@article {pmid40449428,
year = {2025},
author = {Hussain, M and Ullah, K and Tayyab, M and Ullah, S and Shah, AA and Zhang, J and Tong, Z and Liu, X and Rahman, ZU},
title = {Data-driven multi-hazard susceptibility and community perceptions assessment using a mixed-methods approach.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126009},
doi = {10.1016/j.jenvman.2025.126009},
pmid = {40449428},
issn = {1095-8630},
mesh = {Humans ; Floods ; Pakistan ; Surveys and Questionnaires ; Perception ; Climate Change ; Disaster Planning ; Landslides ; Geographic Information Systems ; },
abstract = {Assessing multi-hazard susceptibility and understanding community insights are important for effective disaster risk management; however, limited research has been conducted to study these aspects together. This study uses a data-driven approach to assess multi-hazard susceptibility and community perceptions, aiming to deepen climate change mitigation strategies. We employed a two-stage framework in Eastern Hindukush, Pakistan, which is based on machine learning, remote sensing, geographical information systems, and index-based methods. In the first stage, flood and landslide inventories were generated, and predictive factors were analyzed using logistic regression, resulting in an integrated multi-hazard susceptibility map. In the second stage, a survey of 410 household heads assessed community risk perception, communication, and preparedness, using a structured questionnaire with 28 Likert-scale indicators, and a composite index was calculated. The findings indicate that 25.81 % and 35.43 % of the study area are susceptible to flooding and landslides, respectively, with 15.07 % vulnerable to both hazards concurrently. On the other hand, the community is generally aware of flood and landslide risks; however, there are significant gaps in coping abilities and preparedness, including insufficient insurance coverage and training. Moreover, socioeconomic challenges, such as limited access to information and low trust in local authorities, further complicate disaster preparedness efforts. This study provides a holistic framework for identifying multi-hazard hotspots and assessing community perceptions, facilitating targeted interventions to enhance disaster preparedness and resilience in the region.},
}
@article {pmid40468364,
year = {2025},
author = {Pan, X and Shan, Z and Tian, X and Niu, Y and Liu, Y and Li, Z and Li, Y and Huang, Y and Ye, J},
title = {Evaluating conservation gaps of China's national key protected wild plants: insights from county-level distribution data.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {156},
pmid = {40468364},
issn = {1741-7007},
support = {202206193000001//Shenzhen Science and Technology Program/ ; 20220816162653003//Shenzhen Science and Technology Program/ ; 32270233//National Natural Science Foundation of China/ ; 32200177//National Natural Science Foundation of China/ ; 2022YFF0802300//National Key Research Development Program of China/ ; 2023BSZR014//Doctoral Research Foundation of Jiangxi University of Chinese Medicine/ ; Jiangxi Traditional Chinese Medicine Comprehensive Word No. 3 (2024)//Construction of National Heritage Studio for Old Medicine Workers/ ; },
mesh = {*Conservation of Natural Resources ; China ; *Endangered Species ; *Plants/classification ; Biodiversity ; Databases, Factual ; },
abstract = {BACKGROUND: The National Key Protected Wild Plants (NKPWPs) list serves as China's primary legal framework for plant diversity protection, with the species categorized into Level I (critically endangered, strictly protected) and Level II (lower risk but still requiring protection). However, the geographical distribution of these species and gaps in their conservation remain elusive due to the limited availability of data on species distribution. Thus, to address these gaps and support precise conservation, we developed a county-level distribution database for the NKPWP species using information primarily sourced from literature. Using this database, we elucidated the geographical distribution patterns of NKPWPs and identified the gaps in both in situ and ex situ conservation.<br><br>RESULTS: The NKPWPs analyzed in the study included 1,128 plant species. We compiled a county-level distribution database for these species with 30,397 records. Detailed analysis of this data revealed that these species were concentrated in the mountainous regions of southern China, including the Eastern Himalaya-Hengduan Mountains, south Yunnan, the Yunnan-Guizhou-Guangxi border, and the Wuling Mountains. Among the 1,118 embryophyte species of the checklist, 1,060 (94.81%) were found conserved in situ, 681 (60.91%) were found conserved ex situ, and 660 (59.03%) through both approaches. Besides, species with a higher threat level and limited distribution range exhibited lower conservation coverage in both ex situ and in situ approaches; 37 species received no conservation (3.31%).<br><br>CONCLUSIONS: The county-level distribution database developed in this study comprehensively depicts the geographical distribution patterns of NKPWP in China, offering valuable data for planning species conservation and providing a foundational framework for addressing the existing gaps in their conservation across China. This database will ultimately support targeted conservation and resource allocation to protect plant diversity effectively. We also suggest adopting an integrated evaluation approach for conservation strategies in other areas, globally, or for other biological groups.},
}
@article {pmid40465754,
year = {2025},
author = {Duan, Z and Wang, G and Hu, J and Yu, T and Chen, S and Zhang, Y and Wang, Y and Liu, H and Zhao, X and Chen, H},
title = {Spatiotemporal dynamics of northern Caspian shorelines (1985-2023) and implications for coastal management: Lessons from the Aral Sea.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325546},
pmid = {40465754},
issn = {1932-6203},
mesh = {Oceans and Seas ; *Conservation of Natural Resources ; Spatio-Temporal Analysis ; Ecosystem ; Geographic Information Systems ; Biodiversity ; },
abstract = {Dynamic changes to the northern Caspian Sea shoreline have significant ecological implications, including impacts to biodiversity and the surrounding environment. This study employs Landsat datasets, historical records, and geographic information systems (GIS) to quantitatively analyze spatiotemporal variations along the northern Caspian Sea coastline from 1985 to 2023. The findings demonstrate pronounced cyclic variations in the Caspian Sea's water level. Compared to 1930, the water level decreased by 2.6 m by 2023, with 1935 marking the onset of a significant downward trend. From 1995 to 2023, a pronounced decline in the water level at a rate of 6.1 cm/year was observed. Multiscale temporal oscillations in water levels revealed periodic rises and falls with cycles ranging from 6-8 years to 10-16 years. Due to the broad and shallow morphology of the northern Caspian Sea, fluctuations in water level have resulted in significant displacements of the northern coastline. Between 1985 and 2023, the shoreline length decreased by 262 km, which is equivalent to a 17% reduction. The intensity of the coastline length index reached a critical point during from 2010 to 2015, after which it declined sharply by 3.67. By 2023, the coastline had shifted seaward by 1.33 × 10[4] km2 relative to that in 1985. This continuous retreat of the shoreline poses a severe threat to the ecological stability of the northern Caspian Sea. If the trend persists, then the disappearance of the eastern basin of the South Aral Sea may be replicated in the northern Caspian Sea by 2100. These findings provide critical insights for formulating effective coastal management strategies and conservation initiatives.},
}
@article {pmid40463795,
year = {2025},
author = {Petrou, E and Davies, H and Aoun, M and Radford, AD and Singleton, D and Noble, PM and Killick, DR},
title = {First opinion practice electronic health records are a useful source of descriptions of medication errors.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1560652},
pmid = {40463795},
issn = {2297-1769},
abstract = {BACKGROUND: Medication error (MedE) is a leading global cause of harm in human healthcare with significance both in patient morbidity and mortality, and consequent legal and financial issues. Despite this, MedEs are a poorly explored area in veterinary medicine. Research has so far focussed on survey work and errors spontaneously reported to third parties, such as professional indemnity providers.<br><br>AIM: Determine if MedEs can be successfully identified in first opinion electronic health records (EHRs).<br><br>ANIMALS: EHRs pertaining to animals treated in UK first opinion practice.<br><br>MATERIALS AND METHODS: Regular expressions (REGEX) were designed (with assistance from a domain expert) to identify explicit reference to MedEs in the SAVSNET EHR dataset. Identified MedEs were then classified by the linear sequence of medication therapy, the degree of harm caused, the role of the person who made the error, and the medication type involved.<br><br>RESULTS: In total, 6,665 EHRs were identified by the REGEX, of which a random 2,847 were manually reviewed, with 1,023 (35.9%) matching the MedEs case definition. Of these MedEs, 29.5% (n&#x202f;=&#x202f;302) caused mild harm to the patient, 2.8% (n&#x202f;=&#x202f;27) moderate harm and 0.2% (n&#x202f;=&#x202f;2) severe harm. MedEs were most frequent during the "drug administered" phase (51.4%) and within this phase, "dosing errors" were most common (68.1%). The most common medication types, associated with "drug administered" phase MedEs were vaccinations (27.1%) and non-steroidal anti-inflammatory drugs (19.0%).<br><br>CONCLUSION: EHRs are a useful source of data on MedEs. MedEs are a common cause of patient harm in veterinary practice. The data provided here highlights drug classes at higher risk of problems for which mitigating action and/or education interventions are indicated.},
}
@article {pmid40463267,
year = {2025},
author = {Brook, JBH and Salo, T and Luo, AC and Bagautdinova, J and Rush, S and Alexander-Bloch, AF and Baller, EB and Calkins, ME and Cieslak, M and Cooper, EC and Detre, JA and Elliot, MA and Fair, DA and Freedman, P and Gehrman, PR and Gur, RC and Gur, RE and Klein, A and Laney, N and Laumann, TO and Mehta, K and Merikangas, K and Milham, MP and Mitchell, JA and Moore, TM and Nelson, SM and Ruparel, K and Sevchik, BL and Shanmugan, S and Shou, H and Taso, M and White, LK and Wolf, DH and Tisdall, MD and Roalf, DR and Satterthwaite, TD},
title = {An open, fully-processed data resource for studying mood and sleep variability in the developing brain.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40463267},
issn = {2692-8205},
abstract = {Brain development during adolescence and early adulthood coincides with shifts in emotion regulation and sleep. Despite this, few existing datasets simultaneously characterize affective dynamics, sleep variation, and multimodal measures of brain development. Here, we describe the study protocol and initial release (n = 10) of an open data resource of neuroimaging paired with densely sampled behavioral measures in adolescents and young adults. All participants complete multi-echo functional MRI, compressed-sensing diffusion MRI, and advanced arterial spin-labeled MRI. Behavioral measures include ecological momentary assessment, actigraphy, extensive cognitive assessments, and detailed clinical phenotyping focused on emotion regulation. Raw and processed data are openly available without a data use agreement and will be regularly updated as accrual continues. Together, this resource will accelerate research on the links between mood, sleep, and brain development.},
}
@article {pmid40455595,
year = {2025},
author = {Fetters, AM and Cantalupo, PG and Robles, MTS and Pipas, JM and Ashman, TL},
title = {Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf073},
pmid = {40455595},
issn = {1557-7023},
abstract = {Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether 1) life history, floral traits, or pollination generalism were associated with viral richness, and 2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.},
}
@article {pmid40450230,
year = {2025},
author = {Leung, WKC and Yau, CYC and Lam, SC},
title = {Facilitators, barriers, and recommendations for mobile health applications among Chinese older populations: a scoping review.},
journal = {BMC geriatrics},
volume = {25},
number = {1},
pages = {396},
pmid = {40450230},
issn = {1471-2318},
support = {CRG2023/01//Tung Wah College/ ; CRG2023/01//Tung Wah College/ ; },
mesh = {Aged ; Aged, 80 and over ; Humans ; Middle Aged ; China ; *COVID-19/epidemiology ; *Mobile Applications ; *Telemedicine ; East Asian People ; },
abstract = {BACKGROUND: Mobile health (mHealth) applications have become indispensable in people's daily lives and are now incorporated into a multitude of healthcare services. However, due to inappropriate designs and ineffective promotional strategies, the rates of uptake and continued use of mHealth applications in older adults are usually low. Given that recent evidence has reported distinct mHealth adoption patterns between Chinese and non-Chinese populations, the aim of this scoping review was to map relevant evidence on the end-user perceptions and age-appropriate recommendations for interface design, persuasive features, and promotional strategies among Chinese older adults.<br><br>METHODS: All primary studies conducted in Chinese older people aged 60&#x2009;+&#x2009;years, including quantitative, qualitative, and mixed methods research, examining end-user perceptions (e.g., motivators, barriers, and design) of mHealth applications were considered eligible for inclusion. Four electronic databases (PubMed, CINAHL, PsycINFO, and Medline) were searched from their inceptions through 31 May 2024. A narrative approach was adopted for data analyses relevant to the study aim.<br><br>RESULTS: A total of 23 studies (n&#x2009;=&#x2009;8,203) were included. End-user perceptions (facilitators and barriers) of older people were narratively synthesized according to the socio-ecological model (individual/product, interpersonal, community, and societal). In Chinese deaf and hard-of-hearing older adults, the lack of proficiency in mastering operations of smartphone, Internet, and mHealth applications greatly jeopardized their communication with family or friends, accessibility to online medical consultations, and access to public places amidst COVID-19 pandemic. Recommended interface designs were categorized into various aspects of functional impairments (vision, manual dexterity, and cognition) of elderly users. Seven promotional strategies were also highlighted, whereas more than half of the studies recommended education measures (e.g., personalized family/peer- or health professional-led training program) and technical support (e.g., face-to-face instructions, detailed manual instructions, and timely consultation services). Other recommendations included increased publicity, co-creation, and supportive government policies.<br><br>CONCLUSION: This review synthesizes the existing relevant evidence and hence provides age-friendly recommendations for interface designs, persuasive features, and promotional strategies in Chinese older populations. Overall, this study empirically offers actionable guidelines for mHealth developers to meet the multifaceted needs of older people.},
}
@article {pmid40443799,
year = {2025},
author = {Broad, GR and Lees, DC and Boyes, D and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Straw-barred Pearl moth, Pyrausta despicata Scopoli, 1763.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {151},
pmid = {40443799},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Pyrausta despicata (Straw-barred Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 481.83 megabases. Most of the assembly (99.61%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.29 kilobases.},
}
@article {pmid40442647,
year = {2025},
author = {Maździarz, M and Zając, S and Paukszto, &#x141; and Sawicki, J},
title = {RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU).},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {141},
pmid = {40442647},
issn = {1471-2105},
support = {2024/53/N/NZ8/02829//The National Science Center Krak&#xf3;w, Poland/ ; 12.610.002-110//University of Warmia and Mazury in Olsztyn/ ; },
mesh = {*Codon Usage ; *Software ; *Codon ; *Computational Biology/methods ; },
abstract = {BACKGROUND: Synonymous codon usage bias, a significant factor in gene expression and genome evolution, was extensively studied in genomics and molecular biology. Although the genetic code is universal, significant variations in synonymous codon usage have been observed among and within organisms. This bias was linked to various factors, including gene expression levels, tRNA abundance, protein structure, and environmental adaptation. Relative Synonymous Codon Usage (RSCU), a normalized measure, was used to quantify this bias. By analyzing RSCU values, researchers uncovered patterns and trends related to the underlying mechanisms driving codon usage bias.<br><br>RESULTS: We present an R package named RSCUcaller designed for the analysis of coding nucleotide sequences at the level of relative synonymous codon usage (RSCU). The package enables both visualization of data and the performance of advanced statistical analyses. RSCUcaller accepts as input a multi-fasta file containing coding sequences (CDS) and an accompanying description table. Alternatively, the user may provide separate fasta files for each sequence along with the corresponding table. The program merges the provided sequences and calculates RSCU values for each. Implemented visualization features include creating heatmaps and dendrograms based on these heatmaps. Furthermore, the package allows for the presentation of data in the form of histograms. The calculated RSCU values can also be used to create matrices that can be subjected to further analysis by the user. RSCUcaller offers the functionality of correlation analysis between any two organisms. Additionally, to compare the frequency of amino acid occurrence between different groups of sequences, statistical&#xa0;tests have been implemented.<br><br>CONCLUSIONS: RSCUcaller enabled comparative RSCU analysis between coding sequences of different organisms or individuals of the same species. It facilitated visualization and statistical analysis among codons and user-defined groups. The RSCUcaller package is available at https://github.com/Mordziarz/RSCUcaller under the GPL-3 license.},
}
@article {pmid40442224,
year = {2025},
author = {Sun, Y and Meng, W and Wang, F and Han, H and Sui, M and Jian, Z},
title = {Spatio-temporal evolution and coupling relationship between biodiversity and urbanization in the areas along the Yellow River of Shandong province.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18876},
pmid = {40442224},
issn = {2045-2322},
support = {20221830//cultivation platform for integrating production, science, and education jointly built by Shandong Province and Peking University/ ; 42301320//National Natural Science Fund of China/ ; },
mesh = {*Biodiversity ; *Urbanization ; China ; *Rivers ; Spatio-Temporal Analysis ; Ecosystem ; Conservation of Natural Resources ; Sustainable Development ; },
abstract = {Mastering the coupling relationship and driving mechanism between urbanization and biodiversity is of great significance to ecological protection and regional sustainable development. The study took areas along the Yellow River of Shandong province (AYRSP) as the study area, which have the most rich and unique biodiversity resources in the whole basin. First, this study constructed a new indicator system of biodiversity based on remote-sensing data from species, ecosystem, and landscape to monitor and evaluate the spatial heterogeneity. The result was quantified by the proportion of key biodiversity areas, based on Sustainable Development Goal 15.1.2 from The United Nations. Then, the urbanization system was evaluated based on panel data. At last, the coordination relationship, lead-lag type between biodiversity and urbanization, and key influencing factors of coupling system at the county scale in 2015-2021 were identified by combining multiple models. The results demonstrated that the biodiversity level was gradually declining, with a distribution pattern of "low in the western, and high in mid-southern and eastern regions." The AYRSP still faced certain challenges in the sustainable development of biodiversity. The coupling coordination degree between biodiversity and urbanization showed an increasing trend with continuous improvement in the urbanization level. Only two counties were types of biodiversity-urbanization synchronous development. The results of grey relation degree model indicated that most of indicators were above 0.6 and the urbanization had a significant impact on the coupling system. This study established the evaluation system for biodiversity and urbanization at the small scale, which could provide theoretical reference for the sustainable development of county-level administrative region.},
}
@article {pmid40441709,
year = {2025},
author = {Dang, T and Fuji, Y and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Narukawa, M and Toda, Y and Sakurai, K and Yamasaki, Y and Tsujimoto, H and Hirai, MY and Ichihashi, Y and Iwata, H},
title = {I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
pmid = {40441709},
issn = {1477-4054},
support = {JP21J21850//JSPS KAKENHI/ ; JPMJCR1602//JST-CREST Program/ ; JPMJMI120C7//JST-Mirai Program/ ; JPMJAN23D1//JST ALCA-Next Program/ ; },
mesh = {*Microbiota ; Mice ; Animals ; Humans ; Stochastic Processes ; Bayes Theorem ; Glycine max/microbiology ; *Metabolomics/methods ; Algorithms ; *Computational Biology/methods ; Metabolome ; Cluster Analysis ; Multiomics ; },
abstract = {High-dimensional multi-omics microbiome data play an important role in elucidating microbial community interactions with their hosts and environment in critical diseases and ecological changes. Although Bayesian clustering methods have recently been used for the integrated analysis of multi-omics data, no method designed to analyze multi-omics microbiome data has been proposed. In this study, we propose a novel framework called integrative stochastic variational variable selection (I-SVVS), which is an extension of stochastic variational variable selection for high-dimensional microbiome data. The I-SVVS approach addresses a specific Bayesian mixture model for each type of omics data, such as an infinite Dirichlet multinomial mixture model for microbiome data and an infinite Gaussian mixture model for metabolomic data. This approach is expected to reduce the computational time of the clustering process and improve the accuracy of the clustering results. Additionally, I-SVVS identifies a critical set of representative variables in multi-omics microbiome data. Three datasets from soybean, mice, and humans (each set integrated microbiome and metabolome) were used to demonstrate the potential of I-SVVS. The results indicate that I-SVVS achieved improved accuracy and faster computation compared to existing methods across all test datasets. It effectively identified key microbiome species and metabolites characterizing each cluster. For instance, the computational analysis of the soybean dataset, including 377 samples with 16 943 microbiome species and 265 metabolome features, was completed in 2.18 hours using I-SVVS, compared to 2.35 days with Clusternomics and 1.12 days with iClusterPlus. The software for this analysis, written in Python, is freely available at https://github.com/tungtokyo1108/I-SVVS.},
}
@article {pmid40440249,
year = {2025},
author = {Guevara Rodríguez, DM and Pichihua Grandez, JD and Dianderas, FV and Del Carmen Sara, J},
title = {Incidence of cerebrovascular disease in Peru from 2015 to 2023.},
journal = {PLOS global public health},
volume = {5},
number = {5},
pages = {e0004559},
pmid = {40440249},
issn = {2767-3375},
abstract = {Cerebrovascular disease (stroke) is one of the leading causes of mortality and disability worldwide, particularly in low- and middle-income countries. This study aims to estimate the incidence of stroke in Peru between 2015 and 2023 using national hospital discharge data provided by the National Health Superintendency. We conducted a mixed ecological study using records of stroke cases reported across various healthcare systems, including the Ministry of Health, Social Security, and private entities. Hospitalizations were categorized according to ICD-10 codes (I60-I64) and stratified by age, sex, and region. Incidence rates were calculated using population projections from the National Institute of Statistics and Informatics. A total of 89,776 hospital discharges for stroke were analyzed, yielding an incidence rate of 3.11 per 10,000 persons over the study period, with a predominance in men and individuals over 60 years of age. Cerebral infarction was the most common diagnosis, particularly among those over 40 years old. Incidence varied significantly across regions, with Lima and Callao consistently exceeding the national average. The results highlight disparities in healthcare access and the need for targeted public health interventions. Our findings provide a 9-year overview of stroke in Peru, offering evidence to estimate hospital bed demand and prioritize preventive and management strategies-particularly in regions with higher vulnerability.},
}
@article {pmid40381407,
year = {2025},
author = {Lei, L and Sha, W and Liu, Q and Liu, S and Zhou, Y and Li, R and Duan, Y and Fu, S and Li, H and Liao, R and Li, L and Zhou, R and Zhou, C and Liu, H},
title = {Hepatotoxic effects of exposure to different concentrations of Dibutyl phthalate (DBP) in Schizothorax prenanti: Insights from a multi-omics analysis.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {285},
number = {},
pages = {107390},
doi = {10.1016/j.aquatox.2025.107390},
pmid = {40381407},
issn = {1879-1514},
mesh = {*Dibutyl Phthalate/toxicity ; Animals ; *Liver/drug effects/pathology/metabolism ; *Water Pollutants, Chemical/toxicity ; *Cyprinidae/physiology ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {Dibutyl phthalate (DBP) is one of the most widely used phthalate esters (PAEs) that raise increasing ecotoxicological concerns due to their harmful effects on living organisms and ecosystems. Recently, while PAEs pollution in the Yangtze River has attracted significant attention, little research has been conducted on the impact of PAEs stress on S. prenanti, an endemic and valuable species in the Yangtze River. In this study, one control group (C-L) and three experimental groups: T1-L (3 µg/L), T2-L (30 µg/L), and T3-L (300 µg/L) were established with reference to the DBP concentration in the environment. For the first time, we investigated the effects of DBP stress on the liver of S. prenanti using histomorphological, physiological, and biochemical indexes, as well as a joint multi-omics analysis. The results revealed that compared to the C-L group, liver structural damage and stress were not significant in the environmental concentration group (T1-L) and the number of differential genes and differential metabolites were lower. However, as DBP stress concentration increased, the liver damage became severe, with significant vacuolation and hemolysis observed in the T2-L and T3-L groups. The TUNEL assay revealed a significant increase in the number of apoptotic cells along with a notable rise in differential genes and metabolites in the T2-L and T3-L groups. Oxidative stress markers (T-AOC, SOD, CAT, and GSH-PX) were also significantly higher in the T2-L and T3-L groups. RNA-Seq analysis showed that the protein processing in the endoplasmic reticulum pathway was most significantly -enriched differential gene pathway shared by both C-L vs T2-L and C-L vs T3-L, with most of the genes in this pathway showing significant up-regulation. This suggests that the protein processing in the endoplasmic reticulum pathway may play a key role in protecting the liver from injuries caused by high DBP stress. Interestingly, C XI, C XII, C XIII, C XIV and C XV in the chemical carcinogenesis - reactive oxygen species pathway were significantly down-regulated in the T2-L and T3-L groups based on combined transcriptomic and metabolomic analyses, suggesting that DBP causes liver injury by disrupting mitochondria. This comprehensive histomorphometric and multi-omics study demonstrated that the current DBP concentration in the habitat of S. prenanti in the upper reaches of the Yangtze River temporarily causes less liver damage. However, with increasing of DBP concentration, DBP could still cause serious liver damage to S. prenanti. This study provides a new mechanistic understanding of the liver response mechanism of S. prenanti under different concentrations of DBP stress and offers basic data for the ecological protection of the Yangtze River.},
}
@article {pmid40288322,
year = {2025},
author = {Zhou, H and Wu, Z and Wang, X and Jiang, L and Sun, H and Li, H and Yan, Z and Wang, Y and Yao, X and Zhang, C and Tang, J},
title = {6PPD-quinone exposure induces oxidative damage and physiological disruption in Eisenia fetida: An integrated analysis of phenotypes, multi-omics, and intestinal microbiota.},
journal = {Journal of hazardous materials},
volume = {493},
number = {},
pages = {138334},
doi = {10.1016/j.jhazmat.2025.138334},
pmid = {40288322},
issn = {1873-3336},
mesh = {*Oligochaeta/drug effects/physiology/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Soil Pollutants/toxicity ; *Oxidative Stress/drug effects ; *Phenylenediamines/toxicity ; Phenotype ; Reactive Oxygen Species/metabolism ; Metabolomics ; Transcriptome/drug effects ; Multiomics ; Benzoquinones ; },
abstract = {The environmental prevalence of the tire wear-derived emerging pollutant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) has increasingly raised public concern. However, knowledge of the adverse effects of 6PPD-Q on soil fauna is scarce. In this study, we elucidated its impact on soil fauna, specifically on the earthworm Eisenia fetida. Our investigation encompassed phenotypic, multi-omics, and microbiota analyses to assess earthworm responses to a gradient of 6PPD-Q contamination (10, 100, 1000, and 5000 μg/kg dw soil). Post-28-day exposure, 6PPD-Q was found to bioaccumulate in earthworms, triggering reactive oxygen species production and consequent oxidative damage to coelomic and intestinal tissues. Transcriptomic and metabolomic profiling revealed several physiological perturbations, including inflammation, immune dysfunction, metabolic imbalances, and genetic toxicity. Moreover, 6PPD-Q perturbed the intestinal microbiota, with high dosages significantly suppressing microbial functions linked to metabolism and information processing (P < 0.05). These alterations were accompanied by increased mortality and weight loss in the earthworms. Specifically, at an environmental concentration of 6PPD-Q (1000 μg/kg), we observed a substantial reduction in survival rate and physiological disruptions. This study provides important insights into the environmental hazards of 6PPD-Q to soil biota and reveals the underlying toxicological mechanisms, underscoring the need for further research to mitigate its ecological footprint.},
}
@article {pmid40233751,
year = {2025},
author = {McKenzie, PF and Berardi, AE and Hopkins, R},
title = {Delayed flowering phenology of red-flowering plants in response to hummingbird migration.},
journal = {Current biology : CB},
volume = {35},
number = {9},
pages = {2175-2182.e3},
pmid = {40233751},
issn = {1879-0445},
support = {R35 GM142742/GM/NIGMS NIH HHS/United States ; },
mesh = {*Birds ; Animals ; *Flowers/growth &amp; development/physiology ; Animal Migration ; Pollination ; North America ; Datasets as Topic ; Seasons ; Pigmentation ; Time Factors ; *Magnoliopsida/physiology ; Crowdsourcing ; },
abstract = {The radiation of angiosperms is marked by a phenomenal diversity of floral size, shape, color, scent, and reward.[1][,][2][,][3][,][4] The multi-dimensional response to selection to optimize pollination has generated correlated suites of these floral traits across distantly related species, known as "pollination syndromes."[5][,][6][,][7][,][8][,][9] The ability to test the broad utility of pollination syndromes and expand upon the generalities of these syndromes is constrained by limited trait data, creating a need for new approaches that can integrate vast, unstructured records from community-science platforms. Here, we compile the largest North American flower color dataset to date, using GPT-4 with Vision to classify color in over 11,000 species across more than 1.6 million iNaturalist observations. We discover that red- and orange-flowering species (classic "hummingbird pollination" colors) bloom later in eastern North America compared with other colors, corresponding to the arrival of migratory hummingbirds. Our findings reveal how seasonal flowering phenology, in addition to floral color and morphology, can contribute to the hummingbird pollination syndrome in regions where these pollinators are migratory. Our results highlight phenology as an underappreciated dimension of pollination syndromes and underscore the utility of integrating artificial intelligence with community-science data. The potential breadth of analysis offered by community-science datasets, combined with emerging data extraction techniques, could accelerate discoveries about the evolutionary and ecological drivers of biological diversity.},
}
@article {pmid40435619,
year = {2025},
author = {Matuszewska, D and Kiedrzyńska, E and Jóźwik, A and Kiedrzyński, M},
title = {An analysis of catchment factors associated with heavy metal export into the Baltic Sea and nature-based solutions aimed at its limitation.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138727},
doi = {10.1016/j.jhazmat.2025.138727},
pmid = {40435619},
issn = {1873-3336},
abstract = {The aim of the article was to determine the shares of individual Baltic countries participating in the inflow of metal loads to the Baltic Sea and identify patterns of similarity between these countries regarding the causes of heavy metal load generation. The analyses used HELCOM and EUROSTAT data. The findings indicate that Finland and Sweden generate the highest total loads of heavy metals flowing in through rivers. However, Lithuania and Finland are distinguished by high metal loads calculated per km[2] of catchment area. Clustering countries in terms of their similarity in the heavy metal loads provided to the Baltic resulted in three groups. Finland and Lithuania generates the highest mean loads of cadmium, chromium, nickel and zinc per unit area [kg/km[2]/year]. Estonia and Latvia generates the highest mean annual loads of lead, mercury and copper. Poland, Germany and Sweden generates the lowest heavy metal loads. Multidimensional data analysis showed a strong correlation between aquaculture production in the Baltic Sea catchment area, the number of cattle, beef, mutton, pigs, poultry, and meat produced from them, the amount of waste, trucks, cereal production, the use of nitrogen fertilizers, and the loads of heavy metals reaching the Baltic Sea with river waters. Therefore, there is a need for continuous monitoring of the loads and transfer of heavy metals to the Baltic Sea, and for activities aimed at eliminating them from the environment. For this purpose, Nature-Based Solutions can be used, as they represent inexpensive, nature-friendly methods for removing pollutants from surface waters.},
}
@article {pmid39890763,
year = {2025},
author = {Kuru, A and Yüzer, MA and Yüzer, A&#x15e; and Güney, BG and Yüzer, ME},
title = {Integrated site selection model for industrial areas: case study for İnegöl furniture industry.},
journal = {Environmental science and pollution research international},
volume = {32},
number = {8},
pages = {4771-4793},
pmid = {39890763},
issn = {1614-7499},
mesh = {*Interior Design and Furnishings ; *Industry ; Noise ; Odorants/analysis ; Environmental Monitoring ; Socioeconomic Factors ; Geographic Information Systems ; *Environment ; },
abstract = {Industrial activities in the central area have adverse effects such as noise, odor, and traffic congestion. Simultaneously, due to changing technological and economic advances, existing industrial areas cannot meet the needs, spatial inadequacies obstruct competition, and production capacity decreases. Decentralizing industrial activities from urban centers are ecologically and economically necessary. Various elements on a macro and micro scale need to be considered to select suitable sites for new industrial areas. Natural, socioeconomic, and built environment features must be examined to ensure sustainability. The objective of this study is to develop an integrated industrial site location model that considers the needs of authorities and industrial stakeholders, as well as economic and ecological sustainability for the İnegöl district, one of Turkey's leading settlements in the furniture industry. Thirty-seven criteria were evaluated using GIS based multi-criteria decision making methods. The criteria were defined through spatial analysis, expert opinions, and in-depth interviews with industry and local government representatives. Using weighted linear combination process the five sub-regions exhibiting the lowest economic costs and the least environmental degradation have been identified. Advantages and disadvantages were identified through the use of sketches and comparisons between the sub-regions. A decision support system was developed for local and central government institutions to be used in industrial site selection processes.},
}
@article {pmid40435606,
year = {2025},
author = {Guo, J and Xie, Y and Dou, X and Qi, W and Liao, Y and Cao, X and Peng, J and Liu, H},
title = {Combining source identification and risk assessment to uncover spatial risk patterns in an agricultural lake.},
journal = {Journal of environmental management},
volume = {387},
number = {},
pages = {125966},
doi = {10.1016/j.jenvman.2025.125966},
pmid = {40435606},
issn = {1095-8630},
mesh = {*Lakes ; Agriculture ; *Environmental Monitoring/methods ; Risk Assessment ; Geologic Sediments ; Water Pollutants, Chemical/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; Metals, Heavy/analysis ; Bayes Theorem ; Water Quality ; Rivers ; },
abstract = {Pollutant source identification and risk assessment underpin environmental management, necessitating innovative methods for both pollution source identification and comprehensive evaluation to enhance management efficiency. In this study, we developed a novel integrated framework that combines Bayesian isotope mixing, positive matrix factorization (PMF), random forest, and spatial autocorrelation for multi-pollutant source identification and risk assessment. The Bayesian isotope mixing model revealed that fertilizers accounted for 61 % of the nitrate in the lake and 46 % of the nitrate in the river. Furthermore, PMF analysis indicated that polycyclic aromatic hydrocarbons (PAHs) in sediments and soil were primarily sourced from vehicular emissions (32 %), while heavy metals (40 %) were mainly from vehicular emissions and agricultural activities. Using a comprehensive pollution assessment framework for water and sediment quality, we found that water quality ranged from "medium" to "excellent", and sediment quality ranged from "good" to "excellent". Among various evaluation indices, CODMn, As, F[-], TP, Pb, and Zn were pivotal in determining comprehensive water quality. Key indices for sediment quality evaluation included Flua, BaP, BaA, Pyr, Ant, Pb, and As, primarily sourced from automobile emissions and agricultural activities. Spatial autocorrelation analysis demonstrated a spatial relationship between water quality and sediment quality, covering 43 % of the area. High-pollution areas (13 %) were concentrated around natural river inlets, while low-pollution zones (17 %) were located near ecological water replenishment river inlets. This underscores the significant influence of inflowing water quality on sediment conditions. This study highlights the development of a comprehensive pollution assessment framework to evaluate sediment and soil pollution, as well as to identify high-risk zones of compound pollution in water and sediment. Furthermore, the framework's universal applicability for agricultural lake systems enables the identification of high-risk zones through water-sediment interaction analysis.},
}
@article {pmid40435494,
year = {2025},
author = {Berger, M and Ehlers, JP and Nitsche, J},
title = {Aligning With the Goals of the Planetary Health Concept Regarding Ecological Sustainability and Digital Health: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e71795},
doi = {10.2196/71795},
pmid = {40435494},
issn = {1438-8871},
mesh = {*Telemedicine ; Climate Change ; Humans ; Global Health ; Delivery of Health Care ; Artificial Intelligence ; Digital Health ; },
abstract = {BACKGROUND: Climate change, driven by greenhouse gas emissions, threatens human health and biodiversity. While the digitalization of health care, including telemedicine and artificial intelligence, offers sustainability benefits, it also raises concerns about energy use and electronic waste. Balancing these factors is key to a sustainable health care future.<br><br>OBJECTIVE: The objective of this review was to examine the extent to which digitalization in the health care sector influences environmental sustainability. Specifically, it aimed to assess how digitalization can contribute to reducing the health care sector's impact on global climate change. From these findings, conclusions were drawn regarding the extent to which digitalization aligns with the objectives of the Planetary Health movement and how these 2 movements may mutually reinforce each other.<br><br>METHODS: A scoping review guided by the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) 2020 guidelines using databases such as PubMed and Scopus was conducted, and 58 quantitative studies from 2009 to 2024 were analyzed for environmental, social, and economic outcomes aligned with Planetary Health goals.<br><br>RESULTS: This review analyzed 58 studies on the environmental impact of digitalization in health care primarily focusing on telemedicine, which was examined in 91% (53/58) of the studies. Most studies (56/58, 97%) quantified transport-related emissions avoided through digitalization, with some also assessing emissions from health care facilities, medical equipment, and energy consumption. Findings indicated that telemedicine significantly reduces carbon dioxide emissions, with total avoided emissions amounting to approximately 830 million kg. A substantial proportion of the studies (36/58, 62%) focused on social aspects, highlighting factors such as patient satisfaction, time efficiency, and overall convenience. In addition, economic considerations were analyzed in 48% (28/58) of the studies, emphasizing cost reductions and resource optimization. However, only 12% (7/58) of the studies evaluated the full life cycle impact of digital technologies, highlighting the need for further research on their long-term environmental sustainability.<br><br>CONCLUSIONS: This review calls for further research beyond telemedicine, advocating for life cycle analyses and actionable strategies for a sustainable digitalization in health care systems. The Planetary Health framework is highlighted as a guide for ensuring sustainable digital transformation in health care.},
}
@article {pmid39892263,
year = {2025},
author = {Yang, W and Liu, Y and Shao, H and Iravani, M and Yu, Z and Weber, M},
title = {Developing a cloud-based WebGIS tool for communicating integrated ecosystem services assessment modeling to conservation stakeholders.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124372},
doi = {10.1016/j.jenvman.2025.124372},
pmid = {39892263},
issn = {1095-8630},
mesh = {*Cloud Computing ; *Geographic Information Systems ; Ecosystem ; *Agriculture/economics/methods/statistics &amp; numerical data ; *Conservation of Natural Resources/economics/methods/statistics &amp; numerical data ; Environmental Monitoring ; Models, Statistical ; Farms/economics/statistics &amp; numerical data ; Cost-Effectiveness Analysis ; Alberta ; Agroecology/economics/methods/statistics &amp; numerical data ; Stakeholder Participation ; Hydrology ; },
abstract = {Various modeling efforts have been conducted to evaluate ecosystem services (ES) of agricultural conservation practices but typically these models are too complex for conservation stakeholders to use. This research developed a cloud-based WebGIS tool for communicating integrated ES modeling to conservation stakeholders. The integrated ES modeling was developed by linking farm economic, watershed hydrologic, and soil carbon modeling within a spatial optimization framework for identifying conservation practices to minimize economic costs subject to multiple ES targets including water quality and soil carbon improvement benefits. The WebGIS tool, named "Ecosystem Services Assessment Tool" (ESAT), has a suite of functions to visualize watershed characteristics, summarize the effectiveness of existing agricultural conservation practices, examine the cost, effectiveness, and cost-effectiveness of future agricultural conservation practices, and further, identify optimal sets of conservation practices for achieving cost-effectiveness. The study area for the integrated ES modeling and WebGIS tool development was the 4,820-km[2] Modeste watershed in Alberta, Canada. The ESAT application demonstrated its functionalities to support decision making, particularly in identifying cost-effective conservation practices for achieving sediment, phosphorus or nitrogen reduction, or soil carbon increase target. In the research, conservation stakeholders including municipal and provincial governments, conservation management agencies, and NGOs were actively engaged in data collection, modeling development, WebGIS tool development, and training for the use of the WebGIS tool. Conservation stakeholders assessed that the ESAT is a very useful tool for supporting decision making in agri-environmental programs. However, the WebGIS tool can be further simplified and streamlined to improve the user-friendliness of the ESAT.},
}
@article {pmid37732396,
year = {2025},
author = {Lajmi, A and Glinka, F and Privman, E},
title = {Optimizing ddRAD sequencing for population genomic studies with ddgRADer.},
journal = {Molecular ecology resources},
volume = {25},
number = {5},
pages = {e13870},
doi = {10.1111/1755-0998.13870},
pmid = {37732396},
issn = {1755-0998},
support = {2017319//US-Israel Binational Science Foundation/ ; },
mesh = {*Sequence Analysis, DNA/methods ; *Genetics, Population/methods ; *Software ; *Computational Biology/methods ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; },
abstract = {Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.},
}
@article {pmid37526650,
year = {2025},
author = {Robledo-Ruiz, DA and Austin, L and Amos, JN and Castrejón-Figueroa, J and Harley, DKP and Magrath, MJL and Sunnucks, P and Pavlova, A},
title = {Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment.},
journal = {Molecular ecology resources},
volume = {25},
number = {5},
pages = {e13844},
doi = {10.1111/1755-0998.13844},
pmid = {37526650},
issn = {1755-0998},
support = {//Australian Government Department of Education/ ; DP180102359//Australian Research Council/ ; DP210102275//Australian Research Council/ ; LP160100482//Australian Research Council/ ; //Department of Biodiversity, Conservation and Attractions (Western Australia)/ ; //Department of Environment, Land, Water and Planning (Victoria)/ ; //Diversity Arrays Technology/ ; //Ecological Society of Australia Incorporated/ ; //Environment, Planning &amp; Sustainable Development Directorate (ACT)/ ; //Monash University Faculty of Science/ ; //Revive &amp; Restore/ ; //Zoos Victoria/ ; },
mesh = {Animals ; Birds/genetics ; *Genomics/methods ; Male ; *Sex Determination Processes ; *Computational Biology/methods ; Female ; Mammals/genetics ; *Software ; Sex Chromosomes/genetics ; },
abstract = {Identifying sex-linked markers in genomic datasets is important because their presence in supposedly neutral autosomal datasets can result in incorrect estimates of genetic diversity, population structure and parentage. However, detecting sex-linked loci can be challenging, and available scripts neglect some categories of sex-linked variation. Here, we present new R functions to (1) identify and separate sex-linked loci in ZW and XY sex determination systems and (2) infer the genetic sex of individuals based on these loci. We tested these functions on genomic data for two bird and one mammal species and compared the biological inferences made before and after removing sex-linked loci using our function. We found that our function identified autosomal loci with ≥98.8% accuracy and sex-linked loci with an average accuracy of 87.8%. We showed that standard filters, such as low read depth and call rate, failed to remove up to 54.7% of sex-linked loci. This led to (i) overestimation of population FIS by up to 24%, and the number of private alleles by up to 8%; (ii) wrongly inferring significant sex differences in heterozygosity; (iii) obscuring genetic population structure and (iv) inferring ~11% fewer correct parentages. We discuss how failure to remove sex-linked markers can lead to incorrect biological inferences (e.g. sex-biased dispersal and cryptic population structure) and misleading management recommendations. For reduced-representation datasets with at least 15 known-sex individuals of each sex, our functions offer convenient resources to remove sex-linked loci and to sex the remaining individuals (freely available at https://github.com/drobledoruiz/conservation_genomics).},
}
@article {pmid37357835,
year = {2025},
author = {Chi, L and Zhang, X and Xue, Y and Chen, H},
title = {fastHaN: a fast and scalable program for constructing haplotype network for large-sample sequences.},
journal = {Molecular ecology resources},
volume = {25},
number = {5},
pages = {e13829},
doi = {10.1111/1755-0998.13829},
pmid = {37357835},
issn = {1755-0998},
support = {2021YFC0863400//National Key Research and Development Program of China/ ; 2021YFC2301305//National Key Research and Development Program of China/ ; 2020YFC0847000//National Key Research and Development Program of China/ ; KJZ-SW-L14//the Key Program of Chinese Academy of Sciences/ ; },
mesh = {*Haplotypes ; *Software ; *Computational Biology/methods ; Algorithms ; *Sequence Analysis, DNA/methods ; },
abstract = {Haplotype networks can be used to demonstrate the genealogical relationships of DNA sequences within species, and thus are widely applied in population genetics, molecular ecology, epidemiology and evolutionary studies. However, existing programs become computationally infeasible as the sample size increases. Here, we present fastHaN, an efficient and scalable program suitable for constructing haplotype networks for large samples. On a data set with the haplotype length of 30 kb, the Median Joining Network (MJN) algorithm implemented by fastHaN is 3000 times faster than PopART and 70 times faster than NETWORK in single-threaded mode. The implementation of the Templeton-Crandall-Sing (TCS) algorithm is 100 times faster than PopART and 5800 times faster than the TCS software. Moreover, fastHaN also enables multi-threaded mode with scalability. The source code is freely available on https://github.com/ChenHuaLab/fastHaN/. A web-based version is also available on https://ngdc.cncb.ac.cn/haplotype/.},
}
@article {pmid36458971,
year = {2025},
author = {Huang, K and Li, W and Yang, B and Wang, D and He, S and Shen, Y and Ao, J and Li, Y and Cui, Y and Kong, Y and Li, W and Li, N and Dunn, DW and Li, B},
title = {vcfpop: Performing population genetics analyses for autopolyploids and aneuploids based on next-generation sequencing data sets.},
journal = {Molecular ecology resources},
volume = {25},
number = {5},
pages = {e13744},
doi = {10.1111/1755-0998.13744},
pmid = {36458971},
issn = {1755-0998},
support = {XDB31020302//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 31730104//National Natural Science Foundation of China/ ; 31770411//National Natural Science Foundation of China/ ; 32070453//National Natural Science Foundation of China/ ; 32170515//National Natural Science Foundation of China/ ; 2021KJXX-026//Innovation Capability Support Program of Shaanxi/ ; },
mesh = {*Software ; *Polyploidy ; *Genetics, Population/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; *Plants/genetics ; },
abstract = {Polyploids are cells or organisms with a genome consisting of more than two sets of homologous chromosomes. Polyploid plants have important traits that facilitate speciation and are thus often model systems for evolutionary, molecular ecology and agricultural studies. However, due to their unusual mode of inheritance and double-reduction, diploid models of population genetic analysis cannot properly be applied to autopolyploids. To overcome this problem, we developed a software package entitled vcfpop to perform a variety of population genetic analyses for autopolyploids, such as parentage analysis, analysis of molecular variance, principal coordinates analysis, hierarchical clustering analysis and Bayesian clustering. We used three data sets to evaluate the capability of vcfpop to analyse large data sets on a desktop computer. This software is freely available at http://github.com/huangkang1987/vcfpop.},
}
@article {pmid40433986,
year = {2024},
author = {He, Y and Mulqueeney, JM and Watt, EC and Salili-James, A and Barber, NS and Camaiti, M and Hunt, ESE and Kippax-Chui, O and Knapp, A and Lanzetti, A and Rangel-de Lázaro, G and McMinn, JK and Minus, J and Mohan, AV and Roberts, LE and Adhami, D and Grisan, E and Gu, Q and Herridge, V and Poon, STS and West, T and Goswami, A},
title = {Opportunities and Challenges in Applying AI to Evolutionary Morphology.},
journal = {Integrative organismal biology (Oxford, England)},
volume = {6},
number = {1},
pages = {obae036},
pmid = {40433986},
issn = {2517-4843},
abstract = {Artificial intelligence (AI) is poised to revolutionize many aspects of science, including the study of evolutionary morphology. While classical AI methods such as principal component analysis and cluster analysis have been commonplace in the study of evolutionary morphology for decades, recent years have seen increasing application of deep learning to ecology and evolutionary biology. As digitized specimen databases become increasingly prevalent and openly available, AI is offering vast new potential to circumvent long-standing barriers to rapid, big data analysis of phenotypes. Here, we review the current state of AI methods available for the study of evolutionary morphology, which are most developed in the area of data acquisition and processing. We introduce the main available AI techniques, categorizing them into 3 stages based on their order of appearance: (1) machine learning, (2) deep learning, and (3) the most recent advancements in large-scale models and multimodal learning. Next, we present case studies of existing approaches using AI for evolutionary morphology, including image capture and segmentation, feature recognition, morphometrics, and phylogenetics. We then discuss the prospectus for near-term advances in specific areas of inquiry within this field, including the potential of new AI methods that have not yet been applied to the study of morphological evolution. In particular, we note key areas where AI remains underutilized and could be used to enhance studies of evolutionary morphology. This combination of current methods and potential developments has the capacity to transform the evolutionary analysis of the organismal phenotype into evolutionary phenomics, leading to an era of "big data" that aligns the study of phenotypes with genomics and other areas of bioinformatics.},
}
@article {pmid40378593,
year = {2025},
author = {Broel, N and Daumüller, F and Ali, A and Lemanschick, J and Maibach, K and Mewe, C and Bunk, B and Spröer, C and Baschien, C and Zorn, H and Schlüter, H and Rühl, M and Janssen, S and Gand, M},
title = {Unravelling the enzymatic wood decay repertoire of Cerrena zonata: A multi-omics approach.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128214},
doi = {10.1016/j.micres.2025.128214},
pmid = {40378593},
issn = {1618-0623},
mesh = {Lignin/metabolism ; *Wood/metabolism/microbiology ; Fungal Proteins/genetics/metabolism ; Glycoside Hydrolases/metabolism/genetics ; Peroxidases/metabolism/genetics ; Laccase/metabolism/genetics ; Biomass ; *Basidiomycota/enzymology/genetics/metabolism ; Genomics ; Gene Expression Profiling ; Genome, Fungal ; Proteomics ; Hydrolysis ; Multiomics ; },
abstract = {Lignocellulosic biomass (LCB), such as wheat straw, bagasse, or wood, is a cost-effective, sustainable carbon source but remains challenging to utilize due to the recalcitrance of lignin, which hinders efficient carbohydrate hydrolysis. Effective LCB degradation demands a wide range of enzymes, and commercial enzyme cocktails often require physical or chemical pretreatments. A fully enzymatic degradation could drastically improve the efficiency of these processes. Basidiomycota fungi naturally possess diverse enzymes suited for LCB breakdown. The white-rot fungus Cerrena zonata, a member of the phylum Basidiomycota, was analyzed for its Carbohydrate-Active Enzymes (CAZymes) using a multi-omics approach. Genomic and transcriptomic analyses of C. zonata identified 20,816 protein-encoding genes, including 487 CAZymes (2.3 %). Cultivating C. zonata with and without LCB addition revealed a total of 147 proteins, of which 36 were CAZymes (13 auxiliary activities (AA), 3 carbohydrate esterases, and 20 glycoside hydrolases). In accordance, laccase, manganese peroxidase (MnP) as well as versatile peroxidase (VP) activities were detected in the fungal culture supernatants. Furthermore, relevant enzymes were visualized via zymography. Consistent with these results, five putative peroxidases (AA2) and three putative laccases (AA1_1) were identified in all -omics dimensions. Further structure and sequence analysis of AA2 proteins supports that two proteins were classified as VPs and three as MnPs, based on their active and Mn[2 +] binding sites. In summary, C. zonata possesses a broad enzyme spectrum expressed under varied conditions, highlighting its potential for identifying efficient lignin-degrading enzymes for enzymatic pretreatment of food industry side streams and other LCBs.},
}
@article {pmid39856573,
year = {2025},
author = {Sun, Z and Zhang, F and Zhong, N and Zhou, K and Tang, J},
title = {Genome sequence resources for three strains of the genus Clonostachys.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {8},
pmid = {39856573},
issn = {2730-6844},
support = {No. 2022AH051346 and No. KJ2021A0676//the Key Natural Science Research Projects in Anhui Universities/ ; No. KJTS2022002; No. KJTS2022003//Science and Technology Innovation Capability Enhancement Projects in Fuyang National Agricultural Sci-Tech Park/ ; No. 2022AH020081//Natural Science Foundation of Universities of Anhui Province for Distinguished Young Project/ ; No. 2020KYQD0023//The Fuyang Normal University Research Project/ ; [2023]13//Biological and Medical Sciences of Applied Summit Nurturing Disciplines in Anhui Province, Anhui Education Secretary Department/ ; },
mesh = {*Ascomycota/classification/genetics ; Datasets as Topic ; Genome, Fungal ; Molecular Sequence Annotation ; Biological Control Agents ; },
abstract = {OBJECTIVE: Clonostachys, a genus with rich morphological and ecological diversity in Bionectriaceae, has a wide distribution among diverse habitats. Several studies have reported Clonostachys fungi as effective biological agents against multiple fungal plant pathogens. To clarify the diversity and biocontrol mechanisms of the Clonostachys fungi, this study was undertaken to sequence and assemble the genomes of two C. chloroleuca and one C. rhizophaga.<br><br>DATA DESCRIPTION: Here, we performed genomic sequencing of three strains of genus Clonostachys collected from the China General Microbiological Culture Collection Center (CGMCC) using Illumina HiSeq 2500 sequencing technology. Whole genome analysis indicated that their genomes consist of 58,484,224&#xa0;bp with a GC content of 48.58%, 58,114,960&#xa0;bp with a GC content of 47.74% and 58,450,453&#xa0;bp with a GC content of 48.58%, respectively. BUSCO analysis of the genome assembly indicated that the completeness of these genomes was at least 98%. In summary, these datasets provide a valuable resource for ongoing studies that include further exploration of biological function, marker development, enhanced biological control ability of Clonostachys fungi, and population diversity.},
}
@article {pmid40432488,
year = {2025},
author = {Min, J and Kim, B and Park, Y and Son, Y and Park, W},
title = {Bacterial cell wall synthesis and recycling: new antimicrobial targets and vaccine development.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/1040841X.2025.2510250},
pmid = {40432488},
issn = {1549-7828},
abstract = {Almost all bacteria have peptidoglycan (PG) components that are essential for virulence and are absent in humans, making them a top-priority target for antibiotics and vaccines. The rise of multidrug-resistant bacteria (MRB) necessitates urgent expansion of our arsenal of inhibitors targeting the PG cell wall. This review addresses our understanding of PG biosynthesis and recycling processes, emphasizing the need to identify novel target proteins and redesign existing PG-targeted antimicrobial peptides. Building on our understanding of cell wall biochemistry and biogenesis derived from Escherichia coli, we also aim to compare and elucidate the cell wall processes in other pathogens, such as Acinetobacter baumannii and Salmonella Typhimurium, where knowledge remains incomplete. We cover in detail the distinct roles of PG-related proteins in Gram-negative bacteria, strategies to block PG biosynthesis/recycling pathways, and their potential as novel antibiotic targets to address the growing challenge of antibiotic resistance. Finally, we review the application of rigorous immuno-informatics analysis and several immune filters to construct epitope-specific vaccines displaying PG-related proteins on the surface of outer membrane vesicles (OMVs), aiming to combat MRB proliferation.},
}
@article {pmid40431635,
year = {2025},
author = {Rodrigues, GVP and Santos, JPN and Ferreira, LYM and Conceição, LBA and Porto, JAM and Aguiar, ERGR},
title = {Theobroma cacao Virome: Exploring Public RNA-Seq Data for Viral Discovery and Surveillance.},
journal = {Viruses},
volume = {17},
number = {5},
pages = {},
pmid = {40431635},
issn = {1999-4915},
support = {Financial Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; //Conselho Nacional de Pesquisa Cient&#xed;fica (CNPq)/ ; },
mesh = {*Cacao/virology ; *Virome/genetics ; Plant Diseases/virology ; RNA-Seq ; Computational Biology/methods ; Phylogeny ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; Badnavirus/genetics/isolation &amp; purification/classification ; Microbiota ; },
abstract = {Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant-virus-microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production.},
}
@article {pmid40427823,
year = {2025},
author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG},
title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {5},
pages = {},
pmid = {40427823},
issn = {1660-4601},
support = {PTDC/CTA AMB/29586/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; },
mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation &amp; purification/genetics ; },
abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.},
}
@article {pmid40334559,
year = {2025},
author = {Semcesen, PO and Wells, MG and Sherlock, C and Gutierrez, RF and Rochman, CM},
title = {Wind driven transport of macroplastic debris in a large urban harbour measured by GPS-tracked drifters.},
journal = {Marine pollution bulletin},
volume = {217},
number = {},
pages = {118034},
doi = {10.1016/j.marpolbul.2025.118034},
pmid = {40334559},
issn = {1879-3363},
mesh = {*Wind ; *Plastics/analysis ; *Environmental Monitoring/methods ; Ontario ; Geographic Information Systems ; },
abstract = {The transport pathways of floating plastic debris in Toronto Harbour, Ontario, Canada, were assessed using a series of GPS-tracked drifter bottles. The drifter trajectories were largely controlled by winds, and they could traverse the 2 km wide harbour within a day. The average ratio of drifter speed to wind speed (the wind factor) is consistent with values of 2-5 % used in modelling dispersion of marine debris. However, significant variability in wind factors meant some drifters travelled 2-5 times faster than expected in small waterbodies (Toronto Harbour), and as much as 7 times faster in large waterbodies (Lake Ontario). Importantly, based on our calculated wind factor equations and the coincident accumulation of our drifters with real plastic debris, we can justify the use of wind factors when studying plastic debris transport. Most (75 %) of the drifters that were released in the harbour, stayed within the harbour, accumulating downwind. However, 14 of all 66 drifters escaped Toronto Harbour, where ∼70 % escaped through the West Gap while ∼30 % escaped via the Outer Harbour. One drifter made a 290 km journey across Lake Ontario in a period of 14 days, demonstrating that Toronto is a potential source of plastic debris throughout Lake Ontario.},
}
@article {pmid40426056,
year = {2025},
author = {Charest, J and Loebenstein, P and Mach, RL and Mach-Aigner, AR},
title = {FunFEA: an R package for fungal functional enrichment analysis.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {138},
pmid = {40426056},
issn = {1471-2105},
mesh = {*Genome, Fungal ; *Software ; Molecular Sequence Annotation/methods ; *Fungi/genetics ; Gene Ontology ; Databases, Genetic ; Genomics/methods ; Computational Biology/methods ; },
abstract = {BACKGROUND: The functional annotation of fungal genomes is critical for understanding their biological processes and ecological roles. While existing tools support functional enrichment analysis from publicly available annotations of well-established model organisms, few are tailored to the specific needs of the fungal research community. Furthermore, many tools struggle with processing functional annotations of novel species, for which no publicly available functional annotations are yet available.<br><br>RESULTS: FunFEA is an R package designed for functional enrichment analysis of fungal genomes. It supports COG/KOG (Clusters of Orthologous Genes), GO (Gene Ontology), and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations, and generates background frequency models from publicly available annotations for overrepresentation analysis, within a set of experimentally defined genes or proteins. Additionally, FunFEA can process eggNOG-mapper annotations, thus enabling functional enrichment analysis of novel genomes. The package offers a suite of tools for generation of background frequency models, functional enrichment analysis, as well as visualization of enriched functional categories. On release, the package includes precomputed models for 65 commonly used fungal strains in academic research and strains listed on the WHO fungal priority pathogens list.<br><br>CONCLUSIONS: FunFEA fills a critical need for a specialized tool in fungal genomics, providing valuable insights into fungal biology. Additionally, its ability to process eggNOG-mapper annotations makes it an essential resource for researchers, helping to drive further exploration of fungal functional diversity and pathways and derive biological insights from novel genomes.},
}
@article {pmid40425680,
year = {2025},
author = {Péter, SA and Gallo, T and Mullinax, J and Roess, A and Palomo-Munoz, G and Anderson, T},
title = {Integrating human mobility and animal movement data reveals complex space-use between humans and white-tailed deer in urban environments.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18588},
pmid = {40425680},
issn = {2045-2322},
support = {AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; AP23OA000000C003//Animal and Plant Health Inspection Service/ ; },
mesh = {Animals ; *Deer/physiology ; Humans ; Zoonoses/transmission ; Animals, Wild ; Ecosystem ; Maryland ; Cities ; Wasting Disease, Chronic/transmission ; COVID-19/transmission/epidemiology/virology ; SARS-CoV-2 ; Geographic Information Systems ; },
abstract = {Human expansion into wildlife habitats has increased the need to understand human-wildlife interactions, necessitating interdisciplinary approaches to assess zoonotic disease transmission risks and public health impacts. This study integrated fine-grained human foot traffic data with hourly GPS data from 38 white-tailed deer (Odocoileus virginianus), a species linked to SARS-CoV-2, brucella, and chronic wasting disease, in Howard County, Maryland. We explored spatial and temporal overlap between human and deer activity over 24 months (2018-2019) across a hexagonal tessellation with metrics like hourly popularity and visit counts. Negative binomial models were fitted to the visit counts of each deer and humans per tessellation area, using landscape features as predictors. A separate deer-only model included commercial human activity as another predictor. Spatial analysis showed deer and humans sharing spaces in the study area, with results indicating deer using more populated residential areas and areas with commercial activity. Temporal analysis showed deer avoiding commercial spaces during daytime but using them in late evening and early morning. These findings highlight the complex space use between species and the importance of integrating detailed human mobility and animal movement data when managing wildlife-human conflict and zoonotic disease transmission, particularly in urban areas with a high probability of deer-human interactions.},
}
@article {pmid40425079,
year = {2025},
author = {Mambully, S and Ramesh, V and Rani, S and Khatoon, M and Jayashree, A and Patil, AV and Palavesam, A and Sengupta, PP and Patil, SS and Suresh, KP},
title = {Genotype Patterns and Evolutionary Rates: Uncovering Japanese Encephalitis Virus Spread Across Asia's Climate Regions.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107676},
doi = {10.1016/j.actatropica.2025.107676},
pmid = {40425079},
issn = {1873-6254},
abstract = {Japanese Encephalitis Virus (JEV) is a highly endemic zoonotic virus, consistently found in Asia and parts of the Western Pacific, and it's a major cause of human encephalitis. JEV belongs to a family of antigenically related viruses such as West Nile Virus (WNV), Murray Valley encephalitis virus (MVEV), and Aichi Lake Fever Virus (ALFV) and is transmitted by mosquitoes. Persistent outbreaks of the disease necessitate detailed studies to understand their transmission dynamics and develop effective prevention strategies. This study explores the evolutionary dynamics and spatial transmission of JEV, concentrating on the envelope protein (E) structural gene sequences obtained from across Asia's diverse climatic regions. Evolutionary modeling of the JEV E gene revealed a higher evolutionary rate in tropical regions compared to temperate regions, with nucleotide substitution rates estimated at 1.12 × 10[-3] per site per year for tropical regions and 5.284 × 10[-4] for temperate regions. The time to the most recent common ancestor (tMRCA) was traced to 1796 from Korea for temperate regions, and 1865 from Indonesia for tropical regions. Among the five genotypes of JEV, Genotype I (GI) and III (GIII) were established all over Southeast Asia; moreover, GI revealed a higher evolutionary rate, reflecting its adaptability to diverse ecological niches. The phylogeographic analysis highlighted significant contributions to virus diffusion by China, Korea, and Japan in temperate zones and by Vietnam in tropical zones. By analyzing genetic sequences from various regions and time periods, this study delivered valuable intuitions into transmission pathways. The findings highlighted the necessity of ongoing surveillance and evolutionary monitoring to track the spread and emergence of novel variations of JEV, which are crucial not just for managing JEV outbreaks but also for guiding immunization programs and public health initiatives.},
}
@article {pmid40419494,
year = {2025},
author = {Jucker, T and Fischer, FJ and Chave, J and Coomes, DA and Caspersen, J and Ali, A and Loubota Panzou, GJ and Feldpausch, TR and Falster, D and Usoltsev, VA and Jackson, TD and Adu-Bredu, S and Alves, LF and Aminpour, M and Angoboy Ilondea, B and Anten, NPR and Antin, C and Askari, Y and Ayyappan, N and Banin, LF and Barbier, N and Battles, JJ and Beeckman, H and Bocko, YE and Bond-Lamberty, B and Bongers, F and Bowers, S and van Breugel, M and Chantrain, A and Chaudhary, R and Dai, J and Dalponte, M and Dimobe, K and Domec, JC and Doucet, JL and Dupuy Rada, JM and Duursma, RA and Enríquez, M and van Ewijk, KY and Farfán-Rios, W and Fayolle, A and Ferretti, M and Forni, E and Forrester, DI and Gilani, H and Godlee, JL and Haeni, M and Hall, JS and He, JK and Hemp, A and Hernández-Stefanoni, JL and Higgins, SI and Holdaway, RJ and Hussain, K and Hutley, LB and Ichie, T and Iida, Y and Jiang, HS and Joshi, PR and Kaboli, H and Kazempour Larsary, M and Kenzo, T and Kloeppel, BD and Kohyama, TS and Kunwar, S and Kuyah, S and Kvasnica, J and Lin, S and Lines, ER and Liu, H and Lorimer, C and Loumeto, JJ and Malhi, Y and Marshall, PL and Mattsson, E and Matula, R and Meave, JA and Mensah, S and Mi, X and Momo, ST and Moncrieff, GR and Mora, F and Muñoz, R and Nissanka, SP and Nur Hajar, ZS and O'Hara, KL and Pearce, S and Pelissier, R and Peri, PL and Ploton, P and Poorter, L and Pour, MJ and Pourbabaei, H and Ribeiro, SC and Ryan, C and Sanaei, A and Sanger, J and Schlund, M and Sellan, G and Shenkin, A and Sonké, B and Sterck, FJ and Svátek, M and Takagi, K and Trugman, AT and Vadeboncoeur, MA and Valipour, A and Vanderwel, MC and Vovides, AG and Waldner, P and Wang, W and Wang, LQ and Wirth, C and Woods, M and Xiang, W and de Aquino Ximenes, F and Xu, Y and Yamada, T and Zavala, MA and Zimmermann, NE},
title = {The global spectrum of tree crown architecture.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4876},
pmid = {40419494},
issn = {2041-1723},
support = {NE/S01537X/1//RCUK | Natural Environment Research Council (NERC)/ ; },
mesh = {*Trees/anatomy &amp; histology/physiology/classification ; Ecosystem ; *Plant Stems/anatomy &amp; histology ; Photosynthesis ; Climate ; Biological Evolution ; Phylogeny ; },
abstract = {Trees can differ enormously in their crown architectural traits, such as the scaling relationships between tree height, crown width and stem diameter. Yet despite the importance of crown architecture in shaping the structure and function of terrestrial ecosystems, we lack a complete picture of what drives this incredible diversity in crown shapes. Using data from 374,888 globally distributed trees, we explore how climate, disturbance, competition, functional traits, and evolutionary history constrain the height and crown width scaling relationships of 1914 tree species. We find that variation in height-diameter scaling relationships is primarily controlled by water availability and light competition. Conversely, crown width is predominantly shaped by exposure to wind and fire, while also covarying with functional traits related to mechanical stability and photosynthesis. Additionally, we identify several plant lineages with highly distinctive stem and crown forms, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legume trees in African savannas. Our study charts the global spectrum of tree crown architecture and pinpoints the processes that shape the 3D structure of woody ecosystems.},
}
@article {pmid40417563,
year = {2024},
author = {Foreman, MA and Ross, A and Burgess, APH and Myneni, S and Franklin, A},
title = {Barriers and Facilitators of Digital Health Use for Self-Management of Hypertensive Disorders by Black Pregnant Women.},
journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium},
volume = {2024},
number = {},
pages = {433-442},
pmid = {40417563},
issn = {1942-597X},
mesh = {Humans ; Female ; Pregnancy ; *Self-Management ; *Black or African American ; *Hypertension, Pregnancy-Induced/therapy/ethnology ; Adult ; Interviews as Topic ; Telemedicine ; Digital Health ; White ; },
abstract = {Although digital health tools are increasingly common for managing health conditions, these applications are often developed without consideration of differences across user populations. A reproducible framework is needed to support tailoring applications to include cultural considerations, potentially leading to better adoption and more effective use. As a first step, this study captures a snapshot of Black women's barriers and facilitators in using digital health products for self-management of hypertensive disorders of pregnancy (HDP). One-on-one semi-structured interviews were conducted with 17 Black pregnant women with HDP. We established a unique model for cultural tailoring with these experiences using Black feminist theory and the CDC's Social-Ecological Model (SEM). 38 themes across the four levels of SEM were found through grounded theory. These themes can inform the feature development of a digital health intervention. Future work will instantiate and validate a framework that provides theoretical constructs for developing culturally tailored digital health interventions.},
}
@article {pmid40359589,
year = {2025},
author = {Silva, MKP and Nicoleti, VYU and Rodrigues, BDPP and Araujo, ASF and Ellwanger, JH and de Almeida, JM and Lemos, LN},
title = {Exploring deep learning in phage discovery and characterization.},
journal = {Virology},
volume = {609},
number = {},
pages = {110559},
doi = {10.1016/j.virol.2025.110559},
pmid = {40359589},
issn = {1096-0341},
mesh = {*Deep Learning ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Metagenomics/methods ; Computational Biology/methods ; Genome, Viral ; Neural Networks, Computer ; Metagenome ; Algorithms ; },
abstract = {Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.},
}
@article {pmid40258091,
year = {2025},
author = {Hashem, I and Wang, J and Van Impe, JFM},
title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012974},
doi = {10.1371/journal.pcbi.1012974},
pmid = {40258091},
issn = {1553-7358},
mesh = {*Algorithms ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Biofilms/growth &amp; development ; },
abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.},
}
@article {pmid40416669,
year = {2025},
author = {Gaievskyi, S and Delfrate, N and Ragazzoni, L and Bahattab, A},
title = {Use of multi-criteria decision analysis (MCDA) to support decision-making during health emergencies: a scoping review.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1584026},
pmid = {40416669},
issn = {2296-2565},
mesh = {Humans ; *Decision Support Techniques ; *Decision Making ; *Emergencies ; },
abstract = {BACKGROUND: The mismatch between the health needs of populations affected by emergencies and resources devoted to response is projected to further increase. Making the response more effective is one of the solutions to meet the growing needs. Multi-criteria decision analysis (MCDA) has been successfully used to increase effectiveness in various fields by supporting decision-making. However, no review of its application to all-hazard health emergencies has been done to date.<br><br>METHODS: A review of peer-reviewed English-language articles published since 2004 was conducted in May 2024 using Scopus, PubMed and Web of Science databases. The review focused on the empirical application of MCDA to support decision-making during health emergencies. The review was guided by the Joanna Briggs Institute methodology for scoping reviews and adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Quantitative data were analyzed using summary statistics and qualitative data were analyzed using content analysis.<br><br>RESULTS: Seventy-one articles were included after screening. The articles described the MCDA application to support a variety of decision problems related to health emergency management. However, the technique was mostly applied to infectious hazards management and only seldom to other hazards. The review also found a lack of standardized methodology for identifying alternatives and criteria, weighting, computation of model output, methods of dealing with uncertainty, and stakeholder engagement.<br><br>CONCLUSION: The review provides an overview of the current use of the MCDA approach to support decision-making in health emergency management and informs areas of future development. The review emphasizes that while MCDA is already used for infectious hazards, it is underutilized for other types of health emergencies. Developing tailored MCDA approaches for health emergencies, including defining evaluation criteria and stakeholder engagement, may improve uptake of the technique and benefit the efforts to meet the growing health needs of the population affected by emergencies, https://osf.io/6kd5s/.},
}
@article {pmid40344154,
year = {2025},
author = {Babič, J and Kunavar, T and Oztop, E and Kawato, M},
title = {Success-efficient/failure-safe strategy for hierarchical reinforcement motor learning.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1013089},
doi = {10.1371/journal.pcbi.1013089},
pmid = {40344154},
issn = {1553-7358},
mesh = {Humans ; *Reinforcement, Psychology ; *Learning/physiology ; Male ; Female ; Computational Biology ; Movement/physiology ; Adult ; Young Adult ; Psychomotor Performance/physiology ; Motor Skills/physiology ; },
abstract = {Our study explores how ecological aspects of motor learning enhance survival by improving movement efficiency and mitigating injury risks during task failures. Traditional motor control theories mainly address isolated body movements and often overlook these ecological factors. We introduce a novel computational motor control approach, incorporating ecological fitness and a strategy that alternates between success-driven movement efficiency and failure-driven safety, akin to win-stay/lose-shift tactics. In our experiments, participants performed squat-to-stand movements under novel force perturbations. They adapted effectively through various adaptive motor control mechanisms to avoid falls, reducing failure rates rapidly. The results indicate a high-level ecological controller in human motor learning that switches objectives between safety and movement efficiency, depending on failure or success. This approach is supported by policy learning, internal model adaptation, and adaptive feedback control. Our findings offer a comprehensive perspective on human motor control, integrating risk management in a hierarchical reinforcement learning framework for real-world environments.},
}
@article {pmid40091604,
year = {2025},
author = {Tu, M and Liu, N and He, ZS and Dong, XM and Gao, TY and Zhu, A and Yang, JB and Zhang, SB},
title = {Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum.},
journal = {Plant biotechnology journal},
volume = {23},
number = {6},
pages = {2162-2181},
doi = {10.1111/pbi.70025},
pmid = {40091604},
issn = {1467-7652},
support = {202403AC100032//Key Research and Development Program of Yunnan Province/ ; YNWR-CYJS-2020-023//High-level Talent Support Plan of Yunnan Province/ ; XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32170393//National Natural Science Foundation of China/ ; 2024YFF1306703//National Key Research and Development Program of China/ ; 202201AU070123//Yunnan Fundamental Research Project/ ; 202301AT070306//Yunnan Fundamental Research Project/ ; },
mesh = {*Flowers/metabolism/genetics ; *Orchidaceae/genetics/metabolism ; *Odorants/analysis ; Terpenes/metabolism ; Gene Expression Regulation, Plant ; Transcriptome ; Volatile Organic Compounds/metabolism ; Genomics ; Plant Proteins/metabolism/genetics ; Multiomics ; },
abstract = {Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.},
}
@article {pmid40415801,
year = {2025},
author = {Yang, P and Wang, X and Yang, J and Yan, B and Sheng, H and Li, Y and Yang, Y and Wang, J},
title = {AI-Driven Multiscale Study on the Mechanism of Polygonati Rhizoma in Regulating Immune Function in STAD.},
journal = {ACS omega},
volume = {10},
number = {19},
pages = {19770-19796},
pmid = {40415801},
issn = {2470-1343},
abstract = {Polygonati Rhizoma, a traditional Chinese medicine, has demonstrated immunomodulatory and anticancer properties, yet its precise mechanisms in stomach adenocarcinoma (STAD) remain underexplored. This study aims to uncover the multitarget mechanisms of Polygonati Rhizoma in regulating the tumor immune microenvironment in STAD using artificial intelligence (AI)-driven network pharmacology, bioinformatics, and single-cell RNA sequencing, offering new insights into its immunotherapeutic potential. This study harnessed the power of AI to unravel the molecular mechanisms underlying Polygonati Rhizoma's effects. AI-driven methodologies screened 38 putative constituents, retaining 8 based on ADME criteria. Machine Learning algorithms predicted potential targets, which were cross-referenced with 5,569 immune-related genes from GeneCards, revealing 52 immune-associated targets. Differential expression analysis of the STAD data set identified 18 overlapping DEGs with prognostic significance and immune cell infiltration correlations. Key targets (AKT1, TP53, PTGS2 and VEGFA) emerged as central nodes in the network, with AI-assisted molecular docking confirming strong binding affinities, particularly between diosgenin and these core proteins. Molecular dynamics simulations further validated these interactions. Single-cell RNA sequencing revealed distinct target-gene expression patterns across malignant, stromal, and immune cell subsets in digestive-system tumors. In vitro, Polygonati Rhizoma extract significantly inhibited HGC-27 cell viability and increased intracellular ROS levels. These findings underscore the critical role of AI in integrating multiscale analyses, unveiling a multitarget immunomodulatory and antitumor mechanism for Polygonati Rhizoma in STAD, and providing a foundation for future preclinical and clinical studies.},
}
@article {pmid40414987,
year = {2025},
author = {Jia, L and Liu, Z and Li, Y},
title = {Spatiotemporal dynamics of rural settlement evolution in Guangdong Province, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18244},
pmid = {40414987},
issn = {2045-2322},
support = {23BDJ019//National Planning Office of Philosophy and Social Science/ ; 23BDJ019//National Planning Office of Philosophy and Social Science/ ; },
mesh = {China ; *Rural Population/statistics &amp; numerical data ; Humans ; *Urbanization/trends ; Spatio-Temporal Analysis ; *Population Dynamics ; Socioeconomic Factors ; Industrial Development ; Geographic Information Systems ; },
abstract = {This study analyzes the spatiotemporal dynamics of rural settlement evolution in Guangdong Province, China, examining their transformation amid rapid urbanization and industrialization over the past 20 years. Rural settlements serve as primary spatial carriers for production and living activities, embodying multiple functions including production, living, ecological, and cultural aspects. Using GIS-based analytical tools, including landscape pattern indices, average nearest neighbor index, kernel density estimation, and geographical detector methods, we examined settlement evolution patterns and their driving factors. Results show a continuous decline in settlement numbers, while patch areas exhibited a U-shaped trend of decreasing then increasing. Settlement patterns shifted from "reduction" to "integration", with intensifying spatial agglomeration over time. The Pearl River Delta and Eastern Guangdong regions followed similar trajectories, reflecting the impact of urbanization and industrialization on rural development. Multiple factors, including natural conditions, socioeconomic variables, and locational accessibility, drove these changes. The spatial distribution of rural settlements demonstrates an overall trend of agglomeration, which has gradually intensified over time, leading to significant variations in settlement density across different regions. The findings reveal significant regional disparities and temporal changes in settlement patterns, highlighting the complex interplay between rural transformation and urban development. This research contributes to understanding rural transformation processes in developing countries and emphasizes the need for differentiated approaches in spatial planning and rural revitalization strategies to address the challenges of disordered land expansion and population hollowing while promoting sustainable rural development.},
}
@article {pmid40414334,
year = {2025},
author = {Dou, X and Liu, Q and Fan, Q and Guo, J and Qi, W},
title = {Comprehensive Analysis of Common Heavy Metals in the Yellow River Over 20 Years: Spatiotemporal distribution, Migration Characteristics, Traceability, and Potential Risk Evaluation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121931},
doi = {10.1016/j.envres.2025.121931},
pmid = {40414334},
issn = {1096-0953},
abstract = {Heavy metal pollution posed a great threat to the global aquatic ecological environment, especially in the Yellow River where the utilization rate of water resources was as high as 80%. This study addressed the spatiotemporal distribution, sources, and ecological risks of seven heavy metals (As, Cd, Cr, Cu, Ni, Pb, Zn) in the Yellow River by analyzing historical data collected from 2000 to 2020. The annual heavy metal fluxes increased from Qinghai to Henan section, then decreased from Henan to Shandong section. Similarly, concentrations of Cu, Ni, Pb, and Zn peaked in the sediments of the Henan section. These trends might be attributed to the interception effects of the Xiaolangdi and Sanmenxia Dams. The annual fluxes from 2016-2020 increased by an average of 162.6% compared to that from 2011-2015, likely reflecting the impact of ongoing economic growth (33.36%) and SS increase (69.68%). The annual fluxes of SS demonstrated a significant correlation with all heavy metal fluxes, underscoring their role as a critical transport medium in aquatic ecosystem. The fluxes of Cd and Pb were most strongly influenced by human factors. While most metals in surface water present negligible risks to aquatic life, Cd in sediments presents a considerable ecological threat. Furthermore, the highest potential ecological risk index (RI) was observed in the river sections in Gansu and Inner Mongolia, mainly due to Cd, which contributed up to 85.87%. The findings establish a fundamental framework for safeguarding the aquatic ecosystem of the Yellow River and managing its heavy metal contamination.},
}
@article {pmid40413228,
year = {2025},
author = {Fan, J and Zhang, Y and Nie, X and Liu, Y and Wei, S and Peng, H and Li, H and Zhang, M and Ning, L and Wang, S and Qin, L and Zheng, Y and Xing, Y},
title = {Comprehensive curation and validation of genomic datasets for chestnut.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {860},
pmid = {40413228},
issn = {2052-4463},
mesh = {*Fagaceae/genetics ; *Genome, Plant ; Genomics ; Databases, Genetic ; Molecular Sequence Annotation ; Data Curation ; },
abstract = {The Chinese chestnut (Castanea mollissima) stands out as a plant with significant ecological and economic value, excellent nutritional quality and natural resistance to pests and diseases. Recent strides in high-throughput techniques have enabled the continuous accumulation of genomic data on chestnuts, presenting a promising future for genetic research and advancing traits in this species. To facilitate the accessibility and utility of this data, we have curated and analyzed a collection of genomic datasets for eight Castanea species, including functional annotations, 213 RNA-Seq samples, and 330 resequencing samples. These datasets are publicly available on Figshare and are also available through other platforms such as GEO and EVA, providing a valuable resource for researchers studying Castanea genetics, functional genomics, and evolutionary biology. Furthermore, the datasets are integrated into the Castanea Genome Database (CGD, http://castaneadb.net), which serves as a complementary platform, offering advanced data mining and analysis tools, including BLAST, Batch Query, GO/KEGG Enrichment Analysis, and Synteny Viewer, to enhance the usability of the curated datasets.},
}
@article {pmid40412934,
year = {2025},
author = {Zhu, Q and Cai, Y and Hu, Z},
title = {Effects of bactericides and sulphate reducing bacteria addition on acidification and microbial community structure of newly produced coal gangue.},
journal = {Journal of environmental sciences (China)},
volume = {156},
number = {},
pages = {311-320},
doi = {10.1016/j.jes.2024.06.024},
pmid = {40412934},
issn = {1001-0742},
mesh = {*Coal ; Sulfates/metabolism ; *Bacteria/metabolism ; Hydrogen-Ion Concentration ; *Microbiota ; *Soil Microbiology ; },
abstract = {Microbiologically driven acidic pollution of coal gangue has become a major environmental problem in coal gangue dumps in coal mining areas. Addition of bactericides and sulphate reducing bacteria (SRB) is an effective means to control the acidic pollution of coal gangue, but their mechanism of action has not been fully investigated. By adding bactericide, SRB and bactericide-SRB to the newly produced coal gangue, respectively, the effects of these treatments on the microbial community structure were observed. Changes in pH and electrical conductivity (EC) of the gangue leaching solution, as well as the microbial community composition and functional abundance on the gangue surface were analysed by leaching simulation experiments and 16S rRNA sequencing. The results showed that (1) the addition of bactericide-SRB was the most effective treatment to elevate pH before 8 d, while the addition of SRB performed best after 22 d (2) The addition of bactericide and SRB drastically changed the microbial community structure on the gangue surface. Simultaneous addition of both had the best inhibitory effect on pathogenic bacteria and Thiobacillus. (3) All three treatments promote higher abundance of genes related to nitrogen cycling, but reflected in different gene functions. Microorganisms with sulfate respiration function in the experimental group all showed different increases. The abundance of other sulfur cycle genes decreased substantially. However, Human Pathogens All had higher abundance than control check (CK) in each treatment, which may indicate that the addition of either bactericides or SRB increases the risk of microbial pathogenicity to humans.},
}
@article {pmid40410961,
year = {2025},
author = {Zhang, L and Zhang, L and Gao, S and Huang, C and Dai, Q},
title = {Structural balance and evolution of cooperation in a population with hybrid interactions.},
journal = {Physical review. E},
volume = {111},
number = {4-1},
pages = {044309},
doi = {10.1103/PhysRevE.111.044309},
pmid = {40410961},
issn = {2470-0053},
abstract = {This study explores the evolution of cooperation in populations with mixed pairwise and three-body interactions, investigating the impact of higher-order interaction density ρ and individual interaction preference α. Our results reveal that sparse higher-order interactions markedly boost cooperation, exhibiting two critical phase transitions as ρ changes. These transitions underscore the delicate equilibrium needed for optimal cooperation, as excessive higher-order interactions can diminish returns. The preference parameter α significantly influences cooperation sustainability, with intermediate values maximizing cooperative outcomes, particularly when the temptation to defect r is not strong. Crucially, our findings demonstrate that hybrid social dilemmas structurally encode emergent cooperation pathways that are unattainable within homogeneous interaction frameworks, emphasizing the importance of modeling mixed interactions to capture real-world complexity. These insights offer valuable guidance for designing systems aimed at promoting cooperative behavior across social, ecological, and artificial domains.},
}
@article {pmid40408306,
year = {2025},
author = {Bukat, A and Bukowicki, M and Bykowski, M and Kuczkowska, K and Nowakowski, S and Śliwińska, A and Kowalewska, &#x141;},
title = {GRANA: An AI-based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf212},
pmid = {40408306},
issn = {1532-2548},
abstract = {Grana are fundamental structural units of the intricate chloroplast membrane network. Investigating their nanomorphology is essential for understanding photosynthetic efficiency regulation. Here, we present GRANA (Graphical Recognition and Analysis of Nanostructural Assemblies), an AI-enhanced, user-friendly software tool that recognizes grana on thylakoid network electron micrographs and generates a complex set of their structural parameters. GRANA employs three artificial neural networks of different architectures and binds them in a one-click workflow. Its output is designed to facilitate hybrid intelligence analysis, securing fast and reliable results from large datasets. The GRANA tool is over 100 times faster compared with currently used manual approaches. As a proof of concept, we have successfully applied GRANA software to diverse grana structures across different land plant species grown under various conditions, demonstrating the wide range of potential applications for our software. GRANA tool supports large-scale analysis of grana nanomorphological features, facilitating advancements in photosynthesis-oriented studies.},
}
@article {pmid40408146,
year = {2025},
author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP},
title = {MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {5},
pages = {},
doi = {10.1093/bioinformatics/btaf174},
pmid = {40408146},
issn = {1367-4811},
support = {BB/W013770/1//Bioengineered Cells &amp; Systems/ ; BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Software ; *Microbiota ; Bayes Theorem ; *Computational Biology/methods ; *Microbial Interactions ; Machine Learning ; Computer Simulation ; },
abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analyzing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.<br><br>MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.},
}
@article {pmid40407930,
year = {2025},
author = {Bate, JB and Dagamac, NHA},
title = {Wallow land suitability assessment using GIS-based multicriteria decision-making framework.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {6},
pages = {668},
pmid = {40407930},
issn = {1573-2959},
mesh = {*Geographic Information Systems ; *Conservation of Natural Resources/methods ; Animals ; *Environmental Monitoring/methods ; Ecosystem ; Philippines ; Decision Making ; Biodiversity ; },
abstract = {Protected areas are the frontlines of biodiversity conservation, featuring critical landscapes and microhabitats that are fitted for the survival of the organisms that have restricted populations. The determination of land suitability and habitat connectivity in these protected areas are important for species with specialized adaptive behavior that requires favorable conditions to survive. The Bubalus mindorensis is a critically endangered bovine of the Philippines which utilizes mud or water puddles to address heat stress through body submersion, known as wallowing. With Mts. Iglit-Baco National Park (MIBNP) harboring the largest remaining subpopulation of the tamaraw, the preservation of its natural landscapes is critical for tamaraw survival. Here, the potential wallows in MIBNP were determined using the weighted overlay analysis (WOA) assisted by the analytical hierarchy process (AHP). Using environmental variables that were influential to the creation of wallows, an equal-weighed scenario and an AHP-assisted scenario wallow suitability map was generated. Moderate and highly suitable areas were found at the north-central portion of the mountain, coinciding with the current and future conservation zones of the tamaraw, whereas low suitable areas dominate the other half, aggregating at the corners due to build areas and agriculture. The result of the study provides supplementary information in constructing future conservation strategies for an endemic species with global importance, particularly in its possible range expansion within the park. Furthermore, this study provides a framework for future conservation efforts, which helps in the management of critical landscapes for species with specialized adaptive behaviors through GIS-based multicriteria decision-making.},
}
@article {pmid40407563,
year = {2025},
author = {Araujo, ACB and Souza, OF and Kersanach, BB and Mozzer, JSC and Feitosa, VL and Brandão, VA and Alencar, FEC and Oliveira, NS and Silva, AVBD and Abreu, LC},
title = {Trends in Congenital Syphilis Incidence and Mortality in Brazil's Southeast Region: A Time-Series Analysis (2008-2022).},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {6},
number = {2},
pages = {},
pmid = {40407563},
issn = {2673-3986},
support = {182023//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Esp&#xed;rito Santo/ ; },
abstract = {Congenital syphilis (CS) is an important infectious cause of miscarriage, stillbirth, and neonatal morbidity and mortality. Despite the advances in diagnosis and treatment, CS continues to challenge health systems with increasing incidence and mortality rates in recent years worldwide. Given this, the present study aims to comparatively analyze the temporal trends in CS incidence and mortality in Brazil's Southeast Region from 2008 to 2022. This is an ecological time-series study using secondary data on congenital syphilis from the states of Espírito Santo, Minas Gerais, Rio de Janeiro, and São Paulo. The data was extracted from the Brazilian Health System Informatics Department. Incidence and mortality rates were calculated per 100,000 live births. Joinpoint regression models were employed to identify trends in annual percentage change and average annual percentage change with 95% confidence intervals. The temporal trend of CS incidence in Brazil's Southeast Region increased 12.8% between 2008 and 2022. Minas Gerais, São Paulo, Espírito Santo, and Rio de Janeiro showed increasing temporal trends of 21.4%, 14.1%, 14.0%, and 10.9%, respectively. The temporal trend of CS mortality in Brazil's Southeast Region rose 11.9% between 2008 and 2022. Minas Gerais, São Paulo, and Rio de Janeiro exhibited increasing mortality temporal trends of 21.9%, 20.8%, and 10.1%, respectively. In contrast, Espírito Santo showed reduced mortality, with no deaths in 2021 and 2022. The temporal trend of CS incidence increased in all states of Brazil's Southeast Region between 2008 and 2022, highlighting the need to reassess control measures. The temporal trend of CS mortality also increased during the same period, except in Espírito Santo. Considering that CS is preventable with adequate prenatal care and low-cost measures, these findings can serve as instruments to support strengthening public health policies.},
}
@article {pmid40407387,
year = {2025},
author = {Wang, M and Chen, X and Liu, M and Luo, H and Zhang, S and Guo, J and Wang, J and Zhou, L and Zhang, N and Li, H and Wang, C and Li, L and Wang, Z and Wang, H and Guo, Z and Li, Y and Wang, Y},
title = {Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
pmid = {40407387},
issn = {1477-4054},
support = {2021CXGC010509//2021 Shandong Provincial Key RD Program (Major Technological Innovation Project)/ ; 2022ZDYF0410//Key RD Projects of Ningxia Hui Nationality Autonomous Region in 2022/ ; },
mesh = {*Medicine, Chinese Traditional/methods ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Humans ; Arthritis, Rheumatoid/drug therapy ; Databases, Factual ; Animals ; },
abstract = {Traditional Chinese medicine (TCM) utilizes intricate herbal formulations that exemplify the principles of compatibility and synergy. However, the rapid proliferation of herbal data has resulted in redundant information, complicating the understanding of their potential mechanisms. To address this issue, we first established a comprehensive database that encompasses 992 herbs, 18 681 molecules, and 2168 targets. Consequently, we implemented a multi-network strategy based on a core information screening method to elucidate the highly intertwined relationships among the targets of various herbs and to refine herbal target information. Within a non-redundant network framework, separation and overlap analysis demonstrated that the networking of herbs preserves essential clinical information, including their properties, meridians, and therapeutic classifications. Furthermore, two notable trends emerged from the statistical analyses of classical TCM formulas: the separation of herbs and the overlap between herbs and diseases. This phenomenon is termed the herbal combination model (HCM), validated through statistical analyses of two representative case studies: the common cold and rheumatoid arthritis. Additionally, in vivo and in vitro experiments with the new formula YanChuanQin (YanHuSuo-Corydalis Rhizoma, ChuanWu-Aconiti Radix, and QinJiao-Gentianae Macrophyllae Radix) for acute gouty arthritis further support the HCM. Overall, this computational method provides a systematic network strategy for exploring herbal combinations in complex and poorly understood diseases from a non-redundant perspective.},
}
@article {pmid40341906,
year = {2025},
author = {Shoemaker, WR and Sánchez, &#xc1; and Grilli, J},
title = {Macroecological patterns in experimental microbial communities.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1013044},
doi = {10.1371/journal.pcbi.1013044},
pmid = {40341906},
issn = {1553-7358},
mesh = {*Models, Biological ; *Ecology/methods ; Biodiversity ; Ecosystem ; *Microbiota/physiology ; Computational Biology ; },
abstract = {Ecology has historically benefited from the characterization of statistical patterns of biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal patterns of diversity and abundance that can be captured by effective models. Experimentation has simultaneously played a crucial role, as the advent of high-replication community time-series has allowed researchers to investigate underlying ecological forces. However, there remains a gap between experiments performed in the laboratory and macroecological patterns documented in natural systems, as we do not know whether these patterns can be recapitulated in the lab and whether experimental manipulations produce macroecological effects. This work aims at bridging the gap between experimental ecology and macroecology. Using high-replication time-series, we demonstrate that microbial macroecological patterns observed in nature exist in a laboratory setting, despite controlled conditions, and can be unified under the Stochastic Logistic Model of growth (SLM). We found that demographic manipulations (e.g., migration) impact observed macroecological patterns. By modifying the SLM to incorporate said manipulations alongside experimental details (e.g., sampling), we obtain predictions that are consistent with macroecological outcomes. By combining high-replication experiments with ecological models, microbial macroecology can be viewed as a predictive discipline.},
}
@article {pmid40407023,
year = {2025},
author = {Pang, D and Zhu, R and Zhao, H and Wang, T},
title = {Probabilistic exponential family inverse regression and its applications.},
journal = {Biometrics},
volume = {81},
number = {2},
pages = {},
doi = {10.1093/biomtc/ujaf065},
pmid = {40407023},
issn = {1541-0420},
support = {12222111//National Natural Science Foundation of China/ ; 12331009//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Algorithms ; Computer Simulation ; *Models, Statistical ; Regression Analysis ; Likelihood Functions ; *Biometry/methods ; Data Interpretation, Statistical ; },
abstract = {Rapid advances in high-throughput sequencing technologies have led to the fast accumulation of high-dimensional data, which is harnessed for understanding the implications of various factors on human disease and health. While dimension reduction plays an essential role in high-dimensional regression and classification, existing methods often require the predictors to be continuous, making them unsuitable for discrete data, such as presence-absence records of species in community ecology and sequencing reads in single-cell studies. To identify and estimate sufficient reductions in regressions with discrete predictors, we introduce probabilistic exponential family inverse regression (PrEFIR), assuming that, given the response and a set of latent factors, the predictors follow one-parameter exponential families. We show that the low-dimensional reductions result not only from the response variable but also from the latent factors. We further extend the latent factor modeling framework to the double exponential family by including an additional parameter to account for the dispersion. This versatile framework encompasses regressions with all categorical or a mixture of categorical and continuous predictors. We propose the method of maximum hierarchical likelihood for estimation, and develop a highly parallelizable algorithm for its computation. The effectiveness of PrEFIR is demonstrated through simulation studies and real data examples.},
}
@article {pmid40406849,
year = {2025},
author = {Han, Y and Cai, J and Chen, Y and Zhang, Y and Jin, LN and Chen, T and Li, J and Zhang, G and Chen, J},
title = {Concurrent Formation of Low-Maturity EC and BrC in Biomass and Coal Burning: O-PAH as a Precursor.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c13299},
pmid = {40406849},
issn = {1520-5851},
abstract = {Black carbon (BC) significantly influences climate change through light absorption. Traditional emission inventories equate BC with elemental carbon (EC) and overlook the variability in its properties across sources, leading to uncertainties in climate predictions. This study shows that EC from solid fuel combustion contains substantial low-maturity EC (char), whose emissions increase alongside the light absorption of soluble organic carbon (OC) as the fuel aromaticity rises. Concurrently, the abundance of oxygenated polycyclic aromatic hydrocarbons (O-PAHs) in soluble OC also increases. This suggests that char and brown carbon (BrC) share similar formation pathways with O-PAHs as key precursors. Time-resolved analysis during combustion cycles revealed a significant positive correlation between O-PAHs, the light absorption of soluble OC, and char emissions, further supporting this shared pathway. The nonbonding orbitals in BrC and char facilitate n → π* transitions in the visible region, which are more wavelength-dependent than the π → π* transition in high-maturity EC (soot). This study highlights char as a light-absorbing intermediate, influencing light absorption of EC emitted from solid fuel combustion. These insights into the formation pathways and optical properties of carbonaceous aerosols enhance our understanding of their climate impacts and underscore the need to differentiate between char and soot in climate models to improve accuracy.},
}
@article {pmid40404926,
year = {2025},
author = {Pringle, S and Dallimer, M and Goddard, MA and Le Goff, LK and Hart, E and Langdale, SJ and Fisher, JC and Abad, SA and Ancrenaz, M and Angeoletto, F and Auat Cheein, F and Austen, GE and Bailey, JJ and Baldock, KCR and Banin, LF and Banks-Leite, C and Barau, AS and Bashyal, R and Bates, AJ and Bicknell, JE and Bielby, J and Bosilj, P and Bush, ER and Butler, SJ and Carpenter, D and Clements, CF and Cully, A and Davies, KF and Deere, NJ and Dodd, M and Drinkwater, R and Driscoll, DA and Dutilleux, G and Dyrmann, M and Edwards, DP and Farhadinia, MS and Faruk, A and Field, R and Fletcher, RJ and Foster, CW and Fox, R and Francksen, RM and Franco, AMA and Gainsbury, AM and Gardner, CJ and Giorgi, I and Griffiths, RA and Hamaza, S and Hanheide, M and Hayward, MW and Hedblom, M and Helgason, T and Heon, SP and Hughes, KA and Hunt, ER and Ingram, DJ and Jackson-Mills, G and Jowett, K and Keitt, TH and Kloepper, LN and Kramer-Schadt, S and Labisko, J and Labrosse, F and Lawson, J and Lecomte, N and de Lima, RF and Littlewood, NA and Marshall, HH and Masala, GL and Maskell, LC and Matechou, E and Mazzolai, B and McConnell, A and Melbourne, BA and Miriyev, A and Nana, ED and Ossola, A and Papworth, S and Parr, CL and Payo-Payo, A and Perry, G and Pettorelli, N and Pillay, R and Potts, SG and Prendergast-Miller, MT and Qie, L and Rolley-Parnell, P and Rossiter, SJ and Rowcliffe, M and Rumble, H and Sadler, JP and Sandom, CJ and Sanyal, A and Schrodt, F and Sethi, SS and Shabrani, A and Siddall, R and Smith, SC and Snep, RPH and Soulsbury, CD and Stanley, MC and Stephens, PA and Stephenson, PJ and Struebig, MJ and Studley, M and Svátek, M and Tang, G and Taylor, NK and Umbers, KDL and Ward, RJ and White, PJC and Whittingham, MJ and Wich, S and Williams, CD and Yakubu, IB and Yoh, N and Zaidi, SAR and Zmarz, A and Zwerts, JA and Davies, ZG},
title = {Opportunities and challenges for monitoring terrestrial biodiversity in the robotics age.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
pmid = {40404926},
issn = {2397-334X},
abstract = {With biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more 'difficult' taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively.},
}
@article {pmid40404775,
year = {2025},
author = {Wang, J and Xu, Y and Zhu, H and Chen, C and Zhao, Y and Wang, Y},
title = {CheloniansTraits: a comprehensive trait database of global turtles and tortoises.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {840},
pmid = {40404775},
issn = {2052-4463},
support = {32271734//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Turtles/anatomy &amp; histology ; Animals ; Databases, Factual ; Biological Evolution ; Life History Traits ; Conservation of Natural Resources ; },
abstract = {Turtles and tortoises (chelonians) possess a variety of ecological characteristics, including long lifespans and protective shells, which have enabled them to survive and adapt to environmental challenges since the Triassic period. However, many characteristics of chelonians have turned into disadvantages for their populations in the Anthropocene. Currently, there remains a lack of comprehensive data on the morphological, life-history, and ecological characteristics of all chelonians on a global scale. Consequently, our study aims to collect a complete trait database of global chelonians (CheloniansTraits), which may help bridge the knowledge gap regarding the identity and ecology of global chelonians and thereby aiding future conservation endeavors. We compiled 69 trait data for all 358 recognized chelonian species, utilizing ~2,000 literature sources, covering 33 morphological, 21 life-history, 7 ecological traits, and 8 conservation information. This database serves as a uniquely valuable resource for exploring evolutionary, biogeographical, and ecological inquiries related to chelonians, as well as elucidating key aspects of ecological strategy variation among species.},
}
@article {pmid40404082,
year = {2025},
author = {Zhang, S and Qiang, J and Liu, H and Zhou, J and Li, J and Chen, J and Ding, Q and Qian, K},
title = {An efficient and precise (micro)plastic identification method: feature infrared spectra extraction based on EIS-VIP-CARS and ANN modeling.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121916},
doi = {10.1016/j.envres.2025.121916},
pmid = {40404082},
issn = {1096-0953},
abstract = {Understanding microplastics' (MPs) ecological impact necessitates their precise identification. To address the issue of the competitive adaptive reweighted sampling (CARS) algorithm extracting numerous feature wavenumber points (FWPs) that often miss transmittance peaks (TPs), resulting in high computational load and low accuracy in artificial neural network (ANN) models, this study introduces a novel approach. Initially, the equal interval sampling (EIS) method is employed to capture the main information of the full spectra. Subsequently, the variable importance in projection (VIP) is innovatively integrated into the CARS to formulate the EIS-VIP-CARS method for extracting feature spectra (FS). Using 20 typical MPs as the subjects, this study compares the identification performance of ANN models using full-spectra, EIS, CARS, EIS-CARS, VIP-CARS, and EIS-VIP-CARS. The results show that VIP-CARS extracts 128 FWPs, a reduction of 49.41% compared to CARS. Moreover, the distribution of these FWPs is more concentrated around the TPs and their vicinity. The accuracy of MPs by the ANN model based on VIP-CARS is generally higher than that of CARS. EIS-VIP-CARS extracts 55 FWPs, representing a reduction of 58.65% and 57.03% compared to EIS and VIP-CARS, respectively. The overall distribution of these points closely aligns with the distribution of functional groups. The ANN model based on EIS-VIP-CARS can achieve a similar accuracy for MPs as the model based on EIS, both greater than 99%, demonstrating good generalization ability. The accuracies of the MNN and convolutional neural network (CNN) models are higher than those of the SNN model, but the modeling time is longer. The ANN model established using the EIS-VIP-CARS is an efficient and precise approach for the identification of MPs in infrared spectroscopy. This study provides technical references for the research on the environmental behavior of MPs and is also of significant importance for the classification and management of plastic waste.},
}
@article {pmid40403917,
year = {2025},
author = {Wang, H and Lei, W and Wu, M and Guo, J and He, S and Shen, N and Li, C and Wang, L},
title = {Spatial distribution and ecological risks of neonicotinoids in surface waters of Eastern China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {378},
number = {},
pages = {126507},
doi = {10.1016/j.envpol.2025.126507},
pmid = {40403917},
issn = {1873-6424},
abstract = {Over the past two decades, neonicotinoid insecticides (NNIs) have been extensively used in agricultural activities. Due to its high-water solubility, NNIs are primarily found in surface waters, contaminating them and posing significant ecological risks. However complex watershed environments pose challenges in elucidating the pollution characteristics and ecological risks of NNIs in large-scale waters. This study focused on typical surface waters in Eastern China, exploring the spatial characteristics, driving factors, and ecological risks of NNIs. The total concentration of NNIs (Σ8NNIs) ranges from 2.3 ng/L to 1377.8 ng/L. This concentration range exceeded the European water environment toxicity thresholds, with 86 of the sites surpassing the chronic toxicity threshold (8.3 ng/L) and 14 of the sites exceeding the acute toxicity threshold (200 ng/L). Thiamethoxam (THIA), imidacloprid (IMI), and dinotefuran (DIN) were detected with high rates and concentrations. Spatially, the Σ8NNIs in the Yangtze River (YZ, 140.0 ng/L) are significantly higher than in the north of Beijing-Hangzhou Grand Canal (BHN, 62.8 ng/L), Taihu Lake (TH, 36.6 ng/L), and Taihu Basin (THB, 21.9 ng/L). Moreover, Σ8NNIs in the south of Beijing-Hangzhou Grand Canal (BHS, 326.5 ng/L) are significantly higher than in BHN (62.8 ng/L). The spatial distribution of NNI components indicated that DIN and THIA dominated in YZ (37 %), THIA (34 %) and DIN (20 %) in BHN, IMI (53 %) in BHS, DIN (53 %) in TH, and THIA (49 %) and DIN (31 %) in THB. Correlation analysis and linear mixed modeling identified land use, pH, and dissolved oxygen (DO) as significant factors influencing the occurrence of NNIs, with DO emerging as a crucial element. The species sensitivity distribution (SSD) results showed the acute and chronic toxicity thresholds of NNIs for 5 % of aquatic species were 716 ng/L and 166 ng/L respectively with 19 sites exceeding the chronic toxicity threshold and 1 sites surpassing the acute toxicity threshold.},
}
@article {pmid40402004,
year = {2025},
author = {Brunk, KM and Kramer, HA and Peery, MZ and Kahl, S and Wood, CM},
title = {Assessing spatial variability and efficacy of surrogate species at an ecosystem scale.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e70058},
doi = {10.1111/cobi.70058},
pmid = {40402004},
issn = {1523-1739},
support = {//Arthur Vining Davis Foundations/ ; FKZ 01|S22072//German Federal Ministry of Education and Research/ ; //Josh Holshuh/ ; //University of Wisconsin's Office of the Vice Chancellor for Research/ ; 20-ECOF20-0017//NASA Biodiversity and Ecological Forecasting Program/ ; //National Park Service/ ; 19-RP-NEU-043//California Climate Investment Forest Health Research Program/ ; FKZ 67KI31040E//German Federal Ministry of Environment, Nature Conservation, and Nuclear Safety/ ; //USDA Forest Service Region 5/ ; },
abstract = {Preserving biodiversity is a central goal of conservation, but, in practice, monitoring biodiversity often involves assessing population trends for one or a handful of species that are presumed proxies for biodiversity. Despite the popularity of surrogate species strategies, the links between biodiversity and surrogate species are rarely tested, especially across the broad spatial scales at which they are applied. We quantitatively evaluated a prominent surrogate species strategy across 25,000 km[2] of California's Sierra Nevada, an ecosystem undergoing substantial forest loss due to changing fire regimes and climate. We used passive acoustic monitoring and multispecies occupancy models to quantify pairwise co-occurrence among 6 indicator species and much of the avian community (63 species). We found that 95% of the sampled avian community had a positive association with at least one indicator species and that latitude played an important role in shaping co-occurrence for many species. Our work provides an important test of a long-standing conservation tool, suggests that a well-chosen suite of surrogate species can represent the occurrence patterns of a large portion of the rest of the community, and demonstrates the importance of explicitly considering the spatial scale over which surrogate species are effective.},
}
@article {pmid40399277,
year = {2025},
author = {Petit, MJ and Flory, C and Gu, Q and Fares, M and Lamont, D and Score, A and Davies, K and Bell-Sakyi, L and Scaturro, P and Brennan, B and Kohl, A},
title = {Multi-omics analysis of SFTS virus infection in Rhipicephalus microplus cells reveals antiviral tick factors.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4732},
pmid = {40399277},
issn = {2041-1723},
support = {MC_UU_00034/5//RCUK | Medical Research Council (MRC)/ ; SC 314/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 210462/Z/18/Z//Wellcome Trust (Wellcome)/ ; TICKITS 890970//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; MC_UU_12014/8//RCUK | Medical Research Council (MRC)/ ; /WT_/Wellcome Trust/United Kingdom ; MC_UU_00034/4//RCUK | Medical Research Council (MRC)/ ; },
mesh = {Animals ; *Rhipicephalus/virology/genetics/immunology ; Cell Line ; Proteomics/methods ; Virus Replication ; *Phlebovirus/physiology/genetics ; Transcriptome ; Host-Pathogen Interactions/genetics ; RNA Helicases/metabolism/genetics ; Proteome ; *Severe Fever with Thrombocytopenia Syndrome/virology ; Gene Expression Profiling ; Multiomics ; },
abstract = {The increasing prevalence of tick-borne arboviral infections worldwide necessitates advanced control strategies, particularly those targeting vectors, to mitigate the disease burden. However, the cellular interactions between arboviruses and ticks, especially for negative-strand RNA viruses, remain largely unexplored. Here, we employ a proteomics informed by transcriptomics approach to elucidate the cellular response of the Rhipicephalus microplus-derived BME/CTVM6 cell line to severe fever with thrombocytopenia syndrome virus (SFTSV) infection. We generate the de novo transcriptomes and proteomes of SFTSV- and mock-infected tick cells, identifying key host responses and regulatory pathways. Additionally, interactome analysis of the viral nucleoprotein (N) integrated host responses with viral replication and dsRNA-mediated gene silencing screen reveals two anti-SFTSV effectors: the N interacting RNA helicases DHX9 and UPF1. Collectively, our results provide insights into the antiviral responses of R. microplus vector cells and highlight critical SFTSV restriction factors, while enriching transcriptomic and proteomic resources for future research.},
}
@article {pmid40397662,
year = {2025},
author = {Li, S and Zou, J and Wu, J and Sun, B and Zhao, M and Liu, D and Cheng, Q and Tan, H and Ma, J},
title = {New Insights into Natural Polyphenol-Enhanced Fe(III)/Peracetic Acid System under Acidic pH Conditions: The Overlooked Role of Coexisting Hydrogen Peroxide.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01622},
pmid = {40397662},
issn = {1520-5851},
abstract = {Natural polyphenols have been extensively utilized as reducing agents to enhance contaminant degradation in the Fe(III)/peracetic acid (PAA) system. However, the roles of coexisting hydrogen peroxide (H2O2) remain insufficiently explored. This study, using protocatechuic acid (PCA) as a representative natural polyphenol, demonstrated that contaminant removal within the PCA/Fe(III)/PAA system under acidic pH conditions exhibited two kinetic stages: an initial rapid stage driven by PAA, followed by a slower stage driven by H2O2. The presence of H2O2 facilitated the complete degradation (100%) of contaminants even at low concentrations (<1.0 μM). Interestingly, these two stages contributed differently to various contaminants' degradation. Mechanistic investigations revealed that Fe(IV) was the major reactive species (RSs) for contaminant degradation during the PAA stage, while [•]OH dominated during the H2O2 stage. In brief, H2O2 enriched the generation pathways and types of RSs. Notably, besides PCA itself, the reaction intermediates (i.e., phenoxy radicals) formed during the reaction between PCA and RSs also played a key role in reducing Fe(III), which explained why the PCA/Fe(III)/PAA system was able to maintain sufficient Fe(II) to further interact with H2O2. Overall, this study highlighted the synergistic role of coexisting H2O2 and provided valuable insights for optimizing various contaminants' degradation in actual waters using PAA-based Fenton-like systems.},
}
@article {pmid40393855,
year = {2025},
author = {Zhivkoplias, E and da Silva, JM and Blasiak, R},
title = {How transdisciplinarity can help biotech-driven biodiversity research.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.04.008},
pmid = {40393855},
issn = {1879-3096},
abstract = {The Kunming-Montreal Global Biodiversity Framework marks a significant step toward conserving genetic diversity on a global scale. Sequencing advancements have broadened biodiversity studies by enabling the mapping of species distributions, increasing understanding of ecological interactions, and monitoring genetic diversity. However, these tools are hindered by inequalities and biases, particularly in biodiversity-rich developing countries. To navigate these challenges, we propose strategies using the existing biotechnological toolbox to make biodiversity data more accessible and useful for research and development. This includes increasing funding for database curation, improving metadata standards, addressing inequalities in technological capacity, and supporting holistic capacity-building programmes. Implementing these strategies can unlock new opportunities for biodiversity research aligned with sustainable development principles and can contribute to improved conservation outcomes.},
}
@article {pmid40393068,
year = {2025},
author = {Williams, CM and Scelza, BA and Slack, SD and Font-Porterias, N and Al-Hindi, DR and Mathias, RA and Watson, H and Barnes, KC and Lange, E and Johnson, RK and Gignoux, CR and Ramachandran, S and Henn, BM},
title = {A rapid accurate approach to inferring pedigrees in endogamous populations.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyaf094},
pmid = {40393068},
issn = {1943-2631},
abstract = {Accurate reconstruction of pedigrees from genetic data remains a challenging problem. Many relationship categories (e.g. half-sibships versus avuncular) can be difficult to distinguish without external information. Pedigree inference algorithms are often trained on European-descent families in urban locations. Thus, existing methods tend to perform poorly in endogamous populations for which there may be reticulations within the pedigrees and elevated haplotype sharing. We present a simple, rapid algorithm which initially uses only high-confidence first-degree relationships to seed a machine learning step based on summary statistics of identity-by-descent (IBD) sharing. One of these statistics, our ``haplotype score'', is novel and can be used to: (1) distinguish half-sibling pairs from avuncular or grandparent-grandchildren pairs; and (2) assign individuals to ancestor versus descendant generation. We test our approach in a sample of ∼700 individuals from northern Namibia, sampled from an endogamous population called the Himba. Due to a culture of concurrent relationships in the Himba, there is a high proportion of half-sibships. We accurately identify first through fourth-degree relationships and distinguish between various second-degree relationships: half-sibships, avuncular pairs, and grandparent-grandchildren. We further validate our approach in a second African-descent dataset, the Barbados Asthma Genetics Study (BAGS), and a European-descent founder population from Quebec. Accurate reconstruction of relatives facilitates estimation of allele frequencies, tracing allele trajectories, improved phasing, heritability and other population genomic questions.},
}
@article {pmid40389091,
year = {2025},
author = {Narita, M and Matsugaki, R and Muramatsu, K and Fushimi, K and Matsuda, S},
title = {Obesity and risk of post-operative pneumonia among older adult patients with hip fracture: an obesity paradox.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.05.020},
pmid = {40389091},
issn = {2405-4577},
abstract = {BACKGROUND &amp; AIM: Hip fracture is a condition with a high incidence among older adults and is associated with a high post-operative mortality rate. Post-operative pneumonia is one of the most important risk factors for mortality, making its prevention essential. In recent years, reports on obesity paradoxes have increasingly been documented. Therefore, this study aimed to investigate the relationship between body mass index (BMI) and the risk of developing post-operative pneumonia using a large database.<br><br>METHOD: We included 407,203 patients aged 75 years or older who underwent surgery for hip fracture between 2014 and 2018 using Diagnosis Procedure Combination data, a healthcare reimbursement system. Patients were classified into six BMI categories: <16.0, 16.0-16.9, 17.0-18.4, 18.5-24.9, 25.0-29.9, and &#x2265;30 kg/m[2]. Multilevel logistic regression analysis was performed based on BMI 18.5-24.9 kg/m[2] to determine odds ratios for post-operative pneumonia.<br><br>RESULTS: The data of 332,768 patients were included in the final analysis. Those with BMI <18.5 kg/m[2] demonstrated significantly higher odds of developing post-operative pneumonia compared to those with BMI between 18.5-24.9 kg/m[2], BMI <16.0 kg/m[2] (adjusted odds ratio [AOR: 2.14, 95% confidence interval [CI: 2.01-2.27 p<0.001); BMI 16.0-16.9 kg/m[2] (AOR: 1.57, 95% CI: 1.46-1.69, p<0.001); and BMI 17.0-18.4 kg/m[2] (AOR: 1.31, 95% CI: 1.24-1.39, p<0.001). Conversely, patients with BMI 25.0-29.9 kg/m[2] showed a risk of post-operative pneumonia compared to the other groups (AOR: 0.83, 95% CI: 0.76-0.91, p<0.001). Notably, a J-curve relationship was observed between BMI and the incidence of post-operative pneumonia.<br><br>CONCLUSION: Patients with higher BMI had a lower risk of developing post-operative pneumonia, revealing the presence of an obesity paradox between hip fracture and post-operative pneumonia. Patients with low BMI are at a higher risk and may benefit from enhanced preventive measures to mitigate the risk of pneumonia.},
}
@article {pmid40386950,
year = {2025},
author = {Cordeiro, AL and Cusack, DF and Guerrero-Ramírez, N and Norby, RJ and Toro, L and Wong, MY and Wright, SJ and Cabugao, KGM and Andersen, KM and Fuchslueger, L and Iversen, CM and Soper, F and Ghimire, OP and Lugli, LF and Miron, AC and Valverde-Barrantes, O and Arnaud, M and Batterman, SA and Dietterich, LH and Lee, MY and Weemstra, M and Yaffar, D and Addo-Danso, SD and Pierick, K and Bridges, R and Easton, C and Felsing, I and Gonçalves, NB and Krudop, R and McKinzie, MR and Perbohner, J and Pozzoli-Oropeza, AN and Samaniego, M and Smilor, AW and Vargas, IS and Webb, L and Powers, JS and McCormack, ML},
title = {TropiRoot 1.0: Database of tropical root characteristics across environments.},
journal = {Ecology},
volume = {106},
number = {5},
pages = {e70074},
doi = {10.1002/ecy.70074},
pmid = {40386950},
issn = {1939-9170},
mesh = {*Plant Roots/physiology/anatomy &amp; histology ; *Tropical Climate ; *Databases, Factual ; Ecosystem ; Biodiversity ; },
abstract = {Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.},
}
@article {pmid40386543,
year = {2025},
author = {Ramos, E and Schweizer, M and Wu, MY and Sahli, C and Latt, C and Lunak, M and Crochet, PA and Salzburger, W and Meier, J and Marques, DA and , and , and , and , and , },
title = {The genome sequence of the Yellow-legged Gull, Larus michahellis Naumann, 1840.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {129},
pmid = {40386543},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Larus michahellis (Yellow-legged Gull; Chordata; Aves; Charadriiformes; Laridae). The genome sequence has a total length of 1,405.56 megabases. Most of the assembly (90.55%) is scaffolded into 35 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.79 kilobases in length.},
}
@article {pmid40379663,
year = {2025},
author = {Iminjili, V and Crowther, A and Fisher, MT and Kay, A and Roberts, P and Goldstein, S and Boivin, N and Fernandes, R},
title = {A dataset of scientific dates from archaeological sites in eastern Africa spanning 5000 BCE to 1800 CE.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {801},
pmid = {40379663},
issn = {2052-4463},
mesh = {*Archaeology ; Africa, Eastern ; History, Ancient ; History, 18th Century ; Humans ; },
abstract = {Large collections of archaeological spatiotemporal data can reveal past cultural and demographic trends, land use strategies, and processes of environmental adaptation. Within Africa, archaeological Big Data can contribute to the study of the spread of agriculture, domesticated species, and specific artefacts and technologies, as well as their ecological impacts. Although reviews addressing these topics are available for different parts of the continent, existing mid-late Holocene archaeology datasets have yet to be compiled into a central, open-access, standardized informatic-oriented dataset. Here we present Wanyika, a dataset of scientific dates from archaeological sites in eastern Africa spanning almost 7 millennia, from ~5000 BCE to 1800 CE. This dataset compiles published scientific dates and associated botanical, faunal, iron, and ceramic finds from sites in Kenya, Tanzania, the Comoros Islands, and Madagascar. The records also include data for megafauna extinctions in Madagascar. We describe the spatiotemporal coverage of the dataset, how the data were collected, the structure of the dataset, and the applied quality control measures.},
}
@article {pmid40378227,
year = {2025},
author = {Ha, MK and Postovskaya, A and Kuznetsova, M and Meysman, P and Van Deuren, V and Van Ierssel, S and De Reu, H and Schippers, J and Peeters, K and Besbassi, H and Heyndrickx, L and Willems, B and Mariën, J and Bartholomeus, E and Vercauteren, K and Beutels, P and Van Damme, P and Lion, E and Vlieghe, E and Laukens, K and Coenen, S and Naesens, R and Ariën, KK and Ogunjimi, B},
title = {Celluloepidemiology-A paradigm for quantifying infectious disease dynamics on a population level.},
journal = {Science advances},
volume = {11},
number = {20},
pages = {eadt2926},
pmid = {40378227},
issn = {2375-2548},
mesh = {Humans ; *COVID-19/epidemiology/immunology/virology ; *SARS-CoV-2/immunology ; T-Lymphocytes/immunology ; Machine Learning ; Receptors, Antigen, T-Cell/immunology/metabolism ; Flow Cytometry ; *Communicable Diseases/epidemiology/immunology ; },
abstract = {To complement serology as a tool in public health interventions, we introduced the "celluloepidemiology" paradigm where we leveraged pathogen-specific T cell responses at a population level to advance our epidemiological understanding of infectious diseases, using SARS-CoV-2 as a model. Applying flow cytometry and machine learning on data from more than 500 individuals, we showed that the number of T cells with positive expression of functional markers not only could distinguish patients who recovered from COVID-19 from controls and pre-COVID donors but also identify previously unrecognized asymptomatic patients from mild, moderate, and severe recovered patients. The celluloepidemiology approach was uniquely capable to differentiate health care worker groups with different SARS-CoV-2 exposures from each other. T cell receptor (TCR) profiling strengthened our analysis by revealing that SARS-CoV-2-specific TCRs were more abundant in patients than in controls. We believe that adding data on T cell reactivity will complement serology and augment the value of infection morbidity modeling for populations.},
}
@article {pmid40376739,
year = {2025},
author = {Arnold, LE and Hendrix, K and Pan, X and Vollebregt, MA and Yu, M and Kerson, C and Arns, M and Hatsu, IE and DeBeus, R and Hollway, J and Roley-Roberts, ME},
title = {Lifestyle Effects in a Randomized Controlled Trial of Neurofeedback for Attention-Deficit/Hyperactivity Disorder.},
journal = {Journal of child and adolescent psychopharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cap.2025.0019},
pmid = {40376739},
issn = {1557-8992},
abstract = {Objectives/Background: Multiple factors influence symptom severity in Attention Deficit/Hyperactivity Disorder (ADHD). We examined four of these: diet, sleep hygiene, exercise, and lighting, in the International Collaborative ADHD Neurofeedback (ICAN) randomized clinical trial, which found large significant improvement with both active neurofeedback and control condition without treatment difference. Methods: A total of 142 participants aged 7-10 had breakfast and lunch intake and exercise recorded at each neurofeedback session. Parents completed the Children's Sleep Habits Questionnaire (CSHQ). Parents and teachers rated inattention on Conners3. Lifestyle changes were correlated with inattention changes. Results: At baseline, CSHQ correlated with parent-rated inattention (r = 0.17, p = 0.04), and length of sleep correlated with teacher-rated inattention (r = 0.20, p = 0.03). From baseline to treatment end food group variety (p = 0.029, d = 0.22) and sleep problems (p < 0.0001, d = -0.49) improved significantly, exercise time and protein intake marginally (p = 0.06 - 0.08). Parent-rated inattention improvement correlated with CSHQ improvement (Rho = 0.26, p = 0.002) and marginally with protein intake increase (Rho = 0.18, p = 0.06). The three components of the light-emitting-diode (LED)-induced circadian pathway hypothesis were significant. Conclusions: Most measures improved, but few significantly. How much they impact classroom attention remains unclear. Although parent ratings of inattention improvement correlated with sleep problems improvement, composited parent/teacher ratings (primary outcome) did not. The circadian pathway hypothesis associated with LED lighting was supported. These findings warrant further studies examining the role sleep hygiene can play in improving ADHD symptoms. Meanwhile, attention to sleep hygiene seems appropriate in any treatment plan for ADHD.},
}
@article {pmid40371923,
year = {2025},
author = {Cirino, T and Pinto, L and Iwan, M and Dougha, A and Lučić, B and Kraljević, A and Navoyan, Z and Tevosyan, A and Yeghiazaryan, H and Khondkaryan, L and Abelyan, N and Atoyan, V and Babayan, N and Iwashita, Y and Kimura, K and Komasaka, T and Shishido, K and Nakamura, T and Asada, M and Jain, S and Zakharov, AV and Wang, H and Liu, W and Chupakhin, V and Uesawa, Y},
title = {Consensus Modeling Strategies for Predicting Transthyretin Binding Affinity from Tox24 Challenge Data.},
journal = {Chemical research in toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrestox.5c00018},
pmid = {40371923},
issn = {1520-5010},
abstract = {Transthyretin (TTR) is a key transporter of the thyroid hormone thyroxine, and chemicals that bind to TTR, displacing the hormone, can disrupt the endocrine system, even at low concentrations. This study evaluates computational modeling strategies developed during the Tox24 Challenge, using a data set of 1512 compounds tested for TTR binding affinity. Individual models from nine top-performing teams were analyzed for performance and uncertainty using regression metrics and applicability domains (AD). Consensus models were developed by averaging predictions across these models, with and without consideration of their ADs. While applying AD constraints in individual models generally improved external prediction accuracy (at the expense of reduced chemical space coverage), it had limited additional benefit for consensus models. Results showed that consensus models outperformed individual models, achieving a root-mean-square error (RMSE) of 19.8% on the test set, compared to an average RMSE of 20.9% for the nine individual models. Outliers consistently identified in several of these models indicate potential experimental artifacts and/or activity cliffs, requiring further investigation. Substructure importance analysis revealed that models prioritized different chemical features, and consensus averaging harmonized these divergent perspectives. These findings highlight the value of consensus modeling in improving predictive performance and addressing model limitations. Future work should focus on expanding chemical space coverage and refining experimental data sets to support public health protection.},
}
@article {pmid40371524,
year = {2025},
author = {Li, YH and Zhang, Y},
title = {[Wilderness network construction in Lincang City of Yunnan Province, Southwest China based on landscape connectivity].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {4},
pages = {1233-1243},
doi = {10.13287/j.1001-9332.202504.026},
pmid = {40371524},
issn = {1001-9332},
mesh = {China ; *Conservation of Natural Resources/methods ; *Ecosystem ; Geographic Information Systems ; *Wilderness ; Cities ; *Environment Design ; Models, Theoretical ; *City Planning ; },
abstract = {Constructing wilderness networks based on landscape connectivity is crucial for wilderness conservation. We calculated the continuous spectrum of the wilderness with GIS, identified wilderness sources with morphological spatial pattern analysis (MSPA), constructed wilderness corridors and networks and extracted wilderness strategic points with minimum cumulative resistance model (MCR) and circuit theory. We further analyzed the characte-ristics of the wilderness network, and proposed wilderness protection strategies and ecological planning suggestions for Lincang City. Results showed that wilderness was mainly distributed at 1000-2500 m elevation, with a spatial pattern of more in the south and east, less in the north and west in Lincang City. Grade 3 wilderness covered 55% of the total area, indicating high quality of the study area. Based on the MSPA analysis, we found 27 wilderness sources, most of which were distributed in the eastern and southern areas such as Linxiang and Cangyuan. The western and northern such as Fengqing and Yongde had fewer wilderness sources. There were 63 wilderness corridors in the wilderness network, including 16 important corridors and 47 general corridors. There were 186 strategic points in the wilderness network, including 53 wilderness nodes and 133 barrier points. We constructed the wilderness network of Lincang based in the identified wilderness source areas and extracted wilderness corridors, which had the advantages of high stability, strong resistance to interference, efficient connectivity. Finally, we proposed the "three-zone as a whole" protection strategy and ecological planning suggestions, which had referential value for establishing an ecological security pattern in Lincang City and the practicalization of wilderness protection in China.},
}
@article {pmid40371522,
year = {2025},
author = {Dong, WZ and Su, WC and Gou, R and Zhou, HY and Liu, DY},
title = {[Spatial and temporal evolution of ecological risk in Guizhou Province, China from the perspective of ecosystem services and ecosystem health].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {4},
pages = {1211-1221},
doi = {10.13287/j.1001-9332.202504.021},
pmid = {40371522},
issn = {1001-9332},
mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; Risk Assessment ; Rivers ; Spatio-Temporal Analysis ; Geographic Information Systems ; *Environmental Monitoring/methods ; Ecology ; Models, Theoretical ; },
abstract = {Guizhou Province is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River. Karst landform in Guizhou is developed, with fragile ecological background. The ecological risk assessment and control of Karst landform are of great significance to ecological security and sustainable development of southwest China and the upper reaches of those two rivers. Based on the InVEST model and vigor-organization-resi-lience model, we quantitatively evaluated the ecosystem services and ecosystem health and constructed the ecological risk assessment model of Guizhou Province. With the help of GIS technology, spatial autocorrelation analysis method and gravity center migration model, we analyzed the spatial and temporal variations of ecological risk in Guizhou Province from 2000 to 2020. The results showed that ecosystem services in Guizhou Province increased from 2000 to 2020, with an annual average growth rate of 0.3%. The ecosystem health status was generally well and showed a good trend, and the annual average growth rate of ecosystem health was 12.6%. The ecological risk was dominated by medium ecological risk. The proportion of extremely low ecological risk area and low ecological risk area increased, the proportion of medium and above ecological risk area decreased, and the overall ecological risk showed a downward trend. The low ecological risk areas were mainly located in the south and southeast of Guizhou Province, while the high ecological risk areas were distributed in the central, western and northern parts of Guizhou Province. The global Moran's I of ecological risk in 2000, 2005, 2010, 2015, and 2020 were 0.856, 0.836, 0.844, 0.804, and 0.768, respectively, indicating that the positive correlation of ecological risk in spatial distribution, but the spatial correlation and spatial agglomeration characteristics were weakened. During the study period, the centroid and trajectory of ecological risk in Guizhou Province were consistent with the distribution area of its corresponding ecological risk. From 2000 to 2020, the spatial distribution pattern of ecological risk in Guizhou Pro-vince was relatively stable. With the evolution of time, the dispersion of spatial distribution of extremely high ecological risk and low ecological risk increased. Ecological risk assessment based on ecosystem services and ecosystem health would provide scientific basis for regional ecological risk management and control.},
}
@article {pmid40369670,
year = {2025},
author = {Wu, B and Luo, D and Yue, Y and Yan, H and He, M and Ma, X and Zhao, B and Xu, B and Zhu, J and Wang, J and Jia, J and Sun, M and Xie, Z and Wang, X and Huang, L},
title = {New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {128},
pmid = {40369670},
issn = {1474-760X},
support = {2021YFYZ0013//Sichuan Province Research Grant/ ; SCCXTD-2020-16//Modern Agricultural Industry System Sichuan Forage Innovation Team/ ; 32071867//National Natural Science Foundation of China/ ; },
mesh = {*Panicum/genetics/physiology ; *Haplotypes ; *Genome, Plant ; *Cold-Shock Response/genetics ; Ecotype ; Gene Expression Regulation, Plant ; Genome-Wide Association Study ; Cold Temperature ; Gene Expression Profiling ; Plant Proteins/genetics/metabolism ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear.<br><br>RESULTS: Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region.<br><br>CONCLUSIONS: Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.},
}
@article {pmid40369175,
year = {2025},
author = {Barroux, M and Househam, J and Lakatos, E and Ronel, T and Baker, AM and Salié, H and Mossner, M and Smith, K and Kimberley, C and Nowinski, S and Berner, A and Gunasri, V and Borgmann, M and Liffers, S and Jansen, M and Caravagna, G and Steiger, K and Slotta-Huspenina, J and Weichert, W and Zapata, L and Giota, E and Lorenzen, S and Alberstmeier, M and Chain, B and Friess, H and Bengsch, B and Schmid, RM and Siveke, JT and Quante, M and Graham, TA},
title = {Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of esophageal adenocarcinoma.},
journal = {Nature cancer},
volume = {},
number = {},
pages = {},
pmid = {40369175},
issn = {2662-1347},
abstract = {Locally advanced esophageal adenocarcinoma remains difficult to treat and the ecological and evolutionary dynamics responsible for resistance and recurrence are incompletely understood. Here, we performed longitudinal multiomic analysis of patients with esophageal adenocarcinoma in the MEMORI trial. Multi-region multi-timepoint whole-exome and paired transcriptome sequencing was performed on 27 patients before, during and after neoadjuvant treatment. We found major transcriptomic changes during treatment with upregulation of immune, stromal and oncogenic pathways. Genetic data revealed that clonal sweeps through treatment were rare. Imaging mass cytometry and T cell receptor sequencing revealed remodeling of the tumor microenvironment during treatment. The presence of genetic immune escape, a less-cytotoxic T cell phenotype and a lack of clonal T cell expansions were linked to poor treatment response. In summary, there were widespread transcriptional and environmental changes through treatment, with limited clonal replacement, suggestive of phenotypic plasticity.},
}
@article {pmid40368894,
year = {2025},
author = {Yi, S and Li, X and Liu, Y and Dong, X and Tu, W},
title = {A sub-meter resolution urban surface albedo dataset for 34 U.S. cities based on deep learning.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {789},
pmid = {40368894},
issn = {2052-4463},
support = {2314709//National Science Foundation (NSF)/ ; },
abstract = {Surface albedo is a key determinant of urban heat islands, which modulates the amount of solar energy absorbed or reflected by urban surfaces, influencing microclimate and thermal comfort. However, high-resolution albedo is usually not available, which makes the understanding of the urban thermal environment at hyperlocal difficult. This study presents the first high-resolution urban albedo maps for 34 major U.S. cities using advanced deep learning models and multisource remote sensing data. By differentiating between impervious and pervious surfaces using a combination of NAIP imagery, roof albedo data, building footprints, land cover classifications, and Sentinel-2 imagery, this work achieves sub-meter resolution in albedo mapping. Employing U-Net for impervious surface classification along with impervious (ISA) and pervious surface albedo (PSA) prediction, these models were validated in selected cities, with ISA showing an R[2] of 0.9028 and MAE of 0.0057, and PSA demonstrating an R[2] of 0.9538 and MAE of 0.0027, highlighting the precision and reliability. The datasets, made publicly available, offer essential insights for urban planning and environmental monitoring.},
}
@article {pmid40365044,
year = {2025},
author = {Ogba, P and Baumann, A and Alabi, T and Archer, N and Eniojukan, J and Ibhawoh, B and DiLiberto, DD},
title = {Enhancing IPTp-SP uptake: Community and stakeholder recommendations for improving access and utilisation - insights from a study in Bayelsa-Nigeria.},
journal = {MalariaWorld journal},
volume = {16},
number = {},
pages = {9},
pmid = {40365044},
issn = {2214-4374},
abstract = {BACKGROUND: Malaria remains a major global health challenge, disproportionately affecting pregnant women and children. In Nigeria, malaria in pregnancy contributes to 70.5% of maternal morbidity and 41.1% of maternal mortality. Recognising these risks, the World Health Organization recommends intermittent preventive treatment with sulfadoxine-pyrimethamine (IPTp-SP) as a key strategy for malaria in pregnancy prevention. However, despite its proven effectiveness, pregnant women's uptake of IPTp-SP remains unacceptably low. This study presents participant-driven recommendations to enhance IPTp-SP uptake, structured within the socio-ecological framework.<br><br>MATERIALS AND METHODS: This study employed an exploratory descriptive qualitative approach to examine the community-level contextual factors influencing IPTp-SP uptake. Data were collected from 53 participants in two communities in Bayelsa, Nigeria. Individual interviews were conducted with 17 key stakeholders (spouses, mothers-in-law, religious leaders, community leaders, and traditional birth attendants) and 6 focus group discussions with 36 pregnant women. Data management and coding were conducted using NVivo 14 QSR International software, following an inductive-deductive thematic analysis approach.<br><br>RESULTS: Participants proposed multi-level interventions to address barriers to IPTp-SP uptake at the individual, interpersonal, community, and healthcare system levels. Key recommendations include: Community-wide education campaigns to raise awareness of IPTp-SP's benefits; comprehensive training for healthcare providers to enhance their knowledge and prescription of IPTp-SP; integration of traditional birth attendants into the formal healthcare system; community-level distribution of IPTp-SP to improve access for pregnant women who do not attend antenatal care; government intervention to ensure the functionality of health centers; addressing workforce shortages, and guaranteeing a consistent supply of IPTp-SP.<br><br>CONCLUSION: These evidence-based, participant-driven recommendations offer a holistic and scalable strategy to improve pregnant women's uptake of IPTp-SP in Nigeria and other malaria-endemic regions. Implementing these recommendations can strengthen malaria prevention efforts, improve maternal and child health outcomes, and support broader public health initiatives.},
}
@article {pmid40197051,
year = {2025},
author = {Shamash, M and Sinha, A and Maurice, CF},
title = {Improving gut virome comparisons using predicted phage host information.},
journal = {mSystems},
volume = {10},
number = {5},
pages = {e0136424},
doi = {10.1128/msystems.01364-24},
pmid = {40197051},
issn = {2379-5077},
mesh = {*Bacteriophages/genetics/classification/physiology ; *Virome/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; Feces/virology/microbiology ; Metagenomics/methods ; Computational Biology/methods ; Bacteria/virology ; },
abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.<br><br>IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.},
}
@article {pmid40361718,
year = {2025},
author = {Nițescu, M and Nedelescu, MM and Moroşan, E and Simionescu, AA and Furtunescu, FL and Ştefănescu, BE and Tusaliu, M and Panaitescu, E and Stanciu, AM and Stoian, IM},
title = {Assessment of Food Safety Knowledge and Practices Among Medical Students.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
pmid = {40361718},
issn = {2304-8158},
abstract = {Food safety is an important requirement for protecting human health worldwide. In particular, medical students' education on food safety is essential for them as future physicians, and university education is the first step in acquiring this knowledge. We performed an online survey with 1277 respondents among medical students to assess knowledge, attitudes, and practices (KAPs) related to food safety regarding microbiological contamination. Our findings showed that more than half of the respondents presented a low level of food safety knowledge, with a score between 11-60 points, and only 6% managed to score between 81 and 100 points, which was considered a high level of knowledge. On the contrary, we found that most participants had a high level of good practice: 58% scored more than 25 points, 39% had an average level of good practice (scoring between 21 and 25 points), and 3% of respondents had a low level of good practice (scoring below 21 points). We also noticed a statistically significant difference between total scores of preclinical and clinical years of study among medical students (p = 0.005) regarding food safety knowledge. The frequency of cooking was positively correlated with the level of food safety knowledge, but not with food safety practices. Our study shows that better knowledge on food safety is needed among medical students. Improving knowledge and awareness of food safety in relation to microbiological contamination is a good way to protect themselves and to promote the correct food safety knowledge and measures among their patients.},
}
@article {pmid40361012,
year = {2025},
author = {Barkan, R and Cooke, I and Watson, SA and Strugnell, JM},
title = {Synthesis of transcriptomic studies reveals a core response to heat stress in abalone (genus Haliotis).},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {474},
pmid = {40361012},
issn = {1471-2164},
mesh = {Animals ; *Gastropoda/genetics/physiology ; *Heat-Shock Response/genetics ; *Gene Expression Profiling ; *Transcriptome ; Computational Biology/methods ; },
abstract = {BACKGROUND: As climate change causes marine heat waves to become more intense and frequent, marine species increasingly suffer from heat stress. This stress can result in reduced growth, disrupted breeding cycles, vulnerability to diseases and pathogens, and increased mortality rates. Abalone (genus Haliotis) are an ecologically significant group of marine gastropods and are among the most highly valued seafood products. However, heat stress events have had devastating impacts on both farmed and wild populations. Members of this genus are among the most susceptible marine species to climate change impacts, with over 40% of all abalone species listed as threatened with extinction. This has motivated researchers to explore the genetics linked to heat stress in abalone. A substantial portion of publicly available studies has employed transcriptomic approaches to investigate abalone genetic response to heat stress. However, to date, no meta-analysis has been conducted to determine the common response to heat stress (i.e. the core response) across the genus. This study uses a standardized bioinformatic pipeline to reanalyze and compare publicly available RNA-seq datasets from different heat stress studies on abalone.<br><br>RESULTS: Nine publicly available RNA-seq datasets from nine different heat-stress studies on abalone from seven different abalone species and three hybrids were included in the meta-analysis. We identified a core set of 74 differentially expressed genes (DEGs) in response to heat stress in at least seven out of nine studies. This core set of DEGs mainly included genes associated with alternative splicing, heat shock proteins (HSPs), Ubiquitin-Proteasome System (UPS), and other protein folding and protein processing pathways.<br><br>CONCLUSIONS: The detection of a consistent set of genes that respond to heat stress across various studies, despite differences in experimental design (e.g. stress intensity, species studied-geographical distribution, preferred temperature range, etc.), strengthens our proposal that these genes are key elements of the heat stress response in abalone. The identification of the core response to heat stress in abalone lays an important foundation for future research. Ultimately, this study will aid conservation efforts and aquaculture through the identification of resilient populations, genetic-based breeding programs, possible manipulations such as early exposure to stress, gene editing and the use of immunostimulants to enhance thermal tolerance.},
}
@article {pmid40357641,
year = {2025},
author = {Pourmohsenin, B and Wiese, A and Ziemert, N},
title = {AutoMLST2: a web server for phylogeny and microbial taxonomy.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf397},
pmid = {40357641},
issn = {1362-4962},
support = {101000794//H2020-FNR-11-2020: SECRETED/ ; TTU09.717//German Center for Infection Research/ ; 390838134//Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection/ ; },
abstract = {Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology, ecology, and drug discovery, yet it remains a challenging task. AutoMLST2 (https://automlst2.ziemertlab.com) is a web server designed to facilitate automated phylogenetic reconstruction and microbial taxonomy analysis for bacterial and archaeal genomes. It builds on the foundation of AutoMLST, which remains widely used due to its user-friendly interface compared to similar tools. Given its continued popularity and utility, we have enhanced AutoMLST to leverage newer reference databases and computational tools. AutoMLST2 integrates the Genome Taxonomy Database, extends support to archaeal genomes, and improves analytical flexibility. Key improvements include more customizable processing modes, containerization to prevent queue accumulations, and parallel computing for large-scale studies. By incorporating up-to-date databases and workflows, AutoMLST2 continues to provide an accessible and efficient platform for researchers in microbiology, evolutionary ecology, and natural product discovery.},
}
@article {pmid40344895,
year = {2025},
author = {Kičić, M and Scheuer, S and Korpilo, S and Vuletić, D and Seletković, A and Haase, D and Krajter Ostoić, S},
title = {Relationships between urban green space types, cultural ecosystem services and disservices - a Public Participation Geographic Information System study in Zagreb, Croatia.},
journal = {The Science of the total environment},
volume = {981},
number = {},
pages = {179549},
doi = {10.1016/j.scitotenv.2025.179549},
pmid = {40344895},
issn = {1879-1026},
mesh = {Croatia ; *Geographic Information Systems ; Cities ; *Ecosystem ; *Conservation of Natural Resources/methods ; *Community Participation ; Humans ; *Parks, Recreational ; },
abstract = {Urban green spaces are important providers of ecosystem services in cities, however cultural ecosystem services remain difficult to quantify. Different types of urban green spaces provide various cultural ecosystem services and differ in how they are perceived and utilized by citizens. In this study, we used a Public Participation GIS (PPGIS) survey to collect data on citizens' perceptions and use of cultural ecosystem services and disservices provided by different types of urban green spaces in Zagreb, Croatia. We collected spatial data from 384 respondents on the perceived provision of 19 different attributes of cultural ecosystem services and disservices in 20 defined types of urban green spaces. We used descriptive statistics, spatial metrics, multivariate analysis and visualization techniques to explore and explain 5757 spatial points collected with the PPGIS questionnaire. Results confirm the importance of parks and forests but also that the water elements and greenery around residential buildings serve as important urban green space for providing benefits for citizens of Zagreb. Based on results presented, cultural ecosystem services are perceived as more important than disservices but in some places both co-exist. Our study builds on current literature by providing a systematic, city-wide assessment of cultural ecosystem services related to different types of urban green spaces, while advancing the availability of methods for their quantification.},
}
@article {pmid40194740,
year = {2025},
author = {Nieman, DC and Sakaguchi, CA and Williams, JC and Lawson, J and Lambirth, KC and Omar, AM and Mulani, FA and Zhang, Q},
title = {Gut Prevotella copri abundance linked to elevated post-exercise inflammation.},
journal = {Journal of sport and health science},
volume = {14},
number = {},
pages = {101039},
doi = {10.1016/j.jshs.2025.101039},
pmid = {40194740},
issn = {2213-2961},
abstract = {PURPOSE: This study aimed to examine the linkage between gut microbiome taxa and exercise-induced inflammation.<br><br>METHODS: Twenty-five cyclists provided 4 stool samples during a 10-week period and cycled vigorously for 2.25 h at 67% maximal oxygen uptake (VO2max) in a laboratory setting. Blood samples were collected pre- and post-exercise, with additional samples collected at 1.5-h, 3-h, and 24-h post exercise. Primary outcomes included stool microbiome composition and alpha diversity via whole genome shotgun (WGS) sequencing (averaged from 4 stool samples) and a targeted panel of 75 plasma oxylipins. A total of 5719 taxa were identified, and the 339 that were present in more than 20% of stool samples were used in the analysis. Alpha diversity was calculated by evenness, and the Analysis of Composition of Microbiomes (ANCOM) differential abundance analysis was performed using Quantitative Insights Into Microbial Ecology-2 (QIIME2). A composite variable was calculated from 8 pro-inflammatory oxylipins generated from arachidonic acid (ARA) and cytochrome P-450 (CYP).<br><br>RESULTS: ARA-CYP oxylipins were significantly elevated for at least 3-h post-exercise (p < 0.001); they were strongly and positively related to Prevotella copri (P. copri) abundance (R[2]&#x202f;=&#x202f;0.676, p < 0.001) and negatively related to gut microbiome alpha diversity (R[2]&#x202f;=&#x202f;0.771, p < 0.001).<br><br>CONCLUSION: This analysis revealed for the first time a novel, positive relationship between gut microbiome P. copri abundance in cyclists and post-exercise pro-inflammatory oxylipins. These data demonstrate that about two-thirds of the wide variance in inflammation following prolonged and intensive exercise is largely explained by the abundance of a single gut bacterial species: P. copri.},
}
@article {pmid40147302,
year = {2025},
author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD},
title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.},
journal = {Water research},
volume = {280},
number = {},
pages = {123511},
doi = {10.1016/j.watres.2025.123511},
pmid = {40147302},
issn = {1879-2448},
mesh = {*Floods ; Salinity ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology ; Metabolomics ; Microbiota ; Multiomics ; },
abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.},
}
@article {pmid40352255,
year = {2025},
author = {Seminar, KB and Damayanthi, E and Priandana, K and Imantho, H and Ligar, BW and Seminar, AU and Krishnajaya, AD and Aditya, MR and Suherman, MIH and Fillah, IF},
title = {AI-based system for food and beverage selection towards precision nutrition in Indonesian restaurants.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1590523},
pmid = {40352255},
issn = {2296-861X},
abstract = {The complexity surrounding food selection is attributable to the variability in foods, restaurants, and diners. The diversity of foods, where each dish may have a unique recipe across different restaurants, needs to be accounted for in personalized nutrition. However, personalized food selection poses a combinatorial challenge in selecting the most suitable food at a specific restaurant. The key question is how a diner visiting a particular restaurant can be assisted in selecting optimal foods and beverages based on factors such as sex, age, height, weight, and history of non-communicable diseases (NCDs). In this study, a genetic algorithm (GA) is used to develop a system that can address this issue in the context of Indonesian restaurants. In this system, a database with data on registered diners and foods is maintained. Foods comprise staple foods, side dishes, vegetables, and beverages, each containing its energy and nutrient content for a given restaurant. The nutritional adequacy of a single meal is determined by comparing the energy and nutrient content of the menu with the diner's nutritional needs. The novelty of the proposed system lies in combining scientific nutritional data with individual diner profiles for the selection of the best meal for a diner. This system differs from the existing food recommender applications in Indonesia, which typically do not consider specific diners, personalized nutrition, and NCD history. The proposed system is the first developed application prototype for Indonesian restaurants to overcome the inefficiency of the existing applications. In this study, the structure and chromosome content of the food, its corresponding energy and nutrient contents, and GA operators such as crossover, mutation, and tournament selection for determining the best meal using the defined fitness functions are discussed. The proposed system has been tested at Karimata Restaurant and proved to be highly suitable for the ultimate goal of meal selection for individual diners with different needs, and it can be replicated at other restaurants. Furthermore, user-centered evaluation has revealed that the system (a) increases nutritional understanding and health awareness; (b) is easy to use with comprehensive functions; and (c) promotes user satisfaction with personalized recommendations.},
}
@article {pmid40351335,
year = {2024},
author = {Li, S and Fan, C and Kargarandehkordi, A and Sun, Y and Slade, C and Jaiswal, A and Benzo, RM and Phillips, KT and Washington, P},
title = {Monitoring Substance Use with Fitbit Biosignals: A Case Study on Training Deep Learning Models Using Ecological Momentary Assessments and Passive Sensing.},
journal = {AI (Basel, Switzerland)},
volume = {5},
number = {4},
pages = {2725-2738},
pmid = {40351335},
issn = {2673-2688},
support = {U54 GM138062/GM/NIGMS NIH HHS/United States ; },
abstract = {Substance use disorders affect 17.3% of Americans. Digital health solutions that use machine learning to detect substance use from wearable biosignal data can eventually pave the way for real-time digital interventions. However, difficulties in addressing severe between-subject data heterogeneity have hampered the adaptation of machine learning approaches for substance use detection, necessitating more robust technological solutions. We tested the utility of personalized machine learning using participant-specific convolutional neural networks (CNNs) enhanced with self-supervised learning (SSL) to detect drug use. In a pilot feasibility study, we collected data from 9 participants using Fitbit Charge 5 devices, supplemented by ecological momentary assessments to collect real-time labels of substance use. We implemented a baseline 1D-CNN model with traditional supervised learning and an experimental SSL-enhanced model to improve individualized feature extraction under limited label conditions. Results: Among the 9 participants, we achieved an average area under the receiver operating characteristic curve score across participants of 0.695 for the supervised CNNs and 0.729 for the SSL models. Strategic selection of an optimal threshold enabled us to optimize either sensitivity or specificity while maintaining reasonable performance for the other metric. Conclusion: These findings suggest that Fitbit data have the potential to enhance substance use monitoring systems. However, the small sample size in this study limits its generalizability to diverse populations, so we call for future research that explores SSL-powered personalization at a larger scale.},
}
@article {pmid40348945,
year = {2025},
author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H},
title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {114},
number = {5},
pages = {77},
pmid = {40348945},
issn = {1432-0800},
support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; },
mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; },
abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.},
}
@article {pmid40346497,
year = {2025},
author = {Sigwart, JD and Wong, NLWS and González, VL and Machado, FM and Greve, C and Schell, T and Chen, Z},
title = {Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {460},
pmid = {40346497},
issn = {1471-2164},
mesh = {Animals ; *Bivalvia/genetics/anatomy &amp; histology/classification ; Phylogeny ; *Genome ; *Animal Shells/anatomy &amp; histology ; *Geologic Sediments ; *Adaptation, Physiological/genetics ; *Genomics/methods ; },
abstract = {BACKGROUND: In this study, we present the first chromosome-scale genome of Verpa penis (Linnaeus, 1758), and the first for the bivalve clade Anomalodesmata. The present study has two separate foci. Primarily, we provide the genetic resource to bridge further studies from genome to phenome and propose hypotheses to guide future empirical investigations. Secondarily, based on morphology, we outline a conceptual exploration to address their adaptation. Watering-pot shells have been called "the weirdest bivalves" for their fused tubular shell resembling the spout of a watering can. This adventitious tube arose twice convergently in clavagelloidean bivalves. However, previous literature has never provided a convincing adaptive pathway.<br><br>RESULTS: The genome assembly of V. penis was about 507&#xa0;Mb, with contig N50 of 5.33&#xa0;Mb, and has 96.5% of sequences anchored onto 19 pseudochromosomes. Phylogenomic analyses of this new genome in context of other bivalves confirms the placement for Anomalodesmata as sister to the clade Imparidentia. Contrary to expectations from its highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral karyotype of heterodont bivalves (1&#xa0;N&#x2009;=&#x2009;19). Drawing on established principles from engineering as well as morphology, the thought experiment about the adventitious tube seeks to extend current understanding by exploring parallels with other built structures. A new hypothesis explains one possible interpretation of the adaptive significance of this body form: it is potentially structurally optimised for vertical stability in relatively soft sediments, with parallels to the engineering principles of a suction anchor.<br><br>CONCLUSIONS: While the conclusions presented here on morphological interpretations are theoretical, this serves as a foundation for further empirical validation and refinement. Our study offers new insights to a long-standing mystery in molluscan body forms and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.},
}
@article {pmid40346072,
year = {2025},
author = {Bosso, L and Saviano, S and Abagnale, M and Bellardini, D and Bolinesi, F and Botte, V and Buondonno, A and Carotenuto, Y and Casotti, R and Chiusano, ML and Cipolletta, F and Conversano, F and De Domenico, F and Del Gaizo, G and Donnarumma, V and Furia, M and Iudicone, D and Kokoszka, F and Laface, F and Licandro, P and Mangoni, O and Margiotta, F and Mazzocchi, MG and Miralto, M and Montresor, M and Pansera, M and Pedà, C and Percopo, I and Raffini, F and Russo, L and Romeo, T and Saggiomo, M and Sarno, D and Trano, AC and Vannini, J and Vargiu, M and Zampicinini, G and Zingone, A and Cianelli, D and D'Alelio, D},
title = {GIS-based integration of marine data for assessment and management of a highly anthropized coastal area.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16200},
pmid = {40346072},
issn = {2045-2322},
mesh = {Italy ; *Geographic Information Systems ; *Environmental Monitoring/methods ; Ecosystem ; Humans ; *Conservation of Natural Resources ; Oceans and Seas ; Animals ; Food Chain ; },
abstract = {Monitoring coastal marine environments by evaluating and comparing their chemical, physical, biological, and anthropogenic components is essential for ecological assessment and socio-economic development. In this study, we conducted an integrated multivariate analysis to assess the descriptors of the Marine Strategy Framework Directive at a regional scale in the Tyrrhenian Sea (Italy), with a specific focus on the densely populated coastal zone of the Campania region. Physical, chemical, and biological data were collected and analyzed in 22 sampling sites during three oceanographic surveys in the Gulf of Gaeta (GoG), Naples (GoN), and Salerno (GoS) in autumn 2020. Our results indicated that these three gulfs were distinct overall, with GoN being more divergent and heterogeneous than GoG and GoS. The marine area studied in the GoN had more favorable hydrographic and trophic conditions and food web characteristics, except for the mesozooplankton biomass, and was closer to socio-economic factors compared to the GoS and GoG. Our analysis helped us find the key ecological features that define different sub-regions and connect them to social and economic factors, including human activities. We highlighted the relevance of primary and secondary variables in terms of the comprehensive ecological assessment of a marine area and its impact on specific socio-economic activities. These findings support the need to describe and integrate multiple descriptors at the spatial scale.},
}
@article {pmid40345178,
year = {2025},
author = {O'Callaghan, ME and Casey, M and Pearl, D and Hickey, O and Fosse, A and Sigurðsson, SE and Savage, DW and Vehviläinen-Julkunen, K and Bykachev, K and Parviainen, A and Parker, H and Condell, J and Leavey, G and Hart, N and Weihe, P and Petersen, MS and Glynn, L},
title = {COVID-19 open data: An ecological study and international collaboration examining pandemic trends in Northern Periphery arctic countries.},
journal = {Health informatics journal},
volume = {31},
number = {2},
pages = {14604582251315588},
doi = {10.1177/14604582251315588},
pmid = {40345178},
issn = {1741-2811},
mesh = {Humans ; *COVID-19/epidemiology/mortality ; Arctic Regions/epidemiology ; *International Cooperation ; *Pandemics ; SARS-CoV-2 ; },
abstract = {Objectives: In the early stages of the COVID-19 pandemic, evidence generation lagged behind public health responses. This study describes an international collaboration of frontline clinicians who used open data describing COVID-19 trends to generate "practice-based evidence". Methods: Open data resources from nine Northern Periphery and Arctic (NPA) countries were harnessed using the open-source programming language 'R' and our collaborations analyses and insights were published on a public-facing website. The website's visualisations guided teleconference discussions from September 2020 to March 2021, focusing on contextualizing national responses, especially in rural regions. Results: This project facilitated shared learning from COVID-19 trends and highlighted key aspects of national responses. Notably, rural NPA regions experienced less COVID-19 cases and mortality in the first year of the pandemic. Conclusion: This international collaborative effort, driven by open data analysis, provided a platform to share real-world insights. The study offers a potential template for future pandemics and emphasises the importance of sustaining open data resources, including granular data like excess mortality, for effective pandemic learning.},
}
@article {pmid40344217,
year = {2025},
author = {Schindler, Z and Larysch, E and Fornoff, F and Kröner, K and Obladen, N and Klein, AM and Seifert, T and Vonderach, C and Morhart, C},
title = {Flower power: Modeling floral resources of wild cherry (Prunus avium L.) for bee pollinators based on 3D data.},
journal = {Ecology},
volume = {106},
number = {5},
pages = {e70103},
pmid = {40344217},
issn = {1939-9170},
support = {2819NA071//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft/ ; },
mesh = {*Pollination/physiology ; *Flowers/physiology ; Animals ; Bees/physiology ; *Models, Biological ; *Prunus avium/physiology ; },
abstract = {Pollinator declines pose a threat to ecosystems and food production. Agriculture contributes to, but also suffers from, the erosion of pollination services. Our study explores the potential of trees in agricultural landscapes to support pollinators by providing floral resources. Our overarching objective is the quantification of floral resources produced by wild cherry (Prunus avium L.) that can be used by flower-visiting and pollinating insects such as bees. Using an innovative approach, we combine pollen measurements with manual counts of flowers on branches and 3D data derived from terrestrial laser scanning. This approach allows us to scale up flower numbers from branches to entire trees. The derived models for estimating the probability of flower occurrence (R[2] c = 0.52, R[2] m = 0.50) and the number of flowers per branch (R[2] c = 0.88, R[2] m = 0.84), as well as the number of flowers per tree (R[2] = 0.83), show good model fits with only a small set of predictors. The model fits indicate that, at the branch level, predicting flowering probability is more challenging than predicting flower abundance. We found differences in the number of flowers per branch in different crown sections, suggesting that floral resources are heterogeneously distributed. Furthermore, we demonstrate that the number of flowers per tree increases exponentially with tree dimension (stem diameter, crown volume). Therefore, large trees provide disproportionately more floral resources than small trees and are particularly worthy of conservation efforts. For example, our models estimate that a single tree with a stem diameter of 25 cm carries 195,535 flowers (95% CI: 159,991-237,318), thus providing about 57 cm[3] (95% CI: 32-88 cm[3]) of pollen and producing 170 g (95% CI: 48-345 g) nectar sugar per 24 h. This amount of pollen is sufficient to rear, for example, 5202 larvae (95% CI: 2886-8022) of Lasioglossum laticeps, a common and generalist sweat bee of cherry trees. In contrast, a smaller tree with a stem diameter of 10 cm provides only 8% of these resources. In conclusion, we demonstrate how our results contribute to the broader single-large-or-several-small debate in nature conservation by highlighting the value of large trees. Additionally, we show how information gathered at the branch level may be nondestructively upscaled to entire trees.},
}
@article {pmid40344046,
year = {2025},
author = {Ramihangihajason, TA and Weber, JL and Rakotondraompiana, S and Roger, E and Faramalala, MH and Rakotoniaina, S},
title = {Natural capital accounting as a decision support tool for environmental management of a protected area in Madagascar.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321948},
pmid = {40344046},
issn = {1932-6203},
mesh = {Madagascar ; *Conservation of Natural Resources/methods ; Ecosystem ; Biodiversity ; Forests ; Animals ; *Decision Support Techniques ; Humans ; Birds ; },
abstract = {Ecosystem change affects the availability of resources and services provided by nature. Ecosystem Natural capital accounting helps track these changes and supports better decision-making for managing the environment. This approach aims to assess changes in the stocks and flows of natural resources and the possibility to integrate them into economic and political decisions. The protected area of Mahavavy-Kinkony Complex, in North-Western of Madagascar, was chosen to implement this approach due to its many types of ecosystems as well as important reserves of threatened birds. In five years (2013-2018), we have observed a reduction in woodland cover (forest and mangrove) due to both regulated and illegal logging, linked to urban expansion and increasing of human pressure. This loss of woodland compromises not only biodiversity but also the capacity of ecosystems to provide ecosystem services. At the same time, the silting up of surface waters is compromising water quality and the health of aquatic ecosystems. In addition, the increase in agricultural land at the expense of forested areas raises concerns about the continuing degradation of natural ecosystems. All of these changes can be observed inside local socio-ecological landscape type. Each socio-ecological landscape type shows the potential variation in the production of ecosystem services.},
}
@article {pmid40343940,
year = {2025},
author = {Longo, L and Veronese, M and Cagnato, C and Sorrentino, G and Tetruashvili, A and Belfer-Cohen, A and Jakeli, N and Meshveliani, T and Meneghetti, M and Zoleo, A and Marcomini, A and Artioli, G and Badetti, E and Hardy, K},
title = {Direct evidence for processing Isatis tinctoria L., a non-nutritional plant, 32-34,000 years ago.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321262},
pmid = {40343940},
issn = {1932-6203},
mesh = {*Plant Leaves/chemistry/ultrastructure ; Humans ; *Isatis/chemistry/anatomy &amp; histology ; Spectrum Analysis, Raman ; Spectroscopy, Fourier Transform Infrared ; Archaeology ; History, Ancient ; },
abstract = {Recovering evidence for the intentional use of plants in the Palaeolithic is challenging due to their perishable nature as, unlike chipped stone or bone artefacts, plant remains are rarely preserved. This has created a paradigm for the Palaeolithic in which plants seldom feature, resulting in a partial and skewed perspective; in fact, plants were as essential to human life then as they are today. Here, we combine morphological and spectroscopic analyses (µ-Raman, µ-FTIR) to provide robust multiscale physical and biomolecular evidence for the deliberate pounding and grinding of Isatis tinctoria L. leaves 34-32,000 years ago. The leaf epidermis fragments were found entrapped in the topography of the used surface of unmodified pebbles, in association with use-wear traces. Although their bitter taste renders them essentially inedible, the leaves have well-recognised medicinal properties and contain indigotin precursors, the chromophore responsible for the blue colour of woad, a plant-based dye that is insoluble in water. We used a stringent approach to contamination control and biomolecular analysis to provide evidence for a new perspective on human behaviour, and the applied technical and ecological knowledge that is likely to have prevailed in the Upper Palaeolithic. Whether this plant was used as a colourant, as medicine, or indeed for both remains unknown, but offers a new perspective on the fascinating possibilities of non-edible plant use.},
}
@article {pmid40343039,
year = {2025},
author = {Cuenca, PR and Souza, FN and do Nascimento, RC and da Silva, AG and Eyre, MT and Santana, JO and de Oliveira, DS and de Souza, EVR and Palma, FAG and de Carvalho Santiago, DC and Dos Santos Ribeiro, P and Read, JM and Cremonese, C and Costa, F and Giorgi, E},
title = {Using step selection functions to analyse human mobility using telemetry data in infectious disease epidemiology: a case study of leptospirosis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40343039},
abstract = {Human movement plays a critical role in the transmission of infectious diseases, especially those with environmental drivers like leptospirosis-a zoonotic bacterial infection linked to mud and water contact. Using GPS loggers, we collected detailed telemetry data to understand how fine-scale movements can be analysed in the context of an infectious disease. We recruited individuals living in urban slums in Salvador, Brazil to analyse how they interact with environmental risk factors such as domestic rubbish piles, open sewers, and a local stream. We aimed to identify differences in movement patterns inside the study areas by gender, age, and leptospirosis serological status. Step-selection functions, a spatio-temporal model used in animal movement ecology, estimated selection coefficients to represent the likelihood of movement toward specific environmental factors. With 124 participants wearing GPS devices for 24 to 48 hours, recording locations every 35 seconds during active daytime hours, we segmented movements into morning, midday, afternoon, and evening. Our results suggested women moved closer to the central stream and farther from open sewers compared to men, while serologically positive individuals avoided open sewers. This study introduces a novel method for analysing human telemetry data in infectious disease research, providing critical insights for targeted interventions.},
}
@article {pmid40339581,
year = {2025},
author = {Pekar, JE and Lytras, S and Ghafari, M and Magee, AF and Parker, E and Wang, Y and Ji, X and Havens, JL and Katzourakis, A and Vasylyeva, TI and Suchard, MA and Hughes, AC and Hughes, J and Rambaut, A and Robertson, DL and Dellicour, S and Worobey, M and Wertheim, JO and Lemey, P},
title = {The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.03.035},
pmid = {40339581},
issn = {1097-4172},
abstract = {The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.},
}
@article {pmid40338955,
year = {2025},
author = {Benjamin, JR and Neibauer, J and Anthony, H and Vazquez, J and Rawhouser, A and Dunham, JB},
title = {A partner-driven decision support model to inform the reintroduction of bull trout.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323427},
pmid = {40338955},
issn = {1932-6203},
mesh = {Animals ; *Trout/physiology ; *Conservation of Natural Resources/methods ; Ecosystem ; *Decision Support Techniques ; Decision Making ; },
abstract = {Assessments of species reintroductions involve a series of complex decisions that include human perspectives and ecological contexts. Here, we present a reintroduction assessment involving bull trout (Salvelinus confluentus) using a structured decision-making process. We approached this assessment by engaging partners representing public utilities, government agencies, and Tribes with shared interests in a potential reintroduction. These individuals identified objectives, decision alternatives, and ecological scenarios that were incorporated into a co-produced simulation-based model of potential reintroduction outcomes. The model included mathematical representations of habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Within each recipient stream, partners chose to explore a wide range of decision alternatives and simulated scenarios affecting reintroduction success. Results suggested that 1) reintroductions using eggs or adults were most optimal, 2) adding more individuals resulted in diminishing returns, 3) access to migratory habitat could improve success, and 4) the diversity of opportunities for life history expression led to improved reintroduction opportunities. In addition, modeled scenarios indicated some recipient streams consistently produced lower abundance of reintroduced bull trout. This work contributes a novel example to a growing portfolio of reintroduction assessments that may inform future conservation for bull trout and many other species facing similar challenges.},
}
@article {pmid40335533,
year = {2025},
author = {Pakulnicka, J and Kruk, M},
title = {Water beetle networks differences and migration between natural lakes and post-exploitation water bodies.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15898},
pmid = {40335533},
issn = {2045-2322},
mesh = {Animals ; *Coleoptera/physiology ; *Lakes ; Ecosystem ; *Animal Migration ; Biodiversity ; },
abstract = {Water deficits are a serious problem around the world, which also affects young landscapes, where lakes are most abundant. This poses a threat to many habitats and biological diversity found here. The relationships between species in the ecological networks of lakes at different stages of development and in nearby post-exploitation water bodies remain poorly understood. To better understand the functioning of beetle communities in different ecosystems, we created five network models that we subjected to graph analysis. By analysing the general attributes of the network (number of neighbours, shortest path, characteristic path length, clustering coefficient, network centralisation, network density and network heterogeneity) and those related to the nodes (NCC-Node Closeness Centrality, NBC-Node Betweenness Centrality, NDC-Node Degree Centrality) and to the edges (EBC-Edge Betweenness Centrality and correlations between the biomass of species as nodes), we were able to determine the role of each species in the networks and the relationships between the species. We then used the machine learning ensemble modelling XGBoost-SHAP to identify species that are particularly important in migrations between water bodies and to assess the direction and strength of migrations using Shapley values. Our analyses are based on faunal material from 25 lakes (mesotrophic, eutrophic, dystrophic) and 31-post-exploitation water bodies (clay pits and gravel pits) in northern Poland, in the Masurian Lake District. We found a total of 169 species representing different ecological and functional components. We have shown that the structures of the network between the biomass of species in the analysed five water types differ significantly. The highest value for network density was recorded in eutrophic lakes and clay ponds, the lowest in dystrophic lakes. In eutrophic lakes these are mainly eurybionts, in clay pits-rheophiles and in gravel pits-argilophiles and tyrphophiles. The relationship between the species with the highest NBC and EBC values is particularly important in order to maintain the stability of the network. The periphery of the network usually consists of larger predators that do not compete with each other. By analysing the migration directions of beetles between different ecosystems, we were able to demonstrate a greater affinity of the beetle fauna, especially the argilophiles (e.g. Scarodytes halensis and Laccobius minutus) inhabiting gravel pits, to dystrophic lakes. The beetles in clay pits originate mainly from mesotrophic lakes. These are mainly rheophiles, mostly weakly flying species, such as: Haliplus fluviatilis, Haliplus fulvus, Ilybius fenestratus, Hygrotus vericolor and Haliplus flavicollis. These species are important for the stability of ecological networks in the studied lake types. Their movements between the ecosystems studied in turn contribute to the functional connectivity between the individual lakes, which ensures the stabilisation of biotic relationships at the landscape level. At the same time, they generally also indicate the optimisation of environmental conditions in post-exploitation water bodies, which makes them potential substitute habitats for natural lakes.},
}
@article {pmid40324147,
year = {2025},
author = {Gilpin, W},
title = {Optimization hardness constrains ecological transients.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1013051},
pmid = {40324147},
issn = {1553-7358},
mesh = {*Ecosystem ; *Models, Biological ; Computer Simulation ; Computational Biology ; Biological Evolution ; },
abstract = {Living systems operate far from equilibrium, yet few general frameworks provide global bounds on biological transients. In high-dimensional biological networks like ecosystems, long transients arise from the separate timescales of interactions within versus among subcommunities. Here, we use tools from computational complexity theory to frame equilibration in complex ecosystems as the process of solving an analogue optimization problem. We show that functional redundancies among species in an ecosystem produce difficult, ill-conditioned problems, which physically manifest as transient chaos. We find that the recent success of dimensionality reduction methods in describing ecological dynamics arises due to preconditioning, in which fast relaxation decouples from slow solving timescales. In evolutionary simulations, we show that selection for steady-state species diversity produces ill-conditioning, an effect quantifiable using scaling relations originally derived for numerical analysis of complex optimization problems. Our results demonstrate the physical toll of computational constraints on biological dynamics.},
}
@article {pmid40132265,
year = {2025},
author = {Gu, J and Shen, Y and Guo, L and Chen, Z and Zhou, D and Ji, G and Gu, A},
title = {Investigation of the mechanisms of liver injury induced by emamectin benzoate exposure at environmental concentrations in zebrafish: A multi-omics approach to explore the role of the gut-liver axis.},
journal = {Journal of hazardous materials},
volume = {491},
number = {},
pages = {138008},
doi = {10.1016/j.jhazmat.2025.138008},
pmid = {40132265},
issn = {1873-3336},
mesh = {Animals ; Zebrafish ; *Ivermectin/analogs &amp; derivatives/toxicity ; *Liver/drug effects/metabolism/pathology ; Gastrointestinal Microbiome/drug effects ; *Chemical and Drug Induced Liver Injury/metabolism/pathology/etiology ; *Water Pollutants, Chemical/toxicity ; Metabolomics ; Lipid Metabolism/drug effects ; *Insecticides/toxicity ; RNA, Ribosomal, 16S/genetics ; Multiomics ; },
abstract = {Emamectin benzoate (EMB) is a lipophilic pesticide that enters aquatic systems and adversely affects non-target organisms. This study investigated the long-term effects of EMB on zebrafish, exposing them to concentrations of 0, 0.1, 1, and 10 μg/L from the 4-hour post-fertilization (hpf) embryo stage to the 120-day post-fertilisation (dpf) adult stage. We found that exposure to 1 μg/L EMB induced liver damage, manifested as impaired liver function (elevated aspartate aminotransferase (AST) and alanine aminotransferase (ALT)), histopathological damage (lipid accumulation), as well as inflammatory and oxidative damage, with a dose - dependent effect. Non-targeted metabolomic analysis revealed an increase in lipid molecules in the liver, affecting the pathways related to glycerophospholipid metabolism. In addition, EMB exposure resulted in damage to the intestinal barrier and inflammatory responses in zebrafish. 16S rRNA sequencing demonstrated that EMB exposure resulted in notable alterations in the gut microbiota composition. Notably, the abundance of Plesiomonas and Cetobacterium increased in the EMB exposure group and exhibited a positive correlation with the majority of liver lipid metabolites. In contrast, reductions in Muribaculaceae and Alloprevotella were negatively correlated. The results of this study indicate that long-term exposure to EMB disrupts the gut microbiota, leading to the dysregulation of hepatic phospholipid metabolism. These findings provide new insights into the health risks associated with EMB and highlight its potential threats to higher organisms, including mammals.},
}
@article {pmid40117176,
year = {2025},
author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP},
title = {Healthy microbiome-moving towards functional interpretation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40117176},
issn = {2047-217X},
support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Dysbiosis/microbiology ; Phylogeny ; *Microbiota ; Principal Component Analysis ; Computational Biology/methods ; },
abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.<br><br>FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.<br><br>CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).},
}
@article {pmid40017036,
year = {2025},
author = {Han, Y and Du, Q and Dai, Y and Gu, S and Lei, M and Liu, W and Zhang, W and Zhu, M and Feng, L and Si, H and Liu, J and Zan, Y},
title = {EasyOmics: A graphical interface for population-scale omics data association, integration, and visualization.},
journal = {Plant communications},
volume = {6},
number = {5},
pages = {101293},
doi = {10.1016/j.xplc.2025.101293},
pmid = {40017036},
issn = {2590-3462},
mesh = {*Software ; *Genomics/methods ; Genome-Wide Association Study ; *Computational Biology/methods ; User-Computer Interface ; Computer Graphics ; Quantitative Trait Loci ; Proteomics ; Metabolomics ; },
abstract = {The rapid growth of population-scale whole-genome resequencing, RNA sequencing, bisulfite sequencing, and metabolomic and proteomic profiling has led quantitative genetics into the era of big omics data. Association analyses of omics data, such as genome-, transcriptome-, proteome-, and methylome-wide association studies, along with integrative analyses of multiple omics datasets, require various bioinformatics tools, which rely on advanced programming skills and command-line interfaces and thus pose challenges for wet-lab biologists. Here, we present EasyOmics, a stand-alone R Shiny application with a user-friendly interface that enables wet-lab biologists to perform population-scale omics data association, integration, and visualization. The toolkit incorporates multiple functions designed to meet the increasing demand for population-scale omics data analyses, including data quality control, heritability estimation, genome-wide association analysis, conditional association analysis, omics quantitative trait locus mapping, omics-wide association analysis, omics data integration, and visualization. A wide range of publication-quality graphs can be prepared in EasyOmics by pointing and clicking. EasyOmics is a platform-independent software that can be run under all operating systems, with a docker container for quick installation. It is freely available to non-commercial users at Docker Hub https://hub.docker.com/r/yuhan2000/easyomics.},
}
@article {pmid38319551,
year = {2025},
author = {Fuller, TJ and Lambert, DN and DiClemente, RJ and Wingood, GM},
title = {Reach and Capacity of Black Protestant Health Ministries as Sites of Community-Wide Health Promotion: A Qualitative Social Ecological Model Examination.},
journal = {Journal of racial and ethnic health disparities},
volume = {12},
number = {2},
pages = {887-898},
pmid = {38319551},
issn = {2196-8837},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Black or African American/statistics &amp; numerical data/psychology ; Georgia ; *Health Promotion/organization &amp; administration ; Interviews as Topic ; *Protestantism ; Qualitative Research ; Secondary Data Analysis ; },
abstract = {Black communities in the Southeast United States experience a disproportionate burden of illness and disease. To address this inequity, public health practitioners are partnering with Black Protestant churches to deliver health promotion interventions. Yet, the reach of these programs beyond the organizational level of the Social Ecological Model (SEM) is not well defined. Thus, the aim of this study is to understand Black Protestant church leaders' and members' perceptions about the capacity of their ministries to reach into their communities, beyond their congregations, as providers or hosts of health education or promotion interventions. From 20 Black Protestant churches in Atlanta, GA, 92 church leaders and members participated in semi-structured interviews. Grounded theory guided data analysis and a diverse team coded the interviews. Most participating churches had health ministries. Participants saw the boundaries between their churches at the organizational level of the SEM and the broader Black community to be porous. Those who described their "community" as being broader than their congregation also tended to describe community-wide health promotion their church engaged in. They described church-based health fairs as a strategy to promote engagement in their communities. Some participants, particularly those in a health-related profession, discussed visions of how to utilize their church as a site for community-wide health promotion. We suggest these participants may be boundary leaders who can build relationships between public health professionals, pastors, and congregants. Based on the findings, we suggest that church-based health fairs may be effective sites of community-wide health promotion.},
}
@article {pmid40333133,
year = {2025},
author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO},
title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40333133},
issn = {2076-0817},
support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; },
abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.},
}
@article {pmid40319682,
year = {2025},
author = {Hwang, H and Kim, D and Kim, S and Kim, JY and Kim, ES and Yang, T and Lee, N and Piao, Y and Park, BJ and Lee, DK},
title = {Optimizing urban green spaces using a decision-support model for carbon sequestration and ecological connectivity.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125058},
doi = {10.1016/j.jenvman.2025.125058},
pmid = {40319682},
issn = {1095-8630},
mesh = {*Carbon Sequestration ; *Decision Support Techniques ; Cities ; *Conservation of Natural Resources/methods ; Ecosystem ; },
abstract = {Urban green spaces (UGSs) are vital for enhancing urban ecological health and resident well-being. However, their diverse functions need to be balanced based on spatial limitations and varying stakeholder preferences. Integrated planning approaches are needed to exploit the multiple benefits of UGSs. This study introduces a multi-objective decision-support model designed to optimize UGS planning by simultaneously addressing carbon sequestration, ecological connectivity, and cost constraints. The model incorporates the non-dominated sorting genetic algorithm II to identify Pareto-optimal solutions for tailored decision-making strategies that balance different priorities. The model indicated that ecological connectivity can be improved by 7.57 % while meeting carbon-reduction and budgetary targets. The model effectively balanced trade-offs, underscoring the importance of both the quantity and strategic placement of green space. This decision-support framework empowers decision-makers to rapidly simulate and validate optimal scenarios, effectively balance competing objectives, and provide a scientific basis through verifiable feedback, ultimately promoting the development of sustainable urban environments.},
}
@article {pmid40273607,
year = {2025},
author = {Nkoh, JN and Ye, T and Shang, C and Li, C and Tu, J and Li, S and Wu, Z and Chen, P and Hussain, Q and Esemu, SN},
title = {Deciphering the mechanisms for preferential tolerance of Escherichia coli BL21 to Cd(II) over Cu(II) and Ni(II): A combined physiological, biochemical, and multiomics perspective.},
journal = {Ecotoxicology and environmental safety},
volume = {297},
number = {},
pages = {118195},
doi = {10.1016/j.ecoenv.2025.118195},
pmid = {40273607},
issn = {1090-2414},
mesh = {*Escherichia coli/drug effects/physiology/metabolism ; *Cadmium/toxicity ; *Nickel/toxicity ; *Copper/toxicity ; Oxidative Stress/drug effects ; Escherichia coli Proteins/metabolism/genetics ; Hydrogen Peroxide/metabolism ; Multiomics ; },
abstract = {Environmental pollution severely affects ecological functions/health, and nondegradable pollutants such as heavy metals (HMs) cause significant damage to living organisms. Escherichia coli is one of the most studied life forms, and its response to oxidative stress is driven by a complex ensemble of mechanisms driven by transcriptomic-level adjustments. However, the magnitude of the physiological, metabolic, and biochemical alterations and their relationships with transcriptomic changes remain unclear. Studying the growth of E. coli in Cd-, Cu-, and Ni-polluted media at pH 5.0, we observed that (i) downregulation of the alkyl hydroperoxide complex, glutathione reductase, and glutathione S-transferase by Cd inhibited H2O2 degradation, and the accumulated H2O2 was respectively 2.7, 1.7, and 2.4 times greater than that in the control, Cu, and Ni treatments; (ii) Zn-associated resistance protein (ZraP) was the major scavenger of Cd, with a 140.7-fold increase in its expression; (iii) the P-type Cu[+] transporter (CopA), multicopper oxidase (CueO), and heteromultimeric transport system (CusCBAF) controlled the excretion and detoxification of Cu; (iv) the Cd[2+]/Zn[2+]/Pb[2+]-exporting P-type ATPase (ZntA) and transcriptional activator ZntR were the major transporters of Ni; (v) Cd upregulated biofilm formation and synthesis of secondary metabolites more than Cu and Ni, which resulted in increased adsorption and improved tolerance; and (vi) the activity of superoxide dismutase in Cu-spiked cells was 153.2 %, 141.7 %, and 172.7 % higher and corresponded to 85.7 %, 524.5 %, and 491.5 % lower O2[●][-] in the control, Cd-, and Ni-spiked cells, respectively. This study reveals E. coli's preferential tolerance mechanisms to Cd rather than Cu and Ni and demonstrates mechanisms for its survival in highly polluted environments.},
}
@article {pmid40332368,
year = {2025},
author = {Zheng, K and Feng, Y and Liu, R and Zhang, Y and Fan, D and Zhong, K and Tang, X and Zhang, Q and Cao, S},
title = {Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
pmid = {40332368},
issn = {1422-0067},
mesh = {*Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; Phylogeny ; *Evolution, Molecular ; *Computational Biology/methods ; *Plant Proteins/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; *Multigene Family ; *Adaptation, Physiological/genetics ; *Poaceae/genetics ; Indoleacetic Acids/metabolism ; Promoter Regions, Genetic ; },
abstract = {Auxin response factors (ARFs) are pivotal transcription factors that regulate plant growth, development, and stress responses. Yet, the genomic characteristics and functions of ARFs in Phoebe bournei remain undefined. In this study, 25 PbARF genes were identified for the first time across the entire genome of P. bournei. Phylogenetic analysis categorized these genes into five subfamilies, with members of each subfamily displaying similar conserved motifs and gene structures. Notably, Classes III and V contained the largest number of members. Collinearity analysis suggested that segmental duplication events were the primary drivers of PbARF gene family expansion. Structural analysis revealed that all PbARF genes possess a conserved B3 binding domain and an auxin response element, while additional motifs varied among different classes. Promoter cis-acting element analysis revealed that PbARF genes are extensively involved in hormonal responses-particularly to abscisic acid and jasmonic acid and abiotic stresses-as well as abiotic stresses, including heat, drought, light, and dark. Tissue-specific expression analysis showed that PbARF25, PbARF23, PbARF19, PbARF22, and PbARF20 genes (class III), and PbARF18 and PbARF11 genes (class V) consistently exhibited high expression levels in the five tissues. In addition, five representative PbARF genes were analyzed using qRT-PCR. The results demonstrated significant differences in the expression of PbARF genes under various abiotic stress conditions (drought, salt stress, light, and dark), indicating their important roles in stress response. This study laid a foundation for elucidating the molecular evolution mechanism of ARF genes in P. bournei and for determining the candidate genes for stress-resistance breeding.},
}
@article {pmid40331936,
year = {2025},
author = {Li, H and Wang, R and Pan, J and Chen, J and Hao, X},
title = {Bioinformatics Analysis of the Glutamate-Gated Chloride Channel Family in Bursaphelenchus xylophilus.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
pmid = {40331936},
issn = {1422-0067},
support = {202403//Key Laboratory of National Forestry and Grassland Administration on Prevention and Control Technology of Pine Wilt Disease/ ; 202401BD070001-115//Yunnan Fundamental Research Projects/ ; LXXK-2023M06, LXXK-2024Z04//Southwest Forestry University Forestry major in Yunnan Province First-Class Construction Discipline/ ; },
mesh = {*Chloride Channels/genetics/metabolism/chemistry ; Animals ; *Computational Biology/methods ; Phylogeny ; *Tylenchida/genetics/metabolism ; Multigene Family ; Amino Acid Sequence ; },
abstract = {Glutamate-gated chloride channels (GluCls), a class of ion channels found in the nerve and muscle cells of invertebrates, are involved in vital life processes. Bursaphelenchus xylophilus, the pathogen of pine wilt disease, has induced major economic and ecological losses in invaded areas of Asia and Europe. We identified 33 GluCls family members by sequence alignment analysis. A subsequent bioinformatic analysis revealed the physicochemical properties, protein structure, and gene expression patterns in different developmental stages. The results showed that GluCls genes are distributed across all six chromosomes of B. xylophilus. These proteins indicated a relatively conserved structure by NCBI-conserved domains and InterPro analysis. A gene structure analysis revealed that GluCls genes consist of 5 to 14 exons. Expression pattern analysis revealed BxGluCls were extensively involved in the development of second instar larvae of B. xylophilus. Furthermore, BxGluCls15, BxGluCls25, and BxGluCls28 were mainly associated with the development of eggs of B. xylophilus. BxGluCls12, BxGluCls18, and BxGluCls32 were predominantly linked to nematode resistance and adaptation. Investigation the structure and expression patterns of BxGluCls is crucial to understand the developmental trends of B. xylophilus. It also helps identify molecular targets for the development of biopesticides or drugs designed to control this nematode.},
}
@article {pmid40053042,
year = {2025},
author = {Duarte, T and Martin, GM and Anjos-Santos, D and Pessacq, P},
title = {Unraveling Plecoptera Diversity in Two Protected Areas of Argentine Patagonia.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {97},
number = {1},
pages = {e20240085},
doi = {10.1590/0001-3765202520240085},
pmid = {40053042},
issn = {1678-2690},
mesh = {Animals ; Argentina ; *Biodiversity ; *Neoptera/classification ; Forests ; Population Density ; Cluster Analysis ; *Animal Distribution ; *Insecta/classification ; Conservation of Natural Resources ; Parks, Recreational ; Geographic Information Systems ; },
abstract = {The Plecoptera taxonomy in Patagonia is well-documented, yet their distribution remains poorly understood, hindering comprehensive ecological and biogeographical studies. This study enhances knowledge of stonefly distribution in two Patagonian national parks: Nahuel Huapi and Los Alerces. Extensive fieldwork, georeferenced species records, and geographic information system data integration were conducted. Species richness was calculated using polygons (0.1° x 0.1° pixels) across ecoregions, with species indexed from rare to ubiquitous. Cluster analyses revealed faunal affinities across ecosystem complexes, and richness estimators (Jack1, Jack2, and Chao2) highlighted knowledge gaps. Results showed uneven species distribution, with the highest richness polygon (n = 19) in Los Alerces. The Northern Moist Forests hosted the most species, followed by the Transitional Cypress-Beech Forests. The rarest species were also found in these two complexes, as well as the Ecotone Steppe-Forest. Cluster analysis revealed strong affinities between the Northern Moist Forests of Nahuel Huapi and Ecotone Steppe-Forest. Richness estimators suggested up to 23 undocumented species. Though much remains to be learned about Plecoptera distribution in Patagonia, this study emphasizes the critical role of national parks in conserving biodiversity and provides a foundation for future conservation strategies, identifying new taxa records, including southernmost distributions.},
}
@article {pmid40045055,
year = {2025},
author = {Shi, J and Gong, J and Zhang, Y and Kan, G},
title = {Spatiotemporal change in ecological quality of the Qinghai-Tibetan Plateau based on an improved remote sensing ecological index and Google Earth Engine platform.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {4},
pages = {355},
pmid = {40045055},
issn = {1573-2959},
mesh = {*Remote Sensing Technology ; *Environmental Monitoring/methods ; *Ecosystem ; China ; Tibet ; Spatio-Temporal Analysis ; Conservation of Natural Resources ; Geographic Information Systems ; },
abstract = {The Qinghai-Tibetan Plateau (QTP) serves as a vital ecological security barrier in China and globally. Evaluating changes in ecological quality on the QTP provides critical insights for regional conservation initiatives. This study, tailored to the unique characteristics of the region, develops an Improved Remote Sensing Ecological Index (IRSEI) framework by integrating Gross Primary Productivity (GPP) with the Normalized Difference Vegetation Index (NDVI), humidity (WET), Land Surface Temperature (LST), and the Negative Drought Index (NDBSI). This comprehensive index aims to provide a more precise assessment of the environmental quality of the alpine ecosystem. It investigates spatial and temporal variations in ecological quality across the QTP, as well as within individual geographic subregions from 2000 to 2020. The first principal component accounts for an average variance of 63.69%. Over the past 20 years, the spatial distribution pattern of IRSEI on the QTP has shown lower values in the northwest, higher values in the southeast, and predominantly poor grades throughout the region. The mean trend coefficient for IRSEI was 0.002, indicating a gradual improvement in ecological quality on the QTP over time. Among 11 influencing factors examined, NDVI and GPP exhibit significant positive correlation with ecological quality, with q statistics of 0.942 and 0.932, respectively, underscoring the substantial impact of vegetation cover on ecosystem quality. These findings provide a robust theoretical foundation for supporting ecological management, restoration efforts, and the evaluation of ecological restoration within the QTP, thereby promoting ecosystem balance.},
}
@article {pmid40329811,
year = {2025},
author = {Yang, Y and Liu, X and Wu, J and Svenning, JC and Liu, J and Shrestha, N},
title = {A comprehensive county-level distribution database of alien and invasive plants in China.},
journal = {Ecology},
volume = {106},
number = {5},
pages = {e70084},
pmid = {40329811},
issn = {1939-9170},
support = {2022YFC2601100//National Key Research and Development Program of China/ ; DNRF173//Danmarks Grundforskningsfond/ ; },
mesh = {*Introduced Species ; China ; *Plants/classification ; *Databases, Factual ; Biodiversity ; },
abstract = {Over the past half century, international trade and exchange have continued to increase in China, resulting in the widespread introduction of alien plant species. The accumulation of these alien species has accelerated invasion events, posing serious threats to local ecological security and economic development. Comprehensive and accurate species distribution records are extremely important for early detection, understanding dispersal dynamics, and supporting various management strategies and research initiatives. However, biodiversity databases, both global and local, often lack comprehensive and high-resolution distribution data for alien invasive plant species (AIPs). This limitation is particularly evident in China, where local databases typically provide coarse spatial data, often restricted to the provincial level, leading to a substantial underestimation of the actual distribution of AIPs. Here, we fill this gap by creating the most comprehensive distribution database for AIPs in China at a much finer spatial resolution. By integrating 73,469 distribution records from China's online herbarium, biodiversity databases, flora, published literature, and 173,396 georeferenced records from GBIF, we built the county-level distribution database for 400 AIPs and report for the first time their presence in 2684 administrative counties in China (92.5% of the total counties). Notably, our database provides 2.58 times more distribution records than global biodiversity data repositories such as GBIF and also includes the earliest introduction dates for each AIP. The temporal range of the records spans from 1607 to 2023, capturing over 400 years of AIP presence in China. These rigorously quality-controlled georeferenced data can be used to examine the dynamics and influencing factors of plant invasions in China. They can also serve as the most updated data reference for policy makers in designing effective AIP management policies in China. We encourage users to cite this data paper when utilizing the data, and there are no restrictions on its use for non-commercial purposes.},
}
@article {pmid40294093,
year = {2025},
author = {Williams, B and Balvanera, SM and Sethi, SS and Lamont, TAC and Jompa, J and Prasetya, M and Richardson, L and Chapuis, L and Weschke, E and Hoey, A and Beldade, R and Mills, SC and Haguenauer, A and Zuberer, F and Simpson, SD and Curnick, D and Jones, KE},
title = {Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1013029},
pmid = {40294093},
issn = {1553-7358},
mesh = {*Coral Reefs ; Animals ; Acoustics ; *Unsupervised Machine Learning ; *Artificial Intelligence ; Ecosystem ; Algorithms ; Neural Networks, Computer ; Computational Biology ; Fishes/physiology ; Machine Learning ; Environmental Monitoring/methods ; },
abstract = {Passive acoustic monitoring can offer insights into the state of coral reef ecosystems at low-costs and over extended temporal periods. Comparison of whole soundscape properties can rapidly deliver broad insights from acoustic data, in contrast to detailed but time-consuming analysis of individual bioacoustic events. However, a lack of effective automated analysis for whole soundscape data has impeded progress in this field. Here, we show that machine learning (ML) can be used to unlock greater insights from reef soundscapes. We showcase this on a diverse set of tasks using three biogeographically independent datasets, each containing fish community (high or low), coral cover (high or low) or depth zone (shallow or mesophotic) classes. We show supervised learning can be used to train models that can identify ecological classes and individual sites from whole soundscapes. However, we report unsupervised clustering achieves this whilst providing a more detailed understanding of ecological and site groupings within soundscape data. We also compare three different approaches for extracting feature embeddings from soundscape recordings for input into ML algorithms: acoustic indices commonly used by soundscape ecologists, a pretrained convolutional neural network (P-CNN) trained on 5.2 million hrs of YouTube audio, and CNN's which were trained on each individual task (T-CNN). Although the T-CNN performs marginally better across tasks, we reveal that the P-CNN offers a powerful tool for generating insights from marine soundscape data as it requires orders of magnitude less computational resources whilst achieving near comparable performance to the T-CNN, with significant performance improvements over the acoustic indices. Our findings have implications for soundscape ecology in any habitat.},
}
@article {pmid40329386,
year = {2025},
author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y},
title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {114},
pmid = {40329386},
issn = {2049-2618},
support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; },
mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.<br><br>RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).<br><br>CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.},
}
@article {pmid40328721,
year = {2025},
author = {Zhang, H and Wen, T and Wang, Z and Zhao, X and Wu, H and Xiang, P and Ma, Y},
title = {[Multi-omics analysis of hormesis effect of lanthanum chloride on carotenoid synthesis in Rhodotorula mucilaginosa].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {4},
pages = {1631-1648},
doi = {10.13345/j.cjb.240537},
pmid = {40328721},
issn = {1872-2075},
mesh = {*Lanthanum/pharmacology ; *Rhodotorula/metabolism/drug effects/genetics ; *Carotenoids/metabolism ; *Hormesis/drug effects ; Fermentation ; Multiomics ; },
abstract = {Hormesis effect has been observed in the secondary metabolite synthesis of microorganisms induced by rare earth elements. However, the underlying molecular mechanism remains unclear. To analyze the molecular mechanism of the regulatory effect of Rhodotorula mucilaginosa in the presence of lanthanum chloride, different concentrations of lanthanum chloride were added to the fermentation medium of Rhodotorula mucilaginosa, and the carotenoid content was subsequently measured. It was found that the concentrations of La[3+] exerting the promotional and inhibitory effects were 0-100 mg/L and 100-400 mg/L, respectively. Furthermore, the expression of 33 genes and the synthesis of 55 metabolites were observed to be up-regulated, while the expression of 85 genes and the synthesis of 123 metabolites were found to be down-regulated at the concentration range of the promotional effect. Notably, the expression of carotenoid synthesis-related genes except AL1 was up-regulated. Additionally, the content of β-carotene, lycopene, and astaxanthin demonstrated increases of 10.74%, 5.02%, and 3.22%, respectively. The expression of 5 genes and the synthesis of 91 metabolites were up-regulated, while the expression of 35 genes and the synthesis of 138 metabolites were down-regulated at the concentration range of the inhibitory effect. Meanwhile, the content of β-carotene, lycopene, and astaxanthin decreased by 21.73%, 34.81%, and 35.51%, respectively. In summary, appropriate concentrations of rare earth ions can regulate the synthesis of secondary metabolites by modulating the activities of various enzymes involved in metabolic pathways, thereby exerting the hormesis effect. The findings of this study not only contribute to our comprehension for the mechanism of rare earth elements in organisms but also offer a promising avenue for the utilization of rare earth elements in diverse fields, including agriculture, pharmaceuticals, and healthcare.},
}
@article {pmid40325107,
year = {2025},
author = {Pitogo, KME and Meneses, CG and Flores, ABA and Saavedra, AJL and Amarga, AKS and Angeles, MD and Lucañas, CC and Decena, SCP and Venturina, REL and Fidelino, JS and Pantinople, D and Cabañas, AJC and Herr, MW and Bernstein, JM and Chan, KO and Sanguila, MB and Mallari, NA and Brown, RM and Supsup, CE},
title = {Caught in statistical noise: pitfalls of a unidimensional approach to understanding biodiversity-conflict relationships.},
journal = {npj biodiversity},
volume = {4},
number = {1},
pages = {17},
pmid = {40325107},
issn = {2731-4243},
}
@article {pmid40324092,
year = {2025},
author = {Compton, ZT and Vincze, O and Mellon, W and Tollis, M and Abegglen, L and Schiffman, JD and Giraudeau, M and Boddy, AM and Maley, CC},
title = {Paradoxical indeed.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {19},
pages = {e2504512122},
doi = {10.1073/pnas.2504512122},
pmid = {40324092},
issn = {1091-6490},
support = {T32 CA272303/CA/NCI NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; },
}
@article {pmid40323496,
year = {2025},
author = {Oyelayo, EA and Taiwo, TJ and Oyelude, SO and Alao, JO},
title = {The global impact of industrialisation and climate change on antimicrobial resistance: assessing the role of Eco-AMR Zones.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {6},
pages = {625},
pmid = {40323496},
issn = {1573-2959},
mesh = {*Industrial Development ; *Drug Resistance, Microbial/genetics ; *Climate Change ; Temperature ; Environmental Monitoring ; Genes, Microbial ; Computational Biology ; Anti-Bacterial Agents ; },
abstract = {This study examines the relationship between industrialisation, climate change, and antimicrobial resistance (AMR) gene prevalence. Data analysis from the top 20 highly industrialised and the top 20 least industrialised nations revealed that industrial activities significantly contribute to global warming, with temperature increases of up to 2 °C observed in highly industrialised regions. These environmental changes influence the distribution and evolution of AMR genes, as rising temperatures can affect bacterial resistance in a manner similar to antibiotics. Through a bioinformatics approach, a marked disparity in AMR gene frequencies was observed between highly industrialised and less industrialised nations, with developed countries reporting higher frequencies due to extensive antibiotic use and advanced monitoring systems. 'Eco-AMR Zones' is proposed as a solution to specialised areas by promoting sustainable industrial practices, enforcing pollution controls, and regulating antibiotic use to mitigate AMR's environmental and public health impacts. These zones, supported by collaboration across various sectors, offer a promising approach to preserving antibiotic effectiveness and reducing environmental degradation. The study emphasises the importance of integrated global strategies that address both the ecological and public health challenges posed by AMR, advocating for sustainable practices, international collaboration, and ongoing research to combat the evolving threats of climate change and antimicrobial resistance.},
}
@article {pmid40112992,
year = {2025},
author = {Wei, L and Luo, Z and Wu, X and Liu, C and Shi, Y and Zhang, Q and Chen, M and Qin, W},
title = {Multi-omics analysis provided insights into the fruit softening of postharvest okra under carboxymethyl chitosan treatment.},
journal = {International journal of biological macromolecules},
volume = {307},
number = {Pt 3},
pages = {142149},
doi = {10.1016/j.ijbiomac.2025.142149},
pmid = {40112992},
issn = {1879-0003},
mesh = {*Chitosan/analogs &amp; derivatives/pharmacology ; *Fruit/drug effects/metabolism/genetics ; *Abelmoschus/genetics/metabolism/drug effects ; Gene Expression Regulation, Plant/drug effects ; Transcriptome/drug effects ; *Metabolomics/methods ; Metabolome/drug effects ; Gene Expression Profiling ; Pectins/metabolism ; Multiomics ; },
abstract = {To understand the potential regulatory mechanism of carboxymethyl chitosan (CMCS) treatment on postharvest softening of okra, a joint analysis of physiologic index, transcriptome and metabolome was used. The results showed that CMCS could delay the deterioration of the apparent quality of okra and reduce the degradation of chlorophyll. CMCS can reduce the accumulation of WSP and CSP and the decrease of NSP, and inhibit the enzyme activities of pectin degradation (PE, PG, PL). The results of metabolic pathways related to quality and texture showed that CMCS could increase the metabolic level of pentose phosphate pathway (PPP), inhibit the expression of membrane lipid degradation-related genes, and balance the expression of antioxidant-related genes. Ethylene and abscisic acid (ABA) are two important phytohormones. CMCS down-regulates the biosynthesis of ethylene and increases the expression of ABA. The combined analysis of transcriptome and metabolome showed that CMCS could significantly up-regulate flavonoid biosynthesis metabolites and transcriptional expression levels. Cellulose and pectin are important polymers to maintain the rigidity of okra cell wall. CMCS treatment can slow down the accumulation of cellulose by regulating the expression of DEGs related to cellulose synthesis (CesA) and degradation (EGase). CMCS slowed down the degradation of pectin by down-regulating the expression of pectin degradation-related genes. These results indicate that the quality of okra is deteriorated and the fruit is softened during cold storage. CMCS treatment can improve the nutritional quality of okra and slow down its texture decline. In this study, the regulatory effect of CMCS on softening and quality deterioration of okra during cold storage was discussed at the molecular level, which provided a reference for improving the quality of postharvest okra.},
}
@article {pmid40089216,
year = {2025},
author = {Torres-Roman, JS and Quispe-Vicuña, C and Benavente-Casas, A and Julca-Marin, D and Rios-Garcia, W and Challapa-Mamani, MR and Rio-Muñiz, LD and Ybaseta-Medina, J},
title = {Trends in stroke mortality in Latin America and the Caribbean from 1997 to 2020 and predictions to 2035: An analysis of gender, and geographical disparities.},
journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
volume = {34},
number = {6},
pages = {108286},
doi = {10.1016/j.jstrokecerebrovasdis.2025.108286},
pmid = {40089216},
issn = {1532-8511},
mesh = {Humans ; Latin America/epidemiology ; Female ; Male ; *Stroke/mortality/diagnosis ; Caribbean Region/epidemiology ; Risk Factors ; Sex Factors ; Middle Aged ; Sex Distribution ; Time Factors ; Databases, Factual ; Aged ; Adult ; *Health Status Disparities ; Age Distribution ; Forecasting ; Risk Assessment ; Age Factors ; Young Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Stroke is a leading cause of death and disability globally, with significant public health implications. In Latin America, while mortality rates have declined, the number of stroke cases has increased due to prevalent risk factors like high blood pressure and obesity. Unlike Europe, recent trends in stroke mortality in this region remain underreported.<br><br>OBJECTIVE: This study evaluates stroke mortality rates in Latin America Latin American and Caribbean (LAC) countries from 1997 to 2020 and predictions to 2035.<br><br>METHODS: This ecological observational study utilized mortality data from the World Health Organization database. Trends were analyzed using Joinpoint regression to evaluate the annual percent change (APC) by sex and country. Predicted mortality rates through 2035 were calculated using the Nordpred package in R. Changes in stroke mortality were assessed by disentangling the effects of population growth, aging, and risk factor modifications, based on age-specific rates and projections. Results were presented as absolute case numbers and relative percentages.<br><br>RESULTS: From 1997 to 2020, twelve countries presented significant reductions in stroke mortality rates for men in LAC, the main ones being Chile (-4.2 %), El Salvador (-4.2 %), and Puerto Rico (-4.0 %). Thirteen countries reported a reduction in their mortality for women, mainly in Puerto Rico (-4.3 %), Chile (-3.7 %), Argentina, El Salvador, and Uruguay (-3.5 %). By 2035, an increase in deaths among men and women is expected, mainly due to the increase in population structure and size. However, a decrease in the mortality rate will be reported, mainly due to the reduction of risk factors.<br><br>CONCLUSION: Our final findings show a reduction in stroke mortality trends in LAC countries between 1997 and 2020, due to creating public awareness about vascular risk factors by authorities and the implementation of effective health policies. By 2035, an overall increase in mortality is expected, mainly due to population change in each country.},
}
@article {pmid40102961,
year = {2025},
author = {Hinojosa-Alvarez, S and Mendoza-Portillo, V and Chavez-Santoscoy, RA and Hernández-Pérez, J and Felix-Ceniceros, A and Magallón-Gayón, E and Mar-Silva, AF and Ochoa-Zavala, M and Díaz-Jaimes, P},
title = {The draft genome assembly of the cosmopolitan pelagic fish dolphinfish Coryphaena hippurus.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {5},
pages = {},
doi = {10.1093/g3journal/jkaf059},
pmid = {40102961},
issn = {2160-1836},
support = {CF-2023-G-493//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; },
mesh = {Animals ; *Genome ; Molecular Sequence Annotation ; *Genomics/methods ; *Perciformes/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; *Fishes/genetics ; Whole Genome Sequencing ; Computational Biology/methods ; },
abstract = {For the first time, the complete genome assembly of the dolphinfish (Coryphaena hippurus), a tropical cosmopolitan species with commercial fishing importance was sequenced. Using a combination of Illumina and Nanopore sequencing technologies, a draft genome of 497.8 Mb was assembled into 6,044 contigs, with an N50 of 200.9 kb and a BUSCO genome completeness score of 89%. This high-quality genome assembly provides a valuable resource to study adaptive evolutionary processes and supports conservation and management strategies for this ecologically and economically significant species.},
}
@article {pmid40319413,
year = {2025},
author = {Wang, Y and Mao, Z and Yu, J and Feng, B and Zhang, Z and Zhong, L and Tang, Y},
title = {Construction of risk management system for polluted sites in coal industry clusters.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {6},
pages = {195},
pmid = {40319413},
issn = {1573-2983},
mesh = {*Coal Industry ; *Risk Management/methods ; China ; *Coal ; *Environmental Pollution/prevention &amp; control/statistics &amp; numerical data ; Soil/chemistry ; Groundwater/chemistry ; Environmental Restoration and Remediation ; Environmental Monitoring ; Risk Assessment ; Decision Making, Organizational ; *Coal Mining ; Decision Making, Computer-Assisted ; Algorithms ; *Environmental Pollutants/analysis ; },
abstract = {Coal has always been the main source of energy in China, accounting for more than 60% of primary energy production and consumption. As a result of coal mining, coal industry agglomerations such as mining, coal chemical industry, and so on have been gradually formed, and there are many types of industries in the agglomerations, complex sources of pollutants, and sensitive soil and water environments, and all kinds of industrial sites and solid waste dumps of coal-related industries may pollute the soil and groundwater, and have a certain impact on the ecological environment. However, at present, there is a lack of a targeted region-wide pollution risk management technology system for the polluted sites in the agglomeration area, therefore, it is particularly important to construct a scientific and complete soil-groundwater risk management system and propose more targeted and effective control strategies for the polluted sites in the coal industry agglomeration area. Based on the domestic and international experience and historical data, this paper takes the coal industry cluster area as the research object classifies the land in the area according to the land use type into construction land, agricultural land, and another ecological land, and carries out the risk zoning and grading based on the dosage-effect model and the potential ecological hazard index method respectively, assesses the appropriateness, feasibility, and necessity of the implementation of risk control for the polluted plots, and then designs and develops a risk control decision-making framework by using the hierarchical analysis method. Hierarchical analysis was used to design and develop a decision-making framework for risk management, and finally, the optimal risk management and remediation strategy was proposed based on the AHP + TOPSIS algorithm, which combined with the contaminated land conditions to propose a suitable solution.},
}
@article {pmid40318965,
year = {2025},
author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C},
title = {Corrigendum to "Integrating 'nature' in the water-energy-food nexus: Current perspectives and future directions" [Science of The Total Environment, Volume 966, 2025, 178600].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {179482},
doi = {10.1016/j.scitotenv.2025.179482},
pmid = {40318965},
issn = {1879-1026},
}
@article {pmid40318638,
year = {2025},
author = {Aguilar-Gómez, D and Bejder, J and Graae, J and Ko, Y and Vaughn, A and Clement, K and Tristani-Firouzi, M and Lee, JY and Nordsborg, NB and Nielsen, R and Ilardo, M},
title = {Genetic and training adaptations in the Haenyeo divers of Jeju, Korea.},
journal = {Cell reports},
volume = {},
number = {},
pages = {115577},
doi = {10.1016/j.celrep.2025.115577},
pmid = {40318638},
issn = {2211-1247},
abstract = {Natural selection and relative isolation have shaped the genetics and physiology of unique human populations from Greenland to Tibet. Another such population is the Haenyeo, the all-female Korean divers renowned for their remarkable diving abilities in frigid waters. Apnea diving induces considerable physiological strain, particularly in females diving throughout pregnancy. In this study, we explore the hypothesis that breath-hold diving has shaped physiological and genetic traits in the Haenyeo. We identified pronounced bradycardia during diving, a likely training effect. We paired natural selection and genetic association analyses to investigate adaptive genetic variation that may mitigate the effects of diving on pregnancy through an associated reduction of diastolic blood pressure. Finally, we identified positively selected variation in a gene previously associated with cold water tolerance, which may contribute to reduced hypothermia susceptibility. These findings highlight the importance of traditional diving populations for understanding genetic and physiological adaptation.},
}
@article {pmid40318544,
year = {2025},
author = {Gomes, MLS and Cestari, VRF and Florêncio, RS and Yamamura, M and Santos, JO and Sales, LBF and Silva, RR and Oriá, MOB},
title = {Spatial-temporal analysis of cervical cancer screening and social and health indicators in Brazil.},
journal = {Public health},
volume = {243},
number = {},
pages = {105747},
doi = {10.1016/j.puhe.2025.105747},
pmid = {40318544},
issn = {1476-5616},
abstract = {OBJECTIVE: To identify the spatial-temporal patterns of cervical cancer (CC) screening in Brazil from 2013 to 2022 and its relationship with social and health indicators.<br><br>STUDY DESIGN: This ecological study uses data from the Cancer Information System (SISCAN) of the Brazilian Unified Health System's Department of Informatics.<br><br>METHODS: The study analyzed women aged 25 to 64 who underwent CC screening in 5570 municipalities across Brazil. Global Moran's I and the Local Index of Spatial Autocorrelation (LISA) were employed to investigate clustering. The purely spatial scan statistic technique was used for spatial cluster detection. Temporal trends were assessed using joinpoint regression. GeoDa, SaTScan, GWR, and QGIS software were used for the analysis.<br><br>RESULTS: The global clustering analysis of CC screening proportions revealed significant spatial autocorrelation (Moran's I&#xa0;=&#xa0;0.530). Clusters of municipalities with low screening rates were significantly observed in the Northern (Amap&#xe1;, Amazonas, Rond&#xf4;nia, Roraima) and Northeastern (Piau&#xed;, Pernambuco) regions. The Gini Index (&#x3b2;&#xa0;=&#xa0;-2.60), the Municipal Human Development Index (MHDI) (&#x3b2;&#xa0;=&#xa0;-10.5), and the Social Vulnerability Index (SVI) (&#x3b2;&#xa0;=&#xa0;-9.14) showed negative associations. Conversely, Family Health Strategy (FHS) coverage (&#x3b2;&#xa0;=&#xa0;2.18) demonstrated a positive impact on screening rates. In terms of temporal trends, the screening proportion gradually increased from 5.4&#xa0;% in 2014 to 10.5&#xa0;% in 2022.<br><br>CONCLUSION: Areas with a high risk of low CC screening rates were identified in the Northern and Northeastern regions of Brazil, which are characterized by socioeconomic and demographic disparities, vulnerabilities, and inequalities.},
}
@article {pmid40317095,
year = {2025},
author = {Seizer, L and Pascher, A and Branz, S and Schmitt, N and Löchner, J and Schuller, BW and Rohleder, N and Renner, TJ},
title = {Bridging acute and chronic stress effects on inflammation: protocol for a mixed-methods intensive longitudinal study.},
journal = {BMC psychology},
volume = {13},
number = {1},
pages = {464},
pmid = {40317095},
issn = {2050-7283},
mesh = {Humans ; Longitudinal Studies ; *Stress, Psychological/metabolism/immunology/complications ; *Inflammation/metabolism/psychology/immunology ; Saliva/chemistry ; Male ; Female ; Young Adult ; Chronic Disease ; Adult ; Ecological Momentary Assessment ; Biomarkers/metabolism ; Cytokines/metabolism ; Research Design ; },
abstract = {Acute stress triggers adaptive physiological responses-including transient increases in inflammatory cytokines-while chronic stress is associated with sustained inflammatory activity that may underlie the development of various disorders. Despite extensive research on each stress type individually, the transition and interaction between them remain underexplored. This study aims to address this gap by employing an intensive longitudinal measurement burst design. Healthy university students will be recruited and monitored over three one-week assessment bursts, spaced by three-month breaks. Participants will complete ecological momentary assessments four times daily, recording their emotional states, stress experiences, and daily incidents. Simultaneously, saliva samples will be collected at matching time points to measure biomarkers of immune and stress system activity. In addition, daily audio diaries will provide qualitative context through advanced speech analysis techniques. Data will be analyzed using a multi-level modeling approach to differentiate within-person dynamics from between-person variability, accounting for potential moderators. The findings are expected to shed light on how repeated acute stressors transition into chronic stress and how chronic stress burden may influence acute stress responses.},
}
@article {pmid39937595,
year = {2025},
author = {Royaux, C and Mihoub, JB and Jossé, M and Pelletier, D and Norvez, O and Reecht, Y and Fouilloux, A and Rasche, H and Hiltemann, S and Batut, B and Marc, E and Seguineau, P and Massé, G and Amossé, A and Bissery, C and Lorrilliere, R and Martin, A and Bas, Y and Virgoulay, T and Chambon, V and Arnaud, E and Michon, E and Urfer, C and Trigodet, E and Delannoy, M and Loïs, G and Julliard, R and Grüning, B and Le Bras, Y and , },
title = {Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {39937595},
issn = {2047-217X},
support = {2020-1-NL01-KA203-064717//European Union/ ; //Agence Nationale de la Recherche/ ; //Mus&#xe9;um National d'Histoire Naturelle/ ; //Ministry of Higher Education and Research/ ; },
mesh = {*Ecology/methods/standards ; *Software ; *Data Analysis ; Reproducibility of Results ; *Computational Biology/methods/standards ; },
abstract = {Numerous conceptual frameworks exist for best practices in research data and analysis (e.g., Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical procedures from individual research projects to production-level analytical pipelines. We introduce the concept of atomization to identify analytical steps that support generalization by allowing us to go beyond single analyses. The term atomization is employed to convey the idea of single analytical steps as "atoms" composing an analytical procedure. When generalized, "atoms" can be used in more than a single case analysis. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomized and generalized.},
}
@article {pmid40316929,
year = {2025},
author = {Demsash, AW and Abebe, R and Gezimu, W and Kitil, GW and Tizazu, MA and Lembebo, A and Bekele, F and Alemu, SS and Jarso, MH and Dube, G and Wedajo, LF and Purohit, S and Kalayou, MH},
title = {Data-driven machine learning algorithm model for pneumonia prediction and determinant factor stratification among children aged 6-23 months in Ethiopia.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {647},
pmid = {40316929},
issn = {1471-2334},
mesh = {Humans ; Ethiopia/epidemiology ; Infant ; *Pneumonia/epidemiology/diagnosis ; *Machine Learning ; Female ; Male ; Algorithms ; Risk Factors ; },
abstract = {INTRODUCTION: Pneumonia is the leading cause of child morbidity and mortality and accounts for 5.6 million under-five child deaths. Pneumonia has a significant impact on the quality of life, the country's economy, and the survival of children. Therefore, this study aimed to develop data-driven predictive model using machine learning algorithms to predict pneumonia and stratify the determinant factors among children aged 6-23 months in Ethiopia.<br><br>METHODS: A total of 2035 samples of children were used from the 2016 Ethiopian Demographic and Health Survey dataset. Jupyter Notebook from Anaconda Navigators was used for data management and analysis. Important libraries such as Pandas, Seaborn, and Numpy were imported from Python. The data was pre-processed into a training and testing dataset with a 4:1 ratio, and tenfold cross-validation was used to reduce bias and enhance the models' performance. Six machine learning algorithms were used for model building and comparison, and confusion matrix elements were used to evaluate the performance of each algorithm. Principal component analysis and heatmap function were used for correlation detection between features. Feature importance score was used to identify and stratify the most important predictors of pneumonia.<br><br>RESULTS: From 2035 total samples, 16.6%, 20.1%, and 24.2% of children had short rapid breath, fever, and cough respectively. The overall magnitude of pneumonia among children aged 6-23&#xa0;months was 31.3% based on the 2016 EDHS report. A random forest algorithm is the relatively best performance model to predict pneumonia and stratify its determinates with 91.3% accuracy. The health facility visits, child sex, initiation of breastfeeding, birth interval, birth weight, husbands' education, women's age, and region, are the top eight important predictors of pneumonia among children with important scores of more than 5% to 20% respectively.<br><br>CONCLUSIONS: Random forest is the best model to predict pneumonia and stratify its determinant factors. The implications of this study are profound for advanced research methodology, tailored to promote effective health interventions such as lifestyle modification and behavioral intervention, based on individuals' unique features, specifically for stakeholders to take proactive childcare interventions. The study would serve as pioneering evidence for future research, and researchers are recommended to use deep learning algorithms to enhance prediction accuracy.},
}
@article {pmid40307287,
year = {2025},
author = {Wu, J and He, D and Wang, Y and Liu, S and Du, Y and Wang, H and Tan, S and Zhang, D and Xie, J},
title = {An integrated transcriptome, metabolome, and microbiome dataset of Populus under nutrient-poor conditions.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {717},
pmid = {40307287},
issn = {2052-4463},
mesh = {*Metabolome ; *Microbiota ; Nutrients ; Plant Roots/microbiology/metabolism ; *Populus/microbiology/genetics/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Transcriptome ; Datasets as Topic ; },
abstract = {The rhizosphere microbiota recruited by plants contributes significantly to maintaining host productivity and resisting stress. However, the genetic mechanisms by which plants regulate this recruitment process remain largely unclear. Here, we generated a comprehensive dataset, including 27 root transcriptomes, 27 root metabolomes, and 54 bulk or rhizosphere soil 16S rRNA amplicons across nine poplar species from four sections grown in nutrient-poor natural soil, along with eleven growth phenotype data. We provided a thorough description of this dataset, followed by a comprehensive co-expression network analysis example that broke down the wall of the four-way relationship between plant gene-metabolite-microbe-phenotype, thus identifying the links between plant gene expression, metabolite accumulation, growth behavior, and rhizosphere microbiome variation under nutrient-poor conditions. Overall, this dataset enhances our understanding of plant and microbe interactions, offering valuable strategies and novel insights for resolving how plants regulate rhizosphere microbial compositions and functions, thereby improving host fitness, which will benefit future research.},
}
@article {pmid40314555,
year = {2025},
author = {Yu, Z and Li, S and Yang, W and Chen, J and Rahman, MA and Wang, C and Ma, W and Yao, X and Xiong, J and Xu, C and Zhou, Y and Chen, J and Huang, K and Gao, X and Fensholt, R and Weng, Q and Zhou, W},
title = {Enhancing Climate-Driven Urban Tree Cooling with Targeted Nonclimatic Interventions.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c14275},
pmid = {40314555},
issn = {1520-5851},
abstract = {Urban trees play a pivotal role in mitigating heat, yet the global determinants and patterns of their cooling efficiency (CE) remain elusive. Here, we quantify the diel CE of 229 cities across four climatic zones and employ a machine-learning model to assess the influence of variables on CE. We found that for every 10% increase in tree cover, surface temperatures are reduced by 0.25 °C during the day and 0.04 °C at night. Trees in humid regions exhibit the highest daytime CE, while those in arid zones demonstrate the greatest cooling effect at night. This can be explained by the difference in canopy density between the humid and arid zones. During the day, the high canopy density in the humid zone converts more solar radiation into latent heat flux. At night, the low canopy density in the arid zone intercepts less longwave radiation, which favors surface cooling. While climatic factors contribute nearly twice as much to CE as nonclimatic ones, our findings suggest that optimizing CE is possible by managing variables within specific thresholds due to their nonlinear effects. For instance, we revealed that in arid regions, an impervious surface coverage of approximately 60% is optimal, whereas in humid areas, reducing it to around 40% maximizes cooling benefits. These insights underscore the need for targeted management of nonclimatic factors to sustain tree cooling benefits and offer practical guidance for designing climate-resilient, nature-based urban strategies.},
}
@article {pmid40312707,
year = {2025},
author = {Ketchaji, A and Fokam, J and Assah, F and Ateba, F and Wandji, ML and Pamen, JNB and Djoko, GRP and Seugnou, CDN and Kah, E and Atangana, AF and Ateudjieu, J},
title = {The impact of short message service reminders or peer home visits on adherence to antiretroviral therapy and viral load suppression among HIV-Infected adolescents in Cameroon: a randomized controlled trial.},
journal = {AIDS research and therapy},
volume = {22},
number = {1},
pages = {49},
pmid = {40312707},
issn = {1742-6405},
mesh = {Humans ; *HIV Infections/drug therapy/virology ; Adolescent ; Female ; Cameroon/epidemiology ; Male ; *Viral Load/drug effects ; *Text Messaging ; *House Calls ; Young Adult ; *Medication Adherence ; *Anti-HIV Agents/therapeutic use ; *Reminder Systems ; Peer Group ; },
abstract = {BACKGROUND: Adherence to antiretroviral therapy (ART) and viral load suppression (VLS) constitute one of the key challenges to control human immunodeficiency virus (HIV), especially during adolescence. This trial aimed at assessing the impact of short message services (SMS) or peer home visits (PHV) on adherence to ART and VL suppression among adolescents living with HIV (ALWHIV) in Cameroon.<br><br>METHODS: A randomized controlled trial (RCT) was conducted from July 2018 to February 2019 at the Mother and Child Center of the Chantal Biya Foundation in Yaounde. Eligible ALWHIV (15-19 years), with a fully disclosed HIV status, with availability of phone and guardian's consent, were randomly assigned to receive either daily SMS or bi-weekly PHV for a six-months period. The control-group received standard of care according to the national guidelines. Study investigators and participants were not blinded to the interventions group allocation, and no adverse events or side effects were observed. Adjusted logistic regression was used to assess the impact of interventions on outcomes. The study was approved by The Pan-African Clinical Trials Registry with PACTR201904582515723 at (www.pactr.org).<br><br>RESULTS: Adherence to ART increased in the PHV (aRR: 4.3; 95% CI: 2.2-8.3; p&#x2009;<&#x2009;0.001) and SMS (aRR: 3.1, 95% CI: 2.1-5.3; p&#x2009;<&#x2009;0.001) groups compared to the control-group. Likewise, VL suppression was higher in PHV (aRR: 2.1; 95% CI: 1.9-7.5 p&#x2009;<&#x2009;0.001) and SMS (aRR: 3.2; 95% CI: 1.8-5.4; p&#x2009;<&#x2009;0.001) groups compared to the control-group. Based on CI, both interventions showed similar benefits on improving adherence and VLS.<br><br>CONCLUSIONS: Among ALHIV, SMS or PHV contribute substantially to improving adherence and VL suppression among ALWHIV. Implementing such strategies would support efforts in eliminating pediatric AIDS in low- and middle-income countries.},
}
@article {pmid40120189,
year = {2025},
author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y},
title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.},
journal = {Water research},
volume = {279},
number = {},
pages = {123497},
doi = {10.1016/j.watres.2025.123497},
pmid = {40120189},
issn = {1879-2448},
mesh = {*Sewage ; *Ammonia ; Anaerobiosis ; Iron/chemistry ; Methane ; *Peracetic Acid/chemistry ; Multiomics ; },
abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.},
}
@article {pmid39871222,
year = {2025},
author = {Diongue, FB and Faye, A and Loucoubar, C and Sougou, NM and Sy, I and Tall, A and Ndiaye, Y and Sarr, SC},
title = {Situational analysis of the quality of maternal, child, and adolescent health data in the health districts of Thiès, Mbour, Kédougou, and Saraya in Senegal.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {337},
pmid = {39871222},
issn = {1471-2458},
mesh = {Senegal ; Humans ; Adolescent ; Female ; *Data Accuracy ; Child ; *Health Information Systems/standards ; *Child Health/statistics &amp; numerical data ; *Adolescent Health/statistics &amp; numerical data ; Qualitative Research ; Lot Quality Assurance Sampling ; *Maternal Health ; },
abstract = {INTRODUCTION: In Senegal, the Routine Health Information System (RHIS) captures the majority of data from the Ministry of Health and Social Action (MHSA) public structures and very little health data from the private sector and other ministerial departments. Quality data strengthens the validity and reliability of research results. Common areas of data quality include accuracy, completeness, consistency, credibility, and timeliness. The work aims to assess the quality of routine maternal, child, and adolescent health data in Senegal.<br><br>MATERIALS AND METHODS: A mixed quantitative and qualitative design was chosen in four health districts, including Thi&#xe8;s, Mbour, K&#xe9;dougou, and Saraya. The study included functional health structures that produce maternal, child, and adolescent health data. For the quantitative part, a descriptive and analytical study was carried out. Lot Quality Assurance Sampling (LQAS) was used as the sampling method. Data were collected using Performance of Routine Information Systems Management (PRISM) data collection tools and the ODK application and analyzed (univariate and bivariate) using R and Stata with an alpha risk of 5%. The following data quality indicators (accuracy, completeness, and promptness) were estimated. An exploratory case study and purposive sampling supported the qualitative part by implementing individual interviews.<br><br>RESULTS: The study showed an accuracy ratio of 1 in the intervention districts, a difference in the control districts, and a disparity in the transmission of guidelines between districts (inter- and intra-region). The average level of completeness was 0.64 (+/- 0.44) for all regions combined, with no significant difference between districts. The promptness rate for K&#xe9;dougou, Saraya, Thi&#xe8;s, and Mbour districts was 81%, 75.9%, 72.2%, and 86.7%, respectively. Between 40% and 60% of facilities in each district carried out self-assessments. Data collection tools were considered to be numerous. A large number of tools were easy to use. The recording space was appreciated. On the other hand, the length of the forms was little or not appreciated by the providers. Few of the providers in the 4 districts had been trained to record data in DHIS2.<br><br>CONCLUSION: Assessment of data quality in the districts studied shows shortcomings in terms of completeness and timeliness. Many factors influence the SMEA data quality situation, including knowledge or application of RHIS policies, standards, and protocols, perception of the importance of RHIS, ease of use of data collection tools, training of providers, and diversity of data production sources.},
}
@article {pmid40307720,
year = {2025},
author = {Moreau, SJM and Marchal, L and Boulain, H and Musset, K and Labas, V and Tomas, D and Gauthier, J and Drezen, JM},
title = {Multi-omic approach to characterize the venom of the parasitic wasp Cotesia congregata (Hymenoptera: Braconidae).},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {431},
pmid = {40307720},
issn = {1471-2164},
support = {ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0001//Agence Nationale de la Recherche/ ; SMHART project 35069//European Regional Development Fund/ ; SMHART project 35069//European Regional Development Fund/ ; },
mesh = {Animals ; *Wasps/genetics/virology/metabolism ; *Wasp Venoms/genetics/metabolism/chemistry ; Female ; *Proteomics/methods ; Insect Proteins/genetics/metabolism/chemistry ; Multiomics ; },
abstract = {BACKGROUND: Cotesia congregata is a parasitoid Hymenoptera belonging to the Braconidae family and carrying CCBV (Cotesia congregata Bracovirus), an endosymbiotic polydnavirus. CCBV virus is considered as the main virulence factor of this species, which has raised questions, over the past thirty years, about the potential roles of venom in the parasitic interaction between C. congregata and its host, Manduca sexta (Lepidoptera: Sphingidae). To investigate C. congregata venom composition, we identified genes overexpressed in the venom glands (VGs) compared to ovaries, analyzed the protein composition of this fluid and performed a detailed analysis of conserved domains of these proteins.<br><br>RESULTS: Of the 14 140 known genes of the C. congregata genome, 659 genes were significantly over-expressed (with 10-fold or higher changes in expression) in the VGs of female C. congregata, compared with the ovaries. We identified 30 proteins whose presence was confirmed in venom extracts by proteomic analyses. Twenty-four of these were produced as precursor molecules containing a predicted signal peptide. Six of the proteins lacked a predicted signal peptide, suggesting that venom production in C. congregata also involves non-canonical secretion mechanisms. We have also analysed 18 additional proteins and peptides of interest whose presence in venom remains uncertain, but which could play a role in VG function.<br><br>CONCLUSIONS: Our results show that the venom of C. congregata not only contains proteins (including several enzymes) homologous to well-known venomous compounds, but also original proteins that appear to be specific to this species. This exhaustive study sheds a new light on this venom composition, the molecular diversity of which was unexpected. These data pave the way for targeted functional analyses and to better understand the evolutionary mechanisms that have led to the formation of the venomous arsenals we observe today in parasitoid insects.},
}
@article {pmid39849009,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K},
title = {The influence of depth on the global deep-sea plasmidome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2959},
pmid = {39849009},
issn = {2045-2322},
support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrector&#xed;a de Investigacion de la Universidad Costa Rica/ ; },
mesh = {*Plasmids/genetics ; *Metagenome ; *Seawater/microbiology ; Ecosystem ; Gammaproteobacteria/genetics ; Alphaproteobacteria/genetics ; Oceans and Seas ; Bacteria/genetics ; Computational Biology/methods ; Indian Ocean ; },
abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.},
}
@article {pmid40306212,
year = {2025},
author = {Nica, I and Georgescu, I},
title = {The ecological impact of agricultural production on CO2 emissions in India: Pathways to sustainable agriculture.},
journal = {Journal of environmental management},
volume = {384},
number = {},
pages = {125548},
doi = {10.1016/j.jenvman.2025.125548},
pmid = {40306212},
issn = {1095-8630},
abstract = {This study examines the relationship between CO2 emissions and agricultural production in India from 1990 to 2023, using an Autoregressive Distributed Lag (ARDL) model. Key agricultural indicators analyzed include the Food Production Index (FPI), Cereal Production (CP), Livestock Production Index (LPI), and the value added by Agriculture, Forestry, and Fishing (AFF). The results show that on the long run, a 1 % increase in FPI leads to a 7.86 unit increase in CO2 emissions per capita, while a 1 % increase in livestock production results in a 3.28 unit decrease in CO2 emissions per capita. In the short run, a similar increase in food production and livestock production also influences CO2 emissions, with notable but varying impacts over time. These findings underline the environmental trade-offs between food security and CO2 emissions, emphasizing the need for sustainable agricultural practices. This research contributes to existing literature by utilizing a broad set of agricultural indicators and robust ARDL analysis to examine both short- and long-term effects, providing a more comprehensive understanding of agricultural sustainability. The study was prompted by India's rapid agricultural growth, driven by its growing population and economic expansion, which has raised significant environmental concerns. Unlike prior research that often takes a generalized or global approach, this study offers an India-specific analysis that captures the country's distinct socio-economic and ecological conditions. By focusing on nationally relevant agricultural indicators and sustainability challenges, the research provides context-sensitive insights that can support effective and targeted policy design. The findings highlight the importance of policies that align agricultural productivity with sustainability, supporting the UN Sustainable Development Goals on climate action and food security.},
}
@article {pmid40305182,
year = {2025},
author = {Uemura, NA and Nakane, D},
title = {Type IV Pili in Thermophilic Bacteria: Mechanisms and Ecological Implications.},
journal = {Biomolecules},
volume = {15},
number = {4},
pages = {},
pmid = {40305182},
issn = {2218-273X},
support = {24KJ1131//Japan Society for the Promotion of Science/ ; 21K07020//Japan Society for the Promotion of Science/ ; 22H05066//Japan Society for the Promotion of Science/ ; },
mesh = {*Fimbriae, Bacterial/metabolism/physiology ; *Thermus thermophilus/metabolism/physiology/genetics ; },
abstract = {Type IV pili (T4P) machinery is critical for bacterial surface motility, protein secretion, and DNA uptake. This review highlights the ecological significance of T4P-dependent motility in Thermus thermophilus, a thermophilic bacterium isolated from hot springs. Unlike swimming motility, the T4P machinery enables bacteria to move over two-dimensional surfaces through repeated cycles of extension and retraction of pilus filaments. Notably, T. thermophilus exhibits upstream-directed migration under shear stress, known as rheotaxis, which appears to represent an adaptive strategy unique to thermophilic bacteria thriving in rapid water flows. Furthermore, T4P contributes to the capture of DNA and phages, indicating their multifunctionality in natural environments. Understanding the T4P dynamics provides insights into bacterial survival and evolution in extreme habitats.},
}
@article {pmid40303041,
year = {2024},
author = {McDuie, F and T Overton, C and A Lorenz, A and L Matchett, E and L Mott, A and A Mackell, D and T Ackerman, J and De La Cruz, SEW and Patil, VP and Prosser, DJ and Takekawa, JY and Orthmeyer, DL and Pitesky, ME and Díaz-Muñoz, SL and Riggs, BM and Gendreau, J and Reed, ET and Petrie, MJ and Williams, CK and Buler, JJ and Hardy, MJ and Ladman, BS and Legagneux, P and Bêty, J and Thomas, PJ and Rodrigue, J and Lefebvre, J and Casazza, ML},
title = {Mitigating Risk: Predicting H5N1 Avian Influenza Spread with an Empirical Model of Bird Movement.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {5525298},
pmid = {40303041},
issn = {1865-1682},
mesh = {Animals ; *Influenza in Birds/epidemiology/virology/transmission/prevention &amp; control ; *Influenza A Virus, H5N1 Subtype/physiology ; *Animal Migration ; Birds ; Geographic Information Systems ; Disease Outbreaks/veterinary ; Animals, Wild ; },
abstract = {Understanding timing and distribution of virus spread is critical to global commercial and wildlife biosecurity management. A highly pathogenic avian influenza virus (HPAIv) global panzootic, affecting ~600 bird and mammal species globally and over 83 million birds across North America (December 2023), poses a serious global threat to animals and public health. We combined a large, long-term waterfowl GPS tracking dataset (16 species) with on-ground disease surveillance data (county-level HPAIv detections) to create a novel empirical model that evaluated spatiotemporal exposure and predicted future spread and potential arrival of HPAIv via GPS tracked migratory waterfowl through 2022. Our model was effective for wild waterfowl, but predictions lagged HPAIv detections in poultry facilities and among some highly impacted nonmigratory species. Our results offer critical advance warning for applied biosecurity management and planning and demonstrate the importance and utility of extensive multispecies tracking to highlight potential high-risk disease spread locations and more effectively manage outbreaks.},
}
@article {pmid39852552,
year = {2025},
author = {Yang, H and Luo, X and Shang, Z and Li, K and Cai, J and Chen, Y and Xin, L and Ju, J},
title = {Metabolic Blockade-Based Genome Mining of Malbranchea circinata SDU050: Discovery of Diverse Secondary Metabolites.},
journal = {Marine drugs},
volume = {23},
number = {1},
pages = {},
pmid = {39852552},
issn = {1660-3397},
support = {U2106207//National Natural Science Foundation of China/ ; 2022YFC2804100//National Key Research and Development Program of China/ ; 22037006//National Natural Science Foundation of China/ ; SYS202205//Shandong Laboratory Program/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology/isolation &amp; purification ; *Secondary Metabolism/genetics ; Multigene Family ; Polyketide Synthases/genetics/metabolism ; Biosynthetic Pathways/genetics ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Genome, Fungal ; Microbial Sensitivity Tests ; Gram-Positive Bacteria/drug effects ; Staphylococcus aureus/drug effects ; Bacillus subtilis/drug effects ; *Ascomycota/genetics/metabolism ; Isocoumarins/pharmacology ; Computational Biology ; Geologic Sediments/microbiology ; },
abstract = {Malbranchea circinata SDU050, a fungus derived from deep-sea sediment, is a prolific producer of diverse secondary metabolites. Genome sequencing revealed the presence of at least 69 biosynthetic gene clusters (BGCs), including 30 encoding type I polyketide synthases (PKSs). This study reports the isolation and identification of four classes of secondary metabolites from wild-type M. circinata SDU050, alongside five additional metabolite classes, including three novel cytochalasins (7-9), obtained from a mutant strain through the metabolic blockade strategy. Furthermore, bioinformatic analysis of the BGC associated with the isocoumarin sclerin (1) enabled the deduction of its biosynthetic pathway based on gene function predictions. Bioactivity assays demonstrated that sclerin (1) and (-)-mycousnine (10) exhibited weak antibacterial activity against Gram-positive bacteria such as Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Bacillus subtilis. These findings underscore the chemical diversity and biosynthetic potential of M. circinata SDU050 and highlight an effective strategy for exploring marine fungal metabolites.},
}
@article {pmid40303815,
year = {2023},
author = {Wielgus, E and Klamm, A and Conraths, FJ and Dormann, CF and Henrich, M and Kronthaler, F and Heurich, M},
title = {First-Passage Time Analysis Based on GPS Data Offers a New Approach to Estimate Restricted Zones for the Management of Infectious Diseases in Wildlife: A Case Study Using the Example of African Swine Fever.},
journal = {Transboundary and emerging diseases},
volume = {2023},
number = {},
pages = {4024083},
pmid = {40303815},
issn = {1865-1682},
mesh = {Animals ; *African Swine Fever/prevention &amp; control/epidemiology/transmission ; *Geographic Information Systems ; Swine ; Animals, Wild ; *Sus scrofa ; Germany/epidemiology ; Female ; Disease Outbreaks/veterinary/prevention &amp; control ; Male ; African Swine Fever Virus ; },
abstract = {An essential part of any disease containment and eradication policy is the implementation of restricted zones, but determining the appropriate size of these zones can be challenging for managers. We designed a new method, based on animal movement, to help assess how large restricted zones should be after a spontaneous outbreak to successfully control infectious diseases in wildlife. Our approach uses first-passage time (FPT) analysis and Cox proportional hazard (CPH) models to calculate and compare the risk of an animal leaving different-sized areas. We illustrate our approach using the example of the African swine fever (ASF) virus and its wild pig reservoir host species, the wild boar (Sus scrofa), and we investigate the feasibility of applying this method to other systems. Using GPS data from 57 wild boar living in the Hainich National Park, Germany, we calculate the time spent by each individual in areas of different sizes using FPT analysis. We apply CPH models on the derived data to compare the risk of leaving areas of different sizes and to assess the effects of season and the sex of the wild boar on the risk of leaving. We conduct survival analyses to estimate the risk of leaving an area over time. Our results indicate that the risk of leaving an area decreases exponentially by 10% for each 100 m increase in radius size so that the differences were more pronounced for small sizes. Furthermore, the probability of leaving increases exponentially with time. Wild boar had a similar risk of leaving an area of a given size throughout the year, except in spring and winter, when females had a much lower risk of leaving. Our findings are in agreement with the literature on wild boar movement, further validating our method, and repeated analyses with location data resampled at different rates gave similar results. Our results may be applicable only to our study area, but they demonstrate the applicability of the proposed method to any ecosystem where wild boar populations are likely to be infected with ASF and where restricted zones should be established accordingly. The outlined approach relies solely on the analysis of movement data and provides a useful tool to determine the optimal size of restricted zones. It can also be applied to future outbreaks of other diseases.},
}
@article {pmid40298711,
year = {2025},
author = {Prado, SI and Novais, MAP},
title = {Acute viral bronchiolitis in Brazil: characteristics of length of stay and hospital costs.},
journal = {Ciencia &amp; saude coletiva},
volume = {30},
number = {4},
pages = {e07402023},
doi = {10.1590/1413-81232025304.07402023},
pmid = {40298711},
issn = {1678-4561},
mesh = {Humans ; Brazil ; Infant ; Retrospective Studies ; *Length of Stay/statistics &amp; numerical data/economics ; Acute Disease ; Child, Preschool ; *Hospitalization/economics/statistics &amp; numerical data ; *Bronchiolitis, Viral/economics/therapy/epidemiology ; *Hospital Costs/statistics &amp; numerical data ; Longitudinal Studies ; Male ; Female ; National Health Programs/economics ; },
abstract = {The objective of the study was to evaluate the length of stay in pediatric hospitalizations for acute viral bronchiolitis in the Brazilian Health System (SUS) and the costs of hospitalizations. This was a quantitative, observational, and ecological study, based on a retrospective and longitudinal analysis of data from the Department of Informatics of the Unified Health System (DATASUS; 2012-2021) using descriptive statistics and Tukey's paired test. Regarding the mean value of AIH/HAA Hospital Admission Authorization, among the regions, the high costs of hospitalizations are located more frequent in the Southeast region and the lowest proportion is directed to the corresponds to the North region. In the length of hospital stay among the regions, the shortest mean stay was identified in the Central West region (2.5 days) and the greatest stay in the Northeast region (3.1 days). Considering the age group of one year of life, its representativeness was 57% when compared to the age group of 1-4 years (43%). The fragility of the implementation of primary public policies in the prevention of bronchiolitis contributes to high hospital costs and significant economic impacts on the national healthcare system.},
}
@article {pmid39969985,
year = {2025},
author = {Zhang, J and Gao, X and Liang, C and Zhang, M and Zhang, S},
title = {Spatiotemporal pattern evolution analysis of ecological networks based on morphological spatial pattern analysis: a case study of Ningbo City, China.},
journal = {Integrated environmental assessment and management},
volume = {21},
number = {3},
pages = {540-554},
doi = {10.1093/inteam/vjaf027},
pmid = {39969985},
issn = {1551-3793},
support = {202148/WT_/Wellcome Trust/United Kingdom ; },
mesh = {China ; *Environmental Monitoring/methods ; Spatio-Temporal Analysis ; *Ecosystem ; Cities ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Biodiversity ; Urbanization ; },
abstract = {The exponential expansion of urban areas has precipitated a concomitant deterioration in the natural environment. Constructing ecological networks is vital in improving landscape connectivity, protecting biodiversity, and maintaining regional sustainable development. Ningbo, China, was set as the research area. Geographic information system and morphological spatial pattern analysis (MSPA) were used to determine the ecological source area. Subsequently, the corridor design model Linkage Mapper was used to ascertain and assess the linkages between the designated ecological source areas. The results showed that from 2000-2020, there was a large-scale change in land use type in Ningbo, with increasing complexity of patches and landscape fragmentation. The ecological sources of the three periods in Ningbo were primarily situated in the western, southern, and Hangzhou Bay coastal regions, exhibiting an uneven distribution in the eastern and western areas. The number of primary ecological corridors in Ningbo underwent a significant reduction, from 26 to 17, between the years 2000-2020. In terms of the distribution of ecological corridors, the primary corridors were concentrated in the central, southern, and western regions of the study area in 2000. By 2020, however, the primary ecological corridors within the study region were distributed mainly in a southerly direction. The interaction between north and south ecological sources was weakened, which adversely affected the species spread and ecosystem stability. After optimization, 12 ecological corridors and four ecological nodes were incorporated into Ningbo, 67 ecological breakpoints were identified, and four stepping stone patches were added. The study used spatiotemporal change trends, including land use type and landscape pattern, to examine the ecological network of Ningbo. In conclusion, the proposed optimization strategy is aligned with the current urban development context, offering a particularly pertinent reference point for Ningbo's ecological protection initiatives.},
}
@article {pmid40297776,
year = {2025},
author = {Schwarzerova, J and Olesova, D and Jureckova, K and Kvasnicka, A and Kostoval, A and Friedecky, D and Sekora, J and Pomenkova, J and Provaznik, V and Popelinsky, L and Weckwerth, W},
title = {Enhanced metabolomic predictions using concept drift analysis: identification and correction of confounding factors.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf073},
pmid = {40297776},
issn = {2635-0041},
abstract = {MOTIVATION: The increasing use of big data and optimized prediction methods in metabolomics requires techniques aligned with biological assumptions to improve early symptom diagnosis. One major challenge in predictive data analysis is handling confounding factors-variables influencing predictions but not directly included in the analysis.<br><br>RESULTS: Detecting and correcting confounding factors enhances prediction accuracy, reducing false negatives that contribute to diagnostic errors. This study reviews concept drift detection methods in metabolomic predictions and selects the most appropriate ones. We introduce a new implementation of concept drift analysis in predictive classifiers using metabolomics data. Known confounding factors were confirmed, validating our approach and aligning it with conventional methods. Additionally, we identified potential confounding factors that may influence biomarker analysis, which could introduce bias and impact model performance.<br><br>Based on biological assumptions supported by detected concept drift, these confounding factors were incorporated into correction of prediction algorithms to enhance their accuracy. The proposed methodology has been implemented in Semi-Automated Pipeline using Concept Drift Analysis for improving Metabolomic Predictions (SAPCDAMP), an open-source workflow available at https://github.com/JanaSchwarzerova/SAPCDAMP.},
}
@article {pmid40295976,
year = {2025},
author = {Liberati, F and Pose Marino, TM and Bottoni, P and Canestrelli, D and Castrignanò, T},
title = {HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {113},
pmid = {40295976},
issn = {1471-2105},
mesh = {*Software ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Computational Biology/methods ; Databases, Genetic ; RNA-Seq/methods ; },
abstract = {BACKGROUND: Recent years have seen a substantial increase in RNA-seq data production, with this technique becoming the primary approach for gene expression studies across a wide range of non-model organisms. The majority of these organisms lack a well-annotated reference genome to serve as a basis for studying differentially expressed genes (DEGs). As an alternative cost-effective protocol to using a reference genome, the assembly of RNA-seq raw reads is performed to produce what is referred to as a 'de novo transcriptome,' serving as a reference for subsequent DEGs' analysis. This assembly step for conventional DEGs analysis pipelines for non-model organisms is a computationally expensive task. Furthermore, the complexity of the de novo transcriptome assembly workflows poses a challenge for researchers in implementing best-practice techniques and the most recent software versions, particularly when applied to various organisms of interest.<br><br>RESULTS: To address computational challenges in transcriptomic analyses of non-model organisms, we present HPC-T-Assembly, a tool for de novo transcriptome assembly from RNA-seq data on high-performance computing (HPC) infrastructures. It is designed for straightforward setup via a Web-oriented interface, allowing analysis configuration for several species. Once configuration data is provided, the entire parallel computing software for assembly is automatically generated and can be launched on a supercomputer with a simple command line. Intermediate and final outputs of the assembly pipeline include additional post-processing steps, such as assembly quality control, ORF prediction, and transcript count matrix construction.<br><br>CONCLUSION: HPC-T-Assembly allows users, through a user-friendly Web-oriented interface, to configure a run for simultaneous assemblies of RNA-seq data from multiple species. The parallel pipeline, launched on HPC infrastructures, significantly reduces computational load and execution times, enabling large-scale transcriptomic and meta-transcriptomics analysis projects.},
}
@article {pmid40295704,
year = {2024},
author = {Grunnill, M and Eshaghi, A and Damodaran, L and Nagra, S and Gharouni, A and Braukmann, T and Clark, S and Peci, A and Isabel, S and Banh, P and Plessis, LD and Murall, CL and Colijn, C and Mubareka, S and Hasso, M and Bahl, J and Mostafa, HH and Gubbay, JB and Patel, SN and Wu, J and Duvvuri, VR},
title = {Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks.},
journal = {Npj viruses},
volume = {2},
number = {1},
pages = {34},
pmid = {40295704},
issn = {2948-1767},
abstract = {Enterovirus D68 (EV-D68) has emerged as a significant cause of acute respiratory illness in children globally, notably following its extensive outbreak in North America in 2014. A recent outbreak of EV-D68 was observed in Ontario, Canada, from August to October 2022. Our phylogenetic analysis revealed a notable genetic similarity between the Ontario outbreak and a concurrent outbreak in Maryland, USA. Utilizing Bayesian phylodynamic modeling on whole genome sequences (WGS) from both outbreaks, we determined the median peak time-varying reproduction number (Rt) to be 2.70, 95% HPD (1.76, 4.08) in Ontario and 2.10, 95% HPD (1.41, 3.17) in Maryland. The Rt trends in Ontario closely matched those derived via EpiEstim using reported case numbers. Our study also provides new insights into the median infection duration of EV-D68, estimated at 7.94 days, 95% HPD (4.55, 12.8) in Ontario and 10.8 days, 95% HPD (5.85, 18.6) in Maryland, addressing the gap in the existing literature surrounding EV-D68's infection period. We observed that the estimated Time since the Most Recent Common Ancestor (TMRCA) and the epidemic's origin coincided with the easing of COVID-19 related social contact restrictions in both areas. This suggests that the relaxation of non-pharmaceutical interventions, initially implemented to control COVID-19, may have inadvertently facilitated the spread of EV-D68. These findings underscore the effectiveness of phylodynamic methods in public health, demonstrating their broad application from local to global scales and underscoring the critical role of pathogen genomic data in enhancing public health surveillance and outbreak characterization.},
}
@article {pmid40245036,
year = {2025},
author = {Hu, J and Weber, JN and Fuess, LE and Steinel, NC and Bolnick, DI and Wang, M},
title = {A spectral framework to map QTLs affecting joint differential networks of gene co-expression.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012953},
pmid = {40245036},
issn = {1553-7358},
mesh = {*Quantitative Trait Loci/genetics ; *Gene Regulatory Networks/genetics ; Animals ; Computational Biology/methods ; *Chromosome Mapping/methods ; Phenotype ; Genotype ; Models, Genetic ; Gene Expression Profiling/methods ; },
abstract = {Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype → expression → phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype → network → phenotype mechanism. Here, we develop a network-based method, called spectral network quantitative trait loci analysis (snQTL), to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.},
}
@article {pmid39808116,
year = {2024},
author = {Zárate, A and Díaz-González, L and Taboada, B},
title = {VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39808116},
issn = {1477-4054},
mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Viral Proteins/genetics ; Humans ; *Eukaryota/virology ; *Viruses/genetics ; Genome, Viral ; Artificial Intelligence ; Computational Biology/methods ; Metagenome ; Convolutional Neural Networks ; },
abstract = {This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.},
}
@article {pmid40293859,
year = {2025},
author = {Wastler, HM and Cowan, HR and Breitborde, NJK and Tabares, JV and Yu, M and Pan, X and Boettner, B and Browning, C and Bryan, CJ},
title = {Ecological Momentary Assessment of Emotion Regulation and Suicidal Ideation in First-Episode Psychosis.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf042},
pmid = {40293859},
issn = {1745-1701},
support = {YIG-0-184-20//American Foundation for Suicide Prevention/ ; },
abstract = {Individuals with first-episode psychosis (FEP) are at increased risk for suicide, though few studies have examined the extent to which emotion regulation abnormalities contribute to this risk. The current study sought to address this gap by examining which stages of emotion regulation (ie, identification, selection, implementation) are related to suicidal ideation among individuals with FEP. Forty-one participants completed 28 days of ecological momentary assessment to assess suicidal ideation, negative affect, and emotion regulation in real-time. Results indicated that all 3 stages of emotion regulation were related to suicidal ideation in FEP. Specifically, within-person emotion regulation interacted with between-person negative affect to predict concurrent suicidal ideation (identification stage). Additionally, decreased use of adaptive strategies and increased use of maladaptive strategies were associated with more severe suicidal ideation (selection stage). Finally, decreased emotion regulation effectiveness was associated with more severe suicidal ideation (implementation stage). These findings suggest that emotion regulation difficulties might contribute to the high rates of suicide risk among individuals with FEP. Additional research is needed to determine whether these emotion regulation difficulties are unique to FEP or if they also appear in other high-risk groups.},
}
@article {pmid40292360,
year = {2025},
author = {Andersen, ZJ and Badyda, A and Tzivian, L and Dzhambov, AM and Paunovic, K and Savic, S and Jacquemin, B and Dragic, N},
title = {Air pollution inequalities in Europe: A deeper understating of challenges in Eastern Europe and pathways forward towards closing the gap between East and West.},
journal = {Environmental epidemiology (Philadelphia, Pa.)},
volume = {9},
number = {3},
pages = {e383},
pmid = {40292360},
issn = {2474-7882},
}
@article {pmid40292044,
year = {2025},
author = {Edelson, JB and Huang, J and Wang, Z and Tam, V and Lefktowitz, D and O'Connor, MJ and White, R and Ha, L and Wittlieb-Weber, CA and Rossano, JW and Lin, K and Cousino, MK and Lane-Fall, M and O'Byrne, ML},
title = {Identifying the determinants of health-related quality of life in children after heart transplant.},
journal = {JHLT open},
volume = {8},
number = {},
pages = {100250},
pmid = {40292044},
issn = {2950-1334},
abstract = {BACKGROUND: Pediatric heart transplant (PHT) recipients have impaired health-related quality of life (HRQOL) that is not fully explained by cardiac limitations. Environment is known to influence HRQOL in other chronic disease populations but is less understood in PHT. Understanding the determinants of HRQOL is a necessary step in identifying high-risk groups and designing actionable interventions.<br><br>METHODS: This cross-sectional study includes 8- to 18-year heart transplant (HT) recipients and their families. Generalized estimating equations were used to evaluate the associations of individual characteristics (diagnosis, pulmonary capillary wedge pressure [PCWP], cardiac index [CI]), microenvironment (parent education level, financial security, parental stress [PSI], assessment of child anxiety) and macroenvironment [Child Opportunity Index (COI)] with HRQOL.<br><br>RESULTS: Of 31 participants, 32% self-identified as Black, and 40% had congenital heart disease. On cardiac catheterization, 61% had a CI &#x2265;3&#xa0;liter/min/m[2] and PCWP &#x2264;10&#xa0;mm&#xa0;Hg. Most households had &#x2265;1 parent who had completed college (58%); 28% of households expressed difficulty paying bills. The PSI showed elevated parental stress [64.5 (interquartile range [IQR] 52.0, 77.8)], while the COI was low [73.0 (IQR 44.5, 89.0)] as was HRQOL [Pediatric Quality of Life 4.0 Core Scales 71.7 (IQR 64.2-82.5), Pediatric Cardiac Quality of Life Index 61.8 (IQR 55.7-74.8)]. Higher parental stress (p = 0.036), higher parental perception of child anxiety (p = 0.058), lower Max VO2 (p = 0.059), and higher PCWP (p = 0.006) were independently associated with worse quality of life.<br><br>CONCLUSIONS: HRQOL in children after heart transplant is reduced and determined not only by traditional measures of cardiovascular function, but also by patient psychology and their household environment, highlighting the utility of using an adapted ecological systems framework to understand HRQOL.},
}
@article {pmid40287834,
year = {2025},
author = {Mohanty, A and Srinivasan, A and Udupaa, P and Catchpoole, D},
title = {Multiomics and tumor banking: comprehensive plaforms- integrating cancer diversity, biomarker discovery and personalised cancer care in India.},
journal = {Human molecular genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/hmg/ddaf033},
pmid = {40287834},
issn = {1460-2083},
abstract = {Biobanks are innovative biomedical research infrastructures that play a crucial role in advancing cancer research by supporting investigations into the etiology, progression, and therapeutic interventions of the disease. Biobanks have significantly contributed to personalized medicine by providing high-quality bio specimen resources and expertise in tissue handling, essential for understanding the interplay of genetic, ecological, and lifestyle factors on cancer biology, human health, and mortality. By linking bio specimens with clinical, pathological, and epidemiological data, biobanks are central in the discovery and development of cancer therapeutics through biomarkers. In this review, the importance of managing biobanks as integral parts of data generation and analytics continuum driving precision medicine is pointed out. The advent of multi-OMICS analytics, combined with artificial intelligence, systems biology, and deep machine learning, has elevated the importance of bio banking human bio specimens as not only a biological resource but also an informatics asset. Here, we examine the impact of bio banking in facilitating translational, bench-to-bedside cancer research, with a focus on multi-OMICS data-driven biomarker discovery and precision oncology. In addition, we discuss one of the major innovations in biobank management: the hub-and-spoke model. This centralized system leverages core expertise and resources while collecting bio specimens from diverse geographic regions, thereby capturing the heterogeneity of cancer biology. The hub-and-spoke approach is particularly advantageous for countries like India, characterized by vast geographic and demographic diversity. It ensures complete coverage of the different types of cancers, disease stages, and population groups in addressing the complexity and diversity of cancer biology.},
}
@article {pmid39724139,
year = {2024},
author = {Stephens, JL and Fraga, LAO and Ferreira, JA and De Mondesert, L and Kitron, U and Clennon, JA and Fairley, JK},
title = {Spatial associations of Hansen's disease and schistosomiasis in endemic regions of Minas Gerais, Brazil.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {12},
pages = {e0012682},
pmid = {39724139},
issn = {1935-2735},
mesh = {Humans ; Brazil/epidemiology ; *Leprosy/epidemiology ; *Endemic Diseases ; Female ; Male ; Spatial Analysis ; Adult ; Incidence ; Adolescent ; Middle Aged ; Young Adult ; Child ; Geographic Information Systems ; Animals ; *Schistosomiasis mansoni/epidemiology ; *Schistosomiasis/epidemiology ; Child, Preschool ; Aged ; },
abstract = {BACKGROUND: Brazil has the second highest case count of Hansen's disease (leprosy, HD), but factors contributing to transmission in highly endemic areas of the country remain unclear. Recent studies have shown associations of helminth infection and leprosy, supporting a biological plausibility for increased leprosy transmission in areas with helminths. However, spatial analyses of the overlap of these infections are limited. Therefore, we aimed to spatially analyze these two diseases in a co-endemic area of Minas Gerais, Brazil, in order to identify potential epidemiologic associations.<br><br>METHODS: An ecological study using public health surveillance records and census data was conducted to investigate whether the occurrence of HD -and specifically multibacillary (MB) disease- was associated with the presence of schistosomiasis in a community of 41 municipalities in eastern Minas Gerais, Brazil from 2011 to 2015. Multivariate logistic regression and spatial cluster analyses using geographic information systems (GIS) were performed.<br><br>RESULTS: The average annual incidence of HD in the study area was 35.3 per 100,000 while Schistosoma mansoni average annual incidence was 26 per 100,000. Both HD and schistosomiasis were spatially distributed showing significant clustering across the study area. Schistosomiasis was present in 10.4% of the tracts with HD and thirteen high-high clusters of local bivariate autocorrelation for HD and schistosomiasis cases were identified. A multivariate non-spatial analysis found that census tracts with MB disease were more likely to have schistosomiasis when adjusted for population density, household density, and household income (aOR = 1.7, 95% CI 1.0, 2.7). This remained significant when accounting for spatial correlation (aOR = 1.1, 95% CI (1.0, 1.2)).<br><br>CONCLUSION: We found clustering of both HD and schistosomiasis in this area with some statistically significant overlap of multibacillary HD with S. mansoni infection. Not only did we provide an effective approach to study the epidemiology of two endemic neglected tropical diseases with geographic spatial analyses, we highlight the need for further clinical and translational studies to study the potential epidemiologic associations uncovered.},
}
@article {pmid40287826,
year = {2025},
author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
pmid = {40287826},
issn = {1362-4962},
support = {DBI1356288NSF//NSF/ ; },
mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; },
abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.},
}
@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {Workflow ; *Software ; *Gene Expression Profiling/methods ; *Computational Biology/methods ; *Transcriptome ; Microbiota/genetics ; Humans ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}
@article {pmid40286849,
year = {2025},
author = {Bartas, M and Petrovič, M and Brázda, V and Trenz, O and Ďurčanský, A and Štastný, J},
title = {CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {108537},
doi = {10.1016/j.jbc.2025.108537},
pmid = {40286849},
issn = {1083-351X},
abstract = {With continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation; with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/#/analyse/cpg.},
}
@article {pmid40286830,
year = {2025},
author = {Yu, X and Yao, R and Yao, R and Jin, X and Huang, J and Liang, Q and Jin, LN and Sun, J},
title = {Mechanistic understanding of the toxic effects of tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP) to Escherichia coli: Evidence from alterations in biomarker expression and perturbations of the metabolic network.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {},
number = {},
pages = {110211},
doi = {10.1016/j.cbpc.2025.110211},
pmid = {40286830},
issn = {1532-0456},
abstract = {Tri-n-butyl phosphate (TnBP) and tricresyl phosphate (TCP), emerging flame retardants and plasticizers, have garnered increasing attention due to their potential risks to ecosystem. A few researches regarding the toxicological mechanisms of TnBP and TCP had been performed, while molecular-level toxic effects of them and metabolic response using microbial models are the lack of relevant investigation. Thus, we investigated the cytotoxicity, oxidative stress response, and metabolic response in E. coli exposed to TnBP and TCP. Exposure to them significantly increased the activities of antioxidant enzymes, indicating activation of the antioxidant defense system. Excessive accumulation of reactive oxygen species (ROS) triggered various biological events, including a reduction in membrane potential (MP), decrease of adenosine triphosphatase (ATPase) activity, and increased malondialdehyde (MDA) content. These findings suggested that oxidative damage compromised membrane proteins function, membrane stability, and intracellular homeostasis. GC-MS and LC-MS-based metabolomics analyses revealed that TnBP and TCP strongly disrupted multiple metabolic pathways, including carbohydrate metabolism, nucleotide metabolism, lipid metabolism, beta-alanine metabolism, pyruvate metabolism and oxidative phosphorylation. These disruptions highlighted the inhibitory effects on molecular functions and metabolic processes. Notably, lipids biomarkers e.g., PC(11:0/16:0), PA(17:1(9Z)/18:2(9Z,12Z)), PE(17:0/14:1(9Z)), and LysoPE(0:0/18:1(11Z)) were significantly altered, verifying that the regulation of lipid-associated metabolite synthesis plays a protective role in maintaining cellular membrane function. In summary, this study enhances our understanding of TnBP and TCP toxicity in E. coli, providing novel insights into their toxicological mechanisms at molecular and network levels. These findings underscore the ecological risks posed by organophosphate flame retardants in aquatic ecosystem.},
}
@article {pmid38163964,
year = {2025},
author = {Bhardwaj, N and S, S and Tripathi, N and Kumar, S and Lal, UR and G, R and Guru, SK and Jain, SK},
title = {Mahamanalactone A, a new triterpenoid from Dysoxylum malabaricum bark: a case study for rapid identification of new metabolites via LC-HRMS profiling and database mining strategy.},
journal = {Natural product research},
volume = {39},
number = {9},
pages = {2438-2443},
doi = {10.1080/14786419.2023.2298721},
pmid = {38163964},
issn = {1478-6427},
mesh = {Humans ; *Triterpenes/chemistry/isolation &amp; purification/pharmacology ; *Plant Bark/chemistry ; Cell Line, Tumor ; *Antineoplastic Agents, Phytogenic/chemistry/pharmacology/isolation &amp; purification ; Chromatography, Liquid ; Molecular Structure ; Mass Spectrometry ; *Meliaceae/chemistry ; Data Mining ; Plant Extracts/chemistry ; },
abstract = {In this recent investigation, the focus centred on exploring the potential phytoconstituents within the bark of Dysoxylum malabaricum. A profiling strategy employing LC-HRMS (Liquid Chromatography-High Resolution Mass Spectrometry) was implemented for the rapid identification of compounds from the bark extract. The crude extract underwent fractionation, resulting in the isolation of four previously known compounds (1-4) and a novel cycloartane triterpenoid named Mahamanalactone A (5). Compound 5 represents a cycloartane triterpenoid with a modified ring-A, featuring £-caprolactone fusion at positions 4 and 5, distinguishing it from other reported compounds where £-caprolactone is typically fused at positions 3 and 4. Cytotoxicity assessment revealed that the newly identified compound 5 exhibited a moderate cytotoxic profile (IC50 29 to 78 µM) against a panel of cancer cell lines.},
}
@article {pmid40284070,
year = {2025},
author = {Lu, F and Yi, B and Qin, K and Bu, ZJ},
title = {Long-Term Nitrogen Addition Eliminates the Cooling Effect on Climate in a Temperate Peatland.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {40284070},
issn = {2223-7747},
support = {U23A2003//National Natural Science Foundation of China/ ; 42407354//National Natural Science Foundation of China/ ; 42371050//National Natural Science Foundation of China/ ; 20210402032GH//Jilin Provincial Science and Technology Development Pro-ject/ ; 20230203002SF//Jilin Provincial Science and Technology Development Pro-ject/ ; JP230021//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Peatlands play a crucial role in global carbon (C) sequestration, but their response to long-term nitrogen (N) deposition remains uncertain. This study investigates the effects of 12 years of simulated N addition on CO2 and CH4 fluxes in a temperate peatland through in situ monitoring. The results demonstrate that long-term N addition significantly reduces net ecosystem exchange (NEE), shifting the peatland from a C sink to a C source. This transition is primarily driven by a decline in aboveground plant productivity, as Sphagnum mosses were suppressed and even experienced mortality, while graminoid plants thrived under elevated N conditions. Although graminoid cover increased, it did not compensate for the GPP loss caused by Sphagnum decline. Instead, it further increased CH4 emissions. These findings suggest that sustained N input may diminish the C sequestration function of peatlands, significantly weakening their global cooling effect.},
}
@article {pmid40278529,
year = {2025},
author = {Fabio, RA and Semino, M and Perina, M and Martini, M and Riccio, E and Pili, G and Pani, D and Chessa, M},
title = {Virtual Reality as a Tool for Upper Limb Rehabilitation in Rett Syndrome: Reducing Stereotypies and Improving Motor Skills.},
journal = {Pediatric reports},
volume = {17},
number = {2},
pages = {},
pmid = {40278529},
issn = {2036-749X},
abstract = {BACKGROUND/OBJECTIVES: Rett Syndrome (RTT) is a rare neurodevelopmental disorder that causes the loss of motor, communicative, and cognitive skills. While no cure exists, rehabilitation plays a crucial role in improving quality of life. Virtual Reality (VR) has shown promise in enhancing motor function and reducing stereotypic behaviors in RTT. This study aims to assess the impact of VR training on upper limb motor skills in RTT patients, focusing on reaching and hand-opening tasks, as well as examining its role in motivation and engagement during rehabilitation.<br><br>METHODS: Twenty RTT patients (aged 5-33) were randomly assigned to an experimental group (VR training) and a control group (standard rehabilitation). Pre- and post-tests evaluated motor skills and motivation in both VR and real-world contexts. The VR training involved 40 sessions over 8 weeks, focusing on fine motor tasks. Non-parametric statistical methods were used to analyze the data.<br><br>RESULTS: Results indicated significant improvements in the experimental group for motor parameters, including reduced stereotypy intensity and frequency, faster response times, and increased correct performance. These improvements were consistent across VR and ecological conditions. Moreover, attention time increased, while the number of aids required decreased, highlighting enhanced engagement and independence. However, motivation levels remained stable throughout the sessions.<br><br>CONCLUSIONS: This study demonstrates the potential of VR as a tool for RTT rehabilitation, addressing both motor and engagement challenges. Future research should explore the customization of VR environments to maximize the generalization of skills and sustain motivation over extended training periods.},
}
@article {pmid40277515,
year = {2025},
author = {Kargarandehkordi, A and Li, S and Lin, K and Phillips, KT and Benzo, RM and Washington, P},
title = {Fusing Wearable Biosensors with Artificial Intelligence for Mental Health Monitoring: A Systematic Review.},
journal = {Biosensors},
volume = {15},
number = {4},
pages = {},
pmid = {40277515},
issn = {2079-6374},
support = {MedRes_2023_00002689//Hawai'i Community Foundation/ ; 2406251//U.S. National Science Foundation/ ; 1U54GM138062-02A1/NH/NIH HHS/United States ; U54 GM138062/GM/NIGMS NIH HHS/United States ; U54GM138062/GM/NIGMS NIH HHS/United States ; },
mesh = {*Wearable Electronic Devices ; *Biosensing Techniques ; Humans ; *Artificial Intelligence ; *Mental Health ; Monitoring, Physiologic ; Heart Rate ; },
abstract = {The development of digital instruments for mental health monitoring using biosensor data from wearable devices can enable remote, longitudinal, and objective quantitative benchmarks. To survey developments and trends in this field, we conducted a systematic review of artificial intelligence (AI) models using data from wearable biosensors to predict mental health conditions and symptoms. Following PRISMA guidelines, we identified 48 studies using a variety of wearable and smartphone biosensors including heart rate, heart rate variability (HRV), electrodermal activity/galvanic skin response (EDA/GSR), and digital proxies for biosignals such as accelerometry, location, audio, and usage metadata. We observed several technical and methodological challenges across studies in this field, including lack of ecological validity, data heterogeneity, small sample sizes, and battery drainage issues. We outline several corresponding opportunities for advancement in the field of AI-driven biosensing for mental health.},
}
@article {pmid40276974,
year = {2025},
author = {Blin, K and Shaw, S and Vader, L and Szenei, J and Reitz, ZL and Augustijn, HE and Cediel-Becerra, JDD and de Crécy-Lagard, V and Koetsier, RA and Williams, SE and Cruz-Morales, P and Wongwas, S and Segurado Luchsinger, AE and Biermann, F and Korenskaia, A and Zdouc, MM and Meijer, D and Terlouw, BR and van der Hooft, JJJ and Ziemert, N and Helfrich, EJN and Masschelein, J and Corre, C and Chevrette, MG and van Wezel, GP and Medema, MH and Weber, T},
title = {antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf334},
pmid = {40276974},
issn = {1362-4962},
support = {NNF20CC0035580//Novo Nordisk Foundation/ ; //Microbial Secondary Metabolites/ ; DNRF137//Danish National Research Foundation/ ; MSC 101072485//Horizon Europe Programme/ ; 101000392//Horizon 2020/ ; KICH1.LWV04.21.013//NWO/ ; 101055020//ERC/ ; RM1GM145426/NH/NIH HHS/United States ; TTU09.716//German Center for Infection Research/ ; //The Royal Thai Government/ ; 504947087//German Research Foundation/ ; //Hessian Ministry for Science and the Arts/ ; //Translational Biodiversity Genomics/ ; I008520N//FWO/ ; },
abstract = {Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in microbial interactions and soil health, but are also crucial for the development of pharmaceuticals or agrochemicals. Over the past decades, advancements in genome sequencing have enabled the identification of large numbers of biosynthetic gene clusters directly from microbial genomes. Since its inception in 2011, antiSMASH (https://antismash.secondarymetabolites.org/), has become the leading tool for detecting and characterizing these gene clusters in bacteria and fungi. This paper introduces version 8 of antiSMASH, which has increased the number of detectable cluster types from 81 to 101, and has improved analysis support for terpenoids and tailoring enzymes, as well as improvements in the analysis of modular enzymes like polyketide synthases and nonribosomal peptide synthetases. These modifications keep antiSMASH up-to-date with developments in the field and extend its overall predictive capabilities for natural product genome mining.},
}
@article {pmid40275196,
year = {2025},
author = {Li, Q},
title = {Assessing and adjusting for bias in ecological analysis using multiple sample datasets.},
journal = {BMC medical research methodology},
volume = {25},
number = {1},
pages = {112},
pmid = {40275196},
issn = {1471-2288},
mesh = {Humans ; Bias ; Kenya ; *Ecology/methods ; *Datasets as Topic ; Health Surveys ; Models, Statistical ; Data Interpretation, Statistical ; Computer Simulation ; },
abstract = {BACKGROUND: Ecological analysis utilizes group-level aggregate measures to investigate the complex relationships between individuals or groups and their environment. Despite its extensive applications across various disciplines, this approach remains susceptible to several biases, including ecological fallacy.<br><br>METHODS: Our study identified another significant source of bias in ecological analysis when using multiple sample datasets, a common practice in fields such as public health and medical research. We show this bias is proportional to the sampling fraction used during data collection. We propose two adjustment methods to address this bias: one that directly accounts for the sampling fraction and another based on measurement error models. The effectiveness of these adjustments is evaluated through formal mathematical derivations, simulations, and empirical analysis using data from the 2014 Kenya Demographic and Health Survey.<br><br>RESULTS: Our findings reveal that the sampling fraction bias can lead to significant underestimation of true relationships when using aggregate measures from multiple sample datasets. Both adjustment methods effectively mitigate this bias, with the measurement-error-adjusted estimator showing particular robustness in real-world applications. The results highlight the importance of accounting for sampling fraction bias in ecological analyses to ensure accurate inference.<br><br>CONCLUSION: Beyond the ecological fallacy uncovered by Robinson's seminar work, our research identified another critical bias in ecological analysis that is likely just as prevalent and consequential. The proposed adjustment methods provide potential tools for researchers to adjust for this bias, thereby improving the validity of ecological inferences. This study underscores the need for caution when pooling aggregate measures from multiple sample datasets and offers potential solutions to enhance the reliability of ecological analyses in various research domains.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40275133,
year = {2025},
author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A},
title = {Correction: High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {517},
doi = {10.1186/s12870-025-06560-4},
pmid = {40275133},
issn = {1471-2229},
}
@article {pmid40273274,
year = {2025},
author = {Chen, N},
title = {The impact of the rural digital economy on China's new-type urbanization.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321663},
doi = {10.1371/journal.pone.0321663},
pmid = {40273274},
issn = {1932-6203},
mesh = {China ; *Urbanization/trends ; *Rural Population ; Humans ; *Economic Development/trends ; Agriculture ; },
abstract = {The Chinese government is vigorously implementing the rural revitalization strategy and accelerating the process of new-type urbanization. The rapid development of the rural digital economy has emerged as a new driving force for new-type urbanization. This study aims to explore how the rural digital economy impacts China's new-type urbanization from direct, heterogeneous, and indirect perspectives. Using the provincial-level panel data in China from 2014 to 2022, a mixed-methods approach is employed for the empirical research. The CRITIC and Entropy TOPSIS are used to assess the comprehensive development level and temporal characteristics of the rural digital economy and new-type urbanization. Moreover, a global-local auto-correlation analysis is carried out to depict the spatial distribution of the two variables. Subsequently, a two-way fixed effects model is constructed to verify the direct impact of the rural digital economy on new-type urbanization, as well as its structural and spatial heterogeneity characteristics. Finally, an mediating effect model is established to explore the impact paths through which the rural digital economy impacts new-type urbanization. The results show that the rural digital economy has significantly promoted new-type urbanization. Specifically, rural digital infrastructure, digital transformation of agriculture, agricultural production service informatization have a significant positive effect, while the role of rural life digitization is not significant. The rural digital economy has more significant positive impact on population agglomeration and economic growth, followed by social public service, but has no significant impact on ecological environmental protection and urban-rural coordination. Additionally, the qualitative analysis identifies geographical region, poverty, demographic structure and social equality as notable influencing factors in this impact. Further mechanism analysis result indicates that the rural digital economy impacts new-type urbanization through rural human capital improvement, agricultural economic growth and rural industrial structure upgrading. This research contributes to the existing body of knowledge by providing the practical path of rural development to promote new-type urbanization in the context of the digital economy, also clarifies the weak points and key links in this process. It also highlights the need for further research into the institutional factors that influence this relationship to enhances the policy applicability.},
}
@article {pmid39475336,
year = {2025},
author = {Menssen, M and Dammann, M and Fneish, F and Ellenberger, D and Schaarschmidt, F},
title = {Prediction Intervals for Overdispersed Poisson Data and Their Application in Medical and Pre-Clinical Quality Control.},
journal = {Pharmaceutical statistics},
volume = {24},
number = {2},
pages = {e2447},
pmid = {39475336},
issn = {1539-1612},
mesh = {Humans ; *Quality Control ; Poisson Distribution ; Monte Carlo Method ; Algorithms ; Computer Simulation ; Models, Statistical ; Multiple Sclerosis ; Data Interpretation, Statistical ; },
abstract = {In pre-clinical and medical quality control, it is of interest to assess the stability of the process under monitoring or to validate a current observation using historical control data. Classically, this is done by the application of historical control limits (HCL) graphically displayed in control charts. In many applications, HCL are applied to count data, for example, the number of revertant colonies (Ames assay) or the number of relapses per multiple sclerosis patient. Count data may be overdispersed, can be heavily right-skewed and clusters may differ in cluster size or other baseline quantities (e.g., number of petri dishes per control group or different length of monitoring times per patient). Based on the quasi-Poisson assumption or the negative-binomial distribution, we propose prediction intervals for overdispersed count data to be used as HCL. Variable baseline quantities are accounted for by offsets. Furthermore, we provide a bootstrap calibration algorithm that accounts for the skewed distribution and achieves equal tail probabilities. Comprehensive Monte-Carlo simulations assessing the coverage probabilities of eight different methods for HCL calculation reveal, that the bootstrap calibrated prediction intervals control the type-1-error best. Heuristics traditionally used in control charts (e.g., the limits in Shewhart c- or u-charts or the mean ± 2 SD) fail to control a pre-specified coverage probability. The application of HCL is demonstrated based on data from the Ames assay and for numbers of relapses of multiple sclerosis patients. The proposed prediction intervals and the algorithm for bootstrap calibration are publicly available via the R package predint.},
}
@article {pmid40273037,
year = {2025},
author = {Wu, KC and Belza, B and Berry, D and Lewis, F and Zaslavsky, O and Hartzler, A},
title = {UTI risk factors in older people living with dementia: A conceptual framework and a scoping review.},
journal = {Dementia (London, England)},
volume = {},
number = {},
pages = {14713012251326129},
doi = {10.1177/14713012251326129},
pmid = {40273037},
issn = {1741-2684},
abstract = {Background and Aims: UTIs greatly impact hospitalization rates for people living with dementia. This study aims to craft a framework through a scoping review, assessing UTI symptoms, risk factors, and non-pharmacological prevention strategies in older people living with dementia. Research Design and Methods: Our scoping review followed PRISMA-ScR guidelines, exploring databases (PubMed, CINAHL, Embase, Web of Science) for topics like geriatric care, urinary tract issues published from January 1977 to April 2023. Two reviewers assessed data, organizing it using the Social-Ecological Model to construct the UTI Prevention (UTIP) framework. Results: The literature review scrutinized 1394 articles, selecting 14 through rigorous evaluation. It detailed demographic characteristics, synthesized UTI symptoms, 14 risk factors, and seven outcomes for older people living with dementia. Moreover, it outlined ten preventive domains and proposed a comprehensive UTI Prevention (UTIP) framework spanning individual, relational, community, and societal levels. This framework aims to prevent UTIs among older people living with dementia, integrating risk factors and outcomes to bolster effective prevention strategies for this population. Discussion and Implications: The review introduced a UTIP framework, and non-pharmacological preventive measures tailored for elderly people living with dementia. However, some factors in the framework require further validation to strengthen their associations with outcomes. Preventive measures from studies had limitations like small sample sizes, bias risks, and inconsistent findings. Future research should prioritize robust randomized trials with strong statistical power, strict criteria, and consistent individual-level interventions to boost outcome reliability and validity. Such efforts will enhance the credibility of findings and contribute significantly to refining preventive strategies for this vulnerable population.},
}
@article {pmid40266389,
year = {2025},
author = {Xinyi, B and Qingbiao, G and Songbo, W and Jin, L and Jiren, X},
title = {Identifying the spatio-temporal evolution and driving mechanisms of ecosystem service value in high groundwater table coal mining areas.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {5},
pages = {581},
pmid = {40266389},
issn = {1573-2959},
support = {No. 2024cx2152//the Graduate Innovation Fund Project of Anhui University of Science and Technology/ ; 2024cxcysj094//the Provincial graduate student innovation and entrepreneurship practice project/ ; NO. KSXTJC202401//Engineering Research Center of Mining Area Environmental And Disaster Cooperative Monitoring (Anhui University of Science and Technology)/ ; No. 52274164//the Natural Science Foundation of China/ ; No. 2308085Y31//the Anhui Provincial Natural Science Foundation/ ; No. 2022QNRC001//the Young Elite Scientists Sponsorship Program by CAST/ ; No. GJNY-21-41-15//the Open Fund of State Key Laboratory of Water Resource Protection and Utilization in Coal Mining/ ; },
mesh = {*Coal Mining ; *Environmental Monitoring ; *Ecosystem ; *Groundwater/chemistry ; *Conservation of Natural Resources/methods ; Spatio-Temporal Analysis ; China ; },
abstract = {In coal mining areas with high groundwater tables, surface subsidence has emerged as a non-negligible phenomenon, stemming from long-term coal mining activities. Employing the Huainan mining area as an exemplar, this research meticulously examines the temporal and spatial attributes of ecosystem service value (ESV) across distinct timeframes of 2005, 2010, 2015, and 2020, utilizing the refined equivalent factor approach in conjunction with spatial analysis methodologies. To delve into the primary forces driving the observed changes, the optimal parameter-based geographical detector (OPGD) model is subsequently utilized as a tool for analysis. Lastly, the study delves into the trade-offs and synergies existing between four exemplary services at the grid level, utilizing Spearman correlation coefficient and bivariate spatial autocorrelation. The findings suggest that: (1) From 2005 to 2020, the total ESV in the Huainan mining area demonstrated a general increasing tendency, primarily attributed to the increase in waters. (2) Throughout the research period, the ecosystem service functions in the coal mining area all exhibited relatively significant hydrological regulation and waste treatment capabilities. (3) Vegetation factors significantly influenced the ESV in the Huainan mining area. (4) The Huainan mining area predominantly exhibited synergistic effects among ecosystem services, with the most pronounced synergy occurring between cultural services (CS) and regulating services (RS). All services were transitioning towards an enhanced trend of synergistic effects. (5) Significant spatial variations are present in the observed trade-offs and synergies among diverse ecosystem services. The aforementioned research findings will provide scientific theoretical guidance for rational mining activities and ecological environmental governance in coal mining areas.},
}
@article {pmid40263346,
year = {2025},
author = {Yamamoto, PK and Takasuka, K and Mori, M and Masuda, T and Kono, N},
title = {Non-invasive molecular species identification using spider silk proteomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13844},
pmid = {40263346},
issn = {2045-2322},
support = {23K21203//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Spiders/genetics/classification/metabolism ; *Proteomics/methods ; *Silk/chemistry/genetics/metabolism ; Species Specificity ; Amino Acid Sequence ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; },
abstract = {Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.},
}
@article {pmid40259303,
year = {2025},
author = {Yano, KM and Zucchi, P and Novais, MAP},
title = {Psychiatric hospitalizations in the Unified Health System: an observational study on hospitalization rates from 2012 to 2023.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {1463},
pmid = {40259303},
issn = {1471-2458},
support = {2022/10716-2//S&#xe3;o Paulo State Research Foundation (FAPESP)/ ; },
mesh = {Humans ; *Hospitalization/trends/statistics &amp; numerical data ; Brazil/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; *Mental Disorders/therapy/epidemiology ; Aged ; Young Adult ; Aged, 80 and over ; Child ; Infant ; Child, Preschool ; *National Health Programs/statistics &amp; numerical data ; Infant, Newborn ; },
abstract = {BACKGROUND: Psychiatric care in Brazil is based on the National Mental Health Policy and is aligned with the guidelines of the Brazilian Unified Health System. It is based on the preeminence of care in the extra-hospital context over the hospital context. Hospital admissions should occur solely when extra-hospital resources prove insufficient for the proper management of the mental health condition.<br><br>METHOD: It refers to a time series investigation of a descriptive, ecological, and observational nature. We used publicly available hospital admissions data from the Brazilian Unified Health System's Department of Informatics. The study looked at information on diseases in ICD-10 group V that affected both men and women aged 0 to 80 or older, from 2012 to 2023. The information was analyzed using the statistical software SPSS 20.0, as well as Jointpoint, through permutation tests, with the aim of evaluating the temporal trend of hospitalization and mortality rates. The joinpoint regression model used a log-linear method to set up a series of connected lines on a logarithmic scale and the Monte Carlo permutation method to figure out the direction or statistical significance. A significance level of 5% was established for the execution of all statistical tests.<br><br>RESULTS: Overall, a trend of reduction in psychiatric hospitalization rates was observed. However, these trends exhibited fluctuations when analyzed in isolation with respect to the type of disorder, gender, and age group. In contrast to the general trend, the number of hospitalizations for affective disorders and disorders linked to stress and somatization went up. This was especially true between 2021 and 2023, when the number of hospitalizations for other disorders went down more significantly. The predominance of hospitalizations in the male gender was significant. However, the trends of decrease were less pronounced in the male group, especially regarding hospitalizations associated with alcohol and other substance use, which draws attention to the hospitalization rates of the female sex. As it relates to dementias, the national picture shows that hospitalizations are going down, and most of the patients are women and older adults or people who are very old. However, an analysis of the state scenario showed that hospitalizations went up for adults, more than for the elderly combined, with more men than women.<br><br>CONCLUSION: the results achieved in this research confirm the findings, both nationally and internationally. Studies have shown that investments made through the National Mental Health Policy and the effects of Covid-19 led to a drop in the number of people admitted to psychiatric hospitals. This was because of the restructuring of the care model, which meant that hospitalizations had to be prioritized to meet the needs of Covid-19, which hurt people with mental disorders.},
}
@article {pmid40208899,
year = {2025},
author = {Minier, L and Rouch, J and Sabbagh, B and Bertucci, F and Parmentier, E and Lecchini, D and Sèbe, F and Mathevon, N and Emonet, R},
title = {Visualization and quantification of coral reef soundscapes using CoralSoundExplorer software.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012050},
doi = {10.1371/journal.pcbi.1012050},
pmid = {40208899},
issn = {1553-7358},
mesh = {*Coral Reefs ; *Software ; Animals ; Acoustics ; Anthozoa/physiology ; Sound ; Machine Learning ; Computational Biology ; Polynesia ; Ecosystem ; *Environmental Monitoring/methods ; },
abstract = {Despite hosting some of the highest concentrations of biodiversity and providing invaluable goods and services in the oceans, coral reefs are under threat from global change and other local human impacts. Changes in living ecosystems often induce changes in their acoustic characteristics, but despite recent efforts in passive acoustic monitoring of coral reefs, rapid measurement and identification of changes in their soundscapes remains a challenge. Here we present the new open-source software CoralSoundExplorer, which is designed to study and monitor coral reef soundscapes. CoralSoundExplorer uses machine learning approaches and is designed to eliminate the need to extract conventional acoustic indices. To demonstrate CoralSoundExplorer's functionalities, we use and analyze a set of recordings from three coral reef sites, each with different purposes (undisturbed site, tourist site and boat site), located on the island of Bora-Bora in French Polynesia. We explain the CoralSoundExplorer analysis workflow, from raw sounds to ecological results, detailing and justifying each processing step. We detail the software settings, the graphical representations used for visual exploration of soundscapes and their temporal dynamics, along with the analysis methods and metrics proposed. We demonstrate that CoralSoundExplorer is a powerful tool for identifying disturbances affecting coral reef soundscapes, combining visualizations of the spatio-temporal distribution of sound recordings with new quantification methods to characterize soundscapes at different temporal scales.},
}
@article {pmid40173380,
year = {2025},
author = {Zagorščak, M and Abdelhakim, L and Rodriguez-Granados, NY and Široká, J and Ghatak, A and Bleker, C and Blejec, A and Zrimec, J and Novák, O and Pěnčík, A and Baebler, &#x160; and Perez Borroto, L and Schuy, C and Županič, A and Afjehi-Sadat, L and Wurzinger, B and Weckwerth, W and Pompe Novak, M and Knight, MR and Strnad, M and Bachem, C and Chaturvedi, P and Sonnewald, S and Sasidharan, R and Panzarová, K and Gruden, K and Teige, M},
title = {Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato.},
journal = {Plant physiology},
volume = {197},
number = {4},
pages = {},
doi = {10.1093/plphys/kiaf126},
pmid = {40173380},
issn = {1532-2548},
support = {//H2020-SFS-2019-2/ ; P4-0165//Slovenian Research Agency/ ; //Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.1.01/0.0/0.0/16_026/0008446//European Regional Development Fund-Project/ ; },
mesh = {*Solanum tuberosum/physiology/genetics/metabolism ; *Stress, Physiological/genetics ; Phenotype ; Droughts ; Proteomics ; Metabolomics ; Gene Expression Regulation, Plant ; Transcriptome ; Plant Leaves/physiology ; Plant Tubers ; Multiomics ; },
abstract = {Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.},
}
@article {pmid40253432,
year = {2025},
author = {Kelliher, JM and Aljumaah, M and Bordenstein, SR and Brister, JR and Chain, PSG and Dundore-Arias, JP and Emerson, JB and Fernandes, VMC and Flores, R and Gonzalez, A and Hansen, ZA and Hatcher, EL and Jackson, SA and Kellogg, CA and Madupu, R and Miller, CML and Mirzayi, C and Moustafa, AM and Mungall, C and Oliver, A and Pariente, N and Pett-Ridge, J and Record, S and Reji, L and Reysenbach, AL and Rich, VI and Richardson, L and Schriml, LM and Shabman, RS and Sierra, MA and Sullivan, MB and Sundaramurthy, P and Thibault, KM and Thompson, LR and Tighe, S and Vereen, E and Eloe-Fadrosh, EA},
title = {Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {40},
pmid = {40253432},
issn = {2524-6372},
support = {2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; },
abstract = {Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12-13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.},
}
@article {pmid40249863,
year = {2025},
author = {Wu, Q and Cheng, S and Zhang, W and Zhao, J and Zhang, L and Lv, M and Ma, J and Ding, J and Wang, S and Zheng, X and Gao, J and Liu, R and Yin, Y and Shi, J and Qu, G and Jiang, G},
title = {Heterogeneous Single-Cell Distribution of Trace-Level Metal Mixtures in Tetrahymena thermophila Using Mass Cytometry.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12818},
pmid = {40249863},
issn = {1520-5851},
abstract = {The uptake of heavy metals by unicellular organisms can lead to the bioaccumulation of these metals in higher organisms, detrimentally affecting organismal health and ultimately impacts the ecosystems. By studying the uptake and accumulation of heavy metals in unicellular organisms, we gain insights into potential risks associated with low-dose heavy metal exposure in aquatic environments. Thus, to investigate the accumulation characteristics of Mo, Ag, Cd, Sn, Sb, Hg, Tl, and Pb mixtures in single Tetrahymena thermophila cells, we developed a label-free approach for the simultaneous absolute quantification of multiple metals in a single cell using mass cytometry. Our results demonstrated the dynamic changes in metal concentrations in T. thermophila, and the competition between metals in uptake and excretory pathways resulted in heterogeneous accumulation and bioconcentration of these metals. Additionally, our findings revealed the limited capacity of T. thermophila to excrete Cd and Hg, suggesting a higher risk for T. thermophila cells when exposed to Cd and Hg over an extended period. Therefore, the current study provides valuable data for a more comprehensive understanding of the impact of low-dose heavy metals on aquatic ecosystems.},
}
@article {pmid40188731,
year = {2025},
author = {Li, Y and Huang, S and Jiang, S and Yang, L and Huang, J and Yang, Q and Jiang, Z and Shi, J and Ma, Z and Li, E and Zhou, F},
title = {Multi-omics insights into antioxidant and immune responses in Penaeus monodon under ammonia-N, low salinity, and combined stress.},
journal = {Ecotoxicology and environmental safety},
volume = {295},
number = {},
pages = {118156},
doi = {10.1016/j.ecoenv.2025.118156},
pmid = {40188731},
issn = {1090-2414},
mesh = {Animals ; *Penaeidae/immunology/physiology/drug effects ; *Ammonia/toxicity ; Salinity ; *Antioxidants/metabolism ; *Water Pollutants, Chemical/toxicity ; Oxidative Stress ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Stress, Physiological ; Transcriptome ; Nitrogen/toxicity ; Multiomics ; },
abstract = {Ammonia nitrogen and salinity are critical environmental factors that significantly impact marine organisms and present substantial threats to Penaeus monodon species within aquaculture systems. This study utilized a comprehensive multi-omics approach, encompassing transcriptomics, metabolomics, and gut microbiome analysis, to systematically examine the biological responses of shrimp subjected to low salinity, ammonia nitrogen stress, and their combined conditions. Metabolomic analysis demonstrated that exposure to ammonia nitrogen stress markedly influenced the concentrations of antioxidant-related metabolites, such as glutathione, suggesting that shrimp mitigate oxidative stress by augmenting their antioxidant capacity. The transcriptomic analysis revealed an upregulation of genes linked to energy metabolism and immune responses and antioxidant enzymes. Concurrently, gut microbiome analysis demonstrated that ammonia nitrogen stress resulted in a marked increase in Vibrio populations and a significant decrease in Photobacterium, indicating that alterations in microbial community structure are intricately associated with the shrimp stress response. A comprehensive analysis further indicated that the combined stressors of ammonia nitrogen and salinity exert a synergistic effect on the immune function and physiological homeostasis of shrimp by modulating antioxidant metabolic pathways and gut microbial communities. These findings provide critical systematic data for elucidating the mechanisms through which ammonia nitrogen and salinity influence marine ecosystems, offering substantial implications for environmental protection and ecological management.},
}
@article {pmid40248649,
year = {2025},
author = {Boyes, D and Januszczak, I and , and , and , and , and , and , and , and , and Mitchell, R},
title = {The genome sequence of the Warted Knot-Horn moth, Acrobasis repandana Fabricius, 1798.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {50},
pmid = {40248649},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female specimen of Acrobasis repandana (Warted Knot-Horn moth; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence has a total length of 620.40 megabases. Most of the assembly (99.78%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.21 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,522 protein-coding genes.},
}
@article {pmid40247661,
year = {2025},
author = {Abraham, AJ and Duvall, ES and Doughty, CE and Riond, B and Ortmann, S and Terranova, M and le Roux, E and Clauss, M},
title = {Sodium Retention in Large Herbivores: Physiological Insights and Zoogeochemical Consequences.},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.2924},
pmid = {40247661},
issn = {2471-5646},
support = {//A.J.A. acknowledges Horizon Europe Marie Sk&#x142;odowska-Curie Actions Grant Agreement No. 101062339./ ; },
abstract = {The assimilation, retention, and release of nutrients by animals fundamentally shapes their physiology and contributions to ecological processes (e.g., zoogeochemistry). Yet, information on the transit of nutrients through the bodies of large mammals remains scarce. Here, we examined how sodium (Na), a key element for animal health and ecosystem functioning, travels differently through fecal and urinary systems of cows (Bos taurus) and horses (Equus ferus caballus). We provided a large dose of Na and compared its timing of release in feces and urine to that of nonabsorbable markers. Na excretion by urine occurred approximately twice as fast as excretion by feces, yet both were shorter than indigestible particle markers. These differences correspond to rapid absorption of Na in the upper gastrointestinal tract and transport by blood to the kidneys (urine Na excretion) or resecretion of Na into the lower intestinal tract (fecal Na excretion). Interestingly, for cows, we found a second peak of Na excretion in urine and feces > 96 h after dosage. This result may indicate that surplus Na can be rapidly absorbed and stored in specific body cells (e.g., skin), from which it is later released. Using a propagule dispersal model, we found that the distance of cattle- and horse-driven nutrient dispersal by urine was 31% and 36% less than the fecal pathway and 60% and 41% less than the particle marker pathway, which is commonly used to estimate nutrient dispersal. Future physiological and zoogeochemical studies should resolve different pathways of nutrient retention and release from large mammals.},
}
@article {pmid40247093,
year = {2025},
author = {Yang, J and Chen, YN and Fang, CY and Li, Y and Ke, HQ and Guo, RQ and Xiang, P and Xiao, YL and Zhang, LW and Liu, H},
title = {Investigating immune cell infiltration and gene expression features in pterygium pathogenesis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13352},
pmid = {40247093},
issn = {2045-2322},
support = {ZKF2024042//National clinical key specialty ophthalmology open foundation/ ; ZKF2024041//National clinical key specialty ophthalmology open foundation/ ; 202208535051//China Scholarship Council/ ; 81860171//National Natural Science Foundation of China/ ; 82460201//National Natural Science Foundation of China/ ; 202205AC160016//Yunnan Young and middle-aged Academic and technical leader Project/ ; L2019029//Yunnan Provincial Health Committee Training program for leading medical talents/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; },
mesh = {Humans ; *Pterygium/genetics/immunology/pathology ; Gene Expression Profiling ; Computational Biology/methods ; Conjunctiva/pathology/metabolism/immunology ; Transcriptome ; *Gene Expression Regulation ; Biomarkers/metabolism ; },
abstract = {Pterygium is a prevalent ocular disease characterized by abnormal conjunctival tissue proliferation, significantly impacting patients' quality of life. However, the underlying molecular mechanisms driving pterygium pathogenesis remain inadequately understood. This study aimed to investigate gene expression changes following pterygium excision and their association with immune cell infiltration. Clinical samples of pterygium and adjacent relaxed conjunctival tissue were collected for transcriptomic analysis using RNA sequencing combined with bioinformatics approaches. Machine learning algorithms, including LASSO, SVM-RFE, and Random Forest, were employed to identify potential diagnostic biomarkers. GO, KEGG, GSEA, and GSVA were utilized for enrichment analysis. Single-sample GSEA was employed to analyze immune infiltration. The GSE2513 and GSE51995 datasets from the GEO database, along with clinical samples, were selected for validation analysis. Differentially expressed genes (DEGs) were identified from the PRJNA1147595 and GSE2513 datasets, revealing 2437 DEGs and 172 differentially regulated genes (DRGs), respectively. There were 52 co-DEGs shared by both datasets, and four candidate biomarkers (FN1, SPRR1B, SERPINB13, EGR2) with potential diagnostic value were identified through machine learning algorithms. Single-sample GSEA demonstrated increased Th2 cell infiltration and decreased CD8 + T cell presence in pterygium tissues, suggesting a crucial role of the immune microenvironment in pterygium pathogenesis. Analysis of the GSE51995 dataset and qPCR results revealed significantly higher expression levels of FN1 and SPRR1B in pterygium tissues compared to conjunctival tissues, but SERPINB13 and EGR2 expression levels were not statistically significant. Furthermore, we identified four candidate drugs targeting the two feature genes FN1 and SPRR1B. This study provides valuable insights into the molecular characteristics and immune microenvironment of pterygium. The identification of potential biomarkers FN1 and SPRR1B highlights their significance in pterygium pathogenesis and lays a foundation for further exploration aimed at integrating these findings into clinical practice.},
}
@article {pmid40163742,
year = {2025},
author = {Ghassemi Nedjad, C and Bolteau, M and Bourneuf, L and Paulevé, L and Frioux, C},
title = {Seed2LP: seed inference in metabolic networks for reverse ecology applications.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {4},
pages = {},
doi = {10.1093/bioinformatics/btaf140},
pmid = {40163742},
issn = {1367-4811},
support = {//French National Research Agency/ ; },
mesh = {*Metabolic Networks and Pathways ; *Software ; *Computational Biology/methods ; Models, Biological ; Algorithms ; },
abstract = {MOTIVATION: A challenging problem in microbiology is to determine nutritional requirements of microorganisms and culture them, especially for the microbial dark matter detected solely with culture-independent methods. The latter foster an increasing amount of genomic sequences that can be explored with reverse ecology approaches to raise hypotheses on the corresponding populations. Building upon genome-scale metabolic networks (GSMNs) obtained from genome annotations, metabolic models predict contextualized phenotypes using nutrient information.<br><br>RESULTS: We developed the tool Seed2LP, addressing the inverse problem of predicting source nutrients, or seeds, from a GSMN and a metabolic objective. The originality of Seed2LP is its hybrid model, combining a scalable and discrete Boolean approximation of metabolic activity, with the numerically accurate flux balance analysis (FBA). Seed inference is highly customizable, with multiple search and solving modes, exploring the search space of external and internal metabolites combinations. Application to a benchmark of 107 curated GSMNs highlights the usefulness of a logic modelling method over a graph-based approach to predict seeds, and the relevance of hybrid solving to satisfy FBA constraints. Focusing on the dependency between metabolism and environment, Seed2LP is a computational support contributing to address the multifactorial challenge of culturing possibly uncultured microorganisms.<br><br>Seed2LP is available on https://github.com/bioasp/seed2lp.},
}
@article {pmid40246854,
year = {2025},
author = {He, B and Zhang, H and Qin, T and Shi, B and Wang, Q and Dong, W},
title = {A simultaneous EEG and eye-tracking dataset for remote sensing object detection.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {651},
pmid = {40246854},
issn = {2052-4463},
support = {42230103//National Science Foundation of China | Key Programme/ ; },
mesh = {*Electroencephalography ; Humans ; *Eye-Tracking Technology ; *Remote Sensing Technology ; Artificial Intelligence ; },
abstract = {We introduce the EEGET-RSOD, a simultaneous electroencephalography (EEG) and eye-tracking dataset for remote sensing object detection. This dataset contains EEG and eye-tracking data when 38 remote sensing experts located specific objects in 1,000 remote sensing images within a limited time frame. This task reflects the typical cognitive processes associated with human visual search and object identification in remote sensing imagery. To our knowledge, EEGET-RSOD is the first publicly available dataset to offer synchronized eye-tracking and EEG data for remote sensing images. This dataset will not only advance the study of human visual cognition in real-world environment, but also bridge the gap between human cognition and artificial intelligence, enhancing the interpretability and reliability of AI models in geospatial applications.},
}
@article {pmid40245396,
year = {2025},
author = {Melia, R and Musacchio Schafer, K and Rogers, ML and Wilson-Lemoine, E and Joiner, TE},
title = {The Application of AI to Ecological Momentary Assessment Data in Suicide Research: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e63192},
doi = {10.2196/63192},
pmid = {40245396},
issn = {1438-8871},
mesh = {Humans ; *Ecological Momentary Assessment ; *Artificial Intelligence ; *Suicide ; *Suicidal Ideation ; },
abstract = {BACKGROUND: Ecological momentary assessment (EMA) captures dynamic processes suitable to the study of suicidal ideation and behaviors. Artificial intelligence (AI) has increasingly been applied to EMA data in the study of suicidal processes.<br><br>OBJECTIVE: This review aims to (1) synthesize empirical research applying AI strategies to EMA data in the study of suicidal ideation and behaviors; (2) identify methodologies and data collection procedures used, suicide outcomes studied, AI applied, and results reported; and (3) develop a standardized reporting framework for researchers applying AI to EMA data in the future.<br><br>METHODS: PsycINFO, PubMed, Scopus, and Embase were searched for published articles applying AI to EMA data in the investigation of suicide outcomes. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines were used to identify studies while minimizing bias. Quality appraisal was performed using CREMAS (adapted STROBE [Strengthening the Reporting of Observational Studies in Epidemiology] Checklist for Reporting Ecological Momentary Assessment Studies).<br><br>RESULTS: In total, 1201 records were identified across databases. After a full-text review, 12 (1%) articles, comprising 4398 participants, were included. In the application of AI to EMA data to predict suicidal ideation, studies reported mean area under the curve (0.74-0.86), sensitivity (0.64-0.81), specificity (0.73-0.86), and positive predictive values (0.72-0.77). Studies met between 4 and 13 of the 16 recommended CREMAS reporting standards, with an average of 7 items met across studies. Studies performed poorly in reporting EMA training procedures and treatment of missing data.<br><br>CONCLUSIONS: Findings indicate the promise of AI applied to self-report EMA in the prediction of near-term suicidal ideation. The application of AI to EMA data within suicide research is a burgeoning area hampered by variations in data collection and reporting procedures. The development of an adapted reporting framework by the research team aims to address this.<br><br>TRIAL REGISTRATION: Open Science Framework (OSF); https://doi.org/10.17605/OSF.IO/NZWUJ and PROSPERO CRD42023440218; https://www.crd.york.ac.uk/PROSPERO/view/CRD42023440218.},
}
@article {pmid40240877,
year = {2025},
author = {Li, W and Chu, C and Zhang, T and Sun, H and Wang, S and Liu, Z and Wang, Z and Li, H and Li, Y and Zhang, X and Geng, Z and Wang, Y and Li, Y and Zhang, H and Fan, W and Wang, Y and Xu, X and Cheng, L and Zhang, D and Xiong, Y and Li, H and Zhou, B and Guan, Q and Deng, CH and Han, Y and Ma, H and Han, Z},
title = {Pan-genome analysis reveals the evolution and diversity of Malus.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40240877},
issn = {1546-1718},
support = {CARS-27//Earmarked Fund for China Agriculture Research System/ ; 32172522//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32422077//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2019M661344//China Postdoctoral Science Foundation/ ; },
abstract = {Malus Mill., a genus of temperate perennial trees with great agricultural and ecological value, has diversified through hybridization, polyploidy and environmental adaptation. Limited genomic resources for wild Malus species have hindered the understanding of their evolutionary history and genetic diversity. We sequenced and assembled 30 high-quality Malus genomes, representing 20 diploids and 10 polyploids across major evolutionary lineages and geographical regions. Phylogenomic analyses revealed ancient gene duplications and conversions, while six newly defined genome types, including an ancestral type shared by polyploid species, facilitated the detection of strong signals for extensive introgressions. The graph-based pan-genome captured shared and species-specific structural variations, facilitating the development of a molecular marker for apple scab resistance. Our pipeline for analyzing selective sweep identified a mutation in MdMYB5 having reduced cold and disease resistance during domestication. This study advances Malus genomics, uncovering genetic diversity and evolutionary insights while enhancing breeding for desirable traits.},
}
@article {pmid40179878,
year = {2025},
author = {Li, Y and Liu, X and Guo, L and Han, K and Fang, S and Wan, X and Wang, D and Xu, X and Jiang, L and Fan, G and Xu, M},
title = {SpaGRN: Investigating spatially informed regulatory paths for spatially resolved transcriptomics data.},
journal = {Cell systems},
volume = {16},
number = {4},
pages = {101243},
doi = {10.1016/j.cels.2025.101243},
pmid = {40179878},
issn = {2405-4720},
mesh = {Animals ; *Transcriptome/genetics ; *Gene Expression Profiling/methods ; Humans ; *Gene Regulatory Networks/genetics ; Drosophila/genetics ; Computational Biology/methods ; },
abstract = {Cells spatially organize into distinct cell types or functional domains through localized gene regulatory networks. However, current spatially resolved transcriptomics analyses fail to integrate spatial constraints and proximal cell influences, limiting the mechanistic understanding of tissue organization. Here, we introduce SpaGRN, a statistical framework that reconstructs cell-type- or functional-domain-specific, dynamic, and spatial regulons by coupling intracellular spatial regulatory causality with extracellular signaling path information. Benchmarking across synthetic and real datasets demonstrates SpaGRN's superior precision over state-of-the-art tools in identifying context-dependent regulons. Applied to diverse spatially resolved transcriptomics platforms (Stereo-seq, STARmap, MERFISH, CosMx, Slide-seq, and 10x Visium), complex cancerous samples, and 3D datasets of developing Drosophila embryos and larvae, SpaGRN not only provides a versatile toolkit for decoding receptor-mediated spatial regulons but also reveals spatiotemporal regulatory mechanisms underlying organogenesis and inflammation.},
}
@article {pmid40238767,
year = {2025},
author = {Rodrigues, RDS and Cionek, VM and Barreto, AS and Branco, JO},
title = {Seabird strandings on the Brazilian coast: What influences spatial and temporal patterns?.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0317335},
doi = {10.1371/journal.pone.0317335},
pmid = {40238767},
issn = {1932-6203},
mesh = {Animals ; Brazil ; *Animal Migration/physiology ; *Birds/physiology ; Seasons ; Spatio-Temporal Analysis ; Ecosystem ; Biodiversity ; },
abstract = {Seabirds exhibit physiological adaptations that allow them to forage in the marine environment and undertake long-distance migrations during non-reproductive periods. As a result, they face various natural and anthropogenic pressures, which can lead to extreme fatigue and even death. Stranded bodies that float in the sea can wash ashore, providing valuable ecological information. This study aimed to analyze seabird strandings along the south and southeast coasts of Brazil between 2016 and 2019, focusing on spatiotemporal and potential environmental and anthropogenic influences. Using data from the Santos Basin Beach Monitoring Project, we calculated ecological indices of abundance, richness, and diversity for the entire seabird community and separately by migratory behavior (resident, southern migratory, northern migratory). Statistical modeling revealed a strong decreasing trend in strandings from south to north, with higher events on the southern coast (Santa Catarina and Paraná) and lower on the southeast coast (São Paulo). Resident species and northern migratory species showed peak strandings in spring, while southern migratory peaked in winter. These spatial and temporal patterns reflected birds' home ranges, reproductive cycles, and migratory behaviors. Environmental variables influenced strandings differently depending on species migration behavior and ecological indices, highlighting the role of oceanographic processes in carcass drift and the impact of climatic events on species mortality. This study is the first to demonstrate a spatiotemporal pattern of seabird strandings on the Brazilian coast, providing valuable insights into seabird dynamics in the Santos Basin and offering important data for conservation efforts.},
}
@article {pmid40238239,
year = {2025},
author = {Sutori, S and Eliasson, ET and Mura, F and Ortiz, V and Catrambonephd, V and Hadlaczky, G and Todorov, I and Alfeo, AL and Cardi, V and Cimino, MGCA and Mioni, G and Raya, MA and Valenza, G and Carli, V and Gentili, C},
title = {Acceptability, Usability, and Insights Into Cybersickness Levels of a Novel Virtual Reality Environment for the Evaluation of Depressive Symptoms: Exploratory Observational Study.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e68132},
doi = {10.2196/68132},
pmid = {40238239},
issn = {2561-326X},
mesh = {Humans ; *Virtual Reality ; Male ; Female ; Adult ; *Depression/diagnosis/psychology ; Young Adult ; Italy ; Surveys and Questionnaires ; User-Computer Interface ; Pilot Projects ; Self Report ; },
abstract = {BACKGROUND: There is a clear need for enhanced mental health assessment, depressive symptom (DS) evaluation being no exception. A promising approach to this aim is using virtual reality (VR), which entails the potential of adding a wider set of assessment domains with enhanced ecological validity. However, whilst several studies have used VR for both diagnostic and treatment purposes, its acceptance, in particular how exposure to virtual environments affects populations with psychiatric conditions remains unknown.<br><br>OBJECTIVE: This study aims to report on the acceptability, usability, and cybersickness levels of a pilot VR environment designed for the purpose of differentiating between individuals with DSs.<br><br>METHODS: The exploratory study, conducted in Italy, included 50 healthy controls and 50 young adults with mild-to-moderate DSs (without the need for a formal diagnosis). The study used an observational design with approximately 30 minutes of VR exposure followed by a self-report questionnaire battery. The battery included a questionnaire based on the Theoretical Framework of Acceptability, the System Usability Scale as well as the Simulator Sickness Questionnaire.<br><br>RESULTS: Results indicate that the majority found VR acceptable for the purposes of mental health screening and treatment. However, for diagnostics, there was a clear preference for VR to be used by mental health professionals as a supplementary tool, as opposed to a stand-alone solution. In practice, following exposure to the pilot VR environment, generally, good levels of acceptability and usability were reported, but areas in need of improvement were identified (such as self-efficacy). Self-reported cybersickness levels were comparable to literature averages but were considerably higher among those with DSs.<br><br>CONCLUSIONS: These findings raise questions about the potential interplay between underlying somatic symptoms of depression and VR-induced cybersickness and call for more attention from the scientific community both in terms of methodology as well as potential clinical and theoretical implications. Conclusively, user support indicates a potential for VR to aid mental health assessment, but further research is needed to understand how exposure to virtual environments might affect populations with varying severity and other forms of psychiatric symptoms.<br><br>RR2-10.1186/ISRCTN16396369.},
}
@article {pmid40235568,
year = {2025},
author = {Davies, H and Noble, PJ and Fins, IS and Pinchbeck, G and Singleton, D and Pirmohamed, M and Killick, D},
title = {Developing electronic health records as a source of real-world data for veterinary pharmacoepidemiology.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1550468},
pmid = {40235568},
issn = {2297-1769},
abstract = {Spontaneous reporting of adverse events (AEs) by veterinary professionals and the public is the cornerstone of post-marketing safety surveillance for veterinary medicinal products (VMPs). However, studies suggest that most veterinary AEs remain unreported. Veterinary medicine regulators, including the United Kingdom Veterinary Medicines Directorate and the European Medicines Agency, have included the exploration of big data utilization to support pharmacovigilance efforts in their regulatory strategies. In this study, we describe the application of veterinary electronic healthcare records (EHRs) from the SAVSNET veterinary first opinion informatics system to conduct pharmacoepidemiological analyses. Five VMP-AE pairs were selected for investigation in a proof-of-concept study, where drug exposure was identified from semi-structured treatment data and AEs from the unstructured free-text clinical narrative. Dictionaries were developed to identify AEs based on standard terminology. The precision of these dictionaries improved when they were expanded using word vectorization and expert opinion. A key strength of first-opinion EHR datasets is their ability to enable cohort studies and facilitate calculations of absolute incidence and relative risk. Thus, we demonstrate that unstructured free-text clinical narratives can be used to identify outcomes for veterinary pharmacoepidemiological studies and, consequently, support and expand pharmacovigilance efforts based on spontaneous AE reports.},
}
@article {pmid40232549,
year = {2025},
author = {Xu, F and Jiang, C and Liu, Q and Yang, R and Li, W and Wei, Y and Bao, L and Tong, H},
title = {Source identification of polycyclic aromatic hydrocarbons (PAHs) in river sediments within a hilly agricultural watershed of Southwestern China: an integrated study based on Pb isotopes and PMF method.},
journal = {Environmental geochemistry and health},
volume = {47},
number = {5},
pages = {174},
pmid = {40232549},
issn = {1573-2983},
support = {NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2023YFC3705904//National Key Research and Development Plan of China/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 2021-043//Stationing Point Tracking Research of Ecological Barrier Construction in the upper Yangtze River of Sichuan Province/ ; NO. 41977169//National Natural Science Foundation of China/ ; NO. 41977169//National Natural Science Foundation of China/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; SKLGP2022Z009//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; },
mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Geologic Sediments/chemistry/analysis ; *Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring/methods ; *Lead/analysis ; Agriculture ; Isotopes/analysis ; Geographic Information Systems ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) in sediments represent a pervasive environmental issue that poses significant ecological risks. This study employed a combination of geographic information systems, diagnostic ratios, correlation analysis, Pb isotope ratios, and positive matrix factorization (PMF) to elucidate the potential sources of 16 priority PAHs in river sediments from a hilly agricultural watershed in Southwestern China. The results indicated that PAHs concentrations ranged from 55.9 to 6083.5 ng/g, with a mean value of 1582.1 ± 1528.9 ng/g, reflecting high levels of contamination throughout the watershed. The predominant class of PAHs identified was high molecular weight (HMW) PAHs. Diagnostic ratios and correlation analysis suggested that the presence of PHAs is likely attributed primarily to emissions from industrial dust and combustion of coal and petroleum. Furthermore, correlation analysis revealed a significant association between Pb and PAHs, indicating potential shared sources for both pollutants. Additionally, Pb isotopic analysis demonstrated that aerosols may be the primary contributor to Pb accumulation within this environment. Given the similarity in origins between Pb and PAHs, it can be inferred that PAHs predominantly originate from aerosols associated with coal combustion, industrial dust emissions, and vehicle exhaust. This inference is further supported by PMF results which yielded consistent findings with those derived from Pb isotopes analysis. Moreover, PMF estimated three major sources contributing 57.63%, 23.57%, and 18.80%, respectively. These findings provide novel insights into identifying the sources of PAHs in river sediments within hilly agricultural watersheds in Southwest China, thereby establishing a scientific foundation for enhancing environmental quality in agricultural regions.},
}
@article {pmid40198742,
year = {2025},
author = {Choi, H and Lee, CH},
title = {The impact of climate change on ecology of tick associated with tick-borne diseases.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012903},
doi = {10.1371/journal.pcbi.1012903},
pmid = {40198742},
issn = {1553-7358},
mesh = {*Climate Change ; *Tick-Borne Diseases/transmission/epidemiology/prevention &amp; control ; Animals ; *Ticks/physiology ; Humans ; *Models, Biological ; Population Dynamics ; Computational Biology ; },
abstract = {Infectious diseases have caused significant economic and human losses worldwide. Growing concerns exist regarding climate change potentially exacerbating the spread of these diseases, particularly those transmitted by vectors such as ticks and mosquitoes. Tick-borne diseases, such as Severe Fever with Thrombocytopenia Syndrome (SFTS), can be particularly detrimental to elderly and immunocompromised individuals. This study utilizes a mathematical modeling approach to predict changes in tick populations under climate change scenarios, incorporating tick ecology and climate-sensitive parameters. Sensitivity analysis is performed to investigate the factors influencing tick population dynamics. The study further explores effective tick control strategies and their cost-effectiveness in the context of climate change. The findings indicate that the efficacy of tick population reduction varies greatly depending on the timing of control measure implementation and the effectiveness of the control strategies exhibits a strong dependence on the duration of implementation. Furthermore, as climate change intensifies, tick populations are projected to increase, leading to a rise in control costs and SFTS cases. In light of these findings, identifying and implementing appropriate control measures to manage tick populations under climate change will be increasingly crucial.},
}
@article {pmid40229317,
year = {2025},
author = {Sabadel, AJM and Riekenberg, P and Ayala-Diaz, M and Belk, MC and Bennett, J and Bode, A and Bury, SJ and Dabouineau, L and Delgado, J and Finucci, B and García-Seoane, R and Giari, L and Henkens, J and IJsseldijk, LL and Joling, T and Kerr-Hislop, O and MacLeod, CD and Meyer, L and McGill, RAR and Negro, E and Quillfeldt, P and Reed, C and Roberts, C and Sayyaf Dezfuli, B and Schmidt, O and Sturbois, A and Suchomel, AD and Thieltges, DW and van der Lingen, CD and van der Meer, MTJ and Viana, IG and Weston, M and Willis, TJ and Filion, A},
title = {Establishing a comprehensive host-parasite stable isotope database to unravel trophic relationships.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {623},
pmid = {40229317},
issn = {2052-4463},
support = {CAWX2207//Ministry of Business, Innovation and Employment (MBIE)/ ; },
mesh = {*Host-Parasite Interactions ; Animals ; Nitrogen Isotopes/analysis ; Carbon Isotopes ; *Databases, Factual ; Sulfur Isotopes/analysis ; *Parasites ; },
abstract = {Over the past decades, stable isotopes have been infrequently used to characterise host-parasite trophic relationships. This is because we have not yet identified consistent patterns in stable isotope values between parasites and their host tissues across species, which are crucial for understanding host-parasite dynamics. To address this, we initiated a worldwide collaboration to establish a unique database of stable isotope values of novel host-parasite pairs, effectively doubling the existing data in published literature. This database includes nitrogen, carbon, and sulphur stable isotope values. We present 3213 stable isotope data entries, representing 586 previously unpublished host-parasite pairs. Additionally, while existing literature was particularly limited in sulphur isotope values, we tripled information on this crucial element. By publishing unreported host-parasite pairs from previously unsampled areas of the world and using appropriate host tissues, our dataset stands unparalleled. We anticipate that end-users will utilise our database to uncover generalisable patterns, deepening our understanding of the complexities of parasite-host relationships and driving future research efforts in stable isotope parasitology.},
}
@article {pmid40229216,
year = {2025},
author = {Zhang, X and Lu, B and Jin, LN and Yang, S and Wang, C and Tai, J and Li, D and Chen, J},
title = {Emission Dynamics and Public Health Implications of Airborne Pathogens and Antimicrobial Resistance from Urban Waste Collection Facilities.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12108},
pmid = {40229216},
issn = {1520-5851},
abstract = {Airborne pathogens and antimicrobial resistance (AMR) present significant global health threats. Household waste collection facilities (WCFs), crucial initial nodes in urban waste management systems, have been understudied in regards to their role in emitting these hazards. This study investigated the abundance, composition, sources, driving mechanisms, and health risks associated with pathogens and AMR originating from WCFs in a major city, using culture-based analysis, high-throughput sequencing, and health risk modeling, respectively. The atmospheric escape rates of culturable bacteria (43.4%), fungi (71.7%), and antibiotic-resistant bacteria (ARB) (43.7%) were estimated based on the concentration differences between the interior and exterior of the WCFs by using SourceTracker2 analysis. Health risk assessments showed that annual infection risks for waste-handling workers ranged from 0.194 to 0.489, far exceeding the World Health Organization's acceptable limit of 10[-4]. Community exposure risks were notable up to 220 m downwind from WCFs, marking the maximum extent of pathogen dispersion. Our analysis suggests that approximately 6.3% of the megacity's area (equivalent to 400 km[2]) is within potential risk zones influenced by WCF emissions. These results underscore the critical need to evaluate and mitigate the public health risks posed by airborne pathogens and AMR emitted from WCFs in megacities globally.},
}
@article {pmid40227267,
year = {2025},
author = {Cassaro, A and Pacelli, C and Fanelli, G and Baqué, M and Maturilli, A and Leo, P and Lelli, V and de Vera, JP and Onofri, S and Timperio, A},
title = {Biomarker Preservation in Antarctic Sandstones after Prolonged Space Exposure Outside the International Space Station During the ESA EXPOSE-E Lichens and Fungi Experiment.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2024.0068},
pmid = {40227267},
issn = {1557-8070},
abstract = {A primary aim of current and future space exploration missions is the detection and identification of chemical and biological indicators of life, namely biomarkers, on Mars. The Mars Sample Return NASA-ESA program will bring to Earth samples of martian soil, acquired from up to 7 cm depth. The ESA Rosalind Franklin rover will search for signs of life in the subsurface (down to a depth of 2 meters), given the highly radioactive conditions on Mars' surface, which are not ideal for life as we know it and for the preservation of its traces. In the frame of the Lichens and Fungi Experiment, small fragments of Antarctic sandstones colonized by cryptoendolithic microbial communities were exposed to space and simulated martian conditions in low Earth orbit for 18 months, aboard the EXPOSE-E payload. Through the use of Raman and infrared spectroscopies, as well as a metabolomic approach, we aimed to detect organic compounds in a quartz mineral matrix. The results show that pigments, such as melanin, carotenoids, and chlorophyll, lipids, and amino acids, maintained their stability within minerals under simulated martian conditions in space, which makes them ideal biomarkers for the exploration of putative life on Mars.},
}
@article {pmid40226649,
year = {2024},
author = {Tamm, J and Takano, K and Just, L and Ehring, T and Rosenkranz, T and Kopf-Beck, J},
title = {Ecological Momentary Assessment versus Weekly Questionnaire Assessment of Change in Depression.},
journal = {Depression and anxiety},
volume = {2024},
number = {},
pages = {9191823},
pmid = {40226649},
issn = {1520-6394},
mesh = {Humans ; *Ecological Momentary Assessment ; Male ; Female ; Adult ; Middle Aged ; Surveys and Questionnaires/standards ; *Depression/diagnosis/therapy ; *Outcome Assessment, Health Care/methods ; Reproducibility of Results ; Pessimism/psychology ; Psychiatric Status Rating Scales ; Rumination, Cognitive ; },
abstract = {OBJECTIVE: Ecological momentary assessment (EMA) is increasingly used to monitor depressive symptoms in clinical trials, but little is known about the comparability of its outcomes to those of clinical interviews and questionnaires. In our study, we administered EMA and questionnaires to measure change in depressive symptoms and repetitive negative thinking (RNT) in a clinical trial and investigated (a) the size of intervention effects associated with both techniques and (b) their validity in predicting clinical interview outcomes (i.e., global functioning).<br><br>MATERIALS AND METHODS: Seventy-one depressed patients were randomly assigned to one of three psychological interventions. The EMA comprised a concise item set (four items per scale) and was administered three times per day during a 7-week intervention period. Conversely, questionnaires were assessed weekly (WQA), encompassing their full sets of items of depressive symptoms and RNT.<br><br>RESULTS: While EMA excelled in detecting significant intervention effects, WQA demonstrated greater strength in predicting clinician ratings of global functioning. Additionally, we observed significant differences in time effects (slopes) between the two techniques. WQA scores decreased steeper over time and were more extreme, e.g., higher at baseline and lower postintervention, than EMA scores.<br><br>CONCLUSIONS: Although clinical interviews, questionnaires, and EMA outcomes are related, they assess changes in depression differently. EMA may be more sensitive to intervention effects, but all three methods harbor potential bias, raising validity and reliability questions. Therefore, to enhance the validity and reliability of clinical trial assessments, we emphasize the importance of EMA approaches that combine subjective self-reports with objectively measured behavioral markers. This trial is registered with osf.io/9fuhn.},
}
@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}
@article {pmid40222989,
year = {2025},
author = {Mu, K and Wang, Z and Tang, J and Zhang, J and Han, W},
title = {The satisfaction of ecological environment in sports public services by artificial intelligence and big data.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12748},
pmid = {40222989},
issn = {2045-2322},
mesh = {Humans ; *Artificial Intelligence ; *Big Data ; *Sports ; Surveys and Questionnaires ; Neural Networks, Computer ; *Personal Satisfaction ; },
abstract = {In order to gain a more accurate understanding and enhance the relationship between the fitness ecological environment and artificial intelligence (AI)-driven sports public services, this study combines a Convolutional Neural Network (CNN) approach based on residual modules and attention mechanisms with the SERVQUAL evaluation model. The method employed involves the analysis of big data collected from questionnaire surveys, literature reviews, and interviews. This study critically examines the impact of advanced AI technologies on residents' satisfaction with the fitness ecological environment in sports public services and conducts theoretical analysis of the obtained data. The results show that the quality of sports public services empowered by AI significantly influences residents' satisfaction with the fitness ecological environment, such as running, swimming, ball games and other sports with high requirements for sports service quality and ecological environment. Only the good public sports service quality matching with them can meet the needs of the ecological environment for fitness, and stimulate the enthusiasm of the people for fitness. The study also shows that swimming, running and all kinds of ball games account for the largest proportion of all sports. To sum up, the satisfaction of residents' fitness ecological environment is greatly affected by the quality of public sports services, which is mainly reflected in the good and perfect sports environment and facilities that can provide residents with a wealth of fitness options, greatly improving the sports ecological environment. This study is helpful to realize the relationship between sports public service and sports ecological environment. It contributes to understanding the role of AI and deep learning in enhancing the correlation between sports public service and the ecological environment of sports.},
}
@article {pmid39031316,
year = {2025},
author = {Chakraborty, K and Saha, S and Mandal, D},
title = {Hydrological modelling using SWAT for the assessment of streamflow dynamics in the Ganga River basin.},
journal = {Environmental science and pollution research international},
volume = {32},
number = {16},
pages = {10258-10278},
doi = {10.1007/s11356-024-34385-5},
pmid = {39031316},
issn = {1614-7499},
mesh = {*Rivers ; Hydrology ; *Models, Theoretical ; *Environmental Monitoring/methods ; Geographic Information Systems ; *Water Movements ; Rain ; },
abstract = {Growing concerns over water availability arise from the problems of population growth, rapid industrialization, and human interferences, necessitating accurate streamflow estimation at the river basin scale. It is extremely challenging to access stream flow data of a transboundary river at a spatio-temporal scale due to data unavailability caused by water conflicts for assessing the water availability.Primarily, this estimation is done using rainfall-runoff models. The present study addresses this challenge by applying the soil and water assessment tool (SWAT) for hydrological modelling, utilizing high-resolution geospatial inputs. Hydrological modelling using remote sensing and GIS (Geographic Information System) through this model is initiated to assess the water availability in the Ganga River basin at different locations. The outputs are calibrated and validated using the observed station data from Global Runoff Data Centre (GRDC). To check the performance of the model, Nash-Sutcliffe efficiency (NSE), percent bias (PBIAS), coefficient of determination (R[2]), and RSR efficacy measures are initiated in ten stations using the observed and simulated stream flow data. The R[2] values of eight stations range from 0.82 to 0.93, reflecting the efficacy of the model in rainfall-runoff modelling. Moreover, the results obtained from this hydrological modelling can serve as valuable resources for water resource planners and geographers for future reference.},
}
@article {pmid40218748,
year = {2025},
author = {Meng, J and Wang, Y and Liu, W and Yang, X and He, P},
title = {Research on the Development of an Inland Lake Bathymetry Estimation Model Based on Multispectral Data.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {7},
pages = {},
pmid = {40218748},
issn = {1424-8220},
support = {41901285//the National Natural Science Foundation of China/ ; },
abstract = {Lakes play a crucial role in regional economic development and ecological construction. The variation in lake water depth has a direct impact on local economic activities, such as agriculture, livestock farming, and fisheries, as well as the stability of hydrological conditions and water ecology. In response to the lack of unified evaluation in the application of remote sensing water-depth estimation models for inland lakes, this study systematically compares the performance of numerical models and machine learning models for water-depth estimation in inland lakes. A machine learning-based water-depth estimation model construction methodology suitable for inland lakes is proposed. This study introduces an innovative approach by integrating machine learning techniques with multispectral remote sensing data, improving the accuracy and applicability of water-depth estimation models for inland lakes. The results show the following: (1) The machine learning models based on random forest (RF), BP neural networks (BP), and AdaBoost demonstrate better performance (R[2] = 0.88, 0.72, and 0.61; MAE = 0.12 m, 0.24 m, and 0.31 m; RMSE = 0.32 m, 0.48 m, and 0.57 m) compared to the multi-band logarithmic ratio (MLR) model (R[2] = 0.59; MAE = 0.32 m; RMSE = 0.58 m); (2) the machine learning water-depth estimation model constructed based on this methodology exhibits improved precision (R[2] = 0.92, 0.89, and 0.80; MAE = 0.11 m, 0.17 m, and 0.25 m; RMSE = 0.25 m, 0.30 m, and 0.41 m). This suggests that the methodology is more suitable for the estimation of water depth in medium- and small-sized lakes; (3) The machine learning model developed in this study, combined with multispectral remote sensing imagery, achieves the accuracy required for the evaluation of water depths for practical water resources. This model enables the rapid acquisition of high-precision underwater three-dimensional topographic maps, providing more accurate and timely hydrological data support for lake water resource management.},
}
@article {pmid40213769,
year = {2025},
author = {Yi, S and Liu, Y and Wu, Q and Zhao, D and Li, Z and Peng, X and Liao, G and Wang, S},
title = {Glycosylation of oral bacteria in modulating adhesion and biofilm formation.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2486650},
pmid = {40213769},
issn = {2000-2297},
abstract = {BACKGROUND: Glycosylation is a ubiquitous biochemical process that covalently attaches glycans to proteins or lipids, which plays a pivotal role in modulating the structure and function of these biomolecules. This post-translational modification is prevalent in living organisms and intricately regulates various biological processes, including signaling transduction, recognition, and immune responses. In the oral environment, bacteria ingeniously use glycosylation to enhance their adhesion to oral surfaces, which is a key step in biofilm formation and subsequent development. This adhesion process is intimately associated with the onset and progression of oral diseases, including dental caries and periodontal disease.<br><br>OBJECTIVE: This review aims to describe the types and mechanisms of glycosylation in oral bacteria, and to understand the role of glycosylation in the adhesion, biofilm formation and virulence of oral bacteria.<br><br>METHODS: We reviewed articles on glycosylation in a variety of oral bacteria.<br><br>CONCLUSION: In cariogenic bacteria and periodontopathic pathogens, glycosylation facilitates adhesion and subsequent biofilm maturation on tooth surface. &#xa0;&#xa0;Distinct glycosylation patterns in oral bacteria shape biofilm structure and function, influencing microbial interactions and community stability. &#xa0;&#xa0;Pathogen-specific glycosylation signatures enhance virulence and ecological competitiveness, contributing to disease progression. Glycosylation plays a critical role in bacterial virulence and community &#xa0;interactions, with significant implications for oral health and disease development.},
}
@article {pmid40213351,
year = {2025},
author = {Fehér, &#xc1;M and Bajory, Z and Czimbalmos, N and Burián, K and Lázár, A and Rárosi, F and Köves, B},
title = {Single-dose vs prolonged antibiotic prophylaxis of fosfomycin for transrectal prostate biopsy: a single-center prospective, randomized, controlled trial.},
journal = {Prostate international},
volume = {13},
number = {1},
pages = {28-33},
pmid = {40213351},
issn = {2287-8882},
abstract = {BACKGROUND: Transrectal prostate biopsy is a commonly performed urological procedure in which antibiotic prophylaxis is recommended. Fluoroquinolone-type antibiotics are no longer acceptable in the EU. Fosfomycin-trometamol may be used, but there is no evidence regarding its ideal dose and administration time.<br><br>METHODS: Patients who underwent prostate biopsy between 2021 and 2023 were evaluated prospectively. 204 patients were randomized into two arms: 102 patients (Arm A) received a single-dose of fosfomycin-trometamol one hour before surgery, and 102 patients (Arm B) received one additional dose of fosfomycin-trometamol 48&#xa0;hours after the first dose. Urine tests and questionnaires were administered during the postoperative period and the subsequent four weeks to identify any symptoms, infectious, or other complications.<br><br>RESULTS: There was no statistical difference in the rate of asymptomatic bacteriuria (4.90% (5) vs. 8.82% (9), P&#xa0;=&#xa0;0.27) symptomatic urinary tract infection (0% (0) vs. 1.96% (2), P&#xa0;=&#xa0;0.50), or febrile urinary tract infection (0% (0) vs. 0.98% (1), P&#xa0;=&#xa0;1) between the groups. Only hematuria was significantly more common in Arm B (6.86% (7) vs. 16.67% (17), P&#xa0;=&#xa0;0.03), whereas other complications did not differ significantly. There was no statistical difference in hospitalization (0.98% (1) vs. 2.94 (3), P&#xa0;=&#xa0;0.62) or mortality rate (0 % (0) vs. 0.98% (1), P&#xa0;=&#xa0;1). Sub-group analysis of previous antibiotic users showed no difference in terms of complications.<br><br>CONCLUSION: There is no significant difference in infectious complications between single-dose and prolonged prophylaxis of fosfomycin-trometamol for transrectal prostate biopsy. A single-dose of fosfomycin one hour before biopsy is an ideal choice with a better ecological impact compared with prolonged antibiotic prophylaxis for transrectal prostate biopsy.},
}
@article {pmid40211980,
year = {2025},
author = {Elena Schmitz, J and Rahmann, S},
title = {A comprehensive review and evaluation of species richness estimation.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf158},
pmid = {40211980},
issn = {1477-4054},
mesh = {*Biodiversity ; Computer Simulation ; Animals ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The statistical problem of estimating the total number of distinct species in a population (or distinct elements in a multiset), given only a small sample, occurs in various areas, ranging from the unseen species problem in ecology to estimating the diversity of immune repertoires. Accurately estimating the true richness from very small samples is challenging, in particular for highly diverse populations with many rare species. Depending on the application, different estimation strategies have been proposed that incorporate explicit or implicit assumptions about either the species distribution or about the sampling process. These methods are scattered across the literature, and an extensive overview of their assumptions, methodology, and performance is currently lacking.<br><br>RESULTS: We comprehensively review and evaluate a variety of existing methods on real and simulated data with different compositions of rare and abundant species. Our evaluation shows that, depending on species composition, different methods provide the most accurate richness estimates. Simple methods based on the observed number of singletons yield accurate asymptotic lower bounds for several of the tested simulated species compositions, but tend to underestimate the true richness for heterogeneous populations and small samples containing 1% to 5% of the population. When the population size is known, upsampling (extrapolating) estimators such as PreSeq and RichnEst yield accurate estimates of the total species richness in a sample that is up to 10 times larger than the observed sample.<br><br>AVAILABILITY: Source code for data simulation and richness estimation is available at https://gitlab.com/rahmannlab/speciesrichness.},
}
@article {pmid40205052,
year = {2025},
author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Monfort Anez, G and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Rocha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE},
title = {Complete sequencing of ape genomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40205052},
issn = {1476-4687},
abstract = {The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies[1-3]. Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved reference genomes and comparative analyses of six ape species: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang. We achieve chromosome-level contiguity with substantial sequence accuracy (<1 error in 2.7 megabases) and completely sequence 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, to provide in-depth evolutionary insights. Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome. Such regions include newly minted gene families in lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes and subterminal heterochromatin. This resource serves as a comprehensive baseline for future evolutionary studies of humans and our closest living ape relatives.},
}
@article {pmid40048849,
year = {2025},
author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK},
title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.},
journal = {EBioMedicine},
volume = {114},
number = {},
pages = {105630},
pmid = {40048849},
issn = {2352-3964},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Metagenomics/methods ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenome ; Female ; Interspersed Repetitive Sequences ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.<br><br>METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.<br><br>FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E.&#xa0;coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.<br><br>INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.<br><br>FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Troms&#xf8; Research Foundation, Norway.},
}
@article {pmid40169791,
year = {2025},
author = {Ding, DY and Tang, Z and Zhu, B and Ren, H and Shalek, AK and Tibshirani, R and Nolan, GP},
title = {Quantitative characterization of tissue states using multiomics and ecological spatial analysis.},
journal = {Nature genetics},
volume = {57},
number = {4},
pages = {910-921},
pmid = {40169791},
issn = {1546-1718},
mesh = {Humans ; *Spatial Analysis ; *Genomics/methods ; Single-Cell Analysis/methods ; Multiomics ; },
abstract = {The spatial organization of cells in tissues underlies biological function, and recent advances in spatial profiling technologies have enhanced our ability to analyze such arrangements to study biological processes and disease progression. We propose MESA (multiomics and ecological spatial analysis), a framework drawing inspiration from ecological concepts to delineate functional and spatial shifts across tissue states. MESA introduces metrics to systematically quantify spatial diversity and identify hot spots, linking spatial patterns to phenotypic outcomes, including disease progression. Furthermore, MESA integrates spatial and single-cell multiomics data to facilitate an in-depth, molecular understanding of cellular neighborhoods and their spatial interactions within tissue microenvironments. Applying MESA to diverse datasets demonstrates additional insights it brings over prior methods, including newly identified spatial structures and key cell populations linked to disease states. Available as a Python package, MESA offers a versatile framework for quantitative decoding of tissue architectures in spatial omics across health and disease.},
}
@article {pmid40200522,
year = {2025},
author = {Dsouza, N and Cohen, E and Ossebaard, H and van Meurs, H and Sijm-Eeken, M},
title = {The Ecological Footprint of Gynecology: Lessons from Dutch Hospitals and Implications for Future Healthcare Management.},
journal = {Studies in health technology and informatics},
volume = {323},
number = {},
pages = {424-428},
doi = {10.3233/SHTI250125},
pmid = {40200522},
issn = {1879-8365},
mesh = {Netherlands ; *Gynecology/organization &amp; administration ; Humans ; Quality Improvement/organization &amp; administration ; Female ; Models, Organizational ; },
abstract = {In 2023, global temperatures reached record-breaking highs, highlighting the urgent need for climate action. Healthcare is responsible for 4-8% of global carbon emissions, contributing to global warming and impacting the health of billions of people. Within healthcare, gynecology has a significant ecological footprint due to its high volume and broad range of care services. However, little is known on how gynecology departments' management structures, information systems and processes can be optimized to reduce the ecological footprint of this specialty. Therefore, a sustainability maturity model based on Donabedian's structure-process-outcome model for quality improvement was used to assess sustainability performance in two gynecology practices with different organizational structures (centralized vs. decentralized). Maturity model scores and interview findings were analyzed to extract lessons and recommendations for optimizing sustainability within gynecology. As the first assessment of its kind, this study provides a foundation for healthcare management seeking to improve environmental performance in gynecological care.},
}
@article {pmid40200140,
year = {2025},
author = {Antala, M and Kovar, M and Sporinová, L and Filacek, A and Juszczak, R and Zivcak, M and Shomali, A and Prasad, R and Brestic, M and Rastogi, A},
title = {High-throughput phenotyping of buckwheat (Fagopyrum esculentum Moench.) genotypes under water stress: exploring drought resistance for sustainable agriculture.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {444},
pmid = {40200140},
issn = {1471-2229},
support = {23-04221 L//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 731013//Horizon 2020 Framework Programme/ ; 2021/43/I/NZ9/01356//Narodowym Centrum Nauki/ ; BWS/BIL/2022/1/00120//Narodowa Agencja Wymiany Akademickiej/ ; },
mesh = {*Fagopyrum/genetics/physiology/growth &amp; development ; Genotype ; *Droughts ; Phenotype ; Dehydration ; Crops, Agricultural/genetics/physiology ; Agriculture ; Stress, Physiological ; Plant Breeding ; Drought Resistance ; },
abstract = {BACKGROUND: As global agriculture faces the challenge of climate change, characterized by longer and more severe drought episodes, there is an increasing need for crop diversification and improved plant breeding. Buckwheat is one of the climate-resilient candidates for future important crops with remarkable adaptability to various biotic and abiotic stresses. As an underbred crop, a large number of genotypes should be assessed for the breeding of superior plants. Therefore, this study investigates the response of various buckwheat genotypes to water stress by high-throughput phenotyping and auxiliary plant physiology measurements.<br><br>RESULTS: We assessed six buckwheat genotypes from different regions under mild and severe water stress, focusing on morphological and physiological changes to understand drought tolerance mechanisms. Our findings revealed that reallocation of assimilated carbon from growth to secondary metabolite production is a common response to drought stress. Among the genotypes tested, Panda emerged as the most drought-resistant, with its morphology remaining the most stable under mild water stress and its ability to rapidly accumulate protective pigments in response to drought. Silver Hull also demonstrated resilience, maintaining its aboveground biomass under mild water stress at levels comparable to the control group. Additionally, the response magnitude to drought stress was linked to the biomass production potential of the genotypes, which was higher for those from warmer regions (Bhutan, Zimbabwe) and lower for those from colder regions (Poland, Canada).<br><br>CONCLUSION: The diversity in genotypic responses highlights the significant role of genetic variability in shaping drought resistance strategies in buckwheat. This research not only enhances our understanding of buckwheat's physiological responses to water stress but also holds promise for developing drought-resistant buckwheat varieties. These advancements are crucial for promoting sustainable agriculture in the face of climate change.},
}
@article {pmid40200134,
year = {2025},
author = {Hu, X and Pan, L and Fu, C and Zhu, Q and Hao, J and Wang, X and Nawaz, M and Qu, J and Zhang, J and Chen, Y and Zong, J and Liao, L and Tang, M and Wang, Z},
title = {A multi-omics analysis reveals candidate genes for Cd tolerance in Paspalum vaginatum.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {441},
pmid = {40200134},
issn = {1471-2229},
support = {No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; No.321RC475//Hainan Natural Science Foundation high-level Talents Project/ ; ZDYF2023XDNY078//the Hainan Province Science and Technology Special Fund/ ; XTCX2022STC10//Collaborative Innovation Center Project of Ecological Civilization in Hainan University/ ; KJRC2023C21//Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; No.32060409//the National Natural Science Foundation of China/ ; XTCX2022NYB08//Collaborative Innovation Center Project of Nanfan and High-Efficiency Tropical Agriculture in Hainan University/ ; },
mesh = {*Cadmium/toxicity ; *Paspalum/genetics/drug effects/metabolism/physiology ; Genome-Wide Association Study ; *Genes, Plant ; Gene Expression Regulation, Plant ; Multiomics ; },
abstract = {Cadmium (Cd) pollution in the farmland has become a serious global issue threatening both human health and plant biomass production. Seashore paspalum (Paspalum vaginatum Sw.), a halophytic turfgrass, has been recognized as a Cd-tolerant species. However, the underlying genetic basis of natural variations in Cd tolerance still remains unknown. This study is possibly the first to apply genome-wide association studies (GWAS) and selective sweep analysis to identify potential Cd stress-responsive genes in P. vaginatum. We identified a total of 89 candidate genes and 656 putative selective sweeps regions. Based on the correlation analysis of differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs), we identified the 55 key genes associated with metabolic changes induced by Cd treatment as the Cd tolerance-related genes. These genes showed significantly higher expression in Cd-tolerant accessions as compared to Cd-susceptive accessions. Therefore, our multi-omics study revealed the molecular and genetic basis of Cd tolerance, which may help develop Cd tolerant crop varieties.},
}
@article {pmid40199921,
year = {2025},
author = {Chaudhary, VB and Nokes, LF and González, JB and Cooper, PO and Katula, AM and Mares, EC and Pehim Limbu, S and Robinson, JN and Aguilar-Trigueros, CA},
title = {TraitAM, a global spore trait database for arbuscular mycorrhizal fungi.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {588},
pmid = {40199921},
issn = {2052-4463},
support = {DEB-2205650//National Science Foundation (NSF)/ ; Feodor Lynen Fellowship//Alexander von Humboldt-Stiftung (Alexander von Humboldt Foundation)/ ; },
mesh = {*Mycorrhizae/genetics ; *Spores, Fungal ; Phylogeny ; Symbiosis ; Databases, Factual ; },
abstract = {Knowledge regarding organismal traits supports a better understanding of the relationship between form and function and can be used to predict the consequences of environmental stressors on ecological and evolutionary processes. Most plants on Earth form symbioses with mycorrhizal fungi, but our ability to make trait-based inferences for these fungi is limited due to a lack of publicly available trait data. Here, we present TraitAM, a comprehensive database of multiple spore traits for all described species of the most common group of mycorrhizal fungi, the arbuscular mycorrhizal (AM) fungi (subphylum Glomeromycotina). Trait data for 344 species were mined from original species descriptions and used to calculate newly developed fungal trait metrics that can be employed to explore both intra- and inter-specific variation in traits. TraitAM also includes an updated phylogenetic tree that can be used to conduct phylogenetically-informed multivariate analyses of AM fungal traits. TraitAM will aid our further understanding of the biology, ecology, and evolution of these globally widespread, symbiotic fungi.},
}
@article {pmid40198914,
year = {2025},
author = {Holmqvist, S and Kaplan, M and Chaturvedi, R and Shou, H and Giovannetti, T},
title = {Longitudinal and Combined Smartwatch and Ecological Momentary Assessment in Racially Diverse Older Adults: Feasibility, Adherence, and Acceptability Study.},
journal = {JMIR human factors},
volume = {12},
number = {},
pages = {e69952},
doi = {10.2196/69952},
pmid = {40198914},
issn = {2292-9495},
mesh = {Humans ; *Ecological Momentary Assessment/statistics &amp; numerical data ; Male ; Aged ; Female ; Feasibility Studies ; Middle Aged ; *Patient Compliance/statistics &amp; numerical data ; Aged, 80 and over ; Longitudinal Studies ; *Smartphone ; *Mobile Applications ; *Cognitive Dysfunction/diagnosis ; *Wearable Electronic Devices/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Due to the rising prevalence of Alzheimer disease and related dementias, easily deployable tools to quantify risk are needed. Smartphones and smartwatches enable unobtrusive and continuous monitoring, but there is limited information regarding the feasibility, adherence, and acceptability of digital data collection among racially diverse older adults.<br><br>OBJECTIVE: This paper examined the feasibility, adherence, and acceptability of a 4-week combined smartwatch monitoring and ecological momentary assessment (EMA) study in a racially diverse sample of older adults.<br><br>METHODS: A total of 44 older adults (aged &#x2265;55 y) with either mild cognitive impairment or healthy cognition completed an informed consent comprehension quiz, baseline cognitive testing, training regarding digital data collection, and questionnaires. Participants were instructed to wear a Garmin Vivosmart 4 smartwatch for 23 h/d for 4 weeks, sync 2 smartphone apps (Garmin and Labfront) daily, and complete a daily EMA survey with automated prompts for surveys and charging. Training time, smartwatch adherence (eg, wear time), daily EMA survey response rate, and performance on the consent quiz were quantified. Associations between feasibility and adherence metrics and participant factors were evaluated. Self-reported usability of the apps and smartwatch was collected at study end.<br><br>RESULTS: Consent comprehension quiz scores were high (mean 97.33%, SD 6.86% correct), and training sessions lasted on average 17.93 (SD 6.89) minutes. During the 4-week study, participants wore the smartwatch for an average of 21 h/d (SD 1.53) and showed an average response rate of 94% (SD 9.58%) to daily EMA surveys. In unadjusted bivariate analyses, age, race, and cognition were associated with feasibility and adherence measures, but only age and race remained significant in multivariate models. After accounting for all participant factors, older age was a significant predictor of longer training time, and Black race was a significant predictor of lower daily wear time. On the usability survey, all participants (45/45, 100%) indicated willingness to participate in future smartwatch studies, >80% (37/45) had a positive experience, and >90% (41/45) were satisfied with smartphone app syncing.<br><br>CONCLUSIONS: Smartwatch monitoring, requiring daily wear, smartphone syncing, and daily EMA survey completion, is highly feasible in older adults because adherence to daily wear and EMA surveys was high, as was general satisfaction on usability surveys. Although older participants may require more training on smartwatch and smartphone procedures and automated prompting during the study period, longitudinal monitoring with the Garmin Vivosmart 4 smartwatch and Labfront app is acceptable and feasible for collecting nearly continuous data in Black and White older adults, including those with mild cognitive impairment and those without.},
}
@article {pmid40198416,
year = {2025},
author = {Huan, F and Gao, S and Gu, Y and Ni, L and Wu, M and Li, Y and Liu, M and Yang, Y and Xiao, A and Liu, G},
title = {Molecular Allergology: Epitope Discovery and Its Application for Allergen-Specific Immunotherapy of Food Allergy.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {68},
number = {1},
pages = {37},
pmid = {40198416},
issn = {1559-0267},
support = {32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 32472449//the grant from the National Natural Science Foundation of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; 2022YFF1100103//the grant from the National Key R&amp;D Program of China/ ; },
mesh = {Humans ; *Food Hypersensitivity/therapy/immunology ; *Allergens/immunology/chemistry/genetics ; *Desensitization, Immunologic/methods ; Animals ; *Epitopes, T-Lymphocyte/immunology ; *Epitopes, B-Lymphocyte/immunology ; *Epitopes/immunology ; Computational Biology ; Epitope Mapping ; },
abstract = {The prevalence of food allergy continues to rise, posing a significant burden on health and quality of life. Research on antigenic epitope identification and hypoallergenic agent design is advancing allergen-specific immunotherapy (AIT). This review focuses on food allergens from the perspective of molecular allergology, provides an overview of integration of bioinformatics and experimental validation for epitope identification, highlights hypoallergenic agents designed based on epitope information, and offers a valuable guidance to the application of hypoallergenic agents in AIT. With the development of molecular allergology, the characterization of the amino acid sequence and structure of the allergen at the molecular level facilitates T-/B-cell epitope identification. Alignment of the identified epitopes in food allergens revealed that the amino acid sequence of T-/B-cell epitopes barely overlapped, providing crucial data to design allergen molecules as a promising form for treating (FA) food allergy. Manipulating antigenic epitopes can reduce the allergenicity of allergens to obtain hypoallergenic agents, thereby minimizing the severe side effects associated with AIT. Currently, hypoallergenic agents are mainly developed through synthetic epitope peptides, genetic engineering, or food processing methods based on the identified epitope. New strategies such as DNA vaccines, signaling molecules coupling, and nanoparticles are emerging to improve efficiency. Although significant progress has been made in designing hypoallergenic agents for AIT, the challenge in clinical translation is to determine the appropriate dose and duration of treatment to induce long-term immune tolerance.},
}
@article {pmid40196448,
year = {2025},
author = {Rotstein, NM and Cohen, ZD and Welborn, A and Zbozinek, TD and Akre, S and Jones, KG and Null, KE and Pontanares, J and Sanchez, KL and Flanagan, DC and Halavi, SE and Kittle, E and McClay, MG and Bui, AAT and Narr, KL and Welsh, RC and Craske, MG and Kuhn, TP},
title = {Investigating low intensity focused ultrasound pulsation in anhedonic depression-A randomized controlled trial.},
journal = {Frontiers in human neuroscience},
volume = {19},
number = {},
pages = {1478534},
pmid = {40196448},
issn = {1662-5161},
abstract = {INTRODUCTION: Anhedonic depression is a subtype of depression characterized by deficits in reward processing. This subtype of depression is associated with higher suicide risk and longer depressive episodes, underscoring the importance of effective treatments. Anhedonia has also been found to correlate with alterations in activity in several subcortical regions, including the caudate head and nucleus accumbens. Low intensity focused ultrasound pulsation (LIFUP) is an emerging technology that enables non-invasive stimulation of these subcortical regions, which were previously only accessible with surgically-implanted electrodes.<br><br>METHODS: This double-blinded, sham-controlled study aims to investigate the effects of LIFUP to the left caudate head and right nucleus accumbens in participants with anhedonic depression. Participants in this protocol will undergo three sessions of LIFUP over the span of 5-9 days. To investigate LIFUP-related changes, this 7-week protocol collects continuous digital phenotyping data, an array of self-report measures of depression, anhedonia, and other psychopathology, and magnetic resonance imaging (MRI) before and after the LIFUP intervention. Primary self-report outcome measures include Ecological Momentary Assessment, the Positive Valence Systems Scale, and the Patient Health Questionnaire. Primary imaging measures include magnetic resonance spectroscopy and functional MRI during reward-based tasks and at rest. Digital phenotyping data is collected with an Apple Watch and participants' personal iPhones throughout the study, and includes information about sleep, heart rate, and physical activity.<br><br>DISCUSSION: This study is the first to investigate the effects of LIFUP to the caudate head or nucleus accumbens in depressed subjects. Furthermore, the data collected for this protocol covers a wide array of potentially affected modalities. As a result, this protocol will help to elucidate potential impacts of LIFUP in individuals with anhedonic depression.},
}
@article {pmid39218423,
year = {2025},
author = {Morris, JS},
title = {Tracking vaccine effectiveness in an evolving pandemic, countering misleading hot takes and epidemiologic fallacies.},
journal = {American journal of epidemiology},
volume = {194},
number = {4},
pages = {898-907},
doi = {10.1093/aje/kwae280},
pmid = {39218423},
issn = {1476-6256},
mesh = {Humans ; *COVID-19 Vaccines/immunology ; *Vaccine Efficacy ; *COVID-19/prevention &amp; control/epidemiology ; *Pandemics/prevention &amp; control ; SARS-CoV-2/immunology ; Social Media ; Bias ; },
abstract = {With the emergence of Omicron during the pandemic and the establishment of antibody waning over time, vaccine effectiveness, especially against infection, declined sharply from the original levels seen after the initial rollout. However, studies have demonstrated that they still provided substantial protection vs severe/fatal disease even with Omicron and after waning. Social media has been rife with reports claiming vaccines provided no benefit and some even claiming they made things worse, often driven by simple presentations of raw observational data using erroneous arguments involving epidemiologic fallacies including the base rate fallacy, Simpson's paradox, and the ecological fallacy and ignoring the extensive bias especially from confounding that is an inherent feature of these data. Similar fallacious arguments have been made by some in promoting vaccination policies, as well. Generally, vaccine effectiveness cannot be accurately estimated from raw population summaries but instead require rigorous, careful studies using epidemiologic designs and statistical analysis tools attempting to adjust for key confounders and sources of bias. This article summarizes what aggregated evidence across studies reveals about effectiveness of the mRNA vaccines as the pandemic has evolved, chronologically summarized with emerging variants and highlighting some of the fallacies and flawed arguments feeding social media-based claims that have obscured society's collective understanding.},
}
@article {pmid40186616,
year = {2025},
author = {Chen, L and Guo, Y and López-Güell, K and Ma, J and Dong, Y and Xie, J and Alhambra, DP},
title = {Immunity Debt for Seasonal Influenza After the COVID-19 Pandemic and as a Result of Nonpharmaceutical Interventions: An Ecological Analysis and Cohort Study.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2410513},
doi = {10.1002/advs.202410513},
pmid = {40186616},
issn = {2198-3844},
support = {82373593//National Natural Science Foundation of China/ ; },
abstract = {Non-pharmaceutical interventions (NPIs) during the COVID-19 pandemic significantly reduced influenza transmission. This study explores the hypothesis of "immunity debt" which suggests increased vulnerability to influenza following reduced exposure during the pandemic. World Health Organization aggregated data on influenza from 116 countries and its association with NPI intensity as measured by the COVID-19 Stringency Index is analyzed. Where individual-level data available (France, the United Kingdom, Spain, Italy, Belgium, and Romania), the analyses of influenza monthly rates in six European countries (France, the United Kingdom, Spain, Italy, Belgium, and Romania) are replicated. The results indicate globally a 46.3% (95%CI: 15.79-70.78%) reduction in influenza cases during COVID-19 restrictions in the winter season, followed by a 131.7% (95%CI: 34.95-255.78%) increase in the first postrelaxation winter and a 161.2% (95%CI: 31.88-382.16%) increase in the summer as compared to the predicted level based on historical influenza epidemic trends. In addition, a positive association between the Stringency Index and post-relaxation influenza surge is observed globally (R[2] = 0.14-0.17) and replicated regionally. The findings support the population immunity debt hypothesis for influenza and call for proactive preparations against its consequences in future pandemics.},
}
@article {pmid39689860,
year = {2025},
author = {Wu, Z and Huang, Z and Tang, N and Wang, K and Bian, C and Li, D and Kuraki, V and Schmid, F},
title = {Research on Sports Injury Rehabilitation Detection Based on IoT Models for Digital Health Care.},
journal = {Big data},
volume = {13},
number = {2},
pages = {144-160},
doi = {10.1089/big.2023.0134},
pmid = {39689860},
issn = {2167-647X},
mesh = {Humans ; *Internet of Things ; *Athletic Injuries/rehabilitation/diagnosis ; Delivery of Health Care ; Telemedicine ; Digital Health ; },
abstract = {Physical therapists specializing in sports rehabilitation detection help injured athletes recover from their wounds and avoid further harm. Sports rehabilitators treat not just commonplace sports injuries but also work-related musculoskeletal injuries, discomfort, and disorders. Sensor-equipped Internet of Things (IoT) monitors the real-time location of medical equipment such as scooters, cardioverters, nebulizer treatments, oxygenation pumps, or other monitor gear. Analysis of medicine deployment across sites is possible in real time. Health care delivery based on digital technology to improve access, affordability, and sustainability of medical treatment is known as digital health care. The challenging characteristics of such sports injury rehabilitation for digital health care are playing position, game strategies, and cybersecurity. Hence, in this research, health care IoT-enabled body area networks (HIoT-BAN) have been designed to improve sports injury rehabilitation detection for digital health care. The health care sector may benefit significantly from IoT adoption since it allows for enhanced patient safety; health care investment management includes controlling the hospital's pharmaceutical stock and monitoring the heat and humidity levels. Digital health describes a group of programmers made to aid health care delivery, whether by assisting with clinical decision-making or streamlining back-end operations in health care institutions. A HIoT-BAN effectively predicts the rise in sports injury rehabilitation detection with faster digital health care based on IoT. The research concludes that the HIoT-BAN effectively indicates sports injury rehabilitation detection for digital health care. The experimental analysis of HIoT-BAN outperforms the IoT method in terms of performance, accuracy, prediction ratio, and mean square error rate.},
}
@article {pmid40185844,
year = {2025},
author = {Amin, NU and Islam, F and Umar, M and Muhammad, W and Rahman, SU and Gaafar, AZ and Shah, TA and Dauelbait, M and Bourhia, M},
title = {Evaluation of crop phenology using remote sensing and decision support system for agrotechnology transfer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11582},
pmid = {40185844},
issn = {2045-2322},
mesh = {*Remote Sensing Technology/methods ; *Crops, Agricultural/growth &amp; development ; Biomass ; *Agriculture/methods ; *Decision Support Techniques ; Plant Leaves/growth &amp; development ; Seasons ; },
abstract = {The decision support system for agro-technology transfer (DSSAT) is a worldwide crop modeling platform used for crops growth, yield, leaf area index (LAI), and biomass estimation under varying climatic, soil and management conditions. This study integrates DSSAT with satellite remote sensing (RS) data to estimates canopy state variables like LAI and biomass. For LAI estimation, Moderate Resolution Imaging Spectroradiometer (MODIS) product (MCD15A3H for LAI and MOD17A2 / MOD17A3 products for biomass) are used. Field data for Sheikhupura district is provided by National Agriculture Research Council (NARC) and used for the calibration and validation of the model. The results indicate strong agreement between the DSSAT and RS derived estimates. Correlation coefficients (R[2]) for LAI varied from 0.82 to 0.90, while for biomass ranged from 0.92 to 0.99 over two farms and two growing seasons (2012-2014). The index of agreement (D-index) ranged from 0.79 to 0.96 across the two farms and two growing seasons (2012-2014) affirming the model's durability. However, the biomass estimated from RS data is underestimated due to saturation phenomenon in the optical RS. The performance metrics, comprising the coefficient of residual mass (CRM) and normalized root mean square error (nRMSE), further substantiate the approach utilized. This study will help decision and policymakers and researchers to apply geospatial techniques for the sustainable agriculture practices.},
}
@article {pmid40181527,
year = {2025},
author = {Mills, MB and Shenkin, A and Wilkes, P and Disney, M and Page, S and Berrio, JC and Kaduk, J and Malhi, Y and Robert, R and Nilus, R and Riutta, T},
title = {Investigating the accuracy of tropical woody stem CO2 efflux estimates: scaling methods, and vertical and diel variation.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70122},
pmid = {40181527},
issn = {1469-8137},
support = {CA20118//European Cooperation in Science and Technology/ ; PRA 11.23//Royal Geographical Society/ ; NE/P011780/1//Natural Environment Research Council/ ; NE/Y006216/1//National Centre for Earth Observation/ ; NE/S007350/1//Central England NERC Training Alliance/ ; },
abstract = {Stem CO2 efflux (EA) significantly contributes to autotrophic and ecosystem respiration in tropical forests, but field methodologies often introduce biases and uncertainty. This study evaluates these biases and their impact on scaling EA at the stand-level. Diel and vertical patterns of EA were investigated, along with the accuracy of estimating stem surface area from allometric equations vs terrestrial light dection and ranging (LiDAR) scanning (TLS) in Maliau Basin Conservation Area, Sabah, Malaysian Borneo. Diel EA exhibited no uniform pattern due to inter-tree variability, but results suggest measuring EA before 15:00 h. EA was significantly higher on buttresses and above the first major branching point, but vertical variations in EA did not impact stand-level EA when stem surface area was accurately estimated. Allometric equations underestimated total stem surface area by c. 40% compared with TLS, but applying a site-specific correction factor yielded a similar stand-level EA and total stem surface area to TLS. This study provides guidance for measuring EA in the field and suggests that measuring at one time point and one height along the stem can produce accurate results if conducted using the correct time frame and if stem surface area is accurately estimated.},
}
@article {pmid40180992,
year = {2025},
author = {González, AL and Merder, J and Andraczek, K and Brose, U and Filipiak, M and Harpole, WS and Hillebrand, H and Jackson, MC and Jochum, M and Leroux, SJ and Nessel, MP and Onstein, RE and Paseka, R and Perry, GLW and Rugenski, A and Sitters, J and Sperfeld, E and Striebel, M and Zandona, E and Aymes, JC and Blanckaert, A and Bluhm, SL and Doi, H and Eisenhauer, N and Farjalla, VF and Hood, J and Kratina, P and Labonne, J and Lovelock, CE and Moody, EK and Mozsár, A and Nash, L and Pollierer, MM and Potapov, A and Romero, GQ and Roussel, JM and Scheu, S and Scheunemann, N and Seeber, J and Steinwandter, M and Susanti, WI and Tiunov, A and Dézerald, O},
title = {StoichLife: A Global Dataset of Plant and Animal Elemental Content.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {569},
pmid = {40180992},
issn = {2052-4463},
support = {DFG HI848/26-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR 5000//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG 493345801//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RGPIN-2020-04132//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 310119/2018-9//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (National Council for Scientific and Technological Development)/ ; 310119/2018-9//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (National Council for Scientific and Technological Development)/ ; NAF\R2\180791//Royal Society/ ; DP0986179//Department of Education and Training | Australian Research Council (ARC)/ ; DP160103669//Department of Education and Training | Australian Research Council (ARC)/ ; 22-14-00363)//Russian Science Foundation (RSF)/ ; },
mesh = {*Plants/chemistry ; Animals ; Ecosystem ; Phosphorus/analysis ; Nitrogen/analysis ; Carbon/analysis ; },
abstract = {The elemental content of life is a key trait shaping ecology and evolution, yet organismal stoichiometry has largely been studied on a case-by-case basis. This limitation has hindered our ability to identify broad patterns and mechanisms across taxa and ecosystems. To address this, we present StoichLife, a global dataset of 28,049 records from 5,876 species spanning terrestrial, freshwater, and marine realms. Compiled from published and unpublished sources, StoichLife documents elemental content and stoichiometric ratios (%C, %N, %P, C:N, C:P, and N:P) for individual plants and animals. The dataset is standardized and, where available, includes information on taxonomy, habitat, body mass (for animals), geography, and environmental conditions such as temperature, solar radiation, and nutrient availability. By providing an unprecedented breadth of organismal stoichiometry, StoichLife enables the exploration of global patterns, ecological and evolutionary drivers, and context-dependent variations. This resource advances our understanding of the chemical makeup of life and its responses to environmental change, supporting progress in ecological stoichiometry and related fields.},
}
@article {pmid39936183,
year = {2025},
author = {Brait, N and Hackl, T and Lequime, S},
title = {detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14083},
doi = {10.1111/1755-0998.14083},
pmid = {39936183},
issn = {1755-0998},
mesh = {*Computational Biology/methods ; *Genomics/methods ; *Software ; Genome, Viral ; *Viruses/genetics ; Sensitivity and Specificity ; },
abstract = {Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during their life cycle; however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr) EVEs. Detecting nrEVEs poses challenges because of their sequence and genomic structural diversity, contributing to the scarcity of specific tools designed for nrEVEs detection. Here, we introduce detectEVE, a user-friendly and open-source tool designed for the accurate identification of nrEVEs in genomic assemblies. detectEVE deviates from other nrEVE detection pipelines, which usually classify sequences in a more rigid manner as either virus-associated or not. Instead, we implemented a scaling system assigning confidence scores to hits in protein sequence similarity searches, using bit score distributions and search hints related to various viral characteristics, allowing for higher sensitivity and specificity. Our benchmarking shows that detectEVE is computationally efficient and accurate, as well as considerably faster than existing approaches, because of its resource-efficient parallel execution. Our tool can help to fill current gaps in both host-associated fields and virus-related studies. This includes (i) enhancing genome annotations with metadata for EVE loci, (ii) conducting large-scale paleo-virological studies to explore deep viral evolutionary histories, and (iii) aiding in the identification of actively expressed EVEs in transcriptomic data, reducing the risk of misinterpretations between exogenous viruses and EVEs.},
}
@article {pmid39925235,
year = {2025},
author = {Shi, T and Gao, Z and Zhang, Y and Rausher, MD and Chen, J},
title = {A Strategy of Assessing Gene Copy Number Differentiation Between Populations Using Ultra-Fast De Novo Assembly of Next-Generation Sequencing Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14080},
doi = {10.1111/1755-0998.14080},
pmid = {39925235},
issn = {1755-0998},
support = {31570220//National Natural Science Foundation of China/ ; 31870208//National Natural Science Foundation of China/ ; 32170240//National Natural Science Foundation of China/ ; KFJ-BRP-007-009//Biological Resources Program, CAS/ ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *DNA Copy Number Variations ; *Computational Biology/methods ; *Genetics, Population/methods ; *Gene Dosage ; Sequence Analysis, DNA/methods ; },
abstract = {Gene duplication and loss play pivotal roles in the evolutionary dynamics of genomes, contributing to species phenotypic diversity and adaptation. However, detecting copy number variations (CNVs) in homoploid populations and newly-diverged species using short reads from next-generation sequencing (NGS) with traditional methods can often be challenging due to uneven read coverage caused by variations in GC content and the presence of repetitive sequences. To address these challenges, we developed a novel pipeline, ST4gCNV, which leverages ultra-fast de novo assemblies of NGS data to detect gene-specific CNVs between populations. The pipeline effectively reduces the variance of read coverage due to technical factors such as GC bias, providing a reliable CNV detection with a minimum sequencing depth of 10. We successfully apply ST4gCNV to the resequencing analysis of homoploid species Nelumbo nucifera and Nelumbo lutea (lotus). We reveal significant CNV-driven differentiation between these species, particularly in genes related to petal colour diversity such as those involved in the anthocyanin pathway. By highlighting the extensive gene duplication and loss events in Nelumbo, our study demonstrates the utility of ST4gCNV in population genomics and underscores its potential of integrating genomic CNV analysis with traditional SNP-based resequencing analysis.},
}
@article {pmid39801085,
year = {2025},
author = {Anderson, EC and Giglio, RM and DeSaix, MG and Smyser, TJ},
title = {gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14069},
doi = {10.1111/1755-0998.14069},
pmid = {39801085},
issn = {1755-0998},
support = {//National Wildlife Research Center/ ; //Southwest Fisheries Science Center/ ; },
mesh = {*Computer Simulation ; *Computational Biology/methods ; *Genetics, Population/methods ; Genotype ; *Software ; },
abstract = {While a best practice for evaluating the behaviour of genetic clustering algorithms on empirical data is to conduct parallel analyses on simulated data, these types of simulation techniques often involve sampling genetic data with replacement. In this paper we demonstrate that sampling with replacement, especially with large marker sets, inflates the perceived statistical power to correctly assign individuals (or the alleles that they carry) back to source populations-a phenomenon we refer to as resampling-induced, spurious power inflation (RISPI). To address this issue, we present gscramble, a simulation approach in R for creating biologically informed individual genotypes from empirical data that: (1) samples alleles from populations without replacement and (2) segregates alleles based on species-specific recombination rates. This framework makes it possible to simulate admixed individuals in a way that respects the physical linkage between markers on the same chromosome and which does not suffer from RISPI. This is achieved in gscramble by allowing users to specify pedigrees of varying complexity in order to simulate admixed genotypes, segregating and tracking haplotype blocks from different source populations through those pedigrees, and then sampling-using a variety of permutation schemes-alleles from empirical data into those haplotype blocks. We demonstrate the functionality of gscramble with both simulated and empirical data sets and highlight additional uses of the package that users may find valuable.},
}
@article {pmid40180917,
year = {2025},
author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA},
title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3204},
pmid = {40180917},
issn = {2041-1723},
support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; },
abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.},
}
@article {pmid40179423,
year = {2025},
author = {Dejeante, R and Valeix, M and Chamaillé-Jammes, S},
title = {Do Mixed-Species Groups Travel as One? An Investigation on Large African Herbivores Monitored Using Animal-Borne Video Collars.},
journal = {The American naturalist},
volume = {205},
number = {4},
pages = {451-458},
doi = {10.1086/734410},
pmid = {40179423},
issn = {1537-5323},
mesh = {Animals ; Video Recording ; *Herbivory ; *Giraffes/physiology ; *Equidae/physiology ; *Antelopes/physiology ; Social Behavior ; Geographic Information Systems ; Ecosystem ; },
abstract = {AbstractAlthough prey foraging in mixed-species groups benefit from a reduced risk of predation, whether heterospecific groupmates move together in the landscape, and more generally to what extent mixed-species groups remain cohesive over time and space, remains unknown. Here, we used GPS collars with video cameras to investigate the movements of plains zebras (Equus quagga) in mixed-species groups. Blue wildebeest (Connochaetes taurinus), impalas (Aepyceros melampus), and giraffes (Giraffa camelopardalis) commonly form mixed-species groups with zebras in savanna ecosystems. We found that zebras adjust their movement decisions solely on the basis of the presence of giraffes, being more likely to move in zebra-giraffe herds, and this was correlated with a higher cohesion of such groups. Additionally, zebras moving with giraffes spent more time grazing, suggesting that zebras benefit from foraging in the proximity of giraffes. Our results provide new insights into animal movements in mixed-species groups, contributing to a better consideration of mutualism in movement ecology.},
}
@article {pmid40179162,
year = {2025},
author = {Davín, AA and Woodcroft, BJ and Soo, RM and Morel, B and Murali, R and Schrempf, D and Clark, JW and Álvarez-Carretero, S and Boussau, B and Moody, ERR and Szánthó, LL and Richy, E and Pisani, D and Hemp, J and Fischer, WW and Donoghue, PCJ and Spang, A and Hugenholtz, P and Williams, TA and Szöllősi, GJ},
title = {A geological timescale for bacterial evolution and oxygen adaptation.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {eadp1853},
doi = {10.1126/science.adp1853},
pmid = {40179162},
issn = {1095-9203},
mesh = {*Oxygen/metabolism ; Phylogeny ; *Biological Evolution ; Oxidation-Reduction ; *Bacteria/metabolism/classification/genetics ; Machine Learning ; Photosynthesis ; Adaptation, Physiological ; Cyanobacteria/genetics/metabolism ; },
abstract = {Microbial life has dominated Earth's history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE). We combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial time tree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Phanerozoic. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, in the cyanobacterial ancestor, aerobic metabolism likely predated the GOE, which may have facilitated the evolution of oxygenic photosynthesis.},
}
@article {pmid40178345,
year = {2025},
author = {Riobueno-Naylor, A and Gomez, I and Quan, S and Hutt Vater, C and Montes, M and Hoskova, B and Lai, BS},
title = {Methods for integrating public datasets: insights from youth disaster mental health research.},
journal = {European journal of psychotraumatology},
volume = {16},
number = {1},
pages = {2481699},
doi = {10.1080/20008066.2025.2481699},
pmid = {40178345},
issn = {2000-8066},
mesh = {Humans ; Adolescent ; *Disasters ; United States/epidemiology ; *Mental Health/statistics &amp; numerical data ; Male ; Female ; *Depression/epidemiology ; *Datasets as Topic ; Databases, Factual ; },
abstract = {Introduction: Weather-related disasters pose significant risks to youth mental health. Exposure to multiple disasters is becoming more common; however, the effects of such exposure remain understudied. This study demonstrates the application of integrative data approaches and FAIR (Findable, Accessible, Interoperable, Reusable) data principles to evaluate the relationship between cumulative disaster exposure and youth depression and suicidality in the United States, taking into account contextual factors across levels of social ecology.Methods: We combined data from five public sources, including the Youth Risk Behavior Surveillance System (YRBS), Federal Emergency Management Agency (FEMA), United States Census Bureau, Center for Homeland Defense and Security School Shooting Safety Compendium, and Global Terrorism Database. The integrative dataset included 415,701 youth from 37 districts across the United States who completed the YRBS between 1999 and 2021. The YRBS served as the core dataset.Results: This data note highlights strategies for harmonizing diverse data formats, addressing geographic and temporal inconsistencies, and validating integrated datasets. Automated data cleaning and visualization techniques enhance accuracy and efficiency. Planning for sensitivity analyses before data cleaning is recommended to improve the data integration process and enhance the robustness of findings.Discussion: This integrative approach demonstrates how leveraging FAIR principles can advance trauma research by facilitating large-scale analyses of complex public health questions. The methods provide a replicable framework for examining population-level impacts of phenomena and highlight opportunities for expanding trauma research.},
}
@article {pmid40175550,
year = {2025},
author = {Pärtel, M and Tamme, R and Carmona, CP and Riibak, K and Moora, M and Bennett, JA and Chiarucci, A and Chytrý, M and de Bello, F and Eriksson, O and Harrison, S and Lewis, RJ and Moles, AT and Öpik, M and Price, JN and Amputu, V and Askarizadeh, D and Atashgahi, Z and Aubin, I and Azcárate, FM and Barrett, MD and Bashirzadeh, M and Bátori, Z and Beenaerts, N and Bergholz, K and Birkeli, K and Biurrun, I and Blanco-Moreno, JM and Bloodworth, KJ and Boisvert-Marsh, L and Boldgiv, B and Brancalion, PHS and Brearley, FQ and Brown, C and Bueno, CG and Buffa, G and Cahill, JF and Campos, JA and Cangelmi, G and Carbognani, M and Carcaillet, C and Cerabolini, BEL and Chevalier, R and Clavel, JS and Costa, JM and Cousins, SAO and Čuda, J and Dairel, M and Dalle Fratte, M and Danilova, A and Davison, J and Deák, B and Del Vecchio, S and Dembicz, I and Dengler, J and Dolezal, J and Domene, X and Dvorsky, M and Ejtehadi, H and Enrico, L and Epikhin, D and Eskelinen, A and Essl, F and Fan, G and Fantinato, E and Fazlioglu, F and Fernández-Pascual, E and Ferrara, A and Fidelis, A and Fischer, M and Flagmeier, M and Forte, TGW and Fraser, LH and Fujinuma, J and Furquim, FF and Garris, B and Garris, HW and Giorgis, MA and Giusso Del Galdo, G and González-Robles, A and Good, MK and Guardiola, M and Guarino, R and Guerrero, I and Guillemot, J and Güler, B and Guo, Y and Haesen, S and Hejda, M and Heleno, RH and Høye, TT and Hrivnák, R and Huang, Y and Hunter, JT and Iakushenko, D and Ibáñez, R and Ingerpuu, N and Irl, SDH and Janíková, E and Jansen, F and Jeltsch, F and Jentsch, A and Jiménez-Alfaro, B and Jõks, M and Jouri, MH and Karami, S and Katal, N and Kelemen, A and Khairullin, BI and Khuroo, AA and Komatsu, KJ and Konečná, M and Kook, E and Korell, L and Koroleva, N and Korznikov, KA and Kozhevnikova, MV and Kozub, &#x141; and Laanisto, L and Lager, H and Lanta, V and Lasagno, RG and Lembrechts, JJ and Li, L and Lisner, A and Liu, H and Liu, K and Liu, X and Lucas-Borja, ME and Ludewig, K and Lukács, K and Luther-Mosebach, J and Macek, P and Marignani, M and Michalet, R and Miglécz, T and Moeslund, JE and Moeys, K and Montesinos, D and Moreno-Jiménez, E and Moysiyenko, I and Mucina, L and Muñoz-Rojas, M and Murillo, RA and Nambahu, SM and Neuenkamp, L and Normand, S and Nowak, A and Nuche, P and Oja, T and Onipchenko, VG and Pachedjieva, KL and Paganeli, B and Peco, B and Peralta, AML and Pérez-Haase, A and Peri, PL and Petraglia, A and Peyre, G and Plaza-Álvarez, PA and Plue, J and Prentice, HC and Prokhorov, VE and Radujković, D and Rahmanian, S and Reitalu, T and Ristow, M and Robin, AA and Robles, AB and Rodríguez Ginart, DA and Román, R and Roos, RE and Rosati, L and Sádlo, J and Salimbayeva, K and Sánchez de Dios, R and Sanchir, K and Sattler, C and Scasta, JD and Schmiedel, U and Schrader, J and Schultz, NL and Sellan, G and Serra-Diaz, JM and Silan, G and Skálová, H and Skobel, N and Sonkoly, J and Štajerová, K and Svitková, I and Świerszcz, S and Tanentzap, AJ and Tanentzap, FM and Tarifa, R and Tejero, P and Tekeev, DK and Tholin, M and Thormodsæter, RS and Tian, Y and Tokaryuk, A and Tölgyesi, C and Tomaselli, M and Tordoni, E and Török, P and Tóthmérész, B and Toussaint, A and Touzard, B and Trindade, DPF and Tsakalos, JL and Türkiş, S and Valencia, E and Valerio, M and Valkó, O and Van Meerbeek, K and Vandvik, V and Villellas, J and Virtanen, R and Vítková, M and Vojík, M and von Hessberg, A and von Oppen, J and Wagner, V and Wan, JZ and Wang, CJ and Wani, SA and Weiss, L and Wevill, T and Xiao, S and Zárate Martínez, O and Zobel, M},
title = {Global impoverishment of natural vegetation revealed by dark diversity.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40175550},
issn = {1476-4687},
abstract = {Anthropogenic biodiversity decline threatens the functioning of ecosystems and the many benefits they provide to humanity[1]. As well as causing species losses in directly affected locations, human influence might also reduce biodiversity in relatively unmodified vegetation if far-reaching anthropogenic effects trigger local extinctions and hinder recolonization. Here we show that local plant diversity is globally negatively related to the level of anthropogenic activity in the surrounding region. Impoverishment of natural vegetation was evident only when we considered community completeness: the proportion of all suitable species in the region that are present at a site. To estimate community completeness, we compared the number of recorded species with the dark diversity-ecologically suitable species that are absent from a site but present in the surrounding region[2]. In the sampled regions with a minimal human footprint index, an average of 35% of suitable plant species were present locally, compared with less than 20% in highly affected regions. Besides having the potential to uncover overlooked threats to biodiversity, dark diversity also provides guidance for nature conservation. Species in the dark diversity remain regionally present, and their local populations might be restored through measures that improve connectivity between natural vegetation fragments and reduce threats to population persistence.},
}
@article {pmid40173850,
year = {2025},
author = {Vivien, R and Martin, P},
title = {Maintaining taxonomic accuracy in genetic databases: A duty for taxonomists-Reanalysis of the DNA sequences from Mercan et al. (2024) on the genus Potamothrix (Annelida, Clitellata) in Turkish lakes.},
journal = {Zootaxa},
volume = {5575},
number = {4},
pages = {555-562},
doi = {10.11646/zootaxa.5575.4.5},
pmid = {40173850},
issn = {1175-5334},
mesh = {Turkey ; Animals ; Lakes ; Phylogeny ; *Databases, Genetic/standards ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; *Polychaeta/classification/genetics ; },
abstract = {Public DNA sequence databases such as GenBank are widely used for identification of organisms in ecological and taxonomic studies. It is important that these public databases contain as few mistakes as possible and that any errors detected in these databases are reported. Here, we reanalyzed the COI sequences of Mercan et al. (2024) and showed that they were mistakenly considered by these authors as belonging to different populations (haplotypes) within the species Potamothrix hammoniensis (Tubificinae). We found that they corresponded to four distinct Tubificinae lineages (species), Pothamothrix alatus paravanicus, Potamothrix bavaricus, Tubifex sp. and Potamothrix sp. Despite these identification errors, the data from Mercan et al. (2024) remain interesting as they provide new information on the diversity of the genus Potamothrix in Turkey. Prompt measures must be taken to correct these errors and prevent them from being detrimental to future studies.},
}
@article {pmid40111995,
year = {2025},
author = {Eales, O and Shearer, FM and McCaw, JM},
title = {How immunity shapes the long-term dynamics of influenza H3N2.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012893},
pmid = {40111995},
issn = {1553-7358},
mesh = {Humans ; *Influenza, Human/immunology/epidemiology/transmission/virology ; *Influenza A Virus, H3N2 Subtype/immunology/genetics ; Computational Biology ; *Models, Immunological ; Adult ; Aged ; Middle Aged ; Adolescent ; },
abstract = {Since its emergence in 1968, influenza A H3N2 has caused yearly epidemics in temperate regions. While infection confers immunity against antigenically similar strains, new antigenically distinct strains that evade existing immunity regularly emerge ('antigenic drift'). Immunity at the individual level is complex, depending on an individual's lifetime infection history. An individual's first infection with influenza typically elicits the greatest response with subsequent infections eliciting progressively reduced responses ('antigenic seniority'). The combined effect of individual-level immune responses and antigenic drift on the epidemiological dynamics of influenza are not well understood. Here we develop an integrated modelling framework of influenza transmission, immunity, and antigenic drift to show how individual-level exposure, and the build-up of population level immunity, shape the long-term epidemiological dynamics of H3N2. Including antigenic seniority in the model, we observe that following an initial decline after the pandemic year, the average annual attack rate increases over the next 80 years, before reaching an equilibrium, with greater increases in older age-groups. Our analyses suggest that the average attack rate of H3N2 is still in a growth phase. Further increases, particularly in the elderly, may be expected in coming decades, driving an increase in healthcare demand due to H3N2 infections.},
}
@article {pmid39880083,
year = {2025},
author = {Vande Moortele, T and Verschaffelt, P and Huang, Q and Doncheva, NT and Holstein, T and Jachmann, C and Dawyndt, P and Martens, L and Mesuere, B and Van Den Bossche, T},
title = {PathwayPilot: A User-Friendly Tool for Visualizing and Navigating Metabolic Pathways.},
journal = {Molecular &amp; cellular proteomics : MCP},
volume = {24},
number = {3},
pages = {100918},
pmid = {39880083},
issn = {1535-9484},
mesh = {*Software ; *Metabolic Networks and Pathways ; Humans ; *Proteomics/methods ; Gastrointestinal Microbiome ; User-Computer Interface ; Proteome/metabolism ; *Computational Biology/methods ; Caloric Restriction ; },
abstract = {Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool effectively combines pathway analysis with peptide- or protein-level data. We here introduce PathwayPilot, a web-based application designed to improve metaproteomic data analysis by integrating pathway analysis with peptide- and protein-level data, filling a critical gap in current metaproteomics bioinformatics tools. By allowing users to compare functional annotations across different samples or multiple organisms within a sample, PathwayPilot provides valuable insights into microbial functions. In the re-analysis of a study examining the effects of caloric restriction on gut microbiota, the tool successfully identified shifts in enzyme expressions linked to short-chain fatty acid biosynthesis, aligning with its original findings. PathwayPilot's user-friendly interface and robust capabilities make it a significant advancement in metaproteomics, with the potential for widespread application in microbial ecology and health sciences. All code is open source under the Apache2 license and is available at https://pathwaypilot.ugent.be.},
}
@article {pmid39609363,
year = {2025},
author = {Xu, S and Akhatayeva, Z and Liu, J and Feng, X and Yu, Y and Badaoui, B and Esmailizadeh, A and Kantanen, J and Amills, M and Lenstra, JA and Johansson, AM and Coltman, DW and Liu, GE and Curik, I and Orozco-terWengel, P and Paiva, SR and Zinovieva, NA and Zhang, L and Yang, J and Liu, Z and Wang, Y and Yu, Y and Li, M},
title = {Genetic advancements and future directions in ruminant livestock breeding: from reference genomes to multiomics innovations.},
journal = {Science China. Life sciences},
volume = {68},
number = {4},
pages = {934-960},
pmid = {39609363},
issn = {1869-1889},
mesh = {Animals ; *Livestock/genetics ; *Genomics/methods ; *Breeding/methods ; *Ruminants/genetics ; *Genome ; Phenotype ; Multiomics ; },
abstract = {Ruminant livestock provide a rich source of products, such as meat, milk, and wool, and play a critical role in global food security and nutrition. Over the past few decades, genomic studies of ruminant livestock have provided valuable insights into their domestication and the genetic basis of economically important traits, facilitating the breeding of elite varieties. In this review, we summarize the main advancements for domestic ruminants in reference genome assemblies, population genomics, and the identification of functional genes or variants for phenotypic traits. These traits include meat and carcass quality, reproduction, milk production, feed efficiency, wool and cashmere yield, horn development, tail type, coat color, environmental adaptation, and disease resistance. Functional genomic research is entering a new era with the advancements of graphical pangenomics and telomere-to-telomere (T2T) gap-free genome assembly. These advancements promise to improve our understanding of domestication and the molecular mechanisms underlying economically important traits in ruminant livestock. Finally, we provide new perspectives and future directions for genomic research on ruminant genomes. We suggest how ever-increasing multiomics datasets will facilitate future studies and molecular breeding in livestock, including the potential to uncover novel genetic mechanisms underlying phenotypic traits, to enable more accurate genomic prediction models, and to accelerate genetic improvement programs.},
}
@article {pmid40175491,
year = {2025},
author = {Zhang, H and Guo, G and Li, H and Wang, T and Ni, J and Meng, H},
title = {A new numerical method for calculating residual deformation in mined-out areas considering water-rock interaction and its application.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11207},
pmid = {40175491},
issn = {2045-2322},
support = {2023YFC3804201//National Key R&amp;D Program of China/ ; },
abstract = {Globally, extensive land regions have fallen victim to coal mining subsidence, rendering the reuse of goaf sites a crucial concern. The residual deformation amount of these sites is the linchpin for determining their reusability. Presently, numerical computations of residual deformation in goafs, which overlook water-rock coupling, breed significant errors, posing severe threats to the safety of on-site structures. To remedy the situation, this research hinges on the mechanical experiment results of fractured rock masses under water-rock interaction within the goaf. By leveraging an embedded programming language, it pinpoints the irregular damage range of overlying strata due to water-rock effects. Then, corresponding mechanical parameters are allocated to the surrounding rocks at diverse spatial positions, with the erosive impact of water-soaked coal pillars also factored in. This gives rise to a novel numerical method that more precisely gauges groundwater's influence on strata movement and surface subsidence. Using the 01 working face of a Shandong mine as a practical backdrop, the new method verifies its reliability and accuracy. When contrasted with traditional approaches, be it neglecting water filling or assuming full saturation in the goaf, it slashes the calculation error by 20%, furnishing new approaches for residual deformation calculation and novel perspectives for evaluating site stability under complex geological conditions.},
}
@article {pmid40171521,
year = {2025},
author = {Boyes, D and Hutchinson, F and Crowley, LM and , and , and , and , and , and , and , },
title = {The genome sequence of the Large Birch Bell moth, Large Birch Roller, Epinotia brunnichana (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {101},
pmid = {40171521},
issn = {2398-502X},
abstract = {We present a genome assembly from a female Epinotia brunnichana (Large Birch Bell, Large Birch Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 943.10 megabases. Most of the assembly (99.68%) is scaffolded into 29 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,003 protein-coding genes.},
}
@article {pmid40170100,
year = {2025},
author = {Sato, K and Watanabe, S and Noda, T and Koizumi, T and Yoda, K and Watanabe, YY and Sakamoto, KQ and Isokawa, T and Yoshida, MA and Aoki, K and Takahashi, A and Iwata, T and Nishizawa, H and Maekawa, T and Kawabe, R and Watanuki, Y},
title = {Biologging intelligent Platform (BiP): an integrated and standardized platform for sharing, visualizing, and analyzing biologging data.},
journal = {Movement ecology},
volume = {13},
number = {1},
pages = {23},
pmid = {40170100},
issn = {2051-3933},
abstract = {Sharing biologging data can facilitate collaborative research and biological conservation by providing maps showing animals' distribution and movements. It is a critical social mission to preserve not only horizontal position data, but also behavioral data such as diving depth, flight altitude, speed, and acceleration, as well as physiological data such as body temperature, along with related metadata, ensuring their preservation for future generation. Moreover, although biologging was initially developed in the field of biology, it now contributes to diverse fields such as meteorology and oceanography, leading to expanded opportunities for secondary data utilization. In light of social and academic requirements, we developed "Biologging intelligent Platform (BiP)", which adheres to internationally recognized standards for sensor data and metadata storage. As a result, BiP not only stores sensor data along with metadata but also standardizes this information to facilitate secondary data analysis, facilitating broader applications of biologging data across various disciplines. By visiting the website (https://www.bip-earth.com) and completing the user registration, data owners can interactively upload sensor data, input metadata associated with individual animals, devices, and deployments, standardize data formats, and choose between open and private settings for sharing data. Anyone interested in utilizing the data can access metadata and visualized route maps, irrespective of the data's open or private status. Users can freely download open datasets that are available under the CC BY 4.0 license, which permits copying, redistribution, and modification while adhering to the metadata's credit requirements. To use private datasets, users can contact the data owner to request permission. A unique feature of BiP is the Online Analytical Processing (OLAP) tools that calculate environmental parameters, such as surface currents, ocean winds, and waves from data collected by animals. Algorithms published in some previous studies are integrated into the OLAP which can estimate the environmental and behavioral parameters. To enhance data accessibility, BiP allows users to search for datasets using the DOI of the paper in which the data was used. We believe that linking with other databases for data exchange and multi-repository storage could enhance the sustainability of the data itself.},
}
@article {pmid39934999,
year = {2025},
author = {De Moor, D and Skelton, M and , and Amici, F and Arlet, ME and Balasubramaniam, KN and Ballesta, S and Berghänel, A and Berman, CM and Bernstein, SK and Bhattacharjee, D and Bliss-Moreau, E and Brotcorne, F and Butovskaya, M and Campbell, LAD and Carosi, M and Chatterjee, M and Cooper, MA and Cowl, VB and De la O, C and De Marco, A and Dettmer, AM and Dhawale, AK and Erinjery, JJ and Evans, CL and Fischer, J and García-Nisa, I and Giraud, G and Hammer, R and Hansen, MF and Holzner, A and Kaburu, S and Konečná, M and Kumara, HN and Larrivaz, M and Leca, JB and Legrand, M and Lehmann, J and Li, JH and Lezé, AS and MacIntosh, A and Majolo, B and Maréchal, L and Marty, PR and Massen, JJM and Maulany, RI and McCowan, B and McFarland, R and Merieau, P and Meunier, H and Micheletta, J and Mishra, PS and Sah, SAM and Molesti, S and Morrow, KS and Müller-Klein, N and Ngakan, PO and Palagi, E and Petit, O and Pflüger, LS and di Sorrentino, EP and Raghaven, R and Raimbault, G and Ram, S and Reichard, UH and Riley, EP and Rincon, AV and Ruppert, N and Sadoughi, B and Santhosh, K and Schino, G and Sheeran, LK and Silk, JB and Singh, M and Sinha, A and Sosa, S and Stribos, MS and Sueur, C and Tiddi, B and Tkaczynski, PJ and Trebouet, F and Widdig, A and Whitehouse, J and Wooddell, LJ and Xia, DP and von Fersen, L and Young, C and Schülke, O and Ostner, J and Neumann, C and Duboscq, J and Brent, LJN},
title = {MacaqueNet: Advancing comparative behavioural research through large-scale collaboration.},
journal = {The Journal of animal ecology},
volume = {94},
number = {4},
pages = {519-534},
doi = {10.1111/1365-2656.14223},
pmid = {39934999},
issn = {1365-2656},
support = {864461//H2020 European Research Council/ ; LSC-AF2023_03//Leibniz ScienceCampus EEGA/ ; },
mesh = {Animals ; *Behavioral Research/methods ; Macaca/physiology ; Behavior, Animal ; Databases, Factual ; Social Behavior ; },
abstract = {There is a vast and ever-accumulating amount of behavioural data on individually recognised animals, an incredible resource to shed light on the ecological and evolutionary drivers of variation in animal behaviour. Yet, the full potential of such data lies in comparative research across taxa with distinct life histories and ecologies. Substantial challenges impede systematic comparisons, one of which is the lack of persistent, accessible and standardised databases. Big-team approaches to building standardised databases offer a solution to facilitating reliable cross-species comparisons. By sharing both data and expertise among researchers, these approaches ensure that valuable data, which might otherwise go unused, become easier to discover, repurpose and synthesise. Additionally, such large-scale collaborations promote a culture of sharing within the research community, incentivising researchers to contribute their data by ensuring their interests are considered through clear sharing guidelines. Active communication with the data contributors during the standardisation process also helps avoid misinterpretation of the data, ultimately improving the reliability of comparative databases. Here, we introduce MacaqueNet, a global collaboration of over 100 researchers (https://macaquenet.github.io/) aimed at unlocking the wealth of cross-species data for research on macaque social behaviour. The MacaqueNet database encompasses data from 1981 to the present on 61 populations across 14 species and is the first publicly searchable and standardised database on affiliative and agonistic animal social behaviour. We describe the establishment of MacaqueNet, from the steps we took to start a large-scale collective, to the creation of a cross-species collaborative database and the implementation of data entry and retrieval protocols. We share MacaqueNet's component resources: an R package for data standardisation, website code, the relational database structure, a glossary and data sharing terms of use. With all these components openly accessible, MacaqueNet can act as a fully replicable template for future endeavours establishing large-scale collaborative comparative databases.},
}
@article {pmid39760247,
year = {2025},
author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S},
title = {Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms.},
journal = {Proteomics},
volume = {25},
number = {7},
pages = {e202400208},
doi = {10.1002/pmic.202400208},
pmid = {39760247},
issn = {1615-9861},
support = {//Joint UKRI Natural Environment Research Council (NERC) and National Research Foundation (NRF) Singapore/ ; NE/V009621/1//UKRI NERC/NRF/ ; NRF-SEAP-2020-0001//UKRI NERC/NRF/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership (DTP)/ ; },
mesh = {*Biofilms/growth &amp; development ; *Bacterial Proteins/metabolism/genetics ; Proteomics/methods ; Plastics/metabolism ; Proteome/metabolism/analysis ; Bacteria/genetics/metabolism/classification ; Microbiota/genetics/physiology ; Metagenome/genetics ; Polyethylene/metabolism ; Metagenomics/methods ; Multiomics ; },
abstract = {Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, the early metabolic interactions driving the plastisphere formation remain unclear. This study utilised metaproteomic and metagenomic approaches to explore early plastisphere formation on low-density polyethylene (LDPE) over 3 (D3) and 7 (D7) days, focusing on microbial diversity, activity and biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas and Marinomonas, with near-complete metagenome-assembled genomes (MAGs). Pseudomonas dominated at D3, whilst at D7, Marinomonas, along with Acinetobacter, Vibrio and other genera became more prevalent. Pseudomonas and Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated with oxidative stress regulation, whilst granule formation, and alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes and other xenobiotic degradation enzymes were expressed by five genera. The expression of toxins, several type VI secretion system (TVISS) proteins, and biofilm formation proteins by Pseudomonas indicated their competitive advantage against other taxa. Upregulated metabolic pathways relating to substrate transport also suggested enhanced nutrient cross-feeding within the more diverse biofilm community. These insights enhance our understanding of plastisphere ecology and its potential for biotechnological applications.},
}
@article {pmid39660842,
year = {2025},
author = {Xu, C and Song, LY and Li, J and Zhang, LD and Guo, ZJ and Ma, DN and Dai, MJ and Li, QH and Liu, JY and Zheng, HL},
title = {MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data.},
journal = {Plant, cell &amp; environment},
volume = {48},
number = {5},
pages = {2950-2962},
doi = {10.1111/pce.15318},
pmid = {39660842},
issn = {1365-3040},
support = {//This work was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581); the National Key Research and Development Program of China (2017YFC0506102)/ ; },
mesh = {*Databases, Genetic ; Transcriptome ; Avicennia/genetics ; Gene Expression Profiling ; Computational Biology/methods ; Multiomics ; },
abstract = {Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.},
}
@article {pmid40168108,
year = {2025},
author = {Wang, TY and Wu, YW and Lu, HJ and Liao, TY and Tai, JH and Huang, SP and Wang, FY and Yu, TH and Ting, CT and Chaw, SM and Wang, HY},
title = {Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14110},
doi = {10.1111/1755-0998.14110},
pmid = {40168108},
issn = {1755-0998},
support = {23-23//Biodiversity Research Center, Academia Sinica/ ; MOST 102-2311-B-001-019//National Science and Technology Council/ ; MOST 108-2621-B-001-002//National Science and Technology Council/ ; MOST 109-2311-B-002-023-MY3//National Science and Technology Council/ ; 113L7223//National Taiwan University/ ; },
abstract = {The percomorph fish clade Gobioidei is a suborder that comprises over 2200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their species diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, an early-diverging group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 594 Mb, and a rise in species diversity from early-diverging to more recently diverged lineages is mirrored by enlarged genomes and a higher presence of transposable elements (TEs), particularly DNA transposons. These DNA transposons are enriched in genic and regulatory regions and their copy number increase is strongly correlated with substitution rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an overrepresentation of synaptic function genes, with genes putatively under selection linked to synapse organisation and calcium signalling, implicating a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed new light on the loach goby's survival mechanisms and the broader evolutionary trends within Gobioidei.},
}
@article {pmid40165685,
year = {2025},
author = {Gu, Y and Meng, L and Wang, Y and Wu, Z and Pan, Y and Zhao, Y and Detto, M and Wu, J},
title = {Uncovering the role of solar radiation and water stress factors in constraining decadal intra-site spring phenology variability in diverse ecosystems across the Northern Hemisphere.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70104},
pmid = {40165685},
issn = {1469-8137},
support = {#2017804//Carbon Mitigation Initiative of Princeton University and NSF grant/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme/ ; #17305321//Hong Kong Research Grant Council General Research Fund/ ; #C5062-21GF//Hong Kong Research Grant Council Collaborative Research Fund/ ; #31922090//National Natural Science Foundation of China/ ; //Innovation and Technology Fund (funding support to State Key Laboratories of Agrobiotechnology)/ ; //HKU Science Faculty RAE Improvement Fund 2023-24/ ; },
abstract = {The spring phenology has advanced significantly over recent decades with climate change, impacting large-scale biogeochemical cycles, climate feedback, and other essential ecosystem processes. Although numerous prognostic models have been developed for spring phenology, regional analyses of the optimality (OPT) strategy model that incorporate environmental variables beyond temperature and photoperiod remain lacking. We investigated the roles of solar radiation (SR) and three water stress factors (precipitation (P), soil moisture, and vapor pressure deficit (VPD)) on spring phenology from 1982 to 2015 using the OPT model with Global Inventory Modeling and Mapping Studies NDVI3g dataset and environmental data from TerraClimate, CRU_TS, and Global Land Data Assimilation System across the Northern Hemisphere (> 30°N). Our results show that SR and water stress factors significantly impacted intrasite decadal spring phenology variability, with water stress factors dominant in grassland ecosystems while SR dominated in the rest of the ecosystem types. Enhanced models incorporating SR (OPT-S) and VPD (OPT-VPD) outperformed the original OPT model, likely due to improved representation of the adaptive strategy of spring phenology to optimize photosynthetic carbon gain while minimizing frost risk. Our research enhances the understanding of the key environmental drivers influencing decadal spring phenology variation in the Northern Hemisphere and contributes to more accurate forecasts of ecological responses to global environmental change.},
}
@article {pmid40155956,
year = {2025},
author = {van Kessel, SAM and Wielders, CCH and Schoffelen, AF and Verbon, A},
title = {Enhancing antimicrobial resistance surveillance and research: a systematic scoping review on the possibilities, yield and methods of data linkage studies.},
journal = {Antimicrobial resistance and infection control},
volume = {14},
number = {1},
pages = {25},
pmid = {40155956},
issn = {2047-2994},
mesh = {Humans ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Stewardship ; Information Storage and Retrieval ; },
abstract = {BACKGROUND: Surveillance data on antimicrobial resistance (AMR) determinants such as antibiotic use, prevalence of AMR, antimicrobial stewardship, and infection prevention and control are mostly analysed and reported separately, although they are inextricably linked to each other. The impact of surveillance and research can be enhanced by linking these data. This systematic scoping review aims to summarize the studies that link AMR data and evaluate whether they yield new results, implications, or recommendations for practice.<br><br>METHODS: For this review, data linkage is defined as the process of linking records, from at least two independent data sources on either (I) at least two AMR determinants or (II) one AMR determinant and one or more general population characteristics. Data linkage should be performed on the level of a certain entity which, in the context of this review, can encompass persons, healthcare institutes, geographical regions or countries. A systematic literature search was performed on February 7th 2025 in Embase.com, PubMed and Scopus to identify AMR data linkage studies.<br><br>RESULTS: Forty-eight articles were included in our review. Most data linkage studies used two data sources, and most studies were published in the last 5 years (n&#x2009;=&#x2009;23 in 2020-2024). A predominance of studies linked data on geographical location, and thirteen studies linked data on individual patient level. Findings demonstrate that the majority of studies (43/48) had added value and provided recommendations for clinical practice and future policies or had suggestions for further research and surveillance. Additionally, data linkage studies appeared to be suitable for hypothesis generating. Several limitations were identified. Most studies had ecological designs, which are prone to ecological fallacy and unobserved confounding, making it hard to establish causality.<br><br>CONCLUSION: This systematic scoping review showed that AMR data linkage studies are increasingly performed. They have potential to gain a more comprehensive understanding of AMR dynamics by generating hypotheses, assisting in optimisation of surveillance, and interpretation of data in the context of guideline/policy development. To increase the added value of data linkage, more studies should be performed to improve knowledge on methodological approaches, data access, data management, and governance issues.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid40036964,
year = {2025},
author = {Jyoti, J and Hütt, MT},
title = {Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {4},
pages = {},
doi = {10.1093/bioinformatics/btaf095},
pmid = {40036964},
issn = {1367-4811},
mesh = {*Algorithms ; Humans ; *Microbial Interactions ; Microbiota ; Computational Biology/methods ; },
abstract = {MOTIVATION: Inferring microbial interaction networks from microbiome data is a core task of computational ecology. An avenue of research to create reliable inference methods is based on a stylized view of microbiome data, starting from the assumption that the presences and absences of microbiomes, rather than the quantitative abundances, are informative about the underlying interaction network. With this starting point, inference algorithms can be based on the notion of attractors (asymptotic states) in Boolean networks. Boolean network framework offers a computationally efficient method to tackle this problem. However, often existing algorithms operating under a Boolean network assumption, fail to provide networks that can reproduce the complete set of initial attractors (abundance patterns). Therefore, there is a need for network inference algorithms capable of reproducing the initial stable states of the system.<br><br>RESULTS: We study the change of attractors in Boolean threshold dynamics on signed undirected graphs under small changes in network architecture and show, how to leverage these relationships to enhance network inference algorithms. As an illustration of this algorithmic approach, we analyse microbial abundance patterns from stool samples of humans with inflammatory bowel disease (IBD), with colorectal cancer and from healthy individuals to study differences between the interaction networks of the three conditions. The method reveals strong diversity in IBD interaction networks. The networks are first partially deduced by an earlier inference method called ESABO, then we apply the new algorithm developed here, EDAME, to this result to generate a network that comes nearest to satisfying the original attractors.<br><br>Implementation code is freely available at https://github.com/Jojo6297/edame.git.},
}
@article {pmid40086783,
year = {2025},
author = {Yang, JZ and Li, JH and Liu, JL and Zhou, AD and Wang, H and Xie, XL and Zhang, KK and Wang, Q},
title = {Multiomics analysis revealed the effects of polystyrene nanoplastics at different environmentally relevant concentrations on intestinal homeostasis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {372},
number = {},
pages = {126050},
doi = {10.1016/j.envpol.2025.126050},
pmid = {40086783},
issn = {1873-6424},
mesh = {Animals ; Mice ; *Polystyrenes/toxicity ; *Homeostasis/drug effects ; *Gastrointestinal Microbiome/drug effects ; Microplastics/toxicity ; Nanoparticles/toxicity ; Male ; Mice, Inbred C57BL ; Colon/drug effects ; Intestines/drug effects ; Multiomics ; },
abstract = {Nanoplastics pollution is a global issue, with the digestive tract being one of the first affected organs, requiring further research on its impact on intestinal health. This study involved orally exposing mice to polystyrene nanoplastics (PS-NPs) at doses of 0.1, 0.5, or 2.5 mg/d for 42 days. The effects on intestinal health were thoroughly assessed via microbiomics, metabolomics, transcriptomics, and molecular biology. Our study demonstrated that the administration of all three doses of PS-NPs resulted in increased colonic permeability, heightened colonic and peripheral inflammation, reduced levels of antimicrobial peptides, and shortened colonic length. These effects may be attributed to a reduction in the abundance of probiotic bacteria, such as Clostridia_UCG-014, Roseburia, and Akkermansia, alongside an increase in the abundance of the pathogenic bacterium Desulfovibrionaceae induced by PS-NPs. Furthermore, we underscored the crucial role of histidine metabolism in PS-NPs-induced colonic injury, characterized by a significant reduction of L-histidine, which is closely related to microbial ecological dysregulation. Corresponding to microbiota deterioration and metabolic dysregulation, transcriptome analysis revealed that PS-NPs may disrupt colonic immune homeostasis by activating the TLR4/MyD88/NF-κB/NLRP3 signaling pathway. In conclusion, this study provided novel insights into the mechanisms by which PS-NPs disrupt intestinal homeostasis through integrated multiomics analysis, revealing critical molecular pathway and providing a scientific basis for future risk assessment of nanoplastics exposure.},
}
@article {pmid40155652,
year = {2025},
author = {Rehbein, M and Escobari, B and Fischer, S and Güntsch, A and Haas, B and Matheisen, G and Perschl, T and Wieshuber, A and Engel, T},
title = {Quantitative and qualitative Data on historical Vertebrate Distributions in Bavaria 1845.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {525},
pmid = {40155652},
issn = {2052-4463},
support = {442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 442032008//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Vertebrates ; Germany ; Animals ; *Biodiversity ; History, 19th Century ; Ecosystem ; Conservation of Natural Resources ; Forests ; },
abstract = {Archival collections contain an underutilized wealth of biodiversity data, encapsulated in government files and other historical documents. In 1845, the Bavarian government conducted a comprehensive national survey on the occurrence of 44 selected vertebrate species across the country. The detailed expert responses from 119 forestry offices, totalling 520 handwritten pages, have been preserved in the Bavarian State Archives. In this study, we digitized, annotated, geographically referenced, and published these historical records, making them widely available as data for research and conservation planning. Our dataset, openly accessible through the Global Biodiversity Information Facility (GBIF) and Zenodo, contains 5,467 species occurrence records from 1845. Besides the binary presence/absence data, we have also published the original textual survey responses, which contain rich qualitative information, such as species abundances, population trends, habitats, forest management practices, and human-nature relationships. This information can be further processed and interpreted to address a range of questions in historical and contemporary ecology.},
}
@article {pmid40144399,
year = {2021},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the poplar hawk-moth, Laothoe populi (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {237},
pmid = {40144399},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Laothoe populi (the poplar hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.},
}
@article {pmid40143245,
year = {2025},
author = {Culot, A and Abriat, G and Furlong, KP},
title = {High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy.},
journal = {Viruses},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/v17030314},
pmid = {40143245},
issn = {1999-4915},
mesh = {*Genome, Viral ; *Bacteriophages/genetics/classification ; *Molecular Sequence Annotation ; *Computational Biology/methods ; *Phage Therapy/methods ; Humans ; },
abstract = {Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict-but potentially huge-consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20-30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics' tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE's 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics' rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.},
}
@article {pmid40140737,
year = {2025},
author = {Tahir Ul Qamar, M and Fatima, K and Rao, MJ and Tang, Q and Sadaqat, M and Ding, B and Chen, LL and Zhu, XT},
title = {Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {388},
pmid = {40140737},
issn = {1471-2229},
mesh = {*Citrus/genetics ; *Multigene Family ; *Genome, Plant ; Genomics ; Plant Diseases/genetics/microbiology ; Plant Proteins/genetics/metabolism ; Genetic Variation ; Phylogeny ; Genes, Plant ; Gene Expression Regulation, Plant ; Disease Resistance/genetics ; },
abstract = {Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin-like proteins (GLPs) gene family involved in disease responsiveness. The developed sequence-based pangenome contains 954 Mb sequence and 74,755 genes. The comparative genomics analysis revealed the presence-absence variations (PAVs) among the Citrus genomes and species-specific protein-coding genes. Gene-based pangenome analysis revealed 4,936 new genes missing in the reference genome and highlighted the core and shell genes with putative functions in stress regulation. The pangenome-wide identification of GLP gene family members indicated the intraspecies diversity among the members across 11 genomes by analyzing their gene structure, motifs, and chromosomal distribution patterns. The synteny and evolutionary constraints analyses of Citrus GLPs provide detailed evidence of their evolutionary conservation and divergence. Further, the interaction, functional enrichment, and promoter analysis revealed their involvement in abiotic-, biotic-stress, signaling, and development-related pathways. The expression patterns of C. sinensis GLPs were studied in Huanglongbing (HLB) and Citrus canker disease. Several genes including CsGLPs1-2 and CsGLPs8-4 showed changes in expression patterns under both disease conditions. The qRT-PCR analysis revealed that these two genes were highly expressed in leaves infected with HLB disease across seven HLB-tolerant and susceptible citrus species. This Citrus pangenome and pangenes family study offers a comprehensive resource and new insights into the structural and functional diversity, identifying candidate genes that are important for future research to understand the stress-responsive mechanisms in Citrus.},
}
@article {pmid40139213,
year = {2025},
author = {Tam, CC and Young, SD and Harrison, S and Li, X and Litwin, AH},
title = {Theory-Based Social Media Intervention for Nonmedical Use of Prescription Opioids in Young Adults: Protocol for a Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e65847},
doi = {10.2196/65847},
pmid = {40139213},
issn = {1929-0748},
mesh = {Humans ; *Social Media ; Young Adult ; Male ; Female ; Analgesics, Opioid ; Adult ; Adolescent ; Opioid-Related Disorders/psychology ; },
abstract = {BACKGROUND: The nonmedical use of prescription opioids (NMUPO) in young adults in the United States is concerning and is robustly influenced by many psychosocial factors. Given the advantages of flexibility, wide coverage, and real-time responses and assessment, using social media appears to be a promising and innovative approach to delivering psychosocial intervention to young adults. However, few theory-based social media interventions are available for NMUPO targeting this at-risk population.<br><br>OBJECTIVE: Guided by the information-motivation-behavioral skills model, the proposed research aims to address critical gaps by theoretically exploring psychosocial content associated with NMUPO among young adults via formative assessment. These findings will then be used to develop and evaluate the feasibility and preliminary efficacy of a peer-led social media intervention to reduce NMUPO among young adults.<br><br>METHODS: The proposed study will comprise serial research activities. First, formative research will be conducted through semistructured interviews among 30 young adults engaged in NMUPO. Qualitative data will be synthesized using a pragmatic approach for identifying psychosocial content associated with NMUPO. Second, qualitative findings will be used for developing a peer-led social media intervention to reduce NMUPO among young adults by integrating promising psychotherapy principles and incorporating them with well-trained recovery coaches. Third, the social media intervention will be evaluated through a 12-week randomized controlled trial among 70 young adults (n=35, 50% in the intervention group and control group) engaged in NMUPO via mixed methods, including pre- and postintervention surveys, social media paradata (eg, time-series reactions to posts) collection, and ecological momentary assessment during the intervention. The control group will not receive an intervention but will complete the pre- and postintervention surveys. The primary outcomes will be feasibility, usability, and acceptability, while the secondary outcomes will be psychosocial and behavioral measures, such as past-3-month NMUPO, intention, psychological distress, self-efficacy, resilience, and coping strategies.<br><br>RESULTS: The proposed study was funded in May 2024. Social media campaigns have received responses from a total of 379 individuals, with 24 (6.3%) identified as eligible. As of February 10, 2025, we have completed formative interviews with 8 eligible participants.<br><br>CONCLUSIONS: The proposed study will be one of the first efforts to develop and deliver a theory-based peer-led intervention on social media, incorporating empirical findings on the psychosocial mechanism of NMUPO. The findings of the proposed study will provide valuable insights into opioid risk reduction for young adults through an innovative approach. If the tested trial is found to be feasible, the proposed study will contribute to future scaled-up and fully powered psychosocial interventions among young adults and other key populations at risk for NMUPO.<br><br>TRIAL REGISTRATION: ClincialTrials.gov NCT06469749; https://clinicaltrials.gov/study/NCT06469749.<br><br>DERR1-10.2196/65847.},
}
@article {pmid40139065,
year = {2025},
author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Wedyan, M and Cunsolo, F and Forlani, G and Sfriso, A and Ferretti, G and Coltorti, M and Munari, C and Mistri, M},
title = {Microbial dynamics in seagrass restoration: Unveiling hidden indicators of ecological success.},
journal = {Marine environmental research},
volume = {208},
number = {},
pages = {107089},
doi = {10.1016/j.marenvres.2025.107089},
pmid = {40139065},
issn = {1879-0291},
abstract = {Seagrass transplantation significantly alters sediment microbial communities, shaping their composition and metabolic functions. One year after Zostera marina transplantation, the microbial community structure and functions at the recipient site began shifting toward those of the donor site. Key microbial taxa associated with seagrass meadow sediment, such as Firmicutes (Hungateiclostridiaceae, Defluviitaleaceae) and Campylobacterota (Sulfurovum), increased in abundance, correlating with sediment organic matter content and carbon availability. Four functional groups were identified, each with distinct metabolic roles: (1) Opportunistic Anaerobic Degraders, (2) Seagrass-Driven Carbon Recyclers, (3) Anaerobic Fermenters and Hydrocarbon Recyclers and (4) Oxygen-Linked Carbon and Sulfur Cyclers. The sediments of transplanted Z. marina meadows exhibited increased cellulolysis and aerobic chemoheterotrophy, along with a reduction in nitrogen metabolism one year post transplant. Despite these microbial shifts, sediment isotopic signatures remained indicative of algal biomass, suggesting an incomplete transition toward a mature seagrass environment. Multivariate analysis further confirmed that the microbial community at the recipient site had not yet fully converged with that of the donor meadow, indicating that complete sediment maturation may require longer timescales. These findings demonstrate that microbial community composition and functional annotations serve as early indicators of seagrass restoration success. Long-term monitoring is essential to track ecosystem recovery and assess the stabilization of sediment conditions.},
}
@article {pmid40136166,
year = {2025},
author = {Ferrari, YAC and Jesus, CVF and Batista, JFC and Silva, BEBD and Cavalcante, AB and Lima, CA},
title = {Secular trend of cervical cancer mortality in Brazil and regions.},
journal = {Ciencia &amp; saude coletiva},
volume = {30},
number = {3},
pages = {e09962023},
doi = {10.1590/1413-81232025303.09962023},
pmid = {40136166},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; Female ; *Uterine Cervical Neoplasms/mortality ; Adult ; Middle Aged ; Mortality/trends ; Young Adult ; Aged ; Adolescent ; National Health Programs/organization &amp; administration/trends ; },
abstract = {The scope of this study was to describe the secular trend of cervical cancer mortality in Brazil and its various regions from 1980 to 2021. It involved a populational and ecological study, based on data available at the Department of Informatics of the Unified Health System, using codes 180 and C53. Crude rates, age-specific rates, and age-standardized rates were calculated for the Brazilian and world population. The Average Annual Percent Change (AAPC) was obtained by trend analysis using the Joinpoint Regression Program, with a significance level of 0.05 and 95% confidence intervals (95%CI). There were 171,793 deaths from cervical cancer. In Brazil (AAPC -0.3; CI95%-1.0; 0.4), North (AAPC 0.6; 95%CI -0.1; 1.3) and South (AAPC 0.0; 95%CI -0.5; 0.5) the trends were stationary, increasing in the Northeast (AAPC 0.6; 95%CI 0.3; 0.8) and in the Midwest (AAPC -1.3; 95%CI -1.5; -1.1), and decreasing in the Southeast (AAPC -0.9; 95%CI -1.4; -0.5). Regional differences indicate that public policies need to be improved regarding women's access to a health system that offers adequate prevention, screening and treatment through management strategies that include the most vulnerable population.},
}
@article {pmid40133528,
year = {2025},
author = {Pekar, JE and Wang, Y and Wang, JC and Shao, Y and Taki, F and Forgione, LA and Amin, H and Clabby, T and Johnson, K and Torian, LV and Braunstein, SL and Pathela, P and Omoregie, E and Hughes, S and Suchard, MA and Vasylyeva, TI and Lemey, P and Wertheim, JO},
title = {Transmission dynamics of the 2022 mpox epidemic in New York City.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40133528},
issn = {1546-170X},
support = {AI135992//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI153044//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135995//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI135992//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; PS21-2102//U.S. Department of Health &amp; Human Services | Centers for Disease Control and Prevention (CDC)/ ; },
abstract = {The 2022 global mpox epidemic was caused by transmission of MPXV clade IIb, lineage B.1 through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing phylogeographic analysis of MPXV genomes sampled from 757 individuals in NYC between April 2022 and April 2023, and 3,287 MPXV genomes sampled around the world, we identify over 200 introductions of MPXV into NYC with at least 84 leading to onward transmission. These infections primarily occurred among men who have sex with men, transgender women and nonbinary individuals. Through a comparative analysis with HIV in NYC, we find that both MPXV and HIV genomic cluster sizes are best fit by scale-free distributions, and that people in MPXV clusters are more likely to have previously received an HIV diagnosis and be a member of a recently growing HIV transmission cluster. We model MPXV transmission through sexual contact networks and show that highly connected individuals would be disproportionately infected at the start of an epidemic, which would likely result in the exhaustion of the most densely connected parts of the network, and, therefore, explain the rapid expansion and decline of the NYC outbreak. By coupling the genomic epidemiology of MPXV and HIV with epidemic modeling, we demonstrate that the transmission dynamics of MPXV in NYC can be understood by general principles of sexually transmitted pathogens.},
}
@article {pmid40132633,
year = {2025},
author = {Liu, X and Milesi, E and Fontsere, C and Owens, HL and Heinsohn, R and Gilbert, MTP and Crates, R and Nogués-Bravo, D and Morales, HE},
title = {Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2043},
pages = {20242480},
doi = {10.1098/rspb.2024.2480},
pmid = {40132633},
issn = {1471-2954},
support = {//The European Molecular Biology Organization/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //Danish National Research Foundation/ ; /ERC_/European Research Council/International ; 25925//Villum Fonden/ ; },
mesh = {Animals ; *Endangered Species ; *Extinction, Biological ; Conservation of Natural Resources ; Ecosystem ; Genomics ; Biodiversity ; Genetic Variation ; Australia ; Birds/genetics ; Passeriformes/genetics/physiology ; },
abstract = {Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.},
}
@article {pmid40096239,
year = {2025},
author = {Dinnage, R and Kleineberg, M},
title = {Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012887},
pmid = {40096239},
issn = {1553-7358},
mesh = {Animals ; *Birds/anatomy &amp; histology ; *Imaging, Three-Dimensional/methods ; *Artificial Intelligence ; Beak/anatomy &amp; histology ; Computational Biology ; Deep Learning ; },
abstract = {Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phenotypes at unprecedented scales. However, in order to meet the potential of this revolution we need new data analysis tools to deal with the complexity and heterogeneity of large-scale phenotypic data such as 3D shapes. In this study we explore the potential of generative Artificial Intelligence to help organize and extract meaning from complex 3D data. Specifically, we train a deep representational learning method known as DeepSDF on a dataset of 3D scans of the bills of 2,020 bird species. The model is designed to learn a continuous vector representation of 3D shapes, along with a 'decoder' function, that allows the transformation from this vector space to the original 3D morphological space. We find that approach successfully learns coherent representations: particular directions in latent space are associated with discernible morphological meaning (such as elongation, flattening, etc.). More importantly, learned latent vectors have ecological meaning as shown by their ability to predict the trophic niche of the bird each bill belongs to with a high degree of accuracy. Unlike existing 3D morphometric techniques, this method has very little requirements for human supervised tasks such as landmark placement, increasing it accessibility to labs with fewer labour resources. It has fewer strong assumptions than alternative dimension reduction techniques such as PCA. Once trained, 3D morphology predictions can be made from latent vectors very computationally cheaply. The trained model has been made publicly available and can be used by the community, including for finetuning on new data, representing an early step toward developing shared, reusable AI models for analyzing organismal morphology.},
}
@article {pmid40136165,
year = {2025},
author = {Aquino, &#xc9;C and Borowicc, SL and Alves-Souza, SN and Teixeira, RA and Ishitani, LH and Malta, DC and Morais Neto, OL},
title = {Distribution of garbage codes in the Mortality Information System, Brazil, 2000 to 2020.},
journal = {Ciencia &amp; saude coletiva},
volume = {30},
number = {3},
pages = {e09442023},
doi = {10.1590/1413-81232025303.09442023},
pmid = {40136165},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; *Information Systems/statistics &amp; numerical data/standards ; *Cause of Death/trends ; Linear Models ; Mortality/trends ; Time Factors ; },
abstract = {The analysis of the causes of death is essential to understand the main problems that affect the health level of the population of a region or country. The garbage codes (GC) provide little useful information about causes of death. This study aims to identify the proportion of GC among the deaths registered and to analyze their temporal distribution in Brazil from 2000 to 2020. It's an ecological time-series study of the evolution of the proportion of GC in Brazil. Time series analysis was performed using segmented linear regression models (joinpoint). Between 2000 and 2020, 39.9% of deaths that occurred in Brazil were coded with GC. Between 2000 and 2007, there was a continuous and persistent reduction in the proportion of GC (APC -2.1; P < 0.001). Between 2007 and 2015, there continued to be a reduction, albeit to a lesser extent (APC = -0.7; P = 0.013). Between 2015 and 2018, there was no significant trend of the proportion of GC (APC = -2.3; P = 0.172), which persisted from 2018 (APC 3.2; P < 0.079). Although a reduction in the proportion of GC in Brazil was observed until 2018, this trend did not persist after that year. Reducing the proportion of GC allows managers to plan health policies more adequately for the population.},
}
@article {pmid40073274,
year = {2025},
author = {Aucello, R and Pernice, S and Tortarolo, D and Calogero, RA and Herrera-Rincon, C and Ronchi, G and Geuna, S and Cordero, F and Lió, P and Beccuti, M},
title = {UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
pmid = {40073274},
issn = {1367-4811},
support = {//Ministero dell'Univerisita' e della Ricerca/ ; },
mesh = {*Models, Biological ; Humans ; Software ; Escherichia coli/metabolism ; Systems Biology/methods ; Computational Biology/methods ; Computer Simulation ; },
abstract = {MOTIVATION: Computational models are crucial for addressing critical questions about systems evolution and deciphering system connections. The pivotal feature of making this concept recognizable from the biological and clinical community is the possibility of quickly inspecting the whole system, bearing in mind the different granularity levels of its components. This holistic view of system behaviour expands the evolution study by identifying the heterogeneous behaviours applicable, e.g. to the cancer evolution study.<br><br>RESULTS: To address this aspect, we propose a new modelling paradigm, UnifiedGreatMod, which allows modellers to integrate fine-grained and coarse-grained biological information into a unique model. It enables functional studies by combining the analysis of the system's multi-level stable states with its fluctuating conditions. This approach helps to investigate the functional relationships and dependencies among biological entities. This is achieved, thanks to the hybridization of two analysis approaches that capture a system's different granularity levels. The proposed paradigm was then implemented into the open-source, general modelling framework GreatMod, in which a graphical meta-formalism is exploited to simplify the model creation phase and R languages to define user-defined analysis workflows. The proposal's effectiveness was demonstrated by mechanistically simulating the metabolic output of Escherichia coli under environmental nutrient perturbations and integrating a gene expression dataset. Additionally, the UnifiedGreatMod was used to examine the responses of luminal epithelial cells to Clostridium difficile infection.<br><br>GreatMod https://qbioturin.github.io/epimod/, epimod_FBAfunctions https://github.com/qBioTurin/epimod_FBAfunctions, first case study E. coli &#xa0;https://github.com/qBioTurin/Ec_coli_modelling, second case study C. difficile &#xa0;https://github.com/qBioTurin/EpiCell_CDifficile.},
}
@article {pmid40125538,
year = {2025},
author = {Broad, GR and Holt, S and Sivess, L and Boyes, D and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Scorched Wing moth, Plagodis dolabraria (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {111},
doi = {10.12688/wellcomeopenres.23761.1},
pmid = {40125538},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Plagodis dolabraria (Scorched Wing; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 939.07 megabases. Most of the assembly (99.59%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.97 kilobases in length.},
}
@article {pmid40121238,
year = {2025},
author = {Kelliher, JM and Rodriguez, FE and Johnson, LYD and Roux, S and Smith, M and Clum, A and Lynch, W and Bias, CH and Finks, SS and Keenum, I and Kiledal, EA and Lin, HA and Longley, R and McDonald, R and Pitot, TM and Rodríguez-Ramos, J and Shen, J and Sprockett, DD and Swift, J and Yadav, A and Eloe-Fadrosh, EA},
title = {Quantifying the impact of workshops promoting microbiome data standards and data stewardship.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9887},
pmid = {40121238},
issn = {2045-2322},
support = {The work conducted by the National Microbiome Data Collaborative (https://ror.org/05cwx3318) is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).//U.S. Department of Energy/ ; },
mesh = {*Microbiota ; Humans ; Surveys and Questionnaires ; Research Personnel ; },
abstract = {The field of microbiome research continues to grow at a rapid pace, with multi-omics approaches becoming widely used to interrogate diverse microbiome samples. However, due to lagging awareness and implementation of standards and data stewardship, many datasets are produced that are not comparable, reproducible, or reusable. In 2021, the National Microbiome Data Collaborative launched its Ambassador Program, which utilizes a community-learning model to annually train a cohort of early-career researchers in microbiome data stewardship best practices. These Ambassadors then host workshops and other events to communicate these themes to their respective microbiome research communities. To quantify the impact of this learning model for promoting awareness of and experience with microbiome data, we conducted a survey of workshop participants from events hosted by the 2023 Ambassador cohort. The 2023 cohort of 13 National Microbiome Data Collaborative Ambassadors collectively hosted 21 events, reaching over 550 researchers. The Ambassadors distributed an anonymous post-workshop survey to their event participants to quantify the effectiveness of the training materials, the workshop format, and the thematic content. From the 21 events, survey results were successfully collected for 15 of those events from a total of 122 researchers. Overall, 122 participants working with a range of microbiome types and from a variety of institutions responded to the survey and reported overwhelmingly positive experiences with the workshop content and materials, with 98% of respondents reporting that they gained knowledge from the event. Participants across the events also reported an increase in their post-workshop understanding of metadata standards, principles for microbiome data management and reporting, and the importance of standardization in microbiome data processing. Participants also expressed a willingness to apply what they learned about microbiome data stewardship to their own research. The results of this study demonstrate the effectiveness of hands-on workshops and community-learning for communicating data stewardship best practices to microbiome researchers. The lessons learned and details about the implementation of this cohort-based learning model contained herein are intended to assist other groups in their efforts to create or improve similar learning strategies.},
}
@article {pmid40121181,
year = {2025},
author = {Eaton, WD and McGee, KM and Glahn, A and Lemenze, A and Soteropoulos, P},
title = {Use of a logging road in a Costa Rican forest changes the composition and stability of soil microbial decomposer communities, and the conversion of organic carbon into biomass.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf075},
pmid = {40121181},
issn = {1365-2672},
abstract = {AIMS: The effects of a tropical forest logging road on soil C and N, and the compositions of Actinobacteria, Acidobacteria, and wood rot/lignin-degrading fungal (WRT/LD) decomposer communities were evaluated.<br><br>METHODS AND RESULTS: Soils from a healthy Costa Rican old growth forest before Hurricane Otto and from an adjacent, recently formed logging road built after Hurricane Otto were collected over 4 years and assessed for C and N metrics, and characteristics of the 3 decomposer communities determined by Illumina amplicon sequencing methods. The Logging Road negatively impacted the soil total organic C, respiration, biomass C, qCO2, and total N, while the Actinobacterial and Acidobacterial communities changed from stable compositions of copiotrophic taxa in the rich forest soil to stable compositions of oligotrophic taxa in the poor logging road soil, and the wood rot/lignin degrading (WRT/LD) community changed from stable compositions of copiotrophic taxa in the forest soils to an unstable community of oligotrophic taxa with almost no overlap in genera between Logging Road soils.<br><br>CONCLUSIONS: The logging road negatively influenced 3 decomposer communities and associated C and N metrics, with the two bacterial communities taxonomically stabilizing, but the fungal community taxonomically diverging into an unstable composition over time. Monitoring efforts are on-going to provide local forest land managers with potential indicators of soil ecosystem damage and recovery.},
}
@article {pmid40121109,
year = {2025},
author = {Hanly, J and Anon, and Perret, J and Khan, A},
title = {Disability in ecology and evolution.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2025.02.005},
pmid = {40121109},
issn = {1872-8383},
}
@article {pmid40120582,
year = {2025},
author = {Pinkert, S and Reuber, V and Krug, LM and Heidrich, L and Rehling, F and Brandl, R and Farwig, N},
title = {Burrowing facilitated the survival of mammals in harsh and fluctuating climates.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.02.064},
pmid = {40120582},
issn = {1879-0445},
abstract = {Species' ability to cope with climatic instability varies greatly, influenced by factors such as dispersal, physiological adaptations, and phylogenetic conservatism. Here, we investigate how burrowing behavior, a key component of species' endurance strategies and ecosystem functioning, shaped the contemporary patterns of species richness and range size as well as the diversification of mammalian lineages. Analyzing 4,407 terrestrial mammal species, excluding bats, combined with novel trait data on 3,096 species, we reveal contrasting responses to climatic factors between burrowing and non-burrowing species. Burrowing lineages are disproportionately species-rich at lower temperatures and productivity. Both range size and species richness steeply increase with climate seasonality in burrowing species as opposed to non-burrowing species. The proportion of burrowing species increases with latitude, with regions above 20°, especially those exhibiting greater Pleistocene temperature changes, being almost exclusively composed of burrowing species. Trait conservatism, higher net diversification rates, and Eocene peak diversification provide the evolutionary context for these contemporary patterns, underscoring the role of burrowing for mammalian radiations into temperate climates. Moreover, the lower extinction rate of burrowing species and peak diversification at the Cretaceous-Paleogene (K-Pg) boundary support the longstanding hypothesis that burrowing behavior promoted survival during the "impact winter" that marks the replacement of non-avian dinosaurs by mammals. Our study highlights the potential of readily available trait information for understanding the ecological and evolutionary processes that shape species distributions through space and time. The careful integration of divergent environmental constraints bears vast improvements for forecasts of species' responses to climatic changes and global models of biodiversity patterns.},
}
@article {pmid40049043,
year = {2025},
author = {Huang, JN and Gao, CC and Ren, HY and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ},
title = {Multi-omics association pattern between gut microbiota and host metabolism of a filter-feeding fish in situ exposed to microplastics.},
journal = {Environment international},
volume = {197},
number = {},
pages = {109360},
doi = {10.1016/j.envint.2025.109360},
pmid = {40049043},
issn = {1873-6750},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Microplastics ; *Water Pollutants, Chemical/metabolism/toxicity ; *Carps/microbiology ; Liver/metabolism ; Zebrafish ; Multiomics ; },
abstract = {Microplastics (MPs) are widespread in water environments and can affect gut microbiota and host metabolism of fish, but whether changes in host metabolism under MPs are mediated by gut microbiota remains unclear. Here, silver carp, a filter-feeding fish with important ecological functions, was in-situ exposure to environmentally relevant MPs. Multi-omics analysis and fecal microbiota transplantation were used to reveal the metabolic responses of carp along gut-liver-muscle axis. After three months of in situ exposure to MPs, community structure of gut microbiota of carp was reshaped, and five dominate phyla were significantly changed, including increased Cyanobacteria, Chloroflexi and Planctomycetota but decreased Firmicutes and Fusobacteriota. Weighted gene co-expression network analysis was further performed between these phyla and liver transcription spectrum, showing that the hub gene module contained up-regulated hppD, maiA and plg and activated ubiquinone and other terpenoid-quinone biosynthesis and phenylalanine metabolism. By fecal microbiota transplantation, the key gene module associated with core microbiota phyla of carp was verified in germ-free zebrafish. Interestingly, up-regulated hppD, maiA and plg and enriched phenylalanine metabolism were also observed in this module. Subsequently, metabolome performed in carp liver also shared activated phenylalanine metabolism, including increased trans-cinnamic acid and L-tyrosine. Furthermore, high-associated mapping showed that the differentially expressed metabolites (gamma-aminobutyric acid, ornithine and L-serine) related to amino acid metabolism in carp muscle were significantly accompanied with increased L-tyrosine in its liver. Overall, MPs exposure could change gut microbiome of silver carp and alter host metabolism especially amino acid metabolism along the gut-liver-muscle axis.},
}
@article {pmid39833389,
year = {2025},
author = {Schroeder, MW and Frumkin, MR and Mace, RA},
title = {Proof-of-concept for integrating multimodal digital health assessments into lifestyle interventions for older adults with dementia risk factors.},
journal = {Journal of behavioral medicine},
volume = {48},
number = {2},
pages = {373-384},
pmid = {39833389},
issn = {1573-3521},
support = {1 K23 AG075257-01/AG/NIA NIH HHS/United States ; 1 K23 AG075257-01/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Aged ; Female ; Male ; *Actigraphy/instrumentation ; *Dementia/psychology/therapy ; *Ecological Momentary Assessment ; *Mindfulness ; Pilot Projects ; Life Style ; Middle Aged ; Risk Factors ; Proof of Concept Study ; Aged, 80 and over ; Sleep ; Digital Health ; },
abstract = {Multimodal digital health assessments overcome the limitations of patient-reported outcomes by allowing for continuous and passive monitoring but remain underutilized in older adult lifestyle interventions for brain health. Therefore, we aim to (1) report ecological momentary assessment (EMA) and ActiGraph adherence among older adults during a lifestyle intervention; and (2) use dynamic data collected via EMA and ActiGraph to examine person-specific patterns of mindfulness, steps, and sleep throughout the intervention. We analyzed EMA and ActiGraph data from a pilot study of the 8-week My Healthy Brain program (N = 10) lifestyle group for older adults (60+) with subjective cognitive decline. EMA adherence metrics included proportion of EMA completed and the proportion of days with at least 10 mindfulness minutes. ActiGraph GT9X adherence metrics included the number of valid wear days (≥ 7 h) and the number of days participants achieved their step goal. We used linear mixed-effects models to examine person-specific patterns of step count, sleep efficiency, and mindfulness practice. On average, participants completed 39 of the 49 possible EMAs (80%) during the program. ActiGraph adherence was slightly higher than EMA (M = 61.40 days, 87.71%). Participants achieved the daily mindfulness goal (10 min/day) and step goal on 46.32% and 55.10% of days, respectively. Dynamic data revealed that on average, participant step counts increased by approximately 16.5 steps per day (b = 16.495, p = 0.002). However, some participants exhibited no changes while improvements made by other participants returned to baseline levels of activity. There was substantial heterogeneity in trajectories of mindfulness practice and sleep efficiency. EMA and ActiGraph are feasible for older adults enrolled in dementia risk reduction lifestyle interventions. Future studies are needed to better understand how mechanisms of lifestyle behaviors captured by EMA and ActiGraph are related to cognitive outcomes in older adults.},
}
@article {pmid38582819,
year = {2025},
author = {Li, M and Wu, L and Shi, Y and Wu, L and Afzal, F and Jia, Y and Huang, Y and Hu, B and Chen, J and Huang, J},
title = {Bioinformatics and Functional Analysis of OsASMT1 Gene in Response to Abiotic Stress.},
journal = {Biochemical genetics},
volume = {63},
number = {2},
pages = {1527-1540},
pmid = {38582819},
issn = {1573-4927},
support = {2023NSFSC1270//The Sichuan Natural Science Foundation Project/ ; SKL-KF202316//The Open Project Program of State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/ ; },
mesh = {*Stress, Physiological ; *Computational Biology/methods ; *Oryza/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Gene Expression Regulation, Plant ; Sodium Chloride/pharmacology ; Salt Stress ; },
abstract = {The study aimed to elucidate the functional characteristics of OsASMT1 gene under copper (Cu) or sodium chloride (NaCl) stress. Bioinformatics scrutiny unveiled that OsASMT1 is situated on chromosome 9. Its protein architecture, comprising dimerization and methyltransferase domains, showed significant similarities to OsASMT2 and OsASMT3. High expression in roots and panicles, along with abiotic stress putative cis-regulatory elements in the promoter, indicated potential stress responsiveness. Real-time quantitative PCR confirmed OsASMT1 induction under Cu and NaCl stress in rice. Surprisingly, yeast expressing OsASMT1 did not exhibit enhanced resistance to abiotic stresses. The results of subcellular localization analysis indicated that OsASMT1 plays a role in the cytoplasm. While OsASMT1 responded to Cu and NaCl stress in rice, its heterologous expression in yeast failed to confer abiotic stress resistance, highlighting the need for further investigation of its functional implications.},
}
@article {pmid40115327,
year = {2025},
author = {Hesson, JC and Haba, Y and McBride, CS and Sheerin, E and Mathers, TC and Paulini, M and Pointon, DB and Torrance, JW and Sadasivan Baby, C and Wood, JMD and , and , and McCarthy, SA and Lawniczak, MKN and Makunin, A},
title = {A chromosomal reference genome sequence for the northern house mosquito, Culex pipiens form pipiens, Linnaeus, 1758.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {107},
pmid = {40115327},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Culex pipiens sensu stricto (the northern house mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Sweden. The genome sequence is 533 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.},
}
@article {pmid40108281,
year = {2025},
author = {Dong, J and Dai, W and Xu, J and Zhang, H and Li, Y and Xie, F},
title = {Impact and elastic modulus of coal mining on terrestrial ecosystems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9454},
pmid = {40108281},
issn = {2045-2322},
support = {CSC202306420029//China Scholarship Council/ ; Lumeidike (2022) No.14//Key Research Projects of Shandong Bureau of Coal Geology/ ; },
abstract = {The energy consumption structure is gradually evolving into a "diversified energy structure" against the backdrop of the global implementation of energy-saving and low-carbon policies. Coal, as the main energy source in China, is difficult to change in the short term, given the characteristics of China's energy and resource endowments, as well as the actual social and economic development at the present stage. Nevertheless, coal mining inevitably leads to a range of ecological issues. Identifying the impact of coal mining on terrestrial ecosystems and adopting resilient recovery measures are crucial prerequisites for advancing green coal mining efforts and attaining carbon peaking and carbon neutrality goals. Using China's open-pit coal mining as a case study: (1) the research examines the fundamental attributes and evolving patterns of spatial distribution among these mines within the country. Furthermore, it delineates the life cycle stages and distinctive features of the five principal open-pit coal mines. The life cycle of a coal mining area is divided into four distinct development phases: the initial phase, the accelerated phase, the stable phase, and the declining phase. The spatial relationship between the life cycle stages of coal mining and ecosystem succession is elucidated by examining the evolutionary types of ecosystems within coal mine area. In the accelerated and stable development phase, the adverse effects of coal mining on the ecosystem are in a long-term increasing trend, causing the key elements of the ecosystem to gradually surpass their threshold values. The ecosystem is out of balance, severely damaged, and gradually undergoing degradation or extreme degradation. The types of ecological succession in coal mining areas can be categorized as follows: terrestrial succession leading to a new terrestrial ecosystem, terrestrial to aquatic ecosystem transitions, or the development of an amphibious symbiotic ecosystem. (2) The research quantitatively assessed the impact of surface coal mining on terrestrial ecosystems by utilizing remote sensing data in conjunction with coal production information. In 2022, the affected areas of the five major open-pit coal mines due to coal mining activities amounted to approximately 0.02% of China's total land area. Meanwhile, the nationwide affected areas of all open-pit coal mines combined reached to approximately 0.13% of China's land area. Open-pit coal mining activities have a significant impact on the surface. (3) By incorporating the ecological resilience theory, we establish a model for the ecosystem's elastic modulus in coal mining areas, taking into account landscape diversity, vegetation coverage, land type, and climate factors, which are based on the concepts of elastic strength and elastic limit. A conceptual model for recognizing ecological thresholds in coal mining areas is developed by incorporating the comprehensive integrity index of the ecosystem. The comprehensive integrity of the ecosystem within a coal mining area undergoes significant alterations as it crosses three distinct ecological thresholds: the elastic point, the yield point, and the mutational point. There should be a corresponding constant (or constant interval) at the three ecological thresholds of ecosystem resilience, the elastic point, the yield point, and the mutational point, which is closely related to the scale of mining operations, mining technology, and the service life in coal mining areas. The established models for identifying ecological thresholds and the resilience modulus degree serve as both theoretical references and practical bases for managing the progress and trends of ecosystem changes during coal resource extraction, making ecological restoration in coal mine areas more target-oriented and specific.},
}
@article {pmid40108248,
year = {2025},
author = {Mammides, C and Ieronymidou, C and Papadopoulos, H},
title = {An ecoacoustic dataset collected on the island of Cyprus in the Mediterranean Basin biodiversity hotspot.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {461},
pmid = {40108248},
issn = {2052-4463},
support = {101090273//European Commission (EC)/ ; },
mesh = {Cyprus ; *Biodiversity ; Animals ; *Acoustics ; Vocalization, Animal ; Mediterranean Region ; Islands ; },
abstract = {There is growing interest in using novel technologies for large-scale biodiversity monitoring. Passive acoustic monitoring (PAM) represents a promising approach for surveying vocalizing animals. However, further development of PAM methods is needed to improve their accuracy. The availability of extensive ecoacoustic datasets from biodiverse areas can facilitate this development. In this study, we present a large ecoacoustic dataset (1.58 TB) collected at sixty-one study sites on the island of Cyprus between March and May 2023. The dataset comprises >313,000 audio files, representing over 5,200 hours of recordings. It can be used for a range of applications, such as developing and refining species identification algorithms, acoustic indices, and protocols for processing acoustic data to exclude non-focal sounds, e.g., those produced by human activities. It can also be used to explore fundamental ecological questions. To facilitate its use, the complete dataset has been made available on the Hugging Face repository and the ARBIMON platform, operated by Rainforest Connection[TM], which offers a range of free tools for ecoacoustic analyses.},
}
@article {pmid40067093,
year = {2025},
author = {Zhang, G and Ristola, P and Su, H and Kumar, B and Zhang, B and Hu, Y and Elliot, MG and Drobot, V and Zhu, J and Staal, J and Larralde, M and Wang, S and Yi, Y and Yu, H},
title = {BioArchLinux: community-driven fresh reproducible software repository for life sciences.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {3},
pages = {},
doi = {10.1093/bioinformatics/btaf106},
pmid = {40067093},
issn = {1367-4811},
mesh = {*Software ; *Computational Biology/methods ; *Biological Science Disciplines/methods ; Programming Languages ; Reproducibility of Results ; },
abstract = {MOTIVATION: The BioArchLinux project was initiated to address challenges in bioinformatics software reproducibility and freshness. Relying on Arch Linux's user-driven ecosystem, we aim to create a comprehensive and continuously updated repository for life sciences research.<br><br>RESULTS: BioArchLinux provides a PKGBUILD-based system for seamless software packaging and maintenance, enabling users to access the latest bioinformatics tools across multiple programming languages. The repository includes Docker images, Windows Subsystem for Linux (WSL) support, and Junest for nonroot environments, enhancing accessibility across platforms. Although being developed and maintained by a small core team, BioArchLinux is a fast-growing bioinformatics repository that offers a participatory and community-driven environment.<br><br>The repository, documentation, and tools are freely available at https://bioarchlinux.org and https://github.com/BioArchLinux. Users and developers are encouraged to contribute and expand this open-source initiative.},
}
@article {pmid40102624,
year = {2025},
author = {Rank, M and Kather, A and Wilke, D and Steib-Bauert, M and Kern, WV and Röder, I and de With, K},
title = {Limitations of estimating antibiotic resistance using German hospital consumption data - a comprehensive computational analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9244},
pmid = {40102624},
issn = {2045-2322},
mesh = {Germany/epidemiology ; Humans ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Hospitals ; Drug Resistance, Microbial ; Drug Resistance, Bacterial ; Neural Networks, Computer ; },
abstract = {For almost a century, antibiotics have played an important role in the treatment of infectious diseases. However, the efficacy of these very drugs is now threatened by the development of resistances, which pose major challenges to medical professionals and decision-makers. Thereby, the consumption of antibiotics in hospitals is an important driver that can be targeted directly. To illuminate the relation between consumption and resistance depicts a very important step in this procedure. With the help of comprehensive ecological and clinical data, we applied a variety of different computational approaches ranging from classical linear regression to artificial neural networks to analyze antibiotic resistance in Germany. These mathematical and statistical models demonstrate that the amount and particularly the structure of currently available data sets lead to contradictory results and do, therefore, not allow for profound conclusions. More effort and attention on both data collection and distribution is necessary to overcome this problem. In particular, our results suggest that at least monthly or quarterly antibiotic use and resistance data at the department and ward level for each hospital (including application route and type of specimen) are needed to reliably determine the extent to which antibiotic consumption influences resistance development.},
}
@article {pmid39066964,
year = {2025},
author = {Árvay, J and Hauptvogl, M and Demková, L and Jančo, I and Jakabová, S and Mleczek, M},
title = {GIS-based Visualization of Elemental Distribution in Neoboletus Luridiformis Fruiting Body.},
journal = {Biological trace element research},
volume = {203},
number = {4},
pages = {2271-2283},
pmid = {39066964},
issn = {1559-0720},
support = {1/0602/22//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; },
mesh = {*Fruiting Bodies, Fungal/chemistry/metabolism ; Trace Elements/analysis ; Geographic Information Systems ; Agaricales/chemistry/metabolism ; },
abstract = {The fruiting body of Neoboletus luridiformis (Scarletina bolete) mushroom was used to determine the level of bioconcentration and subsequent distribution of seventeen elements (Ag, Al, Ba, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, Pb, Se, Sr, and Zn). A two-centimeter-thick vertical section of the entire fruit body was divided into 101 partial sub-samples where the contents of the studied elements were determined using ICP OES. The actual distribution of the elements in the fruiting body profile was visualized using a GIS interpolation method resulting in distribution maps. The study provides valuable insights into the distribution patterns of 17 elements within the fruiting body of N. luridiformis. Based on the visualization of the elemental content, the determined elements can be divided into three categories. Elements accumulated primarily (i) in the cap (Al, Ag, Ca, Cd, Cu, Fe, K, Mg, Ni, and Zn), (ii) in the stipe (Ba, Mn, Na, Pb, and Se), and (iii) elements with non-specific distribution (Cr and Sr). Since such detailed information supported by graphical visualization has not been published to date, the information in this study will help to better understand the accumulation and distribution of elements within the fruiting bodies of wild as well as cultivated mushroom species.},
}
@article {pmid40099017,
year = {2025},
author = {Sivell, O and Sivell, D and Mitchell, R and Webb, J and , and , and , and , and , and , and , },
title = {The genome sequence of the Small Red Damselfly, Ceriagrion tenellum (de Villers, 1789).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {79},
pmid = {40099017},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Ceriagrion tenellum (Small Red Damselfly; Arthropoda; Insecta; Odonata; Coenagrionidae). The genome sequence has a total length of 2,077.00 megabases. Most of the assembly (99.28%) is scaffolded into 14 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.21 kilobases in length.},
}
@article {pmid39938845,
year = {2025},
author = {Rakkannan, G and Mohanty, AK and Das, II and Nayak, S and Sahoo, L and Kumar, R and Rasal, A and Rather, MA and Ahmad, I and Sundaray, JK},
title = {Triflumezopyrim induced oxidative stress, DNA damage and apoptosis on Labeo rohita: Insights from Bioinformatics, Histopathological and Molecular approaches.},
journal = {International journal of biological macromolecules},
volume = {304},
number = {Pt 2},
pages = {140911},
doi = {10.1016/j.ijbiomac.2025.140911},
pmid = {39938845},
issn = {1879-0003},
mesh = {Animals ; *Oxidative Stress/drug effects ; *DNA Damage/drug effects ; *Apoptosis/drug effects ; Computational Biology/methods ; Carps/metabolism/genetics ; Water Pollutants, Chemical/toxicity ; Molecular Docking Simulation ; Cyprinidae ; 8-Hydroxy-2'-Deoxyguanosine/metabolism ; Liver/drug effects/pathology/metabolism ; },
abstract = {Triflumezopyrim is a novel mesoionic pesticide used in Asian rice fields to control brown plant hopper, which can reach aquatic environments through drift during application or surface runoff. Thus, this study aimed to investigate the effect of chronic exposure of sub-lethal concentrations of triflumezopyrim (2.468 ppm, 1.480 ppm, and 0.740 ppm) on freshwater carp, Labeo rohita.This study encompassed a multi-pronged approach, including molecular docking studies to elucidate the interactions between triflumezopyrim and selected proteins, an assessment of 8-OHdG (8-hydroxy-2-deoxyguanosine) activity to gauge DNA damage, histopathological examinations to identify cellular alterations, and expression of genes involved in oxidative stress, DNA repair, and apoptosis in L. rohita. We observed dose-dependent responses in 8-OHdG activity and the expression of select genes, with higher concentrations of triflumezopyrim yielding more pronounced transcriptional alterations. Notably, histopathological examinations of liver and brain tissues vividly portrayed the impact of triflumezopyrim on L. rohita. These findings contribute to the assessment of biological toxicity and the environmental footprint left by chemical pollutants such as triflumezopyrim. The study emphasizes the crucial role of monitoring histopathological alterations, 8-OHdG activity and gene expression changes as potential biomarkers for assessing exposures to triflumezopyrim. This research provides valuable insights into the ecological implications of triflumezopyrim in aquatic ecosystems.},
}
@article {pmid24192328,
year = {2013},
author = {Weston, ED and Whitfield, DP and Travis, JM and Lambin, X},
title = {When do young birds disperse? Tests from studies of golden eagles in Scotland.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {42},
pmid = {24192328},
issn = {1472-6785},
mesh = {*Animal Distribution ; Animals ; Geographic Information Systems ; Raptors/*physiology ; Scotland ; },
abstract = {BACKGROUND: Dispersal comprises three broad stages - departure from the natal or breeding locations, subsequent travel, and settlement. These stages are difficult to measure, and vary considerably between sexes, age classes, individuals and geographically. We used tracking data from 24 golden eagles, fitted with long-lived GPS satellite transmitters as nestlings, which we followed during their first year. We estimated the timing of emigration from natal sites using ten previously published methods. We propose and evaluate two new methods. The first of these uses published ranging distances of parents as a measure of the natal home range, with the requirement that juveniles must exceed it for a minimum of 10 days (a literature-based measure of the maximum time that a juvenile can survive without food from its parents). The second method uses the biggest difference in the proportion of locations inside and outside of the natal home range smoothed over a 30 day period to assign the point of emigration. We used the latter as the standard against which we compared the ten published methods.<br><br>RESULTS: The start of golden eagle dispersal occurred from 39 until 250 days after fledging (based on method 12). Previously published methods provided very different estimates of the point of emigration with a general tendency for most to apparently assign it prematurely. By contrast the two methods we proposed provided very similar estimates for the point of emigration that under visual examination appeared to fit the definition of emigration much better.<br><br>CONCLUSIONS: We have used simple methods to decide when an individual has dispersed - they are rigorous and repeatable. Despite one method requiring much more information, both methods provided robust estimates for when individuals emigrated at the start of natal dispersal. Considerable individual variation in recorded behaviour appears to account for the difficulty capturing the point of emigration and these results demonstrate the potential pitfalls associated with species exhibiting complex dispersal behaviour. We anticipate that coupled with the rapidly increasing availability of tracking data, our new methods will, for at least some species, provide a far simpler and more biologically representative approach to determine the timing of emigration.},
}
@article {pmid23587026,
year = {2013},
author = {Hardisty, A and Roberts, D and , and Addink, W and Aelterman, B and Agosti, D and Amaral-Zettler, L and Ariño, AH and Arvanitidis, C and Backeljau, T and Bailly, N and Belbin, L and Berendsohn, W and Bertrand, N and Caithness, N and Campbell, D and Cochrane, G and Conruyt, N and Culham, A and Damgaard, C and Davies, N and Fady, B and Faulwetter, S and Feest, A and Field, D and Garnier, E and Geser, G and Gilbert, J and Grosche, and Grosser, D and Hardisty, A and Herbinet, B and Hobern, D and Jones, A and de Jong, Y and King, D and Knapp, S and Koivula, H and Los, W and Meyer, C and Morris, RA and Morrison, N and Morse, D and Obst, M and Pafilis, E and Page, LM and Page, R and Pape, T and Parr, C and Paton, A and Patterson, D and Paymal, E and Penev, L and Pollet, M and Pyle, R and von Raab-Straube, E and Robert, V and Roberts, D and Robertson, T and Rovellotti, O and Saarenmaa, H and Schalk, P and Schaminee, J and Schofield, P and Sier, A and Sierra, S and Smith, V and van Spronsen, E and Thornton-Wood, S and van Tienderen, P and van Tol, J and Tuama, &#xc9;&#xd3; and Uetz, P and Vaas, L and Vignes Lebbe, R and Vision, T and Vu, D and De Wever, A and White, R and Willis, K and Young, F},
title = {A decadal view of biodiversity informatics: challenges and priorities.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {16},
pmid = {23587026},
issn = {1472-6785},
mesh = {Animals ; *Biodiversity ; Computational Biology/*instrumentation/*methods ; Ecosystem ; Humans ; Information Dissemination ; },
abstract = {Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.},
}
@article {pmid23497177,
year = {2013},
author = {Tonk, L and Bongaerts, P and Sampayo, EM and Hoegh-Guldberg, O},
title = {SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef.},
journal = {BMC ecology},
volume = {13},
number = {},
pages = {7},
pmid = {23497177},
issn = {1472-6785},
mesh = {Animals ; Anthozoa/*microbiology ; Australia ; *Coral Reefs ; DNA, Ribosomal Spacer/genetics ; *Databases, Genetic ; Dinoflagellida/classification/*genetics ; Genetic Markers ; Internet ; Sequence Analysis, DNA ; Symbiosis ; User-Computer Interface ; },
abstract = {BACKGROUND: The algal endosymbionts (genus Symbiodinium) associated with scleractinian corals (and other reef invertebrates) have received a lot of research attention in the past decade, particularly as certain host-symbiont associations appear more affected by increasing seawater temperatures than others. With the rapid accumulation of information on the diversity of Symbiodinium, it is becoming increasingly difficult to compare newly acquired Symbiodinium data with existing data to detect patterns of host-symbiont specificity on broader spatial scales. The lack of a general consensus on the classification of Symbiodinium species coupled with the variety of different markers used to identify the genus Symbiodinium (ITS1, ITS2, LSU D1/D2, chloroplast 23S rDNA and psbA minicircle) further complicate direct comparison.<br><br>DESCRIPTION: The SymbioGBR database compiles all currently available Symbiodinium sequences and associated host information of data collected from the Great Barrier Reef into a single relational database that is accessible via a user-friendly, searchable web-based application (http://www.SymbioGBR.org). SymbioGBR allows users to query Symbiodinium types or sequences sourced from various genetic markers (e.g. ITS1, ITS2, LSU D1/D2 and chloroplast 23S) and invertebrate host species to explore their reported associations. In addition, as the database includes sequence information of multiple genetic markers, it allows cross-referencing between conventional (e.g. ITS2 region) and novel markers that exhibit low intragenomic variability (e.g. psbA region). Finally, the database is based on the collection details of individual specimens. Such host-symbiont associations can be assessed quantitatively and viewed in relation to their environmental and geographic context.<br><br>CONCLUSIONS: The SymbioGBR database provides a comprehensive overview of Symbiodinium diversity and host-associations on the Great Barrier Reef. It provides a quick, user-friendly means to compare newly acquired data on Symbiodinium (e.g. raw sequences or characterized Symbiodinium types) with previous data on the diversity of invertebrate host-symbiont associations on the GBR. The inclusion of psbAncr sequence information allows for validation of widely used ITS1/ITS2 markers and their ability to accurately identify relevant sequences. Most importantly, centralization of sequence information from multiple genetic markers will aid the classification of Symbiodinium species diversity and allow researchers to easily compare patterns of host-Symbiodinium associations.},
}
@article {pmid23173946,
year = {2012},
author = {Renaud, AK and Savage, J and Adamowicz, SJ},
title = {DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits.},
journal = {BMC ecology},
volume = {12},
number = {},
pages = {24},
pmid = {23173946},
issn = {1472-6785},
mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; *Databases, Genetic ; Female ; Genes, Insect ; Male ; Muscidae/*classification/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate "species" diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues.<br><br>RESULTS: Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected.<br><br>CONCLUSIONS: Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.},
}
@article {pmid23095476,
year = {2012},
author = {Sherwood, AR and Wang, N and Carlile, AL and Neumann, JM and Wolfgruber, TK and Presting, GG},
title = {The Hawaiian Freshwater Algal Database (HfwADB): a laboratory LIMS and online biodiversity resource.},
journal = {BMC ecology},
volume = {12},
number = {},
pages = {22},
pmid = {23095476},
issn = {1472-6785},
mesh = {*Biodiversity ; *Chlorophyta ; *Clinical Laboratory Information Systems ; *Cyanobacteria ; *Databases, Factual ; *Diatoms ; Fresh Water ; Hawaii ; Internet ; *Rhodophyta ; User-Computer Interface ; },
abstract = {BACKGROUND: Biodiversity databases serve the important role of highlighting species-level diversity from defined geographical regions. Databases that are specially designed to accommodate the types of data gathered during regional surveys are valuable in allowing full data access and display to researchers not directly involved with the project, while serving as a Laboratory Information Management System (LIMS). The Hawaiian Freshwater Algal Database, or HfwADB, was modified from the Hawaiian Algal Database to showcase non-marine algal specimens collected from the Hawaiian Archipelago by accommodating the additional level of organization required for samples including multiple species.<br><br>DESCRIPTION: The Hawaiian Freshwater Algal Database is a comprehensive and searchable database containing photographs and micrographs of samples and collection sites, geo-referenced collecting information, taxonomic data and standardized DNA sequence data. All data for individual samples are linked through unique 10-digit accession numbers ("Isolate Accession"), the first five of which correspond to the collection site ("Environmental Accession"). Users can search online for sample information by accession number, various levels of taxonomy, habitat or collection site. HfwADB is hosted at the University of Hawaii, and was made publicly accessible in October 2011. At the present time the database houses data for over 2,825 samples of non-marine algae from 1,786 collection sites from the Hawaiian Archipelago. These samples include cyanobacteria, red and green algae and diatoms, as well as lesser representation from some other algal lineages.<br><br>CONCLUSIONS: HfwADB is a digital repository that acts as a Laboratory Information Management System for Hawaiian non-marine algal data. Users can interact with the repository through the web to view relevant habitat data (including geo-referenced collection locations) and download images of collection sites, specimen photographs and micrographs, and DNA sequences. It is publicly available at http://algae.manoa.hawaii.edu/hfwadb/.},
}
@article {pmid21929792,
year = {2011},
author = {Gonzalez, SC and Soto-Centeno, JA and Reed, DL},
title = {Population distribution models: species distributions are better modeled using biologically relevant data partitions.},
journal = {BMC ecology},
volume = {11},
number = {},
pages = {20},
pmid = {21929792},
issn = {1472-6785},
mesh = {Animals ; Geographic Information Systems ; Mice/genetics/*physiology ; *Models, Biological ; *Population Dynamics ; ROC Curve ; Southeastern United States ; Statistics as Topic ; },
abstract = {BACKGROUND: Predicting the geographic distribution of widespread species through modeling is problematic for several reasons including high rates of omission errors. One potential source of error for modeling widespread species is that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We contrast a presence-only maximum entropy model for the widely distributed oldfield mouse (Peromyscus polionotus) that includes all available presence locations for this species, with two composite maximum entropy models. The composite models either subdivided the total species distribution into four geographic quadrants or by fifteen subspecies to capture spatially relevant variation in P. polionotus distributions.<br><br>RESULTS: Despite high Area Under the ROC Curve (AUC) values for all models, the composite species distribution model of P. polionotus generated from individual subspecies models represented the known distribution of the species much better than did the models produced by partitioning data into geographic quadrants or modeling the whole species as a single unit.<br><br>CONCLUSIONS: Because the AUC values failed to describe the differences in the predictability of the three modeling strategies, we suggest using omission curves in addition to AUC values to assess model performance. Dividing the data of a widespread species into biologically relevant partitions greatly increased the performance of our distribution model; therefore, this approach may prove to be quite practical and informative for a wide range of modeling applications.},
}
@article {pmid17900366,
year = {2007},
author = {Blundell, AG and Burkey, TV},
title = {A database of schemes that prioritize sites and species based on their conservation value: focusing business on biodiversity.},
journal = {BMC ecology},
volume = {7},
number = {},
pages = {10},
pmid = {17900366},
issn = {1472-6785},
mesh = {Animals ; *Biodiversity ; Birds ; Conservation of Natural Resources/*methods ; *Databases, Factual ; Plants ; Wetlands ; },
abstract = {BACKGROUND: Biodiversity offsets are conservation projects used mainly by business to counterbalance the environmental impacts of their operations, with the aim of achieving a net neutral or even beneficial outcome for biodiversity. Companies considering offsets need to know: (1) if there are areas of such biological importance that no impact is acceptable, and outside of these no-go areas, (2) the relative importance of biodiversity in the impacted site versus the site(s) proposed for protection, to ensure that the offset is of equal or greater status than that lost through the company's operations. We compiled a database of 40 schemes that use various methods to assess conservation priorities, and we examined if the schemes would allow companies to answer the above questions.<br><br>DESCRIPTION: Overall, schemes tend to be designed to guide conservation organizations in their own priority setting or they categorize species based on conservation status. Generally, the schemes do not provide all the necessary information for offsets because they operate at a broad spatial scale or with low spatial resolution, which make it difficult to assess sites at the project level. Furthermore, most schemes do not explicitly incorporate threat, which we consider key to assessing whether offsets protect habitats or species that would otherwise be lost (i.e., provide additionality). The schemes are useful, however, for identifying the major conservation issues in different ecosystems around the globe.<br><br>CONCLUSION: Companies can proceed by first avoiding, reducing, and mitigating impacts, and then using existing schemes to identify i) no-go areas and ii) appropriate offsets to compensate for any unavoidable loss in biodiversity. If existing schemes are inadequate, then companies should use integrated conservation planning techniques to define offset options within the region of their operations.},
}
@article {pmid17144922,
year = {2006},
author = {Johnson, K and Neville, TB and Neville, P},
title = {GIS habitat analysis for lesser prairie-chickens in southeastern New Mexico.},
journal = {BMC ecology},
volume = {6},
number = {},
pages = {18},
pmid = {17144922},
issn = {1472-6785},
mesh = {Agriculture ; Animals ; *Conservation of Natural Resources ; *Ecosystem ; *Galliformes ; *Geographic Information Systems ; Herbicides ; New Mexico ; },
abstract = {BACKGROUND: We conducted Geographic Information System (GIS) habitat analyses for lesser prairie-chicken (LPCH, Tympanuchus pallidicinctus) conservation planning. The 876,799 ha study area included most of the occupied habitat for the LPCH in New Mexico. The objectives were to identify and quantify: 1. suitable LPCH habitat in New Mexico, 2. conversion of native habitats, 3. potential for habitat restoration, and 4. unsuitable habitat available for oil and gas activities.<br><br>RESULTS: We found 16% of suitable habitat (6% of the study area) distributed in 13 patches of at least 3,200 ha and 11% of suitable habitat (4% of the study area) distributed in four patches over 7,238 ha. The area converted from native vegetation types comprised 17% of the study area. Ninety-five percent of agricultural conversion occurred on private lands in the northeastern corner of the study area. Most known herbicide-related conversions (82%) occurred in rangelands in the western part of the study area, on lands managed primarily by the US Bureau of Land Management (BLM). We identified 88,190 ha (10% of the study area) of habitats with reasonable restoration potential. Sixty-two percent of the primary population area (PPA) contained occupied, suitable, or potentially suitable habitat, leaving 38% that could be considered for oil and gas development.<br><br>CONCLUSION: Although suitable LPCH habitat appears at first glance to be abundant in southeastern New Mexico, only a fraction of apparently suitable vegetation types constitute quality habitat. However, we identified habitat patches that could be restored through mesquite control or shin-oak reintroduction. The analysis also identified areas of unsuitable habitat with low restoration potential that could be targeted for oil and gas exploration, in lieu of occupied, high-quality habitats. Used in combination with GIS analysis and current LPCH population data, the habitat map represents a powerful conservation and management tool.},
}
@article {pmid40088887,
year = {2025},
author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ},
title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100808},
doi = {10.1016/j.xgen.2025.100808},
pmid = {40088887},
issn = {2666-979X},
abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here, we characterize fully assembled centromeres in the eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha-satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence that this epigenetic feature is conserved in the absence of satellite arrays. We uncovered a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, we identify duplications and deletions in HLE centromeres that distinguish them from other gibbons. Finally, we observed differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, and thus propose that a combination of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.},
}
@article {pmid40087683,
year = {2025},
author = {Mbuba, E and Mañas-Chavernas, N and Moore, SJ and Ruzige, PD and Kobe, D and Moore, J and Philipo, R and Kisoka, N and Pontiggia, G and Chacky, F and Mwalimu, CD and Cattin, PC and Wolleb, J and Sandkuehler, R and Ross, A},
title = {Estimating the hole surface area of insecticide-treated nets using image analysis, manual hole counting and exact hole measurements.},
journal = {Malaria journal},
volume = {24},
number = {1},
pages = {82},
pmid = {40087683},
issn = {1475-2875},
mesh = {*Image Processing, Computer-Assisted/methods ; *Insecticide-Treated Bednets/statistics &amp; numerical data ; Mosquito Control/methods ; Animals ; Insecticides ; },
abstract = {BACKGROUND: The physical integrity of insecticidal-treated nets (ITNs) is important for creating a barrier against host-seeking mosquitoes and, therefore, influences people's perception of the net's effectiveness and their willingness to use it. Monitoring the physical integrity of ITNs over time provides information for replenishment schedules and purchasing decisions. Currently, the assessment of physical integrity of ITNs is conducted by manually counting holes and estimating their size to class the net as functional or not. This approach is laborious to routinely conduct during field surveys of ITNs. Automated image analysis may provide a rapid assessment of the physical integrity of ITNs but it is not known if the images can capture sufficient information. As a first step, this study aimed to assess the agreement between estimated hole surface areas derived from (1) manually segmented images, (2) manual hole counting compared to (3) ground truth obtained by calibrated close-up shots of individual holes.<br><br>METHODS: The physical integrity of 75 ITNs purposely selected from an ongoing study was assessed by manual hole counting, image analysis and ground truth. For the image analysis, a graphical user interface was developed and used for the segmentation of holes visible in photographs taken from each side of the net. The hole surface area was then computed from this data. The agreement between the estimates from image analysis and manual hole counting was compared to the ground truth using the Bland-Altman method.<br><br>RESULTS: There was substantial agreement between the manually segmented image analysis estimates and the ground truth hole surface areas. The overall bias was small, with a mean ratio of the hole surface area from image analysis to the ground truth of 0.70, and the 95% limits of agreement ranging from 0.35 to 1.38. Manual hole counting underestimated the hole surface area compared to the ground truth, particularly among nets with holes above 10&#xa0;cm in diameter.<br><br>CONCLUSION: Images coupled with manual segmentation contain sufficient information to calculate hole surface area. This lays the groundwork for incorporating automatic hole detection, and then assessing whether this method will offer a fast and objective method for routine assessment of physical integrity of ITNs. While the WHO method underestimated the hole surface area, it remains useful in classifying nets as either serviceable or too torn because the cut-off is specific to this method.},
}
@article {pmid40086213,
year = {2025},
author = {Dong, L and Mu, L and Huang, X},
title = {Exploring lipid remodeling and antioxidant responses in Chlorella pyrenoidosa exposed to streptomycin sulfate stress.},
journal = {Food chemistry},
volume = {478},
number = {},
pages = {143565},
doi = {10.1016/j.foodchem.2025.143565},
pmid = {40086213},
issn = {1873-7072},
abstract = {Microalgae, particularly Chlorella pyrenoidosa, are valuable for bioactive compounds and biofuel production, but antibiotic use in large-scale cultivation can impact growth and biochemical productivity. This study examines the physiological and molecular responses of C. pyrenoidosa to streptomycin sulfate (STRS) stress. STRS exposure significantly reduced cell density (15.31 × 10[6] to 11.20 × 10[6] cells/mL, p < 0.001) and photosynthetic efficiency (Fv/fm from 0.45 to 0.15). Multi-omics analysis revealed a dual adaptive strategy: (1) activation of antioxidant defenses, including upregulated superoxide dismutase (SOD, 19-fold) and ascorbate peroxidase (APX, 32-fold); (2) lipid remodeling, with increased α-linolenic acid (ALA) content (17.43 % to 21.25 %, p < 0.001) due to β-oxidation downregulation. These findings enhance understanding of microalgal stress adaptation and highlight potential applications in biofuel and food/feed industries. Future studies should optimize genetic and cultivation strategies to enhance these adaptive traits while ensuring ecological sustainability.},
}
@article {pmid40074806,
year = {2025},
author = {Tang, Y and Hu, H and Chen, S and Hao, B and Xu, X and Zhu, H and Zhan, W and Zhang, T and Hu, H and Chen, G},
title = {Multi-omics analysis revealed the novel role of NQO1 in microenvironment, prognosis and immunotherapy of hepatocellular carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8591},
pmid = {40074806},
issn = {2045-2322},
support = {24B0413//the Scientific Research Project of the Hunan Provincial Department of Education/ ; 2024JJ7455//Natural Science Foundation of Hunan Province/ ; 20224310NHYCG04//University of South China Clinical Research 4310 Program/ ; 20224310NHYCG01//University of South China Clinical Research 4310 Program/ ; 82473965//National Natural Science Foundation of China/ ; 2023JJ50156//the Natural Science Foundation of Hunan Province/ ; 202250045223//Science and technology innovation Program of Hengyang City/ ; ZYYD2024CG17//Central Government Guided Local Science and Technology Development Fund Project in Xinjiang Uygur Autonomous Region/ ; 2024WK4008//Hunan Province Innovation Ecological Construction Plan Science and Technology Assistance Project in Xinjiang Uygur Autonomous Region/ ; SYTG-Y202429//Health Technology Promotion Project in Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Carcinoma, Hepatocellular/therapy/genetics/immunology/pathology ; *NAD(P)H Dehydrogenase (Quinone)/genetics/metabolism ; Humans ; *Liver Neoplasms/therapy/genetics/immunology/pathology ; *Tumor Microenvironment/immunology ; Prognosis ; *Immunotherapy/methods ; Gene Expression Regulation, Neoplastic ; Biomarkers, Tumor/genetics ; Male ; Female ; Nomograms ; Tumor-Associated Macrophages/immunology/metabolism ; Middle Aged ; Multiomics ; },
abstract = {NAD(P)H dehydrogenase quinone 1 (NQO1) is overexpressed in various cancers and is strongly associated with an immunosuppressive microenvironment and poor prognosis. In this study, we explored the role of NQO1 in the microenvironment, prognosis and immunotherapy of Hepatocellular carcinoma (HCC) using multi-omics analysis and machine learning. The results revealed that NQO1 was significantly overexpressed in HCC cells. NQO1[+]HCC cells were correlated with poor prognosis and facilitated tumor-associated macrophages (TAMs) polarization to M2 macrophages. We identified core NQO1-related genes (NRGs) and developed the NRGs-related risk-scores in hepatocellular carcinoma (NRSHC). The comprehensive nomogram integrating NRSHC, age, and pathological tumor-node-metastasis (pTNM) Stage achieved an area under the curve (AUC) above 0.7, demonstrating its accuracy in predicting survival outcomes and immunotherapy responses of HCC patients. High-risk patients exhibited worse prognoses but greater sensitivity to immunotherapy. Additionally, a web-based prediction tool was designed to enhance clinical utility. In conclusion, NQO1 may play a critical role in M2 polarization and accelerates HCC progression. The NRSHC model and accompanying tools offer valuable insights for personalized HCC treatment.},
}
@article {pmid40074756,
year = {2025},
author = {Wei, P and Song, Y and Tian, R and Wang, Y and Chen, J and Yuan, Z and Zhou, W},
title = {CaecilianTraits, an individual level trait database of Caecilians worldwide.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {428},
pmid = {40074756},
issn = {2052-4463},
support = {32170445//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Amphibians/classification ; Animals ; *Databases, Factual ; Biodiversity ; Biological Evolution ; },
abstract = {Functional traits differ among species, which determine the ecological niche a species occupies and its ability to adapt to environment. However, differences in traits also exist at intraspecific level. Such variations shape differences in individual survival capabilities. Investigating intraspecific differences of functional traits is important for ecology, evolutionary biology and biodiversity conservation. Individual trait-based approaches have been applied in plant ecology. But for animals, most databases only provide data at the species level. In this study, we presented a global database of morphological traits for caecilians (Amphibia, Gymnophiona) at both species and individual level. Caecilians are a unique group of amphibians characterized by their secretive habits, which have limited our understanding of this taxon. We compiled the most comprehensive database covering 218 out of 222 known species, with 215 of them have individual level data. This database will facilitate research in the ecology, evolutionary biology, conservation biology, and taxonomy of caecilians. Furthermore, this dataset can be utilized to test ecological and evolutionary hypotheses at the individual level.},
}
@article {pmid40070804,
year = {2025},
author = {Vršanský, P and Sendi, H and Kotulová, J and Szwedo, J and Havelcová, M and Palková, H and Vršanská, L and Sakala, J and Puškelová, L and Golej, M and Biroň, A and Peyrot, D and Quicke, D and Néraudeau, D and Uher, P and Maksoud, S and Azar, D},
title = {Jurassic Park approached: a coccid from Kimmeridgian cheirolepidiacean Aintourine Lebanese amber.},
journal = {National science review},
volume = {12},
number = {3},
pages = {nwae200},
pmid = {40070804},
issn = {2053-714X},
abstract = {With the exception of a fly and a mite from the Triassic of Italy, all Mesozoic amber arthropods are from the Cretaceous. Late Jurassic Lebanese amber from Aintourine revealed a completely preserved adult coccid male (wing length 0.8 mm), Jankotejacoccus libanogloria gen. et sp. n., the earliest record of a plant sucking scale insect. Associated plant material included the cheirolepidiaceans Protopodocarpoxylon, Brachyphyllum and Classostrobus, plus Classopolis pollen, suggesting a forested temporary swamp habitat with ferns, tree ferns, water ferns, tall araucarian and ginkgoacean trees and shrubs. (Sub)tropic lateritic soil with vegetation debris underwent incomplete microbial decomposition in an anoxic water environment of peat swamp development. Strata-associated marine organisms support the Kimmeridgian age revealed by zircons. The discovery opens a new field of research in Jurassic amber fossils.},
}
@article {pmid40069723,
year = {2025},
author = {Pieroni, A and Zocchi, DM and Alrhmoun, M and Sulaiman, N and Bavorova, M and Sõukand, R},
title = {Not "just necessity"? Two-x-eco-cultural dilemmas and the ethnobiological importance of the informal grannies' markets in Moldova.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {21},
number = {1},
pages = {17},
pmid = {40069723},
issn = {1746-4269},
support = {714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; },
mesh = {Moldova ; Humans ; Female ; *Commerce ; Food Supply ; Conservation of Natural Resources ; Middle Aged ; Agriculture ; Rural Population ; Culture ; Anthropology, Cultural ; Aged ; Biodiversity ; },
abstract = {Informal food markets, particularly those managed by (elderly) women in post-communist Eastern Europe, represent a biocultural phenomenon of profound significance since globalisation and increasingly strict legal frameworks often threaten these reservoirs of biocultural food heritage. In the fall of 2022 and 2023, a preliminary field study was conducted by visiting the informal markets of six Moldovan centres: Chișinău, Orhei, Bălți, Călărași, Comrat, and Taraclia, and conversing with approximately 40 mid-aged and elderly sellers. We argue that these markets are crucial in sustaining small-scale farming, preserving biodiversity, and maintaining a connection between urban communities and rural communities and, ultimately, between these rural citizens and their nature, keeping small-scale family farming and domestic traditional gastronomic activities alive. By trading fresh, homegrown, and homemade food and goods (including handicrafts), these mid-aged and elderly vendors support local economies, promote environmental sustainability, and safeguard traditional ecological knowledge and cultural heritage. This paper explores how grannies' markets contribute to biocultural diversity and sustainable food practices, especially amid the country's recent turbulent political, socioeconomic, and demographic challenges. The analysis advocates for the survival rights of these ecological, economic, and cultural (2-x-eco-cultural) refugia and invites ethnobiologists, food studies and cultural heritage scholars, rural sociologists, and agricultural economists to defend the biocultural diversity of informal food markets, moving them from an "out of necessity" status to a solid pillar of a possible future, new, family farming and small-scale ecological and gastronomic (conscientious) tourism. Policymakers should protect and enhance these informal spaces, especially the socioecological farming systems behind them, as essential socioeconomic and environmental assets. They should emphasise their importance as hubs for biological diversity, cultural preservation, community cohesion, and ecological sustainability.},
}
@article {pmid40066908,
year = {2025},
author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T},
title = {Intrapartum Care Experiences Associated With Postpartum Visit Attendance.},
journal = {Birth (Berkeley, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1111/birt.12910},
pmid = {40066908},
issn = {1523-536X},
support = {//Wisconsin Alumni Research Foundation/ ; },
abstract = {INTRODUCTION: The postpartum visit is an important opportunity to prevent pregnancy-related morbidity and mortality; however, about 1 in 10 birthing people do not attend this visit. Intrapartum care experiences are an understudied factor that may contribute to postpartum healthcare engagement.<br><br>MATERIALS AND METHODS: We analyze data from a novel survey supplement on intrapartum care experiences administered to a probability-based population sample of people who have recently given birth through the Wisconsin Pregnancy Risk Assessment Monitoring System.<br><br>RESULTS: In regression models adjusting for a robust set of individual characteristics and birth hospital clustering, we find that lower provider responsiveness during intrapartum care is associated with increased odds of forgoing the postpartum visit (aOR 1.4, 95% CI 1.0-2.0).<br><br>DISCUSSION: The quality of care received during the birth hospitalization may shape how birthing people feel about health care providers and their willingness to attend future visits. Experiences of care during the intrapartum period may contribute to future health care utilization. Improving these experiences is an opportunity to promote long-term health.},
}
@article {pmid40064850,
year = {2025},
author = {Roman, J and Abraham, AJ and Kiszka, JJ and Costa, DP and Doughty, CE and Friedlaender, A and Hückstädt, LA and Marcondes, M and Wetsel, E and Pershing, AJ},
title = {Migrating baleen whales transport high-latitude nutrients to tropical and subtropical ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2125},
pmid = {40064850},
issn = {2041-1723},
mesh = {Animals ; *Animal Migration/physiology ; *Ecosystem ; *Whales/physiology/metabolism ; *Nutrients/metabolism ; Tropical Climate ; Seasons ; Nitrogen/metabolism ; Biomass ; Female ; },
abstract = {Baleen whales migrate from productive high-latitude feeding grounds to usually oligotrophic tropical and subtropical reproductive winter grounds, translocating limiting nutrients across ecosystem boundaries in their bodies. Here, we estimate the latitudinal movement of nutrients through carcasses, placentas, and urea for four species of baleen whales that exhibit clear annual migration, relying on spatial data from publicly available databases, present and past populations, and measurements of protein catabolism and other sources of nitrogen from baleen whales and other marine mammals. Migrating gray, humpback, and North Atlantic and southern right whales convey an estimated 3784 tons N yr[-1] and 46,512 tons of biomass yr[-1] to winter grounds, a flux also known as the "great whale conveyor belt"; these numbers might have been three times higher before commercial whaling. We discuss how species recovery might help restore nutrient movement by whales in global oceans and increase the resilience and adaptative capacity of recipient ecosystems.},
}
@article {pmid40064777,
year = {2025},
author = {Crespo-Bellido, A and Martin, DP and Duffy, S},
title = {Recombination Analysis of Geminiviruses Using Recombination Detection Program (RDP).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2912},
number = {},
pages = {125-143},
pmid = {40064777},
issn = {1940-6029},
mesh = {*Geminiviridae/genetics ; *Recombination, Genetic ; Software ; Algorithms ; Sequence Alignment ; Genome, Viral ; Evolution, Molecular ; Computational Biology/methods ; Phylogeny ; },
abstract = {Geminiviruses are recombination-prone, and characterizing this evolutionary process within their genomes is a frequent goal of researchers. RDP is a stand-alone Windows program combining many algorithms that detect and characterize recombination. It has been widely used by the geminivirus community (and beyond). Here we describe the use of RDP4 and RDP5 for analysis of geminiviral nucleotide sequences including: (i) obtaining a reasonable dataset for analysis, (ii) making a credible multiple sequence alignment and (iii) analyzing an alignment with RDP on that alignment. RDP to both characterize recombination events and to produce statistically recombination-free datasets for other molecular evolution analyses.},
}
@article {pmid40063696,
year = {2025},
author = {Smith, LB and Ahlich, E and Lang, B and Bollepalli, S and Prioleau, T and Bartolome, A and Hughes Lansing, A and Rancourt, D},
title = {Glycemic variability and weight-focused eating behaviors among adolescents and young adults with type 1 diabetes†.},
journal = {Journal of pediatric psychology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpepsy/jsaf009},
pmid = {40063696},
issn = {1465-735X},
support = {//Dexcom, Inc/ ; },
abstract = {OBJECTIVE: Type 1 diabetes (T1D) disease management and associated glycemic fluctuations can disrupt experiences of hunger and satiety, which may increase risk for disordered eating behaviors. Glycemic variability may be a useful trigger for just-in-time interventions for disordered eating behaviors. In this exploratory study, we hypothesized that two metrics of glycemic variability would be associated with greater hunger and predict eating behaviors for weight loss or maintenance in adolescents and young adults with T1D.<br><br>METHODS: Individuals with T1D were recruited from a university diabetes clinic (N&#x2009;=&#x2009;34; 50% female, Mage&#x2009;=&#x2009;19.53&#x2009;years, MHbA1c&#x2009;=&#x2009;7.98%; 29% Hispanic/Latinx; 79% White). Participants wore a blinded continuous glucose monitor for 5&#xa0;days, and completed ecological momentary assessments (four prompts per day) that included measures of hunger and eating behaviors for weight loss or maintenance purposes. Generalized and linear mixed models were used to test hypotheses.<br><br>RESULTS: Approximately 30% of participants were at risk for an eating disorder based on Diabetes Eating Problem Survey-Revised scores. Greater glycemic variability did not predict hunger, but was associated with increased odds of endorsing any eating behavior for weight loss or maintenance purposes within-person (ps<.05). Greater hunger was associated with increased odds of endorsing disordered eating behavior within-person (p<.05).<br><br>CONCLUSIONS: This exploratory study provides some preliminary evidence that times of greater hunger and glycemic variability may be when individuals with T1D may be at higher risk of engaging in behaviors to lose or maintain weight.},
}
@article {pmid39823836,
year = {2025},
author = {Li, Z and Meng, C and Azad, MAK and Zhu, Q and Lin, W and Cui, Y and Lan, W and He, Q and Kong, X},
title = {Effects of the Salvia miltiorrhiza, Ligustrum lucidum, and Taraxacum mongolicum ultra-fine powder formula on meat quality of aged layers by multi-omics.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104783},
pmid = {39823836},
issn = {1525-3171},
mesh = {*Taraxacum/chemistry ; Animals ; *Ligustrum/chemistry ; *Salvia miltiorrhiza/chemistry ; *Meat/analysis ; *Drugs, Chinese Herbal/pharmacology/administration &amp; dosage/chemistry ; *Diet/veterinary ; *Animal Feed/analysis ; *Dietary Supplements/analysis ; *Chickens/physiology ; Female ; Powders/chemistry ; Aging/drug effects ; Multiomics ; },
abstract = {This study was aimed to identify the targets of 1% ultra-fine Chinese medicine formula (UCMF, 0.5% Salvia miltiorrhiza Bge. + 0.25% Ligustrum lucidum Ait. + 0.25% Taraxacum mongolicum Hand.-Mazz.) in delaying aging and explore its impacts on meat quality of aged layers. The effective components of the above three Chinese herbs were screened, and the network pharmacology analysis identified 91 common targets and enriched pathways between herbs and aging. The results showed that cellular response to chemical stimulus, response to oxidative stress, and response to oxygen-containing compound pathways were crucial for UCMF to resist aging. Further in vivo analyses confirmed that UCMF supplementation enhanced the antioxidant function in breast muscles of aged layers by upregulating (P < 0.05) the SOD2 gene expression. Meanwhile, UCMF supplementation reduced (P < 0.05) yellowness (b* value) and drip loss while enhancing (P < 0.05) cooked meat percentage of aged layers. For the health lipid indices in breast muscles, UCMF supplementation increased (P < 0.05) polyunsaturated fatty acids/saturated fatty acids and hypocholesterolemic/hypercholesterolemic ratios and decreased (P < 0.05) the thrombogenic index. The UCMF supplementation optimized the cecal microbiota of aged layers by enhancing the relative abundance of Firmicutes and reducing the relative abundances of Bacteroidetes and Spirochaetes (P < 0.05), which may be related to improving meat quality. In conclusion, dietary UCMF supplementation may be an effective strategy for improving antioxidant function and the meat quality of aged layers.},
}
@article {pmid39752826,
year = {2025},
author = {Zhao, X and Jiang, WY and Liu, JJ and Yan, WJ and Zhang, YH and Zhang, Z and Zhang, PD},
title = {Unraveling the impact of PFOA toxicity on Zostera marina using a multi-omics approach: Insights from growth, physiological, transcriptomic, and metabolomic signatures.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {137024},
doi = {10.1016/j.jhazmat.2024.137024},
pmid = {39752826},
issn = {1873-3336},
mesh = {*Caprylates/toxicity ; *Water Pollutants, Chemical/toxicity ; *Transcriptome/drug effects ; *Zosteraceae/genetics/drug effects/metabolism ; *Fluorocarbons/toxicity ; *Metabolomics ; Photosynthesis/drug effects ; Gene Expression Profiling ; Multiomics ; },
abstract = {Perfluorooctanoic acid (PFOA), an anthropogenic organic pollutant known for its persistence, resistance to degradation, and toxicity, has raised significant concerns about its potential ecological impacts. Zostera marina, a common submerged seagrass species in temperate offshore areas, is highly vulnerable to pollutant stressors. However, the impact of PFOA on Z. marina remains unclear. In this study, Z. marina was exposed to different concentrations of PFOA (0, 0.5, 1, 5, 10, and 20 μg/L) for 14 days. We subsequently assessed survival rates, growth patterns, physiological indices, transcriptomic profiles, and metabolomic characteristics. The results revealed dose-dependent PFOA accumulation in Z. marina tissues and significant growth inhibition. Furthermore, exposure to PFOA resulted in a significant reduction in photosynthetic pigment content (IBRv2 indices: 2.78-10.29) and elevated enzyme activity (IBRv2 indices: 2.90-8.96). Transcriptomic analysis identified 1511 differentially expressed genes associated with 11 KEGG pathways predominantly affected by PFOA exposure. Weighted gene co-expression network analysis highlighted the crucial role of the hydroxyphenylpyruvate reductase (hppr) gene in antioxidant defense mechanisms and detoxification processes against PFOA-induced stress. Metabolomics identified 412 differentially expressed metabolites, mainly consisting of flavonoids, organic acids, and lipids. In summary, PFOA exposure resulted in the down-regulation of gene expression related to photosynthesis and energy metabolism while also affecting metabolite synthesis. The response of Z. marina to PFOA stress involves modulation of the cytoskeletal dynamics and signal transduction pathways, as well as activation of a suite of genes and metabolites to initiate defense mechanisms.},
}
@article {pmid39724715,
year = {2025},
author = {Zhang, L and Du, Y and Li, Y and Wang, T and Pan, Y and Xue, X and Mu, X and Qiu, J and Qian, Y},
title = {Mitochondrial mechanism of florfenicol-induced nonalcoholic fatty liver disease in zebrafish using multi-omics technology.},
journal = {Journal of hazardous materials},
volume = {486},
number = {},
pages = {136958},
doi = {10.1016/j.jhazmat.2024.136958},
pmid = {39724715},
issn = {1873-3336},
mesh = {Animals ; *Zebrafish ; *Non-alcoholic Fatty Liver Disease/chemically induced/metabolism/pathology ; *Thiamphenicol/analogs &amp; derivatives/toxicity ; *Anti-Bacterial Agents/toxicity ; Mitochondria/drug effects/metabolism ; Oxidative Stress/drug effects ; Liver/drug effects/metabolism/pathology ; Metabolomics ; Water Pollutants, Chemical/toxicity ; Energy Metabolism/drug effects ; Lipidomics ; Multiomics ; },
abstract = {Florfenicol (FF), a third-generation chloramphenicol antibiotic widely used in food-producing animals, has become a "pseudopersistent" environmental contaminant, raising concerns about its potential ecological and human health impacts. However, its bioaccumulation behavior and hepatotoxic mechanisms remain poorly understood. This study aims to address these gaps with a 28-day exposure experiment in adult zebrafish at 0.05 and 0.5 mg/L FF. Multiomic analyses (metabolomics, lipidomics, and transcriptomics), combined with histological and mitochondrial function assessments, were employed. Higher bioaccumulation was observed at 0.05 mg/L, potentially due to metabolic saturation at higher concentrations. Histological analysis revealed significant hepatic steatosis (>5 % steatosis area), indicative of moderate nonalcoholic fatty liver disease (NAFLD). Multiomic data demonstrated global dysregulation in energy metabolism, including marked alterations in lipids (accumulation of toxic sphingolipids, excessive fatty acids, and acylglycerol), amino acids, tricarboxylic acid cycle intermediates, and nucleotides. Crucially, mitochondrial dysfunction was identified as a central mechanism, with impaired respiratory chain activities, adenosine triphosphate depletion, elevated reactive oxygen species, and oxidative stress promoting NAFLD progression. These findings highlight mitochondrial impairment and oxidative stress as key drivers of FF-induced hepatotoxicity, providing novel insights into its toxicological mechanisms and emphasizing the ecological risks posed by antibiotic pollution in aquatic systems.},
}
@article {pmid40062320,
year = {2025},
author = {Boyes, D and Davis, J and , and , and , and , and , and , },
title = {The genome sequence of the Sandy Carpet moth, Perizoma flavofasciatum (Thunberg, 1792).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {40},
pmid = {40062320},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Perizoma flavofasciatum (Sandy Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 369.30 megabases. Most of the assembly (99.88%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,915 protein-coding genes.},
}
@article {pmid40062319,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Alder Moth, Acronicta alni (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {68},
pmid = {40062319},
issn = {2398-502X},
abstract = {We present a genome assembly from a male Acronicta alni (Alder Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 470.37 megabases and 472.86 megabases. Most of haplotype 1 (98.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 15.38 kilobases in length.},
}
@article {pmid40061226,
year = {2025},
author = {Ab Kadir, MA and Abdul Manaf, R and Mokhtar, SA and Ismail, LI},
title = {Identifying leptospirosis hotspots in Selangor: uncovering climatic connections using remote sensing and developing a predictive model.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18851},
pmid = {40061226},
issn = {2167-8359},
mesh = {*Leptospirosis/epidemiology ; Humans ; Cross-Sectional Studies ; Malaysia/epidemiology ; *Remote Sensing Technology/methods ; *Geographic Information Systems ; Male ; Female ; Adult ; Adolescent ; Incidence ; Machine Learning ; Middle Aged ; Child ; Young Adult ; Climate Change ; Aged ; Rain ; Child, Preschool ; },
abstract = {BACKGROUND: Leptospirosis is an endemic disease in countries with tropical climates such as South America, Southern Asia, and Southeast Asia. There has been an increase in leptospirosis incidence in Malaysia from 1.45 to 25.94 cases per 100,000 population between 2005 and 2014. With increasing incidence in Selangor, Malaysia, and frequent climate change dynamics, a study on the disease hotspot areas and their association with the hydroclimatic factors could enhance disease surveillance and public health interventions.<br><br>METHODS: This ecological cross-sectional study utilised a geographic information system (GIS) and remote sensing techniques to analyse the spatiotemporal distribution of leptospirosis in Selangor from 2011 to 2019. Laboratory-confirmed leptospirosis cases (n&#xa0;= 1,045) were obtained from the Selangor State Health Department. Using ArcGIS Pro, spatial autocorrelation analysis (Moran's I) and Getis-Ord Gi* (hotspot analysis) was conducted to identify hotspots based on the monthly aggregated cases for each subdistrict. Satellite-derived rainfall and land surface temperature (LST) data were acquired from NASA's Giovanni EarthData website and processed into monthly averages. These data were integrated into ArcGIS Pro as thematic layers. Machine learning algorithms, including support vector machine (SVM), Random Forest (RF), and light gradient boosting machine (LGBM) were employed to develop predictive models for leptospirosis hotspot areas. Model performance was then evaluated using cross-validation and metrics such as accuracy, precision, sensitivity, and F1-score.<br><br>RESULTS: Moran's I analysis revealed a primarily random distribution of cases across Selangor, with only 20 out of 103 observed having a clustered distribution. Meanwhile, hotspot areas were mainly scattered in subdistricts throughout Selangor with clustering in the central region. Machine learning analysis revealed that the LGBM algorithm had the best performance scores compared to having a cross-validation score of 0.61, a precision score of 0.16, and an F1-score of 0.23. The feature importance score indicated river water level and rainfall contributes most to the model.<br><br>CONCLUSIONS: This GIS-based study identified a primarily sporadic occurrence of leptospirosis in Selangor with minimal spatial clustering. The LGBM algorithm effectively predicted leptospirosis hotspots based on the analysed hydroclimatic factors. The integration of GIS and machine learning offers a promising framework for disease surveillance, facilitating targeted public health interventions in areas at high risk for leptospirosis.},
}
@article {pmid40055331,
year = {2025},
author = {Guerrero, PC and Contador, T and Díaz, A and Escobar, C and Orlando, J and Marín, C and Medina, P},
title = {Southern Islands Vascular Flora (SIVFLORA) dataset: A global plant database from Southern Ocean islands.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {397},
pmid = {40055331},
issn = {2052-4463},
mesh = {*Biodiversity ; *Islands ; *Plants ; Databases, Factual ; Ecosystem ; Climate Change ; Oceans and Seas ; },
abstract = {The Southern Islands Vascular Flora (SIVFLORA) dataset is a globally significant, open-access resource that compiles essential biodiversity data on vascular plants from islands across the Southern Ocean. The SIVFLORA dataset was generated through five steps: study area delimitation, compiling the dataset, validating and harmonizing taxonomy, structuring dataset attributes, and establishing file format and open access. Covering major taxonomic divisions, SIVFLORA offers a comprehensive overview of plant occurrences, comprising 14,589 records representing 886 species, 95 families, and 42 orders. This dataset documents that 58.62% of the taxa are native, 9.61% are endemic, and 31.77% are alien species. The Falkland/Malvinas Archipelago, the most species-rich, contrast sharply with less diverse islands like the South Orkney Archipelago. SIVFLORA serves as a taxonomically harmonized, interoperable resource for investigating plant diversity patterns, ecosystem responses to climate change in extreme environments, island biogeography, endemism, and the effects of anthropogenic pressures on Southern Ocean flora.},
}
@article {pmid40055329,
year = {2025},
author = {Ferrer-Paris, JR and Sánchez-Mercado, A and Cornwell, WK and Ooi, M and Tozer, M and Mackenzie, BDE and Woodward, R and Denham, AJ and Auld, TD and Keith, DA},
title = {Fire ecology database for documenting plant responses to fire events in Australia.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {399},
pmid = {40055329},
issn = {2052-4463},
mesh = {*Databases, Factual ; *Fires ; *Plants ; Biodiversity ; Australia ; New South Wales ; },
abstract = {An understanding of fire-response traits is essential for predicting how fire regimes structure plant communities and for informing fire management strategies for biodiversity conservation. Quantification of these traits is complex, encompassing several levels of data abstraction scaling up from field observations of individuals, to general categories of species responses. We developed the Fire Ecology Database to accommodate this complexity. Its conceptual framework is underpinned by a flexible data pipeline enabling links between fire-related trait data and event information at individual, population, and community levels. Key features include: (a) concise and documented trait and method vocabularies; (b) documented uncertainty in observations and aggregation; and (c) documented origin of data including field observations, laboratory experiments, and expert elicitation. We demonstrated application of our framework using data from new field surveys and existing data sets in New South Wales, Australia. The database includes 14 traits for 6,287 plant species derived from 8,936 field work records from 2007 to 2018, 7,054 field records from surveys after 2019, and 48,306 records from 301 existing sources.},
}
@article {pmid40054299,
year = {2025},
author = {Guarischi, M and Montagnani, E and Catalano, G and Saligari, E and Signorini, S and Gori, M},
title = {From motion to interaction: How multisensory information shapes motor behaviors in children with visual impairment.},
journal = {Research in developmental disabilities},
volume = {159},
number = {},
pages = {104956},
doi = {10.1016/j.ridd.2025.104956},
pmid = {40054299},
issn = {1873-3379},
abstract = {BACKGROUND: The ability to move independently enables children to develop perceptual, cognitive, and social interaction skills. Concerning this, vision holds a key role. As a result, children with visual impairment (VI) might be more challenged in their ability to move within their surroundings and interact with their caregivers.<br><br>AIM: This study investigated whether the use of multisensory stimuli could influence the motor exploration of children with VI and shape their interaction with the caregivers. For this, the present work examined the variability of children's motor trajectory and the distance between children and caregivers in a setting with and without multisensory cues.<br><br>METHODS AND PROCEDURES: A Motion Capture System was used within an ecological playroom environment. The Strange Situation paradigm was simplified and adapted by placing three TechARMs in the corners of the playroom to deliver audio-visual stimuli, used instead of the stranger.<br><br>OUTCOMES AND RESULTS: Children with VI showed larger variability within their motor trajectory and kept a shorter distance from the caregivers when multisensory cues were introduced in the playroom.<br><br>CONCLUSIONS AND IMPLICATIONS: Multisensory signals were considered unusual and influenced the kinematic parameters. Motor control of the environment was achieved by managing attention flexibility. WHAT DOES THIS PAPER ADD?: This study enriches available evidence about the study of motor and social interaction in children with VI, highlighting how multisensory stimuli could either support or hinder social and motor behaviors. Moreover, enhancing ecological validity could drive progress in the development and application of technological devices to clinical and research setting.},
}
@article {pmid40045231,
year = {2025},
author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD},
title = {Cross-validation for training and testing co-occurrence network inference algorithms.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {74},
pmid = {40045231},
issn = {1471-2105},
support = {2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; },
mesh = {*Algorithms ; *Microbiota ; Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.<br><br>RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.<br><br>CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.},
}
@article {pmid39749403,
year = {2025},
author = {Bougiouri, K},
title = {Mind the Gap: A Neural Network Framework for Imputing Genotypes in Non-Model Species.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14066},
doi = {10.1111/1755-0998.14066},
pmid = {39749403},
issn = {1755-0998},
mesh = {*Neural Networks, Computer ; *Genotype ; Genotyping Techniques/methods ; Haplotypes/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Reduced representation sequencing (RRS) has proven to be a cost-effective solution for sequencing subsets of the genome in non-model species for large-scale studies. However, the targeted nature of RRS approaches commonly introduces large amounts of missing data, leading to reduced statistical power and biased estimates in downstream analyses. Genotype imputation, the statistical inference of missing sites across the genome, is a powerful alternative to overcome the caveats associated with missing sites. Typically, genotype imputation requires the presence of a reference panel of haplotypes, however, this is not always feasible for non-model species. In this issue of Molecular Ecology Resources, Mora-Márquez et al. (2024) develop gtImputation, an unsupervised machine learning imputation tool with an interactive GUI, which leverages information from the underlying data structure itself, without the need for a reference panel. They showcase that their method performs equally well and even surpasses existing haplotype-clustering and unsupervised machine learning algorithms, particularly for sites with low minor allele frequency (MAF) and for data sets with strong underlying population structure. This innovative framework adds to the ongoing efforts to expand the applicability of imputation to non-model species, offering the opportunity to apply varied types of analyses requiring dense sets of markers, while also maintaining lower sequencing costs.},
}
@article {pmid39739202,
year = {2025},
author = {Bard, NW and Davies, TJ and Cronk, QCB},
title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14056},
doi = {10.1111/1755-0998.14056},
pmid = {39739202},
issn = {1755-0998},
support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Fungi/genetics/classification/isolation &amp; purification ; *Genome, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Plants/microbiology ; DNA, Fungal/genetics ; Endophytes/genetics/classification/isolation &amp; purification ; DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.},
}
@article {pmid39611246,
year = {2025},
author = {Armstrong, EE and Li, C and Campana, MG and Ferrari, T and Kelley, JL and Petrov, DA and Solari, KA and Mooney, JA},
title = {A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14048},
doi = {10.1111/1755-0998.14048},
pmid = {39611246},
issn = {1755-0998},
mesh = {*Polymorphism, Single Nucleotide ; *Genetics, Population/methods ; Genotyping Techniques/methods ; Computational Biology/methods ; Animals ; },
abstract = {Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.},
}
@article {pmid39552382,
year = {2025},
author = {Beemelmanns, A and Bouchard, R and Michaelides, S and Normandeau, E and Jeon, HB and Chamlian, B and Babin, C and Hénault, P and Perrot, O and Harris, LN and Zhu, X and Fraser, D and Bernatchez, L and Moore, JS},
title = {Development of SNP Panels from Low-Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14040},
doi = {10.1111/1755-0998.14040},
pmid = {39552382},
issn = {1755-0998},
support = {//Genome Canada/ ; //G&#xe9;nome Qu&#xe9;bec/ ; //Ontario Genomics/ ; NST-1718-0036//Polar Knowledge Canada/ ; //Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; IT16149//Mitacs/ ; //Fisheries and Oceans Canada (DFO)/ ; //Ressources Aquatiques Qu&#xe9;bec (RAQ)/ ; },
mesh = {Animals ; *Polymorphism, Single Nucleotide ; *Fisheries ; *Salmonidae/genetics/classification ; Whole Genome Sequencing/methods ; Genotyping Techniques/methods ; Genotype ; Trout/genetics/classification ; Canada ; Genetics, Population/methods ; Nunavut ; Quebec ; Northwest Territories ; Computational Biology/methods ; },
abstract = {Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational and subsistence mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout (Salvelinus fontinalis) and Lake Whitefish (Coregonus clupeaformis) are among the most harvested and consumed fish species in Northern Indigenous communities in Canada, contributing significantly to food security, culture, tradition and economy. However, genetic resources supporting Indigenous fisheries have not been widely accessible to northern communities (e.g. Inuit, Cree, Dene). Here, we developed Genotyping-in-Thousands by sequencing (GT-seq) panels for population assignment and mixed-stock analyses of three salmonids, to support fisheries stewardship or co-management in Northern Canada. Using low-coverage Whole Genome Sequencing data from 418 individuals across source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest Territories), James Bay (Québec) and Mistassini Lake (Québec), we developed a bioinformatic SNP filtering workflow to select informative SNP markers from genotype likelihoods. These markers were then used to design GT-seq panels, thus enabling high-throughput genotyping for these species. The three GT-seq panels yielded an average of 413 autosomal loci and were validated using 525 individuals with an average assignment accuracy of 83%. Thus, these GT-seq panels are powerful tools for assessing population structure and quantifying the relative contributions of populations/stocks in mixed-stock fisheries across multiple regions. Interweaving genomic data derived from these tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in Indigenous communities, contributing to food security programmes and the economy in Northern Canada.},
}
@article {pmid39545396,
year = {2025},
author = {Li, J and Gao, Y and Shu, G and Chen, X and Zhu, J and Zheng, S and Chen, T},
title = {HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14046},
doi = {10.1111/1755-0998.14046},
pmid = {39545396},
issn = {1755-0998},
support = {2021YFF1201300//National Key Research and Development Program of China/ ; 2021YFF1201303//National Key Research and Development Program of China/ ; 2022YFC2703105//National Key Research and Development Program of China/ ; 2023M731976//Postdoctoral Research Foundation of China/ ; },
mesh = {*Microbiota/genetics ; Animals ; *Phylogeny ; *Amphibians/microbiology ; *Symbiosis/genetics ; Reptiles/microbiology ; Host Microbial Interactions/genetics ; Databases, Factual ; },
abstract = {Symbiotic microbiota strongly impact host physiology. Amphibians and reptiles occupy a pivotal role in the evolutionary history of Animalia, and they are of significant ecological, economic, and scientific value. Many prior studies have found that symbiotic microbiota in herpetofaunal species are closely associated with host phylogeny, physiological traits, and environmental factors; however, insufficient integrated databases hinder researchers from querying, accessing, and reanalyzing these resources. To rectify this, we built the first herpetofaunal microbiota database (HMicroDB; https://herpdb.com/) that integrates 11,697 microbiological samples from 337 host species (covering 23 body sites and associated with 23 host phenotypic or environmental factors), and we identified 11,084 microbial taxa by consistent annotation. The standardised analysis process, cross-dataset integration, user-friendly interface, and interactive visualisation make the HMicroDB a powerful resource for researchers to search, browse, and explore the relationships between symbiotic microbiota, hosts, and environment. This facilitates research in host-microbiota coevolution, biological conservation, and resource utilisation.},
}
@article {pmid40044867,
year = {2025},
author = {Aguirre-Gutiérrez, J and Rifai, SW and Deng, X and Ter Steege, H and Thomson, E and Corral-Rivas, JJ and Guimaraes, AF and Muller, S and Klipel, J and Fauset, S and Resende, AF and Wallin, G and Joly, CA and Abernethy, K and Adu-Bredu, S and Alexandre Silva, C and de Oliveira, EA and Almeida, DRA and Alvarez-Davila, E and Asner, GP and Baker, TR and Benchimol, M and Bentley, LP and Berenguer, E and Blanc, L and Bonal, D and Bordin, K and Borges de Lima, R and Both, S and Cabezas Duarte, J and Cardoso, D and de Lima, HC and Cavalheiro, L and Cernusak, LA and Dos Santos Prestes, NCC and da Silva Zanzini, AC and da Silva, RJ and Dos Santos Alves da Silva, R and de Andrade Iguatemy, M and De Sousa Oliveira, TC and Dechant, B and Derroire, G and Dexter, KG and Rodrigues, DJ and Espírito-Santo, M and Silva, LF and Domingues, TF and Ferreira, J and Simon, MF and Girardin, CAJ and Hérault, B and Jeffery, KJ and Kalpuzha Ashtamoorthy, S and Kavidapadinjattathil Sivadasan, A and Klitgaard, B and Laurance, WF and Dan, ML and Magnusson, WE and Campos-Filho, EM and Manoel Dos Santos, R and Manzatto, AG and Silveira, M and Marimon-Junior, BH and Martin, RE and Vieira, DLM and Metzker, T and Milliken, W and Moonlight, P and Moraes de Seixas, MM and Morandi, PS and Muscarella, R and Nava-Miranda, MG and Nyirambangutse, B and Silva, JO and Oliveras Menor, I and Francisco Pena Rodrigues, PJ and Pereira de Oliveira, C and Pereira Zanzini, L and Peres, CA and Punjayil, V and Quesada, CA and Réjou-Méchain, M and Riutta, T and Rivas-Torres, G and Rosa, C and Salinas, N and Bergamin, RS and Marimon, BS and Shenkin, A and Silva Rodrigues, PM and Figueiredo, AES and Garcia, QS and Spósito, T and Storck-Tonon, D and Sullivan, MJP and Svátek, M and Vieira Santiago, WT and Arn Teh, Y and Theruvil Parambil Sivan, P and Nascimento, MT and Veenendaal, E and Zo-Bi, IC and Dago, MR and Traoré, S and Patacca, M and Badouard, V and de Padua Chaves E Carvalho, S and White, LJT and Zhang-Zheng, H and Zibera, E and Zwerts, JA and Burslem, DFRP and Silman, M and Chave, J and Enquist, BJ and Barlow, J and Phillips, OL and Coomes, DA and Malhi, Y},
title = {Canopy functional trait variation across Earth's tropical forests.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40044867},
issn = {1476-4687},
abstract = {Tropical forest canopies are the biosphere's most concentrated atmospheric interface for carbon, water and energy[1,2]. However, in most Earth System Models, the diverse and heterogeneous tropical forest biome is represented as a largely uniform ecosystem with either a singular or a small number of fixed canopy ecophysiological properties[3]. This situation arises, in part, from a lack of understanding about how and why the functional properties of tropical forest canopies vary geographically[4]. Here, by combining field-collected data from more than 1,800 vegetation plots and tree traits with satellite remote-sensing, terrain, climate and soil data, we predict variation across 13 morphological, structural and chemical functional traits of trees, and use this to compute and map the functional diversity of tropical forests. Our findings reveal that the tropical Americas, Africa and Asia tend to occupy different portions of the total functional trait space available across tropical forests. Tropical American forests are predicted to have 40% greater functional richness than tropical African and Asian forests. Meanwhile, African forests have the highest functional divergence-32% and 7% higher than that of tropical American and Asian forests, respectively. An uncertainty analysis highlights priority regions for further data collection, which would refine and improve these maps. Our predictions represent a ground-based and remotely enabled global analysis of how and why the functional traits of tropical forest canopies vary across space.},
}
@article {pmid40041564,
year = {2025},
author = {Zhang, J and Qian, H and Wang, X},
title = {An online version and some updates of R package U.Taxonstand for standardizing scientific names in plant and animal species.},
journal = {Plant diversity},
volume = {47},
number = {1},
pages = {166-168},
pmid = {40041564},
issn = {2468-2659},
abstract = {•We present 'U.Taxonstand Online', a user-friendly web application for scientific name matching of both plants and animals.•U.Taxonstand Online provides a solution for the users with limited abilities of programming and data mining.•We add several new functions to clean and format the data for R package U.Taxonstand.},
}
@article {pmid40038315,
year = {2025},
author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C},
title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {378},
pmid = {40038315},
issn = {2052-4463},
support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; },
mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; },
abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.},
}
@article {pmid39990470,
year = {2025},
author = {Edwards, SV and Fang, B and Khost, D and Kolyfetis, GE and Cheek, RG and DeRaad, DA and Chen, N and Fitzpatrick, JW and McCormack, JE and Funk, WC and Ghalambor, CK and Garrison, E and Guarracino, A and Li, H and Sackton, TB},
title = {Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39990470},
issn = {2692-8205},
support = {R01 GM123489/GM/NIGMS NIH HHS/United States ; R01 HG011485/HG/NHGRI NIH HHS/United States ; R35 GM133412/GM/NIGMS NIH HHS/United States ; U01 DA047638/DA/NIDA NIH HHS/United States ; },
abstract = {Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.},
}
@article {pmid40034275,
year = {2025},
author = {Veneros, J and Hansen, AJ and Jantz, P and Roberts, D and Noguera-Urbano, E and García, L},
title = {Analysis of changes in temperature and precipitation in South American countries and ecoregions: Comparison between reference conditions and three representative concentration pathways for 2050.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42459},
pmid = {40034275},
issn = {2405-8440},
abstract = {Climate change is a global concern, and its impact on environmental variables such as temperature and annual precipitation is unknown spatially in the desert, andes, and rainforest ecoregions of Peru, Ecuador, and Colombia. In this study, we conducted a general review of climate drivers for South America (SA) and explored climate data using the GCM compareR package (General Circulation Models) and average ensembles for temperature and precipitation. Our results showed that all GCMs demonstrated increases in the annual mean temperature (BIO1) and in the mean temperature of the driest quarter (BIO9) for Peru, Ecuador, and Colombia for 2050 in three RCPs (2.6, 4.5, and 8.5). Also, most of the GCMs showed increases in the annual precipitation (BIO12) and the precipitation in the driest quarter (BIO17). We conducted non-parametric tests (Kruskal-Wallis Test) to assess if the medians of temperature and precipitation in the three ecoregions are equal for both the baseline and the climate change scenarios. We rejected the null hypothesis that the medians are equal for both temperatures and precipitation in the baseline vs. 2050 RCPs (2.6, 4.5, and 8.5). A spatial analysis was conducted to visualize the variations in temperature and precipitation between the RCPs versus the baseline, and the spatial variation at the country or ecoregion level can be observed. The annual mean temperature (°C) or annual precipitation (mm) divided by its standard deviation for each ecoregion (M metric) was analyzed to see how much the average temperature or the annual precipitation is relatively large compared to the variability or dispersion of temperatures or precipitation respectively; the average temperature and the annual precipitation for the baseline and the three RCPs are relatively large and associated with the variability or dispersion of their temperatures in the Napo moist forest compared to the other ecoregions. Our study provides important insights into the potential impacts of climate change on these ecosystems. Prospects in the Napo moist forest ecoregion, where significant changes in temperature and humidity have already occurred, and new species have invaded or evolved in the western Amazon rainforest, are particularly highlighted and reflected in terms of risk mitigation, ecosystem restoration, surveillance, and monitoring.},
}
@article {pmid40033715,
year = {2025},
author = {Gorné, LD and Hendry, AP and Pelletier, F and Sanderson, S and Correa, C and Arias, C and Beausoleil, MO and Boisjoly, M and Crispo, E and Berner, D and De León, LF and DiBattista, JD and Haines, GE and Haller, BC and Kinnison, MT and Muttalib, S and McKellar, AE and O'Dea, RE and Reyes-Corral, WD and Ritchot, Y and Oke, KB and Wood, ZT and Farrugia, T and Gotanda, KM},
title = {PROCEED v6.1: Phenotypic rates of change evolutionary and ecological database.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70009},
doi = {10.1002/ecy.70009},
pmid = {40033715},
issn = {1939-9170},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Le Fonds Qu&#xe9;b&#xe9;cois de la Recherche sur la Nature et les Technologies/ ; //McGill University/ ; //National Science Foundation/ ; //Brock University/ ; },
mesh = {*Biological Evolution ; Animals ; *Phenotype ; *Databases, Factual ; Ecosystem ; },
abstract = {Populations must continuously respond to environmental change or risk extinction. These responses can be measured as phenotypic rates of change, which allow researchers to predict their contemporary evolutionary responses. In 1999, a database of phenotypic rates of change in wild populations was compiled. Since then, researchers have used (and expanded) this database to examine the phenotypic responses as a function of the features of the study system (i.e., the population or set of populations, of a given species, that experienced a specific driver or disturbance), the measured traits, and methodological approaches. Therefore, PROCEED (Phenotypic Rates of Change Evolutionary and Ecological Database) is an ongoing compilation of rates of phenotypic change, typically calculated as Haldanes and Darwins, published in peer-reviewed literature (but also including data from theses and technical reports). Studies in this database measure the intraspecific change in quantitative (continuous or discrete) traits and report either the time elapsed from the onset of environmental novelty, or reference a historical or biological event reported in other sources (e.g., a mine opening or a well-documented biological invasion). Included studies either follow a single population through time (allochronic design) or compare two or more populations that diverged at a known time (synchronic design). Some included studies account for the total phenotypic variability in the field (i.e., phenotypic studies), while others employed common-garden or other quantitative genetic approaches to account for the heritable component of the phenotypic change (i.e., genetic studies). PROCEED includes systems in both natural and experimental conditions, provided that reproduction was not manipulated (i.e., artificial selection experiments were excluded). In the included experimental systems, the environment of the focal populations was manipulated (e.g., an herbivory exclusion experiment, where the type and load of herbivory are manipulated) but the studies did not deliberately select for trait values in the study population (e.g., the plant height). PROCEED does not include systems where the phenotypic change is presumably due to interspecific hybridization, polyploidy, or other chromosomal alterations. Here, we present the most recently updated PROCEED (Version 6.1). This new, curated version has 9263 records (n) collated from 326 studies, 1801 systems, and 428 species. The database includes records belonging to mammals (n = 686), birds (n = 1475), reptiles (n = 96), amphibians (n = 23), fishes (n = 3671), invertebrates (n = 1141, mostly arthropods), and plants (n = 2171). The maximum elapsed time between the environmental change and the sampling is 500 years but is typically less than 100 years (third quartile 89.5; median 45 years). The database also includes a set of variables describing biological and methodological aspects of the study system and measured traits, along with features of the sampling design in the primary source of information. This new version of PROCEED also includes a time series dataset comprising a subset of records included in the general dataset. These are allochronic studies with three or more sampling times throughout the entire study period. The time series dataset contains 655 time series (s)-belonging to 61 studies, from 156 systems, and 77 species-including mammals (s = 140), birds (s = 77), reptiles (s = 4), amphibians (s = 8), fishes (s = 404), and plants (s = 22). The data are released under a Creative Commons CC0 1.0 Universal Public Domain Dedication license.},
}
@article {pmid38995706,
year = {2024},
author = {Dietrich, SW and Ma, W and Ding, Y and Watanabe, KH and Zelinski, MB and Sluka, JP},
title = {MOTHER-DB: A Database for Sharing Nonhuman Ovarian Histology Images.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {21},
number = {6},
pages = {2598-2603},
pmid = {38995706},
issn = {1557-9964},
support = {P51 OD011092/OD/NIH HHS/United States ; },
mesh = {Female ; *Databases, Factual ; *Ovary/pathology ; Animals ; Metadata ; Information Dissemination/methods ; Image Processing, Computer-Assisted/methods ; Computational Biology/methods ; },
abstract = {The goal of the Multispecies Ovary Tissue Histology Electronic Repository (MOTHER) project is to establish a collection of nonhuman ovary histology images for multiple species as a resource for researchers and educators. An important component of sharing scientific data is the inclusion of the contextual metadata that describes the data. MOTHER extends the Ecological Metadata Language (EML) for documenting research data, leveraging its data provenance and usage license with the inclusion of metadata for ovary histology images. The design of the MOTHER metadata includes information on the donor animal, including reproductive cycle status, the slide and its preparation. MOTHER also extends the ezEML tool, called ezEML+MOTHER, for the specification of the metadata. The design of the MOTHER database (MOTHER-DB) captures the metadata about the histology images, providing a searchable resource for discovering relevant images. MOTHER also defines a curation process for the ingestion of a collection of images and its metadata, verifying the validity of the metadata before its inclusion in the MOTHER collection. A Web search provides the ability to identify relevant images based on various characteristics in the metadata itself, such as genus and species, using filters.},
}
@article {pmid40030035,
year = {2025},
author = {Jin, J and Zhang, R and Li, J and Gao, F and Liao, Z and Yu, Y and Wang, Y and Bucci, D and Xiao, M and Ma, R and Ma, Q and Gao, S and Lio, J and Novais, F and Huang, SC and Zhu, J and Ghoneim, H and Wen, H and Li, Z and Sun, N and Xin, G},
title = {The NAE1-mediated neddylation operates as an essential post-translational modification checkpoint for effector CD8[+] T cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2424061122},
doi = {10.1073/pnas.2424061122},
pmid = {40030035},
issn = {1091-6490},
support = {1R01CA269984//HHS | NIH | National Cancer Institute (NCI)/ ; CCR231013713//Susan G. Komen (SGK)/ ; RSG-23-1036499-01//American Cancer Society (ACS)/ ; },
mesh = {*CD8-Positive T-Lymphocytes/immunology/metabolism ; Humans ; *Protein Processing, Post-Translational ; Animals ; Mice ; *NEDD8 Protein/metabolism/genetics ; Ubiquitin-Activating Enzymes/metabolism/genetics ; NFATC Transcription Factors/metabolism/genetics ; Lymphocyte Activation ; Receptors, Antigen, T-Cell/metabolism ; Colonic Neoplasms/immunology/metabolism/genetics/pathology ; Signal Transduction ; Mice, Inbred C57BL ; },
abstract = {Optimal activation of CD8+ T cells is crucial for immunity-mediated destruction of cancer, requiring a substantial amount of proteins involved in metabolism, proliferation, and effector function. Despite extensive studies emphasizing the role of transcriptional regulation in this process, paired transcriptomic and proteomic analyses reveal that the RNA profile is poorly correlated with protein levels. This discrepancy underscores the importance of post-translational modifications (PTMs) in controlling protein abundance during activation. However, the impact of PTMs on the CD8+ T cell protein dynamic remains underexplored. We identify that neddylation, a recently discovered PTM, is activated in response to T cell receptor (TCR) stimulation and enriched in effector CD8+ T cells from colon cancer patients. Mechanistically, we found the rate-limiting enzyme of neddylation, neural precursor cell expressed developmentally down-regulated protein 8 activating enzyme E1 (NAE1), is induced by the NFATc1, a critical transcription factor downstream of TCR signaling. Our observation revealed that genetic ablation of NAE1 significantly disturbed the proteomic landscape related to activation and mitochondrial function. As a result, CD8+ T cells lacking NAE1 exhibited severely compromised activation, proliferation, and survival, which was accompanied by impaired mitochondrial function. Consistently, deletion of NAE1 in CD8+ T cells abolished their antitumor function and promoted tumor progression. By contrast, the overexpression of NAE1 significantly improved the function of tumor-infiltrating CD8+ T cells. Overall, we uncovered neddylation, a previously underappreciated PTM, as a proteomic checkpoint for CD8+ T cell activation. Enforced expression of NAE1 offers promising therapeutic potential for boosting the antitumor CD8+ T cell responses.},
}
@article {pmid40029426,
year = {2025},
author = {Zhang, J and Wang, Q and Gao, H and Qi, Q and He, W and Li, J and Yao, S and Li, W},
title = {Ecological suitability distribution of hop based on MaxEnt modeling.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {4},
pages = {346},
pmid = {40029426},
issn = {1573-2959},
mesh = {China ; *Environmental Monitoring ; *Humulus/growth &amp; development ; *Ecosystem ; Geographic Information Systems ; Climate ; Soil/chemistry ; },
abstract = {Hop has been widely utilized in both food production and traditional medicine owing to their distinctive flavor and various pharmacological effects. In recent years, the increasing demand for hop has led to their cultivation in many regions across China. However, hops require specific ecological conditions, including climate, soil, precipitation, and temperature, which significantly affect their distribution and growth. To facilitate the standardization and scientific cultivation of hops, it is essential to clarify the distribution of their ecological suitability. In this study, we collected data from 95 hops distribution locations and 115 ecological factors to determine the areas suitable for hops cultivation using the Maximum Entropy (MaxEnt) model and Geographic Information System (GIS). The highly suitable areas are primarily located in the northwestern part of the Xinjiang Uygur Autonomous Region, the eastern part of Gansu Province, Shaanxi Province, the southwestern part of Shanxi Province, and parts of Ningxia Hui Autonomous Region and Yunnan Province. These findings provide valuable guidance for the scientific cultivation of hops, ensuring the efficient use of ecological resources and promoting sustainable cultivation practices.},
}
@article {pmid40028932,
year = {2025},
author = {Eisaguirre, JM and Lohman, MG and Frye, GG and Johnson, HE and Riecke, TV and Williams, PJ},
title = {Estimating Spatially Explicit Survival and Mortality Risk From Telemetry Data With Thinned Point Process Models.},
journal = {Ecology letters},
volume = {28},
number = {3},
pages = {e70092},
doi = {10.1111/ele.70092},
pmid = {40028932},
issn = {1461-0248},
support = {//U.S. Geological Survey/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //Institute for Wetland and Waterfowl Research Bonnycastle Fellowship for Wetland and Waterfowl Research/ ; },
mesh = {Animals ; *Telemetry ; Alaska ; Ecosystem ; Models, Biological ; Mortality ; Geographic Information Systems ; },
abstract = {Mortality risk for animals often varies spatially and can be linked to how animals use landscapes. While numerous studies collect telemetry data on animals, the focus is typically on the period when animals are alive, even though there is important information that could be gleaned about mortality risk. We introduce a thinned spatial point process (SPP) modelling framework that couples relative abundance and space use with a mortality process to formally treat the occurrence of mortality events across the landscape as a spatial process. We show how this model can be embedded in a hierarchical statistical framework and fit to telemetry data to make inferences about how spatial covariates drive both space use and mortality risk. We apply the method to two data sets to study the effects of roads and habitat on spatially explicit mortality risk: (1) VHF telemetry data collected for willow ptarmigan in Alaska, and (2) hourly GPS telemetry data collected for black bears in Colorado. These case studies demonstrate the applicability of this method for different species and data types, making it broadly useful in enabling inferences about the mechanisms influencing animal survival and spatial population processes while formally treating survival as a spatial process, especially as the development and implementation of joint analyses continue to progress.},
}
@article {pmid40028774,
year = {2025},
author = {Fuzessy, L and Pizo, MA},
title = {NeoFrugivory: A comprehensive database for frugivory interactions and functional traits in the Neotropics.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70049},
doi = {10.1002/ecy.70049},
pmid = {40028774},
issn = {1939-9170},
support = {2023/12469-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 21/02943-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151167/2023-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304742/2019-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; *Fruit/physiology ; Vertebrates/physiology ; Databases, Factual ; Tropical Climate ; Plants/classification ; Feeding Behavior ; Herbivory ; Ecosystem ; },
abstract = {Frugivory plays a crucial role in shaping Neotropical ecosystems, influencing plant dispersal, community dynamics, and ecosystem function. Despite its ecological significance, a systematic understanding of frugivore-fruit interactions spanning the entire Neotropical realm has been lacking. Therefore, we compiled the NeoFrugivory database, which addresses this gap by synthesizing data from a wide range of sources, including peer-reviewed literature, field studies, and existing databases. NeoFrugivory represents a comprehensive compilation of 10,175 unique frugivory interactions across the Neotropical region, the most diverse in terms of vertebrate frugivores, and consolidates information from 419 studies spanning from 1967 to 2023. It includes 2375 plant species and 758 terrestrial vertebrate species. In addition to documenting frugivory interactions, NeoFrugivory includes information on functional traits for both plants and vertebrates, such as body mass, diet, fruit morphology, and seed characteristics. The database encompasses diverse terrestrial vertebrate taxa, including species belonging to taxonomic groups such as Primates, Chiroptera, Birds, Artiodactyla/Perissodactyla, Reptilia, Carnivora, Marsupialia, and Rodentia. By providing a centralized repository of frugivory interactions, NeoFrugivory facilitates comprehensive analyses of ecological networks, evolutionary patterns, and ecosystem dynamics across the Neotropics, and NeoFrugivory provides a unique resource for researchers interested in exploring the intricate dynamics of plant-animal frugivory interactions in the Neotropics. This database enables researchers to explore the ecological roles of different frugivore taxa, identify keystone species, assess the resilience of mutualistic networks, and evaluate the impacts of environmental change on fruit-frugivore interactions. Furthermore, NeoFrugivory serves as a valuable resource for conservation practitioners, supporting the design and implementation of targeted conservation strategies aimed at preserving biodiversity and ecosystem function in the Neotropical region. Overall, NeoFrugivory represents a significant advancement in our understanding of frugivory dynamics in the Neotropics and provides a foundation for future research and conservation efforts in this ecologically diverse and critically important region. There are no copyright restrictions on the data; this paper should be cited when data are used in publications.},
}
@article {pmid40027489,
year = {2025},
author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX},
title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e70001},
pmid = {40027489},
issn = {2770-596X},
abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.},
}
@article {pmid40023237,
year = {2025},
author = {Munteanu, A and Bortolini, M and Feltracco, M and Alterio, A and Cairns, WRL and Turetta, C and Barbaro, E and Barbante, C and Gambaro, A and Azzaro, M},
title = {Contamination by benzothiazoles in the Arctic: first evidence in the seawater of the Greenland Sea.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125943},
doi = {10.1016/j.envpol.2025.125943},
pmid = {40023237},
issn = {1873-6424},
abstract = {Benzothiazoles (BTHs), used in industrial chemistry, consumer products, and pharmaceuticals, are emerging contaminants due to their environmental presence and toxicological risks to aquatic life and human health. However, their environmental fate in seawater remains poorly investigated. This study reports for the first time the occurrence and distribution of six BTHs in the sub-Arctic seawater of the Greenland Sea. Using solid-phase extraction combined with ultrahigh performance liquid chromatography tandem mass spectrometry, total BTHs were detected at concentrations ranging from 0.2 to 1043 ng L[-1]. Benzothiazole, 2-hydroxy-benzothiazole, 2-methylthio-benzothiazole, and 2-methyl-benzothiazole exhibited higher mean concentrations (355 ± 335, 114 ± 80, 34 ± 7, 15 ± 8 ng L[-1], respectively) compared to 2-thiocyanomethylthio-benzothiazole (0.5 ± 0.9 ng L[-1]) and 2-amino-benzothiazole (0.3 ± 0.2 ng L[-1]). Local emissions and both short- and long-range transport may account for BTHs presence in the Greenland Sea. The spatial distribution of BTHs along the 75° N transect and in the water column appears influenced by the Greenland Sea Gyre circulation and deep convection processes. Total BTHs distribution showed no significant differences between superficial and water column concentrations or between the outermost and innermost transect zones, as determined by the Mann-Whitney test, although concentrations were generally higher in the zone influenced by the Norwegian Atlantic Current. The ecological risks of BTHs, assessed using the risk quotient methodology, indicate a low threat to aquatic life. This research underscores the need for monitoring BTHs in the Arctic to understand their sources, transport, and environmental fate, providing a foundation for future studies.},
}
@article {pmid40022802,
year = {2025},
author = {Wang, H and Liu, C and Li, L and Kong, Y and Akbar, A and Zhou, X},
title = {High-precision inversion of urban river water quality via integration of riparian spatial structures and river spectral signatures.},
journal = {Water research},
volume = {278},
number = {},
pages = {123378},
doi = {10.1016/j.watres.2025.123378},
pmid = {40022802},
issn = {1879-2448},
abstract = {With the ongoing process of urbanization, it poses challenges to the monitoring of water quality in urban rivers. The mainstream methods for remote sensing water quality monitoring rely on the optical characteristics of water to achieve water quality inversion, while overlooking the correlation between water quality and riparian zones. The spatial arrangement and scale fluctuation of the riparian zones exert a substantial influence on water quality as it serves as an intermediary region connecting riverine and terrestrial ecosystems. Therefore, this study firstly employed unmanned aerial vehicle (UAV)-borne multispectral remote sensing technology to capture the subtle variations in urban river water quality and obtain detailed spatial information of the riparian zone. The Liang-Kleeman information flow was subsequently employed to quantitatively assess the causal responses of the spatial composition of riparian zone to water quality parameters across various spatial scales. Finally, we developed a hierarchical ensemble learning model for water quality assessment by integrating the spatial characteristics of the riparian zone with the spectral properties of the water body. The result demonstrates that this model accurately delineated water quality grades for three key parameters: ammonia nitrogen (NH3N), chemical oxygen demand (COD), and total phosphorus (TP), achieving accuracies of 94.87 %, 92.31 %, and 89.74 %, respectively. Our study presents a water quality inversion method for urban rivers, which holds significant guidance for the monitoring and management of urban rivers and contributes to further promoting the sustainable development of cities.},
}
@article {pmid39974046,
year = {2025},
author = {Slack, SD and Esquinca, E and Arehart, CH and Boorgula, MP and Szczesny, B and Romero, A and Campbell, M and Chavan, S and Rafaels, N and Watson, H and Landis, RC and Hansel, NN and Rotimi, CN and Olopade, CO and Figueiredo, CA and Ober, C and Liu, AH and Kenny, EE and Kammers, K and Ruczinski, I and Taub, MA and Daya, M and Gignoux, CR and Kechris, K and Barnes, KC and Mathias, RA and Johnson, RK},
title = {Prediction and Characterization of Genetically Regulated Expression of Target Tissues in Asthma.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39974046},
support = {R01 AI132476/AI/NIAID NIH HHS/United States ; R01 HL104608/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Genetic control of gene expression in asthma-related tissues is not well-characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma in those populations.<br><br>OBJECTIVE: To create novel transcriptome prediction models for asthma tissues (nasal epithelium and CD4+ T cells) and apply them in transcriptome-wide association study (TWAS) to discover candidate asthma genes.<br><br>METHODS: We developed and validated gene expression prediction databases for unstimulated CD4+ T cells (CD4+T) and nasal epithelium using an elastic net framework. Combining these with existing prediction databases (N=51), we performed TWAS of 9,284 individuals of African-ancestry to identify tissue-specific and cross-tissue candidate genes for asthma. For detailed Methods, please see the Supplemental Methods.<br><br>RESULTS: Novel databases for CD4+T and nasal epithelial gene expression prediction contain 8,351 and 10,296 genes, respectively, including four asthma loci (SCGB1A1, MUC5AC, ZNF366, LTC4S) not predictable with existing public databases. Prediction performance was comparable to existing databases and was most accurate for populations sharing ancestry with the training set (e.g. African ancestry). From TWAS, we identified 17 candidate causal asthma genes (adjusted P<0.1), including genes with tissue-specific (IL33 in nasal epithelium) and cross-tissue (CCNC and FBXW7) effects.<br><br>CONCLUSIONS: Expression of IL33, CCNC, and FBXW7 may affect asthma risk in African ancestry populations by mediating inflammatory responses. The addition of CD4+T and nasal epithelium prediction databases to the public sphere will improve ancestry representation and power to detect novel gene-trait associations from TWAS.},
}
@article {pmid40025088,
year = {2025},
author = {Kim, SY and Cheon, S and Park, C and Soh, HY},
title = {Integrating DNA metabarcoding and morphological analysis improves marine zooplankton biodiversity assessment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7283},
pmid = {40025088},
issn = {2045-2322},
support = {RS-2018-KS181192//Korea Institute of Marine Science &amp; Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea/ ; RS-2018-KS181192//Korea Institute of Marine Science &amp; Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries, Korea/ ; No. RS-2024-00442775)//Global-Learning &amp; Academic research institution for Master's &#xb7; PhD students, and Postdocs (LAMP) Program of the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education/ ; Grant number: 2018-3416//Chonnam National University/ ; },
mesh = {Animals ; *Zooplankton/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Copepoda/genetics/classification ; Ecosystem ; China ; Oceans and Seas ; Aquatic Organisms/genetics/classification ; },
abstract = {Marine copepod communities play crucial roles in ocean ecosystems. However, their accurate assessment remains challenging due to taxonomic complexities. This study combines morphological and DNA metabarcoding approaches to evaluate copepod diversity and community structure in the northern East China Sea. Zooplankton samples were collected from 10 stations along a coastal-offshore gradient in August 2019. Morphological analysis identified 34 species from 25 genera, while DNA metabarcoding detected 31 species from 20 genera. Both methods revealed distinct coastal and offshore assemblages, with Paracalanus parvus s.l. as the dominant species across all stations. A significant positive correlation was found between morphology-based individual counts and metabarcoding sequence reads (Spearman's Rho = 0.58, p < 0.001), improving at the genus level (Rho = 0.70, p < 0.001). Redundancy analysis revealed that salinity, temperature, and phytoplankton density significantly influenced copepod distribution. Although both approaches captured similar broad-scale patterns, they provided complementary insights into community structure. Morphological identification was more effective for detecting Cyclopoida diversity, whereas DNA metabarcoding had greater sensitivity for specific Calanoid species. This study underscores the value of integrating traditional and molecular methods for marine biodiversity assessment, especially in the context of global environmental changes.},
}
@article {pmid40021550,
year = {2025},
author = {Post, AK and Richardson, AD},
title = {Predicting end-of-season timing across diverse North American grasslands.},
journal = {Oecologia},
volume = {207},
number = {3},
pages = {44},
pmid = {40021550},
issn = {1432-1939},
support = {EF-1065029//National Science Foundation/ ; EF-1702697//National Science Foundation/ ; DESC0016011//U.S. Department of Energy/ ; },
mesh = {*Grassland ; *Seasons ; *Climate Change ; North America ; Ecosystem ; },
abstract = {Climate change is altering the timing of seasonal vegetation cycles (phenology), with cascading consequences on larger ecosystem processes. Therefore, understanding the drivers of vegetation phenology is critical to predicting ecological impacts of climate change. While numerous phenology models exist to predict the timing of the start of the growing season (SOS), there are fewer end-of-season (EOS) models, and most perform poorly in grasslands, since they were made for forests. Our objective was to develop an improved EOS grassland phenology model. We used repeat digital imagery from the PhenoCam Network to extract EOS dates for 44 diverse North American grassland sites (212 site-years) that we fit to 20 new and 3 existing EOS models. All new EOS models (RMSE = 22-33 days between observed and predicted dates) performed substantially better than existing ones (RMSE = 43-46 days). The top model predicted EOS after surpassing a threshold of either accumulated cold temperatures or dryness, but only after a certain number of days following SOS. Including SOS date improved all model fits, indicating a strong correlation between start- and end-of-season timing. Model performance was further improved by independently optimizing parameters for six distinct climate regions (RMSE = 4-19 days). While the best model varied slightly by region, most included similar drivers as the top all-sites model. Thus, across diverse grassland sites, EOS is influenced by both weather (temperature, moisture) and SOS timing. Incorporating these new EOS models into Earth System Models should improve predictions of grassland dynamics and associated ecosystem processes.},
}
@article {pmid39955977,
year = {2025},
author = {Otay, EN and Uzun, P and Üstün, A},
title = {Multifactorial risk mapping of oil spill accidents for emergency response areas at regional, national and international scales.},
journal = {Marine pollution bulletin},
volume = {213},
number = {},
pages = {117670},
doi = {10.1016/j.marpolbul.2025.117670},
pmid = {39955977},
issn = {1879-3363},
mesh = {*Petroleum Pollution ; Risk Assessment ; Geographic Information Systems ; Turkey ; Environmental Monitoring/methods ; Risk Management ; Accidents/statistics &amp; numerical data ; },
abstract = {Quantification and mapping of oil spill risk are essential for emergency response and mitigation of marine accidents. Large-scale risk management involves geographical identification of hazards and sensitivities in coastal and offshore regions. In this study, a multifactorial oil spill risk model was developed on a national scale by determining the frequency (probability) and sensitivity (severity) of marine and coastal accidents. Seven accident frequency and 51 sensitivity factors were investigated within the Turkish Emergency Response Area (TERA) of 660,908 km[2]. Hydrographical, meteorological, oceanographical, and maritime conditions were analyzed to calculate accident frequency. The sensitive areas were mapped using the geographical distribution of ecologic, social, and economic assets. Using data analytics, digital maps of accident frequency, sensitivity and risk were produced in a GIS grid of 21,410 cells with 3NM resolution. Accident hotspots were identified from scalable frequency maps showing regions of high accident probability. Sensitivity factors were analyzed from environmental, social, and economic vulnerabilities. Using their geographic distribution, a sensitivity map was generated and hotspots were identified. Frequency and sensitivity indices were combined to obtain the grid-based high-resolution oil spill risk map on a scalable GIS platform. High-risk areas were identified for future research on oil spill simulations and emergency response plans. The methodology may help scientists and environmental experts develop regional, national, and global risk assessment tools. The outcomes within the TERA may serve as planning and decision support tools for lawmakers, environmental experts, and oil spill response professionals to manage oil pollution risk across the TERA.},
}
@article {pmid40016792,
year = {2025},
author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R},
title = {Correction: Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {21},
number = {1},
pages = {11},
doi = {10.1186/s13002-025-00763-7},
pmid = {40016792},
issn = {1746-4269},
}
@article {pmid40014700,
year = {2025},
author = {Chen, Z and Baeza, JA and Chen, C and Gonzalez, MT and González, VL and Greve, C and Kocot, KM and Arbizu, PM and Moles, J and Schell, T and Schwabe, E and Sun, J and Wong, NLWS and Yap-Chiongco, M and Sigwart, JD},
title = {A genome-based phylogeny for Mollusca is concordant with fossils and morphology.},
journal = {Science (New York, N.Y.)},
volume = {387},
number = {6737},
pages = {1001-1007},
doi = {10.1126/science.ads0215},
pmid = {40014700},
issn = {1095-9203},
mesh = {Animals ; *Phylogeny ; *Mollusca/genetics/classification/anatomy &amp; histology ; *Genome ; *Fossils ; },
abstract = {Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.},
}
@article {pmid40012989,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Olive Crescent, Trisateles emortualis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {178},
pmid = {40012989},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Trisateles emortualis (the Olive Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 565.5 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.01 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,176 protein coding genes.},
}
@article {pmid40012987,
year = {2024},
author = {McGregor, AP and Sumner-Rooney, L and Burkmar, R and Schoenauer, A and , and , and , and , and , and , and , },
title = {The genome sequence of the silver stretch spider, Tetragnatha montana (Simon, 1874) (Araneae: Tetragnathidae).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {288},
pmid = {40012987},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Tetragnatha montana (the silver stretch spider; Arthropoda; Arachnida; Araneae; Tetragnathidae). The genome sequence is 784.7 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.49 kilobases in length.},
}
@article {pmid40011724,
year = {2025},
author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, Z and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS},
title = {Reply to: Causal claims, causal assumptions and protected area impact.},
journal = {Nature},
volume = {638},
number = {8052},
pages = {E42-E44},
pmid = {40011724},
issn = {1476-4687},
}
@article {pmid40011233,
year = {2025},
author = {Dos Santos, AP and da Silva Junior, AX and Nery, LM and Gomes, G and Toniolo, BP and da Cunha E Silva, DC and Lourenço, RW},
title = {Random forest algorithm applied to model soil textural classification in a river basin.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {3},
pages = {330},
pmid = {40011233},
issn = {1573-2959},
mesh = {*Soil/chemistry ; *Environmental Monitoring/methods ; *Rivers/chemistry ; *Algorithms ; Agriculture ; Machine Learning ; Geographic Information Systems ; Conservation of Natural Resources/methods ; Random Forest ; },
abstract = {The proportion of sand, silt, and clay defines soil texture, significantly influencing agricultural and ecological practices. However, conventional classification methods are costly and limit evaluation frequency and scope. In contrast, machine learning algorithms, such as random forest, provide a more efficient solution for accurate soil texture predictions. This study aims to address this knowledge gap by integrating geoprocessing, precision agriculture, and machine learning to classify soil texture in the Sorocabuçu River Basin (SRB), predominantly agricultural. Twenty-seven sampling points were selected based on topography and land use, ensuring the representativeness of area variations and the reliability of classification. Granulometric analysis was performed using the pipette method to separate sand, silt, and clay. The data were spatially interpolated using geographic information system (GIS) techniques. Soil texture was classified using the random forest algorithm, trained on 70% of the data and tested on 30%, evaluating overall accuracy, kappa index, sensitivity, and specificity. Fifty trees (ntree) and four features per split (ntry) were used, considering the variability of parameters to ensure satisfactory results. The varied spatial distribution of clay, along with high levels of sand and silt, suggests greater vulnerability to erosion without conservation management practices. The random forest model achieved an out-of-bag (OOB) error of 2.78%, a kappa index of 0.88, and an overall accuracy of 0.92, demonstrating excellent predictive capacity. The variability of sand was essential, but the Sandy Clay Loam (SCL) class posed challenges due to its intermediate characteristics between sand and clay, resulting in classification overlaps. This integrated methodology enhances understanding of soil structure in the SRB and provides a foundation for future research and practical applications, supporting food security and environmental sustainability. The model can be applied in other locations and agricultural contexts. In homogeneous soils, the method can be improved through the application of machine learning algorithms to enhance accuracy.},
}
@article {pmid39742992,
year = {2025},
author = {Kim, DH and Kim, Y},
title = {Factors Associated With Habitual Drug Use Among Adolescents: A Secondary Data Analysis.},
journal = {Asian nursing research},
volume = {19},
number = {1},
pages = {78-85},
doi = {10.1016/j.anr.2024.12.006},
pmid = {39742992},
issn = {2093-7482},
mesh = {Humans ; Adolescent ; Female ; Male ; Republic of Korea/epidemiology ; *Substance-Related Disorders/epidemiology ; *Adolescent Behavior/psychology ; Risk Factors ; Risk-Taking ; Prevalence ; Cross-Sectional Studies ; Secondary Data Analysis ; },
abstract = {PURPOSE: Drug use during adolescence can have lasting health consequences, and understanding the factors that contribute to drug use is essential for effective prevention. This study aimed to identify the factors influencing habitual drug use among South Korean adolescents. It employed Bronfenbrenner's ecological model to examine personal, familial, school-related, and social factors.<br><br>METHODS: The study analyzed data from the 19th Korea Youth Risk Behavior Survey for 41,928 students from 1st grade of middle school to 3rd grade of high school. Data analysis involved cross-tabulation and logistic regression for complex samples.<br><br>RESULTS: The prevalence of habitual drug use was 1.4%. Significant personal factors included smoking [adjusted odds ratio (aOR)&#xa0;=&#xa0;2.61], alcohol consumption (aOR&#xa0;=&#xa0;1.55), sexual intercourse (aOR&#xa0;=&#xa0;1.45), smartphone overdependence (high-risk group aOR&#xa0;=&#xa0;2.04, potential risk group aOR&#xa0;=&#xa0;1.31), suicidal ideation (aOR&#xa0;=&#xa0;2.66), depressed mood (aOR&#xa0;=&#xa0;1.87), and loneliness (aOR&#xa0;=&#xa0;1.88). Significant family factors included non-cohabitation with family (aOR&#xa0;=&#xa0;1.86) and both parents being foreign-born (aOR&#xa0;=&#xa0;3.36). Experience of violence (aOR&#xa0;=&#xa0;2.95) was also a significant factor.<br><br>CONCLUSION: This study highlights the need for an integrated approach to prevent adolescent drug use by addressing adolescents' personal behaviors, family dynamics, and school environments. Prevention programs should account for the influence of multiple systems on habitual drug use. School and community nurses should adopt a comprehensive, multi-dimensional strategy that involves families, schools, and communities to prevent adolescent drug use. Additionally, there is a need to develop family-centered and culturally sensitive drug prevention programs for adolescents.},
}
@article {pmid39297890,
year = {2025},
author = {Daich Varela, M and Sanders Villa, A and Pontikos, N and Crossland, MD and Michaelides, M},
title = {Digital health and wearable devices for retinal disease monitoring.},
journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie},
volume = {263},
number = {2},
pages = {279-289},
pmid = {39297890},
issn = {1435-702X},
support = {206619/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Wearable Electronic Devices ; *Telemedicine/instrumentation ; *Retinal Diseases/diagnosis/therapy/physiopathology ; Monitoring, Physiologic/instrumentation/methods ; Artificial Intelligence ; Digital Health ; },
abstract = {Digital health is wielding a growing influence across all areas of healthcare, encompassing various facets such as telemedicine, artificial intelligence (AI), and electronic healthcare records. In Ophthalmology, digital health innovations can be broadly divided into four categories: (i) self-monitoring home devices and apps, (ii) virtual and augmented reality visual aids, (iii) AI software, and (iv) wearables. Wearable devices can work in the background, collecting large amounts of objective data while we do our day-to-day activities, which may be ecologically more valid and meaningful to patients than that acquired in traditional hospital settings. They can be a watch, wristband, piece of clothing, glasses, cane, smartphone in our pocket, earphones, or any other device with a sensor that we carry with us. Focusing on retinal diseases, a key challenge in developing novel therapeutics has been to prove a meaningful benefit in patients' lives and the creation of objective patient-centred endpoints in clinical trials. In this review, we will discuss wearable devices collecting different aspects of visual behaviour, visual field, central vision, and functional vision, as well as their potential implementation as outcome measures in research/clinical trial settings. The healthcare landscape is facing a paradigm shift. Clinicians have a key role of collaborating with the development and fine-tuning of digital health innovations, as well as identifying opportunities where they can be leveraged to enhance our understanding of retinal diseases and improve patient outcomes.},
}
@article {pmid40007820,
year = {2024},
author = {Grieco, F and Parisi, S and Simmenroth, A and Eichinger, M and Zirkel, J and König, S and Jünger, J and Geck, E and Schwienhorst-Stich, EM},
title = {Planetary health education in undergraduate medical education in Germany: results from structured interviews and an online survey within the national PlanetMedEd Project.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1507515},
pmid = {40007820},
issn = {2296-858X},
abstract = {BACKGROUND: In light of the accumulating evidence, awareness and urgency to act upon the three planetary crises - climate change, biodiversity loss, and pollution - the concept of Planetary Health underscores their profound implications for health and promotes actionable solutions to advance both wellbeing and ecological sustainability. Despite (inter)national calls to integrate Planetary Health into health workers' curricula, the current status of Planetary Health Education in undergraduate medical education in Germany is unclear. This study therefore aimed (a) to assess the current implementation of Planetary Health in undergraduate medical education in Germany and (b) to explore its characteristics as a foundation to develop evidence-informed recommendations for mainstreaming Planetary Health Education in medical schools in Germany.<br><br>METHODS: The study comprised structured interviews followed by an online survey, both targeting all 39 medical schools in Germany. In 2021, structured interviews were conducted with students, educators and deanery staff at medical schools. In 2023, educators and deanery staff participated in an online survey based on the findings from the interviews.<br><br>FINDINGS: In total, 80% of the 39 medical schools participated in the interviews, while 90% took part in the online survey. Based on integrated findings, 35 medical schools (90%) offered Planetary Health Education, with a median of two educational activities, including both stand-alone courses and lectures integrated into other courses. Despite an overall increase since winter semester 2021/2022, most educational activities were electives and not part of the mandatory curriculum. Innovative educational approaches and learning objectives differed significantly between mandatory and elective formats. In contrast to mandatory educational activities, student involvement was reported for the majority of electives and was significantly associated with transformative learning objectives.<br><br>INTERPRETATION: Despite a steady rise in teaching activities, mandatory Planetary Health Education remains insufficiently integrated into undergraduate medical education in Germany. Key criteria defining high-quality Planetary Health Education, such as innovative educational approaches, practical skills, and transformative learning, were primarily reflected in electives, that reach only a minority of students. To adequately equip the future healthcare workforce, the current barriers to successfully integrating Planetary Health into medical education must be systematically addressed and overcome.},
}
@article {pmid40007688,
year = {2025},
author = {Boyes, D and Lees, DC and Coates, BS and , and , and , and , and , and , and , and , },
title = {The genome sequence of the European Corn Borer, Ostrinia nubilalis Hübner, 1796.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {12},
pmid = {40007688},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female specimen of Ostrinia nubilalis (European Corn Borer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a total length of 495.50 megabases. Most of the assembly (99.87%) is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,780 protein-coding genes.},
}
@article {pmid40007687,
year = {2025},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , },
title = {The genome sequence of Red Underwing, Catocala nupta Linnaeus, 1767.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {36},
pmid = {40007687},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female specimen of Catocala nupta (Red Underwing; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 930.40 megabases. Most of the assembly (99.82%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,889 protein-coding genes.},
}
@article {pmid40004070,
year = {2025},
author = {Brzhozovskiy, AG and Semenov, SD and Zherebker, AY and Bugrova, AE and Yurova, MN and Zhernov, YV and Kovaleva, OA and Semenov, AL and Abroskin, DP and Kruglov, SS and Fedoros, EI and Kononikhin, AS and Nikolaev, EN},
title = {Hepatoprotective Activity of Nature-Derived Polyphenols Studied by Mass Spectrometry Based Multi-OMICS Approach.},
journal = {International journal of molecular sciences},
volume = {26},
number = {4},
pages = {},
doi = {10.3390/ijms26041604},
pmid = {40004070},
issn = {1422-0067},
support = {22-75-10140//Russian Science Foundation/ ; },
mesh = {Animals ; *Polyphenols/pharmacology ; Mice ; *Metabolomics/methods ; *Carbon Tetrachloride ; *Mice, Inbred BALB C ; *Protective Agents/pharmacology/chemistry ; Liver/drug effects/metabolism ; Mass Spectrometry/methods ; Proteomics/methods ; Pueraria/chemistry ; Metabolome/drug effects ; Plant Extracts/pharmacology/chemistry ; Male ; Proteome/drug effects/metabolism ; Multiomics ; },
abstract = {The aim of this study was to examine the hepatoprotective activity of multicomponent mixtures of natural origin in the BALB/C mouse model, with subacute liver failure (SALF) induced by the administration of toxin carbon tetrachloride (CCl4). The hepatoprotective activity of activated hydrolytic lignin (BP-Cx-1), humic acid peloids (HA), and isoflavones from kudzu Pueraria lobata roots (IFL) was evaluated using mass spectrometry (MS)-based omics technologies. Our MS-based approach revealed new insights into the molecular mechanisms of the hepatoprotective activity of multicomponent mixtures of natural origin. Significant differences were observed in the proteome and metabolome profiles of the urine and liver of BALB/c mice with SALF between a control group with CCl4 administration, intact controls, and groups receiving potential hepatoprotectors of natural origin (BP-Cx-1, HA, IFL). Proteomic and metabolomics analyses demonstrated that among the hepatoprotectors, IFL possessed the highest hepatoprotective potential, which correlated well with the relative effectiveness of the drugs recorded during in vitro studies. These results correlate with the relative effectiveness of the drugs recorded in previous in vitro and in vivo studies. The leading IFL activity may be attributed to a higher content of active polyphenolic components compared to heterogeneous HA and BP-Cx-1. Enrichment with active components by fractionation is a direction that can be explored for developing hepatoprotective agents based on natural complex polyphenols.},
}
@article {pmid39996333,
year = {2025},
author = {Medeiros, W and Kralova, S and Oliveira, V and Ziemert, N and Sehnal, L},
title = {Antarctic bacterial natural products: from genomic insights to drug discovery.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00045e},
pmid = {39996333},
issn = {1460-4752},
abstract = {Covering: up to the end of 2024Microbial life dominates the extreme continent Antarctica, playing a pivotal role in ecosystem functioning and serving as a reservoir of specialized metabolites known as natural products (NPs). NPs not only contribute to microbial adaptation to harsh conditions but also modulate microbial community structure. Long-term isolation and environmental pressures have shaped the genomes of Antarctic bacteria, suggesting that they also encode unique NPs. Since NPs are also an important source of drugs, we argue that investigating Antarctic bacterial NPs is essential not only for understanding their ecological role and evolution, but also for discovering new chemical structures, biosynthetic mechanisms, and potential new drugs. Yet, despite advances in omics technologies and increased scientific activities in Antarctica, relatively few new bacterial NPs have been discovered. The lack of systematic research activities focused on the exploration of Antarctic bacteria and their NPs constitutes a big problem considering the climate change issue, to which ecosystems in polar regions are the most sensitive areas on the Earth. Here, we highlight the currently available data on Antarctic bacteria, their biosynthetic potential, and the successful NP discoveries, while addressing the challenges in NP research and advocating for systematic, collaborative efforts aligned with the Antarctic Treaty System and the Antarctic Conservation Biogeographic Regions.},
}
@article {pmid39995465,
year = {2025},
author = {Huang, J and Bibri, SE and Keel, P},
title = {Generative spatial artificial intelligence for sustainable smart cities: A pioneering large flow model for urban digital twin.},
journal = {Environmental science and ecotechnology},
volume = {24},
number = {},
pages = {100526},
pmid = {39995465},
issn = {2666-4984},
abstract = {Rapid urbanization, alongside escalating resource depletion and ecological degradation, underscores the critical need for innovative urban development solutions. In response, sustainable smart cities are increasingly turning to cutting-edge technologies-such as Generative Artificial Intelligence (GenAI), Foundation Models (FMs), and Urban Digital Twin (UDT) frameworks-to transform urban planning and design practices. These transformative tools provide advanced capabilities to analyze complex urban systems, optimize resource management, and enable evidence-based decision-making. Despite recent progress, research on integrating GenAI and FMs into UDT frameworks remains scant, leaving gaps in our ability to capture complex urban flows and multimodal dynamics essential to achieving environmental sustainability goals. Moreover, the lack of a robust theoretical foundation and real-world operationalization of these tools hampers comprehensive modeling and practical adoption. This study introduces a pioneering Large Flow Model (LFM), grounded in a robust foundational framework and designed with GenAI capabilities. It is specifically tailored for integration into UDT systems to enhance predictive analytics, adaptive learning, and complex data management functionalities. To validate its applicability and relevance, the Blue City Project in Lausanne City is examined as a case study, showcasing the ability of the LFM to effectively model and analyze urban flows-namely mobility, goods, energy, waste, materials, and biodiversity-critical to advancing environmental sustainability. This study highlights how the LFM addresses the spatial challenges inherent in current UDT frameworks. The LFM demonstrates its novelty in comprehensive urban modeling and analysis by completing impartial city data, estimating flow data in new locations, predicting the evolution of flow data, and offering a holistic understanding of urban dynamics and their interconnections. The model enhances decision-making processes, supports evidence-based planning and design, fosters integrated development strategies, and enables the development of more efficient, resilient, and sustainable urban environments. This research advances both the theoretical and practical dimensions of AI-driven, environmentally sustainable urban development by operationalizing GenAI and FMs within UDT frameworks. It provides sophisticated tools and valuable insights for urban planners, designers, policymakers, and researchers to address the complexities of modern cities and accelerate the transition towards sustainable urban futures.},
}
@article {pmid39995103,
year = {2025},
author = {Campbell, IH and Needham, N and Grossi, H and Kamenska, I and Luz, S and Sheehan, S and Thompson, G and Thrippleton, MJ and Gibbs, MC and Leitao, J and Moses, T and Burgess, K and Rigby, BP and Simpson, SA and McIntosh, E and Brown, R and Meadowcroft, B and Creasy, F and Mitchell-Grigorjeva, M and Norrie, J and McLellan, A and Fisher, C and Zieliński, T and Gaggioni, G and Campbell, H and Smith, DJ},
title = {A pilot study of a ketogenic diet in bipolar disorder: clinical, metabolic and magnetic resonance spectroscopy findings.},
journal = {BJPsych open},
volume = {11},
number = {2},
pages = {e34},
doi = {10.1192/bjo.2024.841},
pmid = {39995103},
issn = {2056-4724},
abstract = {BACKGROUND: Preliminary evidence suggests that a ketogenic diet may be effective for bipolar disorder.<br><br>AIMS: To assess the impact of a ketogenic diet in bipolar disorder on clinical, metabolic and magnetic resonance spectroscopy outcomes.<br><br>METHOD: Euthymic individuals with bipolar disorder (N = 27) were recruited to a 6- to 8-week single-arm open pilot study of a modified ketogenic diet. Clinical, metabolic and MRS measures were assessed before and after the intervention.<br><br>RESULTS: Of 27 recruited participants, 26 began and 20 completed the ketogenic diet. For participants completing the intervention, mean body weight fell by 4.2 kg (P < 0.001), mean body mass index fell by 1.5 kg/m[2] (P < 0.001) and mean systolic blood pressure fell by 7.4 mmHg (P < 0.041). The euthymic participants had average baseline and follow-up assessments consistent with them being in the euthymic range with no statistically significant changes in Affective Lability Scale-18, Beck Depression Inventory and Young Mania Rating Scale. In participants providing reliable daily ecological momentary assessment data (n = 14), there was a positive correlation between daily ketone levels and self-rated mood (r = 0.21, P < 0.001) and energy (r = 0.19 P < 0.001), and an inverse correlation between ketone levels and both impulsivity (r = -0.30, P < 0.001) and anxiety (r = -0.19, P < 0.001). From the MRS measurements, brain glutamate plus glutamine concentration decreased by 11.6% in the anterior cingulate cortex (P = 0.025) and fell by 13.6% in the posterior cingulate cortex (P = <0.001).<br><br>CONCLUSIONS: These findings suggest that a ketogenic diet may be clinically useful in bipolar disorder, for both mental health and metabolic outcomes. Replication and randomised controlled trials are now warranted.},
}
@article {pmid39909332,
year = {2025},
author = {Cheng, Z and He, Y and Wang, N and Wu, L and Xu, J and Shi, J},
title = {Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {368},
number = {},
pages = {125787},
doi = {10.1016/j.envpol.2025.125787},
pmid = {39909332},
issn = {1873-6424},
mesh = {*Cadmium/metabolism ; *Glycine max/genetics/microbiology/metabolism ; *Rhizosphere ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Microbiota ; Soil/chemistry ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Metagenomics ; Metagenome ; Multiomics ; },
abstract = {Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha[-1] and 1950 kg ha[-1]) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.},
}
@article {pmid39882857,
year = {2025},
author = {Grettenberger, C and Gold, DA and Brown, CT},
title = {Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs.},
journal = {mSphere},
volume = {10},
number = {2},
pages = {e0101324},
doi = {10.1128/msphere.01013-24},
pmid = {39882857},
issn = {2379-5042},
mesh = {*Cyanobacteria/genetics/classification/metabolism ; *Oxygen/metabolism ; *Ecosystem ; *Photosynthesis ; Phototrophic Processes ; Biological Evolution ; Computational Biology/methods ; Phylogeny ; Metagenome ; },
abstract = {The evolution of oxygenic photosynthesis in the Cyanobacteria was one of the most transformative events in Earth history, eventually leading to the oxygenation of Earth's atmosphere. However, it is difficult to understand how the earliest Cyanobacteria functioned or evolved on early Earth in part because we do not understand their ecology, including the environments in which they lived. Here, we use a cutting-edge bioinformatics tool to survey nearly 500,000 metagenomes for relatives of the taxa that likely bookended the evolution of oxygenic photosynthesis to identify the modern environments in which these organisms live. Ancestral state reconstruction suggests that the common ancestors of these organisms lived in terrestrial (soil and/or freshwater) environments. This restricted distribution may have increased the lag between the evolution of oxygenic photosynthesis and the oxygenation of Earth's atmosphere.IMPORTANCECyanobacteria generate oxygen as part of their metabolism and are responsible for the rise of oxygen in Earth's atmosphere over two billion years ago. However, we do not know how long this process may have taken. To help constrain how long this process would have taken, it is necessary to understand where the earliest Cyanobacteria may have lived. Here, we use a cutting-edge bioinformatics tool called branch water to examine the environments where modern Cyanobacteria and their relatives live to constrain those inhabited by the earliest Cyanobacteria. We find that these species likely lived in non-marine environments. This indicates that the rise of oxygen may have taken longer than previously believed.},
}
@article {pmid39240386,
year = {2025},
author = {Han, S and Hogue, W},
title = {Assessing Human Influence and Vegetative Dune Dynamics on Barrier Islands via Satellite Raster Classification.},
journal = {Environmental management},
volume = {75},
number = {3},
pages = {524-537},
pmid = {39240386},
issn = {1432-1009},
mesh = {Alabama ; *Islands ; Humans ; *Conservation of Natural Resources/methods ; *Ecosystem ; Mississippi ; Satellite Imagery ; Geographic Information Systems ; Climate Change ; Environmental Monitoring/methods ; },
abstract = {Barrier islands support ecological diversity and offshore ecosystems and provide critical protection to coastal communities. Climate change has intensified the frequency and severity of hurricanes affecting these islands, leading to ongoing erosion. The primary goal of this study was to explore the relationship between human intervention such as development and construction and the vegetative dune systems on Gulf Coast barrier islands in Alabama and Mississippi, USA. This research employed two decades of satellite images of three neighboring barrier islands and employed GIS raster classification to track changes in the vegetative dune system in terms of: (1) dune coverage (surface area of the vegetation), (2) vegetative maturity (vegetation type), and (3) stability (fluctuations in the vegetative coverage over time). Time series and trend analyses were used to compare the results for three neighboring islands. The findings show that Dauphin Island, which features both commercial facilities and vacation homes, exhibited a decrease in total area over time, and had the lowest percentage of vegetative dune coverage and highest level of vegetative fluctuation. In contrast, Petit Bois and Horn Islands, which remain untouched by human activity, displayed significantly higher levels of vegetative maturity and coverage and comparatively less fluctuation. This research provides a foundation for those advocating for dune restoration strategies, development limitations, and conservation regulations as nature-based infrastructure solutions to combat erosion on barrier islands and serves as a point of entry for future inquiries in the field of environmental management.},
}
@article {pmid39990132,
year = {2025},
author = {Keet, JH and Hui, C},
title = {One-hectare fine-scale dataset of a fynbos plant community in the Cape Floristic Region.},
journal = {Data in brief},
volume = {59},
number = {},
pages = {111334},
pmid = {39990132},
issn = {2352-3409},
abstract = {Cape fynbos, which forms part of the Cape Floristic Region (CFR) of South Africa, a global biodiversity hotspot, is renowned for its high levels of plant species endemism and diversity. This extraordinary ecosystem, characterised by nutrient-poor soils and fire-adapted vegetation, is a treasure trove of endemic flora. However, this fragile system faces increasing threats from habitat loss, climate change, and invasive species. Pristine fynbos, naturally high in plant diversity and which forms a large part of the CFR, presents an ideal opportunity to gather fine-scale data on community assembly patterns. Most fynbos vegetation surveys use a plot size of about 100 m[2], with no spatial structures within plots to demarcate individual subplots. Here, a groundbreaking dataset is presented that fully covers 1-hectare of pristine fynbos, systematically gridded into 50 × 50 subplots, each measuring 2 × 2 m, arranged evenly within a square-shaped survey site. Each plot was assigned a unique Y-X coordinate combination. For each plot, all plant species present were recorded, along with their total percentage covers and maximum height values. Total percentage covers were also recorded for bare soil, rock, and termite mounds. This dataset provides a valuable contribution to the field of fynbos ecology, as well as plant community ecology in general, and establishes a benchmark for future one-hectare surveys of similar fynbos vegetation types, delineating the fine-scale composition and structure of fynbos in the CFR. The dataset will be useful for a wide audience, including community and spatial ecologists, plant and environmental scientists, and biodiversity informaticians and statistical ecologists, offering ideal data for testing new metrics of diversity and compositional turnover.},
}
@article {pmid39989610,
year = {2024},
author = {Liu, C and Downey, RJ and Salminen, JS and Rojas, SA and Richer, N and Pliner, EM and Hwang, J and Cruz-Almeida, Y and Manini, TM and Hass, CJ and Seidler, RD and Clark, DJ and Ferris, DP},
title = {Electrical brain activity during human walking with parametric variations in terrain unevenness and walking speed.},
journal = {Imaging neuroscience (Cambridge, Mass.)},
volume = {2},
number = {},
pages = {},
pmid = {39989610},
issn = {2837-6056},
abstract = {Mobile brain imaging with high-density electroencephalography (EEG) can provide insight into the cortical processes involved in complex human walking tasks. While uneven terrain is common in the natural environment and poses challenges to human balance control, there is limited understanding of the supraspinal processes involved with traversing uneven terrain. The primary objective of this study was to quantify electrocortical activity related to parametric variations in terrain unevenness for neurotypical young adults. We used high-density EEG to measure brain activity when 32 young adults walked on a novel custom-made uneven terrain treadmill surface with four levels of difficulty at a walking speed tailored to each participant. We identified multiple brain regions associated with uneven terrain walking. Alpha (8 - 13 Hz) and beta (13 - 30 Hz) spectral power decreased in the sensorimotor and posterior parietal areas with increasing terrain unevenness while theta (4 - 8 Hz) power increased in the mid/posterior cingulate area with terrain unevenness. We also found that within stride spectral power fluctuations increased with terrain unevenness. Our secondary goal was to investigate the effect of parametric changes in walking speed (0.25 m/s, 0.5 m/s, 0.75 m/s, 1.0 m/s) to differentiate the effects of walking speed from uneven terrain. Our results revealed that electrocortical activities only changed substantially with speed within the sensorimotor area but not in other brain areas. Together, these results indicate there are distinct cortical processes contributing to the control of walking over uneven terrain versus modulation of walking speed on smooth, flat terrain. Our findings increase our understanding of cortical involvement in an ecologically valid walking task and could serve as a benchmark for identifying deficits in cortical dynamics that occur in people with mobility deficits.},
}
@article {pmid39918865,
year = {2025},
author = {Astill Wright, L and Moore, M and Reeves, S and Vallejos, EP and Morriss, R},
title = {Improving the Utility, Safety, and Ethical Use of a Passive Mood-Tracking App for People With Bipolar Disorder Using Coproduction: Qualitative Focus Group Study.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e65140},
pmid = {39918865},
issn = {2561-326X},
mesh = {Humans ; *Bipolar Disorder/psychology/therapy ; *Focus Groups ; Male ; Female ; Adult ; Middle Aged ; *Mobile Applications ; *Qualitative Research ; Affect ; },
abstract = {BACKGROUND: Coproduction with users of new digital technology, such as passive mood monitoring, is likely to improve its utility, safety, and successful implementation via improved design and consideration of how such technology fits with their daily lives. Mood-monitoring interventions are commonly used by people with bipolar disorder (BD) and have promising potential for digitization using novel technological methods.<br><br>OBJECTIVE: This study aims to explore how a passive behavioral monitoring platform, Remote Assessment of Disease and Relapse, would meet the needs of people with BD by specifically considering purpose and function, diversity of need, personal preference, essential components and potential risks, and harms and mitigation strategies through an iterative coproduction process.<br><br>METHODS: A total of 17 people with BD were recruited via national charities. We conducted 3 web-based focus groups as a part of an iterative coproduction process in line with responsible research and innovation principles and with consideration of clinical challenges associated with BD. Data were analyzed thematically. Results were cross-checked by someone with lived experience of BD.<br><br>RESULTS: Focus groups were transcribed and analyzed using thematic analysis. Six themes were identified as follows: (1) the purpose of using the app, (2) desired features, (3) when to use the app, (4) risks of using the app, (5) sharing with family and friends, and (6) sharing with health care professionals.<br><br>CONCLUSIONS: People with BD who are interested in using passive technology to monitor their mood wish to do so for a wide variety of purposes, identifying several preferences and potential risks. Principally, people with BD wished to use this novel technology to aid them in self-managing their BD with greater insight and a better understanding of potential triggers. We discuss key features that may aid this functionality and purpose, including crisis plans and sharing with others. Future development of passive mood-monitoring technologies should not assume that the involvement of formal mental health services is desired.},
}
@article {pmid39987271,
year = {2025},
author = {Wuyun, D and Sun, L and Chen, Z and Li, Y and Han, M and Shi, Z and Ren, T and Zhao, H},
title = {A 10-meter resolution dataset of abandoned and reclaimed cropland from 2016 to 2023 in Inner Mongolia, China.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {317},
pmid = {39987271},
issn = {2052-4463},
abstract = {Amid growing global food security concerns and frequent armed conflicts, real-time monitoring of abandoned cropland is essential for strategic planning and crisis management. This study develops a method to map abandoned cropland accurately, crucial for maintaining the food supply chain and ecological balance. Utilizing Sentinel-1/2 satellite data, we employed multi-feature stacking and machine learning to create the ARCC10-IM (Abandoned and Reclaimed Cropland Classification at 10-meter resolution in Inner Mongolia) dataset, which tracks annual cropland activity. A novel temporal segmentation algorithm was developed to extract cropland abandonment and reclamation patterns annually, using sliding time windows over several years. This research differentiates cropland states-active cultivation, unstable fallowing, continuous abandonment, and reclamation-providing continuous, regional-scale maps with 10-meter resolution. ARCC10-IM is crucial for land planning, environmental monitoring, and agricultural management in arid areas like Inner Mongolia, enhancing decision-making and technology in land use tracking.},
}
@article {pmid39986902,
year = {2025},
author = {Lee, S and Kaufmann, CN and Lippi, CA and Ryan, SJ and Guo, Y},
title = {Untreated insomnia as a contributor to geographic disparities in risk for Alzheimer's disease and related dementias.},
journal = {Sleep health},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.sleh.2025.01.002},
pmid = {39986902},
issn = {2352-7226},
}
@article {pmid39842565,
year = {2025},
author = {Zheng, JY and Jiang, G and Gao, FH and Ren, SN and Zhu, CY and Xie, J and Li, Z and Yin, W and Xia, X and Li, Y and Wang, HL},
title = {MCTASmRNA: A deep learning framework for alternative splicing events classification.},
journal = {International journal of biological macromolecules},
volume = {300},
number = {},
pages = {139941},
doi = {10.1016/j.ijbiomac.2025.139941},
pmid = {39842565},
issn = {1879-0003},
mesh = {*Deep Learning ; *Alternative Splicing/genetics ; RNA, Messenger/genetics ; Humans ; Animals ; Computational Biology/methods ; Software ; },
abstract = {Alternative splicing (AS) plays crucial post-transcriptional gene function regulation roles in eukaryotic. Despite progress in studying AS at the RNA level, existing methods for AS event identification face challenges such as inefficiency, lengthy processing times, and limitations in capturing the complexity of RNA sequences. To overcome these challenges, we evaluated 10 AS detection tools and selected rMATS for dataset construction. We then developed a multi-scale convolutional and Transformer-based model (MCTASmRNA) to classify AS events in mRNA sequences without relying on a reference genome. To handle the problem of large intra-class and small inter-class difference in AS event sequences, we incorporated an efficient channel attention mechanism and designed a new joint loss function to optimize MCTASmRNA training. MCTASmRNA outperformed baseline models, with an accuracy improvement and exhibited enhanced cross-species generalizability. This model provides valuable support for AS research across different organisms. Future work will focus on optimizing and expanding the model to further explore the complex mechanisms underlying AS.},
}
@article {pmid39982558,
year = {2025},
author = {Li, L and Gupta, A and Zhu, C and Xu, K and Watanabe, Y and Tanaka, M and Seki, M and Mochida, K and Kanno, Y and Seo, M and Nguyen, KH and Tran, CD and Chu, HD and Yin, H and Jia, KP and Tran, LP and Yin, X and Li, W},
title = {Strigolactone and karrikin receptors regulate phytohormone biosynthetic and catabolic processes.},
journal = {Plant cell reports},
volume = {44},
number = {3},
pages = {60},
pmid = {39982558},
issn = {1432-203X},
support = {XDA28110100//State Key Laboratory of Microbial Resources, Chinese Academy of Sciences/ ; 2022YFD1500505//National Key Research and Development Program of China/ ; 32370321//Natural Science Foundation of Jilin Province/ ; },
mesh = {*Plant Growth Regulators/metabolism ; *Lactones/metabolism ; *Arabidopsis/genetics/metabolism ; *Gene Expression Regulation, Plant ; *Arabidopsis Proteins/metabolism/genetics ; *Indoleacetic Acids/metabolism ; *Pyrans/metabolism ; *Cyclopentanes/metabolism ; *Furans/metabolism ; Oxylipins/metabolism ; Gibberellins/metabolism ; Abscisic Acid/metabolism ; Cytokinins/metabolism ; Receptors, Cell Surface/metabolism/genetics ; Salicylic Acid/metabolism ; Signal Transduction ; Mutation ; Gene Expression Profiling ; },
abstract = {Karrikin plays a more critical role in affecting the homeostasis of ABA and cytokinins, while strigolactones play a more critical role in influencing the homeostasis of jasmonic acid and gibberellins. Strigolactones (SLs) and karrikins (KARs) regulate plant growth and development through their crosstalk, and through the crosstalk between them and other phytohormones, such as abscisic acid (ABA) and auxin. However, how SL and KAR signaling pathways influence the levels of other phytohormones is still unknown. Here, we performed a comparative transcriptome analysis of the Arabidopsis thaliana double mutant dwarf14 karrikin-insensitive 2 (d14 kai2), deficient in SL and KAR perception, and the wild-type (WT) using their rosette leaves. Ten gene ontology terms related to phytohormones were enriched with differentially expressed genes derived from the 'd14 kai2 vs WT' comparison. Our data revealed that the levels of auxin, ABA and salicylic acid (SA) were higher in d14 and kai2 single and d14 kai2 mutant plants than in WT, which was consistent with the results of previous investigations. In contrast, the levels of cytokinins (CKs) were found to be lower in all single and double mutants than in WT. The levels of active gibberellins were lower in d14 and d14 kai2 mutants than in WT, while they were comparable in kai2 and WT plants. Similarly, the levels of jasmonic acid (JA) were lower in d14 and d14 kai2 plants, but higher in kai2 plants than in WT. Both transcriptome and qRT-PCR analyses indicated that SL and KAR signaling pathways affect the levels of auxin, SA, CKs, gibberellin 4 (GA4) and ABA by influencing the expression of their biosynthetic (in case of auxin, SA, GA4 and CKs) and catabolic (in case of ABA) genes. Collectively, our data demonstrated that KAI2 plays a more critical role in the homeostasis of ABA and CKs, while D14 plays a more critical role in the homeostasis of JA and gibberellins. Findings of this study indicate a complex and broad crosstalk among various phytohormones in plants, which can be considered for future exogenous applications and hormone engineering.},
}
@article {pmid39982516,
year = {2025},
author = {Elkin-Frankston, S and McIntyre, J and Brunyé, TT and Gardony, AL and Hancock, CL and O'Donovan, MP and Bode, VG and Miller, EL},
title = {Beyond boundaries: a location-based toolkit for quantifying group dynamics in diverse contexts.},
journal = {Cognitive research: principles and implications},
volume = {10},
number = {1},
pages = {10},
pmid = {39982516},
issn = {2365-7464},
support = {W911QY1920003//U.S. Army Combat Capabilities Development Command Soldier Center/ ; 1934553//National Science Foundation/ ; 1931978//National Science Foundation/ ; },
mesh = {Humans ; *Group Processes ; *Military Personnel ; Geographic Information Systems ; Social Behavior ; Movement/physiology ; Models, Theoretical ; Group Dynamics ; },
abstract = {Existing toolkits for analyzing movement dynamics in animal ecology primarily focus on individual or group behavior in habitats without predefined boundaries, while methods for studying human activity often cater to bounded environments, such as team sports played on defined fields. This leaves a gap in tools for modeling and analyzing human group dynamics in large-scale, unbounded, or semi-constrained environments. Examples of such contexts include tourist groups, cycling teams, search and rescue teams, and military units. To address this issue, we survey existing methods and metrics for characterizing individual and collective movement in humans and animals. Using a rich GPS dataset from groups of military personnel engaged in a foot march, we develop a comprehensive, general-purpose toolkit for quantifying group dynamics using location-based metrics during goal-directed movement in open environments. This toolkit includes a repository of Python functions for extracting and analyzing movement data, integrating cognitive factors such as decision-making, situational awareness, and group coordination. By extending location-based analytics to non-traditional domains, this toolkit enhances the understanding of collective movement, group behavior, and emergent properties shaped by cognitive processes. To demonstrate its practical utility, we present a use case utilizing metrics derived from the foot march data to predict group performance during a subsequent strategic and tactical exercise, highlighting the influence of cognitive and decision-making behaviors on team effectiveness.},
}
@article {pmid39982380,
year = {2025},
author = {Blumenstiel, JP and Kingan, SB and Garrigan, D and Hill, T and Vedanayagam, J},
title = {Nested likelihood-ratio testing of the nonsynonymous:synonymous ratio suggests greater adaptation in the piRNA machinery of Drosophila melanogaster compared with Drosophila ananassae and Drosophila willistoni, two species with higher repeat content.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf017},
pmid = {39982380},
issn = {2160-1836},
support = {1413532//NSF MCB/ ; P20GM103638//NIH-NIGMS/COBRE/ ; P20GM103418//NIH-NIGMS/KINBRE/ ; //University of Kansas/ ; DEB1209536//NSF-DDIG/ ; R00GM137077//NIH-NIGMS/ ; //University of Texas at San Antonio/ ; //KU Medical Center Genome Sequencing Facility/ ; NIH U54 HD090216/GF/NIH HHS/United States ; UL1TR002366//Frontiers CTSA/ ; },
abstract = {Numerous studies have revealed a signature of strong adaptive evolution in the piwi-interacting RNA (piRNA) machinery of Drosophila melanogaster, but the cause of this pattern is not understood. Several hypotheses have been proposed. One hypothesis is that transposable element (TE) families and the piRNA machinery are co-evolving under an evolutionary arms race, perhaps due to antagonism by TEs against the piRNA machinery. A related, though not co-evolutionary, hypothesis is that recurrent TE invasion drives the piRNA machinery to adapt to novel TE strategies. A third hypothesis is that ongoing fluctuation in TE abundance leads to adaptation in the piRNA machinery that must constantly adjust between sensitivity for detecting new elements and specificity to avoid the cost of off-target gene silencing. Rapid evolution of the piRNA machinery may also be driven independently of TEs, and instead from other functions such as the role of piRNAs in suppressing sex-chromosome meiotic drive. We sought to evaluate the impact of TE abundance on adaptive evolution of the piRNA machinery in D. melanogaster and 2 species with higher repeat content-Drosophila ananassae and Drosophila willistoni. This comparison was achieved by employing a likelihood-based hypothesis testing framework based on the McDonald-Kreitman test. We show that we can reject a faster rate of adaptive evolution in the piRNA machinery of these 2 species. We propose that the high rate of adaptation in D. melanogaster is either driven by a recent influx of TEs that have occurred during range expansion or selection on other functions of the piRNA machinery.},
}
@article {pmid39981105,
year = {2025},
author = {Plaitano, EG and McNeish, D and Bartels, SM and Bell, K and Dallery, J and Grabinski, M and Kiernan, M and Lavoie, HA and Lemley, SM and Lowe, MR and MacKinnon, DP and Metcalf, SA and Onken, L and Prochaska, JJ and Sand, CL and Scherer, EA and Stoeckel, LE and Xie, H and Marsch, LA},
title = {Adherence to a digital therapeutic mediates the relationship between momentary self-regulation and health risk behaviors.},
journal = {Frontiers in digital health},
volume = {7},
number = {},
pages = {1467772},
pmid = {39981105},
issn = {2673-253X},
abstract = {INTRODUCTION: Smoking, obesity, and insufficient physical activity are modifiable health risk behaviors. Self-regulation is one fundamental behavior change mechanism often incorporated within digital therapeutics as it varies momentarily across time and contexts and may play a causal role in improving these health behaviors. However, the role of momentary self-regulation in achieving behavior change has been infrequently examined. Using a novel momentary self-regulation scale, this study examined how targeting self-regulation through a digital therapeutic impacts adherence to the therapeutic and two different health risk behavioral outcomes.<br><br>METHODS: This prospective interventional study included momentary data for 28 days from 50 participants with obesity and binge eating disorder and 50 participants who smoked regularly. An evidence-based digital therapeutic, called Laddr&#x2122;, provided self-regulation behavior change tools. Participants reported on their momentary self-regulation via ecological momentary assessments and health risk behaviors were measured as steps taken from a physical activity tracker and breathalyzed carbon monoxide. Medical regimen adherence was assessed as daily Laddr usage. Bayesian dynamic mediation models were used to examine moment-to-moment mediation effects between momentary self-regulation subscales, medical regimen adherence, and behavioral outcomes.<br><br>RESULTS: In the binge eating disorder sample, the perseverance [&#x3b2; 1&#x2009;=&#x2009;0.17, 95% CI&#x2009;=&#x2009;(0.06, 0.45)] and emotion regulation [&#x3b2; 1&#x2009;=&#x2009;0.12, 95% CI&#x2009;=&#x2009;(0.03, 0.27)] targets of momentary self-regulation positively predicted Laddr adherence on the following day, and higher Laddr adherence was subsequently a positive predictor of steps taken the same day for both perseverance [&#x3b2; 2&#x2009;=&#x2009;0.335, 95% CI&#x2009;=&#x2009;(0.030, 0.717)] and emotion regulation [&#x3b2; 2&#x2009;=&#x2009;0.389, 95% CI&#x2009;=&#x2009;(0.080, 0.738)]. In the smoking sample, the perseverance target of momentary self-regulation positively predicted Laddr adherence on the following day [&#x3b2;&#x2009;=&#x2009;0.91, 95% CI&#x2009;=&#x2009;(0.60, 1.24)]. However, higher Laddr adherence was not a predictor of CO values on the same day [&#x3b2; 2&#x2009;=&#x2009;-0.09, 95% CI&#x2009;=&#x2009;(-0.24, 0.09)].<br><br>CONCLUSIONS: This study provides evidence that a digital therapeutic targeting self-regulation can modify the relationships between momentary self-regulation, medical regimen adherence, and behavioral health outcomes. Together, this work demonstrated the ability to digitally assess the transdiagnostic mediating effect of momentary self-regulation on medical regimen adherence and pro-health behavioral outcomes.<br><br>CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier (NCT03774433).},
}
@article {pmid39980689,
year = {2025},
author = {Su, Z and Liu, L and Zhang, J and Guo, J and Wang, G and Zeng, X},
title = {A scientometric visualization analysis of the gut microbiota and gestational diabetes mellitus.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1485560},
pmid = {39980689},
issn = {1664-302X},
abstract = {BACKGROUND: The prevalence of gestational diabetes mellitus (GDM), a condition that is widespread globally, is increasing. The relationship between the gut microbiota and GDM has been a subject of research for nearly two decades, yet there has been no bibliometric analysis of this correlation. This study aimed to use bibliometrics to explore the relationship between the gut microbiota and GDM, highlighting emerging trends and current research hotspots in this field.<br><br>RESULTS: A total of 394 papers were included in the analysis. China emerged as the preeminent nation in terms of the number of publications on the subject, with 128 papers (32.49%), whereas the United States had the most significant impact, with 4,874 citations. The University of Queensland emerged as the most prolific institution, contributing 18 publications. Marloes Dekker Nitert was the most active author with 16 publications, and Omry Koren garnered the most citations, totaling 154. The journal Nutrients published the most studies (28 publications, 7.11%), whereas PLoS One was the most commonly co-cited journal, with a total of 805 citations. With respect to keywords, research focuses can be divided into 4 clusters, namely, "the interrelationship between the gut microbiota and pregnancy, childbirth," "the relationship between adverse metabolic outcomes and GDM," "the gut microbiota composition and metabolic mechanisms" and "microbiota and ecological imbalance." Key areas of focus include the interactions between the gut microbiota and individuals with GDM, as well as the formation and inheritance of the gut microbiota. Increasing attention has been given to the impact of probiotic supplementation on metabolism and pregnancy outcomes in GDM patients. Moreover, ongoing research is exploring the potential of the gut microbiota as a biomarker for GDM. These topics represent both current and future directions in this field.<br><br>CONCLUSION: This study provides a comprehensive knowledge map of the gut microbiota and GDM, highlights key research areas, and outlines potential future directions.},
}
@article {pmid39980161,
year = {2025},
author = {Smith, AR and Mueller, ER and Lewis, CE and Markland, A and Smerdon, C and Smith, AL and Sutcliffe, S and Wyman, JF and Low, LK and Miller, JM and , },
title = {Assessment of Environmental, Sociocultural, and Physiological Influences on Women's Toileting Decisions and Behaviors Using "Where I Go": Pilot Study of a Mobile App.},
journal = {JMIR mHealth and uHealth},
volume = {13},
number = {},
pages = {e56533},
doi = {10.2196/56533},
pmid = {39980161},
issn = {2291-5222},
mesh = {Humans ; Female ; *Mobile Applications/standards/statistics &amp; numerical data ; Adult ; Pilot Projects ; Middle Aged ; Aged ; Aged, 80 and over ; Urination/physiology ; Decision Making ; Surveys and Questionnaires ; },
abstract = {BACKGROUND: Little is known about women's decisions around toileting for urination and how those decisions influence moment-to-moment behaviors to manage bladder needs. The new smartphone app "Where I Go" captures such nuanced and granular data in real-world environments.<br><br>OBJECTIVE: This study aims to describe participant engagement with "Where I Go", variation in novel parameters collected, and readiness for the data collection tool's use in population-based studies.<br><br>METHODS: "Where I Go" has three components: (1) real-time data, (2) short look-back periods (3-4 h), and (3) event location (GPS recorded at each interaction). The sample size was 44 women. Recording of real-time toileting events and responding to look-back questions was measured over 2 days of data collection. The participant's self-entered location descriptions and the automatic GPS recordings were compared.<br><br>RESULTS: A total of 44 women with an average age of 44 (range 21-85) years interacted with the app. Real-time reporting of at least 1 toileting event per day was high (38/44, 86%, on day 1 and 40/44, 91%, on day 2) with a median of 5 (IQR 3-7 on day 1 and IQR 3-8 on day 2) toileting events recorded each day. Toileting most commonly occurred at home (85/140, 61%, on day 1 and 129/171, 75%, on day 2) due to a need to go (114/140, 66%, on day 1 and 153/171, 74%, on day 2). The most common reasons for delaying toileting were "work duties" (33/140, 21%, on day 1 and 21/171, 11%, on day 2) and "errands or traveling" (19/140, 12%, on day 1 and 19/171, 10%, on day 2). Response to at least 1 look-back notification was similarly high (41/44, 93%, on day 1 and 42/44, 95%, on day 2), with number of responses higher on average on day 2 compared with day 1 (mean on day 1=3.2, 95% CI 3.0-3.5; mean on day 2=4.3, 95% CI 3.9-4.7; P<.001). Median additional toileting events reported on the look-back survey were 1 (IQR 1-2) and 2 (IQR 1-2) on days 1 and 2, respectively. Overall concordance between self-reported location recording and GPS was 76% (188/247). Participants reported lower urge ratings when at home versus away when reporting real-time toileting (median rating 61, IQR 41-84 vs 72, IQR 56-98), and daily fluid intake showed a small to medium positive correlation with toileting frequency (day 1 r=0.3, day 2 r=0.24). Toileting frequency reported in "Where I Go" showed a small positive correlation with the frequency item from the International Consultation on Incontinence Questionnaire (r=0.31 with day 1 toileting frequency and r=0.21 with day 2 toileting frequency).<br><br>CONCLUSIONS: "Where I Go" has potential to increase the understanding of factors that affect women's toileting decisions and long-term bladder health. We anticipate its use as a data collection tool in population-based studies.},
}
@article {pmid39900590,
year = {2025},
author = {Chen, Y and Zheng, L and Ma, J and Zhu, H and Gan, Y},
title = {The Mediating Role of Meaning-Making in the Relationship Between Mental Time Travel and Positive Emotions in Stress-Related Blogs: Big Data Text Analysis Research.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e63407},
doi = {10.2196/63407},
pmid = {39900590},
issn = {1438-8871},
mesh = {Humans ; *Stress, Psychological/psychology ; *Emotions ; *Big Data ; *Blogging ; Social Media ; },
abstract = {BACKGROUND: Given the ubiquity of stress, a key focus of stress research is exploring how to better coexist with stress.<br><br>OBJECTIVE: This study conducted text analysis on stress-related Weibo posts using a web crawler to investigate whether these posts contained positive emotions, as well as elements of mental time travel and meaning-making. A mediation model of mental time travel, meaning-making, and positive emotions was constructed to examine whether meaning-making triggered by mental time travel can foster positive emotions under stress.<br><br>METHODS: Using Python 3.8, the original public data from active Weibo users were crawled, yielding 331,711 stress-related posts. To avoid false positives, these posts were randomly divided into two large samples for cross-validation (sample 1: n=165,374; sample 2: n=166,337). Google's natural language processing application programming interface was used for word segmentation, followed by text and mediation analysis using the Chinese psychological analysis system "Wenxin." A mini-meta-analysis of the mediation path coefficients was conducted. Text analysis identified mental time travel words, meaning-making words, and positive emotion words in stress-related posts.<br><br>RESULTS: The constructed mediation model of mental time travel words (time words), meaning-making words (causal and insightful words), and positive poststress emotions validated positive adaptation following stress. A mini-meta-analysis of two different mediation models constructed in the two subsamples indicated a stable mediation effect across the 2 random subsamples. The combined effect size (B) obtained was .013 (SE 0.003, 95% CI 0.007-0.018; P<.001), demonstrating that meaning-making triggered by mental time travel in stress-related blog posts can predict positive emotions under stress.<br><br>CONCLUSIONS: Individuals can adapt positively to stress by engaging in meaning-making processes that are triggered by mental time travel and reflected in their social media posts. The study's mediation model confirmed that mental time travel leads to meaning-making, which fosters positive emotional responses to stress. Mental time travel serves as a psychological strategy to facilitate positive adaptation to stressful situations.},
}
@article {pmid39975655,
year = {2025},
author = {Gutiérrez, ME and Lahoz-Beltrá, R and Donayre-Torres, AJ},
title = {Editorial: Towards the embedding of artificial intelligence into synthetic organisms: engineering intelligence in microorganisms.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1562092},
doi = {10.3389/fgene.2025.1562092},
pmid = {39975655},
issn = {1664-8021},
}
@article {pmid39973193,
year = {2025},
author = {Beltran, RS and Kilpatrick, AM and Adamczak, SK and Beumer, LT and Czapanskiy, MF and Davidson, SC and McLean, BS and Mueller, T and Payne, AR and Soria, CD and Weeks, BC and Williams, TM and Salguero-Gómez, R},
title = {Integrating animal tracking and trait data to facilitate global ecological discoveries.},
journal = {The Journal of experimental biology},
volume = {228},
number = {Suppl_1},
pages = {},
doi = {10.1242/jeb.247981},
pmid = {39973193},
issn = {1477-9145},
support = {IOS 2052497//National Science Foundation/ ; //Office of Naval Research/ ; //David and Lucile Packard Foundation/ ; //Arnold and Mabel Beckman Foundation/ ; //Elysea Fund/ ; NE/X013766/1//Natural Environment Research Council/ ; 101044740//European Union/ ; //University of California/ ; 80NSSC21K1182/NASA/NASA/United States ; },
mesh = {Animals ; *Ecology/methods ; Databases, Factual ; Animal Migration ; Big Data ; },
abstract = {Understanding animal movement is at the core of ecology, evolution and conservation science. Big data approaches for animal tracking have facilitated impactful synthesis research on spatial biology and behavior in ecologically important and human-impacted regions. Similarly, databases of animal traits (e.g. body size, limb length, locomotion method, lifespan) have been used for a wide range of comparative questions, with emerging data being shared at the level of individuals and populations. Here, we argue that the proliferation of both types of publicly available data creates exciting opportunities to unlock new avenues of research, such as spatial planning and ecological forecasting. We assessed the feasibility of combining animal tracking and trait databases to develop and test hypotheses across geographic, temporal and biological allometric scales. We identified multiple research questions addressing performance and distribution constraints that could be answered by integrating trait and tracking data. For example, how do physiological (e.g. metabolic rates) and biomechanical traits (e.g. limb length, locomotion form) influence migration distances? We illustrate the potential of our framework with three case studies that effectively integrate trait and tracking data for comparative research. An important challenge ahead is the lack of taxonomic and spatial overlap in trait and tracking databases. We identify critical next steps for future integration of tracking and trait databases, with the most impactful being open and interlinked individual-level data. Coordinated efforts to combine trait and tracking databases will accelerate global ecological and evolutionary insights and inform conservation and management decisions in our changing world.},
}
@article {pmid39973045,
year = {2025},
author = {Panayi, P and Contreras, A and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Mason, L and Varese, F},
title = {A temporal network analysis of complex post-traumatic stress disorder and psychosis symptoms.},
journal = {Psychological medicine},
volume = {55},
number = {},
pages = {e43},
doi = {10.1017/S0033291725000030},
pmid = {39973045},
issn = {1469-8978},
support = {2488414//Economic and Social Research Council/ ; NIHR128623//Health Technology Assessment Programme/ ; //NIHR Maudsley Biomedical Research Centre/ ; },
mesh = {Humans ; *Stress Disorders, Post-Traumatic/physiopathology ; *Psychotic Disorders/physiopathology ; Adult ; Male ; Female ; Middle Aged ; Ecological Momentary Assessment ; Young Adult ; Self Concept ; Comorbidity ; },
abstract = {BACKGROUND: Symptoms of complex post-traumatic stress disorder (cPTSD) may play a role in the maintenance of psychotic symptoms. Network analyses have shown interrelationships between post-traumatic sequelae and psychosis, but the temporal dynamics of these relationships in people with psychosis and a history of trauma remain unclear. We aimed to explore, using network analysis, the temporal order of relationships between symptoms of cPTSD (i.e. core PTSD and disturbances of self-organization [DSOs]) and psychosis in the flow of daily life.<br><br>METHODS: Participants with psychosis and comorbid PTSD (N&#xa0;=&#xa0;153) completed an experience-sampling study involving multiple daily assessments of psychosis (paranoia, voices, and visions), core PTSD (trauma-related intrusions, avoidance, hyperarousal), and DSOs (emotional dysregulation, interpersonal difficulties, negative self-concept) over six consecutive days. Multilevel vector autoregressive modeling was used to estimate three complementary networks representing different timescales.<br><br>RESULTS: Our between-subjects network suggested that, on average over the testing period, most cPTSD symptoms related to at least one positive psychotic symptom. Many average relationships persist in the contemporaneous network, indicating symptoms of cPTSD and psychosis co-occur, especially paranoia with hyperarousal and negative self-concept. The temporal network suggested that paranoia reciprocally predicted, and was predicted by, hyperarousal, negative self-concept, and emotional dysregulation from moment to moment. cPTSD did not directly relate to voices in the temporal network.<br><br>CONCLUSIONS: cPTSD and positive psychosis symptoms mutually maintain each other in trauma-exposed people with psychosis via the maintenance of current threat, consistent with cognitive models of PTSD. Current threat, therefore, represents a valuable treatment target in phased-based trauma-focused psychosis interventions.},
}
@article {pmid39969100,
year = {2025},
author = {Miller, L and Beaney, T and Hope, R and Cunningham, M and Robotham, JV and Pouwels, KB and Costelloe, CE},
title = {General practice antibiotic prescriptions attributable to respiratory syncytial virus by age and antibiotic class: an ecological analysis of the English population.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1093/jac/dkaf043},
pmid = {39969100},
issn = {1460-2091},
support = {MRF-145-0004-TPG-AVISO//Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research/ ; //National Institute for Health and Care Research (NIHR) Royal Marsden/ ; //Institute of Cancer Research Biomedical Research Centre/ ; 2016-10-95//NIHR/ ; //National Institute for Health Research Health Protection Research Unit/ ; //Healthcare Associated Infections and Antimicrobial Resistance/ ; //University of Oxford/ ; NIHR200915//UK Health Security Agency (UKHSA)/ ; /WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: Respiratory syncytial virus (RSV) may contribute to a substantial volume of antibiotic prescriptions in primary care. However, data on the type of antibiotics prescribed for such infections are only available for children <5 years in the UK. Understanding the contribution of RSV to antibiotic prescribing would facilitate predicting the impact of RSV preventative measures on antibiotic use and resistance. The objective of this study was to estimate the proportion of antibiotic prescriptions in English general practice attributable to RSV by age and antibiotic class.<br><br>METHODS: Generalized additive models examined associations between weekly counts of general practice antibiotic prescriptions and laboratory-confirmed respiratory infections from 2015 to 2018, adjusting for temperature, practice holidays and remaining seasonal confounders. We used general practice records from the Clinical Practice Research Datalink and microbiology tests for RSV, influenza, rhinovirus, adenovirus, parainfluenza, human metapneumovirus, Mycoplasma pneumoniae and Streptococcus pneumoniae from England's Second Generation Surveillance System.<br><br>RESULTS: An estimated 2.1% of antibiotics were attributable to RSV, equating to an average of 640 000 prescriptions annually. Of these, adults &#x2265;75&#x2005;years contributed to the greatest volume, with an annual average of 149&#x200a;078 (95% credible interval: 93&#x200a;733-206&#x200a;045). Infants 6-23&#x2005;months had the highest average annual rate at 6580 prescriptions per 100&#x200a;000 individuals (95% credible interval: 4522-8651). Most RSV-attributable antibiotic prescriptions were penicillins, macrolides or tetracyclines. Adults &#x2265;65&#x2005;years had a wider range of antibiotic classes associated with RSV compared with younger age groups.<br><br>CONCLUSIONS: Interventions to reduce the burden of RSV, particularly in older adults, could complement current strategies to reduce antibiotic use in England.},
}
@article {pmid39968615,
year = {2025},
author = {Klarevas-Irby, JA and Nyaguthii, B and Farine, DR},
title = {Moving as a group imposes constraints on the energetic efficiency of movement.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2041},
pages = {20242760},
doi = {10.1098/rspb.2024.2760},
pmid = {39968615},
issn = {1471-2954},
support = {//Centre for the Advanced Study of Collective Behaviour/ ; //Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Association for the Study of Animal Behaviour/ ; //H2020 European Research Council/ ; //Max Planck Society/ ; //Deutsche Forschungsgemeinschaft/ ; //Max Planck-Yale Center for Biodiversity Movement and Global Change/ ; },
mesh = {Animals ; *Energy Metabolism ; *Galliformes/physiology ; Social Behavior ; Movement ; Female ; Geographic Information Systems ; },
abstract = {Movement is a key part of life for many species. In solitary animals, the energetic costs of movement can be mitigated through energetically efficient strategies that produce faster, straighter movements. However, little is known about whether moving as part of a collective enhances or limits the ability of individual group members to express such strategies. Drawing on 6 years of population-level, high-resolution (1 Hz) GPS tracking of group-living vulturine guineafowl (Acryllium vulturinum), we detected 886 events from 94 tagged individuals where their groups made large, range-shifting displacements in response to changing environmental conditions. We contrasted these movements with data from 94 similarly large displacement events by 19 lone, dispersing individuals. Our results suggest that individuals in groups can significantly reduce their energetic cost of transport when making large displacements (15.3% more efficient relative to their normal daily ranging) by increasing the speed and straightness of their movements. However, even during their most efficient movements, individuals in groups could not achieve or maintain comparable increases in speed to lone individuals, resulting in significantly limited efficiency gains (35.7% less efficient than solitary individuals). Overall, this study provides evidence for a substantial energetic cost arising from collective movement.},
}
@article {pmid39963945,
year = {2025},
author = {Giglio, VJ and Adelir-Alves, J and Balzaretti Merino, N and Bravo-Olivas, ML and Camp, EF and Casoli, E and Chávez-Dagostino, RM and Ferretti, E and Fraser, D and Grillo, AC and Jiménez-Guiérrez, S and Leite, KL and Lucrezi, S and Luiz, OJ and Luna-Pérez, B and McBride, J and Milanese, M and Moity, N and Pinheiro, JV and Renfro, B and Roche, R and Saliba, BM and Sara, A and Schiavetti, A and Toso, Y and Valle-Pérez, C and Ferreira, CEL},
title = {DiverReef: A global database of the behavior of recreational divers and their interactions with reefs over 20 years.},
journal = {Ecology},
volume = {106},
number = {2},
pages = {e4519},
doi = {10.1002/ecy.4519},
pmid = {39963945},
issn = {1939-9170},
support = {17/22273-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 111.210/2014//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; },
mesh = {*Diving/physiology ; *Coral Reefs ; *Databases, Factual ; *Recreation ; Animals ; Humans ; Male ; Female ; Time Factors ; },
abstract = {Recreational diving is an important activity in reef environments worldwide, providing income and employment for coastal communities and connecting visiting divers to these ecosystems promoting conservation and stewardship. However, if poorly managed, diving has the potential to cause detrimental effects on benthic communities via mechanical damage caused by physical contact of divers with the reef, often in the form of unintentional fin kicks resulting from poor buoyancy. Understanding diver-reef interaction patterns is important to elucidate the potential impacts of diving tourism on the reef biota. The DiverReef database provides the first public dataset on the underwater behavior of recreational divers in shallow reef environments (<25 m depth) globally and their interactions with the reef seascape and/or reef benthic sessile organisms. The dataset comprises 20 years of data (2004-2023) by observing the behavior of 2311 recreational divers in nine countries at 19 diving destinations and 176 diving sites; 93% of the observations were in marine protected areas. The data were collected through on-site observations of divers' behavior during tourism activities and their physical interactions with the reef structure and/or benthic sessile reef organisms. Observers discreetly followed divers and recorded their behavior and interactions with the reef over set periods. Interactions were described as "contact" or "damage," the latter referring to when physical damage to a benthic organism or the reef structure was observed. Besides behavior, observers also recorded data on the type of diving activity (scuba or snorkeling), profiles of the divers (gender and experience), use of cameras by the divers, visibility, type of reef formation, and marine protection status of the dive site. The authors of this research expect that the data provided will be useful in advancing knowledge of how divers interact with reefs and in developing strategies to mitigate the potential detrimental effects of the diving industry on reef biota. Part of the data has already been used in reports and scientific articles. This dataset can be freely used for noncommercial purposes; we request that users of these data cite this data paper in all publications resulting from the use of this dataset.},
}
@article {pmid39963041,
year = {2025},
author = {Lima-Cordón, R and Mohabir, JT and Sooklall, M and Zurita, AM and Shieh, M and Knox, C and Gobran, S and Johnson, Z and Laws, M and Panchal, R and Niles-Robin, R and Cox, H and Grillet, ME and Moreno, JE and Herrera, S and Quinones, M and Early, AM and Tennessen, JA and Neafsey, DE},
title = {A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14088},
doi = {10.1111/1755-0998.14088},
pmid = {39963041},
issn = {1755-0998},
support = {INV-009416/GATES/Bill &amp; Melinda Gates Foundation/United States ; U19AI110818//National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services/ ; },
abstract = {Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.},
}
@article {pmid39960184,
year = {2025},
author = {Ferdousee, S and Alam, MS and Hwangbo, M and Kim, J},
title = {Visualizing Methane-Cycling Microbial Dynamics in Coastal Wetlands.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {215},
pages = {},
doi = {10.3791/67715},
pmid = {39960184},
issn = {1940-087X},
mesh = {*Wetlands ; *Methane/metabolism ; Texas ; Geographic Information Systems ; },
abstract = {Coastal wetlands are the largest biotic source of methane, where methanogens convert organic matter into methane and methanotrophs oxidize methane, thus playing a critical role in regulating the methane cycle. The wetlands in South Texas, which are subject to frequent weather events, fluctuating salinity levels, and anthropogenic activities due to climate change, influence methane cycling. Despite the ecological importance of these processes, methane cycling in South Texas coastal wetlands remains insufficiently explored. To address this gap, we developed and optimized a method for detecting genes related to methanogens and methanotrophs, including mcrA as a biomarker for methanogens and pmoA1, pmoA2, and mmoX as biomarkers for methanotrophs. Additionally, this study aimed to visualize the spatial and temporal distribution patterns of methanogen and methanotroph abundance utilizing the geographic information system (GIS) software ArcGIS Pro. The integration of these molecular techniques with advanced geospatial visualization provided critical insights into the spatial and temporal distribution of methanogen and methanotroph communities across South Texas wetlands. Thus, the methodology established in this study offers a robust framework for mapping microbial dynamics in wetlands, enhancing our understanding of methane cycling under varying environmental conditions, and supporting broader ecological and environmental change studies.},
}
@article {pmid39957502,
year = {2025},
author = {Latini, L and Burini, G and Mazza, V and Grignani, G and De Donno, R and Bello, E and Tricarico, E and Malavasi, S and Nascetti, G and Canestrelli, D and Carere, C},
title = {Early-life environment shapes claw bilateral asymmetry in the European lobster (Homarus gammarus).},
journal = {Biology open},
volume = {},
number = {},
pages = {},
doi = {10.1242/bio.061901},
pmid = {39957502},
issn = {2046-6390},
support = {//Universite degli Studi della Tuscia/ ; //Universite degli Studi di Firenze/ ; //Universite Ca' Foscari Venezia/ ; },
abstract = {Developmental plasticity refers to an organism's ability to adjust its development in response to changing environmental conditions, leading to changes in behaviour, physiology, or morphology. This adaptability is crucial for survival and helps organisms to cope with environmental challenges throughout their lives. Understanding the mechanisms underlying developmental plasticity, particularly how environmental and ontogenetic factors shape functional traits, is fundamental for both evolutionary biology and conservation efforts. In this study we investigated the effects of early-life environmental conditions on the development of claw asymmetry in juvenile European lobsters (Homarus gammarus, N=244), a functional trait essential for survival and ecological success. Juveniles were randomly divided between four different rearing conditions characterized by the presence or absence of physical enrichments (e.g., substrate and shelters), which were introduced at different developmental stages in separated groups to assess the timing and nature of their effect. Results revealed that exposure to substrate alone, without additional stimuli, consistently promoted claw asymmetry, regardless of the timing of its introduction, while the 6th developmental stage emerged as the critical period for claw differentiation. By identifying the environmental factors that influence developmental outcomes in lobsters, and the timing of these effects, this study improves our understanding of developmental plasticity and offers valuable insights for optimizing conservation aquaculture and reintroduction strategies.},
}
@article {pmid39955351,
year = {2025},
author = {Yang, Y and Yang, Y and Yang, S and Zhang, J},
title = {Pollution control mechanism of national water network with water quality differences based on differential game and case study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5588},
pmid = {39955351},
issn = {2045-2322},
support = {51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; 51679089//National Nature Science Foundation of China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; GXJD004//Intelligent Water Conservancy Project of the Discipline Innovation Introduction Base of Henan Province, China/ ; },
abstract = {The construction of the national water network optimizes water resource allocation but also causes a redistribution of pollutants due to water quality differences, posing urgent challenges for water pollution management. Taking the South-to-North Water Diversion Project and Yangtze-to-Hanjiang River Water Diversion Project (YHRWDP) as an example and considering the pressure brought by the redistribution of pollutants to the polluting enterprises (PE) and water diversion enterprises (WDE) situated in areas where pollution is aggravated, a differential game model of pollution control among the central government, water-supply area (WSA), PE and WDE is constructed based on the cost-sharing mechanism. The results show that: (1) The pressure coefficient has an apparent negative correlation with the effort level of the affected subject. (2) An increase in the amount of pollution elimination per unit of pollution control effort of WSA and PE will lead to their own investment in more efforts to improve the ecology of the basin, thus benefiting all participants in the system. (3) The cost-sharing rate of the central government on the WSA of the YHRWDP, the PE, and the WDE is influenced by several factors, which shows a stable monotonically increasing or decreasing relation. The results are an useful supplement to the research on natural river pollution control, and can also provide a reference for designing pollution control mechanisms of national water network.},
}
@article {pmid39952648,
year = {2025},
author = {Siddiqui, JA and Fan, R and Liu, Y and Syed, AH and Benlin, Y and Chu, Q and Ding, Z and Ghani, MI and Liu, X and Wakil, W and Liu, DD and Chen, X and Cernava, T and Smagghe, G},
title = {The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12983},
pmid = {39952648},
issn = {1365-2583},
support = {32360705//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; GCC[2023]070//Guizhou Provincial Science and Technology Program/ ; HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; 2019-1410//Guizhou Provincial Science and Technology Program/ ; [2023]1-4//Guiyang Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities/ ; },
abstract = {Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.},
}
@article {pmid39952543,
year = {2025},
author = {Chaemsaithong, P and Romero, R and Pongchaikul, P and Warintaksa, P and Mongkolsuk, P and Bhuwapathanapun, M and Kotchompoo, K and Nimsamer, P and Kruasuwan, W and Amnuaykiatlert, O and Vivithanaporn, P and Meyyazhagan, A and Awonuga, A and Settacomkul, R and Singhsnaeh, A and Laolerd, W and Santanirand, P and Thaipisuttikul, I and Wongsurawat, T and Jenjaroenpun, P},
title = {The rapid diagnosis of intraamniotic infection with nanopore sequencing.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2025.02.011},
pmid = {39952543},
issn = {1097-6868},
abstract = {BACKGROUND: Intraamniotic infection (defined as intraamniotic inflammation with microorganisms) is an important cause of the preterm labor syndrome. Methods for the detection of microorganisms in amniotic fluid are culture and/or polymerase chain reaction. However, both methods take time, and results are rarely available for clinical decision-making. Nanopore sequencing technology offers real-time, long-read sequencing that can produce rapid results.<br><br>OBJECTIVES: To determine 1) the diagnostic performance of the 16S rDNA nanopore sequencing method for the identification of microorganisms in patients with intraamniotic inflammation; and 2) the relationship between microbial burden and the intensity of the amniotic fluid inflammatory response.<br><br>STUDY DESIGN: We performed a prospective cohort study that included singleton pregnancies presenting with symptoms of preterm labor with intact membranes or of preterm prelabor rupture of the membranes. Amniotic fluid samples were obtained for the evaluation of bacteria in the amniotic cavity using cultivation and polymerase chain reaction-based 16S Sanger sequencing methods. Participants were classified into 4 groups according to the results of an amniotic fluid culture, 16S Sanger sequencing, and an amniotic fluid interleukin-6 concentration: 1) no intraamniotic infection and intraamniotic inflammation (interleukin-6 <2.6 ng/mL and no microorganisms in the amniotic cavity determined by culture or 16S Sanger sequencing); 2) microbial invasion of the amniotic cavity without intraamniotic inflammation, defined by the presence of bacteria detected by culture or 16S Sanger sequencing; 3) sterile intraamniotic inflammation (interleukin-6 &#x2265;2.6 ng/mL without microbial invasion of the amniotic cavity); and 4) intraamniotic infection (interkeukin-6 &#x2265;2.6 ng/mL with microbial invasion of the amniotic cavity). Patients who underwent a midtrimester amniocentesis, had no intraamniotic infection or intraamniotic inflammation, and delivered at term represented the control group. 16S rDNA nanopore sequencing was performed and the diagnostic indices for the identification of intraamniotic infection were determined. Bioinformatic analysis was carried out to identify microorganisms, and a read count of at least 100 or a read count exceeding that of the background species from the control group, along with a relative abundance of no less than 1%, was used.<br><br>RESULTS: 1) 16S nanopore sequencing had a sensitivity of 88.9% (8/9), specificity of 95.4% (41/43), positive predictive value of 80.0% (8/10), negative predictive value of 97.6% (41/42), positive likelihood ratio of 19.1 (95% CI, 4.8-75.4), negative likelihood ratio of 0.1 (95% CI, 0.02-0.7), and an accuracy of 94.2% (49/52) for the identification of intraamniotic infection [prevalence, 17% (9/52)]; 2) the microbial load determined by 16S nanopore sequencing had a strong positive correlation with the intensity of an intraamniotic inflammatory response (amniotic fluid interleukin-6 concentration; Spearman's correlation 0.9; p = 0.002); and 3) a subgroup of patients with intraamniotic inflammation did not have bacteria determined by culture, Sanger sequencing, or nanopore 16S, thus confirming the existence of sterile intraamniotic inflammation.<br><br>CONCLUSION: 16S nanopore sequencing has high diagnostic indices, predictive values, likelihood ratios, and accuracy in the diagnosis of intraamniotic infection.},
}
@article {pmid39952461,
year = {2025},
author = {Shi, W and Lu, P and Yang, H and Han, J and Wang, Q},
title = {Quantifying the relative importance of natural and human factors on vegetation dynamics in China's western frontiers during 2010-2021.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121120},
doi = {10.1016/j.envres.2025.121120},
pmid = {39952461},
issn = {1096-0953},
abstract = {Vegetation is a core component of terrestrial ecosystems, thus understanding the drivers of its dynamics is crucial for ecological conservation and management, especially in regions rich in natural resources but ecologically fragile. Here, we examined vegetation cover changes in China's western frontiers and quantified the relative importance of key drivers of vegetation dynamics. First, we employed the Dimidiate Pixel Model (DPM) via Google Earth Engine (GEE) to estimate fractional vegetation cover (FVC), followed by trend analysis using the Theil-Sen median and Mann-Kendall methods to examine FVC dynamics from 2010 to 2021. Next, we applied the optimal parameter-based geographic detector (OPGD) to further assess the impact of natural (ie., temperature, precipitation, and elevation) and human (ie., land use and population density) factors on FVC. Our results revealed that approximately 61.26% of the vegetation-covered regions in China's western frontiers have shown improvement. In Xinjiang, population density, land use, and precipitation were the primary drivers of FVC changes, with Q values exceeding 0.20. In Xizang, precipitation, elevation, temperature, and land use changes were the dominant drivers, with Q values greater than 0.30. Furthermore, interactions between natural and human factors significantly influenced FVC variation. Our findings have the potential to provide references for promoting sustainable vegetation management in western China.},
}
@article {pmid39823671,
year = {2025},
author = {Liu, T and Wang, M and Wang, M and Xiong, Q and Jia, L and Ma, W and Sui, S and Wu, W and Guo, X},
title = {Identification of the primary pollution sources and dominant influencing factors of soil heavy metals using a random forest model optimized by genetic algorithm coupled with geodetector.},
journal = {Ecotoxicology and environmental safety},
volume = {290},
number = {},
pages = {117731},
doi = {10.1016/j.ecoenv.2025.117731},
pmid = {39823671},
issn = {1090-2414},
mesh = {*Soil Pollutants/analysis ; *Metals, Heavy/analysis ; China ; *Environmental Monitoring/methods ; *Algorithms ; Geographic Information Systems ; Soil/chemistry ; Risk Assessment ; Environmental Pollution/analysis/statistics &amp; numerical data ; Monte Carlo Method ; Principal Component Analysis ; Random Forest ; },
abstract = {Identifying and quantifying the dominant factors influencing heavy metal (HM) pollution sources are essential for maintaining soil ecological health and implementing effective pollution control measures. This study analyzed soil HM samples from 53 different land use types in Jiaozuo City, Henan Province, China. Pollution sources were identified using Absolute Principal Component Score (APCS), with 8 anthropogenic factors, 9 natural factors, and 4 soil physicochemical properties mapped using Geographic Information System (GIS) kernel density estimation. Geodetector and a genetic algorithm optimized random forest model (GA-RF) were employed to quantify the dominant factors and precisely identify pollution sources. A Monte Carlo model was further applied to assess source-oriented health risk probabilities across age groups in the study area. The results revealed three principal components representing pollution sources, with contribution rates of 47.2 %, 33.3 %, and 19.5 %, respectively. For pollution source 1, industrial activities were dominant, with factory density (27.7 %) and distance from the factory (36.3 %) identified as the main factors. Cr, Cu, Mn, and Ni had high loads in this source. Pollution source 2, a combination of natural and transportation influences, was primarily affected by the normalized difference vegetation index (NDVI, 37.8 %), road network density (16.8 %), and proximity to roads (15.3 %). Pollution source 3 was linked to agricultural activities, with cultivated land density (CLD) contributing 39.1 %. As exhibited a high load (91.1 %) in this source, with an exceedance rate of 93 % in cultivated soil, a moderate enrichment factor of 2.33, and a strong ecological risk index of 615.72, making it the most polluted metal in the area. The source-oriented Health Risk Assessment (HRA) showed that agricultural activities contributed 88.7 % to the carcinogenic risk from As in cultivated land. Overall, 99.3 % of the population faced an acceptable cancer risk level. Unlike traditional source apportionment methods, the GA-RF model effectively quantified the contributions of specific influencing factors (e.g., factory density) to pollution sources, rather than merely estimating the percentage contributions of the sources themselves. This approach provides a novel perspective for HM source apportionment under complex environmental conditions.},
}
@article {pmid39742640,
year = {2025},
author = {Zhang, H and Dong, S and Shan, H and Yang, C and Wang, F},
title = {Application of the DEB-TKTD model with multi-omics data: Prediction of life history traits of Chinese mitten crab (Eriocheir sinensis) under different salinities.},
journal = {Ecotoxicology and environmental safety},
volume = {290},
number = {},
pages = {117635},
doi = {10.1016/j.ecoenv.2024.117635},
pmid = {39742640},
issn = {1090-2414},
mesh = {Animals ; *Brachyura/physiology/drug effects/growth &amp; development/genetics ; *Salinity ; *Aquaculture ; Life History Traits ; Reproduction/drug effects ; Fresh Water ; Female ; Oxidative Stress ; Water Pollutants, Chemical/toxicity ; Osmoregulation ; Multiomics ; },
abstract = {Saline-alkaline aquaculture plays a crucial role in the ecological restoration of saline soils, yet high water salinity can significantly restrict the growth of cultured organisms. The Chinese mitten crab (Eriocheir sinensis) is typically farmed in freshwater, to evaluate the effects of salinity stress on these crabs, this study conducted laboratory aquaculture experiments at salinities of ≤ 0.5 (freshwater), 6, 12, and 18 ‰. Regular data on crab survival and growth were collected over 35 days. Subsequently, tissues including the eyestalk, posterior gill, hepatopancreas, and ovary were sampled from crabs in both the freshwater control group and the 18 ‰ salinity treatment group for transcriptional and metabolomic analysis. The omics data were used to ascertain the physiological mode of action (pMoA) affected by salinity in the crabs. A dynamic energy budget toxicokinetic-toxicodynamic (DEB-TKTD) model was built based on these pMoAs to predict the life history traits of crabs across different salinities, including survival, growth, and reproduction. The omics results indicated that at 18 ‰, the osmoregulatory capacity and oxidative stress resistance were enhanced, and vitellogenin synthesis was stimulated. This suggests that the two pMoAs involved increasing maintenance costs and reallocating energy between soma and reproduction. DEB-TKTD model predictions fit well with the observed data, with high R[2] values (0.9704 for survival, 0.9842 for carapace width, and 0.9283 for reproduction) and low NRMSE (0.0093, 0.1175, and 0.0778, respectively). The predictions indicate that after 60 days, survival rates under salinities of 6, 12, and 18 ‰ decreased by 35.7 %, 56.7 %, and 66.2 %, respectively, compared to freshwater conditions. Growth in carapace width was similarly affected, with reductions of 21.5 %, 42.3 %, and 62.5 %, respectively. The maturation process was accelerated for crabs in saline conditions, with puberty achieved at 45, 36, and 31 days, compared to the freshwater group that had not matured. Furthermore, the LC50 for salinity decreased from 9.07 ‰ (95 % CI: 7.33-10.15 ‰) at 35 days to 4.59 ‰ (95 % CI: 3.12-5.83 ‰) at 60 days. The findings of this study indicate the significant impact of salinity on the survival, growth, and maturation of Chinese mitten crabs by altering maintenance costs and energy allocation. The DEB-TKTD model, informed by omics data, accurately predicts the life history traits of crabs under saline stress. This approach provides an innovative tool for ecological toxicological research in the aquaculture environment.},
}
@article {pmid39730187,
year = {2025},
author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z},
title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.},
journal = {Genome research},
volume = {35},
number = {2},
pages = {368-378},
doi = {10.1101/gr.279825.124},
pmid = {39730187},
issn = {1549-5469},
mesh = {Animals ; *Ruminants/microbiology ; *Deep Learning ; *Fungi/genetics/classification ; Rumen/microbiology/parasitology ; Databases, Protein ; Metagenome ; Metagenomics/methods ; Eukaryota/genetics/classification ; Gastrointestinal Microbiome ; Computational Biology/methods ; },
abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.},
}
@article {pmid39891349,
year = {2025},
author = {Wang, Y and Li, J and Chiu, TP and Gompel, N and Rohs, R},
title = {DNAdesign: feature-aware in silico design of synthetic DNA through mutation.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {2},
pages = {},
doi = {10.1093/bioinformatics/btaf052},
pmid = {39891349},
issn = {1367-4811},
support = {RGP0021/2018//Human Frontier Science Program/ ; },
mesh = {*DNA/chemistry/genetics ; *Mutation ; *Software ; Nucleic Acid Conformation ; Binding Sites ; Computer Simulation ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; },
abstract = {MOTIVATION: DNA sequence and shape readout represent different modes of protein-DNA recognition. Current tools lack the functionality to simultaneously consider alterations in different readout modes caused by sequence mutations. DNAdesign is a web-based tool to compare and design mutations based on both DNA sequence and shape characteristics. Users input a wild-type sequence, select sites to introduce mutations and choose a set of DNA shape parameters for mutation design.<br><br>RESULTS: DNAdesign utilizes Deep DNAshape to provide ultra-fast predictions of DNA shape based on extended k-mers and offers multiple encoding methods for nucleotide sequences, including the physicochemical encoding of DNA through their functional groups in the major and minor groove. DNAdesign provides all mutation candidates along the sequence and shape dimensions, with interactive visualization comparing each candidate with the wild-type DNA molecule. DNAdesign provides an approach to studying gene regulation and applications in synthetic biology, such as the design of synthetic enhancers and transcription factor binding sites.<br><br>The DNAdesign webserver and documentation are freely accessible at https://dnadesign.usc.edu.},
}
@article {pmid39623597,
year = {2024},
author = {Félix, CR and Navarro, HMC and Landell, MF},
title = {The Hidden Global Diversity of the Yeast Genus Carlosrosaea: A Biodiversity Databases Perspective.},
journal = {Yeast (Chichester, England)},
volume = {41},
number = {11-12},
pages = {658-667},
doi = {10.1002/yea.3986},
pmid = {39623597},
issn = {1097-0061},
support = {//This work was supported by Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq, number of grants 475378/2013-0, 312889/2021-6 and 311553/2018-4), Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES) and Funda&#xe7;&#xe3;o de amparo a Pesquisa de Alagoas (FAPEAL). This work is also part of the project "INCT Yeasts: Biodiversity, preservation and biotechnological innovation", funded by Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq), grant #406564/2022-1./ ; },
mesh = {*Biodiversity ; Phylogeny ; Saccharomycetales/classification/genetics/isolation &amp; purification ; Databases, Factual ; },
abstract = {Biodiversity gaps in microorganisms, such as yeasts, blur our understanding of microbial diversity, introducing biases in their biogeography, ecology, and taxonomy. The genus Carlosrosaea is a potential plant growth booster, yet it is still a little-known yeast group. Considering that databases like GBIF and GenBank are powerful tools for exploring biodiversity data, we aimed to map the geographic distribution, ecological patterns, and taxonomic potential of the genus Carlosrosaea. We found 176 records of the genus, with about 70% associated with plant material, mostly leaves. Furthermore, 55% of the records pertained to the tropical region and only 12% to the temperate. The data indicates the existence of more than a dozen possible new species of the genus, cataloged yet undescribed. This study advances our understanding of the geographic, ecological, and taxonomic aspects of Carlosrosaea. It also highlights how public databases and literature reviews provide accessible ways to analyze information about microbial groups with limited data.},
}
@article {pmid39949385,
year = {2023},
author = {Lohse, K and , and , and , and Vila, R and , },
title = {The genome sequence of the Common Blue, Polyommatus icarus (Rottemburg, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {72},
pmid = {39949385},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Polyommatus icarus (the Common Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 512 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases long. Gene annotation of this assembly on Ensembl identified 13,350 protein-coding genes.},
}
@article {pmid39948527,
year = {2025},
author = {Rakshasa-Loots, AM and Steyn, C and Swiffen, D and Marwick, KFM and Semple, RK and Reynolds, RM and Burgess, K and Lawrie, SM and Lightman, SL and Luz, S and Smith, DJ},
title = {Metabolic biomarkers of clinical outcomes in severe mental illness (METPSY): protocol for a prospective observational study in the Hub for metabolic psychiatry.},
journal = {BMC psychiatry},
volume = {25},
number = {1},
pages = {122},
pmid = {39948527},
issn = {1471-244X},
support = {MR/Z503563/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {People with severe mental illness have high rates of obesity, type 2 diabetes, and cardiovascular disease. Emerging evidence suggests that metabolic dysfunction may be causally linked to the risk of severe mental illness. However, more research is needed to identify reliable metabolic markers which may have an impact on mental health outcomes, and to determine the mechanisms behind their impact. In the METPSY research study, we will investigate the relationship between metabolic markers and clinical outcomes of severe mental illness in young adults. We will recruit 120 young adults aged 16-25 years living in Scotland with major depressive disorder, bipolar disorder, schizophrenia, or no severe mental illness (controls) for a prospective observational study. We will assess clinical symptoms at three in-person visits (baseline, 6 months, and 12 months) using the Structured Clinical Interview for DSM-5, and collect blood samples at each of these visits for agnostic profiling of metabolic biomarkers through an untargeted metabolomic screen, using the rapid hydrophilic interaction liquid chromatography ion mobility mass spectrometry method (RHIMMS). Participants will also complete remote assessments at 3 and 9 months after the baseline visit: Ecological Momentary Assessments to measure mental health, wrist actigraphy to measure rhythms of rest and activity, and continuous glucose monitoring to measure metabolic changes. Throughout the 12-month enrolment period, we will also measure objective markers of sleep using a radar sleep monitor (Somnofy). Using advanced statistical techniques and machine learning analysis, we will seek to better understand the mechanisms linking metabolic health with mental health in young adults with schizophrenia, bipolar disorder, and severe depression. Clinical trial number: Not applicable.},
}
@article {pmid39945053,
year = {2025},
author = {Tittes, S and Lorant, A and McGinty, SP and Holland, JB and de Jesus Sánchez-González, J and Seetharam, A and Tenaillon, M and Ross-Ibarra, J},
title = {The population genetics of convergent adaptation in maize and teosinte is not locally restricted.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.92405},
pmid = {39945053},
issn = {2050-084X},
support = {1822330//National Science Foundation/ ; 1238014//National Science Foundation/ ; CA-D-PLS-2066-H 548//U.S. Department of Agriculture/ ; },
mesh = {*Zea mays/genetics/physiology ; *Adaptation, Physiological/genetics ; *Genetics, Population ; Genetic Variation ; Selection, Genetic ; },
abstract = {What is the genetic architecture of local adaptation and what is the geographic scale over which it operates? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are also frequently shared by several populations, and often between subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, even after domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, our results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations but smaller than the species range.},
}
@article {pmid39943576,
year = {2025},
author = {Cleveland, P and Morrison, A},
title = {Sông Sài Gòn: Extreme Plastic Pollution Pathways in Riparian Waterways.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {3},
pages = {},
doi = {10.3390/s25030937},
pmid = {39943576},
issn = {1424-8220},
support = {2023//Annual Award, School of Future Environments, Auckland University of Techolology/ ; },
mesh = {*Plastics ; *Rivers/chemistry ; *Environmental Monitoring/methods ; Vietnam ; Water Pollutants, Chemical/analysis ; Water Pollution/analysis ; Geographic Information Systems ; Ecosystem ; },
abstract = {Plastic pollution in waterways poses a significant global challenge, largely stemming from land-based sources and subsequently transported by rivers to marine environments. With a substantial percentage of marine plastic waste originating from land-based sources, comprehending the trajectory and temporal experience of single-use plastic bottles assumes paramount importance. This project designed, developed, and released a plastic pollution tracking device, coinciding with Vietnam's annual Plastic Awareness Month. By mapping the plastic tracker's journey through the Saigon River, this study generated high-fidelity data for comprehensive analysis and bolstered public awareness through regular updates on the Re-Think Plastics Vietnam website. The device, equipped with technologies such as drone flight controller, open-source software, embedded computing, and cellular networking effectively captured GPS position, track, and localized conditions experienced by the plastic bottle tracker on its journey. This amalgamation of data contributes to the understanding of plastic pollution behaviors and serves as a data set for future initiatives aimed at plastic prevention in the ecologically sensitive Mekong Delta. By illuminating the transportation of single-use plastic bottles in the riparian waterways of Ho Chi Minh City and beyond, this study plays a role in collective efforts to understand plastic pollution and preserve aquatic ecosystems. By deploying a GPS-enabled plastic tracker, this study provides novel, high-resolution empirical data on plastic transport in urban tidal systems. These findings contribute to improving waste interception strategies and informing environmental policies aimed at reducing plastic accumulation in critical retention zones.},
}
@article {pmid39939924,
year = {2025},
author = {Lorková, Z and Cimermanová, M and Piknová, M and Adhvaryu, S and Pristaš, P and Kisková, J},
title = {Environmental impact on the genome shaping of putative new Streptomyces species.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {72},
pmid = {39939924},
issn = {1471-2180},
support = {VEGA 1/0779/21//Grant Agency of the Ministry of Education, Science, Research and Sport, Slovak Republic and the Slovak Academy of Sciences/ ; },
mesh = {*Streptomyces/genetics/classification/metabolism/isolation &amp; purification ; *Genome, Bacterial/genetics ; *Phylogeny ; *Metals, Heavy/metabolism ; Siderophores/metabolism ; Multigene Family ; Poland ; Secondary Metabolism/genetics ; Adaptation, Physiological/genetics ; Mining ; Computational Biology/methods ; },
abstract = {BACKGROUND: The bacterial evolution and the emergence of new species are likely influenced by multiple forces, including long-term environmental pressure such as living in extreme conditions. In this study, the genomes of two potentially new Streptomyces species isolated from a former mine heap in Tarnowskie Góry in Poland, were analyzed.<br><br>RESULTS: A bioinformatic approach revealed notable phylogenetic and metabolic differences between the studied Streptomyces strains, despite originating from the same environment. While both strains are characterized by genetic features common to actinomycetes, additional unique biosynthetic gene clusters were also predicted in their genomes. The comparative genomic analysis with other Streptomyces spp. revealed a high conservation in heavy metal adaptive mechanisms, indicating a preadaptation to extreme conditions. The difference observed in the cad and mer operons could be attributed to the specific adaptations to heavy metal contamination. The high metal tolerance of examined strains was also confirmed by an agar dilution assay in the presence of several heavy metals. The confirmed siderophore production represents an additional mechanism allowing streptomycetes to survive in extreme conditions. On the other hand, both of studied genomes show significant differences in energy acquisition processes and the production of putative novel secondary metabolites. The isolates showed these differences not only among themselves but also compared to other Streptomyces species, indicating their uniqueness.<br><br>CONCLUSIONS: Our results demonstrate that extreme environmental conditions can lead to the development of various adaptation mechanisms in the Streptomyces spp. Furthermore, the results indicate that diverse Streptomyces species have developed conserved adaptation mechanisms against the heavy metals under extreme conditions, indicating the emergence of preadaptations that allow bacteria to respond rapidly to polluted environments and evolve their genomes accordingly up to the evolution of new species.},
}
@article {pmid38452336,
year = {2024},
author = {Vacchi, L and Zirone, E and Strina, V and Cavaletti, G and Ferrarese, C},
title = {Mobile Applications to Support Multiple Sclerosis Communities: The Post-COVID-19 Scenario.},
journal = {Telemedicine journal and e-health : the official journal of the American Telemedicine Association},
volume = {30},
number = {6},
pages = {e1615-e1628},
doi = {10.1089/tmj.2023.0515},
pmid = {38452336},
issn = {1556-3669},
mesh = {Humans ; Access to Information ; COVID-19/epidemiology/prevention &amp; control ; *Digital Health/trends ; Health Knowledge, Attitudes, Practice ; Italy/epidemiology ; *Mobile Applications/trends ; *Multiple Sclerosis/diagnosis/therapy ; Social Networking ; *Telemedicine/trends ; },
abstract = {Introduction: The increase in the use of mobile apps since the COVID-19 pandemic, even among people with multiple sclerosis (PwMS) and health care providers (HCPs), has enabled access to reliable information, symptoms monitoring and management, and social connections. The pandemic has undoubtedly contributed to the acceleration of the "digital revolution." But how far has it progressed for the MS communities? Methods: Italian Google Play and App Store were queried, selecting MS-specific apps in English or Italian language and usable by a wide public. Results: Fifty-four (n = 54) MS-specific apps were identified; most were PwMS-oriented (83%), free of charge (94%), and in English language (76%). The 45 PwMS-oriented apps focused on increasing MS knowledge (71%), tracking symptoms (33%), and promoting networking with peers or HCPs (38%). The 13 HCPs-oriented tools addressed education and updates on MS (62%), disease assessment and management (54%), and research (15%). Google Search tool was also queried to find non-MS-specific apps to fulfill some unmet domains (as sleep, pain, sexual or mental health). Twenty-four additional apps were listed to provide a valuable contribution. Conclusion: The "digital revolution" led to increasingly customized tools for PwMS, especially as m-health or social-networking apps. However, apps to support other specific MS-relevant domains, appealing HCPs-oriented apps, and specific mobile tools for MS caregivers are still lacking. The absence of data assessing the usability and quality of MS apps in ecologically contexts leads to not reliable conclusions about potential benefits. A strong dialogue between MS communities and the digital industry is encouraged to fill this gap.},
}
@article {pmid39938295,
year = {2025},
author = {Zhuo, W and Wu, N and Shi, R and Cui, Y and Zhang, C and Liu, S and Zhu, F and Zhang, B and Liu, P},
title = {Assessing the impacts of reclamation and invasion on ecological dynamics of coastal wetland vegetation in the Yangtze Estuary from 1985 to 2019:A case study of Chongming Island, China.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124505},
doi = {10.1016/j.jenvman.2025.124505},
pmid = {39938295},
issn = {1095-8630},
abstract = {The distribution of coastal wetland vegetation is influenced by biological invasions, human reclamations and climate changes, which continually reshape vegetation structures. However, limited attention has been given to the impact of biological invasion on native vegetation and tidal wetlands. This study focuses on the wetlands of Chongming Island, employing a multi-feature dataset combining spectral, phenological, and temporal information on the Google Earth Engine (GEE) platform. Using the Random Forest (RF) classification method, we analyzed annual vegetation distribution changes and examined the distinct effects of natural and anthropogenic factors. The research results indicate that: (1) From 1985 to 2019, the total area of Chongming Island expanded, while wetland vegetation decreased due to embankment construction and island connection projects. (2) The total area of wetland vegetation on Chongming Island dropped to its lowest point in 2002 (3812.76 ha), and then gradually recovered. (3) Human reclamation was the primary driver of vegetation changes from 1985 to 1995. (4) Vegetation distribution in Dongtan was influenced by both human and natural factors, whereas Beiliuyao affected by the invasion and expansion of the S. alterniflor. These findings provide valuable insights into the drivers of long-term vegetation distribution changes, offering essential data and theoretical support for sustainable development and management of Chongming Island's ecosystems.},
}
@article {pmid39936843,
year = {2025},
author = {Kim, KK and Backonja, U},
title = {Digital health equity frameworks and key concepts: a scoping review.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {},
number = {},
pages = {},
doi = {10.1093/jamia/ocaf017},
pmid = {39936843},
issn = {1527-974X},
support = {//The MITRE Innovation Program/ ; //MITRE Corporation/ ; },
abstract = {OBJECTIVES: Digital health equity, the opportunity for all to engage with digital health tools to support good health outcomes, is an emerging priority across the world. The field of digital health equity would benefit from a comprehensive and systematic understanding of digital health, digital equity, and health equity, with a focus on real-world applications. We conducted a scoping review to identify and describe published frameworks and concepts relevant to digital health equity interventions.<br><br>MATERIALS AND METHODS: We conducted a scoping review of published peer-reviewed literature guided by the PRISMA Extension for Scoping Reviews. We searched 5 databases for frameworks related to or applied to digital health or equity interventions. Using deductive and inductive approaches, we analyzed frameworks and concepts based on the socio-ecological model.<br><br>RESULTS: Of the 910 publications initially identified, we included 44 (4.8%) publications in our review that described 42 frameworks that sought to explain the ecosystem of digital and/or health equity, but none were comprehensive. From the frameworks we identified 243 concepts grouped into 43 categories including characteristics of individuals, communities, and organizations; societal context; perceived value of the intervention by and impacts on individuals, community members, and the organization; partnerships; and access to digital health services, in-person services, digital services, and data and information, among others.<br><br>DISCUSSION: We suggest a consolidated definition of digital health equity, highlight illustrative frameworks, and suggest concepts that may be needed to enhance digital health equity intervention development and evaluation.<br><br>CONCLUSION: The expanded understanding of frameworks and relevant concepts resulting from this study may inform communities and stakeholders who seek to achieve digital inclusion and digital health equity.},
}
@article {pmid39936690,
year = {2025},
author = {Krefer, LT and Oliveira, WF},
title = {[Reformulations in the national mental health policy: analysis of assistance data in the period from 2012 to 2022].},
journal = {Ciencia &amp; saude coletiva},
volume = {30},
number = {2},
pages = {e13372023},
doi = {10.1590/1413-81232025302.13372023},
pmid = {39936690},
issn = {1678-4561},
mesh = {Brazil ; Humans ; *Health Policy ; *Mental Health Services/organization &amp; administration ; *Hospitals, Psychiatric/organization &amp; administration/statistics &amp; numerical data ; Longitudinal Studies ; *Deinstitutionalization/trends ; Primary Health Care/organization &amp; administration ; Mental Health ; Ambulatory Care/statistics &amp; numerical data ; Health Care Reform ; Health Information Systems/organization &amp; administration ; },
abstract = {This article aims to analyze data on care in the field of public mental healthcare in Brazil from 2012 to 2022, corresponding to the years before and after the implementation of the New Mental Health Policy. For this purpose, quantitative methodology, of the longitudinal ecological study type, was used. Data was extracted for the period from 2012 to 2022. The sources used were Health Information Systems. The data was compiled into time series and analyzed using descriptive statistical techniques. The results pointed to the enhancement of outpatient services and a decrease in the expansion of Psychosocial Care Centers and Primary Care facilities after 2017, indicating compliance with the New Policy guidelines to deprioritize territorial and community-based services. The number of psychiatric hospitals showed little variation for the entire period, indicating not only alignment with the strengthening of hospital institutions indicated in the New Policy, but also weaknesses in the deinstitutionalization policy of the period prior to 2017. This study concludes that the effects of the changes in national policies on the organization, management and execution of the health system can be seen, but at the same time there is continuity in various aspects.},
}
@article {pmid39889433,
year = {2025},
author = {Shukla, S and Khan, R and Chrzanowski, &#x141; and Vagliasindi, FGA and Roccaro, P},
title = {Advancing sustainable agriculture through multi-omics profiling of biosolids for safe application: A review.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124292},
doi = {10.1016/j.jenvman.2025.124292},
pmid = {39889433},
issn = {1095-8630},
mesh = {*Agriculture/methods ; Soil/chemistry ; Wastewater/chemistry ; Multiomics ; },
abstract = {Biosolids, derived from wastewater treatment processes, are valuable resources for soil amendment in agriculture due to their nutrient-rich composition. However, various contaminants of concern (CEC) such as pharmaceuticals, per-and poly-fluoroalkyl substances, endocrine disruptive chemicals, surfactants, pathogens, nanoplastics, and microplastics, are also reported in biosolids. The use of biosolids for agriculture may introduce these CEC into the soil, which raises concerns about their environmental and human health impacts. Moreover, the presence of pathogens (Escherichia coli, Salmonella sp., Shigella, Giardia, Rotavirus, etc.) even after treatment calls for microbial profiling of biosolids, especially in developing countries. Multi-omics approaches can be used as powerful tools for characterizing microbial communities and highlighting metabolic pathways. Moreover, these approaches also help in predicting the ecological and agronomic effects of biosolids application in agricultural soils. This review discusses the advantages and challenges of using biosolids in agriculture, considering the range of different CEC reported in biosolids. Moreover, the current legislation for the use of biosolids in agriculture is also presented, highlighting the limitations with respect to guidelines for emerging contaminants in biosolids. Furthermore, the role of the multi-omics approach in biosolids management, focusing on genomics, transcriptomics, proteomics, and metabolomics is also assessed. Multi-omics also allows for real-time monitoring, ensuring continuous optimization of biosolids towards changing environmental conditions. This dynamic approach not only enhances the safe use, but also enhances the sustainability of waste management practices, minimizing the negative effects. Finally, the future research directions for integrating the multi-omics approach into biosolid management practices are also suggested. The need for updating the legislative framework, continued innovation to promote sustainable and robust agricultural systems, bringing the process closer to the principles of a circular bioeconomy is also empahasized.},
}
@article {pmid39854904,
year = {2025},
author = {Ghimire, SR and Schumacher, B and Swanson, S and Hall, R and Hall, ES and Zambrana, J and Johnston, JM},
title = {Assessing riparian functioning condition for improved ecosystem services: A case study of the Back Creek watershed (Virginia, USA).},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124154},
doi = {10.1016/j.jenvman.2025.124154},
pmid = {39854904},
issn = {1095-8630},
mesh = {*Ecosystem ; *Rivers ; Virginia ; *Environmental Monitoring/methods ; Water Quality ; Conservation of Natural Resources ; Hydrology ; Geographic Information Systems ; },
abstract = {Riparian functioning condition refers to a rating and description of the current ecological status of a reach of a riparian ecosystem in consideration of its potential hydrology, vegetation, and geomorphology. Reach rating options are Proper Functioning Condition (PFC), Functional-At-Risk (FAR), Non-Functional, and apparent or monitored trends. We assessed the functioning condition of flowing riverbank areas of Back Creek located in Virginia (USA) following a PFC protocol developed by the U.S. Department of the Interior and the U.S. Department of Agriculture. The PFC protocol involves 17 qualitative assessment items that address three categories of attributes (hydrology, vegetation, and geomorphology); each is answered as "yes", "no," or "not applicable" with an explanation. We discussed key PFC items driving stream water quality contextualizing the previously modeled riparian buffer zones and ecosystem services tradeoffs in the Back Creek watershed published by U.S. Environmental Protection Agency. Using the remote sensing data in the Geographic Information System, we delineated and characterized 26 Back Creek reaches of 41.1 km length. We also analyzed the 38-year (1981-2018) daily datasets of the precipitation, surface runoff, temperature, soil moisture pattern, and vegetation types for the watershed. Then, we conducted the PFC assessments using field reconnaissance of 10 reaches, 19.3 km of the Back Creek. The field assessments concluded that 52% of the assessed length of Back Creek was in PFC, attributed to diverse vegetation, maintained channel characteristics, floodplain accessibility (where appropriate), and balanced water and sediment loading supplied by individual headwater streams to the Back Creek. 48% of the assessed length was in FAR condition due to land use changes and urban road network. This study provides an exemplar of nonpoint source (diffused pollution generated by land runoff) methodology for identifying key riparian functioning issues and assessing effectiveness of the non-point source best management practice programs.},
}
@article {pmid39848196,
year = {2025},
author = {Wang, S and Liping, Y and Arif, M},
title = {Evolutionary analysis of ecological-production-living space-carrying capacity in tourism-centric traditional villages in Guangxi, China.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124182},
doi = {10.1016/j.jenvman.2025.124182},
pmid = {39848196},
issn = {1095-8630},
mesh = {China ; *Tourism ; Humans ; Conservation of Natural Resources ; Geographic Information Systems ; Ecology ; },
abstract = {The carrying capacity of ecological-production-living space (EPLS) is pivotal to the development of traditional villages and the optimization of their tourism industries. However, research on tourism-centric traditional villages in China remains limited. This study addresses this gap by examining EPLS carrying capacity in tourism-focused villages in Guangxi, China. Using remote sensing imagery of Chengyang Bazhai (CYBZ) along with data on local tourism and socio-economic development, the study classifies different types of EPLS and establishes a comprehensive indicator system. Geographic information system spatial analysis, combined with grey correlation analysis, was employed to assess the evolution of EPLS carrying capacity and its influencing factors in CYBZ. The findings indicate that between 2006 and 2015, the overall carrying capacity of EPLS experienced a decline. While the carrying capacity of production spaces remained relatively stable, ecological and living spaces saw notable decreases. However, from 2015 to 2021, EPLS carrying capacity increased substantially. The most substantial growth was observed in Pingyan Village, followed by Chengyang Village, with Pingfu Village exhibiting the smallest improvement. The expansion of the tourism industry has significantly influenced the evolution of EPLS carrying capacity in CYBZ, creating a greater need for strategic future planning. Optimal EPLS and durable tourism development require continuous enhancements in EPLS capacity, reductions in negative interactions between carrying capacity and tourism growth, as well as ecological revitalization. This study contributes to the existing literature by enhancing EPLS carrying capacity understanding. It offers theoretical guidance for its optimization in Chengyang and practical insights into sustainable tourism development in similar regions.},
}
@article {pmid39294488,
year = {2024},
author = {Zhang, WH and Gao, JW and Lau, CC and Jiang, ZF and Yeong, YS and Mok, WJ and Zhou, W},
title = {Effects of different trophic conditions on total fatty acids, amino acids, pigment and gene expression profiles in Euglena gracilis.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {10},
pages = {325},
pmid = {39294488},
issn = {1573-0972},
support = {22zxbtsn00020//Tianjin Municipal Science and Technology Bureau/ ; },
mesh = {*Euglena gracilis/genetics/growth &amp; development/metabolism/ultrastructure ; *Gene Expression Profiling ; *Amino Acids/metabolism ; *Fatty Acids/metabolism ; *Pigments, Biological/metabolism ; Biomass ; Gene Ontology ; Gene Expression Regulation, Developmental ; Heterotrophic Processes ; },
abstract = {Euglena gracilis is a unique microalga that lacks a cell wall and is able to grow under different trophic culture conditions. In this study, cell growth, biomass production, and changes in the ultrastructure of E. gracilis cells cultivated photoautotrophically, mixotrophically, and under sequential-heterotrophy-photoinduction (SHP) were assessed. Mixotrophy induced the highest cell growth and biomass productivity (6.27 ± 0.59 mg/L/d) in E. gracilis, while the highest content of fatty acids, 2.69 ± 0.04% of dry cell weight (DCW) and amino acids, 38.16 ± 0.08% of DCW was obtained under SHP condition. E. gracilis also accumulated significantly higher saturated fatty acids and lower unsaturated fatty acids when cultivated under SHP condition. Transcriptomic analysis showed that the expression of photosynthetic genes (PsbA, PsbC, F-type ATPase alpha and beta) was lower, carbohydrate and protein synthetic genes (glnA, alg14 and fba) were expressed higher in SHP-culture cells when compared to other groups. Different trophic conditions also induced changes in the cell ultrastructure, where paramylon and starch granules were more abundant in SHP-cultured cells. The findings generated in this study illustrated that aerobic SHP cultivation of E. gracilis possesses great potential in human and animal feed applications.},
}
@article {pmid39934908,
year = {2025},
author = {Wang, L and Simopoulos, CMA and Serrana, JM and Ning, Z and Li, Y and Sun, B and Yuan, J and Figeys, D and Li, L},
title = {PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {50},
pmid = {39934908},
issn = {2049-2618},
support = {201906015034//China Scholarship Council/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; 32370050//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.<br><br>RESULTS: Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.<br><br>CONCLUSIONS: Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.},
}
@article {pmid39931107,
year = {2024},
author = {Boyes, D and Murray, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Bird-cherry Ermine moth, Yponomeuta evonymella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {618},
pmid = {39931107},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Yponomeuta evonymella (the Bird-cherry Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence has a total length of 572.70 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the trivalent sex chromosomes Z 1, Z 2 and W. The mitochondrial genome has also been assembled and is 16.16 kilobases in length.},
}
@article {pmid39899595,
year = {2025},
author = {McKenzie-Smith, GC and Wolf, SW and Ayroles, JF and Shaevitz, JW},
title = {Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012753},
doi = {10.1371/journal.pcbi.1012753},
pmid = {39899595},
issn = {1553-7358},
mesh = {Animals ; *Drosophila melanogaster/physiology ; *Behavior, Animal/physiology ; *Locomotion/physiology ; *Circadian Rhythm/physiology ; *Posture/physiology ; Computational Biology ; Deep Learning ; Grooming/physiology ; Female ; Male ; },
abstract = {Animal behavior spans many timescales, from short, seconds-scale actions to daily rhythms over many hours to life-long changes during aging. To access longer timescales of behavior, we continuously recorded individual Drosophila melanogaster at 100 frames per second for up to 7 days at a time in featureless arenas on sucrose-agarose media. We use the deep learning framework SLEAP to produce a full-body postural dataset for 47 individuals resulting in nearly 2 billion pose instances. We identify stereotyped behaviors such as grooming, proboscis extension, and locomotion and use the resulting ethograms to explore how the flies' behavior varies across time of day and days in the experiment. We find distinct daily patterns in all stereotyped behaviors, adding specific information about trends in different grooming modalities, proboscis extension duration, and locomotion speed to what is known about the D. melanogaster circadian cycle. Using our holistic measurements of behavior, we find that the hour after dawn is a unique time point in the flies' daily pattern of behavior, and that the behavioral composition of this hour tracks well with other indicators of health such as locomotion speed and the fraction of time spend moving vs. resting. The method, data, and analysis presented here give us a new and clearer picture of D. melanogaster behavior across timescales, revealing novel features that hint at unexplored underlying biological mechanisms.},
}
@article {pmid39793648,
year = {2025},
author = {Ji, G and Wang, Y and Lu, Z and Long, G and Xu, C},
title = {Associations between ambient benzene and stroke, and the mediating role of accelerated biological aging: Findings from the UK biobank.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {367},
number = {},
pages = {125656},
doi = {10.1016/j.envpol.2025.125656},
pmid = {39793648},
issn = {1873-6424},
mesh = {*Benzene ; Humans ; United Kingdom ; Male ; *Stroke/epidemiology/chemically induced ; Middle Aged ; Female ; *Environmental Exposure/statistics &amp; numerical data ; *Air Pollutants/analysis ; Aged ; *Aging ; *Biological Specimen Banks ; Adult ; Cohort Studies ; Risk Factors ; UK Biobank ; },
abstract = {Benzene can cause respiratory diseases. However, the associations between benzene and stroke are unclear. A total of 13,116 patients with stroke and 377,120 controls from the UK Biobank were included. The benzene exposure concentrations were matched on the basis of the address information of each participant via a data form from the UK Department for Environment, Food and Rural Affairs. Weighted Cox regression was used to investigate the association between benzene and stroke risk. The polygenic risk score (PRS) was used to observe the joint effects of benzene exposure and genetic factors on stroke risk. We conducted a mediation analysis to investigate the mediating role of accelerated biological aging in this cohort study. After adjusting for covariates, every 1 μg/m[3] increase in benzene exposure increased the risk of stroke by 70%, which may be mediated by accelerated biological aging. The population with high benzene exposure concentrations and high PRSs had a 44% greater risk of stroke than did those with low benzene exposure concentrations and low PRSs. Benzene exposure and the PRS have joint effects on the risk of stroke. Benzene exposure was associated with stroke risk, possibly through increased biological aging, and the PRS modified this association.},
}
@article {pmid39929026,
year = {2025},
author = {Song, J and Zhou, S and Kwan, MP and Song, G and Long, J and Song, W},
title = {The time-lagged effect of noise exposure on noise annoyance: The role of temporal, spatial and social contexts.},
journal = {Social science &amp; medicine (1982)},
volume = {368},
number = {},
pages = {117817},
doi = {10.1016/j.socscimed.2025.117817},
pmid = {39929026},
issn = {1873-5347},
abstract = {While some research has examined the time-lagged effect of restorative soundscape in specific contexts (e.g., parks), how the time-lagged effect of noise annoyance during people's daily activities may vary across different temporal, spatial, and social contexts remains largely unknown. To address this research gap, we utilized Ecological Momentary Assessment (EMA) data to measure people's real-time noise annoyance and activity diary data to assess their time-lagged noise annoyance. Real-time noise exposure was captured by portable noise sensors. We employed fixed effects ordered panel logistic regression to examine the effects of different thresholds of noise levels on people's time-lagged noise annoyance, and how it varied across different temporal, spatial, and social contexts. The results indicated that: (1) there were significant time-lagged effects between participants' real-time noise exposure and their time-lagged noise annoyance; (2) participants' time-lagged noise annoyance associated with an activity was influenced by its temporal, spatial, and social contexts, particularly on weekdays; (3) participants' time-lagged noise annoyance was significantly associated with measured noise levels, with the highest coefficient for 65 dB, followed by 70 dB; and (4) there were significant interaction effects between noise levels and temporal-spatial-social contexts on participants' time-lagged noise annoyance (particularly when noise levels exceeded 70 dB). These findings enhance our understanding and have crucial implications for the implementation of noise control policies, which should consider not only noise levels but also the time-lagged effects of noise, particularly on weekdays, at outdoor recreational activity sites, as well as the potential vulnerabilities of individuals experiencing noise exposure in isolation.},
}
@article {pmid39928107,
year = {2025},
author = {Güneri, FD and Karaarslan, F and Özen, H and Odabaşi, E},
title = {Medical mud-pack treatment with different temperatures in patients with knee osteoarthritis.},
journal = {International journal of biometeorology},
volume = {},
number = {},
pages = {},
pmid = {39928107},
issn = {1432-1254},
abstract = {To compare the effects of medical mud-pack (MMP) treatments applied at different temperatures on the pain and joint functions of patients with knee osteoarthritis (KOA). Kellgren Lawrence (KL) stage 3 or 4 KOA patients were included and randomized into three groups. Patients in groups 1, 2, and 3 took MMP treatment to both knees at 39 °C, 42 °C, and 45 °C, respectively. The treatment was performed for 12 days (only weekdays) and was 30 min long per day. The same blinded physician evaluated the patients at baseline and at the end of the treatment. The assessments were done before and after the intervention. The primary outcome was to achieve a minimal clinically important improvement (MCII) for KOA (decrease of at least 19 mm (-40.8%) on the VAS for pain, a decrease of 18.3 mm (-39%) on the patient's global assessment (PGA), and/or a decrease of at least 9.1 points (-26%) on the Western Ontario and McMaster Universities Osteoarthritis Index function subscale (WOMAC-FS). Secondary outcomes were pain (VAS), patient's global assessment (VAS), physician's global assessment (VAS), Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Patient's health state, Patient Acceptable Symptom State (PASS). 217 patients were analyzed. Groups 1, 2, and 3 had 68, 81,68 patients, respectively. The MCII measurement revealed that MMP treatment did not show a significant difference between groups 2 and 3 (p > 0.05). Also, it was observed that more patients in groups 2 and 3 reached the MCII compared to group 1 (p < 0.001). For the secondary outcomes, significant improvements were observed within-group evaluations for each of the three groups (p < 0.001). Between groups comparisons, the improvements at the end of the treatment were found to be superior for group 2 and group 3 compared to group 1 (p < 0.001). There was no statistically significant difference between groups 2 and 3 for any parameters (p > 0.05). The number of patients who achieved the PASS was statistically lower for group 1 compared to groups 2 and 3 (p < 0.001). We observed significant improvements in all groups after treatment. The main result, as measured by MCII, suggests that MMP treatments at 42-45 °C is more effective than at 39 °C in managing severe KOA patients' pain and functional status. We found no significant difference in pain and joint function improvement between 42 °C and 45 °C after MMP.},
}
@article {pmid39899643,
year = {2025},
author = {Hozé, N and Pons-Salort, M and Metcalf, CJE and White, M and Salje, H and Cauchemez, S},
title = {RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012777},
doi = {10.1371/journal.pcbi.1012777},
pmid = {39899643},
issn = {1553-7358},
mesh = {Seroepidemiologic Studies ; Humans ; *Software ; *Bayes Theorem ; Computational Biology/methods ; Computer Simulation ; Disease Outbreaks/statistics &amp; numerical data ; Communicable Diseases/epidemiology/transmission ; },
abstract = {Population-based serological surveys are a key tool in epidemiology to characterize the level of population immunity and reconstruct the past circulation of pathogens. A variety of serocatalytic models have been developed to estimate the force of infection (FOI) (i.e., the rate at which susceptible individuals become infected) from age-stratified seroprevalence data. However, few tool currently exists to easily implement, combine, and compare these models. Here, we introduce an R package, Rsero, that implements a series of serocatalytic models and estimates the FOI from age-stratified seroprevalence data using Bayesian methods. The package also contains a series of features to perform model comparison and visualise model fit. We introduce new serocatalytic models of successive outbreaks and extend existing models of seroreversion to any transmission model. The different features of the package are illustrated with simulated and real-life data. We show we can identify the correct epidemiological scenario and recover model parameters in different epidemiological settings. We also show how the package can support serosurvey study design in a variety of epidemic situations. This package provides a standard framework to epidemiologists and modellers to study the dynamics of past pathogen circulation from cross-sectional serological survey data.},
}
@article {pmid38866716,
year = {2024},
author = {Brock, MT and Morrison, HG and Maignien, L and Weinig, C},
title = {Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
doi = {10.1093/femsle/fnae044},
pmid = {38866716},
issn = {1574-6968},
support = {IOS-1444571//NSF/ ; },
mesh = {*Specimen Handling ; *Soil Microbiology ; *Microbiota ; *Preservation, Biological ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Data Curation ; Phylogeny ; Biodiversity ; Principal Component Analysis ; },
abstract = {Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.},
}
@article {pmid39923474,
year = {2025},
author = {Lucca, E and Kofinas, D and Avellán, T and Kleemann, J and Mooren, CE and Blicharska, M and Teutschbein, C and Sperotto, A and Sušnik, J and Milliken, S and Fader, M and Đorđević, D and Dašić, T and Vasilić, V and Taiwo, B and Baubekova, A and Pineda-Martos, R and Spyropoulou, A and Baganz, GFM and El Jeitany, J and Oral, HV and Merheb, M and Castelli, G and Pagano, A and Sambo, B and Suškevičs, M and Arnold, M and Rađenović, T and Psomas, A and Masia, S and La Jeunesse, I and Amorocho-Daza, H and Das, SS and Bresci, E and Munaretto, S and Brouwer, F and Laspidou, C},
title = {Integrating "nature" in the water-energy-food Nexus: Current perspectives and future directions.},
journal = {The Science of the total environment},
volume = {966},
number = {},
pages = {178600},
doi = {10.1016/j.scitotenv.2025.178600},
pmid = {39923474},
issn = {1879-1026},
abstract = {Integrated approaches for managing natural resources are said to meet increasing demand for water, energy, and food, while maintaining the integrity of ecosystems, and ensuring equitable access to resources. The Water-Energy-Food (WEF) Nexus has been proposed as a cross-sectoral approach to manage trade-offs and exploit synergies that arise among these sectors. Although not initially included as a component of the Nexus, the role of nature in sustaining the water, energy, and food sectors and in regulating their interrelationships is increasingly recognised by Nexus researchers and practitioners. To converge existing approaches that integrate nature into the WEF Nexus and suggest a common framework, we - an interdisciplinary group of natural resources management researchers and systems thinkers from the European research network NEXUSNET COST Action - followed a collaborative process of knowledge creation combining literature review, elicitation of expert opinion and collaborative writing. Our results reveal a multiplicity of concepts utilised in the literature to represent, partially or fully, "nature" in the Nexus, such as "environment", "ecosystems", "ecosystem services", "social-ecological systems", and "biodiversity". Disparity was also found in the role attributed to nature, represented by three key paradigms: (1) ecosystems as the fourth component of an expanded Nexus, i.e., the WEF-Ecosystems (WEFE) Nexus; (2) ecosystems as a foundational layer to the Nexus; and (3) the WEF Nexus as a central component of social-ecological systems (SES). By creating a hybrid approach that brings together the benefits of the respective paradigms, we present a forward-looking WEFE Nexus conceptualisation. This paradigm expands the mutual interlinkages among water, energy and food to the entirety of SES, thus acknowledging the social-ecological processes that are affected by and affect the WEF Nexus. The results of this collaborative research effort intend to provide researchers and stakeholders with means to better understand and ultimately manage Nexus issues towards a transformative change.},
}
@article {pmid39923291,
year = {2025},
author = {de Melo, LRS and Dos Santos Pereira, J and Melo, MS and Andrade, LA and Bezerra-Santos, M and Lima, CA and Dos Santos, AD},
title = {Spatial and temporal dynamic of colorectal cancer mortality in Brazil: A nationwide population-based study of four decades (1980-2021).},
journal = {Cancer epidemiology},
volume = {95},
number = {},
pages = {102766},
doi = {10.1016/j.canep.2025.102766},
pmid = {39923291},
issn = {1877-783X},
abstract = {BACKGROUND: Regardless of being preventable through screening strategies and prompt diagnosis, deaths from colorectal cancer (CRC) still represent a serious public health concern in Brazil, with more than 20 thousand deaths annually. Herein, we aimed to assess the temporal trends and spatiotemporal patterns of CRC mortality in all Brazilian states.<br><br>METHODS: An ecological study using temporal and spatial analysis techniques on deaths due to CRC as the underlying cause in Brazil from 1980 to 2021 was conducted. Death certificate and population data were provided by the Department of Informatics of the Unified Health System (DATASUS) and by the Brazilian Institute of Geography and Statistics (IBGE), respectively.<br><br>RESULTS: A total of 395,782 deaths from CRC were recorded in this period and most of them were in female (205,479; 51.92&#x202f;%), &#x2265;&#x202f;65 years old (233,059; 58.89&#x202f;%), diagnosed with malignant neoplasm of the colon (212,277; 53.63&#x202f;%), with 1-7 years of education (157.564; 39.81&#x202f;%), married (192.276; 48.58&#x202f;%), hospital as place of death (331.393; 83.73&#x202f;%) and white (212.666; 65.07&#x202f;%). Moreover, there was an increasing temporal trend in the Northeast region (APC: 2.6; p&#x202f;<&#x202f;0.05), men (APC: 1.5; p&#x202f;<&#x202f;0.05) and 45-64 years old (APC: 1.2; p&#x202f;<&#x202f;0.05). Also, the spatial analysis showed positive spatial autocorrelation in all periods, with the South and Southeast regions presenting the highest concentration of high-risk clusters CRC deaths. Nevertheless, high-risk clusters were also observed in capitals and municipalities in metropolitan regions in the Northeast region.<br><br>CONCLUSIONS: In general, a temporal and spatial expansion of CRC mortality has been observed in Brazil over the last few decades.},
}
@article {pmid39921816,
year = {2025},
author = {Asuako, PAG and Stojan, R and Bock, O and Mack, M and Voelcker-Rehage, C},
title = {Multitasking: does task-switching add to the effect of dual-tasking on everyday-like driving behavior?.},
journal = {Cognitive research: principles and implications},
volume = {10},
number = {1},
pages = {5},
pmid = {39921816},
issn = {2365-7464},
support = {SPP 1772//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; Female ; Young Adult ; Male ; Adult ; *Automobile Driving ; Adolescent ; *Psychomotor Performance/physiology ; *Multitasking Behavior/physiology ; *Executive Function/physiology ; Reaction Time/physiology ; Attention/physiology ; },
abstract = {It is well established that performing multiple tasks simultaneously (dual-tasking) or sequentially (task-switching) degrades performance on one or both tasks. However, it is unknown whether task-switching adds to the effects of dual-tasking in a single setup. We investigated this in a simulated everyday-like car driving scenario. We expected an additive effect of task-switching on dual-tasking, leading to a stronger deterioration of driving performance due to the increased cognitive load required to handle multiple task-sets. Forty-five young adults aged 18 to 30 years (age: 23.62 ± 2.51, 28 females) were instructed to follow a lead car driving at a constant speed of 70 km/h through a rural landscape while concurrently performing additional tasks. The additional tasks were typing and arguing, in response to stimuli presented visually or auditorily. The tasks were presented either in separate blocks or in intermixed order (conditions: repetitive vs. switching). Driving performance was assessed by use of the average velocity and the standard deviation of lateral position, and performance in the additional tasks was assessed by reaction time. Linear-mixed effect models revealed better performance in the repetitive, compared to the switch condition only for the standard deviation of the lateral lane position while performing the additional typing task. This provides limited evidence for the view that task-switching adds to the challenges of dual-tasking. We therefore posit that already dual-tasking alone involves processing demands that are not substantially increased by adding switching demands.},
}
@article {pmid39615103,
year = {2025},
author = {Sha, J and Liu, X and Wang, H and Song, X and Bao, M and Yu, Q and Wen, G and Wei, M},
title = {Status and habitat suitability evaluation: A case study of the typical temperate seagrass beds in the Bohai Sea, China.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106873},
doi = {10.1016/j.marenvres.2024.106873},
pmid = {39615103},
issn = {1879-0291},
mesh = {*Ecosystem ; China ; *Environmental Monitoring/methods ; *Conservation of Natural Resources ; Oceans and Seas ; Geographic Information Systems ; },
abstract = {Seagrass beds serve crucial ecological functions, yet they are facing a severe decline necessitating immediate conservation and restoration efforts. Current assessments of seagrass habitat suitability are insufficient, thus hindering the restoration effects. This study used a combination of field surveys and satellite remote sensing to conduct a three-year monitoring of typical temperate seagrass beds in the Caofeidian and Xingcheng areas of the Bohai Sea. The relationships between seagrass community factors and environmental factors were investigated using Spearman correlation analysis, BIOENV analysis, and redundancy analysis (RDA). Subsequently, the weights of each environmental factor were determined using the Analytic Hierarchy Process (AHP), leading to the development of the Habitat Suitability Index (HSI). Seagrass habitat suitability maps for Caofeidian and Xingcheng areas were then generated using Geographic Information System (GIS). The results indicate that both seagrass ecosystems degraded during the study period, which coincided with a decreasing trend in habitat suitability shown by the suitability maps. This study provides a methodology for seagrass bed habitat suitability assessment, thereby contributing to the conservation and restoration of these vital ecosystems.},
}
@article {pmid39917311,
year = {2025},
author = {Lysholm, S and Chaters, GL and Di Bari, C and Hughes, EC and Huntington, B and Rushton, J and Thomas, L},
title = {A framework for quantifying the multisectoral burden of animal disease to support decision making.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1476505},
pmid = {39917311},
issn = {2297-1769},
abstract = {Animal diseases have wide-ranging impacts in multiple societal arenas, including agriculture, public health and the environment. These diseases cause significant economic losses for farmers, disrupt food security and present zoonotic risks to human populations. Additionally, they contribute to antimicrobial resistance and a range of environmental issues such as greenhouse gas emissions. The societal and ecological costs of livestock diseases are frequently underrepresented or unaddressed in policy decisions and resource allocations. Social cost-benefit analysis (SCBA) offers a comprehensive framework to evaluate the broad impacts of animal diseases across different sectors. This approach aligns with the One Health concept, which seeks to integrate and optimize the health of humans, animals and the environment. Traditional economic evaluations often focus narrowly on profit maximization within the livestock sector, neglecting wider externalities such as public health and environmental impacts. In contrast, SCBA takes a multi-sectoral whole-system view, considering multiple factors to guide public and private sector investments toward maximizing societal benefits. This paper discusses three separate sector specific (Animal health, Human health, Environmental health) methodologies for quantifying the burden of animal diseases. It then discusses how these estimates can be combined to generate multisectoral estimates of the impacts of animal diseases on human societies and the environment using monetary values. Finally this paper explores how this framework can support the evaluation of interventions from a One Health perspective though SCBA. This integrated assessment framework supports informed decision-making and resource allocation, ultimately contributing to improved public health outcomes, enhanced animal welfare, and greater environmental sustainability.},
}
@article {pmid39567690,
year = {2025},
author = {Borton, MA and McGivern, BB and Willi, KR and Woodcroft, BJ and Mosier, AC and Singleton, DM and Bambakidis, T and Pelly, A and Daly, RA and Liu, F and Freiburger, A and Edirisinghe, JN and Faria, JP and Danczak, R and Leleiwi, I and Goldman, AE and Wilkins, MJ and Hall, EK and Pennacchio, C and Roux, S and Eloe-Fadrosh, EA and Good, SP and Sullivan, MB and Wood-Charlson, EM and Miller, CS and Ross, MRV and Henry, CS and Crump, BC and Stegen, JC and Wrighton, KC},
title = {A functional microbiome catalogue crowdsourced from North American rivers.},
journal = {Nature},
volume = {637},
number = {8044},
pages = {103-112},
pmid = {39567690},
issn = {1476-4687},
support = {P30 CA046934/CA/NCI NIH HHS/United States ; },
mesh = {*Crowdsourcing ; *Microbiota/genetics ; *Rivers/microbiology ; United States ; Water Microbiology ; Transcriptome ; Carbon Cycle ; Metagenome ; Databases, Factual ; },
abstract = {Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.},
}
@article {pmid39915771,
year = {2025},
author = {Gould, E and Fraser, HS and Parker, TH and Nakagawa, S and Griffith, SC and Vesk, PA and Fidler, F and Hamilton, DG and Abbey-Lee, RN and Abbott, JK and Aguirre, LA and Alcaraz, C and Aloni, I and Altschul, D and Arekar, K and Atkins, JW and Atkinson, J and Baker, CM and Barrett, M and Bell, K and Bello, SK and Beltrán, I and Berauer, BJ and Bertram, MG and Billman, PD and Blake, CK and Blake, S and Bliard, L and Bonisoli-Alquati, A and Bonnet, T and Bordes, CNM and Bose, APH and Botterill-James, T and Boyd, MA and Boyle, SA and Bradfer-Lawrence, T and Bradham, J and Brand, JA and Brengdahl, MI and Bulla, M and Bussière, L and Camerlenghi, E and Campbell, SE and Campos, LLF and Caravaggi, A and Cardoso, P and Carroll, CJW and Catanach, TA and Chen, X and Chik, HYJ and Choy, ES and Christie, AP and Chuang, A and Chunco, AJ and Clark, BL and Contina, A and Covernton, GA and Cox, MP and Cressman, KA and Crotti, M and Crouch, CD and D'Amelio, PB and de Sousa, AA and Döbert, TF and Dobler, R and Dobson, AJ and Doherty, TS and Drobniak, SM and Duffy, AG and Duncan, AB and Dunn, RP and Dunning, J and Dutta, T and Eberhart-Hertel, L and Elmore, JA and Elsherif, MM and English, HM and Ensminger, DC and Ernst, UR and Ferguson, SM and Fernandez-Juricic, E and Ferreira-Arruda, T and Fieberg, J and Finch, EA and Fiorenza, EA and Fisher, DN and Fontaine, A and Forstmeier, W and Fourcade, Y and Frank, GS and Freund, CA and Fuentes-Lillo, E and Gandy, SL and Gannon, DG and García-Cervigón, AI and Garretson, AC and Ge, X and Geary, WL and Géron, C and Gilles, M and Girndt, A and Gliksman, D and Goldspiel, HB and Gomes, DGE and Good, MK and Goslee, SC and Gosnell, JS and Grames, EM and Gratton, P and Grebe, NM and Greenler, SM and Griffioen, M and Griffith, DM and Griffith, FJ and Grossman, JJ and Güncan, A and Haesen, S and Hagan, JG and Hager, HA and Harris, JP and Harrison, ND and Hasnain, SS and Havird, JC and Heaton, AJ and Herrera-Chaustre, ML and Howard, TJ and Hsu, BY and Iannarilli, F and Iranzo, EC and Iverson, ENK and Jimoh, SO and Johnson, DH and Johnsson, M and Jorna, J and Jucker, T and Jung, M and Kačergytė, I and Kaltz, O and Ke, A and Kelly, CD and Keogan, K and Keppeler, FW and Killion, AK and Kim, D and Kochan, DP and Korsten, P and Kothari, S and Kuppler, J and Kusch, JM and Lagisz, M and Lalla, KM and Larkin, DJ and Larson, CL and Lauck, KS and Lauterbur, ME and Law, A and Léandri-Breton, DJ and Lembrechts, JJ and L'Herpiniere, K and Lievens, EJP and de Lima, DO and Lindsay, S and Luquet, M and MacLeod, R and Macphie, KH and Magellan, K and Mair, MM and Malm, LE and Mammola, S and Mandeville, CP and Manhart, M and Manrique-Garzon, LM and Mäntylä, E and Marchand, P and Marshall, BM and Martin, CA and Martin, DA and Martin, JM and Martinig, AR and McCallum, ES and McCauley, M and McNew, SM and Meiners, SJ and Merkling, T and Michelangeli, M and Moiron, M and Moreira, B and Mortensen, J and Mos, B and Muraina, TO and Murphy, PW and Nelli, L and Niemelä, P and Nightingale, J and Nilsonne, G and Nolazco, S and Nooten, SS and Novotny, JL and Olin, AB and Organ, CL and Ostevik, KL and Palacio, FX and Paquet, M and Parker, DJ and Pascall, DJ and Pasquarella, VJ and Paterson, JH and Payo-Payo, A and Pedersen, KM and Perez, G and Perry, KI and Pottier, P and Proulx, MJ and Proulx, R and Pruett, JL and Ramananjato, V and Randimbiarison, FT and Razafindratsima, OH and Rennison, DJ and Riva, F and Riyahi, S and Roast, MJ and Rocha, FP and Roche, DG and Román-Palacios, C and Rosenberg, MS and Ross, J and Rowland, FE and Rugemalila, D and Russell, AL and Ruuskanen, S and Saccone, P and Sadeh, A and Salazar, SM and Sales, K and Salmón, P and Sánchez-Tójar, A and Santos, LP and Santostefano, F and Schilling, HT and Schmidt, M and Schmoll, T and Schneider, AC and Schrock, AE and Schroeder, J and Schtickzelle, N and Schultz, NL and Scott, DA and Scroggie, MP and Shapiro, JT and Sharma, N and Shearer, CL and Simón, D and Sitvarin, MI and Skupien, FL and Slinn, HL and Smith, GP and Smith, JA and Sollmann, R and Whitney, KS and Still, SM and Stuber, EF and Sutton, GF and Swallow, B and Taff, CC and Takola, E and Tanentzap, AJ and Tarjuelo, R and Telford, RJ and Thawley, CJ and Thierry, H and Thomson, J and Tidau, S and Tompkins, EM and Tortorelli, CM and Trlica, A and Turnell, BR and Urban, L and Van de Vondel, S and van der Wal, JEM and Van Eeckhoven, J and van Oordt, F and Vanderwel, KM and Vanderwel, MC and Vanderwolf, KJ and Vélez, J and Vergara-Florez, DC and Verrelli, BC and Vieira, MV and Villamil, N and Vitali, V and Vollering, J and Walker, J and Walker, XJ and Walter, JA and Waryszak, P and Weaver, RJ and Wedegärtner, REM and Weller, DL and Whelan, S and White, RL and Wolfson, DW and Wood, A and Yanco, SW and Yen, JDL and Youngflesh, C and Zilio, G and Zimmer, C and Zimmerman, GM and Zitomer, RA},
title = {Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {35},
pmid = {39915771},
issn = {1741-7007},
abstract = {Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small "many analyst" study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.},
}
@article {pmid39910401,
year = {2025},
author = {Fatima, M and Butt, I and MohammadEbrahimi, S and Kiani, B and Gruebner, O},
title = {Spatiotemporal clusters of acute respiratory infections associated with socioeconomic, meteorological, and air pollution factors in South Punjab, Pakistan.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {469},
pmid = {39910401},
issn = {1471-2458},
abstract = {BACKGROUND: In Pakistan, acute respiratory infections (ARI) continue to be a major public health problem. However, there is still a lack of scholarly work regarding different environmental and socioeconomic influencing factors and how they interact with respiratory infections. Furthermore, we do not know much about geographic variation in this context. Therefore, our study examines the ecological-level spatial and temporal patterns of acute respiratory infection incidence (ARI) and their geographic relationship with selected socio-economic, meteorological, and air pollution factors in Pakistan.<br><br>METHODS: We applied the spatiotemporal scan statistics to examine the purely temporal, spatial, and spatiotemporal clusters of ARI in South Punjab, Pakistan for five years (2016-2020). Generalized Linear Model (GLM) and geographically weighted regression (GWR) were also applied to model the linear and non-linear spatial relationships between selected variables and ARI.<br><br>RESULTS: Our results indicate that in the central and northern regions of Pakistan, two spatial clusters of ARI were present, accounting for 28.5% of the total cases. A spatiotemporal cluster with a relative risk of 1.57 was discovered in the northeastern area. The results obtained from the season-based GLM highlighted the significance of climatic factors (temperature, fog, dust storms) and air pollutants (NO2) in influencing ARI incidence, while socio-economic variables (rural population, literacy) had limited impact. In addition, GWR revealed that the relationships between predictors and ARI incidence varied across locations, emphasizing the importance of considering local settings. Season-based non-stationary GLM revealed a multifaceted interaction among socio-economic, meteorological, and air pollution factors.<br><br>CONCLUSIONS: Our study provides evidence about environmental and socio-economic factors significantly associated with ARI incidence. In addition, this study provides the first baseline of ARI cases in Pakistan to plan for intervention and adaptation strategies and may be replicated in other regions of comparable settings worldwide.},
}
@article {pmid39907430,
year = {2025},
author = {Hebert, JD and Tang, YJ and Szamecz, M and Andrejka, L and Lopez, SS and Petrov, DA and Boross, G and Winslow, MM},
title = {Combinatorial in vivo genome editing identifies widespread epistasis and an accessible fitness landscape during lung tumorigenesis.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf023},
pmid = {39907430},
issn = {1537-1719},
abstract = {Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the evolutionary interactions that drive tumorigenesis in vivo.},
}
@article {pmid39906497,
year = {2025},
author = {Palande, S and Arsenault, J and Basurto-Lozada, P and Bleich, A and Brown, BNI and Buysse, SF and Connors, NA and Das Adhikari, S and Dobson, KC and Guerra-Castillo, FX and Guerrero-Carrillo, MF and Harlow, S and Herrera-Orozco, H and Hightower, AT and Izquierdo, P and Jacobs, M and Johnson, NA and Leuenberger, W and Lopez-Hernandez, A and Luckie-Duque, A and Martínez-Avila, C and Mendoza-Galindo, EJ and Plancarte, DC and Schuster, JM and Shomer, H and Sitar, SC and Steensma, AK and Thomson, JE and Villaseñor-Amador, D and Waterman, R and Webster, BM and Whyte, M and Zorilla-Azcué, S and Montgomery, BL and Husbands, AY and Krishnan, A and Percival, S and Munch, E and VanBuren, R and Chitwood, DH and Rougon-Cardoso, A},
title = {Expression-based machine learning models for predicting plant tissue identity.},
journal = {Applications in plant sciences},
volume = {13},
number = {1},
pages = {e11621},
pmid = {39906497},
issn = {2168-0450},
abstract = {PREMISE: The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.<br><br>METHODS: Here, we examine the ability of models based on Arabidopsis gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on Arabidopsis data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on Arabidopsis data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.<br><br>RESULTS: The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from Arabidopsis. k-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.<br><br>DISCUSSION: Our data-driven results highlight that the assertion that knowledge from Arabidopsis is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on Arabidopsis and prioritize plant diversity.},
}
@article {pmid39611775,
year = {2025},
author = {Andorf, CM and Ross-Ibarra, J and Seetharam, AS and Hufford, MB and Woodhouse, MR},
title = {A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {2},
pages = {},
doi = {10.1093/g3journal/jkae281},
pmid = {39611775},
issn = {2160-1836},
support = {5030-21000-072-00-D//US. Department of Agriculture, Agricultural Research Service/ ; //Corn Insects and Crop Genetics Research Unit in Ames, Iowa/ ; //Iowa State University/ ; //SCINet/ ; 0201-88888-003-000D//AI Center of Excellence of the USDA Agricultural Research Service/ ; CA-D-PLS-2066-H//USDA/ ; },
mesh = {*Zea mays/genetics ; *Genome, Plant ; *Polymorphism, Single Nucleotide ; *Genomics/methods ; *Databases, Genetic ; Software ; Molecular Sequence Annotation ; Linkage Disequilibrium ; Genotype ; Genetic Variation ; },
abstract = {Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.},
}
@article {pmid39904391,
year = {2025},
author = {Mihaljevic, JR and Páez, DJ},
title = {Systematic shifts in the variation among host individuals must be considered in climate-disease theory.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2040},
pages = {20242515},
doi = {10.1098/rspb.2024.2515},
pmid = {39904391},
issn = {1471-2954},
support = {//Exxon Valdez Oil Spill Trustee Council/ ; //Division of Environmental Biology/ ; },
mesh = {*Climate Change ; Animals ; *Host-Pathogen Interactions ; Temperature ; Population Dynamics ; Models, Biological ; Disease Susceptibility ; },
abstract = {To make more informed predictions of host-pathogen interactions under climate change, studies have incorporated the thermal performance of host, vector and pathogen traits into disease models to quantify effects on average transmission rates. However, this body of work has omitted the fact that variation in susceptibility among individual hosts affects disease spread and long-term patterns of host population dynamics. Furthermore, and especially for ectothermic host species, variation in susceptibility is likely to be plastic, influenced by variables such as environmental temperature. For example, as host individuals respond idiosyncratically to temperature, this could affect the population-level variation in susceptibility, such that there may be predictable functional relationships between variation in susceptibility and temperature. Quantifying the relationship between temperature and among-host trait variation will therefore be critical for predicting how climate change and disease will interact to influence host-pathogen population dynamics. Here, we use a model to demonstrate how short-term effects of temperature on the distribution of host susceptibility can drive epidemic characteristics, fluctuations in host population sizes and probabilities of host extinction. Our results emphasize that more research is needed in disease ecology and climate biology to understand the mechanisms that shape individual trait variation, not just trait averages.},
}
@article {pmid39903560,
year = {2025},
author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Nordgren, CE and Lampson, M and Levine, M and Searle, JB and Good, JM},
title = {The genomic landscape, causes, and consequences of extensive phylogenomic discordance in murine rodents.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf017},
pmid = {39903560},
issn = {1759-6653},
abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents - a large and ecologically diverse group that gave rise to the laboratory mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust time-calibrated species tree. We then used whole genomes to examine finer-scale patterns of discordance across ∼12 million years of divergence. We found that proximate chromosomal regions tended to have more similar phylogenetic histories. There was no clear relationship between local tree similarity and recombination rates in house mice, but we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to appreciably less discordance. Finally, we show that assuming a single species tree can result in substantial deviation from the results with gene trees when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.},
}
@article {pmid39745426,
year = {2025},
author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A},
title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.},
journal = {Microbiology spectrum},
volume = {13},
number = {2},
pages = {e0106624},
doi = {10.1128/spectrum.01066-24},
pmid = {39745426},
issn = {2165-0497},
mesh = {*Prophages/genetics/isolation &amp; purification ; *Retroelements ; Humans ; *Metagenomics ; Genome, Viral/genetics ; Gastrointestinal Microbiome ; Computational Biology/methods ; Host Specificity ; Bacteriophages/genetics/classification/isolation &amp; purification/physiology ; Genome, Bacterial/genetics ; Phylogeny ; Genetic Variation ; },
abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.},
}
@article {pmid39900973,
year = {2025},
author = {Vysakh, VG and Sukumaran, S and Sebastian, W and Gopalakrishnan, A},
title = {The transcriptomic footprint of Mytella strigata: de novo transcriptome assembly of a major invasive species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {201},
pmid = {39900973},
issn = {2052-4463},
mesh = {*Introduced Species ; Animals ; *Transcriptome ; Mytilidae/genetics ; South America ; Gene Ontology ; Molecular Sequence Annotation ; },
abstract = {Mytella strigata, a potentially invasive species native to South America, is rapidly spreading across various aquatic ecosystems around the globe, posing a threat to native mussels. This study presents the first comprehensive de novo transcriptome assembly of M. strigata. We generated 254 million reads, which were processed and assembled using the Trinity assembler, resulting in 60362 transcripts with an N50 of 1,578 bp and over 93-98% completeness, as confirmed by BUSCO analysis with multiple ortho-datasets. A number of databases were used for functional annotation, including UniProt, KEGG, Reactome, InterPro, and eggNOG. Gene Ontology and pathway analyses identified transcripts associated with key biological processes, including those associated with cell signalling, metabolism, stress responses, cancer pathways, and immune regulation. This dataset enriches the bivalve database by advancing the understanding of the adaptive success and evolutionary resilience of this invasive species. The present study provides a fundamental framework for future research on the ecological and evolutionary impacts of this invasive species.},
}
@article {pmid39899630,
year = {2025},
author = {Sheen, JK and Kennedy-Shaffer, L and Levy, MZ and Metcalf, CJE},
title = {Design of field trials for the evaluation of transmissible vaccines in animal populations.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012779},
doi = {10.1371/journal.pcbi.1012779},
pmid = {39899630},
issn = {1553-7358},
mesh = {Animals ; *Vaccines/immunology ; Vaccination/methods ; Computational Biology ; Sample Size ; Research Design ; },
abstract = {Vaccines which can transmit from vaccinated to unvaccinated animals may be especially useful for increasing immunity in hard to reach populations or in populations where achieving high coverage is logistically infeasible. However, gauging the public health utility for future use of such transmissible vaccines and assessing their risk-benefit tradeoff, given their potential for unintended evolution, hinges on accurate estimates of their indirect protective effect. Here, we establish the conditions under which a two-stage randomized field trial can characterize the protective effects of a transmissible vaccine relative to a traditional vaccine. We contrast the sample sizes required to adequately power these trials when the vaccine is weakly and strongly transmissible. We also identify how required sample sizes change based on the characteristics of host ecology such as the overdispersion of the contact structure of the population, as well as the efficacy of the vaccine and timing of vaccination. Our results indicate the range of scenarios where two-stage randomized field trial designs are feasible and appropriate to capture the protective effects of transmissible vaccines. Our estimates identify the protective benefit of using transmissible vaccines compared to traditional vaccines, and thus can be used to weigh against evolutionary risks.},
}
@article {pmid39897903,
year = {2025},
author = {Doshi, P and Klas, M and Kyzek, S and Zahoranová, A and Šerá, B},
title = {Investigating the effect of plasma activated water on entomopathogenic nematodes under laboratory conditions.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e42038},
pmid = {39897903},
issn = {2405-8440},
abstract = {Entomopathogenic nematodes are currently being tested for their efficiency in controlling several insect pests. In recent years, non-thermal plasma has been investigated as a state-of-the-art technology for its disinfection/decontamination properties on the seed surface. In addition, it is also used to induce seed germination. In this investigation, the effect of plasma activated water (PAW) was tested on three EPN species, namely Steinernema feltiae Filipjev (1934), S. carpocapsae Weiser (1955), and Heterorhabditis bacteriophora Poinar (1976). Seven different PAW prepared at different treatment times, that is, (1s, 3s, 5s, 10s, 20s, 60s, 90s) were tested directly on the three selected nematode species. Distilled water was used as a control treatment (0s). In the case of H. bacteriophora, significantly higher mortality was observed in PAW preparation times of 5, 10, 20, 60 and 90s compared to the control. In the case of S. feltiae, significantly high mortality was observed for PAW preparation times of 10, 20, 60 and 90s. However, S. carpocapsae was found to have the least sensitivity against all PAW treatments, with a maximum mortality of 14 % (<20 %), indicating the potential synergy between PAW and EPNs. The possibility of combined treatments in the context of integrated pest management is presented and discussed.},
}
@article {pmid39897842,
year = {2025},
author = {Loukili, I and Laamrani, A and El Ghorfi, M and El Moutak, S and Ghafiri, A},
title = {Monitoring land changes at an open mine site using remote sensing and multi-spectral indices.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41845},
pmid = {39897842},
issn = {2405-8440},
abstract = {This study investigates the growth of mining activities in Benguerir, one of Morocco's largest and fastest-growing phosphate mines and a global leader in phosphate production, using remote sensing and ancillary data. The study examines spatio-temporal changes in land use and land cover (LULC) within this phosphate mining city to analyze the impacts of mining on agricultural areas, built-up lands, and water bodies over time. A series of images from 1984 to 2021 were processed in to assess patterns of change within the city. Five LULC maps were generated using supervised classification with the maximum likelihood method, providing detailed insights into both urban and non-urban transformations during the study period. Classification quality was evaluated using accuracy assessment and the Kappa index. Additionally, multi-spectral indices, including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), and Normalized Difference Built-up Index (NDBI), were simulated and analyzed across four intervals. The results reveal significant variations in LULC and ecological indices over time, which are associated with mining activities, water stress, urban sprawl, and socio-economic changes in the region.These results provide a valuable means for decision-makers and planners to effectively manage the spaces and lands in the future.},
}
@article {pmid39897809,
year = {2025},
author = {Milling, M and Rampp, SDN and Triantafyllopoulos, A and Plaza, MP and Brunner, JO and Traidl-Hoffmann, C and Schuller, BW and Damialis, A},
title = {Automating airborne pollen classification: Identifying and interpreting hard samples for classifiers.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41656},
pmid = {39897809},
issn = {2405-8440},
abstract = {Deep-learning-based classification of pollen grains has been a major driver towards automatic monitoring of airborne pollen. Yet, despite an abundance of available datasets, little effort has been spent to investigate which aspects pose the biggest challenges to the (often black-box- resembling) pollen classification approaches. To shed some light on this issue, we conducted a sample-level difficulty analysis based on the likelihood for one of the largest automatically-generated datasets of pollen grains on microscopy images and investigated the reason for which certain airborne samples and specific pollen taxa pose particular problems to deep learning algorithms. It is here concluded that the main challenges lie in A) the (partly) co-occurring of multiple pollen grains in a single image, B) the occlusion of specific markers through the 2D capturing of microscopy images, and C) for some taxa, a general lack of salient, unique features. Our code is publicly available under https://github.com/millinma/SDPollen.},
}
@article {pmid39897501,
year = {2025},
author = {Fuster-Calvo, A and Valentin, S and Tamayo, WC and Gravel, D},
title = {Evaluating the feasibility of automating dataset retrieval for biodiversity monitoring.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18853},
pmid = {39897501},
issn = {2167-8359},
mesh = {*Biodiversity ; *Databases, Factual ; Feasibility Studies ; Information Storage and Retrieval/methods ; Algorithms ; Quebec ; Conservation of Natural Resources/methods ; },
abstract = {AIM: Effective management strategies for conserving biodiversity and mitigating the impacts of global change rely on access to comprehensive and up-to-date biodiversity data. However, manual search, retrieval, evaluation, and integration of this information into databases present a significant challenge to keeping pace with the rapid influx of large amounts of data, hindering its utility in contemporary decision-making processes. Automating these tasks through advanced algorithms holds immense potential to revolutionize biodiversity monitoring.<br><br>INNOVATION: In this study, we investigate the potential for automating the retrieval and evaluation of biodiversity data from Dryad and Zenodo repositories. We have designed an evaluation system based on various criteria, including the type of data provided and its spatio-temporal range, and applied it to manually assess the relevance for biodiversity monitoring of datasets retrieved through an application programming interface (API). We evaluated a supervised classification to identify potentially relevant datasets and investigate the feasibility of automatically ranking the relevance. Additionally, we applied the same appraoch on a scientific literature source, using data from Semantic Scholar for reference. Our evaluation centers on the database utilized by a national biodiversity monitoring system in Quebec, Canada.<br><br>MAIN CONCLUSIONS: We retrieved 89 (55%) relevant datasets for our database, showing the value of automated dataset search in repositories. Additionally, we find that scientific publication sources offer broader temporal coverage and can serve as conduits guiding researchers toward other valuable data sources. Our automated classification system showed moderate performance in detecting relevant datasets (with an F-score up to 0.68) and signs of overfitting, emphasizing the need for further refinement. A key challenge identified in our manual evaluation is the scarcity and uneven distribution of metadata in the texts, especially pertaining to spatial and temporal extents. Our evaluative framework, based on predefined criteria, can be adopted by automated algorithms for streamlined prioritization, and we make our manually evaluated data publicly available, serving as a benchmark for improving classification techniques.},
}
@article {pmid39808665,
year = {2025},
author = {Fonseca, LL and Böttcher, L and Mehrad, B and Laubenbacher, RC},
title = {Optimal control of agent-based models via surrogate modeling.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012138},
doi = {10.1371/journal.pcbi.1012138},
pmid = {39808665},
issn = {1553-7358},
mesh = {*Algorithms ; *Computational Biology/methods ; Humans ; Computer Simulation ; Systems Analysis ; Models, Biological ; },
abstract = {This paper describes and validates an algorithm to solve optimal control problems for agent-based models (ABMs). For a given ABM and a given optimal control problem, the algorithm derives a surrogate model, typically lower-dimensional, in the form of a system of ordinary differential equations (ODEs), solves the control problem for the surrogate model, and then transfers the solution back to the original ABM. It applies to quite general ABMs and offers several options for the ODE structure, depending on what information about the ABM is to be used. There is a broad range of applications for such an algorithm, since ABMs are used widely in the life sciences, such as ecology, epidemiology, and biomedicine and healthcare, areas where optimal control is an important purpose for modeling, such as for medical digital twin technology.},
}
@article {pmid39889380,
year = {2025},
author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T},
title = {Racial disparities in intrapartum care experiences and birth hospital characteristics.},
journal = {Social science &amp; medicine (1982)},
volume = {367},
number = {},
pages = {117720},
doi = {10.1016/j.socscimed.2025.117720},
pmid = {39889380},
issn = {1873-5347},
abstract = {Policymakers and researchers have posited intrapartum care as a potential mediator of racial inequities in perinatal outcomes. However, few studies have measured patient-centered quality of intrapartum care or explored differences by race. To address this gap, we developed a survey supplement using cognitive interviewing and administered it to a probability-based race-stratified random sample of people who recently gave birth in Wisconsin in 2020, including oversamples of non-Hispanic Black and Indigenous birthing people. We estimate overall and race-specific prevalences of intrapartum care experiences and use survey-weighted mixed effects ordinal and logistic regression to estimate differences in intrapartum care experiences by race/ethnicity and hospital characteristics. We find significant racial differences in the population prevalence of negative experiences of intrapartum care providers, including disrespect, lack of responsiveness, inclusion in decision-making about care, and pressure to use epidural analgesia. In unadjusted models, both non-Hispanic Indigenous (American Indian/Alaska Native) and non-Hispanic Black respondents had higher odds (than non-Hispanic White birthing people) of reporting several negative intrapartum experiences, including feeling disrespected by providers and experiencing a lower level of care team responsiveness. In adjusted models, Indigenous respondents had significantly higher odds of reporting that intrapartum care providers withheld information, showed disrespect, and were less responsive. Giving birth at a low birth-volume hospital was associated with higher odds of reporting greater participation in decision-making. CONCLUSION: While all birthing people are entitled to respectful and person-centered care, in practice, Indigenous and Black birthing persons are more likely than their white counterparts to endure negative intrapartum experiences including disrespect and lack of responsiveness to their needs. Equitable implementation of person-centered care principles will require concerted efforts to institutionalize practices that preserve patient dignity and autonomy.},
}
@article {pmid39888239,
year = {2025},
author = {Giles, EC and González, VL and Carimán, P and Leiva, C and Suescún, AV and Lemer, S and Guillemin, ML and Ortiz-Barrientos, D and Saenz-Agudelo, P},
title = {Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14075},
doi = {10.1111/1755-0998.14075},
pmid = {39888239},
issn = {1755-0998},
support = {2190878//BECA CONICYT-PCHA/Doctorado Nacional Chile/2019/ ; 1190710//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; OIA-1946352//National Science Foundation NSF-EPSCoR/ ; },
abstract = {Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.},
}
@article {pmid39854567,
year = {2025},
author = {Moody, NM and Williams, CM and Ramachandran, S and Fuxjager, MJ},
title = {Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012740},
doi = {10.1371/journal.pcbi.1012740},
pmid = {39854567},
issn = {1553-7358},
mesh = {Animals ; Female ; Male ; *Aggression/physiology ; *Territoriality ; Birds/physiology ; Computational Biology ; Social Behavior ; Behavior, Animal/physiology ; Sexual Behavior, Animal/physiology ; },
abstract = {Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response. Here, we investigate the possibility that resident female and male downy woodpeckers guard their breeding territories from conspecific intruders by deploying defensive behavior in context-specific patterns. To study whether this is the case, we use correlation networks to reveal how suites of agonistic behavior are interrelated. We find that residents do organize their defense into definable patterns, with female and male social mates deploying their behaviors non-randomly in a correlated fashion. We then employ spectral clustering analyses to further distill these responses into distinct behavioral motifs. Our results show that this population of woodpeckers adjusts the defensive motifs deployed according to threat context. When we combine this approach with behavioral transition analyses, our results reveal that pair coordination is a common feature of territory defense in this species. However, if simulated intruders are less threatening, residents are more likely to defend solo, where only one bird deploys defensive behaviors. Overall, our study supports the hypothesis that nonhuman animals can pattern their behavior in a strategic and coordinated manner, while demonstrating the power of systems approaches for analyzing multiagent behavioral dynamics.},
}
@article {pmid38112302,
year = {2025},
author = {Marques, PH and Rodrigues, TCV and Santos, EH and Bleicher, L and Aburjaile, FF and Martins, FS and Oliveira, CJF and Azevedo, V and Tiwari, S and Soares, S},
title = {Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches.},
journal = {Journal of biomolecular structure &amp; dynamics},
volume = {43},
number = {4},
pages = {1788-1803},
doi = {10.1080/07391102.2023.2293256},
pmid = {38112302},
issn = {1538-0254},
mesh = {*Cholera/prevention &amp; control/immunology ; *Computational Biology/methods ; Humans ; *Cholera Vaccines/immunology ; *Vaccinology/methods ; Epitopes, T-Lymphocyte/immunology/chemistry ; Epitopes/immunology/chemistry ; Epitopes, B-Lymphocyte/immunology/chemistry ; Vibrio Infections/prevention &amp; control/immunology ; Molecular Docking Simulation ; Immunoinformatics ; },
abstract = {Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.},
}
@article {pmid39834325,
year = {2025},
author = {Chen, L and Xu, Z and He, Y and Zhang, X and Li, L and Zhu, R and Zhang, Z and Lin, H and Hong, G},
title = {Multiomics Analysis Reveals Key Targeted Metabolic Pathways Underlying the Hormesis and Detrimental Effects of Enrofloxacin on Rice Plants.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {4},
pages = {2678-2695},
doi = {10.1021/acs.jafc.4c09001},
pmid = {39834325},
issn = {1520-5118},
mesh = {*Oryza/metabolism/growth &amp; development/drug effects/genetics/chemistry ; *Enrofloxacin/metabolism ; *Hormesis/drug effects ; *Metabolic Networks and Pathways/drug effects ; Anti-Bacterial Agents/pharmacology ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant/drug effects ; Multiomics ; },
abstract = {Fluoroquinolone antibiotic enrofloxacin (ENR) is frequently detected in agricultural environments. The hormesis and detrimental effects of ENR on crops have been extensively observed. However, the molecular mechanisms underlying these crops' responses to ENR remain limited. Here, integrated physiological, transcriptomic, and metabolomic analysis revealed the key metabolic pathway responses underlying the ENR-induced effects on rice. The results showed that ENR mainly affected three metabolic pathways: 'biosynthesis of amino acids', "tryptophan metabolism", and 'phenylpropanoid/flavonoid biosynthesis'. A low level of ENR treatment promoted root elongation and enhanced the antioxidant capacity by increasing the phytohormone gibberellin A3 and the flavonol quercetin-3-O-neohesperidoside, respectively. However, the high dose of ENR significantly stimulated ROS production, inhibited photosynthesis, and ultimately impaired plant growth. In response to high ENR toxicity, plants accumulated more quercetin derivatives as antioxidants and produced defense-related substances, such as N-hydroxytryptamine, indole-3-acetonitrile, and jasmonic acid, to combat biotic stress. In conclusion, this study provides new insights into the molecular mechanism accounting for the ecological effects of antibiotic pollution in farmland.},
}
@article {pmid39874571,
year = {2025},
author = {Sahandi Far, M and Fischer, JM and Senge, S and Rathmakers, R and Meissner, T and Schneble, D and Narava, M and Eickhoff, SB and Dukart, J},
title = {Cross-Platform Ecological Momentary Assessment App (JTrack-EMA+): Development and Usability Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e51689},
doi = {10.2196/51689},
pmid = {39874571},
issn = {1438-8871},
mesh = {Humans ; *Ecological Momentary Assessment ; *Mobile Applications ; Smartphone ; },
abstract = {BACKGROUND: Traditional in-clinic methods of collecting self-reported information are costly, time-consuming, subjective, and often limited in the quality and quantity of observation. However, smartphone-based ecological momentary assessments (EMAs) provide complementary information to in-clinic visits by collecting real-time, frequent, and longitudinal data that are ecologically valid. While these methods are promising, they are often prone to various technical obstacles. However, despite the potential of smartphone-based EMAs, they face technical obstacles that impact adaptability, availability, and interoperability across devices and operating systems. Deficiencies in these areas can contribute to selection bias by excluding participants with unsupported devices or limited digital literacy, increase development and maintenance costs, and extend deployment timelines. Moreover, these limitations not only impede the configurability of existing solutions but also hinder their adoption for addressing diverse clinical challenges.<br><br>OBJECTIVE: The primary aim of this research was to develop a cross-platform EMA app that ensures a uniform user experience and core features across various operating systems. Emphasis was placed on maximizing the integration and adaptability to various study designs, all while maintaining strict adherence to security and privacy protocols. JTrack-EMA+ was designed and implemented per the FAIR (findable, accessible, interpretable, and reusable) principles in both its architecture and data management layers, thereby reducing the burden of integration for clinicians and researchers.<br><br>METHODS: JTrack-EMA+ was built using the Flutter framework, enabling it to run seamlessly across different platforms. This platform comprises two main components. JDash (Research Centre J&#xfc;lich, Institute of Neuroscience and Medicine, Brain and Behaviour [INM-7]) is an online management tool created using Python (Python Software Foundation) with the Django (Django Software Foundation) framework. This online dashboard offers comprehensive study management tools, including assessment design, user administration, data quality control, and a reminder casting center. The JTrack-EMA+ app supports a wide range of question types, allowing flexibility in assessment design. It also has configurable assessment logic and the ability to include supplementary materials for a richer user experience. It strongly commits to security and privacy and complies with the General Data Protection Regulations to safeguard user data and ensure confidentiality.<br><br>RESULTS: We investigated our platform in a pilot study with 480 days of follow-up to assess participants' compliance. The 6-month average compliance was 49.3%, significantly declining (P=.004) from 66.7% in the first month to 42% in the sixth month.<br><br>CONCLUSIONS: The JTrack-EMA+ platform prioritizes platform-independent architecture, providing an easy entry point for clinical researchers to deploy EMA in their respective clinical studies. Remote and home-based assessments of EMA using this platform can provide valuable insights into patients' daily lives, particularly in a population with limited mobility or inconsistent access to health care services.},
}
@article {pmid39813804,
year = {2025},
author = {Ahmad, S and Peng, X and Ashraf, A and Yin, D and Chen, Z and Ahmed, R and Israr, M and Jia, H},
title = {Building resilient urban drainage systems by integrated flood risk index for evidence-based planning.},
journal = {Journal of environmental management},
volume = {374},
number = {},
pages = {124130},
doi = {10.1016/j.jenvman.2025.124130},
pmid = {39813804},
issn = {1095-8630},
mesh = {*Floods ; *Cities ; Geographic Information Systems ; Climate Change ; Risk Management/methods ; Urbanization ; Risk Assessment ; },
abstract = {Urban flooding poses a significant risk to cities worldwide, exacerbated by increasing urbanization and climate change. Effective flood risk management requires comprehensive assessments considering the complex interaction of social, economic, and environmental factors. This study developed an innovative Urban Flood Risk Index (FRI) to quantify and assess flood risk at the sub-catchment level, providing a tool for evidence-based planning and resilient infrastructure development. This study integrates Geographic Information System (GIS), Storm Water Management Model (SWMM), Analytic Hierarchy Process (AHP), and the Pressure-State-Response (PSR) framework. The FRI incorporates seven pressure and state indicators and three response indicators weighted by expert judgment. The FRI was calculated by combining the weighted sub-indices, classifying flood risk into five levels. Results showed that 51% of the study area experienced high pressure, with 26% facing very-high pressure. The state index indicated that 55% of the area falls under a moderate state, while 21% exhibits a high state. Importantly, the response index highlighted the effectiveness of Low Impact Development (LID) practices, with 20% of the area showing high to very-high response levels. The integrated FRI demonstrated an overall moderate flood risk level for maximum sub-catchments, emphasizing the positive impact of LID practices in mitigating flood risk despite existing pressures and system limitations. This evidence-based assessment provides a valuable tool for sub-catchment level flood risk assessment. It empowers decision-makers to prioritize investments, target interventions, and develop adaptive strategies to enhance urban resilience in a changing climate.},
}
@article {pmid39809974,
year = {2025},
author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB},
title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.},
journal = {Nature metabolism},
volume = {7},
number = {1},
pages = {16-34},
pmid = {39809974},
issn = {2522-5812},
mesh = {Humans ; China/epidemiology ; *Diabetes Mellitus/epidemiology ; Risk Factors ; Prevalence ; Metabolomics ; Multiomics ; },
abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.},
}
@article {pmid39648557,
year = {2025},
author = {Huang, Y and Wang, T and Li, Y and Wang, Z and Cai, X and Chen, J and Li, R and Li, X},
title = {In Vitro-to-In Vivo Extrapolation on Lung Toxicity Induced by Metal Oxide Nanoparticles via Data-Mining.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {3},
pages = {1673-1682},
doi = {10.1021/acs.est.4c06186},
pmid = {39648557},
issn = {1520-5851},
mesh = {*Lung/drug effects/pathology ; Animals ; *Metal Nanoparticles/toxicity ; Mice ; *Oxides/toxicity ; Data Mining ; Humans ; },
abstract = {While in silico analyses are commonly employed for chemical risk assessments, predicting chronic lung toxicity induced by engineered nanoparticles (ENMs) in vivo still faces many challenges due to complex interactions at multiple nanobio interfaces. In this study, we developed a rigorous method to compile published evidence on the in vivo lung toxicity of metal oxide nanoparticles (MeONPs) and revealed previously overlooked in vitro-to-in vivo extrapolation (IVIVE) relationships. A comprehensive multidimensional data set containing 1102 in vivo data points, 75 pulmonary toxicological biomarkers, and 20 features (covering in vitro effects, physicochemical properties, and exposure conditions) was constructed. An IVIVE approach that related effects at the cellular level to in vivo lung toxicity in rodent model was established with prediction accuracy reaching 89 and 80% in training and test sets. Experimental validation was conducted by testing chronic lung fibrosis of 8 new MeONPs in 32 independent mice, with prediction accuracy reaching 88%. The IVIVE model indicated that the proinflammatory cytokine IL-1β in THP-1 cells could serve as an in vitro marker to predict lung toxicity. The IVIVE model showed great promise for minimizing unnecessary animal tests and understanding toxicological mechanisms.},
}
@article {pmid39871100,
year = {2025},
author = {Terauds, A and Lee, JR and Wauchope, HS and Raymond, B and Bergstrom, DM and Convey, P and Mason, C and Patterson, CR and Robinson, SA and Van de Putte, A and Watts, D and Chown, SL},
title = {The biodiversity of ice-free Antarctica database.},
journal = {Ecology},
volume = {106},
number = {1},
pages = {e70000},
doi = {10.1002/ecy.70000},
pmid = {39871100},
issn = {1939-9170},
support = {n&#xb0;FR/36/AN1/AntaBIS(EU-LifeWatch)//Belgian Science Policy Office/ ; n&#xb0;RT/23/ADVANCE//Belgian Science Policy Office/ ; //Royal Commission for the Exhibition of 1851 Research Fellowship/ ; SRIEAS-SR200100005//Australian Research Council/ ; //Securing Antarctica's Environmental Future/ ; AAS 4296//Australian Antarctic Division/ ; AAS 4297//Australian Antarctic Division/ ; },
abstract = {Antarctica is one of Earth's most untouched, inhospitable, and poorly known regions. Although knowledge of its biodiversity has increased over recent decades, a diverse, wide-ranging, and spatially explicit compilation of the biodiversity that inhabits Antarctica's permanently ice-free areas is unavailable. This absence hinders both Antarctic biodiversity research and the integration of Antarctica in global biodiversity-related studies. Fundamental and applied research on biodiversity patterns, ecological structure and function, and options for conservation are reliant on spatially resolved, taxonomically consistent observations. Such information is especially important for modern, data-driven biodiversity science, in both Antarctica and globally, and forms the backbone of biodiversity informatics, reflected, for example, in the Darwin Core Standard used by the Global Biodiversity Information Facility. Biodiversity data are also essential to fulfill the conservation requirements for Antarctica, as set out in the Protocol on Environmental Protection to the Antarctic Treaty and inform the design of systematic surveys to address biodiversity and ecological knowledge gaps, for both specific taxa and ecosystems. Such surveys are key requirements for understanding and mitigating the impacts of environmental change on the region's biodiversity. Here, we address these requirements through the public release of The Biodiversity of Ice-free Antarctica Database. In 2008, we extracted a subset of biodiversity records only from terrestrial ice-free areas from the Scientific Committee on Antarctic Research (SCAR) Antarctic Biodiversity Database. We have subsequently added thousands of records from a range of sources: checking, and where necessary (and possible), correcting the spatial location, clarifying, cross-referencing, and harmonizing taxonomy with globally recognized sources, and documenting the original source of records. The Biodiversity of Ice-free Antarctica Database spans the early 1800s to 2019 (with most records collected after 1950) and represents the most comprehensive consolidation of Antarctic ice-free biodiversity occurrence data yet compiled into a single database. The Biodiversity of Ice-free Antarctica Database contains 35,654 records of 1890 species in over 800 genera across six kingdoms and spans all Antarctic Conservation Biogeographic Regions. These data are released under a CC BY Attribution License (http://creativecommons.org/licenses/by/4.0/).},
}
@article {pmid39870942,
year = {2025},
author = {Lazaro, A and Tiago, I and Mendes, J and Ribeiro, J and Bernardes, A and Oliveira, F and Regateiro, F and Caramelo, F and Silva, H},
title = {Sleeve Gastrectomy and Gastric Bypass Impact in Patient's Metabolic, Gut Microbiome, and Immuno-inflammatory Profiles-A Comparative Study.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {39870942},
issn = {1708-0428},
abstract = {BACKGROUND: Bariatric surgery is the most long-term effective treatment option for severe obesity. The role of gut microbiome (GM) in either the development of obesity or in response to obesity management strategies has been a matter of debate. This study aims to compare the impact of two of the most popular procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (GB), on metabolic syndrome parameters and gut bacterial microbiome and in systemic immuno-inflammatory response.<br><br>METHODS: A prospective observational study enrolled 24 patients with severe obesity, 14 underwent SG and 10&#xa0;GB. Evaluations before (0&#xa0;M) and 6&#xa0;months (6&#xa0;M) after surgical procedures included clinical and biochemical parameters, expression of 17 immuno-inflammatory genes in peripheral blood leukocytes, and assessment of gut microbiome profile using 16&#xa0;s rRNA next-generation sequencing approach. Statistical significance was set to a p value&#x2009;<&#x2009;0.05 with an FDR&#x2009;<&#x2009;0.1.<br><br>RESULTS: A significant and similar decrease in weight-associated parameters and for most metabolic markers was achieved with both surgeries. Considering the gut microbiome in the whole study population, there was an increase in alpha diversity at family-level taxa. Beta diversity between SG and GB at 6&#xa0;M showed near significant differences (p&#x2009;=&#x2009;0.042) at genus levels. Analysis of the relative abundance of individual taxonomic groups highlighted differences between pre- and post-surgical treatment and between both approaches, namely, a higher representation of family Enterobacteriaceae and genera Veillonella and Enterobacteriaceae_unclassified after GB. Increased expression of immune-inflammatory genes was observed mainly for SG patients.<br><br>CONCLUSIONS: We conclude that SG and GB have similar clinical and metabolic outcomes but different impacts in the gut bacterial microbiome. Results also suggest reactivation of immune response after bariatric surgery.},
}
@article {pmid39870652,
year = {2025},
author = {Koizumi, T and Suzuki, K and Mizuki, I and Kumaishi, K and Ichihashi, Y},
title = {A quantitative prediction method utilizing whole omics data for biosensing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1928},
pmid = {39870652},
issn = {2045-2322},
support = {21J00762//Japan Society for the Promotion of Science/ ; Technologies for Smart Bio-industry and Agriculture//the Cabinet Office, Goverment of Japan/ ; },
mesh = {*Biosensing Techniques/methods ; *Biomarkers ; Transcriptome ; Humans ; Metabolomics/methods ; Gene Regulatory Networks ; Genomics/methods ; Computational Biology/methods ; Metabolome ; Microbiota/genetics ; Gene Expression Profiling/methods ; },
abstract = {Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. However, omics data have not been fully utilized because current prediction methods in biomarker construction are susceptible to data multidimensionality and noise. We developed OmicSense, a quantitative prediction method that uses a mixture of Gaussian distributions as the probability distribution, yielding the most likely objective variable predicted for each biomarker. Our benchmark test using a transcriptome dataset revealed that OmicSense achieves accurate and robust prediction against background noise without overfitting. Weighted gene co-expression network analysis revealed that OmicSense preferentially utilized hub nodes of the network, indicating the interpretability of the method. Application of OmicSense to single-cell transcriptome, metabolome, and microbiome datasets confirmed high prediction performance (r > 0.8), suggesting applicability to diverse scientific fields. Given the recent rapidly expanding availability of omics data, the developed prediction tool OmicSense, can accelerate the use of omics data as a "biosensor" based on an assemblage of potential biomarkers.},
}
@article {pmid39870651,
year = {2025},
author = {Ridgway, J and Wesner, J},
title = {A global dataset of freshwater fish trophic interactions.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {160},
pmid = {39870651},
issn = {2052-4463},
mesh = {Animals ; *Fishes ; *Fresh Water ; Food Chain ; Diet/veterinary ; Predatory Behavior ; Databases, Factual ; },
abstract = {Freshwater management and research frequently rely on trophic data to manage freshwater fishes, yet it is difficult to perform a simple search of dietary information for any one species. FishBase represents the largest effort to organize freshwater dietary data into a singular, navigable dataset. Nonetheless, FishBase excludes a large portion of the ecological literature because it was developed before the creation of most modern scientific search engines. Our project, TroPhish, builds upon FishBase by digitizing over 100 years of data from the fish predation literature. Data from 1,106 published papers, theses, dissertations, and government reports were filtered, scanned in through third-party software (Able2Extract), reorganized, and consolidated with FishBase to form a unified dataset. This dataset contains 54,750 observations of data on 4,571 unique dietary samples, representing 9% (982) of all freshwater fish species and 43% (111) of all freshwater fish families. Fish species and family representation varied by continent, ranging from 3-32% and 34-75%, respectively. Users are encouraged to submit errors or additional data through GitHub's fork and pull model.},
}
@article {pmid39869900,
year = {2025},
author = {Yeom, JW and Kim, H and Pack, SP and Lee, HJ and Cheong, T and Cho, CH},
title = {Exploring the Psychological and Physiological Insights Through Digital Phenotyping by Analyzing the Discrepancies Between Subjective Insomnia Severity and Activity-Based Objective Sleep Measures: Observational Cohort Study.},
journal = {JMIR mental health},
volume = {12},
number = {},
pages = {e67478},
doi = {10.2196/67478},
pmid = {39869900},
issn = {2368-7959},
mesh = {Humans ; Middle Aged ; Male ; *Sleep Initiation and Maintenance Disorders/physiopathology/psychology/diagnosis ; Female ; Adult ; *Severity of Illness Index ; Aged ; Cohort Studies ; *Wearable Electronic Devices ; Young Adult ; Ecological Momentary Assessment ; Sleep/physiology ; Exercise/psychology/physiology ; Self Report ; },
abstract = {BACKGROUND: Insomnia is a prevalent sleep disorder affecting millions worldwide, with significant impacts on daily functioning and quality of life. While traditionally assessed through subjective measures such as the Insomnia Severity Index (ISI), the advent of wearable technology has enabled continuous, objective sleep monitoring in natural environments. However, the relationship between subjective insomnia severity and objective sleep parameters remains unclear.<br><br>OBJECTIVE: This study aims to (1) explore the relationship between subjective insomnia severity, as measured by ISI scores, and activity-based objective sleep parameters obtained through wearable devices; (2) determine whether subjective perceptions of insomnia align with objective measures of sleep; and (3) identify key psychological and physiological factors contributing to the severity of subjective insomnia complaints.<br><br>METHODS: A total of 250 participants, including both individuals with and without insomnia aged 19-70 years, were recruited from March 2023 to November 2023. Participants were grouped based on ISI scores: no insomnia, mild, moderate, and severe insomnia. Data collection involved subjective assessments through self-reported questionnaires and objective measurements using wearable devices (Fitbit Inspire 3) that monitored sleep parameters, physical activity, and heart rate. The participants also used a smartphone app for ecological momentary assessment, recording daily alcohol consumption, caffeine intake, exercise, and stress. Statistical analyses were used to compare groups on subjective and objective measures.<br><br>RESULTS: Results indicated no significant differences in general sleep structure (eg, total sleep time, rapid eye movement sleep time, and light sleep time) among the insomnia groups (mild, moderate, and severe) as classified by ISI scores (all P>.05). Interestingly, the no insomnia group had longer total awake times and lower sleep quality compared with the insomnia groups. Among the insomnia groups, no significant differences were observed regarding sleep structure (all P>.05), suggesting similar sleep patterns regardless of subjective insomnia severity. There were significant differences among the insomnia groups in stress levels, dysfunctional beliefs about sleep, and symptoms of restless leg syndrome (all P&#x2264;.001), with higher severity associated with higher scores in these factors. Contrary to expectations, no significant differences were observed in caffeine intake (P=.42) and alcohol consumption (P=.07) between the groups.<br><br>CONCLUSIONS: The findings demonstrate a discrepancy between subjective perceptions of insomnia severity and activity-based objective sleep parameters, suggesting that factors beyond sleep duration and quality may contribute to subjective sleep complaints. Psychological factors, such as stress, dysfunctional sleep beliefs, and symptoms of restless legs syndrome, appear to play significant roles in the perception of insomnia severity. These results highlight the importance of considering both subjective and objective assessments in the evaluation and treatment of insomnia and suggest potential avenues for personalized treatment strategies that address both psychological and physiological aspects of sleep disturbances.<br><br>TRIAL REGISTRATION: Clinical Research Information Service KCT0009175; https://cris.nih.go.kr/cris/search/detailSearch.do?seq=26133.},
}
@article {pmid39868965,
year = {2025},
author = {Grikscheit, K and Berger, A and Rabenau, H and Kohmer, N and Appel, KS and Scherer, M and Bals, R and Blaschke, S and Hamprecht, A and Hopff, SM and Krefting, D and Meybohm, P and Nürnberger, C and Heuschmann, P and Pley, C and Nunes de Miranda, SM and Dahl, E and Jensen, B and Illig, T and Anton, G and Vehreschild, JJ and Ciesek, S},
title = {Occurrence and clinical correlates of SARS-CoV-2 viremia in two German patient cohorts.},
journal = {Emerging microbes &amp; infections},
volume = {},
number = {},
pages = {2459137},
doi = {10.1080/22221751.2025.2459137},
pmid = {39868965},
issn = {2222-1751},
abstract = {Viremia defined as detectable SARS-CoV-2 RNA in the blood is a potential marker of disease severity and prognosis in COVID-19 patients. Here, we determined the frequency of viremia in serum of two independent COVID-19 patient cohorts within the German National Pandemic Cohort Network (German: Nationales Pandemie Kohorten Netzwerk, NAPKON) with diagnostic RT-PCR against SARS-CoV-2. A cross-sectional cohort with 1,122 COVID-19 patients (German: Sektorenuebergreifende Platform, SUEP) and 299 patients recruited in a high-resolution platform with patients at high risk to develop severe courses (German: Hochaufloesende Plattform, HAP) were tested for viremia. Our study also involved a comprehensive analysis and association of serological, diagnostic and clinical parameters of the NAPKON medical dataset. Prevalence of viremia at the recruitment visit was 12,8% (SUEP) and 13% (HAP) respectively. Serological analysis revealed that viremic patients had lower levels of SARS-CoV-2 specific antibodies as well as lower neutralizing antibodies compared to aviremic patients. Viremia was associated with severity (<0.0001 SUEP; 0.002 HAP) and mortality of COVID-19 (both cohorts <0.0001) compared to aviremic patients. While rare, viremia was also detected in patients with mild disease (0.7%). In patients of the SUEP cohort with acute kidney disease (p = 0.0099) and hematooncological conditions (p = 0.0091), viremia was detected more frequently. Compared to the aviremic group, treatment with immunomodulating drugs as well as elevated levels of inflammatory markers in the blood was more frequent in the viremic group. In conclusion, our analysis revealed that detectable viremia correlates with hyperinflammatory conditions and higher risk for severe COVID-19 disease.},
}
@article {pmid39830079,
year = {2024},
author = {Couch, J and Arnaout, R and Arnaout, R},
title = {Beyond Size and Class Balance: Alpha as a New Dataset Quality Metric for Deep Learning.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {39830079},
issn = {2331-8422},
support = {R01 AI148747/AI/NIAID NIH HHS/United States ; R01 HL150394/HL/NHLBI NIH HHS/United States ; },
abstract = {In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, the current best practice-maximizing dataset size and class balance-does not guarantee dataset diversity. We hypothesized that, for a given model architecture, model performance can be improved by maximizing diversity more directly. To test this hypothesis, we introduce a comprehensive framework of diversity measures from ecology that generalizes familiar quantities like Shannon entropy by accounting for similarities among images. (Size and class balance emerge as special cases.) Analyzing thousands of subsets from seven medical datasets showed that the best correlates of performance were not size or class balance but A -"big alpha"-a set of generalized entropy measures interpreted as the effective number of image-class pairs in the dataset, after accounting for image similarities. One of these, A 0 , explained 67% of the variance in balanced accuracy, vs. 54% for class balance and just 39% for size. The best pair of measures was size-plus- A 1 (79%), which outperformed size-plus-class-balance (74%). Subsets with the largest A 0 performed up to 16% better than those with the largest size (median improvement, 8%). We propose maximizing A as a way to improve deep learning performance in medical imaging.},
}
@article {pmid39866757,
year = {2023},
author = {Gudelj Rakić, J and Maksimović, M and Vlajinac, H and Janković, J and Vukašinović, D and Marinković, J},
title = {TRENDS IN OVERWEIGHT AND OBESITY AMONG SERBIAN ADULT POPULATION 2000-2013.},
journal = {Acta clinica Croatica},
volume = {62},
number = {4},
pages = {605-614},
pmid = {39866757},
issn = {1333-9451},
mesh = {Humans ; Male ; Serbia/epidemiology ; Female ; Adult ; *Obesity/epidemiology ; *Overweight/epidemiology ; Prevalence ; Middle Aged ; *Body Mass Index ; Cross-Sectional Studies ; Health Surveys ; Young Adult ; Aged ; },
abstract = {The aim of the study was to determine changes in body mass index (BMI) and in the prevalence of overweight and obesity in Serbian adult population. Data for this study were obtained from three National Health Interview Surveys, carried out as cross-sectional, nationally representative surveys in 2000, 2006 and 2013. The values of p for trends of sociodemographic and health related behavioral characteristics, of BMI distribution, and of overweight and obesity prevalence were determined by univariate and multivariate linear and logistic regression analyses, with year of survey as a continuous variable. The mean values of BMI and standard deviations in surveys were 26.09±3.92, 26.28±4.02 and 26.87±4.33 in men, and 25.91±5.25, 25.77±5.22 and 26.35±5.58 in women, respectively (trend p<0.001 both). The prevalence of obesity was 14.3%, 16.5% and 21.4% in men, and 20.0%, 19.7% and 23.3% in women, respectively (trend p<0.001 both). The prevalence of overweight did not change significantly during the observed period. In conclusion, the prevalence of obesity showed an increasing trend in both men and women, demanding targeted public health interventions.},
}
@article {pmid39865039,
year = {2024},
author = {Alekseeva, AO and Zolotovskaia, MA and Sorokin, MI and Suntsova, MV and Zakharova, GS and Pugacheva, PA and Tinkov, AA and Korobeinikova, TV and Sekacheva, MI and Poddubskaya, EV and Skalny, AV and Kushlinskii, NE and Buzdin, AA},
title = {The First Multiomics Association Study of Trace Element and Mineral Concentration and RNA Sequencing Profiles in Human Cancers.},
journal = {Biochemistry. Biokhimiia},
volume = {89},
number = {12},
pages = {2274-2286},
doi = {10.1134/S0006297924120150},
pmid = {39865039},
issn = {1608-3040},
mesh = {Humans ; *Trace Elements/metabolism/analysis ; Minerals/metabolism ; Sequence Analysis, RNA ; Neoplasms/genetics/metabolism ; Male ; Colorectal Neoplasms/genetics/metabolism ; Female ; Gene Expression Profiling ; Multiomics ; },
abstract = {Integration of various types of omics data is an important trend in contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained gene expression profiles (RNA sequencing) and essential and trace element profiles (inductively coupled plasma mass spectrometry) for a set of human cancer samples. The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 18 for other solid cancer types (16 types). Mass spectrometry profiles were obtained for 45 chemical elements: Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, and Zr. The expression levels were profiled for 36,596 known human genes, and the activation levels were assessed for 10,520 human intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels for both colorectal cancer samples and at the pan-cancer level. In total, 222/137, 122/220, 1/0, 239/186, 71/44, 1/0, 354/294, 69/82 gene/pathway biomarkers were detected for Ca, Cu, Fe, K, Mg, Na, P, and Zn, respectively. We believe that this first-in-class database provided here will be valuable for multiomics cancer research.},
}
@article {pmid39860723,
year = {2025},
author = {Dewmini, H and Meedeniya, D and Perera, C},
title = {Elephant Sound Classification Using Deep Learning Optimization.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {2},
pages = {},
doi = {10.3390/s25020352},
pmid = {39860723},
issn = {1424-8220},
mesh = {*Elephants/physiology ; *Deep Learning ; Animals ; *Vocalization, Animal/physiology ; *Bayes Theorem ; Sound Spectrography/methods ; Sound ; Algorithms ; },
abstract = {Elephant sound identification is crucial in wildlife conservation and ecological research. The identification of elephant vocalizations provides insights into the behavior, social dynamics, and emotional expressions, leading to elephant conservation. This study addresses elephant sound classification utilizing raw audio processing. Our focus lies on exploring lightweight models suitable for deployment on resource-costrained edge devices, including MobileNet, YAMNET, and RawNet, alongside introducing a novel model termed ElephantCallerNet. Notably, our investigation reveals that the proposed ElephantCallerNet achieves an impressive accuracy of 89% in classifying raw audio directly without converting it to spectrograms. Leveraging Bayesian optimization techniques, we fine-tuned crucial parameters such as learning rate, dropout, and kernel size, thereby enhancing the model's performance. Moreover, we scrutinized the efficacy of spectrogram-based training, a prevalent approach in animal sound classification. Through comparative analysis, the raw audio processing outperforms spectrogram-based methods. In contrast to other models in the literature that primarily focus on a single caller type or binary classification that identifies whether a sound is an elephant voice or not, our solution is designed to classify three distinct caller-types namely roar, rumble, and trumpet.},
}
@article {pmid39856257,
year = {2025},
author = {Gulakhmadov, A and Chen, X and Gulahmadov, N and Rizwan, M and Gulakhmadov, M and Nadeem, MU and Rakhimova, M and Liu, T},
title = {Modeling of historical and future changes in temperature and precipitation in the Panj River Basin in Central Asia under the CMIP5 RCP and CMIP6 SSP scenarios.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3037},
pmid = {39856257},
issn = {2045-2322},
support = {42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; },
abstract = {This study examines the complexities of climate modeling, specifically in the Panj River Basin (PRB) in Central Asia, to evaluate the transition from CMIP5 to CMIP6 models. The research aimed to identify differences in historical simulations and future predictions of rainfall and temperature, examining the accuracy of eight General Circulation Models (GCMs) used in both CMIP5 (RCP4.5 and 8.5) and CMIP6 (SSP2-4.5 and 5-8.5). The evaluation metrics demonstrated that the GCMs have a high level of accuracy in reproducing maximum temperature (Tmax) with a correlation coefficient of 0.96. The models also performed well in replicating minimum temperature (Tmin) with a correlation coefficient of 0.94. This suggests that the models have improved modeling capabilities in both CMIPs. The performance of Max Plank Institute (MPI) across all variables in CMIP6 models was exceptional. Within the CMIP5 domain, Geophysical Fluid Dynamics (GFDL) demonstrated outstanding skill in reproducing maximum temperature (Tmax) and precipitation (KGE 0.58 and 0.34, respectively), while (Institute for Numerical Mathematics) INMCM excelled in replicating minimum temperature (Tmin) (KGE 0.28). The uncertainty analysis revealed a significant improvement in the CMIP6 precipitation bias bands, resulting in a more precise depiction of diverse climate zones compared to CMIP5. Both CMIPs consistently tended to underestimate Tmax in the Csa zone and overestimate it in the Bwk zone throughout all months. Nevertheless, the CMIP6 models demonstrated a significant decrease in uncertainty, especially in ensemble simulations, suggesting improvements in forecasting PRB climate dynamics. The projections revealed a complex story, as the CMIP6 models predict a relatively small increase in temperature and a simultaneous drop in precipitation. This indicates a trend towards more uniform temperature patterns across different areas. Nevertheless, the precipitation forecasts exhibited increased variability, highlighting the intricate interaction of climate dynamics in the PRB area under the impact of global warming scenarios. Hydrological components in global climate models can be further improved and developed with the theoretical reference provided by this study.},
}
@article {pmid39854555,
year = {2025},
author = {Zhou, J and Johnson, VC and Shi, J and Tan, ML and Zhang, F},
title = {Multi-scenario land use change simulation and spatial-temporal evolution of carbon storage in the Yangtze River Delta region based on the PLUS-InVEST model.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0316255},
doi = {10.1371/journal.pone.0316255},
pmid = {39854555},
issn = {1932-6203},
mesh = {China ; *Rivers ; *Conservation of Natural Resources/methods ; *Carbon/metabolism/analysis ; Models, Theoretical ; Carbon Sequestration ; Ecosystem ; Spatio-Temporal Analysis ; Computer Simulation ; Humans ; Agriculture/methods ; },
abstract = {Influenced by urban expansion, population growth, and various socio-economic activities, land use in the Yangtze River Delta (YRD) area has undergone prominent changes. Modifications in land use have resulted in adjustments to ecological structures, leading to subsequent fluctuations in carbon storage. This study focuses on YRD region and analyzes the characteristics of land use changes in the area using land use data from 2000 to 2020, with a 10-year interval. Utilizing InVEST Model's Carbon Storage module in combination with PLUS model (patch-generating land use simulation), we simulated and projected future land use patterns and carbon storage across YRD region under five scenarios including natural development (ND), urban development (UD), ecological protection (EP), cropland protection (CP), and balanced development (BD). Upon comparing carbon storage levels predicted for 2030 under the five scenarios with those in 2020, carbon stocks decrease in the initial four scenarios and then increase in the fifth scenario. In the initial four declining scenarios, CP scenario had the least reduction in carbon storage, followed by EP scenario. The implementation of policies aimed at safeguarding cropland and preserving ecological integrity can efficaciously curtail the expansion of developed land into woodland and cropland, enhance the structure of land use, and mitigate the loss of carbon storage.},
}
@article {pmid39854538,
year = {2025},
author = {Katchali, M and Richard, E and Tonnang, HEZ and Tanga, CM and Beesigamukama, D and Senagi, K},
title = {Mathematical and computational modeling for organic and insect frass fertilizer production: A systematic review.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0292418},
doi = {10.1371/journal.pone.0292418},
pmid = {39854538},
issn = {1932-6203},
mesh = {*Fertilizers/analysis ; Animals ; *Insecta ; Models, Theoretical ; Agriculture/methods ; Computer Simulation ; },
abstract = {Organic fertilizers have been identified as a sustainable agricultural practice that can enhance productivity and reduce environmental impact. Recently, the European Union defined and accepted insect frass as an innovative and emerging organic fertilizer. In the wider domain of organic fertilizers, mathematical and computational models have been developed to optimize their production and application conditions. However, with the advancement in policies and regulations, modelling has shifted towards efficiencies in the deployment of these technologies. Therefore, this paper reviews and critically analyzes the recent developments in the mathematical and computation modeling that have promoted various organic fertilizer products including insect frass. We reviewed a total of 35 studies and discussed the methodologies, benefits, and challenges associated with the use of these models. The results show that mathematical and computational modeling can improve the efficiency and effectiveness of organic fertilizer production, leading to improved agricultural productivity and reduced environmental impact. Mathematical models such as simulation, regression, dynamics, and kinetics have been applied while computational data driven machine learning models such as random forest, support vector machines, gradient boosting, and artificial neural networks have also been applied as well. These models have been used in quantifying nutrients concentration/release, effects of nutrients in agro-production, and fertilizer treatment. This paper also discusses prospects for the use of these models, including the development of more comprehensive and accurate models and integration with emerging technologies such as Internet of Things.},
}
@article {pmid39853577,
year = {2025},
author = {Pierrat, ZA and Magney, TS and Richardson, WP and Runkle, BRK and Diehl, JL and Yang, X and Woodgate, W and Smith, WK and Johnston, MR and Ginting, YRS and Koren, G and Albert, LP and Kibler, CL and Morgan, BE and Barnes, M and Uscanga, A and Devine, C and Javadian, M and Meza, K and Julitta, T and Tagliabue, G and Dannenberg, MP and Antala, M and Wong, CYS and Santos, ALD and Hufkens, K and Marrs, JK and Stovall, AEL and Liu, Y and Fisher, JB and Gamon, JA and Cawse-Nicholson, K},
title = {Proximal remote sensing: an essential tool for bridging the gap between high-resolution ecosystem monitoring and global ecology.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20405},
pmid = {39853577},
issn = {1469-8137},
support = {//National Research Council Postdoctoral Research Associateship Program/ ; 2020/37/B/ST10/01213//National Science Centre of Poland/ ; //TVL E-13 work contract at the Climate Monitoring Group of the University of Bonn/ ; //The LEMONTREE project by E. Schmidt and W. Schmidt/ ; 1926090//National Science Foundation/ ; 2044818//National Science Foundation/ ; 2131853//National Science Foundation/ ; IOS-2005574 OPP-2023205//National Science Foundation/ ; 80NSSC20K1805/NASA/NASA/United States ; 80NSSC21K1002/NASA/NASA/United States ; 80NSSC21K1639/NASA/NASA/United States ; 80NSSC21K1707/NASA/NASA/United States ; 80NSSC23K0109/NASA/NASA/United States ; 80NSSC23K0309/NASA/NASA/United States ; 80NSSC24K0135/NASA/NASA/United States ; NNH20ZDA001N-BIODIV/NASA/NASA/United States ; DE190101182//Australian Research Council/ ; },
abstract = {A new proliferation of optical instruments that can be attached to towers over or within ecosystems, or 'proximal' remote sensing, enables a comprehensive characterization of terrestrial ecosystem structure, function, and fluxes of energy, water, and carbon. Proximal remote sensing can bridge the gap between individual plants, site-level eddy-covariance fluxes, and airborne and spaceborne remote sensing by providing continuous data at a high-spatiotemporal resolution. Here, we review recent advances in proximal remote sensing for improving our mechanistic understanding of plant and ecosystem processes, model development, and validation of current and upcoming satellite missions. We provide current best practices for data availability and metadata for proximal remote sensing: spectral reflectance, solar-induced fluorescence, thermal infrared radiation, microwave backscatter, and LiDAR. Our paper outlines the steps necessary for making these data streams more widespread, accessible, interoperable, and information-rich, enabling us to address key ecological questions unanswerable from space-based observations alone and, ultimately, to demonstrate the feasibility of these technologies to address critical questions in local and global ecology.},
}
@article {pmid39843543,
year = {2025},
author = {Gioiosa, S and Gasparini, S and Presutti, C and Rinaldi, A and Castrignanò, T and Mannironi, C},
title = {Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2778},
pmid = {39843543},
issn = {2045-2322},
support = {GJC22071//Cariplo Telethon Alliance/ ; },
mesh = {*Rett Syndrome/genetics ; Humans ; Animals ; *Alternative Splicing ; Mice ; *Disease Models, Animal ; *Methyl-CpG-Binding Protein 2/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Computational Biology/methods ; Mutation ; },
abstract = {Mutations of the MECP2 gene lead to Rett syndrome (RTT), a rare developmental disease causing severe intellectual and physical disability. How the loss or defective function of MeCP2 mediates RTT is still poorly understood. MeCP2 is a global gene expression regulator, acting at transcriptional and post-transcriptional levels. Little attention has been given so far to the contribution of alternative splicing (AS) dysregulation to RTT pathophysiology. To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. Our comparative analysis across studies indicates common species-specific differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes. Human and mouse dysregulated genes are involved in two main functional categories: cell-extracellular matrix adhesion regulation and synaptic functions, the first category more significantly enriched in human datasets. Our extensive bioinformatics study indicates, for the first time, a significant dysregulation of AS in human RTT datasets, suggesting the crucial contribution of altered RNA processing to the pathophysiology of RTT.},
}
@article {pmid39841777,
year = {2025},
author = {Cardoso, ADRO and Ferreira, ACG and Rabahi, MF},
title = {Asthma-related deaths in Brazil: data from an ecological study.},
journal = {Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia},
volume = {50},
number = {6},
pages = {e20240296},
doi = {10.36416/1806-3756/e20240296},
pmid = {39841777},
issn = {1806-3756},
mesh = {Humans ; Brazil/epidemiology ; *Asthma/mortality/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Hospitalization/statistics &amp; numerical data ; Young Adult ; Adolescent ; Child ; Sex Distribution ; Age Distribution ; Child, Preschool ; Aged ; Infant ; Sex Factors ; Age Factors ; Cause of Death ; Time Factors ; },
abstract = {OBJECTIVE: The aim of this study was to present epidemiological data on hospitalizations and deaths related to asthma in Brazil over the past 11 years.<br><br>METHODS: An ecological study was conducted on asthma-related hospitalizations and mortality in Brazil from 2013 to 2023, using data extracted from the Department of Informatics of the Brazilian Unified Health System and the Mortality Information System.<br><br>RESULTS: Asthma-related deaths showed an increasing trend during the analyzed period. A surge in deaths was observed in 2022 compared to 2014 (difference between means = 56.08 &#xb1; 19.7; 95% CI = 15.2-96.9). The mean number of deaths was higher among females, with their rate remaining stable, while the rate for males increased. Individuals aged >60 years accounted for approximately 65% of all asthma-related deaths from 2013 to 2023, with a strong direct correlation observed between age and the number of deaths, regardless of sex. During the same period, the total number of asthma-related hospitalizations in Brazil showed a declining trend, decreasing from 134,322 in 2013 to 87,707 in 2023.<br><br>CONCLUSION: Over the past 11 years, asthma-related deaths have increased in Brazil, with the majority occurring among females. Older individuals accounted for most asthma-related deaths, and a positive correlation was observed between age and the number of deaths.},
}
@article {pmid39840283,
year = {2024},
author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S},
title = {Recent advances in deep learning and language models for studying the microbiome.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1494474},
pmid = {39840283},
issn = {1664-8021},
abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.},
}
@article {pmid39838963,
year = {2024},
author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y},
title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf014},
pmid = {39838963},
issn = {1477-4054},
support = {11209823//City University of Hong Kong/ ; },
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; },
abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.},
}
@article {pmid39558756,
year = {2025},
author = {Paris, JR and King, RA and Ferrer Obiol, J and Shaw, S and Lange, A and Bourret, V and Hamilton, PB and Rowe, D and Laing, LV and Farbos, A and Moore, K and Urbina, MA and van Aerle, R and Catchen, JM and Wilson, RW and Bury, NR and Santos, EM and Stevens, JR},
title = {The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers.},
journal = {Molecular ecology},
volume = {34},
number = {1},
pages = {e17591},
pmid = {39558756},
issn = {1365-294X},
support = {BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //University of Exeter/ ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; Charityno.1135007,Companyno.06545646//Westcountry Rivers Trust, UK/ ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //Environment Agency, UK/ ; },
mesh = {*Genome ; *Transcription, Genetic/drug effects ; *Adaptation, Physiological/drug effects/genetics ; *Rivers ; *Water Pollutants, Chemical/toxicity ; *Salmon/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; *Metals/toxicity ; United Kingdom ; Genetic Loci ; Gene Library ; Metagenomics ; Organ Specificity/drug effects ; Gene Ontology ; Animals ; },
abstract = {Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.},
}
@article {pmid39833495,
year = {2025},
author = {Akar, SE and Nwachukwu, W and Adewuyi, OS and Ahumibe, AA and Akanimo, I and Okunromade, O and Babatunde, O and Ihekweazu, C and Hitachi, M and Kato, K and Takamatsu, Y and Hirayama, K and Kaneko, S},
title = {Epidemiology of Yellow Fever in Nigeria: Analysis of Climatic, Ecological, Socio-Demographic, and Clinical Factors Associated with Viral Positivity Among Suspected Cases Using National Surveillance Data, 2017-2023.},
journal = {Journal of epidemiology and global health},
volume = {15},
number = {1},
pages = {2},
pmid = {39833495},
issn = {2210-6014},
mesh = {Humans ; Nigeria/epidemiology ; *Yellow Fever/epidemiology ; Male ; Female ; Adolescent ; Retrospective Studies ; Adult ; Middle Aged ; Young Adult ; Child ; Child, Preschool ; Infant ; Climate ; Disease Outbreaks/statistics &amp; numerical data ; Yellow fever virus ; Risk Factors ; Socioeconomic Factors ; Sociodemographic Factors ; Population Surveillance/methods ; },
abstract = {BACKGROUND: Since its resurgence in 2017, Yellow fever (YF) outbreaks have continued to occur in Nigeria despite routine immunization and the implementation of several reactive mass vaccinations. Nigeria, Africa's most populous endemic country, is considered a high-priority country for implementing the End Yellow fever Epidemics strategy.<br><br>METHODS: This retrospective analysis described the epidemiological profile, trends, and factors associated with Yellow fever viral positivity in Nigeria. We conducted a multivariable binary logistic regression analysis to identify factors associated with YF viral positivity.<br><br>RESULTS: Of 16,777 suspected cases, 8532(50.9%) had laboratory confirmation with an overall positivity rate of 6.9%(585). Predictors of YFV positivity were the Jos Plateau, Derived/Guinea Savanah, and the Freshwater/Lowland rainforest compared to the Sahel/Sudan Savannah; dry season compared to rainy season; the hot dry or humid compared to the temperate, dry cool/humid climatic zone; 2019, 2020, 2021, 2022, and 2023 epidemic years compared to compared to 2017; first, third, and fourth quarters compared to the second; male sex compared to female; age group&#x2009;>&#x2009;=&#x2009;15 years compared to <&#x2009;15 years; working in outdoor compared to indoor settings; having traveled within the last two weeks; being of unknown vaccination status compared to being vaccinated; and vomiting.<br><br>CONCLUSION: Ecological, climatic, and socio-demographic characteristics are drivers of YF outbreaks in Nigeria, and public health interventions need to target these factors to halt local epidemics and reduce the risk of international spread. Inadequate vaccination coverage alone may not account for the recurrent outbreaks of YF in Nigeria.},
}
@article {pmid39833104,
year = {2024},
author = {Liu, F and Zhao, Z and Liu, Y},
title = {PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf017},
pmid = {39833104},
issn = {1477-4054},
support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Natural Science Foundation of Jilin Province, China/ ; },
mesh = {*Bacteriophages/genetics ; Algorithms ; Software ; Computational Biology/methods ; Host-Pathogen Interactions/genetics ; Bacteria/virology/genetics ; Phage Therapy ; },
abstract = {Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity. Accurate prediction of phage hosts is essential for successfully applying phage therapy. However, existing prediction models may not fully encapsulate the complex dynamics of phage-host interactions in diverse microbial environments, indicating a need for improved accuracy through more sophisticated modeling techniques. In response to this challenge, this study introduces a novel phage-host prediction model, PHPGAT, which leverages a multimodal heterogeneous knowledge graph with the advanced GATv2 (Graph Attention Network v2) framework. The model first constructs a multimodal heterogeneous knowledge graph by integrating phage-phage, host-host, and phage-host interactions to capture the intricate connections between biological entities. GATv2 is then employed to extract deep node features and learn dynamic interdependencies, generating context-aware embeddings. Finally, an inner product decoder is designed to compute the likelihood of interaction between a phage and host pair based on the embedding vectors produced by GATv2. Evaluation results using two datasets demonstrate that PHPGAT achieves precise phage host predictions and outperforms other models. PHPGAT is available at https://github.com/ZhaoZMer/PHPGAT.},
}
@article {pmid39832988,
year = {2025},
author = {Shimels, T and Kantelhardt, EJ and Assefa, M and Fenta, TG},
title = {Spatiotemporal dynamics and prevention strategies of cervical cancer incidence in Addis Ababa, Ethiopia: an ecological study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e089521},
doi = {10.1136/bmjopen-2024-089521},
pmid = {39832988},
issn = {2044-6055},
mesh = {Humans ; Ethiopia/epidemiology ; *Uterine Cervical Neoplasms/epidemiology/prevention &amp; control ; Female ; Incidence ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Young Adult ; Bayes Theorem ; Aged ; Geographic Information Systems ; Adolescent ; Papillomavirus Vaccines ; },
abstract = {OBJECTIVE: This study analysed the spatial and temporal patterns of cervical cancer incidence in Addis Ababa from 2012 to 2021.<br><br>DESIGN: An ecological study was conducted from 1 September to 30 November 2023 to examine the spatiotemporal trends of cervical cancer incidence.<br><br>SETTING: The research was conducted in Addis Ababa, the capital city of Ethiopia.<br><br>PARTICIPANTS: Included were all patients with clinically and/or histopathologically confirmed diagnoses of cervical cancer.<br><br>DATA ANALYSIS: The study employed advanced analytical tools including R programming, Quantum Geographic Information System V.3.36.0, GeoDa V.1.2.2 and System for Automated Geoscientific Analyses GIS V.9.3.2. Techniques such as Bayesian empirical testing with a block weighting matrix for hotspot identification, Global Moran's I for spatial autocorrelation, nearest neighbour imputation and universal Kriging interpolation were used to manage data gaps. Joinpoint trend analysis and direct age-standardised incidence rate (ASIR) using the Segi's World standard population was applied to compare trends across subcities. A statistical significance threshold was set at p<0.05.<br><br>RESULTS: Between 2012 and 2021, a total of 2435 new cervical cancer cases were recorded in the Addis Ababa City Population-based Cancer Registry, with significant spatial clustering observed in Nifas Silk Lafto, Bole, Kirkos as well as parts of Gulele and Yeka sub cities (z score>1.96) in 2018. The citywide age-standardised incidence rate varied from 19 to 26 cases per 100&#x2009;000&#x2009;women-years during 2013 and 2016, respectively. Subcity trends varied significantly, with increases and decreases noted in Akaki Kality and Kolfe Keraniyo over different periods while Bole subcity showed modest increase at 4.2% APC (95% CI: 0.6% to 7.9%; p=0.026).<br><br>CONCLUSION: The study highlights substantial fluctuations in ASIR and significant geographic disparities in cervical cancer throughout Addis Ababa. To address these challenges, the implementation of school-based human papillomavirus vaccination programmes, alongside targeted interventions, active campaigns and sustained surveillance, is critical. These strategies are essential to effectively reduce the cervical cancer burden and improve health outcomes in the community.},
}
@article {pmid39832144,
year = {2024},
author = {Ištoňová, M and Dorko, E and Knap, V and Stehlíková, B and Murgová, A and Ondová, P and Rimárová, K},
title = {Assessment of depressive disorders and states of anxiety in patients following cerebrovascular accidents in connection with health care provision.},
journal = {Central European journal of public health},
volume = {32},
number = {Supplement},
pages = {18-24},
pmid = {39832144},
issn = {1210-7778},
mesh = {Humans ; Female ; Male ; Middle Aged ; Aged ; Slovakia/epidemiology ; Aged, 80 and over ; *Stroke/epidemiology/psychology ; Anxiety/epidemiology ; Depressive Disorder/epidemiology ; Surveys and Questionnaires ; Depression/epidemiology ; Anxiety Disorders/epidemiology ; },
abstract = {OBJECTIVE: Anxiety and depression in patients following cerebrovascular accidents are among frequently occurring complications of the medical condition. The consequences affect personal, family, professional, and social life. They cause severe functional and cognitive impairments, limit the ability to perform normal daily activities, which can result in complete disability. The aim of the study was to monitor the occurrence of anxiety and depression in patients following cerebrovascular accidents hospitalized in neurological departments in the region of eastern Slovakia.<br><br>METHODS: A total of 101 patients following cerebrovascular accidents, aged from 48-86 years, were included in the descriptive study. Demographic and clinical data were obtained from patients and from medical records. We determined the occurrence of anxiety disorders, depression and emotional distress in patients following cerebrovascular accidents using a standardized Hospital Anxiety and Depression Scale (HADS) questionnaire.<br><br>RESULTS: Data analysis confirms a high incidence of anxiety in the HADS-A subscale (9.23 &#xb1; 4.13) and depression in the HADS-D subscale (9.09 &#xb1; 4.43) during the hospitalization phase of the disease. It demonstrates the pathological occurrence of anxiety states in 37%, depression in 36%, emotional distress in 36%, and a serious degree of combination of pathological values of the anxiety subscale and the depression subscale in 27% of patients. The existence of a strong positive correlation between anxiety and depression indicators was confirmed.<br><br>CONCLUSION: The results confirm a high prevalence of anxiety and depression in the acute phase of the disease. The findings indicate that patients recovering from cerebrovascular accidents not only face physical difficulties and loss of independence but also struggle with anxiety and depression, which can negatively impact and slow their recovery. Given the high frequency of these psychological conditions, further research is needed to enhance the quality and effectiveness of care provided to patients with cerebrovascular accidents.},
}
@article {pmid39832137,
year = {2025},
author = {Iobbi, V and Parisi, V and Giacomini, M and De Riccardis, F and Brun, P and Núñez-Pons, L and Drava, G and Giordani, P and Monti, MC and Poggi, R and Murgia, Y and De Tommasi, N and Bisio, A},
title = {Sesterterpenoids: sources, structural diversity, biological activity, and data management.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00041b},
pmid = {39832137},
issn = {1460-4752},
abstract = {Reviewing the literature published up to October 2024.Sesterterpenoids are one of the most chemically diverse and biologically promising subgroup of terpenoids, the largest family of secondary metabolites. The present review article summarizes more than seven decades of studies on isolation and characterization of more than 1600 structurally novel sesterterpenoids, supplemented by biological, pharmacological, ecological, and geographic distribution data. All the information have been implemented in eight tables available on the web and a relational database https://sesterterpenoids.unige.net/. The interface has two sections, one open to the public for reading only and the other, protected by an authentication mechanism, for timely updating of published results.},
}
@article {pmid39830898,
year = {2025},
author = {Gartler, S and Scheer, J and Meyer, A and Abass, K and Bartsch, A and Doloisio, N and Falardeau, J and Hugelius, G and Irrgang, A and Haukur Ingimundarson, J and Jungsberg, L and Lantuit, H and Nymand Larsen, J and Lodi, R and Martin, VS and Mercer, L and Nielsen, D and Overduin, P and Povoroznyuk, O and Rautio, A and Schweitzer, P and Speetjens, NJ and Tomaškovičová, S and Timlin, U and Vanderlinden, JP and Vonk, J and Westerveld, L and Ingeman-Nielsen, T},
title = {A transdisciplinary, comparative analysis reveals key risks from Arctic permafrost thaw.},
journal = {Communications earth &amp; environment},
volume = {6},
number = {1},
pages = {21},
doi = {10.1038/s43247-024-01883-w},
pmid = {39830898},
issn = {2662-4435},
abstract = {Permafrost thaw poses diverse risks to Arctic environments and livelihoods. Understanding the effects of permafrost thaw is vital for informed policymaking and adaptation efforts. Here, we present the consolidated findings of a risk analysis spanning four study regions: Longyearbyen (Svalbard, Norway), the Avannaata municipality (Greenland), the Beaufort Sea region and the Mackenzie River Delta (Canada) and the Bulunskiy District of the Sakha Republic (Russia). Local stakeholders' and scientists' perceptions shaped our understanding of the risks as dynamic, socionatural phenomena involving physical processes, key hazards, and societal consequences. Through an inter- and transdisciplinary risk analysis based on multidirectional knowledge exchanges and thematic network analysis, we identified five key hazards of permafrost thaw. These include infrastructure failure, disruption of mobility and supplies, decreased water quality, challenges for food security, and exposure to diseases and contaminants. The study's novelty resides in the comparative approach spanning different disciplines, environmental and societal contexts, and the transdisciplinary synthesis considering various risk perceptions.},
}
@article {pmid39826720,
year = {2025},
author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR},
title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {139980},
doi = {10.1016/j.ijbiomac.2025.139980},
pmid = {39826720},
issn = {1879-0003},
abstract = {Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer (HGT) in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters (BGCs), including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.},
}
@article {pmid39817434,
year = {2025},
author = {Blum, J and Brüll, M and Hengstler, JG and Dietrich, DR and Gruber, AJ and Dipalo, M and Kraushaar, U and Mangas, I and Terron, A and Fritsche, E and Marx-Stoelting, P and Hardy, B and Schepky, A and Escher, S and Hartung, T and Landsiedel, R and Odermatt, A and Sachana, M and Koch, K and Dönmez, A and Masjosthusmann, S and Bothe, K and Schildknecht, S and Beilmann, M and Beltman, JB and Fitzpatrick, S and Mangerich, A and Rehm, M and Tangianu, S and Zickgraf, FM and Kamp, H and Burger, G and van de Water, B and Kleinstreuer, N and White, A and Leist, M},
title = {The long way from raw data to NAM-based information: Overview on data layers and processing steps.},
journal = {ALTEX},
volume = {42},
number = {1},
pages = {167-180},
doi = {10.14573/altex.2412171},
pmid = {39817434},
issn = {1868-8551},
abstract = {Toxicological test methods generate raw data and provide instructions on how to use these to determine a final outcome such as a classification of test compounds as hits or non-hits. The data processing pipeline provided in the test method description is often highly complex. Usually, multiple layers of data, ranging from a machine-generated output to the final hit definition, are considered. Transition between each of these layers often requires several data processing steps. As changes in any of these processing steps can impact the final output of new approach methods (NAMs), the processing pipeline is an essential part of a NAM description and should be included in reporting templates such as the ToxTemp. The same raw data, processed in different ways, may result in different final outcomes that may affect the readiness status and regulatory acceptance of the NAM, as an altered output can affect robustness, performance, and relevance. Data management, pro­cessing, and interpretation are therefore important elements of a comprehensive NAM definition. We aim to give an overview of the most important data levels to be considered during the devel­opment and application of a NAM. In addition, we illustrate data processing and evaluation steps between these data levels. As NAMs are increasingly standard components of the spectrum of toxi­cological test methods used for risk assessment, awareness of the significance of data processing steps in NAMs is crucial for building trust, ensuring acceptance, and fostering the reproducibility of NAM outcomes.},
}
@article {pmid39652873,
year = {2025},
author = {Naderian, M and Norland, K and Schaid, DJ and Kullo, IJ},
title = {Development and Evaluation of a Comprehensive Prediction Model for Incident Coronary Heart Disease Using Genetic, Social, and Lifestyle-Psychological Factors: A Prospective Analysis of the UK Biobank.},
journal = {Annals of internal medicine},
volume = {178},
number = {1},
pages = {1-10},
doi = {10.7326/ANNALS-24-00716},
pmid = {39652873},
issn = {1539-3704},
mesh = {Humans ; Male ; United Kingdom/epidemiology ; Middle Aged ; *Coronary Disease/epidemiology ; Female ; Prospective Studies ; Risk Assessment ; *Life Style ; Risk Factors ; Incidence ; Social Determinants of Health ; Machine Learning ; UK Biobank ; },
abstract = {BACKGROUND: Clinical risk calculators for coronary heart disease (CHD) do not include genetic, social, and lifestyle-psychological risk factors.<br><br>OBJECTIVE: To improve CHD risk prediction by developing and evaluating a prediction model that incorporated a polygenic risk score (PRS) and a polysocial score (PSS), the latter including social determinants of health and lifestyle-psychological factors.<br><br>DESIGN: Cohort study.<br><br>SETTING: United Kingdom.<br><br>PARTICIPANTS: UK Biobank participants recruited between 2006 and 2010.<br><br>MEASUREMENTS: Incident CHD (myocardial infarction and/or coronary revascularization); 10-year clinical risk based on pooled cohort equations (PCE), Predicting Risk of cardiovascular disease EVENTs (PREVENT), and QRISK3; PRS (Polygenic Score Catalog identification: PGS000018) for CHD (PRSCHD); and PSSCHD from 100 related covariates. Machine-learning and time-to-event analyses and model performance indices.<br><br>RESULTS: In 388&#x2009;224 participants (age, 55.5 [SD, 8.1] years; 42.5% men; 94.9% White), the hazard ratio for 1 SD increase in PSSCHD for incident CHD was 1.43 (95% CI, 1.38 to 1.49; P&#x2009;<&#x2009;0.001) and for 1 SD increase in PRSCHD was 1.59 (CI, 1.53 to 1.66, P&#x2009;<&#x2009;0.001). Non-White persons had higher PSSCHD than White persons. The effects of PSSCHD and PRSCHD on CHD were independent and additive. At a 10-year CHD risk threshold of 7.5%, adding PSSCHD and PRSCHD to PCE reclassified 12% of participants, with 1.86 times higher CHD risk in the up- versus down-reclassified persons and showed superior performance compared with PCE as reflected by improved net benefit while maintaining good calibration relative to the clinical risk calculators. Similar results were seen when incorporating PSSCHD and PRSCHD into PREVENT and QRISK3.<br><br>LIMITATION: A predominantly White cohort; possible healthy participant effect and ecological fallacy.<br><br>CONCLUSION: A PSSCHD was associated with incident CHD and its joint modeling with PRSCHD improved the performance of clinical risk calculators.<br><br>PRIMARY FUNDING SOURCE: National Human Genome Research Institute.},
}
@article {pmid39830091,
year = {2023},
author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful Golden Y, Autographa pulchrina (Haworth, 1809).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {375},
doi = {10.12688/wellcomeopenres.19840.1},
pmid = {39830091},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Autographa pulchrina (the Beautiful Golden Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 426.2 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein coding genes.},
}
@article {pmid39825388,
year = {2025},
author = {Burthe, SJ and Kumbar, B and Schäfer, SM and Purse, BV and Vanak, AT and Balakrishnan, N and Hassall, R and Hoti, SL and Narayanaswamy, D and Potadar, S and Rahman, M and Chanda, MM},
title = {First evidence of transovarial transmission of Kyasanur Forest disease virus in Haemaphysalis and Rhipicephalus ticks in the wild.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {14},
pmid = {39825388},
issn = {1756-3305},
support = {MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; },
mesh = {Animals ; Female ; *Encephalitis Viruses, Tick-Borne/physiology/isolation &amp; purification/genetics ; *Kyasanur Forest Disease/transmission/virology ; India/epidemiology ; *Larva/virology ; *Rhipicephalus/virology ; *Ixodidae/virology ; Arachnid Vectors/virology ; },
abstract = {BACKGROUND: Kyasanur forest disease virus (KFDV) is a tick-borne flavivirus causing debilitating and potentially fatal disease in people in the Western Ghats region of India. The transmission cycle is complex, involving multiple vector and host species, but there are significant gaps in ecological knowledge. Empirical data on pathogen-vector-host interactions and incrimination have not been updated since the last century, despite significant local changes in land use and the expansion of KFD to new areas. Mathematical models predict that transovarial transmission, whereby adult female ticks pass KFDV infections to their offspring, plays an important role in the persistence of KFD, but this has not been shown in the wild. Here we set out to establish whether transovarial transmission of KFDV was occurring under natural field conditions by assessing whether host-seeking larvae were positive for KFDV.<br><br>METHODS: Ticks were sampled by dragging and flagging across a broad range of habitats within the agro-forest matrix at 49 sites in two districts: Shivamogga, Karnataka and Wayanad, Kerala (September 2018-March 2019), and larvae were tested for KFDV by PCR.<br><br>RESULTS: In total, larval ticks from 7 of the 49 sites sampled tested positive for KFDV, indicating that transovarial transmission is occurring. Of the 13 KFDV-positive larval samples, 3 came from around houses and gardens, 5 from crops (3 from harvested rice paddy and 2 from areca plantation), 1 from teak plantation and 4 (2 from 1 transect) from forests. Five different tick species were found to have KFDV-positive larvae: Haemaphysalis spinigera, H. bispinosa, Rhipicephalus annulatus, R. microplus and an unidentifiable species of Haemaphysalis (no close match in GenBank).<br><br>CONCLUSIONS: Our empirical confirmation of transovarial transmission has important implications for understanding and predicting KFD dynamics, suggesting that ticks may act as a reservoir for KFDV. Moreover, small mammals and cattle may play crucial roles in transmission if small mammals are the main hosts for larvae infected via transovarial transmission, and cattle support large numbers of infected female adult ticks. This first report of transovarial transmission of KFDV, and within a hitherto undescribed range of vectors and habitats, will help disease managers improve KFD surveillance and mitigation strategies, ultimately leading to communities becoming more resilient to the risk of this tick-transmitted disease.},
}
@article {pmid39441382,
year = {2025},
author = {Canzler, S and Schubert, K and Rolle-Kampczyk, UE and Wang, Z and Schreiber, S and Seitz, H and Mockly, S and Kamp, H and Haake, V and Huisinga, M and Bergen, MV and Buesen, R and Hackermüller, J},
title = {Evaluating the performance of multi-omics integration: a thyroid toxicity case study.},
journal = {Archives of toxicology},
volume = {99},
number = {1},
pages = {309-332},
pmid = {39441382},
issn = {1432-0738},
support = {C5 - XomeTox//European Chemical Industry Council/ ; 101057014//HORIZON EUROPE Framework Programme/ ; },
mesh = {Animals ; *Thyroid Gland/drug effects/pathology ; *Propylthiouracil/toxicity ; Rats ; Metabolomics ; Proteomics ; Transcriptome/drug effects ; Male ; Genomics ; Risk Assessment ; Female ; Antithyroid Agents/toxicity ; Rats, Sprague-Dawley ; Proteome/metabolism ; Multiomics ; },
abstract = {Multi-omics data integration has been repeatedly discussed as the way forward to more comprehensively cover the molecular responses of cells or organisms to chemical exposure in systems toxicology and regulatory risk assessment. In Canzler et al. (Arch Toxicol 94(2):371-388. https://doi.org/10.1007/s00204-020-02656-y), we reviewed the state of the art in applying multi-omics approaches in toxicological research and chemical risk assessment. We developed best practices for the experimental design of multi-omics studies, omics data acquisition, and subsequent omics data integration. We found that multi-omics data sets for toxicological research questions were generally rare, with no data sets comprising more than two omics layers adhering to these best practices. Due to these limitations, we could not fully assess the benefits of different data integration approaches or quantitatively evaluate the contribution of various omics layers for toxicological research questions. Here, we report on a multi-omics study on thyroid toxicity that we conducted in compliance with these best practices. We induced direct and indirect thyroid toxicity through Propylthiouracil (PTU) and Phenytoin, respectively, in a 28-day plus 14-day recovery oral rat toxicity study. We collected clinical and histopathological data and six omics layers, including the long and short transcriptome, proteome, phosphoproteome, and metabolome from plasma, thyroid, and liver. We demonstrate that the multi-omics approach is superior to single-omics in detecting responses at the regulatory pathway level. We also show how combining omics data with clinical and histopathological parameters facilitates the interpretation of the data. Furthermore, we illustrate how multi-omics integration can hint at the involvement of non-coding RNAs in post-transcriptional regulation. Also, we show that multi-omics facilitates grouping, and we assess how much information individual and combinations of omics layers contribute to this approach.},
}
@article {pmid39822595,
year = {2024},
author = {Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the Poplar Grey moth, Subacronicta megacephala (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {696},
doi = {10.12688/wellcomeopenres.23371.1},
pmid = {39822595},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Subacronicta megacephala (Poplar Grey moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 424.20 megabases. Most of the assembly (99.02%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,189 protein-coding genes.},
}
@article {pmid39822261,
year = {2025},
author = {Proença Neto, MA and De Sousa, MPA},
title = {Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e138257},
doi = {10.3897/BDJ.13.e138257},
pmid = {39822261},
issn = {1314-2828},
abstract = {BACKGROUND: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.<br><br>NEW INFORMATION: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise. Tests on spreadsheets derived from datasets published in the Global Biodiversity Information Facility (GBIF) demonstrated its effectiveness in identifying and resolving taxonomic errors. By mitigating the propagation of inaccuracies from researchers' datasets to global biodiversity databases, pytaxon supports more reliable conservation decisions and robust scientific investigations. Its contributions enhance data integrity and promote informed biodiversity management in a rapidly evolving global environment.},
}
@article {pmid39821365,
year = {2025},
author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y},
title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.},
journal = {Drug development research},
volume = {86},
number = {1},
pages = {e70045},
doi = {10.1002/ddr.70045},
pmid = {39821365},
issn = {1098-2299},
support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; },
mesh = {Humans ; *Famotidine/adverse effects ; *Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; United States/epidemiology ; *Histamine H2 Antagonists/adverse effects ; *Pharmacovigilance ; *United States Food and Drug Administration ; Female ; Male ; Adult ; Middle Aged ; Aged ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Databases, Factual ; Infant ; },
abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.},
}
@article {pmid39423319,
year = {2025},
author = {Tian, Y and Yang, L and Ding, S and Zhang, D and Yuan, L and Liu, Z and Hu, QN},
title = {BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.},
journal = {ACS synthetic biology},
volume = {14},
number = {1},
pages = {285-289},
doi = {10.1021/acssynbio.4c00347},
pmid = {39423319},
issn = {2161-5063},
mesh = {*Synthetic Biology/methods ; *Knowledge Bases ; Databases, Factual ; Software ; Computational Biology/methods ; },
abstract = {Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references. It is freely available at http://www.synbiohealth.cn/biotry. To our knowledge, BioTRY is the first available database on biosynthesis TRY data from original research. We anticipate that BioTRY will become a useful tool that aids researchers and decision-makers in understanding the current development state of biosynthesis and allows them to foresee potential prospects and applications for biosynthesis.},
}
@article {pmid38383603,
year = {2025},
author = {Nevers, Y and Warwick Vesztrocy, A and Rossier, V and Train, CM and Altenhoff, A and Dessimoz, C and Glover, NM},
title = {Quality assessment of gene repertoire annotations with OMArk.},
journal = {Nature biotechnology},
volume = {43},
number = {1},
pages = {124-133},
pmid = {38383603},
issn = {1546-1696},
mesh = {*Software ; *Molecular Sequence Annotation ; *Proteome/genetics ; Animals ; Databases, Protein ; Genomics/methods ; },
abstract = {In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.},
}
@article {pmid39814778,
year = {2025},
author = {Gómez-Gras, D and Linares, C and Viladrich, N and Zentner, Y and Grinyó, J and Gori, A and McFadden, CS and Fabricius, KE and Madin, JS},
title = {The Octocoral Trait Database: a global database of trait information for octocoral species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {82},
pmid = {39814778},
issn = {2052-4463},
mesh = {*Anthozoa/classification ; Animals ; *Databases, Factual ; *Coral Reefs ; Biodiversity ; Ecosystem ; },
abstract = {Trait-based approaches are revolutionizing our understanding of high-diversity ecosystems by providing insights into the principles underlying key ecological processes, such as community assembly, species distribution, resilience, and the relationship between biodiversity and ecosystem functioning. In 2016, the Coral Trait Database advanced coral reef science by centralizing trait information for stony corals (i.e., Subphylum Anthozoa, Class Hexacorallia, Order Scleractinia). However, the absence of trait data for soft corals, gorgonians, and sea pens (i.e., Class Octocorallia) limits our understanding of ecosystems where these organisms are significant members and play pivotal roles. To address this gap, we introduce the Octocoral Trait Database, a global, open-source database of curated trait data for octocorals. This database houses species- and individual-level data, complemented by contextual information that provides a relevant framework for analyses. The inaugural dataset, OctocoralTraits v2.2, contains over 97,500 global trait observations across 98 traits and over 3,500 species. The database aims to evolve into a steadily growing, community-led resource that advances future marine science, with a particular emphasis on coral reef research.},
}
@article {pmid39813953,
year = {2025},
author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL},
title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109260},
doi = {10.1016/j.envint.2025.109260},
pmid = {39813953},
issn = {1873-6750},
abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.},
}
@article {pmid39813347,
year = {2025},
author = {Gu, S and Shao, Z and Qu, Z and Zhu, S and Shao, Y and Zhang, D and Allen, R and He, R and Shao, J and Xiong, G and Jousset, A and Friman, VP and Wei, Z and Kümmerli, R and Li, Z},
title = {Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq5038},
doi = {10.1126/sciadv.adq5038},
pmid = {39813347},
issn = {2375-2548},
mesh = {*Iron/metabolism ; *Siderophores/metabolism ; *Evolution, Molecular ; Ecosystem ; Pseudomonas/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Ligases/metabolism/genetics ; Humans ; Computational Biology/methods ; Bacterial Outer Membrane Proteins ; Receptors, Cell Surface ; },
abstract = {Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.},
}
@article {pmid39809329,
year = {2025},
author = {Amino, K and Hirakawa, T and Yago, M and Matsuo, T},
title = {Dorsoventral comparison of intraspecific variation in the butterfly wing pattern using a convolutional neural network.},
journal = {Biology letters},
volume = {21},
number = {1},
pages = {20240446},
doi = {10.1098/rsbl.2024.0446},
pmid = {39809329},
issn = {1744-957X},
support = {//ACT-X/ ; //Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Butterflies/anatomy &amp; histology/genetics ; *Wings, Animal/anatomy &amp; histology ; *Neural Networks, Computer ; *Sex Characteristics ; Male ; Female ; Species Specificity ; Biological Mimicry ; },
abstract = {Butterfly wing patterns exhibit notable differences between the dorsal and ventral surfaces, and morphological analyses of them have provided insights into the ecological and behavioural characteristics of wing patterns. Conventional methods for dorsoventral comparisons are constrained by the need for homologous patches or shared features between two surfaces, limiting their applicability across species. We used a convolutional neural network (CNN)-based analysis, which can compare images of the two surfaces without focusing on homologous patches or features, to detect dorsoventral bias in two types of intraspecific variation: sexual dimorphism and mimetic polymorphism. Using specimen images of 29 species, we first showed that the level of sexual dimorphism calculated by CNN-based analysis corresponded well with traditional assessments of sexual dissimilarity, demonstrating the validity of the method. Dorsal biases were widely detected in sexual dimorphism, suggesting that the conventional hypothesis of dorsally biased sexual selection can be supported in a broader range of species. In contrast, mimetic polymorphism showed no such bias, indicating the importance of both surfaces in mimicry. Our study demonstrates the potential versatility of CNN in comparing wing patterns between the two surfaces, while elucidating the relationship between dorsoventrally different selections and dorsoventral biases in intraspecific variations.},
}
@article {pmid39807382,
year = {2024},
author = {Smith, SD and Geraghty, EM and Rivas, AL and Fasina, FO and Kosoy, M and Malania, L and Hoogesteijn, AL and Fair, JM},
title = {Multidimensional perspectives of geo-epidemiology: from interdisciplinary learning and research to cost-benefit oriented decision-making.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1492426},
pmid = {39807382},
issn = {2296-2565},
mesh = {Humans ; *Cost-Benefit Analysis ; *Decision Making ; Epidemiology/education ; Geographic Information Systems ; Learning ; },
abstract = {Research typically promotes two types of outcomes (inventions and discoveries), which induce a virtuous cycle: something suspected or desired (not previously demonstrated) may become known or feasible once a new tool or procedure is invented and, later, the use of this invention may discover new knowledge. Research also promotes the opposite sequence-from new knowledge to new inventions. This bidirectional process is observed in geo-referenced epidemiology-a field that relates to but may also differ from spatial epidemiology. Geo-epidemiology encompasses several theories and technologies that promote inter/transdisciplinary knowledge integration, education, and research in population health. Based on visual examples derived from geo-referenced studies on epidemics and epizootics, this report demonstrates that this field may extract more (geographically related) information than simple spatial analyses, which then supports more effective and/or less costly interventions. Actual (not simulated) bio-geo-temporal interactions (never captured before the emergence of technologies that analyze geo-referenced data, such as geographical information systems) can now address research questions that relate to several fields, such as Network Theory. Thus, a new opportunity arises before us, which exceeds research: it also demands knowledge integration across disciplines as well as novel educational programs which, to be biomedically and socially justified, should demonstrate cost-effectiveness. Grounded on many bio-temporal-georeferenced examples, this report reviews the literature that supports this hypothesis: novel educational programs that focus on geo-referenced epidemic data may help generate cost-effective policies that prevent or control disease dissemination.},
}
@article {pmid39806613,
year = {2024},
author = {Shen, A and Ye, J and Zhao, H and Qiang, W and Zhao, H and Huang, Y and Zhou, Y and Wang, Y and Li, X and Zhang, Z and Bian, J and Zhang, L and Wu, P and Wang, Y and Lu, Q},
title = {Risk factors and prediction model of breast cancer-related lymphoedema in a Chinese cancer centre: a prospective cohort study protocol.},
journal = {BMJ open},
volume = {14},
number = {12},
pages = {e089769},
doi = {10.1136/bmjopen-2024-089769},
pmid = {39806613},
issn = {2044-6055},
mesh = {Humans ; Female ; Prospective Studies ; China/epidemiology ; Risk Factors ; *Breast Neoplasms/complications/surgery ; *Breast Cancer Lymphedema/epidemiology/etiology ; Incidence ; Risk Assessment ; Middle Aged ; Adult ; Lymphedema/epidemiology/etiology ; Research Design ; East Asian People ; },
abstract = {INTRODUCTION: Lymphoedema is a distressing and long-term complication for breast cancer survivors. However, the reported incidence of lymphoedema varies, and its risk factors remain underexplored. Currently, a well-established risk prediction model is still lacking. This study aims to describe the rationale, objectives, protocol and baseline characteristics of a prospective cohort study focused on examining the incidence and risk factors of breast cancer-related lymphoedema (BCRL), as well as developing a risk prediction model.<br><br>METHODS AND ANALYSIS: This study is an ongoing single-centre prospective observational cohort study recruiting 1967 patients with breast cancer scheduled for surgery treatment in northern China between 15 February 2022 and 21 June 2023. Assessments will be conducted presurgery and at 1, 3, 6, 12, 18, 24, 30 and 36 months postsurgery. Bilateral limb circumferences will be measured by patients at home or by researchers at the outpatient clinics during follow-up visits. The diagnosis of lymphoedema is based on a relative limb volume increase of &#x2265;10% from the preoperative assessment. Self-reported symptoms will be assessed to assist in diagnosis. Potential risk factors are classified into innate personal traits, behavioural lifestyle, interpersonal networks, socioeconomic status and macroenvironmental factors, based on health ecology model. Data collection, storage and management were conducted using the online 'H6WORLD' data management platform. Survival analysis using the Kaplan-Meier estimate will determine the incidence of BCRL. Risk factors of BCRL will be analysed using log-rank test and COX-LASSO regression. Traditional COX regression analysis and seven common survival analysis machine learning algorithms (COX, CARST, RSF, GBSM, XGBS, SSVM and SANN) will be employed for model construction and validation.<br><br>ETHICS AND DISSEMINATION: The study protocol was approved by the Biomedical Ethics Committee of Peking University (IRB00001052-21124) and the Research Ethics Committee of Tianjin Medical University Cancer Institute and Hospital (bc2023013). The results of this study will be published in peer-reviewed journals and will be presented at several research conferences.<br><br>TRIAL REGISTRATION NUMBER: ChiCTR2200057083.},
}
@article {pmid39671935,
year = {2025},
author = {Paulukonis, EA and Purucker, ST},
title = {Spatiotemporally derived agricultural field delineations for species effects assessments and environmental decision support.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {177967},
doi = {10.1016/j.scitotenv.2024.177967},
pmid = {39671935},
issn = {1879-1026},
mesh = {*Agriculture/methods ; *Environmental Monitoring/methods ; Crops, Agricultural ; Pesticides/analysis ; Risk Assessment/methods ; Decision Support Techniques ; United States ; Geographic Information Systems ; Ecosystem ; },
abstract = {Rural landscapes are strongly defined by the spatial distribution of agricultural fields. GIS layers that capture this information have much utility in many decision support contexts, particularly with regards to the intersection of agricultural pesticide use and endangered species habitat. The United States Department of Agriculture's Cropland Data Layer (CDL) is a georeferenced, annual resource that often serves a crucial role in pesticide risk-related decision support applications. However, CDL agriculture timeseries data are not mapped to explicit field boundaries, contributing to increased uncertainty regarding differentiated crop type spatial homogeneity and geographic extent, inherently adding complexity to multi-temporal crop monitoring and analyses efforts. We describe the development and testing of an approach for field delineation based on timeseries information from the 2008-2021 CDL at spatial scales relevant for endangered species risk assessment. We validate and test the approach against quantitative crop information and contextualize the outputs as part of a case study reconstructing past agricultural pesticide exposures to non-target species to demonstrate the utility of the method for ecological risk assessment decision support. The approach resulted in delineated field unit boundaries that effectively incorporated the unmodified CDL crop type generalized spatial distribution patterns; derived metrics closely corresponded with reported crop metrics for landscapes with proportionally significant agriculture use. When modified to reflect areas of mixed/small crop acreages, the method can provide a useful framework for large-scale field delineation of the CDL, which can complement ongoing environmental risk assessment and conservation efforts in agricultural landscapes.},
}
@article {pmid39584487,
year = {2025},
author = {Daru, BH},
title = {A global database of butterfly species native distributions.},
journal = {Ecology},
volume = {106},
number = {1},
pages = {e4462},
doi = {10.1002/ecy.4462},
pmid = {39584487},
issn = {1939-9170},
support = {2345994//National Science Foundation/ ; 2416314//National Science Foundation/ ; },
mesh = {*Butterflies/physiology ; Animals ; *Animal Distribution ; Databases, Factual ; Species Specificity ; Ecosystem ; },
abstract = {Butterflies represent a diverse group of insects, playing key ecosystem roles such as pollination and their larval form engage in herbivory. Despite their importance, comprehensive global distribution data for butterfly species are lacking. This lack of comprehensive global data has hindered many large-scale questions in ecology, evolutionary biology, and conservation at the regional and global scales. Here, I use an integrative workflow that combines occurrence records, alpha hull polygons, species' dispersal capacity, and natural habitat and environmental variables within a framework of species distribution models to generate species-level native distributions for butterflies at a global scale in the contemporary period. The database releases native range maps for 10,372 extant species of butterflies at a spatial grain resolution of 5 arcmin (~10 km). This database has the potential to allow unprecedented large-scale analyses in ecology, biogeography, and conservation of butterflies. The maps are available in the WGS84 coordinate reference system (EPSG:4326 code) and stored as vector polygons in the GEOPACKAGE format for maximum compression, allowing easy data manipulation using a standard computer. I additionally provide each species' spatial raster. All maps and R scripts are open access and available for download in Dryad and Zenodo, respectively, and are guided by FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. By making these data available to the scientific community, I aim to advance the sharing of biological data to stimulate more comprehensive research in ecology, biogeography, and conservation of butterflies.},
}
@article {pmid39805953,
year = {2025},
author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C},
title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39805953},
issn = {2058-5276},
abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.},
}
@article {pmid39763978,
year = {2024},
author = {Palma-Martínez, MJ and Posadas-García, YS and López-Ángeles, BE and Quiroz-López, C and Lewis, ACF and Bird, KA and Lasisi, T and Zaidi, AA and Sohail, M},
title = {The multi-scale complexity of human genetic variation beyond continental groups.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39763978},
issn = {2692-8205},
support = {K99 HG012809/HG/NHGRI NIH HHS/United States ; R00 GM137076/GM/NIGMS NIH HHS/United States ; },
abstract = {Traditional clustering and visualization approaches in human genetics often operate under frameworks that assume inherent, discrete groupings[1,2]. These methods can inadvertently simplify multifaceted relationships, functioning to entrench the idea of typological groups[3]. We introduce a network-based pipeline and visualization tool grounded in relational thinking[4], which constructs networks from a variety of genetic similarity metrics. We identify communities at multiple resolutions, departing from typological models of analysis and interpretation that categorize individuals into a (predefined) number of sets. We applied our pipeline to a dataset merged from the 1000 Genomes and Human Genome Diversity Project[5], revealing the limitations of traditional groupings and capturing the complexities introduced by demographic events and evolutionary processes. This method embraces the context-specificity of genetic similarities that are salient depending on the question, markers of interest, and study individuals. Different numbers of communities are revealed depending on the resolution chosen and metric used, underscoring a fluid spectrum of genetic relationships and challenging the notion of universal categorization. We provide a web application (https://sohail-lab.shinyapps.io/GG-NC/) for interactive visualization and engagement with these intricate genetic landscapes.},
}
@article {pmid39799926,
year = {2025},
author = {Fridman, M and Krasko, O and Veyalkin, I},
title = {The incidence trends of papillary thyroid carcinoma in Belarus during the post-Chernobyl epoch.},
journal = {Cancer epidemiology},
volume = {95},
number = {},
pages = {102745},
doi = {10.1016/j.canep.2025.102745},
pmid = {39799926},
issn = {1877-783X},
abstract = {BACKGROUND: The increase of papillary thyroid cancer (PTC) rate among children who were exposed to post-Chernobyl 131-I release was reported only four years after the accident, first in Belarus where the heaviest fallout happened. The evolution of the occurrence of thyroid carcinoma based on the age-period-cohort analysis and the effects of age, period, and birth cohort on time trends aimed to reveal if post-Chernobyl follicular cells irradiation still has been impacting on incidence rate of papillary thyroid carcinoma nowadays.<br><br>METHODS: The Belarusian Cancer Registry was used to identify patients with PTC diagnosed during the years 1980-2019. The incidence trends were analysed using Join-point regression software.<br><br>RESULTS: The highest peak of age-specific incidence curve was shown during the years 1980-2001 in the age group of 15-19 years old that was associated also with short-latency cases of post-Chernobyl PTC. This is the same age group that demonstrated significant growth of the incidence rate during the years 2006-2019, largely because of the increasing number of non-exposed patients with PTC (p&#x202f;<&#x202f;0.001). Influence of post-Chernobyl exposure also can be seen in the young adults age-groups of patients (for 20-24 years old during the years 1980-2003 and 2013-2019, p&#x202f;<&#x202f;0.001; for 25-29 years old during the years 1980-1999 and 1999-2011, p&#x202f;<&#x202f;0.001).<br><br>CONCLUSION: After the Chernobyl accident, epidemiological waves that reflect the age shift of the group of children exposed to 131-I have consistently emerged. Currently, the incidence rate continues to increase only in the cohort of patients aged 20-44 years.},
}
@article {pmid39798660,
year = {2025},
author = {Li, J and Lu, Y and Chen, X and Wang, L and Cao, Z and Lei, H and Zhang, Z and Wang, P and Sun, B},
title = {Seasonal variation of microbial community and diversity in the Taiwan Strait sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120809},
doi = {10.1016/j.envres.2025.120809},
pmid = {39798660},
issn = {1096-0953},
abstract = {Human activities and ocean currents in the Taiwan Strait exhibit significant seasonal variation, yet the response of marine microbes to ocean changes under anthropogenic and climatic stress remains unclear. Using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics and functional variations of microbial communities in sediment samples. Our findings revealed distinct seasonal patterns in microbial diversity and composition. Proteobacteria, Desulfobacterota, and Crenarchaeota dominated at the phylum level, while Candidatus Nitrosopumilus, Woeseia, and Subgroup 10 were prevalent at the genus level. Iron concentrations, heavy metals and C/N ratio were primary factors influencing microbial communities during specific seasons, whereas sulfur content, temperature fluctuations, and heavy metals shaped the entire microbial structure and diversity. Core microbial groups, including Desulfobulbus, Subgroup 10, Unidentified Latescibacterota, and Sumerlaea, played essential roles in regulating community structure and functional transitions. Marker species, such as Aliidiomarina sanyensis, Spirulina platensis, Croceimarina litoralis and Sulfuriflexus mobilis, acted as seasonal indicators. Bacteria exhibited survival strategy akin to higher organisms, encompassing process of synthesis, growth, dormancy, and disease resistance throughout the seasonal cycle. Core microbial groups and marker species in specific seasons can serve as indicators for monitoring and assessing the health of the Taiwan Strait ecosystem.},
}
@article {pmid39794649,
year = {2025},
author = {Mohammad, L and Bandyopadhyay, J and Mondal, I and Altuwaijri, HA and Khatun, S and Hossain, SKA and Juliev, M},
title = {Assessing cropping system dynamics over three decades: remote sensing and GIS insights in Murshidabad-Jiaganj Block.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {2},
pages = {164},
pmid = {39794649},
issn = {1573-2959},
mesh = {*Environmental Monitoring/methods ; *Remote Sensing Technology ; *Agriculture/methods ; *Geographic Information Systems ; Crops, Agricultural/growth &amp; development ; Seasons ; },
abstract = {Agriculture is a significant contributor to the country's economic development. We used multiple Landsat images from 1990 to 2021 in the Murshidabad-Jiaganj Block to assess changes in the agricultural system and their underlying causes. The Rabi season saw a 10.99% growth in agrarian regions from 1990 to 2000 and an 8.86% increase in 2010, yet it declined by 28.12% in 2021. During the summer, the cultivated lands diminished by 26.63%, 19.43%, and 19.64%, while in the Kharif season, they declined by 21.78%, 15.68%, and 11.99% from 1990 in the years 2000, 2010, and 2021, respectively. The agricultural area had 36.82%, 34.16%, and 19.01% increases between 1990 and 2021, respectively. Regarding direction, farmland acreage decreased in all zones except the SSE, which had a 0.95% increase. Mono-, double-, and triple-cropping systems have decreased in area, while multi-cropping systems have experienced increases of 43.51%, 4.50%, and 18.49% in 1990-2021, respectively. The multi-cropping system has a good correlation with all agroclimatic factors. The reduction of irrigated lands post-2009 significantly affected the agriculture system. The fall in agricultural employment in recent decades is attributable to migration seeking higher-paying occupations. The advancement of accurate remote sensing-based modeling is crucial for mitigating food security risks, particularly those posed by climate change, and informing policy decisions.},
}
@article {pmid39794678,
year = {2025},
author = {Sasia, I and Bueno, G and Etxano, I},
title = {Amalur EIS: a system for calculating the environmental impacts of industrial sites from E-PRTR records.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {2},
pages = {163},
pmid = {39794678},
issn = {1573-2959},
support = {IT 1567-22 Ekopol Research Group&#xa0;(UPV/EHU)//Department of Education of the Basque Government/ ; IT 1567-22 Ekopol Research Group&#xa0;(UPV/EHU)//Department of Education of the Basque Government/ ; IT 1567-22 Ekopol Research Group&#xa0;(UPV/EHU)//Department of Education of the Basque Government/ ; },
mesh = {*Environmental Monitoring/methods ; Climate Change ; Environment ; Europe ; Databases, Factual ; Industry ; Environmental Pollutants/analysis ; Environmental Pollution/statistics &amp; numerical data ; },
abstract = {This article presents Amalur EIS (https://www.amalur-eis.eus/), an Environmental Information System that estimates environmental impacts using data sourced from the European Pollutant Release and Transfer Register database (E-PRTR). The system uses data on the releases into land, air and water of 31,556 European industrial facilities for the period 2007-2021. Amalur EIS calculates environmental impacts of industrial releases using 31 life cycle impact assessment methods (LCIA) and covering 78 of the 91 pollutants regulated by the PRTR Protocol. The system has been constructed using a two-layer software infrastructure: (i) a data layer supported by a relational database built in Postgres and (ii) a presentation layer built in Tableau, so it provides user-friendly access to the information. For an illustrative analysis of the tool, the EF 3.0 LCIA method recommended by the European Commission was used, including normalisation and weighting steps for a better comparison. The analysis concludes that the climate change impact category contributes the most (68.6%) to the total impacts, while the largest contributor from an economic activity perspective is the energy sector (59.5%). Geographically, both elements coincide in the German regions of Düsseldorf, Köln and Brandenburg, resulting in the concentration of the largest impacts at the European regional level. In fact, Germany is the country with the highest impact (20.3% of total). Beyond this analysis, Amalur EIS is poised to be a valuable tool for tracking the transition towards sustainability, particularly in Europe.},
}
@article {pmid39793033,
year = {2025},
author = {Clauss, M and Roller, M and Bertelsen, MF and Rudolf von Rohr, C and Müller, DWH and Schiffmann, C and Kummrow, M and Encke, D and Ferreira, S and Duvall, ES and Maré, C and Abraham, AJ},
title = {Zoos must embrace animal death for education and conservation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {1},
pages = {e2414565121},
doi = {10.1073/pnas.2414565121},
pmid = {39793033},
issn = {1091-6490},
support = {101062339//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; },
}
@article {pmid39792995,
year = {2025},
author = {Soeishi, T and Nakata, A and Nagata, T and Akutsu, S and Tondokoro, T and Inoue, Y and Katsumura, F and Kikunaga, K},
title = {Predicting depressive symptoms and psychological distress by circulating inflammatory mediators: A 16-month prospective study in Japanese white-collar employees.},
journal = {Journal of occupational and environmental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/JOM.0000000000003307},
pmid = {39792995},
issn = {1536-5948},
abstract = {OBJECTIVE: Although increasing evidence suggests that depression/distress involves inflammatory processes, its potential sex differences and the temporal directions for this association remain elusive.<br><br>METHODS: We examined the temporal association between serum inflammatory mediators and depression/distress as measured by the Center for Epidemiologic Studies Depression Scale (CES-D) and the Kessler Psychological Distress Scale (K6), in non-depressed working men and women (n = 61 and 43, respectively) by a 16-month prospective design.<br><br>RESULTS: Fully-adjusted partial correlation analyses revealed that in men, a lower IFN-&#x3b3; predicted subsequent increases in CES-D and K6 scores, while a higher TNF-&#x3b1; predicted increased K6 scores. In women, a higher IFN-&#x3b3; predicted a subsequent increase in the CES-D score. CES-D and K6 scores did not predict inflammatory mediators at follow-up.<br><br>CONCLUSIONS: The finding suggests that inflammatory activation precedes depression/distress with distinct sex differences.},
}
@article {pmid39792790,
year = {2025},
author = {Kherroubi Garcia, I and Erdmann, C and Gesing, S and Barton, M and Cadwallader, L and Hengeveld, G and Kirkpatrick, CR and Knight, K and Lemmen, C and Ringuette, R and Zhan, Q and Harrison, M and Mac Gabhann, F and Meyers, N and Osborne, C and Till, C and Brenner, P and Buys, M and Chen, M and Lee, A and Papin, J and Rao, Y},
title = {Ten simple rules for good model-sharing practices.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012702},
doi = {10.1371/journal.pcbi.1012702},
pmid = {39792790},
issn = {1553-7358},
mesh = {*Information Dissemination/methods ; Humans ; *Computational Biology ; Computer Simulation ; },
abstract = {Computational models are complex scientific constructs that have become essential for us to better understand the world. Many models are valuable for peers within and beyond disciplinary boundaries. However, there are no widely agreed-upon standards for sharing models. This paper suggests 10 simple rules for you to both (i) ensure you share models in a way that is at least "good enough," and (ii) enable others to lead the change towards better model-sharing practices.},
}
@article {pmid39789290,
year = {2025},
author = {Sağlam, S and Özdemir, E and Özden, &#xd6; and Makineci, E and Özkan, UY and Bingöl, D and Güzelçimen, F},
title = {The effects of some chemical compounds on the sound absorbing ability of tree bark.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {39789290},
issn = {2676-8607},
abstract = {Tree bark is an important natural polymer for sound absorption. The main components in the bark of different tree species are polymers with high molecular weight such as cellulose, hemicellulose, and lignin. The aim of this study is to determine the noise reduction coefficient (NRC), lignin, alcohol-benzene solubility (ABS), carbon (C), and nitrogen (N) contents in samples taken from the bark of different tree species-black locust (Robinia pseudoacacia), narrow-leaved ash (Fraxinus angustifolia), stone pine (Pinus pinea), silver lime (Tilia tomentosa), sweet chestnut (Castanea sativa), sessile oak (Quercus petraea), and maritime pine (Pinus pinaster) and to investigate the relationship between these chemical properties and sound absorption measurements. Tree species showed a statistically significant difference in terms of all measured variables. In the correlation matrix obtained as a result of the analysis, only ABS showed a significant and the highest positive correlation with the NRC, with a correlation coefficient of r = 0.812. ABS in bark is seen as the most important chemical factor regarding sound retention, indicating the abundance of extractives in barks of different tree species. An investigation into the relationship between sound retention and different extractive substance and contents of different extractive substances in bark is recommended for further studies.},
}
@article {pmid39789035,
year = {2025},
author = {Li, F and Xia, H and Miao, J and Yang, J},
title = {Changes of the ecological environment status in villages under the background of traditional village preservation: a case study in Enshi Tujia and Miao Autonomous Prefecture.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1504},
pmid = {39789035},
issn = {2045-2322},
support = {42271318//National Natural Science Foundation of China/ ; },
mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; China ; Humans ; Rural Population ; Geographic Information Systems ; },
abstract = {The preservation of Chinese traditional villages plays a crucial role in promoting the sustainable development of rural natural, cultural, and ecological environments. It is also a key strategy for achieving rural revitalization. Current research on traditional villages predominantly focuses on the realm of cultural landscapes, with an emphasis on preserving the cultural ecological value of these communities. In comparison, discussions on the quality of the ecological environment of villages from the perspectives of natural environment, economic environment, and the social organizational environment within regional development are relatively scarce. Our study employed GIS and RS technology and refers to the Technical Criterion for Ecosystem Status Evaluation. Several sub-indices of the ecological environment status, including the biological richness index, vegetation coverage index, water network density index, and land stress index, were selected to construct an ecological environment assessment model. This model was used to analyze the spatial-temporal changes in the ecological environment status of each county, county-level city, and traditional village within the jurisdiction of Enshi Tujia and Miao Autonomous Prefecture and its surrounding areas from 2010 to 2020. The study quantitatively evaluated the ecological environment status of each county, county-level city, and village in Enshi before and after the implementation of traditional village preservation policies. Through comparative analysis, the study revealed the impact of these policies on the natural ecological environment of the study area. The results indicated the following: (1) From 2010 to 2020, the ecological index (EI) values in the villages of Enshi Prefecture exhibited a similar trend to the EI values in the respective counties and county-level cities they are located in, although significant differences in magnitude of change were observed. (2) The EI values in the counties, county-level cities, and villages demonstrated greater variation in the latter five years of the decade (2015-2020) compared to the previous five years (2010-2015). (3) In 2020, the EI value of the villages experienced more significant changes compared to 2010, whereas the overall EI value of the counties and county-level cities showed less pronounced changes. The findings of this study suggest that the traditional village preservation policies implemented in Enshi Prefecture have both positive and negative impacts on the ecological environment of the surrounding areas of protected villages, and these impacts become increasingly evident over time. By comparing and analyzing the ecological changes in the surrounding areas of traditional villages in Enshi Prefecture with the overall ecological changes in the respective counties and county-level cities, our study employs quantitative analytical methods to delve into the impact of traditional village conservation policies on the natural ecological environment. It assesses the effects of policy implementation on the natural ecological environment of traditional villages, analyzing both the positive and negative impacts brought about by the execution of these policies, with the aim of effectively guiding the natural ecological conditions of traditional villages towards a more healthy trajectory of development.},
}
@article {pmid39788970,
year = {2025},
author = {Sánchez-Jardón, L and Hernández de Diego, A and Mackenzie, R and Villodre, M and Arnaiz-Schmitz, C and Schmitz, MF and Acosta-Gallo, B},
title = {Bryophyte literature records database of Aysén, Chilean sub-Antarctic ecoregion.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {36},
pmid = {39788970},
issn = {2052-4463},
mesh = {*Bryophyta ; Chile ; *Biodiversity ; Antarctic Regions ; Ecosystem ; Databases, Factual ; },
abstract = {The Chilean sub-Antarctic ecoregion hosts the largest expanse of temperate forests, wetlands and peatlands, as well as the largest proportion of protected areas in the southern hemisphere. Bryophytes are highly diverse and ecologically essential in sub-Antarctic ecosystems and are considered as biodiversity loss indicators caused by the current socio-ecological crisis. However, knowledge about their biodiversity is rather limited. Integrating the available information on bryophyte diversity in regional platforms such as SIB-Aysén can be useful to acknowledge their ecological importance and remarkable biodiversity. This article integrates 345 records of 273 bryophyte taxa known in the region of Aysén and emphasizes the need to include citizen science as a tool to increase observations in lesser-known taxonomic groups.},
}
@article {pmid39787642,
year = {2024},
author = {Aanes, H and Vigeland, MD and Star, B and Gilfillan, GD and Mattingsdal, M and Trøan, S and Strand, M and Eide, LM and Hanssen, EN},
title = {Heating up three cold cases in Norway using investigative genetic genealogy.},
journal = {Forensic science international. Genetics},
volume = {76},
number = {},
pages = {103217},
doi = {10.1016/j.fsigen.2024.103217},
pmid = {39787642},
issn = {1878-0326},
abstract = {With the advent of commercial DNA databases, investigative genetic genealogy (IGG) has emerged as a powerful forensic tool, rivalling the impact of STR analyses, introduced four decades ago. IGG has been frequently applied in the US and tested in other countries, but never in Norway. Here, we apply IGG to three cold criminal cases and successfully identify the donor of the DNA in two of these cases. Our findings suggest that when combined with phenotypic prediction and case information, IGG holds substantial potential for resolving both active and cold cases in Norway. This potential is amplified by the digitalization of archives and the transparent and structured nature of society in Norway. Additionally, the databases exhibit sufficient representation to yield matches with distant relatives. Moreover, this work has uncovered a series of lingering research questions spanning the entire workflow from DNA extraction to genealogy research. Finally, we highlight the possibility that more insights can be gleaned from genetic profiles, for instance using an accurate age prediction method. The results show that IGG can be successfully applied in Norway, having reached a level of maturity that enables identification of unknown individuals in cases where DNA is accessible.},
}
@article {pmid39787194,
year = {2025},
author = {Bantie, GM and Tadege, M and Nigussie, TZ and Woya, AA and Tekile, AK and Melese, AA and Ayalew, S and Beyene, BB and Wubetu, GY},
title = {Regional disparities of full pentavalent vaccine uptake and the determinants in Ethiopia: Mapping and spatial analysis using the EDHS data.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0312514},
doi = {10.1371/journal.pone.0312514},
pmid = {39787194},
issn = {1932-6203},
mesh = {Humans ; Ethiopia ; Infant ; Female ; Adult ; *Spatial Analysis ; Male ; *Vaccination/statistics &amp; numerical data ; Diphtheria-Tetanus-Pertussis Vaccine/administration &amp; dosage ; Hepatitis B Vaccines/administration &amp; dosage ; Young Adult ; Immunization Programs/statistics &amp; numerical data ; Middle Aged ; Haemophilus Vaccines ; Adolescent ; Vaccination Coverage/statistics &amp; numerical data ; Vaccines, Combined ; },
abstract = {BACKGROUND: The full pentavalent (DPT-HepB-Hib) vaccination is the main strategy to prevent five communicable diseases in early childhood, especially in countries with huge communicable disease burdens like Ethiopia. Exploring spatial distributions and determinants of full pentavalent vaccination status in minor ecological areas in Ethiopia is crucial for creating targeted immunization campaigns and monitoring the advancement of accomplishing sustainable development goals. This study aimed to investigate the spatial disparities and determinants of full pentavalent vaccination among 12-23-month-old children in Ethiopia.<br><br>METHOD: The data on pentavalent vaccine uptake was found in the Ethiopian Health and Demographic Survey (EDHS, 2019). A two-stage cluster sampling method was applied to collect the EDHS data. The enumeration area was the primary sample unit while the household served as the secondary sampling unit. The geographical variations of full pentavalent vaccine uptake were explored using Quantum Geographic Information System (QGIS) software. The significant predictors of full pentavalent vaccination were identified using a simple logistic regression model through R version 4.1 software.<br><br>RESULT: The national full pentavalent vaccine uptake was 59.2%. The spatial distribution of full pentavalent vaccine uptake was not uniform in Ethiopia. Spatial cluster analysis revealed that most of low coverage regions for full pentavalent vaccine uptake were Afar, Somali, and Harari. The regions with the highest and lowest rates of vaccine uptake were Tigray and Harari region, respectively. Maternal age of 35-49 years (AOR = 3.42; 95% CI: 1.99, 5.87), and 25-34 years (AOR = 1.55; 95% CI: 1.17, 2.19), primary education attended (AOR = 1.51; 95%CI: 1.07, 2.11), richness wealth index (AOR = 1.96; 95% CI: 1.40, 2.75), birth order of 1-3 (AOR = 1.88; 95% CI: 1.19, 2.96), and delivery in the health facility (AOR = 3.41: 95% CI: 2.52, 4.61) were the determinants of full pentavalent vaccine uptake in Ethiopia.<br><br>CONCLUSION: Ethiopia's full pentavalent vaccine uptake was far lower than the global target. Older maternal age, maternal education, wealth index, birth order, and giving birth in a health facility were the determinants of full pentavalent vaccine uptake. Special attention should be given to Afar, Somali, and Harari regions, to strengthen the vaccine uptake. Moreover, improved socioeconomic status and getting maternal health services during delivery are necessary to enhance vaccine uptake.},
}
@article {pmid39750058,
year = {2024},
author = {Jain, S and Srinivasan, R and Helton, TJ and Karthikeyan, R},
title = {TXSELECT: a web-based decision support system for regional assessment of potential E. coli loads using a spatially explicit approach.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering},
volume = {59},
number = {10},
pages = {550-561},
doi = {10.1080/10934529.2024.2445953},
pmid = {39750058},
issn = {1532-4117},
mesh = {*Escherichia coli/isolation &amp; purification ; Texas ; *Internet ; Environmental Monitoring/methods ; Water Microbiology ; Decision Support Techniques ; },
abstract = {Bacterial source characterization and allocation are imperative to watershed planning and identifying best management practices. The Spatially Explicit Load Enrichment Calculation Tool (SELECT) has been extensively utilized in watershed protection plans to evaluate the potential bacteria loads and sources in impaired watersheds. However, collecting data, compiling inputs, and spatially mapping sources can be arduous, time-intensive, expensive, and iterative until potential bacteria loads are appropriately allocated to sources based on stakeholder recommendations. We developed a web-based decision support system (DSS), TXSELECT (https://tx.select.tamu.edu), providing a user-friendly interface to run the SELECT model on Texas watersheds. The DSS includes pre-determined watershed-specific inputs that can be readily adjusted within the interface based on user preference and stakeholder recommendations, obviating the necessity for expensive GIS tools and data extraction. To illustrate the applications of TXSELECT, we implemented it in the entire coverage area to identify the potential hotspots and source contributions for Escherichia coli at a regional scale. Median potential E. coli loads were significantly higher in subwatersheds not supporting recreation use. Overall, the large-scale application of SELECT has the potential to aid in prioritizing management measures in watersheds that are less frequently monitored but could have an elevated risk of impairment.},
}
@article {pmid39560426,
year = {2025},
author = {Zhu, H-H and Liu, M-M and Boekhout, T and Wang, Q-M},
title = {Improvement of a MALDI-TOF database for the reliable identification of Candidozyma auris (formally Candida auris) and related species.},
journal = {Microbiology spectrum},
volume = {13},
number = {1},
pages = {e0144424},
pmid = {39560426},
issn = {2165-0497},
mesh = {*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Humans ; *Candidiasis/microbiology/diagnosis ; Candida auris/chemistry/isolation &amp; purification/classification ; Databases, Factual ; Mycological Typing Techniques/methods ; Candida/classification/isolation &amp; purification/chemistry ; },
abstract = {UNLABELLED: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising technique for the rapid identification microorganisms. The aim of this study was to create a new database for the accurate identification of Candidozyma auris (formerly known as Candida auris) and 11 species of the Candidozyma haemuli species complex, including C. chanthaburiensis, C. duobushaemuli, C. haemuli, C. heveicola, C. khanbhai, C. konsanensis, C. metrosideri, C. ohialehuae, C. pseudohaemuli, C. ruelliae, and C. vulturna. Seventy-one Candidozyma isolates from different national institutions were studied. Thirty-seven strains were used to create a MALDI-TOF (microTyper MS) database using the formic acid extraction method. The validation of this database was performed with 34 other strains of the genus Candidozyma, and the result was compared with the identification results when using DBRs v1.0.0.4 (Tianrui, China). Our library allowed a 100% identification of the evaluated strains with all strains showing log scores of >2.0. Repeatability and reproducibility tests result showed a coefficient of variation of the log score values of less than 5%. The MALDI-TOF MS system can identify C. auris and related species quickly and accurately. This method will play a crucial role in accurately diagnosing infectious agents of the genus Candidozyma in clinical practice.<br><br>IMPORTANCE: Importance Candidozyma auris, also known as Candida auris, has quickly spread across the world, and prompt identification of C. auris from infected individuals is critical. However, a standard identification method is lacking for the identification of C. auris in clinical and public health laboratories. To make matters worse, its biochemical assimilation profile was found to be similar to that of closely related and even no-related species, leading to frequent misidentification. To improve diagnostics of this and closely related species, we created a database of reference mass spectra resulting in the efficient and correct identification of all Candidozyma species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, potential pathogenic species of Candidozyma can be effectively identified by MALDI-TOF MS, and differentiated from non-clinically relevant phylogenetic relatives. Thus, MALDI-TOF MS may help expedite laboratory diagnosis and treatment of C. auris and related species of clinical importance and help the clinician to decide on early treatment.},
}
@article {pmid39304763,
year = {2025},
author = {Pakkir Shah, AK and Walter, A and Ottosson, F and Russo, F and Navarro-Diaz, M and Boldt, J and Kalinski, JJ and Kontou, EE and Elofson, J and Polyzois, A and González-Marín, C and Farrell, S and Aggerbeck, MR and Pruksatrakul, T and Chan, N and Wang, Y and Pöchhacker, M and Brungs, C and Cámara, B and Caraballo-Rodríguez, AM and Cumsille, A and de Oliveira, F and Dührkop, K and El Abiead, Y and Geibel, C and Graves, LG and Hansen, M and Heuckeroth, S and Knoblauch, S and Kostenko, A and Kuijpers, MCM and Mildau, K and Papadopoulos Lambidis, S and Portal Gomes, PW and Schramm, T and Steuer-Lodd, K and Stincone, P and Tayyab, S and Vitale, GA and Wagner, BC and Xing, S and Yazzie, MT and Zuffa, S and de Kruijff, M and Beemelmanns, C and Link, H and Mayer, C and van der Hooft, JJJ and Damiani, T and Pluskal, T and Dorrestein, P and Stanstrup, J and Schmid, R and Wang, M and Aron, A and Ernst, M and Petras, D},
title = {Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.},
journal = {Nature protocols},
volume = {20},
number = {1},
pages = {92-162},
pmid = {39304763},
issn = {1750-2799},
support = {EXC 2124//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Metabolomics/methods ; Chromatography, Liquid/methods ; Software ; Tandem Mass Spectrometry/methods ; Data Interpretation, Statistical ; },
abstract = {Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks (https://github.com/Functional-Metabolomics-Lab/FBMN-STATS). Additionally, the protocol is accompanied by a web application with a graphical user interface (https://fbmn-statsguide.gnps2.org/) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.},
}
@article {pmid39778451,
year = {2025},
author = {Lausch, A and Selsam, P and Heege, T and von Trentini, F and Almeroth, A and Borg, E and Klenke, R and Bumberger, J},
title = {Monitoring and modelling landscape structure, land use intensity and landscape change as drivers of water quality using remote sensing.},
journal = {The Science of the total environment},
volume = {960},
number = {},
pages = {178347},
doi = {10.1016/j.scitotenv.2024.178347},
pmid = {39778451},
issn = {1879-1026},
abstract = {The interactions between landscape structure, land use intensity (LUI), climate change, and ecological processes significantly impact hydrological processes, affecting water quality. Monitoring these factors is crucial for understanding their influence on water quality. Remote sensing (RS) provides a continuous, standardized approach to capture landscape structures, LUI, and landscape changes over long-term time series. In this study, RS-based indicators from Landsat data (2018-2021) were used to assess landscape structure, LUI, and land use change for a study area in northern Germany, applying the ESIS/Imalys tool. These indicators were then used to model and predict water quality (Chla) in 119 standing waters. Various machine learning methods, including Generalised Linear Models, Support Vector Machines, Deep Learning, Decision Trees, Random Forest, and Gradient Boosted Trees, were tested. The Random Forest model performed best, with a correlation of 0.744 ± 0.11. Indicators related to landscape structure, such as diversity_mean (0.376) and relation_mean (0.292), had the highest global correlation weights, while LUI and land use change indicators like NirV2_mean (0.369) and NirV_regme (0.284) were also significant. All indicators and their effects on water quality (Chla) are discussed in detail. The study highlights the potential of the ESIS/Imalys tool for quantifying landscape structure, LUI, and land use change with RS to model and predict water quality and suggests directions for future model improvements by incorporating additional influencing factors.},
}
@article {pmid39777935,
year = {2025},
author = {Mond, L and Geyer, S and Tetzlaff, J and Weißenborn, K and Schneider, J and Epping, J},
title = {More Drugs and Fewer Strokes? Time Trends in CVD Medication and Incidence of Stroke With German Health Insurance Data.},
journal = {Pharmacoepidemiology and drug safety},
volume = {34},
number = {1},
pages = {e70077},
doi = {10.1002/pds.70077},
pmid = {39777935},
issn = {1099-1557},
support = {//Allgemeine Ortskrankenkasse Niedersachsen/ ; GE 1167/15-1//Deutsche Forschungsgemeinschaft/ ; GE 1167/19-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; *Stroke/epidemiology/prevention &amp; control ; Adult ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/prevention &amp; control ; Young Adult ; Adolescent ; *Insurance, Health/statistics &amp; numerical data ; Prevalence ; Cardiovascular Agents/therapeutic use/adverse effects ; Age Factors ; Time Factors ; Databases, Factual ; },
abstract = {BACKGROUND: Successful prevention of cardiovascular diseases (CVD) may reduce the burden of diseases. Preventive medication is an important measure to decrease the risks of cardiovascular events, in particular myocardial infarction and stroke. The aim of this study is to analyze the prevalence of CVD preventive medication in Germany over time with respect to sex and age and to compare it with the temporal development of strokes.<br><br>METHODS: The study is based on statutory health insurance claims data from the AOK Niedersachsen (AOKN) covering the years 2005-2018. The study population comprises all AOKN insured persons aged 18&#x2009;years and older (N&#x2009;=&#x2009;2&#x2009;088&#x2009;495). Age-standardized time trends of the prevalence of CVD preventive medication and incidence of stroke were calculated for men and women in different age groups. After that, the relationship of both measures was examined in an ecological correlation.<br><br>RESULTS: We found a clear increase in medication prevalence over time. In 2018, about 35% of the total population and about 85% of those over 85&#x2009;years of age received CVD preventive medication. At the same time, age-standardized incidence rates of ischemic stroke were decreasing slightly. The ecological correlation showed a negative association between medication prevalence and stroke incidence especially in the higher age groups.<br><br>CONCLUSION: High correlation coefficients indicate that higher medication prevalence could be linked to better population health. Further research is needed to draw conclusions about the effects of increasing medicalization, including adverse risks and side effects at the population level.},
}
@article {pmid39776539,
year = {2024},
author = {Chandel, N and Maile, A and Shrivastava, S and Verma, AK and Thakur, V},
title = {Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations.},
journal = {Gut microbiome (Cambridge, England)},
volume = {5},
number = {},
pages = {e8},
doi = {10.1017/gmb.2024.6},
pmid = {39776539},
issn = {2632-2897},
abstract = {Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity. India is home to the largest human population in the world. It is spread across diverse ecological and geographical locations. With variable dietary habits and lifestyles, Indians have unique gut microbial composition. This review captures contrasting and common trends of gut bacterial community establishment in infants (born through different modes of delivery), and how that bacterial community manifests itself along infancy, through old age between Indian and global populations. Because dysbiosis of the gut community structure is associated with various diseases, this review also highlights the common and unique bacterial species associated with various communicable as well as noncommunicable diseases such as diarrhoea, amoebiasis, malnutrition, type 2 diabetes, obesity, colorectal cancer, inflammatory bowel disease, and gut inflammation and damage to the brain in the global and Indian population.},
}
@article {pmid39776261,
year = {2025},
author = {Nolasco, M and Balzarini, M},
title = {Assessment of temporal aggregation of Sentinel-2 images on seasonal land cover mapping and its impact on landscape metrics.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {2},
pages = {142},
pmid = {39776261},
issn = {1573-2959},
mesh = {*Environmental Monitoring/methods ; *Ecosystem ; *Seasons ; Satellite Imagery ; Geographic Information Systems ; },
abstract = {Landscape metrics (LM) play a crucial role in fields such as urban planning, ecology, and environmental research, providing insights into the ecological and functional dynamics of ecosystems. However, in dynamic systems, generating thematic maps for LM analysis poses challenges due to the substantial data volume required and issues such as cloud cover interruptions. The aim of this study was to compare the accuracy of land cover maps produced by three temporal aggregation methods: median reflectance, maximum normalised difference vegetation index (NDVI), and a two-date image stack using Sentinel-2 (S2) and then to analyse their implications for LM calculation. The Google Earth Engine platform facilitated data filtering, image selection, and aggregation. A random forest algorithm was employed to classify five land cover classes across ten sites, with classification accuracy assessed using global measurements and the Kappa index. LM were then quantified. The analysis revealed that S2 data provided a high-quality, cloud-free dataset suitable for analysis, ensuring a minimum of 25 cloud-free pixels over the study period. The two-date and median methods exhibited superior land cover classification accuracy compared to the max NDVI method. In particular, the two-date method resulted in lower fragmentation-heterogeneity and complexity metrics in the resulting maps compared to the median and max NDVI methods. Nevertheless, the median method holds promise for integration into operational land cover mapping programmes, particularly for larger study areas exceeding the width of S2 swath coverage. We find patch density combined with conditional entropy to be particularly useful metrics for assessing fragmentation and configuration complexity.},
}
@article {pmid39771200,
year = {2024},
author = {Sedmáková, D and Jaloviar, P and Mišíková, O and Šumichrast, L and Slováčková, B and Kucbel, S and Vencurik, J and Bosela, M and Sedmák, R},
title = {Small Gap Dynamics in High Mountain Central European Spruce Forests-The Role of Standing Dead Trees in Gap Formation.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
doi = {10.3390/plants13243502},
pmid = {39771200},
issn = {2223-7747},
support = {APVV-21-0199//Slovak Research and Development Agency/ ; APVV-19-0183//Slovak Research and Development Agency/ ; APVV-20-0408//Slovak Research and Development Agency/ ; 1/0515/23//The Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; },
abstract = {Gap dynamics are driving many important processes in the development of temperate forest ecosystems. What remains largely unknown is how often the regeneration processes initialized by endogenous mortality of dominant and co-dominant canopy trees take place. We conducted a study in the high mountain forests of the Central Western Carpathians, naturally dominated by the Norway spruce. Based on the repeated forest inventories in two localities, we quantified the structure and amount of deadwood, as well as the associated mortality of standing dead canopy trees. We determined the basic specific gravity of wood and anatomical changes in the initial phase of wood decomposition. The approach for estimating the rate of gap formation and the number of canopy trees per unit area needed for intentional gap formation was formulated based on residence time analysis of three localities. The initial phase of gap formation (standing dead tree in the first decay class) had a narrow range of residence values, with a 90-95% probability that gap age was less than 10 or 13 years. Correspondingly, a relatively constant absolute number of 12 and 13 canopy spruce trees per hectare died standing in 10 years, with a mean diameter reaching 50-58 cm. Maximum diameters trees (70-80 cm) were represented by 1-4 stems per hectare. The values of the wood-specific gravity of standing trees were around 0.370-0.380 g.cm[-3], and varied from 0.302 to 0.523 g.cm[-3]. Microscopically, our results point out that gap formation is a continuous long-lasting process, starting while canopy trees are living. We observed early signs of wood degradation and bacteria, possibly associated with bark beetles, that induce a strong effect when attacking living trees with vigorous defenses. New information about the initial phase of gap formation has provided a basis for the objective proposal of intervals and intensities of interventions, designed to promote a diversified structure and the long-term ecological stability of the mountain spruce stands in changing climate conditions.},
}
@article {pmid39656924,
year = {2025},
author = {Bastian, FB and Cammarata, AB and Carsanaro, S and Detering, H and Huang, WT and Joye, S and Niknejad, A and Nyamari, M and Mendes de Farias, T and Moretti, S and Tzivanopoulou, M and Wollbrett, J and Robinson-Rechavi, M},
title = {Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D878-D885},
pmid = {39656924},
issn = {1362-4962},
support = {//University of Lausanne/ ; U01CA215010/GF/NIH HHS/United States ; //Service de la Sant&#xe9; Publique, Canton de Vaud/ ; U01 CA215010/CA/NCI NIH HHS/United States ; 31003A_173048/SNSF_/Swiss National Science Foundation/Switzerland ; 863410//Horizon 2020 - Research and Innovation Framework Programme/ ; //swissuniversities Programme Open Science/ ; //SIB Swiss Institute of Bioinformatics/ ; },
mesh = {Animals ; *Single-Cell Analysis/methods ; *RNA-Seq/methods ; *Software ; *Databases, Genetic ; Humans ; Internet ; Molecular Sequence Annotation ; Gene Expression Profiling/methods ; Data Curation ; Single-Cell Gene Expression Analysis ; },
abstract = {Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integrated and made comparable between species thanks to consistent data annotation and processing. In the past years, we have integrated single-cell RNA-sequencing expression data into Bgee through careful curation of public datasets in multiple species. We have fully integrated this new technology along with the wealth of other data existing in Bgee. As a result, Bgee can now provide one definitive answer all the way to the cell resolution about a gene's expression pattern, comparable between species. We have updated our programmatic access tools to adapt to these changes accordingly. We have introduced a new web interface, providing detailed access to our annotations and expression data. It enables users to retrieve data, e.g. for specific organs, cell types or developmental stages, and leverages ontology reasoning to build powerful queries. Finally, we have expanded our species count from 29 to 52, emphasizing fish species critical for vertebrate genome studies, species of agronomic and veterinary importance and nonhuman primates.},
}
@article {pmid39475188,
year = {2025},
author = {Kemmler, E and Lemfack, MC and Goede, A and Gallo, K and Toguem, SMT and Ahmed, W and Millberg, I and Preissner, S and Piechulla, B and Preissner, R},
title = {mVOC 4.0: a database of microbial volatiles.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D1692-D1696},
pmid = {39475188},
issn = {1362-4962},
support = {Pi153/36-1//German Research Foundation/ ; //University of Rostock/ ; 428445448//Food allergy and tolerance (FOOD@)/ ; },
mesh = {*Volatile Organic Compounds/metabolism/chemistry ; *Bacteria/metabolism/genetics ; Microbiota ; Metabolomics/methods ; Databases, Factual ; Humans ; Metabolome ; Terpenes/metabolism/chemistry ; Databases, Chemical ; },
abstract = {Metabolomic microbiome research has become an important topic for understanding agricultural, ecological as well as health correlations. Only the determination of both the non-volatile and the volatile organic compound (mVOC) production by microorganisms allows a holistic view for understanding the complete potential of metabolomes and metabolic capabilities of bacteria. In the recent past, more and more bacterial headspaces and culture media were analyzed, leading to an accumulation of about 3500 mVOCs in the updated mVOC 4.0 database, including compounds synthesized by the newly discovered non-canonical terpene pathway. Approximately 10% of all mVOCs can be assigned with a biological function, some mVOCs have the potential to impact agriculture in the future (e.g. eco-friendly pesticides) or animal and human health care. mVOC 4.0 offers various options for exploring extensively annotated mVOC data from different perspectives, including improved mass spectrometry matching. The mVOC 4.0 database includes literature searches with additional relevant keywords, making it the most up-to-date and comprehensive publicly available mVOC platform at: http://bioinformatics.charite.de/mvoc.},
}
@article {pmid39470715,
year = {2025},
author = {Miao, Z and Ren, Y and Tarabini, A and Yang, L and Li, H and Ye, C and Liti, G and Fischer, G and Li, J and Yue, JX},
title = {ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel.},
journal = {Nucleic acids research},
volume = {53},
number = {D1},
pages = {D852-D863},
pmid = {39470715},
issn = {1362-4962},
support = {32070592//National Natural Science Foundation of China/ ; 2022A1515010717//Guangdong Basic and Applied Basic Research Foundation/ ; 2019QN01Y183//Guangdong Pearl River Talents Program/ ; YTP-SYSUCC-0042//Sun Yat-sen University Cancer Center/ ; 24qnpy293//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Saccharomyces cerevisiae/genetics/metabolism ; *Genome, Fungal ; *Databases, Genetic ; *Genomics/methods ; Telomere/genetics ; Molecular Sequence Annotation ; Proteomics ; Multiomics ; },
abstract = {As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.},
}
@article {pmid39761773,
year = {2025},
author = {Banakar, SN and Karan, R and Prasanna Kumar, MK and Venkateshbabu, G and Harish, J and Patil, SS and Chandrashekar, BS and Mahesh, HB and Devanna, P and Manjunatha, C and Vamsidharreddy, N and Pallavi, KN and Sarangi, AN and Vaidya, K and Guru Murthy, DS},
title = {Unveiling Fusarium falciforme: Genome sequencing of a Novel wilt causing pathogen in Subabul (Leucaena leucocephala L.) in India.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107281},
doi = {10.1016/j.micpath.2025.107281},
pmid = {39761773},
issn = {1096-1208},
abstract = {Subabul (Leucaena leucocephala L.) is a leguminous species often referred to as the "miracle tree," it provides numerous ecosystem services and exhibits robust ecological characteristics. However, the infection caused by phytopathogenic fungi is poorly understood in Subabul. Therefore, this study provides comprehensive insights into the molecular and genomic characteristics of Fusarium falciforme, the causal agent of wilt disease in Subabul (Leucaena leucocephala). Pathogen isolation from infected samples, followed by morpho-molecular characterization through DNA sequencing of key markers (ITS, LSU, TEF1α) and phylogenetic analysis, confirmed the identity of F. falciforme. Host range analysis demonstrated the pathogen's ability to infect additional leguminous crops, including chickpea (Cicer arietinum) and soybean (Glycine max). A complete genome assembly revealed a genome size of 59.19 Mb, comprising 18,853 protein-coding genes. Comparative genomic analysis elucidated evolutionary relationships with other Fusarium species, while functional annotation identified critical virulence factors, such as polyketide synthases, ABC transporters, and secretory proteins, which facilitate host tissue invasion. These findings enhance the understanding of F. falciforme pathogenicity, enabling improved diagnostic tools and management strategies for controlling wilt disease in Subabul and related legumes.},
}
@article {pmid39761073,
year = {2025},
author = {Sangeetha, S and Sajeev, S and Hamza, MK and Shome, BR and Raisen, C and Holmes, MA and Sivaraman, GK},
title = {Whole-Genome Sequencing of Antimicrobial Resistant Klebsiella quasipneumoniae, a Novel Sequence Type 5655 from Retail Fish Market, Assam, India.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {},
doi = {10.1089/fpd.2023.0017},
pmid = {39761073},
issn = {1556-7125},
abstract = {Klebsiella quasipneumoniae is a recently described species that can be differentiated from Klebsiella pneumoniae. However, in clinical settings, they are frequently misidentified as K. pneumoniae. In this study, our objective was to conduct genomic characterization and bioinformatics analysis of K. quasipneumoniae subsp. quasipneumoniae (KpII-A) isolated from a sample obtained from a retail fish market in Assam, India. Notably, this particular isolate was identified as K. pneumoniae when identified using BD Pheonix™ M50 (BD Difco, USA). This represents a serious pitfall of conventional microbiological methods for distinguishing between K. pneumoniae and K. quasipneumoniae. In this connection, identifying differences in nuclear gene content is key to avoid misidentification. The isolate was confirmed to be KpII-A using species identification by Mash Screen and whole-genome sequencing by the Illumina platform. We report the draft genome sequence of this strain, comprising of 53 contigs with an average GC content of 58.11%. The annotation revealed 5,095 protein coding sequences, 69 tRNA genes, and 4 rRNA genes. The isolated strain acknowledges the presence of oqxA, oqxB, fosA, and blaOKP-A-3 antimicrobial resistance genes (ARGs). Additionally two phage genomes were detected in contigs 3 and 19 of the bacterial genome. Based on the multilocus sequence typing and genome sequencing, the isolate was identified as a novel sequence type, ST5655, within the species K. quasipneumoniae under the phylogroup KpII-A. The presence of antimicrobial resistance genes in KpII-A, isolated from retail fish samples, raises concerns regarding transmission across barriers in ecological niches and possible transmission to consumers. Given that fish may serve as a potential vehicle for ARG transmission, our findings are highly relevant and paramount to human health. Moreover, our study supports the robustness of the sequence-based microbial identification.},
}
@article {pmid39753746,
year = {2025},
author = {Allegretti, E and D'Innocenzo, G and Coco, MI},
title = {The Visual Integration of Semantic and Spatial Information of Objects in Naturalistic Scenes (VISIONS) database: attentional, conceptual, and perceptual norms.},
journal = {Behavior research methods},
volume = {57},
number = {1},
pages = {42},
pmid = {39753746},
issn = {1554-3528},
support = {PTDC/PSI-ESP/30958/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LISBOA-01-0145-FEDER-0309//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Humans ; *Semantics ; *Attention/physiology ; Female ; Adult ; Male ; Young Adult ; *Space Perception/physiology ; *Visual Perception/physiology ; Databases, Factual ; Eye-Tracking Technology ; Adolescent ; },
abstract = {The complex interplay between low- and high-level mechanisms governing our visual system can only be fully understood within ecologically valid naturalistic contexts. For this reason, in recent years, substantial efforts have been devoted to equipping the scientific community with datasets of realistic images normed on semantic or spatial features. Here, we introduce VISIONS, an extensive database of 1136 naturalistic scenes normed on a wide range of perceptual and conceptual norms by 185 English speakers across three levels of granularity: isolated object, whole scene, and object-in-scene. Each naturalistic scene contains a critical object systematically manipulated and normed regarding its semantic consistency (e.g., a toothbrush vs. a flashlight in a bathroom) and spatial position (i.e., left, right). Normative data are also available for low- (i.e., clarity, visual complexity) and high-level (i.e., name agreement, confidence, familiarity, prototypicality, manipulability) features of the critical object and its embedding scene context. Eye-tracking data during a free-viewing task further confirms the experimental validity of our manipulations while theoretically demonstrating that object semantics is acquired in extra-foveal vision and used to guide early overt attention. To our knowledge, VISIONS is the first database exhaustively covering norms about integrating objects in scenes and providing several perceptual and conceptual norms of the two as independently taken. We expect VISIONS to become an invaluable image dataset to examine and answer timely questions above and beyond vision science, where a diversity of perceptual, attentive, mnemonic, or linguistic processes could be explored as they develop, age, or become neuropathological.},
}
@article {pmid38979368,
year = {2024},
author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Gillies, RJ and Prasanna, P and Chen, C and Damaghi, M},
title = {Eco-evolutionary Guided Pathomics Analysis to Predict DCIS Upstaging.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38979368},
issn = {2692-8205},
support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA249016/CA/NCI NIH HHS/United States ; R01 CA272601/CA/NCI NIH HHS/United States ; U01 CA261841/CA/NCI NIH HHS/United States ; },
abstract = {Cancers evolve in a dynamic ecosystem. Thus, characterizing cancer's ecological dynamics is crucial to understanding cancer evolution and can lead to discovering novel biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts. In this study, we show that ecological habitat analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. First, we developed a novel eco-evolutionary designed approach to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, we identified cancer cells with metabolic phenotypes attributed to their habitat conditions, such as the expression of CA9 indicating hypoxia responding phenotype, and LAMP2b indicating the acid adaptation. Traditionally these markers have shown limited predictive capabilities for DCIS upstaging, if any. However, when analyzed from an ecological perspective, their power to differentiate between pure DCIS and upstaged DCIS increased significantly. Second, using eco-evolutionary guided computational and digital pathology techniques, we discovered distinct niches with spatial patterns of these biomarkers and used the distribution of such niches to predict patient upstaging. The niches patterns were characterized by pattern analysis of both cellular and spatial features. With a 5-fold validation on the biopsy cohort, we trained a random forest classifier to achieve the area under curve (AUC) of 0.74. Our results affirm the importance of using eco-evolutionary-designed approaches in biomarkers discovery studies in the era of digital pathology by demonstrating the role of tumor ecological habitats and niches.},
}
@article {pmid39753915,
year = {2025},
author = {Davidson, SC and Cagnacci, F and Newman, P and Dettki, H and Urbano, F and Desmet, P and Bajona, L and Bryant, E and Carneiro, APB and Dias, MP and Fujioka, E and Gambin, D and Hoenner, X and Hunter, C and Kato, A and Kot, CY and Kranstauber, B and Lam, CH and Lepage, D and Naik, H and Pye, JD and Sequeira, AMM and Tsontos, VM and van Loon, E and Vo, D and Rutz, C},
title = {Establishing bio-logging data collections as dynamic archives of animal life on Earth.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
pmid = {39753915},
issn = {2397-334X},
support = {80NSSC21K1182//National Aeronautics and Space Administration (NASA)/ ; Fellowship at Fondation Im&#xe9;RA//Institut de Recherche pour le D&#xe9;veloppement (French Research Institute for Development)/ ; CN00000033//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca (Ministry of Education, University and Research)/ ; LifeWatch//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; DP210103091//Department of Education and Training | Australian Research Council (ARC)/ ; GBMF9881//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; NGS-82515R-20//National Geographic Society/ ; },
abstract = {Rapid growth in bio-logging-the use of animal-borne electronic tags to document the movements, behaviour, physiology and environments of wildlife-offers opportunities to mitigate biodiversity threats and expand digital natural history archives. Here we present a vision to achieve such benefits by accounting for the heterogeneity inherent to bio-logging data and the concerns of those who collect and use them. First, we can enable data integration through standard vocabularies, transfer protocols and aggregation protocols, and drive their wide adoption. Second, we need to develop integrated data collections on standardized data platforms that support data preservation through public archiving and strategies that ensure long-term access. We outline pathways to reach these goals, highlighting the need for resources to govern community data standards and guide data mobilization efforts. We propose the launch of a community-led coordinating body and provide recommendations for how stakeholders-including government data centres, museums and those who fund, permit and publish bio-logging work-can support these efforts.},
}
@article {pmid39753264,
year = {2025},
author = {Aguirre Vergara, F and Pinker, I and Fischer, A and Seuring, T and Tichomirowa, MA and de Beaufort, C and Kamp, SM and Fagherazzi, G and Aguayo, GA},
title = {Readiness of adults with type 1 diabetes and diabetes caregivers for diabetes distress monitoring using a voice-based digital health solution: insights from the PsyVoice mixed methods study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e088424},
doi = {10.1136/bmjopen-2024-088424},
pmid = {39753264},
issn = {2044-6055},
abstract = {OBJECTIVES: Diabetes distress can negatively affect the well-being of individuals with type 1 diabetes (T1D). Voice-based (VB) technology can be used to develop inexpensive and ecological tools for managing diabetes distress. This study explored the competencies to engage with digital health services, needs and preferences of individuals with T1D or caring for a child with this condition regarding VB technology to inform the tailoring of a co-designed tool for supporting diabetes distress management.<br><br>DESIGN: We used a mixed methods design. We performed a qualitative reflexive thematic analysis of semistructured interviews of people living with T1D or caring for a child with T1D, complemented by quantitative analysis (descriptive statistics).<br><br>SETTING: 12 adults living with T1D who attended diabetes centres or cared for a child with this condition participated in semistructured interviews to collect opinions about voice technology. They also responded to three questionnaires on sociodemographics and diabetes management, diabetes distress and e-health literacy.<br><br>OUTCOME MEASURES: Main: Patient experiences and perceptions derived from the coded transcriptions of interview data. Secondary: Quantitative data generated from Socio-Demographic and Diabetes Management questionnaire; Problem Areas in Diabetes Scale and e-Health Literacy Questionnaire.<br><br>RESULTS: Five major themes were generated from the participants' interview responses: (1) Experience of T1D, (2) Barriers to VB technology use, (3) Facilitators of VB technology, (4) Expectations of VB technology management in T1D, (5) Role of healthcare professionals in implementing VB technology for T1D. Most participants expressed a favourable view of voice technology for diabetes distress management. Trust in technology and healthcare professionals emerged as the predominant sentiment, with participants' current device type impacting anticipated barriers to adopting new technologies.<br><br>CONCLUSION: The results highlighted positive participant views towards VB technology. Device use, previous experience and health professional endorsement were influential facilitators of novel VB digital health solutions. Further research involving younger people with T1D could further contribute to the successful development of these tools.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov, NCT05517772.},
}
@article {pmid39749768,
year = {2025},
author = {Fifield, K and Veerakanjana, K and Hodsoll, J and Kuntsi, J and Tye, C and Simblett, S},
title = {Completion Rates of Smart Technology Ecological Momentary Assessment (EMA) in Populations With a Higher Likelihood of Cognitive Impairment: A Systematic Review and Meta-Analysis.},
journal = {Assessment},
volume = {},
number = {},
pages = {10731911241306364},
doi = {10.1177/10731911241306364},
pmid = {39749768},
issn = {1552-3489},
abstract = {Ecological Momentary Assessment using smartphone technology (smart EMA) has grown substantially over the last decade. However, little is known about the factors associated with completion rates in populations who have a higher likelihood of cognitive impairment. A systematic review of Smart EMA studies in populations who have a higher likelihood of cognitive impairment was carried out (PROSPERO; ref no CRD42022375829). Smartphone EMA studies in neurological, neurodevelopmental and neurogenetic conditions were included. Six databases were searched, and bias was assessed using Egger's test. Completion rates and moderators were analyzed using meta-regression. Fifty-five cohorts were included with 18 cohorts reporting confirmed cognitive impairment. In the overall cohort, the completion rate was 74.4% and EMA protocol characteristics moderated completion rates. Participants with cognitive impairment had significantly lower completion rates compared with those without (p = .021). There were no significant moderators in the cognitive impairment group. Limitations included significant methodological issues in reporting of completion rates, sample characteristics, and associations with completion and dropout rates. These findings conclude that smart EMA is feasible for people with cognitive impairment. Future research should focus on the efficacy of using smart EMA within populations with cognitive impairment to develop an appropriate methodological evidence base.},
}
@article {pmid39747897,
year = {2025},
author = {Petrovic, M and Salovic, B and Tomic, A and Jesic-Petrovic, T and Matejic, A and Radovic, I and Babic, S and Korugic, A and Jelovac, D and Mikovic, N and Jakovljevic, S and Pelemis, S and Dimitrijevic, M and Milovanovic, J and Jotic, A and Trivic, A and Dimitrijevic, A and Bulatovic, S and Dudvarski, Z and Soldatovic, I and Ilic-Zivojinovic, J},
title = {Functional assessment of cancer therapy - head &amp; neck (FACT-HN) translation and validation in Serbian.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {298},
pmid = {39747897},
issn = {2045-2322},
mesh = {Humans ; *Head and Neck Neoplasms/therapy/psychology ; Male ; Serbia ; Female ; *Quality of Life ; Middle Aged ; *Psychometrics/methods ; Surveys and Questionnaires ; Aged ; Reproducibility of Results ; Adult ; Translations ; },
abstract = {This study aimed to translate and validate the Functional Assessment of Cancer Therapy - Head &amp; Neck (FACT-HN) in a Serbian-speaking population, assessing its psychometric properties and utility in evaluating the quality of life in head and neck cancer patients. The research focuses on determining the translated questionnaire's reliability, validity, and cultural relevance. A total of 106 Serbian-speaking head and neck cancer patients completed the translated FACT-HN, along with other validated instruments, including the EORTC QLQ-C30, EORTC QLQ-HN43, CES-D, and GAD-7. The translation followed a standard internationally accepted procedure. Psychometric analyses were conducted using confirmatory and exploratory factor analysis, Pearson correlations, and reliability measures such as Cronbach's alpha and intraclass correlation coefficients. The Serbian version of the FACT-HN showed excellent internal consistency across all subscales, with Cronbach's alpha ranging from 0.70 to 0.89. Confirmatory factor analysis confirmed the five-factor structure. Strong correlations were observed between the FACT-HN and other validated QoL measures, particularly with the EORTC QLQ-C30 and EORTC QLQ-HN43. Convergent validity was satisfactory for all components except the Social Well-Being component. The Serbian version of the FACT-HN is a valid and reliable tool for assessing the quality of life in head and neck cancer patients. It provides a comprehensive assessment of physical, social, emotional, and functional well-being, making it valuable for clinical and research applications in Serbian-speaking populations. Further research is needed to assess its sensitivity to longitudinal treatment-related changes.},
}
@article {pmid39747514,
year = {2025},
author = {Liu, X and Tan, Y and Dong, J and Wu, J and Wang, X and Sun, Z},
title = {Assessing habitat selection parameters of Arabica coffee using BWM and BCM methods based on GIS.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {8},
pmid = {39747514},
issn = {2045-2322},
support = {51979133//National Natural Science Foundation of China/ ; 202301AS070030//Yunnan Fundamental Research Projects/ ; 202302AE090024//Yunnan Major Science and Technology Special Plan/ ; },
mesh = {*Ecosystem ; *Geographic Information Systems ; *Coffea/growth &amp; development ; China ; Coffee ; Climate ; Decision Making ; Conservation of Natural Resources/methods ; Soil/chemistry ; },
abstract = {Arabica coffee, as one of the world's three native coffee species, requires rational planning for its growing areas to ensure ecological and sustainable agricultural development. This study aims to establish a decision-making framework using Geographic Information Systems (GIS) and Multi-Criteria Decision-Making (MCDM), with a focus on assessing the habitat suitability of Arabica coffee in Yunnan Province, China. The impacts of climate, topography, soil, and socio-economic factors were considered by selecting 13 criteria through correlation analysis. Indicator weights were determined using the Best-Worst Method (BWM), while weighted processing was conducted using the Base-Criterion Method (BCM). Sensitivity analysis was performed to verify the accuracy and stability of the model. Additionally, several decision models were evaluated to investigate regionalizing Arabica coffee habitats in Yunnan. The results highlighted that minimum temperature during the coldest month is crucial for evaluation purposes. The BWM-GIS model identified suitable areas comprising 13.55% of the total area as most suitable, 27.46% as suitable, and 59.00% as unsuitable, whereas corresponding values for the BCM-GIS model were 9.97%, 30.43%, and 59.59%. Despite employing different decision-making methods, both models yielded similar and consistent results. The suitable areas mainly encompass Dehong, Pu'er, Lincang, Xishuangbanna, Baoshan, southern Chuxiong, eastern Honghe, southern Yuxi, and parts of Wenshan. BWM-GIS achieved an area under curve (AUC) value of 0.891, while BCM-GIS obtained an AUC value of 0.890, indicating the stability and reliability of the models. Among them, the evaluation process of BCM-GIS was simpler and more realistic. Therefore, it has high feasibility and practical value in practical application. The findings from this study provide a significant scientific foundation for optimizing Yunnan Province.},
}
@article {pmid39373541,
year = {2025},
author = {Zuo, YW and Quan, MH and Liu, GH and Zhang, X and Long, NN and You, SQ and Peng, Y and Deng, HP},
title = {Multi-Omics Analysis Reveals Molecular Responses of Alkaloid Content Variations in Lycoris aurea Across Different Locations.},
journal = {Plant, cell &amp; environment},
volume = {48},
number = {2},
pages = {953-964},
doi = {10.1111/pce.15187},
pmid = {39373541},
issn = {1365-3040},
support = {//This study was supported by General Program of the Chongqing Natural Science Foundation and National Natural Science Foundation of China./ ; },
mesh = {*Lycoris/metabolism/genetics ; *Alkaloids/metabolism ; Gene Expression Regulation, Plant ; Metabolomics ; Transcriptome ; Soil Microbiology ; Protein Interaction Maps ; Gene Expression Profiling ; Photosynthesis ; Metabolome ; Genes, Plant ; Multiomics ; },
abstract = {Lycoris aurea, celebrated for its visually striking flowers and significant medicinal value due to the presence of alkaloids such as lycorine and galanthamine, has intricate yet poorly understood regulatory mechanisms. This study provides a detailed examination of the transcriptomic, metabolomic and ecological dynamics of L. aurea, aiming to elucidate the underlying molecular mechanisms of alkaloid biosynthesis. Our comparative analysis across different ecological settings highlighted key genes involved in alkaloid biosynthesis, such as genes encoding aldehyde dehydrogenase and norbelladine 4'-O-methyltransferase, which were distinctively increased in the high alkaloids-producing group. We identified a total of 6871 differentially expressed genes and 915 metabolites involved in pathways like terpenoid backbone biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis. Protein interaction network analysis revealed significant upregulation of photosynthesis, photosystem and photosynthetic membrane pathways in the alkaloids-producing region. Furthermore, our research delineated the interactions among soil microbial communities, genes and plant and soil biochemical properties, noting that bacterial populations correlate with soil properties that favour the activation of metabolic pathways essential for alkaloid production. Collectively, this study advances our understanding of the genetic and metabolic alkaloid biosynthesis pathways in L. aurea, shedding light on the complex interactions that govern alkaloid production.},
}
@article {pmid39746011,
year = {2025},
author = {Wohltjen, S and Colón, YI and Zhu, Z and Miller, K and Huang, WC and Mutlu, B and Li, Y and Niedenthal, PM},
title = {Uniting theory and data: the promise and challenge of creating an honest model of facial expression.},
journal = {Cognition &amp; emotion},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/02699931.2024.2446945},
pmid = {39746011},
issn = {1464-0600},
abstract = {People routinely use facial expressions to communicate successfully and to regulate other's behaviour, yet modelling the form and meaning of these facial behaviours has proven surprisingly complex. One reason for this difficulty may lie in an over-reliance on the assumptions inherent in existing theories of facial expression - specifically that (1) there is a putative set of facial expressions that signal an internal state of emotion, (2) patterns of facial movement have been empirically linked to the prototypical emotions in this set, and (3) static, non-social, posed images from convenience samples are adequate to validate the first two assumptions. These assumptions have guided the creation of datasets, which are then used to train unrepresentative computational models of facial expression. In this article, we discuss existing theories of facial expression and review how they have shaped current facial expression recognition tools. We then discuss the resources that are available to help researchers build a more ecologically valid model of facial expressions.},
}
@article {pmid39736019,
year = {2024},
author = {Kobzeva, K and Ivenkov, M and Gromov, R and Bushueva, O},
title = {HSP90 Family Members, Their Regulators and Ischemic Stroke Risk: A Comprehensive Molecular-Genetics and Bioinformatics Analysis.},
journal = {Frontiers in bioscience (Scholar edition)},
volume = {16},
number = {4},
pages = {19},
doi = {10.31083/j.fbs1604019},
pmid = {39736019},
issn = {1945-0524},
support = {22-15-00288//Russian Science Foundation/ ; },
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *HSP90 Heat-Shock Proteins/genetics/metabolism ; *Ischemic Stroke/genetics ; Male ; Female ; Middle Aged ; *Computational Biology ; Aged ; *Genetic Predisposition to Disease ; Russia/epidemiology ; Risk Factors ; Case-Control Studies ; Heat Shock Transcription Factors/genetics/metabolism ; },
abstract = {BACKGROUND: Disruptions in proteostasis are recognized as key drivers in cerebro- and cardiovascular disease progression. Heat shock proteins (HSPs), essential for maintaining protein stability and cellular homeostasis, are pivotal in neuroperotection. Consequently, deepening the understanding the role of HSPs in ischemic stroke (IS) risk is crucial for identifying novel therapeutic targets and advancing neuroprotective strategies.<br><br>AIM: Our objective was to examine the potential correlation between single nucleotide polymorphisms (SNPs) in genes that encode members of the Heat shock protein 90 (HSP90), small heat shock proteins (HSPB), and heat shock factors (HSF) families, and the risk and clinical characteristics of IS.<br><br>METHODS: 953 IS patients and 1265 controls from Central Russia were genotyped for nine SNPs in genes encoding HSP90AA1, HSFs, and HSPBs using the MassArray-4 system and probe-based polymerase chain reaction (PCR).<br><br>RESULTS: In smokers, SNP rs1133026 HSPB8 increased the risk of IS (risk allele A, odds ratio (OR) = 1.43, 95% Confidence Interval (CI) 1.02-2.02, p = 0.035), and rs556439 HSF2 increased the brain infarct size (risk allele A, p = 0.02). In non-smokers, SNPs rs4279640 HSF1 (protective allele T, OR = 0.58, 95% CI 0.37-0.92, p = 0.02) and rs4264324 HSP90AA1 (protective allele C, OR = 0.11, 95% CI 0.01-0.78, p = 0.001) lowered the risk of recurrent stroke; SNP rs7303637 HSPB8 increased the age of onset of IS (protective allele T, p = 0.04). In patients with body mass index (BMI) &#x2265;25, SNPs rs556439 HSF2 (risk allele A, OR = 1.33, 95% CI 1.04-1.69, p = 0.02) and rs549302 HSF2 (risk allele G, OR = 1.34, 95% CI 1.02-1.75, p = 0.03) were linked to a higher risk of IS.<br><br>CONCLUSIONS: The primary molecular mechanisms through which the studied SNPs contribute to IS pathogenesis were found to be the regulation of cell death, inflammatory and oxidative stress responses.},
}
@article {pmid39730727,
year = {2024},
author = {Kato, H},
title = {Daily walking time effects of the opening of a multifunctional facility "ONIKURU" using propensity score matching and GPS tracking techniques.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {31047},
pmid = {39730727},
issn = {2045-2322},
support = {24K17421//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; Female ; *Walking/physiology ; Male ; Adult ; *Geographic Information Systems ; *Propensity Score ; Middle Aged ; Young Adult ; Exercise/physiology ; Adolescent ; Environment Design ; Time Factors ; Smartphone ; },
abstract = {Urban design focused on improving walkability has received attention as a method of increasing physical activity among the population. However, only a few studies have examined the effect of walking time of opening multifunctional facilities as an architecture-scale intervention. This study aimed to clarify the effect of opening a multifunctional facility on residents' daily walking time. In addition, this study analyzed the gender and age subgroups. The natural experiment was conducted using the case of the Ibaraki City Cultural and Childcare Complex "ONIKURU," a public multifunctional facility. This study used GPS-trajectory data based on GPS tracking techniques, which is anonymized location data for smartphone users. The causal relationship was analyzed using propensity score matching and difference-in-differences analysis. The results showed that the opening of ONIKURU significantly increased the average walking time of visitors to 3.165 [- 1.697, 8.027] min/day compared with that of non-visitors. Specifically, visitors' average daily walking time improved to a level comparable to that of non-visitors after the opening of ONIKURU. In addition, opening ONIKURU significantly increased female young adults' average walking time to 3.385 [- 4.906, 11.676] min/day. Therefore, this study provides theoretical contributions to a health-promoting built environment significantly affecting walking at an architecture-scale intervention.},
}
@article {pmid39729740,
year = {2024},
author = {Gupta, AK and Ravikumar, K and Gopal, V and Begum, N and Tabassum, and Sangeetha, S and Narendran, P and Shankar, D},
title = {A trans-disciplinary agro-ecology strategy to grow medicinal plants.},
journal = {Journal of Ayurveda and integrative medicine},
volume = {16},
number = {1},
pages = {100985},
doi = {10.1016/j.jaim.2024.100985},
pmid = {39729740},
issn = {0975-9476},
abstract = {The scope of the emerging field of Ayurvedic-biology visualized thus far is confined to studies on dimensions pertaining to clinical and experimental pharmacology, basic trans-disciplinary science and drug design. However, given the multiple facets of classical Ayurveda knowledge system, its application in the field of organic agriculture perhaps also needs to be urgently explored. The urgency is due to the growing public acceptance of Ayurveda as a preferred clinical choice for well-being and disease management. The turnover of the sector across manufacturing and health services is estimated to be around Rs.1,00,000 crores per annum. Medicinal plants today and in the coming decade will therefore be required in large volumes and given that their applications are solely for enhancing health of humans, livestock (Pashu Ayurveda) and crops (Vriksh Ayurveda), it is imperative that they be cultivated in an organic manner employing the fusion of best available inter-cultural knowledge. The Ayurvedic subjects relevant for organic agriculture are Desh vichar, Dravya guna Shastra and Vriksh Ayurveda. From the perspective of modern biology subjects like soil micro biome, genetics, plant physiology and the natural geographical distribution of species are relevant. It must be stated at the very outset that this article is largely theoretical. While experiments in Vriksh Ayurveda have been attempted on a small scale, the fusion of Ayurveda and biology for improving organic agriculture of medicinal plants has thus far not been systematically explored.},
}
@article {pmid39727132,
year = {2024},
author = {Xin, PY and Tian, T and Zhang, ML and Han, WZ and Song, YT},
title = {[Assessment of habitat quality changes and driving factors in Jilin Province based on InVEST model and geodetector].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {10},
pages = {2853-2860},
doi = {10.13287/j.1001-9332.202410.026},
pmid = {39727132},
issn = {1001-9332},
mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; *Models, Theoretical ; Environmental Monitoring ; Forests ; Trees/growth &amp; development ; Geographic Information Systems ; },
abstract = {Jilin Province is an important ecological security barrier in Northeast China as it is located at the junction of the Northeast forest belts and the northern sand prevention belts. In recent years, Jilin Province has actively carried out ecological protection and restoration projects, resulting in a continuous improvement trend for the overall ecological environment. However, the evolution patterns and mechanisms of habitat quality are largely unkown. We applied the InVEST model and geographic detector method to analyze the changes in habitat quality and evaluate the main driving factors from 2000 to 2020. The results showed that the average habitat quality in Jilin Province showed a slight downward trend, and that the spatial heterogeneity characteristics of habitat quality in east and west gradually increased. The degree of habitat degradation presented a single nuclear radiation pattern centered on Changchun City. Vegetation factors and terrain factors were the first and secondary causes of spatial heterogeneity of habitat quality, respectively. The average habitat quality within the eco-redline of Jilin Province was showing an increasing trend year by year, which was consistent with the overall distribution of regions with extremely high habitat quality levels. There was a local spatial dislocation (the phenomenon of extremely high habitat quality levels not within the eco-redline) in the eastern part of Jilin Province. Our results could provide reference basis for ecosystem protection and the spatial pattern optimization.},
}
@article {pmid39727130,
year = {2024},
author = {Jia, J and Su, X and Zhang, J and Lu, CL and Zhang, MY and Li, X and Dong, YG and Ren, HC},
title = {[Land use changes and driving forces of landslide area in Tongwei County, Gansu Province, Northwest China from 1985 to 2020.].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {10},
pages = {2833-2841},
doi = {10.13287/j.1001-9332.202410.020},
pmid = {39727130},
issn = {1001-9332},
mesh = {China ; *Landslides ; *Conservation of Natural Resources ; *Crops, Agricultural/growth &amp; development ; Ecosystem ; Trees/growth &amp; development ; Forests ; Grassland ; Environmental Monitoring/methods ; Disasters ; Geographic Information Systems ; Poaceae/growth &amp; development ; },
abstract = {Accurately analyzing the type of land use and change characteristics of disaster damage in landslide areas is of great significance to scientifically promote the optimization of regional land use pattern and disaster prevention and mitigation. We analyzed the characteristic parameters of landslides as well as the characteristics and driving factors of land use change from 1985 to 2020 in Tongwei County, Gansu Province, using ALOS DEM data and 1985-2020 land use data, GIS spatial analysis, land-use dynamic attitude, transfer matrix, and Geodetector. The results showed that a total of 1012 landslide samples were identified, characterized by medium elevation, gentle gradient, low elevation difference, short length, and small size. During 1985-2020, landslide area land use types were cropland, woodland, grassland, bare land and impervious surface, dominated by grassland and cropland. During 2015-2020, each category of single land use dynamic attitude reached the largest, with the value of cropland, grassland, woodland, bare land, and the combined land use being 3.1%, 3.0%, 10.9%, 20.0%, 1.5%, respectively. During the study period, land use change was dominated by cropland and grassland, with a total reduction of 4.39 km[2] in cultivated land area, which was converted into grassland and forest. There was no change in bare land and impervious surfaces. We investigated the driving factors of land use change across 2000-2005 and 2015-2020. Slope and normalized difference vegetation index had a stronger explanatory power for land use change during 2000-2005, while slope, population density and total population had a stronger explanatory power during 2015-2020. The land use mode of regional individual landslide tended to be unified, and the increase of grassland enhanced the vegetation cover of the region. The findings would provide a scientific basis for the development and reuse of disaster damaged land and ecological restoration.},
}
@article {pmid39720717,
year = {2024},
author = {Luo, Z and Zhou, F and Jiang, S and Huang, J and Yang, L and Yang, Q and Shi, J and Li, E and Ma, Z and Li, Y},
title = {Immune and physiological responses in Penaeus monodon to ammonia-N stress: a multi-omics approach.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1510887},
pmid = {39720717},
issn = {1664-3224},
mesh = {Animals ; *Penaeidae/immunology ; *Ammonia/metabolism ; *Stress, Physiological/immunology ; *Oxidative Stress ; Transcriptome ; Metabolomics ; Immunity, Innate ; Gene Expression Profiling ; Nitrogen/metabolism ; Aquaculture ; Biomarkers ; Hepatopancreas/immunology/metabolism ; Multiomics ; },
abstract = {Ammonia-N stress is a significant environmental factor that adversely affects the health and productivity of aquaculture species. This study investigates the effects of ammonia-N stress on the shrimp Penaeus monodon through a combination of biochemical, histological, transcriptomic, and metabolomic analyses. Shrimp were exposed to ammonia-N stress for 12 and 96 hours, and key markers of oxidative stress, nitrogen metabolism, immune response, and overall health were assessed. The results showed that prolonged ammonia-N exposure causes significant hepatopancreatic damage, including atrophy and deformation. Transcriptomic analysis revealed significant changes in gene expression related to apoptosis, immune response, and key metabolic pathways, with particular emphasis on the disruption of innate immune signaling and defense mechanisms. Metabolomic analysis identified disruptions in nucleotide turnover, antioxidant defenses, and fundamental metabolic processes. These findings suggest that ammonia-N stress induces a multifaceted stress response in shrimp, involving oxidative stress, immune activation, and metabolic disturbances. Understanding these immune-related and metabolic mechanisms provides valuable insights into the molecular responses of crustaceans to environmental stress, laying the foundation for assessing the ecological risk of ammonia-N and identifying potential immunological biomarkers for monitoring and mitigating its adverse effects in aquaculture systems.},
}
@article {pmid39719706,
year = {2024},
author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ},
title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100725},
doi = {10.1016/j.xgen.2024.100725},
pmid = {39719706},
issn = {2666-979X},
abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.},
}
@article {pmid39718830,
year = {2024},
author = {Kicsiny, R and Hufnagel, L and Lóczi, L and Székely, L and Varga, Z},
title = {Modeling the Mutation and Competition of Certain Nutrient-Producing Protocells by Means of Specific Turing Machines.},
journal = {Artificial life},
volume = {},
number = {},
pages = {1-29},
doi = {10.1162/artl_a_00463},
pmid = {39718830},
issn = {1530-9185},
abstract = {It is very important to model the behavior of protocells as basic lifelike artificial organisms more and more accurately from the level of genomes to the level of populations. A better understanding of basic protocell communities may help us in describing more complex ecological systems accurately. In this article, we propose a new comprehensive, bilevel mathematical model of a community of three protocell species (one generalist and two specialists). The aim is to achieve a model that is as basic/fundamental as possible while already displaying mutation, selection, and complex population dynamics phenomena (like competitive exclusion and keystone species). At the microlevel of genetic codes, the protocells and their mutations are modeled with Turing machines (TMs). The specialists arise from the generalist by means of mutation. Then the species are put into a common habitat, where, at the macrolevel of populations, they have to compete for the available nutrients, a part of which they themselves can produce. Because of different kinds of mutations, the running times of the species as TMs (algorithms) are different. This feature is passed on to the macrolevel as different reproduction times. At the macrolevel, a discrete-time dynamic model describes the competition. The model displays complex lifelike behavior known from population ecology, including the so-called competitive exclusion principle and the effect of keystone species. In future works, the bilevel model will have a good chance of serving as a simple and useful tool for studying more lifelike phenomena (like evolution) in their pure/abstract form.},
}
@article {pmid39717656,
year = {2024},
author = {Nguyen, TTT and de A Santiago, ALCM and Hallsworth, JE and Cordeiro, TRL and Voigt, K and Kirk, PM and Crous, PW and Júnior, MAM and Elsztein, C and Lee, HB},
title = {New Mucorales from opposite ends of the world.},
journal = {Studies in mycology},
volume = {109},
number = {},
pages = {273-321},
pmid = {39717656},
issn = {0166-0616},
abstract = {The Mucorales is a group of ancient fungi with global distribution. In the current study we accessed mucoralean fungi isolated from two countries on opposite sides of the Earth and in different hemispheres: South Korea and Brazil. Mucorales isolates were obtained from freshwater, soil, invertebrates, and fruit seeds and identified using phenotypic techniques combined with the DNA sequence data. These analyses revealed 15 new species including one that we affiliated to a newly proposed genus, Neofennellomyces. Names proposed for these 15 new species are Absidia cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, A. tarda, A. variiprojecta, A. variispora, Backusella varians, Mucor albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and Neofennellomyces jeongsukae. Of these new species, 12 were isolated from South Korea: A. cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, B. varians, M. albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and N. jeongsukae, and three from Brazil: A. tarda, A. variiprojecta, and A. variispora. Niche specificity of these fungi is discussed including newly recorded invertebrate hosts and a new geographic distribution for species of Backusella, Circinella, Cunninghamella, and Mucor. Given these findings, we provide an inventory of Mucorales. Taxonomic novelties: New genus: Neofennellomyces Hyang B. Lee &amp; T.T.T. Nguyen. New species: Absidia cheongyangensis Hyang B. Lee &amp; T.T.T. Nguyen, Absidia fluvii Hyang B. Lee, A.L. Santiago, P.M. Kirk, K. Voigt &amp; T.T.T. Nguyen, Absidia kunryangriensis Hyang B. Lee &amp; T.T.T. Nguyen, Absidia paracylindrospora Hyang B. Lee &amp; T.T.T. Nguyen, Absidia tarda T.R.L. Cordeiro, Hyang B. Lee &amp; A.L. Santiago, Absidia variiprojecta T.R.L. Cordeiro &amp; A.L. Santiago, Absidia variispora T.R.L. Cordeiro &amp; A.L. Santiago, Backusella varians Hyang B. Lee &amp; T.T.T. Nguyen, Mucor aurantiacus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor cryophilus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor albicolonia Hyang B. Lee &amp; T.T.T. Nguyen, Mucor glutinatus Hyang B. Lee &amp; T.T.T. Nguyen, Mucor paraorantomantidis Hyang B. Lee &amp; T.T.T. Nguyen, Mucor timomeni Hyang B. Lee &amp; T.T.T. Nguyen, Neofennellomyces jeongsukae Hyang B. Lee &amp; T.T.T. Nguyen. Citation: Nguyen TTT, de A. Santiago ALCM, Hallsworth JE, Cordeiro TRL, Voigt K, Kirk PM, Crous PW, Júnior MAM, Elsztein C, Lee HB (2024). New Mucorales from opposite ends of the world. Studies in Mycology 109: 273-321. doi: 10.3114/sim.2024.109.04.},
}
@article {pmid39717508,
year = {2025},
author = {Wang, T and Campbell, C and Stockdale, AJ and Todd, S and McIntyre, K and Frankland, A and Jaworski, J and Glampson, B and Papadimitriou, D and Mercuri, L and Mayer, E and Jones, CR and Salih, H and Roadknight, G and Little, S and Noble, T and Várnai, KA and Davis, C and Heinson, AI and George, M and Borca, F and English, L and Romão, L and Ramlakhan, D and , and Woods, K and Davies, J and Nastouli, E and Khakoo, SI and Gelson, W and Cooke, GS and Barnes, E and Matthews, PC},
title = {Distinct virologic trajectories in chronic hepatitis B identify heterogeneity in response to nucleos(t)ide analogue therapy.},
journal = {JHEP reports : innovation in hepatology},
volume = {7},
number = {1},
pages = {101229},
pmid = {39717508},
issn = {2589-5559},
abstract = {BACKGROUND &amp; AIMS: The dynamics of HBV viral load (VL) in patients with chronic hepatitis B (CHB) on nucleos(t)ide analogue (NA) treatment and its relationship with liver disease are poorly understood. We aimed to study longitudinal VL patterns and their associations with CHB clinical outcomes.<br><br>METHODS: Utilising large scale, routinely collected electronic health records from six centres in England, collated by the National Institute for Health and Care Research Health Informatics Collaborative (NIHR HIC), we applied latent class mixed models to investigate VL trajectory patterns in adults receiving NA treatment. We assessed associations of VL trajectory with alanine transaminase, and with liver fibrosis/cirrhosis.<br><br>RESULTS: We retrieved data from 1,885 adults on NA treatment (median follow-up 6.2 years, IQR 3.7-9.3 years), with 21,691 VL measurements (median 10 per patient, IQR 5-17). Five VL classes were identified from the derivation cohort (n&#xa0;= 1,367, discrimination: 0.93, entropy: 0.90): class 1 'long term suppression' (n&#xa0;= 827, 60.5%), class 2 'timely virological suppression' (n&#xa0;= 254, 18.6%), class 3 'persistent moderate viraemia' (n&#xa0;= 140, 10.2%), class 4 'persistent high-level viraemia' (n&#xa0;= 44, 3.2%), and class 5 'slow virological suppression' (n&#xa0;= 102, 7.5%). The model demonstrated a discrimination of 0.93 and entropy of 0.88 for the validation cohort (n&#xa0;= 518). Alanine transaminase decreased variably over time in VL-suppressed groups (classes 1, 2, 5; all p <0.001), but did not significantly improve in those with persistent viraemia (classes 3, 4). Patients in class 5 had twofold increased hazards of fibrosis/cirrhosis compared with class 1 (adjusted hazard ratio, 2.00; 95% CI, 1.33-3.02).<br><br>CONCLUSIONS: Heterogeneity exists in virological response to NA therapy in CHB patients, with over 20% showing potentially suboptimal responses. Slow virological suppression is associated with liver disease progression.<br><br>IMPACT AND IMPLICATIONS: Treatment recommendations for people living with chronic hepatitis B virus (HBV) infection are becoming less stringent, meaning that more of the population will be eligible to receive therapy with nucleos(t)ide analogue agents. We explored outcomes of HBV treatment in a large UK dataset, describing different responses to treatment, and showing that the viral load is not completely suppressed after 1 year in about one in five cases, associated with an increased risk of liver complications. As treatment is rolled out more widely, patients and clinicians need to be aware of the potential for incomplete virologic responses. The findings can support the identification of high-risk individuals, improve early fibrosis and cirrhosis prediction, guide monitoring and preventive interventions, and support public health elimination goals.},
}
@article {pmid39716198,
year = {2024},
author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R},
title = {Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {20},
number = {1},
pages = {108},
pmid = {39716198},
issn = {1746-4269},
mesh = {*Fisheries ; Philippines ; *Ethnobotany ; Humans ; *Knowledge ; *Conservation of Natural Resources ; *Lakes ; Ecosystem ; Fishes ; Animals ; Ecology ; Female ; Male ; Middle Aged ; Adult ; Plants ; },
abstract = {BACKGROUND: Ethnobotanical knowledge about plant roles in fisheries is crucial for sustainable resource management. Local ecological knowledge helps understand dynamics of the lake ecosystem. Fishers use plants based on availability and characteristics while adapting to the changes in the environment. Studying fishery related uses of plants and algae and the challenges interconnected with them from local perspectives can provide insights into their beneficial uses and impacts to the ecosystem.<br><br>METHODS: The study investigates the botanical knowledge of three fishing villages in Laguna Lake or Laguna de Bay (LB), Philippines, including Buhangin, Sampiruhan, and Mabato-Azufre, each with varying degrees of industrialization. The ethnobotanical study, which gathered 27 interviews between June 2022 and July 2024, included plant collection with the help of local collaborators, including local fishers as research guides.<br><br>RESULTS: Fishers in LB highlighted positive and negative plant-fishing interactions. The most frequently mentioned plant applications were fish habitat and fish hiding places. Fish food, spawning sites, conservation, and a number of challenges such as navigational concerns and aquaculture fish deaths had been previously reported in local use reports. The remaining observations provide new insights into plant-fishing interactions, including indicators of food quality and food sources for fish, the decrease in the action of waves, and how plants help in improving the quality of the water.<br><br>CONCLUSION: These results highlight that the knowledge of fishers regarding the ecosystem in which they conduct their fishing activities provides baseline information about the positive and negative relationships between plants and fishing activities in the region, which is vital for further understanding its biodiversity and ecosystem interactions. It is crucial to consider fisher knowledge and involve them as equal partners in conservation efforts of LB.},
}
@article {pmid39716000,
year = {2025},
author = {Chunduri, JR and Sagar, SP},
title = {Insect Brain Proteomics: A Case Study of Periplaneta americana.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2884},
number = {},
pages = {99-118},
pmid = {39716000},
issn = {1940-6029},
mesh = {Animals ; *Periplaneta/metabolism ; *Proteomics/methods ; *Brain/metabolism ; *Insect Proteins/metabolism/analysis ; *Proteome ; Chromatography, Liquid/methods ; Mass Spectrometry/methods ; Computational Biology/methods ; },
abstract = {Insects are known invertebrate species with economic, ecological, pathological, and medicinal value, as well as closely associated with human populations. Entomophagy and entomotherapy are future promising prospects largely attributable to the abundant availability, high protein content, and climatic sustainability of insects. In particular, the insect brain is an important system with a secluded, compact, and protective exoskeleton. It is immunologically privileged and capable of producing a robust immune response against pathogens. It is also a source of materials that initiate key activity throughout the body. Proteomic interrogation of Periplaneta americana enables understanding the role of this insect in the fields of food and pharmacology. Proximate analyses of P. americana highlights its richness in proteins. Here we perform a simple proteomic analysis to study the brain proteome of P. americana. The processes applied during the study include gel-based isolation and separation of proteins, followed by NanoLC-MS (Orbitrap) analyses and bioinformatic interrogation of the data. The results demonstrated that this insect proteome comprises antimicrobial proteins, allergens, and proteins required for metabolic processes.},
}
@article {pmid39713561,
year = {2024},
author = {Blair, ME and Noguera-Urbano, EA and Ochoa-Quintero, JM and Paz, A and Lopez-Gallego, C and Echeverry-Galvis, M&#xc1; and Zuloaga, J and Rodríguez, P and Lemus-Mejia, L and Ersts, P and López-Lozano, DF and Aiello-Lammens, ME and Arango, HM and Buitrago, L and Chang Triguero, S and Cruz-Rodríguez, CA and Díaz-Nieto, JF and Escobar, D and Grisales-Betancur, V and Johnson, BA and Kass, JM and Londoño-Murcia, MC and Merow, C and Muñoz-Rodríguez, CJ and Olaya-Rodríguez, MH and Parra, JL and Pinilla-Buitrago, GE and Roach, NS and Rojas-Soto, O and Roncancio-Duque, N and Suárez-Valencia, E and Urbina-Cardona, JN and Velásquez-Tibatá, J and Zapata-Martinez, CA and Anderson, RP},
title = {Software codesign between end users and developers to enhance utility for biodiversity conservation.},
journal = {Bioscience},
volume = {74},
number = {12},
pages = {867-873},
pmid = {39713561},
issn = {0006-3568},
abstract = {Creating software tools that address the needs of a wide range of decision-makers requires the inclusion of differing perspectives throughout the development process. Software tools for biodiversity conservation often fall short in this regard, partly because broad decision-maker needs may exceed the toolkits of single research groups or even institutions. We show that participatory, collaborative codesign enhances the utility of software tools for better decision-making in biodiversity conservation planning, as demonstrated by our experiences developing a set of integrated tools in Colombia. Specifically, we undertook an interdisciplinary, multi-institutional collaboration of ecological modelers, software engineers, and a diverse profile of potential end users, including decision-makers, conservation practitioners, and biodiversity experts. We leveraged and modified common paradigms of software production, including codesign and agile development, to facilitate collaboration through all stages (including conceptualization, development, testing, and feedback) to ensure the accessibility and applicability of the new tools to inform decision-making for biodiversity conservation planning.},
}
@article {pmid39710433,
year = {2024},
author = {Yuan, H and Hicks, P and Ahmadian, M and Johnson, KA and Valtadoros, L and Krishnan, A},
title = {Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
pmid = {39710433},
issn = {1477-4054},
support = {2328140//National Science Foundation/ ; },
mesh = {*Metadata ; *Natural Language Processing ; *Machine Learning ; Humans ; Computational Biology/methods ; Proteomics/methods ; Vocabulary, Controlled ; },
abstract = {Reusing massive collections of publicly available biomedical data can significantly impact knowledge discovery. However, these public samples and studies are typically described using unstructured plain text, hindering the findability and further reuse of the data. To combat this problem, we propose txt2onto 2.0, a general-purpose method based on natural language processing and machine learning for annotating biomedical unstructured metadata to controlled vocabularies of diseases and tissues. Compared to the previous version (txt2onto 1.0), which uses numerical embeddings as features, this new version uses words as features, resulting in improved interpretability and performance, especially when few positive training instances are available. Txt2onto 2.0 uses embeddings from a large language model during prediction to deal with unseen-yet-relevant words related to each disease and tissue term being predicted from the input text, thereby explaining the basis of every annotation. We demonstrate the generalizability of txt2onto 2.0 by accurately predicting disease annotations for studies from independent datasets, using proteomics and clinical trials as examples. Overall, our approach can annotate biomedical text regardless of experimental types or sources. Code, data, and trained models are available at https://github.com/krishnanlab/txt2onto2.0.},
}
@article {pmid39709508,
year = {2024},
author = {De Wint, FC and Nicholson, S and Koid, QQ and Zahra, S and Chestney-Claassen, G and Seelan, JSS and Xie, J and Xing, S and Fayle, TM and Haelewaters, D},
title = {Introducing a global database of entomopathogenic fungi and their host associations.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1418},
pmid = {39709508},
issn = {2052-4463},
support = {2023 Student Mobility Grant to F.C.D.W.//EC | Erasmus+/ ; Senior Postdoctoral Fellowship 1206024N to D.H.//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
mesh = {*Insecta/microbiology ; Animals ; *Databases, Factual ; *Hypocreales ; Host Specificity ; Biodiversity ; },
abstract = {Pathogens significantly influence natural and agricultural ecosystems, playing a crucial role in the regulation of species populations and maintaining biodiversity. Entomopathogenic fungi (EF), particularly within the Hypocreales order, exemplify understudied pathogens that infect insects and other arthropods globally. Despite their ecological importance, comprehensive data on EF host specificity and geographical distribution are lacking. To address this, we present EntomoFun 1.0, an open-access database centralizing global records of EF-insect associations in Hypocreales. This database includes 1,791 records detailing EF species, insect host taxa, countries of occurrence, life stages of hosts, and information sources. EntomoFun 1.0 is constructed based on 600 literature sources, as well as herbarium specimens of the Royal Botanical Gardens, Kew. This database is intended to test hypotheses, identify knowledge gaps, and stimulate future research. Contents of the EntomoFun 1.0 database are visualized with a global map, taxonomic chart, bipartite community network, and graphs.},
}
@article {pmid39709502,
year = {2024},
author = {Jakobsson, M and Mohammad, R and Karlsson, M and Salas-Romero, S and Vacek, F and Heinze, F and Bringensparr, C and Castro, CF and Johnson, P and Kinney, J and Cardigos, S and Bogonko, M and Accettella, D and Amblas, D and An, L and Bohan, A and Brandt, A and Bünz, S and Canals, M and Casamor, JL and Coakley, B and Cornish, N and Danielson, S and Demarte, M and Di Franco, D and Dickson, ML and Dorschel, B and Dowdeswell, JA and Dreutter, S and Fremand, AC and Hall, JK and Hally, B and Holland, D and Hong, JK and Ivaldi, R and Knutz, PC and Krawczyk, DW and Kristofferson, Y and Lastras, G and Leck, C and Lucchi, RG and Masetti, G and Morlighem, M and Muchowski, J and Nielsen, T and Noormets, R and Plaza-Faverola, A and Prescott, MM and Purser, A and Rasmussen, TL and Rebesco, M and Rignot, E and Rysgaard, S and Silyakova, A and Snoeijs-Leijonmalm, P and Sørensen, A and Straneo, F and Sutherland, DA and Tate, AJ and Travaglini, P and Trenholm, N and van Wijk, E and Wallace, L and Willis, JK and Wood, M and Zimmermann, M and Zinglersen, KB and Mayer, L},
title = {The International Bathymetric Chart of the Arctic Ocean Version 5.0.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1420},
pmid = {39709502},
issn = {2052-4463},
abstract = {Knowledge about seafloor depth, or bathymetry, is crucial for various marine activities, including scientific research, offshore industry, safety of navigation, and ocean exploration. Mapping the central Arctic Ocean is challenging due to the presence of perennial sea ice, which limits data collection to icebreakers, submarines, and drifting ice stations. The International Bathymetric Chart of the Arctic Ocean (IBCAO) was initiated in 1997 with the goal of updating the Arctic Ocean bathymetric portrayal. The project team has since released four versions, each improving resolution and accuracy. Here, we present IBCAO Version 5.0, which offers a resolution four times as high as Version 4.0, with 100 × 100 m grid cells compared to 200 × 200 m. Over 25% of the Arctic Ocean is now mapped with individual depth soundings, based on a criterion that considers water depth. Version 5.0 also represents significant advancements in data compilation and computing techniques. Despite these improvements, challenges such as sea-ice cover and political dynamics still hinder comprehensive mapping.},
}
@article {pmid39707199,
year = {2024},
author = {Zhang, M and Sun, Y and Lan, Y and Cheng, L and Lv, Z and Han, M and Yang, L},
title = {Multiomics joint analysis reveals the potential mechanism of differences in the taproot thickening between cultivated ginseng and mountain-cultivated ginseng.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1228},
pmid = {39707199},
issn = {1471-2164},
support = {20230204001YY//the Key Research and Development Projects of Jilin Province Science and Technology Development Plan/ ; 20200504002YY//the Major Projects of Jilin Province Science and Technology Development Plan/ ; CARS-21//the National Modern Agricultural Industrial Technology System Fund Project/ ; },
mesh = {*Panax/genetics/growth &amp; development/metabolism ; *Plant Roots/genetics/growth &amp; development/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Transcriptome ; Metabolomics ; Starch/metabolism ; Sucrose/metabolism ; Phenotype ; Genomics ; Multiomics ; },
abstract = {Panax ginseng is an important medicinal plant in China and is classified into two types: cultivated ginseng (CFCG) and mountain-cultivated ginseng (MCG). The two types of genetic varieties are the same, but the growth environments and management practices are different, resulting in substantial differences in their taproot morphology. Currently, there is a paucity of research on the internal mechanisms that regulate the phenotypic differences between cultivated ginseng and mountain-cultivated ginseng. In this study, we explored the potential mechanisms underlying their phenotypic differences using transcriptomic and metabolomic techniques. The results indicate that the taproot thickening of CFCG was significantly greater than that of MCG. Compared with MCG-4, MCG-10, and MCG-18, the diameters of the taproots of CFCG-4 increased by 158.96, 81.57, and 43.21%, respectively. Additionally, the contents of sucrose and starch in the taproot, as well as TRA and DHZR, were markedly elevated. Transcriptome analysis revealed that compared with MCG of different age groups, genes associated with starch and sucrose metabolism pathways (PgSUS1, PgSPS1, PgSPS3, and PgglgC1) were significantly upregulated in CFCG-4, whereas genes involved in the phenylpropanoid biosynthesis pathway (PgPER3, PgPER51, and PgPER12) were significantly downregulated in CFCG-4. This imbalance in the metabolic pathways suggests that these genes play crucial roles in ginseng taproot thickening. PgbHLH130 and PgARF18 may be key regulators of transcriptional changes in these pathways. These findings elucidate the molecular mechanisms governing ginseng taproot thickening, and have important implications for enhancing the overall quality and value of ginseng.},
}
@article {pmid39703500,
year = {2024},
author = {Townsend, HA and Rosenberger, KJ and Vanderlinden, LA and Inamo, J and Zhang, F},
title = {Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1454263},
pmid = {39703500},
issn = {1664-3224},
mesh = {*Single-Cell Analysis/methods ; Humans ; *Genome-Wide Association Study ; Inflammation/genetics ; Arthritis, Rheumatoid/genetics/immunology ; Polymorphism, Single Nucleotide ; Genetic Predisposition to Disease ; Colitis, Ulcerative/genetics/immunology ; Algorithms ; Sequence Analysis, RNA/methods ; },
abstract = {BACKGROUND: Understanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.<br><br>METHODS: We present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. First, we applied and compared the results of three recent algorithms, based on pathways (scGWAS), single-cell disease scores (scDRS), or both (scPagwas), according to accuracy/sensitivity and interpretability. While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,173 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC). Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools' resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas. Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.<br><br>RESULTS: We first found that single-cell based tools scDRS and scPagwas called superior numbers of supported cell states that were overlooked by scGWAS. While scGWAS and scPagwas were advantageous for gene exploration, scDRS effectively accounted for batch effect and captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5' scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn's disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.},
}
@article {pmid39701966,
year = {2024},
author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L},
title = {Unraveling the ancient fungal DNA from the Iceman gut.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1225},
pmid = {39701966},
issn = {1471-2164},
mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; },
abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).<br><br>METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.<br><br>RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.<br><br>CONCLUSION: We suggest that &#xd6;tzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.},
}
@article {pmid39700981,
year = {2024},
author = {Wong, SY and Machado-de-Lima, NM and Wilkins, D and Zhang, E and Ferrari, BC},
title = {Fine-scale landscape heterogeneity drives microbial community structure at Robinson Ridge, East Antarctica.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {177964},
doi = {10.1016/j.scitotenv.2024.177964},
pmid = {39700981},
issn = {1879-1026},
abstract = {Life at Robinson Ridge, located in the Windmill Islands region of East Antarctica, is susceptible to a changing climate. At this site, responses of the vegetation communities and moss-beds have been well researched, but corresponding information for microbial counterparts is still lacking. To bridge this knowledge gap, we established baseline data for monitoring the environmental drivers shaping the soil microbial community on the local 'hillslope' scale. Using triplicate 300-m long transects encompassing a hillslope with wind-exposed arid soils near the top, and snowmelt-sustained-moss beds at the bottom, we assessed the fine-scale heterogeneity of the soil environmental and microbial properties. Moist, low-lying, and vegetated soils exhibited higher soil fertility and unique biodiversity, with taxa adapted to thrive in moist conditions (i.e., Tardigrada, Phragmoplastophyta, Chloroflexi) and those that have previously demonstrated strong specificity for moss species (i.e., Fibrobacterota, Mucoromycota and Cyanobacteria) dominating. In contrast, elevated soils with limited moisture and nutrients were dominated by metabolically diverse phyla like Actinobacteriota and Ascomycota. Significant differences in microbial communities were observed at both hillslope (50-300 m) and fine spatial scales, as small as 0.1 m. Vertical heterogeneity was observed with higher abundances of Cyanobacteria and micro-algae in surfaces compared to subsoil, potentially indicating early biocrust formation. Stochastic and deterministic processes governing phylogenetic assembly were linked to soil positional groups and microbial domains rather than soil depth. Gradient Forest modeling identified critical environmental thresholds, such as ammonia, manganese, and sulphur, responsible for drastic community changes following level alterations. This reinforces the existence of strong niche preferences and distinct distribution patterns within the local microbial communities. This study highlights the need for finer-scale investigations considering site topography to better understand the relationship between environmental drivers and local microbiota. Ultimately, these insights enable us to understand environmental drivers and predict Antarctic ecosystem responses, helping safeguard this fragile environment.},
}
@article {pmid39700412,
year = {2024},
author = {Duan, HN and Hearne, G and Polikar, R and Rosen, GL},
title = {The Naïve Bayes Classifier ++ for Metagenomic Taxonomic Classification-Query Evaluation.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae743},
pmid = {39700412},
issn = {1367-4811},
abstract = {MOTIVATION: This study examines the query performance of the NBC ++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC ++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.<br><br>RESULTS: NBC&#x2009;++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC&#x2009;++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC&#x2009;++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.<br><br>AVAILABILITY: Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online, and databases are available at Zenodo records #11657719 and #11643985.},
}
@article {pmid39695923,
year = {2024},
author = {Zhang, Z and Li, Q and Li, H and Wei, S and Yu, W and Peng, Z and Wei, F and Zhou, W},
title = {Integrative multi-omics analysis reveals the contribution of neoVTX genes to venom diversity of Synanceia verrucosa.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1210},
pmid = {39695923},
issn = {1471-2164},
support = {2023YFF1304900//Ministry of Science and Technology of the People's Republic of China/ ; 2024A1515013196//Science and Technology Department of Guangdong Province/ ; SLYJ2023B4004//Guangdong Forestry Administration/ ; GML2020GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; GML2022GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 32222014//National Natural Science Foundation of China/ ; 2021YFF0502804//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Transcriptome ; Fish Venoms/genetics/chemistry ; Genomics/methods ; Proteomics ; Proteome ; Alternative Splicing ; Fishes/genetics ; Phylogeny ; Gene Expression Profiling ; Multiomics ; },
abstract = {BACKGROUND: Animal venom systems are considered as valuable model for investigating the molecular mechanisms underlying phenotypic evolution. Stonefish are the most venomous and dangerous fish because of severe human envenomation and occasionally fatalities, whereas the genomic background of their venom has not been fully explored compared with that in other venomous animals.<br><br>RESULTS: In this study, we followed modern venomic pipelines to decode the Synanceia verrucosa venom components. A catalog of 478 toxin genes was annotated based on our assembled chromosome-level genome. Integrative analysis of the high-quality genome, the transcriptome of the venom gland, and the proteome of crude venom revealed mechanisms underlying the venom complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit genes were identified as the major source for the neoVTX protein production. Further isoform sequencing revealed massive alternative splicing events with a total of 411 isoforms demonstrated by the six genes, which further contributed to the venom diversity. We then characterized 12 dominantly expressed toxin genes in the venom gland, and 11 of which were evidenced to produce the venom protein components, with the neoVTX proteins as the most abundant. Other major venom proteins included a presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, and hyaluronidase. Besides, a few of highly abundant non-toxin proteins were also characterized and they were hypothesized to function in housekeeping or hemostasis maintaining roles in the venom gland. Notably, gastrotropin like non-toxin proteins were the second highest abundant proteins in the venom, which have not been reported in other venomous animals and contribute to the unique venom properties of S. verrucosa.<br><br>CONCLUSIONS: The results identified the major venom composition of S. verrucosa, and highlighted the contribution of neoVTX genes to the diversity of venom composition through tandem-duplication and alternative splicing. The diverse neoVTX proteins in the venom as lethal particles are important for understanding the adaptive evolution of S. verrucosa. Further functional studies are encouraged to exploit the venom components of S. verrucosa for pharmaceutical innovation.},
}
@article {pmid39695260,
year = {2024},
author = {Ma, X and Zheng, G and Xu, C and Moskal, LM and Gong, P and Guo, Q and Huang, H and Li, X and Liang, X and Pang, Y and Wang, C and Xie, H and Yu, B and Zhao, B and Zhou, Y},
title = {A global product of 150-m urban building height based on spaceborne lidar.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1387},
pmid = {39695260},
issn = {2052-4463},
support = {42171340//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Urban building height, as a fundamental 3D urban structural feature, has far-reaching applications. However, creating readily available datasets of recent urban building heights with fine spatial resolutions and global coverage remains a challenging task. Here, we provide a 150-m global urban building heights dataset around 2020 by combining the spaceborne lidar (Global Ecosystem Dynamics Investigation, GEDI), multi-sourced data (Landsat-8, Sentinel-2, and Sentinel-1), and topographic data. The validation results revealed that the GEDI-estimated building height samples were effective compared to the reference data (Pearson's r = 0.81, RMSE = 3.58 m). The mapping product also demonstrated good performance, as indicated by its strong correlation with the reference data (Pearson's r = 0.71, RMSE = 4.73 m). Compared with the currently existing datasets, it holds the ability to provide a spatial resolution (150 m) with a great level of inherent details about the spatial heterogeneity and flexibility of updating using the GEDI samples as inputs. This product will boost future urban studies across many fields, including environmental, ecological, and social sciences.},
}
@article {pmid39694720,
year = {2024},
author = {Reynolds, SA and Beery, S and Burgess, N and Burgman, M and Butchart, SHM and Cooke, SJ and Coomes, D and Danielsen, F and Di Minin, E and Durán, AP and Gassert, F and Hinsley, A and Jaffer, S and Jones, JPG and Li, BV and Mac Aodha, O and Madhavapeddy, A and O'Donnell, SAL and Oxbury, WM and Peck, L and Pettorelli, N and Rodríguez, JP and Shuckburgh, E and Strassburg, B and Yamashita, H and Miao, Z and Sutherland, WJ},
title = {The potential for AI to revolutionize conservation: a horizon scan.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2024.11.013},
pmid = {39694720},
issn = {1872-8383},
abstract = {Artificial Intelligence (AI) is an emerging tool that could be leveraged to identify the effective conservation solutions demanded by the urgent biodiversity crisis. We present the results of our horizon scan of AI applications likely to significantly benefit biological conservation. An international panel of conservation scientists and AI experts identified 21 key ideas. These included species recognition to uncover 'dark diversity', multimodal models to improve biodiversity loss predictions, monitoring wildlife trade, and addressing human-wildlife conflict. We consider the potential negative impacts of AI adoption, such as AI colonialism and loss of essential conservation skills, and suggest how the conservation field might adapt to harness the benefits of AI while mitigating its risks.},
}
@article {pmid39692459,
year = {2024},
author = {Shitindo, M},
title = {Interactions between wild pigs and the spread of disease.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39692459},
issn = {2050-084X},
mesh = {Animals ; *Animals, Wild ; Swine ; Swine Diseases ; Geographic Information Systems ; Humans ; },
abstract = {Tracking wild pigs with GPS devices reveals how their social interactions could influence the spread of disease, offering new strategies for protecting agriculture, wildlife, and human health.},
}
@article {pmid39691468,
year = {2024},
author = {Winders, S and Yoo, L and Heitkemper, M and Kamp, K},
title = {Multilevel Factors and Sleep in Adults With Inflammatory Bowel Disease: A Qualitative Study.},
journal = {Crohn's &amp; colitis 360},
volume = {6},
number = {4},
pages = {otae075},
pmid = {39691468},
issn = {2631-827X},
abstract = {BACKGROUND: This study aimed to describe the patient-reported factors that impact sleep among individuals with inflammatory bowel disease (IBD), aligning with the Social Ecological Model of Sleep. This addresses the gap in IBD sleep research, which predominantly focuses on individual-level factors and their impact on sleep.<br><br>METHODS: Adults (ages 18-65) with IBD were recruited online through ResearchMatch in June 2023. Participants filled out survey questions on their demographic characteristics, health history, sleep, and IBD-related symptoms. Content analysis was conducted on 2 open-ended questions about factors that impacted their sleep.<br><br>RESULTS: This analysis included 163 adults with IBD (M&#x2005;=&#x2005;39 years of age, 76.7% White, 91.4% non-Hispanic or Latino, 66.9% female, and 83.4% active IBD) who answered open-ended questions with comments about their sleep. Most participants indicated an individual-level factor impacted their sleep quality (85.3%, n&#x2005;=&#x2005;139), categorized into 5 subthemes: Mental health, health, behavior and choices, physiology, and attitudes. Additionally, participants (43.6%, n&#x2005;=&#x2005;71) mentioned social-level factors divided into 7 subthemes: Family, work, home, neighborhood, social network, and school. A smaller group of participants (17.2%, n&#x2005;=&#x2005;28) mentioned societal-level factors designated into 4 subthemes: Natural environment and geography, technology, 24/7 society, and economics.<br><br>CONCLUSIONS: This study highlights the need for tailored sleep interventions for those with IBD that consider not only disease activity but also mental health, family, work, and the natural environment. IBD clinics should prioritize sleep health using an interdisciplinary approach to holistically address the unique needs of those with IBD.},
}
@article {pmid39689854,
year = {2024},
author = {Radice, VZ and Hernández-Agreda, A and Pérez-Rosales, G and Booker, R and Bellworthy, J and Broadribb, M and Carpenter, GE and Diaz, C and Eckert, RJ and Foster, NL and Gijsbers, JC and Gress, E and Laverick, JH and Micaroni, V and Pierotti, M and Rouzé, H and Stevenson, A and Sturm, AB and Bongaerts, P},
title = {Recent trends and biases in mesophotic ecosystem research.},
journal = {Biology letters},
volume = {20},
number = {12},
pages = {20240465},
pmid = {39689854},
issn = {1744-957X},
mesh = {*Ecosystem ; Animals ; Oceans and Seas ; Research/trends ; Anthozoa/physiology ; Bias ; Databases, Factual ; },
abstract = {Mesophotic ecosystems (approx. 30-150 m) represent a significant proportion of the world's oceans yet have long remained understudied due to challenges in accessing these deeper depths. Owing to advances in underwater technologies and a growing scientific and management interest, there has been a major expansion in research of both (sub)tropical mesophotic coral ecosystems and temperate mesophotic ecosystems. Here, we characterize the recent global trends in mesophotic research through an updated release of the 'mesophotic.org' database (www.mesophotic.org) where we reviewed and catalogued 1500 scientific publications. In doing so, we shed light on four major research biases: a gross imbalance in (a) the geographical spread of research efforts, differences in (b) the focal depth range and (c) research fields associated with study organisms and research platforms, and (d) the lack of temporal studies. Overall, we are optimistic about the future of mesophotic research and hope that by highlighting current trends and imbalances, we can raise awareness and stimulate discussion on the future directions of this emerging field.},
}
@article {pmid39689059,
year = {2024},
author = {Bernadou, A and Jeanson, R},
title = {Randomness as a driver of inactivity in social groups.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012668},
pmid = {39689059},
issn = {1553-7358},
mesh = {Animals ; *Ants/physiology ; *Social Behavior ; Behavior, Animal/physiology ; Models, Biological ; Bees/physiology ; Computational Biology ; Computer Simulation ; Social Group ; },
abstract = {Social insects, such as ants and bees, are known for their highly efficient and structured colonies. Division of labour, in which each member of the colony has a specific role, is considered to be one major driver of their ecological success. However, empirical evidence has accumulated showing that many workers, sometimes more than half, remain idle in insect societies. Several hypotheses have been put forward to explain these patterns, but none provides a consensual explanation. Task specialisation exploits inter-individual variations, which are mainly influenced by genetic factors beyond the control of the colony. As a result, individuals may also differ in the efficiency with which they perform tasks. In this context, we aimed to test the hypothesis that colonies generate a large number of individuals in order to recruit only the most efficient to perform tasks, at the cost of producing and maintaining a fraction of workers that remain inactive. We developed a model to explore the conditions under which variations in the scaling of workers' production and maintenance costs, along with activity costs, allow colonies to sustain a fraction of inactive workers. We sampled individual performances according to different random distributions in order to simulate the variability associated with worker efficiency. Our results show that the inactivity of part of the workforce can be beneficial for a wide range of parameters if it allows colonies to select the most efficient workers. In decentralised systems such as insect societies, we suggest that inactivity is a by-product of the random processes associated with the generation of individuals whose performance levels cannot be controlled.},
}
@article {pmid39688289,
year = {2024},
author = {Bao, Y and Jia, F and Geng, Y and Song, G and Xu, R and Wang, H and Mu, Y and Tong, HHY and Zhang, F and Guo, J},
title = {Uncovering the Differed Susceptibility of Fusarium oxysporum (Fo32931 and FocII5) to Fungicide Phenamacril: From Computational and Experimental Perspectives.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c07865},
pmid = {39688289},
issn = {1520-5118},
abstract = {Fo32931 and FoCII5 are two subtypes of Fusarium oxysporum (Fo), a pathogenic filamentous fungus. Phenamacril (PHA), a Fusarium-specific fungicide that targets myosin I, exhibits significant hyphal growth inhibition in Fo32931 but shows weak resistance in FocII5, despite only two amino acid differences in the PHA-binding pocket of myosin I. In this study, we aim to elucidate the molecular basis for the differential sensitivity ofF. oxysporum myosin I variants (FoMyoI[32931] and FoMyoI[cII5]) to phenamacril through computational methods and biochemical validation. The results suggest that phenamacril functions as an allosteric inhibitor for FoMyoI[32931], inhibiting the large oscillation of the converter lever domain (CLD) upon ATP binding and promoting the opening of the outer cleft, further impairing protein function. PHA significantly reduced the coupling between the CLD, especially the converter, and the catalytic center, diminishing the response of the CLD to the motor domain in FoMyoI[32931]. From the residue mutation experiment, we found that the S418T substitution in FoMyoI[cII5] is the key to the reduced phenamacril sensitivity of FocII5. According to the microscale thermophoresis (MST) assay and pocket conformation analysis, the S418T mutation disturbs the orientation of pocket residues, especially Lys537, leading to a looser pocket and reduced interaction between Lys537 and phenamacril, which lowers the binding affinity of FoMyoI[cII5] for phenamacril. These findings provide deeper insights into the reasons for the lower sensitivity of FoCII5 to phenamacril from both molecular and structural perspectives and will also guide the design of novel inhibitors against resistant Fusarium spp., like FoCII5.},
}
@article {pmid39684926,
year = {2024},
author = {Liu, R and Zhang, P and Bai, J and Zhong, Z and Shan, Y and Cheng, Z and Zhang, Q and Guo, Q and Zhang, H and Zhang, B},
title = {Integrated Transcriptomic and Proteomic Analyses of Antler Growth and Ossification Mechanisms.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684926},
issn = {1422-0067},
support = {23CB063 and 24CE-BGS-09//Beijing Academy of Science and Technology Financial Support Projects/ ; },
mesh = {*Antlers/growth &amp; development/metabolism ; Animals ; *Osteogenesis/genetics ; *Deer/genetics/growth &amp; development ; *Transcriptome ; *Proteomics/methods ; Proteome/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; },
abstract = {Antlers are the sole mammalian organs capable of continuous regeneration. This distinctive feature has evolved into various biomedical models. Research on mechanisms of antler growth, development, and ossification provides valuable insights for limb regeneration, cartilage-related diseases, and cancer mechanisms. Here, ribonucleic acid sequencing (RNA-seq) and four-dimensional data-independent acquisition (4D DIA) technologies were employed to examine gene and protein expression differences among four tissue layers of the Chinese milu deer antler: reserve mesenchyme (RM), precartilage (PC), transition zone (TZ), cartilage (CA). Overall, 4611 differentially expressed genes (DEGs) and 2388 differentially expressed proteins (DEPs) were identified in the transcriptome and proteome, respectively. Among the 828 DEGs common to both omics approaches, genes from the collagen, integrin, and solute carrier families, and signaling molecules were emphasized for their roles in the regulation of antler growth, development, and ossification. Bioinformatics analysis revealed that in addition to being regulated by vascular and nerve regeneration pathways, antler growth and development are significantly influenced by numerous cancer-related signaling pathways. This indicates that antler growth mechanisms may be similar to those of cancer cell proliferation and development. This study lays a foundation for future research on the mechanisms underlying the rapid growth and ossification of antlers.},
}
@article {pmid39684378,
year = {2024},
author = {Zhang, KL and Leng, YN and Hao, RR and Zhang, WY and Li, HF and Chen, MX and Zhu, FY},
title = {Adaptation of High-Altitude Plants to Harsh Environments: Application of Phenotypic-Variation-Related Methods and Multi-Omics Techniques.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684378},
issn = {1422-0067},
support = {KYCX24_1376//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; 2023ZD0405602//STI 2030&#xff0d;Major Projects/ ; CX (21)2023//Jiangsu Agricultural Science and Technology Innovation Fund/ ; BK20240668//Basic Research Program of Jiangsu Province/ ; },
mesh = {*Altitude ; *Metabolomics/methods ; *Plants/metabolism/genetics ; *Proteomics/methods ; *Adaptation, Physiological ; *Genomics/methods ; *Phenotype ; Plant Physiological Phenomena ; Acclimatization ; Transcriptome ; Multiomics ; },
abstract = {High-altitude plants face extreme environments such as low temperature, low oxygen, low nutrient levels, and strong ultraviolet radiation, causing them to adopt complex adaptation mechanisms. Phenotypic variation is the core manifestation of ecological adaptation and evolution. Many plants have developed a series of adaptive strategies through long-term natural selection and evolution, enabling them to survive and reproduce under such harsh conditions. This article reviews the techniques and methods used in recent years to study the adaptive evolution of high-altitude plants, including transplantation techniques, genomics, transcriptomics, proteomics, and metabolomics techniques, and their applications in high-altitude plant adaptive evolution. Transplantation technology focuses on phenotypic variation, which refers to natural variations in morphological, physiological, and biochemical characteristics, exploring their key roles in nutrient utilization, photosynthesis optimization, and stress-resistance protection. Multiple omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revealed genes, regulatory pathways, and metabolic networks associated with phenotypic variations at the genetic and molecular levels. At the same time, the limitations and deficiencies of current technologies used to study plant adaptation to high-altitude environments were discussed. In addition, we propose future improvements to existing technologies and advocate for the integration of different technologies at multiple levels to study the molecular mechanisms of plant adaptation to high-altitude environments, thus providing insights for future research in this field.},
}
@article {pmid39683090,
year = {2024},
author = {Chaligava, O and Zinicovscaia, I and Peshkova, A and Yushin, N and Frontasyeva, M and Vergel, K and Nurkassimova, M and Cepoi, L},
title = {Major and Trace Airborne Elements and Ecological Risk Assessment: Georgia Moss Survey 2019-2023.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {23},
pages = {},
pmid = {39683090},
issn = {2223-7747},
abstract = {The study, carried out as part of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops, involved collecting 95 moss samples across the territory of Georgia during the period from 2019 to 2023. Primarily samples of Hypnum cupressiforme were selected, with supplementary samples of Abietinella abietina, Pleurozium schreberi, and Hylocomium splendens in cases of the former's absence. The content of 14 elements (Al, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, S, Sr, V, and Zn) was detected using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), while the Hg content was determined using a Direct Mercury Analyzer. To identify any relationships between chemical elements and to depict their sources, multivariate statistics was applied. Principal component analysis identified three main components: PC1 (geogenic, 43.4%), PC2 (anthropogenic, 13.3%), and PC3 (local anomalies, 8.5%). The results were compared with the first moss survey conducted in Georgia in the period from 2014 to 2017, offering insights into temporal trends of air quality. Utilizing GIS, a spatial map illustrating pollution levels across Georgia, based on the Pollution Load Index, was generated. The Potential Environmental Risk Index emphasized significant risks associated with mercury and cadmium at several locations. The study highlights the utility of moss biomonitoring in assessing air pollution and identifying hotspots of contamination. The findings from this study could be beneficial for future biomonitoring research in areas with varying physical and geographical conditions.},
}
@article {pmid39679384,
year = {2024},
author = {Khosravi, M and Mojtabaeian, SM and Sarvestani, MA},
title = {A Systematic Review on the Outcomes of Climate Change in the Middle-Eastern Countries: The Catastrophes of Yemen and Syria.},
journal = {Environmental health insights},
volume = {18},
number = {},
pages = {11786302241302270},
pmid = {39679384},
issn = {1178-6302},
abstract = {The Middle East is facing serious climate change challenges, rendering it as one of the most affected regions worldwide. This paper aimed to investigate the outcomes of climate change in the Middle East. In 2024, a qualitative study was conducted employing a methodology that integrated systematic review for data collection and thematic analysis for data analysis. Such integration of the approaches provided valuable insights into the findings within the literature in a comprehensive and categorized format. PubMed, Scopus, ProQuest, and the Cochrane Database of Systematic Reviews were searched for relevant studies published between 2000 and 2024. The quality of these studies was assessed using the AACODS (Accuracy, Coverage, Objectivity, Date, Significance) checklist. The data extracted from the included studies underwent a thematic analysis utilizing Braun and Clarke's methodology. After completing the screening process, a total of 93 papers were deemed suitable for inclusion in the study. The quality assessment of these selected studies demonstrated a notably high standard, particularly in terms of authority, accuracy, coverage, objectivity, and significance. Moreover, minimal levels of bias were observed within the included studies. Subsequent thematic analysis of the findings from the systematic review identified 6 overarching themes: "Human Health Outcomes," "Animal Health Outcomes," "Plant Health Outcomes," "Ecological Outcomes," "Economic Outcomes," and "Political Outcomes." The study revealed ecological outcomes as the most prevalent consequences of climate change in the Middle East, including alterations in habitat distribution, temperature increase, water scarcity, and more. The outcomes seemed to be interconnected, exacerbating each other. Yemen and Syria had faced severe consequences, leading to political unrest and humanitarian crises in which Yemen ranking among the most water-stressed nations globally, while Syria contending with millions of displaced individuals living in dire conditions.},
}
@article {pmid39675288,
year = {2024},
author = {Mu, X and Chen, C and Fan, Q and Zhang, W and Liu, F and Guo, J and Qi, W and Liu, H},
title = {Removal and ecological impact of sulfamethoxazole and N-acetyl sulfamethoxazole in mesocosmic wetlands dominated by submerged plants: Plant tolerance, microbial response, and nitrogen transformation.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178034},
doi = {10.1016/j.scitotenv.2024.178034},
pmid = {39675288},
issn = {1879-1026},
abstract = {Sulfamethoxazole (SMX) and its human metabolite N-acetylsulfamethoxazole (N-SMX) are frequently detected in aquatic environments, posing potential threats to freshwater ecosystem health. Constructed wetlands are pivotal for wastewater treatment, with plant species serving as key determinants of pollutant removal efficiency. In this study, wetlands dominated by three submerged plants (Myriophyllum verticillatum, Vallisneria spiralis, Hydrilla verticillata) were respectively constructed to investigate the removal of SMX and N-SMX, and the impact on wetland ecology regarding plant tolerance, microbial response, and nitrogen transformation. Results showed that wetlands removed N-SMX (82.3-99.8 %) more effectively than SMX (54.3-80.2 %), with the wetland dominated by Myriophyllum verticillatum showing the highest removal efficiency. However, high concentrations (5 mg/L) of SMX and N-SMX significantly reduced NH4[+]-N and TN removal (p < 0.05), accompanied by shifts in microbial communities, especially a decreased abundance of Proteobacteria and key nitrogen-transforming genes. A total of 22 different ARGs (antibiotic resistance genes) were detected. SMX significantly increased the relative abundance of sulfonamide resistance genes (sul1, sul2) (p < 0.05), while major denitrifying genera, such as Thiobacillus, which were not the primary hosts of these genes, showed a significant negative correlation with sul1 and sul2 (p < 0.05). This study provides a reference for ecological remediation of wetlands in response to antibiotic contamination.},
}
@article {pmid39656857,
year = {2024},
author = {Alvarado, M and Gómez-Navajas, JA and Blázquez-Muñoz, MT and Gómez-Molero, E and Fernández-Sánchez, S and Eraso, E and Munro, CA and Valentín, E and Mateo, E and de Groot, PWJ},
title = {The good, the bad, and the hazardous: comparative genomic analysis unveils cell wall features in the pathogen Candidozyma auris typical for both baker's yeast and Candida.},
journal = {FEMS yeast research},
volume = {24},
number = {},
pages = {},
pmid = {39656857},
issn = {1567-1364},
support = {PID2020-117983RB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; SBPLY/23/180225/000029//UCLM/ ; //European Regional Development Fund/ ; JDC2023-051226-I//European Social Fund Plus/ ; },
mesh = {*Cell Wall/metabolism ; *Saccharomyces cerevisiae/genetics/metabolism ; Computational Biology ; Genomics ; Candida auris/genetics/metabolism/drug effects ; beta-Glucans/metabolism ; Genome, Fungal ; Fungal Proteins/genetics/metabolism ; Glycosylphosphatidylinositols/metabolism/genetics ; Candida albicans/genetics/pathogenicity ; Candida/genetics/metabolism/pathogenicity ; },
abstract = {The drug-resistant pathogenic yeast Candidozyma auris (formerly named Candida auris) is considered a critical health problem of global importance. As the cell wall plays a crucial role in pathobiology, here we performed a detailed bioinformatic analysis of its biosynthesis in C. auris and related Candidozyma haemuli complex species using Candida albicans and Saccharomyces cerevisiae as references. Our data indicate that the cell wall architecture described for these reference yeasts is largely conserved in Candidozyma spp.; however, expansions or reductions in gene families point to subtle alterations, particularly with respect to β--1,3--glucan synthesis and remodeling, phosphomannosylation, β-mannosylation, and glycosylphosphatidylinositol (GPI) proteins. In several aspects, C. auris holds a position in between C. albicans and S. cerevisiae, consistent with being classified in a separate genus. Strikingly, among the identified putative GPI proteins in C. auris are adhesins typical for both Candida (Als and Hyr/Iff) and Saccharomyces (Flo11 and Flo5-like flocculins). Further, 26 putative C. auris GPI proteins lack homologs in Candida genus species. Phenotypic analysis of one such gene, QG37_05701, showed mild phenotypes implicating a role associated with cell wall β-1,3-glucan. Altogether, our study uncovered a wealth of information relevant for the pathogenicity of C. auris as well as targets for follow-up studies.},
}
@article {pmid39671449,
year = {2024},
author = {Celiker, E and Woodrow, C and Guadayol, &#xd2; and Davranoglou, LR and Schlepütz, CM and Mortimer, B and Taylor, GK and Humphries, S and Montealegre-Z, F},
title = {Mechanical network equivalence between the katydid and mammalian inner ears.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012641},
pmid = {39671449},
issn = {1553-7358},
mesh = {Animals ; *Ear, Inner/anatomy &amp; histology/physiology ; *Mammals/physiology ; *Hearing/physiology ; Computer Simulation ; Insecta/physiology ; Computational Biology ; Models, Biological ; Cochlea/physiology/anatomy &amp; histology ; X-Ray Microtomography ; },
abstract = {Mammalian hearing operates on three basic steps: 1) sound capturing, 2) impedance conversion, and 3) frequency analysis. While these canonical steps are vital for acoustic communication and survival in mammals, they are not unique to them. An equivalent mechanism has been described for katydids (Insecta), and it is unique to this group among invertebrates. The katydid inner ear resembles an uncoiled cochlea, and has a length less than 1 mm. Their inner ears contain the crista acustica, which holds tonotopically arranged sensory cells for frequency mapping via travelling waves. The crista acustica is located on a curved triangular surface formed by the dorsal wall of the ear canal. While empirical recordings show tonotopic vibrations in the katydid inner ear for frequency analysis, the biophysical mechanism leading to tonotopy remains elusive due to the small size and complexity of the hearing organ. In this study, robust numerical simulations are developed for an in silico investigation of this process. Simulations are based on the precise katydid inner ear geometry obtained by synchrotron-based micro-computed tomography, and empirically determined inner ear fluid properties for an accurate representation of the underlying mechanism. We demonstrate that the triangular structure below the hearing organ drives the tonotopy and travelling waves in the inner ear, and thus has an equivalent role to the mammalian basilar membrane. This reveals a stronger analogy between the inner ear basic mechanical networks of two organisms with ancient evolutionary differences and independent phylogenetic histories.},
}
@article {pmid39671336,
year = {2024},
author = {Karim, AAJ and Mahmud, MZ and Khan, R},
title = {Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012654},
pmid = {39671336},
issn = {1553-7358},
mesh = {Animals ; *Culicidae/classification ; *Deep Learning ; *Computational Biology/methods ; Entomology/methods ; Mosquito Vectors/classification ; Humans ; Algorithms ; Neural Networks, Computer ; },
abstract = {Mosquito-related diseases pose a significant threat to global public health, necessitating efficient and accurate mosquito classification for effective surveillance and control. This work presents an innovative approach to mosquito classification by leveraging state-of-the-art vision transformers and open-set learning techniques. A novel framework has been introduced that integrates Transformer-based deep learning models with comprehensive data augmentation and preprocessing methods, enabling robust and precise identification of ten mosquito species. The Swin Transformer model achieves the best performance for traditional closed-set learning with 99.60% accuracy and 0.996 F1 score. The lightweight MobileViT technique attains an almost equivalent accuracy of 98.90% with significantly reduced parameters and model complexities. Next, the applied deep learning models' adaptability and generalizability in a static environment have been enhanced by using new classes of data samples during the inference stage that have not been included in the training set. The proposed framework's ability to handle unseen classes like insects similar to mosquitoes, even humans, through open-set learning further enhances its practical applicability employing the OpenMax technique and Weibull distribution. The traditional CNN model, Xception, outperforms the latest transformer with higher accuracy and F1 score for open-set learning. The study's findings highlight the transformative potential of advanced deep-learning architectures in entomology, providing a strong groundwork for future research and development in mosquito surveillance and vector control. The implications of this work extend beyond mosquito classification, offering valuable insights for broader ecological and environmental monitoring applications.},
}
@article {pmid39670410,
year = {2025},
author = {Alipio, K and García-Colón, J and Boscarino, N and Fox, K},
title = {Indigenous Data Sovereignty, Circular Systems, and Solarpunk Solutions for a Sustainable Future.},
journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
volume = {30},
number = {},
pages = {717-733},
pmid = {39670410},
issn = {2335-6936},
mesh = {*Artificial Intelligence ; *Computational Biology ; Humans ; Cloud Computing/statistics &amp; numerical data ; Sustainable Development ; Indigenous Peoples/statistics &amp; numerical data ; Conservation of Natural Resources ; },
abstract = {Recent advancements in Artificial Intelligence (AI) and data center infrastructure have brought the global cloud computing market to the forefront of conversations about sustainability and energy use. Current policy and infrastructure for data centers prioritize economic gain and resource extraction, inherently unsustainable models which generate massive amounts of energy and heat waste. Our team proposes the formation of policy around earth-friendly computation practices rooted in Indigenous models of circular systems of sustainability. By looking to alternative systems of sustainability rooted in Indigenous values of aloha 'āina, or love for the land, we find examples of traditional ecological knowledge (TEK) that can be imagined alongside Solarpunk visions for a more sustainable future. One in which technology works with the environment, reusing electronic waste (e-waste) and improving data life cycles.},
}
@article {pmid39664868,
year = {2024},
author = {Boyes, D and Zilli, A and , and , and , and , and , and , and , },
title = {The genome sequence of the Grey Shoulder-knot, Lithophane ornitopus (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {214},
pmid = {39664868},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Lithophane ornitopus (the Grey Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 508.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,397 protein coding genes.},
}
@article {pmid39664717,
year = {2024},
author = {Baker, KS and Millerand, F},
title = {The Incremental Growth of Data Infrastructure in Ecology (1980-2020).},
journal = {Ecology and evolution},
volume = {14},
number = {12},
pages = {e70444},
pmid = {39664717},
issn = {2045-7758},
abstract = {After decades of growth, a research community's network information system and data repository were transformed to become a national data management office and a major element of data infrastructure for ecology and the environmental sciences. Developing functional data infrastructures is key to the support of ongoing Open Science and Open Data efforts. This example of data infrastructure growth contrasts with the top-down development typical of many digital initiatives. The trajectory of this network information system evolved within a collaborative, long-term ecological research community. This particular community is funded to conduct ecological research while collective data management is also carried out across its geographically dispersed study sites. From this longitudinal ethnography, we describe an Incremental Growth Model that includes a sequence of six relatively stable phases where each phase is initiated by a rapid response to a major pivotal event. Exploring these phases and the roles of data workers provides insight into major characteristics of digital growth. Further, a transformation in assumptions about data management is reported for each phase. Investigating the growth of a community information system over four decades as it becomes data infrastructure reveals details of its social, technical, and institutional dynamics. In addition to addressing how digital data infrastructure characteristics change, this study also considers when the growth of data infrastructure begins.},
}
@article {pmid39663400,
year = {2024},
author = {Carter, KR and Cavaleri, MA and Atkin, OK and Bahar, NHA and Cheesman, AW and Choury, Z and Crous, KY and Doughty, CE and Dusenge, ME and Ely, KS and Evans, JR and Fonseca da Silva, J and Mau, AC and Medlyn, BE and Meir, P and Norby, RJ and Read, J and Reed, SC and Reich, PB and Rogers, A and Serbin, SP and Slot, M and Schwartz, EC and Tribuzy, ES and Uddling, J and Vårhammar, A and Walker, AP and Winter, K and Wood, TE and Wu, J},
title = {Photosynthetic responses to temperature across the tropics: a meta-analytic approach.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcae206},
pmid = {39663400},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Tropical forests exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial biome. Yet, uncertainty in the projected carbon balance over the next century is roughly three-times greater for the tropics than other ecosystems. Our limited knowledge of tropical plant physiological responses, including photosynthetic, to climate change is a substantial source of uncertainty in our ability to forecast the global terrestrial carbon sink.<br><br>METHODS: We used a meta-analytic approach, focusing on tropical photosynthetic temperature responses, to address this knowledge gap. Our dataset, gleaned from 18 independent studies, included leaf-level light saturated photosynthetic (Asat) temperature responses from 108 woody species, with additional temperature parameters (35 species) and rates (250 species) of both maximum rates of electron transport (Jmax) and Rubisco carboxylation (Vcmax). We investigated how these parameters responded to mean annual temperature (MAT), temperature variability, aridity, and elevation, as well as also how responses differed among successional strategy, leaf habit, and light environment.<br><br>KEY RESULTS: Optimum temperatures for Asat (ToptA) and Jmax (ToptJ) increased with MAT but not for Vcmax (ToptV). Although photosynthetic rates were higher for "light" than "shaded" leaves, light conditions did not generate differences in temperature response parameters. ToptA did not differ with successional strategy, but early successional species had ~4 &#xb0;C wider thermal niches than mid/late species. Semi-deciduous species had ~1 &#xb0;C higher ToptA than broadleaf evergreen. Most global modeling efforts consider all tropical forests as a single "broadleaf evergreen" functional type, but our data show that tropical species with different leaf habits display distinct temperature responses that should be included in modeling efforts.<br><br>CONCLUSIONS: This novel research will inform modeling efforts to quantify tropical ecosystem carbon cycling and provide more accurate representations of how these key ecosystems will respond to altered temperature patterns in the face of climate warming.},
}
@article {pmid39660611,
year = {2024},
author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V},
title = {Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39660611},
issn = {2050-084X},
support = {R01 AG075283/AG/NIA NIH HHS/United States ; 457837076//Deutsche Forschungsgemeinschaft/ ; W81XWH2020013//Congressionally Directed Medical Research Programs/ ; 1R01AG075283-01A1/NH/NIH HHS/United States ; },
mesh = {*Bacteriocins/pharmacology/genetics/metabolism ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Gram-Negative Bacteria/drug effects/genetics ; Plant Diseases/microbiology ; Microbial Sensitivity Tests ; },
abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered 12 previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella. Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e., Acinetobacter baumannii or Pseudomonas aeruginosa, providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.},
}
@article {pmid39657789,
year = {2024},
author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, &#xc1;T and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1115},
pmid = {39657789},
issn = {1362-4962},
support = {KICH1.LWV04.21.013//NWO/ ; 101000392//Horizon 2020/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; 547394769//German Research Foundation/ ; //University of Sydney/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; IM230100154//Australian Research Council Industry Fellowship/ ; //Hans Fischer Society/ ; //UK Government Department for Environment, Food &amp; Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 101072485//Horizon Europe Marie Sk&#x142;odowska-Curie/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; 101117891-MeDiSyn//ERC Starting/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; //Department of Biotechnology/ ; //National Agri-Food Biotechnology Institute/ ; 101087181//EU/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; 2021YFA0909500//National Key Research and Development Program of China/ ; 32170080//National Natural Science Foundation of China/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 21K06336//KAKENHI/ ; 21/07038-0//S&#xe3;o Paulo Research Foundation/ ; VI.Veni.202.130//NWO Talent/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 222676//USDA Evans-Allen Research/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; //University of Illinois/ ; 802736//European Union Horizon 2020/ ; 735867//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; //NWO Merian/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101066127//European Union/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; K12 GM068524/GM/NIGMS NIH HHS/United States ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Alexander von Humboldt-Stiftung/ ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; NE/T010959/1//Signals in the Soil/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; 495740318//German Research Foundation/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; 101072485//European Union's Horizon/ ; //European Regional Development Fund/ ; 802736//European Union's Horizon 2020/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; //Swiss Federal Government/ ; PS00349981//Fulbright/ ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; DM60066//Italian Ministry of Research/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; NA22NOS4200050//NERRS/ ; BB/V005723/2//BBSRC/ ; 1347411//CONAHCYT/ ; T32GM136583/NH/NIH HHS/United States ; 101130799//European Union's Horizon/ ; CFB 2.0//Novo Nordisk Foundation/ ; //Basic Science Research Program/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; //Werner Siemens Foundation/ ; OCENW.XL21.XL21.088//NWO-XL/ ; DNRF137//Danish National Research Foundation/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; CBET-2032243//U.S. National Science Foundation/ ; //Delta Stewardship Council Delta Science Program/ ; //European Union's Horizon 2020 Research/ ; 852600//Innovation Program ERC St/ ; 101072485//European Union's Horizon Europe/ ; //Conahcyt Mexico International PhD Studentship/ ; //Strathclyde University Global Research Scholarship/ ; 3141-00013A//Innovation Fund Denmark/ ; K445/2022//Leibniz Association/ ; 23/01956-2//S&#xe3;o Paulo Research Foundation/ ; DGE 2241144//NSF GRFP/ ; 024.004.014//MiCRop Consortium/ ; CF22-1239//Carlsberg Foundation/ ; 102022750//SINTEF/ ; 102029187//SEP AGREE/ ; 102024676-14//POS BIOINFO 2024/ ; 101106349//Marie Sklodowska-Curie/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //National Research Fund of Ukraine/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //German Academic Scholarship Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; //Department of Biotechnology/ ; //University Grants Commission/ ; PROYEXCEL_00012//Spanish "Junta de Andaluc&#xed;a"/ ; GNT2021638//National Health and Medical Research Council/ ; DP230102668//Australian Research Council Discovery Project/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 865738/ERC_/European Research Council/International ; T32-GM136629//Chemical-Biology Interface Training/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 757173//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; //Horizon Europe Marie Sk&#x142;odowska-Curie Actions Postdoctoral Fellowship/ ; 101099528//European Innovation Council/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; //Swedish Pharmaceutical Society PostDoc/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; //Saarland University/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; AUFF-E-2022-9-42//AUFF/ ; 101055020-COMMUNITY//ERC Advanced/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; 10.55776/P 34036//Austrian Science Fund/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; },
abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}
@article {pmid39653494,
year = {2024},
author = {Lee, HB and Nguyen, TTT and Noh, SJ and Kim, DH and Kang, KH and Kim, SJ and Kirk, PM and Avery, SV and Medina, A and Hallsworth, JE},
title = {Aspergillus ullungdoensis sp. nov., Penicillium jeongsukae sp. nov., and other fungi from Korea.},
journal = {Fungal biology},
volume = {128},
number = {8 Pt B},
pages = {2479-2492},
doi = {10.1016/j.funbio.2024.05.014},
pmid = {39653494},
issn = {1878-6146},
mesh = {Republic of Korea ; *Phylogeny ; *Penicillium/isolation &amp; purification/classification/genetics ; DNA, Fungal/genetics ; Soil Microbiology ; Aspergillus/isolation &amp; purification/classification/genetics ; Sequence Analysis, DNA ; Cluster Analysis ; DNA, Ribosomal Spacer/genetics/chemistry ; },
abstract = {Eurotiales fungi are thought to be distributed worldwide but there is a paucity of information about their occurrence on diverse substrates or hosts and at specific localities. Some of the Eurotiales, including Aspergillus and Penicillium species, produce an array of secondary metabolites of use for agricultural, medicinal, and pharmaceutical applications. Here, we carried out a survey of the Eurotiales in South Korea, focusing on soil, freshwater, and plants (dried persimmon fruits and seeds of Perilla frutescens, known commonly as shiso). We obtained 11 species that-based on morphology, physiology, and multi-locus (ITS, BenA, CaM, and RPB2) phylogenetic analyses-include two new species, Aspergillus ullungdoensis sp. nov. and Penicillium jeongsukae sp. nov., and nine species that were known, but previously not described in South Korea, Aspergillus aculeatinus, Aspergillus aurantiacoflavus, Aspergillus croceiaffinis, Aspergillus pseudoviridinutans, Aspergillus uvarum, Penicillium ferraniaense, Penicillium glaucoroseum, Penicillium sajarovii, and one, Penicillium charlesii, that was isolated from previously unknown host, woodlouse (Porcellio scaber). We believe that biodiversity survey and identifying new species can contribute to set a baseline for future changes in the context of humanitarian crises such as climate change.},
}
@article {pmid39652754,
year = {2024},
author = {Pillay, R and Watson, JEM and Hansen, AJ and Burns, P and Virnig, ALS and Supples, C and Armenteras, D and González-Del-Pliego, P and Aragon-Osejo, J and A Jantz, P and Ervin, J and Goetz, SJ and Venter, O},
title = {Global rarity of high-integrity tropical rainforests for threatened and declining terrestrial vertebrates.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {51},
pages = {e2413325121},
pmid = {39652754},
issn = {1091-6490},
support = {NNX17AG51G/NASA/NASA/United States ; NNL15AA03/NASA/NASA/United States ; 80NSSC18K0338/NASA/NASA/United States ; },
mesh = {*Rainforest ; Animals ; *Biodiversity ; *Vertebrates/physiology ; *Conservation of Natural Resources/methods ; Tropical Climate ; Endangered Species ; Ecosystem ; },
abstract = {Structurally intact native forests free from major human pressures are vitally important habitats for the persistence of forest biodiversity. However, the extent of such high-integrity forest habitats remaining for biodiversity is unknown. Here, we quantify the amount of high-integrity tropical rainforests, as a fraction of total forest cover, within the geographic ranges of 16,396 species of terrestrial vertebrates worldwide. We found up to 90% of the humid tropical ranges of forest-dependent vertebrates was encompassed by forest cover. Concerningly, however, merely 25% of these remaining rainforests are of high integrity. Forest-dependent species that are threatened and declining and species with small geographic ranges have disproportionately low proportions of high-integrity forest habitat left. Our work brings much needed attention to the poor quality of much of the forest estate remaining for biodiversity across the humid tropics. The targeted preservation of the world's remaining high-integrity tropical rainforests that are currently unprotected is a critical conservation priority that may help alleviate the biodiversity crisis in these hyperdiverse and irreplaceable ecosystems. Enhanced efforts worldwide to preserve tropical rainforest integrity are essential to meet the targets of the Convention on Biological Diversity's 2022 Kunming-Montreal Global Biodiversity Framework which aims to achieve near zero loss of high biodiversity importance areas (including ecosystems of high integrity) by 2030.},
}
@article {pmid39649625,
year = {2024},
author = {Boyes, D and Crowley, LC and Hutchinson, F and Wawman, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the Broad-barred Knot-horn, Acrobasis consociella (Hübner, 1813).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {429},
pmid = {39649625},
issn = {2398-502X},
abstract = {We present a genome assembly from one female Acrobasis consociella (the Broad-barred Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 598.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length.},
}
@article {pmid39647412,
year = {2024},
author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD},
title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.},
journal = {Environment international},
volume = {194},
number = {},
pages = {109155},
doi = {10.1016/j.envint.2024.109155},
pmid = {39647412},
issn = {1873-6750},
mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; },
abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.},
}
@article {pmid39644634,
year = {2024},
author = {Xie, Y and Guo, J and Fan, Q and Huang, S and Qi, W and Cao, X and Peng, J and Chen, Y and Chen, M},
title = {High-density sampling reveals the occurrence, levels and transport flux of 15 polycyclic aromatic hydrocarbons derivatives (PAHs-d) along the Yangtze River.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {177907},
doi = {10.1016/j.scitotenv.2024.177907},
pmid = {39644634},
issn = {1879-1026},
abstract = {Polycyclic aromatic hydrocarbons derivatives (PAHs-d) have higher toxicity levels compared to its parent polycyclic aromatic hydrocarbons (PPAHs). Their partitioning in different media and large-scale transport patterns in rivers remain largely unknown. This study investigated the occurrence of 15 PAHs-d and 19 PPAHs in water and suspended particulate matter (SPM) of the Yangtze River between 2019 and 2020. The range of Σ15PAHs-d concentrations was 20.54 to 2010.03 ng·L[-1] in water and 0.62 to 29.80 μg·g[-1] in SPM. The primary PAHs-d components were 2,6-dimethylnaphthalene, 2-methylnaphthalene, and anthraquinone. The range of Σ19PPAHs concentrations in water and SPM was 34.89 to 739.53 ng·L[-1] and 0.37 to 204.62 μg·g[-1], respectively. And low-ring PAHs-d and PPAHs were more prevalent in water than SPM. Partitioning behaviors indicated that PAHs-d and PPAHs were more readily partitioned into water and SPM during normal and dry periods, respectively. The concentrations of PAHs-d saw significant changes in their spatial distribution, which rose in water and reduced in SPM in downstream of the Three Gorges Dam. This is due to the dam's blocking effect on sediment transport. Positive matrix factorization source analysis revealed biomass combustion upstream and vehicle emissions downstream as primary sources, shaped by the evolving energy consumption patterns of urban areas situated around the Yangtze River. The annual fluxes of PAHs-d in water and SPM of the Yangtze River were 90.40 t·yr[-1] and 11.95 t·yr[-1], representing 88.3 % and 11.7 % of the overall PAHs-d fluxes, respectively. The total fluxes of PAHs-d and PPAHs in water and SPM tended to increase spatially along the river, with growth rates exceeding 76 and 24 times, respectively. Interception within the Three Gorges Reservoir area has resulted in the differences in the concentration and transport distribution of PAHs-d and PPAHs upstream and downstream, which play important roles in reducing PAHs-d and PPAHs entry into the sea. Future studies on PAHs-d in Yangtze River basin tributaries and estuaries are essential.},
}
@article {pmid39643871,
year = {2024},
author = {Zhang, W and Jin, Z and Huang, R and Huang, W and Li, L and He, Y and Zhou, J and Tian, C and Xiao, L and Li, P and Quan, M and Zhang, D and Du, Q},
title = {Multi-omics analysis reveals genetic architecture and local adaptation of coumarins metabolites in Populus.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1170},
pmid = {39643871},
issn = {1471-2229},
support = {No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 6212021//Project of the Natural Science Foundation of Beijing Municipality/ ; QNTD202305//Fundamental Research Funds for Central Universities of the Central South University/ ; },
mesh = {*Populus/genetics/metabolism ; *Coumarins/metabolism ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Adaptation, Physiological/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Multiomics ; },
abstract = {BACKGROUND: Accumulation of coumarins plays key roles in response to immune and abiotic stress in plants, but the genetic adaptation basis of controlling coumarins in perennial woody plants remain unclear.<br><br>RESULTS: We detected 792 SNPs within 334 genes that were significantly associated with the phenotypic variations of 15 single-metabolic traits and multiple comprehensive index, such as principal components (PCs) of coumarins metabolites. Expression quantitative trait locus mapping uncovered that 337 eQTLs associated with the expression levels of 132 associated genes. Selective sweep revealed 55 candidate genes have potential selective signature among three geographical populations, highlighting that the coumarins biosynthesis have been encountered forceful local adaptation. Furthermore, we constructed a genetic network of seven candidate genes that coordinately regulate coumarins biosynthesis, revealing the multiple regulatory patterns affecting coumarins accumulation in Populus tomentosa. Validation of candidate gene variations in a drought-tolerated population and DUF538 heterologous transformation experiments verified the function of candidate genes and their roles in adapting to the different geographical conditions in poplar.<br><br>CONCLUSIONS: Our study uncovered the genetic regulation of the coumarins metabolic biosynthesis of Populus, and offered potential clues for drought-tolerance evaluation and regional improvement in woody plants.},
}
@article {pmid39642727,
year = {2024},
author = {Mendrik, F and Hackney, CR and Cumming, VM and Waller, C and Hak, D and Dorrell, R and Hung, NN and Parsons, DR},
title = {The transport and vertical distribution of microplastics in the Mekong River, SE Asia.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136762},
doi = {10.1016/j.jhazmat.2024.136762},
pmid = {39642727},
issn = {1873-3336},
abstract = {Rivers are primary vectors of plastic debris to oceans, but sources, transport mechanisms, and fate of fluvial microplastics (<5 mm) remain poorly understood, impeding accurate predictions of microplastic flux, ecological risk and socio-economic impacts. We report on microplastic concentrations, characteristics and dynamics in the Mekong River, one of the world's largest and polluting rivers, in Cambodia and Vietnam. Sampling throughout the water column at multiple localities detected an average of 24 microplastics m[-3] (0.073 mg l[-1]). Concentrations increased downstream from rural Kampi, Cambodia (344 km from river mouth; 2 microplastics m[-3,] 0.006 mg l[-1]), to Can Tho, Vietnam (83 km from river mouth; 64 microplastics m[-3], 0.182 mg l[-1]) with most microplastics being fibres (53 %), followed by fragments (44 %) and the most common polymer being polyethylene terephthalate (PET) or polyester. Pathways of microplastic pollution are expected to be from urban wastewater highlighting the need for improved wastewater treatment in this region. On average, 86 % of microplastics are transported within the water column and consequently we identified an optimum sampling depth capturing a representative flux value, highlighting that sampling only the water surface substantially biases microplastic concentration predictions. Additionally, microplastic abundance does not linearly follow discharge changes during annual monsoonal floods or mirror siliciclastic sediment transport, as microplastic concentrations decrease rapidly during higher monsoon flows. The findings reveal complex microplastic transport in large rivers and call for improved sampling methods and predictive models to better assess environmental risk and guide policy.},
}
@article {pmid39642364,
year = {2024},
author = {Lee, TY and Chen, CH and Chen, IM and Chen, HC and Liu, CM and Wu, SI and Hsiao, CK and Kuo, PH},
title = {Dynamic Bidirectional Associations Between Global Positioning System Mobility and Ecological Momentary Assessment of Mood Symptoms in Mood Disorders: Prospective Cohort Study.},
journal = {Journal of medical Internet research},
volume = {26},
number = {},
pages = {e55635},
pmid = {39642364},
issn = {1438-8871},
mesh = {Humans ; *Geographic Information Systems ; *Ecological Momentary Assessment ; Prospective Studies ; Male ; Adult ; Female ; Middle Aged ; *Mood Disorders/psychology ; Smartphone/statistics &amp; numerical data ; Affect ; Mobile Applications ; },
abstract = {BACKGROUND: Although significant research has explored the digital phenotype in mood disorders, the time-lagged and bidirectional relationship between mood and global positioning system (GPS) mobility remains relatively unexplored. Leveraging the widespread use of smartphones, we examined correlations between mood and behavioral changes, which could inform future scalable interventions and personalized mental health monitoring.<br><br>OBJECTIVE: This study aims to investigate the bidirectional time lag relationships between passive GPS data and active ecological momentary assessment (EMA) data collected via smartphone app technology.<br><br>METHODS: Between March 2020 and May 2022, we recruited 45 participants (mean age 42.3 years, SD 12.1 years) who were followed up for 6 months: 35 individuals diagnosed with mood disorders referred by psychiatrists and 10 healthy control participants. This resulted in a total of 5248 person-days of data. Over 6 months, we collected 2 types of smartphone data: passive data on movement patterns with nearly 100,000 GPS data points per individual and active data through EMA capturing daily mood levels, including fatigue, irritability, depressed, and manic mood. Our study is limited to Android users due to operating system constraints.<br><br>RESULTS: Our findings revealed a significant negative correlation between normalized entropy (r=-0.353; P=.04) and weekly depressed mood as well as between location variance (r=-0.364; P=.03) and depressed mood. In participants with mood disorders, we observed bidirectional time-lagged associations. Specifically, changes in homestay were positively associated with fatigue (&#x3b2;=0.256; P=.03), depressed mood (&#x3b2;=0.235; P=.01), and irritability (&#x3b2;=0.149; P=.03). A decrease in location variance was significantly associated with higher depressed mood the following day (&#x3b2;=-0.015; P=.009). Conversely, an increase in depressed mood was significantly associated with reduced location variance the next day (&#x3b2;=-0.869; P<.001). These findings suggest a dynamic interplay between mood symptoms and mobility patterns.<br><br>CONCLUSIONS: This study demonstrates the potential of utilizing active EMA data to assess mood levels and passive GPS data to analyze mobility behaviors, with implications for managing disease progression in patients. Monitoring location variance and homestay can provide valuable insights into this process. The daily use of smartphones has proven to be a convenient method for monitoring patients' conditions. Interventions should prioritize promoting physical movement while discouraging prolonged periods of staying at home.},
}
@article {pmid39642189,
year = {2024},
author = {Graham, AL and Regoes, RR},
title = {Dose-dependent interaction of parasites with tiers of host defense predicts "wormholes" that prolong infection at intermediate inoculum sizes.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012652},
pmid = {39642189},
issn = {1553-7358},
mesh = {*Host-Parasite Interactions/immunology ; Animals ; Computational Biology ; Parasites/physiology/immunology ; Immunity, Innate ; Models, Biological ; },
abstract = {Immune responses are induced by parasite exposure and can in turn reduce parasite burden. Despite such apparently simple rules of engagement, key drivers of within-host dynamics, including dose-dependence of defense and infection duration, have proven difficult to predict. Here, we model how varied inoculating doses interact with multi-tiered host defenses at a site of inoculation, by confronting barrier, innate, and adaptive tiers with replicating and non-replicating parasites across multiple orders of magnitude of dose. We find that, in general, intermediate parasite doses generate infections of longest duration because they are sufficient in number to breach barrier defenses, but insufficient to strongly induce subsequent tiers of defense. These doses reveal "wormholes" in defense from which parasites might profit: Deviation from the hypothesis of independent action, which postulates that each parasite has an independent probability of establishing infection, may therefore be widespread. Interestingly, our model predicts local maxima of duration at two doses-one for each tier transition. While some empirical evidence is consistent with nonlinear dose-dependencies, testing the predicted dynamics will require finer-scale dose variation than experiments usually incorporate. Our results help explain varied infection establishment and duration among differentially-exposed hosts and elucidate evolutionary pressures that shape both virulence and defense.},
}
@article {pmid39642168,
year = {2024},
author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M},
title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012627},
pmid = {39642168},
issn = {1553-7358},
mesh = {*Computational Biology/methods ; Humans ; *Microbiota/physiology ; *Algorithms ; *Gastrointestinal Microbiome/physiology ; Microbial Interactions/physiology ; },
abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.},
}
@article {pmid39638881,
year = {2024},
author = {Vojteková, J and Janizadeh, S and Vojtek, M and Tirpáková, A and Ruttkay, M and Petrovič, F},
title = {Prediction of potential occurrence of historical objects with defensive function in Slovakia using machine learning approach.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {30350},
pmid = {39638881},
issn = {2045-2322},
support = {033UKF-4/2023//Kult&#xfa;rna a Edukacn&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR/ ; },
abstract = {In this article, we aim at the prediction of possible locations of already defunct historical objects with a defensive function (HODFs) in Slovakia, which have not been found and documented so far, using three machine learning methods. Specifically, we used the support vector machine, k-nearest neighbors, and random forest algorithms, which were trained based on the following five factors influencing the possible occurrence of HODFs: elevation, distance from a river, distance from a settlement, lithological rock type, and type of representative geoecosystems. Training and testing datasets were based on a database of already documented 605 HODFs, which were divided into 70% of training samples and 30% of testing samples. All of the three models reached the AUC-ROC value over 0.74 based on the testing dataset. The best performance was recorded by the random forest predictive model with the AUC-ROC value equal to 0.79. The results of the random forest model were also validated with the recently documented HODFs via the archeological research.},
}
@article {pmid39636475,
year = {2024},
author = {Ganie, PA and Posti, R and Bharti, VS and Sehgal, VK and Sarma, D and Pandey, PK},
title = {Erosion landscape characterization in the Himalayan basin: insights from geospatial data and multi-criteria evaluation.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {1},
pages = {29},
pmid = {39636475},
issn = {1573-2959},
mesh = {India ; *Environmental Monitoring ; *Rivers/chemistry ; *Geographic Information Systems ; Soil Erosion ; Conservation of Natural Resources ; Hydrology ; },
abstract = {In regions characterized by mountainous landscapes, such as watersheds with high elevations, steep inclines, and rugged terrains, there exists an inherent susceptibility to water-induced soil erosion. This susceptibility underscores the importance of identifying areas prone to erosion to mitigate the loss of valuable natural resources and ensure their preservation over time. In response to this need, the current research employed a combination of four multi-criteria decision-making (MCDM) models, namely TOPSIS-AHP, VIKOR-AHP, ARAS-AHP, and CODAS-AHP, for the identification of areas susceptible to soil erosion within the Himalayan River basin of Nandakini, Uttarakhand, India. This identification was facilitated through the utilization of remote sensing and geospatial technologies. The study considered a total of 19 prioritization parameters that included morphological, topo-hydrological, climatic, and environmental factors specific to the Nandakini catchment for the purpose of prioritization modeling. The adoption of morphometric parameters in depicting the geological structures and hydrodynamic behavior of the river basin proves to be a crucial approach in locales where hydrological data may be scarce. The investigation delineated twenty watersheds within the catchment by employing SRTM DEM, SOI toposheets, and Geographic Information Systems (GIS), calculating the catchment's total area to be approximately 540.98 km[2]. The analysis determined that the catchment is classified as a 6th-order catchment, exhibiting mainly a sub-dendritic to dendritic drainage pattern. It was identified that the catchment is vulnerable to flooding and subsequent gully erosion due to the slow movement of surface runoff. Furthermore, the catchment's elongated shape and the compactness coefficient suggest a delayed peak runoff. The drainage texture ranged from very coarse to coarse, and the relief characteristics highlighted that the watersheds within the catchment possess a high relief ratio, thereby increasing their erosion vulnerability. Topo-hydrological indices revealed significant topographic variability and spatial differences in water availability and erosion potential across the basin. The efficacy of the MCDM models was evaluated through the Spearman's correlation coefficient test, alongside indices of intensity and percentage of change, to validate the findings. The ARAS-AHP and CODAS-AHP models were found to exhibit superior efficiency and higher accuracy relative to the other methods assessed. The insights gained from the ARAS-AHP and CODAS-AHP models are instrumental in the development of strategies for sustainable catchment management plans and inform decision-making processes regarding water resources management within the catchment.},
}
@article {pmid39635120,
year = {2024},
author = {Qiu, Y and He, Z and Yu, X and Jia, G and Wang, Y},
title = {Analysis of factors influencing groundwater drought in the Loess zone of China.},
journal = {iScience},
volume = {27},
number = {10},
pages = {110929},
pmid = {39635120},
issn = {2589-0042},
abstract = {Understanding the characteristics and factors influencing groundwater resources is important for regional water resources management. The Gravity Recovery and Climate Experiment (GRACE)-based groundwater conditions were used to analyze the spatiotemporal characteristics of and the factors influencing groundwater storage (GWS) distribution in the Loess zone of the Yellow River Basin. The results revealed that the spatiotemporal distribution of GWS anomalies in the Loess zone of China was best explained by the first three components of the empirical orthogonal function (EOF), representing 85.6% of the total variance. The normalized difference vegetation index (NDVI) was significantly correlated with groundwater drought (p < 0.05). In addition, NDVI and evapotranspiration (ET) were the dominant factors influencing groundwater drought. NDVI was the dominant influencing factor in 67% and 80% of the total study area between 2002-2014 and 2015-2021, respectively. This study provides important guidance for a future ecological restoration plan in the Loess zone.},
}
@article {pmid39627996,
year = {2024},
author = {Rodman, KC and Bradford, JB and Formanack, AM and Fulé, PZ and Huffman, DW and Kolb, TE and Miller-Ter Kuile, AT and Normandin, DP and Ogle, K and Pedersen, RJ and Schlaepfer, DR and Stoddard, MT and Waltz, AEM},
title = {Restoration treatments enhance tree growth and alter climatic constraints during extreme drought.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {},
number = {},
pages = {e3072},
doi = {10.1002/eap.3072},
pmid = {39627996},
issn = {1051-0761},
support = {22-DG-11030000-012//U.S. Forest Service/ ; },
abstract = {The frequency and severity of drought events are predicted to increase due to anthropogenic climate change, with cascading effects across forested ecosystems. Management activities such as forest thinning and prescribed burning, which are often intended to mitigate fire hazard and restore ecosystem processes, may also help promote tree resistance to drought. However, it is unclear whether these treatments remain effective during the most severe drought conditions or whether their impacts differ across environmental gradients. We used tree-ring data from a system of replicated, long-term (>20 years) experiments in the southwestern United States to evaluate the effects of forest restoration treatments (i.e., evidence-based thinning and burning) on annual growth rates (i.e., basal area increment; BAI) of ponderosa pine (Pinus ponderosa), a broadly distributed and heavily managed species in western North America. The study sites were established at the onset of the most extreme drought event in at least 1200 years and span much of the climatic niche of Rocky Mountain ponderosa pine. Across sites, tree-level BAI increased due to treatment, where trees in treated units grew 133.1% faster than trees in paired, untreated units. Likewise, trees in treated units grew an average of 85.6% faster than their pre-treatment baseline levels (1985 to ca. 2000), despite warm, dry conditions in the post-treatment period (ca. 2000-2018). Variation in the local competitive environment promoted variation in BAI, and larger trees were the fastest-growing individuals, irrespective of treatment. Tree thinning and prescribed fire altered the climatic constraints on growth, decreasing the effects of belowground moisture availability and increasing the effects of atmospheric evaporative demand over multi-year timescales. Our results illustrate that restoration treatments can enhance tree-level growth across sites spanning ponderosa pine's climatic niche, even during recent, extreme drought events. However, shifting climatic constraints, combined with predicted increases in evaporative demand in the southwestern United States, suggest that the beneficial effects of such treatments on tree growth may wane over the upcoming decades.},
}
@article {pmid39627652,
year = {2024},
author = {Peltier, DMP and Carbone, MS and Ogle, K and Koch, GW and Richardson, AD},
title = {Decades-old carbon reserves are widespread among tree species, constrained only by sapwood longevity.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20310},
pmid = {39627652},
issn = {1469-8137},
support = {149//Save the Redwoods League/ ; 1936205//Division of Integrative Organismal Systems/ ; 2053337//Division of Integrative Organismal Systems/ ; 1832218//Division of Environmental Biology/ ; 2213599//Division of Environmental Biology/ ; },
abstract = {Carbon reserves are distributed throughout plant cells allowing past photosynthesis to fuel current metabolism. In trees, comparing the radiocarbon (Δ[14]C) of reserves to the atmospheric bomb spike can trace reserve ages. We synthesized Δ[14]C observations of stem reserves in nine tree species, fitting a new process model of reserve building. We asked how the distribution, mixing, and turnover of reserves vary across trees and species. We also explored how stress (drought and aridity) and disturbance (fire and bark beetles) perturb reserves. Given sufficient sapwood, young (< 1 yr) and old (20-60+ yr) reserves were simultaneously present in single trees, including 'prebomb' reserves in two conifers. The process model suggested that most reserves are deeply mixed (30.2 ± 21.7 rings) and then respired (2.7 ± 3.5-yr turnover time). Disturbance strongly increased Δ[14]C mean ages of reserves (+15-35 yr), while drought and aridity effects on mixing and turnover were species-dependent. Fire recovery in Sequoia sempervirens also appears to involve previously unobserved outward mixing of old reserves. Deep mixing and rapid turnover indicate most photosynthate is rapidly metabolized. Yet ecological variation in reserve ages is enormous, perhaps driven by stress and disturbance. Across species, maximum reserve ages appear primarily constrained by sapwood longevity, and thus old reserves are probably widespread.},
}
@article {pmid39624726,
year = {2024},
author = {Tian, T and Zhang, X and Zhang, F and Huang, X and Li, M and Quan, Z and Wang, W and Lei, J and Wang, Y and Liu, Y and Wang, JH},
title = {Harnessing AI for advancing pathogenic microbiology: a bibliometric and topic modeling approach.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1510139},
pmid = {39624726},
issn = {1664-302X},
abstract = {INTRODUCTION: The integration of artificial intelligence (AI) in pathogenic microbiology has accelerated research and innovation. This study aims to explore the evolution and trends of AI applications in this domain, providing insights into how AI is transforming research and practice in pathogenic microbiology.<br><br>METHODS: We employed bibliometric analysis and topic modeling to examine 27,420 publications from the Web of Science Core Collection, covering the period from 2010 to 2024. These methods enabled us to identify key trends, research areas, and the geographical distribution of research efforts.<br><br>RESULTS: Since 2016, there has been an exponential increase in AI-related publications, with significant contributions from China and the USA. Our analysis identified eight major AI application areas: pathogen detection, antibiotic resistance prediction, transmission modeling, genomic analysis, therapeutic optimization, ecological profiling, vaccine development, and data management systems. Notably, we found significant lexical overlaps between these areas, especially between drug resistance and vaccine development, suggesting an interconnected research landscape.<br><br>DISCUSSION: AI is increasingly moving from laboratory research to clinical applications, enhancing hospital operations and public health strategies. It plays a vital role in optimizing pathogen detection, improving diagnostic speed, treatment efficacy, and disease control, particularly through advancements in rapid antibiotic susceptibility testing and COVID-19 vaccine development. This study highlights the current status, progress, and challenges of AI in pathogenic microbiology, guiding future research directions, resource allocation, and policy-making.},
}
@article {pmid39622961,
year = {2024},
author = {Jeong, D and Hyun, JY and Marchenkova, T and Matiukhina, D and Cho, S and Lee, J and Kim, DY and Li, Y and Darman, Y and Min, MS and Bardyuk, V and Lee, Y and Pandey, P and Lee, H},
title = {Genetic insights and conservation strategies for Amur tigers in Southwest Primorye Russia.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29985},
pmid = {39622961},
issn = {2045-2322},
support = {550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; },
mesh = {Animals ; *Tigers/genetics ; *Conservation of Natural Resources ; *Genetic Variation ; *Microsatellite Repeats/genetics ; Male ; Female ; *DNA, Mitochondrial/genetics ; Russia ; Genetics, Population ; Population Density ; },
abstract = {Southwest Primorye hosts approximately 9% of the remaining wild Amur tiger population and represents hope for the revival of tigers in Northeast China and the Korean peninsula. Decades of conservation efforts have led to a significant increase in population size, from less than 10 individuals surviving in the region in 1996 to multiple folds today. However, while the population size has recovered since the mid-1900s, the effects of genetic depletion on evolutionary potential are not easily reversed. In this study, a non-invasive genetic analysis of the Amur tiger subpopulation in Southwest Primorye was conducted using microsatellite loci and mitochondrial genes to estimate genetic diversity, relatedness, and determine the impact of historical demographic dynamics. A total of 32 individuals (16 males, 15 females, and 1 unidentified sex) were identified, and signs of bottlenecks were detected, reflecting past demographic events. Low genetic variation observed in mitochondrial DNA also revealed genetic depletion within the population. Most individuals were found to be closely related to each other, raising concerns about inbreeding given the small population size and somewhat isolated environment from the main population in Sikhote-Alin. These findings emphasize the urgent need to establish ecological corridors to neighboring areas to restore genetic diversity and ensure the conservation of the Amur tiger population in Southwest Primorye.},
}
@article {pmid39622813,
year = {2024},
author = {Monadjem, A and Montauban, C and Webala, PW and Laverty, TM and Bakwo-Fils, EM and Torrent, L and Tanshi, I and Kane, A and Rutrough, AL and Waldien, DL and Taylor, PJ},
title = {African bat database: curated data of occurrences, distributions and conservation metrics for sub-Saharan bats.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1309},
pmid = {39622813},
issn = {2052-4463},
mesh = {*Chiroptera/classification/physiology ; Animals ; Africa South of the Sahara ; *Conservation of Natural Resources ; *Databases, Factual ; Ecosystem ; Animal Distribution ; },
abstract = {Accurate knowledge of species distributions is foundational for effective conservation efforts. Bats are a diverse group of mammals, with important roles in ecosystem functioning. However, our understanding of bats and their ecological importance is hindered by poorly defined ranges, mostly as a result of under-recording. This issue is exacerbated in Africa by the ongoing rapid discovery of new species, both de novo and splits of existing species, and by inaccessibility to museum specimens that are mostly hosted outside of the continent. Here we present the African bat database - a curated set of 17,285 unique locality records of all 266 species of bats from sub-Saharan Africa, vouched for by specimens and/or genetic sequencing, and aligned with current taxonomy. Based on these records, we also present Maxent-based distribution models and calculate the IUCN Red List metrics for Extent of Occurrence and Area of Occupancy. This database and online visualization tool provide an important open-source resource and is expected to significantly advance studies in ecology, and aid in bat conservation.},
}
@article {pmid39622351,
year = {2024},
author = {Nishimura, H and Nawa, N and Ogawa, T and Fushimi, K and Schwartz, BS and Fujiwara, T},
title = {Projections of future heat-related emergency hospitalizations for asthma under climate and demographic change scenarios: A Japanese nationwide time-series analysis.},
journal = {Environmental research},
volume = {266},
number = {},
pages = {120498},
doi = {10.1016/j.envres.2024.120498},
pmid = {39622351},
issn = {1096-0953},
abstract = {BACKGROUND: There is growing concern about climate impacts on human health. However, empirical evidence is lacking regarding future projections of heat-related asthma hospitalizations. This study aimed to project excess emergency hospitalizations for heat-related asthma exacerbation in Japan.<br><br>METHODS: Using Japanese nationwide administrative data from 2011 to 2019, we conducted an ecological time-series quasi-Poisson regression analysis to estimate the heat-related relative risk of emergency hospitalization for asthma over a lag of 0-3 days during the warm season (June to September). Heat exposure was defined as the region-specific daily mean temperature exceeding the locally defined minimum morbidity temperature percentile (MMP). Heat-related excess hospitalizations for asthma were projected under future climate and demographic change scenarios based on Shared Socioeconomic Pathways (SSPs).<br><br>RESULTS: We identified 75,829 emergency hospitalizations for asthma. The heat-related relative risk of hospitalization was 1.22 (95% confidence interval (CI): 1.12-1.33) at the 99th percentile temperature relative to the MMP, with the highest estimates for cases aged 0-14 years. Heat-related excess hospitalizations were projected to increase by 6.78 (95%CI: 5.84-7.67) times in 2091-2099 versus 2011-2019 along SSP5-8.5 when constant population structure was assumed. The increasing trend persisted even when the future population decline was considered (4.19 (95%CI: 3.53-4.85) times in 2091-2099 versus 2011-2019 under SSP5-8.5).<br><br>CONCLUSION: Future heat-related impacts on asthma exacerbation are expected to increase in Japan toward the end of this century, even when the future demographic change is considered. Our projections will contribute to resilient health systems adapting to ongoing climate change.},
}
@article {pmid39621910,
year = {2024},
author = {Alfaro-Sánchez, R and Richardson, AD and Smith, SL and Johnstone, JF and Turetsky, MR and Cumming, SG and Le Moine, JM and Baltzer, JL},
title = {Permafrost instability negates the positive impact of warming temperatures on boreal radial growth.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {50},
pages = {e2411721121},
pmid = {39621910},
issn = {1091-6490},
support = {15879//Aurora Research Institute (ARI)/ ; permafrost monitoring in the Mackenzie River Valley//Canadian Government | Natural Resources Canada (NRCan)/ ; MZ2021//Mar&#xed;a Zambrano program/ ; Small Research 2021 - SR21/1291//British Ecological Society (BES)/ ; Environmental Studies Research Fund and Cumulative Impacts Monitoring Program (Project 170)//Environment and Natural Resources, Northwest Territories (ENR, NWT)/ ; Discovery Grant support//Canadian Government | NSERC | RES'EAU-WaterNET/ ; Bonanza Creek LTER DEB-2224776//National Science Foundation (NSF)/ ; },
mesh = {*Permafrost ; *Trees/growth &amp; development ; Temperature ; Taiga ; Global Warming ; Climate Change ; Forests ; },
abstract = {Climate warming can alleviate temperature and nutrient constraints on tree growth in boreal regions, potentially enhancing boreal productivity. However, in permafrost environments, warming also disrupts the physical foundation on which trees grow, leading to leaning trees or "drunken" forests. Tree leaning might reduce radial growth, undermining potential benefits of warming. Here, we found widespread radial growth reductions in southern latitude boreal forests since the 1980s. At mid latitudes, radial growth increased from ~1980 to ~2000 but showed recent signs of decline afterward. Increased growth was evident since the 1980 s at higher latitudes, where radial growth appears to be temperature limited. However, recent changes in permafrost stability, and the associated increased frequency of tree leaning events, emerged as a significant stressor, leading to reduced radial growth in boreal trees at the highest latitudes, where permafrost is extensive. We showed that trees growing in unstable permafrost sites allocated more nonstructural carbohydrate reserves to offset leaning which compromised radial growth and potential carbon uptake benefits of warming. This higher allocation of resources in drunken trees is needed to build the high-density reaction wood, rich in lignin, that is required to maintain a vertical position. With continued climate warming, we anticipate widespread reductions in radial growth in boreal forests, leading to lower carbon sequestration. These findings enhance our understanding of how climate warming and indirect effects, such as ground instability caused by warming permafrost, will affect boreal forest productivity in the future.},
}
@article {pmid39621775,
year = {2024},
author = {Osiecka, AN and Bryndza, P and Briefer, EF and Wojczulanis-Jakubas, K},
title = {Long distance calls: Negligible information loss of little auk social vocalisations due to high frequency propagation losses.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1011961},
doi = {10.1371/journal.pcbi.1011961},
pmid = {39621775},
issn = {1553-7358},
mesh = {Animals ; *Vocalization, Animal/physiology ; Sound Spectrography/methods ; Computational Biology ; Acoustics ; Social Behavior ; },
abstract = {How well does the information contained in vocal signals travel through the environment? To assess the efficiency of information transfer in little auk (Alle alle, an Arctic seabird) calls over distance, we selected two of the social call types with the highest potential for individuality coding. Using available recordings of known individuals, we calculated the apparent source levels, with apparent maximum peak sound pressure level (ASPL) of 63 dB re 20 μPa at 1 m for both call types. Further, we created a sound attenuation model using meteorological data collected in the vicinity of the little auk colony in Hornsund, Spitsbergen. Using this model, we modelled the calls to reflect higher frequency filtering and sound level loss occurring during spherical spreading in perfect local conditions, down to the putative hearing threshold of the species, calculated to equal ASPL of signals "propagated" to roughly one kilometre. Those modelled calls were then used in a permuted discriminant function analysis, support vector machine models, and linear models of Beecher's information statistic, to investigate whether transmission loss will affect the retention of individual information of the signal. Calls could be correctly classified to individuals above chance level independently of the distance, down to and over the putative physiological hearing threshold. Interestingly, the information capacity of the signal did not decrease with its filtering and attenuation. While this study touches on signal properties purely and cannot provide evidence of the actual use by the animals, it shows that little auk signals can theoretically travel long distances with negligible information loss, and supports the hypothesis that vocalisations could facilitate long-distance communication in the species.},
}
@article {pmid39618809,
year = {2024},
author = {Boyes, D and Young, MR and , and , and , and , and , and , and , },
title = {The genome sequence of the Straw Grass-veneer moth, Agriphila straminella (Denis &amp; Schiffermüller), 1775.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {433},
pmid = {39618809},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Straw Grass-veneer moth, Agriphila straminella (Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a length of 511.50 megabases. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,087 protein-coding genes.},
}
@article {pmid39616400,
year = {2024},
author = {Asaaga, FA and Shakeer, I and Sriram, A and Chhotaria, K and Dutta, S and Narayanaswamy, D and Amankwaa, G and Chanda, MM and Hoti, SL and Young, JC and Purse, BV},
title = {Ties that bind: understanding One Health networks and participation for zoonoses prevention and control in India.},
journal = {One health outlook},
volume = {6},
number = {1},
pages = {24},
pmid = {39616400},
issn = {2524-4655},
abstract = {BACKGROUND: Cross-sectoral collaborations as exemplified by the One Health approach, are widely endorsed as pragmatic avenues for addressing zoonotic diseases, but operationalisation remain limited in low-and-middle income countries (LMICs). Complexities and competing interests and agendas of key stakeholders and the underlying politico-administrative context can all shape outcomes of collaborative arrangements. Evidence is building that organised collaborations are complex political initiatives where different objectives; individual and institutional agendas need to be reconciled to incentivise collaborations.<br><br>METHODS: Drawing on a qualitative network analysis of published sources on 'One Health' stakeholders supplemented with 26 multi-scale (national-state-district level) key-informant interviews (including policymakers, disease managers and public health experts), this paper characterises the fragmented and complex characteristics of institutional networks involved in zoonoses prevention and control in India.<br><br>RESULTS: Our results highlight how the local socio-political and institutional contexts interact to modulate how and when collaborations occur (or not), the associated contingencies and stakeholder innovations in circumventing existing barriers (e.g. competing interests, distrust between actors, departmental bureaucracy) to cross-sector collaborations and zoonoses management. Aside from principal actors negotiating common ground in some instance, they also capitalised on political/institutional pressure to subtly 'manipulate' their subordinates as a way of fostering collaboration, especially in instances when the institutional and political stakes are high.<br><br>CONCLUSION: Altogether our findings suggest that cross-sectoral collaborations are by-product of political and institutional tinkering as long as individual actors and institutional interests converge and these dynamics must be embraced to embed meaningful and sustainable collaborations in local socio-political and administrative contexts.},
}
@article {pmid39612036,
year = {2024},
author = {Ma, D and Huang, Q and Wang, Q and Xu, H and Yan, Y},
title = {Detection of spatiotemporal changes in eco-environmental quality based on RSEI and SG filtering and its driving force analysis: a case study in Sichuan Province, China.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {12},
pages = {1274},
pmid = {39612036},
issn = {1573-2959},
support = {ZR2020MD025//Natural Science Foundation of Shandong Province/ ; 42171435//National Natural Science Foundation of China/ ; },
mesh = {China ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Forests ; Ecosystem ; Grassland ; Conservation of Natural Resources/methods ; },
abstract = {Landsat images were extracted using Google Earth Engine (GEE) platform and optimized by Savitzky-Golay (SG) filtering. The Remote Sensing Ecological Index (RSEI) method was used to analyze the eco-environmental quality in Sichuan Province in recent 20 years. In addition, Theil-Sen median method and Mann-Kendall (MK) test were used to test the change trend of eco-environmental quality. Furthermore, drivers were evaluated by partial correlation analysis, 2D scatter plots, and t tests. The results showed that (1) in the past 20 years, the eco-environmental quality of Sichuan Province was on the rise, and the eco-environmental quality in the western region was better than that in the eastern region. The eco-environmental quality was positively correlated with forest and grassland types, and negatively correlated with cultivated land and urban and rural construction land types. (2) The eco-environmental quality of Sichuan Province is linearly correlated with the digital elevation model, but poorly correlated with slope and slope direction. In the range of slope 0° ~ 9° and southeast direction, the eco-environmental quality is the worst. (3) The eco-environmental quality of Sichuan Province was most significantly affected by soil moisture and sunshine hours. The study can help us to understand and assess the health of ecosystems in Sichuan Province, provide a scientific basis for protecting and improving the environment, and guide the formulation and implementation of environmental protection policies.},
}
@article {pmid39609505,
year = {2024},
author = {Alvarez-Mamani, E and Buettner, F and Beltran-Castanon, CA and Ibanez, AJ},
title = {Exploratory analysis of metabolic changes using mass spectrometry data and graph embeddings.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29570},
pmid = {39609505},
issn = {2045-2322},
support = {No. 174-2020-FONDECYT "Doctoral Programs in Peruvian Universities"//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica (CONCYTEC), and Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica (FONDECYT)/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; N&#xba; PE501086715-2024- PROCIENCIA)//CONCYTEC-Prociencia convocatoria E041-2024-01/ ; },
mesh = {*Metabolomics/methods ; *Mass Spectrometry/methods ; *Algorithms ; *Data Mining/methods ; Humans ; Deep Learning ; Metabolic Networks and Pathways ; Metabolome ; },
abstract = {Mass spectrometry (MS)-based metabolomics analysis is a powerful tool, but it comes with its own set of challenges. The MS workflow involves multiple steps before its interpretation in what is denominate data mining. Data mining consists of a two-step process. First, the MS data is ordered, arranged, and presented for filtering before being analyzed. Second, the filtered and reduced data are analyzed using statistics to remove further variability. This holds true particularly for MS-based untargeted metabolomics studies, which focused on understanding fold changes in metabolic networks. Since the task of filtering and identifying changes from a large dataset is challenging, automated techniques for mining untargeted MS-based metabolomic data are needed. The traditional statistics-based approach tends to overfilter raw data, which may result in the removal of relevant data and lead to the identification of fewer metabolomic changes. This limitation of the traditional approach underscores the need for a new method. In this work, we present a novel deep learning approach using node embeddings (powered by GNNs), edge embeddings, and anomaly detection algorithm to analyze the data generated by mass spectrometry (MS)-based metabolomics called GEMNA (Graph Embedding-based Metabolomics Network Analysis), for example for an untargeted volatile study on Mentos candy, the data clusters produced by GEMNA were better than the ones used traditional tools, i.e., GEMNA has [Formula: see text], vs. the traditional approach has [Formula: see text].},
}
@article {pmid39606930,
year = {2024},
author = {Whyte, M and Wambui, KM and Musenge, E},
title = {Nigeria's malaria prevalence in 2015: a geospatial, exploratory district-level approach.},
journal = {Geospatial health},
volume = {19},
number = {2},
pages = {},
doi = {10.4081/gh.2024.1243},
pmid = {39606930},
issn = {1970-7096},
mesh = {Humans ; Nigeria/epidemiology ; *Malaria/epidemiology ; Prevalence ; Child, Preschool ; Infant ; *Spatial Analysis ; Female ; Male ; *Geographic Information Systems ; Socioeconomic Factors ; Adult ; Adolescent ; Child ; Middle Aged ; Young Adult ; },
abstract = {This study used data from the second Nigeria Malaria Indicator Survey (NMIS) conducted in 2015 to investigate the spatial distribution of malaria prevalence in the country and identify its associated factors. Nigeria is divided into 36 states with 109 senatorial districts, most of which are affected by malaria, a major cause of morbidity and mortality in children under five years of age. We carried out an ecological study with analysis at the senatorial district level. A malaria prevalence map was produced combining geographic information systems data from the Nigeria Malaria Indicator Survey (NMIS) of 2015 with shape files from an open data-sharing platform. Spatial autoregressive models were fitted using a set of key covariates. Malaria prevalence in children under-five was highest in Kebbi South senatorial district (70.6%). It was found that poorest wealth index (β = 0.10 (95% CI: 0.01, 0.20), p = 0.04), mothers having only secondary level of education (β = 0.78 (95% CI: 0.05, 1.51), p = 0.04) and households without mosquito bed nets (β = 0.21 (95% CI: 0.02, 0.39), p = 0.03) were all significantly associated with higher malaria prevalence. Moran's I (54.81, p<0.001) showed spatial dependence of malaria prevalence across contiguous districts and spatial autoregressive modelling demonstrated significant spill-over effect of malaria prevalence. Maps produced in this study provide a useful graphical representation of the spatial distribution of malaria prevalence based on NMIS-2015 data. Clustering of malaria prevalence in certain areas further highlights the need for sustained malaria elimination interventions across affected regions in order to break the chain of transmission.},
}
@article {pmid39602490,
year = {2024},
author = {Soares, R and Azevedo, L and Vasconcelos, V and Pratas, D and Sousa, SF and Carneiro, J},
title = {Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation.},
journal = {Journal of chemical information and modeling},
volume = {64},
number = {24},
pages = {9576-9593},
doi = {10.1021/acs.jcim.4c00995},
pmid = {39602490},
issn = {1549-960X},
mesh = {*Cyanobacteria/metabolism ; *Machine Learning ; *Biodegradation, Environmental ; *Drug Discovery ; Molecular Docking Simulation ; Databases, Factual ; Databases, Chemical ; Humans ; Software ; },
abstract = {Cyanobacteria strains have the potential to produce bioactive compounds that can be used in therapeutics and bioremediation. Therefore, compiling all information about these compounds to consider their value as bioresources for industrial and research applications is essential. In this study, a searchable, updated, curated, and downloadable database of cyanobacteria bioactive compounds was designed, along with a machine-learning model to predict the compounds' targets of newly discovered molecules. A Python programming protocol obtained 3431 cyanobacteria bioactive compounds, 373 unique protein targets, and 3027 molecular descriptors. PaDEL-descriptor, Mordred, and Drugtax software were used to calculate the chemical descriptors for each bioactive compound database record. The biochemical descriptors were then used to determine the most promising protein targets for human therapeutic approaches and environmental bioremediation using the best machine learning (ML) model. The creation of our database, coupled with the integration of computational docking protocols, represents an innovative approach to understanding the potential of cyanobacteria bioactive compounds. This resource, adhering to the findability, accessibility, interoperability, and reuse of digital assets (FAIR) principles, is an excellent tool for pharmaceutical and bioremediation researchers. Moreover, its capacity to facilitate the exploration of specific compounds' interactions with environmental pollutants is a significant advancement, aligning with the increasing reliance on data science and machine learning to address environmental challenges. This study is a notable step forward in leveraging cyanobacteria for both therapeutic and ecological sustainability.},
}
@article {pmid39600916,
year = {2021},
author = {Boyes, D and Crowley, LM and , and , and , and , and , and , },
title = {The genome sequence of the harlequin ladybird, Harmonia axyridis (Pallas, 1773).},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {300},
pmid = {39600916},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Harmonia axyridis (the harlequin ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 426 megabases in span. The majority (99.98%) of the assembly is scaffolded into 8 chromosomal pseudomolecules, with the X sex chromosome assembled.},
}
@article {pmid39599286,
year = {2024},
author = {Toghan, A and Alduaij, OK and Sanad, MMS and Elessawy, NA},
title = {Scalable Engineering of 3D Printing Filaments Derived from Recycling of Plastic Drinking Water Bottle and Glass Waste.},
journal = {Polymers},
volume = {16},
number = {22},
pages = {},
pmid = {39599286},
issn = {2073-4360},
support = {IMSIU-RG23086//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University/ ; },
abstract = {The most significant challenge that the world is currently facing is the development of beneficial industrial applications for solid waste. A novel strategy was implemented to produce a composite with varying loadings of glass waste nanoparticles (GWNP) in 5, 10, and 15 wt.% with recycled polyethylene terephthalate drinking water bottle waste (RPET). This strategy was based on glass and drinking water bottle waste. An analysis was conducted to evaluate the performance of the composite as filaments for 3D printer applications. This study evaluated the effect of GWNP addition on the chemical structure, thermal and mechanical characteristics of the composite. The Fourier Transform Infrared (FTIR) spectra of the filament composites and RPET composites exhibited similarities. However, the mechanical strength and thermal stability of the filament composites were enhanced due to the increased GWNP content. Furthermore, the results indicated that the filament developed could be utilized for 3D printing, as demonstrated by the successful fabrication of the filament composite, including 5 wt.% GWNP, using a 3D printer pen. The production of filaments using GWNP and RPET matrix presents a cost-effective, high-yield, and ecologically beneficial alternative. The present study may pave the way for the future advancement and utilization of 3D printing filaments by treating hazardous waste and using more ecologically friendly materials in design applications.},
}
@article {pmid39597377,
year = {2024},
author = {Maślanka, P and Korycki, R},
title = {Material, Aerodynamic, and Operational Aspects of Single-Skin Paraglider.},
journal = {Materials (Basel, Switzerland)},
volume = {17},
number = {22},
pages = {},
pmid = {39597377},
issn = {1996-1944},
abstract = {The operating comfort of a paraglider is created by the aerodynamic parameters as well as the mass and packing volume of the wing. A classic paraglider has upper and lower covers. To reduce the material and manufacturing costs as well as protect the environment, it is possible to introduce a single-skin wing. This article conducts an analysis of a single-skin paraglider covered only with upper panels, whereas the lower cover is applied only at the leading and trailing edges. The analysis is theoretically oriented; aerodynamic and structural calculations were performed using the ANSYS environment. The single-skin structure was evaluated in terms of the predicted behavior during flight and the material's deformation under the influence of a specified pressure and the overloads acting on it. The results show that developing these structures may influence the creation of models with comparable aerodynamic characteristics to traditional ones. Additionally, the reduced masses and packing volumes of difficult-to-degrade materials are strongly correlated with saving costs and an ecological approach. No corresponding studies were found in the available literature. Thus, this presented analysis may result in a greater understanding and application of this paraglider type.},
}
@article {pmid39596552,
year = {2024},
author = {Signore, IA and Donoso, G and Bocchieri, P and Tobar-Calfucoy, EA and Yáñez, CE and Carvajal-Silva, L and Silva, AX and Otth, C and Cappelli, C and Valenzuela Jorquera, H and Zapata-Contreras, D and Espinosa-Parrilla, Y and Zúñiga-Pacheco, P and Fuentes-Guajardo, M and Monardes-Ramírez, VA and Kochifas Velasquez, P and Muñoz, CA and Dorador, C and García-Araya, J and Campillay-Véliz, CP and Echeverria, C and Santander, RA and Cerpa, LC and Martínez, MF and Quiñones, LA and Lamoza Galleguillos, ER and Saez Hidalgo, J and Nova-Lamperti, E and Sanhueza, S and Giacaman, A and Acosta-Jamett, G and Verdugo, C and Plaza, A and Verdugo, C and Selman, C and Verdugo, RA and Colombo, A},
title = {The Chilean COVID-19 Genomics Network Biorepository: A Resource for Multi-Omics Studies of COVID-19 and Long COVID in a Latin American Population.},
journal = {Genes},
volume = {15},
number = {11},
pages = {},
pmid = {39596552},
issn = {2073-4425},
support = {ANID COVID0961, ANID COVID0789, ANID COVID1005, ANID COVID0585, ACT210085, FONDECYT 1170446, FONDECYT 1211480//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; MAG1995//Ministry of Education/ ; RED21193//Interuniversity Center for Healthy Aging/ ; VRID220.085.041-INI//University of Concepci&#xf3;n/ ; },
mesh = {Humans ; *COVID-19/genetics/virology/epidemiology ; Chile ; *Biological Specimen Banks ; *Genomics/methods ; *SARS-CoV-2/genetics ; Male ; Female ; Adult ; Middle Aged ; Aged ; Latin America ; Multiomics ; },
abstract = {Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical course, where ethnic background appears to influence disease severity, with non-Europeans facing higher hospitalization rates. In addition, access to high-quality samples and data is a critical issue for personalized and precision medicine, and it has become clear that the solution lies in biobanks. The creation of the Chilean COVID-19 Biorepository reported here addresses these gaps, representing the first nationwide multicentric Chilean initiative. It operates under rigorous biobanking standards and serves as one of South America's largest COVID cohorts. A centralized harmonization strategy was chosen and included unified standard operating procedures, a sampling coding system, and biobanking staff training. Adults with confirmed SARS-CoV-2 infection provided broad informed consent. Samples were collected to preserve blood, plasma, buffy coat, and DNA. Quality controls included adherence to the standard preanalytical code, incident reporting, and DNA concentration and absorbance ratio 260/280 assessments. Detailed sociodemographic, health, medication, and preexisting condition data were gathered. In five months, 2262 participants were enrolled, pseudonymized, and sorted by disease severity. The average Amerindian ancestry considering all participant was 44.0% [SD 15.5%], and this value increased to 61.2% [SD 19.5%] among those who self-identified as Native South Americans. Notably, 279 participants self-identified with one of 12 ethnic groups. High compliance (>90%) in all assessed quality controls was achieved. Looking ahead, our team founded the COVID-19 Genomics Network (C19-GenoNet) focused on identifying genetic factors influencing SARS-CoV-2 outcomes. In conclusion, this bottom-up collaborative effort aims to promote the integration of Latin American populations into global genetic research and welcomes collaborations supporting this endeavor. Interested parties are invited to explore collaboration opportunities through our catalog, accessible online.},
}
@article {pmid39595758,
year = {2024},
author = {Aras, SG and Runyon, JR and Kazman, JB and Thayer, JF and Sternberg, EM and Deuster, PA},
title = {Is Greener Better? Quantifying the Impact of a Nature Walk on Stress Reduction Using HRV and Saliva Cortisol Biomarkers.},
journal = {International journal of environmental research and public health},
volume = {21},
number = {11},
pages = {},
pmid = {39595758},
issn = {1660-4601},
support = {XX//The Institute for Integrative Health and Nature Sacred/ ; },
mesh = {Humans ; *Hydrocortisone/analysis/metabolism ; *Saliva/chemistry ; *Walking/physiology ; *Heart Rate/physiology ; Male ; Adult ; Female ; *Biomarkers/analysis/metabolism ; Stress, Psychological/metabolism/physiopathology ; Affect/physiology ; Stress, Physiological/physiology ; Young Adult ; Nature ; Middle Aged ; },
abstract = {The physiological impact of walking in nature was quantified via continuous heart rate variability (HRV), pre- and post-walk saliva cortisol measures, and self-reported mood and mindfulness scores for N = 17 participants who walked "The Green Road" at Walter Reed National Military Medical Center in Bethesda, Maryland. For N = 15 of the participants, HRV analysis revealed two main groups: group one individuals had a 104% increase (mean) in the root mean square standard deviation (RMSSD) and a 47% increase (mean) in the standard deviation of NN values (SDNN), indicating an overall reduction in physiological stress from walking the Green Road, and group two individuals had a decrease (mean) of 42% and 31% in these respective HRV metrics, signaling an increase in physiological stresses. Post-walk self-reported scores for vigor and mood disturbance were more robust for the Green Road than for a comparable urban road corridor and showed that a higher HRV during the walk was associated with improved overall mood. Saliva cortisol was lower after taking a walk for all participants, and it showed that walking the Green Road elicited a significantly larger reduction in cortisol of 53%, on average, when compared with 37% of walking along an urban road. It was also observed that the order in which individuals walked the Green Road and urban road also impacted their cortisol responses, with those walking the urban road before the Green Road showing a substantial reduction in cortisol, suggesting a possible attenuation effect of walking the Green Road first. These findings provide quantitative data demonstrating the stress-reducing effects of being in nature, thus supporting the health benefit value of providing access to nature more broadly in many settings.},
}
@article {pmid39594004,
year = {2024},
author = {Alrhmoun, M and Sulaiman, N and Haq, SM and Abidullah, S and Prakofjewa, J and Krigas, N and Pieroni, A and Sõukand, R},
title = {Is Boiling Bitter Greens a Legacy of Ancient Crete? Contemporary Foraging in the Minoan Refugium of the Lasithi Plateau.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {22},
pages = {},
pmid = {39594004},
issn = {2304-8158},
support = {N/A//University of Gastronomic Sciences, Pollenzo, Italy/ ; N/A//Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari Uni-versity of Venice, Italy/ ; },
abstract = {Wild greens (WGs) play a significant role in Mediterranean diets (MDs), reflecting botanical and cultural diversities, mainly influenced by a complex conglomerate of local human ecologies. This study investigates local ecological knowledge (LEK) linked to traditional gathering and consumption of WGs in the Lasithi Plateau of eastern Crete, where human genetic studies one decade ago showed very peculiar patterns, hypothesising that the Minoan civilisation took refuge there before it disappeared. A field ethnobotanical study was conducted to document the diversity of WGs and their detailed local culinary uses in the Lasithi area by interviewing 31 study participants. Fifty-nine folk taxa (species and subspecies) were recorded, corresponding to fifty-eight botanical taxa. A quotation index was measured to assess the cultural significance of WGs in the study areas; logistic regression analysis was adopted to understand the impact of sensory classifications of WGs and their local cooking methods. Lasithi's foraging showed a notable prevalence of bitter-tasting WGs, which play a central role in local cognition and culinary practices. This bitterness aspect of WGs, potentially influenced by cultural preferences and genetic factors, probably suggests a connection to the ancient Lasithi's inhabitants, i.e., Minoan dietary habits. We found that bitterness is the predominant sensory attribute in Lasithi, characterising 45.76% of the WGs. These findings underscore the complex interplay between local ecologies and biodiversity, LEK, and dietary traditions, highlighting the importance of WGs in understanding the evolution of foraging and plant culinary diversities across the Mediterranean.},
}
@article {pmid39592922,
year = {2024},
author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S},
title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1127},
pmid = {39592922},
issn = {1471-2229},
mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; },
abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.},
}
@article {pmid39591252,
year = {2024},
author = {Baradaran, M and Salabi, F and Mahdavinia, M and Mohammadi, E and Vazirianzadeh, B and Avella, I and Kazemi, SM and Lüddecke, T},
title = {ScorpDb: A Novel Open-Access Database for Integrative Scorpion Toxinology.},
journal = {Toxins},
volume = {16},
number = {11},
pages = {},
pmid = {39591252},
issn = {2072-6651},
mesh = {*Scorpion Venoms/chemistry ; *Scorpions ; Animals ; Humans ; Databases, Factual ; Scorpion Stings/drug therapy ; Databases, Protein ; },
abstract = {Scorpion stings are a significant public health concern globally, particularly in tropical and subtropical regions. Scorpion venoms contain a diverse array of bioactive peptides, and different scorpion species around the world typically exhibit varying venom profiles, resulting in a wide range of envenomation symptoms. Despite their harmful effects, scorpion venom peptides hold immense potential for drug development due to their unique characteristics. Therefore, the establishment of a comprehensive database that catalogs scorpions along with their known venom peptides and proteins is imperative in furthering research efforts in this research area. We hereby present ScorpDb, a novel database that offers convenient access to data related to different scorpion species, the peptides and proteins found in their venoms, and the symptoms they can cause. To this end, the ScorpDb database has been primarily advanced to accommodate data on the Iranian scorpion fauna. From there, we propose future community efforts to include a larger diversity of scorpions and scorpion venom components. ScorpDb holds the promise to become a valuable resource for different professionals from a variety of research fields, like toxinologists, arachnologists, and pharmacologists. The database is available at https://www.scorpdb.com/.},
}
@article {pmid39591213,
year = {2024},
author = {Roman-Ramos, H and Ho, PL},
title = {Current Technologies in Snake Venom Analysis and Applications.},
journal = {Toxins},
volume = {16},
number = {11},
pages = {},
pmid = {39591213},
issn = {2072-6651},
support = {2017/18398-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 309741/2023-8//National Council for Scientific and Technological Development/ ; },
mesh = {*Snake Venoms/chemistry ; Animals ; *Proteomics ; Humans ; Genomics ; Computational Biology ; Snakes ; },
abstract = {This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals.},
}
@article {pmid39589804,
year = {2024},
author = {Arias, M and Behrendt, L and Dreßler, L and Raka, A and Perrier, C and Elias, M and Gomez, D and Renoult, JP and Tedore, C},
title = {Testing the equivalency of human "predators" and deep neural networks in the detection of cryptic moths.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voae146},
pmid = {39589804},
issn = {1420-9101},
abstract = {Researchers have shown growing interest in using deep neural networks (DNNs) to efficiently test the effects of perceptual processes on the evolution of color patterns and morphologies. Whether this is a valid approach remains unclear, as it is unknown whether the relative detectability of ecologically relevant stimuli to DNNs actually matches that of biological neural networks. To test this, we compare image classification performance by humans and six DNNs (AlexNet, VGG-16, VGG-19, ResNet-18, SqueezeNet, and GoogLeNet) trained to detect artificial moths on tree trunks. Moths varied in their degree of crypsis, conferred by different sizes and spatial configurations of transparent wing elements. Like humans, four of six DNN architectures found moths with larger transparent elements harder to detect. However, humans and only one DNN architecture (GoogLeNet) found moths with transparent elements touching one side of the moth's outline harder to detect than moths with untouched outlines. When moths were small, the camouflaging effect of transparent elements touching the moth's outline was reduced for DNNs but enhanced for humans. Prey size can thus interact with camouflage type in opposing directions in humans and DNNs, which warrants a deeper investigation of size interactions with a broader range of stimuli. Overall, our results suggest that humans and DNNs responses had some similarities, but not enough to justify the widespread use of DNNs for studies of camouflage.},
}
@article {pmid39586965,
year = {2024},
author = {Gianicolo, E and Russo, A and Di Staso, R and Ronckers, CM and Schmidtmann, I and Wollschläger, D and Blettner, M},
title = {A municipality-specific analysis to investigate persistent increased incidence rates of childhood leukaemia near the nuclear power plant of Krümmel in Germany.},
journal = {European journal of epidemiology},
volume = {39},
number = {12},
pages = {1373-1378},
pmid = {39586965},
issn = {1573-7284},
mesh = {Humans ; Germany/epidemiology ; Child ; *Nuclear Power Plants ; Incidence ; Male ; Child, Preschool ; Female ; *Leukemia/epidemiology ; Adolescent ; Infant ; *Registries ; Leukemia, Radiation-Induced/epidemiology ; Infant, Newborn ; Cities/epidemiology ; Environmental Exposure/adverse effects/statistics &amp; numerical data ; Risk Factors ; },
abstract = {Increased incidence rates for childhood leukaemia have been reported in municipalities close to the nuclear power plant (NPP) Krümmel (Geesthacht, Germany). Methodological challenges arise when analysing this association at ecological level. They include the use of an appropriate reference population, unstable estimates of standardised incidence ratios (SIRs), and the potential role of prevailing winds. The aim of our study is to address these challenges. The German Childhood Cancer Registry provided data on leukaemia in children under 15 years (2004-2019). The German Federal Statistical Office provided the population data. The study region included all municipalities with ≥ 75% surface area within 50 kms from the Krümmel NPP. We calculated SIRs using national and regional reference rates. Smoothed incidence relative rates (IRRs) were calculated and mapped to check for potential patterns associated with prevailing winds. Overall 356 cases of childhood leukaemia were observed in the study region (321 municipalities) during 2004-2019. SIRs based on national reference rates show nearly no difference to those calculated using the regional rates as reference. Increased SIR and IRR were observed in Geesthacht (observed-cases = eight; SIR = 2.29; 95% confidence interval: 0.99-4.51. IRR = 1.80; 95% credibility interval: 0.88-2.79). The analysis of the IRR map does not show patterns associated with prevailing winds. Using a regional population as the reference, we found evidence that there may still be an increased risk for childhood leukaemia in Geesthacht. However, IRR estimates are uncertain and credibility intervals are compatible with the absence of elevated risk. The persistent evidence of risk of childhood leukaemia in Geesthacht warrants further epidemiological surveillance.},
}
@article {pmid39585857,
year = {2024},
author = {Adderley-Heron, K and Chow-Fraser, P},
title = {Unsupervised classification of Blanding's turtle (Emydoidea blandingii) behavioural states from multi-sensor biologger data.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0314291},
pmid = {39585857},
issn = {1932-6203},
mesh = {Animals ; *Turtles/physiology/classification ; Female ; Male ; *Behavior, Animal/physiology ; Accelerometry ; Markov Chains ; Geographic Information Systems ; Nesting Behavior/physiology ; },
abstract = {Classifying animal behaviors in their natural environments is both challenging and ecologically important, but the use of biologgers with multiple sensors has significantly advanced this research beyond the capabilities of traditional methods alone. Here, we show how biologgers containing an integrated tri-axial accelerometer, GPS logger and immersion sensor were used to infer behavioural states of a cryptic, freshwater turtle, the Blanding's turtle (Emydoidea blandingii). Biologgers were attached to three males and five females that reside in two undisturbed coastal marshes in northeastern Georgian Bay (Ontario, Canada) between May and July 2023. Raw acceleration values were separated into static and dynamic acceleration and subsequently used to calculate overall dynamic body acceleration (ODBA) and pitch. The unsupervised Hidden Markov Model (HMM) successfully differentiated five behavioural states as follows: active in water, resting in water, active out of water, resting in water, and nesting. Overall accuracy of the classification was 93.8%, and except for nesting (79%), all other behaviours were above 92%. There were significant differences in daily activity budgets between male and female turtles, with females spending a greater proportion of time active out of water, and inactive out of the water, while males spent a greater proportion of time active in water. These differences were likely a result of large seasonal life-history requirements such as nesting and mate finding. Accurate classification of behavioural states is important for researchers to understand fine-scale activities carried out during the active season and how environmental variables may influence the behaviours of turtles in their natural habitats.},
}
@article {pmid39585479,
year = {2024},
author = {Sahak, AS and Karsli, F and Saraj, MA},
title = {Evaluating the impact of urban sprawl on the urban ecological status using GIS and remote sensing from 2000 to 2021: a case study of Herat City, Afghanistan.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {12},
pages = {1246},
pmid = {39585479},
issn = {1573-2959},
mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; *Urbanization ; *Cities ; Afghanistan ; Conservation of Natural Resources/methods ; Ecosystem ; },
abstract = {Urbanization often incurs environmental costs, as fertile agricultural and forested lands are converted into urban areas. Herat City is currently undergoing significant urban transformation. This research aims to assess the impact of urban sprawl on Herat City's urban ecological status during 2000, 2013, and 2021, using GIS and remote sensing. The urban expansion intensity index was used to measure urban sprawl. The Mean Remote Sensing Ecological Index (MRSEI), integrating known granulation entropy (KGE) and comprehensive distance-based ranking (COBRA) algorithms, was utilized to evaluate urban ecological status. The random forest (RF) supervised machine learning-based algorithm was used to classify the study area into four categories (Built-up, Bare-land, Water, and Vegetation). Findings indicate rapid development from 2000 to 2013, followed by moderate expansion until 2021. Urban ecological quality degradation is observed in various directions over time, with the southeast consistently demonstrating excellent status. Interestingly, while good and excellent urban ecological status decreases over two decades, poor and very poor conditions improve. The research underscores an inverse relationship between urban expansion intensity and ecological status, highlighting the need for improved strategies to mitigate environmental decline. These findings will inform Afghan governmental bodies and international organizations, enabling them to better address resource consumption, ecological disruptions, social inequalities, and foster sustainable development.},
}
@article {pmid39583330,
year = {2024},
author = {Hakkenberg, CR and Clark, ML and Bailey, T and Burns, P and Goetz, SJ},
title = {Ladder fuels rather than canopy volumes consistently predict wildfire severity even in extreme topographic-weather conditions.},
journal = {Communications earth &amp; environment},
volume = {5},
number = {1},
pages = {721},
pmid = {39583330},
issn = {2662-4435},
abstract = {Drivers of forest wildfire severity include fuels, topography and weather. However, because only fuels can be actively managed, quantifying their effects on severity has become an urgent research priority. Here we employed GEDI spaceborne lidar to consistently assess how pre-fire forest fuel structure affected wildfire severity across 42 California wildfires between 2019-2021. Using a spatial-hierarchical modeling framework, we found a positive concave-down relationship between GEDI-derived fuel structure and wildfire severity, marked by increasing severity with greater fuel loads until a decline in severity in the tallest and most voluminous forest canopies. Critically, indicators of canopy fuel volumes (like biomass and height) became decoupled from severity patterns in extreme topographic and weather conditions (slopes >20°; winds > 9.3 m/s). On the other hand, vertical continuity metrics like layering and ladder fuels more consistently predicted severity in extreme conditions - especially ladder fuels, where sparse understories were uniformly associated with lower severity levels. These results confirm that GEDI-derived fuel estimates can overcome limitations of optical imagery and airborne lidar for quantifying the interactive drivers of wildfire severity. Furthermore, these findings have direct implications for designing treatment interventions that target ladder fuels versus entire canopies and for delineating wildfire risk across topographic and weather conditions.},
}
@article {pmid39581005,
year = {2024},
author = {Tinsley, E and Froidevaux, JSP and Jones, G},
title = {The location of solar farms within England's ecological landscape: Implications for biodiversity conservation.},
journal = {Journal of environmental management},
volume = {372},
number = {},
pages = {123372},
doi = {10.1016/j.jenvman.2024.123372},
pmid = {39581005},
issn = {1095-8630},
mesh = {*Biodiversity ; England ; *Conservation of Natural Resources ; *Ecosystem ; Solar Energy ; Farms ; Geographic Information Systems ; Ecology ; Agriculture ; },
abstract = {A global energy transition to using sustainable renewable sources is being driven by global agreements. Simultaneously there is a call for increased biodiversity conservation. This creates a green-green dilemma, where the expansion of renewables could lead to the demise of biodiversity if not carefully assessed, managed and monitored. Recognition of the dilemma is central to the development of Sustainable Development Goals. It is therefore important to understand whether renewable energy sources such as solar farms are being sited in areas where they have minimal impact on biodiversity. If solar farms were sited with minimal impacts on biodiversity, we hypothesised that they would be less likely to be sited close to ecologically sensitive areas than near random points. We used Geographic Information System methods to explore the density of solar photovoltaic (PV) farms in England and assessed their siting relative to sensitive ecological features, including priority habitat types, designated sites, and land conservation initiatives. We compared the area of 25 sensitive ecological features around solar farms and random points across three spatial scales (100 m, 1000 m, and 6000 m radius scales). Solar farms were distributed throughout England, with the highest concentration in South West England. Solar sites were primarily surrounded by habitats with anthropogenic influences, such as agricultural and urban settings. Priority habitats, such as woodland, grassland, wetland and heathland, were more extensive around random points across spatial scales (except for woodland at the largest scale). Most designated sites were significantly more extensive around random points. We conclude that, under current planning regulations, solar sites in England are being placed appropriately with regard to sensitive ecological habitats, and are often sited in areas already impacted by farming and development. Adaptive planning should be implemented to ensure that the evolving research around biodiversity and solar farms is incorporated into decision making, and monitoring is completed across the lifespan of solar farms to assess impacts and effective mitigation.},
}
@article {pmid39580513,
year = {2024},
author = {Li, J and Weckwerth, W and Waldherr, S},
title = {Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian.},
journal = {NPJ systems biology and applications},
volume = {10},
number = {1},
pages = {137},
pmid = {39580513},
issn = {2056-7189},
support = {201806010428//China Scholarship Council (CSC)/ ; },
mesh = {Humans ; *Algorithms ; *Metabolic Networks and Pathways/genetics ; *Breast Neoplasms/metabolism/genetics ; *Metabolomics/methods ; Cell Line, Tumor ; Models, Biological ; Computational Biology/methods ; Female ; Systems Biology/methods ; },
abstract = {Based on high-throughput metabolomics data, the recently introduced inverse differential Jacobian algorithm can infer regulatory factors and molecular causality within metabolic networks close to steady-state. However, these studies assumed perturbations acting independently on each metabolite, corresponding to metabolic system fluctuations. In contrast, emerging evidence puts forward internal network fluctuations, particularly from gene expression fluctuations, leading to correlated perturbations on metabolites. Here, we propose a novel approach that exploits these correlations to quantify relevant metabolic interactions. By integrating enzyme-related fluctuations in the construction of an appropriate fluctuation matrix, we are able to exploit the underlying reaction network structure for the inverse Jacobian algorithm. We applied this approach to a model-based artificial dataset for validation, and to an experimental breast cancer dataset with two different cell lines. By highlighting metabolic interactions with significantly changed interaction strengths, the inverse Jacobian approach identified critical dynamic regulation points which are confirming previous breast cancer studies.},
}
@article {pmid39578727,
year = {2024},
author = {Ang'ang'o, LM and Herren, JK and Tastan Bishop, &#xd6;},
title = {Bioinformatics analysis of the Microsporidia sp. MB genome: a malaria transmission-blocking symbiont of the Anopheles arabiensis mosquito.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1132},
pmid = {39578727},
issn = {1471-2164},
mesh = {*Anopheles/microbiology/parasitology/genetics ; Animals ; *Microsporidia/genetics ; *Symbiosis ; *Computational Biology/methods ; *Genome, Fungal ; Malaria/transmission ; Phylogeny ; Mosquito Vectors/microbiology/genetics ; Genomics/methods ; RNA Interference ; },
abstract = {BACKGROUND: The use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mosquitoes, can be transmitted both vertically and horizontally with minimal effects on its mosquito host. Its genome, recently sequenced from An. arabiensis, comprises a compact 5.9 Mbp.<br><br>RESULTS: Here, we analyze the Microsporidia sp. MB genome, highlighting its major genomic features, gene content, and protein function. The genome contains 2247 genes, predominantly encoding enzymes. Unlike other members of the Enterocytozoonida group, Microsporidia sp. MB has retained most of the genes in the glycolytic pathway. Genes involved in RNA interference (RNAi) were also identified, suggesting a mechanism for host immune suppression. Importantly, meiosis-related genes (MRG) were detected, indicating potential for sexual reproduction in this organism. Comparative analyses revealed similarities with its closest relative, Vittaforma corneae, despite key differences in host interactions.<br><br>CONCLUSION: This study provides an in-depth analysis of the newly sequenced Microsporidia sp. MB genome, uncovering its unique adaptations for intracellular parasitism, including retention of essential metabolic pathways and RNAi machinery. The identification of MRGs suggests the possibility of sexual reproduction, offering insights into the symbiont's evolutionary strategies. Establishing a reference genome for Microsporidia sp. MB sets the foundation for future studies on its role in malaria transmission dynamics and host-parasite interactions.},
}
@article {pmid39576832,
year = {2024},
author = {Devadhasan, A and Kolodny, O and Carja, O},
title = {Competition for resources can reshape the evolutionary properties of spatial structure.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012542},
pmid = {39576832},
issn = {1553-7358},
support = {R35 GM147445/GM/NIGMS NIH HHS/United States ; T32 EB009403/EB/NIBIB NIH HHS/United States ; },
mesh = {*Ecosystem ; Humans ; *Biological Evolution ; Computational Biology ; Mutation ; Models, Biological ; Computer Simulation ; },
abstract = {Many evolving ecosystems have spatial structures that can be conceptualized as networks, with nodes representing individuals or homogeneous subpopulations and links the patterns of spread between them. Prior models of evolution on networks do not take ecological niche differences and eco-evolutionary interplay into account. Here, we combine a resource competition model with evolutionary graph theory to study how heterogeneous topological structure shapes evolutionary dynamics under global frequency-dependent ecological interactions. We find that the addition of ecological competition for resources can produce a reversal of roles between amplifier and suppressor networks for deleterious mutants entering the population. We show that this effect is a nonlinear function of ecological niche overlap and discuss intuition for the observed dynamics using simulations and analytical approximations. We use these theoretical results together with spatial representations from imaging data to show that, for ductal carcinoma, where tumor growth is highly spatially constrained, with cells confined to a tree-like network of ducts, the topological structure can lead to higher rates of deleterious mutant hitchhiking with metabolic driver mutations, compared to tumors characterized by different spatial topologies.},
}
@article {pmid39570994,
year = {2024},
author = {Madden, WG and Jin, W and Lopman, B and Zufle, A and Dalziel, B and E Metcalf, CJ and Grenfell, BT and Lau, MSY},
title = {Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012616},
pmid = {39570994},
issn = {1553-7358},
mesh = {*Measles/epidemiology ; Humans ; *Neural Networks, Computer ; *Disease Outbreaks/statistics &amp; numerical data ; *Endemic Diseases/statistics &amp; numerical data ; England/epidemiology ; Wales/epidemiology ; Computational Biology ; Forecasting/methods ; Epidemiological Models ; },
abstract = {Measles is an important infectious disease system both for its burden on public health and as an opportunity for studying nonlinear spatio-temporal disease dynamics. Traditional mechanistic models often struggle to fully capture the complex nonlinear spatio-temporal dynamics inherent in measles outbreaks. In this paper, we first develop a high-dimensional feed-forward neural network model with spatial features (SFNN) to forecast endemic measles outbreaks and systematically compare its predictive power with that of a classical mechanistic model (TSIR). We illustrate the utility of our model using England and Wales measles data from 1944-1965. These data present multiple modeling challenges due to the interplay between metapopulations, seasonal trends, and nonlinear dynamics related to demographic changes. Our results show that while the TSIR model yields similarly performant short-term (1 to 2 biweeks ahead) forecasts for highly populous cities, our neural network model (SFNN) consistently achieves lower root mean squared error (RMSE) across other forecasting windows. Furthermore, we show that our spatial-feature neural network model, without imposing mechanistic assumptions a priori, can uncover gravity-model-like spatial hierarchy of measles spread in which major cities play an important role in driving regional outbreaks. We then turn our attention to integrative approaches that combine mechanistic and machine learning models. Specifically, we investigate how the TSIR can be utilized to improve a state-of-the-art approach known as Physics-Informed-Neural-Networks (PINN) which explicitly combines compartmental models and neural networks. Our results show that the TSIR can facilitate the reconstruction of latent susceptible dynamics, thereby enhancing both forecasts in terms of mean absolute error (MAE) and parameter inference of measles dynamics within the PINN. In summary, our results show that appropriately designed neural network-based models can outperform traditional mechanistic models for short to long-term forecasts, while simultaneously providing mechanistic interpretability. Our work also provides valuable insights into more effectively integrating machine learning models with mechanistic models to enhance public health responses to measles and similar infectious disease systems.},
}
@article {pmid39570888,
year = {2024},
author = {Cuesta-Aguirre, DR and Malgosa, A and Santos, C},
title = {An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0311115},
pmid = {39570888},
issn = {1932-6203},
mesh = {*DNA, Mitochondrial/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Forensic Genetics/methods ; DNA, Ancient/analysis ; },
abstract = {Genome and transcriptome examinations have become more common due to Next-Generation Sequencing (NGS), which significantly increases throughput and depth coverage while reducing costs and time. Mitochondrial DNA (mtDNA) is often the marker of choice in degraded samples from archaeological and forensic contexts, as its higher number of copies can improve the success of the experiment. Among other sequencing strategies, amplicon-based NGS techniques are currently being used to obtain enough data to be analyzed. There are some pipelines designed for the analysis of ancient mtDNA samples and others for the analysis of amplicon data. However, these pipelines pose a challenge for non-expert users and cannot often address both ancient and forensic DNA particularities and amplicon-based sequencing simultaneously. To overcome these challenges, a user-friendly bioinformatic tool was developed to analyze the non-coding region of human mtDNA from degraded samples recovered in archaeological and forensic contexts. The tool can be easily modified to fit the specifications of other amplicon-based NGS experiments. A comparative analysis between two tools, MarkDuplicates from Picard and dedup parameter from fastp, both designed for duplicate removal was conducted. Additionally, various thresholds of PMDtools, a specialized tool designed for extracting reads affected by post-mortem damage, were used. Finally, the depth coverage of each amplicon was correlated with its level of damage. The results obtained indicated that, for removing duplicates, dedup is a better tool since retains more non-repeated reads, that are removed by MarkDuplicates. On the other hand, a PMDS = 1 in PMDtools was the threshold that allowed better differentiation between present-day and ancient samples, in terms of damage, without losing too many reads in the process. These two bioinformatic tools were added to a pipeline designed to obtain both haplotype and haplogroup of mtDNA. Furthermore, the pipeline presented in the present study generates information about the quality and possible contamination of the sample. This pipeline is designed to automatize mtDNA analysis, however, particularly for ancient samples, some manual analyses may be required to fully validate results since the amplicons that used to be more easily recovered were the ones that had fewer reads with damage, indicating that special care must be taken for poor recovered samples.},
}
@article {pmid39569566,
year = {2024},
author = {Sung, ML and León, C and Reisman, JI and Gordon, KS and Kerns, RD and Li, W and Liu, W and Mitra, A and Yu, H and Becker, WC},
title = {Disparities in Receipt of Medications for Opioid Use Disorder Before and During the COVID-19 Pandemic in the US Veterans Health Administration.},
journal = {Substance use &amp; addiction journal},
volume = {},
number = {},
pages = {29767342241293334},
doi = {10.1177/29767342241293334},
pmid = {39569566},
issn = {2976-7350},
abstract = {BACKGROUND: Populations disproportionately impacted by the opioid epidemic are less likely to receive medications for opioid use disorder (MOUD; OUD). The COVID-19 pandemic exacerbated these disparities. We performed an ecological survey of subpopulations to compare differences in MOUD receipt among Veterans with OUD before versus during the pandemic.<br><br>METHODS: Using 2 cross-sections of 2 time periods of national Veterans Health Administration electronic health record data, we calculated proportions of Veterans with any MOUD receipt by demographics, Elixhauser comorbidity index, and natural language processing (NLP)-derived substance use and social determinants of health in each time period. We evaluated differences in MOUD receipt before and during the pandemic by patient characteristics using Chi-square and Cohen's h for effect size.<br><br>RESULTS: Among 62&#x2009;195 patients with OUD before the pandemic, the proportion prescribed MOUD increased from 46.5% before to 47.5% (P&#x2009;=&#x2009;.0003) during the pandemic. Statistically significant increased receipt of MOUD was observed for patients who were &#x2265;55&#x2009;years, men, White, with Elixhauser comorbidity indices of 2 and &#x2265;5, and with NLP-derived indicators of substance use. There was a decrease that did not achieve statistical significance in MOUD receipt from before to during the pandemic for patients who were women, Black, Latinx, and food insecure.<br><br>CONCLUSIONS: The proportions of patients with OUD prescribed MOUD increased from before to during the pandemic. However, Veterans who were women, Black, Latinx, and food insecure did not experience these increases. These patients may benefit from interventions such as targeted outreach efforts to improve MOUD engagement to reduce OUD harms.},
}
@article {pmid39569448,
year = {2024},
author = {Yu, Y and Edelson, M and Pham, A and Pekar, JE and Johnson, B and Post, K and Kuo, TT},
title = {Distributed, immutable, and transparent biomedical limited data set request management on multi-capacity network.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {},
number = {},
pages = {},
doi = {10.1093/jamia/ocae288},
pmid = {39569448},
issn = {1527-974X},
support = {R01EB031030//U.S. National Institutes of Health/ ; },
abstract = {OBJECTIVE: Our study aimed to expedite data sharing requests of Limited Data Sets (LDS) through the development of a streamlined platform that allows distributed, immutable management of network activities, provides transparent and intuitive auditing of data access history, and systematically evaluated it on a multi-capacity network setting for meaningful efficiency metrics.<br><br>MATERIALS AND METHODS: We developed a blockchain-based system with six types of smart contracts to automate the LDS sharing process among major stakeholders. Our workflow included metadata initialization, access-request processing, and audit-log querying. We evaluated our system using synthetic data on three machines with varying specifications to emulate real-world scenarios. The data employed included &#x223c;1000 researcher requests and &#x223c;360&#xa0;000 log queries.<br><br>RESULTS: On average, it took &#x223c;2.5&#xa0;s to register and respond to a researcher access request. The average runtime for an audit-log query with non-empty output was &#x223c;3&#xa0;ms. The runtime metrics at each institution showed general trends affiliated with their computational capacity.<br><br>DISCUSSION: Our system can reduce the LDS sharing request time from potentially hours to seconds, while enhancing data access transparency in a multi-institutional setting. There were variations in performance across sites that could be attributed to differences in hardware specifications. The performance gains became marginal beyond certain hardware thresholds, pointing to the influence of external factors such as network speeds.<br><br>CONCLUSION: Our blockchain-based system can potentially accelerate clinical research by strengthening the data access process, expediting access and delivery of data links, increasing transparency with clear audit trails, and reinforcing trust in medical data management. Our smart contracts are available at: https://github.com/graceyufei/LDS-Request-Management.},
}
@article {pmid39568559,
year = {2024},
author = {Boyes, D and Hutchinson, F and Crowley, LM and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Silver-barred Sober moth, Aproaerema taeniolella (Zeller, 1839).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {500},
pmid = {39568559},
issn = {2398-502X},
abstract = {We present a genome assembly of a female Silver-barred Sober moth Aproaerema taeniolella (Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a length of 636.60 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,274 protein-coding genes.},
}
@article {pmid39564491,
year = {2024},
author = {Zhang, Y and Wang, M and Huang, M and Zhao, J},
title = {Innovative strategies and challenges mosquito-borne disease control amidst climate change.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1488106},
pmid = {39564491},
issn = {1664-302X},
abstract = {The revival of the transmission dynamics of mosquito-borne diseases grants striking challenges to public health intensified by climate change worldwide. This inclusive review article examines multidimensional strategies and challenges linked to climate change and the epidemiology of mosquito-borne diseases such as malaria, dengue, Zika, chikungunya, and yellow fever. It delves into how the biology, pathogenic dynamics, and vector distribution of mosquitoes are influenced by continuously rising temperatures, modified rainfall patterns, and extreme climatic conditions. We also highlighted the high likelihood of malaria in Africa, dengue in Southeast Asia, and blowout of Aedes in North America and Europe. Modern predictive tools and developments in surveillance, including molecular gears, Geographic Information Systems (GIS), and remote sensing have boosted our capacity to predict epidemics. Integrated data management techniques and models based on climatic conditions provide a valuable understanding of public health planning. Based on recent data and expert ideas, the objective of this review is to provide a thoughtful understanding of existing landscape and upcoming directions in the control of mosquito-borne diseases regarding changing climate. This review determines emerging challenges and innovative vector control strategies in the changing climatic conditions to ensure public health.},
}
@article {pmid39563951,
year = {2024},
author = {Sivell, O and Hawkes, WLS and , and , and , and , and , and , and , },
title = {The genome sequence of the silvery leafcutter bee, Megachile leachella Curtis, 1828.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {415},
pmid = {39563951},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Megachile leachella (the silvery leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 573.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.04 kilobases in length.},
}
@article {pmid39563229,
year = {2024},
author = {Toth, AL and Wyatt, CDR and Masonbrink, RE and Geist, KS and Fortune, R and Scott, SB and Favreau, E and Rehan, SM and Sumner, S and Gardiner, MM and Sivakoff, FS},
title = {New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1106},
pmid = {39563229},
issn = {1471-2164},
support = {20176701326595//USDA National Institute of Food and Agriculture/ ; 1929239//NSF DEB-NERC/ ; },
mesh = {Animals ; Bees/genetics/drug effects ; *Metals, Heavy/toxicity ; *Transcriptome ; Genomics/methods ; Molecular Sequence Annotation ; Gene Expression Profiling ; Genome, Insect ; Toxins, Biological/genetics ; },
abstract = {BACKGROUND: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.<br><br>RESULTS: PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6&#xa0;Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with &#x2265;&#x2009;96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.<br><br>CONCLUSIONS: Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.},
}
@article {pmid39561196,
year = {2024},
author = {Konzen, E and Delahay, RJ and Hodgson, DJ and McDonald, RA and Brooks Pollock, E and Spencer, SEF and McKinley, TJ},
title = {Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012592},
pmid = {39561196},
issn = {1553-7358},
mesh = {Animals ; *Mustelidae/microbiology ; *Tuberculosis, Bovine/epidemiology/transmission/diagnosis ; Cattle ; *Animals, Wild/microbiology ; United Kingdom/epidemiology ; Models, Biological ; Mycobacterium bovis ; Computational Biology/methods ; Disease Reservoirs/microbiology/veterinary ; Ireland/epidemiology ; },
abstract = {Bovine tuberculosis (bTB) has significant socio-economic and welfare impacts on the cattle industry in parts of the world. In the United Kingdom and Ireland, disease control is complicated by the presence of infection in wildlife, principally the European badger. Control strategies tend to be applied to whole populations, but better identification of key sources of transmission, whether individuals or groups, could help inform more efficient approaches. Mechanistic transmission models can be used to better understand key epidemiological drivers of disease spread and identify high-risk individuals and groups if they can be adequately fitted to observed data. However, this is a significant challenge, especially within wildlife populations, because monitoring relies on imperfect diagnostic test information, and even under systematic surveillance efforts (such as capture-mark-recapture sampling) epidemiological events are only partially observed. To this end we develop a stochastic compartmental model of bTB transmission, and fit this to individual-level data from a unique > 40-year longitudinal study of 2,391 badgers using a recently developed individual forward filtering backward sampling algorithm. Modelling challenges are further compounded by spatio-temporal meta-population structures and age-dependent mortality. We develop a novel estimator for the individual effective reproduction number that provides quantitative evidence for the presence of superspreader badgers, despite the population-level effective reproduction number being less than one. We also infer measures of the hidden burden of infection in the host population through time; the relative likelihoods of competing routes of transmission; effective and realised infectious periods; and longitudinal measures of diagnostic test performance. This modelling framework provides an efficient and generalisable way to fit state-space models to individual-level data in wildlife populations, which allows identification of high-risk individuals and exploration of important epidemiological questions about bTB and other wildlife diseases.},
}
@article {pmid39556417,
year = {2024},
author = {Helgeson, SA and Mudgalkar, RM and Jacobs, KA and Lee, AS and Sanghavi, D and Moreno Franco, P and Brooks, IS and , },
title = {Association Between X/Twitter and Prescribing Behavior During the COVID-19 Pandemic: Retrospective Ecological Study.},
journal = {JMIR infodemiology},
volume = {4},
number = {},
pages = {e56675},
pmid = {39556417},
issn = {2564-1891},
support = {U24 TR002306/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Retrospective Studies ; *Hydroxychloroquine/therapeutic use ; *Social Media ; United States/epidemiology ; *COVID-19/epidemiology ; *Practice Patterns, Physicians' ; Pandemics ; COVID-19 Drug Treatment ; Male ; Female ; Middle Aged ; SARS-CoV-2/drug effects ; },
abstract = {BACKGROUND: Social media has become a vital tool for health care providers to quickly share information. However, its lack of content curation and expertise poses risks of misinformation and premature dissemination of unvalidated data, potentially leading to widespread harmful effects due to the rapid and large-scale spread of incorrect information.<br><br>OBJECTIVE: We aim to determine whether social media had an undue association with the prescribing behavior of hydroxychloroquine, using the COVID-19 pandemic as the setting.<br><br>METHODS: In this retrospective study, we gathered the use of hydroxychloroquine in 48 hospitals in the United States between January and December 2020. Social media data from X/Twitter was collected using Brandwatch, a commercial aggregator with access to X/Twitter's data, and focused on mentions of "hydroxychloroquine" and "Plaquenil." Tweets were categorized by sentiment (positive, negative, or neutral) using Brandwatch's sentiment analysis tool, with results classified by date. Hydroxychloroquine prescription data from the National COVID Cohort Collaborative for 2020 was used. Granger causality and linear regression models were used to examine relationships between X/Twitter mentions and prescription trends, using optimum time lags determined via vector auto-regression.<br><br>RESULTS: A total of 581,748 patients with confirmed COVID-19 were identified. The median daily number of positive COVID-19 cases was 1318.5 (IQR 1005.75-1940.3). Before the first confirmed COVID-19 case, hydroxychloroquine was prescribed at a median rate of 559 (IQR 339.25-728.25) new prescriptions per day. A day-of-the-week effect was noted in both prescriptions and case counts. During the pandemic in 2020, hydroxychloroquine prescriptions increased significantly, with a median of 685.5 (IQR 459.75-897.25) per day, representing a 22.6% rise from baseline. The peak occurred on April 2, 2020, with 3411 prescriptions, a 397.6% increase. Hydroxychloroquine mentions on X/Twitter peaked at 254,770 per day on April 5, 2020, compared to a baseline of 9124 mentions per day before January 21, 2020. During this study's period, 3,823,595 total tweets were recorded, with 10.09% (n=386,115) positive, 37.87% (n=1,448,030) negative, and 52.03% (n=1,989,450) neutral sentiments. A 1-day lag was identified as the optimal time for causal association between tweets and hydroxychloroquine prescriptions. Univariate analysis showed significant associations across all sentiment types, with the largest impact from positive tweets. Multivariate analysis revealed only neutral and negative tweets significantly affected next-day prescription rates.<br><br>CONCLUSIONS: During the first year of the COVID-19 pandemic, there was a significant association between X/Twitter mentions and the number of prescriptions of hydroxychloroquine. This study showed that X/Twitter has an association with the prescribing behavior of hydroxychloroquine. Clinicians need to be vigilant about their potential unconscious exposure to social media as a source of medical knowledge, and health systems and organizations need to be more diligent in identifying expertise, source, and quality of evidence when shared on social media platforms.},
}
@article {pmid39555185,
year = {2024},
author = {Yang, D and Hashizume, M and Tobías, A and Honda, Y and Roye, D and Oh, J and Dang, TN and Kim, Y and Abrutzky, R and Guo, Y and Tong, S and Coelho, MSZS and Saldiva, PHN and Lavigne, E and Correa, PM and Ortega, NV and Osorio, S and Kyselý, J and Urban, A and Orru, H and Indermitte, E and Jaakkola, J and Ryti, N and Pascal, M and Huber, V and Schneider, A and Katsouyanni, K and Analitis, A and Entezari, A and Mayvaneh, F and Goodman, P and Zeka, A and Michelozzi, P and de'Donato, F and Alahmad, B and Diaz, MH and la Cruz Valencia, C and Overcenco, A and Houthuijs, D and Ameling, C and Rao, S and Nunes, B and Madureira, J and Holo-Bâc, IH and Scovronick, N and Acquaotta, F and Kim, H and Lee, W and Íñiguez, C and Forsberg, B and Vicedo-Cabrera, AM and Ragettli, MS and Guo, YL and Pan, SC and Li, S and Sera, F and Zanobetti, A and Schwartz, J and Armstrong, B and Gasparrini, A and Chung, Y},
title = {Temporal change in minimum mortality temperature under changing climate: A multicountry multicommunity observational study spanning 1986-2015.},
journal = {Environmental epidemiology (Philadelphia, Pa.)},
volume = {8},
number = {5},
pages = {e334},
pmid = {39555185},
issn = {2474-7882},
support = {MR/R013349/1/MRC_/Medical Research Council/United Kingdom ; MR/V034162/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: The minimum mortality temperature (MMT) or MMT percentile (MMTP) is an indicator of population susceptibility to nonoptimum temperatures. MMT and MMTP change over time; however, the changing directions show region-wide heterogeneity. We examined the heterogeneity of temporal changes in MMT and MMTP across multiple communities and in multiple countries.<br><br>METHODS: Daily time-series data for mortality and ambient mean temperature for 699 communities in 34 countries spanning 1986-2015 were analyzed using a two-stage meta-analysis. First, a quasi-Poisson regression was employed to estimate MMT and MMTP for each community during the designated subperiods. Second, we pooled the community-specific temporally varying estimates using mixed-effects meta-regressions to examine temporal changes in MMT and MMTP in the entire study population, as well as by climate zone, geographical region, and country.<br><br>RESULTS: Temporal increases in MMT and MMTP from 19.5 &#xb0;C (17.9, 21.1) to 20.3 &#xb0;C (18.5, 22.0) and from the 74.5 (68.3, 80.6) to 75.0 (71.0, 78.9) percentiles in the entire population were found, respectively. Temporal change was significantly heterogeneous across geographical regions (P < 0.001). Temporal increases in MMT were observed in East Asia (linear slope [LS] = 0.91, P = 0.02) and South-East Asia (LS = 0.62, P = 0.05), whereas a temporal decrease in MMT was observed in South Europe (LS = -0.46, P = 0.05). MMTP decreased temporally in North Europe (LS = -3.45, P = 0.02) and South Europe (LS = -2.86, P = 0.05).<br><br>CONCLUSIONS: The temporal change in MMT or MMTP was largely heterogeneous. Population susceptibility in terms of optimum temperature may have changed under a warming climate, albeit with large region-dependent variations.},
}
@article {pmid39549265,
year = {2024},
author = {Rayamajhi, N and Rivera-Colón, AG and Minhas, BF and Cheng, CC and Catchen, JM},
title = {The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae267},
pmid = {39549265},
issn = {2160-1836},
abstract = {The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.},
}
@article {pmid39548719,
year = {2024},
author = {Chen, Y and Gao, Y and Zhang, Z and Zhan, A},
title = {Multi-Omics Inform Invasion Risks Under Global Climate Change.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17588},
doi = {10.1111/gcb.17588},
pmid = {39548719},
issn = {1365-2486},
support = {2022GDASZH-2022010106//GDAS Special Project of Science and Technology Development/ ; 2024A1515010914//Guangdong Basic and Applied Basic Research Foundation/ ; 42106098//National Natural Science Foundation of China/ ; 32061143012//National Natural Science Foundation of China/ ; 42276126//National Natural Science Foundation of China/ ; 32371753//National Natural Science Foundation of China/ ; },
mesh = {*Climate Change ; *Introduced Species ; *Genomics ; Urochordata/genetics ; Epigenomics ; Adaptation, Physiological/genetics ; Animals ; Multiomics ; },
abstract = {Global climate change is exacerbating biological invasions; however, the roles of genomic and epigenomic variations and their interactions in future climate adaptation remain underexplored. Using the model invasive ascidian Botryllus schlosseri across the Northern Hemisphere, we investigated genomic and epigenomic responses to future climates and developed a framework to assess future invasion risks. We employed generalized dissimilarity modeling and gradient forest analyses to assess genomic and epigenomic offsets under climate change. Our results showed that populations with genomic maladaptation did not geographically overlap with those experiencing epigenomic maladaptation, suggesting that genomic and epigenomic variations play complementary roles in adaptation to future climate conditions. By integrating genomic and epigenomic offsets into the genome-epigenomic index, we predicted that populations with lower index values were less maladapted, indicating a higher risk of future invasions. Native populations exhibited lower offsets than invasive populations, suggesting greater adaptive potentials and higher invasion risks under future climate change scenarios. These results highlight the importance of incorporating multi-omics data into predictive models to study future climate (mal)adaptation and assess invasion risks under global climate change.},
}
@article {pmid39548060,
year = {2024},
author = {Conrad, RE and Brink, CE and Viver, T and Rodriguez-R, LM and Aldeguer-Riquelme, B and Hatt, JK and Venter, SN and Rossello-Mora, R and Amann, R and Konstantinidis, KT},
title = {Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9906},
pmid = {39548060},
issn = {2041-1723},
support = {1831582//NSF | BIO | Division of Environmental Biology (DEB)/ ; },
mesh = {*Homologous Recombination ; *Escherichia coli/genetics/classification ; Genome, Bacterial ; Microbiota/genetics ; Evolution, Molecular ; Gene Flow ; Phylogeny ; Computational Biology/methods ; },
abstract = {Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.},
}
@article {pmid39547957,
year = {2024},
author = {Kwon, EJ and Lee, H and Shin, U and Kim, ES and Myung, K and Kim, J and Park, JH and Kim, K and Lee, Y and Oh, CK and Kim, YH},
title = {Ionizing radiation inhibits zebrafish embryo hatching through induction of tissue inhibitors of metalloproteinases (TIMPs) expression.},
journal = {The FEBS journal},
volume = {291},
number = {24},
pages = {5470-5485},
doi = {10.1111/febs.17318},
pmid = {39547957},
issn = {1742-4658},
support = {IBS-R022-D1//Institute for Basic Science/ ; RS-2023-00223591//National Research Foundation of Korea/ ; RS-2023-00301938//National Research Foundation of Korea/ ; RS-2024-00439078//National Research Foundation of Korea/ ; //KREONET/ ; },
mesh = {Animals ; *Zebrafish/genetics/embryology/metabolism ; *Radiation, Ionizing ; *Tissue Inhibitor of Metalloproteinases/metabolism/genetics ; *Gene Expression Regulation, Developmental/radiation effects ; *Embryo, Nonmammalian/radiation effects/metabolism ; Zebrafish Proteins/genetics/metabolism ; },
abstract = {Ionizing radiation (IR) has garnered growing attention because of its biological effects on aquatic organisms and humans. Here, we identify the most impacted organs and uncover the molecular mechanisms causing the changes in the context of vertebrate development using single-cell RNA sequencing. Alterations in cellular composition and biological functions were explored using transcriptomic profiling of zebrafish embryos exposed to 5 Gy. Single-cell RNA sequencing analyses unveiled notable shifts in the proportions of brain/central nervous system and hatching gland clusters. Although IR exposure led to increased expression of hatching enzymes, a significant but mild delay in hatching was observed following 5 Gy IR exposure. Gene Ontology analysis showed an increased expression of tissue inhibitors of metalloproteinases (TIMPs), known as matrix metalloproteinase inhibitors, which was confirmed via whole-mount in situ hybridization. Correlation analysis linked TIMPs to transcription factors cebpb and cebpd, which were significantly correlated post-IR exposure. Although no morphological changes were observed in some organs, including the brain, the study reveals substantial alterations in developing vertebrates. Notably, despite increased hatching enzymes, elevated TIMPs in the hatching gland suggest a regulatory mechanism impacting hatching activity. This research contributes to comprehending the ecological repercussions of IR exposure, emphasizing the importance of safety measures for aquatic ecosystems and overall environmental health.},
}
@article {pmid39546825,
year = {2025},
author = {Meyer, A and Ndiaye, B and Larkins, A and Chaters, G and Gilbert, W and Huntington, B and Ilboudo, G and Dione, M and Jemberu, WT and Diouf, MN and Fall, AG and Fall, M and Lo, M and Rushton, J},
title = {Economic assessment of animal disease burden in Senegalese small ruminants.},
journal = {Preventive veterinary medicine},
volume = {234},
number = {},
pages = {106382},
doi = {10.1016/j.prevetmed.2024.106382},
pmid = {39546825},
issn = {1873-1716},
mesh = {Animals ; Senegal/epidemiology ; *Goat Diseases/economics/epidemiology ; *Goats ; Sheep ; *Sheep Diseases/economics/epidemiology ; Cost of Illness ; Animal Husbandry/economics/methods ; },
abstract = {Small ruminant production in sub-Saharan Africa is limited by a range of constraints, including animal health issues. This study aimed at estimating the impact of these issues on the small ruminant production in Senegal in a holistic manner, using an approach developed by the Global Burden of Animal Diseases (GBADs) programme. The estimation focused on the mixed crop-livestock system, representing a large proportion (>60 %) of the small ruminant population in the country. It was based on existing data collected via a systematic literature review, acquisition of secondary datasets from local stakeholders, and expert elicitation. A dynamic population model was used to calculate the gross margin of the sector under both the current health constraints and an ideal health state, where animals are not exposed to causes of morbidity and mortality. The difference between the current and ideal health scenarios, termed the Animal Health Loss Envelope (AHLE), provides a quantitative measure of the farm-level cost of disease in the system. The all-cause AHLE was estimated at 292 billion FCFA (468 million USD, with 95 % prediction interval 216 - 366 billion FCFA) per year for 2022, for a population of 8.8 million animals. The contribution of Peste des Petits Ruminants (PPR) was modelled separately, as an example of attributing part of the AHLE to a specific disease cause. PPR was estimated to contribute 5 % of the total AHLE. The animal disease burden experienced by Senegalese livestock keepers was largely due to loss in animals and production, with relatively small amounts of animal health expenditure. Implementation of this study contributed to the further development of the GBADs approach. Such estimates can support decision making at all levels, from investment decisions at the international level to local disease awareness campaigns targeting livestock keepers.},
}
@article {pmid39545367,
year = {2024},
author = {Heuck, MK and Powell, JR and Kath, J and Birnbaum, C and Frew, A},
title = {Evaluating the Usefulness of the C-S-R Framework for Understanding AM Fungal Responses to Climate Change in Agroecosystems.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17566},
doi = {10.1111/gcb.17566},
pmid = {39545367},
issn = {1365-2486},
support = {DE220100479//Australian Research Council (ARC) Discovery Early Career Researcher Award (DECRA)/ ; FT190100590//Australian Research Council Future Fellowship/ ; },
mesh = {*Climate Change ; *Mycorrhizae/physiology ; *Agriculture ; *Ecosystem ; Symbiosis ; },
abstract = {Arbuscular mycorrhizal (AM) fungi play a key role in terrestrial ecosystems by forming symbiotic relationships with plants and may confer benefits for sustainable agriculture, by reducing reliance on harmful fertiliser and pesticide inputs and enhancing plant resilience against insect herbivores. Despite their ecological importance, critical gaps in understanding AM fungal ecology limit predictions of their responses to global change in agroecosystems. However, predicting climate change impacts on AM fungi is important for maintaining crop productivity and ecosystem stability. Efforts to classify AM fungi based on functional traits, such as the competitor, stress-tolerator, ruderal (C-S-R) framework, aim to address these gaps but face challenges due to the obligate symbiotic nature of the fungi. As the framework is still widely used, we evaluate its applicability in predicting global change impacts on AM fungal communities in agroecosystems. Chagnon's adaptation of the C-S-R framework for AM fungi aligns with some study outcomes (e.g., under the context of water limitation) but faces challenges when used in complex climate change scenarios, varying agricultural conditions and/or extreme climatic conditions. The reliance on a limited dataset to classify AM fungal families further limits accurate predictions of AM fungal community dynamics. Trait data collection could support a nuanced understanding of AM fungi and leveraging AM fungal databases could streamline data management and analysis, enhancing efforts to clarify AM fungal responses to environmental change and guide ecosystem management practices. Thus, while the C-S-R framework holds promise, it requires additional AM fungal trait data for validation and improvement of its predictive power. Conclusively, before designing experiments based on life-history strategies and developing new frameworks tailored to AM fungi a critical first step is to gain a comprehensive understanding of their traits.},
}
@article {pmid39543597,
year = {2024},
author = {Rajovic, N and Grubor, N and Cirkovic, A and Maheswaran, R and Bath, PA and Green, D and Bellantuono, I and Milicevic, O and Kanazir, S and Miljus, D and Zivkovic, S and Vidojevic, D and Mickovski, N and Rakocevic, I and Ivanovic, I and Mladenovic, A and Goyder, E and Milic, N},
title = {Insights into relationship of environmental inequalities and multimorbidity: a population-based study.},
journal = {Environmental health : a global access science source},
volume = {23},
number = {1},
pages = {99},
pmid = {39543597},
issn = {1476-069X},
support = {200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200110/WT_/Wellcome Trust/United Kingdom ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; },
mesh = {Humans ; Middle Aged ; *Multimorbidity ; Adult ; Male ; Female ; Serbia/epidemiology ; Aged ; Young Adult ; *Air Pollutants/analysis ; Adolescent ; Environmental Exposure/adverse effects ; Air Pollution/analysis/adverse effects ; Prevalence ; Water Quality ; Socioeconomic Factors ; },
abstract = {BACKGROUND: Substantial inequalities in the overall prevalence and patterns of multimorbidity have been widely reported, but the causal mechanisms are complex and not well understood. This study aimed to identify common patterns of multimorbidity in Serbia and assess their relationship with air pollutant concentrations and water quality indicators.<br><br>METHODS: This ecological study was conducted on a nationally representative sample of the Serbian population. Data were obtained from the European Health Interview (EHIS) Survey, a periodic study designed to assess population health using widely recognized standardized instruments. The study included 13,069 participants aged 15 and older, randomly selected through a multistage stratified sampling design. Multimorbidity was defined as having two or more self-reported diagnoses of chronic non-communicable diseases. Latent class analysis (LCA) was performed to identify clusters of multimorbidity. Concentrations of particulate matter (PM10), sulfur dioxide (SO2), nitrogen dioxide (NO2), carbon monoxide (CO), and ozone (O3), as well as water quality indicators, were obtained from the Serbian Environmental Protection Agency.<br><br>RESULTS: The overall prevalence of multimorbidity was 33.4% [32.6%-34.2%]. Six latent classes of multimorbidity were identified: Healthy, Multicondition, Cardiovascular, Metabolic syndrome, Respiratory, and Musculoskeletal. Annual increases in PM10 and SO2 concentrations, as well as daily increases in O3 concentrations, significantly raised the odds of having multimorbidity (OR&#x2009;=&#x2009;1.02, 95% CI 1.02-1.03; OR&#x2009;=&#x2009;1.01, 95% CI 1.00-1.02 and OR&#x2009;=&#x2009;1.03, 95% CI 1.02-1.03, respectively). A pattern of increased risk was observed with rising levels of water contamination. Exposure to physico-chemical, microbiological and combined contamination was associated with a 3.92%, 5.17% and 5.54% higher probability, respectively, of having multiple chronic conditions. There was strong evidence that air pollutants, as well as chemical and microbial water contamination, were significantly associated with higher odds of the most common clusters of multimorbidity identified by LCA.<br><br>CONCLUSION: There is compelling evidence of an association between multimorbidity and environmental pollution, suggesting that exposure to air pollutants and water contaminants may contribute to disease accumulation and help explain geographically and socioeconomically patterned inequalities. These findings underscore the need for extensive studies that simultaneously measure both multimorbidity and pollution to explore their complex interrelationships.},
}
@article {pmid39543483,
year = {2024},
author = {Rzehak, T and Praeg, N and Galla, G and Seeber, J and Hauffe, HC and Illmer, P},
title = {Comparison of commonly used software pipelines for analyzing fungal metabarcoding data.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1085},
pmid = {39543483},
issn = {1471-2164},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification ; *Software ; Animals ; Cattle ; Computational Biology/methods ; Feces/microbiology ; Soil Microbiology ; },
abstract = {BACKGROUND: Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.<br><br>RESULTS: Here we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n&#x2009;=&#x2009;18), while DADA2 results for the same replicates were highly heterogeneous.<br><br>CONCLUSIONS: Our study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.},
}
@article {pmid39541885,
year = {2024},
author = {Wang, G and Li, X and Deng, J and Cao, J and Meng, H and Dong, J and Zhang, H},
title = {Assessing soil cadmium quality standards for different land use types: A global synthesis.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136450},
doi = {10.1016/j.jhazmat.2024.136450},
pmid = {39541885},
issn = {1873-3336},
abstract = {The contamination of cadmium (Cd) in soil has become an increasingly serious issue worldwide, presenting significant risks to human health, crop safety, and ecosystems. Despite its importance, there is a lack of standardized soil threshold values for use in regulating exposure to Cd-contaminated surface soil. By synthesizing soil environmental standards for Cd from 61 countries and 75 regions, this study analyzed and categorized these standards by land use types. The distribution of Cd quality standards among various countries was determined, based on available data primarily from the United States, Canada, Europe, Australia, and China. The established soil Cd quality standards were also determined for different land types, including lands for agricultural, residential, industrial, construction, commercial uses, and parks/green spaces. Using the ecological environment criteria - species sensitivity distribution (ECC-SSD) model, Cd levels were analyzed across different land use types, and it was determined that a log-logistic distribution was the best fitted model. Our findings indicated that soil Cd quality standards ranged from 0.11 to 5.20 mg/kg for agricultural land, 1.25 to 171.51 mg/kg for residential land, and 2.58 to 1845.26 mg/kg for industrial land, all within the 5-95 % percentile range. The 5 % hazard concentration (HC5) value was recommended as the latest national quality standards for each land type. This comprehensive assessment of global soil Cd quality standards provides valuable insight for decision-makers tasked with effectively managing and mitigating Cd pollution in soil.},
}
@article {pmid39539549,
year = {2024},
author = {Pappa, T and Rivas, AL and Iandiorio, MJ and Hoogesteijn, AL and Fair, JM and Rojas Gil, AP and Burriel, AR and Bagos, PG and Chatzipanagiotou, S and Ioannidis, A},
title = {Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1430972},
pmid = {39539549},
issn = {1664-3224},
mesh = {Humans ; *Sepsis/immunology/mortality/blood/diagnosis ; Male ; Female ; Middle Aged ; Aged ; *Precision Medicine ; Leukocyte Count ; Biomarkers/blood ; Aged, 80 and over ; Adult ; Immunosuppression Therapy ; },
abstract = {INTRODUCTION: Data overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis.<br><br>METHODS: Blood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions.<br><br>RESULTS: The reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named 'early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other'). Mortality data validated these labels: both 'suppression' subsets revealed 100% mortality, the 'immunocompetence' group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the 'intermediary' suppression expressed an impaired monocyte-related function, the 'late' suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine.<br><br>DISCUSSION: The data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the 'other' group, additional studies are recommended.},
}
@article {pmid39537861,
year = {2024},
author = {Noria, SF and Pratt, KJ and Abdel-Rasoul, M and Diaz, K and Shalash, B and Abul-Khoudoud, D and Needleman, B and Magallanes, M},
title = {The impact of social determinants of health (SDOH) on completing bariatric surgery at a single academic institution.},
journal = {Surgical endoscopy},
volume = {},
number = {},
pages = {},
pmid = {39537861},
issn = {1432-2218},
abstract = {BACKGROUND: Underutilization of bariatric surgery is multifactorial. This study aimed to understand the association of SDOH on not achieving surgery.<br><br>METHODS: 1081 applications for primary MBS from January-December 2021 were stratified into those that completed surgery (COM; n&#x2009;=&#x2009;415), in progress&#x2009;>&#x2009;1-year (IP; n&#x2009;=&#x2009;107), dropped out (DO; n&#x2009;=&#x2009;379), and never started (NS; n&#x2009;=&#x2009;180). Using the American-Community-Survey results (2015-2020) and patient zip-codes, population differences in 4-domains of SDOH (demographic/social/housing/economic) were examined between COM versus the other groups. Additionally, using institutional MBSAQIP and EMR data, patient-specific differences in comorbidities were evaluated for COM versus IP/DO. Univariate analysis using Kruskal-Wallis, chi-squared/Fisher's exact tests were used for continuous and/or categorical variables. For patient-level analysis multinomial logistic regression was used to determine predictors of not achieving surgery. Hypothesis testing was conducted at an overall 5 percent type-I error rate (alpha&#x2009;=&#x2009;0.05) and Bonferroni's method was used to adjust for multiple comparisons.<br><br>RESULTS: Compared to COM, IP-patients resided in zip-codes characterized by fewer married people (43% vs 46%; p&#x2009;=&#x2009;0.019), lower education levels (49% vs 43%; p&#x2009;=&#x2009;0.048), more households where rent was&#x2009;>&#x2009;50% of household income (10% vs 8%, p&#x2009;=&#x2009;0.002), and households below the poverty line (17.6% vs 14.5%, p&#x2009;=&#x2009;0.017). At the patient-level, IP were more likely to be male (27.9% vs 14.9%; p&#x2009;=&#x2009;0.014), publicly insured (44.9% vs 28.4%; p&#x2009;=&#x2009;0.004), Black (35.5% vs 22.2%; p&#x2009;=&#x2009;0.006), an active smoker (8.9% vs 2.2%; p&#x2009;=&#x2009;0.018), have a higher BMI (49.6 vs 47.6; p&#x2009;=&#x2009;0.01), and coronary intervention (5.8% vs 1.7%, p&#x2009;=&#x2009;0.034). Comparison of COM vs DO was similar for both phases. Multinomial multivariable logistic regression demonstrated higher BMI (OR&#x2009;=&#x2009;1.03,[CI]:1.01-1.05, p&#x2009;=&#x2009;0.001), males (OR&#x2009;=&#x2009;1.9,[CI]:1.09-3.32, p&#x2009;=&#x2009;0.024), smoking (OR&#x2009;=&#x2009;4.58,[CI]:1.74-12.02, p&#x2009;=&#x2009;0.002), and Medicaid (OR&#x2009;=&#x2009;2.16,[CI]:1.33-3.49, p&#x2009;=&#x2009;0.002) independently predicted not achieving surgery.<br><br>CONCLUSION: Patient-level data demonstrated social not clinical factors predicted surgery completion. Given zip-codes characterizing the IP/DO groups had a greater prevalence of social risk, more attention needs to be directed patient-level social risks.},
}
@article {pmid39537735,
year = {2024},
author = {Ki, J and Lee, JM and Lee, W and Kim, JH and Jin, H and Jung, S and Lee, J},
title = {Dual-encoder architecture for metal artifact reduction for kV-cone-beam CT images in head and neck cancer radiotherapy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27907},
pmid = {39537735},
issn = {2045-2322},
support = {NRF-2020R1F1A1073430//National Research Foundation of Korea/ ; NRF-2021R1F1A1057818//National Research Foundation of Korea/ ; HI21C1161//Korea Health Industry Development Institute/ ; RS-2020-II201336//Ministry of Science and ICT, South Korea/ ; },
mesh = {*Cone-Beam Computed Tomography/methods ; Humans ; *Head and Neck Neoplasms/radiotherapy/diagnostic imaging ; *Artifacts ; *Metals/chemistry ; Deep Learning ; Image Processing, Computer-Assisted/methods ; Radiotherapy Planning, Computer-Assisted/methods ; Radiotherapy Dosage ; Phantoms, Imaging ; },
abstract = {During a radiotherapy (RT) course, geometrical variations of target volumes, organs at risk, weight changes (loss/gain), tumor regression and/or progression can significantly affect the treatment outcome. Adaptive RT has become the effective methods along with technical advancements in imaging modalities including cone-beam computed tomography (CBCT). Planning CT (pCT) can be modified via deformable image registration (DIR), which is applied to the pair of pCT and CBCT. However, the artifact existed in both pCT and CBCT is a vulnerable factor in DIR. The dose calculation on CBCT is also suggested. Missing information due to the artifacts hinders the accurate dose calculation on CBCT. In this study, we aim to develop a deep learning-based metal artifact reduction (MAR) model to reduce the metal artifacts in CBCT for head and neck cancer RT. To train the proposed MAR model, we synthesized the kV-CBCT images including metallic implants, with and without metal artifacts (simulated image data pairs) through sinogram image handling process. We propose the deep learning architecture which focuses on both artifact removal and reconstruction of anatomic structure using a dual-encoder architecture. We designed four single-encoder models and three dual-encoder models based on UNet (for an artifact removal) and FusionNet (for a tissue restoration). Each single-encoder model contains either UNet or FusionNet, while the dual-encoder models have both UNet and FusionNet architectures. In the dual-encoder models, we implemented different feature fusion methods, including simple addition, spatial attention, and spatial/channel wise attention. Among the models, a dual-encoder model with spatial/channel wise attention showed the highest scores in terms of peak signal-to-noise ratio, mean squared error, structural similarity index, and Pearson correlation coefficient. CBCT images from 34 head and neck cancer patients were used to test the developed models. The dual-encoder model with spatial/channel wise attention showed the best results in terms of artifact index. By using the proposed model to CBCT, one can achieve more accurate synthetic pCT for head and neck patients as well as better tissue recognition and structure delineation for CBCT image itself.},
}
@article {pmid39537340,
year = {2024},
author = {Di Battista, V and Danielsen, PH and Gajewicz-Skretna, A and Kedziorski, A and Seiffert, SB and Ma-Hock, L and Berthing, T and Mortensen, A and Sundermann, A and Skjolding, LM and Vogel, U and Baun, A and Wohlleben, W},
title = {Oxide-Perovskites for Automotive Catalysts Biotransform and Induce Multicomponent Clearance and Hazard.},
journal = {ACS nano},
volume = {18},
number = {47},
pages = {32672-32693},
pmid = {39537340},
issn = {1936-086X},
mesh = {*Oxides/chemistry ; Animals ; Catalysis ; *Lanthanum/chemistry ; Rats ; Mice ; Calcium Compounds/chemistry ; Titanium/chemistry ; Automobiles ; Male ; Biotransformation ; Surface Properties ; Lung/metabolism/drug effects ; },
abstract = {Oxide-perovskites designed for automotive catalysts contain multiple metal elements whose presence is crucial to achieving the targeted performance. They are highly stable in exhaust operating conditions; however, little is known about their stability under physiological conditions. As some of the metallic components are hazardous to humans and the environment, perovskite benefits in cleaner air must be balanced with risks in a Safe and Sustainable Design (SSbD) approach. New approach methodologies (NAMs), including in chemico and in silico methods, were used for testing hazards and benefits, including catalytic activity and tolerance for temporary excess of oxygen under dynamic driving conditions. The composition and surface properties of six different lanthanum-based oxide-perovskites compromised their stability under lung physiological conditions, influencing the oxidative damage of the particles and the bioacessibility of leaching metals. We found consistent biotransformation of the oxide-perovskite materials at pH 4.5. The leached lanthanum ions, but not other metals, respeciated into lanthanum phosphate nanoparticles, which increased the overall oxidative damage in additive synergy. The NAM results in the presented SSbD approach were challenged by in vivo studies in rats and mice, which confirmed multicomponent clearance from lungs into urine and supported the comparative ranking of effects against well-characterized spinel materials. Among the perovskites, the version with reduced nickel content and doped with palladium offered the best SSbD balance, despite not improving the conventional benchmark catalytic performance and related sustainability benefits. Redesign by industry may be necessary to better fulfill all SSbD dimensions.},
}
@article {pmid39536186,
year = {2024},
author = {Corrêa-do-Nascimento, GS and Galvão, C and Leite, GR},
title = {Investigating the distribution of a rare Colombo-Venezuelan kissing bug, Rhodnius neivai, Lent, 1953, using geographical information system-based analyses.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {119},
number = {},
pages = {e240106},
pmid = {39536186},
issn = {1678-8060},
mesh = {Animals ; *Rhodnius ; *Geographic Information Systems ; Colombia ; *Insect Vectors/classification ; *Animal Distribution ; Venezuela ; Chagas Disease/transmission ; Ecosystem ; },
abstract = {BACKGROUND: Rhodnius neivai, a kissing bug found in the dry regions of Colombia and Venezuela, has limited documented occurrences. While it is not deemed a significant vector for Chagas disease, distributional and ecological studies are essential in monitoring species domiciliation and shedding light on the evolutionary aspects of the Rhodniini tribe.<br><br>OBJECTIVES: The study aims to provide a detailed revision of R. neivai distribution and evaluate general spatial data quality for ecological niche modelling (ENM). It will also provide the first published ENM for the species, which may aid species sampling and future analytical improvement.<br><br>METHODS: Registers and other spatial information were gathered by literature review; data georeferencing, preliminary geographical investigations, and model editing were conducted in GIS platforms; ENMs were built using R and explored the uncertainty of parameters and algorithms.<br><br>FINDINGS: Twenty four unique sites were identified, unearthing 17 previously uncovered records. Data lacks robust spatial and temporal precision; however, ENMs had acceptable validations. The models present some variation in suitability but with objective areas for sampling effort.<br><br>MAIN CONCLUSIONS: Rhodnius neivai distribution is better explained by conditions that characterise dry ecotypes, but further sampling is essential to improve modelling and advance with ecological and evolutive matters.},
}
@article {pmid39536049,
year = {2024},
author = {Zhao, Y and Cordero, OX and Tikhonov, M},
title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012590},
pmid = {39536049},
issn = {1553-7358},
mesh = {*Algorithms ; Linear Models ; *Ecosystem ; *Computational Biology/methods ; Models, Biological ; Microbiota/physiology ; Nonlinear Dynamics ; },
abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.},
}
@article {pmid39530726,
year = {2024},
author = {Toledo, MJL and Zawadzki, MJ and Scott, SB and Johnson, JA and Marcusson-Clavertz, D and Kim, J and Lanza, S and Almeida, DM and Sliwinski, MJ and Smyth, JM},
title = {Exploring the Utility of a Real-Time Approach to Characterising Within-Person Fluctuations in Everyday Stress Responses.},
journal = {Stress and health : journal of the International Society for the Investigation of Stress},
volume = {40},
number = {6},
pages = {e3501},
pmid = {39530726},
issn = {1532-2998},
support = {/NH/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; *Stress, Psychological/psychology ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; Aged ; },
abstract = {Few studies have measured components of stress responses in real time-an essential step in designing just-in-time interventions targeting moments of risk. Using ecological momentary assessment (EMA), we characterised stress response components to everyday stressors, including reactivity (the response following a stressor), recovery (the return towards baseline), and pile-up (the accumulation of stressors) (RRPs) by quantifying the dynamics of response indicators (i.e., subjective stress, negative affect, and perseverative cognition). To determine the utility of these novel measures in capturing and characterising acute moments of the stress response, this study evaluated the proportion of variance in RRPs attributed to (1) between-person, (2) between-days, and (3) within-day (momentary) levels. Healthy adults (n = 123; aged 35-65, 79% women, 91% non-Hispanic White) participated in a 14-day study assessing stress response via EMA 6 times a day. RRPs were constructed from 10,065 EMA reports. Multilevel models with moments nested within days nested within persons were used to partition variance in the RRPs. Reactivity and recovery indicators captured the most variation within-days (i.e., across moments; range 76%-80% and 87%-89%, respectively), with small amounts of variance between-person. For pile-up, variation was mostly observed between-days (range 60%-63%) and between-persons (range 27%-31%). In contrast, raw measures of stress response reflected substantial between-person (range 32%-54%) and within-day (range 34%-53%) variance. These results demonstrated that a person-specific approach to measuring stress response components (i.e., RRPs) can capture the dynamic within-person variation in stress response, as it occurs in real time, making it well-suited for use in novel just-in-time interventions targeting moments of risk.},
}
@article {pmid39526854,
year = {2024},
author = {Tan, X and Xue, F and Zhang, C and Wang, T},
title = {mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39526854},
issn = {1477-4054},
support = {12331009//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; Computational Biology/methods ; Algorithms ; Gastrointestinal Microbiome ; },
abstract = {Alterations in human microbial communities are intricately linked to the onset and progression of diseases. Identifying the key microbes driving these community changes is crucial, as they may serve as valuable biomarkers for disease prevention, diagnosis, and treatment. However, there remains a need for further research to develop effective methods for addressing this critical task. This is primarily because defining the driver microbe requires consideration not only of each microbe's individual contributions but also their interactions. This paper introduces a novel framework, called mbDriver, for identifying driver microbes based on microbiome abundance data collected at discrete time points. mbDriver comprises three main components: (i) data preprocessing of time-series abundance data using smoothing splines based on the negative binomial distribution, (ii) parameter estimation for the generalized Lotka-Volterra (gLV) model using regularized least squares, and (iii) quantification of each microbe's contribution to the community's steady state by manipulating the causal graph implied by gLV equations. The performance of nonparametric spline-based denoising and regularized least squares estimation is comprehensively evaluated on simulated datasets, demonstrating superiority over existing methods. Furthermore, the practical applicability and effectiveness of mbDriver are showcased using a dietary fiber intervention dataset and an ulcerative colitis dataset. Notably, driver microbes identified in the dietary fiber intervention dataset exhibit significant effects on the abundances of short-chain fatty acids, while those identified in the ulcerative colitis dataset show a significant correlation with metabolism-related pathways.},
}
@article {pmid39526196,
year = {2024},
author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Pale November moth, Epirrita christyi (Allen, 1906).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {540},
pmid = {39526196},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Pale November moth, Epirrita christyi (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 474.20 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.99 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,983 protein-coding genes.},
}
@article {pmid39521320,
year = {2024},
author = {Coelho, LA and Gonzalez, CLR and Tammurello, C and Campus, C and Gori, M},
title = {Hand and foot overestimation in visually impaired human adults.},
journal = {Neuroscience},
volume = {563},
number = {},
pages = {74-83},
doi = {10.1016/j.neuroscience.2024.10.055},
pmid = {39521320},
issn = {1873-7544},
mesh = {Humans ; Female ; Male ; Adult ; *Hand ; *Foot ; Middle Aged ; *Blindness/physiopathology/psychology ; Visually Impaired Persons/psychology ; Body Image/psychology ; Young Adult ; Sex Characteristics ; },
abstract = {Previous research has shown that visual impairment results in reduced audio, tactile and proprioceptive ability. One hypothesis is that these issues arise from inaccurate body representations. Few studies have investigated metric body representations in a visually impaired population. We designed an ecologically valid behavioural task in which visually impaired adults haptically explored various sized gloves or shoes. They were asked to indicate if they perceived each clothing item as bigger than the size of their hand or foot. In the post-hoc analyses we fit psychometric curves to the data to extract the point of subjective equality. We then compared the results to age/sex matched controls. We hypothesized the blind participants body representations should be more distorted. Because previous research has shown that females are more likely to overestimate body size, we predicted sex differences in the sighted participants. However, because blind adults have no exposure to visual ideals of body size, we predicted that there would be no sex differences. Our results showed thatblind participants overestimated their hands and feetto a similar degree. Sighted controls overestimated their hands significantly more than their feet. Taken together, our results partially support our hypothesis and suggest that visual deprivation, even for short periods result in hand size overestimation.},
}
@article {pmid39520764,
year = {2025},
author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS},
title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.},
journal = {International journal of food microbiology},
volume = {427},
number = {},
pages = {110955},
doi = {10.1016/j.ijfoodmicro.2024.110955},
pmid = {39520764},
issn = {1879-3460},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth &amp; development/classification/genetics/isolation &amp; purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; },
abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.},
}
@article {pmid39516498,
year = {2024},
author = {Weistuch, C and Murgas, KA and Zhu, J and Norton, L and Dill, KA and Tannenbaum, AR and Deasy, JO},
title = {Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27230},
pmid = {39516498},
issn = {2045-2322},
support = {BCRF-17-193//Breast Cancer Research Foundation/ ; W911NF2210292//Army Research Office/ ; FA9550-20-1-0029//Air Force Office of Scientific Research/ ; R01-AG048769/GF/NIH HHS/United States ; R01 AG048769/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Transcriptome ; *Phenotype ; *Gene Expression Regulation, Neoplastic ; Female ; Neoplasms/genetics/pathology/metabolism ; Gene Expression Profiling ; Breast Neoplasms/genetics/pathology/metabolism ; },
abstract = {Cancer transcriptional patterns reflect both unique features and shared hallmarks across diverse cancer types, but whether differences in these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that these shared transcriptomic signatures reflect repurposed versions of functional tasks performed by normal tissues. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.},
}
@article {pmid39512488,
year = {2024},
author = {Lewis, JH and Kojima, H and Suenaga, M and Petsopoulos, D and Fujisawa, Y and Truong, XL and Warren, DL},
title = {The era of cybertaxonomy: X-ray microtomography reveals cryptic diversity and concealed cuticular sculpture in Aphanerostethus Voss, 1957 (Coleoptera, Curculionidae).},
journal = {ZooKeys},
volume = {1217},
number = {},
pages = {1-45},
pmid = {39512488},
issn = {1313-2989},
abstract = {Weevils represent one of the most speciose and economically important animal clades, but remain poorly studied across much of the Oriental Region. Here, an integrative revision of the Oriental, flightless genus Aphanerostethus Voss, 1957 (Curculionidae: Molytinae) based on X-ray microtomography, multi-gene DNA barcoding (CO1, Cytb, 16S), and traditional morphological techniques (light microscopy, dissections) is presented. Twelve new species, namely, A.armatus Lewis &amp; Kojima, sp. nov., A.bifidus Kojima &amp; Lewis, sp. nov., A.darlingi Lewis, sp. nov., A.decoratus Lewis &amp; Kojima, sp. nov., A.falcatus Kojima, Lewis &amp; Fujisawa, sp. nov., A.incurvatus Kojima &amp; Lewis, sp. nov., A.japonicus Lewis &amp; Kojima, sp. nov., A.magnus Lewis &amp; Kojima, sp. nov., A.morimotoi Kojima &amp; Lewis, sp. nov., A.nudus Lewis &amp; Kojima, sp. nov., A.spinosus Lewis &amp; Kojima, sp. nov., and A.taiwanus Lewis, Fujisawa &amp; Kojima, sp. nov. are described from Japan, Taiwan, Vietnam, and Malaysia. A neotype is designated for A.vannideki Voss, 1957. The hitherto monotypic genus Darumazo Morimoto &amp; Miyakawa, 1985, syn. nov. is synonymized under Aphanerostethus based on new morphological data and Aphanerostethusdistinctus (Morimoto &amp; Miyakawa, 1985), comb. nov. is transferred accordingly. X-ray microtomography is successfully used to explore for stable interspecific differences in cuticular, internal and micro morphology. Remarkable species-specific sexual dimorphism in the metatibial uncus is described in seven of the newly described Aphanerostethus species and the evolution of this character is discussed.},
}
@article {pmid39511491,
year = {2024},
author = {Tang, Y and Tian, C and Yao, D and Yang, S and Shi, L and Yi, L and Peng, Q},
title = {Community assembly and potential function analysis of the endophyte in Eucommia ulmoides.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {460},
pmid = {39511491},
issn = {1471-2180},
mesh = {*Endophytes/genetics/metabolism/classification/physiology/isolation &amp; purification ; *Eucommiaceae/microbiology ; *Ascomycota/genetics/growth &amp; development/physiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Iridoid Glucosides/metabolism ; Basidiomycota/genetics/physiology ; Symbiosis ; Fungi/classification/genetics/isolation &amp; purification/metabolism/physiology ; Computational Biology ; },
abstract = {Endophytes play a pivotal role in protecting host plants from both biotic and abiotic stresses, promoting the production of active components (AC) and plant growth. However, the succession of the endophyte community in Eucommia ulmoides (E. ulmoides), particularly the community assembly and function, has not been extensively investigated. In this study, we employed high-throughput sequencing and bioinformatics tools to analyze endophyte diversity across different tree ages, parts, and periods. We examined the population differences, correlations, community assembly mechanisms, and functional roles of these endophytes. Functional predictions via PICRUSt2 revealed that most endophytic fungal functions were linked to biosynthesis, with significant differences in biosynthetic functional abundance across parts and periods. In contrast, the metabolic activity of endophytic bacteria remained stable across different periods and parts. Correlation analysis further confirmed a strong positive relationship between ACs and certain endophytic fungi. Among them, the fungal phyla Ascomycota and Basidiomycota were identified as key contributors to the metabolism of chlorogenic acid (CA), while Aucubin was significantly positively correlated with several endophytic bacteria. These findings provide valuable insights into the functional roles and community assembly mechanism of E. ulmoides endophytes, as well as their symbiotic relationships.},
}
@article {pmid39507254,
year = {2024},
author = {Flores, M and Ho, E and Ly, C and Ceberio, N and Guardado, M and Felix, K and Thorner, HM and Paunovich, M and Godek, C and Kalaydjian, C and Rohlfs, RV},
title = {Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111067},
pmid = {39507254},
issn = {2589-0042},
support = {T32 GM148332/GM/NIGMS NIH HHS/United States ; },
abstract = {Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 83 human groups. We find higher false inclusion rates for mixtures with more contributors and for groups with lower genetic diversity. Even for three-contributor mixtures where two contributors are known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 36 out of 83 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.},
}
@article {pmid39503522,
year = {2024},
author = {Campelo, F and de Oliveira, ALG and Reis-Cunha, J and Fraga, VG and Bastos, PH and Ashford, J and Ekárt, A and Adelino, TER and Silva, MVF and de Melo Iani, FC and de Jesus, ACP and Bartholomeu, DC and de Souza Trindade, G and Fujiwara, RT and Bueno, LL and Lobo, FP},
title = {Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39503522},
issn = {1477-4054},
support = {BIP-00123-23//FAPEMIG/ ; INCT-406441/2022-7//Brazilian National Institutes of Science and Technology/ ; RED-00067-23//Rede Mineira de Imunobiol&#xf3;gicos/ ; APQ-4035/17//State of Minas Gerais Research Support Foundation/ ; 310311/2023-3//National Council for Scientific and Technological Development/ ; 405249/2022-5//MCTI/Brazil/ ; MR/T016019/1//UK Medical Research Council/ ; //EPSRC/UK/ ; },
mesh = {*Phylogeny ; Humans ; *Epitopes, B-Lymphocyte/immunology ; Orthopoxvirus/immunology/genetics ; Computational Biology/methods ; Vaccinia virus/immunology/genetics ; Mpox (monkeypox) ; },
abstract = {We introduce a phylogeny-aware framework for predicting linear B-cell epitope (LBCE)-containing regions within proteins. Our approach leverages evolutionary information by using a taxonomic scaffold to build models trained on hierarchically structured data. The resulting models present performance equivalent or superior to generalist methods, despite using simpler features and a fraction of the data volume required by current state-of-the-art predictors. This allows the utilization of available data for major pathogen lineages to facilitate the prediction of LBCEs for emerging infectious agents. We demonstrate the efficacy of our approach by predicting new LBCEs in the monkeypox (MPXV) and vaccinia viruses. Experimental validation of selected targets using sera from infected patients confirms the presence of LBCEs, including candidates for the differential serodiagnosis of recent MPXV infections. These results point to the use of phylogeny-aware predictors as a useful strategy to facilitate the targeted development of immunodiagnostic tools.},
}
@article {pmid39501271,
year = {2024},
author = {Sijm-Eeken, M and Ossebaard, HC and Čaluković, A and Temme, B and Peute, LW and Jaspers, MW},
title = {Linking theory and practice to advance sustainable healthcare: the development of maturity model version 1.0.},
journal = {BMC health services research},
volume = {24},
number = {1},
pages = {1350},
pmid = {39501271},
issn = {1472-6963},
mesh = {Humans ; *Delivery of Health Care/organization &amp; administration ; Climate Change ; Sustainable Development ; Conservation of Natural Resources/methods ; Models, Theoretical ; Models, Organizational ; },
abstract = {BACKGROUND: Climate change and increased awareness of planetary health have made reducing ecological footprints a priority for healthcare organizations. However, improving healthcare's environmental impact remains difficult. Numerous researchers argue these difficulties are caused by healthcare's environmental impact being multidimensional, influenced throughout the healthcare chain, and often has downstream consequences that are hard to identify or to measure. Even though existing research describes many successful approaches to reduce healthcare's environmental impact, a robust multidimensional framework to assess this impact is lacking. This research aims at developing a maturity model for sustainable healthcare that could be used for self-assessment by healthcare professionals to identify improvement actions and for sharing best practices in environmental sustainability.<br><br>METHODS: A design-oriented approach for maturity model development was combined with an expert panel and six case studies to develop, refine and expand the maturity model for environmentally sustainable healthcare.<br><br>RESULTS: A maturity model was developed containing four domains: 'Governance', 'Organization Structures', 'Processes', and 'Outcomes and Control'. Applying the model in real-world environments demonstrated the model's understandability, ease of use, usefulness, practicality and ability to identify improvement actions for environmental sustainability in healthcare organizations.<br><br>CONCLUSIONS: This study found that healthcare practitioners could apply the maturity model developed and tested in this study in several hours without training to help them gain valuable insights into the environment footprint of the healthcare setting they worked in. Systematically implementing the model developed in this study could help address the urgent need to mitigate the substantial environmental impact of healthcare. These implementations can help evaluate and improve the maturity model.},
}
@article {pmid39497067,
year = {2024},
author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD},
title = {Removal of sequencing adapter contamination improves microbial genome databases.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1033},
pmid = {39497067},
issn = {1471-2164},
mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; },
abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.},
}
@article {pmid39494195,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Case-bearing Clothes moth, Tinea pellionella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {119},
pmid = {39494195},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Tinea pellionella (the Case-bearing Clothes moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 245.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 25.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,811 protein coding genes.},
}
@article {pmid39493766,
year = {2024},
author = {Chakraborty, H and Chakraborty, HJ and Das, BK and Maity, J},
title = {Age-specific changes in the serum proteome of female anadromous, hilsa Tenualosa ilisha: a comparative analysis across developmental stages.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1448627},
pmid = {39493766},
issn = {1664-3224},
mesh = {Female ; *Proteome ; Animals ; Proteomics/methods ; Tandem Mass Spectrometry ; Protein Interaction Maps ; Computational Biology/methods ; Age Factors ; Chromatography, Liquid ; Blood Proteins/metabolism ; Fishes/genetics/blood ; Aging/blood/immunology ; },
abstract = {INTRODUCTION: The proteome profile of the female Tenualosa ilisha (Hamilton, 1822), a species of great ecological and economic importance, across various age groups was investigated to comprehend the functional dynamics of the serum proteome for conservation and aquaculture, as well as sustain the population.<br><br>METHODS: Advanced liquid chromatography-tandem mass spectrometry LC-MS/MS-based proteomic data were analysed and submitted to the ProteomeXchange Consortium via PRIDE (PRoteomics IDEntifications database). Bioinformatics analysis of serum proteome have been done and it showed different proteins associated with GO Gene Ontology () terms, and the genes associated with enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways (such as phagosome, mTOR, Apelin signalling pathways, herpes simplex virus) implicated in immune responses.<br><br>RESULTS: The expression levels of important immunological proteins, such as those involved in cellular defence and inflammatory responses, were significantly different age-dependently. In this study, we annotated 952, 494, 415, and 282 proteins in year classes IV, III, II, and I Hilsa, respectively, and analysed their Protein-Protein Interaction (PPI) networks based on their functional characteristics. From year classes I to IV, new proteins appeared and were more than three-fold. Notably, class I hilsa displayed a lower abundance of proteins than class IV hilsa.<br><br>DISCUSSION: This is the first study, to the best of our knowledge, to report the analysis of the serum proteome of hilsa at different developmental stages, and the results can help improve the understanding of the mechanisms underlying the different changes in protein enrichment during migration in hilsa. This analysis also offers crucial insights into the immune system for hilsa conservation and management.},
}
@article {pmid39493638,
year = {2024},
author = {Reuken, PA and Besteher, B and Bleidorn, J and Brockmann, D and Finke, K and Freytag, A and Lehmann-Pohl, K and Lemhöfer, C and Mikolajczyk, R and Puta, C and Scherag, A and Wiedermann, M and Zippel-Schultz, B and Stallmach, A},
title = {Web-based telemedicine approach for treatment of post-COVID-19 in Thuringia (WATCH).},
journal = {Digital health},
volume = {10},
number = {},
pages = {20552076241291748},
pmid = {39493638},
issn = {2055-2076},
abstract = {OBJECTIVE: After infection with SARS-CoV-2, a substantial proportion of patients develop long-lasting sequelae. These sequelae include fatigue (potentially as severe as that seen in ME/CFS cases), cognitive dysfunction, and psychiatric symptoms. Because the pathophysiology of these sequelae remains unclear, existing therapeutic concepts address the symptoms through pacing strategies, cognitive training, and psychological therapy.<br><br>METHODS: Here, we present a protocol for a digital multimodal structured intervention addressing common symptoms through three intervention modules: BRAIN, BODY, and SOUL. This intervention includes an assessment conducted via a mobile "post-COVID-19 bus" near the patient's home, as well as the use of wearable devices and mobile applications to support pacing strategies and collection of data, including ecological momentary assessment.<br><br>RESULTS: We will focus on physical component subscore of the SF36 as Quality of Life parameter as the primary outcome parameter for WATCH to take into account the holistic approach that is necessary for care of post-COVID patients.<br><br>CONCLUSION: In the current project, we present a protocol for a holistic and multimodal structured therapeutic concept which is easily accessible, and scalable for post-COVID patients.},
}
@article {pmid39488960,
year = {2024},
author = {Tayyab, M and Hussain, M and Zhang, J and Ullah, S and Tong, Z and Rahman, ZU and Al-Aizari, AR and Al-Shaibah, B},
title = {Leveraging GIS-based AHP, remote sensing, and machine learning for susceptibility assessment of different flood types in peshawar, Pakistan.},
journal = {Journal of environmental management},
volume = {371},
number = {},
pages = {123094},
doi = {10.1016/j.jenvman.2024.123094},
pmid = {39488960},
issn = {1095-8630},
mesh = {*Floods ; Pakistan ; *Machine Learning ; *Geographic Information Systems ; Algorithms ; Remote Sensing Technology ; },
abstract = {Due to its diverse topography, Pakistan faces different types of floods each year, which cause substantial physical, environmental, and socioeconomic damage. However, the susceptibility of specific regions to different flood types remains unexplored. To the best of our knowledge for the first time, this study employed an integrated approach by leveraging a GIS-based Analytical Hierarchy Process (AHP), remote sensing, and machine learning (ML) algorithms, to assess susceptibility to three different types of flooding in Peshawar, Pakistan. The study first evaluated the degree of susceptibility to riverine, urban, and flash floods using the GIS-based AHP technique, and then employed ML models, (i.e., specifically Random Forest [RF] and Extreme Gradient Boosting [XG-Boost] to analyze multi-type flood susceptibility in the study region. The performance of the ML models was also evaluated, and the XG-Boost model outperforms RF, demonstrating a higher correlation coefficient (R[2] = 0.561-0.922) and lower mean absolute error (MAE = 0.042-0.354), and root-mean-square error (RMSE = 0.119-0.415) for both training and testing datasets. The superior performance of the XG-Boost was further confirmed by the higher value of the area under the curve (AUC) values, which is relatively higher (0.87) than that of the AHP (0.70) and RF (0.86) models. Based on the relative best performance, the XG-Boost model was chosen for further susceptibility assessment of different types of floods, and the generated flood susceptibility maps revealed that 20.9% of the total area is susceptible to riverine flooding, while 30.27% and 48.68% of the total area is susceptible to urban and flash flooding, respectively. The study's findings are significant, offering valuable insights for relevant stakeholders in guiding future flood risk management and sustainable land use plans in the study area.},
}
@article {pmid39480949,
year = {2024},
author = {Goldshtein, A and Chen, X and Amichai, E and Boonman, A and Harten, L and Yinon, O and Orchan, Y and Nathan, R and Toledo, S and Couzin, ID and Yovel, Y},
title = {Acoustic cognitive map-based navigation in echolocating bats.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6721},
pages = {561-567},
doi = {10.1126/science.adn6269},
pmid = {39480949},
issn = {1095-9203},
mesh = {Animals ; Acoustics ; *Chiroptera/physiology ; *Cognition ; *Echolocation ; Geographic Information Systems ; Homing Behavior ; *Spatial Navigation ; },
abstract = {Bats are known for their ability to use echolocation for obstacle avoidance and orientation. However, the extent to which bats utilize their highly local and directional echolocation for kilometer-scale navigation is unknown. In this study, we translocated wild Kuhl's pipistrelle bats and tracked their homing abilities while manipulating their visual, magnetic, and olfactory sensing and accurately tracked them using a new reverse GPS system. We show that bats can identify their location after translocation and conduct several-kilometer map-based navigation using solely echolocation. This proposition was further supported by a large-scale echolocation model disclosing how bats use environmental acoustic information to perform acoustic cognitive map-based navigation. We also demonstrate that navigation is improved when using both echolocation and vision.},
}
@article {pmid39480880,
year = {2024},
author = {Silva, GAA and Harder, AM and Kirksey, KB and Mathur, S and Willoughby, JR},
title = {Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012566},
pmid = {39480880},
issn = {1553-7358},
mesh = {*Homozygote ; *Genetics, Population/methods ; *Inbreeding ; Animals ; Models, Genetic ; Computational Biology/methods ; Humans ; Computer Simulation ; Polymorphism, Single Nucleotide/genetics ; },
abstract = {Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.},
}
@article {pmid39480818,
year = {2024},
author = {Ramesh, S and Rapp, S and Tapias Gomez, J and Levine, B and Tapias-Gomez, D and Chung, D and Truong, Z},
title = {Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0309707},
pmid = {39480818},
issn = {1932-6203},
mesh = {*User-Computer Interface ; *Software ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Databases, Nucleic Acid ; Web Browser ; },
abstract = {Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.},
}
@article {pmid39483086,
year = {2024},
author = {Behera, BP and Naik, H and Konkimalla, VB},
title = {Peptaloid: A Comprehensive Database for Exploring Peptide Alkaloid.},
journal = {Journal of chemical information and modeling},
volume = {64},
number = {22},
pages = {8387-8395},
doi = {10.1021/acs.jcim.4c01667},
pmid = {39483086},
issn = {1549-960X},
mesh = {*Peptides/chemistry ; *Alkaloids/chemistry/pharmacology ; Databases, Protein ; Machine Learning ; Databases, Factual ; Humans ; },
abstract = {Peptaloid is the first dedicated database for peptide alkaloid molecules, a unique class of naturally derived compounds known for their structural diversity and significant biological activities. Despite their promising potential in drug discovery and therapeutic development, research on peptide alkaloids has been limited by the absence of a comprehensive and centralized resource. Fragmented data across various sources have posed a significant challenge, underscoring the need for a specialized database to facilitate more efficient research and application. Peptaloid addresses this critical gap by providing a database with over 161,000 peptide alkaloid entries, each detailed with structural, physicochemical, and pharmacological properties. By leveraging advanced computational tools and machine learning, Peptaloid generates ADMET profiles, aiding in identifying and optimizing therapeutic candidates. Designed for versatility, the database supports various applications beyond drug discovery, including ecology and material sciences. Peptaloid (as a specialized database for peptide alkaloids) will play a crucial role in innovation and collaboration across scientific disciplines. Peptaloid is accessible at https://peptaloid.niser.ac.in.},
}
@article {pmid39481332,
year = {2025},
author = {Yao, M and Ren, A and Yang, X and Chen, L and Wang, X and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M},
title = {Unveiling the influence of heating temperature on biofilm formation in shower hoses through multi-omics.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122704},
doi = {10.1016/j.watres.2024.122704},
pmid = {39481332},
issn = {1879-2448},
mesh = {*Biofilms ; Proteomics ; Heating ; Metagenomics ; Hot Temperature ; Metagenome ; Multiomics ; },
abstract = {Shower systems provide unique environments that are conducive to biofilm formation and the proliferation of pathogens. The water heating temperature is a delicate decision that can impact microbial growth, balancing safety and energy consumption. This study investigated the impact of different heating temperatures (39 °C, 45 °C, 51 °C and 58 °C) on the shower hose biofilm (exposed to a final water temperature of 39 °C) using controlled full-scale shower setups. Whole metagenome sequencing and metaproteomics were employed to unveil the microbial composition and protein expression profiles. Overall, the genes and enzymes associated with disinfectant resistance and biofilm formation appeared largely unaffected. However, metagenomic analysis revealed a sharp decline in the number of total (86,371 to 34,550) and unique genes (32,279 to 137) with the increase in hot water temperature, indicating a significant reduction of overall microbial complexity. None of the unique proteins were detected in the proteomics experiments, suggesting smaller variation among biofilms on the proteome level compared to genomic data. Furthermore, out of 43 pathogens detected by metagenomics, only 5 could actually be detected by metaproteomics. Most interestingly, our study indicates that 45 °C heating temperature may represent an optimal balance. It minimizes active biomass (ATP) and reduces the presence of pathogens while saving heating energy. Our study offered new insights into the impact of heating temperature on shower hose biofilm formation and proposed optimal parameters that ensure biosafety while conserving energy.},
}
@article {pmid39477106,
year = {2024},
author = {Manzanedo, RD and Chin, ARO and Ettinger, AK and Pederson, N and Pradhan, K and Guiterman, CH and Su, J and Baumgarten, F and Hille Ris Lambers, J},
title = {Moving ecological tree-ring big data forwards: Limitations, data integration, and multidisciplinarity.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {177244},
doi = {10.1016/j.scitotenv.2024.177244},
pmid = {39477106},
issn = {1879-1026},
mesh = {*Ecology ; *Big Data ; *Trees ; *Databases, Factual ; Environmental Monitoring/methods ; Forests ; Ecosystem ; },
abstract = {In recent years, tree-ring databases have emerged as a remarkable resource for ecological research, allowing us to address ecological questions at unprecedented temporal and spatial scales. However, concerns regarding big tree-ring data limitations and risks have also surfaced, leading to questions about their potential to be representative of long-term forest responses. Here, we highlight three paths of action to improve on tree-ring databases in ecology: 1) Implementing consistent bias analyses in large dendroecological databases and promoting community-driven data to address data limitations, 2) Encouraging the integration of tree-ring data with other ecological datasets, and 3) Promoting theory-driven, mechanistic dendroecological research. These issues are increasingly important for tackling pressing cross-disciplinary research questions. Finally, although we focus here on tree ring databases, these points apply broadly across many aggregative databases in ecology.},
}
@article {pmid39475652,
year = {2024},
author = {Chala, D and Endresen, D and Demissew, S and Slaughter, LA and Johnsen, EB and Stenseth, NC},
title = {Stop using racist, unethical, and inappropriate names in taxonomy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {45},
pages = {e2415490121},
pmid = {39475652},
issn = {1091-6490},
}
@article {pmid39473806,
year = {2024},
author = {Ayadi, H and Elbéji, A and Despotovic, V and Fagherazzi, G},
title = {Digital Vocal Biomarker of Smoking Status Using Ecological Audio Recordings: Results from the Colive Voice Study.},
journal = {Digital biomarkers},
volume = {8},
number = {1},
pages = {159-170},
pmid = {39473806},
issn = {2504-110X},
abstract = {INTRODUCTION: The complex health, social, and economic consequences of tobacco smoking underscore the importance of incorporating reliable and scalable data collection on smoking status and habits into research across various disciplines. Given that smoking impacts voice production, we aimed to develop a gender and language-specific vocal biomarker of smoking status.<br><br>METHODS: Leveraging data from the Colive Voice study, we used statistical analysis methods to quantify the effects of smoking on voice characteristics. Various voice feature extraction methods combined with machine learning algorithms were then used to produce a gender and language-specific (English and French) digital vocal biomarker to differentiate smokers from never-smokers.<br><br>RESULTS: A total of 1,332&#x202c; participants were included after propensity score matching (mean age = 43.6 [13.65], 64.41% are female, 56.68% are English speakers, 50% are smokers and 50% are never-smokers). We observed differences in voice features distribution: for women, the fundamental frequency F0, the formants F1, F2, and F3 frequencies and the harmonics-to-noise ratio were lower in smokers compared to never-smokers (p < 0.05) while for men no significant disparities were noted between the two groups. The accuracy and AUC of smoking status prediction reached 0.71 and 0.76, respectively, for the female participants, and 0.65 and 0.68, respectively, for the male participants.<br><br>CONCLUSION: We have shown that voice features are impacted by smoking. We have developed a novel digital vocal biomarker that can be used in clinical and epidemiological research to assess smoking status in a rapid, scalable, and accurate manner using ecological audio recordings.},
}
@article {pmid39473051,
year = {2024},
author = {Wang, Y and Chen, J and Ni, Y and Liu, Y and Gao, X and Tse, MA and Panagiotou, G and Xu, A},
title = {Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2416928},
pmid = {39473051},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Exercise ; Middle Aged ; *Mycobiome ; *Fungi/classification/genetics/isolation &amp; purification ; *Feces/microbiology ; Proteomics ; Prediabetic State/microbiology/metabolism ; Metabolomics ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Adult ; Diabetes Mellitus, Type 2/microbiology/prevention &amp; control ; Metagenomics ; Multiomics ; },
abstract = {BACKGROUND: The importance of gut microbes in mediating the benefits of lifestyle intervention is increasingly recognized. However, compared to the bacterial microbiome, the role of intestinal fungi in exercise remains elusive. With our established randomized controlled trial of exercise intervention in Chinese males with prediabetes (n = 39, ClinicalTrials.gov:NCT03240978), we investigated the dynamics of human gut mycobiome and further interrogated their associations with exercise-elicited outcomes using multi-omics approaches.<br><br>METHODS: Clinical variations and biological samples were collected before and after training. Fecal fungal composition was analyzed using the internal transcribed spacer 2 (ITS2) sequencing and integrated with paired shotgun metagenomics, untargeted metabolomics, and Olink proteomics.<br><br>RESULTS: Twelve&#x2009;weeks of exercise training profoundly promoted fungal ecological diversity and intrakingdom connection. We further identified exercise-responsive genera with potential metabolic benefits, including Verticillium, Sarocladium, and Ceratocystis. Using multi-omics approaches, we elucidated comprehensive associations between changes in gut mycobiome and exercise-shaped metabolic phenotypes, bacterial microbiome, and circulating metabolomics and proteomics profiles. Furthermore, a machine-learning algorithm built using baseline microbial signatures and clinical characteristics predicted exercise responsiveness in improvements of insulin sensitivity, with an area under the receiver operating characteristic (AUROC) of 0.91 (95% CI: 0.85-0.97) in the discovery cohort and of 0.79 (95% CI: 0.74-0.86) in the independent validation cohort (n&#x2009;=&#x2009;30).<br><br>CONCLUSIONS: Our findings suggest that intense exercise training significantly remodels the human fungal microbiome composition. Changes in gut fungal composition are associated with the metabolic benefits of exercise, indicating gut mycobiome is a possible molecular transducer of exercise. Moreover, baseline gut fungal signatures predict exercise responsiveness for diabetes prevention, highlighting that targeting the gut mycobiome emerges as a prospective strategy in tailoring personalized training for diabetes prevention.},
}
@article {pmid39472185,
year = {2024},
author = {Orr, MC and Albert, G and Hughes, AC and Koludarov, I and Luo, A and Qiao, H and Wang, MQ and Chesters, D and Zhu, CD},
title = {Dark data limit the biological sciences.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2024.10.021},
pmid = {39472185},
issn = {2095-9281},
}
@article {pmid39470965,
year = {2024},
author = {Sandin, P and Baard, P and Bülow, W and Helgesson, G},
title = {Authorship and Citizen Science: Seven Heuristic Rules.},
journal = {Science and engineering ethics},
volume = {30},
number = {6},
pages = {53},
pmid = {39470965},
issn = {1471-5546},
support = {2019-00548//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {*Authorship/standards ; Humans ; *Citizen Science/ethics ; *Heuristics ; *Guidelines as Topic ; *Ethics, Research ; *Publishing/ethics/standards ; Editorial Policies ; Research Personnel/ethics ; Volunteers ; Social Responsibility ; },
abstract = {Citizen science (CS) is an umbrella term for research with a significant amount of contributions from volunteers. Those volunteers can occupy a hybrid role, being both 'researcher' and 'subject' at the same time. This has repercussions for questions about responsibility and credit, e.g. pertaining to the issue of authorship. In this paper, we first review some existing guidelines for authorship and their applicability to CS. Second, we assess the claim that the guidelines from the International Committee of Medical Journal Editors (ICMJE), known as 'the Vancouver guidelines', may lead to exclusion of deserving citizen scientists as authors. We maintain that the idea of including citizen scientists as authors is supported by at least two arguments: transparency and fairness. Third, we argue that it might be plausible to include groups as authors in CS. Fourth and finally, we offer a heuristic list of seven recommendations to be considered when deciding about whom to include as an author of a CS publication.},
}
@article {pmid39470730,
year = {2024},
author = {Bağcı, C and Nuhamunada, M and Goyat, H and Ladanyi, C and Sehnal, L and Blin, K and Kautsar, SA and Tagirdzhanov, A and Gurevich, A and Mantri, S and von Mering, C and Udwary, D and Medema, MH and Weber, T and Ziemert, N},
title = {BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae953},
pmid = {39470730},
issn = {1362-4962},
support = {161L0284C//Federal Ministry of Research and Education (BMBF)/ ; TTU09.716//German Centre for Infection Research (DZIF)/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; //Saarland University/ ; //National Agri-Food Biotechnology Institute/ ; 101064285//Horizon Europe-Research and Innovation Framework Programme/ ; //Office of Science/ ; DE-AC02-05CH11231//Department of Energy/ ; },
abstract = {Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.},
}
@article {pmid39469132,
year = {2024},
author = {Bernstein, JM and Bautista, JB and Clores, MA and Brown, RM and Ruane, S and Sanguila, MB and Alis-Besenio, MGJ and Pejo, CLF and Cuesta, MA},
title = {Using mangrove and field observation data to identify fine-scale species distributions: a case study in bockadams (Serpentes: Homalopsidae: Cerberus).},
journal = {Royal Society open science},
volume = {11},
number = {10},
pages = {240483},
pmid = {39469132},
issn = {2054-5703},
abstract = {Characterization of species distributions is a fundamental challenge in biodiversity science, with particular significance for downstream evolutionary studies, conservation efforts, field-based faunal studies and estimates of species diversity. Checklists and phylogenetic studies often focus on poorly known, rare taxa with limited ranges. However, studies of widely distributed, ecologically important species that are abundant in their preferred microhabitats are also important for systematics and local conservation efforts, but less often studied. We collected novel natural history data during fieldwork (2019-2023) for Philippine populations of bockadams (Homalopsidae: Cerberus), one of the most abundant vertebrates in Southeast Asian aquatic systems. Considered a coastal snake, many studies report Cerberus inland. We report the frequency of encounters of Cerberus schneiderii, and the IUCN data-deficient, Philippine-endemic Cerberus microlepis during six expeditions (62 days; 1041 person-hours). We report new occurrence data for 69 C. schneiderii and 6 C. microlepis for coastal and inland populations, water measurements and dietary observations. Regression analyses and ecological niche models show the importance of coastal and mangrove habitats for Cerberus. Our study is the most comprehensive assessment of Philippine Cerberus populations to date and provides critical baseline natural history data for downstream research on widespread and range-restricted species of Southeast Asian snakes.},
}
@article {pmid39469049,
year = {2024},
author = {Chávez-Luzanía, RA and Ortega-Urquieta, ME and Aguilera-Ibarra, J and Morales-Sandoval, PH and Hernández-Coss, JA and González-Vázquez, LA and Jara-Morales, VB and Arredondo-Márquez, SH and Olea-Félix, MJ and de Los Santos-Villalobos, S},
title = {Transdisciplinary approaches for the study of cyanobacteria and cyanotoxins.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100289},
pmid = {39469049},
issn = {2666-5174},
abstract = {Cyanobacteria, ancient aerobic and photoautotrophic prokaryotes, thrive in diverse ecosystems due to their extensive morphological and physiological adaptations. They play crucial roles in aquatic ecosystems as primary producers and resource providers but also pose significant ecological and health risks through blooms that produce harmful toxins, called cyanotoxins. The taxonomic affiliation of cyanobacteria has evolved from morphology-based methods to genomic analysis, which offers detailed structural and physiological insights that are essential for accurate taxonomic affiliation and monitoring. However, challenges posed by uncultured species have been extrapolated to the detection and quantification of cyanotoxins. Current advances in molecular biology and informatics improve the precision of monitoring and allow the analysis of groups of genes related to toxin production, providing crucial information for environmental biosafety and public health. Unfortunately, public genomic databases heavily underrepresent cyanobacteria, which limits the understanding of their diversity and metabolic capabilities. Despite the increasing availability of cyanobacterial genome sequences, research is still largely focused on a few model strains, narrowing the scope of genetic and metabolic studies. The challenges posed by cyanobacterial blooms and cyanotoxins necessitate improved molecular, cultivation, and polyphasic techniques for comprehensive classification and quantification, highlighting the need for advanced genomic approaches to better understand and manage cyanobacteria and toxins. This review explores the application of transdisciplinary approaches for the study of cyanobacteria and cyanotoxins focused on diversity analysis, population quantification, and cyanotoxin monitoring, emphasizing their genomic resources and their potential in the genomic mining of toxin-related genes.},
}
@article {pmid39467848,
year = {2024},
author = {Büttiker, P and Boukherissa, A and Weissenberger, S and Ptacek, R and Anders, M and Raboch, J and Stefano, GB},
title = {Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods.},
journal = {Cellular and molecular neurobiology},
volume = {44},
number = {1},
pages = {72},
pmid = {39467848},
issn = {1573-6830},
mesh = {Humans ; *Molecular Mimicry ; Computational Biology/methods ; Cognition/physiology ; Protein Binding ; Amino Acid Sequence ; Viral Proteins/metabolism/chemistry ; Models, Molecular ; },
abstract = {Neurotropic pathogens, notably, herpesviruses, have been associated with significant neuropsychiatric effects. As a group, these pathogens can exploit molecular mimicry mechanisms to manipulate the host central nervous system to their advantage. Here, we present a systematic computational approach that may ultimately be used to unravel protein-protein interactions and molecular mimicry processes that have not yet been solved experimentally. Toward this end, we validate this approach by replicating a set of pre-existing experimental findings that document the structural and functional similarities shared by the human cytomegalovirus-encoded UL144 glycoprotein and human tumor necrosis factor receptor superfamily member 14 (TNFRSF14). We began with a thorough exploration of the Homo sapiens protein database using the Basic Local Alignment Search Tool (BLASTx) to identify proteins sharing sequence homology with UL144. Subsequently, we used AlphaFold2 to predict the independent three-dimensional structures of UL144 and TNFRSF14. This was followed by a comprehensive structural comparison facilitated by Distance-Matrix Alignment and Foldseek. Finally, we used AlphaFold-multimer and PPIscreenML to elucidate potential protein complexes and confirm the predicted binding activities of both UL144 and TNFRSF14. We then used our in silico approach to replicate the experimental finding that revealed TNFRSF14 binding to both B- and T-lymphocyte attenuator (BTLA) and glycoprotein domain and UL144 binding to BTLA alone. This computational framework offers promise in identifying structural similarities and interactions between pathogen-encoded proteins and their host counterparts. This information will provide valuable insights into the cognitive mechanisms underlying the neuropsychiatric effects of viral infections.},
}
@article {pmid39466727,
year = {2024},
author = {Charniga, K and Park, SW and Akhmetzhanov, AR and Cori, A and Dushoff, J and Funk, S and Gostic, KM and Linton, NM and Lison, A and Overton, CE and Pulliam, JRC and Ward, T and Cauchemez, S and Abbott, S},
title = {Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012520},
pmid = {39466727},
issn = {1553-7358},
mesh = {Humans ; *Communicable Diseases/epidemiology ; *Disease Outbreaks/statistics &amp; numerical data ; Models, Statistical ; Computational Biology/methods ; Epidemiological Models ; },
abstract = {Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strategies. In recent work, we found that censoring, right truncation, and dynamical bias were rarely addressed correctly when estimating delays and that these biases were large enough to have knock-on impacts across a large number of use cases. Here, we formulate a checklist of best practices for estimating and reporting epidemiological delays. We also provide a flowchart to guide practitioners based on their data. Our examples are focused on the incubation period and serial interval due to their importance in outbreak response and modeling, but our recommendations are applicable to other delays. The recommendations, which are based on the literature and our experience estimating epidemiological delay distributions during outbreak responses, can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.},
}
@article {pmid39464503,
year = {2023},
author = {Weir, JC and , and , and , and , and , and , and Boyes, D},
title = {The genome sequence of the Vapourer moth, Orgyia antiqua (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {314},
pmid = {39464503},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Orgyia antiqua specimen (the Vapourer moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 480.1 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,475 protein coding genes.},
}
@article {pmid39464235,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Lewin, T and , },
title = {The genome sequence of the acorn piercer, Pammene fasciana (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {258},
pmid = {39464235},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Pammene fasciana (acorn piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 564 megabases in span. Most of the assembly (99.94%) is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,224 protein-coding genes.},
}
@article {pmid39461044,
year = {2024},
author = {Wu, Y and Wei, C and Zhang, Y and Gu, C and Fang, Y},
title = {Investigating intrinsic and situational predictors of depression among older adults: An analysis of the CHARLS database.},
journal = {Asian journal of psychiatry},
volume = {102},
number = {},
pages = {104279},
doi = {10.1016/j.ajp.2024.104279},
pmid = {39461044},
issn = {1876-2026},
mesh = {Humans ; Female ; Male ; Aged ; Middle Aged ; Aged, 80 and over ; *Depression/epidemiology ; Databases, Factual ; China/epidemiology ; Risk Factors ; Follow-Up Studies ; Depressive Disorder/epidemiology ; Chronic Disease ; },
abstract = {BACKGROUND: This study aimed to investigate the intrinsic and situational predictors of depression under the health ecological model.<br><br>METHODS: Two waves (2011 and 2013) of survey data were collected from the CHARLS. A total of 5845 older adults (&#x2267;60) were included, and depression was defined as CESD-10 score &#x2267;10. Random forest combined with interpretable methods were utilized to select important predictors of depression. Multilevel logit model was used to examine the associations of intrinsic and situational predictors with depression.<br><br>RESULTS: After a 2-year follow up, 1822 individuals (31.17&#x202f;%) developed depression. Interpretable analyses showed that both intrinsic and situational variables were predictive for depression. Multilevel logit model showed that age, gender, number of chronic diseases, number of pain areas, life satisfaction, and toilet distance were significantly associated with depression.<br><br>CONCLUSION: Both intrinsic and situational factors were found to be associated with depression among community older population, highlighting their significance for early prevention from the perspective of public health.},
}
@article {pmid39460934,
year = {2024},
author = {Frazer, SA and Baghbanzadeh, M and Rahnavard, A and Crandall, KA and Oakley, TH},
title = {Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD).},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {39460934},
issn = {2047-217X},
support = {DEB-2153773//National Science Foundation/ ; },
mesh = {*Machine Learning ; *Opsins/genetics/metabolism ; Animals ; *Phenotype ; *Databases, Genetic ; Genetic Association Studies ; Genotype ; Humans ; Mutation ; },
abstract = {BACKGROUND: Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families, including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax-the wavelength of maximum absorbance-which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.<br><br>RESULTS: Here, we report a newly compiled database of all heterologously expressed opsin genes with &#x3bb;max phenotypes that we call the Visual Physiology Opsin Database (VPOD). VPOD_1.0 contains 864 unique opsin genotypes and corresponding &#x3bb;max phenotypes collected across all animals from 73 separate publications. We use VPOD data and deepBreaks to show regression-based machine learning (ML) models often reliably predict &#x3bb;max, account for nonadditive effects of mutations on function, and identify functionally critical amino acid sites.<br><br>CONCLUSION: The ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism's ecological niche, and may be used more broadly for de novo protein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.},
}
@article {pmid39460811,
year = {2024},
author = {Hasan, A and Ibrahim, M and Alonazi, WB and Yu, R and Li, B},
title = {Pangenome analysis of five representative Tropheryma whipplei strains following multiepitope-based vaccine design via immunoinformatic approaches.},
journal = {Molecular genetics and genomics : MGG},
volume = {299},
number = {1},
pages = {101},
pmid = {39460811},
issn = {1617-4623},
mesh = {Humans ; *Tropheryma/genetics/immunology ; *Bacterial Vaccines/immunology/genetics ; Whipple Disease/immunology/microbiology/genetics ; Computational Biology/methods ; Bacterial Proteins/genetics/immunology ; Genome, Bacterial ; Epitopes/immunology/genetics ; Vaccine Development ; Immunodominant Epitopes/immunology/genetics ; Proteomics/methods ; Proteome/genetics/immunology ; },
abstract = {Whipple disease caused by Tropheryma whipplei a gram-positive bacterium is a systemic disorder that impacts not only the gastrointestinal tract but also the vascular system, joints, central nervous system, and cardiovascular system. Due to the lack of an approved vaccine, this study aimed to utilize immunoinformatic approaches to design multiepitope -based vaccine by utilizing the proteomes of five representative T. whipplei strains. The genomes initially comprised a total of 4,844 proteins ranging from 956 to 1012 proteins per strain. We collected 829 nonredundant lists of core proteins, that were shared among all the strains. Following subtractive proteomics, one extracellular protein, WP_033800108.1, a WhiB family transcriptional regulator, was selected for the chimeric-based multiepitope vaccine. Five immunodominant epitopes were retrieved from the WhiB family transcriptional regulator protein, indicating MHC-I and MHC-II with a global population coverage of 70.61%. The strong binding affinity, high solubility, nontoxicity, nonallergenic properties and high antigenicity scores make the selected epitopes more appropriate. Integration of the epitopes into a chimeric vaccine was carried out by applying appropriate adjuvant molecules and linkers, leading to the vaccine construct having enhanced immunogenicity and successfully eliciting both innate and adaptive immune responses. Moreover, the abilityof the vaccine to bind TLR4, a core innate immune receptor, was confirmed. Molecular dynamics simulations have also revealed the promising potential stability of the designed vaccine at 400 ns. In summary, we have designed a potential vaccine construct that has the ability not only to induce targeted immunogenicity for one strain but also for global T. whipplei strains. This study proposes a potential universal vaccine, reducing Whipple's disease risk and laying the groundwork for future research on multi-strain pathogens.},
}
@article {pmid39454020,
year = {2024},
author = {Wong, R and Matulewicz, RS and Talwar, R and Shoenbill, KA and Goldstein, AO and Bjurlin, MA},
title = {Increased tobacco taxation associated with decreased consumption and bladder cancer incidence.},
journal = {Urology practice},
volume = {},
number = {},
pages = {101097UPJ0000000000000743},
doi = {10.1097/UPJ.0000000000000743},
pmid = {39454020},
issn = {2352-0787},
abstract = {PURPOSE: The temporal relationship between smoking exposure and bladder cancer (BC) diagnosis remains ill-defined. This study aims to cross-correlate and temporally associate changes in United States (US) tobacco tax and consumption with BC incidence.<br><br>METHODS: US tobacco consumption, tobacco tax data, and BC incidence rates from 1975-2019 were retrieved. A cross-correlation lag time for tobacco tax and consumption on BC incidence was calculated while controlling for national health expenditure. Proxied lag weighted semi-log linear models to determine the rate of change in BC incidence rates associated with a 1% change in tobacco tax percentages on a national and state level.<br><br>RESULTS: A 1% increase in tobacco tax was associated with a 1.77% decrease in BC incidence over a 6-year period (R[2]=0.9687, p=0.00044). 22 states had a statistically significant decline in BC incidences correlated with increasing tobacco taxation. Reduction in BC incidence >0.5% were observed in states along the Western and Eastern US borders. Montana, Utah, Nebraska, Arkansas, and Tennessee did not have decreasing BC incidences from tobacco tax increases. California had the most drastic decline in BC incidence (1.98%). Nationally, tobacco consumption decrease in 1 pack per capita was associated with a 0.47% decrease in BC incidence over a 28-year period (R[2]=0.984, p=0.00011).<br><br>CONCLUSION: Declining US tobacco consumption may indicate significant reduction in BC incidence through 2047. Primary prevention through adaptation of state-legislated tax changes may contribute to a reduction in BC incidence in states lying within the Central US. A national tobacco tax initative can be considered given the improvement in population health.},
}
@article {pmid39449983,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Currant Clearwing moth, Synanthedon tipuliformis (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {300},
pmid = {39449983},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Synanthedon tipuliformis (the Currant Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 295.8 megabases in span. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 27.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,878 protein-coding genes.},
}
@article {pmid39448189,
year = {2024},
author = {Konečný, L and Peterková, K},
title = {Unveiling the peptidases of parasites from the office chair - The endothelin-converting enzyme case study.},
journal = {Advances in parasitology},
volume = {126},
number = {},
pages = {1-52},
doi = {10.1016/bs.apar.2024.05.003},
pmid = {39448189},
issn = {2163-6079},
mesh = {Animals ; *Computational Biology ; Endothelin-Converting Enzymes/genetics ; Schistosoma mansoni/enzymology/genetics ; Humans ; Peptide Hydrolases/genetics/metabolism ; Proteomics ; },
abstract = {The emergence of high-throughput methodologies such as next-generation sequencing and proteomics has necessitated significant advancements in biological databases and bioinformatic tools, therefore reshaping the landscape of research into parasitic peptidases. In this review we outline the development of these resources along the -omics technologies and their transformative impact on the field. Apart from extensive summary of general and specific databases and tools, we provide a general pipeline on how to use these resources effectively to identify candidate peptidases from these large datasets and how to gain as much information about them as possible without leaving the office chair. This pipeline is then applied in an illustrative case study on the endothelin-converting enzyme 1 homologue from Schistosoma mansoni and attempts to highlight the contemporary capabilities of bioinformatics. The case study demonstrate how such approach can aid to hypothesize enzyme functions and interactions through computational analysis alone effectively and emphasizes how such virtual investigations can guide and optimize subsequent wet lab experiments therefore potentially saving precious time and resources. Finally, by showing what can be achieved without traditional wet laboratory methods, this review provides a compelling narrative on the use of bioinformatics to bridge the gap between big data and practical research applications, highlighting the key role of these technologies in furthering our understanding of parasitic diseases.},
}
@article {pmid39446479,
year = {2024},
author = {Oliveira, J and Aires Dias, J and Correia, R and Pinheiro, R and Reis, V and Sousa, D and Agostinho, D and Simões, M and Castelo-Branco, M},
title = {Exploring Immersive Multimodal Virtual Reality Training, Affective States, and Ecological Validity in Healthy Firefighters: Quasi-Experimental Study.},
journal = {JMIR serious games},
volume = {12},
number = {},
pages = {e53683},
pmid = {39446479},
issn = {2291-9279},
abstract = {BACKGROUND: Firefighters face stressful life-threatening events requiring fast decision-making. To better prepare for those situations, training is paramount, but errors in real-life training can be harmful. Virtual reality (VR) simulations provide the desired realism while enabling practice in a secure and controlled environment. Firefighters' affective states are also crucial as they are a higher-risk group.<br><br>OBJECTIVE: To assess the impact on affective states of 2 simulated immersive experiences in a sample of healthy firefighters (before, during, and after the simulation), we pursued a multivariate approach comprising cognitive performance, situational awareness, depression, anxiety, stress, number of previous adverse events experienced, posttraumatic stress disorder (PTSD) severity, and emotions. The efficacy and ecological validity of an innovative VR haptic system were also tested, exploring its impact on performance.<br><br>METHODS: In collaboration with the Portuguese National Fire Service School, we exposed 22 healthy firefighters to 2 immersive scenarios using the FLAIM Trainer VR system (neutral and arousing scenarios) while recording physiological data in a quasi-experimental study. Baseline cognitive performance, depression, anxiety, stress, number of adverse events, and severity of PTSD symptoms were evaluated. Positive and negative affective states were measured before, between, and after each scenario. Situational awareness, sense of presence, ecological validity, engagement, and negative effects resulting from VR immersion were tested.<br><br>RESULTS: Baseline positive affect score was high (mean 32.4, SD 7.2) and increased after the VR tasks (partial &#x3b7;[2]=0.52; Greenhouse-Geisser F1.82,32.78=19.73; P<.001). Contrarily, mean negative affect score remained low (range 11.0-11.9) throughout the study (partial &#x3b7;[2]=0.02; Greenhouse-Geisser F2.13,38.4=0.39; P=.69). Participants' feedback on the VR sense of presence was also positive, reporting a high sense of physical space (mean score 3.9, SD 0.8), ecological validity (mean score 3.8, SD 0.6), and engagement (mean score 3.8, SD 0.6). Engagement was related to the number of previously experienced adverse events (r=0.49; P=.02) and positive affect (after the last VR task; r=0.55; P=.02). Conversely, participants reported few negative effects (mean score 1.7, SD 0.6). The negative effects correlated positively with negative affect (after the last VR task; r=0.53; P=.03); and avoidance (r=0.73; P<.001), a PTSD symptom, controlling for relevant baseline variables. Performance related to situational awareness was positive (mean 46.4, SD 34.5), although no relation was found to metacognitively perceived situational awareness (r=-0.12; P=.59).<br><br>CONCLUSIONS: We show that VR is an effective alternative to in-person training as it was considered ecologically valid and engaging while promoting positive emotions, with few negative repercussions. This corroborates the use of VR to test firefighters' performance and situational awareness. Further research is needed to ascertain that firefighters with PTSD symptomatology are not negatively affected by VR. This study favors the use of VR training and provides new insights on its emotional and cognitive impact on the trainee.},
}
@article {pmid39445720,
year = {2024},
author = {Compton, ZT and Mellon, W and Harris, VK and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, LN and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Li, CI and Zehnder, A and Graham, TA and Troan, BV and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, CA and Abegglen, LM and Maley, CC and Boddy, AM},
title = {Cancer Prevalence across Vertebrates.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {OF1-OF18},
doi = {10.1158/2159-8290.CD-24-0573},
pmid = {39445720},
issn = {2159-8290},
support = {P01 CA091955/CA/NCI NIH HHS/United States ; OTKA K143421//Agence Nationale de la Recherche (ANR)/ ; U54 CA217376/CA/NCI NIH HHS/United States ; ADHS18-198847//Arizona Biomedical Research Commission (ABRC)/ ; U2C CA233254/CA/NCI NIH HHS/United States ; //Hyundai Hope On Wheels (Hope On Wheels)/ ; BC132057//Congressionally Directed Medical Research Programs (CDMRP)/ ; R01 CA140657/CA/NCI NIH HHS/United States ; R21 CA257980/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; COVER ANR-23-CE02-0019//Agence Nationale de la Recherche (ANR)/ ; },
abstract = {Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes.},
}
@article {pmid39442119,
year = {2024},
author = {Castro-Nunes, P and Palmieri, P and Bellas, H and Soares, A and Viana, J and Carvalho, PVR and Jatobá, A},
title = {Effects of pay for performance in primary care in an under-registration scenario.},
journal = {Revista de saude publica},
volume = {58},
number = {},
pages = {44},
pmid = {39442119},
issn = {1518-8787},
mesh = {Humans ; *Primary Health Care/economics ; Brazil ; *Reimbursement, Incentive/economics ; Female ; National Health Programs/economics ; },
abstract = {OBJECTIVE: To propose a method for detecting and analyzing under-registration and highlight its potential financial effect in view of the implementation of the Previne Brasil Program.<br><br>METHODS: An ecological study was carried out to analyze cytopathological exams in programmatic area 3.1 in the municipality of Rio de Janeiro. The data was collected from the Departamento de Inform&#xe1;tica do Sistema &#xda;nico de Sa&#xfa;de (DATASUS - Department of Informatics of the Unified Health System) database, including information on reports from outsourced cytopathology laboratories and those available in the Sistema de Informa&#xe7;&#xe3;o em Sa&#xfa;de para a Aten&#xe7;&#xe3;o B&#xe1;sica (SISAB - Health Information System for Primary Care) and the Sistema de Informa&#xe7;&#xe3;o do C&#xe2;ncer do Colo do &#xda;tero (SISCOLO - Cervical Cancer Information System) of DATASUS/Ministry of Health.<br><br>RESULTS: The estimated under-registrations per health unit totaled 108,511 exams in the last two years in the programmatic area 3.1 area, which corresponds to an estimated total of R$ 435,129.00 that would have been foregone if the Previne Brasil Program had been in place during the period studied.<br><br>CONCLUSION: The article's main contribution lies in the presentation of empirical evidence of the potential effects of under-registration on Primary Health Care financing. In addition, there are two other significant findings - firstly, it highlights weaknesses in the process of recording health information inherent to vulnerable regions; secondly, it indicates a vicious circle potentially fueled by sudden changes in Primary Health Care funding conditions, in addition to potential consequences for other levels of care.},
}
@article {pmid39440963,
year = {2024},
author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K},
title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.},
journal = {mSystems},
volume = {9},
number = {11},
pages = {e0068224},
pmid = {39440963},
issn = {2379-5077},
support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; },
abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.<br><br>IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.},
}
@article {pmid39439296,
year = {2025},
author = {Rosche, C and Broennimann, O and Novikov, A and Mrázová, V and Boiko, GV and Danihelka, J and Gastner, MT and Guisan, A and Kožić, K and Lehnert, M and Müller-Schärer, H and Nagy, DU and Remelgado, R and Ronikier, M and Selke, JA and Shiyan, NM and Suchan, T and Thoma, AE and Zdvořák, P and Mráz, P},
title = {Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe.},
journal = {The New phytologist},
volume = {245},
number = {1},
pages = {392-405},
pmid = {39439296},
issn = {1469-8137},
mesh = {*Centaurea/genetics/physiology ; Europe ; *Polyploidy ; *Introduced Species ; Phylogeography ; Ecosystem ; Diploidy ; },
abstract = {Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in natural and relict habitats and phylogeographic data, we estimated the native ranges of both cytotypes. Diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids has exponentially increased over time in their expanded but not in their native range. This cryptic invasion predominantly occurred in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. We conclude that spatio-temporally explicit assessments of range shifts, habitat preferences and niche evolution can improve our understanding of cryptic invasions. We also emphasize the value of herbarium specimens for accurate estimation of species´ native ranges, with fundamental implications for the design of research studies and the assessment of biodiversity trends.},
}
@article {pmid39438357,
year = {2024},
author = {Little, AJ and Matthee, CA and Ueckermann, EA and Horak, IG and Hui, C and Matthee, S},
title = {Host and habitat shape ectoparasite diversity on Mastomys natalensis and Mastomys coucha (Muridae).},
journal = {Parasitology},
volume = {151},
number = {8},
pages = {769-783},
pmid = {39438357},
issn = {1469-8161},
support = {R01 AI136832/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Rodent Diseases/parasitology/epidemiology ; *Ecosystem ; *Murinae/parasitology ; Male ; *Ectoparasitic Infestations/parasitology/veterinary ; Female ; Host-Parasite Interactions ; Mites/physiology/classification ; Siphonaptera/classification/physiology ; Biodiversity ; Ticks/classification/physiology ; },
abstract = {Mastomys natalensis and M. coucha are commensal rodent species endemic to Africa. A recent taxonomic revision within Mastomys leaves the parasite–host list of M. natalensis questionable and that of M. coucha incomplete. The current study aimed to develop a better understanding of the ectoparasite diversity associated with the 2 distinct but closely related rodent species and to explore the influence of host and habitat type on ectoparasite infestations. Between 2014 and 2020, 590 rodents were trapped in 3 habitat types (village, agriculture and natural) across a wildlife-human/domestic animal interface. In total 48 epifaunistic species (45 ectoparasitic and 3 predatory) represented by 29 genera from 4 taxonomic groups (fleas, lice, mites and ticks) were recorded. Only 50% of the epifauna were shared between the 2 rodent species, with mites the most speciose taxon in both host species. The abundance of epifaunistic individuals, and also those of mites and fleas, were significantly higher on male M. natalensis, while ticks were significantly higher on reproductively active M. natalensis. For both rodent species, infestations by most epifaunistic taxa (on M. natalensis) and some taxa (on M. coucha) were significantly lower in the village as opposed to the less disturbed agricultural and natural habitat types. The study highlights the importance of host life history, even in closely related rodent species, in shaping parasite profiles and a loss of parasite diversity in more extreme anthropogenic habitats.},
}
@article {pmid39436938,
year = {2024},
author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP},
title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012530},
pmid = {39436938},
issn = {1553-7358},
mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; },
abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.},
}
@article {pmid39436510,
year = {2024},
author = {Zinicovscaia, I and Chernyagina, O and Chaligava, O and Yushin, N and Devyatova, E and Grozov, D},
title = {Moss biomonitoring in areas affected by ashfalls of Shiveluch volcano (Kamchatka).},
journal = {Environmental science and pollution research international},
volume = {31},
number = {52},
pages = {61730-61739},
pmid = {39436510},
issn = {1614-7499},
mesh = {*Bryophyta/chemistry ; *Volcanic Eruptions ; *Environmental Monitoring/methods ; *Biological Monitoring ; Air Pollutants/analysis ; },
abstract = {The moss bag technique was applied on Kamchatka to assess the effect of Shiveluch volcano on the air quality. Moss bags were exposed in settlements located at different distances from the volcano and affected by ashfall to varying degrees. The inductively coupled plasma optical emission spectrometry was used for the determination of the content of Al, Ba, Co, Cd, Cr, Cu, Fe, Mn, P, Pb, Sr, S, V, and Zn in both exposed and unexposed moss samples. Relative accumulation factor revealed enrichment of mosses exposed in the area affected by ashfall with Al, Cr, V, and Zn. Correlation and principal component analysis allowed to identify elements of volcanogenic, geogenic, and anthropogenic origin. Ecological risk values less than 150 indicate low potential ecological risk in the region. Active moss biomonitoring can be considered a cheap and efficient tool for in-depth study of the influence of volcanic activity on air quality on the peninsula.},
}
@article {pmid39435526,
year = {2025},
author = {Kan-Lingwood, NY and Sagi, L and Mazie, S and Shahar, N and Zecherle Bitton, L and Templeton, A and Rubenstein, D and Bouskila, A and Bar-David, S},
title = {Genotyping Error Detection and Customised Filtration for SNP Datasets.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14033},
doi = {10.1111/1755-0998.14033},
pmid = {39435526},
issn = {1755-0998},
support = {2011384//United States-Israel Binational Science Foundation/ ; },
mesh = {*Polymorphism, Single Nucleotide ; *Genotyping Techniques/methods ; Animals ; Genotype ; Computational Biology/methods ; },
abstract = {A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the 'true' genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non-invasive sampling from the Asiatic wild ass (Equus hemionus) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (r) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (p = 0.0002) and a significant increase in relatedness, from r = 0.98 to r = 0.991 (p = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality.},
}
@article {pmid39434036,
year = {2024},
author = {Li, C and Zhang, X and Zhao, L and Liu, S},
title = {Multi-omics profiling reveals the molecular mechanisms of H2O2-induced detrimental effects on Thamnaconus septentrionalis.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {984},
pmid = {39434036},
issn = {1471-2164},
mesh = {Animals ; *Hydrogen Peroxide/metabolism ; Fishes/metabolism/genetics ; Transcriptome/drug effects ; Gene Expression Profiling ; Metabolomics ; Signal Transduction/drug effects ; Metabolome/drug effects ; Multiomics ; },
abstract = {BACKGROUND: Hydrogen peroxide (H2O2), a novel water treatment agent, can be used for disinfection, water quality adjustment, and disease prevention, while excessive H2O2 can injure farm animals, even leading to death. Hydrogen peroxide is a recommended disinfectant and bactericide for treating gill diseases and vibriosis in the greenfin horse-faced filefish Thamnaconus septentrionalis. However, its cumulative effect, toxic molecular mechanism and relevant signal transduction/metabolic networks in marine fishes are largely unknown.<br><br>RESULTS: We employed a multi-omics approach to investigate the detrimental effects of 50&#xa0;mg/L H2O2 exposure (2&#xa0;h/d) on filefish for 2 d, 4 d, and 6 d. Transcriptome sequencing showed that differentially expressed genes (DEGs) were mainly classified into functions such as signal transduction, nervous system, liver and bile acid metabolism, energy metabolism, cell adhesion and communication, inflammation and immune response. Metabolomic analysis found that the significantly changed metabolites (SCMs) were involved in phenylalanine metabolism, inflammatory mediator regulation, linoleic acid metabolism, and necroptosis. The main SCMs were cholic acid, carnitine C12:1, dimethylmalonic acid, glutamic acid, L-lactic acid, shikimic acid, 2-methylsuccinic acid, and others. Moreover, H2O2-induced oxidative stress also disturbs the balance of the gut microbiota, altering the microbial composition and affecting digestive processes.<br><br>CONCLUSIONS: Integrated multiomics analysis revealed that H2O2-induced detrimental impacts include mucosal damage, inflammatory and immune responses, altered energy metabolism, and gut microbiota disorders. These findings offer novel insights into the harmful effects and signal transduction/metabolic pathways triggered by H2O2 exposure in marine fishes.},
}
@article {pmid39432055,
year = {2025},
author = {Zhao, L and Henriksen, RA and Ramsøe, A and Nielsen, R and Korneliussen, TS},
title = {Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e14029},
pmid = {39432055},
issn = {1755-0998},
support = {CF19-0712//Carlsberg Foundation/ ; CF20-0071//Carlsberg Foundation/ ; R302-2018-2155//Lundbeck Foundation/ ; },
mesh = {*DNA, Ancient/analysis ; DNA Damage ; Sequence Analysis, DNA/methods ; Likelihood Functions ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Humans ; },
abstract = {One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.},
}
@article {pmid39430511,
year = {2024},
author = {Shamrat, FMJM and Idna Idris, MY and Zhou, X and Khalid, M and Sharmin, S and Sharmin, Z and Ahmed, K and Moni, MA},
title = {PollenNet: A novel architecture for high precision pollen grain classification through deep learning and explainable AI.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38596},
pmid = {39430511},
issn = {2405-8440},
abstract = {Pollen grains play a critical role in environmental, agricultural, and allergy research despite their tiny dimensions. The accurate classification of pollen grains remains a significant challenge, mainly attributable to their intricate structures and the extensive diversity of species. Traditional methods often lack accuracy and effectiveness, prompting the need for advanced solutions. This study introduces a novel deep learning framework, PollenNet, designed to tackle the intricate challenge of pollen grain image classification. The efficiency of PollenNet is thoroughly evaluated through stratified 5-fold cross-validation, comparing it with cutting-edge methods to demonstrate its superior performance. A comprehensive data preparation phase is conducted, including removing duplicates and low-quality images, applying Non-local Means Denoising for noise reduction, and Gamma correction to adjust image brightness. Furthermore, Explainable AI (XAI) is utilized to enhance the interpretability of the model, while Receiver Operating Characteristic (ROC) curve analysis serves as a quantitative method for evaluating the model's capabilities. PollenNet demonstrates superior performance when compared to existing models, with an accuracy of 98.45 %, precision of 98.20 %, specificity of 98.40 %, recall of 98.30 %, and f1-score of 98.25 %. The model also maintains low Mean Squared Error (0.03) and Mean Absolute Error (0.02) rates. The ROC curve analysis, the low False Positive Rate (0.016), and the False Negative Rate (0.017) highlight the reliability and dependability of the model. This study significantly improves the efficacy of classifying pollen grains, indicating an important advancement in the application of deep learning for ecological research.},
}
@article {pmid39429633,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Hebrew Character, Orthosia gothica (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {90},
pmid = {39429633},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Orthosia gothica (the Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,065.1 megabases in span. Most of the assembly is scaffolded into 37 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,691 protein coding genes.},
}
@article {pmid39429632,
year = {2024},
author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The genome sequence of the smooth giant clam, Tridacna derasa Röding, 1798.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {375},
pmid = {39429632},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Tridacna derasa (the smooth giant clam; Mollusca; Bivalvia;Cardiida; Cardiidae). The genome sequence is 1,060.2 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.95 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,638 protein coding genes.},
}
@article {pmid39424895,
year = {2024},
author = {Melo, MS and Lima, SVMA and Dos Santos, AD and Ribeiro, CJN and Júnior, PAB and Silva, TKS and de Resende, LT and Corrêa, F and Migowski, A and Schiffman, M and Rodriguez, AC and Ribeiro, A and Raiol, T},
title = {Temporal trends, spatial and spatiotemporal clusters of cervical cancer mortality in Brazil from 2000 to 2021.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24436},
pmid = {39424895},
issn = {2045-2322},
support = {Grant number GEREB-Fiocruz/CNPq 440204/2019-4.//Oswaldo Cruz Foundation (Fiocruz) and National Council for Scientific and Technological Development (CNPq)/ ; },
mesh = {Humans ; Female ; Brazil/epidemiology ; *Uterine Cervical Neoplasms/mortality/epidemiology ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Aged ; Young Adult ; Adolescent ; Mortality/trends ; },
abstract = {Cervical cancer, despite being preventable through primary and secondary prevention strategies, remains one of the leading causes of morbidity and mortality among women in Brazil. This study aimed to analyze the temporal, spatial, and space-time patterns of cervical cancer mortality in Brazil. An ecological study was conducted using temporal, spatial, and space-time analysis techniques, using death certificates with cervical cancer as the underlying cause or associated condition among females in Brazil from 2000 to 2021. Death certificate and population data were provided by the Department of Health Informatics of the Unified Health System (DATASUS) and the Brazilian Institute of Geography and Statistics (IBGE), respectively. A total of 123,306 deaths associated with cervical cancer among women were registered during the study period. A rising trend in mortality was detected since 2014 onwards, after 14 years of decline. Particularly, an increase in mortality was observed among the younger age groups, and in the North and Northeast regions regardless of age. Heterogeneity in the spatial distribution of cervical cancer mortality was observed, with high mortality clusters around the country, but mostly concentrated in the North and Northeast regions. These findings suggest a need and an opportunity to develop efficient and effective health policies targeting those regions and groups of women at higher risk which in turn will allow for fast and significant reductions in cervical cancer mortality in Brazil.},
}
@article {pmid39421415,
year = {2024},
author = {Ion, MC and Bloomer, CC and Bărăscu, TI and Oficialdegui, FJ and Shoobs, NF and Williams, BW and Scheers, K and Clavero, M and Grandjean, F and Collas, M and Baudry, T and Loughman, Z and Wright, JJ and Ruokonen, TJ and Chucholl, C and Guareschi, S and Koese, B and Banyai, ZM and Hodson, J and Hurt, M and Kaldre, K and Lipták, B and Fetzner, JW and Cancellario, T and Weiperth, A and Birzaks, J and Trichkova, T and Todorov, M and Balalaikins, M and Griffin, B and Petko, ON and Acevedo-Alonso, A and D'Elía, G and Śliwińska, K and Alekhnovich, A and Choong, H and South, J and Whiterod, N and Zorić, K and Haase, P and Soto, I and Brady, DJ and Haubrock, PJ and Torres, PJ and Şadrin, D and Vlach, P and Kaya, C and Woo Jung, S and Kim, JY and Vermeersch, XHC and Bonk, M and Guiaşu, R and Harlioğlu, MM and Devlin, J and Kurtul, I and Błońska, D and Boets, P and Masigol, H and Cabe, PR and Jussila, J and Vrålstad, T and Beresford, DV and Reid, SM and Patoka, J and Strand, DA and Tarkan, AS and Steen, F and Abeel, T and Harwood, M and Auer, S and Kelly, S and Giantsis, IA and Maciaszek, R and Alvanou, MV and Aksu, &#xd6; and Hayes, DM and Kawai, T and Tricarico, E and Chakandinakira, A and Barnett, ZC and Kudor, &#x15e;G and Beda, AE and Vîlcea, L and Mizeranschi, AE and Neagul, M and Licz, A and Cotoarbă, AD and Petrusek, A and Kouba, A and Taylor, CA and Pârvulescu, L},
title = {World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18229},
pmid = {39421415},
issn = {2167-8359},
mesh = {Animals ; *Astacoidea/microbiology ; *Fresh Water ; Aphanomyces ; Internet ; Ecosystem ; Databases, Factual ; },
abstract = {Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.},
}
@article {pmid39420601,
year = {2024},
author = {Li, Z and Zhang, Y and Peng, B and Qin, S and Zhang, Q and Chen, Y and Chen, C and Bao, Y and Zhu, Y and Hong, Y and Liu, B and Liu, Q and Xu, L and Chen, X and Ma, X and Wang, H and Xie, L and Yao, Y and Deng, B and Li, J and De, B and Chen, Y and Wang, J and Li, T and Liu, R and Tang, Z and Cao, J and Zuo, E and Mei, C and Zhu, F and Shao, C and Wang, G and Sun, T and Wang, N and Liu, G and Ni, JQ and Liu, Y},
title = {A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.},
journal = {Nucleic acids research},
volume = {52},
number = {21},
pages = {13447-13468},
pmid = {39420601},
issn = {1362-4962},
support = {2021YFF1200500//China National Key R&amp;D Program/ ; 32070595//National Natural Science Foundation of China/ ; 20221250020//Ministry of Science and Technology/ ; 20181300988//National Natural Science Foundation of China/ ; },
mesh = {*Enhancer Elements, Genetic ; Animals ; *Deep Learning ; Drosophila melanogaster/genetics ; Drosophila/genetics ; Humans ; Computational Biology/methods ; Gene Expression Regulation ; },
abstract = {Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design. Proficient in uncovering subtle and intricate patterns within extensive enhancer screening data, DREAM achieves cutting-edge sequence-based enhancer activity prediction and highlights critical sequence features implicating strong enhancer activity. Leveraging DREAM, we have engineered enhancers that surpass the potency of the strongest enhancer within the Drosophila genome by approximately 3.6-fold. Remarkably, these synthetic enhancers exhibited conserved functionality across species that have diverged more than billion years, indicating that DREAM was able to learn highly conserved enhancer regulatory grammar. Additionally, we designed silencers and cell line-specific enhancers using DREAM, demonstrating its versatility. Overall, our study not only introduces an interpretable approach for enhancer design but also lays out a general framework applicable to the design of other types of cis-regulatory elements.},
}
@article {pmid39419226,
year = {2024},
author = {Liu, J and Zhu, M and Shi, X and Hui, C and Sun, Y and Zhang, R and Jin, D and Li, Z and Chen, H and Zhao, Z},
title = {Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {176892},
doi = {10.1016/j.scitotenv.2024.176892},
pmid = {39419226},
issn = {1879-1026},
mesh = {*Nitrogen ; *Soil Microbiology ; *Microbiota/drug effects ; *Herbivory ; Animals ; *Insecta/physiology ; Desert Climate ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; China ; },
abstract = {Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.},
}
@article {pmid39417898,
year = {2024},
author = {Khalaf, SMH and Alqahtani, MSM and Ali, MRM and Abdelalim, ITI and Hodhod, MS},
title = {Modeling climate-related global risk maps of rice bacterial blight caused by Xanthomonas oryzae (Ishiyama 1922) using geographical information system (GIS).},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {11},
pages = {1064},
pmid = {39417898},
issn = {1573-2959},
mesh = {*Xanthomonas ; *Oryza/microbiology ; *Climate Change ; *Plant Diseases/microbiology/statistics &amp; numerical data ; *Geographic Information Systems ; Environmental Monitoring ; Climate ; },
abstract = {Rice is a critical staple crop that feeds more than half of the world's population. Still, its production confronts various biotic risks, notably the severe bacterial blight disease produced by Xanthomonas oryzae. Understanding the possible effects of climate change on the geographic distribution of this virus is critical to ensuring food security. This work used ecological niche modeling and the Maxent algorithm to create future risk maps for the range of X. oryzae under several climate change scenarios between 2050 and 2070. The model was trained using 93 occurrence records of X. oryzae and five critical bioclimatic variables. It has an excellent predictive performance, with an AUC of 0.889. The results show that X. oryzae's potential geographic range and habitat suitability are expected to increase significantly under low (RCP2.6) and high (RCP8.5) emission scenarios. Key climatic drivers allowing this development include increased yearly precipitation, precipitation during the wettest quarter, and the wettest quarter's mean temperature. These findings are consistent with broader research revealing that climate change is allowing many plant diseases and other dangerous microbes to spread across the globe. Integrating these spatial predictions with data on host susceptibility, agricultural practices, and socioeconomic vulnerabilities can help to improve targeted surveillance, preventative, and management methods for reducing the growing threat of bacterial blight to rice production. Proactive, multidisciplinary efforts to manage the changing disease dynamics caused by climate change will be critical to assuring global food security in the future decades.},
}
@article {pmid39417330,
year = {2024},
author = {Kershenbaum, A and Akçay, &#xc7; and Babu-Saheer, L and Barnhill, A and Best, P and Cauzinille, J and Clink, D and Dassow, A and Dufourq, E and Growcott, J and Markham, A and Marti-Domken, B and Marxer, R and Muir, J and Reynolds, S and Root-Gutteridge, H and Sadhukhan, S and Schindler, L and Smith, BR and Stowell, D and Wascher, CAF and Dunn, JC},
title = {Automatic detection for bioacoustic research: a practical guide from and for biologists and computer scientists.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.13155},
pmid = {39417330},
issn = {1469-185X},
support = {//A*MIDEX/ ; //Cambridge Centre for Data-Driven Discovery/ ; //African Institute for Mathematical Sciences/ ; NE/W005468/1//Natural Environment Research Council/ ; //Global Affairs Canada/ ; ANR-20-CE23-0012-01 MIM//Agence Nationale de la Recherche/ ; ANR-20-CHIA-0014//Agence Nationale de la Recherche/ ; ANR-16-CONV-0002//Institute of Convergence ILCB/ ; //International Development Research Centre/ ; },
abstract = {Recent years have seen a dramatic rise in the use of passive acoustic monitoring (PAM) for biological and ecological applications, and a corresponding increase in the volume of data generated. However, data sets are often becoming so sizable that analysing them manually is increasingly burdensome and unrealistic. Fortunately, we have also seen a corresponding rise in computing power and the capability of machine learning algorithms, which offer the possibility of performing some of the analysis required for PAM automatically. Nonetheless, the field of automatic detection of acoustic events is still in its infancy in biology and ecology. In this review, we examine the trends in bioacoustic PAM applications, and their implications for the burgeoning amount of data that needs to be analysed. We explore the different methods of machine learning and other tools for scanning, analysing, and extracting acoustic events automatically from large volumes of recordings. We then provide a step-by-step practical guide for using automatic detection in bioacoustics. One of the biggest challenges for the greater use of automatic detection in bioacoustics is that there is often a gulf in expertise between the biological sciences and the field of machine learning and computer science. Therefore, this review first presents an overview of the requirements for automatic detection in bioacoustics, intended to familiarise those from a computer science background with the needs of the bioacoustics community, followed by an introduction to the key elements of machine learning and artificial intelligence that a biologist needs to understand to incorporate automatic detection into their research. We then provide a practical guide to building an automatic detection pipeline for bioacoustic data, and conclude with a discussion of possible future directions in this field.},
}
@article {pmid39415784,
year = {2024},
author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and Harnqvist, S and , and , and , and , and , },
title = {The genome sequence of the Essex Skipper butterfly, Thymelicus lineola (Ochsenheimer, 1808).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {452},
pmid = {39415784},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Essex Skipper butterfly, Thymelicus lineola (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence spans 511.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.24 kilobases in length.},
}
@article {pmid39414803,
year = {2024},
author = {Lončarević, N and Liu, U and Stefanaki, A and Carapeto, A and Ensslin, A and Meade, C and Metzing, D and Peci, D and Fantinato, E and Colling, G and Pankova, H and Akmane, I and Tsvetkov, IN and Sibik, J and Szitár, K and Van Meerbeek, K and Daco, L and Boudagher, M and Klisz, M and Walczak, M and Evju, M and Lužnik, M and Kiehn, M and Sarginci, M and Aksoy, N and Koçer, N and Barazani, O and Anastasiu, P and Stroh, P and Vit, P and Vergeer, P and Puchałka, R and Kahale, R and Godefroid, S and Lanfranco, S and Parpan, T and Kull, T and Rašomavičius, V and Fišer, &#x17d; and Glasnović, P},
title = {Database of European vascular plants red lists as a contribution to more coherent plant conservation.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1138},
pmid = {39414803},
issn = {2052-4463},
support = {R25 CA018201/CA/NCI NIH HHS/United States ; CA18201//European Cooperation in Science and Technology (COST)/ ; },
mesh = {Europe ; *Databases, Factual ; *Conservation of Natural Resources ; *Plants/classification ; Biodiversity ; },
abstract = {We introduce the database of European vascular plant red lists, a compilation of red list categories designated to taxa during in-country conservation assessments. Version 1.0 of the database is a standalone static dataset with open access in an end-user friendly format. Its aim is to fulfil the objectives of European Cooperation in Science and Technology (COST) Action 18201, ConservePlants. The database synthesizes data across 42 red lists from 41 countries, with participation of 39 out of a total of 44 European countries and two additional Mediterranean countries. The database contains 51,109 records representing 21,481 original taxonomic names with 37 different red list categories. During data harmonisation, 20,312 of the original taxonomic names were assigned to 17,873 unique accepted taxonomic names with scientific authorships across 184 families, 1650 genera and 15,593 species; and red list categories were standardised to 13 unique categories. We see this database as a source of information in diverse plant conservation activities and suitable for various stakeholders.},
}
@article {pmid39409485,
year = {2024},
author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F},
title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.},
journal = {Sensors (Basel, Switzerland)},
volume = {24},
number = {19},
pages = {},
pmid = {39409485},
issn = {1424-8220},
support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; },
abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.},
}
@article {pmid39407030,
year = {2024},
author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ},
title = {Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {31},
doi = {10.1038/s44185-024-00065-3},
pmid = {39407030},
issn = {2731-4243},
}
@article {pmid39404811,
year = {2024},
author = {Litavský, J and Majzlan, O and Langraf, V and Žarnovičan, H},
title = {Influence of habitat management and selected environmental parameters on the ground-living communities of harvestmen (Opiliones) in the historical park in Rusovce (Slovakia).},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {11},
pages = {1056},
pmid = {39404811},
issn = {1573-2959},
support = {No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0255/23//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; },
mesh = {*Ecosystem ; *Parks, Recreational ; *Environmental Monitoring ; Animals ; Slovakia ; Biodiversity ; Arachnida ; Conservation of Natural Resources/methods ; Forests ; Microclimate ; },
abstract = {City parks serve as valuable refuges for invertebrates in the urban environment, which are constantly exposed to human influence caused by management practices in the parks. Many harvestman species are suitable bioindicators for monitoring ecological change; however, their effective use in environmental assessment necessitates to expand the insufficient knowledge of ecological environmental specificities of their communities. We studied the diversity and dynamics of harvestman (Opiliones) communities in the historical park in Rusovce, situated in the southwestern part of Bratislava (Slovakia). Seven study sites were investigated, representing areas subjected to different management practices. The research was conducted from March 2019 to April 2020, using pitfall traps. We evaluated the impact of microclimatic variables (soil and air temperature), environmental characteristics (plant diversity and cover of vegetation layers, age of forest stands, thickness of the litter layer), and management practices on the structure of harvestman communities. The study revealed the response of specific harvestman species to temperature variations, emphasizing the importance of microclimatic conditions. Environmental variables, such as the richness of plant species in the shrub layer, the cover of the herb and shrub vegetation layers, and the age of the forest stands, were identified as key factors that influence the dispersal of harvestman species. Furthermore, management practices, especially the presence of monoculture tree plantations, significantly affected the species composition of harvestmen. Examining the sensitivity of Opiliones, important bioindicators, to these factors is crucial for implementing effective conservation strategies in urban green spaces and anthropogenically influenced ecosystems.},
}
@article {pmid39403498,
year = {2024},
author = {Hung, RJ and Low, I and Yeh, HC and Wang, PY and Chen, YS and Chen, LF},
title = {Feedback matters: EEG correlates of empathy involved in the naturalistic communication of emotions.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38574},
pmid = {39403498},
issn = {2405-8440},
abstract = {Empathy involves the processing of complex information related to dynamic interactions between the empathizer and target. One neural signature of empathy is the suppression of electroencephalographic mu rhythm (8-13 Hz) over the sensorimotor region. It is important to consider that few researchers have studied the effects of empathizer feedback on empathy and its underlying neural mechanism, and most previous research has lacked ecological validity due to standardized emotional stimuli and constraints on the experiment environment. Our objective in this study was to investigate the means by which empathizer feedback influences one's own empathy in naturalistic social situations. Our results revealed that empathizer feedback decreases empathic accuracy but does not affect the emotional contagion nor the emotional intensity of the empathizer. We also found that the ability to accurately infer sadness is hindered by empathizer feedback. Empathizers presented lower alpha activity in the sensorimotor cortical areas only while receiving sad narratives and not providing feedback. This study contributes to the emerging research on the influence of empathizer feedback in naturalistic social settings.},
}
@article {pmid39403309,
year = {2024},
author = {Sivell, O and Sivell, D and Webb, JA and Mitchell, R and Ashworth, M and , and , and , and , and , and , and , },
title = {The genome sequence of the acalyptrate fly Dryomyza anilis Fallén, 1820.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {440},
pmid = {39403309},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male acalyptrate fly Dryomyza anilis (Arthropoda; Insecta; Diptera; Dryomyzidae). The genome sequence has a total length of 656.60 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.48 kilobases in length.},
}
@article {pmid39401552,
year = {2024},
author = {Yan, X and Zhao, Z and Feng, S and Zhang, Y and Wang, Z and Li, Z},
title = {Multi-omics analysis reveal the fall armyworm Spodoptera frugiperda tolerate high temperature by mediating chitin-related genes.},
journal = {Insect biochemistry and molecular biology},
volume = {174},
number = {},
pages = {104192},
doi = {10.1016/j.ibmb.2024.104192},
pmid = {39401552},
issn = {1879-0240},
mesh = {Animals ; *Spodoptera/genetics/growth &amp; development/metabolism/physiology ; *Chitin/metabolism ; Hot Temperature ; Larva/genetics/growth &amp; development/metabolism ; CRISPR-Cas Systems ; Insect Proteins/metabolism/genetics ; Thermotolerance ; Transcriptome ; RNA Interference ; Multiomics ; },
abstract = {Climate change facilitates the rapid invasion of agricultural pests, threatening global food security. The fall armyworm Spodoptera frugiperda is a highly polyphagous migratory pest tolerant to high temperatures, allowing its proliferation in harsh thermal environments. We aimed to demonstrate mechanisms of its high-temperature tolerance, particularly transcriptional and metabolic regulation, which are poorly understood. To achieve the aim, we examined the impact and mechanism of heat events on S. frugiperda by using multiple approaches: ecological measurements, transcriptomics, metabolomics, RNAi, and CRISPR/Cas9 technology. We observed that several physiological indices (larval survival rate, larval period, pupation rate, pupal weight, eclosion rate, and average fecundity) decreased as the temperature increased, with the 32 °C treatment displaying a significant difference from the control group at 26 °C. Significantly upregulated expression of genes encoding endochitinase and chitin deacetylase was observed in the chitin-binding, extracellular region, and carbohydrate metabolic process GO terms of hemolymph, fat body, and brain, exhibiting a tissue-specific pattern. Significantly enriched pathways (e.g., cutin, suberin, and wax biosynthesis; oxidative phosphorylation and cofactor biosynthesis; diverse amino acid biosynthesis and degradation; carbon metabolism; and energy metabolism), all of which are essential for S. frugiperda larvae to tolerate temperature, were found in metabolites that were expressed differently. Successful RNA interference targeting of the three chitin-related genes reduced gene expression levels and larval survival rate. Knockout of the endochitinase gene by using the CRISPR/Cas9 system significantly reduced the relative gene expression and increased sensitivity to high-temperature exposure. On the basis of our findings, theoretical foundations for understanding the high-temperature tolerance of S. frugiperda populations and latent genetic control strategies were established.},
}
@article {pmid39401366,
year = {2024},
author = {Posch, BC and Bush, SE and Koepke, DF and Schuessler, A and Anderegg, LLD and Aparecido, LMT and Blonder, BW and Guo, JS and Kerr, KL and Moran, ME and Cooper, HF and Doughty, CE and Gehring, CA and Whitham, TG and Allan, GJ and Hultine, KR},
title = {Intensive leaf cooling promotes tree survival during a record heatwave.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {43},
pages = {e2408583121},
pmid = {39401366},
issn = {1091-6490},
support = {IOS-2140427//NSF (NSF)/ ; IOS-2140428//NSF (NSF)/ ; IOS-2140429//NSF (NSF)/ ; IOS-2003205//NSF (NSF)/ ; IOS-2216855//NSF (NSF)/ ; DEB-1340852//NSF (NSF)/ ; DEB-1340856//NSF (NSF)/ ; DEB-2017895//NSF (NSF)/ ; },
mesh = {*Plant Leaves/physiology ; *Populus/physiology/genetics ; *Trees/physiology/genetics ; *Water ; Soil ; Genotype ; Extreme Heat ; Hot Temperature ; Ecosystem ; },
abstract = {Increasing heatwaves are threatening forest ecosystems globally. Leaf thermal regulation and tolerance are important for plant survival during heatwaves, though the interaction between these processes and water availability is unclear. Genotypes of the widely distributed foundation tree species Populus fremontii were studied in a controlled common garden during a record summer heatwave-where air temperature exceeded 48 °C. When water was not limiting, all genotypes cooled leaves 2 to 5 °C below air temperatures. Homeothermic cooling was disrupted for weeks following a 72-h reduction in soil water, resulting in leaf temperatures rising 3 °C above air temperature and 1.3 °C above leaf thresholds for physiological damage, despite the water stress having little effect on leaf water potentials. Tradeoffs between leaf thermal safety and hydraulic safety emerged but, regardless of water use strategy, all genotypes experienced significant leaf mortality following water stress. Genotypes from warmer climates showed greater leaf cooling and less leaf mortality after water stress in comparison with genotypes from cooler climates. These results illustrate how brief soil water limitation disrupts leaf thermal regulation and potentially compromises plant survival during extreme heatwaves, thus providing insight into future scenarios in which ecosystems will be challenged with extreme heat and unreliable soil water access.},
}
@article {pmid39399683,
year = {2024},
author = {Martin, C and Gitter, A and Anantharaman, K},
title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {39399683},
issn = {2693-5015},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; },
abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.},
}
@article {pmid39399250,
year = {2024},
author = {Arliyani, I and Noori, MT and Ammarullah, MI and Tangahu, BV and Mangkoedihardjo, S and Min, B},
title = {Constructed wetlands combined with microbial fuel cells (CW-MFCs) as a sustainable technology for leachate treatment and power generation.},
journal = {RSC advances},
volume = {14},
number = {44},
pages = {32073-32100},
pmid = {39399250},
issn = {2046-2069},
abstract = {The physical and chemical treatment processes of leachate are not only costly but can also possibly produce harmful by products. Constructed wetlands (CW) has been considered a promising alternative technology for leachate treatment due to less demand for energy, economic, ecological benefits, and simplicity of operations. Various trends and approaches for the application of CW for leachate treatment have been discussed in this review along with offering an informatics peek of the recent innovative developments in CW technology and its perspectives. In addition, coupling CW with microbial fuel cells (MFCs) has proven to produce renewable energy (electricity) while treating contaminants in leachate wastewaters (CW-MFC). The combination of CW-MFC is a promising bio electrochemical that plays symbiotic among plant microorganisms in the rhizosphere of an aquatic plant that convert sun electricity is transformed into bioelectricity with the aid of using the formation of radical secretions, as endogenous substrates, and microbial activity. Several researchers study and try to find out the application of CW-MFC for leachate treatment, along with this system and performance. Several key elements for the advancement of CW-MFC technology such as bioelectricity, reactor configurations, plant species, and electrode materials, has been comprehensively discussed and future research directions were suggested for further improving the performance. Overall, CW-MFC may offer an eco-friendly approach to protecting the aquatic environment and come with built-in advantages for visual appeal and animal habitats using natural materials such as gravel, soil, electroactive bacteria, and plants under controlled condition.},
}
@article {pmid39398940,
year = {2024},
author = {Boyes, D and Hutchinson, F and Crowley, LM and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Common Flat-body moth, Agonopterix heracliana Linnaeus, 1758.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {329},
pmid = {39398940},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Agonopterix heracliana (the Common Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 539.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length.},
}
@article {pmid39398938,
year = {2024},
author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Sinclair, E and Clayton-Lucey, IA and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {366},
pmid = {39398938},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Fragum sueziense (the heart cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The genome sequence is 1,206.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 92.77 kilobases in length. Gene annotation of this assembly on Ensembl identified 70,309 protein-coding genes.},
}
@article {pmid39398937,
year = {2024},
author = {Boyes, D and Crowley, LM and Morley, LM and , and , and , and , and , and , and , },
title = {The genome sequence of the Green Oak Leaf Roller, Tortrix viridana (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {260},
pmid = {39398937},
issn = {2398-502X},
abstract = {We present a genome assembly from a female Tortrix viridana (the Green Oak Leaf Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 456.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length.},
}
@article {pmid39396151,
year = {2025},
author = {Burger, J and Gochfeld, M and Brown, KG and Cortes, M and Ng, K and Kosson, D},
title = {Using the National Land Cover Database as an indicator of shrub-steppe habitat: comparing two large United States federal lands with surrounding regions.},
journal = {Journal of toxicology and environmental health. Part A},
volume = {88},
number = {1},
pages = {1-19},
doi = {10.1080/15287394.2024.2412659},
pmid = {39396151},
issn = {1528-7394},
mesh = {*Ecosystem ; *Conservation of Natural Resources ; Idaho ; Washington ; Databases, Factual ; United States ; Grassland ; Environmental Monitoring/methods ; },
abstract = {There is a need to assess whether ecological resources are being protected on large, federal lands. The aim of this study was to present a methodology which consistently and transparently determines whether two large Department of Energy (U.S. DOE) facilities have protected valuable ecological lands on their sites compared to the surrounding region. The National Land Cover Database (2019) was used to examine the % shrub-scrub (shrub-steppe) and other habitats on the DOE's Hanford Site (HS, Washington) and on the Idaho National Laboratory (INL), compared to a 10-km and 30-km diameter band of land surrounding each site. On both sites, over 95% is in shrub-scrub or grassland, compared to the surrounding region. Approximately 70% of 10 km and 30-km bands around INL, and less than 50% of land surrounding HS is located in these two habitat types. INL has preserved a significantly higher % shrub/scrub habitat than HS, but INL allows grazing on 60% of its land. HS has preserved a significantly higher % grassland than INL but no grazing on site is present. The methodology presented may be used to compare key ecological habitat types such as grasslands, forest, and desert among sites in different parts of the country. This methodology enables managers, resource trustees, and the public to (1) make remediation decisions that protect resources, (2) assess whether landowners and managers have adequately characterized and protected environmental resources on their sites, and (3) whether landowners and managers have protected the integrity of that land as well as its climax vegetation.},
}
@article {pmid39395210,
year = {2025},
author = {Pachade, S and Porwal, P and Kokare, M and Deshmukh, G and Sahasrabuddhe, V and Luo, Z and Han, F and Sun, Z and Qihan, L and Kamata, SI and Ho, E and Wang, E and Sivajohan, A and Youn, S and Lane, K and Chun, J and Wang, X and Gu, Y and Lu, S and Oh, YT and Park, H and Lee, CY and Yeh, H and Cheng, KW and Wang, H and Ye, J and He, J and Gu, L and Müller, D and Soto-Rey, I and Kramer, F and Arai, H and Ochi, Y and Okada, T and Giancardo, L and Quellec, G and Mériaudeau, F},
title = {RFMiD: Retinal Image Analysis for multi-Disease Detection challenge.},
journal = {Medical image analysis},
volume = {99},
number = {},
pages = {103365},
doi = {10.1016/j.media.2024.103365},
pmid = {39395210},
issn = {1361-8423},
mesh = {Humans ; *Retinal Diseases/diagnostic imaging ; Image Interpretation, Computer-Assisted/methods ; Deep Learning ; Fundus Oculi ; Datasets as Topic ; Diabetic Retinopathy/diagnostic imaging ; Databases, Factual ; },
abstract = {In the last decades, many publicly available large fundus image datasets have been collected for diabetic retinopathy, glaucoma, and age-related macular degeneration, and a few other frequent pathologies. These publicly available datasets were used to develop a computer-aided disease diagnosis system by training deep learning models to detect these frequent pathologies. One challenge limiting the adoption of a such system by the ophthalmologist is, computer-aided disease diagnosis system ignores sight-threatening rare pathologies such as central retinal artery occlusion or anterior ischemic optic neuropathy and others that ophthalmologists currently detect. Aiming to advance the state-of-the-art in automatic ocular disease classification of frequent diseases along with the rare pathologies, a grand challenge on "Retinal Image Analysis for multi-Disease Detection" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2021). This paper, reports the challenge organization, dataset, top-performing participants solutions, evaluation measures, and results based on a new "Retinal Fundus Multi-disease Image Dataset" (RFMiD). There were two principal sub-challenges: disease screening (i.e. presence versus absence of pathology - a binary classification problem) and disease/pathology classification (a 28-class multi-label classification problem). It received a positive response from the scientific community with 74 submissions by individuals/teams that effectively entered in this challenge. The top-performing methodologies utilized a blend of data-preprocessing, data augmentation, pre-trained model, and model ensembling. This multi-disease (frequent and rare pathologies) detection will enable the development of generalizable models for screening the retina, unlike the previous efforts that focused on the detection of specific diseases.},
}
@article {pmid39395131,
year = {2024},
author = {Atesoglu, A and Ayyildiz, E and Karakaya, I and Bulut, FS and Serengil, Y},
title = {Land cover and drought risk assessment in Türkiye's mountain regions using neutrosophic decision support system.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {11},
pages = {1046},
pmid = {39395131},
issn = {1573-2959},
mesh = {*Droughts ; *Environmental Monitoring/methods ; *Climate Change ; Risk Assessment ; Ecosystem ; Turkey ; Decision Support Techniques ; Remote Sensing Technology ; Conservation of Natural Resources/methods ; },
abstract = {Earth observation (EO) provides dynamic scientific methods for tracking and defining ecological parameters in mountainous regions. Open-source platforms are frequently utilized in this context to efficiently collect and evaluate spatial data. In this study, we used Collect Earth (CE), an open-source land monitoring platform, to reveal and assess land cover, land cover change, and relevant ecological parameters such as drought risk. Mountain ecosystems were subject to an evaluation for the first time by combining remote sensing with a hybridization of Decision-Making Trial and Evaluation Laboratory (DEMATEL), analytic hierarchy process (AHP), and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) for neutrosophic sets in risk assessment problems of several connected criteria. The high and dispersed high alpine environment of Türkiye accommodates land with relatively less human influence, making it suitable to observe climate change impacts. In the framework of the study, we evaluated more than two decades (2000-2022) of land use and land cover (LULC) changes in the mountain regions of the country. Using nine identified ecological parameters, we also evaluated drought risk. The parameters included were the LULC classes and their change, elevation, slope, aspect, precipitation, temperature, normalized difference vegetation index (NDVI), water deficit, and evapotranspiration (ET). The risk map we produced revealed a high to very high drought risk for almost throughout the Türkiye's mountainous areas. We concluded that integrating geospatial techniques with hybridization is promising for mapping drought risk, helping policymakers prepare effective drought mitigation measures to reasonably adapt to climate change impacts.},
}
@article {pmid39392918,
year = {2024},
author = {Kopania, EEK and Thomas, GWC and Hutter, CR and Mortimer, SME and Callahan, CM and Roycroft, E and Achmadi, AS and Breed, WG and Clark, NL and Esselstyn, JA and Rowe, KC and Good, JM},
title = {Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents.},
journal = {Evolution; international journal of organic evolution},
volume = {79},
number = {1},
pages = {11-27},
pmid = {39392918},
issn = {1558-5646},
support = {DEB-1754096//National Science Foundation/ ; R01-HG009299/HG/NHGRI NIH HHS/United States ; R01-HD073439//National Institute of Child Health and Human Development/ ; },
mesh = {Animals ; Male ; *Spermatozoa/physiology ; Mice/genetics ; *Evolution, Molecular ; *Testis/anatomy &amp; histology ; Phylogeny ; Selection, Genetic ; Sexual Selection ; Spermatogenesis/genetics ; Murinae/genetics/physiology ; Rats ; Reproduction/genetics ; },
abstract = {It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass (RTM), presumably reflecting reduced sperm competition. Several sperm traits were associated with RTM, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller RTM due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction and that broad patterns of molecular evolution may help identify genes that contribute to male fertility.},
}
@article {pmid39390673,
year = {2024},
author = {Udaondo, Z and Ramos, JL and Abram, K},
title = {Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.},
journal = {FEMS microbiology reviews},
volume = {48},
number = {6},
pages = {},
pmid = {39390673},
issn = {1574-6976},
support = {PID2021-123469OB-I00//Plan Nacional sobre Drogas/ ; },
mesh = {*Pseudomonas putida/genetics/classification/drug effects ; *Genome, Bacterial/genetics ; *Genetic Variation ; Drug Resistance, Bacterial/genetics ; Genomics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier "Pseudomonas putida" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as "Pseudomonas putida" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.},
}
@article {pmid39390511,
year = {2024},
author = {Li, Y and Thomas, GWC and Richards, S and Waterhouse, RM and Zhou, X and Pfrender, ME},
title = {Rapid evolution of mitochondrion-related genes in haplodiploid arthropods.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {229},
pmid = {39390511},
issn = {1741-7007},
mesh = {Animals ; *Evolution, Molecular ; *Arthropods/genetics ; *Genes, Mitochondrial/genetics ; Phylogeny ; Haploidy ; Diploidy ; Oxidative Phosphorylation ; Cell Nucleus/genetics ; },
abstract = {BACKGROUND: Mitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes among arthropod lineages have dramatic evolutionary rate differences. Haplodiploid arthropods often show fast-evolving mitochondrial genes. One hypothesis predicts that the small effective population size of haplodiploid species could enhance the effect of genetic drift leading to higher substitution rates in mitochondrial and nuclear genes. Alternatively, positive selection or compensatory changes in nuclear OXPHOS genes could lead to the fast-evolving mitochondrial genes. However, due to the limited number of arthropod genomes, the rates of evolution for nuclear genes in haplodiploid species, besides hymenopterans, are largely unknown. To test these hypotheses, we used data from 76 arthropod genomes, including 5 independently evolved haplodiploid lineages, to estimate the evolutionary rates and patterns of gene family turnover of mitochondrial and nuclear genes.<br><br>RESULTS: We show that five haplodiploid lineages tested here have fast-evolving mitochondrial genes and fast-evolving nuclear genes related to mitochondrial functions, while nuclear genes not related to mitochondrion showed no significant evolutionary rate differences. Among hymenopterans, bees and ants show faster rates of molecular evolution in mitochondrial genes and mitochondrion-related nuclear genes than sawflies and wasps. With genome data, we also find gene family expansions and contractions in mitochondrion-related genes of bees and ants.<br><br>CONCLUSIONS: Our results reject the small population size hypothesis in haplodiploid species. A combination of positive selection and compensatory changes could lead to the observed patterns in haplodiploid species. The elevated evolutionary rates in OXPHOS complex 2 genes of bees and ants suggest a unique evolutionary history of social hymenopterans.},
}
@article {pmid39387871,
year = {2024},
author = {Smith, SJ and Cummins, SF and Motti, CA and Wang, T},
title = {A mass spectrometry database for the identification of marine animal saponin-related metabolites.},
journal = {Analytical and bioanalytical chemistry},
volume = {416},
number = {29},
pages = {6893-6907},
pmid = {39387871},
issn = {1618-2650},
mesh = {*Saponins/analysis/metabolism ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Mass Spectrometry/methods ; Databases, Factual ; },
abstract = {Saponins encompass a diverse group of naturally occurring glycoside molecules exhibiting amphiphilic properties and a broad range of biological activities. There is a resurgence of interest in those saponins produced by marine organisms based on their potential therapeutic benefits, application in food products and most recently their potential involvement in intra- and inter-species chemical communication. The continual advancements in liquid chromatography techniques and mass spectrometry technologies have allowed for greater detection rates, as well as improved isolation and elucidation of saponins. These factors have significantly contributed to the expansion in the catalogue of known saponin structures isolated from marine invertebrates; however, there currently exists no specific chemical library resource to accelerate the discovery process. In this study, a Marine Animal Saponin Database (MASD v1.0) has been developed to serve as a valuable chemical repository for known marine saponin-related data, including chemical formula, molecular mass and biological origin of nearly 1000 secondary metabolites associated with saponins produced by marine invertebrates. We demonstrate its application with an exemplar asteroid extract (Acanthaster cf. solaris, also known as crown-of-thorns starfish; COTS), identifying saponins from the MASD v1.0 that have been previously reported from COTS, as well as 21 saponins isolated from multiple other related asteroid species. This database will help facilitate future research endeavours, aiding researchers in exploring the vast chemical diversity of saponins produced by marine organisms and providing ecological insights, and the realisation of their potential for various applications, including as pharmaceuticals.},
}
@article {pmid39386964,
year = {2024},
author = {Martin, SH and Lohse, K and Ebdon, S and Mackintosh, A and , and , and , and , and , },
title = {The genome sequence of the Pearl-bordered Fritillary, Boloria euphrosyne (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {267},
pmid = {39386964},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Boloria euphrosyne (the Pearl-bordered Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 400.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,138 protein coding genes.},
}
@article {pmid39385455,
year = {2024},
author = {Wu, H and Li, Q and Wu, JC},
title = {Bioinformatics-aided function exploration of GH29 fucosidases from human gut Parabacteroides.},
journal = {Glycobiology},
volume = {34},
number = {12},
pages = {},
doi = {10.1093/glycob/cwae086},
pmid = {39385455},
issn = {1460-2423},
support = {2023GDASZH-2023010102//GDAS' Project of Science and Technology Development/ ; SL2023A04J01435//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022A1515110917//Guangdong Basic and Applied Basic Research Foundation/ ; 32302033//National Natural Science Foundation of China/ ; 2023A04J1494//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022GDASZH-2022010110//GDAS' Project of Science and Technology Development/ ; },
mesh = {Humans ; *alpha-L-Fucosidase/metabolism/genetics/chemistry ; *Computational Biology ; Gastrointestinal Microbiome ; Bacteroidetes/enzymology/genetics ; Polysaccharides/metabolism/chemistry ; Substrate Specificity ; Mucins/metabolism/chemistry ; },
abstract = {Gut microbes produce α-l-fucosidases critical for utilizing human milk oligosaccharides, mucosal and dietary glycans. Although gut Parabacteroides have garnered attention for their impact on host health and disease, their CAZymes remain poorly studied. CAZome analysis of eleven gut Parabacteroides type strains revealed their capacity to degrade mucin O-glycans. Their abundance of GH29 fucosidases caught our attention, and we predicted the functional profiles of 46 GH29 fucosidases using in silico approaches. Our findings showed diverse linkages specificities and species-specific distributions, with over half of GH29 enzymes functioning as α1,3/4 fucosidases, essential for acting on Lewis antigen epitopes of mucin O-glycans. We further enzymatically validated 4 novel GH29 sequences from poorly characterized groups. PgoldGH29A (cluster37GH29BERT, GH29:75.1CUPP) does not act on tested natural substrates. PgoldGH29B (cluster1GH29BERT, GH29:84.1CUPP) functions as a strict α1,3/4 fucosidase. PgoldGH29C (cluster14GH29BERT, GH29:29.1CUPP) displays unprecedented substrate specificity for α1,2/3/4 disaccharides. PgoldGH29D (cluster4GH29BERT, GH29:6.2CUPP) acts on α1,2/3/4/6 linkages similar to enzymes from GH29:6.1CUPP but prefers disaccharides over trisaccharides. These results suggest that PgoldGH29B and PgoldGH29D can contribute to mucin O-glycan degradation via their α1,3/4 and α1,2 fucosidase activity, respectively, while the natural substrates of PgoldGH29A and PgoldGH29C may be irrelevant to host-glycans. These insights enhance our understanding of the ecological niches inhabited by gut Parabacteroides and may guide similar exploration in other intriguing gut microbial species.},
}
@article {pmid39381069,
year = {2024},
author = {Boyes, D and Lees, DC and Sims, I and Phillips, D and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Yellow-dotted Stilt, Euspilapteryx auroguttella Stephens, 1835.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {226},
pmid = {39381069},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Euspilapteryx auroguttella (the Yellow-dotted Stilt; Arthropoda; Insecta; Lepidoptera; Gracillariidae). The genome sequence is 331.9 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.94 kilobases in length.},
}
@article {pmid39379720,
year = {2024},
author = {Klopper, A},
title = {GPS tracking reveals how hares shape lynx populations.},
journal = {Nature},
volume = {634},
number = {8033},
pages = {301},
doi = {10.1038/d41586-024-03272-x},
pmid = {39379720},
issn = {1476-4687},
mesh = {Animals ; *Geographic Information Systems ; *Lynx/physiology ; Population Density ; Population Dynamics ; Alaska ; *Predatory Behavior ; *Hares/physiology ; },
}
@article {pmid39376700,
year = {2024},
author = {Chelliah, DS and Ray, AE and Zhang, E and Terauds, A and Ferrari, BC},
title = {The Vestfold Hills are alive: characterising microbial and environmental dynamics in Old Wallow, eastern Antarctica.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1443491},
pmid = {39376700},
issn = {1664-302X},
abstract = {Old Wallow is an underexplored, hyper-arid coastal desert in Antarctica's Vestfold Hills. Situated near an elephant seal wallow, we examined how stochastic nutrient inputs from the seal wallow affect soil communities amid environmental changes along a spatially explicit sampling transect. We hypothesized that nutrient levels would be elevated due to proximity to the seal wallow, influencing community distributions. While the soil bacterial and eukaryotic communities at the phylum level were similar to other terrestrial environments, analysis at class and family levels revealed a dominance of unclassified taxa that are often linked to marine environments. Elevated nutrient concentrations (NO3 [-], SO4 [2-], SO3) were found at Old Wallow, with conductivity and Cl[-] levels up to 10-fold higher at the lowest elevation soils, correlating with significantly (p < 0.05) higher abundances of halophilic (Halomonadaceace) and uncultivated lineages (Ca Actinomarinales, unclassified Bacillariophyta and unclassified Opisthonkonta). An improved Gradient Forest model was used to quantify microbial responses to 26 soil gradients at OW, revealing variable responses to environmental predictors and identifying critical environmental thresholds or drivers of community turnover. Major tipping points were projected for eukaryotes with SO4 [2-], pH, and SO3, and for bacteria with moisture, Na2O, and Cl[-]. Thus, the Old Wallow ecosystem is primarily shaped by salt, sulphate, and moisture and is dominated by uncultivated taxa, which may be sensitive to environmental changes once critical tipping points are reached. This study provides critical baseline data for future regional monitoring under threats of environmental change.},
}
@article {pmid39374677,
year = {2024},
author = {Ikeda, T and Cooray, U and Matsugaki, R and Suzuki, Y and Takagi, M and Muramatsu, K and Fushimi, K and Murakami, M and Osaka, K and Matsuda, S},
title = {Associations of hypothetical early intensive in-hospital rehabilitation with activities of daily living after hip fracture surgery in patients with and without dementia: emulating a randomized controlled trial using medical claims data.},
journal = {Journal of clinical epidemiology},
volume = {176},
number = {},
pages = {111550},
doi = {10.1016/j.jclinepi.2024.111550},
pmid = {39374677},
issn = {1878-5921},
mesh = {Humans ; *Hip Fractures/surgery/rehabilitation ; Female ; Male ; *Dementia/rehabilitation ; Aged ; *Activities of Daily Living ; Japan ; Aged, 80 and over ; Middle Aged ; Hospitalization/statistics &amp; numerical data ; Recovery of Function ; },
abstract = {OBJECTIVES: To investigate the impact of early intensive in-hospital rehabilitation, initiated within 2 days of surgery and lasting up to 7 days, on the recovery of activities of daily living in patients with and without dementia.<br><br>STUDY DESIGN AND SETTING: Medical claims data from 925 hospitals in Japan were analyzed. We enrolled patients aged &#x2265;50&#xa0;years who underwent hip fracture surgery within 2&#xa0;days of admission between April 1, 2018, and December 31, 2019. Low- (20&#xa0;minutes per day starting on day 2), highest- (60&#xa0;minutes per day starting on day 1), and gradually increasing (20&#xa0;minutes on day 1, 40&#xa0;minutes on days 2-4, and 60&#xa0;minutes per day thereafter) intensity regimens were used as exposures. The outcomes were Barthel Index (BI) scores at 14 and 30&#xa0;days postoperatively. For per-protocol analysis, a target trial emulation framework with the sequential doubly robust estimator was used.<br><br>RESULTS: Among patients without dementia (N&#xa0;=&#xa0;11,461), no significant differences in BI scores were observed at 14&#xa0;days postoperatively across regimens. At 30&#xa0;days postoperatively, significant differences in BI scores were noted between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 15.2 (95% CI, 10.7-19.7) and 14.7 (95% CI, 9.2-20.2), respectively. In patients with dementia (N&#xa0;=&#xa0;14,302), significant differences in BI scores were noted at 14&#xa0;days postoperatively between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 8.7 (95% CI, 5.2-12.2) and 10.7 (95% CI, 5.8-15.6), respectively. At 30&#xa0;days postoperatively, a significant difference in BI scores was observed between gradually increasing intensity and low-intensity regimens, with an additive BI score of 17.9 (95% CI, 11.3-24.5).<br><br>CONCLUSION: Early intensive in-hospital rehabilitation is highly relevant and beneficial for dementia patients.},
}
@article {pmid39373887,
year = {2024},
author = {Dittrich, SP and Adithya, S and Ajith, Y and Athira, N and Athira, KS and Safeer, MS and Preena, P and Aishwarya, A and Athira, K and Nisha, AR and Devi, G and Mäder, M and Beena, V and Jacob, SS},
title = {Parasite diversity among domestic goats of tropical monsoon climatic zone in India.},
journal = {Parasitology research},
volume = {123},
number = {10},
pages = {342},
pmid = {39373887},
issn = {1432-1955},
support = {IN-ME_BI-5550//Deutscher Akademischer Austauschdienst/ ; SRG/2022/000837//Science and Engineering Research Board/ ; SRG/2022/000837//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Goats/parasitology ; India/epidemiology ; *Goat Diseases/parasitology/epidemiology ; *Tropical Climate ; Phylogeny ; Parasitic Diseases, Animal/parasitology/epidemiology ; Parasites/classification/isolation &amp; purification/genetics ; Biodiversity ; },
abstract = {Among different climatic zones in India, the tropical monsoon region comprises a diverse ecosystem characterized by the endemic nature of several parasites including certain emerging and re-emerging vector-borne pathogens of humans, whereas a systematic investigation of the occurrence of different parasites among domestic goats in this area is not yet explored. The goal of the present study is to explore the parasite diversity focusing on molecular identification of vector-borne hemoparasites and its health impacts on domestic goats reared in the tropical monsoon climate zone of Kerala, India. Among 227 goats presented to the Teaching Veterinary Clinical Complex (TVCC) in the monsoon months of 2023, thirty animals were recruited for the study. The animals were screened for the presence of different hemoparasites (Anaplasma spp., Theileria spp., and Babesia spp.), ectoparasites (ticks, lice, and fleas), and gastrointestinal (GI) parasites (hookworms, threadworms, tapeworms, whipworms, and coccidia). The isolated hemoparasites were further characterized by sequencing and phylogenetic analysis. The correlation studies to elucidate the association between the occurrence of different parasites and clinical manifestations (hyperthermia, pallor of mucous membrane, circulatory failure, respiratory signs, neurological instability, and GI signs), blood picture (anemia, leukopenia, thrombocytopenia), demographics (sex and age), and treatment history (hemoparasitic therapy, ectoparasiticidal application, and prophylactic deworming) were conducted. The co-infection status of these parasites was also evaluated. A substantial portion of the goats in the study group was found to be affected by vector-borne hemoparasitic diseases and their arthropod vectors or GI parasites or both. This can be attributed to the constantly warm and humid climate of the region, which is favorable for the survival and growth of different life cycle stages of these parasites and vectors. A strategic parasitic disease surveillance-cum-control program is the need of the hour for ensuring climate resilience and profitable goat farming in the region.},
}
@article {pmid39373528,
year = {2024},
author = {Ros-Rocher, N},
title = {The evolution of multicellularity and cell differentiation symposium: bridging evolutionary cell biology and computational modelling using emerging model systems.},
journal = {Biology open},
volume = {13},
number = {10},
pages = {},
pmid = {39373528},
issn = {2046-6390},
support = {101106415//European Union's Horizon Europe research and innovation funding program/ ; //Institute Pasteur: Institut Pasteur; Baylor College of Medicine/ ; },
mesh = {*Cell Differentiation/genetics ; *Biological Evolution ; Animals ; Computational Biology/methods ; Humans ; Cell Biology ; Models, Biological ; Computer Simulation ; Genomics/methods ; },
abstract = {'The evolution of multicellularity and cell differentiation' symposium, organized as part of the EuroEvoDevo 2024 meeting on June 25-28th in Helsinki (Finland), addressed recent advances on the molecular and mechanistic basis for the evolution of multicellularity and cell differentiation in eukaryotes. The symposium involved over 100 participants and brought together 10 speakers at diverse career stages. Talks covered various topics at the interface of developmental biology, evolutionary cell biology, comparative genomics, computational biology, and ecology using animal, protist, algal and mathematical models. This symposium offered a unique opportunity for interdisciplinary dialog among researchers working on different systems, especially in promoting collaborations and aligning strategies for studying emerging model species. Moreover, it fostered opportunities to promote early career researchers in the field and opened discussions of ongoing work and unpublished results. In this Meeting Review, we aim to promote the research, capture the spirit of the meeting, and present key topics discussed within this dynamic, growing and open community.},
}
@article {pmid39373052,
year = {2024},
author = {Xie, X and Gui, L and Qiao, B and Wang, G and Huang, S and Zhao, Y and Sun, S},
title = {Deep learning in template-free de novo biosynthetic pathway design of natural products.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
pmid = {39373052},
issn = {1477-4054},
support = {2572022BD04//Fundamental Research Funds for the Central Universities/ ; 62001088//National Natural Science Foundation of China/ ; },
mesh = {*Biological Products/metabolism ; *Deep Learning ; *Biosynthetic Pathways ; Algorithms ; Computational Biology/methods ; Humans ; },
abstract = {Natural products (NPs) are indispensable in drug development, particularly in combating infections, cancer, and neurodegenerative diseases. However, their limited availability poses significant challenges. Template-free de novo biosynthetic pathway design provides a strategic solution for NP production, with deep learning standing out as a powerful tool in this domain. This review delves into state-of-the-art deep learning algorithms in NP biosynthesis pathway design. It provides an in-depth discussion of databases like Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and UniProt, which are essential for model training, along with chemical databases such as Reaxys, SciFinder, and PubChem for transfer learning to expand models' understanding of the broader chemical space. It evaluates the potential and challenges of sequence-to-sequence and graph-to-graph translation models for accurate single-step prediction. Additionally, it discusses search algorithms for multistep prediction and deep learning algorithms for predicting enzyme function. The review also highlights the pivotal role of deep learning in improving catalytic efficiency through enzyme engineering, which is essential for enhancing NP production. Moreover, it examines the application of large language models in pathway design, enzyme discovery, and enzyme engineering. Finally, it addresses the challenges and prospects associated with template-free approaches, offering insights into potential advancements in NP biosynthesis pathway design.},
}
@article {pmid39367377,
year = {2024},
author = {Qiao, L and Zhang, C and Zhang, M and Jiang, H and Shi, Y and Zhang, W and Mei, Y and Li, Y and Wang, H},
title = {High-risk spatiotemporal patterns of leprosy in the southeastern region of Yunnan province from 2010 to 2022: an analysis at the township level.},
journal = {BMC public health},
volume = {24},
number = {1},
pages = {2707},
pmid = {39367377},
issn = {1471-2458},
support = {82103748//National Natural Science Foundation of China/ ; 81972950//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Leprosy/epidemiology ; China/epidemiology ; Female ; Male ; *Spatio-Temporal Analysis ; Adult ; Middle Aged ; *Geographic Information Systems ; Adolescent ; Young Adult ; Aged ; Child ; Risk Factors ; },
abstract = {BACKGROUND: Despite being preventable and curable, leprosy remains endemic in some undeveloped regions, including China. Wenshan Zhuang and Miao Autonomous Prefecture (Wenshan prefecture) currently bears the highest leprosy burden in China. In this ecological study, we aimed to analyze the epidemiological characteristics as well as identify and visualize the high-risk townships of Wenshan prefecture using the most updated leprosy data from 2010 to 2022.<br><br>METHODS: Geographical information system combined with spatial scan statistics was used for newly detected leprosy cases abstracted from the Leprosy Management Information System in China. Global Moran's I index was used to uncover the spatial pattern of leprosy at the township level. Spatial scan statistics, encompassing purely temporal, purely spatial, spatial variation in temporal trends, and space-time analysis, were implemented for detecting the risk clusters.<br><br>RESULTS: Between 2010 and 2022, Wenshan prefecture detected 532 new leprosy cases, comprising 352 (66.17%) males and 180 (33.83%) females. The aggregated time primarily occurred between October 2010 and March 2014. The distribution pattern of newly detected leprosy cases was spatially clustered. We identified four high-risk spatial clusters encompassing 54.51% of the new cases. Furthermore, spatial variation in temporal trends highlighted one cluster as a potential high-risk area. Finally, two space-time clusters were detected, and the most likely cluster was predominantly located in the central and northwest regions of Wenshan prefecture, spanning from January 2010 to September 2013.<br><br>CONCLUSIONS: In this ecology study, we characterized the epidemiological features and temporal and spatial patterns of leprosy in Wenshan prefecture using the most recent leprosy data between 2010 and 2022. Our findings offer scientific insights into the epidemiological profiles and spatiotemporal dynamics of leprosy in Wenshan prefecture. Clinicians and policymakers should pay particular attention to the identified clusters for the prevention and control of leprosy.},
}
@article {pmid39367017,
year = {2024},
author = {Zhou, M and Guo, F},
title = {Mechanism and spatial spillover effect of digital economy on common prosperity in the Yellow River Basin of China.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23086},
pmid = {39367017},
issn = {2045-2322},
support = {41801105//National Natural Science Foundation of China/ ; 2022RW040//Shandong Province Higher Education Youth Innovation Technology Support Program/ ; 23CGLJ15//Shandong Province Social Science Planning and Research Project/ ; },
abstract = {The digital economy has emerged as a new trend in economic development and has profoundly influenced the process of achieving common prosperity. However, current research on the correlation between the digital economy and common prosperity from the perspective of a river basin still needs to be strengthened. Based on this, the present study first theoretically elaborates the conceptual meanings of "digital economy" and "common prosperity", as well as the mechanism by which the digital economy empowers common prosperity. Subsequently, a scientifically-constructed performance evaluation index system for the digital economy and common prosperity is established. Considering the Yellow River Basin as an empirical case study area, this study investigates the mechanism and spatial spillover effects of the digital economy in empowering common prosperity from 2005 to 2020. The research findings reveal that: (1) The Yellow River Basin exhibits a basin characteristic with downstream > midstream > upstream areas regarding the level of common prosperity and digital economy. It indicates that a distinct spatial correlation exists between the two factors. However, the ongoing decrease in both high-level and very high-level areas reflects the lengthy and challenging journey of enhancing the quality and efficiency of the digital economy in empowering common prosperity. (2) The digital economy not only directly impacts common prosperity, but also fosters its development through spatial spillover effects. Among the control factors, informatization and housing levels have a major stimulating effect. (3) There exists a clear regional heterogeneity in how the digital economy affects common prosperity in the Yellow River Basin. Specifically, common prosperity of downstream cities is significantly impacted by the digital economy. The spatial spillover effects of the digital economy on common prosperity exhibit a pronounced "neighborhood as a moat" characteristic. (4) The digital economy facilitates the achievement of shared prosperity through the implementation of mechanisms centered on sharing, affluence, and sustainability. These research findings illuminate the empowering mechanisms and spatial spillover pathways of the digital economy in promoting shared prosperity, aligning with national strategies for ecological conservation and high-quality development in the Yellow River Basin.},
}
@article {pmid39364368,
year = {2024},
author = {Bullion, CM and Bahlai, CA},
title = {Data gap or biodiversity gap? Evaluating apparent spatial biases in community science observations of Odonata in the east-central United States.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18115},
pmid = {39364368},
issn = {2167-8359},
mesh = {Animals ; *Biodiversity ; *Odonata ; Humans ; Bias ; United States ; Databases, Factual ; },
abstract = {Odonates (dragonflies and damselflies) have become popular study organisms for insect-based climate studies, due to the taxon's strong sensitivity to environmental conditions, and an enthusiastic following by community scientists due to their charismatic appearance and size. Where formal records of this taxon can be limited, public efforts have provided nearly 1,500,000 open-sourced odonate records through online databases, making real-time spatio-temporal monitoring more feasible. While these databases can be extensive, concerns regarding these public endeavors have arisen from a variety of sources: records may be biased by human factors (ex: density, technological access) which may cause erroneous interpretations. Indeed, records of odonates in the east-central US documented in the popular database iNaturalist bear striking patterns corresponding to political boundaries and other human activities. We conducted a 'ground-truthing' study using a structured sampling method to examine these patterns in an area where community science reports indicated variable abundance, richness, and diversity which appeared to be linked to observation biases. Our observations were largely consistent with patterns recorded by community scientists, suggesting these databases were indeed capturing representative biological trends and raising further questions about environmental drivers in the observed data gaps.},
}
@article {pmid39363544,
year = {2024},
author = {Panayi, P and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Emsley, R and Mason, L and Elliott, R and Varese, F},
title = {Complex PTSD symptoms predict positive symptoms of psychosis in the flow of daily life.},
journal = {Psychological medicine},
volume = {54},
number = {12},
pages = {1-12},
pmid = {39363544},
issn = {1469-8978},
support = {NIHR128623//Health Technology Assessment Programme/ ; NIHR130971//Efficacy and Mechanism Evaluation Programme/ ; N/A//NIHR Maudsley Biomedical Research Centre/ ; },
abstract = {BACKGROUND: Post-traumatic stress disorder (PTSD) has been shown to predict psychotic symptomology. However, few studies have examined the relative contribution of PTSD compared to broader post-traumatic sequelae in maintaining psychosis. Complex PTSD (cPTSD), operationalized using ICD-11 criteria, includes core PTSD (intrusions, avoidance, hyperarousal) as well as additional "disturbances of self-organisation" (DSO; emotional dysregulation, interpersonal difficulties, negative self-concept) symptoms, more likely to be associated with complex trauma histories. It was hypothesized that DSOs would be associated with positive psychotic symptoms (paranoia, voices, and visions) in daily life, over and above core PTSD symptoms.<br><br>METHODS: This study (N = 153) employed a baseline subsample of the Study of Trauma And Recovery (STAR), a clinical sample of participants with comorbid post-traumatic stress and psychosis symptoms. Core PTSD, DSO and psychosis symptoms were assessed up to 10 times per day at quasi-random intervals over six consecutive days using Experience Sampling Methodology.<br><br>RESULTS: DSOs within the preceding 90 min predicted paranoia, voices, and visions at subsequent moments. These relationships persisted when controlling for core PTSD symptoms within this timeframe, which were themselves significant. The associations between DSOs and paranoia but not voices or visions, were significantly stronger than those between psychosis and core PTSD symptoms.<br><br>CONCLUSIONS: Consistent with an affective pathway to psychosis, the findings suggest that DSOs may be more important than core PTSD symptoms in maintaining psychotic experiences in daily life among people with comorbid psychosis and cPTSD, and indicate the potential importance of addressing broad post-traumatic sequelae in trauma-focused psychosis interventions.},
}
@article {pmid39363203,
year = {2024},
author = {Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP and Meirelles, PM},
title = {Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.},
journal = {BMC research notes},
volume = {17},
number = {1},
pages = {291},
pmid = {39363203},
issn = {1756-0500},
support = {2023-PPI-007//Rockefeller Foundation/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; Metagenome/genetics ; Computational Biology/methods ; Reproducibility of Results ; Nasopharynx/microbiology/virology ; },
abstract = {OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment.<br><br>RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4&#xa0;min per sample (processing 1&#xa0;million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.},
}
@article {pmid39362872,
year = {2024},
author = {Fu, SW and Feng, MC and Chi, PW and Ding, TS},
title = {Combining citizen science data and literature to build a traits dataset of Taiwan's birds.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1076},
pmid = {39362872},
issn = {2052-4463},
mesh = {Animals ; Taiwan ; *Birds ; *Citizen Science ; *Ecosystem ; Databases, Factual ; },
abstract = {Trait-based methodologies are gaining traction in the field of ecology, providing deeper insights into ecosystem structure and functions. To this end, trait databases tailored to specific taxonomic groups have become foundational. In Taiwan, the collaborative efforts of avian researchers and dedicated citizen scientists have led to the compilation of a vast array of data. This includes web-sourced images from social media, spatial distribution records from eBird, and morphological metrics from banded birds and specimens. Enriched by peer-reviewed literature, we have meticulously assembled a comprehensive trait dataset encompassing 454 bird species across 73 families. This dataset covers a wide range of traits, including foraging ecology, morphological characteristics, territorial behaviors, breeding attributes, and the roles of bird species in ecosystem regulation. As an invaluable resource, this dataset lays the foundation for in-depth exploration of functional diversity, trait-based community ecology, ecosystem function, and critical insights needed to shape conservation strategies.},
}
@article {pmid39362167,
year = {2024},
author = {Fardullah, M and Hossain, MT and Islam, MS and Islam, MR and Rahman, MR and Akther, K and Uddin, A and Morshed, S and Sultana, N and Alam, MA and Bahadur, NM and Robel, FN},
title = {Occurrence and spatial distribution of microplastics in water and sediments of Hatiya Island, Bangladesh and their risk assessment.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122697},
doi = {10.1016/j.jenvman.2024.122697},
pmid = {39362167},
issn = {1095-8630},
mesh = {*Microplastics/analysis ; Risk Assessment ; Bangladesh ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry/analysis ; Islands ; },
abstract = {This research has evaluated the MPs distribution, characteristics, and potential threats of MPs in surface water and sediments from Hatiya Island. The results showed that the abundance of MPs was 139 ± 44 items/m[3] in surface water and 493 ± 80 items/kg dw in sediments, indicating higher levels of MPs contamination in sediment samples. Fibers were the predominant kind of microplastics, and microscopic sizes (0.3-1.5 mm) MPs were generally more frequent and largely present in both the surface water and sediments. Fourier-transform infrared spectroscopy (FTIR) confirmed that polyethylene terephthalate was the major polymer component of microplastics in surface water, whereas polyethylene was the most abundant polymer in sediments. MPs contamination risk was examined based on multiple risk assessment models. Nemerow pollution index (NPI) and pollutant load index (PLI) show minimal pollution levels of MPs. But potential hazard index (PHI), potential ecological risk factor (Er), and potential ecological risk index (RI), indicate severe MPs contamination due to the presence of polyurethane, polycarbonate, polyvinyl chloride, epoxy that were hazardous MPs and exhibited a critical concern for MPs risk. These statistics will help to understand the environmental difficulties generated by MPs and which hazard is waiting for mankind in the future.},
}
@article {pmid39360250,
year = {2024},
author = {Soni, N and Eyre, MT and Souza, FN and Diggle, PJ and Ko, AI and Begon, M and Pickup, R and Childs, JE and Khalil, H and Carvalho-Pereira, TSA and Pertile, AC and Carvalho, M and de Oliveira, D and Nery, N and Giorgi, E and Costa, F},
title = {Disentangling the influence of reservoir abundance and pathogen shedding on zoonotic spillover of the Leptospira agent in urban informal settlements.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1447592},
pmid = {39360250},
issn = {2296-2565},
mesh = {Animals ; Humans ; *Leptospirosis/epidemiology/microbiology/transmission ; *Leptospira/isolation &amp; purification ; *Disease Reservoirs/microbiology ; Brazil/epidemiology ; Rats ; *Zoonoses/microbiology ; Male ; Female ; Adult ; Bacterial Shedding ; Longitudinal Studies ; Middle Aged ; Risk Factors ; Urban Population/statistics &amp; numerical data ; Adolescent ; Young Adult ; },
abstract = {Rats are major reservoirs for pathogenic Leptospira, the bacteria causing leptospirosis, particularly in urban informal settlements. However, the impact of variation in rat abundance and pathogen shedding rates on spillover transmission to humans remains unclear. This study aimed to investigate how spatial variation in reservoir abundance and pathogen pressure affect Leptospira spillover transmission to humans in a Brazilian urban informal settlement. A longitudinal eco-epidemiological study was conducted from 2013 to 2014 to characterize the spatial distribution of rat abundance and Leptospira shedding rates in rats and determine the association with human infection risk in a cohort of 2,206 community residents. Tracking plates and live-trapping were used to measure rat abundance and quantify rat shedding status and load. In parallel, four sequential biannual serosurveys were used to identify human Leptospira infections. To evaluate the role of shedding on human risk, we built three statistical models for: (1) the relative abundance of rats, (2) the shedding rate by individual rats, and (3) human Leptospira infection, in which "total shedding", obtained by multiplying the predictions from those two models, was used as a risk factor. We found that Leptospira shedding was associated with older and sexually mature rats and varied spatially and temporally-higher at valley bottoms and with seasonal rainfall (December to March). The point estimate for "total shedding" by rat populations was positive, i.e., Leptospira infection risk increased with total shedding, but the association was not significant [odds ratio (OR) = 1.1; 95% confidence interval (CI): 0.9, 1.4]. This positive trend was mainly driven by rat abundance, rather than individual rat shedding (OR = 1.8; 95% CI: 0.6, 5.4 vs. OR = 1.0; 95% CI: 0.7, 1.4]. Infection risk was higher in areas with more vegetative land cover (OR = 2.4; 95% CI: 1.2, 4.8), and when floodwater entered the house (OR = 2.4; 95% CI: 1.6, 3.4). Our findings indicate that environmental and hydrological factors play a more significant role in Leptospira spillover than rat associated factors. Furthermore, we developed a novel approach combining several models to elucidate complex links between animal reservoir abundance, pathogen shedding and environmental factors on zoonotic spillover in humans that can be extended to other environmentally transmitted diseases.},
}
@article {pmid39359327,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Crescent Plume, Marasmarcha lunaedactyla (Haworth, 1811).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {431},
pmid = {39359327},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Marasmarcha lunaedactyla (the Crescent Plume; Arthropoda; Insecta; Lepidoptera; Pterophoridae). The genome sequence is 771.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,571 protein coding genes.},
}
@article {pmid39355992,
year = {2024},
author = {Auffret, AG and Ladouceur, E and Haussmann, NS and Daouti, E and Elumeeva, TG and Kačergytė, I and Knape, J and Kotowska, D and Low, M and Onipchenko, VG and Paquet, M and Rubene, D and Plue, J},
title = {A global database of soil seed bank richness, density, and abundance.},
journal = {Ecology},
volume = {105},
number = {11},
pages = {e4438},
doi = {10.1002/ecy.4438},
pmid = {39355992},
issn = {1939-9170},
mesh = {*Seed Bank ; *Soil ; *Databases, Factual ; *Biodiversity ; *Seeds ; Ecosystem ; Plants/classification ; },
abstract = {A soil seed bank is the collective name for viable seeds that are stored naturally in the soil. At the species or population level, the ability to form a seed bank represents a strategy for (re)colonization following a disturbance or other change in the local environmental conditions. At the community level, seed banks are thought to buffer local diversity during periods of environmental change and are often studied in relation to the potential for passive habitat restoration. The role that seed banks play in plant population and community dynamics, as well as their importance in the agricultural sector, means that they have been widely studied in ecological research. This database is the result of a comprehensive literature search, including all seed bank studies from the Web of Science from which data could be extracted, as well as an additional search of the Russian language literature. The database contains information on the species richness, seed density, and/or seed abundance in 3096 records from at least 1929 locations across the world's seven continents, extracted from 1442 studies published between 1940 and 2020. Records are grouped into five broad habitat categories (aquatic, arable, forest, grassland-including shrubland-and wetland), including information relating to habitat degradation from, or restoration to other habitats (total 14 combinations). Sampling protocols were also extracted for each record, and the database was extensively checked for errors. The location of each record was then used to extract summary climate data and biome classification from external published databases. The database has several potential uses. The large geographical spread relative to many other global biodiversity datasets is relevant for investigating patterns of diversity in biogeographical or macroecological contexts. Habitat type and status (intact, degraded, and restored) can be used to provide insights for biodiversity conservation, while the potential effects of sampling method and effort can be used to inform optimized data collection for future seed bank studies. This database is released under the CC-BY license.},
}
@article {pmid39354608,
year = {2024},
author = {Navratilova, HF and Whetton, AD and Geifman, N},
title = {Artificial intelligence driven definition of food preference endotypes in UK Biobank volunteers is associated with distinctive health outcomes and blood based metabolomic and proteomic profiles.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {881},
pmid = {39354608},
issn = {1479-5876},
support = {202205080261//Lembaga Pengelola Dana Pendidikan/ ; },
mesh = {Humans ; *Food Preferences ; United Kingdom ; Male ; Female ; *Biological Specimen Banks ; Middle Aged ; *Proteomics/methods ; *Metabolomics ; *Artificial Intelligence ; Metabolome ; Adult ; Aged ; Surveys and Questionnaires ; Health ; UK Biobank ; },
abstract = {BACKGROUND: Specific food preferences can determine an individual's dietary patterns and therefore, may be associated with certain health risks and benefits.<br><br>METHODS: Using food preference questionnaire (FPQ) data from a subset comprising over 180,000 UK Biobank participants, we employed Latent Profile Analysis (LPA) approach to identify the main patterns or profiles among participants. blood biochemistry across groups/profiles was compared using the non-parametric Kruskal-Wallis test. We applied the Limma algorithm for differential abundance analysis on 168 metabolites and 2923 proteins, and utilized the Database for Annotation, Visualization and Integrated Discovery (DAVID) to identify enriched biological processes and pathways. Relative risks (RR) were calculated for chronic diseases and mental conditions per group, adjusting for sociodemographic factors.<br><br>RESULTS: Based on their food preferences, three profiles were termed: the putative Health-conscious group (low preference for animal-based or sweet foods, and high preference for vegetables and fruits), the Omnivore group (high preference for all foods), and the putative Sweet-tooth group (high preference for sweet foods and sweetened beverages). The Health-conscious group exhibited lower risk of heart failure (RR&#x2009;=&#x2009;0.86, 95%CI 0.79-0.93) and chronic kidney disease (RR&#x2009;=&#x2009;0.69, 95%CI 0.65-0.74) compared to the two other groups. The Sweet-tooth group had greater risk of depression (RR&#x2009;=&#x2009;1.27, 95%CI 1.21-1.34), diabetes (RR&#x2009;=&#x2009;1.15, 95%CI 1.01-1.31), and stroke (RR&#x2009;=&#x2009;1.22, 95%CI 1.15-1.31) compared to the other two groups. Cancer (overall) relative risk showed little difference across the Health-conscious, Omnivore, and Sweet-tooth groups with RR of 0.98 (95%CI 0.96-1.01), 1.00 (95%CI 0.98-1.03), and 1.01 (95%CI 0.98-1.04), respectively. The Health-conscious group was associated with lower levels of inflammatory biomarkers (e.g., C-reactive Protein) which are also known to be elevated in those with common metabolic diseases (e.g., cardiovascular disease). Other markers modulated in the Health-conscious group, ketone bodies, insulin-like growth factor-binding protein (IGFBP), and Growth Hormone 1 were more abundant, while leptin was less abundant. Further, the IGFBP pathway, which influences IGF1 activity, may be significantly enhanced by dietary choices.<br><br>CONCLUSIONS: These observations align with previous findings from studies focusing on weight loss interventions, which include a reduction in leptin levels. Overall, the Health-conscious group, with preference to healthier food options, has better health outcomes, compared to Sweet-tooth and Omnivore groups.},
}
@article {pmid39352141,
year = {2024},
author = {Coclet, C and Camargo, AP and Roux, S},
title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.},
journal = {mSystems},
volume = {9},
number = {10},
pages = {e0088824},
pmid = {39352141},
issn = {2379-5077},
mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; },
abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.},
}
@article {pmid39352117,
year = {2024},
author = {Gu, S and Shao, Y and Rehm, K and Bigler, L and Zhang, D and He, R and Xu, R and Shao, J and Jousset, A and Friman, VP and Bian, X and Wei, Z and Kümmerli, R and Li, Z},
title = {Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39352117},
issn = {2050-084X},
support = {No. 2021YFF1200500//National Key Research and Development Program of China/ ; No. 42107140//National Natural Science Foundation of China/ ; No.41922053//National Natural Science Foundation of China/ ; No. 32071255//National Natural Science Foundation of China/ ; No. T2321001//National Natural Science Foundation of China/ ; No. BX2021012//National Postdoctoral Program for Innovative Talents/ ; no. 310030_212266/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Siderophores/metabolism/genetics ; *Genome, Bacterial ; *Pseudomonas/genetics/metabolism ; *Computational Biology/methods ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Oligopeptides/metabolism/genetics ; Secondary Metabolism/genetics ; Iron/metabolism ; },
abstract = {Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here, we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data.},
}
@article {pmid39351379,
year = {2024},
author = {Leavy, OC and Russell, RJ and Harrison, EM and Lone, NI and Kerr, S and Docherty, AB and Sheikh, A and Richardson, M and Elneima, O and Greening, NJ and Harris, VC and Houchen-Wolloff, L and McAuley, HJC and Saunders, RM and Sereno, M and Shikotra, A and Singapuri, A and Aul, R and Beirne, P and Bolton, CE and Brown, JS and Choudhury, G and Diar Bakerly, N and Easom, N and Echevarria, C and Fuld, J and Hart, N and Hurst, JR and Jones, M and Parekh, D and Pfeffer, P and Rahman, NM and Rowland-Jones, S and Shah, AM and Wootton, DG and Jolley, C and Thompson, AAR and Chalder, T and Davies, MJ and De Soyza, A and Geddes, JR and Greenhalf, W and Heller, S and Howard, L and Jacob, J and Jenkins, RG and Lord, JM and Man, WD and McCann, GP and Neubauer, S and Openshaw, PJM and Porter, J and Rowland, MJ and Scott, JT and Semple, MG and Singh, SJ and Thomas, D and Toshner, M and Lewis, K and Heaney, LG and Briggs, A and Zheng, B and Thorpe, M and Quint, JK and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Poinasamy, K and Raman, B and Wain, LV and Brightling, CE and Evans, RA},
title = {1-year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study.},
journal = {ERJ open research},
volume = {10},
number = {5},
pages = {},
pmid = {39351379},
issn = {2312-0541},
abstract = {BACKGROUND: In patients with coronavirus disease 2019 (COVID-19) requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) 1 year after discharge.<br><br>METHODS: Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies (Post-hospitalisation COVID-19 and the International Severe Acute Respiratory and emerging Infection Consortium). HRQoL, assessed by the EuroQol-Five Dimensions-Five Levels utility index (EQ-5D-5L UI), pre-hospital and 1 year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient-reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.<br><br>FINDINGS: Of the 1888 participants included in the primary analysis, 1149 received corticosteroids. There was no between-group difference in EQ-5D-5L UI at 1 year (mean difference 0.004, 95% CI -0.026-0.034). A similar reduction in EQ-5D-5L UI was seen at 1 year between corticosteroid exposed and nonexposed groups (mean&#xb1;sd change -0.12&#xb1;0.22 versus -0.11&#xb1;0.22). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a cohort of 109&#x2009;318 patients admitted to hospital with COVID-19, EQ-5D-5L UI at 1 year remained similar between the two groups.<br><br>INTERPRETATION: Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL 1 year after hospital discharge. Treatments to address the persistent reduction in HRQoL are urgently needed.},
}
@article {pmid39351031,
year = {2024},
author = {Wei, C and Cai, Y and Liu, J and Guo, Y and Wu, X and He, X and Hu, D},
title = {Factors influencing user's health information discernment abilities in online health communities: based on SEM and fsQCA.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1379094},
pmid = {39351031},
issn = {2296-2565},
mesh = {Humans ; Surveys and Questionnaires ; Female ; Male ; Adult ; *Internet ; Consumer Health Information ; Latent Class Analysis ; Information Seeking Behavior ; Fuzzy Logic ; Young Adult ; Middle Aged ; },
abstract = {INTRODUCTION: Online health communities have become the main source for people to obtain health information. However, the existence of poor-quality health information, misinformation, and rumors in online health communities increases the challenges in governing information quality. It not only affects users' health decisions but also undermines social stability. It is of great significance to explore the factors that affect users' ability to discern information in online health communities.<br><br>METHODS: This study integrated the Stimulus-Organism-Response Theory, Information Ecology Theory and the Mindsponge Theory to constructed a model of factors influencing users' health information discernment abilities in online health communities. A questionnaire was designed based on the variables in the model, and data was collected. Utilizing Structural Equation Modeling (SEM) in conjunction with fuzzy-set Qualitative Comparative Analysis (fsQCA), the study analyzed the complex causal relationships among stimulus factors, user perception, and the health information discernment abilities.<br><br>RESULTS: The results revealed that the dimensions of information, information environment, information technology, and information people all positively influenced health information discernment abilities. Four distinct configurations were identified as triggers for users' health information discernment abilities. The core conditions included information source, informational support, technological security, technological facilitation, and perceived risk. It was also observed that information quality and emotional support can act as substitutes for one another, as can informational support and emotional support.<br><br>DISCUSSION: This study provides a new perspective to study the influencing factors of health information discernment abilities of online health community users. It can provide experiences and references for online health community information services, information resource construction and the development of users' health information discernment abilities.},
}
@article {pmid39349447,
year = {2024},
author = {Zhou, L and Wu, S and Chen, Y and Huang, R and Cheng, B and Mao, Q and Liu, T and Liu, Y and Zhao, K and Pan, H and Yu, C and Gao, X and Luo, L and Zhang, Q},
title = {Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8469},
pmid = {39349447},
issn = {2041-1723},
mesh = {*Rosa/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Odorants/analysis ; *Genome, Plant ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Genomics/methods ; Eugenol/analogs &amp; derivatives/metabolism ; Plant Proteins/genetics/metabolism ; Pollination ; Multiomics ; },
abstract = {Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.},
}
@article {pmid39346055,
year = {2024},
author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M},
title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17893},
pmid = {39346055},
issn = {2167-8359},
mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation &amp; purification/classification ; Plants/microbiology ; Computational Biology/methods ; },
abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.},
}
@article {pmid39345378,
year = {2024},
author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Gonzalez, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Bayabyan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, G and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, A and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Wagner, J and Xiao, C and Liss, AS and Zook, JM},
title = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39345378},
issn = {2692-8205},
support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; OT2 OD034190/OD/NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; },
abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from thirteen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.},
}
@article {pmid39345343,
year = {2024},
author = {Halpern, B and Vörös, J and Mc Cartney, AM and Formenti, G and Mouton, A and , and , and , and , },
title = {The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis Méhely, 1893.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {404},
pmid = {39345343},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Vipera ursinii rakosiensis (the Hungarian meadow viper; Chordata; Lepidosauria; Squamata; Viperidae). The genome sequence is 1,625.0 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.38 kilobases in length.},
}
@article {pmid39343505,
year = {2024},
author = {Eneli, I and Heeren, FAN and Cason-Wilkerson, RL and Pratt, KJ},
title = {Metabolic and Bariatric Surgery for Adolescents.},
journal = {Pediatric clinics of North America},
volume = {71},
number = {5},
pages = {981-998},
doi = {10.1016/j.pcl.2024.06.007},
pmid = {39343505},
issn = {1557-8240},
mesh = {Humans ; Adolescent ; *Bariatric Surgery/methods ; *Pediatric Obesity/surgery ; Obesity, Morbid/surgery/psychology ; Gastrectomy/methods ; },
abstract = {Obesity is a chronic, complex, and multifactorial disease. Currently, approximately 6% have severe obesity with higher rates seen among racial/ethnic minority subgroups and in rural communities. Severe obesity is associated with cardiometabolic, psychologic, and musculoskeletal comorbidities. Metabolic and bariatric surgery is an effective treatment option for adolescents endorsed by major pediatric organizations. The most common procedure is the vertical sleeve gastrectomy. Pre-operative evaluation includes an in-depth medical, nutrition, physical activity and psychosocial assessment, with a care plan developed by a multidicplinary team with the adolescent and caregiver. The post-operative plan should include monitoring for surgical complications, weight regain, micronutrient deficiencies, psychologic challenges, and transition to adult care.},
}
@article {pmid39341239,
year = {2024},
author = {Adomako, MO and Jin, L and Li, C and Liu, J and Adu, D and Seshie, VI and Yu, FH},
title = {Mechanisms underpinning microplastic effects on the natural climate solutions of wetland ecosystems.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176491},
doi = {10.1016/j.scitotenv.2024.176491},
pmid = {39341239},
issn = {1879-1026},
abstract = {Wetland ecosystems are vital carbon dioxide (CO2) sinks, offering significant nature-based solutions for global climate mitigation. However, the recent influx of microplastic (MP) into wetlands substantially impacts key drivers (e.g., plants and microorganisms) underpinning these wetland functions. While MP-induced greenhouse gas (GHG) emissions and effects on soil organic carbon (SOC) mineralization potentially threaten the long-term wetland C-climate feedbacks, the exact mechanisms and linkage are unclear. This review provides a conceptual framework to elaborate on the interplay between MPs, wetland ecosystems, and the atmospheric milieu. We also summarize published studies that validate possible MP impacts on natural climate solutions of wetlands, as well as provide extensive elaboration on underlying mechanisms. We briefly highlight the relationships between MP influx, wetland degradation, and climate change and conclude by identifying key gaps for future research priorities. Globally, plastic production, MP entry into aquatic systems, and wetland degradation-related emissions are predicted to increase. This means that MP-related emissions and wetland-climate feedback should be addressed in the context of the UN Paris Climate Agreement on net-zero emissions by 2050. This overview serves as a wake-up call on the alarming impacts of MPs on wetland ecosystems and urges a global reconsideration of nature-based solutions in the context of climate mitigation.},
}
@article {pmid39340701,
year = {2024},
author = {Gang, J and Ping, Y and Du, C},
title = {Anti-Magnaporthe oryzae Activity of Streptomyces bikiniensis HD-087 In Vitro and Bioinformatics Analysis of Polyketide Synthase Gene pksL.},
journal = {Current microbiology},
volume = {81},
number = {11},
pages = {379},
pmid = {39340701},
issn = {1432-0991},
support = {32172468//National Natural Science Foundation of China/ ; },
mesh = {*Polyketide Synthases/genetics/metabolism ; *Streptomyces/genetics/metabolism/enzymology ; *Computational Biology ; *Multigene Family ; Bacterial Proteins/genetics/metabolism ; Erythromycin/pharmacology ; Antifungal Agents/pharmacology/metabolism ; Polyketides/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Molecular Docking Simulation ; Ascomycota ; },
abstract = {Streptomyces bikiniensis HD-087 is capable of synthesizing various antimicrobial substances to counter the detrimental effects of hazardous microorganisms. To elucidate whether it produces polyketide antibiotics and the synthesis mechanism of antibiotic substances, the metabolites and related genes of S. bikiniensis HD-087 were analyzed through LC-MS, anti-Magnaporthe oryzae activity detection, and bioinformatics approaches. The result indicated that the strain HD-087 could produce erythromycin, a polyketide antibiotic. The inhibitory zones of the fermentation supernatant of strain HD-087 and methanol solution of erythromycin extract against M. oryzae were 40.84 ± 0.68 mm and 33.18 ± 0.81 mm, respectively. The IC50 value of erythromycin extract for inhibiting spore germination of erythromycin extract was 220.43 μg/mL. There are two polyketide synthesis gene clusters in the genome of strain HD-087, namely t1pks-nrps and t3pks-lantipeptide-t1pks-nrps. The key gene pksL in the t3pks-lantipeptide-t1pks-nrps gene cluster was predicted. The results suggested that it encodes a stable, hydrophilic, and acidic protein, mainly composed of α-helix and random coil. The PksL protein contains dehydrogenase (DH), ketone reductase (KR), acyl carrier protein (ACP), and ketone synthase (KS) domains. Moreover, it can form interaction networks with 11 proteins containing domains, such as polyketide synthase and ACP synthase. The molecular docking between PksL and acetyl-CoA is stable and strong, suggesting that PksL protein could catalyze the synthesis of polyketides with CoA as a substrate. This study provides a theoretical basis for further exploring the polyketides synthesis mechanism and developing antifungal metabolites in S. bikiniensis HD-087.},
}
@article {pmid39337302,
year = {2024},
author = {Romano Spica, V and Volpini, V and Valeriani, F and Carotenuto, G and Arcieri, M and Platania, S and Castrignanò, T and Clementi, ME and Michetti, F},
title = {In Silico Predicting the Presence of the S100B Motif in Edible Plants and Detecting Its Immunoreactive Materials: Perspectives for Functional Foods, Dietary Supplements and Phytotherapies.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
pmid = {39337302},
issn = {1422-0067},
mesh = {*Dietary Supplements ; *S100 Calcium Binding Protein beta Subunit/metabolism ; *Functional Food ; *Plants, Edible/chemistry ; Computer Simulation ; Amino Acid Motifs ; Phytotherapy/methods ; Computational Biology/methods ; Humans ; Fruit/chemistry/metabolism ; Phylogeny ; Plant Proteins/metabolism ; },
abstract = {The protein S100B is a part of the S100 protein family, which consists of at least 25 calcium-binding proteins. S100B is highly conserved across different species, supporting important biological functions. The protein was shown to play a role in gut microbiota eubiosis and is secreted in human breast milk, suggesting a physiological trophic function in newborn development. This study explores the possible presence of the S100B motif in plant genomes, and of S100B-like immunoreactive material in different plant extracts, opening up potential botanical uses for dietary supplementation. To explore the presence of the S100B motif in plants, a bioinformatic workflow was used. In addition, the immunoreactivity of S100B from vegetable and fruit samples was tested using an ELISA assay. The S100B motif was expected in silico in the genome of different edible plants belonging to the Viridiplantae clade, such as Durio zibethinus or Malus domestica and other medicinal species. S100B-like immunoreactive material was also detected in samples from fruits or leaves. The finding of S100B-like molecules in plants sheds new light on their role in phylogenesis and in the food chain. This study lays the foundation to elucidate the possible beneficial effects of plants or derivatives containing the S100B-like principle and their potential use in nutraceuticals.},
}
@article {pmid39332349,
year = {2024},
author = {Sun, Q and Zhang, Z and Ping, Q and Wang, L and Li, Y},
title = {Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures.},
journal = {Water research},
volume = {267},
number = {},
pages = {122502},
doi = {10.1016/j.watres.2024.122502},
pmid = {39332349},
issn = {1879-2448},
mesh = {*Nitrogen/metabolism ; *Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Denitrification ; Nitrification ; Metabolomics ; Metagenomics ; Ammonium Compounds/metabolism ; Multiomics ; },
abstract = {In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m[3]/(m[2]⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.},
}
@article {pmid39331699,
year = {2024},
author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M},
title = {VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.},
journal = {Molecular biology and evolution},
volume = {41},
number = {10},
pages = {},
pmid = {39331699},
issn = {1537-1719},
support = {82341118//National Natural Science Foundation of China/ ; 2022A1515011854//Natural Science Foundation of Guangdong Province of China/ ; JCYJ20210324124414040//Shenzhen Science and Technology Program/ ; //Hong Kong Innovation and Technology Fund (ITF/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC (Australia) Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*RNA Viruses/genetics ; *Software ; *Metagenomics/methods ; *Phylogeny ; Humans ; RNA-Dependent RNA Polymerase/genetics ; Computational Biology/methods ; },
abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.},
}
@article {pmid39331660,
year = {2024},
author = {Pasqualini, J and Facchin, S and Rinaldo, A and Maritan, A and Savarino, E and Suweis, S},
title = {Emergent ecological patterns and modelling of gut microbiomes in health and in disease.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012482},
pmid = {39331660},
issn = {1553-7358},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Models, Biological ; Computational Biology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics.},
}
@article {pmid39331576,
year = {2024},
author = {Qiao, B and Wang, S and Hou, M and Chen, H and Zhou, Z and Xie, X and Pang, S and Yang, C and Yang, F and Zou, Q and Sun, S},
title = {Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {10},
pages = {},
doi = {10.1093/bioinformatics/btae581},
pmid = {39331576},
issn = {1367-4811},
support = {62273086//National Natural Science Foundation of China/ ; },
mesh = {*Deep Learning ; *NLR Proteins/metabolism ; *Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: Nucleotide-binding leucine-rich repeat (NLR) family is a class of immune receptors capable of detecting and defending against pathogen invasion. They have been widely used in crop breeding. Notably, the correspondence between NLRs and effectors (CNE) determines the applicability and effectiveness of NLRs. Unfortunately, CNE data is very scarce. In fact, we've found a substantial 91 291 NLRs confirmed via wet experiments and bioinformatics methods but only 387 CNEs are recognized, which greatly restricts the potential application of NLRs.<br><br>RESULTS: We propose a deep learning algorithm called ProNEP to identify NLR-effector pairs in a high-throughput manner. Specifically, we conceptualized the CNE prediction task as a protein-protein interaction (PPI) prediction task. Then, ProNEP predicts the interaction between NLRs and effectors by combining the transfer learning with a bilinear attention network. ProNEP achieves superior performance against state-of-the-art models designed for PPI predictions. Based on ProNEP, we conduct extensive identification of potential CNEs for 91&#xa0;291 NLRs. With the rapid accumulation of genomic data, we expect that this tool will be widely used to predict CNEs in new species, advancing biology, immunology, and breeding.<br><br>The ProNEP is available at http://nerrd.cn/#/prediction. The project code is available at https://github.com/QiaoYJYJ/ProNEP.},
}
@article {pmid39328967,
year = {2024},
author = {Dey, B and Ferdous, J and Ahmed, R},
title = {Comprehensive stomata image dataset of Sundarbans Mangrove and Ratargul Swamp forest tree species in Bangladesh.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110908},
pmid = {39328967},
issn = {2352-3409},
abstract = {Plants' leaf stomata are crucial for various scientific research, including identifying species, studying ecology, conserving ecosystems, improving agriculture, and advancing the field of deep learning. This dataset, containing 1083 images, encompasses 11 species from two distinct locations in Bangladesh: nine from the Sundarbans mangrove forest and two from the Ratargul Swamp Forest. It is a valuable tool for refining machine learning algorithms that specialize in detecting stomata and categorizing species accurately. Researchers can explore a deeper understanding of plant physiology, adaptation mechanisms, and environmental interactions by employing pattern recognition, deep learning, and feature extraction techniques. Additionally, this dataset could be a potential tool for enhancing research in macroscopic metamaterials, extending its impact beyond traditional biological studies into interdisciplinary fields of technology and material science.},
}
@article {pmid39326744,
year = {2024},
author = {Wang, Y and Feng, Z and Ghani, MI and Wang, Q and Zeng, L and Yang, X and Zhang, X and Chen, C and Li, S and Cao, P and Chen, X and Cernava, T},
title = {Co-exposure to microplastics and soil pollutants significantly exacerbates toxicity to crops: Insights from a global meta and machine-learning analysis.},
journal = {The Science of the total environment},
volume = {954},
number = {},
pages = {176490},
doi = {10.1016/j.scitotenv.2024.176490},
pmid = {39326744},
issn = {1879-1026},
mesh = {*Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Crops, Agricultural ; *Machine Learning ; Environmental Monitoring/methods ; Soil/chemistry ; Environmental Pollution/statistics &amp; numerical data ; },
abstract = {Environmental contamination of microplastics (MPs) is ubiquitous worldwide, and co-contamination of arable soils with MPs and other pollutants is of increasing concern, and may lead to unexpected consequences on crop production. However, the overall implications of this combined effect, whether beneficial or detrimental, remain a subject of current debate. Here, we conducted a global meta and machine-learning analysis to evaluate the effects of co-exposure to MPs and other pollutants on crops, utilizing 3346 biological endpoints derived from 68 different studies. Overall, compared with control groups that only exposure to conventional soil contaminants, co-exposure significantly exacerbated toxicity to crops, particularly with MPs intensifying adverse effects on crop morphology, oxidative damage, and photosynthetic efficiency. Interestingly, our analysis demonstrated a significant reduction in the accumulation of pollutants in the crop due to the presence of MPs. In addition, the results revealed that potential adverse effects were primarily associated with crop species, MPs mass concentration, and exposure duration. Our study reaffirms the substantial consequences of MPs as emerging pollutants on crops within the context of integrated pollution, providing novel insights into improving sustainability in agro-ecosystems.},
}
@article {pmid39326182,
year = {2024},
author = {Li, D and Ping, Q and Mo, R and Guo, W and Zhang, S and Wang, L and Li, Y},
title = {Revealing synergistic mechanisms of biochar-assisted microbial electrolysis cells in enhancing the anaerobic digestion performance of waste activated sludge: Extracellular polymeric substances characterization, enzyme activity assay, and multi-omics analysis.},
journal = {Water research},
volume = {267},
number = {},
pages = {122501},
doi = {10.1016/j.watres.2024.122501},
pmid = {39326182},
issn = {1879-2448},
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Extracellular Polymeric Substance Matrix/metabolism ; Charcoal/chemistry ; Waste Disposal, Fluid/methods ; Electrolysis ; Methane/metabolism ; Multiomics ; },
abstract = {Although biochar (BC)-assisted microbial electrolysis cells (MEC) has been shown to improve anaerobic digestion (AD) performance of waste activated sludge (WAS), the underlying mechanisms remain unclear. This study conducted an in-depth investigation into the mechanism based on analyses of extracellular polymeric substances (EPS) characteristics, enzyme activities and multi-omics. The results showed that compared with the control group, methane production improved by 16.73 %, 21.32 %, and 29.37 % in the BC, MEC, and BC-assisted MEC (BC-MEC) groups, respectively. The reconfiguration of the protein secondary structure increased the hydrophobicity of the EPS, thereby promoting microbial aggregation. In addition, partial least-squares path modeling (PLS-PM) and mantel test based on the enzyme activity and multi-omics analyses revealed that the promotional effect of MEC on the hydrolysis of WAS was superior to that of BC, while BC was more advantageous in promoting electron transfer and biofilm formation regulated by quorum sensing. The synergistic effects of BC and MEC were exemplified in the BC-MEC group. g_norank_Aminicenantales responsible for the hydrolysis of WAS was enriched (29.6 %), and the activities of hydrolytic enzymes including α-glucosidases and proteases were increased by 29.1 % and 43.6 %, respectively. Further, the expressions of genes related to acyl homoserine lactones (AHLs) and diffusible signal factor (DSF) in quorum sensing systems, as well as the genes related to hydrogenase involved in electron transfer (mbhJKL, hyfB-JR, hypA-F, and hoxFHUY), were up-regulated in the BC-MEC group. This facilitated electron transfer and microbial communication, consequently enhancing methane production. This research significantly advances the understanding of the mechanism by which BC-assisted MEC enhances AD performance and provides valuable insights into strategies for improving energy recovery from WAS.},
}
@article {pmid39325874,
year = {2024},
author = {Zhu, Y and Chen, G and Sun, Y},
title = {VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {10},
pages = {},
pmid = {39325874},
issn = {1367-4811},
support = {11206819//City University of Hong Kong, Hong Kong Research Grants Council/ ; //Hong Kong Innovation and Technology Fund/ ; },
mesh = {*RNA Viruses/genetics/classification ; *Software ; RNA, Viral/genetics ; Phylogeny ; Sequence Analysis, RNA/methods ; Genome, Viral ; Algorithms ; Computational Biology/methods ; },
abstract = {SUMMARY: RNA viruses are ubiquitous across a broad spectrum of ecosystems. Therefore, beyond their significant implications for public health, RNA viruses are also key players in ecological processes. High-through sequencing has accelerated the discovery of RNA viruses. Nevertheless, many of these viruses lack taxonomic annotation, posing a challenge to functional inference and evolutionary study. In particular, virus classification at the genus level remains difficult due to the limited reference data and ambiguous boundaries between some closely related genera. We introduce VirTAXA, a robust classification tool that combines remote homology search and tree-based validation to enhance the genus-level taxonomic classification of RNA viruses. VirTAXA is able to predict the genus label of an assembled viral contig and provide evidence type for each prediction. It achieves comparable accuracy to state-of-the-art methods while assigning genus labels to a greater number of sequences. Specifically, on the Global Ocean RNA metatranscriptomic data, VirTAXA can assign genus labels for 18% more contigs than the second-best classification tool. Furthermore, we demonstrated that VirTAXA can be conveniently extended to other types of viruses.<br><br>The source code and data of VirTAXA are available via https://github.com/JudithEllyn/VirTAXA.},
}
@article {pmid39323974,
year = {2022},
author = {Boyes, D and Crowley, LM and , and , and , and , and , and Skojec, C and Plotkin, D and Kawahara, AY and , },
title = {The genome sequence of the 6-spot burnet, Zygaena filipendulae (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {197},
pmid = {39323974},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Zygaena filipendulae (6-spot burnet; Arthropoda; Insecta; Lepidoptera; Zygaenidae). The genome sequence is 365.9 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,493 protein coding genes.},
}
@article {pmid39323166,
year = {2024},
author = {Lin, ML and Hu, ZQ and Peng, WH and Ye, WL and Zhang, CL and Huang, XR and Chen, S and Gui, HR},
title = {[Pollution Assessment and Source Apportionment of Heavy Metals in the Surrounding Soil of Typical Mining Areas in Tongling, Anhui Province].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {9},
pages = {5494-5505},
doi = {10.13227/j.hjkx.202307274},
pmid = {39323166},
issn = {0250-3301},
abstract = {To study the level of heavy metal pollution and ecological risks in the soil around typical mining areas in Tongling, a total of 150 soil samples were collected from the study area. The content characteristics of 10 elements, namely, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, Fe, and Zn, in the soils were analyzed. Methods including enrichment factor, the geo-accumulation index, single-factor pollution index, Nemero comprehensive pollution index, and potential ecological risk index were used to evaluate the pollution status of heavy metals in the soil of the study area. The pollution sources of heavy metals in the soil were also analyzed using correlation analysis, cluster analysis, and principal component analysis. The results showed that except for Cr and Fe, the average contents of the other eight heavy metal elements were higher than the soil background values in the study area. Pb, Zn, As, Cu, and Cd had a high degree of variation and were significantly affected by external interference. The spatial distribution showed that both Cr and Ni showed a decreasing trend from the edge to the central region, whereas the other eight heavy metals showed a decreasing trend from the central region to the surrounding areas. The pollution level of Cd and Cu in the soil of the research area was relatively severe. The overall ecological risk was at a medium to low level. Cd and Hg were the main contributing factors. As, Cd, Cu, Fe, Mn, Pb, and Zn mainly came from agricultural, industrial, and transportation sources, whereas Cr and Ni were mainly from natural sources. However, the sources of Hg were relatively complex. The research results can provide a scientific basis for the prevention and control of soil heavy metal pollution in metal mining areas, as well as the remediation of mine pollution.},
}
@article {pmid39321538,
year = {2024},
author = {Cao, J and Lei, Y and Li, W and Jiang, X and Li, M},
title = {Coupled digital visualization and multi-omics uncover neurobehavioral dysfunction in zebrafish induced by resorcinol bis(diphenylphosphate).},
journal = {Environment international},
volume = {192},
number = {},
pages = {109023},
doi = {10.1016/j.envint.2024.109023},
pmid = {39321538},
issn = {1873-6750},
mesh = {Animals ; *Zebrafish/physiology ; Water Pollutants, Chemical/toxicity ; Blood-Brain Barrier/drug effects ; Resorcinols/toxicity ; Brain/drug effects/metabolism ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Multiomics ; },
abstract = {Resorcinol bis(diphenylphosphate) (RDP) is an emerging pollutant that has been frequently detected in aquatic environments, although its toxicity is poorly characterized. To understand how RDP affects the neural system, two-month-old zebrafish were exposed to RDP at concentrations of 0.1 and 10 μg/L for 60 days. Following exposure, behavioral assessments were conducted, revealing the emergence of anxiety-like symptoms and memory deficits among the adult fish exposed to RDP, especially at the higher concentration. The increased blood-brain barrier (BBB) permeability (4.67-5.58-fold higher than the control group), reduced expression of tight junction proteins and the rapid brain RDP bioaccumulation (15.63 ± 2.34 ng/g wet weight) indicated the neurotoxicity of RDP. Excess reactive oxygen species synthesis (2.20-2.50-fold) was induced by RDP, leading to mitochondrial dysfunction and decreased production of neurotransmitters in the brain, specifically serotonin (5-HT; 16.3 %) and dopamine (DA; 18.1 %). Metabolomic analysis revealed that the low-toxicity RDP dose up-regulated lipid-related metabolites, while the high-toxicity dose up-regulated arachidonic acid metabolism and disrupted amino acid metabolism, including tryptophan and tyrosine metabolism related to dopaminergic and serotonergic pathways. The dysregulation of genes in various cellular processes was identified by transcriptomics, mainly involved in cell adhesion molecules and gap junctions, and oxidative phosphorylation, which were directly associated with BBB permeability and oxidative stress, respectively. Correlation analysis of microbiome-metabolite-host links built a mechanistic hypothesis for alterations in gut microbiota (Actinobacteriota and Proteobacteria) induced by high-dose RDP leading to the alteration of tryptophan, tyrosine, and arachidonic acid metabolism, decreasing the production of 5-HT and DA through the gut-brain axis. This study provides valuable insights into the mechanism underlying RDP-induced neurotoxicity in zebrafish, which can inform ecological risk assessments.},
}
@article {pmid39320588,
year = {2024},
author = {Oroud, IM},
title = {The implications of climate change on freshwater resources in the arid and semiarid Mediterranean environments using hydrological modeling, GIS tools, and remote sensing.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {979},
pmid = {39320588},
issn = {1573-2959},
mesh = {*Climate Change ; *Environmental Monitoring/methods ; *Hydrology ; *Remote Sensing Technology ; *Geographic Information Systems ; Fresh Water/chemistry ; Groundwater/chemistry ; Models, Theoretical ; Mediterranean Region ; Desert Climate ; Water Resources ; },
abstract = {Precipitation partitioning in arid and semiarid environments is not well understood due to scanty precipitation, its temporal distribution, and the lack/absence of adequate measurements of the hydrometeorological components. Simulation methods have the potential to bridge the data gap, thereby providing a window to estimate the water balance components. The present investigation evaluates the water balance components of a typical watershed situated in the southeastern Mediterranean for the period 1979 through 2019 using daily meteorological data and a grid spacing of 250 m. Generated runoff results were commensurate with corresponding values obtained using the SWAT model. Computed groundwater recharge is also compatible with recharge values calculated using the chloride mass balance method. Results show that average runoff and groundwater recharge for the entire period was ⁓24 mm a[-1] and 19 mm a[-1], giving a precipitation ratio of 9.5% and 7.5%, respectively. Substantial interannual variability in the water balance components was observed during the study period which reflected the significant precipitation fluctuations typifying the Eastern Mediterranean. Results show that the period extending from 1998/1999 through 2018/2019 witnessed an 18% drop in annual precipitation, while surface runoff and groundwater recharge experienced a reduction of ⁓34% and ⁓67%, respectively. Although groundwater recharge is a complex function of numerous meteorological and geological factors, the NDVI can provide an excellent indicator of groundwater recharge in marginal Mediterranean environments. This is highly beneficial in areas where climate records are scanty or absent. The presented results emphasize the significant impacts of global warming and aridification on the future availability of water resources in the semiarid marginal climates in the Eastern Mediterranean and point out clearly that water resources in this area will become scarcer, leading to multiple security threats at national and regional levels.},
}
@article {pmid39313745,
year = {2024},
author = {Dabrowski, JK and Yang, EJ and Crofts, SJC and Hillary, RF and Simpson, DJ and McCartney, DL and Marioni, RE and Kirschner, K and Latorre-Crespo, E and Chandra, T},
title = {Probabilistic inference of epigenetic age acceleration from cellular dynamics.},
journal = {Nature aging},
volume = {4},
number = {10},
pages = {1493-1507},
pmid = {39313745},
issn = {2662-8465},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Epigenesis, Genetic ; *Aging/genetics ; *DNA Methylation ; CpG Islands/genetics ; Genome-Wide Association Study ; Aged ; Female ; Male ; Middle Aged ; Models, Statistical ; },
abstract = {The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological aging into a quantitative era; however, while current epigenetic clocks show strong predictive power, they are data-driven in nature and are not based on the underlying biological mechanisms driving methylation dynamics. We show that predictions of these clocks are susceptible to several confounding non-age-related phenomena that make interpretation of these estimates and associations difficult. To address these limitations, we developed a probabilistic model describing methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, which directly reflect perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias corresponds to global changes in methylation levels. Using data from 15,900 participants from the Generation Scotland study, we develop a robust inference framework and show that these are two distinct processes confounding current epigenetic predictors. Our results show improved associations of acceleration and bias with physiological traits known to impact healthy aging, such as smoking and alcohol consumption, respectively. Furthermore, a genome-wide association study of epigenetic age acceleration identified seven genomic loci.},
}
@article {pmid39312537,
year = {2024},
author = {Malamud, J and Guloksuz, S and van Winkel, R and Delespaul, P and De Hert, MAF and Derom, C and Thiery, E and Jacobs, N and Rutten, BPF and Huys, QJM},
title = {Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012457},
pmid = {39312537},
issn = {1553-7358},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Affect/physiology ; *Depression/physiopathology ; *Computational Biology ; Algorithms ; Ecological Momentary Assessment ; Psychometrics/methods ; Male ; Female ; },
abstract = {BACKGROUND: Mood disorders involve a complex interplay between multifaceted internal emotional states, and complex external inputs. Dynamical systems theory suggests that this interplay between aspects of moods and environmental stimuli may hence determine key psychopathological features of mood disorders, including the stability of mood states, the response to external inputs, how controllable mood states are, and what interventions are most likely to be effective. However, a comprehensive computational approach to all these aspects has not yet been undertaken.<br><br>METHODS: Here, we argue that the combination of ecological momentary assessments (EMA) with a well-established dynamical systems framework-the humble Kalman filter-enables a comprehensive account of all these aspects. We first introduce the key features of the Kalman filter and optimal control theory and their relationship to aspects of psychopathology. We then examine the psychometric and inferential properties of combining EMA data with Kalman filtering across realistic scenarios. Finally, we apply the Kalman filter to a series of EMA datasets comprising over 700 participants with and without symptoms of depression.<br><br>RESULTS: The results show a naive Kalman filter approach performs favourably compared to the standard vector autoregressive approach frequently employed, capturing key aspects of the data better. Furthermore, it suggests that the depressed state involves alterations to interactions between moods; alterations to how moods responds to external inputs; and as a result an alteration in how controllable mood states are. We replicate these findings qualitatively across datasets and explore an extension to optimal control theory to guide therapeutic interventions.<br><br>CONCLUSIONS: Mood dynamics are richly and profoundly altered in depressed states. The humble Kalman filter is a well-established, rich framework to characterise mood dynamics. Its application to EMA data is valid; straightforward; and likely to result in substantial novel insights both into mechanisms and treatments.},
}
@article {pmid39309423,
year = {2023},
author = {Boyes, D and Blaxter, ML and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful Hook-tip, Laspeyria flexula (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {529},
pmid = {39309423},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Laspeyria flexula (the Beautiful Hook-tip; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 450.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,281 protein coding genes.},
}
@article {pmid39309224,
year = {2024},
author = {Boyes, D and Lees, DC and Wawman, DC and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis &amp; Schiffermüller) 1775.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {271},
pmid = {39309224},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.64 kilobases in length.},
}
@article {pmid39309222,
year = {2024},
author = {Boyes, D and Wawman, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the Figure of Eighty moth Tethea ocularis Linnaeus, 1767.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {348},
pmid = {39309222},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Tethea ocularis (the Figure of Eighty; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 339.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.28 kilobases in length.},
}
@article {pmid39304543,
year = {2024},
author = {Hossen, MF and Sultana, N},
title = {Landscape transition-induced ecological risk modeling using GIS and remote sensing techniques: a case of Saint Martin Island, Bangladesh.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {964},
pmid = {39304543},
issn = {1573-2959},
mesh = {Bangladesh ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; *Geographic Information Systems ; *Conservation of Natural Resources ; *Islands ; *Ecosystem ; Risk Assessment/methods ; Humans ; Bayes Theorem ; },
abstract = {Uncontrolled human activity and nature are causing the deterioration of Saint Martin Island, Bangladesh's only tropical island, necessitating sustainable land use strategies and ecological practices. Therefore, the present study measures the land use/cover transition from 1974 to 2021, predicts 2032 and 2042, and constructs the spatiotemporal features of the Landscape Ecological Risk Index based on land use changes. The study utilized Maximum Likelihood Classification (MLC) on Landsat images from 1974, 1988, 2001, 2013, and Sentinel 2B in 2021, achieving ≥ 80% accuracy. The MLP-MC approach was also used to predict 2032 and 2042 LULC change patterns. The eco-risk index was developed using landscape disturbance and vulnerability indices, Bayesian Kriging interpolation, and spatial autocorrelations to indicate spatial clustering. The research found that settlements increased from 2.06 to 28.62 ha between 1974 and 2021 and would cover 41.22 ha in 2042, causing considerable losses in agricultural areas, waterbodies, sand, coral reefs, and vegetation. The area under study showed a more uniform and homogenous environment as Shannon's diversity and evenness scores decreased. The ecological risk of Saint Martin Island increased from 4.31 to 31.05 ha between 1974 and 2042 due to natural and human factors like erosion, tidal bores, population growth, coral mining, habitat destruction, and intensive agricultural practices and tourism, primarily in Nazrul Para, Galachipa, and Western Dakhin Para. The findings will benefit St. Martin Island stakeholders and policymakers by providing insights into current and potential landscape changes and land eco-management.},
}
@article {pmid39303692,
year = {2024},
author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Peacock, TP and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F},
title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.},
journal = {Cell},
volume = {187},
number = {19},
pages = {5468-5482.e11},
pmid = {39303692},
issn = {1097-4172},
support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation &amp; purification ; *Animals, Wild/virology ; *Phylogeny ; Humans ; Pandemics ; },
abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.},
}
@article {pmid39301440,
year = {2024},
author = {Morales, HE and Groombridge, JJ and Tollington, S and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton &amp; E. Newton, 1876).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {378},
pmid = {39301440},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.},
}
@article {pmid39295890,
year = {2023},
author = {Boyes, D and Januszczak, I and , and , and , and , and , and , },
title = {The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {545},
pmid = {39295890},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Cosmia pyralina (the Lunar-spotted Pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 803.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,901 protein coding genes.},
}
@article {pmid39294496,
year = {2024},
author = {Khaliq, AM and Rajamohan, M and Saeed, O and Mansouri, K and Adil, A and Zhang, C and Turk, A and Carstens, JL and House, M and Hayat, S and Nagaraju, GP and Pappas, SG and Wang, YA and Zyromski, NJ and Opyrchal, M and Lee, KP and O'Hagan, H and El Rayes, B and Masood, A},
title = {Spatial transcriptomic analysis of primary and metastatic pancreatic cancers highlights tumor microenvironmental heterogeneity.},
journal = {Nature genetics},
volume = {56},
number = {11},
pages = {2455-2465},
pmid = {39294496},
issn = {1546-1718},
mesh = {Humans ; *Tumor Microenvironment/genetics ; *Pancreatic Neoplasms/genetics/pathology ; *Carcinoma, Pancreatic Ductal/genetics/pathology ; *Transcriptome ; *Neoplasm Metastasis/genetics ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling/methods ; Female ; },
abstract = {Although the spatial, cellular and molecular landscapes of resected pancreatic ductal adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology remain elusive. By applying spatially resolved transcriptomics to matched primary and metastatic PDAC samples, we discovered a conserved continuum of fibrotic, metabolic and immunosuppressive spatial ecotypes across anatomical regions. We observed spatial tumor microenvironment heterogeneity spanning beyond that previously appreciated in PDAC. Through comparative analysis, we show that the spatial ecotypes exhibit distinct enrichment between primary and metastatic sites, implying adaptability to the local environment for survival and progression. The invasive border ecotype exhibits both pro-tumorigenic and anti-tumorigenic cell-type enrichment, suggesting a potential immunotherapy target. The ecotype heterogeneity across patients emphasizes the need to map individual patient landscapes to develop personalized treatment strategies. Collectively, our findings provide critical insights into metastatic PDAC biology and serve as a valuable resource for future therapeutic exploration and molecular investigations.},
}
@article {pmid39292721,
year = {2024},
author = {Bastien, GE and Cable, RN and Batterbee, C and Wing, AJ and Zaman, L and Duhaime, MB},
title = {Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011649},
pmid = {39292721},
issn = {1553-7358},
mesh = {*Machine Learning ; Humans ; *Viruses/genetics ; *Computational Biology/methods ; *Host-Pathogen Interactions/genetics/physiology ; Host Microbial Interactions/genetics/physiology ; },
abstract = {Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets.},
}
@article {pmid39292164,
year = {2024},
author = {Sakai, K and Nagata, T and Mori, T and Inoue, S and Fujiwara, H and Odagami, K and Adi, NP and Tatemichi, M and Mori, K},
title = {Research topics in occupational medicine, 1990-2022: A text-mining-applied bibliometric study.},
journal = {Scandinavian journal of work, environment &amp; health},
volume = {50},
number = {7},
pages = {567-576},
pmid = {39292164},
issn = {1795-990X},
support = {240801-01//Industrial Disease Clinical Research Grants from the Ministry of Health, Labor and Welfare/ ; },
mesh = {*Bibliometrics ; *Data Mining ; Humans ; *Occupational Medicine ; Occupational Health ; },
abstract = {OBJECTIVE: Occupational health has been influenced by societal and industrial changes. This study aimed to clarify topic trends in occupational health research in 1990-2022.<br><br>METHODS: We conducted a text-mining-adjusted bibliometric study using research titles in occupational health. Data on research titles and the years of publication were collected from 26 peer-reviewed journals on PubMed. Using morphological and correspondence analyses in text mining, we structured research topics into multiple categories and visualized the relationship between all categories and publication years. Statistical analyses were conducted using the text mining software - KH Coder 3.0.<br><br>RESULTS: We obtained 48 645 articles containing 714 890 words in their titles. The research topics were classified into 4 categories and 17 subcategories, of which those of occupations; countries; non-intervention; psychosocial factors; lifestyle factors; safety; symptoms; therapy and care; and productivity have recently shown an increasing trend. In contrast, the subcategories of risk, chemical factors, disease, and organ damage showed decreasing trends. Chemical factors, which were the main topics in the 1990s, included risk, organ damage, and disease. Productivity, the main topic in the 2020s, co-occurred with lifestyle factors, symptoms, and intervention.<br><br>CONCLUSIONS: Focal areas in occupational-health research shift according to societal trends. Occupational-health research has primarily analyzed issues in developed countries with capitalist values and may not have sufficiently covered issues in developing countries. It is imperative for policymakers and public funding bodies to determine priorities for investigation in the field.},
}
@article {pmid39292040,
year = {2024},
author = {Vasconcelos, NM and Bernal, RTI and Souza, JB and Bordoni, PHC and Stein, C and Coll, CVN and Murray, J and Malta, DC},
title = {Underreporting of violence against women: an analysis of two data sources.},
journal = {Ciencia &amp; saude coletiva},
volume = {29},
number = {10},
pages = {e07732023},
doi = {10.1590/1413-812320242910.07732023},
pmid = {39292040},
issn = {1678-4561},
mesh = {Humans ; Brazil/epidemiology ; Female ; Adult ; Young Adult ; Adolescent ; *Sex Offenses/statistics &amp; numerical data ; Middle Aged ; Health Surveys ; Gender-Based Violence/statistics &amp; numerical data ; Information Systems/statistics &amp; numerical data ; Information Sources ; },
abstract = {This article aims to estimate the underreporting of violence against women (VAW) in the Notifiable Diseases Information System (SINAN), based on data from the National Survey of Health (NSH), in Brazil and subnational units (SU). This work was an ecological study using SINAN and NSH, both from 2019. In SINAN, reports of sexual, physical, and psychological VAW, aged 18 years or older, were selected. In the NSH, women of the same age group who reported psychological, physical, or sexual violence, and who had sought health care due to consequences of the violence were selected. SINAN underreporting was calculated in reference to the NSH's estimated population, for Brazil and each SU. Underreporting of VAW in Brazil was 98.5%, 75.9%, and 89.4% for psychological, physical, and sexual violence, respectively. The North and Northeast states presented the lowest reporting rates among the states. VAW in Brazil is highly underreported by the health sector, showing the need for adequate training of health professionals to recognize situations of violence and raise awareness of the importance of reporting.},
}
@article {pmid39290666,
year = {2024},
author = {Guclu, C and Luk, CL and Ashton, LA and Abbas, S and Boyle, MJW},
title = {Beta diversity subcomponents of plant species turnover and nestedness reveal drivers of community assembly in a regenerating subtropical forest.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70233},
pmid = {39290666},
issn = {2045-7758},
abstract = {Secondary forests represent a significant proportion of global forest cover, with over 70% of forests in East Asia classified as regenerating. While succession has been studied extensively in temperate systems, trajectories of subtropical succession remain poorly characterized in highly disturbed, urban-adjacent forests. Investigating the additive beta diversity components of turnover and nestedness may reveal community assembly mechanisms driving secondary succession. The present study investigates plant community assembly along a successional gradient from 7 to 70 years following the onset of succession in secondary subtropical forests in Hong Kong, China. Plant survey data for 28 plots were analysed, generating additive Simpsons turnover and nestedness beta diversity metrics. Dissimilarity matrices were generated and modelled as a function of environmental matrices including forest plant community age (years following onset of secondary succession), inter-community distance (metres), and soil moisture saturation (%) across three elevational bands using generalized dissimilarity models. Nonmetric multidimensional scaling of plant communities was conducted with Bray-Curtis dissimilarity matrices. Inter-community distance and successional age differentially influenced plant species turnover between lowland and Montane forest types. Models of nestedness found that plot age and soil moisture saturation were significant drivers of nestedness patterns in plant communities across elevational classes. Turnover represented a higher proportion of Sorensen beta diversity than nestedness, while ANOSIM found significant differentiation between plant communities at different successional stages. Turnover patterns suggest a deterministic model of community assembly, with strong patterns of species replacement between communities at fine spatial scales and successional stages, as well as clear compositional shifts between lowland and montane forest types. NMDS analysis and functional compositional assessments suggested a transition from early successional communities with a high proportion of shrub species, to later successional communities with a higher proportion of tree species, with an increase in species turnover with greater age dissimilarity.},
}
@article {pmid39290433,
year = {2024},
author = {Castrillo, M and Aguilar, F and García-Díaz, D},
title = {Dataset on sub-daily vertical profiles of physicochemical parameters and chlorophyll concentration in El Val reservoir, together with its daily meteorological data, storage state and downstream flow (2018-2022).},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110839},
pmid = {39290433},
issn = {2352-3409},
abstract = {The dataset addressed in this article contains parameters about El Val reservoir (province of Zaragoza, Spain). It includes physicochemical variables, the water level, the stored water volume, its meteorological conditions and the flow rate of its effluent, the Queiles River, a few metres downstream of the dam. The El Val reservoir stores water from the Val River, but it also receives water from the Queiles River through a pipeline and from several ravines. The dam releases on the Queiles River, which is a tributary of the Ebro River (the second one in Spain in length and discharge rate). A multiparametric probe (aquaDam, Adasa Systems), hanging from a structure located in the dam, every 6 h makes a vertical profile taking the measurements at each metre of depth from the surface to approximately 573 m above sea level (m.a.s.l.), in other words, between 2 and 3 m above the bottom outlet. This probe collects data of water temperature, pH, ORP, conductivity, dissolved oxygen, turbidity and chlorophyll concentration. Meteorological data are collected in the nearest weather station, located in the municipality of Los Fayos which is about 500 m downstream of the dam. These include daily accumulated precipitation, daily maximum and average solar irradiance, daily maximum, minimum and average air temperature and daily average wind speed. The water level and volume of stored water and the flow rate of the Queiles River are collected in the El Val monitoring station and the Queiles River gauge station respectively, and are also provided on a daily basis. These data are useful to feed deterministic, data driven or hybrid hydrological models with different purposes, like the identification of the impact of meteorological conditions on the physicochemical properties of the reservoir as well as the assessment of different management strategies in the reservoir. This is a data article that additionally supports the work published in Ecological Informatics [1] where the use of common and readily available open data is promoted through its use to feed data driven models, in particular to infer the depth of the thermocline in reservoirs that are periodically or permanently thermally stratified. In that article a dataset derived from the one presented in this article is used.},
}
@article {pmid39290364,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Red Chestnut moth, Cerastis rubricosa (Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {88},
pmid = {39290364},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Cerastis rubricosa (the Red Chestnut moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 678.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,784 protein coding genes.},
}
@article {pmid39290036,
year = {2024},
author = {Monreal-Di Bello, M and González-Bermejo, D and Castillo-Cano, B and Rodriguez-Pascual, A and Montero-Corominas, D},
title = {Impact of Regulatory Interventions on Ulipristal Acetate 5 mg (Esmya) Use in Spain: An Interrupted Time-Series Analysis.},
journal = {Pharmacoepidemiology and drug safety},
volume = {33},
number = {9},
pages = {e70004},
doi = {10.1002/pds.70004},
pmid = {39290036},
issn = {1099-1557},
support = {//Spanish Agency on Medicines and Medical Devices (AEMPS)/ ; },
mesh = {Humans ; Spain/epidemiology ; *Norpregnadienes/administration &amp; dosage/adverse effects/therapeutic use ; *Interrupted Time Series Analysis ; Female ; Databases, Factual ; Electronic Health Records/statistics &amp; numerical data ; Risk Evaluation and Mitigation ; Male ; Adult ; Middle Aged ; },
abstract = {PURPOSE: Since late 2017, the use of ulipristal acetate 5 mg (UPA; Proprietary name: Esmya) has been under review in the European Union, due to an emerging hepatic risk. In February 2018 and in July 2018, the Spanish Agency of Medicines and Medical Devices and the marketing authorization holder put two risk minimization measures (RMM) in place, in order to inform about new safety information and to mitigate this risk. This study aims to assess RMM effectiveness in Spain, by performing an interrupted time-series (ITS) analyses, between 2014 and 2019.<br><br>METHOD: Two quasi-experimental ITS analyses to examine the use of UPA before and after the RMM release were performed: (a) an ecological study using aggregated data from a drug consumption database; and (b) a study using primary healthcare data gathered from electronic clinical records.<br><br>RESULTS: Regulatory interventions were associated with an immediate and significant decrease level of DID (the number of DDD dispensed per 100&#x2009;000 inhabitants and day) and incidence. The DID was 70% less than expected 12&#x2009;months after the interventions. This value was 59% for the incidence. However, a change in the slope was not observed and the use started rising again in the last segment of the study period.<br><br>CONCLUSION: Despite RMM had an immediate strong impact on UPA use, the last segment upward trend in the long-term might have been affected by the lack of comparable therapeutic alternatives. Further studies should be performed to confirm the increase trend observed and analyze subsequent measures and additional data.},
}
@article {pmid39289538,
year = {2024},
author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ},
title = {The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {28},
pmid = {39289538},
issn = {2731-4243},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.},
}
@article {pmid39287883,
year = {2024},
author = {Stolz, BJ and Dhesi, J and Bull, JA and Harrington, HA and Byrne, HM and Yoon, IHR},
title = {Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {11},
pages = {128},
pmid = {39287883},
issn = {1522-9602},
support = {EP/R018472/1//EPSRC/ ; EP/R018472/1, EP/K041096/1, EP/R005125/1, EP/T001968/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; RGF EA 201074, UF150238//Royal Society/ ; CTRQQR-2021/100002/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {*Tumor Microenvironment/immunology ; Humans ; *Mathematical Concepts ; *Models, Biological ; *Neoplasms/pathology/immunology ; Computer Simulation ; Computational Biology ; Macrophages/immunology/pathology ; },
abstract = {Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity (e.g., cells or molecular species). However, state-of-the-art data collection techniques now generate exquisitely detailed multispecies data, prompting a need for methods that can examine and quantify the relations among them. Such heterogeneous data types arise in many contexts, ranging from biomedical imaging, geospatial analysis, to species ecology. Here, we propose two methods for encoding spatial relations among different data types that are based on Dowker complexes and Witness complexes. We apply the methods to synthetic multispecies data of a tumor microenvironment and analyze topological features that capture relations between different cell types, e.g., blood vessels, macrophages, tumor cells, and necrotic cells. We demonstrate that relational topological features can extract biological insight, including the dominant immune cell phenotype (an important predictor of patient prognosis) and the parameter regimes of a data-generating model. The methods provide a quantitative perspective on the relational analysis of multispecies spatial data, overcome the limits of traditional PH, and are readily computable.},
}
@article {pmid39287032,
year = {2024},
author = {Meaume, S and Senet, P and Thomé, B and Aragno, VA and Serge, B and Fortin, S and Boucley, I and Michon-Pasturel, U and Colboc, H},
title = {Impact of primary dressings on healing of venous leg ulcers: a French cohort study from the healthcare insurance database.},
journal = {Journal of wound care},
volume = {33},
number = {9},
pages = {678-686},
doi = {10.12968/jowc.2024.0189},
pmid = {39287032},
issn = {0969-0700},
mesh = {Humans ; Female ; Male ; *Wound Healing ; France ; *Varicose Ulcer/therapy/economics ; Aged ; *Bandages/economics ; Middle Aged ; Cohort Studies ; Databases, Factual ; Aged, 80 and over ; Insurance, Health/statistics &amp; numerical data ; Treatment Outcome ; Health Care Costs/statistics &amp; numerical data ; },
abstract = {OBJECTIVE: Multicomponent bandages (MCBs) are recommended by the French Authority for Health (Haute Autorité de Santé) as first-line treatment for venous leg ulcers (VLUs). A first analysis of the data collected from the French administrative healthcare database (Système National des Données de Santé (SNDS)) on 25,255 patients with a VLU supported superiority of MCBs versus short stretch bandages when considering the healing outcomes and costs associated with closure of these wounds. The aim of this study was to assess how beneficial the primary dressing (technology lipido-colloid nano-oligosaccharide factor (TLC NOSF) or control dressing group (CDG)) could be, when used in combination with MCBs in the treatment of VLUs.<br><br>METHOD: Data from the SNDS were collected for patients meeting the following inclusion criteria: treatment for a VLU with MCBs and with the same dressing type (TLC-NOSF or CDG) during the whole treatment period. Healing outcomes were documented on the global cohorts and propensity score-matched cohorts. The mean healthcare cost and the ecological impact were calculated for those patients healed within the study period.<br><br>RESULTS: In total, 12,507 patients met the criteria for treatment with both MCBs and TLC-NOSF dressings (n=1134) versus MCBs and CDG (n=11,373); with 1134 and 2268 patients per group following propensity score matching. Healing outcomes were favourable for the TLC-NOSF group in the global cohort and were enhanced in the propensity score-matched cohorts. At every point of the analysis, the adjusted healing rates were significantly higher in the TLC-NOSF group than in the CDG group (p<0.001). In the propensity score-matched cohorts (n=3402), the healing rate at three months was 52% in the TLC-NOSF group versus 37% in the CDG group (p<0.001). The median healing time was 87 days versus 125.5 days in the TLC-NOSF and CDG groups, respectively (p<0.0001). TLC-NOSF dressings significantly reduced the average treatment cost per healed ulcer (&#x20ac;2099) by 23.7% compared with dressings without TLC-NOSF (&#x20ac;2751) (p<0.001), as well as the resources used.<br><br>CONCLUSION: This SNDS analysis confirms, in the largest real-life study performed in VLU management, the superiority of the TLC-NOSF dressings versus those not impregnated with the NOSF compound. Better clinical outcomes associated with cost savings and a positive ecological impact support the combination of MCBs and TLC-NOSF dressings and should be considered as an optimal standard of care for the global management of VLUs. These outcomes reinforce the current positions of the international guidelines on the use of NOSF impregnated dressings (UrgoStart range; Laboratoires Urgo, France) in this pathology.},
}
@article {pmid39283951,
year = {2024},
author = {Amaral, AS and Devos, DP},
title = {The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012459},
pmid = {39283951},
issn = {1553-7358},
mesh = {*Proteome/metabolism ; Databases, Protein ; Computational Biology ; Proteins/metabolism/chemistry ; Humans ; Proteomics/methods ; Bacteria/metabolism/genetics ; Animals ; },
abstract = {An often-overlooked aspect of biology is formed by the outliers of the protein length distribution, specifically those proteins with more than 5000 amino acids, which we refer to as huge proteins (HPs). By examining UniprotKB, we discovered more than 41 000 HPs throughout the tree of life, with the majority found in eukaryotes. Notably, the phyla with the highest propensity for HPs are Apicomplexa and Fornicata. Moreover, we observed that certain bacteria, such as Elusimicrobiota or Planctomycetota, have a higher tendency for encoding HPs, even more than the average eukaryote. To investigate if these macro-polypeptides represent "real" proteins, we explored several indirect metrics. Additionally, orthology analyses reveals thousands of clusters of homologous sequences of HPs, revealing functional groups related to key cellular processes such as cytoskeleton organization and functioning as chaperones or as E3-ubiquitin ligases in eukaryotes. In the case of bacteria, the major clusters have functions related to non-ribosomomal peptide synthesis/polyketide synthesis, followed by pathogen-host attachment or recognition surface proteins. Further exploration of the annotations for each HPs supported the previously identified functional groups. These findings underscore the need for further investigation of the cellular and ecological roles of these HPs and their potential impact on biology and biotechnology.},
}
@article {pmid39283104,
year = {2024},
author = {Tedim, AP and Almeida-Santos, AC and Lanza, VF and Novais, C and Coque, TM and Freitas, AR and Peixe, L and , },
title = {Bacteriocin distribution patterns in Enterococcus faecium and Enterococcus lactis: bioinformatic analysis using a tailored genomics framework.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {10},
pages = {e0137624},
pmid = {39283104},
issn = {1098-5336},
support = {EXPL/SAU-INF/0261/2021, UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UI/BD/151317/2021//MCTES | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; },
mesh = {*Bacteriocins/genetics/metabolism ; *Enterococcus faecium/genetics/metabolism/drug effects ; *Genomics ; *Computational Biology ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Enterococcus/genetics/metabolism/drug effects ; },
abstract = {UNLABELLED: Multidrug-resistant Enterococcus faecium strains represent a major concern due to their ability to thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance and virulence mechanisms have been extensively studied, the contribution of bacteriocins to E. faecium's adaptability remains poorly explored. E. faecium, within the Bacillota phylum, is a prominent bacteriocin producer. Here, we developed a tailored database of 76 Bacillota bacteriocins (217 sequences, including 40 novel bacteriocins) and applied it to uncover bacteriocin distribution patterns in 997 quality-filtered E. faecium and Enterococcus lactis (former E. faecium clade B) genomes. Curated using computational pipelines and literature mining, our database demonstrates superior precision versus leading public tools in identifying diverse bacteriocins. Distinct bacteriocin profiles emerged between E. faecium and E. lactis, highlighting species-specific adaptations. E. faecium strains from hospitalized patients were significantly enriched in bacteriocins as enterocin A and bacteriocins 43 (or T8), AS5, and AS11. These bacteriocin genes were strongly associated with antibiotic resistance, particularly vancomycin and ampicillin, and Inc18 rep2_pRE25-derivative plasmids, classically associated with vancomycin resistance transposons. Such bacteriocin arsenal likely enhances the adaptability and competitive fitness of E. faecium in the nosocomial environment. By combining a novel tailored database, whole-genome sequencing, and epidemiological data, our work elucidates meaningful connections between bacteriocin determinants, antimicrobial resistance, mobile genetic elements, and ecological origins in E. faecium and provides a framework for elucidating bacteriocin landscapes in other organisms. Characterizing species- and strain-level differences in bacteriocin profiles may reveal determinants of ecological adaptation, and translating these discoveries could further inform strategies to exploit bacteriocins against high-risk clones.<br><br>IMPORTANCE: This work significantly expands the knowledge on the understudied bacteriocin diversity in opportunistic enterococci, revealing their contribution in the adaptation to different environments. It underscores the importance of placing increased emphasis on genetic platforms carrying bacteriocins as well as on cryptic plasmids that often exclusively harbor bacteriocins since bacteriocin production can significantly contribute to plasmid maintenance, potentially facilitating their stable transmission across generations. Further characterization of strain-level bacteriocin landscapes could inform strategies to combat high-risk clones. Overall, these insights provide a framework for unraveling the therapeutic and biotechnological potential of bacteriocins.},
}
@article {pmid39277496,
year = {2024},
author = {van der Feltz-Cornelis, CM and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A},
title = {Corrigendum to "Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis" [General Hospital Psychiatry volume 88 (2024)10-22 10.1016/j.genhosppsych.2024.02.009].},
journal = {General hospital psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.genhosppsych.2024.09.006},
pmid = {39277496},
issn = {1873-7714},
}
@article {pmid39275913,
year = {2024},
author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T},
title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.},
journal = {FEBS open bio},
volume = {14},
number = {12},
pages = {1972-1984},
pmid = {39275913},
issn = {2211-5463},
support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; Japan ; *Gastrointestinal Microbiome/genetics ; *Birds/microbiology/virology ; *Metagenomics/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; },
abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.},
}
@article {pmid39274728,
year = {2024},
author = {Sąsiadek-Andrzejczak, E and Maras, P and Kozicki, M},
title = {Flexible and Ecological Cotton-Based Dosimeter for 2D UV Surface Dose Distribution Measurements.},
journal = {Materials (Basel, Switzerland)},
volume = {17},
number = {17},
pages = {},
pmid = {39274728},
issn = {1996-1944},
abstract = {This work presents a 2D radiochromic dosimeter for ultraviolet (UV) radiation measurements, based on cotton fabric volume-modified with nitroblue tetrazolium chloride (NBT) as a radiation-sensitive compound. The developed dosimeter is flexible, which allows it to adapt to various shapes and show a color change from yellowish to purple-brown during irradiation. The intensity of the color change depends on the type of UV radiation and is the highest for UVC (253.7 nm). It has been shown that the developed dosimeters (i) can be used for UVC radiation dose measurements in the range of up to 10 J/cm[2]; (ii) can be measured in 2D using a flatbed scanner; and (iii) can have the obtained images after scanning be filtered with a medium filter to improve their quality by reducing noise from the fabric structure. The developed cotton-NBT dosimeters can measure UVC-absorbed radiation doses on objects of various shapes, and when combined with a dedicated computer software package and a data processing method, they form a comprehensive system for measuring dose distributions for objects with complex shapes. The developed system can also serve as a comprehensive method for assessing the quality and control of UV radiation sources used in various industrial processes.},
}
@article {pmid39273837,
year = {2024},
author = {Gatina, E and Zinicovscaia, I and Yushin, N and Chaligava, O and Frontasyeva, M and Sharipova, A},
title = {Assessment of the Atmospheric Deposition of Potentially Toxic Elements Using Moss Pleurozium schreberi in an Urban Area: The Perm (Perm Region, Russia) Case Study.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {17},
pages = {},
pmid = {39273837},
issn = {2223-7747},
abstract = {Assessment of air quality in urban areas is very important because pollutants affect both the environment and human health. In Perm (Russia), a moss biomonitoring method was used to assess the level of air pollution. The concentrations of 15 elements in 87 samples of moss Pleurozium schreberi in the city territory were determined using a direct mercury analyzer and an inductively coupled plasma atomic emission spectroscopy. Using factor and correlation analyses, the grouping of elements and their relationship with emission sources were established. The main sources of emissions of potentially toxic elements are the transportation (road and rail), metallurgical, and chemical industries. The level of atmospheric air pollution was assessed by calculating the environmental risk index, pollutant load index, and pollution coefficient. Based on the values of the pollution index, the level of atmospheric air pollution in Perm varies from unpolluted to highly polluted, with moderate environmental risk.},
}
@article {pmid39273245,
year = {2024},
author = {Damarov, IS and Korbolina, EE and Rykova, EY and Merkulova, TI},
title = {Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273245},
issn = {1422-0067},
support = {23-15-00113//Russian Science Foundation/ ; },
mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/genetics/drug therapy/metabolism ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; Hypoglycemic Agents/therapeutic use/pharmacology ; Quantitative Trait Loci ; Computational Biology/methods ; Leukocytes, Mononuclear/metabolism/drug effects ; Gene Expression Regulation/drug effects ; Promoter Regions, Genetic ; Multiomics ; },
abstract = {The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin.},
}
@article {pmid39271937,
year = {2024},
author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D},
title = {Author Correction: A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {12},
pages = {2336},
doi = {10.1038/s41559-024-02557-8},
pmid = {39271937},
issn = {2397-334X},
}
@article {pmid39271747,
year = {2024},
author = {Shin, S and Baker, AJ and Enk, J and McKenna, DD and Foquet, B and Vandergast, AG and Weissman, DB and Song, H},
title = {Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21377},
pmid = {39271747},
issn = {2045-2322},
support = {DEB-1937815//National Science Foundation/ ; IOS-1253493//National Science Foundation/ ; DEB-1064082//National Science Foundation/ ; Hatch Grant TEX0-2-6584//U.S. Department of Agriculture/ ; },
mesh = {Animals ; *Phylogeny ; *Orthoptera/genetics/classification ; Transcriptome/genetics ; Computational Biology/methods ; DNA Probes/genetics ; Evolution, Molecular ; },
abstract = {Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.},
}
@article {pmid39269993,
year = {2024},
author = {Golumbeanu, M and Briët, O and Champagne, C and Lemant, J and Winkel, M and Zogo, B and Gerhards, M and Sinka, M and Chitnis, N and Penny, M and Pothin, E and Smith, T},
title = {AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011609},
pmid = {39269993},
issn = {1553-7358},
mesh = {Animals ; Humans ; *Malaria/transmission/prevention &amp; control ; *Anopheles/physiology ; *Mosquito Vectors/physiology ; *Mosquito Control/methods ; *Software ; Computational Biology ; Models, Biological ; },
abstract = {In recent decades, field and semi-field studies of malaria transmission have gathered geographic-specific information about mosquito ecology, behaviour and their sensitivity to interventions. Mathematical models of malaria transmission can incorporate such data to infer the likely impact of vector control interventions and hence guide malaria control strategies in various geographies. To facilitate this process and make model predictions of intervention impact available for different geographical regions, we developed AnophelesModel. AnophelesModel is an online, open-access R package that quantifies the impact of vector control interventions depending on mosquito species and location-specific characteristics. In addition, it includes a previously published, comprehensive, curated database of field entomological data from over 50 Anopheles species, field data on mosquito and human behaviour, and estimates of vector control effectiveness. Using the input data, the package parameterizes a discrete-time, state transition model of the mosquito oviposition cycle and infers species-specific impacts of various interventions on vectorial capacity. In addition, it offers formatted outputs ready to use in downstream analyses and by other models of malaria transmission for accurate representation of the vector-specific components. Using AnophelesModel, we show how the key implications for intervention impact change for various vectors and locations. The package facilitates quantitative comparisons of likely intervention impacts in different geographical settings varying in vector compositions, and can thus guide towards more robust and efficient malaria control recommendations. The AnophelesModel R package is available under a GPL-3.0 license at https://github.com/SwissTPH/AnophelesModel.},
}
@article {pmid39269992,
year = {2024},
author = {O'Meara, BC and Beaulieu, JM},
title = {Noise leads to the perceived increase in evolutionary rates over short time scales.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012458},
pmid = {39269992},
issn = {1553-7358},
mesh = {*Computational Biology/methods ; Models, Genetic ; Biological Evolution ; Evolution, Molecular ; Animals ; Models, Statistical ; Humans ; },
abstract = {Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show that plotting a noisy numerator divided by time versus time leads to the observed hyperbolic pattern; in fact, randomizing the amount of change over time generates patterns functionally identical to observed patterns. Ignoring errors can not only obscure true patterns but create novel patterns that have long misled scientists.},
}
@article {pmid39267994,
year = {2024},
author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {258},
pmid = {39267994},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.},
}
@article {pmid39266599,
year = {2024},
author = {He, H and Boehringer, T and Schäfer, B and Heppell, K and Beck, C},
title = {Analyzing spatio-temporal dynamics of dissolved oxygen for the River Thames using superstatistical methods and machine learning.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21288},
pmid = {39266599},
issn = {2045-2322},
support = {VH-NG-1727//Helmholtz Association and the Networking Fund/ ; },
abstract = {By employing superstatistical methods and machine learning, we analyze time series data of water quality indicators for the River Thames (UK). The indicators analyzed include dissolved oxygen, temperature, electrical conductivity, pH, ammonium, turbidity, and rainfall, with a specific focus on the dynamics of dissolved oxygen. After detrending, the probability density functions of dissolved oxygen fluctuations exhibit heavy tails that are effectively modeled using q-Gaussian distributions. Our findings indicate that the multiplicative Empirical Mode Decomposition method stands out as the most effective detrending technique, yielding the highest log-likelihood in nearly all fittings. We also observe that the optimally fitted width parameter of the q-Gaussian shows a negative correlation with the distance to the sea, highlighting the influence of geographical factors on water quality dynamics. In the context of same-time prediction of dissolved oxygen, regression analysis incorporating various water quality indicators and temporal features identify the Light Gradient Boosting Machine as the best model. SHapley Additive exPlanations reveal that temperature, pH, and time of year play crucial roles in the predictions. Furthermore, we use the Transformer, a state-of-the-art machine learning model, to forecast dissolved oxygen concentrations. For long-term forecasting, the Informer model consistently delivers superior performance, achieving the lowest Mean Absolute Error (0.15) and Symmetric Mean Absolute Percentage Error (21.96%) with the 192 historical time steps that we used. This performance is attributed to the Informer's ProbSparse self-attention mechanism, which allows it to capture long-range dependencies in time-series data more effectively than other machine learning models. It effectively recognizes the half-life cycle of dissolved oxygen, with particular attention to critical periods such as morning to early afternoon, late evening to early morning, and key intervals between the 16th and 26th quarter-hours of the previous half-day. Our findings provide valuable insights for policymakers involved in ecological health assessments, aiding in accurate predictions of river water quality and the maintenance of healthy aquatic ecosystems.},
}
@article {pmid39264951,
year = {2024},
author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB},
title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012445},
pmid = {39264951},
issn = {1553-7358},
mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; },
abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.},
}
@article {pmid39264914,
year = {2024},
author = {Zhang, K and Cao, Y and Guo, X and Kong, F and Sun, H and Jing, T and Zhan, Y and Qi, F},
title = {Comparative transcriptome analysis of differentially expressed genes and pathways in male and female flowers of Fraxinus mandshurica.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0308013},
pmid = {39264914},
issn = {1932-6203},
mesh = {*Flowers/genetics/metabolism/growth &amp; development ; *Gene Expression Regulation, Plant ; *Gene Expression Profiling ; *Fraxinus/genetics ; *Transcriptome ; Signal Transduction/genetics ; Plant Proteins/genetics/metabolism ; Gene Ontology ; Genes, Plant ; },
abstract = {Fraxinus mandshurica Rupr. (F. mandshurica) is a dioecious tree species with important ecological and application values. To delve deeper into the regulatory pathways and genes responsible for male and female flowers in F. mandshurica, we conducted transcriptome sequencing on male and female flowers at four distinct stages. The analysis revealed that the female database generated 38,319,967 reads while the male database generated 43,320,907 reads, resulting in 2930 differentially expressed genes with 1441 were up-regulated and 1489 down-regulated in males compared to females. Following an analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), four distinct pathways (hormone signal transduction, energy metabolism, flavonoid biosynthesis, and photoperiod) linked to female and male flowers were identified. Subsequently, qRT-PCR verification revealed that FmAUX/IAA, FmEIN3, and FmA-ARR genes in hormone signal transduction pathway are related to female flower development. Meanwhile, FmABF genes in hormone signal transduction pathway, FmGS and FmGDH genes in energy metabolism pathway, FmFLS genes in flavonoid biosynthesis pathway, and FmCaM, FmCRY, and FmPKA genes in photoperiod pathway are related to male flower development. This study was the first to analyze the transcriptome of male and female flowers of F. mandshurica, providing a reference for the developmental pathways and gene expression levels of male and female plants.},
}
@article {pmid39264239,
year = {2024},
author = {Silva, M and Capps, S and London, JK},
title = {Community-Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants.},
journal = {Birth defects research},
volume = {116},
number = {9},
pages = {e2395},
pmid = {39264239},
issn = {2472-1727},
support = {P30 ES023513/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Environmental Pollutants ; *Databases, Factual ; Risk Assessment/methods ; Environmental Exposure/adverse effects ; United States ; United States Environmental Protection Agency ; Pesticides/adverse effects/toxicity ; },
abstract = {BACKGROUND: The paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR).<br><br>METHODS: CompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center.<br><br>RESULTS: Case #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation.<br><br>CONCLUSIONS: These resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.},
}
@article {pmid39263387,
year = {2024},
author = {Deeleman-Reinhold, CL and Addink, W and Miller, JA},
title = {The genera Chrysillaand Phintelloidesrevisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e129438},
pmid = {39263387},
issn = {1314-2828},
abstract = {BACKGROUND: Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren.<br><br>NEW INFORMATION: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb &amp; Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam &amp; Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as inChrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla andPhintelloidesare redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Pr&#xf3;szy&#x144;ski &amp; Deeleman-Reinhold, 2010 are described. The male and female ofChrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from PhintellaB&#xf6;senberg &amp; Strand, 1906, SilerSimon, 1889, Phintelloides Kanesharatnam &amp; Benjamin, 2019 andProszynskiaKanesharatnam &amp; Benjamin, 2019. The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam &amp; Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloidesversicolor (C. L. Koch, 1846) are redescribed.Phintelloidesmunita(B&#xf6;senberg &amp; Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized withP.versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.},
}
@article {pmid39262445,
year = {2023},
author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, &#xc5;J and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA},
title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {926},
pmid = {39262445},
issn = {2046-1402},
support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; },
abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.<br><br>METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.<br><br>RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.<br><br>CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.},
}
@article {pmid39257810,
year = {2024},
author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ},
title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39257810},
issn = {2692-8205},
support = {P51 OD011092/OD/NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R01 HG010333/HG/NHGRI NIH HHS/United States ; },
abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a "perfect storm" of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.},
}
@article {pmid39257624,
year = {2024},
author = {Lohse, K and Vila, R and Hayward, A and , and , and , and , and , },
title = {The genome sequence of the Lulworth Skipper, Thymelicus acteon (Rottemburg, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {266},
pmid = {39257624},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Thymelicus acteon (the Lulworth Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 537.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,813 protein-coding genes.},
}
@article {pmid39257623,
year = {2024},
author = {Boyes, D and Januszczak, I and Lees, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {96},
pmid = {39257623},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Lomographa bimaculata (the White-pinion Spotted; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 554.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.66 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,749 protein coding genes.},
}
@article {pmid39257281,
year = {2024},
author = {Calabrese, JM and Schüler, L and Fu, X and Gawel, E and Zozmann, H and Bumberger, J and Quaas, M and Wolf, G and Attinger, S},
title = {A novel, scenario-based approach to comparing non-pharmaceutical intervention strategies across nations.},
journal = {Journal of the Royal Society, Interface},
volume = {21},
number = {218},
pages = {20240301},
pmid = {39257281},
issn = {1742-5662},
support = {//Helmholtz-Gemeinschaft/ ; //Bundesministerium f&#xfc;r Bildung und Forschung/ ; //S&#xe4;chsisches Staatsministerium f&#xfc;r Wissenschaft und Kunst/ ; },
mesh = {*COVID-19/epidemiology/prevention &amp; control ; Humans ; New Zealand/epidemiology ; Switzerland/epidemiology ; Germany/epidemiology ; *SARS-CoV-2 ; Pandemics/prevention &amp; control ; },
abstract = {Comparing COVID-19 response strategies across nations is a key step in preparing for future pandemics. Conventional comparisons, which rank individual non-pharmaceutical intervention (NPI) effects, are limited by: (i) a focus on epidemiological outcomes; (ii) NPIs typically being applied as packages of interventions; and (iii) different political, economic and social conditions among nations. Here, we develop a coupled epidemiological-behavioural-macroeconomic model that can transfer NPI effects from a reference nation to a focal nation. This approach quantifies epidemiological, behavioural and economic outcomes while accounting for both packaged NPIs and differing conditions among nations. As a first proof of concept, we take Germany as our focal nation during Spring 2020, and New Zealand and Switzerland as reference nations with contrasting NPI strategies. Our results suggest that, while New Zealand's more aggressive strategy would have yielded modest epidemiological gains in Germany, it would have resulted in substantially higher economic costs while dramatically reducing social contacts. In contrast, Switzerland's more lenient strategy would have prolonged the first wave in Germany, but would also have increased relative costs. More generally, these findings indicate that our approach can provide novel, multifaceted insights on the efficacy of pandemic response strategies, and therefore merits further exploration and development.},
}
@article {pmid39255632,
year = {2024},
author = {Amenu, K and Daborn, C and Huntington, B and Knight-Jones, T and Rushton, J and Grace, D},
title = {Prioritization, resource allocation and utilization of decision support tools in animal health: Results of qualitative interviews with experts.},
journal = {Preventive veterinary medicine},
volume = {233},
number = {},
pages = {106333},
doi = {10.1016/j.prevetmed.2024.106333},
pmid = {39255632},
issn = {1873-1716},
mesh = {Animals ; *Resource Allocation ; Decision Support Techniques ; Health Priorities ; Decision Making ; Animal Husbandry/methods ; Surveys and Questionnaires ; },
abstract = {A follow up to an online questionnaire survey (in a kind of a sequential study design), qualitative assessment was made on the views of selected animal health experts on disease prioritization methods, resource allocation and use of decision-support tools. This was done through in-depth interviews with experts working for national or international organizations and sectors. A semi-structured question guide was formulated based on the information generated in the online questionnaire and a systematic content analysis of animal and human health manuals for disease prioritization and resource allocation. In-depth, one-on-one, online interviews on the process of disease prioritization, animal health decision-making, types of prioritization tools and aspects of improvements in the tools were conducted during March and April 2022 with 20 expert informants. Prioritization approaches reported by experts were either single criterion-based or multiple criteria-based. Experts appreciated the single-criterion-based approach (quantitative) for its objectivity in contrast to multicriteria prioritization approaches which were criticized for their subjectivity. Interviews with the experts revealed a perceived lack of quality and reliable data to inform disease prioritization, especially in smallholder livestock production systems. It was found that outputs of disease prioritization exercises do not generally directly influence resource allocation in animal health and highlighted the paucity of funding for animal health compared to other agricultural sectors. The experts considered that the available decision-support tools in animal health need improvement in terms of data visualization for interpretation, management decision making and advocacy. Further recommendations include minimizing subjective biases by increasing the availability and quality of data and improving the translation of disease prioritization outputs into actions and the resources to deliver those actions. DATA AVAILABILITY STATEMENT: The data can be obtained from the corresponding author upon request.},
}
@article {pmid39255272,
year = {2024},
author = {Sylla, A and Chevillon, C and Djidjiou-Demasse, R and Seydi, O and Campos, CAV and Dogbe, M and Fast, KM and Pechal, JL and Rakestraw, A and Scott, ME and Sandel, MW and Jordan, H and Benbow, ME and Guégan, JF},
title = {Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012435},
pmid = {39255272},
issn = {1553-7358},
mesh = {Humans ; *Ecosystem ; Mycobacterium ulcerans/pathogenicity ; Buruli Ulcer/transmission/microbiology ; Models, Biological ; Computational Biology ; Animals ; },
abstract = {Pathogens such as bacteria, fungi and viruses are important components of soil and aquatic communities, where they can benefit from decaying and living organic matter, and may opportunistically infect human and animal hosts. One-third of human infectious diseases is constituted by sapronotic disease agents that are natural inhabitants of soil or aquatic ecosystems. They are capable of existing and reproducing in the environment outside of the host for extended periods of time. However, as ecological research on sapronosis is infrequent and epidemiological models are even rarer, very little information is currently available. Their importance is overlooked in medical and veterinary research, as well as the relationships between free environmental forms and those that are pathogenic. Here, using dynamical models in realistic aquatic metacommunity systems, we analyze sapronosis transmission, using the human pathogen Mycobacterium ulcerans that is responsible for Buruli ulcer. We show that the persistence of bacilli in aquatic ecosystems is driven by a seasonal upstream supply, and that the attachment and development of cells to aquatic living forms is essential for such pathogen persistence and population dynamics. Our work constitutes the first set of metacommunity models of sapronotic disease transmission, and is highly flexible for adaptation to other types of sapronosis. The importance of sapronotic agents on animal and human disease burden needs better understanding and new models of sapronosis disease ecology to guide the management and prevention of this important group of pathogens.},
}
@article {pmid39255143,
year = {2024},
author = {Jiang, W and Windl, M and Tag, B and Sarsenbayeva, Z and Mayer, S},
title = {An Immersive and Interactive VR Dataset to Elicit Emotions.},
journal = {IEEE transactions on visualization and computer graphics},
volume = {30},
number = {11},
pages = {7343-7353},
doi = {10.1109/TVCG.2024.3456202},
pmid = {39255143},
issn = {1941-0506},
mesh = {Humans ; *Emotions/physiology ; *Virtual Reality ; Female ; Male ; *Computer Graphics ; Adult ; Young Adult ; User-Computer Interface ; Databases, Factual ; Video Recording ; },
abstract = {Images and videos are widely used to elicit emotions; however, their visual appeal differs from real-world experiences. With virtual reality becoming more realistic, immersive, and interactive, we envision virtual environments to elicit emotions effectively, rapidly, and with high ecological validity. This work presents the first interactive virtual reality dataset to elicit emotions. We created five interactive virtual environments based on corresponding validated 360° videos and validated their effectiveness with 160 participants. Our results show that our virtual environments successfully elicit targeted emotions. Compared with the existing methods using images or videos, our dataset allows virtual reality researchers and practitioners to integrate their designs effectively with emotion elicitation settings in an immersive and interactive way.},
}
@article {pmid39253482,
year = {2024},
author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V},
title = {Expanding the toolbox: Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.12.05.570296},
pmid = {39253482},
issn = {2692-8205},
abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally-produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered twelve previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella . Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e. Acinetobacter baumannii or Pseudomonas aeruginosa , providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.},
}
@article {pmid39250076,
year = {2024},
author = {Zancolli, G and von Reumont, BM and Anderluh, G and Caliskan, F and Chiusano, ML and Fröhlich, J and Hapeshi, E and Hempel, BF and Ikonomopoulou, MP and Jungo, F and Marchot, P and de Farias, TM and Modica, MV and Moran, Y and Nalbantsoy, A and Procházka, J and Tarallo, A and Tonello, F and Vitorino, R and Zammit, ML and Antunes, A},
title = {Web of venom: exploration of big data resources in animal toxin research.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {39250076},
issn = {2047-217X},
support = {//European Cooperation in Science and Technology/ ; //Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Animals ; *Venoms ; *Internet ; *Computational Biology/methods ; *Big Data ; Databases, Factual ; },
abstract = {Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.},
}
@article {pmid39244927,
year = {2024},
author = {Ibrahim, AS and Kuuire, V and Kepe, T},
title = {On mapping urban community resilience: Land use vulnerability, coping and adaptive strategies in Ghana.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122426},
doi = {10.1016/j.jenvman.2024.122426},
pmid = {39244927},
issn = {1095-8630},
mesh = {Ghana ; *Floods ; Humans ; *Cities ; Climate Change ; Urban Population ; Geographic Information Systems ; },
abstract = {Cities across the globe are prioritizing resilience in the wake of increasing climate change-related disasters. About 44% of these disasters are floods and their manifestation in cities is more pronounced, threatening urban social, ecological, and economic systems. This study draws on community resilience and participatory GIS, to examine land use vulnerability to flooding and local coping and adaptive strategies to achieve resilience. Using Ghana as a case study, the results show that participatory mapping offers community resilience benefits by providing context to community resilience challenges and potentials, enabling a deeper understanding of socio-environmental coupling that contributes to flood vulnerability and builds on community adaptive strategies through harnessing local community knowledge. We identified that topography, poor drainage and road network, rainfall variability, residents' land use practices, and land use planning conundrum drive disparities in land use vulnerability to flooding. Participants underscored the necessity of critical urban infrastructure in facilitating community adaptability to floods. The findings indicate that socio-spatial inequities threaten urban community resilience, especially in increasingly cosmopolitan urban contexts, by putting the marginalized urban population in a more vulnerable position. We recommend the prioritization of recognitional equity in community resilience planning efforts to allow for the targeting of resilient interventions that reflect and respect social differentiation in the urban environment so that outcomes will not exacerbate or generate new urban socio-spatial inequalities.},
}
@article {pmid39242865,
year = {2023},
author = {Karakulak, A and Tepe, B and Dimitrova, R and Abdelrahman, M and Akaliyski, P and Alaseel, R and Alkamali, YA and Amin, A and Lizarzaburu Aguinaga, DA and Andres, A and Aruta, JJBR and Assiotis, M and Avanesyan, H and Ayub, N and Bacikova-Sleskova, M and Baikanova, R and Bakkar, B and Bartoluci, S and Benitez, D and Bodnar, I and Bolatov, A and Borchet, J and Bosnar, K and Broche-Pérez, Y and Buzea, C and Cassibba, R and Carbonell, MM and Chen, BB and Dimitrovska, GR and Công Doanh, D and Dominguez Espinosa, ADC and Edine, WG and Ferenczi, N and Fernández-Morales, R and Gaete, J and Gan, Y and Giolo, S and Giordani, RCF and Friehs, MT and Gindi, S and Gjoneska, B and Godoy, JC and Del Pilar Grazioso, M and Hancheva, C and Hapunda, G and Hihara, S and Husain, MS and Islam, MS and Janovská, A and Javakhishvili, N and Jovanović, V and Kabir, RS and Abdul Kadir, NB and Karl, J and Katović, D and Kauyzbay, Z and Kawashima, TD and Kazmierczak, M and Khanna, R and Khosla, M and Klicperová-Baker, M and Kozina, A and Krauss, SE and Landabur, R and Lefringhausen, K and Lewandowska-Walter, A and Liang, YH and Makashvili, A and Malik, S and Manrique-Millones, D and Mastrotheodoros, S and McGrath, B and Mechili, EA and Mejía, M and Mhizha, S and Michalek-Kwiecien, J and Miconi, D and Mohsen, F and Moreta-Herrera, R and Muhl, C and Muradyan, M and Musso, P and Naterer, A and Nemat, A and Neto, F and Neto, J and Palacio, LMA and Okati-Aliabad, H and Orellana, CI and Orellana, LM and Mishra, SK and Park, J and Pavlova, I and Peralta, E and Petrytsa, P and Pišot, S and Prot, F and Rasia, J and Rivera, R and Riyanti, BPD and Samekin, A and Seisembekov, T and Serapinas, D and Silletti, F and Sharma, P and Shukla, S and Skrzypińska, K and Šolcová, IP and Solomontos-Kountouri, O and Stanciu, A and Stefenel, D and Steinmetz, LCL and Stogianni, M and Stuart, J and Sudarnoto, LF and Sugimura, K and Sultana, S and Suryani, AO and Tair, E and Tavitian-Elmadjan, L and Thome, LD and Uka, F and Valickienė, RP and Walter, B and Wendt, GW and Yang, PJ and Yıldırım, E and Yu, Y and Yunes, MAM and Zanoni da Silva, M and Rudnev, M},
title = {Trust in government moderates the association between fear of COVID-19 as well as empathic concern and preventive behaviour.},
journal = {Communications psychology},
volume = {1},
number = {1},
pages = {43},
pmid = {39242865},
issn = {2731-9121},
abstract = {With the COVID-19 pandemic, behavioural scientists aimed to illuminate reasons why people comply with (or not) large-scale cooperative activities. Here we investigated the motives that underlie support for COVID-19 preventive behaviours in a sample of 12,758 individuals from 34 countries. We hypothesized that the associations of empathic prosocial concern and fear of disease with support towards preventive COVID-19 behaviours would be moderated by trust in the government. Results suggest that the association between fear of disease and support for COVID-19 preventive behaviours was strongest when trust in the government was weak (both at individual- and country-level). Conversely, the association with empathic prosocial concern was strongest when trust in the government was high, but this moderation was only found at individual-level scores of governmental trust. We discuss how motivations may be shaped by socio-cultural context, and outline how findings may contribute to a better understanding of collective action during global crises.},
}
@article {pmid39242702,
year = {2023},
author = {Santangeli, A and Haukka, A and Morris, W and Arkkila, S and Delhey, K and Kempenaers, B and Valcu, M and Dale, J and Lehikoinen, A and Mammola, S},
title = {What drives our aesthetic attraction to birds?.},
journal = {npj biodiversity},
volume = {2},
number = {1},
pages = {20},
pmid = {39242702},
issn = {2731-4243},
abstract = {In the Anthropocene, the era when the imprint of humans on nature is pervasive across the planet, it is of utmost importance to understand human relationships with other species. The aesthetics of nature, and of species, is one of the values that plays a role in shaping human-nature relationships. Birds are ubiquitous across the world. The beauty of birds exerts a powerful tug on human emotions, and bird-rich areas attract scores of eco-tourists. People naturally find some birds more beautiful or interesting than others, but we currently lack a global understanding of the specifics of what makes a species aesthetically attractive. Here, we used a global citizen-science database on bird attractiveness covering nearly all extant bird species, to show that there are specific visual features that drive our aesthetic appeal for some bird species over others. First, our aesthetic attraction is highest for smaller birds with specific, vivid colors (e.g., blue and red, and departing from brown-grey) and extreme ornaments (a long crest or tail). Second, our aesthetic attraction is highest for species with broad ranges, possibly because such species may be more familiar to us. The features that make us attracted to a particular bird strongly align with broad human visual aesthetic preferences in modern society. Unveiling the visual features underpinning our aesthetic attraction to birds is a critical step towards optimizing conservation (e.g., via conservation marketing) and education campaigns, and leverage the cultural ecosystem service potential of birds.},
}
@article {pmid39240878,
year = {2024},
author = {Shipley, ON and Dabrowski, AJ and Bowen, GJ and Hayden, B and Pauli, JN and Jordan, C and Anderson, L and Bailey, A and Bataille, CP and Cicero, C and Close, HG and Cook, C and Cook, JA and Desai, AR and Evaristo, J and Filley, TR and France, CAM and Jackson, AL and Kim, SL and Kopf, S and Loisel, J and Manlick, PJ and McFarlin, JM and McMeans, BC and O'Connell, TC and Pilaar Birch, SE and Putman, AL and Semmens, BX and Stantis, C and Stricker, CA and Szejner, P and Trammell, TLE and Uhen, MD and Weintraub-Leff, S and Wooller, MJ and Williams, JW and Yarnes, CT and Vander Zanden, HB and Newsome, SD},
title = {Design, development, and implementation of IsoBank: A centralized repository for isotopic data.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0295662},
pmid = {39240878},
issn = {1932-6203},
mesh = {*Databases, Factual ; *Metadata ; Isotopes ; Internet ; },
abstract = {Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank (www.isobank.org), a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.},
}
@article {pmid39239169,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Elephant Hawk-moth, Deilephila elpenor (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {104},
pmid = {39239169},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Deilephila elpenor (the Elephant Hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 414.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,748 protein coding genes.},
}
@article {pmid39235751,
year = {2025},
author = {Lemée, P and Bridier, A},
title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {289-309},
pmid = {39235751},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; },
abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.},
}
@article {pmid39233902,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Green Silver-lines, Pseudoips prasinana (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {117},
pmid = {39233902},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Pseudoips prasinana (the Green Silver-lines; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 1,125.7 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,065 protein coding genes.},
}
@article {pmid39233899,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {31},
pmid = {39233899},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Callimorpha dominula (the Scarlet Tiger moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 658.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,234 protein coding genes.},
}
@article {pmid39233418,
year = {2024},
author = {Li, X and Zhang, LY and Wu, C},
title = {Vegetation changes and influencing factors in different watersheds of Henan Province based on GEE and geographic detectors.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {7},
pages = {1887-1896},
doi = {10.13287/j.1001-9332.202407.021},
pmid = {39233418},
issn = {1001-9332},
mesh = {China ; *Rivers ; *Ecosystem ; *Environmental Monitoring/methods ; Conservation of Natural Resources ; Plant Development ; Geographic Information Systems ; Plants ; },
abstract = {Clarifying vegetation changes and the driving factors can provide references for ecological restoration and sustainable social development. We analyzed vegetation distribution and trend changes in Henan Province and its basin zoning (Haihe River basin zoning, Yellow River basin zoning, Huaihe River basin zoning, Yangtze River basin zoning), with fractional vegetation cover data from 2000 to 2020 based on the Google Earth Engine platform, and by combining Theil-Sen Median trend analysis, Mann-Kendall test, and Hurst index. We also utilized factor detection and factor interaction to explore the individual and mutual influences of natural and anthropogenic factors on vegetation at different scales. The results showed that the fractional vegetation cover (FVC) in Henan Province exhibited a distribution pattern of higher coverage in the south and lower in the north during the study period, predominantly characterized by moderate to high vegetation coverage. The Yangtze River basin zoning had the highest coverage. FVC in Henan Province and its zoning exhibited a consistent pattern of fluctuating upward trends, with all areas showing significant improvement. Particularly, the Yangtze River basin zoning had the largest area of improvement. According to the Hurst index, apart from the possibility of continued improvement in the Huaihe River basin zoning, other zoning would be likely to shift from improvement to degradation in the future. Vegetation changes in Henan Province and its zoning were the result of combined effects of anthropogenic and natural factors, with the influence of these factors changing over time and the dominant factors varying by region. Anthropogenic factors such as land use/cover type and nighttime lighting had a stronger impact on vegetation than natural factors like elevation, slope, and annual mean low temperature. The interaction between factors, particularly between anthropogenic and natural factors, exhibited a nonlinear enhancing pattern.},
}
@article {pmid39233286,
year = {2024},
author = {Long, XB and Yao, CR and Li, SY and Zhang, JG and Lu, ZJ and Ma, DD and Jiang, YX and Ying, GG and Shi, WJ},
title = {Multiomics analysis reveal the impact of 17α-Ethinylestradiol on mortality in juvenile zebrafish.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {286},
number = {},
pages = {110027},
doi = {10.1016/j.cbpc.2024.110027},
pmid = {39233286},
issn = {1532-0456},
mesh = {Animals ; *Zebrafish ; *Ethinyl Estradiol/toxicity ; *Water Pollutants, Chemical/toxicity ; Endocrine Disruptors/toxicity ; Transcriptome/drug effects ; Multiomics ; },
abstract = {17α-Ethinylestradiol (EE2) is known for its endocrine-disrupting effects on embryonic and adult fish. However, its impact on juvenile zebrafish has not been well established. In this study, juvenile zebrafish were exposed to EE2 at concentrations of 5 ng/L (low dose, L), 10 ng/L (medium dose, M), and 50 ng/L (high dose, H) from 21 days post-fertilization (dpf) to 49 dpf. We assessed their growth, development, behavior, transcriptome, and metabolome. The findings showed that the survival rate in the EE2-H group was 66.8 %, with all surviving fish displaying stunted growth and swollen, transparent abdomens by 49 dpf. Moreover, severe organ deformities were observed in the gills, kidneys, intestines, and heart of fish in both the EE2-H and EE2-M groups. Co-expression analysis of mRNA and lncRNA revealed that EE2 downregulated the transcription of key genes involved in the cell cycle, DNA replication, and Fanconi anemia signaling pathways. Additionally, metabolomic analysis indicated that EE2 influenced metabolism and development-related signaling pathways. These pathways were also significantly identified based on the genes regulated by lncRNA. Consequently, EE2 induced organ deformities and mortality in juvenile zebrafish by disrupting signaling pathways associated with development and metabolism. The results of this study offer new mechanistic insights into the adverse effects of EE2 on juvenile zebrafish based on multiomics analysis. The juvenile zebrafish are highly sensitive to EE2 exposure, which is not limited to adult and embryonic stages. It is a potential model for studying developmental toxicity.},
}
@article {pmid39233066,
year = {2024},
author = {Wen, J and Chuai, X and Xiang, A and Liu, Y and Wang, T and Luo, Y and Miao, L and Zhang, L and Li, J and Zhao, R},
title = {Re-identifying farmland carbon neutrality gap under a new carbon counting and the framework of regional interactions in China.},
journal = {The Science of the total environment},
volume = {952},
number = {},
pages = {175996},
doi = {10.1016/j.scitotenv.2024.175996},
pmid = {39233066},
issn = {1879-1026},
abstract = {The farmland ecosystem, with its numerous material cycles and energy flows, is an important part of the carbon cycle in terrestrial ecosystems. Focusing on the carbon neutrality of farmland is meaningful for mitigating global warming and serving national low-carbon strategies. This study enriches the carbon accounting items of farmland and establishes a new research framework to check the carbon neutrality of farmland from the aspect of regional interactions and, subsequently, the inequality among China's provinces. The results revealed that there is still a great gap in the capability of China[']s farmland to reach carbon neutrality, with a gap value of up to 10,503 × 10[4] t C. All of the provinces presented net carbon emissions, and the per unit area carbon neutrality gaps showed spatial regularity decreasing from the coastal regions to the inland areas. Anthropogenic carbon emissions on farmland played a dominant role compared with soil organic carbon. Five provinces had reduced interior-regional carbon emissions through grain trade, and the amounts were especially high for developed regions, such as Guangdong, Zhejiang, Beijing, Shanghai and Jiangsu. Sixteen provinces gained external carbon emissions through trade; these were the less developed regions located mainly in the north, such as Inner Mongolia, Hebei, Jilin, Heilongjiang and Xinjiang. Under regional inequality, 15 provinces added to the net amount of the carbon emissions generated in external regions, with China's megacities adding the highest percentage, especially Beijing, with 389.95 % compared with its original emissions. Inequality showed that most provinces had a moderate status. Sichuan and Hunan experienced weak advantages, and six provinces had disadvantages. Therefore, constructing compensation and trade-based rights and responsibilities traceability mechanisms is important.},
}
@article {pmid39230451,
year = {2024},
author = {Hendrix, JG and Robitaille, AL and Kusch, JM and Webber, QMR and Vander Wal, E},
title = {Faithful pals and familiar locales: differentiating social and spatial site fidelity during reproduction.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1912},
pages = {20220525},
pmid = {39230451},
issn = {1471-2970},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Female ; *Reproduction ; *Reindeer/physiology ; Newfoundland and Labrador ; Social Behavior ; Geographic Information Systems ; },
abstract = {Site fidelity-the tendency to reuse familiar spaces-is expected to improve fitness. Familiarity with the local environment is particularly crucial when resource demands or predation risk are high. Consequently, site fidelity often peaks during reproduction when energetic costs are high and offspring are vulnerable. For many species, the environment they experience is not solely a function of geography but also of the social environment. Social fidelity, the selection for familiar social environments, could constitute an independent or parallel strategy to spatial fidelity when considering behaviour at the spatial-social interface. Using global positioning system locations from caribou across Newfoundland, we tested whether females selected calving sites based on proximity to familiar conspecifics, in addition to geographical (spatial) fidelity. These strategies were synergistic, not alternative, and correlated across the population but more variable within individuals. We also tested whether either form of fidelity affected reproductive success. We failed to detect an effect of spatial or social fidelity on reproductive success in this population. Nevertheless, given the association between social and spatial fidelity and the demonstrated fitness consequences of site fidelity in other systems, familiar conspecifics and the potential benefits these social partners provide may be an underappreciated component driving site fidelity.This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.},
}
@article {pmid39229001,
year = {2024},
author = {Obbard, DJ and , and , and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Drosophila limbata von Roser 1840.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {365},
pmid = {39229001},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Drosophila limbata (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 233.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.09 kilobases in length.},
}
@article {pmid39226337,
year = {2024},
author = {Rahman, AU and Tikhonov, G and Oksanen, J and Rossi, T and Ovaskainen, O},
title = {Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011914},
pmid = {39226337},
issn = {1553-7358},
mesh = {*Algorithms ; *Computational Biology/methods ; *Software ; Models, Biological ; Machine Learning ; Computer Graphics ; Models, Statistical ; Humans ; },
abstract = {Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging. In this study, we aim to enhance JSDM scalability by leveraging high-performance computing (HPC) resources for an existing fitting method. Our work focuses on the Hmsc R-package, a widely used JSDM framework that supports the integration of various dataset types into a single comprehensive model. We developed a GPU-compatible implementation of its model-fitting algorithm using Python and the TensorFlow library. Despite these changes, our enhanced framework retains the original user interface of the Hmsc R-package. We evaluated the performance of the proposed implementation across various model configurations and dataset sizes. Our results show a significant increase in model fitting speed for most models compared to the baseline Hmsc R-package. For the largest datasets, we achieved speed-ups of over 1000 times, demonstrating the substantial potential of GPU porting for previously CPU-bound JSDM software. This advancement opens promising opportunities for better utilizing the rapidly accumulating new biodiversity data resources for inference and prediction.},
}
@article {pmid39225619,
year = {2024},
author = {Liu, Z and Sun, Y and Li, Y and Ma, A and Willaims, NF and Jahanbahkshi, S and Hoyd, R and Wang, X and Zhang, S and Zhu, J and Xu, D and Spakowicz, D and Ma, Q and Liu, B},
title = {An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {11},
number = {41},
pages = {e2403393},
pmid = {39225619},
issn = {2198-3844},
support = {2020YFA0712400//National Key Research and Development Program of China/ ; 62272270//National Nature Science Foundation of China/ ; 11931008//National Nature Science Foundation of China/ ; ZR2023JQ002//Shandong Provincial Natural Science Foundation for Distinguished Young Scholars/ ; },
mesh = {Mice ; *Microbiota ; Animals ; *Neoplasms/microbiology ; *Neural Networks, Computer ; Humans ; Reproducibility of Results ; Disease Models, Animal ; },
abstract = {Microbes are extensively present among various cancer tissues and play critical roles in carcinogenesis and treatment responses. However, the underlying relationships between intratumoral microbes and tumors remain poorly understood. Here, a MIcrobial Cancer-association Analysis using a Heterogeneous graph transformer (MICAH) to identify intratumoral cancer-associated microbial communities is presented. MICAH integrates metabolic and phylogenetic relationships among microbes into a heterogeneous graph representation. It uses a graph transformer to holistically capture relationships between intratumoral microbes and cancer tissues, which improves the explainability of the associations between identified microbial communities and cancers. MICAH is applied to intratumoral bacterial data across 5 cancer types and 5 fungi datasets, and its generalizability and reproducibility are demonstrated. After experimentally testing a representative observation using a mouse model of tumor-microbe-immune interactions, a result consistent with MICAH's identified relationship is observed. Source tracking analysis reveals that the primary known contributor to a cancer-associated microbial community is the organs affected by the type of cancer. Overall, this graph neural network framework refines the number of microbes that can be used for follow-up experimental validation from thousands to tens, thereby helping to accelerate the understanding of the relationship between tumors and intratumoral microbiomes.},
}
@article {pmid39224879,
year = {2023},
author = {Boyes, D and Mulley, JF and , and , and , and , and , and , },
title = {The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {441},
pmid = {39224879},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hemistola chrysoprasaria (the Small Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 438.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,512 protein coding genes.},
}
@article {pmid39224768,
year = {2024},
author = {Jentoft, S and Tørresen, OK and Tooming-Klunderud, A and Skage, M and Kollias, S and Jakobsen, KS and , and , and , and , and , },
title = {The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {189},
pmid = {39224768},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.},
}
@article {pmid39224703,
year = {2024},
author = {Shi, Y and Zhang, W and Li, L and Wu, W and Li, M and Xiao, K and Wang, K and Sheng, Z and Xie, F and Wang, X and Shi, X and Tong, Y and Xie, L},
title = {Evaluation of phage-based decontamination in respiratory intensive care unit environments using ddPCR and 16S rRNA targeted sequencing techniques.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1442062},
pmid = {39224703},
issn = {2235-2988},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Klebsiella pneumoniae/virology/genetics ; *Intensive Care Units ; *Decontamination/methods ; *Bacteriophages/genetics ; Humans ; Polymerase Chain Reaction/methods ; Cross Infection/prevention &amp; control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention &amp; control/microbiology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important.<br><br>METHODS: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity.<br><br>RESULTS: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance.<br><br>DISCUSSION: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control.},
}
@article {pmid39222768,
year = {2024},
author = {Yushin, N and Jakhu, R and Chaligava, O and Grozdov, D and Zinicovscaia, I},
title = {Evaluation of the potentially toxic elements and radionuclides in the soil sample of Novaya Zemlya in the Arctic Circle.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124871},
doi = {10.1016/j.envpol.2024.124871},
pmid = {39222768},
issn = {1873-6424},
mesh = {Arctic Regions ; *Soil/chemistry ; Russia ; Environmental Monitoring/methods ; Soil Pollutants/analysis ; Thorium/analysis ; Cesium Radioisotopes/analysis ; Soil Pollutants, Radioactive/analysis ; Radiation Monitoring/methods ; Animals ; Birds ; Radioisotopes/analysis ; Radium ; },
abstract = {The study presented here elucidate the concentrations of radionuclides and potentially toxic elements in the soil samples around the Novaya Zemlya in the Russian Arctic zone, determined using HPGe gamma spectrometry, inductively coupled plasma optical emission spectrometry and direct mercury analyzer. The average detected concentrations for [226]Ra, [232]Th, [40]K, [235]U and [137]Cs were 36.40, 46.06, 768, 2.06 and 4.71 Bq/kg, respectively. At many sampling sites, the concentrations of potentially toxic elements (Zn, Cu, Pb, Cd, Ni, and Cr) were higher than the natural levels. Positive Matrix Factorization analysis revealed the contribution of oil dumps (32%), natural sources (16%), bird colonies (32%) and atmospheric deposition (20%) for elevated elements content. In the case of radionuclides, the natural occurring contamination (38%) was primary source followed by dumped material (32%) and bird colonies (30%). The radiological risk from radionuclides was relatively high, yet still under permissible levels. For potentially toxic elements, Fe was predominant non-carcinogenic pollutant and Ni emerged as major carcinogenic contaminant. Keeping in view the high content of some elements, future studies are required to keep the human and ecological risk low, and to establish scientific grounds for the contribution of settled bird species. The findings of the study advance the present knowledge about the contamination of the study area and lays the path for further effort.},
}
@article {pmid39222062,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: coverage-based analysis for identification of microbiome.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
pmid = {39222062},
issn = {1477-4054},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid39222055,
year = {2024},
author = {Xu, C and Wang, JC and Sun, L and Zhuang, LH and Guo, ZJ and Ding, QS and Ma, DN and Song, LY and Li, J and Tang, HC and Zhu, XY and Zheng, HL},
title = {Genome-Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi-Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves.},
journal = {Plant, cell &amp; environment},
volume = {47},
number = {12},
pages = {5498-5510},
doi = {10.1111/pce.15132},
pmid = {39222055},
issn = {1365-3040},
support = {//This study was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581) and&#xa0;the National Key Research and Development Program of China (2017YFC0506102)./ ; },
mesh = {*Plant Leaves/genetics/metabolism ; *Genome-Wide Association Study ; *Plant Proteins/genetics/metabolism ; Multigene Family ; RNA Editing/genetics ; Rhizophoraceae/genetics/physiology ; Phylogeny ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Genes, Plant ; Genome, Plant ; Multiomics ; },
abstract = {Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of PPR genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove Kandelia obovata, we systematically identified 298 PPR genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point, and so forth. Furthermore, we combined genome-wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential PPR genes associated with propagule leaves colour variations of K. obovata. As a result, we prioritized 16 PPR genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS-type) and Maker00003187 (P-type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (rps14, rpoC1 and rpoC2) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of rps14, rpoC1, and rpoC2 in our previous study and the verification of interaction between Maker00002998 and rps14 transcript using in vitro RNA pull-down assays revealed that Maker00002998 PPR protein might be involved in the post-transcriptional process of chloroplast genes. Our result provides new insights into the roles of PPR genes in the albinism mechanism of K. obovata propagule leaves.},
}
@article {pmid39221663,
year = {2024},
author = {Crawford, AD and Slavin, R and Tabar, M and Radhakrishnan, K and Wang, M and Estrada, A and McGrath, JM},
title = {Methodological approaches in developing and implementing digital health interventions amongst underserved women.},
journal = {Public health nursing (Boston, Mass.)},
volume = {41},
number = {6},
pages = {1612-1621},
doi = {10.1111/phn.13410},
pmid = {39221663},
issn = {1525-1446},
mesh = {Humans ; Female ; *Telemedicine ; Texas ; Vulnerable Populations ; Women's Health ; Medically Underserved Area ; Artificial Intelligence ; Adult ; Mobile Applications ; Digital Health ; },
abstract = {BACKGROUND: Minority populations are utilizing mobile health applications more frequently to access health information. One group that may benefit from using mHealth technology is underserved women, specifically those on community supervision.<br><br>OBJECTIVE: Discuss methodological approaches for navigating digital health strategies to address underserved women's health disparities.<br><br>Using an intersectional lens, we identified strategies for conducting research using digital health technology and artificial intelligence amongst the underserved, particularly those with community supervision.<br><br>We explore (1) methodological approaches that combine traditional research methods with precision medicine, digital phenotyping, and ecological momentary assessment; (2) implications for artificial intelligence; and (3) ethical considerations with data collection, storage, and engagement.<br><br>DISCUSSION: Researchers must address gendered differences related to health, social, and economic disparities concurrently with an unwavering focus on the protection of human subjects when addressing the unique needs of underserved women while utilizing digital health methodologies.<br><br>PUBLIC CONTRIBUTION: Women on community supervision in South Central Texas helped inform the design of JUN, the mHealth app we reported in the case exemplar. JUN is named after the Junonia shell, a native shell to South Texas, which means strength, power, and self-sufficiency, like the participants in our preliminary studies.},
}
@article {pmid39221442,
year = {2024},
author = {Morales, HE and Norris, K and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Groombridge, JJ and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {312},
pmid = {39221442},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Falco punctatus (the Mauritius kestrel; Chordata; Aves; Falconiformes; Falconidae). The genome sequence is 1,279.3 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.},
}
@article {pmid39219129,
year = {2024},
author = {Xie, Z and Hu, D and Jiang, F and Fu, X and Li, R and Zheng, D and Zhao, L and Xu, J and Yuan, X and Bao, Y and Zhou, H and Wang, B and Wang, Q},
title = {Assessment of urban flood resilience based on the socio-ecological composite index model: a case study in Wuhua District, Kunming City, China.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {89},
number = {2},
pages = {252-270},
doi = {10.2166/wst.2023.413},
pmid = {39219129},
issn = {0273-1223},
mesh = {China ; *Floods ; *Cities ; Models, Theoretical ; Geographic Information Systems ; Socioeconomic Factors ; },
abstract = {Global climate change and rapid urbanization have increased the frequency of flooding, making urban flood resilience a critical objective. This article introduces a methodology for assessing urban flood resilience, utilizing a social-ecological synthesis index that integrates geographical and temporal data with Geographic Information System (GIS). The study focuses on ten administrative subdistricts in Wuhua District, Kunming City, China, and selects 18 social-ecological indicators. These indicators, chosen from social and ecological perspectives, are weighted using the entropy weight method to determine their significance in the assessment system. By combining scores for each subdistrict, the study quantifies flood resilience and creates a spatial distribution map using ArcGIS. Key findings reveal that out of the ten administrative subdistricts, five in Wuhua District, particularly in the core urban area of Kunming, demonstrate strong overall flood resilience. Influenced by social-ecological indicators, there is significant spatial differentiation in flood resilience within Wuhua District, with a decreasing trend radiating from the city center to areas farther from the urban core. The research indicates that regions with well-established transportation infrastructure, a wide distribution of government institutions, improved water management facilities, and a substantial population with higher education levels contribute significantly to enhancing urban flood resilience.},
}
@article {pmid39209912,
year = {2024},
author = {Yuan, R and Qu, Q and Lu, Z and Geng, X and Tian, S and Jin, Y and Gong, J and Ye, X and Tang, P and Chen, X},
title = {A chromosome-level genome assembly of the gall maker pest inquiline, Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {944},
pmid = {39209912},
issn = {2052-4463},
support = {32070467//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31920103005//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Chromosomes, Insect ; Genome Size ; *Genome, Insect ; *Hymenoptera/genetics ; Wasps/parasitology ; Datasets as Topic ; },
abstract = {Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae) is an inquiline of gall maker Aiolomorphus rhopaloides Walker (Hymenoptera: Eurytomidae). They are of significant economic significance and predominantly inhabit bamboo forest. So far, only four scaffold-level genomes have been published for the family Torymidae. In this study, we present a high-quality genome assembly of D. aiolomorphi at the chromosome level, achieved through the integration of Nanopore (ONT) long-read, Illumina pair-end DNA short-read, and High-through Chromosome Conformation Capture (Hi-C) sequencing methods. The final assembly was 1,084.56 Mb in genome size, with 1,083.41 Mb (99.89%) assigned to five pseudochromosomes. The scaffold N50 length reached 224.87 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 97.3%. The genome contained 762.12 Mb of repetitive elements, accounting for 70.27% of the total genome size. A total of 18,011 protein-coding genes were predicted, with 17,829 genes being functionally annotated. The high-quality genome assembly of D. aiolomorphi presented in this study will serve as a valuable genomic resource for future research on parasitoid wasps. The results of this study may also contribute to the development of biological control strategies for pest management in bamboo forests, enhancing ecological balance and economic sustainability.},
}
@article {pmid39209853,
year = {2024},
author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H},
title = {Massive expansion of the pig gut virome based on global metagenomic mining.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {76},
pmid = {39209853},
issn = {2055-5008},
mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; },
abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.},
}
@article {pmid39213392,
year = {2024},
author = {Du, Q and Zhang, Z and Yang, W and Zhou, X and Zhou, N and Wu, C and Bao, J},
title = {CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {39213392},
issn = {1758-0463},
support = {31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; 31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; },
mesh = {Humans ; *Databases, Genetic ; *Data Curation/methods ; Genome-Wide Association Study/methods ; Genetic Predisposition to Disease ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CRISPR-Cas Systems ; Disease/genetics ; },
abstract = {The field of understanding the association between genes and diseases is rapidly expanding, making it challenging for researchers to keep up with the influx of new publications and genetic datasets. Fortunately, there are now several regularly updated databases available that focus on cataloging gene-disease relationships. The development of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system has revolutionized the field of gene editing, providing a highly efficient, accurate, and reliable method for exploring gene-disease associations. However, currently, there is no resource specifically dedicated to collecting and integrating the latest experimentally supported gene-disease association data derived from genome-wide CRISPR screening. To address this gap, we have developed the CRISPR-Based Gene-Disease Associations (CBGDA) database, which includes over 200 manually curated gene-disease association data derived from genome-wide CRISPR screening studies. Through CBGDA, users can explore gene-disease association data derived from genome-wide CRISPR screening, gaining insights into the expression patterns of genes in different diseases, associated chemical data, and variant information. This provides a novel perspective on understanding the associations between genes and diseases. What is more, CBGDA integrates data from several other databases and resources, enhancing its comprehensiveness and utility. In summary, CBGDA offers a fresh perspective and comprehensive insights into the research on gene-disease associations. It fills the gap by providing a dedicated resource for accessing up-to-date, experimentally supported gene-disease association data derived from genome-wide CRISPR screening. Database URL: http://cbgda.zhounan.org/main.},
}
@article {pmid39213378,
year = {2024},
author = {Wang, M and Li, Z and Wang, H and Zhao, J and Zhang, Y and Lin, K and Zheng, S and Feng, Y and Zhang, Y and Teng, W and Tong, Y and Zhang, W and Xue, Y and Mao, H and Li, H and Zhang, B and Rasheed, A and Bhavani, S and Liu, C and Ling, HQ and Hu, YQ and Zhang, Y},
title = {A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development.},
journal = {Molecular biology and evolution},
volume = {41},
number = {9},
pages = {},
pmid = {39213378},
issn = {1537-1719},
support = {//National Natural Science Foundation of China/ ; //National Key R&amp;D Program of China/ ; //Yangfan Project of Shanghai Science and Technology Commission/ ; //State Key Laboratory of Genetic Engineering/ ; //State Key Laboratory of Crop Gene Exploration and Utilization in Southwest/ ; //State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/ ; //Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; },
mesh = {*Single-Cell Analysis/methods ; *Polyploidy ; Animals ; Computational Biology/methods ; },
abstract = {Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.},
}
@article {pmid39209112,
year = {2024},
author = {Ji, N and Kumar, A and Joe, W and Kuriyan, R and Sethi, V and Finkelstein, JL and Mehta, S},
title = {Prevalence and Correlates of Double and Triple Burden of Malnutrition Among Children and Adolescents in India: The Comprehensive National Nutrition Survey.},
journal = {The Journal of nutrition},
volume = {154},
number = {10},
pages = {2932-2947},
doi = {10.1016/j.tjnut.2024.08.021},
pmid = {39209112},
issn = {1541-6100},
mesh = {Humans ; India/epidemiology ; Adolescent ; Child ; Female ; Male ; Prevalence ; *Nutrition Surveys ; Child, Preschool ; *Malnutrition/epidemiology ; Nutritional Status ; Young Adult ; Overnutrition/epidemiology ; Socioeconomic Factors ; Child Nutrition Disorders/epidemiology ; },
abstract = {BACKGROUND: Limited information on the co-prevalence of undernutrition, micronutrient deficiencies, overnutrition, and abnormal levels of noncommunicable disease biomarkers at the same time in children and adolescents in India hinders efforts to comprehensively address their health.<br><br>OBJECTIVES: This study aimed to examine the prevalence and correlates of double burden of malnutrition (DBM) and triple burden of malnutrition (TBM) among children and adolescents (5-19 y) to inform policies and programs.<br><br>METHODS: A total of 17,599 children (5-9 y) and 16,184 adolescents (10-19 y) with available biomarker data from the Comprehensive National Nutrition Survey were included. Malnutrition was defined based on either undernutrition based on anthropometry, overnutrition/abnormal metabolic markers, and anemia/micronutrient deficiency. DBM was defined as the coexistence of any 2 forms of malnutrition. DBM+ was defined as the coexistence of undernutrition and/or micronutrient deficiency along with overnutrition. TBM was defined as having the coexistence of all 3 forms of malnutrition. The prevalence of DBM, DBM+, and TBM was estimated accounting for probabilistic selection. We used mixed-effect binomial regression to determine correlates of DBM/TBM in children and adolescents separately.<br><br>RESULTS: The prevalence of DBM, DBM+, and TBM was 50.8%, 37.2%, and 14.4%, respectively, in children and 53.4%, 36.1%, and 12.7%, respectively, in adolescents. The prevalence of DBM+ was significantly higher in girls compared to in boys in the 5-9 y age group. In children, being in a disadvantaged caste group, having a lower wealth index, having inadequate diet diversity, having no maternal schooling, and having a recent history of acute illness were associated with DBM. In adolescents, being in a disadvantaged caste group, maternal occupation, and lower paternal age were correlated with DBM. A similar set of variables was associated with TBM in both age groups.<br><br>CONCLUSIONS: The prevalence of DBM and TBM is substantial in children and adolescents in India and varies across states. Socioeconomic factors and acute illness were the main correlates for DBM and TBM.},
}
@article {pmid39208288,
year = {2024},
author = {Ishigohoka, J and Bascón-Cardozo, K and Bours, A and Fuß, J and Rhie, A and Mountcastle, J and Haase, B and Chow, W and Collins, J and Howe, K and Uliano-Silva, M and Fedrigo, O and Jarvis, ED and Pérez-Tris, J and Illera, JC and Liedvogel, M},
title = {Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.},
journal = {Evolution; international journal of organic evolution},
volume = {78},
number = {12},
pages = {1916-1935},
doi = {10.1093/evolut/qpae117},
pmid = {39208288},
issn = {1558-5646},
support = {MFFALIMN0001//The Max Planck Society/ ; 395940726//Magnetoreception and Navigation in Vertebrates/ ; 407495230//DFG Research Infrastructure/ ; 423957469//Next Generation Sequencing Competence Network/ ; 1ZIAHG200398//Intramural Research Program of the NHGRI/ ; //Spanish Ministry of Science/ ; //Innovation and Universities/ ; PGC2018-097575-B-I00//The European Regional Development Fund/ ; },
mesh = {Animals ; *Haplotypes ; *Recombination, Genetic ; *Genetic Variation ; *Songbirds/genetics ; Selection, Genetic ; Genome ; },
abstract = {Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.},
}
@article {pmid39208193,
year = {2024},
author = {Naser, AY},
title = {Insights into hospitalization pattern for drug, medicament, and biological substance poisoning, adverse effect, and underdosing in Australia: An ecological study between 1998 and 2019.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0309362},
pmid = {39208193},
issn = {1932-6203},
mesh = {Humans ; *Hospitalization/statistics &amp; numerical data/trends ; Australia/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Poisoning/epidemiology ; Child, Preschool ; Infant ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Aged, 80 and over ; Databases, Factual ; },
abstract = {BACKGROUND: Drug, medicament, and biological substance poisoning, adverse effects, and underdosing are significant public health concerns. Gaining insight into the patterns and trends in hospitalizations caused by these occurrences is essential for the development of preventative initiatives, optimization of treatment regimens, and improvement of patient safety. The aim of this study is to examine the trend of hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019.<br><br>METHODS: This is an ecological descriptive study that examined hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019. A nationwide hospital admissions database was used for this study.<br><br>RESULTS: Between 1998 and 2019, a total of 683,869 hospital admission episodes were recorded in Australia. The overall annual number of hospital admissions for various reasons increased by 20.5% from 29,854 in 1998 to 35,960 in 2019, representing a decrease in hospital admission rate of 10.6% [from 158.69 (95% CI 156.90-160.49) in 1998 to 141.91 (95% CI 140.44-143.37) in 2019 per 100,000 persons, trend test, p<0.05]. Overnight-stay admissions accounted for 69.2% of the total number of hospital admissions, and 30.8% were same-day admissions. Rates of same-day hospital admission decreased by 13.3% [from 50.55 (95%CI 49.54-51.57) in 1998 to 43.81 (95%CI 43.00-44.63) in 2019 per 100,000 persons]. Rates of overnight-stay hospital admission decreased by 11.1% [from 108.14 (95%CI 106.66-109.63) in 1998 to 96.17 (95%CI 94.96-97.38) in 2019 per 100,000 persons]. Admissions related to antiepileptic, sedative-hypnotic and antiparkinsonism drugs was the most prevalent hospital admissions type accounting for 26.8%. Females were responsible for 418,751 hospital admission episodes, representing 61.5% of the total number of hospital admission.<br><br>CONCLUSION: This study found that while the overall annual number of admissions increased, the rate of admission decreased over the same period. The most common reasons for admissions were antiepileptic, sedative-hypnotic, and anti-parkinsonism drugs. The study also noted increases in admissions related to anaesthetics, therapeutic gases, hormones, and their synthetic substitutes. These findings suggest a concerning rise in the suboptimal use of these medications. In order to combat the increasing incidence of this type of admissions, it is imperative to strengthen public awareness initiatives on medicine safety and abuse.},
}
@article {pmid39205176,
year = {2024},
author = {Vanslembrouck, A and Jansen, S and De Witte, J and Janssens, C and Vereecken, S and Helms, M and Lange, U and Lühken, R and Schmidt-Chanasit, J and Heitmann, A and Müller, R},
title = {Larval Competition between Aedes and Culex Mosquitoes Carries over to Higher Arboviral Infection during Their Adult Stage.},
journal = {Viruses},
volume = {16},
number = {8},
pages = {},
pmid = {39205176},
issn = {1999-4915},
support = {G0G2319N//BiodivERsA/ ; CA17108//European Cooperation in Science and Technology/ ; 653316//European Union's Horizon 2020 research and innovation program/ ; Dubois-Brigu&#xe9; scholarship//Doctor Albert Dubois Foundation for tropical pathology/ ; },
mesh = {Animals ; *Culex/virology/growth &amp; development ; *Aedes/virology/growth &amp; development/physiology ; *Larva/virology ; *Mosquito Vectors/virology/growth &amp; development ; Arbovirus Infections/transmission/virology ; Arboviruses/physiology ; West Nile virus/physiology ; Female ; Chikungunya virus/physiology ; Encephalitis Virus, Japanese/physiology ; },
abstract = {The common house mosquito (Culex pipiens) is a native vector for West Nile virus (WNV). Invasive species like the tiger mosquito (Aedes albopictus) and Asian bush mosquito (Aedes japonicus) are rapidly spreading through Europe, posing a major threat as vectors for dengue, chikungunya (CHIKV), and Japanese encephalitis virus (JEV). These mosquitoes share a similar ecological niche as larvae, but the carry-over effects of aquatic larval interactions to the terrestrial adult stage remain largely unknown and their medical relevance requires further investigation. This study examines the context dependency of larval interactions among Aedes albopictus, Aedes japonicus, and Culex pipiens. The survival, development time, growth, and energetic storage were measured in different European populations within density-response (intraspecific) experiments and replacement (interspecific) experiments at 20 °C and 26 °C. Overall, Ae. japonicus was the weakest competitor, while competition between Ae. albopictus and Cx. pipiens varied with temperature. Adults emerging from this larval competition were infected as follows: Culex pipiens with WNV, Ae. albopictus with CHIKV, and Ae. japonicus with JEV. While no JEV infection was observed, mosquitoes experiencing interspecific interactions during their larval stages exhibited higher infection rates and viral RNA titers for CHIKV and WNV. This increased susceptibility to viral infection after larval competition suggests a higher risk of arbovirus transmission in co-occurring populations.},
}
@article {pmid39202353,
year = {2024},
author = {Maltseva, PY and Plotnitskaya, NA and Krivoruchko, AV and Beletskiy, AV and Rakitin, AL and Mardanov, AV and Ivshina, IB},
title = {Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
pmid = {39202353},
issn = {2073-4425},
support = {24-14-20015//the Russian Science Foundation/ ; },
mesh = {*Rhodococcus/genetics/metabolism ; *Genome, Bacterial ; *Computational Biology/methods ; *Biotransformation/genetics ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Monoterpenes/metabolism ; },
abstract = {A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.},
}
@article {pmid39202178,
year = {2024},
author = {de Llanza Varona, M and Martínez, M},
title = {Synergy Makes Direct Perception Inefficient.},
journal = {Entropy (Basel, Switzerland)},
volume = {26},
number = {8},
pages = {},
pmid = {39202178},
issn = {1099-4300},
support = {PID2021-127046NA-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CEX2021-001169-M MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2021-SGR-00276//Government of Catalonia/ ; },
abstract = {A typical claim in anti-representationalist approaches to cognition such as ecological psychology or radical embodied cognitive science is that ecological information is sufficient for guiding behavior. According to this view, affordances are immediately perceptually available to the agent (in the so-called "ambient energy array"), so sensory data does not require much further inner processing. As a consequence, mental representations are explanatorily idle: perception is immediate and direct. Here we offer one way to formalize this direct-perception claim and identify some important limits to it. We argue that the claim should be read as saying that successful behavior just implies picking out affordance-related information from the ambient energy array. By relying on the Partial Information Decomposition framework, and more concretely on its development of the notion of synergy, we show that in multimodal perception, where various energy arrays carry affordance-related information, the "just pick out affordance-related information" approach is very inefficient, as it is bound to miss all synergistic components. Efficient multimodal information combination requires transmitting sensory-specific (and not affordance-specific) information to wherever it is that the various information streams are combined. The upshot is that some amount of computation is necessary for efficient affordance reconstruction.},
}
@article {pmid39198944,
year = {2024},
author = {Wang, HT and Li, HY and Lu, QW and He, SL},
title = {[Determination of eight neonicotinoid pesticides in wastewater by solid phase extraction combined with liquid chromatography-tandem mass spectrometry].},
journal = {Se pu = Chinese journal of chromatography},
volume = {42},
number = {9},
pages = {856-865},
pmid = {39198944},
issn = {1872-2059},
mesh = {*Tandem Mass Spectrometry/methods ; *Solid Phase Extraction/methods ; *Wastewater/chemistry/analysis ; *Neonicotinoids/analysis ; *Water Pollutants, Chemical/analysis ; Chromatography, Liquid/methods ; *Nitro Compounds/analysis ; Thiamethoxam/analysis ; Guanidines/analysis ; Thiazoles/analysis ; Pesticides/analysis ; Thiazines/analysis ; Oxazines/analysis ; },
abstract = {Neonicotinoid pesticides are a relatively new class of pesticides that have garnered significant attention owing to their potential ecological risks to nontarget organisms. A method combining solid phase extraction with liquid chromatography-tandem mass spectrometry (SPE-LC-MS/MS) was developed for the rapid and accurate detection of eight neonicotinoid pesticides (dinotefuran, E-nitenpyram, thiamethoxam, clothianidin, imidacloprid, imidaclothiz, acetamiprid, and thiacloprid) in wastewater. The chromatographic mobile phase and MS parameters were selected, and a single-factor method was used to determine the optimal column type, extraction volume, sample loading speed, and pH for SPE. The optimal parameters were as follows: column type, HLB column (500 mg/6 mL); sample extraction volume, 500 mL; sample loading speed, 10 mL/min; and sample pH, 6-8. The matrix effects of the wastewater samples were reduced by optimizing the chromatographic gradient-elution program, examining the dilution factor of the samples, and using the isotope internal standard calibration method. Prior to analysis, the wastewater samples were diluted 5-fold with ultrapure water for pretreatment. Subsequently, 2 mmol/L ammonium acetate aqueous solution containing 0.1% (v/v) formic acid and methanol was used as mobile phases for gradient elution on a ZORBAX Eclipse Plus C18 column (100 mm×2.1 mm, 1.8 μm). The samples were quantified using positive-ion multiple reaction monitoring (MRM) mode for 10 min. Imidacloprid-d4 was used as the isotope internal standard. The SPE process was further optimized by applying response surface methodology to select the type and mass of rinsing and elution solvents. The optimal pretreatment of the SPE column included rinsing with 10% methanol aqueous solution and elution with methanol-acetonitrile (1∶1, v/v) mixture (7 mL). The eight neonicotinoid pesticides showed satisfactory linearity within the relevant range, with linear correlation coefficients (r) all greater than 0.9990. The method detection limits (MDLs) ranged from 0.2 to 1.2 ng/L, and the method quantification limits (MQLs) ranged from 0.8 to 4.8 ng/L. The average recoveries of the eight neonicotinoid pesticides were in the range of 82.6%-94.2% at three spiked levels, with relative standard deviations (RSDs) ranging from 3.9% to 9.4%. Finally, the optimized method was successfully applied to analyze wastewater samples collected from four sewage treatment plants. The results indicated that the eight neonicotinoid pesticides could be generally detected at concentrations ranging from not detected (ND) to 256 ng/L. The developed method has a low MDL and high accuracy, rendering it a suitable choice for the trace detection of the eight neonicotinoid pesticides in wastewater when compared with other similar methods. The proposed method can be utilized to monitor the environmental impact and assess the potential risks of neonicotinoid pesticides in wastewater, thus promoting the protection of nontarget organisms and the sustainable use of these pesticides in agriculture.},
}
@article {pmid39198489,
year = {2024},
author = {Chanda, MM and Campbell, L and Walke, H and Salzer, JS and Hemadri, D and Patil, SS and Purse, BV and Shivachandra, SB},
title = {A thirty-year time series analyses identifies coherence between oscillations in Anthrax outbreaks and El Niño in Karnataka, India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19928},
pmid = {39198489},
issn = {2045-2322},
mesh = {*Anthrax/epidemiology ; India/epidemiology ; *Disease Outbreaks ; Animals ; *El Nino-Southern Oscillation ; Bayes Theorem ; Bacillus anthracis/isolation &amp; purification/pathogenicity ; Humans ; Livestock/microbiology ; },
abstract = {Anthrax is an economically important zoonotic disease affecting both livestock and humans. The disease is caused by a spore forming bacterium, Bacillus anthracis, and is considered endemic to the state of Karnataka, India. It is critical to quantify the role of climatic factors in determining the temporal pattern of anthrax outbreaks, so that reliable forecasting models can be developed. These models will aid in establishing public health surveillance and guide strategic vaccination programs, which will reduce the economic loss to farmers, and prevent the spill-over of anthrax from livestock to humans. In this study, correlation and coherence between time series of anthrax outbreaks in livestock (1987-2016) and meteorological variables and Sea Surface Temperature anomalies (SST) were identified using a combination of cross-correlation analyses, spectral analyses (wavelets and empirical mode decomposition) and further quantified using a Bayesian time series regression model accounting for temporal autocorrelation. Monthly numbers of anthrax outbreaks were positively associated with a lagged effect of rainfall and wet day frequency. Long-term periodicity in anthrax outbreaks (approximately 6-8 years) was coherent with the periodicity in SST anomalies and outbreak numbers increased with decrease in SST anomalies. These findings will be useful in planning long-term anthrax prevention and control strategies in Karnataka state of India.},
}
@article {pmid39198479,
year = {2024},
author = {Zhu, J and Li, Z and Yang, J and Yu, K and Zhang, D and Zhong, J},
title = {Ecological space management and control zoning of Giant Panda National Park from the perspective of ecosystem services and land use.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19951},
pmid = {39198479},
issn = {2045-2322},
support = {GJGY2020-ZD002//Key Project of National Park Research Center, Key Social Science Research Base of Sichuan Province, "National Park Natural Ecosystem Service Function Importance Evaluation and Protection Policy Research"/ ; ZDJS202303//Chengdu University of Technology "Double First-Class" initiative Construction Philosophy and Social Sciences Key Construction Project/ ; },
mesh = {Animals ; Bayes Theorem ; Carbon Sequestration ; China ; Computer Simulation ; *Conservation of Natural Resources/legislation &amp; jurisprudence/methods ; Conservation of Water Resources ; Datasets as Topic ; *Ecosystem ; *Parks, Recreational/legislation &amp; jurisprudence/organization &amp; administration/standards ; Probability ; Soil ; *Ursidae ; Ecology/legislation &amp; jurisprudence/methods/organization &amp; administration ; },
abstract = {Since China proposed building a national park system in 2017, the establishment of a planning system for nature reserves, with national parks as the main body, is being actively promoted around the country. Among them, scientific ecological space management and control zoning (ESMCZ) is an important link in maintaining the ecological stability of national parks. How to zone national parks and how to improve the precision of zoning has become a new task for national parks. Therefore, this study takes the Giant Panda National Park as the study area, takes ecosystem services and land use/cover change as the research perspective, integrates the InVEST model, PLUS model and bayes belief network (BBN) model, and builds a set of ecological space management and control zoning (ESMCZ) spatial zoning framework based on raster scale, dividing the study area into strictly protected zone, ecological buffer zone, ecological control zone and controlled development zone. The results showed that: (1) The study area showed an increasing trend in water conservation, soil conservation and carbon storage from 2005 to 2020, and the habitat quality index was generally high. The spatial heterogeneity of ecosystem services in the study area was significant, and the effect of a single factor on ecosystem services was most pronounced. (2) Large variation in area for different land uses under natural development scenarios and ecological protection scenarios. In both scenarios, the area of cultivated land, the area of grassland and the area of unused land decrease relative to 2020, and the area of forested land, the area of water and the area of constructed land increase relative to 2020. (3) The Giant Panda National Park is divided into strictly protected zone, ecological buffer zone, ecological control zone and control development zone, of which the strictly protected zone have the largest area and the best ecosystem background condition, and the control development zone have the smallest area and the worst ecosystem background condition. (4) The ecological space management and control zoning (ESMCZ) framework provides a more refined method for the secondary zoning of nature reserves such as the Giant Panda National Park, which is valuable for the implementation of zoning and categorization management for ecological conservation in the Giant Panda National Park.},
}
@article {pmid39196880,
year = {2024},
author = {Tsigeman, E and Zemliak, V and Likhanov, M and Papageorgiou, KA and Kovas, Y},
title = {AI can see you: Machiavellianism and extraversion are reflected in eye-movements.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308631},
pmid = {39196880},
issn = {1932-6203},
mesh = {Humans ; *Eye Movements/physiology ; Male ; Female ; Adolescent ; *Extraversion, Psychological ; *Machine Learning ; *Machiavellianism ; Surveys and Questionnaires ; Algorithms ; Personality/physiology ; Eye-Tracking Technology ; },
abstract = {INTRODUCTION: Recent studies showed an association between personality traits and individual patterns of visual behaviour in laboratory and other settings. The current study extends previous research by measuring multiple personality traits in natural settings; and by comparing accuracy of prediction of multiple machine learning algorithms.<br><br>METHODS: Adolescent participants (N = 35) completed personality questionnaires (Big Five Inventory and Short Dark Triad Questionnaire) and visited an interactive museum while their eye movements were recorded with head-mounted eye tracking. To predict personality traits the eye-movement data was analysed using eight machine-learning methods: Random Forest, Adaboost, Naive Bayes, Support Vector Machine, Logistic Regression, k Nearest Neighbours, Decision Tree and a three-layer Perceptron.<br><br>RESULTS AND DISCUSSION: Extracted eye movement features introduced to machine learning algorithms predicted personality traits with above 33% chance accuracy (34%-48%). This result is comparable to previous ecologically valid studies, but lower than in laboratory-based research. Better prediction was achieved for Machiavellianism and Extraversion compared to other traits (10 and 9 predictions above the chance level by different algorithms from different parts of the recording). Conscientiousness, Narcissism and Psychopathy were not reliably predicted from eye movements. These differences in predictability across traits might be explained by differential activation of different traits in different situations, such as new vs. familiar, exciting vs. boring, and complex vs. simple settings. In turn, different machine learning approaches seem to be better at capturing specific gaze patterns (e.g. saccades), associated with specific traits evoked by the situation. Further research is needed to gain better insights into trait-situation-algorithm interactions.},
}
@article {pmid39193916,
year = {2024},
author = {Spöri, Y and Flot, JF},
title = {Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
pmid = {39193916},
issn = {1477-4054},
support = {T.0078.23//Fonds de la Recherche Scientifique - FNRS/ ; },
mesh = {*Computational Biology/methods ; *Programming Languages ; *Software ; },
abstract = {Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe's source code conversion functionality when it comes to implementing bioinformatic software.},
}
@article {pmid39193399,
year = {2024},
author = {Boyes, D and Crowley, LM and Hutchinson, F and Wawman, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the Lesser Yellow Underwing, Noctua comes Hübner, 1813.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {200},
pmid = {39193399},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Noctua comes (the Lesser Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 540.7 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,001 protein coding genes.},
}
@article {pmid39193313,
year = {2024},
author = {Kang, B and Ma, J and Jeong, I and Yoon, S and Kim, JI and Heo, SJ and Oh, SS},
title = {Behavioral marker-based predictive modeling of functional status for older adults with subjective cognitive decline and mild cognitive impairment: Study protocol.},
journal = {Digital health},
volume = {10},
number = {},
pages = {20552076241269555},
pmid = {39193313},
issn = {2055-2076},
abstract = {OBJECTIVE: This study describes a research protocol for a behavioral marker-based predictive model that examines the functional status of older adults with subjective cognitive decline and mild cognitive impairment.<br><br>METHODS: A total of 130 older adults aged &#x2265;65 years with subjective cognitive decline or mild cognitive impairment will be recruited from the Dementia Relief Centers or the Community Service Centers. Data on behavioral and psychosocial markers (e.g. physical activity, mobility, sleep/wake patterns, social interaction, and mild behavioral impairment) will be collected using passive wearable actigraphy, in-person questionnaires, and smartphone-based ecological momentary assessments. Two follow-up assessments will be performed at 12 and 24 months after baseline. Mixed-effect machine learning models: MErf, MEgbm, MEmod, and MEctree, and standard machine learning models without random effects [random forest, gradient boosting machine] will be employed in our analyses to predict functional status over time.<br><br>RESULTS: The results of this study will be fundamental for developing tailored digital interventions that apply deep learning techniques to behavioral data to predict, identify, and aid in the management of functional decline in older adults with subjective cognitive decline and mild cognitive impairment. These older adults are considered the optimal target population for preventive interventions and will benefit from such tailored strategies.<br><br>CONCLUSIONS: Our study will contribute to the development of self-care interventions that utilize behavioral data and machine learning techniques to provide automated analyses of the functional decline of older adults who are at risk for dementia.},
}
@article {pmid39193090,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Small Angle Shades, Euplexia lucipara (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {509},
pmid = {39193090},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Euplexia lucipara (the Small Angle Shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 661.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,395 protein coding genes.},
}
@article {pmid39192185,
year = {2024},
author = {Donthu, R and Marcelino, JAP and Giordano, R and Tao, Y and Weber, E and Avalos, A and Band, M and Akraiko, T and Chen, SC and Reyes, MP and Hao, H and Ortiz-Alvarado, Y and Cuff, CA and Claudio, EP and Soto-Adames, F and Smith-Pardo, AH and Meikle, WG and Evans, JD and Giray, T and Abdelkader, FB and Allsopp, M and Ball, D and Morgado, SB and Barjadze, S and Correa-Benitez, A and Chakir, A and Báez, DR and Chavez, NHM and Dalmon, A and Douglas, AB and Fraccica, C and Fernández-Marín, H and Galindo-Cardona, A and Guzman-Novoa, E and Horsburgh, R and Kence, M and Kilonzo, J and Kükrer, M and Le Conte, Y and Mazzeo, G and Mota, F and Muli, E and Oskay, D and Ruiz-Martínez, JA and Oliveri, E and Pichkhaia, I and Romane, A and Sanchez, CG and Sikombwa, E and Satta, A and Scannapieco, AA and Stanford, B and Soroker, V and Velarde, RA and Vercelli, M and Huang, Z},
title = {HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {278},
pmid = {39192185},
issn = {1471-2105},
support = {PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; USDA-APHIS #AP20PPQS &amp; T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; USDA-APHIS #AP20PPQS &amp; T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; NSF-OISE #1545803//National Science Foundation, United States of America/ ; },
mesh = {Bees/genetics/classification ; Animals ; *Polymorphism, Single Nucleotide/genetics ; Genomics/methods ; },
abstract = {BACKGROUND: Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited.<br><br>RESULTS: We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples.<br><br>CONCLUSION: HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.},
}
@article {pmid39188222,
year = {2024},
author = {Koracevic, G and Stojanovic, M and Zdravkovic, M and Lovic, D and Simic, D and Mladenovic, K},
title = {Proposal of a Modified Classification of Hypertensive Crises: Urgency, Impending Emergency, and Emergency.},
journal = {Current vascular pharmacology},
volume = {22},
number = {3},
pages = {180-186},
pmid = {39188222},
issn = {1875-6212},
mesh = {Humans ; *Hypertension/diagnosis/physiopathology/drug therapy/classification ; *Antihypertensive Agents/therapeutic use/adverse effects ; Risk Assessment ; Risk Factors ; *Blood Pressure/drug effects ; *Emergencies ; Prognosis ; Predictive Value of Tests ; Decision Support Techniques ; Clinical Decision-Making ; Hypertensive Crisis ; },
abstract = {Systemic arterial hypertension (HTN) is the main cause of morbidity and mortality, and HTN crises contribute significantly to an unfavourable clinical course. For decades, HTN crises have been dichotomized into hypertensive emergency (HTN-E) and hypertensive urgency (HTN-U). The main difference between the two is the presence of acute hypertension-mediated organ damage (HMOD) - if HMOD is present, HTN crisis is HTN-E; if not, it is HTN-U. Patients with HTN-E are in a life-threatening situation. They are hospitalized and receive antihypertensive drugs intravenously (IV). On the other hand, patients with HTN-U are usually not hospitalized and receive their antihypertensives orally. We suggest a modification of the current risk stratification scheme for patients with HTN crises. The new category would be the intermediate risk group, more precisely the 'impending HTN-E' group, with a higher risk in comparison to HTN-U and a lower risk than HTN-E. 'Impending HMOD' means that HMOD has not occurred (yet), and the prognosis is, therefore, better than in patients with ongoing HMOD. There are three main reasons to classify patients as having impending HTN-E: excessively elevated BP, high-risk comorbidities, and ongoing bleeding/high bleeding risk. Their combinations are probable. This approach may enable us to prevent some HTNEs by avoiding acute HMOD using a timely blood pressure treatment. This treatment should be prompt but controlled.},
}
@article {pmid39186487,
year = {2024},
author = {Raj, U and Banerjee, A and Ray, S and Bhattacharya, S},
title = {Structure of higher-order interactions in social-ecological networks through Q-analysis of their neighbourhood and clique complex.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0306409},
pmid = {39186487},
issn = {1932-6203},
mesh = {*Ecosystem ; Humans ; Models, Theoretical ; Madagascar ; Algorithms ; Social Networking ; Social Support ; Agriculture ; },
abstract = {This paper studies higher-order interactions in social-ecological networks, which formally represent interactions within the social and ecological units of an ecosystem. Many real-world social ecosystems exhibit not only pairwise interactions but also higher-order interactions among their units. Therefore, the conventional graph-theoretic description of networks falls short of capturing these higher-order interactions due to the inherent limitations of the graph definition. In this work, a mathematical framework for capturing the higher-order interactions of a social-ecological system has been given by incorporating notions from combinatorial algebraic topology. In order to achieve this, two different simplicial complexes, the clique and the neighbourhood complex, have been constructed from a pairwise social-ecological network. As a case study, the Q-analysis and a structural study of the interactions in the rural agricultural system of southern Madagascar have been done at various structural levels denoted by q. The results obtained by calculating all the structural vectors for both simplicial complexes, along with exciting results about the participation of facets of the clique complex at different q-levels, have been discussed. This work also establishes significant theorems concerning the dimension of the neighbourhood complex and clique complex obtained from the parent pairwise network.},
}
@article {pmid39185327,
year = {2024},
author = {Panyushkina, IP and Jull, AJT and Molnár, M and Varga, T and Kontul', I and Hantemirov, R and Kukarskih, V and Sljusarenko, I and Myglan, V and Livina, V},
title = {The timing of the ca-660 BCE Miyake solar-proton event constrained to between 664 and 663 BCE.},
journal = {Communications earth &amp; environment},
volume = {5},
number = {1},
pages = {454},
pmid = {39185327},
issn = {2662-4435},
abstract = {Extreme solar energetic particle events, known as Miyake events, are rare phenomena observed by cosmogenic isotopes, with only six documented. The timing of the ca. 660 BCE Miyake event remains undefined until now. Here, we assign its occurrence to 664-663 BCE through new radiocarbon measurements in gymnosperm larch tree rings from arctic-alpine biomes (Yamal and Altai). Using a 22-box carbon cycle model and Bayesian statistics, we calculate the radiocarbon production rate during the event that is 3.2-4.8 times higher than the average solar modulation, and comparable to the 774-775 CE solar-proton event. The prolonged radiocarbon signature manifests a 12‰ rise over two years. The non-uniform signal in the tree rings is likely driven by the low rate of CO2 gas exchange between the trees and the ambient atmosphere, and the high residence time of radiocarbon in the post-event stratosphere. We caution about using the event's pronounced signature for precise single-year-dating.},
}
@article {pmid39184546,
year = {2024},
author = {Yuan, H and Mancuso, CA and Johnson, K and Braasch, I and Krishnan, A},
title = {Computational strategies for cross-species knowledge transfer and translational biomedicine.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {39184546},
issn = {2331-8422},
support = {R01 OD011116/OD/NIH HHS/United States ; R35 GM128765/GM/NIGMS NIH HHS/United States ; },
abstract = {Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research organisms hinders effective knowledge transfer across species. Here, we review state-of-the-art methods for computationally transferring knowledge across species, primarily focusing on methods that utilize transcriptome data and/or molecular networks. We introduce the term "agnology" to describe the functional equivalence of molecular components regardless of evolutionary origin, as this concept is becoming pervasive in integrative data-driven models where the role of evolutionary origin can become unclear. Our review addresses four key areas of information and knowledge transfer across species: (1) transferring disease and gene annotation knowledge, (2) identifying agnologous molecular components, (3) inferring equivalent perturbed genes or gene sets, and (4) identifying agnologous cell types. We conclude with an outlook on future directions and several key challenges that remain in cross-species knowledge transfer.},
}
@article {pmid39181462,
year = {2024},
author = {de Vries, P},
title = {ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database.},
journal = {Chemosphere},
volume = {364},
number = {},
pages = {143078},
doi = {10.1016/j.chemosphere.2024.143078},
pmid = {39181462},
issn = {1879-1298},
mesh = {*United States Environmental Protection Agency ; *Databases, Factual ; *Software ; United States ; Ecotoxicology/methods ; Risk Assessment/methods ; Reproducibility of Results ; },
abstract = {The US EPA ECOTOX database provides key ecotoxicological data that are crucial in environmental risk assessment. It can be used for computational predictions of toxicity or indications of hazard in a wide range of situations. There is no standardised or formalised method for extracting and subsetting data from the database for these purposes. Consequently, results in such meta-analyses are difficult to reproduce. The present study introduces the software package ECOTOXr, which provides the means to formalise data retrieval from the ECOTOX database in the R scripting language. Three cases are presented to evaluate the performance of the package in relation to earlier data extractions and searches on the website. These cases demonstrate that the package can reproduce data sets relatively well. Furthermore, they illustrate how future studies can further improve traceability and reproducibility by applying the package and adhering to some simple guidelines. This contributes to the FAIR principles, credibility and acceptance of research that uses data from the ECOTOX database.},
}
@article {pmid39181078,
year = {2024},
author = {Wei, Q and Yin, Y and Tong, Q and Gong, Z and Shi, Y},
title = {Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming.},
journal = {Ecotoxicology and environmental safety},
volume = {284},
number = {},
pages = {116916},
doi = {10.1016/j.ecoenv.2024.116916},
pmid = {39181078},
issn = {1090-2414},
mesh = {*Solanum tuberosum/microbiology ; *Fertilizers ; *Nitrogen/analysis ; *Soil Microbiology ; Transcriptome ; Metabolome/drug effects ; Agriculture/methods ; Metagenomics ; Soil/chemistry ; Multiomics ; },
abstract = {Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3[-] increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.},
}
@article {pmid39180071,
year = {2024},
author = {Zhuang, M and Qiao, C and Han, L and Bi, Y and Cao, M and Wang, S and Guo, L and Pang, R and Xie, H},
title = {Multi-omics analyses reveal the responses of wheat (Triticum aestivum L.) and rhizosphere bacterial community to nano(micro)plastics stress.},
journal = {Journal of nanobiotechnology},
volume = {22},
number = {1},
pages = {507},
pmid = {39180071},
issn = {1477-3155},
support = {2023YFD1400902//National Key Research and Development Program of China/ ; J210019//Beijing Municipal Natural Science Foundation/ ; C2021204190//Natural Science Foundation of Hebei Province/ ; 21JCZXJC00110//Natural Science Foundation of Tianjin Municipality/ ; },
mesh = {*Triticum ; *Rhizosphere ; *Bacteria/genetics/metabolism/drug effects ; *Microplastics ; *Soil Microbiology ; Nanoparticles/chemistry ; Stress, Physiological ; Microbiota ; Soil Pollutants ; Particle Size ; Polystyrenes/chemistry ; Multiomics ; },
abstract = {The pervasive existence of nanoplastics (NPs) and microplastics (MPs) in soil has become a worldwide environmental concern. N/MPs exist in the environment in a variety of forms, sizes, and concentrations, while multi-omics studies on the comprehensive impact of N/MPs with different properties (e.g. type and size) on plants remain limited. Therefore, this study utilized multi-omics analysis methods to investigate the effects of three common polymers [polyethylene-NPs (PE-NPs, 50 nm), PE-MPs (PE-MPs, 10 μm), and polystyrene-MPs (PS-MPs, 10 μm)] on the growth and stress response of wheat, as well as the rhizosphere microbial community at two concentrations (0.05 and 0.5 g/kg). PS and PE exhibited different effects for the same particle size and concentration. PE-NPs had the most severe stress effects, resulting in reduced rhizosphere bacteria diversity, plant biomass, and antioxidant enzyme activity while increasing beneficial bacteria richness. N/MPs altered the expression of nitrogen-, phosphorus-, and sulfur-related functional genes in rhizosphere bacteria, thereby affecting photosynthesis, as well as metabolite and gene levels in wheat leaves. Partial least squares pathway models (PLSPMs) indicated that concentration, size, and type play important roles in the impact of N/MPs on the plant ecological environment, which could have essential implications for assessing the environmental risk of N/MPs.},
}
@article {pmid39178805,
year = {2024},
author = {Bravo-Ortiz, MA and Guevara-Navarro, E and Holguín-García, SA and Rivera-Garcia, M and Cardona-Morales, O and Ruz, GA and Tabares-Soto, R},
title = {SpectroCVT-Net: A convolutional vision transformer architecture and channel attention for classifying Alzheimer's disease using spectrograms.},
journal = {Computers in biology and medicine},
volume = {181},
number = {},
pages = {109022},
doi = {10.1016/j.compbiomed.2024.109022},
pmid = {39178805},
issn = {1879-0534},
mesh = {*Alzheimer Disease/classification/physiopathology/diagnosis ; Humans ; *Electroencephalography/methods ; *Signal Processing, Computer-Assisted ; Male ; Female ; Databases, Factual ; Aged ; },
abstract = {Dementia arises from various brain-affecting diseases and injuries, with Alzheimer's disease being the most prevalent, impacting around 55 million people globally. Current clinical diagnosis often relies on biomarkers indicative of Alzheimer's distinctive features. Electroencephalography (EEG) serves as a cost-effective, user-friendly, and safe biomarker for early Alzheimer's detection. This study utilizes EEG signals processed with Short-Time Fourier Transform (STFT) to generate spectrograms, facilitating visualization of EEG signal properties. Leveraging the Brainlat database, we propose SpectroCVT-Net, a novel convolutional vision transformer architecture incorporating channel attention mechanisms. SpectroCVT-Net integrates convolutional and attention mechanisms to capture local and global dependencies within spectrograms. Comprising feature extraction and classification stages, the model enhances Alzheimer's disease classification accuracy compared to transfer learning methods, achieving 92.59 ± 2.3% accuracy across Alzheimer's, healthy controls, and behavioral variant frontotemporal dementia (bvFTD). This article introduces a new architecture and evaluates its efficacy with unconventional data for Alzheimer's diagnosis, contributing: SpectroCVT-Net, tailored for EEG spectrogram classification without reliance on transfer learning; a convolutional vision transformer (CVT) module in the classification stage, integrating local feature extraction with attention heads for global context analysis; Grad-CAM analysis for network decision insight, identifying critical layers, frequencies, and electrodes influencing classification; and enhanced interpretability through spectrograms, illuminating key brain wave contributions to Alzheimer's, frontotemporal dementia, and healthy control classifications, potentially aiding clinical diagnosis and management.},
}
@article {pmid39178313,
year = {2024},
author = {Du, J and Liu, W and Li, M and Li, Z and Li, X and Dai, Y and Liu, G and Wang, X and Zhu, P and Gladyshev, VN and Zhou, X},
title = {Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002778},
pmid = {39178313},
issn = {1545-7885},
mesh = {Animals ; Mice ; *Histones/metabolism ; Humans ; Neoplasms/genetics/metabolism/pathology ; Mole Rats/genetics ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Proteomics/methods ; Fibroblasts/metabolism ; Autophagy/genetics ; Adaptation, Physiological/genetics ; Transcriptome/genetics ; Cell Hypoxia/genetics ; Cell Line, Tumor ; Signal Transduction ; Multiomics ; },
abstract = {The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.},
}
@article {pmid39176874,
year = {2024},
author = {Knak, AK and Roheger, M and Wulff, A},
title = {Challenges in Daily Computerized Assessment of Cognitive Functions of Post-COVID Patients.},
journal = {Studies in health technology and informatics},
volume = {316},
number = {},
pages = {1950-1954},
doi = {10.3233/SHTI240815},
pmid = {39176874},
issn = {1879-8365},
mesh = {Humans ; *COVID-19 ; Cognitive Dysfunction ; Diagnosis, Computer-Assisted/methods ; SARS-CoV-2 ; Fatigue ; Post-Acute COVID-19 Syndrome ; Cognition ; },
abstract = {While it would be quite helpful to learn more about the daily fluctuations of fatigue and cognitive impairments of post-COVID patients, their condition can make investigating these especially challenging. By discussing these issues with post-COVID patients and clinical practitioners, we identified six challenges that specifically apply to daily computerized assessment of cognitive functions of post-COVID patients. We proposed solutions for each of the challenges which can be summarized as offering a carefully planned and flexible study design to participants and monitoring their well-being throughout the assessments. We argue that when the proposed precautions are taken, it is feasible to conduct a study that will generate valuable insights into the trajectories of (cognitive) post-COVID symptoms.},
}
@article {pmid39176504,
year = {2024},
author = {Kokolakis, S and Kokinou, E and Chronaki, C and Moen, A and Datta, G},
title = {Earth Observation and Geoinformatics to Monitoring the Environmental Status of Urban Streams Inextricably Linked to People's Mental Health.},
journal = {Studies in health technology and informatics},
volume = {316},
number = {},
pages = {1560-1564},
doi = {10.3233/SHTI240716},
pmid = {39176504},
issn = {1879-8365},
mesh = {*Environmental Monitoring/methods ; Humans ; *Mental Health ; Rivers ; Geographic Information Systems ; Cities ; },
abstract = {The general condition of urban watercourses is inextricably linked to ecological balance and public health (physical and mental well-being). Given the vulnerability of these systems to climate change and human pollution, this work aims to demonstrate the effective use of environmental indicators to: a) rapidly assess soil and water conditions near urban streams and b) highlight the importance of geoinformatics and earth observation supported by ground-based techniques. There is a great need for new technology and methods for spatial and temporal monitoring and further quantification of environmental quality in urban streams and the land surrounding them to sensitize policymakers and the public to the environmental degradation of these exceptional habitats and to further protect people's mental health.},
}
@article {pmid39173171,
year = {2024},
author = {Barahona, M and Alegría, A and Amstein, C and Cárcamo, M and Barahona, M},
title = {Epidemiology of high-energy trauma in Chile: An ecological analysis using public registries.},
journal = {Medwave},
volume = {24},
number = {7},
pages = {e2929},
doi = {10.5867/medwave.2024.07.2929},
pmid = {39173171},
issn = {0717-6384},
mesh = {Chile/epidemiology ; Humans ; *Accidents, Traffic/statistics &amp; numerical data/mortality ; Male ; Adult ; *Databases, Factual ; *Registries ; Female ; Young Adult ; Middle Aged ; *Multiple Trauma/epidemiology/mortality ; Wounds and Injuries/epidemiology/mortality ; Public Health ; Sex Distribution ; Adolescent ; Age Distribution ; World Health Organization ; Aged ; },
abstract = {High-energy trauma is defined as severe organic injuries resulting from events that generate a large amount of kinetic, electrical, or thermal energy. It represents a significant public health concern, accounting for 10% of global mortality. This article aims to describe the epidemiology of high-energy trauma in Chile. Specifically, it seeks to compare the mortality rate per 100 000 inhabitants among member countries of the World Health Organization (WHO), provide a descriptive analysis of notifications under the Explicit Health Guarantees (GES) for the health issue of polytraumatized patients, and analyze the trend in the mortality rate due to external causes in Chile. This study employs an ecological design using three open-access databases. First, the WHO database on deaths from traffic accidents in 2019 was used. Then, the GES database was consulted for the "Polytraumatized" issue between 2018 and 2022. Finally, the Chilean Department of Health Statistics database on causes of death between 1997 and 2020 was utilized. In 2019, Chile ranked in the middle regarding the mortality rate per 100 000 inhabitants due to traffic accidents. GES notifications for polytrauma predominantly involved men aged 20 to 40 years and those affiliated with the public health system, highlighting a primary focus for prevention efforts. Mortality from accidents showed a decreasing trend, with significant structural changes identified in 2000 and 2007.},
}
@article {pmid39170344,
year = {2024},
author = {D, S and Vellaturi, G and Shaik Ibrahim, SH and Molugu, S and Desanamukula, VS and Kocherla, R and Vatambeti, R},
title = {Enhanced deep learning models for automatic fish species identification in underwater imagery.},
journal = {Heliyon},
volume = {10},
number = {15},
pages = {e35217},
pmid = {39170344},
issn = {2405-8440},
abstract = {Underwater cameras are crucial in marine ecology, but their data management needs automatic species identification. This study proposes a two-stage deep learning approach. First, the Unsharp Mask Filter (UMF) preprocesses images. Then, an enhanced region-based fully convolutional network (R-FCN) detects fish using two-order integrals for position-sensitive score maps and precise region of interest (PS-Pr-RoI) pooling for accuracy. The second stage integrates ShuffleNetV2 with the Squeeze and Excitation (SE) module, forming the Improved ShuffleNetV2 model, enhancing classification focus. Hyperparameters are optimized with the Enhanced Northern Goshawk Optimization Algorithm (ENGO). The improved R-FCN model achieves 99.94 % accuracy, 99.58 % precision and recall, and a 99.27 % F-measure on the Fish4knowledge dataset. Similarly, the ENGO-based ShuffleNetV2 model, evaluated on the same dataset, shows 99.93 % accuracy, 99.19 % precision, 98.29 % recall, and a 98.71 % F-measure, highlighting its superior classification accuracy.},
}
@article {pmid39169276,
year = {2024},
author = {Arcioni, L and Arcieri, M and Martino, JD and Liberati, F and Bottoni, P and Castrignanò, T},
title = {HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {272},
pmid = {39169276},
issn = {1471-2105},
support = {B87G22000450001//Ministry of University and Research, Italy/ ; },
mesh = {*Software ; *Transcriptome/genetics ; *Molecular Sequence Annotation/methods ; Gene Expression Profiling/methods ; Computational Biology/methods ; Databases, Genetic ; },
abstract = {BACKGROUND: The availability of transcriptomic data for species without a reference genome enables the construction of de novo transcriptome assemblies as alternative reference resources from RNA-Seq data. A transcriptome provides direct information about a species' protein-coding genes under specific experimental conditions. The de novo assembly process produces a unigenes file in FASTA format, subsequently targeted for the annotation. Homology-based annotation, a method to infer the function of sequences by estimating similarity with other sequences in a reference database, is a computationally demanding procedure.<br><br>RESULTS: To mitigate the computational burden, we introduce HPC-T-Annotator, a tool for de novo transcriptome homology annotation on high performance computing (HPC) infrastructures, designed for straightforward configuration via a Web interface. Once the configuration data are given, the entire parallel computing software for annotation is automatically generated and can be launched on a supercomputer using a simple command line. The output data can then be easily viewed using post-processing utilities in the form of Python notebooks integrated in the proposed software.<br><br>CONCLUSIONS: HPC-T-Annotator expedites homology-based annotation in de novo transcriptome assemblies. Its efficient parallelization strategy on HPC infrastructures significantly reduces computational load and execution times, enabling large-scale transcriptome analysis and comparison projects, while its intuitive graphical interface extends accessibility to users without IT skills.},
}
@article {pmid39167718,
year = {2024},
author = {Zass, L and Mwapagha, LM and Louis-Jacques, AF and Allali, I and Mulindwa, J and Kiran, A and Hanachi, M and Souiai, O and Mulder, N and Oduaran, OH},
title = {Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {39167718},
issn = {1758-0463},
support = {U24 HG009780/HG/NHGRI NIH HHS/United States ; 1U24HG009780/NH/NIH HHS/United States ; },
mesh = {*Metadata ; *Microbiota ; Humans ; Databases, Factual ; },
abstract = {Microbiome research has made significant gains with the evolution of sequencing technologies. Ensuring comparability between studies and enhancing the findability, accessibility, interoperability and reproducibility of microbiome data are crucial for maximizing the value of this growing body of research. Addressing the challenges of standardized metadata reporting, collection and curation, the Microbiome Working Group of the Human Hereditary and Health in Africa (H3Africa) consortium aimed to develop a comprehensive solution. In this paper, we present the Microbiome Research Data Toolkit, a versatile tool designed to standardize microbiome research metadata, facilitate MIxS-MIMS and PhenX reporting, standardize prospective collection of participant biological and lifestyle data, and retrospectively harmonize such data. This toolkit enables past, present and future microbiome research endeavors to collaborate effectively, fostering novel collaborations and accelerating knowledge discovery in the field. Database URL: https://doi.org/10.25375/uct.24218999.v2.},
}
@article {pmid39162518,
year = {2024},
author = {Hu, D and Zhang, T and He, S and Pu, T and Yin, Y and Hu, Y},
title = {Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.},
journal = {Microbiology spectrum},
volume = {12},
number = {10},
pages = {e0086424},
pmid = {39162518},
issn = {2165-0497},
support = {32370552//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070414,32325010//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Mammals/microbiology ; *Metagenome ; *Multigene Family ; Bacteria/genetics/classification/metabolism ; Polyketides/metabolism ; Data Mining ; Biological Products/metabolism ; Female ; Biosynthetic Pathways/genetics ; },
abstract = {Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.},
}
@article {pmid39161242,
year = {2024},
author = {Setyawati, I and Husaini, AF and Setiawan, AG and Artika, IM and Ambarsari, L and Nurcholis, W and Vidilaseris, K and Kurniatin, PA},
title = {Structural Classification Insights Into the Plant Defensive Peptides.},
journal = {Proteins},
volume = {92},
number = {12},
pages = {1413-1427},
doi = {10.1002/prot.26736},
pmid = {39161242},
issn = {1097-0134},
support = {102/E5/PG.02.00.PL/2023//Ministry of Education, Culture, Research, and Technology, Republic of Indonesia/ ; },
mesh = {*Phylogeny ; *Plant Proteins/chemistry/genetics/metabolism ; *Plants/metabolism/chemistry ; *Databases, Protein ; Evolution, Molecular ; Amino Acid Sequence ; Models, Molecular ; },
abstract = {This study presents a structural phylogenetic analysis of plant defensive peptides, revealing their evolutionary relationships, structural diversification, and functional adaptations. Utilizing a robust dataset comprising both experimental and predicted structures sourced from the RCSB Protein Data Bank and AlphaFold DB, we constructed a detailed phylogenetic tree to elucidate the distinct evolutionary paths of plant defensive peptide families. Our findings showcase the evolutionary intricacies of defensive peptides, highlighting their diversity and the conservation of key structural motifs critical to their antimicrobial or defensive functions. The results also underscore the adaptive significance of defensive peptides in plant evolution, highlighting their roles in responding to ecological pressures and pathogen interactions.},
}
@article {pmid39155119,
year = {2024},
author = {Reitz, ZL},
title = {Predicting metallophore structure and function through genome mining.},
journal = {Methods in enzymology},
volume = {702},
number = {},
pages = {371-401},
doi = {10.1016/bs.mie.2024.06.007},
pmid = {39155119},
issn = {1557-7988},
mesh = {*Genomics/methods ; Genome, Bacterial ; Computational Biology/methods ; Siderophores/metabolism/chemistry/genetics ; Data Mining/methods ; },
abstract = {Metallophores are small molecule chelators that many microbes use to obtain trace metals from their environment. Through genome mining, where genomes are scanned for metallophore biosynthesis genes, one can not only identify which organisms are likely to produce a metallophore, but also predict the metallophore structure, thus preventing undesired reisolation of known compounds and accelerating characterization. Furthermore, the presence of accessory genes for the transport, utilization, and regulation can suggest the biological function and fate of a metallophore. Modern, user-friendly tools have made powerful genomic analyses accessible to scientists with no bioinformatics experience, but these tools are often not utilized to their full potential. This chapter provides an introduction to metallophore genomics and demonstrates how to use the free, publicly available antiSMASH platform to infer metallophore function and structure.},
}
@article {pmid39154763,
year = {2024},
author = {Lin, X and Sun, B and Wang, P and Zhao, M and Liu, D and Zhang, Q and Wu, B and Liu, D},
title = {Enhanced low-concentration phosphate adsorption using magnetic UiO-66@Fe3O4 composite with potential linker exchange.},
journal = {Chemosphere},
volume = {364},
number = {},
pages = {143126},
doi = {10.1016/j.chemosphere.2024.143126},
pmid = {39154763},
issn = {1879-1298},
mesh = {Adsorption ; *Phosphates/chemistry ; *Water Pollutants, Chemical/chemistry ; Water Purification/methods ; Metal-Organic Frameworks/chemistry ; Ferric Compounds/chemistry ; Magnetics ; Phthalic Acids ; },
abstract = {A magnetic FenUiO-66 adsorbent was created to achieve high phosphate adsorption capacity. The incorporation of Fe3O4 facilitated the precipitation and growth of UiO-66 during crystallization, resulting in a shift towards a multilayer heterogeneous distribution of adsorption sites. The increased Fe3O4 content notably enhanced the magnetic properties of FenUiO-66, while negligibly affecting its adsorption performance. The Fe1.5UiO-66 demonstrated exceptional phosphate adsorption capacity (136.54 mg/g), outstanding selectivity, and sustained reusability, with an 80% removal efficiency after nine cycles of treating actual water. The mechanism of phosphate adsorption by FenUiO-66 involved electrostatic attraction, ligand exchange, and linker exchange. Notably, while linker exchange significantly contributed to high adsorption capacity, it resulted in irreversible damage to the FenUiO-66 crystal. These unequivocal findings will serve as a solid foundation for further research and underline the critical role of linkers in the process of phosphate adsorption.},
}
@article {pmid39154477,
year = {2024},
author = {Bai, Z and He, Y and Hu, G and Cheng, L and Wang, M},
title = {Microplastics at an environmentally relevant dose enhance mercury toxicity in a marine copepod under multigenerational exposure: Multi-omics perspective.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135529},
doi = {10.1016/j.jhazmat.2024.135529},
pmid = {39154477},
issn = {1873-3336},
mesh = {Animals ; *Copepoda/drug effects ; *Mercury/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microplastics/toxicity ; Reproduction/drug effects ; Apoptosis/drug effects ; Proteomics ; Multiomics ; },
abstract = {Here, we subjected the marine copepod Tigriopus japonicus to environmentally-relevant concentrations of microplastics (MPs) and mercury (Hg) for three generations (F0-F2) to investigate their physiological and molecular responses. Hg accumulation and phenotypic traits were measured in each generation, with multi-omics analysis conducted in F2. The results showed that MPs insignificantly impacted the copepod's development and reproduction, however, which were significantly compromised by Hg exposure. Interestingly, MPs significantly increased Hg accumulation and consequently aggravated this metal toxicity in T. japonicus, demonstrating their carrier role. Multi-omics analysis indicated that Hg pollution produced numerous toxic events, e.g., induction of apoptosis, damage to cell/organ morphogenesis, and disordered energy metabolism, ultimately resulting in retarded development and decreased fecundity. Importantly, MPs enhanced Hg toxicity mainly via increased oxidative apoptosis, compromised cell/organ morphogenesis, and energy depletion. Additionally, phosphoproteomic analysis revealed extensive regulation of the above processes, and also impaired neuron activity under combined MPs and Hg exposure. These alterations adversely affected development and reproduction of T. japonicus. Overall, our findings should offer novel molecular insights into the response of T. japonicus to long-term exposure to MPs and Hg, with a particular emphasis on the carrier role of MPs on Hg toxicity.},
}
@article {pmid39151562,
year = {2024},
author = {Rahimian, M and Panahi, B},
title = {Metagenome sequence data mining for viral interaction studies: Review on progress and prospects.},
journal = {Virus research},
volume = {349},
number = {},
pages = {199450},
pmid = {39151562},
issn = {1872-7492},
mesh = {*Metagenomics/methods ; *Metagenome ; *Viruses/genetics/classification ; *Computational Biology/methods ; *Data Mining ; *High-Throughput Nucleotide Sequencing ; Humans ; Animals ; },
abstract = {Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research.},
}
@article {pmid39147186,
year = {2024},
author = {Song, J and Zhou, S and Zou, D and Kwan, MP and Cai, J and Lu, J},
title = {Non-linear associations between noise level and people's short-term noise annoyance in different activity contexts.},
journal = {Environmental research},
volume = {260},
number = {},
pages = {119772},
doi = {10.1016/j.envres.2024.119772},
pmid = {39147186},
issn = {1096-0953},
mesh = {Humans ; Male ; Female ; Adult ; *Noise/adverse effects ; Young Adult ; Ecological Momentary Assessment ; Environmental Exposure ; Middle Aged ; Noise, Transportation/adverse effects ; Geographic Information Systems ; Nonlinear Dynamics ; },
abstract = {Recent research has become increasingly interested in the on-linear associations between noise levels and people's short-term noise annoyance. However, there has been limited investigation into measuring short-term noise annoyance and how different activity contexts may affect these non-linear associations. To address this research gap, this study measured people's short-term noise annoyance using real-time Ecological Momentary Assessment (EMA) data and the Day Reconstruction Method's (DRM) recalled data. Corresponding noise levels were captured using Global Positioning Systems and portable noise sensors. Employing the Shapley additive explanations method, we examined the non-linear associations between noise level and people's real-time and recalled noise annoyance across different activity contexts. The results indicated that 1) People had greater sensitivity to noise levels in real-time annoyance (non-linear association threshold: 60 dB) compared to recalled annoyance, which had a higher non-linear association threshold of 70 dB. 2) The non-linear associations between noise level and people's real-time/recalled noise annoyance varied between different activity contexts. People tended to be more sensitive to noise in real-time annoyance than recalled annoyance on travel routes and at workplaces. 3) Among the factors examined, the contribution of noise level varied across activity contexts. Noise level contributed more significantly to people's real-time noise annoyance in outdoor recreational sites and on travel routes. These findings enhance our understanding of the non-linear association between noise level and people's short-term noise annoyance, moving beyond the linear paradigm. Policymakers should consider the non-linear relationships and different activity contexts when implementing noise control measures.},
}
@article {pmid39146704,
year = {2024},
author = {Li, G and Wu, M and Xiao, Y and Tong, Y and Li, S and Qian, H and Zhao, T},
title = {Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {52},
number = {},
pages = {101309},
doi = {10.1016/j.cbd.2024.101309},
pmid = {39146704},
issn = {1878-0407},
mesh = {Animals ; *Bombyx/microbiology/genetics ; *Enterococcus/genetics ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; Proteomics ; Symbiosis ; Multiomics ; },
abstract = {Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.},
}
@article {pmid39146377,
year = {2024},
author = {Nuismer, SL and Basinski, AJ and Schreiner, CL and Eskew, EA and Fichet-Calvet, E and Remien, CH},
title = {Quantifying the risk of spillover reduction programs for human health.},
journal = {PLoS computational biology},
volume = {20},
number = {8},
pages = {e1012358},
pmid = {39146377},
issn = {1553-7358},
support = {R01 GM122079/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Computer Simulation ; *Zoonoses/transmission/epidemiology/prevention &amp; control/virology ; Computational Biology ; Public Health ; Lassa Fever/epidemiology/prevention &amp; control/transmission ; Disease Outbreaks/prevention &amp; control/statistics &amp; numerical data ; Risk Assessment ; Africa, Western/epidemiology ; },
abstract = {Reducing spillover of zoonotic pathogens is an appealing approach to preventing human disease and minimizing the risk of future epidemics and pandemics. Although the immediate human health benefit of reducing spillover is clear, over time, spillover reduction could lead to counterintuitive negative consequences for human health. Here, we use mathematical models and computer simulations to explore the conditions under which unanticipated consequences of spillover reduction can occur in systems where the severity of disease increases with age at infection. Our results demonstrate that, because the average age at infection increases as spillover is reduced, programs that reduce spillover can actually increase population-level disease burden if the clinical severity of infection increases sufficiently rapidly with age. If, however, immunity wanes over time and reinfection is possible, our results reveal that negative health impacts of spillover reduction become substantially less likely. When our model is parameterized using published data on Lassa virus in West Africa, it predicts that negative health outcomes are possible, but likely to be restricted to a small subset of populations where spillover is unusually intense. Together, our results suggest that adverse consequences of spillover reduction programs are unlikely but that the public health gains observed immediately after spillover reduction may fade over time as the age structure of immunity gradually re-equilibrates to a reduced force of infection.},
}
@article {pmid39146316,
year = {2024},
author = {He, YJ and Liao, H and Yang, G and Qiu, W and Xuan, R and Zheng, G and Xu, B and Yang, X and Magnuson, JT and Schlenk, D and Zheng, C},
title = {Perfluorohexanesulfonic Acid (PFHxS) Impairs Lipid Homeostasis in Zebrafish Larvae through Activation of PPARα.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {37},
pages = {16258-16268},
doi = {10.1021/acs.est.4c03053},
pmid = {39146316},
issn = {1520-5851},
mesh = {Animals ; *Zebrafish ; *Larva/drug effects/metabolism ; *Homeostasis ; *PPAR alpha/metabolism ; Lipid Metabolism/drug effects ; Fluorocarbons ; Sulfonic Acids ; },
abstract = {Perfluorohexanesulfonic acid (PFHxS), an emerging short-chain per- and polyfluoroalkyl substance, has been frequently detected in aquatic environments. Adverse outcome pathway studies have shown that perfluorinated compounds impair lipid homeostasis through peroxisome proliferator activated receptors (PPARs). However, many of these studies were performed at high concentrations and may thus be a result of overt toxicity. To better characterize the molecular and key events of PFHxS to biota, early life-stage zebrafish (Danio rerio) were exposed to concentrations detected in the environment (0.01, 0.1, 1, and 10 μg/L). Lipidomic and transcriptomic evaluations were integrated to predict potential molecular targets. PFHxS significantly impaired lipid homeostasis by the dysregulation of glycerophospholipids, fatty acyls, glycerolipids, sphingolipids, prenol lipids, and sterol lipids. Informatic analyses of the lipidome and transcriptome indicated alterations of the PPAR signaling pathway, with downstream changes to retinol, linoleic acid, and glycerophospholipid metabolism. To assess the role of PPARs, potential binding of PFHxS to PPARs was predicted and animals were coexposed to a PPAR antagonist (GW6471). Molecular simulation indicated PFHxS had a 27.1% better binding affinity than oleic acid, an endogenous agonist of PPARα. Antagonist coexposures rescued impaired glycerophosphocholine concentrations altered by PFHxS. These data indicate PPARα activation may be an important molecular initiating event for PFHxS.},
}
@article {pmid39145536,
year = {2024},
author = {Pipes, L and Nielsen, R},
title = {A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39145536},
issn = {2050-084X},
support = {BIO180028//Pittsburgh Supercomputing Center/ ; 1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Advanced Cyberinfrastructure Coordination Ecosystem: Services &amp; Support/ ; R01 GM138634/GM/NIGMS NIH HHS/United States ; K99 GM144747/GM/NIGMS NIH HHS/United States ; },
mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA, Environmental/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical assignment of reads to taxonomic groups. It has long been known that full probabilistic methods for phylogenetic assignment are preferable, but unfortunately, such methods are computationally intensive and are typically inapplicable to modern next-generation sequencing data. We present a fast approximate likelihood method for phylogenetic assignment of DNA sequences. Applying the new method to several mock communities and simulated datasets, we show that it identifies more reads at both high and low taxonomic levels more accurately than other leading methods. The advantage of the method is particularly apparent in the presence of polymorphisms and/or sequencing errors and when the true species is not represented in the reference database.},
}
@article {pmid39145283,
year = {2023},
author = {Boyes, D and Skojec, C and Kawahara, AY and , and , and , and , and , and , },
title = {The genome sequence of the Buff Footman, Eilema depressum (Esper, 1787).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {342},
pmid = {39145283},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Eilema depressum (the Buff Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 622.0 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,038 protein coding genes.},
}
@article {pmid39143756,
year = {2024},
author = {Bauer, IE and Davies, MA and Bona, KA and Hararuk, O and Shaw, CH and Thompson, DK and Kurz, WA and Webster, KL and Garneau, M and McLaughlin, JW and Packalen, MS and Prystupa, E and Sanderson, NK and Tarnocai, C},
title = {Peat profile database from peatlands in Canada.},
journal = {Ecology},
volume = {105},
number = {10},
pages = {e4398},
doi = {10.1002/ecy.4398},
pmid = {39143756},
issn = {1939-9170},
support = {//Government of Canada (Expanding Market Opportunities Program)/ ; },
mesh = {Canada ; *Soil/chemistry ; Databases, Factual ; Ecosystem ; },
abstract = {Peatlands cover approximately 12% of the Canadian landscape and play an important role in the carbon cycle through their centennial- to millennial-scale storage of carbon under waterlogged and anoxic conditions. In recognizing the potential of these ecosystems as natural climate solutions and therefore the need to include them in national greenhouse gas inventories, the Canadian Model for Peatlands module (CaMP v. 2.0) was developed by the Canadian Forest Service. Model parameterization included compiling peat profiles across Canada to calibrate peat decomposition rates from different peatland types, to define typical bulk density profiles, and to describe the hydrological (i.e., water table) response of peatlands to climatic changes. A total of 1217 sites were included in the dataset from published and unpublished sources. The CORESITES table contains site location and summary data for each profile, as well as an estimate of total carbon mass per unit area (in megagrams of C per hectare). Total carbon mass per unit area at each location was calculated using bulk density and carbon content through each profile. The PROFILES table contains data for depth (in centimeters), bulk density (in grams per cubic meter), ash and carbon content (in percentage), and material descriptions for contiguous samples through each peat profile. Data gaps for bulk density and C content were filled using interpolation, regression trees, and assigned values based on material description and/or soil classification to allow for the estimation of total carbon mass per unit area. A subset of the sites (N = 374) also have pH and pore water trace-elemental geochemistry data and are found in the WATER table. The REFERENCES table contains the full citation of each source of the data and is linked to each core location through the SOURCEDATA table. The LOOKUP table defines codes in the database that required more space that what was sufficient in the metadata tables. The data can be accessed on Open Government Canada and will be useful for future work on carbon stock mapping and ecosystem modeling. All metadata and data are provided © Her Majesty the Queen in Right of Canada, 2023 and information contained in this publication may be reproduced for personal or public noncommercial purposes with attribution, whereas commercial reproduction and distribution are prohibited except with written permission from NRCan; complete details are noted in the Supporting Information file Metadata S1 (see Class III.B.3: Copyright restrictions).},
}
@article {pmid39140146,
year = {2024},
author = {Yang, F and Han, QL and Zhao, WD and Zhao, Y},
title = {EC number prediction of protein sequences based on combination of hierarchical and global features.},
journal = {Yi chuan = Hereditas},
volume = {46},
number = {8},
pages = {661-669},
doi = {10.16288/j.yczz.24-102},
pmid = {39140146},
issn = {0253-9772},
mesh = {*Computational Biology/methods ; Amino Acid Sequence ; Proteins/chemistry ; Algorithms ; Sequence Analysis, Protein/methods ; Enzymes/chemistry/metabolism ; },
abstract = {The identification of enzyme functions plays a crucial role in understanding the mechanisms of biological activities and advancing the development of life sciences. However, existing enzyme EC number prediction methods did not fully utilize protein sequence information and still had shortcomings in identification accuracy. To address this issue, we proposed an EC number prediction network using hierarchical features and global features (ECPN-HFGF). This method first utilized residual networks to extract generic features from protein sequences, and then employed hierarchical feature extraction modules and global feature extraction modules to further extract hierarchical and global features of protein sequences. Subsequently, the prediction results of both feature types were combined, and a multitask learning framework was utilized to achieve accurate prediction of enzyme EC numbers. Experimental results indicated that the ECPN-HFGF method performed best in the task of predicting EC numbers for protein sequences, achieving macro F1 and micro F1 scores of 95.5% and 99.0%, respectively. The ECPN-HFGF method effectively combined hierarchical and global features of protein sequences, allowing for rapid and accurate EC number prediction. Compared to current commonly used methods, this method offers significantly higher prediction accuracy, providing an efficient approach for the advancement of enzymology research and enzyme engineering applications.},
}
@article {pmid39139763,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Acer Sober, Anarsia innoxiella (Gregersen &amp; Karsholt, 2017).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {357},
pmid = {39139763},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Anarsia innoxiella (the Acer Sober; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 302.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length.},
}
@article {pmid39139615,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Crescent Groundling, Teleiodes luculella (Hübner, 1813).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {143},
pmid = {39139615},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Teleiodes luculella (the Crescent Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 454.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,943 protein coding genes.},
}
@article {pmid39139614,
year = {2024},
author = {Boyes, D and Crowley, LM and McCulloch, J and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Elm Groundling moth, Carpatolechia fugitivella (Zeller, 1839).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {211},
pmid = {39139614},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Carpatolechia fugitivella (the Elm Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 493.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.26 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,721 protein coding genes.},
}
@article {pmid39137474,
year = {2024},
author = {Tanaka, S and Uraguchi, K and Suzuki, E and Matsumoto, N and Tsumura, M and Fujimoto, S and Miyamoto, S and Yorifuji, T and Ando, M},
title = {Survey of pharyngeal foreign bodies in Japan: An ecological study using the nationwide claims data.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {184},
number = {},
pages = {112055},
doi = {10.1016/j.ijporl.2024.112055},
pmid = {39137474},
issn = {1872-8464},
mesh = {Humans ; *Foreign Bodies/epidemiology ; Japan/epidemiology ; Female ; Male ; Child ; Child, Preschool ; Adolescent ; Infant ; Adult ; *Pharynx ; Young Adult ; Feeding Behavior ; Middle Aged ; Incidence ; Databases, Factual ; Seasons ; Aged ; Sex Distribution ; Age Distribution ; },
abstract = {OBJECTIVE: Pharyngeal foreign bodies (PFBs) are a prevalent disease affected by food culture and dietary habits, with fish bones as the leading cause. Most studies were limited to specific regions, and a nationwide survey was not conducted in Japan. In this ecological study, we aimed to conduct a nationwide analysis of outpatient PFB cases in Japan over three years, focusing on seasonal trends, sex- and age-stratified cases, and regional differences.<br><br>METHODS: We used the National Database of Health Insurance Claims and Specific Health Checkups of Japan open data from April 2019 to March 2022. The case data were analyzed by month, age, sex, and prefecture. Additionally, we calculated the standardized claim ratios (SCRs) for each prefecture and investigated the association between dietary habits, food culture, and SCR of PFBs using a two-level linear regression model.<br><br>RESULTS: We analyzed a total of 164,337 outpatient PFB cases in Japan, revealing an average incidence rate of 45.6 per 100,000 persons. The seasonal trend revealed a peak in July each year from 2019 to 2021, confirming seasonality in PFB incidents. Children reported a higher incidence rate. Living west of Japan and expenditure on fish and shellfish had a strongly positive association with the SCR of PFBs.<br><br>CONCLUSION: Our nationwide survey reveals that, even within Japan, there were regional variations influenced by food culture and dietary habits. The data showed that PFB incidence was higher among children, highlighting the need for preventive education.<br><br>LEVEL OF EVIDENCE: Level 3.},
}
@article {pmid39133313,
year = {2024},
author = {Kuchař, M and Kotěrová, AP and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J},
title = {Correction to: Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.},
journal = {International journal of legal medicine},
volume = {138},
number = {6},
pages = {2739},
doi = {10.1007/s00414-024-03311-2},
pmid = {39133313},
issn = {1437-1596},
}
@article {pmid39132840,
year = {2024},
author = {Vale, FF and Roberts, RJ and Kobayashi, I and Camargo, MC and Rabkin, CS and , },
title = {Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2379440},
pmid = {39132840},
issn = {1949-0984},
support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R03 CA167773/CA/NCI NIH HHS/United States ; K22 CA226395/CA/NCI NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; R01 DK062813/DK/NIDDK NIH HHS/United States ; K07 CA125588/CA/NCI NIH HHS/United States ; P01 CA028842/CA/NCI NIH HHS/United States ; K08 CA252635/CA/NCI NIH HHS/United States ; R01 CA077955/CA/NCI NIH HHS/United States ; R01 CA190612/CA/NCI NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; I01 CX002171/CX/CSRD VA/United States ; R01 ES010178/ES/NIEHS NIH HHS/United States ; R01 DK058587/DK/NIDDK NIH HHS/United States ; },
mesh = {*Helicobacter pylori/genetics/virology ; *Prophages/genetics/physiology ; *Genome, Bacterial ; Humans ; *Phylogeny ; *Genomics ; Helicobacter Infections/microbiology ; },
abstract = {Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.},
}
@article {pmid39131439,
year = {2024},
author = {Menger, J and Magagna, B and Henle, K and Harpke, A and Frenzel, M and Rick, J and Wiltshire, K and Grimm-Seyfarth, A},
title = {FAIR-EuMon: a FAIR-enabling resource for biodiversity monitoring schemes.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e125132},
pmid = {39131439},
issn = {1314-2828},
abstract = {BACKGROUND: Within the scope of the Helmholtz Metadata Collaboration (HMC), the ADVANCE project - Advanced metadata standards for biodiversity survey and monitoring data: supporting of research and conservation - aimed at supporting rich metadata generation with interoperable metadata standards and semantic artefacts that facilitate data access, integration and reuse across terrestrial, freshwater and marine realms. HMC's mission is to facilitate the discovery, access, machine-readability, and reuse of research data across and beyond the Helmholtz Association.<br><br>NEW INFORMATION: We revised, adapted and expanded existing metadata schemas, vocabularies and thesauri to build a FAIR metadata schema and a metadata entry form built on it for users to provide their metadata instances focused on biodiversity monitoring data. The schema is FAIR because it is both machine-interpretable and follows domain-relevant community standards. This report provides a general overview of the project results and instructions on how to access, re-use and complete the metadata form.},
}
@article {pmid39131363,
year = {2024},
author = {Martin, C and Gitter, A and Anantharaman, K},
title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39131363},
issn = {2692-8205},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; },
abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.},
}
@article {pmid39131277,
year = {2024},
author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Anez, GM and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Roha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE},
title = {Complete sequencing of ape genomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39131277},
issn = {2692-8205},
support = {R01 MH120295/MH/NIMH NIH HHS/United States ; UH3 AG064706/AG/NIA NIH HHS/United States ; R35 GM146886/GM/NIGMS NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R01 AG056169/AG/NIA NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; P51 OD011092/OD/NIH HHS/United States ; R56 AG056169/AG/NIA NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; R35 HG011332/HG/NHGRI NIH HHS/United States ; R35 GM133600/GM/NIGMS NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; R35 GM146926/GM/NIGMS NIH HHS/United States ; R35 GM151945/GM/NIGMS NIH HHS/United States ; },
abstract = {We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.},
}
@article {pmid39129912,
year = {2023},
author = {Boyes, D and Hutchinson, F and , and , and , and , and , and , },
title = {The genome sequence of the Brown Rustic, Charanyca ferruginea (Esper, 1785).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {547},
pmid = {39129912},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Charanyca ferruginea (the Brown Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 854.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,126 protein coding genes.},
}
@article {pmid39127755,
year = {2024},
author = {Pekár, S},
title = {Datasets of traits of zodariid spiders (Araneae: Zodariidae).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {862},
pmid = {39127755},
issn = {2052-4463},
mesh = {*Spiders/classification/anatomy &amp; histology/physiology ; Animals ; Ecosystem ; Databases, Factual ; Australia ; },
abstract = {Species traits are essential for inferences on ecology and the evolution of organisms. Spiders are the most abundant and diversified terrestrial predators, playing an important role in a range of ecosystem services. Here, I present datasetse on all traits of zodariid spiders, which are known to be free-living ground-dwellers occurring on all continents (except Antarctica) with the highest species diversity in Australia. I collated the data from published resources. The datasets includes nearly 100 000 trait records on all (90) genera and almost all species (1249) of the family. The majority of the 88 traits collected are morphometric, followed by those relating to ecology, reproduction, and physiology. Morphometric traits were available for the majority of species. Other trait classes were only available for some species. I provide a standardized classification of selected categorical traits (habitat, microhabitat, retreat type, circadian activity, prey, primary defensive, and predators). This is the first complete database of traits of a whole spider family, which is available through the World Spider Trait database.},
}
@article {pmid39122728,
year = {2024},
author = {Hixon, SW and Fernandes, R and Andriamahaihavana, A and Baden, AL and Blanco, MB and Caulier, G and Dammhahn, M and Eeckhaut, I and Eppley, TM and Frédérich, B and Ganzhorn, JU and Garbaras, A and Gibson, D and Goodman, SM and Irwin, M and Kelley, EA and Michel, LN and Lepoint, G and Loudon, JE and Mittelheiser, L and Rakotondranary, J and Rasamisoa, DC and Rasolofonirina, R and Ratovonamana, Y and Razafindramanana, J and Reisdorff, C and Sponheimer, M and Terrana, L and Vasey, N and Crowley, BE},
title = {Introducing IsoMad, a compilation of isotopic datasets for Madagascar.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {857},
pmid = {39122728},
issn = {2052-4463},
mesh = {Madagascar ; *Databases, Factual ; Animals ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; },
abstract = {We present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work by making it easy for researchers to access existing data (even for those who are relatively unfamiliar with the literature) and identify both research gaps and opportunities for using various isotope systems to answer research questions. We also hope that this database will encourage full data reporting in future publications.},
}
@article {pmid39122322,
year = {2024},
author = {Martín, G and Erinjery, JJ and Ediriweera, D and Goldstein, E and Somaweera, R and de Silva, HJ and Lalloo, DG and Iwamura, T and Murray, KA},
title = {Effects of global change on snakebite envenoming incidence up to 2050: a modelling assessment.},
journal = {The Lancet. Planetary health},
volume = {8},
number = {8},
pages = {e533-e544},
pmid = {39122322},
issn = {2542-5196},
mesh = {*Snake Bites/epidemiology ; Incidence ; Sri Lanka/epidemiology ; Humans ; *Climate Change ; Models, Theoretical ; Forecasting ; Animals ; Snakes ; },
abstract = {BACKGROUND: Human activities are driving climate, land cover, and population change (global change), and shifting the baseline geographical distribution of snakebite. The interacting effects of global change on snakes and communities at risk of snakebite are poorly understood, limiting capacity to anticipate and manage future changes in snakebite risk.<br><br>METHODS: In this modelling study, we projected how global change will affect snakebite envenoming incidence in Sri Lanka, as a model system that has a high incidence of snakebite. We used the shared socioeconomic pathway (SSP) scenario analysis framework to integrate forecasts across the domains of: climate change (historical trend from WorldClim plus three underlying regional circulation models [RCMs] in the Coordinated Regional Downscaling Experiment-South Asia repository, with two emissions pathways [representative concentration pathways RCP4.5 and RCP8.5]); land cover change (Dyna-CLUE model); and human population density change (based on Gridded Population of the World data) from Jan 1, 2010 to Dec 31, 2050. Forecasts were integrated under three different development scenarios: a sustainability pathway (SSP1 and no further emissions), a middle-of-the-road pathway (SSP2 and RCP4.5), and a fossil-fuelled pathway (SSP5 and RCP8.5). For SSP2 and SSP5, we nested three different RCMs (CNRM-CM5, GFDL-CCM3, and MPI-ESM-LR; mean averaged to represent consensus) to account for variability in climate predictions. Data were used as inputs to a mechanistic model that predicted snakebite envenoming incidence based on human-snake contact patterns.<br><br>FINDINGS: From 2010 to 2050, at the national level, envenoming incidence in Sri Lanka was projected to decrease by 12&#xb7;0-23&#xb7;0%, depending on the scenario. The rate of decrease in envenoming incidence was higher in SSP5-RCP8.5 than in SSP1 and SSP2-RCP4.5. Change in envenoming incidence was heterogenous across the country. In SSP1, incidence decreased in urban areas expected to have population growth, and with land cover changes towards anthropised classes. In SSP2-RCP4.5 and SSP5-RCP8.5, most areas were projected to have decreases in incidence (SSP5-RCP8.5 showing the largest area with incidence reductions), while areas such as the central highlands and the north of the country showed localised increases. In the model, decreases occurred with human population growth, land use change towards anthropised classes (potentially shifting occupational risk factors), and decreasing abundance of some snake species, potentially due to global warming and reduced climatic and habitat suitability, with displacement of some snake species.<br><br>INTERPRETATION: Snakebite envenoming incidence was projected to decrease overall in the coming decades in Sri Lanka, but with an apparent emerging conflict with sustainability objectives. Therefore, efforts to mitigate snakebite envenoming incidence will need to consider the potential impacts of sustainability interventions, particularly related to climate and land use change and in areas where increases in incidence are projected. In view of global change, neglected tropical diseases and public health issues related to biodiversity, such as snakebite, should be managed collaboratively by both environment and health stakeholders.<br><br>FUNDING: UK Medical Research Council.},
}
@article {pmid39116194,
year = {2024},
author = {Guseva, K and Mohrlok, M and Alteio, L and Schmidt, H and Pollak, S and Kaiser, C},
title = {Bacteria face trade-offs in the decomposition of complex biopolymers.},
journal = {PLoS computational biology},
volume = {20},
number = {8},
pages = {e1012320},
pmid = {39116194},
issn = {1553-7358},
mesh = {Biopolymers/metabolism/chemistry ; *Bacteria/metabolism/enzymology ; Models, Biological ; Computational Biology ; },
abstract = {Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.},
}
@article {pmid39114815,
year = {2023},
author = {Lohse, K and Ebdon, S and Mackintosh, A and Martin, S and Saccheri, IJ and Bourn, NAD and Vila, R and , and , and , and , },
title = {The genome sequence of the Arctic Skipper, Carterocephalus palaemon (Pallas, 1771).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {369},
pmid = {39114815},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Carterocephalus palaemon (the Arctic Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 394.5 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.78 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,032 protein coding genes.},
}
@article {pmid39114490,
year = {2024},
author = {Butlin, R and Mérot, C and , and , and , and , and , },
title = {The genome sequence of a kelp fly, Coelopa pilipes Haliday, 1838.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {197},
pmid = {39114490},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Coelopa pilipes (kelp fly; Arthropoda; Insecta; Diptera; Coelopidae). The genome sequence is 263.0 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length.},
}
@article {pmid39112823,
year = {2024},
author = {Darabi, H and Bazhdar, Y and Ehsani, AH},
title = {Modeling the spatial relationship between landscape services and vulnerability assessment.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {9},
pages = {797},
pmid = {39112823},
issn = {1573-2959},
mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; *Conservation of Natural Resources ; *Ecosystem ; Iran ; Remote Sensing Technology ; Models, Theoretical ; Spatial Analysis ; },
abstract = {Even though many studies have been thus far devoted to landscape services (LS) or vulnerability assessment (VA) alone, the relationship between these two concepts has been less investigated. The current study attempts to model the spatial relationship between LS and VA in the Tarhan area (west of Iran). For this purpose, a combination of the analytic hierarchy process (AHP), remote sensing (RS), and geographic information system (GIS) techniques are applied to assess vulnerability. Variogram models and geostatistical simulations are used for mapping and evaluating landscape services. Moreover, the geographically weighted regression (GWR) is operated to predict the relationship between LS and VA. The results indicate that landform and socioeconomic variables are also two main factors shaping variations in VA. As well, the levels of services provided in the possible landscape are affected by the vulnerability. The assessment accordingly establishes that natural and cultural values have significant effects on services, in terms of their spatial distribution and nature. Exploring the relationship between LS and VA correspondingly depicts that VA has a direct influence on the capacity and entity of LS provision (adjusted R[2] = 0.67). The outcomes of the study provide a foundation for nature management and conservation, although it is less able to analyze the trade-off between ecosystem degradation and future development trends. The nexus of LS and future ecological processes in an integrated system can be thus the subject of further research.},
}
@article {pmid39109333,
year = {2024},
author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful China-mark moth Nymphula nitidulata (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {135},
pmid = {39109333},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Nymphula nitidulata (the Beautiful China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 635.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,031 protein coding genes.},
}
@article {pmid39109332,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Brown Ash Ermine moth, Zelleria hepariella Stainton, 1849.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {242},
pmid = {39109332},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from a male Zelleria hepariella (the Brown Ash Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 428.8 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,718 protein coding genes.},
}
@article {pmid39108663,
year = {2023},
author = {Taylor, SC and Crowley, LM and Luker, S and Harvey, M and , and , and , and , and , and , and , },
title = {The genome sequence of the Downland Villa bee-fly, Villa cingulata (Meigen, 1804).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {526},
pmid = {39108663},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Villa cingulata (the Downland Villa bee-fly; Arthropoda; Insecta; Diptera; Bombyliidae). The genome sequence is 412.6 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 22.43 kilobases in length.},
}
@article {pmid39103962,
year = {2024},
author = {Prakofjewa, J and Sartori, M and Kalle, R and Łuczaj, &#x141; and Karbarz, M and Mattalia, G and Šarka, P and Prūse, B and Stryamets, N and Anegg, M and Kuznetsova, N and Kolosova, V and Belichenko, O and Aziz, MA and Pieroni, A and Sõukand, R},
title = {"But how true that is, I do not know": the influence of written sources on the medicinal use of fungi across the western borderlands of the former Soviet Union.},
journal = {IMA fungus},
volume = {15},
number = {1},
pages = {22},
pmid = {39103962},
issn = {2210-6340},
support = {714874//HORIZON EUROPE European Research Council/ ; },
abstract = {Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanita muscaria, Boletus edulis, Lycoperdon, Morchella, Phallus impudicus and Cetraria islandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotus obliquus, Kombucha) or later popular publications (Cantharellus cibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities.},
}
@article {pmid39103035,
year = {2024},
author = {Shi, C and Cheng, L and Yu, Y and Chen, S and Dai, Y and Yang, J and Zhang, H and Chen, J and Geng, N},
title = {Multi-omics integration analysis: Tools and applications in environmental toxicology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {360},
number = {},
pages = {124675},
doi = {10.1016/j.envpol.2024.124675},
pmid = {39103035},
issn = {1873-6424},
mesh = {*Environmental Pollutants/toxicity ; *Ecotoxicology/methods ; *Proteomics ; Genomics ; Metabolomics ; Animals ; Humans ; Multiomics ; },
abstract = {Nowadays, traditional single-omics study is not enough to explain the causality between molecular alterations and toxicity endpoints for environmental pollutants. With the development of high-throughput sequencing technology and high-resolution mass spectrometry technology, the integrative analysis of multi-omics has become an efficient strategy to understand holistic biological mechanisms and to uncover the regulation network in specific biological processes. This review summarized sample preparation methods, integration analysis tools and the application of multi-omics integration analyses in environmental toxicology field. Currently, omics methods have been widely applied being as the sensitivity of early biological response, especially for low-dose and long-term exposure to environmental pollutants. Integrative omics can reveal the overall changes of genes, proteins, and/or metabolites in the cells, tissues or organisms, which provide new insights into revealing the overall toxicity effects, screening the toxic targets, and exploring the underlying molecular mechanism of pollutants.},
}
@article {pmid39102402,
year = {2024},
author = {Saad-Roy, CM and Morris, SE and Boots, M and Baker, RE and Lewis, BL and Farrar, J and Marathe, MV and Graham, AL and Levin, SA and Wagner, CE and Metcalf, CJE and Grenfell, BT},
title = {Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy.},
journal = {PLoS computational biology},
volume = {20},
number = {8},
pages = {e1012211},
pmid = {39102402},
issn = {1553-7358},
support = {U01 CK000555/CK/NCEZID CDC HHS/United States ; },
mesh = {Humans ; *COVID-19/immunology/prevention &amp; control/epidemiology ; *SARS-CoV-2/immunology ; *COVID-19 Vaccines/immunology ; Vaccination Hesitancy/statistics &amp; numerical data ; Severity of Illness Index ; Vaccination/statistics &amp; numerical data ; Pandemics/prevention &amp; control ; Computational Biology ; },
abstract = {The SARS-CoV-2 pandemic has generated a considerable number of infections and associated morbidity and mortality across the world. Recovery from these infections, combined with the onset of large-scale vaccination, have led to rapidly-changing population-level immunological landscapes. In turn, these complexities have highlighted a number of important unknowns related to the breadth and strength of immunity following recovery or vaccination. Using simple mathematical models, we investigate the medium-term impacts of waning immunity against severe disease on immuno-epidemiological dynamics. We find that uncertainties in the duration of severity-blocking immunity (imparted by either infection or vaccination) can lead to a large range of medium-term population-level outcomes (i.e. infection characteristics and immune landscapes). Furthermore, we show that epidemiological dynamics are sensitive to the strength and duration of underlying host immune responses; this implies that determining infection levels from hospitalizations requires accurate estimates of these immune parameters. More durable vaccines both reduce these uncertainties and alleviate the burden of SARS-CoV-2 in pessimistic outcomes. However, heterogeneity in vaccine uptake drastically changes immune landscapes toward larger fractions of individuals with waned severity-blocking immunity. In particular, if hesitancy is substantial, more robust vaccines have almost no effects on population-level immuno-epidemiology, even if vaccination rates are compensatorily high among vaccine-adopters. This pessimistic scenario for vaccination heterogeneity arises because those few individuals that are vaccine-adopters are so readily re-vaccinated that the duration of vaccinal immunity has no appreciable consequences on their immune status. Furthermore, we find that this effect is heightened if vaccine-hesitants have increased transmissibility (e.g. due to riskier behavior). Overall, our results illustrate the necessity to characterize both transmission-blocking and severity-blocking immune time scales. Our findings also underline the importance of developing robust next-generation vaccines with equitable mass vaccine deployment.},
}
@article {pmid39102091,
year = {2024},
author = {Kuchař, M and Pilmann Kotěrová, A and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J},
title = {Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.},
journal = {International journal of legal medicine},
volume = {138},
number = {6},
pages = {2647-2658},
pmid = {39102091},
issn = {1437-1596},
mesh = {Humans ; *Sex Determination by Skeleton/methods ; Male ; Female ; *Pelvic Bones/diagnostic imaging ; *Algorithms ; *Imaging, Three-Dimensional ; *Forensic Anthropology/methods ; Adult ; Middle Aged ; Aged ; Young Adult ; Portugal ; Aged, 80 and over ; },
abstract = {Thanks to technical progress and the availability of virtual data, sex estimation methods as part of a biological profile are undergoing an inevitable evolution. Further reductions in subjectivity, but potentially also in measurement errors, can be brought by approaches that automate the extraction of variables. Such automatization also significantly accelerates and facilitates the specialist's work. The aim of this study is (1) to apply a previously proposed algorithm (Kuchař et al. 2021) to automatically extract 10 variables used for the DSP2 sex estimation method, and (2) to test the robustness of the new automatic approach in a current heterogeneous population. For the first aim, we used a sample of 240 3D scans of pelvic bones from the same individuals, which were measured manually for the DSP database. For the second aim a sample of 108 pelvic bones from the New Mexico Decedent Image Database was used. The results showed high agreement between automatic and manual measurements with rTEM below 5% for all dimensions except two. The accuracy of final sex estimates based on all 10 variables was excellent (error rate 0.3%). However, we observed a higher number of undetermined individuals in the Portuguese sample (25% of males) and the New Mexican sample (36.5% of females). In conclusion, the procedure for automatic dimension extraction was successfully applied both to a different type of data and to a heterogeneous population.},
}
@article {pmid39101049,
year = {2024},
author = {Boyes, D and Lees, DC and Holland, PWH and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Oak Beauty, Biston strataria (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {35},
pmid = {39101049},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Biston strataria (the Oak Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 424.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,406 protein coding genes.},
}
@article {pmid39100235,
year = {2024},
author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A},
title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.},
journal = {Evolution letters},
volume = {8},
number = {4},
pages = {526-538},
pmid = {39100235},
issn = {2056-3744},
abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.},
}
@article {pmid39099847,
year = {2024},
author = {Kapsetaki, SE and Compton, ZT and Dolan, J and Harris, V&#x39a; and Mellon, W and Rupp, SM and Duke, EG and Harrison, TM and Aksoy, S and Giraudeau, M and Vincze, O and McGraw, KJ and Aktipis, A and Tollis, M and Boddy, A&#x39c; and Maley, CC},
title = {Life history traits and cancer prevalence in birds.},
journal = {Evolution, medicine, and public health},
volume = {12},
number = {1},
pages = {105-116},
pmid = {39099847},
issn = {2050-6201},
support = {R01 CA140657/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND AND OBJECTIVES: Cancer is a disease that affects nearly all multicellular life, including the broad and diverse taxa of Aves. While little is known about the factors that contribute to cancer risk across Aves, life history trade-offs may explain some of this variability in cancer prevalence. We predict birds with high investment in reproduction may have a higher likelihood of developing cancer. In this study, we tested whether life history traits are associated with cancer prevalence in 108 species of birds.<br><br>METHODOLOGY: We obtained life history data from published databases and cancer data from 5,729 necropsies from 108 species of birds across 24 taxonomic orders from 25 different zoological facilities. We performed phylogenetically controlled regression analyses between adult body mass, lifespan, incubation length, clutch size, sexually dimorphic traits, and both neoplasia and malignancy prevalence. We also compared the neoplasia and malignancy prevalence of female and male birds.<br><br>RESULTS: Providing support for a life history trade-off between somatic maintenance and reproduction, we found a positive relationship between clutch size and cancer prevalence across Aves. There was no significant association with body mass, lifespan, incubation length, sexual dimorphism, and cancer.<br><br>CONCLUSIONS AND IMPLICATIONS: Life history theory presents an important framework for understanding differences in cancer defenses across various species. These results suggest a trade-off between reproduction and somatic maintenance, where Aves with small clutch sizes get less cancer.},
}
@article {pmid39099645,
year = {2023},
author = {Obbard, DJ and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Chymomyza fuscimana (Drosophilidae) (Zetterstedt, 1838).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {477},
pmid = {39099645},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Chymomyza fuscimana (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 338.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.47 kilobases in length.},
}
@article {pmid39092794,
year = {2024},
author = {Ma, X and Huete, A and Liu, Y and Zhu, X and Nguyen, H and Miura, T and Chen, M and Li, X and Asrar, G},
title = {A holistic big data approach to understand and manage increasing pollen-induced respiratory allergies under global change.},
journal = {Global change biology},
volume = {30},
number = {8},
pages = {e17451},
doi = {10.1111/gcb.17451},
pmid = {39092794},
issn = {1365-2486},
support = {1027576//National Institute of Food and Agriculture/ ; DP210100347//Australian Research Council/ ; 42171305//National Natural Science Foundation of China/ ; },
mesh = {*Pollen/immunology ; *Big Data ; *Climate Change ; Humans ; Respiratory Hypersensitivity/etiology ; },
}
@article {pmid39092001,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Orange-tailed Clearwing, Synanthedon andrenaeformis (Laspeyres, 1801).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {160},
pmid = {39092001},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Synanthedon andrenaeformis (the Orange-tailed Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 348.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.65 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,867 protein coding genes.},
}
@article {pmid39090383,
year = {2024},
author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H},
title = {Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.},
journal = {Nature methods},
volume = {21},
number = {10},
pages = {1959},
doi = {10.1038/s41592-024-02395-3},
pmid = {39090383},
issn = {1548-7105},
}
@article {pmid39089617,
year = {2024},
author = {Chen, SH and Chen, CH and Lin, HC and Yeh, SA and Hwang, TL and Chen, PJ},
title = {Drug repurposing of cyclin-dependent kinase inhibitors for neutrophilic acute respiratory distress syndrome and psoriasis.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.07.026},
pmid = {39089617},
issn = {2090-1224},
abstract = {BACKGROUND: Neutrophilic inflammation, characterized by dysregulated neutrophil activation, triggers a variety of inflammatory responses such as chemotactic infiltration, oxidative bursts, degranulation, neutrophil extracellular traps (NETs) formation, and delayed turnover. This type of inflammation is pivotal in the pathogenesis of acute respiratory distress syndrome (ARDS) and psoriasis. Despite current treatments, managing neutrophil-associated inflammatory symptoms remains a significant challenge.<br><br>AIM OF REVIEW: This review emphasizes the role of cyclin-dependent kinases (CDKs) in neutrophil activation and inflammation. It aims to highlight the therapeutic potential of repurposing CDK inhibitors to manage neutrophilic inflammation, particularly in ARDS and psoriasis. Additionally, it discusses the necessary precautions for the clinical application of these inhibitors due to potential off-target effects and the need for dose optimization.<br><br>CDKs regulate key neutrophilic functions, including chemotactic responses, degranulation, NET formation, and apoptosis. Repurposing CDK inhibitors, originally developed for cancer treatment, shows promise in controlling neutrophilic inflammation. Clinical anticancer drugs, palbociclib and ribociclib, have demonstrated efficacy in treating neutrophilic ARDS and psoriasis by targeting off-label pathways, phosphoinositide 3-kinase (PI3K) and phosphodiesterase 4 (PDE4), respectively. While CDK inhibitors offer promising therapeutic benefits, their clinical repurposing requires careful consideration of off-target effects and dose optimization. Further exploration and clinical trials are necessary to ensure their safety and efficacy in treating inflammatory conditions.},
}
@article {pmid39086664,
year = {2023},
author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , },
title = {The genome sequence of the Rose-flounced Tabby, Endotricha flammealis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {516},
pmid = {39086664},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Endotricha flammealis (the Rose-flounced Tabby; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 473.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,578 protein coding genes.},
}
@article {pmid39083325,
year = {2024},
author = {Webb, EK and Stevens, JS and Ely, TD and Lebois, LAM and van Rooij, SJH and Bruce, SE and House, SL and Beaudoin, FL and An, X and Neylan, TC and Clifford, GD and Linnstaedt, SD and Germine, LT and Bollen, KA and Rauch, SL and Haran, JP and Storrow, AB and Lewandowski, C and Musey, PI and Hendry, PL and Sheikh, S and Jones, CW and Punches, BE and Swor, RA and Murty, VP and Hudak, LA and Pascual, JL and Seamon, MJ and Datner, EM and Pearson, C and Peak, DA and Domeier, RM and Rathlev, NK and O'Neil, BJ and Sergot, P and Sanchez, LD and Joormann, J and Pizzagalli, DA and Harte, SE and Kessler, RC and Koenen, KC and Ressler, KJ and McLean, SA and Harnett, NG},
title = {Neighborhood Resources Associated With Psychological Trajectories and Neural Reactivity to Reward After Trauma.},
journal = {JAMA psychiatry},
volume = {81},
number = {11},
pages = {1090-1100},
pmid = {39083325},
issn = {2168-6238},
support = {K01 MH129828/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Stress Disorders, Post-Traumatic/physiopathology/diagnostic imaging ; Female ; Male ; *Reward ; Adult ; *Magnetic Resonance Imaging ; *Resilience, Psychological ; Longitudinal Studies ; *Residence Characteristics ; Middle Aged ; Young Adult ; Brain/physiopathology/diagnostic imaging ; Survivors/psychology ; },
abstract = {IMPORTANCE: Research on resilience after trauma has often focused on individual-level factors (eg, ability to cope with adversity) and overlooked influential neighborhood-level factors that may help mitigate the development of posttraumatic stress disorder (PTSD).<br><br>OBJECTIVE: To investigate whether an interaction between residential greenspace and self-reported individual resources was associated with a resilient PTSD trajectory (ie, low/no symptoms) and to test if the association between greenspace and PTSD trajectory was mediated by neural reactivity to reward.<br><br>As part of a longitudinal cohort study, trauma survivors were recruited from emergency departments across the US. Two weeks after trauma, a subset of participants underwent functional magnetic resonance imaging during a monetary reward task. Study data were analyzed from January to November 2023.<br><br>EXPOSURES: Residential greenspace within a 100-m buffer of each participant's home address was derived from satellite imagery and quantified using the Normalized Difference Vegetation Index and perceived individual resources measured by the Connor-Davidson Resilience Scale (CD-RISC).<br><br>MAIN OUTCOME AND MEASURES: PTSD symptom severity measured at 2 weeks, 8 weeks, 3 months, and 6 months after trauma. Neural responses to monetary reward in reward-related regions (ie, amygdala, nucleus accumbens, orbitofrontal cortex) was a secondary outcome. Covariates included both geocoded (eg, area deprivation index) and self-reported characteristics (eg, childhood maltreatment, income).<br><br>RESULTS: In 2597 trauma survivors (mean [SD] age, 36.5 [13.4] years; 1637 female [63%]; 1304 non-Hispanic Black [50.2%], 289 Hispanic [11.1%], 901 non-Hispanic White [34.7%], 93 non-Hispanic other race [3.6%], and 10 missing/unreported [0.4%]), 6 PTSD trajectories (resilient, nonremitting high, nonremitting moderate, slow recovery, rapid recovery, delayed) were identified through latent-class mixed-effect modeling. Multinominal logistic regressions revealed that for individuals with higher CD-RISC scores, greenspace was associated with a greater likelihood of assignment in a resilient trajectory compared with nonremitting high (Wald z test&#x2009;=&#x2009;-3.92; P&#x2009;<&#x2009;.001), nonremitting moderate (Wald z test&#x2009;=&#x2009;-2.24; P&#x2009;=&#x2009;.03), or slow recovery (Wald z test&#x2009;=&#x2009;-2.27; P&#x2009;=&#x2009;.02) classes. Greenspace was also associated with greater neural reactivity to reward in the amygdala (n&#x2009;=&#x2009;288; t277&#x2009;=&#x2009;2.83; adjusted P value&#x2009;=&#x2009;0.02); however, reward reactivity did not differ by PTSD trajectory.<br><br>CONCLUSIONS AND RELEVANCE: In this cohort study, greenspace and self-reported individual resources were significantly associated with PTSD trajectories. These findings suggest that factors at multiple ecological levels may contribute to the likelihood of resiliency to PTSD after trauma.},
}
@article {pmid39082646,
year = {2024},
author = {Mallawaarachchi, V and Wickramarachchi, A and Xue, H and Papudeshi, B and Grigson, SR and Bouras, G and Prahl, RE and Kaphle, A and Verich, A and Talamantes-Becerra, B and Dinsdale, EA and Edwards, RA},
title = {Solving genomic puzzles: computational methods for metagenomic binning.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
pmid = {39082646},
issn = {1477-4054},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; /NH/NIH HHS/United States ; DP220102915//Australian Research Council/ ; RC2DK116713/DK/NIDDK NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Algorithms ; Genomics/methods ; },
abstract = {Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research.},
}
@article {pmid39082518,
year = {2024},
author = {Cabral, BVB and Sousa, GJB and Cordeiro, LI and Maranhão, TA and Pereira, MLD},
title = {Temporal Pattern and Spatial Distribution of Tuberculosis Prevalence Associated with Multimorbidity in Brazil.},
journal = {Revista da Sociedade Brasileira de Medicina Tropical},
volume = {57},
number = {},
pages = {e00408},
pmid = {39082518},
issn = {1678-9849},
mesh = {Humans ; Brazil/epidemiology ; Prevalence ; *Tuberculosis/epidemiology ; *Spatio-Temporal Analysis ; Male ; *Multimorbidity ; Female ; Adult ; Middle Aged ; Chronic Disease/epidemiology ; Socioeconomic Factors ; },
abstract = {BACKGROUND: Four main chronic conditions may be involved in the tuberculosis pathogenic process and/or clinical evolution: HIV/AIDS, diabetes mellitus, mental illness, and Chronic Obstructive Pulmonary Disease. This study aimed to determine the spatiotemporal pattern of tuberculosis (TB) associated with multimorbidity in Brazil.<br><br>METHODS: Ecological study use data from the Notifiable Diseases Information System (SINAN), collected from the electronic portal of the Department of Informatics of the SUS (DATASUS). These data included TB cases that were reported between 2007 and 2021 and were associated with two or more chronic clinical health conditions (multimorbidity).<br><br>RESULTS: A total of 7,795 cases of TB associated with multimorbidity were recorded, with an average growth trend of 4.6% per year (95% Confidence Interval (CI): 3.3-5.9; p<0.001) and higher growth in the first temporal segment (2007 to 2011) (8.9%; 95%CI: 4.2-13.9; p=0.002). The spatial analysis, after Bayesian smoothing, highlighted the main municipalities states of the study, namely: S&#xe3;o Paulo (19.8%; n = 297), Porto Alegre (23.6%; n = 354), and Rio de Janeiro (44.8%; n = 672). The proportion of extremely poor (&#x3b2;=-0.002), the bolsa fam&#xed;lia program (&#x3b2;=0.002), the average per-person income (&#x3b2;=0.001), and the percentage of the population living in households with a density of more than 2 people per bedroom (&#x3b2;=0.001) were related to chronic health conditions.<br><br>CONCLUSIONS: These findings will stimulate public action to manage this situation. However, as this is still a recent topic in the literature, we encourage the development of studies on the synergistic characteristics of TB and other clinical conditions.},
}
@article {pmid39082244,
year = {2024},
author = {Farrell, MJ and Le Guillarme, N and Brierley, L and Hunter, B and Scheepens, D and Willoughby, A and Yates, A and Mideo, N},
title = {The changing landscape of text mining: a review of approaches for ecology and evolution.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2027},
pages = {20240423},
pmid = {39082244},
issn = {1471-2954},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Data Mining ; *Ecology/methods ; *Biological Evolution ; *Natural Language Processing ; Machine Learning ; },
abstract = {In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data from literature are often arduous. Researchers may manually process hundreds to thousands of articles for systematic reviews, meta-analyses, and compiling synthetic datasets. As relevant articles expand to tens or hundreds of thousands, computer-based approaches can increase the efficiency, transparency and reproducibility of literature-based research. Methods available for text mining are rapidly changing owing to developments in machine learning-based language models. We review the growing landscape of approaches, mapping them onto three broad paradigms (frequency-based approaches, traditional Natural Language Processing and deep learning-based language models). This serves as an entry point to learn foundational and cutting-edge concepts, vocabularies, and methods to foster integration of these tools into ecological and evolutionary research. We cover approaches for modelling ecological texts, generating training data, developing custom models and interacting with large language models and discuss challenges and possible solutions to implementing these methods in ecology and evolution.},
}
@article {pmid39081076,
year = {2024},
author = {Levy, O and Shahar, S},
title = {Artificial Intelligence for Climate Change Biology: From Data Collection to Predictions.},
journal = {Integrative and comparative biology},
volume = {64},
number = {3},
pages = {953-974},
doi = {10.1093/icb/icae127},
pmid = {39081076},
issn = {1557-7023},
support = {300/22//Israeli Science Foundation/ ; NGS-84241T-21//National Geographic Society/ ; IOS-1754949//National Science Foundation/ ; },
mesh = {*Climate Change ; *Artificial Intelligence ; Animals ; Big Data ; Microclimate ; Data Collection/methods ; },
abstract = {In the era of big data, ecological research is experiencing a transformative shift, yet big-data advancements in thermal ecology and the study of animal responses to climate conditions remain limited. This review discusses how big data analytics and artificial intelligence (AI) can significantly enhance our understanding of microclimates and animal behaviors under changing climatic conditions. We explore AI's potential to refine microclimate models and analyze data from advanced sensors and camera technologies, which capture detailed, high-resolution information. This integration can allow researchers to dissect complex ecological and physiological processes with unprecedented precision. We describe how AI can enhance microclimate modeling through improved bias correction and downscaling techniques, providing more accurate estimates of the conditions that animals face under various climate scenarios. Additionally, we explore AI's capabilities in tracking animal responses to these conditions, particularly through innovative classification models that utilize sensors such as accelerometers and acoustic loggers. For example, the widespread usage of camera traps can benefit from AI-driven image classification models to accurately identify thermoregulatory responses, such as shade usage and panting. AI is therefore instrumental in monitoring how animals interact with their environments, offering vital insights into their adaptive behaviors. Finally, we discuss how these advanced data-driven approaches can inform and enhance conservation strategies. In particular, detailed mapping of microhabitats essential for species survival under adverse conditions can guide the design of climate-resilient conservation and restoration programs that prioritize habitat features crucial for biodiversity resilience. In conclusion, the convergence of AI, big data, and ecological science heralds a new era of precision conservation, essential for addressing the global environmental challenges of the 21st century.},
}
@article {pmid39080706,
year = {2024},
author = {Hamamoto, K and Mizuyama, M and Nishijima, M and Maeda, A and Gibu, K and Poliseno, A and Iguchi, A and Reimer, JD},
title = {Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {54},
pmid = {39080706},
issn = {2524-6372},
support = {20H00653//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.<br><br>RESULTS: The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.<br><br>CONCLUSION: Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.},
}
@article {pmid39079269,
year = {2024},
author = {Tian, Y and Liu, Y and Yue, L and Zhao, X and Zhou, Q and Uwaremwe, C and Wang, Y and Chen, G and Sha, Y and Zhang, Y and Wang, R},
title = {Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions.},
journal = {Microbiological research},
volume = {287},
number = {},
pages = {127855},
doi = {10.1016/j.micres.2024.127855},
pmid = {39079269},
issn = {1618-0623},
mesh = {*Solanum tuberosum/microbiology/growth &amp; development ; *Fertilizers/analysis ; *Soil Microbiology ; Bacillus amyloliquefaciens/growth &amp; development ; Transcriptome ; Plant Tubers/microbiology/growth &amp; development ; Microbiota ; Soil/chemistry ; Metabolome ; Rhizosphere ; Sucrose/metabolism ; Plant Development ; Metabolomics/methods ; Multiomics ; },
abstract = {Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.},
}
@article {pmid39075558,
year = {2024},
author = {Pinheiro-Junior, EL and Alirahimi, E and Peigneur, S and Isensee, J and Schiffmann, S and Erkoc, P and Fürst, R and Vilcinskas, A and Sennoner, T and Koludarov, I and Hempel, BF and Tytgat, J and Hucho, T and von Reumont, BM},
title = {Diversely evolved xibalbin variants from remipede venom inhibit potassium channels and activate PKA-II and Erk1/2 signaling.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {164},
pmid = {39075558},
issn = {1741-7007},
support = {2016/04761-4//S&#xe3;o Paulo Research Foundation/ ; GOC2319 N//F.W.O.-Vlaanderen/ ; GOA4919 N//F.W.O.-Vlaanderen/ ; G0E7120N//F.W.O.-Vlaanderen/ ; PDM/19/164//KU Leuven funding/ ; CA19144 EUVEN//EU COST Action/ ; },
mesh = {Animals ; *Potassium Channels/metabolism/genetics ; MAP Kinase Signaling System/drug effects ; Phylogeny ; Mice ; Cyclic AMP-Dependent Protein Kinases/metabolism/genetics ; Evolution, Molecular ; Humans ; Arthropod Venoms/chemistry ; },
abstract = {BACKGROUND: The identification of novel toxins from overlooked and taxonomically exceptional species bears potential for various pharmacological applications. The remipede Xibalbanus tulumensis, an underwater cave-dwelling crustacean, is the only crustacean for which a venom system has been described. Its venom contains several xibalbin peptides that have an inhibitor cysteine knot (ICK) scaffold.<br><br>RESULTS: Our screenings revealed that all tested xibalbin variants particularly inhibit potassium channels. Xib1 and xib13 with their eight-cysteine domain similar to spider knottins also inhibit voltage-gated sodium channels. No activity was noted on calcium channels. Expanding the functional testing, we demonstrate that xib1 and xib13 increase PKA-II and Erk1/2 sensitization signaling in nociceptive neurons, which may initiate pain sensitization. Our phylogenetic analysis suggests that xib13 either originates from the common ancestor of pancrustaceans or earlier while xib1 is more restricted to remipedes. The ten-cysteine scaffolded xib2 emerged from xib1, a result that is supported by our phylogenetic and machine learning-based analyses.<br><br>CONCLUSIONS: Our functional characterization of synthesized variants of xib1, xib2, and xib13 elucidates their potential as inhibitors of potassium channels in mammalian systems. The specific interaction of xib2 with Kv1.6 channels, which are relevant to treating variants of epilepsy, shows potential for further studies. At higher concentrations, xib1 and xib13 activate the kinases PKA-II and ERK1/2 in mammalian sensory neurons, suggesting pain sensitization and potential applications related to pain research and therapy. While tested insect channels suggest that all probably act as neurotoxins, the biological function of xib1, xib2, and xib13 requires further elucidation. A novel finding on their evolutionary origin is the apparent emergence of X. tulumensis-specific xib2 from xib1. Our study is an important cornerstone for future studies to untangle the origin and function of these enigmatic proteins as important components of remipede but also other pancrustacean and arthropod venoms.},
}
@article {pmid39074140,
year = {2024},
author = {Melo, D and Pallares, LF and Ayroles, JF},
title = {Reassessing the modularity of gene co-expression networks using the Stochastic Block Model.},
journal = {PLoS computational biology},
volume = {20},
number = {7},
pages = {e1012300},
pmid = {39074140},
issn = {1553-7358},
support = {R01 ES029929/ES/NIEHS NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; },
mesh = {*Drosophila melanogaster/genetics ; Animals ; *Gene Regulatory Networks/genetics ; *Stochastic Processes ; *Algorithms ; *Computational Biology/methods ; Models, Genetic ; Gene Expression Profiling/methods ; },
abstract = {Finding communities in gene co-expression networks is a common first step toward extracting biological insight from these complex datasets. Most community detection algorithms expect genes to be organized into assortative modules, that is, groups of genes that are more associated with each other than with genes in other groups. While it is reasonable to expect that these modules exist, using methods that assume they exist a priori is risky, as it guarantees that alternative organizations of gene interactions will be ignored. Here, we ask: can we find meaningful communities without imposing a modular organization on gene co-expression networks, and how modular are these communities? For this, we use a recently developed community detection method, the weighted degree corrected stochastic block model (SBM), that does not assume that assortative modules exist. Instead, the SBM attempts to efficiently use all information contained in the co-expression network to separate the genes into hierarchically organized blocks of genes. Using RNAseq gene expression data measured in two tissues derived from an outbred population of Drosophila melanogaster, we show that (a) the SBM is able to find ten times as many groups as competing methods, that (b) several of those gene groups are not modular, and that (c) the functional enrichment for non-modular groups is as strong as for modular communities. These results show that the transcriptome is structured in more complex ways than traditionally thought and that we should revisit the long-standing assumption that modularity is the main driver of the structuring of gene co-expression networks.},
}
@article {pmid39071792,
year = {2023},
author = {Falk, S and Gorše, I and , and , and , and , and , and , },
title = {The genome sequence of the hawkweed Cheilosia, Cheilosia urbana (Meigen, 1822).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {311},
pmid = {39071792},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Cheilosia urbana (the hawkweed Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 546.9 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length.},
}
@article {pmid39069513,
year = {2024},
author = {Xu, R and Xu, C and Li, Z and Zheng, T and Yu, W and Yang, C},
title = {Boundary guidance network for medical image segmentation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17345},
pmid = {39069513},
issn = {2045-2322},
support = {2019YFC0117800//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Urinary Bladder Neoplasms/diagnostic imaging/pathology ; Image Processing, Computer-Assisted/methods ; Deep Learning ; Magnetic Resonance Imaging/methods ; Tomography, X-Ray Computed/methods ; Neural Networks, Computer ; Algorithms ; Cystoscopy/methods ; Image Interpretation, Computer-Assisted/methods ; },
abstract = {Accurate segmentation of the tumor area is crucial for the treatment and prognosis of patients with bladder cancer. Cystoscopy is the gold standard for diagnosing bladder tumors. However, The vast majority of current work uses deep learning to identify and segment tumors from CT and MRI findings, and rarely involves cystoscopy findings. Accurately segmenting bladder tumors remains a great challenge due to their diverse morphology and fuzzy boundaries. In order to solve the above problems, this paper proposes a medical image segmentation network with boundary guidance called boundary guidance network. This network combines local features extracted by CNNs and long-range dependencies between different levels inscribed by Parallel ViT, which can capture tumor features more effectively. The Boundary extracted module is designed to extract boundary features and utilize the boundary features to guide the decoding process. Foreground-background dual-channel decoding is performed by boundary integrated module. Experimental results on our proposed new cystoscopic bladder tumor dataset (BTD) show that our method can efficiently perform accurate segmentation of tumors and retain more boundary information, achieving an IoU score of 91.3%, a Hausdorff Distance of 10.43, an mAP score of 85.3%, and a F1 score of 94.8%. On BTD and three other public datasets, our model achieves the best scores compared to state-of-the-art methods, which proves the effectiveness of our model for common medical image segmentation.},
}
@article {pmid39068884,
year = {2024},
author = {Fan, Q and Huang, S and Guo, J and Xie, Y and Chen, M and Chen, Y and Qi, W and Liu, H and Jia, Z and Hu, H and Qu, J},
title = {Spatiotemporal distribution and transport flux of organophosphate esters in the sediment of the Yangtze River.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135312},
doi = {10.1016/j.jhazmat.2024.135312},
pmid = {39068884},
issn = {1873-3336},
abstract = {The Yangtze River Basin is an important area for organophosphate esters (OPEs) consumption and emission. Studies proved high OPE detection in Yangtze River water, but there is limited information about the spatiotemporal distribution and transport flux of OPEs in sediment. The present study investigated 16 OPEs in sediment from upstream to mid-downstream of the Yangtze River. The mean concentration of OPEs was 84.30 ng/g, and alkyl-OPEs was the primary component. Great specific surface area and high content of organic carbon significantly increased OPE concentration in Three Gorges Reservoir (TGR) by physical adsorption and chemical bonds (p < 0.05), making TGR the most contaminated area in mainstream. No significant differences in OPE constituents were found in seasonal distribution. Four potential sources of OPEs were identified by principal component analysis and self-organizing maps, and traffic emissions were the dominant source for OPEs. The hazard quotient model results indicated that aryl-OPEs showed moderate risks in the mainstream of Yangtze River, alkyl-OPEs and Cl-OPEs showed low risks. TGR was a significant sink of OPEs in Yangtze River and buried 7.41 tons of OPEs in 2020, a total of 14.87 tons of OPE were transported into the sea by sediment.},
}
@article {pmid39066932,
year = {2024},
author = {Seldeslachts, A and Maurstad, MF and Øyen, JP and Undheim, EAB and Peigneur, S and Tytgat, J},
title = {Exploring oak processionary caterpillar induced lepidopterism (Part 1): unveiling molecular insights through transcriptomics and proteomics.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {81},
number = {1},
pages = {311},
pmid = {39066932},
issn = {1420-9071},
support = {GOC2319N, GOA4919N, and G0E7120N//Fonds Wetenschappelijk Onderzoek/ ; 12W7822N//Fonds Wetenschappelijk Onderzoek/ ; 1S51521N and 1S51523N//Fonds Wetenschappelijk Onderzoek/ ; CA19144 EUVEN//European Cooperation in Science and Technology/ ; FRIPRO-YRT Fellowship no. 287462//Norwegian Research Council/ ; 101039862//H2020 European Research Council/ ; },
mesh = {Animals ; *Proteomics/methods ; *Transcriptome ; *Moths/genetics ; Arthropod Venoms ; Larva/metabolism ; Quercus ; Gene Expression Profiling ; Allergens/immunology ; Insect Proteins/genetics/metabolism ; Proteome/metabolism ; Computational Biology/methods ; },
abstract = {Lepidopterism, a skin inflammation condition caused by direct or airborne exposure to irritating hairs (setae) from processionary caterpillars, is becoming a significant public health concern. Recent outbreaks of the oak processionary caterpillar (Thaumetopoea processionea) have caused noteworthy health and economic consequences, with a rising frequency expected in the future, exacerbated by global warming promoting the survival of the caterpillar. Current medical treatments focus on symptom relief due to the lack of an effective therapy. While the source is known, understanding the precise causes of symptoms remain incomplete understood. In this study, we employed an advanced method to extract venom from the setae and identify the venom components through high-quality de novo transcriptomics, venom proteomics, and bioinformatic analysis. A total of 171 venom components were identified, including allergens, odorant binding proteins, small peptides, enzymes, enzyme inhibitors, and chitin biosynthesis products, potentially responsible for inflammatory and allergic reactions. This work presents the first comprehensive proteotranscriptomic database of T. processionea, contributing to understanding the complexity of lepidopterism. Furthermore, these findings hold promise for advancing therapeutic approaches to mitigate the global health impact of T. processionea and related caterpillars.},
}
@article {pmid39060281,
year = {2024},
author = {Khaki, JJ and Meiring, JE and Thindwa, D and Henrion, MYR and Jere, TM and Msuku, H and , and Heyderman, RS and Gordon, MA and Giorgi, E},
title = {Modelling Salmonella Typhi in high-density urban Blantyre neighbourhood, Malawi, using point pattern methods.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17164},
pmid = {39060281},
issn = {2045-2322},
support = {106158/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 617 OPP1141321//Bill and Melinda Gates Foundation/ ; },
mesh = {Humans ; *Typhoid Fever/epidemiology/microbiology ; *Salmonella typhi/isolation &amp; purification ; Adolescent ; Child ; Malawi/epidemiology ; Adult ; Child, Preschool ; Male ; Female ; Young Adult ; Incidence ; Infant ; Risk Factors ; Sanitation ; Urban Population ; },
abstract = {Salmonella Typhi is a human-restricted pathogen that is transmitted by the faecal-oral route and causative organism of typhoid fever. Using health facility data from 2016 to 2020, this study focuses on modelling the spatial variation in typhoid risk in Ndirande township in Blantyre. To pursue this objective, we developed a marked inhomogeneous Poisson process model that allows us to incorporate both individual-level and environmental risk factors. The results from our analysis indicate that typhoid cases are spatially clustered, with the incidence decreasing by 54% for a unit increase in the water, sanitation, and hygiene (WASH) score. Typhoid intensity was also higher in children aged below 18 years than in adults. However, our results did not show evidence of a strong temporal variation in typhoid incidence. We also discuss the inferential benefits of using point pattern models to characterise the spatial variation in typhoid risk and outline possible extensions of the proposed modelling framework.},
}
@article {pmid39060268,
year = {2024},
author = {Tagliaferro, S and Maio, S and Pirona, F and Stanisci, I and Sarno, G and Silvi, P and Kermenidou, M and Papaioannou, N and Perchard, R and Prpic, I and Polanska, K and Jerzynska, J and Ramos, E and Rovira, J and Belmonte, J and Snoj Tratnik, JS and Horvat, M and Kocman, D and Spiric, Z and Zickella, J and Fasola, S and La Grutta, S and Malizia, V and Montalbano, L and , and , and Baldacci, S and Annesi-Maesano, I},
title = {Assessing external exposome by implementing an Environmental Data Management System using Open Data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17142},
pmid = {39060268},
issn = {2045-2322},
support = {603946//European Commission/ ; },
mesh = {Humans ; Male ; Female ; *Exposome ; Environmental Exposure ; Data Management ; Environmental Monitoring/methods ; Europe ; Aged, 80 and over ; Cities ; Aged ; },
abstract = {Due to the increasing importance of exposome in environmental epidemiology, feasibility and usefulness of an Environmental Data Management System (EDMS) using Open Data was evaluated. The EDMS includes data from 10 European cities (Celje (Slovenia), Łódź (Poland), Manchester (UK), Palermo (Italy), Paris (France), Porto (Portugal), Regensburg (Germany), Reus (Spain), Rijeka (Croatia), Thessaloniki (Greece)) about external non-specific and specific exposome factors at the city or country level (2017-2020). Findings showed that the highest values of life expectancy were in Reus females (86 years) and Palermo males (81 years). UK had the highest obesity rate (28%), Croatia the highest prescribed drug consumption (62%), Greece and Portugal the highest smoking rates (37%, 42%) and daily alcohol consumption (21%), respectively. The most polluted cities were Thessaloniki for PM10 (38 µg/m[3]), Łódź for PM2.5 (25 µg/m[3]), Porto for NO2 (62 µg/m[3]) and Rijeka for O3 (92 µg/m[3]). Thessaloniki had the highest grey space (98%) and Łódź the highest cumulative amount of pollen (39,041 p/m[3]). The highest daily noise levels ≥ 55 dB was in Reus (81% to traffic) and Regensburg (21% to railway). In drinking water, arsenic had the highest value in Thessaloniki (6.4 µg/L), boron in Celje (24 mg/L) and lead in Paris (46.7 µg/L). Portugal and Greece showed the highest pesticide residues in food (7%). In conclusion, utilizing open-access databases enables the translation of research findings into actionable strategies for public health interventions.},
}
@article {pmid39059890,
year = {2024},
author = {Tikhomirov, L and Semmler, C and McCradden, M and Searston, R and Ghassemi, M and Oakden-Rayner, L},
title = {Medical artificial intelligence for clinicians: the lost cognitive perspective.},
journal = {The Lancet. Digital health},
volume = {6},
number = {8},
pages = {e589-e594},
doi = {10.1016/S2589-7500(24)00095-5},
pmid = {39059890},
issn = {2589-7500},
mesh = {*Artificial Intelligence ; Humans ; *Clinical Decision-Making/methods ; Cognition ; Decision Support Systems, Clinical ; Radiology ; },
abstract = {The development and commercialisation of medical decision systems based on artificial intelligence (AI) far outpaces our understanding of their value for clinicians. Although applicable across many forms of medicine, we focus on characterising the diagnostic decisions of radiologists through the concept of ecologically bounded reasoning, review the differences between clinician decision making and medical AI model decision making, and reveal how these differences pose fundamental challenges for integrating AI into radiology. We argue that clinicians are contextually motivated, mentally resourceful decision makers, whereas AI models are contextually stripped, correlational decision makers, and discuss misconceptions about clinician-AI interaction stemming from this misalignment of capabilities. We outline how future research on clinician-AI interaction could better address the cognitive considerations of decision making and be used to enhance the safety and usability of AI models in high-risk medical decision-making contexts.},
}
@article {pmid39057817,
year = {2024},
author = {Chanda, MM and Purse, BV and Sedda, L and Benz, D and Prasad, M and Reddy, YN and Yarabolu, KR and Byregowda, SM and Carpenter, S and Prasad, G and Rogers, DJ},
title = {Bluetongue Risk Map for Vaccination and Surveillance Strategies in India.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {39057817},
issn = {2076-0817},
support = {BB/H009167/1//BBSRC, DFID, Scottish government/ ; },
abstract = {Bluetongue virus (BTV, Sedoreoviridae: Orbivirus) causes an economically important disease, namely, bluetongue (BT), in domestic and wild ruminants worldwide. BTV is endemic to South India and has occurred with varying severity every year since the virus was first reported in 1963. BT can cause high morbidity and mortality to sheep flocks in this region, resulting in serious economic losses to subsistence farmers, with impacts on food security. The epidemiology of BTV in South India is complex, characterized by an unusually wide diversity of susceptible ruminant hosts, multiple vector species biting midges (Culicoides spp., Diptera: Ceratopogonidae), which have been implicated in the transmission of BTV and numerous co-circulating virus serotypes and strains. BT presence data (1997-2011) for South India were obtained from multiple sources to develop a presence/absence model for the disease. A non-linear discriminant analysis (NLDA) was carried out using temporal Fourier transformed variables that were remotely sensed as potential predictors of BT distribution. Predictive performance was then characterized using a range of different accuracy statistics (sensitivity, specificity, and Kappa). The top ten variables selected to explain BT distribution were primarily thermal metrics (land surface temperature, i.e., LST, and middle infrared, i.e., MIR) and a measure of plant photosynthetic activity (the Normalized Difference Vegetation Index, i.e., NDVI). A model that used pseudo-absence points, with three presence and absence clusters each, outperformed the model that used only the recorded absence points and showed high correspondence with past BTV outbreaks. The resulting risk maps may be suitable for informing disease managers concerned with vaccination, prevention, and control of BT in high-risk areas and for planning future state-wide vector and virus surveillance activities.},
}
@article {pmid39056317,
year = {2024},
author = {Stulberg, EL and Lisabeth, L and Schneider, ALC and Skolarus, L and Kershaw, KN and Zheutlin, AR and Harris, BRE and Sarpong, D and Wong, KH and Sheth, KN and de Havenon, A},
title = {Correlations of Socioeconomic and Clinical Determinants with United States County-Level Stroke Prevalence.},
journal = {Annals of neurology},
volume = {96},
number = {4},
pages = {739-744},
doi = {10.1002/ana.27039},
pmid = {39056317},
issn = {1531-8249},
support = {R01 NS107463/NH/NIH HHS/United States ; 1R38HL167282-01/HI/NHLBI NIH HHS/United States ; R01MD016178/NS/NINDS NIH HHS/United States ; R01NS110721/NS/NINDS NIH HHS/United States ; HT9425-23-1-0981//Department of Defense/ ; R01 HL152741/NH/NIH HHS/United States ; R01 HL156906/NH/NIH HHS/United States ; //American Heart Association/American Stroke Association/ ; U24NS107136/NS/NINDS NIH HHS/United States ; R01EB301114/NS/NINDS NIH HHS/United States ; R01NR018335/NS/NINDS NIH HHS/United States ; /MD/NIMHD NIH HHS/United States ; /AG/NIA NIH HHS/United States ; R01NS130189/NS/NINDS NIH HHS/United States ; U24NS129500/NS/NINDS NIH HHS/United States ; W81XWH-21-1-0590//Department of Defense/ ; K23NS123340/NS/NINDS NIH HHS/United States ; R38 HL167282/HL/NHLBI NIH HHS/United States ; U24NS107215/NS/NINDS NIH HHS/United States ; R01 NS038916/NH/NIH HHS/United States ; U01NS106513/NS/NINDS NIH HHS/United States ; UG3NS130228/NS/NINDS NIH HHS/United States ; K23NS105924/NS/NINDS NIH HHS/United States ; },
mesh = {Humans ; *Stroke/epidemiology ; United States/epidemiology ; Prevalence ; Socioeconomic Factors ; Risk Factors ; Social Class ; Male ; Female ; Adult ; Middle Aged ; Health Services Accessibility ; Aged ; },
abstract = {Socioeconomic status (SES) is a multi-faceted theoretical construct associated with stroke risk and outcomes. Knowing which SES measures best correlate with population stroke metrics would improve its accounting in observational research and inform interventions. Using the Centers for Disease Control and Prevention's (CDC) Population Level Analysis and Community Estimates (PLACES) and other publicly available databases, we conducted an ecological study comparing correlations of different United States county-level SES, health care access and clinical risk factor measures with age-adjusted stroke prevalence. The prevalence of adults living below 150% of the federal poverty level most strongly correlated with stroke prevalence compared to other SES and non-SES measures (correlation coefficient = 0.908, R[2] = 0.825; adjusted partial correlation coefficient: 0.589, R[2] = 0.347). ANN NEUROL 2024;96:739-744.},
}
@article {pmid39056051,
year = {2024},
author = {Navarro-Farfán, MDM and García-Romero, L and Martínez-Cinco, MA and Domínguez-Sánchez, C and Sánchez-Quispe, ST},
title = {Methodology for the assessment of poor-data water resources.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17755},
pmid = {39056051},
issn = {2167-8359},
mesh = {*Water Resources ; Models, Theoretical ; Hydrology/methods ; Environmental Monitoring/methods ; },
abstract = {Surface hydrologic modeling becomes a problem when insufficient spatial and temporal information is available. It is common to have useful modeling periods of less than 15 years. The purpose of this work is to develop a methodology that allows the selection of meteorological and hydrometric stations that are suitable for modeling when information is scarce in the area. Based on the scarcity of data, a series of statistical tests are proposed to eliminate stations according to a decision-making process. Although the number of stations decreases drastically, the information used is reliable and of adequate quality, ensuring less uncertainty in the surface simulation models. Individual basin modeling can be carried out considering the poor data. The transfer of parameters can be applied through the nesting of basins to have information distributed over an extensive area. Therefore, temporally and spatially extended modeling can be achieved with information that preserves statistical parameters over time. If data management and validation is performed, the modeled watersheds are well represented; if this is not done, only 26% to 50% of the runoff is represented.},
}
@article {pmid39053536,
year = {2024},
author = {He, M and Cui, J and Yi, Y and Chen, HW and Zhang, Q and Li, L and Huang, L and Hong, S},
title = {Vegetation increases global climate vulnerability risk by shifting climate zones in response to rising atmospheric CO2.},
journal = {The Science of the total environment},
volume = {949},
number = {},
pages = {174810},
doi = {10.1016/j.scitotenv.2024.174810},
pmid = {39053536},
issn = {1879-1026},
mesh = {*Carbon Dioxide/analysis ; *Climate Change ; *Ecosystem ; Atmosphere/chemistry ; },
abstract = {Global climate zones are experiencing widespread shifts with ongoing rise in atmospheric CO2, influencing vegetation growth and shifting its distributions to challenge ecosystem structure and function, posing threats on ecological and societal safety. However, how rising atmospheric CO2 affects the pace of global climate zone shifts is highly uncertain. More attentions are urgently required to understand the underlying mechanisms and quantifications of regional climate vulnerability in response to rising CO2. In this study, we employ nine Earth system models from CMIP6 to investigate global climate zone shifts with rising CO2, unravel the effects of vegetation physiological response (PHY), and categorize climate vulnerable regions depending on the extent of climate zone shifts. We find that climate zone shifts over half of the global land area, 16.8% of which is contributed by PHY at 4 × CO2. Intriguingly, besides warming, PHY-induced precipitation changes and their interactions with warming dominate about two-fifths of PHY-forced shifts, providing potential direction for model improvement in future predictions of climate zone shifts. Aided with PHY effects, 4 × CO2 imposes substantial climate zone shifts over about one-fifth of the global land area, suggesting substantial changes in local climate and ecosystem structure and functions. Hence, those regions would experience strong climate vulnerability, and face high risk of climate extremes, water scarcity and food production. Our results quantitatively identify the vulnerable regions and unravel the underlying drivers, providing scientific insights to prioritize conservation and restoration efforts to ensure ecological and social safety globally.},
}
@article {pmid39051209,
year = {2024},
author = {de Souza, OF and Araújo, ACB and Vieira, LB and Bachur, JA and Lopez, AGP and Gonçalves, TG and de Abreu, LC},
title = {Sex Disparity in Stroke Mortality among Adults: A Time Series Analysis in the Greater Vitoria Region, Brazil (2000-2021).},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {5},
number = {3},
pages = {402-410},
pmid = {39051209},
issn = {2673-3986},
abstract = {The disparity between the sexes in stroke mortality has been demonstrated in people from different locations. The objective of this study was to analyze the disparity between sexes in stroke mortality in adults in the metropolitan area of Greater Vitoria between 2000 and 2021. Ecological time series design was conducted with a database of the Brazilian Health System Informatics Department. The annual percentage change and average annual percentage change were calculated through joinpoint regression. Pairwise comparisons using parallelism and coincidence tests were applied to compare temporal trends between men and women. Men had higher mortality rates in most years between 2000 and 2021. In contrast, women had higher proportional mortality values in all years evaluated from 2000 to 2021. The paired comparison revealed a disparity between the sexes in the proportional mortality time series (parallelism test: p = 0.003; coincidence test: p < 0.001). However, the time series of the mortality rates showed no disparity between the sexes (parallelism test: p = 0.114; coincidence test: p = 0.093). From 2000 to 2021, there was a disparity in proportional mortality from stroke between the sexes of the population in the metropolitan area of Greater Vitoria, Brazil. However, the time series of mortality rates between the sexes did not reveal any disparity in the study period.},
}
@article {pmid39050029,
year = {2024},
author = {Kryukov, K and Nakahama, N and Kuraku, S},
title = {Genome assembly catalog for species in the Japanese Red List: unlocking endangered biodiversity through genomic inventory.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {583},
pmid = {39050029},
issn = {2046-1402},
mesh = {Animals ; *Biodiversity ; *Endangered Species ; Genome ; *Genomics/methods ; Japan ; },
abstract = {Improvements in DNA sequencing technology are allowing the dramatic increase of whole genome data for a wide variety of species. Such genome sequence data can assist the monitoring of intraspecific genetic diversity, but is often lacking for threatened species. In this project, we focused on the national Red List, a catalog of extinct and threatened species, issued by the Japanese government. We combined the data included in it with the record of genome assembly in NCBI and tabulated the assembly availability of the species in the list. The combined data shows a low percentage (2.1%) of the availability of whole genome sequence data for the taxa ranked on the Japanese Red List as well as a strong bias towards mammals and birds in Animalia and vascular plants in Plantae. Our data presentation highlights potential systematic limitations in genome sequencing (e.g., budget for sequencing large genomes of amphibians) and instructs future policies including which taxon needs more effort for genome sequencing. The resultant tables are available in the original website https://treethinkers.nig.ac.jp/redlist/ and are regularly updated.},
}
@article {pmid39049113,
year = {2024},
author = {Yurkov, A and Visagie, CM and Crous, PW and Hashimoto, A and Baschien, C and Begerow, D and Kemler, M and Schoutteten, N and Stadler, M and Wijayawardene, NN and Hyde, KD and Zhang, N and Boekhout, T and , and May, TW and Thines, M and Hawksworth, DL},
title = {Cultures as types and the utility of viable specimens for fungal nomenclature.},
journal = {IMA fungus},
volume = {15},
number = {1},
pages = {20},
pmid = {39049113},
issn = {2210-6340},
abstract = {The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.},
}
@article {pmid39048683,
year = {2024},
author = {Gauci, V and Pangala, SR and Shenkin, A and Barba, J and Bastviken, D and Figueiredo, V and Gomez, C and Enrich-Prast, A and Sayer, E and Stauffer, T and Welch, B and Elias, D and McNamara, N and Allen, M and Malhi, Y},
title = {Global atmospheric methane uptake by upland tree woody surfaces.},
journal = {Nature},
volume = {631},
number = {8022},
pages = {796-800},
pmid = {39048683},
issn = {1476-4687},
mesh = {*Atmosphere/chemistry ; *Forests ; *Methane/metabolism/analysis ; Taiga ; *Trees/chemistry/metabolism/microbiology ; Tropical Climate ; *Wood/chemistry/metabolism/microbiology ; Greenhouse Gases/analysis/metabolism ; Carbon Isotopes ; Forestry ; Global Warming/prevention &amp; control/statistics &amp; numerical data ; Greenhouse Effect/prevention &amp; control/statistics &amp; numerical data ; },
abstract = {Methane is an important greenhouse gas[1], but the role of trees in the methane budget remains uncertain[2]. Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base[3,4], it has also been suggested that upland trees can serve as a net sink for atmospheric methane[5,6]. Here we examine in situ woody surface methane exchange of upland tropical, temperate and boreal forest trees. We find that methane uptake on woody surfaces, in particular at and above about 2 m above the forest floor, can dominate the net ecosystem contribution of trees, resulting in a net tree methane sink. Stable carbon isotope measurement of methane in woody surface chamber air and process-level investigations on extracted wood cores are consistent with methanotrophy, suggesting a microbially mediated drawdown of methane on and in tree woody surfaces and tissues. By applying terrestrial laser scanning-derived allometry to quantify global forest tree woody surface area, a preliminary first estimate suggests that trees may contribute 24.6-49.9 Tg of atmospheric methane uptake globally. Our findings indicate that the climate benefits of tropical and temperate forest protection and reforestation may be greater than previously assumed.},
}
@article {pmid39048062,
year = {2024},
author = {Kondak, S and Kondak, D and Kabadayi, O and Erdei, L and Rónavári, A and Kónya, Z and Galbács, G and Kolbert, Z},
title = {Current insights into the green synthesis, in planta characterization and phytoeffects of nickel nanoparticles and their agricultural implications.},
journal = {Environmental research},
volume = {260},
number = {},
pages = {119665},
doi = {10.1016/j.envres.2024.119665},
pmid = {39048062},
issn = {1096-0953},
mesh = {*Nickel/toxicity ; *Metal Nanoparticles/toxicity ; Plants/drug effects ; Agriculture ; Green Chemistry Technology ; },
abstract = {The intensifying production and release into the environment as well as the increasing potential in agricultural applications make the relationship between plants and nickel nanoparticles (Ni NPs) a relevant and timely topic. The aim of this review is to give an overview and discuss the latest findings about the relationship of Ni NPs and plants. Ni NPs can be synthesized using phytochemicals derived from plant parts in an environmentally friendly manner. There are several ways for these nanoparticles to enter plant cells and tissues. This can be demonstrated through various imaging and chemical mapping approaches (e.g., transmission electron microscopy, X-ray fluorescence spectroscopy etc.). NiO NPs affect plants at multiple levels, including subcellular, cellular, tissue, organ, and whole-plant levels. However, the effects of Ni NPs on plants' ecological partners (e.g., rhizobiome, pollinators) remain largely unknown despite their ecotoxicological significance. The main cause of the Ni NPs-triggered damages is the reactive oxygen species imbalance as a consequence of the modulation of antioxidants. In non-tolerant plants, the toxicity of NiO NPs can be mitigated by exogenous treatments such as the application of silicon, salicylic acid, or jasmonic acid, which induce defense mechanisms whereas Ni-hypertolerant plant species possess endogenous defense systems, such as cell wall modifications and nitrosative signaling against NiO NP stress. Research highlights the role of Ni NPs in managing fungal diseases, showcasing their antifungal properties against specific pathogens. Due to the essentiality of Ni, the application of Ni NPs as nanofertilizers might be promising and has recently started to come into view.},
}
@article {pmid39047578,
year = {2024},
author = {Maxion, A and Gaebler, AJ and Röhrig, R and Mathiak, K and Zweerings, J and Kutafina, E},
title = {Spectral changes in electroencephalography linked to neuroactive medications: A computational pipeline for data mining and analysis.},
journal = {Computer methods and programs in biomedicine},
volume = {255},
number = {},
pages = {108319},
doi = {10.1016/j.cmpb.2024.108319},
pmid = {39047578},
issn = {1872-7565},
mesh = {Humans ; *Electroencephalography/methods ; *Data Mining/methods ; Carbamazepine/therapeutic use/pharmacology ; Risperidone ; Antipsychotic Agents/pharmacology ; Anticonvulsants/pharmacology/therapeutic use ; Brain/drug effects ; },
abstract = {BACKGROUND AND OBJECTIVES: The increasing amount of open-access medical data provides new opportunities to gain clinically relevant information without recruiting new patients. We developed an open-source computational pipeline, that utilizes the publicly available electroencephalographic (EEG) data of the Temple University Hospital to identify EEG profiles associated with the usage of neuroactive medications. It facilitates access to the data and ensures consistency in data processing and analysis, thus reducing the risk of errors and creating comparable and reproducible results. Using this pipeline, we analyze the influence of common neuroactive medications on brain activity.<br><br>METHODS: The pipeline is constructed using easily controlled modules. The user defines the medications of interest and comparison groups. The data is downloaded and preprocessed, spectral features are extracted, and statistical group comparison with visualization through a topographic EEG map is performed. The pipeline is adjustable to answer a variety of research questions. Here, the effects of carbamazepine and risperidone were statistically compared with control data and with other medications from the same classes (anticonvulsants and antipsychotics).<br><br>RESULTS: The comparison between carbamazepine and the control group showed an increase in absolute and relative power for delta and theta, and a decrease in relative power for alpha, beta, and gamma. Compared to antiseizure medications, carbamazepine showed an increase in alpha and theta for absolute powers, and for relative powers an increase in alpha and theta, and a decrease in gamma and delta. Risperidone compared with the control group showed a decrease in absolute and relative power for alpha and beta and an increase in theta for relative power. Compared to antipsychotic medications, risperidone showed a decrease in delta for absolute powers. These results show good agreement with state-of-the-art research. The database allows to create large groups for many different medications. Additionally, it provides a collection of records labeled as "normal" after expert assessment, which is convenient for the creation of control groups.<br><br>CONCLUSIONS: The pipeline allows fast testing of different hypotheses regarding links between medications and EEG spectrum through ecological usage of readily available data. It can be utilized to make informed decisions about the design of new clinical studies.},
}
@article {pmid39045996,
year = {2024},
author = {Lima, AGCF and Ribeiro, CJN and Lima, SVMA and Barbosa, YM and Oliveira, IM and Araújo, KCGM},
title = {Space-time analysis of work-related musculoskeletal disorders in Brazil: an ecological study.},
journal = {Cadernos de saude publica},
volume = {40},
number = {7},
pages = {e00141823},
pmid = {39045996},
issn = {1678-4464},
mesh = {Humans ; Brazil/epidemiology ; *Musculoskeletal Diseases/epidemiology ; *Occupational Diseases/epidemiology ; *Spatio-Temporal Analysis ; Incidence ; Male ; Female ; Bayes Theorem ; Risk Factors ; Adult ; },
abstract = {This study aimed to analyze the incidence of work-related musculoskeletal disorders (WMSD) in Brazil from 2007 to 2019, examining the spatial, temporal, and spatiotemporal patterns of their occurrence. An ecological time series study was conducted using spatial analysis techniques. WMSD morbidity data from 2007 to 2019 were collected from the Brazilian Information System for Notificable Diseases of the Brazilian Health Informatics Department. Incidence rates were standardized and smoothed using the local empirical Bayes' theorem. Time trends were analyzed by segmented linear regression. Spatial analysis was performed using Moran's univariate global (I) and local (LISA) indexes. The spatiotemporal scan statistic was used to identify high-risk spatiotemporal clusters for WMSD. A total of 93,387 cases of WMSD were recorded in Brazil. Temporal trends showed an increase in all regions except the Northeast, which remained stable. The incidence of WMSD showed a spatial dependence, with spatial and space-time clusters identified, especially in the Southeast region, overlapping the largest economic-industrial center of the country. The spatiotemporal clustering observed in one region suggests the highest level of industrial and economic development. Our findings highlight the need to implement intersectoral surveillance policies, inspect working conditions, and invest in the prevention and promotion of workers' health.},
}
@article {pmid39045504,
year = {2024},
author = {Märtz, J and Tallian, A and Wikenros, C and Heeres, RW},
title = {"ClusterApp": A Shiny R application to guide cluster studies based on GPS data.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11695},
pmid = {39045504},
issn = {2045-7758},
abstract = {The rapid evolution of GPS devices, and therefore, collection of GPS data can be used to investigate a wide variety of topics in wildlife research. The combination of remotely collected GPS data with on-the-ground field investigations is a powerful tool for exploring behavioral ecology. "GPS cluster studies" are aimed at pinpointing and investigating identified clusters in the field. Activity clusters can be based on various parameters (e.g., distance between GPS locations and the number of locations needed to establish a cluster), which are closely related to the set research questions. Variation in methods across years within the same study may result in data collection biases. Therefore, a streamlined method to parametrize, generate interactive maps, and extract activity cluster data using a predefined approach will limit biases, and make field work and data management straightforward for field technicians. We developed the "ClusterApp" Shiny application in the R software to facilitate a step-by-step guide to execute cluster analyses and data management of cluster studies on any species using GPS data. We illustrate the use of the "ClusterApp" with two location datasets constructed by data collected on brown bears (Ursus arctos) and gray wolves (Canis lupus).},
}
@article {pmid39032255,
year = {2024},
author = {Hossain, M and Wiegand, B and Reza, A and Chaudhuri, H and Mukhopadhyay, A and Yadav, A and Patra, PK},
title = {A machine learning approach to investigate the impact of land use land cover (LULC) changes on groundwater quality, health risks and ecological risks through GIS and response surface methodology (RSM).},
journal = {Journal of environmental management},
volume = {366},
number = {},
pages = {121911},
doi = {10.1016/j.jenvman.2024.121911},
pmid = {39032255},
issn = {1095-8630},
mesh = {*Groundwater/analysis ; *Machine Learning ; *Water Quality ; *Geographic Information Systems ; India ; Environmental Monitoring/methods ; Bayes Theorem ; Humans ; Agriculture ; },
abstract = {Groundwater resources are enormously affected by land use land cover (LULC) dynamics caused by increasing urbanisation, agricultural and household discharge as a result of global population growth. This study investigates the impact of decadal LULC changes in groundwater quality, human and ecological health from 2009 to 2021 in a diverse landscape, West Bengal, India. Using groundwater quality data from 479 wells in 2009 and 734 well in 2021, a recently proposed Water Pollution Index (WPI) was computed, and its geospatial distribution by a machine learning-based 'Empirical Bayesian Kriging' (EBK) tool manifested a decline in water quality since the number of excellent water category decreased from 30.5% to 28% and polluted water increased from 44% to 45%. ANOVA and Friedman tests revealed statistically significant differences (p < 0.0001) in year-wise water quality parameters as well as group comparisons for both years. Landsat 7 and 8 satellite images were used to classify the LULC types applying machine learning tools for both years, and were coupled with response surface methodology (RSM) for the first time, which revealed that the alteration of groundwater quality were attributed to LULC changes, e.g. WPI showed a positive correlation with built-up areas, village-vegetation cover, agricultural lands, and a negative correlation with surface water, barren lands, and forest cover. Expansion in built-up areas by 0.7%, and village-vegetation orchards by 2.3%, accompanied by a reduction in surface water coverage by 0.6%, and 2.4% in croplands caused a 1.5% drop in excellent water and 1% increase in polluted water category. However, ecological risks through the ecological risk index (ERI) exhibited a lower risk in 2021 attributed to reduced high-risk potential zones. This study highlights the potentiality in linking LULC and water quality changes using some advanced statistical tools like GIS and RSM for better management of water quality and landscape ecology.},
}
@article {pmid39032150,
year = {2024},
author = {Kim, J and Foo, JC and Murata, T and Togo, F},
title = {Reduced heart rate variability is related to fluctuations in psychological stress levels in daily life.},
journal = {Stress and health : journal of the International Society for the Investigation of Stress},
volume = {40},
number = {5},
pages = {e3447},
doi = {10.1002/smi.3447},
pmid = {39032150},
issn = {1532-2998},
support = {19K24283//Japan Society for the Promotion of Science/ ; 21K17681//Japan Society for the Promotion of Science/ ; 031L0190A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {Humans ; *Heart Rate/physiology ; *Stress, Psychological/physiopathology/psychology ; Male ; Female ; Adult ; *Ecological Momentary Assessment ; Young Adult ; Affect/physiology ; Exercise/psychology/physiology ; },
abstract = {Laboratory-based studies have shown that psychological stress caused by response to various stressors triggers acute changes in the cardiovascular system. A better understanding is needed of the emerging evidence on temporal associations between psychological stress and cardiovascular responses in natural settings. This study examined the association of psychological stress and heart rate variability (HRV) in daily life, at high resolution over 2 weeks, taking the effect of physical activity into account. Participants (n = 34) completed ecological momentary assessments (EMA) 6 times per day, reporting levels of perceived stress, low-arousal negative affect (LNA), and high-arousal negative affect. Chest-mounted heart-rate monitors were worn to assess HRV. Multilevel models were used to examine the association between psychological stress levels and preceding/subsequent HRV. Reduced time domain HRV measures (mean and standard deviation of R-wave to R-wave intervals) during the prior hour predicted higher levels of perceived stress. Frequency domain HRV measures higher low to high frequency (LF/HF) and lower HF to total power (HF nu) ratios during the preceding 10 min predicted higher perceived stress levels, suggesting the dominance of sympathetic nervous system activity. EMA reports of higher perceived stress levels were associated with reduced time domain HRV measures during the following 10 min. On the other hand, higher LNA were related to increased HRV measures, such as lower LF/HF and higher HF nu during the following hour. The dynamic associations observed may have therapeutic implications for 'just-in-time' interventions in the management of daily stress and cardiovascular health.},
}
@article {pmid39031697,
year = {2024},
author = {Zembere, K and Jones, CM and Mthawanji, R and Nkolokosa, C and Kamwezi, R and Kalonde, PK and Stanton, MC},
title = {Small dams drive Anopheles abundance during the dry season in a high malaria burden area of Malawi.},
journal = {Medical and veterinary entomology},
volume = {38},
number = {4},
pages = {375-392},
doi = {10.1111/mve.12733},
pmid = {39031697},
issn = {1365-2915},
support = {215184/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Anopheles/physiology ; Malawi ; *Seasons ; *Mosquito Vectors/physiology ; *Malaria/transmission ; *Population Density ; Larva/physiology/growth &amp; development ; Female ; },
abstract = {This study explores the influence of small dams on the exposure to malaria vectors during the dry season in Kasungu district, Malawi, an area recently identified as high priority for malaria interventions by the National Malaria Control Programme. Small dam impoundments provide communities with a continuous supply of water for domestic and agricultural activities across sub-Saharan Africa and are considered vital to food security and climate change resilience. However, these permanent water bodies also create ideal breeding sites for mosquitoes in typically arid landscapes. The study focuses on a specific dam impoundment and its vicinity, aiming to assess its spatial and temporal influence on indoor vector densities. From May to August 2021, CDC light traps were used to measure indoor mosquito densities for two consecutive nights per month in three communities located at increasing distances from the dam (0, ~1 and ~2 km). Simultaneously, drone imagery was captured for each community, enabling the identification of additional standing water within approximately 400 m of selected households. Larval sampling was carried out within the impoundment periphery and in additional water bodies identified in the drone imagery. Generalised linear mixed models (GLMMs) were employed to analyse the indoor Anopheles abundance data, estimating the effects of household structure (open/closed eaves), month, temperature and water proximity on malaria vector exposure. Throughout 685 trapping nights, a total of 1256 mosquitoes were captured, with 33% (412) being female Anopheles. Among these, 91% were morphologically identified as Anopheles funestus s.l., and 5% as Anopheles gambiae s.l. Catches progressively decline in each consecutive trapping month as the environment became drier. This decline was much slower in Malangano, the community next to the dam, with abundance being notably higher in June and July. Further, the majority of An. gambiae s.l. were caught in May, with none identified in July and August. Anopheles larvae were found both in the impoundment and other smaller water bodies such as irrigation wells in each survey month; however, the presence of these smaller water bodies did not have a significant impact on adult female mosquito catches in the GLMM. The study concludes that proximity to the dam impoundment was the primary driver of differences between survey communities with the abundance in Chikhombwe (~1 km away) and Chiponde (~2 km away) being 0.35 (95% confidence interval [CI], 0.19-0.66) and 0.28 (95% CI, 0.16-0.47) lower than Malangano, respectively, after adjusting for other factors. These findings underscore the importance of targeted interventions, such as larval source management or housing improvements, near small dams to mitigate malaria transmission risks during the dry season. Further research is needed to develop cost-effective strategies for vector control within and around these impoundments.},
}
@article {pmid39029911,
year = {2024},
author = {Tyagi, S and Katara, P},
title = {Metatranscriptomics: A Tool for Clinical Metagenomics.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {8},
pages = {394-407},
doi = {10.1089/omi.2024.0130},
pmid = {39029911},
issn = {1557-8100},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; Metagenome/genetics ; },
abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.},
}
@article {pmid39027808,
year = {2024},
author = {Falk, S and Poole, O and , and , and , and , and , and , and , },
title = {The genome sequence of a hoverfly, Cheilosia impressa (Loew, 1840).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {74},
pmid = {39027808},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Cheilosia impressa (hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 395.0 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.87 kilobases in length.},
}
@article {pmid39026607,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brindled Beauty, Lycia hirtaria (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {303},
pmid = {39026607},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Lycia hirtaria (the Brindled Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 552.0 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length.},
}
@article {pmid39026606,
year = {2023},
author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Little Grey, Eudonia lacustrata (Panzer, 1804).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {302},
pmid = {39026606},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eudonia lacustrata (the Little Grey; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 699.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,652 protein coding genes.},
}
@article {pmid39026203,
year = {2024},
author = {Piacenza, F and Di Rosa, M and Soraci, L and Montesanto, A and Corsonello, A and Cherubini, A and Fabbietti, P and Provinciali, M and Lisa, R and Bonfigli, AR and Filicetti, E and Greco, GI and Muglia, L and Lattanzio, F and Volpentesta, M and Biscetti, L},
title = {Interactions between patterns of multimorbidity and functional status among hospitalized older patients: a novel approach using cluster analysis and association rule mining.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {669},
pmid = {39026203},
issn = {1479-5876},
support = {RF-2013-02358848//Ministero della Salute/ ; },
mesh = {Humans ; Male ; Female ; *Multimorbidity ; Aged ; Cluster Analysis ; *Hospitalization ; Aged, 80 and over ; *Activities of Daily Living ; Functional Status ; Data Mining ; Retrospective Studies ; },
abstract = {BACKGROUND: Multimorbidity (MM) is generally defined as the presence of 2 or more chronic diseases in the same patient and seems to be frequently associated with frailty and poor quality of life. However, the complex interplay between MM and functional status in hospitalized older patients has not been fully elucidated so far. Here, we implemented a 2-step approach, combining cluster analysis and association rule mining to explore how patterns of MM and disease associations change as a function of disability.<br><br>METHODS: This retrospective cohort study included 3366 hospitalized older patients discharged from acute care units of Ancona and Cosenza sites of Italian National Institute on Aging (INRCA-IRCCS) between 2011 and 2017. Cluster analysis and association rule mining (ARM) were used to explore patterns of MM and disease associations in the whole population and after stratifying by dependency in activities of daily living (ADL) at discharge. Sensitivity analyses in men and women were conducted to test for robustness of study findings.<br><br>RESULTS: Out of 3366 included patients, 78% were multimorbid. According to functional status, 22.2% of patients had no disability in ADL (functionally independent group), 22.7% had 1 ADL dependency (mildly dependent group), and 57.4% 2 or more ADL impaired (moderately-severely dependent group). Two main MM clusters were identified in the whole general population and in single ADL groups. ARM revealed interesting within-cluster disease associations, characterized by high lift and confidence. Specifically, in the functionally independent group, the most significant ones involved atrial fibrillation (AF)-anemia and chronic kidney disease (CKD) (lift&#x2009;=&#x2009;2.32), followed by coronary artery disease (CAD)-AF and heart failure (HF) (lift&#x2009;=&#x2009;2.29); in patients with moderate-severe ADL disability, the most significant ARM involved CAD-HF and AF (lift&#x2009;=&#x2009;1.97), thyroid dysfunction and AF (lift&#x2009;=&#x2009;1.75), cerebrovascular disease (CVD)-CAD and AF (lift&#x2009;=&#x2009;1.55), and hypertension-anemia and CKD (lift&#x2009;=&#x2009;1.43).<br><br>CONCLUSIONS: Hospitalized older patients have high rates of MM and functional impairment. Combining cluster analysis to ARM may assist physicians in discovering unexpected disease associations in patients with different ADL status. This could be relevant in the view of individuating personalized diagnostic and therapeutic approaches, according to the modern principles of precision medicine.},
}
@article {pmid39024004,
year = {2024},
author = {Hernandez, R and Hoogendoorn, C and Gonzalez, JS and Pyatak, EA and Crespo-Ramos, G and Schneider, S},
title = {Reliability and Validity of Ecological Momentary Assessment Response Time-Based Measures of Emotional Clarity: Secondary Data Analysis.},
journal = {JMIR mental health},
volume = {11},
number = {},
pages = {e58352},
pmid = {39024004},
issn = {2368-7959},
support = {R01 DK121298/DK/NIDDK NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; UL1 TR001855/TR/NCATS NIH HHS/United States ; UL1 TR000130/TR/NCATS NIH HHS/United States ; R01 AG068190/AG/NIA NIH HHS/United States ; U2C AG060408/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Ecological Momentary Assessment ; Female ; Male ; Reproducibility of Results ; Adult ; *Emotions ; Middle Aged ; Diabetes Mellitus, Type 1/psychology ; Reaction Time/physiology ; Emotional Regulation/physiology ; Data Analysis ; Personal Satisfaction ; Surveys and Questionnaires ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Emotional clarity has often been assessed with self-report measures, but efforts have also been made to measure it passively, which has advantages such as avoiding potential inaccuracy in responses stemming from social desirability bias or poor insight into emotional clarity. Response times (RTs) to emotion items administered in ecological momentary assessments (EMAs) may be an indirect indicator of emotional clarity. Another proposed indicator is the drift rate parameter, which assumes that, aside from how fast a person responds to emotion items, the measurement of emotional clarity also requires the consideration of how careful participants were in providing responses.<br><br>OBJECTIVE: This paper aims to examine the reliability and validity of RTs and drift rate parameters from EMA emotion items as indicators of individual differences in emotional clarity.<br><br>METHODS: Secondary data analysis was conducted on data from 196 adults with type 1 diabetes who completed a 2-week EMA study involving the completion of 5 to 6 surveys daily. If lower RTs and higher drift rates (from EMA emotion items) were indicators of emotional clarity, we hypothesized that greater levels (ie, higher clarity) should be associated with greater life satisfaction; lower levels of neuroticism, depression, anxiety, and diabetes distress; and fewer difficulties with emotion regulation. Because prior literature suggested emotional clarity could be valence specific, EMA items for negative affect (NA) and positive affect were examined separately.<br><br>RESULTS: Reliability of the proposed indicators of emotional clarity was acceptable with a small number of EMA prompts (ie, 4 to 7 prompts in total or 1 to 2 days of EMA surveys). Consistent with expectations, the average drift rate of NA items across multiple EMAs had expected associations with other measures, such as correlations of r=-0.27 (P<.001) with depression symptoms, r=-0.27 (P=.001) with anxiety symptoms, r=-0.15 (P=.03) with emotion regulation difficulties, and r=0.63 (P<.001) with RTs to NA items. People with a higher NA drift rate responded faster to NA emotion items, had greater subjective well-being (eg, fewer depression symptoms), and had fewer difficulties with overall emotion regulation, which are all aligned with the expectation for an emotional clarity measure. Contrary to expectations, the validities of average RTs to NA items, the drift rate of positive affect items, and RTs to positive affect items were not strongly supported by our results.<br><br>CONCLUSIONS: Study findings provided initial support for the validity of NA drift rate as an indicator of emotional clarity but not for that of other RT-based clarity measures. Evidence was preliminary because the sample size was not sufficient to detect small but potentially meaningful correlations, as the sample size of the diabetes EMA study was chosen for other more primary research questions. Further research on passive emotional clarity measures is needed.},
}
@article {pmid39023004,
year = {2024},
author = {Rillig, MC and Li, C and Rodríguez Del Río, &#xc1; and Zhu, YG and Jin, L},
title = {Elevated levels of antibiotic resistance genes as a factor of human-caused global environmental change.},
journal = {Global change biology},
volume = {30},
number = {7},
pages = {e17419},
doi = {10.1111/gcb.17419},
pmid = {39023004},
issn = {1365-2486},
support = {C5063-22G//Research Grants Council of Hong Kong/ ; 2021-DST-004//Ningbo S&amp;T/ ; P0044024//Hong Kong Polytechnic University/ ; P0040336//Hong Kong Polytechnic University/ ; //Alexander-von-Humboldt Foundation/ ; },
mesh = {Humans ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Climate Change ; Ecosystem ; Human Activities ; },
abstract = {Antibiotic resistance genes (ARGs) have moved into focus as a critically important response variable in global change biology, given the increasing environmental and human health threat posed by these genes. However, we propose that elevated levels of ARGs should also be considered a factor of global change, not just a response. We provide evidence that elevated levels of ARGs are a global change factor, since this phenomenon is linked to human activity, occurs globally, and affects biota. We explain why ARGs could be considered the global change factor, rather than the organisms containing them; and we highlight the difference between ARGs and the presence of antibiotics, which are not necessarily linked since elevated levels of ARGs are caused by multiple factors. Importantly, shifting the perspective to elevated levels of ARGs as a factor of global change opens new avenues of research, where ARGs can be the experimental treatment. This includes asking questions about how elevated ARG levels interact with other global change factors, or how ARGs influence ecosystem processes, biodiversity or trophic relationships. Global change biology stands to profit from this new framing in terms of capturing more completely the real extent of human impacts on this planet.},
}
@article {pmid39018100,
year = {2024},
author = {Corponi, F and Li, BM and Anmella, G and Valenzuela-Pascual, C and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Young, AH and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A},
title = {Wearable Data From Subjects Playing Super Mario, Taking University Exams, or Performing Physical Exercise Help Detect Acute Mood Disorder Episodes via Self-Supervised Learning: Prospective, Exploratory, Observational Study.},
journal = {JMIR mHealth and uHealth},
volume = {12},
number = {},
pages = {e55094},
pmid = {39018100},
issn = {2291-5222},
mesh = {Humans ; *Supervised Machine Learning ; Prospective Studies ; *Wearable Electronic Devices/statistics &amp; numerical data/standards ; Male ; Female ; *Mood Disorders/diagnosis/psychology ; Adult ; Exercise/psychology/physiology ; Universities/statistics &amp; numerical data/organization &amp; administration ; },
abstract = {BACKGROUND: Personal sensing, leveraging data passively and near-continuously collected with wearables from patients in their ecological environment, is a promising paradigm to monitor mood disorders (MDs), a major determinant of the worldwide disease burden. However, collecting and annotating wearable data is resource intensive. Studies of this kind can thus typically afford to recruit only a few dozen patients. This constitutes one of the major obstacles to applying modern supervised machine learning techniques to MD detection.<br><br>OBJECTIVE: In this paper, we overcame this data bottleneck and advanced the detection of acute MD episodes from wearables' data on the back of recent advances in self-supervised learning (SSL). This approach leverages unlabeled data to learn representations during pretraining, subsequently exploited for a supervised task.<br><br>METHODS: We collected open access data sets recording with the Empatica E4 wristband spanning different, unrelated to MD monitoring, personal sensing tasks-from emotion recognition in Super Mario players to stress detection in undergraduates-and devised a preprocessing pipeline performing on-/off-body detection, sleep/wake detection, segmentation, and (optionally) feature extraction. With 161 E4-recorded subjects, we introduced E4SelfLearning, the largest-to-date open access collection, and its preprocessing pipeline. We developed a novel E4-tailored transformer (E4mer) architecture, serving as the blueprint for both SSL and fully supervised learning; we assessed whether and under which conditions self-supervised pretraining led to an improvement over fully supervised baselines (ie, the fully supervised E4mer and pre-deep learning algorithms) in detecting acute MD episodes from recording segments taken in 64 (n=32, 50%, acute, n=32, 50%, stable) patients.<br><br>RESULTS: SSL significantly outperformed fully supervised pipelines using either our novel E4mer or extreme gradient boosting (XGBoost): n=3353 (81.23%) against n=3110 (75.35%; E4mer) and n=2973 (72.02%; XGBoost) correctly classified recording segments from a total of 4128 segments. SSL performance was strongly associated with the specific surrogate task used for pretraining, as well as with unlabeled data availability.<br><br>CONCLUSIONS: We showed that SSL, a paradigm where a model is pretrained on unlabeled data with no need for human annotations before deployment on the supervised target task of interest, helps overcome the annotation bottleneck; the choice of the pretraining surrogate task and the size of unlabeled data for pretraining are key determinants of SSL success. We introduced E4mer, which can be used for SSL, and shared the E4SelfLearning collection, along with its preprocessing pipeline, which can foster and expedite future research into SSL for personal sensing.},
}
@article {pmid39015757,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {341},
pmid = {39015757},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Ypsolopha scabrella (the Wainscot Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 853.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,594 protein coding genes.},
}
@article {pmid39015615,
year = {2024},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , },
title = {The genome sequence of the Mottled Pug, Eupithecia exiguata (Hübner, 1813).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {65},
pmid = {39015615},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eupithecia exiguata (the Mottled Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 372.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,194 protein coding genes.},
}
@article {pmid39015613,
year = {2024},
author = {Obbard, DJ and , and , and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Drosophila histrio (Meigen, 1830).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {56},
pmid = {39015613},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Drosophila histrio (the drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 189.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.02 kilobases in length.},
}
@article {pmid39015611,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Dotted Grey Groundling, Athrips mouffetella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {42},
pmid = {39015611},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Athrips mouffetella (the Dotted Grey Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 869.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,889 protein coding genes.},
}
@article {pmid39014019,
year = {2024},
author = {Cavaliere, M and Yang, G and De Dreu, CKW and Gross, J},
title = {Cooperation and social organization depend on weighing private and public reputations.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16443},
pmid = {39014019},
issn = {2045-2322},
mesh = {Humans ; *Cooperative Behavior ; Social Networking ; Game Theory ; Interpersonal Relations ; },
abstract = {To avoid exploitation by defectors, people can use past experiences with others when deciding to cooperate or not ('private information'). Alternatively, people can derive others' reputation from 'public' information provided by individuals within the social network. However, public information may be aligned or misaligned with one's own private experiences and different individuals, such as 'friends' and 'enemies', may have different opinions about the reputation of others. Using evolutionary agent-based simulations, we examine how cooperation and social organization is shaped when agents (1) prioritize private or public information about others' reputation, and (2) integrate others' opinions using a friend-focused or a friend-and-enemy focused heuristic (relying on reputation information from only friends or also enemies, respectively). When agents prioritize public information and rely on friend-and-enemy heuristics, we observe polarization cycles marked by high cooperation, invasion by defectors, and subsequent population fragmentation. Prioritizing private information diminishes polarization and defector invasions, but also results in limited cooperation. Only when using friend-focused heuristics and following past experiences or the recommendation of friends create prosperous and stable populations based on cooperation. These results show how combining one's own experiences and the opinions of friends can lead to stable and large-scale cooperation and highlight the important role of following the advice of friends in the evolution of group cooperation.},
}
@article {pmid39008135,
year = {2024},
author = {Urbano, F and Viterbi, R and Pedrotti, L and Vettorazzo, E and Movalli, C and Corlatti, L},
title = {Correction to: Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {8},
pages = {733},
doi = {10.1007/s10661-024-12886-7},
pmid = {39008135},
issn = {1573-2959},
}
@article {pmid39007251,
year = {2024},
author = {Pili, AN and Leroy, B and Measey, JG and Farquhar, JE and Toomes, A and Cassey, P and Chekunov, S and Grenié, M and van Winkel, D and Maria, L and Diesmos, MLL and Diesmos, AC and Zurell, D and Courchamp, F and Chapple, DG},
title = {Forecasting potential invaders to prevent future biological invasions worldwide.},
journal = {Global change biology},
volume = {30},
number = {7},
pages = {e17399},
doi = {10.1111/gcb.17399},
pmid = {39007251},
issn = {1365-2486},
support = {DP210103050//Australian Research Council/ ; FT200100108//Australian Research Council/ ; IL230100175//Australian Research Council/ ; //Monash University Faculty of Science's Dean's Postgraduate Research Scholarship and Dean's International Postgraduate Research Scholarship, and by Monash University Graduate Research Office's Graduate Research Completion Award and Post-Graduate Publication Award/ ; BIFA3_026//the Philippine Department of Environment and Natural Resources FORIS project and the Global Biodiversity Information Facility Biodiversity Fund for Asia Project/ ; },
mesh = {*Introduced Species ; Animals ; *Forecasting ; *Reptiles/physiology ; *Amphibians/physiology ; Risk Assessment/methods ; Models, Theoretical ; Models, Biological ; },
abstract = {The ever-increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history. Here, we aim to support decision-making by developing a quantitative invasion risk assessment tool based on invasion syndromes (i.e., generalising typical attributes of invasive alien species). We implemented a workflow based on 'Multiple Imputation with Chain Equation' to estimate invasion syndromes from imputed datasets of species' life-history and ecological traits and macroecological patterns. Importantly, our models disentangle the factors explaining (i) transport and introduction and (ii) establishment. We showcase our tool by modelling the invasion syndromes of 466 amphibians and reptile species with invasion history. Then, we project these models to amphibians and reptiles worldwide (16,236 species [c.76% global coverage]) to identify species with a risk of being unintentionally transported and introduced, and risk of establishing alien populations. Our invasion syndrome models showed high predictive accuracy with a good balance between specificity and generality. Unintentionally transported and introduced species tend to be common and thrive well in human-disturbed habitats. In contrast, those with established alien populations tend to be large-sized, are habitat generalists, thrive well in human-disturbed habitats, and have large native geographic ranges. We forecast that 160 amphibians and reptiles without known invasion history could be unintentionally transported and introduced in the future. Among them, 57 species have a high risk of establishing alien populations. Our reliable, reproducible, transferable, statistically robust and scientifically defensible quantitative invasion risk assessment tool is a significant new addition to the suite of decision-support tools needed for developing a future-proof preventative biosecurity globally.},
}
@article {pmid39004905,
year = {2024},
author = {Herraiz, C and Triguero-Ocaña, R and Laguna, E and Jiménez-Ruiz, S and Peralbo-Moreno, A and Martínez-López, B and García-Bocanegra, I and Risalde, M&#xc1; and Vicente, J and Acevedo, P},
title = {Movement-driven modelling reveals new patterns in disease transmission networks.},
journal = {The Journal of animal ecology},
volume = {93},
number = {9},
pages = {1275-1287},
doi = {10.1111/1365-2656.14142},
pmid = {39004905},
issn = {1365-2656},
support = {PID2019-111699RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; AGL2013-48523-C3-1-R//Ministerio de Econom&#xed;a y Competitividad/ ; AGL2016-76358-R//Ministerio de Econom&#xed;a y Competitividad/ ; //European Social Fund/ ; //Government of Castilla-La Mancha/ ; //University of Castilla-La Mancha/ ; },
mesh = {Animals ; Cattle ; Swine ; *Models, Biological ; Spain ; Geographic Information Systems ; Tuberculosis, Bovine/transmission/microbiology ; Swine Diseases/transmission/microbiology ; Movement ; },
abstract = {Interspecific interactions are highly relevant in the potential transmission of shared pathogens in multi-host systems. In recent decades, several technologies have been developed to study pathogen transmission, such as proximity loggers, GPS tracking devices and/or camera traps. Despite the diversity of methods aimed at detecting contacts, the analysis of transmission risk is often reduced to contact rates and the probability of transmission given the contact. However, the latter process is continuous over time and unique for each contact, and is influenced by the characteristics of the contact and the pathogen's relationship with both the host and the environment. Our objective was to assess whether a more comprehensive approach, using a movement-based model which assigns a unique transmission risk to each contact by decomposing transmission into contact formation, contact duration and host characteristics, could reveal disease transmission dynamics that are not detected with more traditional approaches. The model was built from GPS-collar data from two management systems in Spain where animal tuberculosis (TB) circulates: a national park with extensively reared endemic cattle, and an area with extensive free-range pigs and cattle farms. In addition, we evaluated the effect of the GPS device fix rate on the performance of the model. Different transmission dynamics were identified between both management systems. Considering the specific conditions under which each contact occurs (i.e. whether the contact is direct or indirect, its duration, the hosts characteristics, the environmental conditions, etc.) resulted in the identification of different transmission dynamics compared to using only contact rates. We found that fix intervals greater than 30 min in the GPS tracking data resulted in missed interactions, and intervals greater than 2 h may be insufficient for epidemiological purposes. Our study shows that neglecting the conditions under which each contact occurs may result in a misidentification of the real role of each species in disease transmission. This study describes a clear and repeatable framework to study pathogen transmission from GPS data and provides further insights to understand how TB is maintained in multi-host systems in Mediterranean environments.},
}
@article {pmid39004875,
year = {2024},
author = {Taylor, A and Sigona, A and Kelly, M},
title = {Centering Amah Mutsun voices in the analysis of a culturally important, fire-managed coastal grassland.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {34},
number = {6},
pages = {e3014},
doi = {10.1002/eap.3014},
pmid = {39004875},
issn = {1051-0761},
support = {//Critical Mission Studies Grant program of the University of California/ ; //Joseph A. Myers Center for Research on Native American Issues, UC Berkeley/ ; //California Native Plant Society (both statewide and from the Santa Clara Valley chapter)/ ; //UC Berkeley Chapter of Sigma Xi/ ; //California Native Grasslands Association/ ; //Department of Environmental Science, Policy, and Management at UC Berkeley/ ; //University of California Graduate Division Fellowship/ ; //Phi Beta Kappa Fellowship, UC Berkeley/ ; //Inter-institutional Network for Food, Agriculture and Sustainability and Intertribal Agriculture Council Tribal Fellowship/ ; //UC Berkeley Graduate Fellowship in Climate Equity/ ; //Ford Foundation Predoctoral Fellowship Program/ ; //Wilderness Society Scholarship/ ; //UC Berkeley Chancellor's Fellowship/ ; },
mesh = {*Grassland ; California ; *Fires ; *Conservation of Natural Resources ; Humans ; Wildfires ; Indigenous Peoples ; },
abstract = {Indigenous communities throughout California, USA, are increasingly advocating for and practicing cultural fire stewardship, leading to a host of social, cultural, and ecological benefits. Simultaneously, state agencies are recognizing the importance of controlled burning and cultural fire as a means of reducing the risk of severe wildfire while benefiting fire-adapted ecosystems. However, much of the current research on the impacts of controlled burning ignores the cultural importance of these ecosystems, and risks further marginalizing Indigenous knowledge systems. Our work adds a critical Indigenous perspective to the study of controlled burning in California's unique coastal grasslands, one of the most biodiverse and endangered ecosystems in the country. In this study, we partnered with the Amah Mutsun Tribal Band to investigate how the abundance and occurrence of shrubs, cultural plants, and invasive plants differed among three adjacent coastal grasslands with varying fire histories. These three sites are emblematic of the state's diverging approaches to grassland management: fire suppression, fire suppression followed by wildfire, and an exceedingly rare example of a grassland that has been repeatedly burned approximately every 2 years for more than 30 years. We found that Danthonia californica was significantly more abundant on the burned sites, whereas all included shrub species (Baccharis pilularis, Frangula californica, and Rubus ursinus) were significantly more abundant on the site with no recorded fire, results that have important implications for future cultural revitalization efforts and the loss of coastal grasslands to shrub encroachment. In addition to conducting a culturally relevant vegetation survey, we used Sentinel-2 satellite imagery to compare the relative severities of the two most recent fire events within the study area. Critically, we used interviews with Amah Mutsun tribal members to contextualize the results of our vegetation survey and remote sensing analysis, and to investigate how cultural burning contrasts from typical Western fire management approaches in this region. Our study is a novel example of how interviews, field data, and satellite imagery can be combined to gain a deeper ecological and cultural understanding of fire in California's endangered coastal grasslands.},
}
@article {pmid39004446,
year = {2024},
author = {Fummey, E and Navarro, P and Plazzer, JP and Frayling, IM and Knott, S and Tenesa, A},
title = {Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.},
journal = {Journal of medical genetics},
volume = {61},
number = {9},
pages = {861-869},
pmid = {39004446},
issn = {1468-6244},
mesh = {Humans ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/epidemiology ; Female ; United Kingdom/epidemiology ; *Biological Specimen Banks ; Middle Aged ; *DNA Mismatch Repair/genetics ; *Genetic Predisposition to Disease ; Aged ; Heterozygote ; Exome Sequencing ; Incidence ; Adult ; Breast Neoplasms/genetics/epidemiology ; Endometrial Neoplasms/genetics/epidemiology ; DNA-Binding Proteins/genetics ; MutL Protein Homolog 1/genetics ; UK Biobank ; MutS Homolog 2 Protein ; },
abstract = {UNLABELLED: BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.<br><br>METHODS: 830 carriers of pathogenic or likely pathogenic (path_MMR) MMR gene variants classified by InSiGHT were identified in 454&#x2009;756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).<br><br>RESULTS: Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in path_MMR carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in path_MMR carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic PMS2 variants in UKB.<br><br>CONCLUSION: These results support offering incidentally identified carriers of any path_MMR surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in MLH1, MSH2 and MSH6 would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.},
}
@article {pmid39004058,
year = {2024},
author = {Guo, J and Jin, Y and Liu, S and Li, T and Ji, D and Hou, C and Tang, H},
title = {Investigation of the causes and mechanisms of hypoxia in the central Bohai Sea in the summer of 2022.},
journal = {Marine pollution bulletin},
volume = {206},
number = {},
pages = {116710},
doi = {10.1016/j.marpolbul.2024.116710},
pmid = {39004058},
issn = {1879-3363},
mesh = {*Seasons ; China ; *Eutrophication ; *Environmental Monitoring ; *Oceans and Seas ; Seawater/chemistry ; Animals ; Temperature ; },
abstract = {The deep-water area in the central Bohai Sea (BS) serves as a spawning ground and nursery for fish, shrimp, and crabs. Frequent hypoxia will affect the ecological environment in the central BS. Data from an on-site investigation of the central BS in the spring and summer of 2022 were used to analyze the relevant factors generating the occurrence of hypoxia in the central BS through the eutrophication index E, apparent oxygen consumption (AOU), and Spearman correlation. The hypoxia area was largely distributed in the study area's deep water section, and stratification was the main cause of hypoxia at the bottom. Organic matter mineralization, degradation, and biological respiration further exacerbated the hypoxia. In the summer of 2022, temperature stratification was the dominant factor influencing hypoxia.},
}
@article {pmid39001963,
year = {2024},
author = {Lu, Y and Xiao, X and Liang, Y and Li, J and Guo, C and Xu, L and Liu, Q and Xiao, Y and Zhou, S},
title = {Distribution and transformation of potentially toxic elements in cracks under coal mining disturbance in farmland.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {9},
pages = {312},
pmid = {39001963},
issn = {1573-2983},
support = {52130402//State Key Program of National Natural Science Foundation of China/ ; },
mesh = {*Soil Pollutants/analysis/toxicity ; *Coal Mining ; *Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Soil/chemistry ; Farms ; Risk Assessment ; },
abstract = {The ground cracks resulting from coal mining activities induce alterations in the physical and chemical characteristics of soil. However, limited knowledge exists regarding the impact of subsidence caused by coal mining on the distribution of potentially toxic elements (PTEs) fractions in farmland soil. In this study, we collected 19 soil profiles at varying depths from the soil surface and at horizontal distances of 0, 1, 2, and 5 m from the vertical crack. Using BCR extraction fractionation, we determined the geochemical fractions and total concentrations of Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd) and lead (Pb) to investigate their ecological risk, spatial fraction distribution, and main influencing factors. Results showed that the E r i values of Cd appearing in 68.7% of the samples were higher than 40 and less than 80, presented a moderate ecological risk. Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), and lead (Pb) were mainly bound to residual fractions (> 60%) with lower mobility and Cd was dominated by F1 (acid-soluble fractions, 50%) and F2 (reducible fractions, 29%) in surface soil (0-20 cm). The geochemical fractionation revealed that the mobile fractions (F1-acid-soluble and F2-reducible) of PTEs were primarily located near the crack, influenced by available potassium. In contrast, the less mobile fractions (F3-oxidizable and F4-residual) exhibited higher concentrations at distances of 2 and 5 m from the crack, except for arsenic, influenced by the presence of clay particles and available phosphorus.},
}
@article {pmid39001714,
year = {2024},
author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ},
title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39001714},
issn = {1751-7370},
support = {GBMF9741//Gordon and Betty Moore Foundation/ ; 714774//European Union's Horizon 2020 Research and Innovation Programme/ ; /ERC_/European Research Council/International ; 947317//European Union's Horizon 2020 Research and Innovation Programme/ ; 735929LPI//Simons Foundation/ ; FL150100038//Australian Research Council Laureate Fellowship/ ; 812811//Simons Foundation/ ; 101087081//European Union's Horizon Europe ERA Chair Program/ ; URF150571//Royal Society University Research Fellowship/ ; },
mesh = {*Phylogeny ; *Archaea/genetics/classification ; Bacteria/genetics/classification ; Evolution, Molecular ; Genome, Bacterial ; Symbiosis ; Ecology ; },
abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.},
}
@article {pmid39000743,
year = {2024},
author = {Macchia, A and Marinelli, L and Barbaccia, FI and de Caro, T and Hansen, A and Schuberthan, LM and Izzo, FC and Pintus, V and Testa Chiari, K and La Russa, MF},
title = {Mattel's ©Barbie: Preventing Plasticizers Leakage in PVC Artworks and Design Objects through Film-Forming Solutions.},
journal = {Polymers},
volume = {16},
number = {13},
pages = {},
pmid = {39000743},
issn = {2073-4360},
abstract = {The main conservation problem of p-PVC artworks is phthalate-based plasticizer migration. Phthalate migration from the bulk to the surface of the materials leads to the formation of a glossy and oily film on the outer layers, ultimately reducing the flexibility of the material. This study aimed to develop a removable coating for the preservation of contemporary artworks and design objects made of plasticized polyvinyl chloride (p-PVC). Several coatings incorporating chitosan, collagen, and cellulose ethers were assessed as potential barriers to inhibiting plasticizer migration. Analytical techniques including optical microscopy (OM), ultraviolet/visible/near-infrared spectroscopy (UV/Vis/NIR), Fourier transform infrared spectroscopy with attenuated total reflection (FTIR-ATR), and scanning electron microscopy (SEM) were utilized to evaluate the optical and chemical stability of selected coating formulations applied to laboratory p-PVC sheet specimens. Subsequently, formulations were tested on a real tangible example of a design object, ©Barbie doll, characterized by the prevalent issue of plasticizer migration. Furthermore, the results obtained with the tested formulations were evaluated by a group of conservators using a tailored survey. Finally, a suitable coating formulation capable of safeguarding plastic substrates was suggested.},
}
@article {pmid39000053,
year = {2024},
author = {Wang, XY and Ren, CX and Fan, QW and Xu, YP and Wang, LW and Mao, ZL and Cai, XZ},
title = {Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance to Sclerotinia sclerotiorum.},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000053},
issn = {1422-0067},
support = {2021C02064//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; LZ18C140002//Zhejiang Provincial Natural Science Foundation of China/ ; 324CXTD430//Hainan Provincial Natural Science Foundation of China/ ; },
mesh = {*Ascomycota/pathogenicity ; *Machine Learning ; *Disease Resistance/genetics ; *Genome-Wide Association Study ; *Plant Diseases/microbiology/genetics ; *Brassica napus/genetics/microbiology/immunology ; *Calcium Signaling/genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Genomics/methods ; Multiomics ; },
abstract = {Sclerotinia sclerotiorum (Ss) is one of the most devastating fungal pathogens, causing huge yield loss in multiple economically important crops including oilseed rape. Plant resistance to Ss pertains to quantitative disease resistance (QDR) controlled by multiple minor genes. Genome-wide identification of genes involved in QDR to Ss is yet to be conducted. In this study, we integrated several assays including genome-wide association study (GWAS), multi-omics co-localization, and machine learning prediction to identify, on a genome-wide scale, genes involved in the oilseed rape QDR to Ss. Employing GWAS and multi-omics co-localization, we identified seven resistance-associated loci (RALs) associated with oilseed rape resistance to Ss. Furthermore, we developed a machine learning algorithm and named it Integrative Multi-Omics Analysis and Machine Learning for Target Gene Prediction (iMAP), which integrates multi-omics data to rapidly predict disease resistance-related genes within a broad chromosomal region. Through iMAP based on the identified RALs, we revealed multiple calcium signaling genes related to the QDR to Ss. Population-level analysis of selective sweeps and haplotypes of variants confirmed the positive selection of the predicted calcium signaling genes during evolution. Overall, this study has developed an algorithm that integrates multi-omics data and machine learning methods, providing a powerful tool for predicting target genes associated with specific traits. Furthermore, it makes a basis for further understanding the role and mechanisms of calcium signaling genes in the QDR to Ss.},
}
@article {pmid38997687,
year = {2024},
author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R},
title = {Knowledge in motion: temporal dynamics of wild food plant use in the Polish-Lithuanian-Belarusian border region.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {20},
number = {1},
pages = {65},
pmid = {38997687},
issn = {1746-4269},
support = {grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {Lithuania ; Poland ; *Plants, Edible/classification ; Republic of Belarus ; Humans ; Knowledge ; Ethnobotany ; },
abstract = {BACKGROUND: Understanding how Local Ecological Knowledge (LEK) evolves over time is crucial for fostering social and environmental responsibility. This study aims to develop a conceptual model of plant knowledge circulation, providing insights into the temporal dynamics of LEK in the Polish-Lithuanian-Belarusian border region. It explores the key patterns and driving forces behind changes in the use of wild plants for food.<br><br>METHODS: Field research was conducted in 60 rural settlements across Podlasie Voivodeship (Poland), Vilnius Region (Lithuania), and Hrodna Region (Belarus). This included 200 semi-structured interviews and participant observation among two local communities, Lithuanians and Poles. To assess the temporal dynamics of wild food use, we performed a cross-ethnic, cross-border analysis over time, dividing the data into three major temporal dimensions: past, continuous, and recently acquired uses.<br><br>RESULTS: Of the 72 wild plant taxa reported by Poles or Lithuanians in the Polish-Lithuanian-Belarusian borderland, 47 were continuously used for food, 58 were utilised in the past, and 41 were recently acquired. Cross-country trends were similar, with Poland showing more past uses. Diachronic comparisons between Poles and Lithuanians in each studied country revealed no significant differences. Recently acquired taxa overlapped considerably with those used continuously and in the past. The most diversely utilised taxa showed the greatest overlaps. By observing the movement of specific plant taxa within various time dimensions, we distinguished overlapping flow variations: retention (3 taxa), decay (11), invention (8), stagnation (17), revitalisation (6), re-invention (3), and knowledge in motion (24). Shifts in the use of wild food plants were influenced by changes in environmental conditions, governmental policies, cultural practices, and economic factors.<br><br>CONCLUSION: The findings of this study have important implications for improving methods of tracking changes in LEK and enhancing our understanding of the relationship between people and nature. Our results underscore the importance of considering knowledge circulation over time in different directions. Recognising the various stages of knowledge circulation might help in pursuing sustainable solutions that balance the needs of human communities with environmental protection.},
}
@article {pmid38995977,
year = {2024},
author = {Rosenblatt, E and Cook, JD and DiRenzo, GV and Grant, EHC and Arce, F and Pepin, KM and Rudolph, FJ and Runge, MC and Shriner, S and Walsh, DP and Mosher, BA},
title = {Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission.},
journal = {PLoS computational biology},
volume = {20},
number = {7},
pages = {e1012263},
pmid = {38995977},
issn = {1553-7358},
mesh = {Animals ; *Deer/virology ; *COVID-19/transmission/epidemiology/veterinary/virology ; *SARS-CoV-2 ; Humans ; Epidemiological Models ; Animals, Wild/virology ; Computational Biology ; Disease Outbreaks/veterinary/statistics &amp; numerical data ; Zoonoses/transmission/epidemiology/virology ; },
abstract = {Emerging infectious diseases with zoonotic potential often have complex socioecological dynamics and limited ecological data, requiring integration of epidemiological modeling with surveillance. Although our understanding of SARS-CoV-2 has advanced considerably since its detection in late 2019, the factors influencing its introduction and transmission in wildlife hosts, particularly white-tailed deer (Odocoileus virginianus), remain poorly understood. We use a Susceptible-Infected-Recovered-Susceptible epidemiological model to investigate the spillover risk and transmission dynamics of SARS-CoV-2 in wild and captive white-tailed deer populations across various simulated scenarios. We found that captive scenarios pose a higher risk of SARS-CoV-2 introduction from humans into deer herds and subsequent transmission among deer, compared to wild herds. However, even in wild herds, the transmission risk is often substantial enough to sustain infections. Furthermore, we demonstrate that the strength of introduction from humans influences outbreak characteristics only to a certain extent. Transmission among deer was frequently sufficient for widespread outbreaks in deer populations, regardless of the initial level of introduction. We also explore the potential for fence line interactions between captive and wild deer to elevate outbreak metrics in wild herds that have the lowest risk of introduction and sustained transmission. Our results indicate that SARS-CoV-2 could be introduced and maintained in deer herds across a range of circumstances based on testing a range of introduction and transmission risks in various captive and wild scenarios. Our approach and findings will aid One Health strategies that mitigate persistent SARS-CoV-2 outbreaks in white-tailed deer populations and potential spillback to humans.},
}
@article {pmid38994633,
year = {2024},
author = {Gómez-García, A and Prinz, AK and Jiménez, DAA and Zamora, WJ and Barazorda-Ccahuana, HL and Chávez-Fumagalli, M&#xc1; and Valli, M and Andricopulo, AD and da S Bolzani, V and Olmedo, DA and Solís, PN and Núñez, MJ and Rodríguez Pérez, JR and Sánchez, HAV and Cortés Hernández, HF and Mosquera Martinez, OM and Koch, O and Medina-Franco, JL},
title = {Updating and profiling the natural product-likeness of Latin American compound libraries.},
journal = {Molecular informatics},
volume = {43},
number = {7},
pages = {e202400052},
doi = {10.1002/minf.202400052},
pmid = {38994633},
issn = {1868-1751},
mesh = {*Biological Products/chemistry/pharmacology ; Latin America ; Small Molecule Libraries/pharmacology/chemistry ; Drug Discovery ; Cheminformatics ; Databases, Chemical ; },
abstract = {Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.},
}
@article {pmid38992177,
year = {2024},
author = {Alvarez-Mora, I and Arturi, K and Béen, F and Buchinger, S and El Mais, AER and Gallampois, C and Hahn, M and Hollender, J and Houtman, C and Johann, S and Krauss, M and Lamoree, M and Margalef, M and Massei, R and Brack, W and Muz, M},
title = {Progress, applications, and challenges in high-throughput effect-directed analysis for toxicity driver identification - is it time for HT-EDA?.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {38992177},
issn = {1618-2650},
abstract = {The rapid increase in the production and global use of chemicals and their mixtures has raised concerns about their potential impact on human and environmental health. With advances in analytical techniques, in particular, high-resolution mass spectrometry (HRMS), thousands of compounds and transformation products with potential adverse effects can now be detected in environmental samples. However, identifying and prioritizing the toxicity drivers among these compounds remain a significant challenge. Effect-directed analysis (EDA) emerged as an important tool to address this challenge, combining biotesting, sample fractionation, and chemical analysis to unravel toxicity drivers in complex mixtures. Traditional EDA workflows are labor-intensive and time-consuming, hindering large-scale applications. The concept of high-throughput (HT) EDA has recently gained traction as a means of accelerating these workflows. Key features of HT-EDA include the combination of microfractionation and downscaled bioassays, automation of sample preparation and biotesting, and efficient data processing workflows supported by novel computational tools. In addition to microplate-based fractionation, high-performance thin-layer chromatography (HPTLC) offers an interesting alternative to HPLC in HT-EDA. This review provides an updated perspective on the state-of-the-art in HT-EDA, and novel methods/tools that can be incorporated into HT-EDA workflows. It also discusses recent studies on HT-EDA, HT bioassays, and computational prioritization tools, along with considerations regarding HPTLC. By identifying current gaps in HT-EDA and proposing new approaches to overcome them, this review aims to bring HT-EDA a step closer to monitoring applications.},
}
@article {pmid38989474,
year = {2024},
author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {129},
pmid = {38989474},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual specimen of Fragum fragum (a heart cockle; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,153.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 22.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,262 protein coding genes.},
}
@article {pmid38986397,
year = {2024},
author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santschi, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY},
title = {Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050.},
journal = {Marine pollution bulletin},
volume = {206},
number = {},
pages = {116664},
doi = {10.1016/j.marpolbul.2024.116664},
pmid = {38986397},
issn = {1879-3363},
mesh = {Taiwan ; *Carbon Dioxide/analysis ; *Carbon Sequestration ; Environmental Monitoring/methods ; Carbon/analysis ; Oceans and Seas ; Forests ; },
abstract = {Taiwan has pledged to achieve net-zero carbon emissions by 2050, but the current extent of carbon sinks in Taiwan remains unclear. Therefore, this study aims to first review the existing nature-based carbon sinks on land and in the oceans around Taiwan. Subsequently, we suggest potential strategies to reduce CO2 emissions and propose carbon dioxide removal methods (CDRs). The natural carbon sinks by forests, sediments, and oceans in and around Taiwan are approximately 21.5, 42.1, and 96.8 Mt-CO2 y[-1], respectively, which is significantly less than Taiwan's CO2 emissions (280 Mt-CO2 y[-1]). Taiwan must consider decarbonization strategies like using electric vehicles, renewable energy, and hydrogen energy by formulating enabling policies. Besides more precisely assessing both terrestrial and marine carbon sinks, Taiwan should develop novel CDRs such as bioenergy with carbon capture and storage, afforestation, reforestation, biochar, seaweed cultivation, and ocean alkalinity enhancement, to reach carbon neutrality by 2050.},
}
@article {pmid38985613,
year = {2024},
author = {Filice, M and Crocco, MC and Agostino, RG and Barberi, RC and Amelio, D and Imbrogno, S and Formoso, V and Cerra, MC},
title = {An X-ray computed μ-tomography analysis for the characterization of 3D-heart shape in a model of cardiac plasticity.},
journal = {Vascular pharmacology},
volume = {155},
number = {},
pages = {107310},
doi = {10.1016/j.vph.2024.107310},
pmid = {38985613},
issn = {1879-3649},
mesh = {Animals ; *Imaging, Three-Dimensional ; *X-Ray Microtomography ; Heart/diagnostic imaging ; Radiographic Image Interpretation, Computer-Assisted ; },
}
@article {pmid38982382,
year = {2024},
author = {Blazanin, M},
title = {gcplyr: an R package for microbial growth curve data analysis.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {232},
pmid = {38982382},
issn = {1471-2105},
mesh = {*Software ; Computational Biology/methods ; Data Analysis ; },
abstract = {BACKGROUND: Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights.<br><br>RESULTS: To address this need, here I present a newly-developed R package: gcplyr. gcplyr can flexibly import growth curve data in common tabular formats, and reshapes it under a tidy framework that is flexible and extendable, enabling users to design custom analyses or plot data with popular visualization packages. gcplyr can also incorporate metadata and generate or import experimental designs to merge with data. Finally, gcplyr carries out model-free (non-parametric) analyses. These analyses do not require mathematical assumptions about microbial growth dynamics, and gcplyr is able to extract a broad range of important traits, including growth rate, doubling time, lag time, maximum density and carrying capacity, diauxie, area under the curve, extinction time, and more.<br><br>CONCLUSIONS: gcplyr makes scripted analyses of growth curve data in R straightforward, streamlines common data wrangling and analysis steps, and easily integrates with common visualization and statistical analyses.},
}
@article {pmid38979877,
year = {2024},
author = {Overgaard, CK and Jamy, M and Radutoiu, S and Burki, F and Dueholm, MKD},
title = {Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.},
journal = {Molecular ecology resources},
volume = {24},
number = {7},
pages = {e13991},
doi = {10.1111/1755-0998.13991},
pmid = {38979877},
issn = {1755-0998},
support = {9041-00236B//Danmarks Frie Forskningsfond/ ; 2021-04055//Vetenskapsr&#xe5;det/ ; 101044505/ERC_/European Research Council/International ; },
mesh = {*Eukaryota/genetics/classification ; *Computational Biology/methods ; *Benchmarking ; *High-Throughput Nucleotide Sequencing/methods ; *rRNA Operon/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA/methods ; Phylogeny ; },
abstract = {The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operon clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing strategies (PacBio circular consensus sequencing and two Nanopore approaches using unique molecular identifiers) and three tools for resolving amplicons sequence variants (ASVs) (USEARCH, VSEARCH, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essentially error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples, which enables us to identify previously undescribed microeukaryotic lineages.},
}
@article {pmid38977855,
year = {2024},
author = {Sharaf, A and Nesengani, LT and Hayah, I and Kuja, JO and Mdyogolo, S and Omotoriogun, TC and Odogwu, BA and Beedessee, G and Smith, RM and Barakat, A and Moila, AM and El Hamouchi, A and Benkahla, A and Boukteb, A and Elmouhtadi, A and Mafwila, AL and Abushady, AM and Elsherif, AK and Ahmed, B and Wairuri, C and Ndiribe, CC and Ebuzome, C and Kinnear, CJ and Ndlovu, DF and Iraqi, D and El Fahime, E and Assefa, E and Ouardi, F and Belharfi, FZ and Tmimi, FZ and Markey, FB and Radouani, F and Zeukeng, F and Mvumbi, GL and Ganesan, H and Hanachi, M and Nigussie, H and Charoute, H and Benamri, I and Mkedder, I and Haddadi, I and Meftah-Kadmiri, I and Mubiru, JF and Domelevo Entfellner, JK and Rokani, JB and Ogwang, J and Daiga, JB and Omumbo, J and Ideozu, JE and Errafii, K and Labuschagne, K and Komi, KK and Tonfack, LB and Hadjeras, L and Ramantswana, M and Chaisi, M and Botes, MW and Kilian, M and Kvas, M and Melloul, M and Chaouch, M and Khyatti, M and Abdo, M and Phasha-Muchemenye, M and Hijri, M and Mediouni, MR and Hassan, MA and Piro, M and Mwale, M and Maaloum, M and Mavhunga, M and Olivier, NA and Aminou, O and Arbani, O and Souiai, O and Djocgoue, PF and Mentag, R and Zipfel, RD and Tata, RB and Megnekou, R and Muzemil, S and Paez, S and Salifu, SP and Kagame, SP and Selka, S and Edwards, S and Gaouar, SBS and Reda, SRA and Fellahi, S and Khayi, S and Ayed, S and Madisha, T and Sahil, T and Udensi, OU and Ras, V and Ezebuiro, V and Duru, VC and David, X and Geberemichael, Y and Tchiechoua, YH and Mungloo-Dilmohamud, Z and Chen, Z and Happi, C and Kariuki, T and Ziyomo, C and Djikeng, A and Badaoui, B and Mapholi, N and Muigai, A and Osuji, JO and Ebenezer, TE},
title = {Establishing African genomics and bioinformatics programs through annual regional workshops.},
journal = {Nature genetics},
volume = {56},
number = {8},
pages = {1556-1565},
pmid = {38977855},
issn = {1546-1718},
mesh = {*Genomics/education ; *Computational Biology/methods/education ; Africa ; Humans ; Biodiversity ; },
abstract = {The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.},
}
@article {pmid38976642,
year = {2024},
author = {Pisarenco, VA and Vizueta, J and Rozas, J},
title = {GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {7},
pages = {},
pmid = {38976642},
issn = {1367-4811},
support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n of Spain/ ; },
mesh = {*Multigene Family ; *Software ; *Computational Biology/methods ; Genome ; Genomics/methods ; Evolution, Molecular ; Humans ; },
abstract = {MOTIVATION: Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.<br><br>RESULTS: To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.<br><br>GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon.},
}
@article {pmid38974014,
year = {2024},
author = {Cassee, FR and Bleeker, EAJ and Durand, C and Exner, T and Falk, A and Friedrichs, S and Heunisch, E and Himly, M and Hofer, S and Hofstätter, N and Hristozov, D and Nymark, P and Pohl, A and Soeteman-Hernández, LG and Suarez-Merino, B and Valsami-Jones, E and Groenewold, M},
title = {Roadmap towards safe and sustainable advanced and innovative materials. (Outlook for 2024-2030).},
journal = {Computational and structural biotechnology journal},
volume = {25},
number = {},
pages = {105-126},
pmid = {38974014},
issn = {2001-0370},
abstract = {The adoption of innovative advanced materials holds vast potential, contingent upon addressing safety and sustainability concerns. The European Commission advocates the integration of Safe and Sustainable by Design (SSbD) principles early in the innovation process to streamline market introduction and mitigate costs. Within this framework, encompassing ecological, social, and economic factors is paramount. The NanoSafety Cluster (NSC) delineates key safety and sustainability areas, pinpointing unresolved issues and research gaps to steer the development of safe(r) materials. Leveraging FAIR data management and integration, alongside the alignment of regulatory aspects, fosters informed decision-making and innovation. Integrating circularity and sustainability mandates clear guidance, ensuring responsible innovation at every stage. Collaboration among stakeholders, anticipation of regulatory demands, and a commitment to sustainability are pivotal for translating SSbD into tangible advancements. Harmonizing standards and test guidelines, along with regulatory preparedness through an exchange platform, is imperative for governance and market readiness. By adhering to these principles, the effective and sustainable deployment of innovative materials can be realized, propelling positive transformation and societal acceptance.},
}
@article {pmid38973368,
year = {2024},
author = {Martínez, L and Zattara, EE and Arbetman, MP and Morales, CL and Masonbrink, RE and Severin, AJ and Aizen, MA and Toth, AL},
title = {Chromosome-Level Assembly and Annotation of the Genome of the Endangered Giant Patagonian Bumble Bee Bombus dahlbomii.},
journal = {Genome biology and evolution},
volume = {16},
number = {7},
pages = {},
doi = {10.1093/gbe/evae146},
pmid = {38973368},
issn = {1759-6653},
support = {//Fulbright Science and Technology Award, Argentina Commission/ ; //Iowa State University Faculty Professional Development Leave/ ; NGS-57001R-19//National Geographic Society/ ; },
mesh = {Animals ; Bees/genetics ; *Endangered Species ; *Molecular Sequence Annotation ; *Genome, Insect ; Male ; Chromosomes, Insect/genetics ; },
abstract = {This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from a single, haploid male collected in Argentina was used for PacBio (HiFi) sequencing, and Hi-C technology was then used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high-quality, near chromosome-level assembly. The sequenced genome size is estimated at 265 Mb. The genome was annotated based on RNA sequencing data of another male from Argentina, and BRAKER3 produced 15,767 annotated genes. The genome and annotation show high completeness, with >95% BUSCO scores for both the genome and annotated genes (based on conserved genes from Hymenoptera). This genome provides a valuable resource for studying the biology of this iconic and endangered species, as well as for understanding the impacts of its decline and designing strategies for its preservation.},
}
@article {pmid38972117,
year = {2024},
author = {Hyman, S and Zhang, J and Lim, YH and Jovanovic Andersen, Z and Cole-Hunter, T and Li, Y and Møller, P and Daras, K and Williams, R and Thomas, ML and Labib, SM and Topping, D},
title = {Residential greenspace and COVID-19 Severity: A cohort study of 313,657 individuals in Greater Manchester, United Kingdom.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108843},
doi = {10.1016/j.envint.2024.108843},
pmid = {38972117},
issn = {1873-6750},
mesh = {*COVID-19/epidemiology/mortality ; Humans ; Male ; Female ; Middle Aged ; Aged ; United Kingdom/epidemiology ; Retrospective Studies ; *Air Pollution/statistics &amp; numerical data ; *Hospitalization/statistics &amp; numerical data ; SARS-CoV-2 ; Adult ; Cohort Studies ; Severity of Illness Index ; Aged, 80 and over ; },
abstract = {BACKGROUND: Greenspaces contribute positively to mental and physical well-being, promote social cohesion, and alleviate environmental stressors, such as air pollution. Ecological studies suggest that greenspace may affect incidence and severity of Coronavirus Disease 2019 (COVID-19).<br><br>OBJECTIVE: This study examines the association between residential greenspace and COVID-19 related hospitalization and death.<br><br>METHOD: In this retrospective cohort based on patient records from the Greater Manchester Care Records, all first COVID-19 cases diagnosed between March 1, 2020, and May 31, 2022 were followed until COVID-19 related hospitalization or death within 28&#xa0;days. Residential greenspace availability was assessed using the Normalized Difference Vegetation Index per lower super output area in Greater Manchester. The association of greenspace with COVID-19 hospitalization and mortality were estimated using multivariate logistic regression models after adjusting for potential individual, temporal, and spatial confounders. We explored potential effect modifications of the associations with greenspace and COVID-19 severity by age, sex, body mass index, smoking, deprivation, and certain comorbidities. Combined effects of greenspace and air pollution (NO2 and PM2.5) were investigated by mutually adjusting pairs with correlation coefficients&#xa0;&#x2264;&#xa0;0&#xb7;7.<br><br>RESULTS: Significant negative associations were observed between greenspace availability and COVID-19 hospitalization and mortality with odds ratios [OR] (95&#xa0;% Confidence Intervals [CI]) of 0&#xb7;96 (0&#xb7;94-0&#xb7;97) and 0&#xb7;84 (0&#xb7;80-0&#xb7;88) (per interquartile range [IQR]), respectively. These were significantly modified by deprivation (P-value for interaction&#xa0;<&#xa0;0.05), showing that those most deprived obtained largest benefits from greenspace. Inclusion of NO2 and PM2.5 diminished associations to null for COVID-19 hospitalization, but only reduced them slightly for mortality, where inverse associations remained.<br><br>CONCLUSION: In the Greater Manchester area, residential greenspace is associated with reduced risk of hospitalization or death in individuals with COVID-19, with deprived groups obtaining the greatest benefits. Associations were strongest for COVID-19 mortality, which were robust to inclusion of air pollutants in the models.},
}
@article {pmid38972039,
year = {2024},
author = {Nurkolis, F and Wiyarta, E and Taslim, NA and Kurniawan, R and Thibault, R and Fernandez, ML and Yang, Y and Han, J and Tsopmo, A and Mayulu, N and Tjandrawinata, RR and Tallei, TE and Hardinsyah, H},
title = {Unraveling diabetes complexity through natural products, miRNAs modulation, and future paradigms in precision medicine and global health.},
journal = {Clinical nutrition ESPEN},
volume = {63},
number = {},
pages = {283-293},
doi = {10.1016/j.clnesp.2024.06.043},
pmid = {38972039},
issn = {2405-4577},
mesh = {Humans ; *Precision Medicine ; *MicroRNAs/genetics ; *Diabetes Mellitus/therapy/genetics ; *Biological Products/therapeutic use ; *Global Health ; Metabolomics ; Computational Biology ; Biomarkers/blood ; Genomics ; },
abstract = {BACKGROUND AND AIMS: The challenge posed by diabetes necessitates a paradigm shift from conventional diagnostic approaches focusing on glucose and lipid levels to the transformative realm of precision medicine. This approach, leveraging advancements in genomics and proteomics, acknowledges the individualistic genetic variations, dietary preferences, and environmental exposures in diabetes management. The study comprehensively analyzes the evolving diabetes landscape, emphasizing the pivotal role of genomics, proteomics, microRNAs (miRNAs), metabolomics, and bioinformatics.<br><br>RESULTS: Precision medicine revolutionizes diabetes research and treatment by diverging from traditional diagnostic methods, recognizing the heterogeneous nature of the condition. MiRNAs, crucial post-transcriptional gene regulators, emerge as promising therapeutic targets, influencing key facets such as insulin signaling and glucose homeostasis. Metabolomics, an integral component of omics sciences, contributes significantly to diabetes research, elucidating metabolic disruptions, and offering potential biomarkers for early diagnosis and personalized therapies. Bioinformatics unveils dynamic connections between natural substances, miRNAs, and cellular pathways, aiding in the exploration of the intricate molecular terrain in diabetes. The study underscores the imperative for experimental validation in natural product-based diabetes therapy, emphasizing the need for in&#xa0;vitro and in&#xa0;vivo studies leading to clinical trials for assessing effectiveness, safety, and tolerability in real-world applications. Global cooperation and ethical considerations play a pivotal role in addressing diabetes challenges worldwide, necessitating a multifaceted approach that integrates traditional knowledge, cultural competence, and environmental awareness.<br><br>CONCLUSIONS: The key components of diabetes treatment, including precision medicine, metabolomics, bioinformatics, and experimental validation, converge in future strategies, embodying a holistic paradigm for diabetes care anchored in cutting-edge research and global healthcare accessibility.},
}
@article {pmid38971026,
year = {2024},
author = {Ou, X and Chen, J and Li, B and Yang, Y and Liu, X and Xu, Z and Xiang, X and Wang, Q},
title = {Multiomics reveals the ameliorating effect and underlying mechanism of aqueous extracts of polygonatum sibiricum rhizome on obesity and liver fat accumulation in high-fat diet-fed mice.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {132},
number = {},
pages = {155843},
doi = {10.1016/j.phymed.2024.155843},
pmid = {38971026},
issn = {1618-095X},
mesh = {Animals ; Male ; Mice ; Akkermansia ; Diet, High-Fat/adverse effects ; Gastrointestinal Microbiome/drug effects ; Lipid Metabolism/drug effects ; *Liver/drug effects/metabolism ; Mice, Inbred C57BL ; Multiomics ; *Non-alcoholic Fatty Liver Disease/drug therapy ; *Obesity/drug therapy/etiology ; Orlistat/pharmacology ; *Plant Extracts/pharmacology ; *Polygonatum/chemistry ; Rhizome/chemistry ; Disease Models, Animal ; },
abstract = {BACKGROUND: Polygonatum sibiricum polysaccharides protect against obesity and NAFLD. However, the potential effects of PS rhizome aqueous extracts (PSRwe) on adiposity and hepatic lipid accumulation remains unexplored.<br><br>PURPOSE: Elucidating the impact and underlying mechanism of PSRwe on HFD-induced obesity and liver fat depostition.<br><br>STUDY DESIGN: 56 male mice, aged eight weeks, were divided into seven groups: Positive, four doses of PSRwe, Model, and Control. HFD was fed for eight weeks, followed by alternate-day gavage of orlistat and PSRwe for an additional eight-week period. Integrative analysis encompassing multiomics, physiological and histopathological, and biochemical indexes was employed.<br><br>METHODS: Body weight (BW); liver, fat and Lee's indexes; TC, TG, LDL-C, HDL-C, AST, ALT, FFA, leptin, and adiponectin in the liver and blood; TNF&#x3b1;, IL-6, and LPS in the colon, plasma, and liver; H&amp;E, PAS and oil red O staining on adipose and liver samples were examined. OGTT and ITT were conducted The gut microbiome, microbial metabolome, colonic and liver transcriptome, plasma and liver metabolites were investigated.<br><br>RESULTS: PSRwe at the dosage of 7.5 mg/kg demonstrated significant and consistent reduction in BW and hepatic fat deposition than orlistat. PSRwe significantly decreased TC, TG, LDL-C, LEP, FFA levels in blood and liver. PSRwe significantly enhanced the relative abundance of probiotics including Akkermansia muciniphila, Bifidobacterium pseudolongum, Lactobacillus reuteri, and metabolic pathways including glycolysis and fatty acids &#x3b2;-oxidation. The 70 up-regulated microbial metabolites in PSRwe-treated mice mainly involved in nucleotides and amino acids metabolism, while 40 decreased metabolites primarily associated with lipid metabolism. The up-regulated colonic differentially expressed genes (DEGs) participate in JAK-STAT/PI3K-Akt/FoxO signaling pathway, serotonergic/cholinergic/glutamatergic synapses, while the down-regulated DEGs predominantly focused on fat absorption and transport. The up-regulated liver DEGs mainly concentrated on fatty acid oxidation and metabolism. Liver metabolisms revealed 131 differential metabolites, among which carnitine and oxidized lipids significantly increased in PSRwe-treated mice. In plasma, the 58 up-regulated metabolites mainly participate in co-factors/vitamins metabolism while 154 down-regulated ones in fatty acids biosynthesis. Comprehensive multiomics association analysis revealed significant associations between gut microbiota and colonic/liver gene expression, and suggested exogenous and endogenous betaine may be active compound in alleviating HFD-induced symptoms.<br><br>CONCLUSION: PSRwe effectively mitigate HFD-induced obesity and hepatic steatosis by increasing beneficial bacteria, reducing colonic fat digestion/absorption, increasing hepatic lipid metabolism, and elevating betaine levels.},
}
@article {pmid38970356,
year = {2024},
author = {Chan, KO},
title = {Next-generation bioinformatics: An ultrafast and user-friendly tool for phylogenomic data exploration.},
journal = {Molecular ecology resources},
volume = {24},
number = {7},
pages = {e13993},
doi = {10.1111/1755-0998.13993},
pmid = {38970356},
issn = {1755-0998},
mesh = {*Computational Biology/methods ; *Software ; *Phylogeny ; Genomics/methods ; User-Computer Interface ; },
abstract = {With increasingly large genomic datasets, even routine bioinformatic tasks can be arduous, computationally demanding, and time-consuming. Additionally, most bioinformatic programs do not have a graphical user interface (GUI) and thus, require users to be minimally competent in command-line. These impediments present significant economic and technological barriers for practitioners who do not have access to advanced computational resources and support. In this issue of Molecular Ecology Resources, Handika and Esselstyn (2024) developed an ultrafast and memory-efficient bioinformatic tool, SEGUL, that performs common manipulations and calculations of summary statistics on phylogenomic datasets. SEGUL has two main features that distinguish it from other bioinformatic programs: (1) it is based on the recently emergent, high-performance programming language Rust, and (2) it has a GUI written using Flutter, a cross-platform programming framework that also supports mobile operating systems (mobile iOS, iPadOS and Android). By leveraging and combining the power of Rust and Flutter, SEGUL achieves significantly faster computation times and lower memory usage across different platforms and CPU architectures compared to similar programs. The unique and innovative features of SEGUL pave the way for a new era of bioinformatics that can be more energy-efficient, inclusive, and available to a broader swathe of users.},
}
@article {pmid38968897,
year = {2024},
author = {Zhu, Y and Chen, F and Jiang, F and Hua, Z and Luo, Z and Ma, J},
title = {Enhanced remediation of PFAS-metal co-contaminated soil by ceramsite supported Fe3O4-MoS2 heterojunction as a high-performance piezocatalyst.},
journal = {Journal of environmental management},
volume = {365},
number = {},
pages = {121716},
doi = {10.1016/j.jenvman.2024.121716},
pmid = {38968897},
issn = {1095-8630},
mesh = {*Soil Pollutants/chemistry/metabolism ; *Soil/chemistry ; *Metals, Heavy/chemistry ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; },
abstract = {In this study, a novel piezoremediation system was developed to remediate an actual soil co-polluted by high contents of per- and polyfluoroalkyl substances (PFAS, 5725 μg/kg soil) and heavy metals (6455 mg/kg soil). Two piezocatalysts, MoS2/ceramsite (MC) and Fe3O4-MoS2/ceramsite (FMC), were synthesized using a facile hydrothermal-coprecipitation method. These two materials were employed to treat the co-contaminated soil in soil slurry environment under sonication. FMC exhibited significantly higher piezoremediation performance than MC, wherein 91.6% of PFAS, 97.8% of Cr[6+] ions and 81% of total metals (Cr, Cu, Zn and Ni) were removed from the soil after 50 min of the FMC piezoremediation process. FMC also exhibited the advantages of easy separation from the slurry phase and excellent reusability. In comparison with MC, the Fe3O4-MoS2 heterojunction in FMC can stabilize MoS2 particles on the surface of ceramsite granules, promote the separation of electron/hole pairs, accelerate charge transfer, therefore enhancing piezocatalytic performance. The electron spin resonance analysis and free radical quenching tests show that [•]OH was the dominant oxidative radical responsible for PFAS degradation. The count of bacteria and the bacterial community structure in the treated soil can be basically restored to the initial states after 30 days of incubation under nutrient stimulation. Overall, this study not only provides a deep insight on soil remediation process, but also offers an efficient and reliable technique for simultaneous decontamination of organic and metal pollutants in soil.},
}
@article {pmid38968305,
year = {2024},
author = {Fu, X and Withers, J and Miyamae, JA and Moore, TY},
title = {ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture.},
journal = {PLoS computational biology},
volume = {20},
number = {7},
pages = {e1012243},
pmid = {38968305},
issn = {1553-7358},
mesh = {*Tendons/physiology/anatomy &amp; histology ; Humans ; Biomechanical Phenomena ; *Software ; *Joints/physiology/anatomy &amp; histology ; *Muscle, Skeletal/physiology/anatomy &amp; histology ; Models, Biological ; Computational Biology ; Computer Simulation ; Animals ; },
abstract = {Computational models of musculoskeletal systems are essential tools for understanding how muscles, tendons, bones, and actuation signals generate motion. In particular, the OpenSim family of models has facilitated a wide range of studies on diverse human motions, clinical studies of gait, and even non-human locomotion. However, biological structures with many joints, such as fingers, necks, tails, and spines, have been a longstanding challenge to the OpenSim modeling community, especially because these structures comprise numerous bones and are frequently actuated by extrinsic muscles that span multiple joints-often more than three-and act through a complex network of branching tendons. Existing model building software, typically optimized for limb structures, makes it difficult to build OpenSim models that accurately reflect these intricacies. Here, we introduce ArborSim, customized software that efficiently creates musculoskeletal models of highly jointed structures and can build branched muscle-tendon architectures. We used ArborSim to construct toy models of articulated structures to determine which morphological features make a structure most sensitive to branching. By comparing the joint kinematics of models constructed with branched and parallel muscle-tendon units, we found that among various parameters-the number of tendon branches, the number of joints between branches, and the ratio of muscle fiber length to muscle tendon unit length-the number of tendon branches and the number of joints between branches are most sensitive to branching modeling method. Notably, the differences between these models showed no predictable pattern with increased complexity. As the proportion of muscle increased, the kinematic differences between branched and parallel models units also increased. Our findings suggest that stress and strain interactions between distal tendon branches and proximal tendon and muscle greatly affect the overall kinematics of a musculoskeletal system. By incorporating complex muscle-tendon branching into OpenSim models using ArborSim, we can gain deeper insight into the interactions between the axial and appendicular skeleton, model the evolution and function of diverse animal tails, and understand the mechanics of more complex motions and tasks.},
}
@article {pmid38968199,
year = {2024},
author = {Stratton, CA and Thompson, Y and Zio, K and Morrison, WR and Murrell, EG},
title = {uafR: An R package that automates mass spectrometry data processing.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0306202},
pmid = {38968199},
issn = {1932-6203},
mesh = {*Gas Chromatography-Mass Spectrometry/methods ; *Algorithms ; *Software ; Cheminformatics/methods ; },
abstract = {Chemical information has become increasingly ubiquitous and has outstripped the pace of analysis and interpretation. We have developed an R package, uafR, that automates a grueling retrieval process for gas -chromatography coupled mass spectrometry (GC -MS) data and allows anyone interested in chemical comparisons to quickly perform advanced structural similarity matches. Our streamlined cheminformatics workflows allow anyone with basic experience in R to pull out component areas for tentative compound identifications using the best published understanding of molecules across samples (pubchem.gov). Interpretations can now be done at a fraction of the time, cost, and effort it would typically take using a standard chemical ecology data analysis pipeline. The package was tested in two experimental contexts: (1) A dataset of purified internal standards, which showed our algorithms correctly identified the known compounds with R2 values ranging from 0.827-0.999 along concentrations ranging from 1 × 10-5 to 1 × 103 ng/μl, (2) A large, previously published dataset, where the number and types of compounds identified were comparable (or identical) to those identified with the traditional manual peak annotation process, and NMDS analysis of the compounds produced the same pattern of significance as in the original study. Both the speed and accuracy of GC -MS data processing are drastically improved with uafR because it allows users to fluidly interact with their experiment following tentative library identifications [i.e. after the m/z spectra have been matched against an installed chemical fragmentation database (e.g. NIST)]. Use of uafR will allow larger datasets to be collected and systematically interpreted quickly. Furthermore, the functions of uafR could allow backlogs of previously collected and annotated data to be processed by new personnel or students as they are being trained. This is critical as we enter the era of exposomics, metabolomics, volatilomes, and landscape level, high-throughput chemotyping. This package was developed to advance collective understanding of chemical data and is applicable to any research that benefits from GC -MS analysis. It can be downloaded for free along with sample datasets from Github at github.org/castratton/uafR or installed directly from R or RStudio using the developer tools: 'devtools::install_github("castratton/uafR")'.},
}
@article {pmid38967613,
year = {2024},
author = {Hanners, A and Melnyk, B and Bedell, T and Conroy, S and Volek, J and Brock, G and Kelley, M},
title = {A pilot study of Keto Prescribed+: A healthy thinking and eating educational program for African American women.},
journal = {Journal of the American Association of Nurse Practitioners},
volume = {36},
number = {7},
pages = {377-384},
pmid = {38967613},
issn = {2327-6924},
support = {L30 HL159699/HL/NHLBI NIH HHS/United States ; UL1TR002733//Center for Clinical and Translational Science, Ohio State University/ ; TL1TR002735//Center for Clinical and Translational Science, Ohio State University/ ; },
mesh = {Adult ; Female ; Humans ; Middle Aged ; *Black or African American/psychology/statistics &amp; numerical data ; Pilot Projects ; Patient Education as Topic ; *Health Promotion ; Healthy Lifestyle ; },
abstract = {African American (AA) women have the highest prevalence of obesity in addition to health disparities in preventable diet-related diseases (i.e., diabetes, hypertension), which places them at increased risk for cardiovascular disease. The purpose of this pilot study was to assess the feasibility, acceptability, and preliminary effectiveness of the Keto Prescribed+ (KetoRx+) program on associated physical and psychosocial outcomes among this population. The KetoRx+ program is a healthy eating and thinking educational intervention. The program combined online and in-person community group sessions over 8 weeks. The Keto Prescribed+ was found to be feasible and acceptable with comments on ways to increase acceptability from participants completing program (n = 10). Physical outcomes changed showed an average decrease in weight of 10lbs (SD = 5), baseline average 226lbs. Waist-to-hip ratio and systolic blood pressure also trended down. Psychosocial outcomes showed improvement trends. The KetoRx+ program is feasible and acceptable for overweight or obese AA women. Preliminary efficacy was established for most physical and psychosocial outcomes. However, more research is needed to identify specific program components contributing to healthy lifestyle behavior change and to establish program efficacy and effectiveness. Culturally adapted community-based biopsychosocial interventions using ketogenic nutrition therapy may help improve cardiovascular health of adult AA women.},
}
@article {pmid38966305,
year = {2024},
author = {Crowley, LM and Roy, HE and Brown, PMJ and , and , and , and , and , and , and , },
title = {The genome sequence of the ten-spot ladybird, Adalia decempunctata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {106},
pmid = {38966305},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Adalia decempunctata (the ten-spot ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 489.4 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.68 kilobases in length.},
}
@article {pmid38964062,
year = {2024},
author = {Jeon, Y and Kwon, YS and Noh, YJ and Lee, SM and Song, JW and Kim, JH and Seo, JS},
title = {Unraveling the mechanisms of benzo[a]pyrene degradation by Pigmentiphaga kullae strain KIT-003 using a multi-omics approach.},
journal = {Ecotoxicology and environmental safety},
volume = {281},
number = {},
pages = {116665},
doi = {10.1016/j.ecoenv.2024.116665},
pmid = {38964062},
issn = {1090-2414},
mesh = {*Benzo(a)pyrene/metabolism/toxicity ; *Biodegradation, Environmental ; Republic of Korea ; Proteomics ; Water Pollutants, Chemical/metabolism/toxicity ; Gas Chromatography-Mass Spectrometry ; Catechols/metabolism ; Rivers/chemistry/microbiology ; Multiomics ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs), notably benzo[a]pyrene (BaP), are environmental contaminants with multiple adverse ecological implications. Numerous studies have suggested the use of BaP biodegradation using various bacterial strains to remove BaP from the environment. This study investigates the BaP biodegradation capability of Pigmentiphaga kullae strain KIT-003, isolated from the Nak-dong River (South Korea) under specific environmental conditions. The optimum conditions of biodegradation were found to be pH 7.0, 35°C, and a salinity of 0 %. GC-MS analysis suggested alternative pathways by which KIT-003 produced catechol from BaP through several intermediate metabolites, including 4-formylchrysene-5-carboxylic acid, 5,6-dihydro-5,6-dihydroxychrysene-5-carboxylic acid (isomer: 3,4-dihydro-3,4-dihydroxychrysene-4-carboxylic acid), naphthalene-1,2-dicarboxylic acid, and 2-hydroxy-1-naphthoic acid. Proteomic profiles indicated upregulation of enzymes associated with aromatic compound degradation, such as nahAc and nahB, and of those integral to the tricarboxylic acid cycle, reflecting the strain's adaptability to and degradation of BaP. Lipidomic analysis of KIT-003 demonstrated that BaP exposure induced an accumulation of glycerolipids such as diacylglycerol and triacylglycerol, indicating their crucial role in bacterial adaptation mechanisms under BaP stress. This study provides significant scientific knowledge regarding the intricate mechanisms involved in BaP degradation by microorganisms.},
}
@article {pmid38961615,
year = {2024},
author = {Papageorgiou, D and Cherono, W and Gall, G and Nyaguthii, B and Farine, DR},
title = {Testing the information centre hypothesis in a multilevel society.},
journal = {The Journal of animal ecology},
volume = {93},
number = {8},
pages = {1147-1159},
doi = {10.1111/1365-2656.14131},
pmid = {38961615},
issn = {1365-2656},
support = {//Max Planck Society/ ; //Wissenschaftskolleg zu Berlin/ ; 422037984//Deutsche Forschungsgemeinschaft/ ; //Deutscher Akademischer Austauschdienst/ ; WW-175ER-17//National Geographic Society/ ; PCEFP3_187058/SNSF_/Swiss National Science Foundation/Switzerland ; 850859/ERC_/European Research Council/International ; },
mesh = {Animals ; *Social Behavior ; *Galliformes/physiology ; Geographic Information Systems ; Female ; Male ; },
abstract = {In various animal species conspecifics aggregate at sleeping sites. Such aggregations can act as information centres where individuals acquire up-to-date knowledge about their environment. In some species, communal sleeping sites comprise individuals from multiple groups, where each group maintains stable membership over time. We used GPS tracking to simultaneously record group movement in a population of wild vulturine guineafowl (Acryllium vulturinum) to investigate whether communal sleeping sites can facilitate the transfer of information among individuals across distinct groups. These birds live in large and stable groups that move both together and apart, often forming communal roosts containing up to five groups. We first test whether roosts provide the opportunity for individuals to acquire information from members of other groups by examining the spatial organization at roosts. The GPS data reveal that groups intermix, thereby providing an opportunity for individuals to acquire out-group information. We next conduct a field experiment to test whether naïve groups can locate novel food patches when co-roosting with knowledgeable groups. We find that co-roosting substantially increases the chances for the members of a naïve group to discover a patch known to individuals from other groups at the shared roost. Further, we find that the discovery of food patches by naïve groups subsequently shapes their space use and inter-group associations. We also draw on our long-term tracking to provide examples that demonstrate natural cases where communal roosting has preceded large-scale multi-group collective movements that extend into areas beyond the groups' normal ranges. Our findings support the extension of the information centre hypothesis to communal sleeping sites that consist of distinct social groups.},
}
@article {pmid38960861,
year = {2024},
author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Sharif, MB and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD},
title = {Unravelling reference bias in ancient DNA datasets.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {7},
pages = {},
pmid = {38960861},
issn = {1367-4811},
support = {2021.0048//Knut and Alice Wallenberg Foundation/ ; },
mesh = {*DNA, Ancient/analysis ; Humans ; *Sequence Analysis, DNA/methods ; Software ; Animals ; Sequence Alignment/methods ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.<br><br>RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.<br><br>AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).},
}
@article {pmid38959816,
year = {2024},
author = {Zhang, Y and Li, D and Li, X and Zhou, X and Newman, G},
title = {The integration of geographic methods and ecological momentary assessment in public health research: A systematic review of methods and applications.},
journal = {Social science &amp; medicine (1982)},
volume = {354},
number = {},
pages = {117075},
pmid = {38959816},
issn = {1873-5347},
support = {R01 MD016587/MD/NIMHD NIH HHS/United States ; },
mesh = {Humans ; *Ecological Momentary Assessment ; *Geographic Information Systems ; *Public Health/methods ; },
abstract = {With the widespread prevalence of mobile devices, ecological momentary assessment (EMA) can be combined with geospatial data acquired through geographic techniques like global positioning system (GPS) and geographic information system. This technique enables the consideration of individuals' health and behavior outcomes of momentary exposures in spatial contexts, mostly referred to as "geographic ecological momentary assessment" or "geographically explicit EMA" (GEMA). However, the definition, scope, methods, and applications of GEMA remain unclear and unconsolidated. To fill this research gap, we conducted a systematic review to synthesize the methodological insights, identify common research interests and applications, and furnish recommendations for future GEMA studies. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines to systematically search peer-reviewed studies from six electronic databases in 2022. Screening and eligibility were conducted following inclusion criteria. The risk of bias assessment was performed, and narrative synthesis was presented for all studies. From the initial search of 957 publications, we identified 47 articles included in the review. In public health, GEMA was utilized to measure various outcomes, such as psychological health, physical and physiological health, substance use, social behavior, and physical activity. GEMA serves multiple research purposes: 1) enabling location-based EMA sampling, 2) quantifying participants' mobility patterns, 3) deriving exposure variables, 4) describing spatial patterns of outcome variables, and 5) performing data linkage or triangulation. GEMA has advanced traditional EMA sampling strategies and enabled location-based sampling by detecting location changes and specified geofences. Furthermore, advances in mobile technology have prompted considerations of additional sensor-based data in GEMA. Our results highlight the efficacy and feasibility of GEMA in public health research. Finally, we discuss sampling strategy, data privacy and confidentiality, measurement validity, mobile applications and technologies, and GPS accuracy and missing data in the context of current and future public health research that uses GEMA.},
}
@article {pmid38956468,
year = {2024},
author = {Li, X and Cao, T and Liu, H and Fu, L and Wang, Q},
title = {Identification and expression analysis of Sox family genes in echinoderms.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {655},
pmid = {38956468},
issn = {1471-2164},
support = {ZR2021QD158//Natural Science Foundation of Shandong Province, China/ ; ZR2021MC151//Natural Science Foundation of Shandong Province, China/ ; 2023XBZD003//Scientific Research Project of Yantai Vocational College/ ; },
mesh = {Animals ; *SOX Transcription Factors/genetics/metabolism ; *Phylogeny ; *Echinodermata/genetics ; *Multigene Family ; Gene Expression Profiling ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; },
abstract = {The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous developmental processes. Echinoderms occupy a pivotal position in many research fields, such as neuroscience, sex determination and differentiation, and embryonic development. However, to date, no comprehensive study has been conducted to characterize and analyze Sox genes in echinoderms. In the present study, the evolution and expression of Sox family genes across 11 echinoderms were analyzed using bioinformatics methods. The results revealed a total of 70 Sox genes, with counts ranging from 5 to 8 across different echinoderms. Phylogenetic analysis revealed that the identified Sox genes could be categorized into seven distinct classes: the SoxB1 class, SoxB2 class, SoxC class, SoxD class, SoxE class, SoxF class and SoxH class. Notably, the SoxB1, SoxB2, and SoxF genes were ubiquitously present in all the echinoderms studied, which suggests that these genes may be conserved in echinoderms. The spatiotemporal expression patterns observed for Sox genes in the three echinoderms indicated that various Sox members perform distinct functional roles. Notably, SoxB1 is likely involved in echinoderm ovary development, while SoxH may play a crucial role in testis development in starfish and sea cucumber. In general, the present investigation provides a molecular foundation for exploring the Sox gene in echinoderms, providing a valuable resource for future phylogenetic and genomic studies.},
}
@article {pmid38955825,
year = {2024},
author = {Pan, H and Wattiez, R and Gillan, D},
title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.},
journal = {Current microbiology},
volume = {81},
number = {8},
pages = {257},
pmid = {38955825},
issn = {1432-0991},
support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; },
mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; Computational Biology/methods ; },
abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.},
}
@article {pmid38954338,
year = {2024},
author = {Yao, Z and Zhou, X and Jin, T and Wang, L and Liu, N and Wu, L},
title = {Remediation of phenanthrene contaminated soil by persulphate coupled with Pseudomonas aeruginosa GZ7 based on oxidation prediction model.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {31},
pages = {44415-44430},
pmid = {38954338},
issn = {1614-7499},
support = {52270171//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 51974314//Innovative Research Group Project of the National Natural Science Foundation of China/ ; },
mesh = {*Phenanthrenes/metabolism ; *Pseudomonas aeruginosa ; *Soil Pollutants ; *Oxidation-Reduction ; *Soil/chemistry ; Soil Microbiology ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; Polycyclic Aromatic Hydrocarbons ; Sulfates/chemistry ; },
abstract = {Chemical oxidation coupled with microbial remediation has attracted widespread attention for the removal of polycyclic aromatic hydrocarbons (PAHs). Among them, the precise evaluation of the feasible oxidant concentration of PAH-contaminated soil is the key to achieving the goal of soil functional ecological remediation. In this study, phenanthrene (PHE) was used as the target pollutant, and Fe[2+]-activated persulphate (PS) was used to remediate four types of soils. Linear regression analysis identified the following important factors influencing remediation: PS dosage and soil PHE content for PHE degradation, Fe[2+] dosage, hydrolysable nitrogen (HN), and available phosphorus for PS decomposition. A comprehensive model of "soil characteristics-oxidation conditions-remediation effect" with a high predictive accuracy was constructed. Based on model identification, Pseudomonas aeruginosa GZ7, which had high PAHs degrading ability after domestication, was further applied to coupling repair remediation. The results showed that the optimal PS dose was 0.75% (w/w). The response relationship between soil physical, chemical, and biological indicators at the intermediate interface and oxidation conditions was analysed. Coupled remediation effects were clarified using microbial diversity sequencing. The introduction of Pseudomonas aeruginosa GZ7 stimulated the relative abundance of Cohnella, Enterobacter, Paenibacillus, and Bacillus, which can promote material metabolism and energy transformation during remediation.},
}
@article {pmid38954067,
year = {2024},
author = {Bazkiaee, PA and Kamkar, B and Amiri, E and Kazemi, H and Rezaei, M and Araji, HA},
title = {Multi-criteria GIS-based land suitability analysis for rice cultivation: a case study in Guilan Province, Iran.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {7},
pages = {680},
pmid = {38954067},
issn = {1573-2959},
mesh = {*Oryza/growth &amp; development ; Iran ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Agriculture/methods ; *Soil/chemistry ; Conservation of Natural Resources ; Climate ; },
abstract = {Ensuring food security and sustainable resource management has become a paramount global concern, prompting significant attention to land suitability analysis for enhancing agricultural production. In this study, an AHP-weighted overlay method was employed to delineate rice cultivation suitability in Guilan province, Iran, a central hub for rice production. Sixteen climatic, topographic, and soil variables were integrated, and individual maps were reclassified to align with the specific requisites for rice production. The results revealed three suitability classes: including 'very suitable,' 'suitable,' and 'moderately suitable', covering 91%, 6%, and 3% of the land, respectively. Soil attributes, particularly organic matter, significantly influenced suitability (weight value of 0.745), with topographic and soil factors outweighing climate in assessment. While salinity is generally absent, organic matter deficiency affects 44% of the land. Phosphorus imbalances are prevalent, with potassium toxicity observed in 10%. Microelement deficiencies, especially in iron and zinc, are noted. Additionally, the results indicated that topographic and soil attributes played a more significant role than climate-related factors in assessing land suitability for rice cultivation within the study area. This research provides a comprehensive spatial analysis of all variables in the study region, shedding light on the complexities of land suitability for rice cultivation. These findings contribute to the understanding of agricultural sustainability and resource management strategies in the context of food security.},
}
@article {pmid38951915,
year = {2024},
author = {Koci, O and Russell, RK and Shaikh, MG and Edwards, C and Gerasimidis, K and Ijaz, UZ},
title = {CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {117},
pmid = {38951915},
issn = {2049-2618},
support = {NE/L011956/1//NERC Environmental Bioinformatics Centre/ ; BB/T010657/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; Metagenome ; Crohn Disease/microbiology/genetics ; },
abstract = {BACKGROUND: Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.<br><br>RESULTS: In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case-control relationships.<br><br>CONCLUSIONS: CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn's disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract.},
}
@article {pmid38949108,
year = {2024},
author = {Bahl, A and Halappanavar, S and Wohlleben, W and Nymark, P and Kohonen, P and Wallin, H and Vogel, U and Haase, A},
title = {Bioinformatics and machine learning to support nanomaterial grouping.},
journal = {Nanotoxicology},
volume = {18},
number = {4},
pages = {373-400},
doi = {10.1080/17435390.2024.2368005},
pmid = {38949108},
issn = {1743-5404},
mesh = {*Machine Learning ; *Nanostructures/chemistry/toxicity ; *Computational Biology/methods ; Humans ; Risk Assessment ; Animals ; },
abstract = {Nanomaterials (NMs) offer plenty of novel functionalities. Moreover, their physicochemical properties can be fine-tuned to meet the needs of specific applications, leading to virtually unlimited numbers of NM variants. Hence, efficient hazard and risk assessment strategies building on New Approach Methodologies (NAMs) become indispensable. Indeed, the design, the development and implementation of NAMs has been a major topic in a substantial number of research projects. One of the promising strategies that can help to deal with the high number of NMs variants is grouping and read-across. Based on demonstrated structural and physicochemical similarity, NMs can be grouped and assessed together. Within an established NM group, read-across may be performed to fill in data gaps for data-poor variants using existing data for NMs within the group. Establishing a group requires a sound justification, usually based on a grouping hypothesis that links specific physicochemical properties to well-defined hazard endpoints. However, for NMs these interrelationships are only beginning to be understood. The aim of this review is to demonstrate the power of bioinformatics with a specific focus on Machine Learning (ML) approaches to unravel the NM Modes-of-Action (MoA) and identify the properties that are relevant to specific hazards, in support of grouping strategies. This review emphasizes the following messages: 1) ML supports identification of the most relevant properties contributing to specific hazards; 2) ML supports analysis of large omics datasets and identification of MoA patterns in support of hypothesis formulation in grouping approaches; 3) omics approaches are useful for shifting away from consideration of single endpoints towards a more mechanistic understanding across multiple endpoints gained from one experiment; and 4) approaches from other fields of Artificial Intelligence (AI) like Natural Language Processing or image analysis may support automated extraction and interlinkage of information related to NM toxicity. Here, existing ML models for predicting NM toxicity and for analyzing omics data in support of NM grouping are reviewed. Various challenges related to building robust models in the field of nanotoxicology exist and are also discussed.},
}
@article {pmid38947430,
year = {2024},
author = {Li, S and Mao, Y and Yang, J and Li, Y and Dong, J and Wang, Z and Jiang, L and He, S},
title = {Efficient integration of covalent triazine frameworks (CTFs) for augmented photocatalytic efficacy: A review of synthesis, strategies, and applications.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e32202},
pmid = {38947430},
issn = {2405-8440},
abstract = {Heterogeneous photocatalysis emerges as an exceptionally appealing technological avenue for the direct capture, conversion, and storage of renewable solar energy, facilitating the generation of sustainable and ecologically benign solar fuels and a spectrum of other pertinent applications. Heterogeneous nanocomposites, incorporating Covalent Triazine Frameworks (CTFs), exhibit a wide-ranging spectrum of light absorption, well-suited electronic band structures, rapid charge carrier mobility, ample resource availability, commendable chemical robustness, and straightforward synthetic routes. These attributes collectively position them as highly promising photocatalysts with applicability in diverse fields, including but not limited to the production of photocatalytic solar fuels and the decomposition of environmental contaminants. As the field of photocatalysis through the hybridization of CTFs undergoes rapid expansion, there is a pressing and substantive need for a systematic retrospective analysis and forward-looking evaluation to elucidate pathways for enhancing performance. This comprehensive review commences by directing attention to diverse synthetic methodologies for the creation of composite materials. And then it delves into a thorough exploration of strategies geared towards augmenting performance, encompassing the introduction of electron donor-acceptor (D-A) units, heteroatom doping, defect Engineering, architecture of Heterojunction and optimization of morphology. Following this, it systematically elucidates applications primarily centered around the efficient generation of photocatalytic hydrogen, reduction of carbon dioxide through photocatalysis, and the degradation of organic pollutants. Ultimately, the discourse turns towards unresolved challenges and the prospects for further advancement, offering valuable guidance for the potent harnessing of CTFs in high-efficiency photocatalytic processes.},
}
@article {pmid38945180,
year = {2024},
author = {Pearl, RL and Donze, LF and Rosas, LG and Agurs-Collins, T and Baskin, ML and Breland, JY and Byker Shanks, C and Cooksey Stowers, K and Johnson, S and Lee, BY and Martin, MY and Mujuru, P and Odoms-Young, A and Panza, E and Pronk, NP and Calicutt, K and Nadglowski, J and Nece, PM and Tedder, M and Chow, LS and Krishnamurti, H and Jay, M and Xi, D and Jastreboff, AM and Stanford, FC},
title = {Ending Weight Stigma to Advance Health Equity.},
journal = {American journal of preventive medicine},
volume = {67},
number = {5},
pages = {785-791},
doi = {10.1016/j.amepre.2024.06.021},
pmid = {38945180},
issn = {1873-2607},
support = {K23 MD015092/MD/NIMHD NIH HHS/United States ; U24 DK132733/DK/NIDDK NIH HHS/United States ; UE5 DK137285/DK/NIDDK NIH HHS/United States ; UM1 TR004921/TR/NCATS NIH HHS/United States ; UL1 TR003142/TR/NCATS NIH HHS/United States ; },
}
@article {pmid38941024,
year = {2024},
author = {Holstein, T and Muth, T},
title = {Bioinformatic Workflows for Metaproteomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2820},
number = {},
pages = {187-213},
pmid = {38941024},
issn = {1940-6029},
mesh = {*Proteomics/methods ; *Computational Biology/methods ; *Workflow ; *Software ; *Microbiota/genetics ; Humans ; Databases, Protein ; Metagenomics/methods ; },
abstract = {The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.},
}
@article {pmid38938637,
year = {2024},
author = {Yang, J and Deng, H and Zhang, Y and Zhou, Y and Miao, T},
title = {Application of amodal segmentation for shape reconstruction and occlusion recovery in occluded tomatoes.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1376138},
pmid = {38938637},
issn = {1664-462X},
abstract = {Common object detection and image segmentation methods are unable to accurately estimate the shape of the occluded fruit. Monitoring the growth status of shaded crops in a specific environment is challenging, and certain studies related to crop harvesting and pest detection are constrained by the natural shadow conditions. Amodal segmentation can focus on the occluded part of the fruit and complete the overall shape of the fruit. We proposed a Transformer-based amodal segmentation algorithm to infer the amodal shape of occluded tomatoes. Considering the high cost of amodal annotation, we only needed modal dataset to train the model. The dataset was taken from two greenhouses on the farm and contains rich occlusion information. We introduced boundary estimation in the hourglass structured network to provide a priori information about the completion of the amodal shapes, and reconstructed the occluded objects using a GAN network (with discriminator) and GAN loss. The model in this study showed accuracy, with average pairwise accuracy of 96.07%, mean intersection-over-union (mIoU) of 94.13% and invisible mIoU of 57.79%. We also examined the quality of pseudo-amodal annotations generated by our proposed model using Mask R-CNN. Its average precision (AP) and average precision with intersection over union (IoU) 0.5 (AP50) reached 63.91%,86.91% respectively. This method accurately and rationally achieves the shape of occluded tomatoes, saving the cost of manual annotation, and is able to deal with the boundary information of occlusion while decoupling the relationship of occluded objects from each other. Future work considers how to complete the amodal segmentation task without overly relying on the occlusion order and the quality of the modal mask, thus promising applications to provide technical support for the advancement of ecological monitoring techniques and ecological cultivation.},
}
@article {pmid38937989,
year = {2024},
author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W},
title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {11},
number = {33},
pages = {e2400058},
pmid = {38937989},
issn = {2198-3844},
support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Cell Proliferation/physiology ; *Stem Cells/metabolism/cytology ; *Lactobacillus/metabolism/genetics ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Swine ; *Lactic Acid/metabolism ; Signal Transduction/physiology ; Wnt Signaling Pathway/physiology/genetics ; Jejunum/microbiology/metabolism/cytology ; Obesity/metabolism/microbiology ; Intestinal Mucosa/metabolism/microbiology/cytology ; },
abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.},
}
@article {pmid38936731,
year = {2024},
author = {Li, Y and Hou, K and Chang, Y and Yuan, B and Li, X},
title = {A methodological study on the identification of ecological security change processes and zoning control strategies -- Based on the perspective of sustainable development.},
journal = {The Science of the total environment},
volume = {946},
number = {},
pages = {174190},
doi = {10.1016/j.scitotenv.2024.174190},
pmid = {38936731},
issn = {1879-1026},
abstract = {Ecological security (ES) is a crucial indicator for assessing the sustainable development of a region. Currently, most studies on ES primarily focus on process analysis, and the integration of environmental variability into the development of tailored control strategies for regions with varying ecological quality is overlooked. Therefore, in this study, we identified regional ES change processes, employed an optimized system to calculate the ecological security index (ESI), and identified ecological corridors (ECs) through the Minimum Constrained Resource (MCR) model to determine zoning strategies for typical arid regions, using the Ningxia region in the Yellow River Basin of China as an example. The findings showed that (1) from 2006 to 2020, the ESI values of most regions were between 0.2 and 0.4, with small but consistent increases in the ESI values over the years. (2) The proportion of regions with high ES ratings increased by 9.08 % across all districts and counties, and the center of gravity of ES shifted in a north-south and east-west direction. (3) The ESI exhibited a strong positive spatial correlation, characterized by spatial diffusion and spillover effects in most regions. (4) The ECs were predominantly distributed in a north-south direction, involving a total of 20 districts and counties. Based on the principles of sustainable development, we developed a model for the dynamic identification and zoning control of regional ES, aiming to provide a practical framework for effective ecological restoration and protection measures. Additionally, the strategies and methodologies presented in this study serve as important references for similar regions worldwide to facilitate the zoning control of ES, highlighting the broader significance and applicability of the study.},
}
@article {pmid38936185,
year = {2024},
author = {Hu, CJ and Lv, YQ and Xian, WD and Jiao, JY and Lian, ZH and Tan, S and Li, MM and Luo, ZH and Liu, ZT and Lv, AP and Liu, L and Ali, M and Liu, WQ and Li, WJ},
title = {Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135017},
doi = {10.1016/j.jhazmat.2024.135017},
pmid = {38936185},
issn = {1873-3336},
mesh = {*Sodium Benzoate/metabolism ; *Biodegradation, Environmental ; *Hot Springs/microbiology ; *Phylogeny ; Water Pollutants, Chemical/metabolism ; Multiomics ; },
abstract = {Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066[T] and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066[T] carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066[T] might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".},
}
@article {pmid38935782,
year = {2024},
author = {Louvet, A and Mantoux, C and Machon, N},
title = {Assessing the extinction risk of the spontaneous flora in urban tree bases.},
journal = {PLoS computational biology},
volume = {20},
number = {6},
pages = {e1012191},
pmid = {38935782},
issn = {1553-7358},
mesh = {*Extinction, Biological ; *Trees ; *Bayes Theorem ; *Cities ; *Ecosystem ; Computational Biology ; Markov Chains ; Models, Biological ; Paris ; },
abstract = {As the spatial arrangement of trees planted along streets in cities makes their bases potential ecological corridors for the flora, urban tree bases may be a key contributor to the overall connectivity of the urban ecosystem. However, these tree bases are also a highly fragmented environment in which extinctions are frequent. The goal of this study was to assess the plant species' ability to survive and spread through urban tree bases. To do so, we developed a Bayesian framework to assess the extinction risk of a plant metapopulation using presence/absence data, assuming that the occupancy dynamics was described by a Hidden Markov Model. The novelty of our approach is to take into account the combined effect of low-distance dispersal and the potential presence of a seed bank on the extinction risk. We introduced a metric of the extinction risk and examined its performance over a wide range of metapopulation parameters. We applied our framework to yearly floristic inventories carried out in 1324 tree bases in Paris, France. While local extinction risks were generally high, extinction risks at the street scale varied greatly from one species to another. We identified 10 plant species that could survive and spread through urban tree bases, and three plant traits correlated with the extinction risk at the metapopulation scale: the maximal height, and the beginning and end of the flowering period. Our results suggest that some plant species can use urban tree bases as ecological corridors despite high local extinction risks by forming a seed bank. We also identified other plant traits correlated with the ability to survive in tree bases, related to the action of gardeners. Moreover, our findings demonstrate that our Bayesian estimation framework based on percolation theory has the potential to be extended to more general metapopulations.},
}
@article {pmid38932245,
year = {2024},
author = {Conradie, T and Caparros-Martin, JA and Egan, S and Kicic, A and Koks, S and Stick, SM and Agudelo-Romero, P},
title = {Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories.},
journal = {Viruses},
volume = {16},
number = {6},
pages = {},
pmid = {38932245},
issn = {1999-4915},
support = {NHMRC115648//National Health and Medical Research Council/ ; Synergy grant APP118364//National Health and Medical Research Council/ ; Theme Collaboration Award 2023//Telethon Kids Institute/ ; N/A//Google cloud education program/ ; Investigator grant 2021/GR000216//National Health and Medical Research Council/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Virome ; *Genome, Viral ; *Respiratory System/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Metagenome ; Computer Simulation ; Phylogeny ; Computational Biology/methods ; Microbiota ; Bacteriophages/genetics/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.<br><br>METHODS: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.<br><br>RESULTS: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.<br><br>CONCLUSION: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.},
}
@article {pmid38926582,
year = {2024},
author = {Tian, SY and Yasuhara, M and Condamine, FL and Huang, HM and Fernando, AGS and Aguilar, YM and Pandita, H and Irizuki, T and Iwatani, H and Shin, CP and Renema, W and Kase, T},
title = {Cenozoic history of the tropical marine biodiversity hotspot.},
journal = {Nature},
volume = {632},
number = {8024},
pages = {343-349},
pmid = {38926582},
issn = {1476-4687},
mesh = {Animals ; *Aquatic Organisms/classification/isolation &amp; purification ; *Biodiversity ; Climate Change ; Datasets as Topic ; Extinction, Biological ; *Fossils ; Genetic Speciation ; History, Ancient ; Time Factors ; *Tropical Climate ; Pacific Ocean ; Coral Reefs ; },
abstract = {The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)[1,2]. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood[3]. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.},
}
@article {pmid38924481,
year = {2024},
author = {Ramos, SR and Reynolds, H and Johnson, C and Melkus, G and Kershaw, T and Thayer, JF and Vorderstrasse, A},
title = {Perceptions of HIV-Related Comorbidities and Usability of a Virtual Environment for Cardiovascular Disease Prevention Education in Sexual Minority Men With HIV: Formative Phases of a Pilot Randomized Controlled Trial.},
journal = {Journal of medical Internet research},
volume = {26},
number = {},
pages = {e57351},
pmid = {38924481},
issn = {1438-8871},
mesh = {Humans ; Male ; *Cardiovascular Diseases/prevention &amp; control ; *HIV Infections/prevention &amp; control/psychology ; Pilot Projects ; *Sexual and Gender Minorities/psychology/statistics &amp; numerical data ; Adult ; Middle Aged ; Comorbidity ; Virtual Reality ; User-Computer Interface ; },
abstract = {BACKGROUND: Sexual minority men with HIV are at an increased risk of cardiovascular disease (CVD) and have been underrepresented in behavioral research and clinical trials.<br><br>OBJECTIVE: This study aims to explore perceptions of HIV-related comorbidities and assess the interest in and usability of a virtual environment for CVD prevention education in Black and Latinx sexual minority men with HIV.<br><br>METHODS: This is a 3-phase pilot behavioral randomized controlled trial. We report on formative phases 1 and 2 that informed virtual environment content and features using qualitative interviews, usability testing, and beta testing with a total of 25 individuals. In phase 1, a total of 15 participants completed interviews exploring HIV-related illnesses of concern that would be used to tailor the virtual environment. In phase 2, usability testing and beta testing were conducted with 10 participants to assess interest, features, and content.<br><br>RESULTS: In phase 1, we found that CVD risk factors included high blood pressure, myocardial infarction, stroke, and diabetes. Cancer (prostate, colon, and others) was a common concern, as were mental health conditions. In phase 2, all participants completed the 12-item usability checklist with favorable feedback within 30 to 60 minutes. Beta-testing interviews suggested (1) mixed perceptions of health and HIV, (2) high risk for comorbid conditions, (3) virtual environment features were promising, and (4) the need for diverse avatar representations.<br><br>CONCLUSIONS: We identified several comorbid conditions of concern, and findings carry significant implications for mitigating barriers to preventive health screenings, given the shared risk factors between HIV and related comorbidities. Highly rated aspects of the virtual environment were anonymity; meeting others with HIV who identify as gay or bisexual; validating lesbian, gay, bisexual, transgender, queer, and others (LGBTQ+) images and content; and accessibility to CVD prevention education. Critical end-user feedback from beta testing suggested more options for avatar customization in skin, hair, and body representation. Our next phase will test the virtual environment as a new approach to advancing cardiovascular health equity in ethnic and racial sexual minority men with HIV.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT04061915; https://clinicaltrials.gov/study/NCT05242952.<br><br>RR2-10.2196/38348.},
}
@article {pmid38920364,
year = {2024},
author = {Mau, RL and Hayer, M and Purcell, AM and Geisen, S and Hungate, BA and Schwartz, E},
title = {Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0080024},
pmid = {38920364},
issn = {1098-5336},
support = {DE-AC52-07NA27344//U.S. Department of Energy (DOE)/ ; DE-SC0020172//U.S. Department of Energy (DOE)/ ; DE-SC0023126//U.S. Department of Energy (DOE)/ ; },
mesh = {*RNA, Ribosomal, 18S/genetics ; *Computational Biology/methods ; *Eukaryota/genetics/classification ; *DNA Primers/genetics ; *Soil Microbiology ; Biodiversity ; Temperature ; Soil/parasitology/chemistry ; Polymerase Chain Reaction ; },
abstract = {Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.},
}
@article {pmid38917931,
year = {2024},
author = {Wang, H and Li, Y and Huang, G and Ma, Y and Zhang, Q and Li, Y},
title = {Analyzing variation of water inflow to inland lakes under climate change: Integrating deep learning and time series data mining.},
journal = {Environmental research},
volume = {259},
number = {},
pages = {119478},
doi = {10.1016/j.envres.2024.119478},
pmid = {38917931},
issn = {1096-0953},
mesh = {*Lakes/chemistry ; *Climate Change ; *Deep Learning ; Data Mining ; Environmental Monitoring/methods ; },
abstract = {The alarming depletion of global inland lakes in recent decades makes it essential to predict water inflow from rivers to lakes (WIRL) trend and unveil the dominant influencing driver, particularly in the context of climate change. The raw time series data contains multiple components (i.e., long-term trend, seasonal periodicity, and random noise), which makes it challenging for traditional machine/deep learning techniques to effectively capture long-term trend information. In this study, a novel FactorConvSTLnet (FCS) method is developed through integrating STL decomposition, convolutional neural networks (CNN), and factorial analysis into a general framework. FCS is more robust in long-term WIRL trend prediction through separating trend information as a modeling predictor, as well as unveiling predominant drivers. FCS is applied to typical inland lakes (the Aral Sea and the Lake Balkhash) in Central Asia, and results indicate that FCS (Nash-Sutcliffe efficiency = 0.88, root mean squared error = 67m[3]/s, mean relative error = 10%) outperforms the traditional CNN. Some main findings are: (i) during 1960-1990, reservoir water storage (WSR) was the dominant driver for the two lakes, respectively contributing to 71% and 49%; during 1991-2014 and 2015-2099, evaporation (EVAP) would be the dominant driver, with the contribution of 30% and 47%; (ii) climate change would shift the dominant driver from human activities to natural factors, where EVAP and surface snow amount (SNW) have an increasing influence on WIRL; (iii) compared to SSP1-2.6, the SNW contribution would decrease by 26% under SSP5-8.5, while the EVAP contribution would increase by 9%. The findings reveal the main drivers of shrinkage of the inland lakes and provide the scientific basis for promoting regional ecological sustainability.},
}
@article {pmid38917628,
year = {2024},
author = {Li, Q and Ma, Q and Zhou, Y and Jiang, X and Parales, RE and Zhao, S and Zhuang, Y and Ruan, Z},
title = {Isolation, identification, and degradation mechanism by multi-omics of mesotrione-degrading Amycolatopsis nivea La24.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {134951},
doi = {10.1016/j.jhazmat.2024.134951},
pmid = {38917628},
issn = {1873-3336},
mesh = {*Herbicides/metabolism/chemistry ; *Cyclohexanones/metabolism ; *Biodegradation, Environmental ; *Amycolatopsis/metabolism/genetics ; Metabolomics ; Sulfonylurea Compounds/metabolism ; Soil Pollutants/metabolism ; Multiomics ; },
abstract = {Mesotrione is a herbicide used in agricultural production; however, its stability and long-term residues pose ecological risks to soil health and subsequent crops. In this research, the strain Amycolatopsis nivea La24 was identified as capable of completely degrading 50 mg∙L[-1] mesotrione within 48 h. It exhibited a broad adaptability to various environment and could degrade three sulfonylurea herbicides (nicosulfuron, chlorimuron-methyl, and cinosulfuron). Non-target metabonomic and mass spectrometry demonstrated that La24 strain broke down the mesotrione parent molecule by targeting the β-diketone bond and nitro group, resulting in the production of five possible degradation products. The differentially expressed genes were significantly enriched in fatty acid degradation, amino acid metabolism, and other pathways, and the differentially metabolites in glutathione metabolism, arginine/proline metabolism, cysteine/methionine metabolism, and other pathways. Additionally, it was confirmed by heterologous expression that nitroreductase was directly involved in the mesotrione degradation, and NDMA-dependent methanol dehydrogenase would increase the resistance to mesotrione. Finally, the intracellular response of La24 during mesotrione degradation was proposed. This work provides insight for a comprehensive understanding of the mesotrione biodegradation mechanism, significantly expands the resources for pollutant degradation, and offers the potential for a more sustainable solution to address herbicide pollution in soil.},
}
@article {pmid38917233,
year = {2024},
author = {Costa, IB and Pimenta, IDSF and Aiquoc, KM and Oliveira, &#xc2;GRDC},
title = {Congenital syphilis, syphilis in pregnancy and prenatal care in Brazil: An ecological study.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0306120},
pmid = {38917233},
issn = {1932-6203},
mesh = {Humans ; Pregnancy ; Female ; Brazil/epidemiology ; *Syphilis, Congenital/epidemiology ; *Prenatal Care ; *Pregnancy Complications, Infectious/epidemiology ; Incidence ; Adult ; Socioeconomic Factors ; Syphilis/epidemiology/diagnosis ; Adolescent ; Young Adult ; },
abstract = {The aim of this research was to evaluate the incidence of congenital syphilis and the ratio between congenital syphilis and syphilis in pregnant women in Brazil according to socioeconomic indicators (inadequate water supply and sanitation; illiteracy at 15 years of age or older; household income per capita; proportion of poor people; Gini index; human development index; and average health expenditure per inhabitant by the health system) and prenatal quality-of-care indicators. We conducted an ecological study using a sample composed of 257 municipalities, each with ≥ 100,000 inhabitants. Data was collected from four public databases: the Brazilian Institute of Geography and Statistics, comprising socioeconomical data from the 2010 census; and the data of 2019 available in the databases of the Department of Informatics of the Brazilian Health System, Information and Management of Primary Care, and the Electronic Citizen Information System. Descriptive analysis of dependent and independent variables and bivariate analysis by Negative Binomial regression were carried out. The mean incidence of congenital syphilis was 38% higher in municipalities with a Human Development Index up to 0.785 (ratio of means [RM] = 1.38; p = 0.049) and 57% higher among populations where less than 50% of primary healthcare services provided a rapid test for syphilis (RM = 1.57; p < 0.001). The ratio between congenital syphilis and syphilis in pregnant women was 29% higher in municipalities with a low household income per capita (RM = 1.29; p < 0.001) and 28% higher in locations where less than 50% of the primary healthcare services provided a rapid test for syphilis (RM = 1.28; p < 0.001). There was no statistical significance of the quality of prenatal care compared to the outcomes. This result underscores the challenges in detecting syphilis infections among pregnant women during prenatal care, consequently increasing the risk of vertical transmission of the disease to the fetus. Traits of inequality in the occurrence of congenital syphilis also draw attention to strategies to reduce health inequities and improve prenatal care.},
}
@article {pmid38916705,
year = {2024},
author = {Yu, J and Chen, S},
title = {The Use of Big Data Analysis in Digital Empowerment of Sustainable Technological Innovation Management of Ecological Enterprises.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {31},
pages = {43956-43966},
pmid = {38916705},
issn = {1614-7499},
mesh = {*Big Data ; China ; Inventions ; Ecology ; Empowerment ; Environmental Monitoring/methods ; Conservation of Natural Resources ; },
abstract = {With the social economy's rapid progress and the popularization of environmental awareness, ecological enterprises have gradually become a crucial trend in the development of modern enterprises. This work intends to promote the development of ecological enterprises to a higher level. This work first analyzes the management mode of ecological enterprises in the context of big data in China. Then, it establishes various indicators to analyze the role of sustainable technological innovation in enterprise development and the impact of digital empowerment on enterprise development. Finally, this work takes China's manufacturing industry and ecological enterprises in Hubei Province as examples to summarize the digital empowerment of sustainable technological innovation management of ecological enterprises under the background of big data. The final result indicates that sustainable technological innovation significantly reduces ecological enterprises' resource consumption and waste emissions. Additionally, it has a significant positive effect on improving enterprise output value and economic benefits. The digital empowerment of enterprises has a significant driving effect on sustainable technological innovation, with a digital driving coefficient of 26. This work provides a feasible scheme for the specific application of big data analysis in the technology innovation management of ecological enterprises, including market demand analysis, environmental monitoring and governance, technology assessment and risk management. This work expounds the role of big data analysis technology in improving decision-making efficiency, optimizing resource allocation and enhancing the competitiveness of enterprises in the digital empowerment of ecological enterprises.},
}
@article {pmid38915508,
year = {2024},
author = {Shukla, HG and Chakraborty, M and Emerson, JJ},
title = {Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38915508},
issn = {2692-8205},
support = {S10 OD021718/OD/NIH HHS/United States ; R35 GM153327/GM/NIGMS NIH HHS/United States ; P30 AR075047/AR/NIAMS NIH HHS/United States ; R01 GM123303/GM/NIGMS NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; R00 GM129411/GM/NIGMS NIH HHS/United States ; },
abstract = {Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and informatic study, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in Drosophila melanogaster, offering significant improvements to the existing community reference assembly. Our work successfully recovers previously elusive segments, including complete reconstructions of the histone locus and the pericentric heterochromatin of the X chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative of crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.},
}
@article {pmid38915006,
year = {2024},
author = {Reininghaus, U and Schwannauer, M and Barne, I and Beames, JR and Bonnier, RA and Brenner, M and Breznoščáková, D and Dančík, D and De Allegri, M and Di Folco, S and Durstewitz, D and Gugel, J and Hajdúk, M and Heretik, A and Izáková, &#x13d; and Katreniakova, Z and Kiekens, G and Koppe, G and Kurilla, A and Marelli, L and Nagyova, I and Nguyen, H and Pečeňák, J and Schulte-Strathaus, JCC and Sotomayor-Enriquez, K and Uyttebroek, L and Weermeijer, J and Wolters, M and Wensing, M and Boehnke, JR and Myin-Germeys, I and Schick, A},
title = {Strategies, processes, outcomes, and costs of implementing experience sampling-based monitoring in routine mental health care in four European countries: study protocol for the IMMERSE effectiveness-implementation study.},
journal = {BMC psychiatry},
volume = {24},
number = {1},
pages = {465},
pmid = {38915006},
issn = {1471-244X},
support = {945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 389624707//DFG/ ; 101063326//Marie Sk&#x142;odowska-Curie fellowship/ ; 1204924N//Research Foundation Flanders/ ; APVV-22-0587//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/ ; },
mesh = {Humans ; Belgium ; Cost-Benefit Analysis/methods ; Ecological Momentary Assessment ; Europe ; Germany ; Mental Disorders/therapy/economics ; *Mental Health Services/economics ; Slovakia ; *Randomized Controlled Trials as Topic ; *Multicenter Studies as Topic ; },
abstract = {BACKGROUND: Recent years have seen a growing interest in the use of digital tools for delivering person-centred mental health care. Experience Sampling Methodology (ESM), a structured diary technique for capturing moment-to-moment variation in experience and behaviour in service users' daily life, reflects a particularly promising avenue for implementing a person-centred approach. While there is evidence on the effectiveness of ESM-based monitoring, uptake in routine mental health care remains limited. The overarching aim of this hybrid effectiveness-implementation study is to investigate, in detail, reach, effectiveness, adoption, implementation, and maintenance as well as contextual factors, processes, and costs of implementing ESM-based monitoring, reporting, and feedback into routine mental health care in four European countries (i.e., Belgium, Germany, Scotland, Slovakia).<br><br>METHODS: In this hybrid effectiveness-implementation study, a parallel-group, assessor-blind, multi-centre cluster randomized controlled trial (cRCT) will be conducted, combined with a process and economic evaluation. In the cRCT, 24 clinical units (as the cluster and unit of randomization) at eight sites in four European countries will be randomly allocated using an unbalanced 2:1 ratio to one of two conditions: (a) the experimental condition, in which participants receive a Digital Mobile Mental Health intervention (DMMH) and other implementation strategies in addition to treatment as usual (TAU) or (b) the control condition, in which service users are provided with TAU. Outcome data in service users and clinicians will be collected at four time points: at baseline (t0), 2-month post-baseline (t1), 6-month post-baseline (t2), and 12-month post-baseline (t3). The primary outcome will be patient-reported service engagement assessed with the service attachment questionnaire at 2-month post-baseline. The process and economic evaluation will provide in-depth insights into in-vivo context-mechanism-outcome configurations and economic costs of the DMMH and other implementation strategies in routine care, respectively.<br><br>DISCUSSION: If this trial provides evidence on reach, effectiveness, adoption, implementation and maintenance of implementing ESM-based monitoring, reporting, and feedback, it will form the basis for establishing its public health impact and has significant potential to bridge the research-to-practice gap and contribute to swifter ecological translation of digital innovations to real-world delivery in routine mental health care.<br><br>TRIAL REGISTRATION: ISRCTN15109760 (ISRCTN registry, date: 03/08/2022).},
}
@article {pmid38914930,
year = {2024},
author = {Jiang, G and Zheng, JY and Ren, SN and Yin, W and Xia, X and Li, Y and Wang, HL},
title = {A comprehensive workflow for optimizing RNA-seq data analysis.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {631},
pmid = {38914930},
issn = {1471-2164},
mesh = {*Workflow ; *RNA-Seq/methods ; *Software ; Fungi/genetics ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Alternative Splicing ; },
abstract = {BACKGROUND: Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge.<br><br>RESULTS: By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz.<br><br>CONCLUSION: The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.},
}
@article {pmid38911902,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the White-point, Mythimna albipuncta (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {62},
pmid = {38911902},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Mythimna albipuncta (the White-point; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 698.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,679 protein coding genes.},
}
@article {pmid38909735,
year = {2024},
author = {Su, F and Huo, D and Yang, H and Sun, L},
title = {CircRNA8388 functions as the sponge for miR-2392 during intestinal regeneration in sea cucumber Apostichopus japonicus.},
journal = {International journal of biological macromolecules},
volume = {274},
number = {Pt 2},
pages = {133302},
doi = {10.1016/j.ijbiomac.2024.133302},
pmid = {38909735},
issn = {1879-0003},
mesh = {Animals ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; *Intestines ; *MicroRNAs/genetics ; *Regeneration/genetics ; *RNA, Circular/genetics ; *Stichopus/genetics ; },
abstract = {The sea cucumber Apostichopus japonicus can expel internal organs under stress and regenerate them subsequently. However, growth is delayed during regeneration, significantly impacting the industry. Circular RNAs (circRNAs) are single-stranded circular RNA molecules produced through alternative splicing of mRNA precursors. They play crucial roles in regulating gene expression via the ceRNA mechanism. In this study, circRNA profiles of control and regenerated intestines were constructed. A total of 15,874 circRNAs were identified, with a length of 300-350 nucleotides (nt) being the most abundant. Sanger sequencing confirmed the circular structure of circRNA398. Compared with the normal intestine, 50 and 83 differentially expressed circRNAs (DE-circRNAs) were identified in the regenerated intestine at 1 and 3 days post evisceration (dpe), respectively. Gene ontology (GO) terms for signal transduction and development regulation were most significantly enriched in 1dpeVScon and 3dpeVScon treatments, respectively. The dual-luciferase assay revealed that circRNA8388 functions as a sponge for miR-2392, participating in the remodeling of the extracellular matrix (ECM). In conclusion, these findings will contribute to the enhancement of the non-coding RNA database for echinoderms and lay the groundwork for future investigations into circRNA regulation during intestinal regeneration.},
}
@article {pmid38908558,
year = {2024},
author = {Yang, Y and Li, Z and Wen, J},
title = {Long term impact of Wenchuan earthquake on population mental and behavioral disorders in heavily-stricken areas: An ecological study based on big data.},
journal = {Journal of affective disorders},
volume = {361},
number = {},
pages = {589-595},
doi = {10.1016/j.jad.2024.06.070},
pmid = {38908558},
issn = {1573-2517},
mesh = {Humans ; *Earthquakes ; China/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Mental Disorders/epidemiology ; *Disasters/statistics &amp; numerical data ; *Survivors/psychology/statistics &amp; numerical data ; Prevalence ; Adolescent ; Aged ; *Big Data ; Young Adult ; Risk Factors ; Child ; Urbanization ; },
abstract = {BACKGROUND: This study aimed to explore and evaluate the development trends and differential changes in the prevalence of mental and behavioral disorders among the earthquake survivors in exposure groups (highly hard-hit areas) and control groups (general disaster areas) from 2015 to 2019, as well as to investigate the potential influencing factors.<br><br>METHODS: Data was obtained from the Sichuan Health Information System and the Sichuan Health Yearbook, the prevalence of the exposure group and the control group were calculated, the difference between the two groups was evaluated using the prevalence rate ratio, and a fixed effect model was developed to investigate the potential influencing factors of the prevalence.<br><br>RESULTS: The prevalence by gender and age in the exposure group was always greater than those in the control group (RR>1), although the disparity between the two proceeded to diminish with time. The urbanization rate (&#x3b2;&#xa0;=&#xa0;0.0448, P&#xa0;<&#xa0;0.05) and disaster area levels (&#x3b2;&#xa0;=&#xa0;0.0104, P&#xa0;<&#xa0;0.05) were risk factors for the prevalence of mental and behavioral disorders.<br><br>LIMITATIONS: The study only collected data at the group level following the Wenchuan earthquake. Consequently, the findings are only applicable at the group level. Furthermore, diagnostic criteria for various types of mental and behavioral disorders diseases were not provided.<br><br>CONCLUSIONS: The earthquake has a significant long-term impact on mental health. It is necessary to continuously monitor the mental health of Wenchuan earthquake survivors and take appropriate post-disaster intervention measures.},
}
@article {pmid38907904,
year = {2024},
author = {Roved, J},
title = {MHCtools 1.5: Analysis of MHC Sequencing Data in R.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2809},
number = {},
pages = {275-295},
pmid = {38907904},
issn = {1940-6029},
mesh = {*Major Histocompatibility Complex/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Software ; Animals ; *Haplotypes/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genetic Variation ; Genotyping Techniques/methods ; Genotype ; },
abstract = {The genes of the major histocompatibility complex (MHC) play a vital role in the vertebrate immune system and have attracted considerable interest in evolutionary biology. While the MHC has been characterized in detail in humans (human leukocyte antigen, HLA) and in model organisms such as the mouse, studies in non-model organisms often lack prior knowledge about structure, genetic variability, and evolutionary properties of this locus. MHC genotyping in non-model species commonly relies on PCR-based amplicon sequencing, and while several published protocols facilitate generation of MHC sequence data, there is a lack of transparent and standardized tools for downstream data analysis.Here, I present the R package MHCtools version 1.5, which contains 15 tools that (i) assist accurate MHC genotyping from high-throughput amplicon sequencing data, and provide standardized methods to analyze (ii) MHC diversity, (iii) MHC supertypes, and (iv) MHC haplotypes.I hope that MHCtools will be helpful in future studies of the MHC in non-model species and that it may help to advance our understanding of the important roles of the MHC in ecology and evolution.},
}
@article {pmid38904377,
year = {2024},
author = {Berasategui, A and Salem, H and Moller, AG and Christopher, Y and Vidaurre Montoya, Q and Conn, C and Read, TD and Rodrigues, A and Ziemert, N and Gerardo, N},
title = {Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants.},
journal = {mSystems},
volume = {9},
number = {7},
pages = {e0057624},
pmid = {38904377},
issn = {2379-5077},
support = {BE6922/1-1//Deutsche Forschungsgemeinschaft (DFG)/ ; EXC 2124 - 390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; 1711545//National Science Foundation (NSF)/ ; 1754595//National Science Foundation (NSF)/ ; 1927411//National Science Foundation (NSF)/ ; 2021/04706-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 2019/03746-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; },
mesh = {*Symbiosis ; *Ants/microbiology ; Animals ; *Secondary Metabolism/genetics ; *Phylogeny ; *Genome, Fungal ; *Hypocreales/genetics/metabolism ; Evolution, Molecular ; Genomics ; Biosynthetic Pathways/genetics ; },
abstract = {The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.},
}
@article {pmid38902323,
year = {2024},
author = {Horváth, G and Sos, T and Bóné, G and Lőrincz, CE and Pap, PL and Herczeg, G},
title = {Integrating behavioural thermoregulatory strategy into the animal personality framework using the common lizard, Zootoca vivipara as a model.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14200},
pmid = {38902323},
issn = {2045-2322},
support = {PD 132041//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innovaci&#xf3;s Alap/ ; },
mesh = {Animals ; *Lizards/physiology ; *Body Temperature Regulation/physiology ; *Behavior, Animal/physiology ; Personality/physiology ; Male ; Female ; },
abstract = {The study of consistent between-individual behavioural variation in single (animal personality) and across two or more behavioural traits (behavioural syndrome) is a central topic of behavioural ecology. Besides behavioural type (individual mean behaviour), behavioural predictability (environment-independent within-individual behavioural variation) is now also seen as an important component of individual behavioural strategy. Research focus is still on the 'Big Five' traits (activity, exploration, risk-taking, sociability and aggression), but another prime candidate to integrate to the personality framework is behavioural thermoregulation in small-bodied poikilotherms. Here, we found animal personality in thermoregulatory strategy (selected body temperature, voluntary thermal maximum, setpoint range) and 'classic' behavioural traits (activity, sheltering, risk-taking) in common lizards (Zootoca vivipara). Individual state did not explain the between-individual variation. There was a positive behavioural type-behavioural predictability correlation in selected body temperature. Besides an activity-risk-taking syndrome, we also found a risk-taking-selected body temperature syndrome. Our results suggest that animal personality and behavioural syndrome are present in common lizards, both including thermoregulatory and 'classic' behavioural traits, and selecting high body temperature with high predictability is part of the risk-prone behavioural strategy. We propose that thermoregulatory behaviour should be considered with equal weight to the 'classic' traits in animal personality studies of poikilotherms employing active behavioural thermoregulation.},
}
@article {pmid38899724,
year = {2024},
author = {Parra, J and Jarmusch, SA and Duncan, KR},
title = {Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems.},
journal = {Environmental microbiology},
volume = {26},
number = {6},
pages = {e16635},
doi = {10.1111/1462-2920.16635},
pmid = {38899724},
issn = {1462-2920},
support = {2-1-4-17-1-037//Ministerio de Ciencia Tecnolog&#xed;a y Telecomunicaciones, Costa Rica/ ; NNF19OC0055625//Novo Nordisk Fonden/ ; DNRF137//Danmarks Grundforskningsfond/ ; },
mesh = {Antibiosis ; *Ecosystem ; Genomics ; Geologic Sediments/microbiology ; *Metabolomics ; Multigene Family ; Multiomics ; *Phylogeny ; *Pseudonocardia/genetics ; },
abstract = {Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free-living Pseudonocardia remains understudied. This study applies a multi-omics approach to investigate the chemical ecology of free-living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry-based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix-assisted laser desorption/ionisation-mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free-living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.},
}
@article {pmid38897481,
year = {2024},
author = {Kepp, KP and Aavitsland, P and Ballin, M and Balloux, F and Baral, S and Bardosh, K and Bauchner, H and Bendavid, E and Bhopal, R and Blumstein, DT and Boffetta, P and Bourgeois, F and Brufsky, A and Collignon, PJ and Cripps, S and Cristea, IA and Curtis, N and Djulbegovic, B and Faude, O and Flacco, ME and Guyatt, GH and Hajishengallis, G and Hemkens, LG and Hoffmann, T and Joffe, AR and Klassen, TP and Koletsi, D and Kontoyiannis, DP and Kuhl, E and La Vecchia, C and Lallukka, T and Lambris, J and Levitt, M and Makridakis, S and Maltezou, HC and Manzoli, L and Marusic, A and Mavragani, C and Moher, D and Mol, BW and Muka, T and Naudet, F and Noble, PW and Nordström, A and Nordström, P and Pandis, N and Papatheodorou, S and Patel, CJ and Petersen, I and Pilz, S and Plesnila, N and Ponsonby, AL and Rivas, MA and Saltelli, A and Schabus, M and Schippers, MC and Schünemann, H and Solmi, M and Stang, A and Streeck, H and Sturmberg, JP and Thabane, L and Thombs, BD and Tsakris, A and Wood, SN and Ioannidis, JPA},
title = {Panel stacking is a threat to consensus statement validity.},
journal = {Journal of clinical epidemiology},
volume = {173},
number = {},
pages = {111428},
doi = {10.1016/j.jclinepi.2024.111428},
pmid = {38897481},
issn = {1878-5921},
mesh = {Humans ; *COVID-19/prevention &amp; control ; *Delphi Technique ; *Consensus ; SARS-CoV-2 ; Conflict of Interest ; Reproducibility of Results ; Pandemics ; },
abstract = {Consensus statements can be very influential in medicine and public health. Some of these statements use systematic evidence synthesis but others fail on this front. Many consensus statements use panels of experts to deduce perceived consensus through Delphi processes. We argue that stacking of panel members toward one particular position or narrative is a major threat, especially in absence of systematic evidence review. Stacking may involve financial conflicts of interest, but nonfinancial conflicts of strong advocacy can also cause major bias. Given their emerging importance, we describe here how such consensus statements may be misleading, by analyzing in depth a recent high-impact Delphi consensus statement on COVID-19 recommendations as a case example. We demonstrate that many of the selected panel members and at least 35% of the core panel members had advocated toward COVID-19 elimination (Zero-COVID) during the pandemic and were leading members of aggressive advocacy groups. These advocacy conflicts were not declared in the Delphi consensus publication, with rare exceptions. Therefore, we propose that consensus statements should always require rigorous evidence synthesis and maximal transparency on potential biases toward advocacy or lobbyist groups to be valid. While advocacy can have many important functions, its biased impact on consensus panels should be carefully avoided.},
}
@article {pmid38896539,
year = {2024},
author = {Sänger, M and De Mecquenem, N and Lewińska, KE and Bountris, V and Lehmann, F and Leser, U and Kosch, T},
title = {A qualitative assessment of using ChatGPT as large language model for scientific workflow development.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {38896539},
issn = {2047-217X},
support = {//German Research Foundation/ ; },
mesh = {*Workflow ; Programming Languages ; Software ; Computational Biology/methods ; Humans ; },
abstract = {BACKGROUND: Scientific workflow systems are increasingly popular for expressing and executing complex data analysis pipelines over large datasets, as they offer reproducibility, dependability, and scalability of analyses by automatic parallelization on large compute clusters. However, implementing workflows is difficult due to the involvement of many black-box tools and the deep infrastructure stack necessary for their execution. Simultaneously, user-supporting tools are rare, and the number of available examples is much lower than in classical programming languages.<br><br>RESULTS: To address these challenges, we investigate the efficiency of large language models (LLMs), specifically ChatGPT, to support users when dealing with scientific workflows. We performed 3 user studies in 2 scientific domains to evaluate ChatGPT for comprehending, adapting, and extending workflows. Our results indicate that LLMs efficiently interpret workflows but achieve lower performance for exchanging components or purposeful workflow extensions. We characterize their limitations in these challenging scenarios and suggest future research directions.<br><br>CONCLUSIONS: Our results show a high accuracy for comprehending and explaining scientific workflows while achieving a reduced performance for modifying and extending workflow descriptions. These findings clearly illustrate the need for further research in this area.},
}
@article {pmid38892087,
year = {2024},
author = {Suárez, I and Collado, IG and Garrido, C},
title = {Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites.},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38892087},
issn = {1422-0067},
support = {PID-2021-1228990-B-C21 and PID-2021-1228990-B-C22//MCIN/AEI/ 10.13039/501100011033 and ERDF A way of making Europe/ ; },
mesh = {*Botrytis/genetics/pathogenicity ; *Secondary Metabolism/genetics ; *Peptide Synthases/genetics/metabolism ; *Polyketide Synthases/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Computational Biology/methods ; Multigene Family ; Genes, Fungal ; },
abstract = {Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with B. cinerea's pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea's biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against B. cinerea. This study sets a foundation for further investigations into the fungus's secondary metabolism, with implications for biotechnology and crop disease management.},
}
@article {pmid38888768,
year = {2024},
author = {Sanderson, H and White, AP},
title = {Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2813},
number = {},
pages = {19-37},
pmid = {38888768},
issn = {1940-6029},
mesh = {*Salmonella/genetics ; Humans ; *Genomics/methods ; *Salmonella Infections/microbiology/epidemiology ; *Phylogeny ; *Genome, Bacterial ; *Molecular Epidemiology/methods ; Virulence Factors/genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.},
}
@article {pmid38882711,
year = {2023},
author = {Waterhouse, RM and Adam-Blondon, AF and Balech, B and Barta, E and Ying Shi Chua, P and Di Cola, V and Heil, KF and Hughes, GM and Jermiin, LS and Kalaš, M and Lanfear, J and Pafilis, E and Palagi, PM and Papageorgiou, AC and Paupério, J and Psomopoulos, F and Raes, N and Burgin, J and Gabaldón, T},
title = {The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {},
pmid = {38882711},
issn = {2046-1402},
mesh = {Humans ; *Biodiversity ; Conservation of Natural Resources ; },
abstract = {Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth's biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.},
}
@article {pmid38882082,
year = {2024},
author = {Fei, J and Jiang, X and Yang, H and Fan, K and Che, Y and Sun, B and Guo, T},
title = {Research and Development of a Big Data Application Platform for Intelligent Blast Furnace Intensive Management and Control.},
journal = {ACS omega},
volume = {9},
number = {23},
pages = {24674-24684},
pmid = {38882082},
issn = {2470-1343},
abstract = {The blast furnaces of Anshan Iron and Steel have completed large-scale modernization, and a large amount of information technology has been popularized and applied to the process of blast furnaces. This paper takes the Anshan Iron and Steel blast furnace group as the research background. Based on big data and industrial Internet technology, combining the smelting process mechanism of blast furnace production and using artificial intelligence, cloud analysis, and other technologies, the data management platform was used to effectively integrate the data of each process of the blast furnace and design the data asset catalogue. The big data application platform for the intensive control of the blast furnace was established. The data were in multidimensional in-depth mining, and the intelligent application model of the blast furnace was established. The visual intelligent monitoring of the safe production and operation of the blast furnace was realized, and the production operation of the blast furnace was guided. The overall information and intelligent level of production operation and management of the blast furnace have been improved.},
}
@article {pmid38880940,
year = {2024},
author = {Medo, A and Ohte, N and Doi, H and Kamdee, K and Koba, K and Arai, N and Mitsunaga, Y and Kume, M and Kojima, D and Nose, T and Yokoyama, A and Viputhanumas, T and Mitamura, H},
title = {Trophic niche partitioning and intraspecific variation in food resource use in the genus Pangasianodon in a reservoir revealed by stable isotope analysis of multiple tissues.},
journal = {Journal of fish biology},
volume = {105},
number = {3},
pages = {814-824},
doi = {10.1111/jfb.15842},
pmid = {38880940},
issn = {1095-8649},
support = {16H05792//Japan Society for the Promotion of Science/ ; 22J13642//Japan Society for the Promotion of Science/ ; 202180216//Japan Society for the Promotion of Science/ ; //Shikata Memorial Trust for Nature Conservation/ ; 25610919060008//Thailand Institute of Nuclear Technology/ ; },
mesh = {Animals ; *Nitrogen Isotopes/analysis ; *Carbon Isotopes/analysis ; *Diet/veterinary ; Food Chain ; Thailand ; Liver/chemistry ; Ecosystem ; Catfishes ; },
abstract = {Understanding the mechanism by which non-native fish species integrate into native communities is crucial for evaluating the possibility of their establishment success. The genus Pangasianodon, comprising Pangasianodon gigas and Pangasianodon hypophthalmus, has been introduced into reservoirs, which are non-native habitats, for fishery stock enhancement. P. gigas and P. hypophthalmus often successfully establish and co-occur in several Thai reservoirs, but there is little information on differences in food resource use between the two species. To investigate the trophic niche width of P. gigas and P. hypophthalmus in a Thai reservoir, we conducted stable carbon and nitrogen ratio (δ[13]C and δ[15]N) analyses. We examined the degree of individual specialization in both species using the δ[13]C and δ[15]N values of muscle and liver tissues, which provides long- and short-term diet information. The isotopic niches did not overlap between P. gigas and P. hypophthalmus. The δ[15]N value of P. gigas was significantly higher than that of P. hypophthalmus, whereas the δ[13]C value did not significantly differ between the two species. The isotopic niche sizes were larger in P. hypophthalmus than in P. gigas. Individual specialization was observed in P. hypophthalmus but not in P. gigas, indicating that intraspecific variation in food resource use was larger in P. hypophthalmus compared to P. gigas. These findings suggest that trophic niche partitioning was one of the factors facilitating the establishment success of P. gigas and P. hypophthalmus in a reservoir, but the establishment process may differ between the two species.},
}
@article {pmid38873190,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Notch-wing Button, Acleris emargana (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {376},
pmid = {38873190},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Acleris emargana (the Notch-wing Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,886 protein coding genes.},
}
@article {pmid38870844,
year = {2024},
author = {Rocha, LP and Machado, &#xcd;E and Fogal, AS and Malta, DC and Velasquez-Melendez, G and Felisbino-Mendes, MS},
title = {Burden of disease and direct costs to the health system attributable to high body mass index in Brazil.},
journal = {Public health},
volume = {233},
number = {},
pages = {121-129},
doi = {10.1016/j.puhe.2024.05.013},
pmid = {38870844},
issn = {1476-5616},
mesh = {Humans ; Brazil/epidemiology ; *Body Mass Index ; Cross-Sectional Studies ; Male ; *Cost of Illness ; Female ; Middle Aged ; Adult ; *Health Care Costs/statistics &amp; numerical data ; Hospitalization/statistics &amp; numerical data/economics ; National Health Programs/economics/statistics &amp; numerical data ; Obesity/epidemiology/economics ; Aged ; Disability-Adjusted Life Years ; },
abstract = {OBJECTIVES: Excess weight, measured by a high body mass index (BMI), is associated with the onset of many diseases, which can, in turn, lead to disability and premature death, subsequently placing a significant burden on healthcare services. This study analysed the burden of disease and the direct costs to the Brazilian Unified Health System (Sistema Único de Saúde [SUS]) attributable to high BMI in the Brazilian population.<br><br>STUDY DESIGN: Ecological study.<br><br>METHODS: This ecological study had two components: (1) a time-series assessment to analyse the burden of diseases attributable to high BMI from 1990 to 2019 in Brazil; and (2) a cross-sectional design to estimate the direct costs of SUS hospitalisations and outpatient procedures attributable to high BMI in 2019. Estimates from the Global Burden of Disease study and the costs of hospital admissions and outpatient procedures from the Department of Informatics of the Brazilian Unified Health System were used. Deaths, years of life lost to premature death (YLLs), years lived with disability (YLDs), and years of life lost adjusted for disability (DALYs) were analysed. The direct health cost was obtained in Brazilian Real (R$) and converted in international Dollars (INT$).<br><br>RESULTS: The current study found a reduction in the number of DALYs, YLLs, and deaths per 100,000 population of cardiovascular disease (CVD) attributable to high BMI and an increase in YLD due to diabetes and cardiovascular disease attributable to high BMI from 1990 to 2019. In 2019, high BMI resulted in 2404 DALYs, 658 YLDs, 1746 YLLs, and 76 deaths per 100,000 inhabitants. In the same year, INT$377.30 million was spent on hospitalisations and high- and medium-complexity procedures to control non-communicable diseases attributable to high BMI. The states in the South and Southeast regions of Brazil presented the highest total cost per 10,000 inhabitants. CVDs and chronic kidney disease showed the highest costs per hospital admission, whereas neoplasms and CVDs presented the highest costs for outpatient procedures.<br><br>CONCLUSIONS: High BMI causes significant disease burden and financial costs. The highest expenses observed were not in locations with the highest burden of disease attributable to high BMI. These findings highlight the need to improve current public policies and apply cost-effective intervention packages, focussing on equity and the promotion of healthier lifestyles to reduce overweight/obesity, especially in localities with low socioeconomic status.},
}
@article {pmid38870774,
year = {2024},
author = {Bucci, S and Berry, N and Ainsworth, J and Berry, K and Edge, D and Eisner, E and Emsley, R and Forbes, G and Hassan, L and Lewis, S and Machin, M and Haddock, G},
title = {Effects of Actissist, a digital health intervention for early psychosis: A randomized clinical trial.},
journal = {Psychiatry research},
volume = {339},
number = {},
pages = {116025},
doi = {10.1016/j.psychres.2024.116025},
pmid = {38870774},
issn = {1872-7123},
mesh = {Humans ; Female ; Male ; Adult ; *Psychotic Disorders/therapy ; *Schizophrenia/therapy ; *Mobile Applications ; *Cognitive Behavioral Therapy/methods ; *Telemedicine ; Young Adult ; Middle Aged ; Outcome Assessment, Health Care ; Treatment Outcome ; Digital Health ; },
abstract = {Schizophrenia affects 24 million people worldwide. Digital health interventions drawing on psychological principles have been developed, but their effectiveness remains unclear. This parallel, assessor-blinded, randomized clinical trial aimed to investigate whether a cognitive behaviour therapy-informed digital health intervention (Actissist app) confers added benefit on psychotic symptoms over and above remote symptom monitoring (ClinTouch app). Participants recruited from UK community health services were randomized 1:1 to receive either Actissist plus treatment as usual (TAU) or ClinTouch plus TAU. Eligible participants were adults with schizophrenia-spectrum psychosis within five years of first episode onset meeting a criterion level of positive symptoms severity. The primary outcome was Positive and Negative Syndrome Scale (PANSS) symptoms total score at 12 weeks post-randomization. Intention-to-treat analysis included 172 participants, with 149 participants (86.6 %) providing primary outcome data. Actissist plus TAU was not associated with greater reduction than an active control remote symptom monitoring app (ClinTouch) in PANSS total score at post-randomization. There were no significant effects between groups across secondary measures. There were no serious adverse reactions. Both groups improved on the primary psychotic symptoms measure at primary end-point and on secondary measures over time. The Actissist app is safe but not superior to digital symptom monitoring.},
}
@article {pmid38868628,
year = {2023},
author = {Obbard, DJ and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Hirtodrosophila cameraria (Haliday, 1833).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {361},
pmid = {38868628},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Hirtodrosophila cameraria (a drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 214.5 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.94 kilobases in length.},
}
@article {pmid38867756,
year = {2024},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , },
title = {The genome sequence of the Marbled White Spot, Protodeltote pygarga (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {7},
pmid = {38867756},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Protodeltote pygarga (the Marbled White Spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 421.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.48 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,784 protein coding genes.},
}
@article {pmid38867206,
year = {2024},
author = {Anjos, C and Duarte, D and Fatsini, E and Matias, D and Cabrita, E},
title = {Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposure.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {591},
pmid = {38867206},
issn = {1471-2164},
support = {SFRH/BD/130910/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CCMAR/Multi/04326/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 0139_VENUS_5_E//Interreg POCTEP/ ; JRA2-H2020-INFRAIA-2016-2017//European Commission/ ; EBB-EAPA_501/2016//Interreg Atlantic Area/ ; },
mesh = {Animals ; *Cryopreservation ; *Crassostrea/genetics/growth &amp; development ; *Cryoprotective Agents/pharmacology/toxicity ; *Larva/genetics/drug effects/growth &amp; development ; *Gene Expression Profiling ; Transcriptome ; Gene Ontology ; },
abstract = {BACKGROUND: The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process.<br><br>RESULTS: Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage.<br><br>CONCLUSIONS: The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.},
}
@article {pmid38865434,
year = {2024},
author = {Iverson, AR and Humple, DL and Cormier, RL and Hahn, TP and Block, TA and Shizuka, D and Lyon, BE and Chaine, AS and Hudson, EJ and Hull, EM},
title = {Winter GPS tagging reveals home ranges during the breeding season for a boreal-nesting migrant songbird, the Golden-crowned Sparrow.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0305369},
pmid = {38865434},
issn = {1932-6203},
mesh = {Animals ; *Seasons ; *Geographic Information Systems ; *Animal Migration/physiology ; *Sparrows/physiology ; *Homing Behavior/physiology ; Breeding ; Ecosystem ; British Columbia ; Alaska ; Nesting Behavior/physiology ; },
abstract = {Determining space use for species is fundamental to understanding their ecology, and tracking animals can reveal insights into their spatial ecology on home ranges and territories. Recent technological advances have led to GPS-tracking devices light enough for birds as small as ~30 g, creating novel opportunities to remotely monitor fine-scale movements and space use for these smaller species. We tested whether miniaturized GPS tags can allow us to understand space use of migratory birds away from their capture sites and sought to understand both pre-breeding space use as well as territory and habitat use on the breeding grounds. We used GPS tags to characterize home ranges on the breeding grounds for a migratory songbird with limited available breeding information, the Golden-crowned Sparrow (Zonotrichia atricapilla). Using GPS points from 23 individuals across 26 tags (three birds tagged twice), we found home ranges in Alaska and British Columbia were on average 44.1 ha (95% kernel density estimate). In addition, estimates of territory sizes based on field observations (mean 2.1 ha, 95% minimum convex polygon [MCP]) were three times smaller than 95% MCPs created using GPS tags (mean 6.5 ha). Home ranges included a variety of land cover classes, with shrubland particularly dominant (64-100% of home range cover for all but one bird). Three birds tracked twice returned to the same breeding area each year, supporting high breeding site fidelity for this species. We found reverse spring migration for five birds that flew up to 154 km past breeding destinations before returning. GPS-tracking technology allowed for critical ecological insights into this migratory species that breeds in very remote locations.},
}
@article {pmid38865431,
year = {2024},
author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S},
title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38865431},
issn = {1758-0463},
support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; },
mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; },
abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.},
}
@article {pmid38863181,
year = {2024},
author = {Wong, RE and Berner, LT and Sullivan, PF and Potter, CS and Dial, RJ},
title = {Pixel walking along the boreal forest-Arctic tundra ecotone: Large scale ground-truthing of satellite-derived greenness (NDVI).},
journal = {Global change biology},
volume = {30},
number = {6},
pages = {e17374},
doi = {10.1111/gcb.17374},
pmid = {38863181},
issn = {1365-2486},
support = {80NSSC22K1247/NASA/NASA/United States ; 80NSSC20M0070//Alaska Space Grant Program/ ; DEB-2133494//National Science Foundation/ ; OPP-1748773//National Science Foundation/ ; OPP-1748849//National Science Foundation/ ; 80NSSC19M0062//Alaska NASA EPSCoR/ ; },
mesh = {Alaska ; Arctic Regions ; *Satellite Imagery ; *Tundra ; Remote Sensing Technology/methods ; Taiga ; Environmental Monitoring/methods ; },
abstract = {In this Technical Advance, we describe a novel method to improve ecological interpretation of remotely sensed vegetation greenness measurements that involved sampling 24,395 Landsat pixels (30 m) across 639 km of Alaska's central Brooks Range. The method goes well beyond the spatial scale of traditional plot-based sampling and thereby more thoroughly relates ground-based observations to satellite measurements. Our example dataset illustrates that, along the boreal-Arctic boundary, vegetation with the greatest Landsat Normalized Difference Vegetation Index (NDVI) is taller than 1 m, woody, and deciduous; whereas vegetation with lower NDVI tends to be shorter, evergreen, or non-woody. The field methods and associated analyses advance efforts to inform satellite data with ground-based vegetation observations using field samples collected at spatial scales that closely match the resolution of remotely sensed imagery.},
}
@article {pmid38862613,
year = {2024},
author = {Venu, V and Roth, C and Adikari, SH and Small, EM and Starkenburg, SR and Sanbonmatsu, KY and Steadman, CR},
title = {Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {721},
pmid = {38862613},
issn = {2399-3642},
support = {20210134ER//DOE | LDRD | Los Alamos National Laboratory (Los Alamos Lab)/ ; },
mesh = {*Chromatin/metabolism/genetics ; Animals ; *Vaccinia virus/genetics/physiology ; Chlorocebus aethiops ; Vero Cells ; Vaccinia/virology/immunology ; Host-Pathogen Interactions/genetics ; Multiomics ; },
abstract = {The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.},
}
@article {pmid38862357,
year = {2024},
author = {Knight, E and Rhinehart, T and de Zwaan, DR and Weldy, MJ and Cartwright, M and Hawley, SH and Larkin, JL and Lesmeister, D and Bayne, E and Kitzes, J},
title = {Individual identification in acoustic recordings.},
journal = {Trends in ecology &amp; evolution},
volume = {39},
number = {10},
pages = {947-960},
doi = {10.1016/j.tree.2024.05.007},
pmid = {38862357},
issn = {1872-8383},
mesh = {*Acoustics ; Animals ; Vocalization, Animal ; },
abstract = {Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.},
}
@article {pmid38860489,
year = {2024},
author = {Toga, K and Sakamoto, T and Kanda, M and Tamura, K and Okuhara, K and Tabunoki, H and Bono, H},
title = {Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae).},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {8},
pages = {},
pmid = {38860489},
issn = {2160-1836},
support = {JPMJPF2010//Center of Innovation for Bio-Digital Transformation/ ; 23K17418//JSPS KAKENHI/ ; },
mesh = {Animals ; Genome, Insect ; Genomics/methods ; Japan ; *Molecular Sequence Annotation ; *Wasps/genetics ; },
abstract = {Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which over two thousand genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae precociously, and their emergence period and aggressive behavior differ between the US and Japanese C. floridanum strains. Genome sequencing expects to contribute to our understanding of the molecular bases underlying the progression of polyembryony. However, only the genome sequence of the US strain generated by the short-read assembly has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structures from those in the US strain. This was accomplished through functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected in amino acid sequences of vasa that play a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detailed genomic regions responsible for the ecological and physiological characteristics of C. floridanum.},
}
@article {pmid38856681,
year = {2024},
author = {Dasgupta, S},
title = {Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {7},
pages = {347-356},
doi = {10.1089/omi.2024.0116},
pmid = {38856681},
issn = {1557-8100},
mesh = {Humans ; *Machine Learning ; *Lung Neoplasms/genetics ; *Tuberculosis/genetics ; *Systems Biology/methods ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Regulatory Networks ; },
abstract = {The traditional way of thinking about human diseases across clinical and narrow phenomics silos often masks the underlying shared molecular substrates across human diseases. One Health and planetary health fields particularly address such complexities and invite us to think across the conventional disease nosologies. For example, tuberculosis (TB) and lung cancer (LC) are major pulmonary diseases with significant planetary health implications. Despite distinct etiologies, they can coexist in a given community or patient. This is both a challenge and an opportunity for preventive medicine, diagnostics, and therapeutics innovation. This study reports a bioinformatics analysis of publicly available gene expression data, identifying overlapping dysregulated genes, downstream regulators, and pathways in TB and LC. Analysis of NCBI-GEO datasets (GSE83456 and GSE103888) unveiled differential expression of CEACAM6, MUC1, ADM, DYSF, PLOD2, and GAS6 genes in both diseases, with pathway analysis indicating association with lysine degradation pathway. Random forest, a machine-learning-based classification, achieved accuracies of 84% for distinguishing TB from controls and 83% for discriminating LC from controls using these specific genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of warfarin to GAS6. Taken together, the present study speaks of the pressing need to rethink clinical diagnostic categories of human diseases and that TB and LC might potentially share molecular substrates. Going forward, planetary health and One Health scholarship are poised to cultivate new ways of thinking about diseases not only across medicine and ecology but also across traditional diagnostic conventions.},
}
@article {pmid38855721,
year = {2023},
author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Cloaked Minor, Mesoligia furuncula (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {251},
pmid = {38855721},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Mesoligia furuncula (the Cloaked Minor; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 889.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,903 protein coding genes.},
}
@article {pmid38854694,
year = {2024},
author = {Christenhusz, MJM and Pannell, JR and Twyford, AD and , and , and , and , and , and , and , },
title = {The genome sequence of the Annual Mercury, Mercurialis annua L., 1753 (Euphorbiaceae).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {102},
pmid = {38854694},
issn = {2398-502X},
abstract = {We present a genome assembly from a diploid female Mercurialis annua (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.},
}
@article {pmid38853065,
year = {2024},
author = {O'Connor, JB and Mottlowitz, M and Wagner, BD and Harris, JK and Laguna, TA},
title = {Metabolomics analysis of bronchoalveolar lavage fluid predicts unique features of the lower airway in pediatric cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {23},
number = {6},
pages = {1087-1094},
doi = {10.1016/j.jcf.2024.04.017},
pmid = {38853065},
issn = {1873-5010},
mesh = {Humans ; *Cystic Fibrosis/microbiology/metabolism/physiopathology ; *Bronchoalveolar Lavage Fluid/chemistry/microbiology ; Child ; Female ; Male ; *Metabolomics/methods ; Microbiota ; Adolescent ; Bronchoscopy/methods ; RNA, Ribosomal, 16S/analysis ; Respiratory Function Tests/methods ; },
abstract = {BACKGROUND: Progressive, obstructive lung disease resulting from chronic infection and inflammation is the leading cause of morbidity and mortality in persons with cystic fibrosis (PWCF). Metabolomics and next -generation sequencing (NGS) of airway secretions can allow for better understanding of cystic fibrosis (CF) pathophysiology. In this study, global metabolomic profiling on bronchoalveolar lavage fluid (BALF) obtained from pediatric PWCF and disease controls (DCs) was performed and compared to lower airway microbiota, inflammation, and lung function.<br><br>METHODS: BALF was collected from children undergoing flexible bronchoscopies for clinical indications. Metabolomic profiling was performed using a platform developed by Metabolon Inc. Total bacterial load (TBL) was measured using quantitative polymerase chain reaction (qPCR), and bacterial communities were characterized using 16S ribosomal RNA (rRNA) sequencing. Random Forest Analysis (RFA), principal component analysis (PCA), and hierarchical clustering analysis (HCA) were performed.<br><br>RESULTS: One hundred ninety-five BALF samples were analyzed, 142 (73 %) from PWCF. Most metabolites (425/665) and summed categories (7/9) were significantly increased in PWCF. PCA of the metabolomic data revealed CF BALF exhibited more dispersed clustering compared to DC BALF. Higher metabolite concentrations correlated with increased inflammation, increased abundance of Staphylococcus, and decreased lung function.<br><br>CONCLUSIONS: The lower airway metabolome of PWCF was defined by a complex expansion of metabolomic activity. These findings could be attributed to heightened inflammation in PWCF and aspects of the CF airway polymicrobial ecology. CF-specific metabolomic features are associated with the unique underlying biology of the CF airway.},
}
@article {pmid38852834,
year = {2024},
author = {Goodus, MT and Alfredo, AN and Carson, KE and Dey, P and Pukos, N and Schwab, JM and Popovich, PG and Gao, J and Mo, X and Bruno, RS and McTigue, DM},
title = {Spinal cord injury-induced metabolic impairment and steatohepatitis develops in non-obese rats and is exacerbated by premorbid obesity.},
journal = {Experimental neurology},
volume = {379},
number = {},
pages = {114847},
doi = {10.1016/j.expneurol.2024.114847},
pmid = {38852834},
issn = {1090-2430},
mesh = {Animals ; *Spinal Cord Injuries/complications/metabolism/pathology ; Rats ; *Obesity/complications/metabolism/pathology ; Male ; Fatty Liver/metabolism/pathology/etiology ; Rats, Sprague-Dawley ; Metabolic Syndrome/metabolism/complications/pathology ; Disease Models, Animal ; Insulin Resistance/physiology ; },
abstract = {Impaired sensorimotor functions are prominent complications of spinal cord injury (SCI). A clinically important but less obvious consequence is development of metabolic syndrome (MetS), including increased adiposity, hyperglycemia/insulin resistance, and hyperlipidemia. MetS predisposes SCI individuals to earlier and more severe diabetes and cardiovascular disease compared to the general population, which trigger life-threatening complications (e.g., stroke, myocardial infarcts). Although each comorbidity is known to be a risk factor for diabetes and other health problems in obese individuals, their relative contribution or perceived importance in propagating systemic pathology after SCI has received less attention. This could be explained by an incomplete understanding of MetS promoted by SCI compared with that from the canonical trigger diet-induced obesity (DIO). Thus, here we compared metabolic-related outcomes after SCI in lean rats to those of uninjured rats with DIO. Surprisingly, SCI-induced MetS features were equal to or greater than those in obese uninjured rats, including insulin resistance, endotoxemia, hyperlipidemia, liver inflammation and steatosis. Considering the endemic nature of obesity, we also evaluated the effect of premorbid obesity in rats receiving SCI; the combination of DIO + SCI exacerbated MetS and liver pathology compared to either alone, suggesting that obese individuals that sustain a SCI are especially vulnerable to metabolic dysfunction. Notably, premorbid obesity also exacerbated intraspinal lesion pathology and worsened locomotor recovery after SCI. Overall, these results highlight that normal metabolic function requires intact spinal circuitry and that SCI is not just a sensory-motor disorder, but also has significant metabolic consequences.},
}
@article {pmid38850116,
year = {2024},
author = {Yi, X and Kemppainen, P and Merilä, J},
title = {SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13985},
doi = {10.1111/1755-0998.13985},
pmid = {38850116},
issn = {1755-0998},
support = {N_HKU763/21//National Natural Science Foundation of China/Research Grants Council (RGC) Joint Research Scheme/ ; },
mesh = {*Linkage Disequilibrium ; *Sex Chromosomes/genetics ; Computational Biology/methods ; Animals ; Male ; Female ; Cluster Analysis ; },
abstract = {Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.},
}
@article {pmid38845010,
year = {2024},
author = {Wang, S and Lee, HC and Lee, S},
title = {Predicting herb-disease associations using network-based measures in human protein interactome.},
journal = {BMC complementary medicine and therapies},
volume = {24},
number = {Suppl 2},
pages = {218},
pmid = {38845010},
issn = {2662-7671},
support = {GIST Research Institute IIBR//Gwangju Institute of Science and Technology/ ; GIST Research Institute (GRI) GIST-MIT research Collaboration//Gwangju Institute of Science and Technology/ ; 2021M3A9G8022959//Ministry of Science and ICT, South Korea/ ; 2021R1C1C1006336//Ministry of Science and ICT, South Korea/ ; HR22C141105//Ministry of Health and Welfare/ ; },
mesh = {Humans ; *Protein Interaction Maps ; Computer Simulation ; Computational Biology/methods ; },
abstract = {BACKGROUND: Natural herbs are frequently used to treat diseases or to relieve symptoms in many countries. Moreover, as their safety has been proven for a long time, they are considered as main sources of new drug development. However, in many cases, the herbs are still prescribed relying on ancient records and/or traditional practices without scientific evidences. More importantly, the medicinal efficacy of the herbs has to be evaluated in the perspective of MCMT (multi-compound multi-target) effects, but most efforts focus on identifying and analyzing a single compound experimentally. To overcome these hurdles, computational approaches which are based on the scientific evidences and are able to handle the MCMT effects are needed to predict the herb-disease associations.<br><br>RESULTS: In this study, we proposed a network-based in silico method to predict the herb-disease associations. To this end, we devised a new network-based measure, WACP (weighted average closest path length), which not only quantifies proximity between herb-related genes and disease-related genes but also considers compound compositions of each herb. As a result, we confirmed that our method successfully predicts the herb-disease associations in the human protein interactome (AUROC&#x2009;=&#x2009;0.777). In addition, we observed that our method is superior than the other simple network-based proximity measures (e.g. average shortest and closest path length). Additionally, we analyzed the associations between Brassica oleracea var. italica and its known associated diseases more specifically as case studies. Finally, based on the prediction results of the WACP, we suggested novel herb-disease pairs which are expected to have potential relations and their literature evidences.<br><br>CONCLUSIONS: This method could be a promising solution to modernize the use of the natural herbs by providing the scientific evidences about the molecular associations between the herb-related genes targeted by multiple compounds and the disease-related genes in the human protein interactome.},
}
@article {pmid38844398,
year = {2024},
author = {Xiao, Z and Robertson, S and Long, E and Flaig, R and Kirby, L and Romaniuk, L and Murray, A and Whalley, H},
title = {Loneliness in the Digital World: protocol for a co-produced ecological momentary assessment study in adolescents.},
journal = {BMJ open},
volume = {14},
number = {6},
pages = {e087374},
pmid = {38844398},
issn = {2044-6055},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Loneliness/psychology ; Adolescent ; *Ecological Momentary Assessment ; *Mental Health ; Female ; Child ; Male ; Social Interaction ; Surveys and Questionnaires ; Research Design ; Depression ; Scotland ; Anxiety ; },
abstract = {INTRODUCTION: Loneliness has been identified as an important public health issue, peaking during adolescence. Previous research has suggested that social interaction is a key factor in loneliness, and positive social interaction can act as a protective factor against loneliness. However, it is unclear whether there are differing impacts of in-person and online social interaction on adolescents' loneliness and mental health. Ecological Momentary Assessment (EMA) designs are ideally suited for better understanding these associations.<br><br>METHOD AND ANALYSIS: In the 'Loneliness in the Digital World' study, we will use a co-developed EMA design to capture daily social interactions, loneliness and mental health such as positive and negative emotions, depression and anxiety in approximately 200 adolescents aged 12-15 years. We will combine this with comprehensive information gathered from online surveys. Analysing the data using techniques such as dynamic structural equation modelling, we will examine, among other research questions, the associations between online and in-person social interaction and feelings of loneliness. The results can help inform interventions to support adolescents with high levels of loneliness and poor mental health.<br><br>ETHICS AND DISSEMINATION: We received the ethics approval for the data collection from The Academic and Clinical Central Office for Research and Development, followed by the College of Medicine and Veterinary Medicine Ethics panel at University of Edinburgh, and finally reviewed by East of Scotland Research Ethics Service. The results will be disseminated through journal publications, conferences and seminar presentations and to relevant stakeholders such as teachers.},
}
@article {pmid38841890,
year = {2024},
author = {Pedersen, MB and Beedholm, K and Hubancheva, A and Koseva, K and Uebel, AS and Hochradel, K and Madsen, PT and Stidsholt, L},
title = {Clutter resilience via auditory stream segregation in echolocating greater mouse-eared bats.},
journal = {The Journal of experimental biology},
volume = {227},
number = {12},
pages = {},
doi = {10.1242/jeb.246889},
pmid = {38841890},
issn = {1477-9145},
support = {//Frands Christian Frantsen Foundation/ ; FP2 0135-00343B//Natur og Univers, Det Frie Forskningsr&#xe5;d/ ; AU337272//Fonden Frands Christian Frantsens Legat/ ; 41386//Villum Fonden/ ; CF16-0405//Carlsbergfondet/ ; },
mesh = {Animals ; *Chiroptera/physiology ; *Echolocation/physiology ; Male ; Female ; Vocalization, Animal/physiology ; },
abstract = {Bats use echolocation to navigate and hunt in darkness, and must in that process segregate target echoes from unwanted clutter echoes. Bats may do this by approaching a target at steep angles relative to the plane of the background, utilizing their directional transmission and receiving systems to minimize clutter from background objects, but it remains unknown how bats negotiate clutter that cannot be spatially avoided. Here, we tested the hypothesis that when movement no longer offers spatial release, echolocating bats mitigate clutter by calling at lower source levels and longer call intervals to ease auditory streaming. We trained five greater mouse-eared bats (Myotis myotis) to land on a spherical loudspeaker with two microphones attached. We used a phantom-echo setup, where the loudspeaker/target transmitted phantom clutter echoes by playing back the bats' own calls at time delays of 1, 3 and 5 ms with a virtual target strength 7 dB higher than the physical target. We show that the bats successfully landed on the target, irrespective of the clutter echo delays. Rather than decreasing their source levels, the bats used similar source level distributions in clutter and control trials. Similarly, the bats did not increase their call intervals, but instead used the same distribution of call intervals across control and clutter trials. These observations reject our hypothesis, leading us to conclude that bats display great resilience to clutter via short auditory integration times and acute auditory stream segregation rather than via biosonar adjustments.},
}
@article {pmid38840517,
year = {2024},
author = {Walker, XJ and Hart, S and Hansen, WD and Jean, M and Brown, CD and Stuart Chapin, F and Hewitt, R and Hollingsworth, TN and Mack, MC and Johnstone, JF},
title = {Factors limiting the potential range expansion of lodgepole pine in Interior Alaska.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {34},
number = {5},
pages = {e2983},
doi = {10.1002/eap.2983},
pmid = {38840517},
issn = {1051-0761},
support = {05-1-2-06//Joint Fire Science Program/ ; //Natural Sciences and Engineering Research Council of Canada/ ; PNW01-JV11261952-23//U.S. Fish and Wildlife Service/ ; RC-2109//Strategic Environmental Research and Development Program/ ; RC-2754//Strategic Environmental Research and Development Program/ ; DEB-0620579//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; DEB-2224776//National Science Foundation/ ; USFS-PNW01-JV11261952-23//National Science Foundation/ ; RJVA-PNW-20-JV-11261932-018//National Science Foundation/ ; OPP-2116862//National Science Foundation/ ; NNX15AT71A/NASA/NASA/United States ; },
mesh = {*Pinus/physiology ; Alaska ; Climate Change ; Models, Biological ; Seedlings ; Demography ; Animals ; Ecosystem ; },
abstract = {Understanding the factors influencing species range limits is increasingly crucial in anticipating migrations due to human-caused climate change. In the boreal biome, ongoing climate change and the associated increases in the rate, size, and severity of disturbances may alter the distributions of boreal tree species. Notably, Interior Alaska lacks native pine, a biogeographical anomaly that carries implications for ecosystem structure and function. The current range of lodgepole pine (Pinus contorta var. latifolia) in the adjacent Yukon Territory may expand into Interior Alaska, particularly with human assistance. Evaluating the potential for pine expansion in Alaska requires testing constraints on range limits such as dispersal limitations, environmental tolerance limits, and positive or negative biotic interactions. In this study, we used field experiments with pine seeds and transplanted seedlings, complemented by model simulations, to assess the abiotic and biotic factors influencing lodgepole pine seedling establishment and growth after fire in Interior Alaska. We found that pine could successfully recruit, survive, grow, and reproduce across our broadly distributed network of experimental sites. Our results show that both mammalian herbivory and competition from native tree species are unlikely to constrain pine growth and that environmental conditions commonly found in Interior Alaska fall well within the tolerance limits for pine. If dispersal constraints are released, lodgepole pine could have a geographically expansive range in Alaska, and once established, its growth is sufficient to support pine-dominated stands. Given the impacts of lodgepole pine on ecosystem processes such as increases in timber production, carbon sequestration, landscape flammability, and reduced forage quality, natural or human-assisted migration of this species is likely to substantially alter responses of Alaskan forest ecosystems to climate change.},
}
@article {pmid38839953,
year = {2024},
author = {Senior, RA and Bagwyn, R and Leng, D and Killion, AK and Jetz, W and Wilcove, DS},
title = {Global shortfalls in documented actions to conserve biodiversity.},
journal = {Nature},
volume = {630},
number = {8016},
pages = {387-391},
pmid = {38839953},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources/methods/statistics &amp; numerical data ; Databases, Factual ; *Endangered Species/statistics &amp; numerical data ; Extinction, Biological ; *Internationality ; Introduced Species/statistics &amp; numerical data ; },
abstract = {Threatened species are by definition species that are in need of assistance. In the absence of suitable conservation interventions, they are likely to disappear soon[1]. There is limited understanding of how and where conservation interventions are applied globally, or how well they work[2,3]. Here, using information from the International Union for Conservation of Nature Red List and other global databases, we find that for species at risk from three of the biggest drivers of biodiversity loss-habitat loss, overexploitation for international trade and invasive species[4]-many appear to lack the appropriate types of conservation interventions. Indeed, although there has been substantial recent expansion of the protected area network, we still find that 91% of threatened species have insufficient representation of their habitats within protected areas. Conservation interventions are not implemented uniformly across different taxa and regions and, even when present, have infrequently led to substantial improvements in the status of species. For 58% of the world's threatened terrestrial species, we find conservation interventions to be notably insufficient or absent. We cannot determine whether such species are truly neglected, or whether efforts to recover them are not included in major conservation databases. If they are indeed neglected, the outlook for many of the world's threatened species is grim without more and better targeted action.},
}
@article {pmid38838462,
year = {2024},
author = {Runge, MC and Shea, K and Howerton, E and Yan, K and Hochheiser, H and Rosenstrom, E and Probert, WJM and Borchering, R and Marathe, MV and Lewis, B and Venkatramanan, S and Truelove, S and Lessler, J and Viboud, C},
title = {Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design.},
journal = {Epidemics},
volume = {47},
number = {},
pages = {100775},
doi = {10.1016/j.epidem.2024.100775},
pmid = {38838462},
issn = {1878-0067},
support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control/transmission ; *Decision Support Techniques ; Forecasting ; SARS-CoV-2 ; Communicable Diseases/epidemiology ; Pandemics/prevention &amp; control ; Decision Making ; Research Design ; },
abstract = {Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, situational awareness, horizon scanning, forecasting, and value of information) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.},
}
@article {pmid38837409,
year = {2024},
author = {Rico-Jiménez, M and Udaondo, Z and Krell, T and Matilla, MA},
title = {Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica.},
journal = {mSystems},
volume = {9},
number = {7},
pages = {e0016524},
pmid = {38837409},
issn = {2379-5077},
support = {PID2020-112612GB-I00//Spanish Ministry for Science and Innovation/ ; PID2019-103972GA-I00//Spanish Ministry for Science and Innovation/ ; 2023AEP002//Consejo Superior de Investigaciones Cient&#xed;ficas (CSIC)/ ; P18-FR-1621//Junta de Andalucia/ ; },
mesh = {*Indoleacetic Acids/metabolism ; *Serratia/metabolism/genetics/drug effects/pathogenicity ; *Cyclic GMP/metabolism/analogs &amp; derivatives ; Gene Expression Regulation, Bacterial/drug effects ; Bacteriophages ; Signal Transduction/drug effects ; Biofilms/drug effects/growth &amp; development ; Bacterial Proteins/metabolism/genetics ; Plant Growth Regulators/metabolism ; Transcriptome/drug effects ; },
abstract = {UNLABELLED: The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.<br><br>IMPORTANCE: Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.},
}
@article {pmid38831386,
year = {2024},
author = {Duo, H and Li, Y and Lan, Y and Tao, J and Yang, Q and Xiao, Y and Sun, J and Li, L and Nie, X and Zhang, X and Liang, G and Liu, M and Hao, Y and Li, B},
title = {Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {145},
pmid = {38831386},
issn = {1474-760X},
support = {KJQN202100538//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; 62101087//National Natural Science Foundation of China/ ; 2021MD703942//China Postdoctoral Science Foundation/ ; YKC23027//Graduate Research Innovation Project of Chongqing Normal University/ ; YNPRAEC-2023004//Open Fund of Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology/ ; },
mesh = {*Single-Cell Analysis/methods ; *Gene Expression Profiling/methods ; Humans ; Software ; Computer Simulation ; Transcriptome ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods/standards ; },
abstract = {BACKGROUND: Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perform unbiased benchmarks, data simulation has been widely adopted by providing explicit ground truth and generating customized datasets. However, the performance of simulation methods under multiple scenarios has not been comprehensively assessed, making it challenging to choose suitable methods without practical guidelines.<br><br>RESULTS: We systematically evaluated 49 simulation methods developed for scRNA-seq and/or SRT data in terms of accuracy, functionality, scalability, and usability using 152 reference datasets derived from 24 platforms. SRTsim, scDesign3, ZINB-WaVE, and scDesign2 have the best accuracy performance across various platforms. Unexpectedly, some methods tailored to scRNA-seq data have potential compatibility for simulating SRT data. Lun, SPARSim, and scDesign3-tree outperform other methods under corresponding simulation scenarios. Phenopath, Lun, Simple, and MFA yield high scalability scores but they cannot generate realistic simulated data. Users should consider the trade-offs between method accuracy and scalability (or functionality) when making decisions. Additionally, execution errors are mainly caused by failed parameter estimations and appearance of missing or infinite values in calculations. We provide practical guidelines for method selection, a standard pipeline Simpipe (https://github.com/duohongrui/simpipe ; https://doi.org/10.5281/zenodo.11178409), and an online tool Simsite (https://www.ciblab.net/software/simshiny/) for data simulation.<br><br>CONCLUSIONS: No method performs best on all criteria, thus a good-yet-not-the-best method is recommended if it solves problems effectively and reasonably. Our comprehensive work provides crucial insights for developers on modeling gene expression data and fosters the simulation process for users.},
}
@article {pmid38826163,
year = {2024},
author = {Onyango, B and Copeland, R and Mbogholi, J and Wamalwa, M and Kibet, C and Tonnang, HEZ and Senagi, K},
title = {WiPFIM: A digital platform for interlinking biocollections of wild plants, fruits, associated insects, and their molecular barcodes.},
journal = {Ecology and evolution},
volume = {14},
number = {6},
pages = {e11457},
pmid = {38826163},
issn = {2045-7758},
abstract = {The current knowledge on insects feeding on fruits is limited, and some of the scarce existing data on the fruit-associated insects are secluded within the host institutions. Consequently, their value is not fully realized. Moreover, in countries like Kenya, the integration of biocollections data within a digital framework has not been fully exploited. To address these gaps, this article presents a description of the development of a web-based platform for data sharing and integrating biodiversity historical data of wild plants, fruits, associated insects, and their molecular barcodes (WiPFIM) while leveraging data science technologies. The barcodes corresponding to the biocollections data were retrieved from BOLD database. The platform is an online resource about fruit-insect interactions that can be of interest to a worldwide community of users and can be useful in building innovative tools. The platform is accessible online at https://test-dmmg.icipe.org/wpfhi.},
}
@article {pmid38825206,
year = {2024},
author = {Wei, Q and Xue, L and Liao, S and Liu, Y},
title = {Ecohydrological indicators and environmental flow assessment in the middle and lower reaches of the Huai River, China.},
journal = {The Science of the total environment},
volume = {940},
number = {},
pages = {173639},
doi = {10.1016/j.scitotenv.2024.173639},
pmid = {38825206},
issn = {1879-1026},
abstract = {The vitality of river ecosystems is vital for the sustainable development of river basins, with the assessment of environmental flow (EF) playing a pivotal role in eco-informatics. This study delves into the middle and lower reaches (MLR) of the Huai River basin (HRB) in China, utilizing hydrological data spanning from 1950 to 2020. Its principal objective lies in the selection of ecohydrological indicators to refine the estimation of EF in the HRB. Employing principal component analysis (PCA), ecologically relevant hydrological indicators (ERHIs) were discerned and scrutinized for their hydrological characteristics. The analysis extended to evaluating hydrological shifts at different stations using ERHIs, determining suitable EF in the MLR, and delineating the trajectories of appropriate intra-annual flows in different hydrological years through HEC-RPT. Based on a variety of mutation test methods, the change point of runoff sequence was determined in 1991. The PCA analysis identified eight ERHIs, reflecting hydrological changes of 49.79 % and 56.26 % at Bengbu and Sanhezha, respectively, which indicate a moderate alteration. Based on ERHIs, the other stations in the HRB exhibited hydrological alterations ranging from 33 % to 47 %, notably highlighting substantial changes in maximal 30d flow and flow fall rate. The optimal flood pulse discharge in the middle reaches is 4150 m[3]/s, 3140 m[3]/s and 2150 m[3]/s in wet, dry and dry years, respectively. Downstream, flood pulse flow in wet, normal and dry years should exceed 4070 m[3]/s, 3110 m[3]/s and 1980 m[3]/s, respectively. The research contributes significantly to the management of rivers and the sustainable conservation of the ecological milieu.},
}
@article {pmid38824636,
year = {2024},
author = {Xie, PZ and Fan, YX and Chapman, C and Ma, C and Wu, CF and Hu, P and Hu, LL and Fan, PF},
title = {Determinants of macaques' space use: A test for the ecological constraints model using GPS collars.},
journal = {American journal of primatology},
volume = {86},
number = {8},
pages = {e23636},
doi = {10.1002/ajp.23636},
pmid = {38824636},
issn = {1098-2345},
support = {33000-42090019//Forestry Administration of Guangdong Province/ ; Basic Research 20180285//Shenzhen Science and Technology Innovation Committee/ ; 23lgzy002//Fundamental Research Funds for the Central Universities, Sun Yat-sun University/ ; },
mesh = {Animals ; *Macaca mulatta/physiology ; *Geographic Information Systems ; *Homing Behavior ; China ; Male ; Female ; Ecosystem ; Temperature ; Seasons ; Islands ; },
abstract = {As a central topic in Behavioral Ecology, animal space use involves dynamic responses to social and ecological factors. We collared 22 rhesus macaques (Macaca mulatta) from six groups on Neilingding Island, China, and collected 80,625 hourly fixes over a year. Using this high-resolution location data set, we quantified the macaques' space use at the individual level and tested the ecological constraints model while considering various environmental and human interfering factors. As predicted by the ecological constraints model, macaques in larger groups had longer daily path lengths (DPLs) and larger home ranges. We found an inverted U-shape relationship between mean daily temperatures and DPLs, indicating that macaques traveled farther on mild temperature days, while they decreased DPLs when temperatures were too high or too low. Anthropogenic food subsidies were positively correlated to DPLs, while the effect of rainfall was negative. Macaques decreased their DPLs and core areas when more flowers and less leaves were available, suggesting that macaques shifted their space use patterns to adapt to the seasonal differences in food resources. By applying GPS collars on a large number of individuals living on a small island, we gained valuable insights into within-group exploitation competition in wild rhesus macaques.},
}
@article {pmid38823656,
year = {2024},
author = {Sundar Panja, A},
title = {The systematic codon usage bias has an important effect on genetic adaption in native species.},
journal = {Gene},
volume = {926},
number = {},
pages = {148627},
doi = {10.1016/j.gene.2024.148627},
pmid = {38823656},
issn = {1879-0038},
mesh = {*Codon Usage ; *Selection, Genetic ; *Evolution, Molecular ; Endangered Species ; Mutation ; Animals ; Codon/genetics ; Adaptation, Physiological/genetics ; Extremophiles/genetics ; },
abstract = {Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.},
}
@article {pmid38823290,
year = {2024},
author = {Lopez-Labrador, FX and Huber, M and Sidorov, IA and Brown, JR and Cuypers, L and Laenen, L and Vanmechelen, B and Maes, P and Fischer, N and Pichler, I and Storey, N and Atkinson, L and Schmutz, S and Kufner, V and van Boheemen, S and Mulders, CE and Grundhoff, A and Blümke, P and Robitaille, A and Cinek, O and Hubáčková, K and Mourik, K and Boers, SA and Stauber, L and Salmona, M and Cappy, P and Ramette, A and Franze', A and LeGoff, J and Claas, ECJ and Rodriguez, C and de Vries, JJC and , },
title = {Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {173},
number = {},
pages = {105695},
doi = {10.1016/j.jcv.2024.105695},
pmid = {38823290},
issn = {1873-5967},
mesh = {*Metagenomics/methods/standards ; Humans ; *Benchmarking ; *Viruses/genetics/classification/isolation &amp; purification ; *Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods/standards ; Virus Diseases/diagnosis/virology ; Computational Biology/methods ; },
abstract = {Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 10[4] copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.},
}
@article {pmid38822995,
year = {2024},
author = {Meier, TA and Refahi, MS and Hearne, G and Restifo, DS and Munoz-Acuna, R and Rosen, GL and Woloszynek, S},
title = {The Role and Applications of Artificial Intelligence in the Treatment of Chronic Pain.},
journal = {Current pain and headache reports},
volume = {28},
number = {8},
pages = {769-784},
pmid = {38822995},
issn = {1534-3081},
mesh = {Humans ; *Chronic Pain/therapy ; *Artificial Intelligence ; Pain Management/methods ; Precision Medicine/methods ; },
abstract = {PURPOSE OF REVIEW: This review aims to explore the interface between artificial intelligence (AI) and chronic pain, seeking to identify areas of focus for enhancing current treatments and yielding novel therapies.<br><br>RECENT FINDINGS: In the United States, the prevalence of chronic pain is estimated to be upwards of 40%. Its impact extends to increased healthcare costs, reduced economic productivity, and strain on healthcare resources. Addressing this condition is particularly challenging due to its complexity and the significant variability in how patients respond to treatment. Current options often struggle to provide long-term relief, with their benefits rarely outweighing the risks, such as dependency or other side effects. Currently, AI has impacted four key areas of chronic pain treatment and research: (1) predicting outcomes based on clinical information; (2) extracting features from text, specifically clinical notes; (3) modeling 'omic data to identify meaningful patient subgroups with potential for personalized treatments and improved understanding of disease processes; and (4) disentangling complex neuronal signals responsible for pain, which current therapies attempt to modulate. As AI advances, leveraging state-of-the-art architectures will be essential for improving chronic pain treatment. Current efforts aim to extract meaningful representations from complex data, paving the way for personalized medicine. The identification of unique patient subgroups should reveal targets for tailored chronic pain treatments. Moreover, enhancing current treatment approaches is achievable by gaining a more profound understanding of patient physiology and responses. This can be realized by leveraging AI on the increasing volume of data linked to chronic pain.},
}
@article {pmid38822898,
year = {2024},
author = {Asefa, A and Reuber, VM and Miehe, G and Wraase, L and Wube, T and Farwig, N and Schabo, DG},
title = {Giant root-rat engineering and livestock grazing activities regulate plant functional trait diversity of an Afroalpine vegetation community in the Bale Mountains, Ethiopia.},
journal = {Oecologia},
volume = {205},
number = {2},
pages = {281-293},
pmid = {38822898},
issn = {1432-1939},
support = {NA 783/12-2, FA-925/14-1 und SCHA-2085/3-1, MI271/33-2]//German Research Council (DFG) within the Research Unit 2358 ("The Mountain Exile Hypothesis")/ ; },
mesh = {Ethiopia ; Animals ; *Livestock ; *Ecosystem ; Rodentia/physiology ; },
abstract = {Disturbances from rodent engineering and human activities profoundly impact ecosystem structure and functioning. Whilst we know that disturbances modulate plant communities, comprehending the mechanisms through which rodent and human disturbances influence the functional trait diversity and trait composition of plant communities is important to allow projecting future changes and to enable informed decisions in response to changing intensity of the disturbances. Here, we evaluated the changes in functional trait diversity and composition of Afroalpine plant communities in the Bale Mountains of Ethiopia along gradients of engineering disturbances of a subterranean endemic rodent, the giant root-rat (Tachyoryctes macrocephalus Rüppell 1842) and human activities (settlement establishment and livestock grazing). We conducted RLQ (co-inertia analysis) and fourth-corner analyses to test for trait-disturbance (rodent engineering/human activities) covariation. Overall, our results show an increase in plant functional trait diversity with increasing root-rat engineering and increasing human activities. We found disturbance specific association with traits. Specifically, we found strong positive association of larger seed mass with increasing root-rat fresh burrow density, rhizomatous vegetative propagation negatively associated with increasing root-rat old burrow, and stolonifereous vegetative propagation positively associated with presence of root-rat mima mound. Moreover, both leaf size and leaf nitrogen content were positively associated with livestock dung abundance but negatively with distance from settlement. Overall, our results suggest that disturbances by rodents filter plant traits related to survival and reproduction strategies, whereas human activities such as livestock grazing act as filters for traits related to leaf economics spectrum along acquisitive resource-use strategy.},
}
@article {pmid38822152,
year = {2024},
author = {Li, X and Bai, Y and Xu, C and Liu, S and Yu, H and Kong, L and Du, S and Li, Q},
title = {OysterDB: A Genome Database for Ostreidae.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {26},
number = {4},
pages = {827-834},
pmid = {38822152},
issn = {1436-2236},
support = {2022LZGCQY010, 2021ZLGX03 and 2021TSGC1240//Shandong Province Agriculture Research System Project/ ; CARS-49//China Agriculture Research System Project/ ; },
mesh = {Animals ; *Databases, Genetic ; *Ostreidae/genetics ; *Genome ; Molecular Sequence Annotation ; Computational Biology ; Genomics ; },
abstract = {The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters (http://oysterdb.com.cn/).},
}
@article {pmid38820292,
year = {2023},
author = {Damian-Serrano, A and Sutherland, KR},
title = {A Developmental Ontology for the Colonial Architecture of Salps.},
journal = {The Biological bulletin},
volume = {245},
number = {1},
pages = {9-18},
doi = {10.1086/730459},
pmid = {38820292},
issn = {1939-8697},
mesh = {Animals ; *Urochordata/growth &amp; development/physiology/anatomy &amp; histology ; Life Cycle Stages/physiology ; Biological Ontologies ; },
abstract = {AbstractColonial animals are composed of clonal individuals that remain physically connected and physiologically integrated. Salps are tunicates with a dual life cycle, including an asexual solitary stage that buds sexual colonies composed of jet-propelling zooids that efficiently swim together as a single unit by multijet propulsion. Colonies from different species develop distinct architectures characterized by their zooid arrangement patterns, but this diversity has received little attention. Thus, these architectures have never been formally defined using a framework of variables and axes that would allow comparative analyses. We set out to define an ontology of the salp colony architecture morphospace and describe the developmental pathways that build the different architectures. To inform these definitions, we collected and photographed live specimens of adult and developing colonies through offshore scuba diving. Since all salp colonies begin their development as a transversal double chain, we characterized each adult colonial architecture as a series of developmental transitions, such as rotations and translations of zooids, relative to their orientation at this early shared stage. We hypothesize that all adult architectures are either final or intermediate stages within three developmental pathways toward bipinnate, cluster, or helical forms. This framework will enable comparative studies on the biomechanical implications, ecological functions, evolutionary history, and engineering applications of the diversity of salp colony architectures.},
}
@article {pmid38819974,
year = {2024},
author = {Tang, Z and Tang, S and Wang, H and Li, R and Zhang, X and Zhang, W and Yuan, X and Zang, Y and Li, Y and Zhou, T and Li, Y},
title = {S2VQ-VAE: Semi-Supervised Vector Quantised-Variational AutoEncoder for Automatic Evaluation of Trail Making Test.},
journal = {IEEE journal of biomedical and health informatics},
volume = {28},
number = {8},
pages = {4456-4470},
doi = {10.1109/JBHI.2024.3407881},
pmid = {38819974},
issn = {2168-2208},
mesh = {Humans ; *Cognitive Dysfunction/diagnosis ; Aged ; Male ; Female ; *Trail Making Test ; Supervised Machine Learning ; Aged, 80 and over ; Algorithms ; Deep Learning ; Diagnosis, Computer-Assisted/methods ; Signal Processing, Computer-Assisted ; },
abstract = {BACKGROUND: Computer-aided detection of cognitive impairment garnered increasing attention, offering older adults in the community access to more objective, ecologically valid, and convenient cognitive assessments using multimodal sensing technology on digital devices.<br><br>METHODOLOGY: In this study, we aimed to develop an automated method for screening cognitive impairment, building on paper- and electronic TMTs. We proposed a novel deep representation learning approach named Semi-Supervised Vector Quantised-Variational AutoEncoder (S2VQ-VAE). Within S2VQ-VAE, we incorporated intra- and inter-class correlation losses to disentangle class-related factors. These factors were then combined with various real-time obtainable features (including demographic, time-related, pressure-related, and jerk-related features) to create a robust feature engineering block. Finally, we identified the light gradient boosting machine as the optimal classifier. The experiments were conducted on a dataset collected from older adults in the community.<br><br>RESULTS: The experimental results showed that the proposed multi-type feature fusion method outperformed the conventional method used in paper-based TMTs and the existing VAE-based feature extraction in terms of screening performance.<br><br>CONCLUSIONS: In conclusion, the proposed deep representation learning method significantly enhances the cognitive diagnosis capabilities of behavior-based TMTs and streamlines large-scale community-based cognitive impairment screening while reducing the workload of professional healthcare staff.},
}
@article {pmid38819559,
year = {2024},
author = {Sanchez, FB and Sato Guima, SE and Setubal, JC},
title = {How to Obtain and Compare Metagenome-Assembled Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2802},
number = {},
pages = {135-163},
pmid = {38819559},
issn = {1940-6029},
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; Software ; Computational Biology/methods ; Databases, Genetic ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; },
abstract = {Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.},
}
@article {pmid38818975,
year = {2024},
author = {Shi, H and Zhu, Y and Wu, X and Jiang, T and Li, X and Liu, J and Di, Y and Chen, F and Gao, J and Xu, X and Xiao, N and Feng, X and Zhang, P and Wu, Y and La, Q and Li, A and Chen, P and Li, X},
title = {CropMetabolome: a comprehensive metabolome database for major crops cross eight categories.},
journal = {The Plant journal : for cell and molecular biology},
volume = {119},
number = {3},
pages = {1613-1626},
doi = {10.1111/tpj.16858},
pmid = {38818975},
issn = {1365-313X},
support = {2023ZD04073//National Key R&amp;D Program of China/ ; XDA24010400//Strategic Priority Research Program of Chinese Academy of Sciences/ ; BE2023336//Key R&amp;D Program of Jiangsu Province Modern Agriculture/ ; 32270719//National Natural Science Foundation of China/ ; 31900470//National Natural Science Foundation of China/ ; 32200093//National Natural Science Foundation of China/ ; CARS-11//Earmarked Fund for China Agriculture Research System/ ; 2022M713144//China Postdoctoral Science Foundation/ ; },
mesh = {*Crops, Agricultural/metabolism/genetics ; *Metabolome ; *Metabolomics/methods ; *Databases, Factual ; Flavonoids/metabolism ; Mass Spectrometry ; },
abstract = {Chemical compositions of crops are of great agronomical importance, as crops serve as resources for nutrition, energy, and medicines for human and livestock. For crop metabolomics research, the lack of crop reference metabolome and high-quality reference compound mass spectra, as well as utilities for metabolic profiling, has hindered the discovery and functional study of phytochemicals in crops. To meet these challenging needs, we have developed the Crop Metabolome database (abbreviated as CropMetabolome) that is dedicated to the construction of crop reference metabolome, repository, and dissemination of crop metabolomic data, and profiling and analytic tools for metabolomics research. CropMetabolome contains a metabolomics database for more than 50 crops (belonging to eight categories) that integrated self-generated raw mass spectral data and public-source datasets. The reference metabolome for 59 crop species was constructed, which have functions that parallel those of reference genome in genomic studies. CropMetabolome also contains 'Standard compound mass spectral library', 'Flavonoids library', 'Pesticide library', and a set of related analytical tools that enable metabolic profiling based on a reference metabolome (CropRefMetaBlast), annotation and identification of new metabolites (CompoundLibBlast), deducing the structure of novel flavonoid derivatives (FlavoDiscover), and detecting possible residual pesticides in crop samples (PesticiDiscover). In addition, CropMetabolome is a repository to share and disseminate metabolomics data and a platform to promote collaborations to develop reference metabolome for more crop species. CropMetabolome is a comprehensive platform that offers important functions in crop metabolomics research and contributes to improve crop breeding, nutrition, and safety. CropMetabolome is freely available at https://www.cropmetabolome.com/.},
}
@article {pmid38816346,
year = {2024},
author = {Locke, MA and Witthaus, LM and Lizotte, RE and Heintzman, LJ and Moore, MT and O'Reilly, A and Wells, RR and Langendoen, EJ and Bingner, RL and Gholson, DM and Taylor, JM and Johnson, FE},
title = {The LTAR Cropland Common Experiment in the Lower Mississippi River Basin.},
journal = {Journal of environmental quality},
volume = {53},
number = {6},
pages = {957-967},
doi = {10.1002/jeq2.20577},
pmid = {38816346},
issn = {1537-2537},
mesh = {*Rivers ; *Agriculture/methods ; *Crops, Agricultural ; Conservation of Natural Resources/methods ; },
abstract = {The Lower Mississippi River Basin Long-Term Agroecosystem Research Site (LMRB-LTAR) encompasses six states from Missouri to the Gulf of Mexico and is coordinated by the USDA-ARS National Sedimentation Laboratory, Oxford, MS. The overarching goal of LTAR is to assess regionally diverse and geographically scalable farming practices for enhanced sustainability of agroecosystem goods and services under changing environment and resource-use conditions. The LMRB-LTAR overall goal is to assess sustainable row crop agricultural production systems that integrate regional environmental and socioeconomic needs. Primary row crops in the region include soybeans, corn, cotton, rice, and sugarcane with crop rotations influenced by commodity crop price and other factors. The field-scale common experiment (CE) includes four row crop farms (26-101 ha) established in 2021 and 2023. Three fields are managed with alternative practices, including reduced tillage, cover crops, and automated prescription irrigation, and three fields are managed with prevailing farming practices, consisting of conventional tillage, no cover crop, and nonprescription irrigation. Treatment effects on crop productivity, soil quality, water use efficiency, water quality, and carbon storage are assessed. Research from the LMRB CE will deliver outcomes linked to overarching LTAR network goals, including innovative agricultural systems, strengthened partnerships, data management technologies, and precision environmental tools.},
}
@article {pmid38814981,
year = {2024},
author = {Mullon, C and Peña, J and Lehmann, L},
title = {The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012071},
pmid = {38814981},
issn = {1553-7358},
mesh = {*Biological Evolution ; *Social Interaction ; Computational Biology ; Phenotype ; Animals ; Environment ; Humans ; },
abstract = {Many social interactions happen indirectly via modifications of the environment, e.g. through the secretion of functional compounds or the depletion of renewable resources. Here, we derive the selection gradient on a quantitative trait affecting dynamical environmental variables that feed back on reproduction and survival in a finite patch-structured population subject to isolation by distance. Our analysis shows that the selection gradient depends on how a focal individual influences the fitness of all future individuals in the population through modifications of the environmental variables they experience, weighted by the neutral relatedness between recipients and the focal. The evolutionarily relevant trait-driven environmental modifications are formalized as the extended phenotypic effects of an individual, quantifying how a trait change in an individual in the present affects the environmental variables in all patches at all future times. When the trait affects reproduction and survival through a payoff function, the selection gradient can be expressed in terms of extended phenotypic effects weighted by scaled relatedness. We show how to compute extended phenotypic effects, relatedness, and scaled relatedness using Fourier analysis, which allow us to investigate a broad class of environmentally mediated social interactions in a tractable way. We use our approach to study the evolution of a trait controlling the costly production of some lasting commons (e.g. a common-pool resource or a toxic compound) that can diffuse in space and persist in time. We show that indiscriminate posthumous spite readily evolves in this scenario. More generally, whether selection favours environmentally mediated altruism or spite is determined by the spatial correlation between an individual's lineage and the commons originating from its patch. The sign of this correlation depends on interactions between dispersal patterns and the commons' renewal dynamics. More broadly, we suggest that selection can favour a wide range of social behaviours when these have carry-over effects in space and time.},
}
@article {pmid38814957,
year = {2024},
author = {Schoenecker, KA and King, SRB and Hennig, JD and Cole, MJ and Scasta, JD and Beck, JL},
title = {Effects of telemetry collars on two free-roaming feral equid species.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303312},
pmid = {38814957},
issn = {1932-6203},
mesh = {Animals ; *Telemetry ; *Equidae/physiology ; *Geographic Information Systems ; Horses ; Female ; Male ; },
abstract = {There are two species of free-roaming feral equids in North America: horses (Equus caballus) and donkeys or "burros" (E. asinus). Both species were introduced as domestic animals to North America in the early 1500s and currently inhabit rangelands across the western United States, Canada, and all continents except Antarctica. Despite their global distribution, little is known about their fine scale spatial ecology. Contemporary research tools to assess space use include global positioning system (GPS) tracking collars, but older models were problematic due to stiff collar belting causing poor fit. We tested modern designs of GPS collars on n = 105 horses and n = 60 burros for 4 years in five populations (3 horse, 2 burro) across the western United States, to assess whether collars posed welfare risks to horses or burros. We found no difference in survival of collared versus uncollared mares and jennies, and no difference in survival of their foals. In 4036 of 4307 observations for horses (93.7%) and 2115 of 2258 observations for burros (93.6%), collars were observed symmetrical, maintaining proper fit on the neck. Fur effects from collars (sweaty neck, indented fur, broken fur) were seen in 3% of horse observations and 25% of burro observations. Superficial effects (chafes and marks on skin surface) were seen in 2% of horse observations and 11% of burro observations; no severe effects from collars were seen. Body condition was not affected by collars; mean body condition of collared horses was 4.70 ± 0.54 (mean ± s.d) and 4.71 ± 0.65 for collared burros. Behavior results indicated minimal effects; collared horses stood slightly more than uncollared, and collared burros stood and foraged more in one population, but not in the other. For 6.3% of observations of horses and 6.4% of observations of burros, we found an effect of time wearing a collar on the cumulative sum of fur effects which increased over time (burros: rs = 0.87, P = <0.0001; horses: rs = 0.31, P = 0.002). Burros also showed an increase over time in the number of superficial effects, but horses did not. Collars occasionally moved into the wrong position, shifting forward over the ears; we observed this on 19 horses and 1 burro. Of those, most collars went over the ears in summer (n = 12). All collars were equipped with a remote release mechanism as well as a timed-release mechanism for redundancy, thus removed when observed in wrong position to avoid rubbing or discomfort. Our finding of no consequential physical effects in 98% of horse observations, and 89% of burro observations suggests the consequences of collars on free-roaming equid welfare and survival is biologically insignificant, although collars should be monitored regularly and continue to be equipped with a remote release mechanism to remove a collar if needed. With frequent welfare-driven, visual monitoring, collaring of free-roaming equids can be a safe and useful tool to increase our understanding of their spatial ecology, demography, habitat use, behavior, and interactions with other wildlife.},
}
@article {pmid38813661,
year = {2024},
author = {Cong, Y and Endo, T},
title = {A Quadruple Revolution: Deciphering Biological Complexity with Artificial Intelligence, Multiomics, Precision Medicine, and Planetary Health.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {6},
pages = {257-260},
doi = {10.1089/omi.2024.0110},
pmid = {38813661},
issn = {1557-8100},
mesh = {*Precision Medicine/methods/trends ; *Artificial Intelligence ; Humans ; Systems Biology/methods ; Genomics/methods ; Machine Learning ; Multiomics ; },
abstract = {A quiet quadruple revolution has been in the making in systems science with convergence of (1) artificial intelligence, machine learning, and other digital technologies; (2) multiomics big data integration; (3) growing interest in the "variability science" of precision/personalized medicine that aims to account for patient-to-patient and between-population differences in disease susceptibilities and responses to health interventions such as drugs, nutrition, vaccines, and radiation; and (4) planetary health scholarship that both scales up and integrates biological, clinical, and ecological contexts of health and disease. Against this overarching background, this article presents and highlights some of the salient challenges and prospects of multiomics research, emphasizing the attendant pivotal role of systems medicine and systems biology. In addition, we emphasize the rapidly growing importance of planetary health research for systems medicine, particularly amid climate emergency, ecological degradation, and loss of planetary biodiversity. Looking ahead, we anticipate that the integration and utilization of multiomics big data and artificial intelligence will drive further progress in systems medicine and systems biology, heralding a promising future for both human and planetary health.},
}
@article {pmid38813550,
year = {2023},
author = {Boyes, D and , and , and , and , and , and , },
title = {The genome sequence of the Six-belted Clearwing, Bembecia ichneumoniformis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {515},
pmid = {38813550},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Bembecia ichneumoniformis (the Six-belted Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 511.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,114 protein coding genes.},
}
@article {pmid38813548,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the July Highflyer, Hydriomena furcata (Thunberg, 1784).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {496},
pmid = {38813548},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Hydriomena furcata (the July Highflyer; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 423.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.89 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,324 protein coding genes.},
}
@article {pmid38813465,
year = {2024},
author = {Falk, S and Poole, O and , and , and , and , and , and , and , },
title = {The genome sequence of the parsley Cheilosia, Cheilosia pagana (Meigen, 1822).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {54},
pmid = {38813465},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Cheilosia pagana (the parsley Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 354.1 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.76 kilobases in length.},
}
@article {pmid38808804,
year = {2024},
author = {Freitas, GA and Marcon, GEB and Welch, JR and Silva, CMFPD},
title = {Analysis of the completeness and consistency of records of violence against indigenous women in the health macro-region of Dourados, Mato Grosso do Sul state, Brazil, 2009-2020.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {33},
number = {},
pages = {e20231075},
pmid = {38808804},
issn = {2237-9622},
mesh = {Adult ; Indians, South American/statistics &amp; numerical data ; Information Systems ; Time Factors ; Female ; South American People ; Humans ; Brazil ; Communication ; Indigenous Peoples/statistics &amp; numerical data ; *Violence/statistics &amp; numerical data ; Educational Status ; Gender-Based Violence/statistics &amp; numerical data ; },
abstract = {OBJECTIVE: To analyze the temporal trend of completeness and consistency of data on notifications of violence against indigenous women in the health macro-region of Dourados, state of Mato Grosso do Sul, Brazil, between 2009 and 2020.<br><br>METHODS: An ecological time series study was conducted using data from the Notifiable Health Conditions Information System; Prais-Winsten regression was used to analyze the trend of data completeness and consistency, as well as the proportion of completed and coherent fields.<br><br>RESULTS: A total of 2,630 cases were reported; completeness was found to be very poor in the variable "occupation" (48.9%) and poor in the variables "schooling" (68.3%) and "time of occurrence" (67.9%); in the analysis of temporal trends, only the variable "occupation" showed a decreasing trend (p = 0.045).<br><br>CONCLUSION: The data analyzed demonstrated the need for improvement in the completeness of the variables "schooling", "occupation" and "time of occurrence" of the violent act.<br><br>MAIN RESULTS: There was a progressive increase in notifications over the years. Most of the variables showed regular or excellent completeness and consistency. In the analysis of temporal trend, only the "occupation" variable showed a decreasing trend.<br><br>IMPLICATIONS FOR SERVICES: Care for victims of violence is part of the daily routine of health services, and it is essential for health professionals to provide adequate compulsory notification for a comprehensive understanding of the victims' profile, thus assisting in addressing this issue.<br><br>PERSPECTIVES: Further studies are needed to understand the factors associated with violence against indigenous women, which could help the development of health promotion actions and violence prevention strategies targeting these women.},
}
@article {pmid38808214,
year = {2024},
author = {Kyalo, H and Tonnang, HEZ and Egonyu, JP and Olukuru, J and Tanga, CM and Senagi, K},
title = {A convolutional neural network with image and numerical data to improve farming of edible crickets as a source of food-A decision support system.},
journal = {Frontiers in artificial intelligence},
volume = {7},
number = {},
pages = {1403593},
pmid = {38808214},
issn = {2624-8212},
abstract = {Crickets (Gryllus bimaculatus) produce sounds as a natural means to communicate and convey various behaviors and activities, including mating, feeding, aggression, distress, and more. These vocalizations are intricately linked to prevailing environmental conditions such as temperature and humidity. By accurately monitoring, identifying, and appropriately addressing these behaviors and activities, the farming and production of crickets can be enhanced. This research implemented a decision support system that leverages machine learning (ML) algorithms to decode and classify cricket songs, along with their associated key weather variables (temperature and humidity). Videos capturing cricket behavior and weather variables were recorded. From these videos, sound signals were extracted and classified such as calling, aggression, and courtship. Numerical and image features were extracted from the sound signals and combined with the weather variables. The extracted numerical features, i.e., Mel-Frequency Cepstral Coefficients (MFCC), Linear Frequency Cepstral Coefficients, and chroma, were used to train shallow (support vector machine, k-nearest neighbors, and random forest (RF)) ML algorithms. While image features, i.e., spectrograms, were used to train different state-of-the-art deep ML models, i,e., convolutional neural network architectures (ResNet152V2, VGG16, and EfficientNetB4). In the deep ML category, ResNet152V2 had the best accuracy of 99.42%. The RF algorithm had the best accuracy of 95.63% in the shallow ML category when trained with a combination of MFCC+chroma and after feature selection. In descending order of importance, the top 6 ranked features in the RF algorithm were, namely humidity, temperature, C#, mfcc11, mfcc10, and D. From the selected features, it is notable that temperature and humidity are necessary for growth and metabolic activities in insects. Moreover, the songs produced by certain cricket species naturally align to musical tones such as C# and D as ranked by the algorithm. Using this knowledge, a decision support system was built to guide farmers about the optimal temperature and humidity ranges and interpret the songs (calling, aggression, and courtship) in relation to weather variables. With this information, farmers can put in place suitable measures such as temperature regulation, humidity control, addressing aggressors, and other relevant interventions to minimize or eliminate losses and enhance cricket production.},
}
@article {pmid38807051,
year = {2024},
author = {Xie, J and Lan, Y and Zou, C and He, J and Huang, Q and Zeng, J and Pan, M and Mei, Y and Luo, J and Zou, D},
title = {Single-nucleus analysis reveals microenvironment-specific neuron and glial cell enrichment in Alzheimer's disease.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {526},
pmid = {38807051},
issn = {1471-2164},
support = {YCSW2023244//the Innovation Project of Guangxi Graduate Education/ ; 2024GXNSFBA010054//the Joint Project on Regional High-Incidence Diseases Research of Guangxi Natural Science Foundation/ ; 2024GXNSFDA010001//the Joint Project on Regional High-Incidence Diseases Research of Guangxi Natural Science Foundation/ ; },
mesh = {*Alzheimer Disease/genetics/pathology/metabolism ; Humans ; *Neuroglia/metabolism/pathology ; *Neurons/metabolism ; *Single-Cell Analysis ; Cellular Microenvironment/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is a complicated neurodegenerative disease. Neuron-glial cell interactions are an important but not fully understood process in the progression of AD. We used bioinformatic methods to analyze single-nucleus RNA sequencing (snRNA-seq) data to investigate the cellular and molecular biological processes of AD.<br><br>METHOD: snRNA-seq data were downloaded from Gene Expression Omnibus (GEO) datasets and reprocessed to identify 240,804 single nuclei from healthy controls and patients with AD. The cellular composition of AD was further explored using Uniform Manifold Approximation and Projection (UMAP). Enrichment analysis for the functions of the DEGs was conducted and cell development trajectory analyses were used to reveal underlying cell fate decisions. iTALK was performed to identify ligand-receptor pairs among various cell types in the pathological ecological microenvironment of AD.<br><br>RESULTS: Six cell types and multiple subclusters were identified based on the snRNA-seq data. A subcluster of neuron and glial cells co-expressing lncRNA-SNHG14, myocardin-related transcription factor A (MRTFA), and MRTFB was found to be more abundant in the AD group. This subcluster was enriched in mitogen-activated protein kinase (MAPK)-, immune-, and apoptosis-related pathways. Through molecular docking, we found that lncRNA-SNHG14 may bind MRTFA and MRTFB, resulting in an interaction between neurons and glial cells.<br><br>CONCLUSIONS: The findings of this study describe a regulatory relationship between lncRNA-SNHG14, MRTFA, and MRTFB in the six main cell types of AD. This relationship may contribute to microenvironment remodeling in AD and provide a theoretical basis for a more in-depth analysis of AD.},
}
@article {pmid38805961,
year = {2024},
author = {Edwin, IE and Chukwuka, O and Ochege, FU and Ling, Q and Chen, B and Nzabarinda, V and Ajaero, C and Hamdi, R and Luo, G},
title = {Quantifying land change dynamics, resilience and feedback: A comparative analysis of the lake Chad basin in Africa and Aral Sea basin in Central Asia.},
journal = {Journal of environmental management},
volume = {361},
number = {},
pages = {121218},
doi = {10.1016/j.jenvman.2024.121218},
pmid = {38805961},
issn = {1095-8630},
mesh = {*Lakes ; *Climate Change ; Africa ; Geographic Information Systems ; Conservation of Natural Resources ; Asia ; },
abstract = {The intricate interaction of natural and anthropogenic factors drives changes in land and water in response to societal demands and climate change. However, there has been insufficient information on the feedback effects in dryland hotspots altered by land change dynamics. This research compared two transboundary inland lakes, the Lake Chad basin (LCB) in Africa and the Aral Sea basin (ASB) in Central Asia, using remote sensing and geographic information system techniques to analyze and quantify present and future land cover dynamics, resilience, and their feedback effects. The study integrated Cellular Automata, Markov Chain, and Multilayer Perceptron models to predict LULC changes up to 2030. Descriptive statistics, ordinary least squares regression, hotspot Gi-Bin, trend analysis, and advanced geostatistical methods were utilized to identify relationships, patterns, magnitudes, and directions of observed changes in the feedback effects. From 2000 to 2030, the analysis unveils intriguing trends, including an increase in cropland from 48% to 51% and a decrease in shrubland from 18% to 15% in the LCB. The grassland increased from 21% to 22%, and the settlement expanded from 0.10 to 0.60% in the ASB. Water bodies remained stable at 1.60 % in LCB, while in ASB, it declined from 3% to 2%. These changes were significantly influenced by population, elevation, and temperature in both basins, with irrigation also playing a significant role in the ASB and slope in LCB. The study further revealed discernible shifts in normalized difference vegetation index, temperature, and precipitation linked to specific land cover conversions, suggesting alterations in surface properties and vegetation health. This study underscores the complex interplay between land cover dynamics, resilience, climate variability, and feedback mechanisms in LCB and ASB.},
}
@article {pmid38805695,
year = {2024},
author = {McElroy, KE and Masonbrink, R and Chudalayandi, S and Severin, AJ and Serb, JM},
title = {A chromosome-level genome assembly of the disco clam, Ctenoides ales.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {9},
pages = {},
pmid = {38805695},
issn = {2160-1836},
support = {DEB 1754331//National Science Foundation/ ; 1726447//NSF/ ; },
mesh = {Animals ; *Bivalvia/genetics ; *Genome ; *Molecular Sequence Annotation ; Chromosomes/genetics ; Genomics/methods ; Phylogeny ; },
abstract = {The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.},
}
@article {pmid38805543,
year = {2024},
author = {Lansch-Justen, L and El Karoui, M and Alexander, HK},
title = {Estimating mutation rates under heterogeneous stress responses.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012146},
pmid = {38805543},
issn = {1553-7358},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Mutation Rate ; *Escherichia coli/genetics ; *Stress, Physiological/genetics ; *Models, Genetic ; SOS Response, Genetics/genetics ; Computer Simulation ; Computational Biology/methods ; Mutation ; },
abstract = {Exposure to environmental stressors, including certain antibiotics, induces stress responses in bacteria. Some of these responses increase mutagenesis and thus potentially accelerate resistance evolution. Many studies report increased mutation rates under stress, often using the standard experimental approach of fluctuation assays. However, single-cell studies have revealed that many stress responses are heterogeneously expressed in bacterial populations, which existing estimation methods have not yet addressed. We develop a population dynamic model that considers heterogeneous stress responses (subpopulations of cells with the response off or on) that impact both mutation rate and cell division rate, inspired by the DNA-damage response in Escherichia coli (SOS response). We derive the mutant count distribution arising in fluctuation assays under this model and then implement maximum likelihood estimation of the mutation-rate increase specifically associated with the expression of the stress response. Using simulated mutant count data, we show that our inference method allows for accurate and precise estimation of the mutation-rate increase, provided that this increase is sufficiently large and the induction of the response also reduces the division rate. Moreover, we find that in many cases, either heterogeneity in stress responses or mutant fitness costs could explain similar patterns in fluctuation assay data, suggesting that separate experiments would be required to identify the true underlying process. In cases where stress responses and mutation rates are heterogeneous, current methods still correctly infer the effective increase in population mean mutation rate, but we provide a novel method to infer distinct stress-induced mutation rates, which could be important for parameterising evolutionary models.},
}
@article {pmid38805169,
year = {2024},
author = {Peng, X and Yang, Y and Zhong, R and Yang, Y and Yan, F and Liang, N and Yuan, S},
title = {Zinc and Inflammatory Bowel Disease: From Clinical Study to Animal Experiment.},
journal = {Biological trace element research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12011-024-04193-6},
pmid = {38805169},
issn = {1559-0720},
support = {2081921001//Chengdu University/ ; CDUCX2024759//Training Program for Innovation and Entrepreneurship of Chengdu University/ ; 32370557//National Natural Science Foundation of China/ ; NCKL202201//Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control/ ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract (GI) with a high incidence rate globally, and IBD patients are often accompanied by zinc deficiency. This review aims to summarize the potential therapeutic value of zinc supplementation in IBD clinical patients and animal models. Zinc supplementation can relieve the severity of IBD especially in patients with zinc deficiency. The clinical severity of IBD were mainly evaluated through some scoring methods involving clinical performance, endoscopic observation, blood biochemistry, and pathologic biopsy. Through conducting animal experiments, it has been found that zinc plays an important role in alleviating clinical symptoms and improving pathological lesions. In both clinical observation and animal experiment of IBD, the therapeutic mechanisms of zinc interventions have been found to be related to immunomodulation, intestinal epithelial repair, and gut microbiota's balance. Furthermore, the antioxidant activity of zinc was clarified in animal experiment. Appropriate zinc supplementation is beneficial for IBD therapy, and the present evidence highlights that alleviating zinc-deficient status can effectively improve the severity of clinical symptoms in IBD patients and animal models.},
}
@article {pmid38803273,
year = {2024},
author = {Wang, Y and Yang, Y and Liu, Y and Liu, C and Xu, M and Fang, M and Mu, X},
title = {CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38803273},
issn = {1758-0463},
support = {2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; 2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; },
mesh = {Animals ; *Fishes/genetics/classification ; *RNA, Ribosomal, 18S/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Phylogeny ; Databases, Nucleic Acid ; },
abstract = {Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL: http://210.22.121.250:8888/CoSFISH/home/indexPage.},
}
@article {pmid38803140,
year = {2024},
author = {Jacobson, OT and Barrett, BJ and Perry, SE and Finerty, GE and Tiedeman, KM and Crofoot, MC},
title = {A new approach to geostatistical synthesis of historical records reveals capuchin spatial responses to climate and demographic change.},
journal = {Ecology letters},
volume = {27},
number = {5},
pages = {e14443},
doi = {10.1111/ele.14443},
pmid = {38803140},
issn = {1461-0248},
support = {//Wenner-Gren Foundation/ ; //American Society of Primatologists/ ; //Alexander von Humboldt-Stiftung/ ; //Max-Planck-Gesellschaft/ ; //Department of Anthropology, University of California, Los Angeles/ ; 20113909//National Geographic Society/ ; 45176R-18//National Geographic Society/ ; 7968-06//National Geographic Society/ ; 8671-09//National Geographic Society/ ; 9795-15//National Geographic Society/ ; 9633991//National Science Foundation/ ; BCS-0613226//National Science Foundation/ ; BCS-1638428//National Science Foundation/ ; BCS-848360//National Science Foundation/ ; DDIG 1232371//National Science Foundation/ ; SE9870429//National Science Foundation/ ; //Achievement Rewards for College Scientists Foundation/ ; //Leakey Foundation/ ; 1650042//National Science Foundation Graduate Research Fellowship Program/ ; Grant 0208/TWCF/TWCF/United States ; },
mesh = {Animals ; Costa Rica ; *Climate Change ; *Cebus/physiology ; Homing Behavior ; Geographic Information Systems ; Population Dynamics ; Demography ; },
abstract = {Recent proliferation of GPS technology has transformed animal movement research. Yet, time-series data from this recent technology rarely span beyond a decade, constraining longitudinal research. Long-term field sites hold valuable historic animal location records, including hand-drawn maps and semantic descriptions. Here, we introduce a generalised workflow for converting such records into reliable location data to estimate home ranges, using 30 years of sleep-site data from 11 white-faced capuchin (Cebus imitator) groups in Costa Rica. Our findings illustrate that historic sleep locations can reliably recover home range size and geometry. We showcase the opportunity our approach presents to resolve open questions that can only be addressed with very long-term data, examining how home ranges are affected by climate cycles and demographic change. We urge researchers to translate historical records into usable movement data before this knowledge is lost; it is essential to understanding how animals are responding to our changing world.},
}
@article {pmid38802965,
year = {2024},
author = {Hosseinzadeh-Shanjani, Z and Khodayari-Zarnaq, R and Khosravi, MF and Arab-Zozani, M and Alizadeh, G},
title = {Factors affecting major depression in Iran: a mixed-method study.},
journal = {Journal of health, population, and nutrition},
volume = {43},
number = {1},
pages = {73},
pmid = {38802965},
issn = {2072-1315},
mesh = {Humans ; Iran/epidemiology ; *Depressive Disorder, Major/epidemiology ; Risk Factors ; Health Policy ; Socioeconomic Factors ; Economic Recession ; Politics ; Female ; Male ; },
abstract = {Depression is a major cause of disability and, if left untreated, can increase the risk of suicide. Evidence on the determinants of depression is incomplete, making it challenging to interpret results across studies. This study aims to identify the social, economic, environmental, political, and technological factors influencing the great recession in Iran. The study was conducted in two parts. The first step involved a literature review to identify the factors, using PubMed, Scopus, and Web of Science for the search. The reference lists of all identified articles were reviewed to find relevant studies, and the extracted information was summarized and reported descriptively. The second steps involved compiling and consulting 14 experts from different fields, using a framework analysis method. Twenty-four articles were used as primary sources of information, and a total of 28 factors were found to exist. After removing duplicates and related factors, 19 of these were subsequently declared as factors, resulting in a total of 36 determinants being identified. Most of these factors belong to the social category. The health policies implemented have a significant impact on disease risk factors and ultimately their occurrence. Political decisions and policy-making processes play a crucial role in all areas, particularly in addressing disease risk factors. Severe depression can disrupt all aspects of the healthcare system, underscoring the importance of access to care. Policies concerning physical education, transportation, nutrition, employment, green spaces, recreational facilities, and tobacco are vital in this context. The influence of health policies on disease risk factors and disease occurrence is profound. Severe depression can have far-reaching effects on the healthcare system, emphasizing the critical need for access to care. The formulation of policies to combat depression must be thoroughly evaluated in terms of economic, political, social, technological, and environmental factors. The findings suggest that addressing social inequalities and emphasizing the role of political action, as highlighted by the social determinants of health, should be top priorities in addressing depression. Efforts to prevent depression should incorporate ecological approaches that consider the impact of the socioeconomic environment on depressive symptoms.},
}
@article {pmid38802223,
year = {2024},
author = {Lv, H and Lu, Z and Fu, G and Lv, S and Jiang, J and Xie, Y and Luo, X and Zeng, J and Xue, S},
title = {Pollution characteristics and quantitative source apportionment of heavy metals within a zinc smelting site by GIS-based PMF and APCS-MLR models.},
journal = {Journal of environmental sciences (China)},
volume = {144},
number = {},
pages = {100-112},
doi = {10.1016/j.jes.2023.09.033},
pmid = {38802223},
issn = {1001-0742},
mesh = {*Metals, Heavy/analysis ; *Zinc/analysis ; *Environmental Monitoring/methods ; *Soil Pollutants/analysis ; *Metallurgy ; Geographic Information Systems ; Models, Chemical ; },
abstract = {The abandoned smelters present a substantial pollution threat to the nearby soil and groundwater. In this study, 63 surface soil samples were collected from a zinc smelter to quantitatively describe the pollution characteristics, ecological risks, and source apportionment of heavy metal(loid)s (HMs). The results revealed that the average contents of Zn, Cd, Pb, As, and Hg were 0.4, 12.2, 3.3, 5.3, and 12.7 times higher than the risk screening values of the construction sites, respectively. Notably, the smelter was accumulated heavily with Cd and Hg, and the contribution of Cd (0.38) and Hg (0.53) to ecological risk was 91.58%. ZZ3 and ZZ7 were the most polluted workshops, accounting for 25.7% and 35.0% of the pollution load and ecological risk, respectively. The influence of soil parent materials on pollution was minor compared to various workshops within the smelter. Combined with PMF, APCS-MLR and GIS analysis, four sources of HMs were identified: P1(25.5%) and A3(18.4%) were atmospheric deposition from the electric defogging workshop and surface runoff from the smelter; P2(32.7%) and A2(20.9%) were surface runoff of As-Pb foul acid; P3(14.5%) and A4(49.8%) were atmospheric deposition from the leach slag drying workshop; P4(27.3%) and A1(10.8%) were the smelting process of zinc products. This paper described the distribution characteristics and specific sources of HMs in different process workshops, providing a new perspective for the precise remediation of the smelter by determining the priority control factors.},
}
@article {pmid38800997,
year = {2025},
author = {Madrigal, G and Minhas, BF and Catchen, J},
title = {Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.},
journal = {Molecular ecology resources},
volume = {25},
number = {1},
pages = {e13982},
pmid = {38800997},
issn = {1755-0998},
support = {1645087//Division of Antarctic Sciences/ ; },
mesh = {Animals ; Bees/genetics ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; Antifreeze Proteins/genetics/chemistry ; High-Throughput Nucleotide Sequencing/methods ; Genome/genetics ; Genomics/methods ; Software ; Fishes/genetics ; },
abstract = {The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees.},
}
@article {pmid38800521,
year = {2024},
author = {Obbard, DJ and , and , and , and , and , and , },
title = {The genome sequence of the drosophilid fruit fly, Drosophila phalerata (Meigen, 1830).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {63},
pmid = {38800521},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Drosophila phalerata (drosophilid fruit fly, Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 223.9 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.14 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,973 protein coding genes.},
}
@article {pmid38800516,
year = {2024},
author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {145},
pmid = {38800516},
issn = {2398-502X},
abstract = {We present a chromosomal-level genome assembly from an individual Tridacna gigas (the giant clam; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,175.9 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 25.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,177 protein coding genes.},
}
@article {pmid38798998,
year = {2023},
author = {Obbard, DJ and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Drosophila funebris (Fabricius, 1789).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {437},
pmid = {38798998},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Drosophila funebris (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 181.1 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.15 kilobases in length.},
}
@article {pmid38798994,
year = {2023},
author = {Hawkes, WLS and Wotton, KR and , and , and , and , and , and , },
title = {The genome sequence of the Common Spotted Hoverfly, Eupeodes luniger (Meigen, 1822).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {472},
pmid = {38798994},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Eupeodes luniger (the Common Spotted Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 616.9 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length.},
}
@article {pmid38798992,
year = {2023},
author = {Hawkes, WLS and Wotton, KR and , and , and , and , and , and , },
title = {The genome sequence of the slender grass hoverfly, Melanostoma scalare (Fabricius, 1794).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {489},
pmid = {38798992},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Melanostoma scalare (the slender grass hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 738.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.08 kilobases in length.},
}
@article {pmid38796535,
year = {2024},
author = {Wenk, EH and Sauquet, H and Gallagher, RV and Brownlee, R and Boettiger, C and Coleman, D and Yang, S and Auld, T and Barrett, R and Brodribb, T and Choat, B and Dun, L and Ellsworth, D and Gosper, C and Guja, L and Jordan, GJ and Le Breton, T and Leigh, A and Lu-Irving, P and Medlyn, B and Nolan, R and Ooi, M and Sommerville, KD and Vesk, P and White, M and Wright, IJ and Falster, DS},
title = {The AusTraits plant dictionary.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {537},
pmid = {38796535},
issn = {2052-4463},
mesh = {*Plants ; Databases, Factual ; Dictionaries as Topic ; },
abstract = {Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.},
}
@article {pmid38796014,
year = {2024},
author = {Graham, CC},
title = {The role of Geographic Information Systems in mitigating plastics pollution in the Global South-A spatial analysis of recycling facilities in Costa Rica.},
journal = {The Science of the total environment},
volume = {937},
number = {},
pages = {173396},
doi = {10.1016/j.scitotenv.2024.173396},
pmid = {38796014},
issn = {1879-1026},
mesh = {Costa Rica ; *Plastics/analysis ; *Geographic Information Systems ; *Recycling ; *Environmental Pollution/statistics &amp; numerical data ; Spatial Analysis ; Conservation of Natural Resources/methods ; Environmental Monitoring ; },
abstract = {Costa Rica is at the forefront of environmental conservation in Central America, with its focus on sustainability and green practices. Building on this foundation, the country joins a cohort of middle-income developing countries that have set forth ambitious goals to eliminate plastic pollution and become plastics-free. Recycling remains one of the most effective ways of removing plastic waste from the environment. Although GIS has been utilized in environmental research, its use is still expanding in developing countries of the Global South. These countries are experiencing unprecedented adverse climate and ecological impacts while also pursuing fundamental socioeconomic growth. The application of more cost-effective and strategic technological solutions, as well as data-driven decision-making, could fast-track the achievement of their urgent environmental goals. Using Geographic Information Systems (GIS) analysis, this study applies hot spot, location-allocation, and time-distance measures to examine Costa Rica's capacity to recycle plastic waste. Focusing specifically on availability and the public's access to recycling facilities, this article offers insights into the resource constraints and evolution of plastics governance in developing countries with environmentally-focused priorities. The findings of this study suggest that while Costa Rica is implementing progressive plastics regulatory policies, the ability to achieve plastics-free status is hampered by shortfalls in the number and distribution of recycling facilities and the public's access to recycling services. Expanding recycling infrastructure, including transportation, and adopting a less canton-centric waste administration system could contribute to resolving these challenges. This study contributes to discourses on global plastics governance and environmental change management in the Global South.},
}
@article {pmid38795997,
year = {2024},
author = {Lu, J and Peng, Q and Song, Y and Lyu, L and Chen, D and Huang, P and Peng, F and Liu, Y},
title = {Characteristics and effects of global sloping land urbanization from 2000 to 2020.},
journal = {The Science of the total environment},
volume = {937},
number = {},
pages = {173348},
doi = {10.1016/j.scitotenv.2024.173348},
pmid = {38795997},
issn = {1879-1026},
abstract = {Cities usually expand on flat land. However, in recent decades, the increasing scarcity of available flat land has compelled many cities to expand to sloping land (sloping land urbanization, SLU), and the understanding for global SLU is still unclear. This study, based on the currently available high-precision global Digital Elevation Model (FABDEM) and global land cover dataset (GlobeLand30), investigated the characteristics and impacts of SLU in 26,402 urban residential areas worldwide from 2000 to 2020. Results show that the total area of SLU globally is 16,383 km[2], accounting for 9.54 % of the overall urban expansion. This phenomenon is widespread globally and relatively concentrated in a few countries, with 42.78 %, 24.35 %, and 21.83 % of the area coming from cultivated land, forest, and grassland respectively. Global SLU has accommodated 34.78 million urban population, and indirectly protected 8922 km[2] of flat cultivated land, while causing a net loss of 4373 km[2] of green ecological land. Deliberately balancing the dual effects of SLU is crucial for advancing sustainable global urbanization.},
}
@article {pmid38791265,
year = {2024},
author = {Bartas, M and Brázda, V and Pečinka, P},
title = {Special Issue "Bioinformatics of Unusual DNA and RNA Structures".},
journal = {International journal of molecular sciences},
volume = {25},
number = {10},
pages = {},
pmid = {38791265},
issn = {1422-0067},
support = {CZ.10.03.01/00/22_003/0000003//Operational Programme Just Transition, European Union/ ; },
mesh = {*RNA/chemistry/metabolism ; *DNA/chemistry/metabolism ; *Computational Biology/methods ; *Nucleic Acid Conformation ; Humans ; },
abstract = {Nucleic acids are not only static carriers of genetic information but also play vital roles in controlling cellular lifecycles through their fascinating structural diversity [...].},
}
@article {pmid38789640,
year = {2024},
author = {Leigh, DM and Vandergast, AG and Hunter, ME and Crandall, ED and Funk, WC and Garroway, CJ and Hoban, S and Oyler-McCance, SJ and Rellstab, C and Segelbacher, G and Schmidt, C and Vázquez-Domínguez, E and Paz-Vinas, I},
title = {Best practices for genetic and genomic data archiving.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {7},
pages = {1224-1232},
pmid = {38789640},
issn = {2397-334X},
support = {31BD30_193900//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Genomics ; Databases, Genetic ; Data Management ; Metadata ; },
abstract = {Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.},
}
@article {pmid38787862,
year = {2024},
author = {Wang, L and Cui, H},
title = {Identification and classification of urban employment centers based on big data: A case study of Beijing.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0299726},
pmid = {38787862},
issn = {1932-6203},
mesh = {Beijing ; Humans ; *Employment/statistics &amp; numerical data ; *Transportation/statistics &amp; numerical data ; Big Data ; Workplace ; Urban Population ; },
abstract = {The layout, scale and spatial form of urban employment centers are important guidelines for the rational layout of public service facilities such as urban transportation, medical care, and education. In this paper, we use Internet cell phone positioning data to identify the workplace and residence of users in the Beijing city area and obtain commuting data of the employed to measure the employment center system in Beijing. Firstly, the employment density distribution is generated using the data of the working places of the employed persons, and the employment centers are identified based on the employment density of Beijing. Then, we use the business registration data of employment centers to measure the industrial diversity within the employment centers by using the ecological Shannon Wiener Diversity Index, and combine the commuting links between employment centers and places of residence to measure the energy level of each employment center, analyze the hinterland and sphere of influence of each center, and finally using the industrial diversity index of employment centers and the average commuting time of employed persons, combined with the K-Means clustering algorithm, to classify the employment centers in Beijing. The employment center identification and classification method based on big data constructed in this study can help solve the limitations of the previous employment center system research in terms of center identification and commuting linkage measurement due to large spatial units and lack of commuting data to a certain extent. The study can provide reference for the regular understanding and technical analysis of employment centers and provide help for the employment multi-center system in Beijing in terms of quantifying the employment spatial structure, guiding the construction of multi-center system, and adjusting the land use rules.},
}
@article {pmid38785034,
year = {2024},
author = {McEachran, MC and Harvey, JA and Mummah, RO and Bletz, MC and Teitelbaum, CS and Rosenblatt, E and Rudolph, FJ and Arce, F and Yin, S and Prosser, DJ and Mosher, BA and Mullinax, JM and DiRenzo, GV and Couret, J and Runge, MC and Grant, EHC and Cook, JD},
title = {Reframing wildlife disease management problems with decision analysis.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {38},
number = {4},
pages = {e14284},
doi = {10.1111/cobi.14284},
pmid = {38785034},
issn = {1523-1739},
support = {//National Science Foundation/ ; 2200310//PIPP Phase 1: International Center for Avian Influenza Pandemic Prediction and Prevention/ ; P.L. 116-136//Coronavirus Aid, Relief, and Economic Security Act/ ; },
mesh = {Animals ; *Animals, Wild ; *Decision Support Techniques ; *Conservation of Natural Resources/methods ; *Decision Making ; COVID-19/epidemiology ; SARS-CoV-2 ; Uncertainty ; },
abstract = {Contemporary wildlife disease management is complex because managers need to respond to a wide range of stakeholders, multiple uncertainties, and difficult trade-offs that characterize the interconnected challenges of today. Despite general acknowledgment of these complexities, managing wildlife disease tends to be framed as a scientific problem, in which the major challenge is lack of knowledge. The complex and multifactorial process of decision-making is collapsed into a scientific endeavor to reduce uncertainty. As a result, contemporary decision-making may be oversimplified, rely on simple heuristics, and fail to account for the broader legal, social, and economic context in which the decisions are made. Concurrently, scientific research on wildlife disease may be distant from this decision context, resulting in information that may not be directly relevant to the pertinent management questions. We propose reframing wildlife disease management challenges as decision problems and addressing them with decision analytical tools to divide the complex problems into more cognitively manageable elements. In particular, structured decision-making has the potential to improve the quality, rigor, and transparency of decisions about wildlife disease in a variety of systems. Examples of management of severe acute respiratory syndrome coronavirus 2, white-nose syndrome, avian influenza, and chytridiomycosis illustrate the most common impediments to decision-making, including competing objectives, risks, prediction uncertainty, and limited resources.},
}
@article {pmid38784435,
year = {2024},
author = {Boyes, D and Crowley, LM and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Summer Chafer, Amphimallon solstitiale (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {138},
pmid = {38784435},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Amphimallon solstitiale (the Summer Chafer; Arthropoda; Insecta; Coleoptera; Scarabaeidae). The genome sequence is 1,584.1 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.29 kilobases in length.},
}
@article {pmid38781445,
year = {2024},
author = {Vuruputoor, VS and Starovoitov, A and Cai, Y and Liu, Y and Rahmatpour, N and Hedderson, TA and Wilding, N and Wegrzyn, JL and Goffinet, B},
title = {Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {7},
pages = {},
pmid = {38781445},
issn = {2160-1836},
support = {DEB-0919284//US National Science Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bryopsida/genetics ; *Genome, Plant ; *Phylogeny ; Genomics/methods ; Molecular Sequence Annotation ; },
abstract = {The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.},
}
@article {pmid38781323,
year = {2024},
author = {Edwards, SV and Cloutier, A and Cockburn, G and Driver, R and Grayson, P and Katoh, K and Baldwin, MW and Sackton, TB and Baker, AJ},
title = {A nuclear genome assembly of an extinct flightless bird, the little bush moa.},
journal = {Science advances},
volume = {10},
number = {21},
pages = {eadj6823},
doi = {10.1126/sciadv.adj6823},
pmid = {38781323},
issn = {2375-2548},
mesh = {Animals ; *Birds/genetics ; *Genome ; *Extinction, Biological ; Cell Nucleus/genetics ; Phylogeny ; Fossils ; Genome, Mitochondrial ; Flight, Animal ; New Zealand ; Male ; DNA Transposable Elements/genetics ; Genomics/methods ; },
abstract = {We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.},
}
@article {pmid38779566,
year = {2024},
author = {Scanu, M and Toto, F and Petito, V and Masi, L and Fidaleo, M and Puca, P and Baldelli, V and Reddel, S and Vernocchi, P and Pani, G and Putignani, L and Scaldaferri, F and Del Chierico, F},
title = {An integrative multi-omic analysis defines gut microbiota, mycobiota, and metabolic fingerprints in ulcerative colitis patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1366192},
pmid = {38779566},
issn = {2235-2988},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; *Bacteria/classification/isolation &amp; purification/metabolism/genetics ; Middle Aged ; *Metabolomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Gas Chromatography-Mass Spectrometry ; *Feces/microbiology ; *Fungi/classification/isolation &amp; purification/metabolism ; Dysbiosis/microbiology ; Metabolome ; Aged ; Young Adult ; Solid Phase Microextraction ; Mycobiome ; Multiomics ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic gut microbial profile has been associated with UC. Our study aimed to characterize the UC gut bacterial, fungal, and metabolic fingerprints by omic approaches.<br><br>METHODS: The 16S rRNA- and ITS2-based metataxonomics and gas chromatography-mass spectrometry/solid phase microextraction (GC-MS/SPME) metabolomic analysis were performed on stool samples of 53 UC patients and 37 healthy subjects (CTRL). Univariate and multivariate approaches were applied to separated and integrated omic data, to define microbiota, mycobiota, and metabolic signatures in UC. The interaction between gut bacteria and fungi was investigated by network analysis.<br><br>RESULTS: In the UC cohort, we reported the increase of Streptococcus, Bifidobacterium, Enterobacteriaceae, TM7-3, Granulicatella, Peptostreptococcus, Lactobacillus, Veillonella, Enterococcus, Peptoniphilus, Gemellaceae, and phenylethyl alcohol; and we also reported the decrease of Akkermansia; Ruminococcaceae; Ruminococcus; Gemmiger; Methanobrevibacter; Oscillospira; Coprococus; Christensenellaceae; Clavispora; Vishniacozyma; Quambalaria; hexadecane; cyclopentadecane; 5-hepten-2-ol, 6 methyl; 3-carene; caryophyllene; p-Cresol; 2-butenal; indole, 3-methyl-; 6-methyl-3,5-heptadiene-2-one; 5-octadecene; and 5-hepten-2-one, 6 methyl. The integration of the multi-omic data confirmed the presence of a distinctive bacterial, fungal, and metabolic fingerprint in UC gut microbiota. Moreover, the network analysis highlighted bacterial and fungal synergistic and/or divergent interkingdom interactions.<br><br>CONCLUSION: In this study, we identified intestinal bacterial, fungal, and metabolic UC-associated biomarkers. Furthermore, evidence on the relationships between bacterial and fungal ecosystems provides a comprehensive perspective on intestinal dysbiosis and ecological interactions between microorganisms in the framework of UC.},
}
@article {pmid38779149,
year = {2024},
author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , and , },
title = {The genome sequence of the Water Veneer, Acentria ephemerella (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {134},
pmid = {38779149},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Acentria ephemerella (the Water Veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 340.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,748 protein coding genes.},
}
@article {pmid38779060,
year = {2023},
author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , },
title = {The genome sequence of the Scarce Umber, Agriopis aurantiaria (Hübner, 1799).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {463},
pmid = {38779060},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agriopis aurantiaria (the Scarce Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 485.4 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,963 protein coding genes.},
}
@article {pmid38779056,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Pinion-streaked Snout, Schrankia costaestrigalis (Stephens, 1834).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {203},
pmid = {38779056},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Schrankia costaestrigalis (the Pinion-streaked Snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 572.0 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,453 protein coding genes.},
}
@article {pmid38779055,
year = {2023},
author = {Boyes, D and , and , and , and , and , and , },
title = {The genome sequence of the Diamondback Moth, Plutella xylostella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {404},
pmid = {38779055},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Plutella xylostella (the Diamondback Moth; Arthropoda; Insecta; Lepidoptera; Plutellidae). The genome sequence is 323.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 35.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,190 protein coding genes.},
}
@article {pmid38779054,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Coxcomb Prominent, Ptilodon capucinus (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {242},
pmid = {38779054},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Ptilodon capucinus (the Coxcomb Prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 348.7 megabases in span. The assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,968 protein coding genes.},
}
@article {pmid38779050,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Grey Poplar Bell, Epinotia nisella (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {281},
pmid = {38779050},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Epinotia nisella (the Grey Poplar Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 585.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,952 protein coding genes.},
}
@article {pmid38779048,
year = {2023},
author = {Boyes, D and Mulley, JF and , and , and , and , and , and , },
title = {The genome sequence of the Six-striped Rustic, Xestia sexstrigata (Haworth, 1809).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {399},
pmid = {38779048},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Xestia sexstrigata (the Six-striped Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 638.3 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,104 protein coding genes.},
}
@article {pmid38779046,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Red-green Carpet, Chloroclysta siterata (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {206},
pmid = {38779046},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Chloroclysta siterata (the Red-green Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437.9 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,814 protein coding genes.},
}
@article {pmid38778011,
year = {2024},
author = {Mercuri, AM and Clò, E and Zappa, J and Bosi, G and Furia, E and Ricucci, C and Di Lena, M and Camerini, F and Florenzano, A},
title = {BRAIN - Holocene archaeo-data for assessing plant-cultural diversity in Italy and other Mediterranean regions.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {520},
pmid = {38778011},
issn = {2052-4463},
mesh = {*Archaeology ; Botany/history ; Italy ; Mediterranean Region ; *Plants ; *Pollen ; Databases as Topic ; },
abstract = {In the field of botany applied to archaeological and palaeoecological studies, the multi- and inter-disciplinary nature of this research produces a lack of data sharing and scattered articles in the specialty literature or in national and international journals. The vast production of archaeobotany and palynology data makes it necessary to develop a tool for the availability, accessibility, and dissemination of existing research. Many databases exist on palaeoecology, archaeobotany or pollen data. There are no collections focused on archaeological sites and human-induced environments and centred on Southern Europe and the Mediterranean. BRAIN - Botanical Records of Archaeobotany Italian Network is the first database listing sites from which all types of plant records are available in Italy and nearby Mediterranean regions. BRAIN represents the largest integrated collection of archaeo/palaeo-botanical data and a range of descriptive information that makes data recovery FAIR ready. This unique network hosts data on the availability of anthropogenic pollen, palynomorphs and plant macroremains in the same database, and experts of different research fields may contribute to it.},
}
@article {pmid38777192,
year = {2024},
author = {Aggarwal, R and Peters, G},
title = {Freshwater ecotoxicity characterization factors for PMT/vPvM substances.},
journal = {Chemosphere},
volume = {360},
number = {},
pages = {142391},
doi = {10.1016/j.chemosphere.2024.142391},
pmid = {38777192},
issn = {1879-1298},
mesh = {*Water Pollutants, Chemical/toxicity ; *Ecotoxicology ; *Fresh Water/chemistry ; Environmental Monitoring/methods ; Risk Assessment ; Germany ; Databases, Factual ; },
abstract = {This study addresses the gap in freshwater ecotoxicological characterization factors (CFs) for Persistent, Mobile, and Toxic (PMT) and Very Persistent and Very Mobile (vPvM) substances. These CFs are vital for integrating the ecotoxicity impacts of these chemicals into life cycle assessments. Our goals are twofold: first, to calculate experimental freshwater CFs for PMT/vPvM substances listed by the German Environment Agency (UBA); second, to compare these CFs with those from the USEtox database. The expanded UBA list includes 343 PMT/vPvM substances, each representing a unique chemical structure, and linked to 474 REACH-registered substances. This study successfully computed CFs for 244 substances, with 107 overlapping the USEtox database and 137 being new. However, ecotoxicity data limitations prevented CF determination for 97 substances. This research enhances our understanding of freshwater CFs for PMT/vPvM substances, covering 72% of UBA's 343 PMT/vPvM substances. Data scarcity remains a significant challenge, which invariably impedes CF calculations. Notably, the disparities observed between CF values in the USEtox database and those derived in this research largely stem from variations in ecotoxicity data. Consequently, this research underscores the dynamic nature of CFs for substances, emphasizing the need for regular updates to ensure their accuracy and relevance.},
}
@article {pmid38776304,
year = {2024},
author = {Karlgren, K and Andersson Franko, M and Kilström, D},
title = {'Experiencing one thing and saying another'-Ecological Momentary Assessment (EMA) of nursing students' competence and challenge during clinical placements compared with retrospective interviews.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0302866},
pmid = {38776304},
issn = {1932-6203},
mesh = {Humans ; *Students, Nursing/psychology ; Female ; Retrospective Studies ; *Clinical Competence ; Male ; *Ecological Momentary Assessment ; Adult ; Young Adult ; Interviews as Topic ; Smartphone ; },
abstract = {UNLABELLED: Clinical placements are essential to nursing education and understanding students' challenges in the clinical context is important for educators. Nevertheless, few studies have investigated students' experiences in the clinical context itself but rely on methods which ask participants to generalize their clinical experiences retrospectively.<br><br>OBJECTIVES: This study aimed to explore nursing students' experiences of clinical activities during and after clinical placements with a focus on feelings of competence and challenge. A particular interest was on comparing momentary assessments in the clinical context with retrospective interview data.<br><br>METHODS: Smartphones were used for ecological momentary assessment of students' experiences of clinical activities during five-week placements at 21 nursing homes. Both quantitative and qualitative data were collected. Interviews were conducted after the placements.<br><br>RESULTS: 575 responses were obtained showing final-year nursing students rated their competence significantly higher and challenge significantly lower than first-year students. An analysis of the quantitative data using the four-channel flow model showed that first-year students' activities were to a significantly higher extent associated with flow and anxiety, compared to those of final-year students. Conversely, the final-year students' activities were to a significantly higher extent associated with boredom than those of first-year students. The analysis of the students' reflections resulted in five themes: Specific activities are challenging, Lack of challenge, Learning and developing, Reflects critically on competence, and Arrangement of the clinical placement.<br><br>DISCUSSION: Final-year nursing students were significantly less challenged during the placements compared to first-year students. There was overlap in how students described their clinical experiences during and after placements, but there were also striking differences. The first-year students were overwhelmed by the challenges during the placements but viewed these experiences as valuable learning experiences afterwards. The final-year students also described several challenging clinical activities during the placements but none of these challenges were brought up afterwards in the interviews and instead a lack of challenge was emphasized. Momentary assessment thus enabled capturing data about clinical activities which may be overlooked by retrospective methods.},
}
@article {pmid38776282,
year = {2024},
author = {MacPhail, VJ and Hatfield, R and Colla, SR},
title = {Bumble Bee Watch community science program increases scientific understanding of an important pollinator group across Canada and the USA.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303335},
pmid = {38776282},
issn = {1932-6203},
mesh = {Animals ; Bees/physiology ; United States ; *Pollination ; Canada ; Databases, Factual ; },
abstract = {In a time of increasing threats to bumble bees (Hymenoptera: Apidae: Bombus), it is important to understand their ecology and distribution. As experts are limited in resources to conduct field surveys, there is potential for community scientists to help. The Bumble Bee Watch (BBW) community science program involves volunteers taking photos of bumble bees in Canada and the USA and submitting them, along with geographic and optional plant information, to a website or through an app. Taxon experts then verify the bee species identification. The Bumble Bees of North America database (BBNA) stores data (no photographs) collected and identified by more traditional scientific methods over the same range. Here we compared BBW data to BBNA data over all years and just 2010-2020 to understand the scientific contribution of community scientists to the state of the knowledge about native bumble bees. We found that BBW had similar geographic and species coverage as BBNA. It had records from all 63 provinces, states, and territories where bumble bees occur (including four more than BBNA in 2010-2020), and represented 41 of the 48 species in BBNA (with ten more species than BBNA in 2010-2020). While BBW contributed only 8.50% of records overall, it contributed 25.06% of all records over 2010-2020. BBW confirmed the persistence of species and identified new locations of species, both inside and outside of the previously known extent of occurrences. BBW also contributed a wealth of ecological information, such as unique plant genera and species data for almost all the bee species. Thus, while BBW had fewer bee records than the BBNA database overall, it helped to fill in data gaps and provided novel information, complementing the traditional methods. This community science program is valuable in helping to inform conservation management for bumble bee species.},
}
@article {pmid38775247,
year = {2024},
author = {Oliveira, S and Marchi, N and Excoffier, L},
title = {Assessing the limits of local ancestry inference from small reference panels.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13981},
doi = {10.1111/1755-0998.13981},
pmid = {38775247},
issn = {1755-0998},
support = {310030_188883//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Genetics, Population/methods ; Humans ; Computational Biology/methods ; },
abstract = {Admixture is a common biological phenomenon among populations of the same or different species. Identifying admixed tracts within individual genomes can provide valuable information to date admixture events, reconstruct ancestry-specific demographic histories, or detect adaptive introgression, genetic incompatibilities, as well as regions of the genomes affected by (associative-) overdominance. Although many local ancestry inference (LAI) methods have been developed in the last decade, their performance was accessed using large reference panels, which are rarely available for non-model organisms or ancient samples. Moreover, the demographic conditions for which LAI becomes unreliable have not been explicitly outlined. Here, we identify the demographic conditions for which local ancestries can be best estimated using very small reference panels. Furthermore, we compare the performance of two LAI methods (RFMix and MOSAIC) with the performance of a newly developed approach (simpLAI) that can be used even when reference populations consist of single individuals. Based on simulations of various demographic models, we also determine the limits of these LAI tools and propose post-painting filtering steps to reduce false-positive rates and improve the precision and accuracy of the inferred admixed tracts. Besides providing a guide for using LAI, our work shows that reasonable inferences can be obtained from a single diploid genome per reference under demographic conditions that are not uncommon among past human groups and non-model organisms.},
}
@article {pmid38775206,
year = {2024},
author = {Veglia, AJ and Rivera-Vicéns, RE and Grupstra, CGB and Howe-Kerr, LI and Correa, AMS},
title = {vAMPirus: A versatile amplicon processing and analysis program for studying viruses.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13978},
doi = {10.1111/1755-0998.13978},
pmid = {38775206},
issn = {1755-0998},
support = {OCE 22-24354//Directorate for Biological Sciences/ ; OCE-2145472//Directorate for Biological Sciences/ ; //Wagoner Foreign Study Award/ ; //Kirk W. Dotson Endowed Graduate Fellowship in Ecology and Evolutionary Biology/ ; //Lewis and Clark Grants for Exploration/ ; 100009646//Gulf Research Program of the National Academies of Sciences/ ; },
mesh = {*Software ; Computational Biology/methods ; DNA Viruses/genetics/classification ; Viruses/genetics/classification/isolation &amp; purification ; RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; },
abstract = {Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user-friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide- and amino acid-based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal-to-noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double-stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef-associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage-specific analyses. The vAMPirus framework is designed to be adaptable; community-driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.},
}
@article {pmid38774958,
year = {2024},
author = {Huson, D and Xavier, JC and Steel, M},
title = {Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry.},
journal = {Journal of the Royal Society, Interface},
volume = {21},
number = {214},
pages = {20230732},
pmid = {38774958},
issn = {1742-5662},
mesh = {*Algorithms ; Catalysis ; Models, Biological ; Biochemistry ; Origin of Life ; },
abstract = {The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.},
}
@article {pmid38772433,
year = {2024},
author = {Chagas, &#xc9;CDS and Ferreira, FADS and Mwangi, VI and Terrazas, WCM and Becker, JN and Simões, RC and Pacífico, EMSS and Silva, ASD and Marques, CDS and Chagas, ECDS and Machado, MB and Figueira, EAG and Castro, DB and Ramos, TCA and Oliveira, JH},
title = {Spatio-temporal analysis of American Tegumentary Leishmaniasis incidences in the Brazilian state of Amazonas: 2011 to 2022.},
journal = {Acta tropica},
volume = {256},
number = {},
pages = {107266},
doi = {10.1016/j.actatropica.2024.107266},
pmid = {38772433},
issn = {1873-6254},
mesh = {Brazil/epidemiology ; Humans ; Incidence ; *Leishmaniasis, Cutaneous/epidemiology ; *Spatio-Temporal Analysis ; *Seasons ; Climate ; Female ; Male ; Adult ; Adolescent ; Young Adult ; Child ; },
abstract = {This study aimed to conduct a spatio-temporal analysis of tegumentary leishmaniasis occurrences in the Amazonas state, Brazil. An ecological study encompassing time series and spatial analysis was performed, exploring the geographic distribution and temporal trends of American Tegumentary Leishmaniasis (ATL) in Amazonas between 2011 and 2022. Secondary data extracted from the Department of Informatics of the Unified Health System (DATASUS) were utilized for this analysis. The study evaluated the relationship between disease cases and environmental/climatic variables (deforestation, temperature, precipitation, and relative humidity). Over the study period, 19,730 cases of tegumentary leishmaniasis were recorded, averaging an incidence of 41.4/100,000 inhabitants across the 62 municipalities of Amazonas state. Disease intensity varied with seasons. Generally, Amazonas state displayed a declining trend in ATL cases. However, certain municipalities, notably Rio Preto da Eva and Presidente Figueiredo, exhibited high incidence rates, while Canutama, Envira, Eirunepé, and Pauini municipalities demand closer attention due to their demonstrated increasing temporal trend of ATL cases. The analysis indicated a correlation between the number of ATL cases reported and relative humidity as well as precipitation. These findings underscore the significance of tegumentary leishmaniasis as a public health issue in the region and emphasize the necessity for public initiatives aimed at preventing this endemic illness.},
}
@article {pmid38771704,
year = {2024},
author = {Warren, WC and Rice, ES and X, M and Roback, E and Keene, A and Martin, F and Ogeh, D and Haggerty, L and Carroll, RA and McGaugh, S and Rohner, N},
title = {Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {8},
pages = {},
pmid = {38771704},
issn = {2160-1836},
support = {//University of Missouri/ ; 1923372//National Science Foundation/ ; WT222155/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R24 OD011198/OD/NIH HHS/United States ; 1R01GM127872-01/GF/NIH HHS/United States ; },
mesh = {Animals ; *Characidae/genetics ; *Chromosomes/genetics ; *Caves ; Phylogeny ; Genome ; Genomics/methods ; Genetic Variation ; Quantitative Trait Loci ; Synteny ; Phenotype ; },
abstract = {The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.},
}
@article {pmid38770718,
year = {2024},
author = {Schwarzerova, J and Hurta, M and Barton, V and Lexa, M and Walther, D and Provaznik, V and Weckwerth, W},
title = {A perspective on genetic and polygenic risk scores-advances and limitations and overview of associated tools.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {3},
pages = {},
pmid = {38770718},
issn = {1477-4054},
support = {FEKT/FIT-J-23-8274//Brno University of Technology intra-university junior project/ ; },
mesh = {Humans ; *Multifactorial Inheritance ; *Genetic Predisposition to Disease ; *Software ; Computational Biology/methods ; Genome-Wide Association Study/methods ; Risk Factors ; Risk Assessment/methods ; Genetic Risk Score ; },
abstract = {Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advantages and shortcomings in comparison with other predictive methods, and discuss their conceptual limitations in light of the complexity of biological systems. Furthermore, we provide a survey of published tools for computing PRS and associated resources. The various tools and software packages are categorized based on their technical utility for users or prospective developers. Understanding the array of available tools and their limitations is crucial for accurately assessing and predicting disease risks, facilitating early interventions, and guiding personalized healthcare decisions. Additionally, we also identify potential new avenues for future bioinformatic analyzes and advancements related to PRS.},
}
@article {pmid38767676,
year = {2024},
author = {Geng, A and Zhang, C and Wang, J and Zhang, X and Qiu, W and Wang, L and Xi, J and Yang, B},
title = {Current advances of chlorinated organics degradation by bioelectrochemical systems: a review.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {7},
pages = {208},
pmid = {38767676},
issn = {1573-0972},
support = {2022YFC3702000//National Key Research and Development Program of China/ ; BE2020773//Social Development Project/ ; 23KJA610008//the Natural Science Foundation of Jiangsu Higher Education Institutions of China/ ; },
mesh = {*Biodegradation, Environmental ; *Electrochemical Techniques ; Wastewater/chemistry ; Hydrocarbons, Chlorinated/metabolism ; Water Pollutants, Chemical/metabolism ; Groundwater/chemistry ; Organic Chemicals/metabolism ; },
abstract = {Chlorinated organic compounds (COCs) are typical refractory organic compounds, having high biological toxicity. These compounds are a type of pervasive pollutants that can be present in polluted soil, air, and various types of waterways, such as groundwater, rivers, and lakes, posing a significant threat to the ecological environment and human health. Bioelectrochemical systems (BESs) are an effective strategy for the degradation of bio-refractory compounds. BESs improve the waste treatment efficiency through the application of weak electrical stimulation. This review discusses the processes of BESs configurations and degradation performances in different environmental media including wastewater, soil, waste gas and groundwater. In addition, the degradation mechanisms and performance-enhancing additives are summarized. The future challenges and perspectives on the development of BES for COCs removal are briefly discussed.},
}
@article {pmid38767452,
year = {2024},
author = {Rashidi, A and Ebadi, M and Rehman, TU and Elhusseini, H and Kazadi, D and Halaweish, H and Khan, MH and Hoeschen, A and Cao, Q and Luo, X and Kabage, AJ and Lopez, S and Ramamoorthy, S and Holtan, SG and Weisdorf, DJ and Khoruts, A and Staley, C},
title = {Multi-omics Analysis of a Fecal Microbiota Transplantation Trial Identifies Novel Aspects of Acute GVHD Pathogenesis.},
journal = {Cancer research communications},
volume = {4},
number = {6},
pages = {1454-1466},
pmid = {38767452},
issn = {2767-9764},
support = {KL2 TR002492/TR/NCATS NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; KL2TR002492//Foundation for the National Institutes of Health (FNIH)/ ; UL1TR002494//Foundation for the National Institutes of Health (FNIH)/ ; P30CA07759//HHS | NIH | National Cancer Institute (NCI)/ ; Chainbreaker grant//UMN | Clinical and Translational Science Institute, University of Minnesota (CTSI)/ ; n/a//Achieving Cures Together/ ; },
mesh = {Humans ; *Graft vs Host Disease/microbiology/immunology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Hematopoietic Stem Cell Transplantation/methods/adverse effects ; Adult ; Leukemia, Myeloid, Acute/therapy/microbiology/immunology ; Transplantation, Homologous/methods/adverse effects ; Faecalibacterium ; Aged ; Acute Disease ; Feces/microbiology ; Metabolome ; Multiomics ; },
abstract = {UNLABELLED: Acute GVHD (aGVHD) is a major complication of allogeneic hematopoietic cell transplantation (alloHCT) associated with gut microbiota disruptions. However, whether therapeutic microbiota modulation prevents aGVHD is unknown. We conducted a randomized, placebo-controlled trial of third-party fecal microbiota transplantation (FMT) administered at the peak of microbiota injury in 100 patients with acute myeloid leukemia receiving induction chemotherapy and alloHCT recipients. Despite improvements in microbiome diversity, expansion of commensals, and shrinkage of potential pathogens, aGVHD occurred more frequently after FMT than placebo. Although this unexpected finding could be explained by clinical differences between the two arms, we asked whether a microbiota explanation might be also present. To this end, we performed multi-omics analysis of preintervention and postintervention gut microbiome and serum metabolome. We found that postintervention expansion of Faecalibacterium, a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, predicted a higher risk for aGVHD. Faecalibacterium expansion occurred predominantly after FMT and was due to engraftment of unique donor taxa, suggesting that donor Faecalibacterium-derived antigens might have stimulated allogeneic immune cells. Faecalibacterium and ursodeoxycholic acid (an anti-inflammatory secondary bile acid) were negatively correlated, offering an alternative mechanistic explanation. In conclusion, we demonstrate context dependence of microbiota effects where a normally beneficial bacteria may become detrimental in disease. While FMT is a broad, community-level intervention, it may need precision engineering in ecologically complex settings where multiple perturbations (e.g., antibiotics, intestinal damage, alloimmunity) are concurrently in effect.<br><br>SIGNIFICANCE: Post-FMT expansion of Faecalibacterium, associated with donor microbiota engraftment, predicted a higher risk for aGVHD in alloHCT recipients. Although Faecalibacterium is a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, our findings suggest that it may become pathogenic in the setting of FMT after alloHCT. Our results support a future trial with precision engineering of the FMT product used as GVHD prophylaxis after alloHCT.},
}
@article {pmid38764972,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Common Emerald, Hemithea aestivaria (Hübner, 1789).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {243},
pmid = {38764972},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hemithea aestivaria (the Common Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 501.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,477 protein coding genes.},
}
@article {pmid38764970,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Pebble Hook-tip, Drepana falcataria (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {207},
pmid = {38764970},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Drepana falcataria (the Pebble Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 326.7 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.},
}
@article {pmid38764134,
year = {2024},
author = {Wang, J and Li, Y and Rahman, MM and Li, B and Yan, Z and Song, G and Zhao, Y and Wu, J and Chu, C},
title = {Unraveling the drivers and impacts of leaf phenological diversity in a subtropical forest: A fine-scale analysis using PlanetScope CubeSats.},
journal = {The New phytologist},
volume = {243},
number = {2},
pages = {607-619},
doi = {10.1111/nph.19850},
pmid = {38764134},
issn = {1469-8137},
support = {20220816162849005//Shenzhen Science and Technology Program/ ; 32301350//National Natural Science Foundation of China/ ; 31925027//National Natural Science Foundation of China/ ; 31922090//National Natural Science Foundation of China/ ; 32271595//National Natural Science Foundation of China/ ; 17305321//Hong Kong Research Grant Council General Research Fund/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme, the Hung Ying Physical Science Research Fund 2021-22/ ; //Innovation and Technology Fund (funding support to State Key Laboratories in Hong Kong of Agrobiotechnology) of the HKSAR, China/ ; LVEC-2023rc01//Key Talent Project of the State Key Laboratory of Vegetation and Environmental Change/ ; },
mesh = {*Plant Leaves/physiology ; *Forests ; *Biodiversity ; *Tropical Climate ; Biomass ; Soil ; China ; },
abstract = {Leaf phenology variations within plant communities shape community assemblages and influence ecosystem properties and services. However, questions remain regarding quantification, drivers, and productivity impacts of intra-site leaf phenological diversity. With a 50-ha subtropical forest plot in China's Heishiding Provincial Nature Reserve (part of the global ForestGEO network) as a testbed, we gathered a unique dataset combining ground-derived abiotic (topography, soil) and biotic (taxonomic diversity, functional diversity, functional traits) factors. We investigated drivers underlying leaf phenological diversity extracted from high-resolution PlanetScope data, and its influence on aboveground biomass (AGB) using structural equation modeling (SEM). Our results reveal considerable fine-scale leaf phenological diversity across the subtropical forest landscape. This diversity is directly and indirectly influenced by abiotic and biotic factors (e.g. slope, soil, traits, taxonomic diversity; r[2] = 0.43). While a notable bivariate relationship between AGB and leaf phenological diversity was identified (r = -0.24, P < 0.05), this relationship did not hold in SEM analysis after considering interactions with other biotic and abiotic factors (P > 0.05). These findings unveil the underlying mechanism regulating intra-site leaf phenological diversity. While leaf phenology is known to be associated with ecosystem properties, our findings confirm that AGB is primarily influenced by functional trait composition and taxonomic diversity rather than leaf phenological diversity.},
}
@article {pmid38764024,
year = {2024},
author = {Trujillano, F and Jimenez, G and Manrique, E and Kahamba, NF and Okumu, F and Apollinaire, N and Carrasco-Escobar, G and Barrett, B and Fornace, K},
title = {Using image segmentation models to analyse high-resolution earth observation data: new tools to monitor disease risks in changing environments.},
journal = {International journal of health geographics},
volume = {23},
number = {1},
pages = {13},
pmid = {38764024},
issn = {1476-072X},
support = {/WT_/Wellcome Trust/United Kingdom ; 221963/Z/20/Z//Wellcome Trust and Royal Society/ ; BB/X511110/1//BBSRC and EPSRC Impact Accelerator Accounts/ ; },
mesh = {Humans ; Animals ; *Climate Change ; Malaria/epidemiology ; Mosquito Vectors ; Remote Sensing Technology/methods ; Geographic Information Systems ; Image Processing, Computer-Assisted/methods ; },
abstract = {BACKGROUND: In the near future, the incidence of mosquito-borne diseases may expand to new sites due to changes in temperature and rainfall patterns caused by climate change. Therefore, there is a need to use recent technological advances to improve vector surveillance methodologies. Unoccupied Aerial Vehicles (UAVs), often called drones, have been used to collect high-resolution imagery to map detailed information on mosquito habitats and direct control measures to specific areas. Supervised classification approaches have been largely used to automatically detect vector habitats. However, manual data labelling for model training limits their use for rapid responses. Open-source foundation models such as the Meta AI Segment Anything Model (SAM) can facilitate the manual digitalization of high-resolution images. This pre-trained model can assist in extracting features of interest in a diverse range of images. Here, we evaluated the performance of SAM through the Samgeo package, a Python-based wrapper for geospatial data, as it has not been applied to analyse remote sensing images for epidemiological studies.<br><br>RESULTS: We tested the identification of two land cover classes of interest: water bodies and human settlements, using different UAV acquired imagery across five malaria-endemic areas in Africa, South America, and Southeast Asia. We employed manually placed point prompts and text prompts associated with specific classes of interest to guide the image segmentation and assessed the performance in the different geographic contexts. An average Dice coefficient value of 0.67 was obtained for buildings segmentation and 0.73 for water bodies using point prompts. Regarding the use of text prompts, the highest Dice coefficient value reached 0.72 for buildings and 0.70 for water bodies. Nevertheless, the performance was closely dependent on each object, landscape characteristics and selected words, resulting in varying performance.<br><br>CONCLUSIONS: Recent models such as SAM can potentially assist manual digitalization of imagery by vector control programs, quickly identifying key features when surveying an area of interest. However, accurate segmentation still requires user-provided manual prompts and corrections to obtain precise segmentation. Further evaluations are necessary, especially for applications in rural areas.},
}
@article {pmid38762947,
year = {2024},
author = {Liu, D and Zhou, M and Tan, H and Xiong, G and Wang, L and Shi, L and Li, C and Wu, W and Qiao, Y},
title = {Metabolomics, volatolomics, and bioinformatics analyses of the effects of ultra-high pressure pretreatment on taste and flavour parameters of cured Culter alburnus.},
journal = {Food chemistry},
volume = {453},
number = {},
pages = {139649},
doi = {10.1016/j.foodchem.2024.139649},
pmid = {38762947},
issn = {1873-7072},
mesh = {Animals ; *Taste ; *Flavoring Agents/chemistry/metabolism ; *Metabolomics ; *Computational Biology ; Fish Products/analysis/microbiology ; Pressure ; Cyprinidae/metabolism/microbiology ; Volatile Organic Compounds/chemistry/metabolism/analysis ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Humans ; Food Handling ; Amino Acids/metabolism/analysis ; },
abstract = {The effects of ultra-high pressure (UHP) pretreatment (50-250 MPa) on the fish curing were studied. UHP increased the overall volatile compound concentration of cured fish. Among 50-250 MPa five treatment groups, 150 MPa UHP group exhibited the highest total free amino acid content (294.34 mg/100 g) with that of the control group being 92.39 mg/100 g. The activity of cathepsin L was increased under 50-200 MPa UHP treatment (62.28-58.15 U/L), compared with that in the control group (53.80 U/L). UHP treatment resulted in a significant increase in small molecule compounds, especially the amino acid dipeptides and ATP metabolic products. Under UHP treatments, the bacterial phyla Actinobacteriota (1.04-5.25 %), Bacteroidota (0.20-4.47 %), and Deinococcota (0.00-0.05 %) exhibited an increased abundance, and they promoted taste and flavor formation. Our results indicated that UHP is a promising pretreatment method to improve taste and flavour in cured fish by affecting the microorganisms, cathepsin, and proteins.},
}
@article {pmid38760814,
year = {2024},
author = {Sakai, K and Igarashi, Y and Tounai, S and Shirai, C and Tsurugi, Y and Kakuno, F and Komasa, Y and Fujimura, M and Uruha, M and Mori, K and Tateishi, S},
title = {Key issues in Japan's public health centers to prepare for future pandemics: a text mining study using a topic model.},
journal = {BMC health services research},
volume = {24},
number = {1},
pages = {636},
pmid = {38760814},
issn = {1472-6963},
mesh = {Humans ; Japan ; *COVID-19/epidemiology ; Cross-Sectional Studies ; *Pandemics ; Surveys and Questionnaires ; Data Mining/methods ; Public Health ; SARS-CoV-2 ; Male ; },
abstract = {BACKGROUND: In Japan, over 450 public health centers played a central role in the operation of the local public health system in response to the COVID-19 pandemic. This study aimed to identify key issues for improving the system for public health centers for future pandemics.<br><br>METHODS: We conducted a cross-sectional study using an online questionnaire. The respondents were first line workers in public health centers or local governments during the pandemic. We solicited open-ended responses concerning improvements needed for future pandemics. Issues were identified from these descriptions using morphological analysis and a topic model with KHcoder3.0. The number of topics was estimated using Perplexity as a measure, and Latent Dirichlet Allocation for meaning identification.<br><br>RESULTS: We received open-ended responses from 784 (48.6%) of the 1,612 survey respondents, which included 111 physicians, 330 nurses, and 172 administrative staff. Morphological analysis processed these descriptions into 36,632 words. The topic model summarized them into eight issues: 1) establishment of a crisis management system, 2) division of functions among public health centers, prefectures, and medical institutions, 3) clear role distribution in public health center staff, 4) training of specialists, 5) information sharing system (information about infectious diseases and government policies), 6) response to excessive workload (support from other local governments, cooperation within public health centers, and outsourcing), 7) streamlining operations, and 8) balance with regular duties.<br><br>CONCLUSIONS: This study identified key issues that need to be addressed to prepare Japan's public health centers for future pandemics. These findings are vital for discussions aimed at strengthening the public health system based on experiences from the COVID-19 pandemic.},
}
@article {pmid38758962,
year = {2024},
author = {Massey, A and Boennec, C and Restrepo-Ortiz, CX and Blanchet, C and Alizon, S and Sofonea, MT},
title = {Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012124},
pmid = {38758962},
issn = {1553-7358},
mesh = {*COVID-19/epidemiology ; Humans ; France/epidemiology ; *Forecasting/methods ; *SARS-CoV-2 ; Computational Biology/methods ; Retrospective Studies ; Models, Statistical ; Pandemics/statistics &amp; numerical data ; Hospitals/statistics &amp; numerical data ; Hospitalization/statistics &amp; numerical data ; Bed Occupancy/statistics &amp; numerical data ; },
abstract = {Projects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes. We present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three baselines derived from standard statistical forecasting methods (a naive model, auto-regression, and an ensemble of exponential smoothing and ARIMA). In terms of median absolute error for forecasting critical care unit occupancy at the two-week horizon, our model only outperformed the naive baseline for 4 out of 14 geographical units and underperformed compared to the ensemble baseline for 5 of them at the 90% confidence level (n = 38). However, for the same level at the 4 week horizon, our model was never statistically outperformed for any unit despite outperforming the baselines 10 times spanning 7 out of 14 geographical units. This implies modest forecasting utility for longer horizons which may justify the application of non-Markovian compartmental models in the context of hospital-strain surveillance for future pandemics.},
}
@article {pmid38752675,
year = {2024},
author = {Schaupp, CM and Byrne, G and Chan, M and Haggard, DE and Hazemi, M and Jankowski, MD and LaLone, CA and LaTier, A and Mattingly, KZ and Olker, JH and Renner, J and Sharma, B and Villeneuve, DL},
title = {An automated computational data pipeline to rapidly acquire, score, and rank toxicological data for ecological hazard assessment.},
journal = {Integrated environmental assessment and management},
volume = {20},
number = {6},
pages = {2203-2217},
doi = {10.1002/ieam.4945},
pmid = {38752675},
issn = {1551-3793},
support = {//USEPA Office of Research and Development, Chemical Safety for Sustainability National Research Program/ ; },
mesh = {Risk Assessment/methods ; *Environmental Monitoring/methods ; Animals ; Endangered Species ; Water Pollutants, Chemical/toxicity/analysis ; Ecotoxicology/methods ; United States ; Quantitative Structure-Activity Relationship ; },
abstract = {Biological Evaluations support Endangered Species Act (ESA) consultation with the US Fish and Wildlife Service and National Marine Fisheries Service by federal action agencies, such as the USEPA, regarding impacts of federal activities on threatened or endangered species. However, they are often time-consuming and challenging to conduct. The identification of pollutant benchmarks or guidance to protect taxa for states and tribes when USEPA has not yet developed criteria recommendations is also of importance to ensure a streamlined approach to Clean Water Act program implementation. Due to substantial workloads, tight regulatory timelines, and the often-protracted length of ESA consultations, there is a need to streamline the development of biological evaluation toxicity assessments for determining the impact of chemical pollutants on ESA-listed species. Moreover, there is limited availability of species-specific toxicity data for many contaminants, further complicating the consultation process. New approach methodologies are being increasingly used in toxicology and chemical safety assessment to rapidly and cost-effectively provide data that can fill gaps in hazard and/or exposure characterization. Here, we present the development of an automated computational pipeline-RASRTox (Rapidly Acquire, Score, and Rank Toxicological data)-to rapidly extract and categorize ecological toxicity benchmark values from curated data sources (ECOTOX, ToxCast) and well-established quantitative structure-activity relationships (TEST, ECOSAR). As a proof of concept, points-of-departure (PODs) generated in RASRTox for 13 chemicals were compared against benchmark values derived using traditional methods-toxicity reference values (TRVs) and water quality criteria (WQC). The RASRTox PODs were generally within an order of magnitude of corresponding TRVs, though less concordant compared with WQC. The greatest utility of RASRTox, however, lies in its ability to quickly and systematically identify critical studies that may serve as a basis for screening value derivation by toxicologists as part of an ecological hazard assessment. As such, the strategy described in this case study can potentially be adapted for other risk assessment contexts and stakeholder needs. Integr Environ Assess Manag 2024;20:2203-2217. © 2024 Society of Environmental Toxicology &amp; Chemistry (SETAC). This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.},
}
@article {pmid38746391,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: Coverage-based Analysis for Identification of Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38746391},
issn = {2692-8205},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid38741754,
year = {2024},
author = {Klatt, S and Otte, FW and Beavan, A and Schumacher, T and Millar, SK},
title = {How did you perform? Investigating football players' perception of self-regulated passing performances under auditory noise environments.},
journal = {Frontiers in psychology},
volume = {15},
number = {},
pages = {1390487},
pmid = {38741754},
issn = {1664-1078},
abstract = {INTRODUCTION: This paper deals with the question on how sport performances may be influenced by internal, emotional processes, which stem from outside feedback.<br><br>METHODS: In terms of methods, players' subjective performance ratings for four experimental auditory cue conditions were examined; these included both 'positive' and 'negative' stadium noise, 'no (auditory) conditions,' and a control/'baseline' condition. This resulted in a qualitative-analytic data set that was obtained succeeding each auditory cue condition using a unique football training machine (i.e., known as 'Footbonaut'). Without having received any coaching/performance feedback, players were asked to rate and individually comment on their perceived performance ratings for each experimental auditory condition.<br><br>RESULTS: Findings indicate stronger and more significant correlations between auditory conditions and subjective ratings compared to the non-auditory condition and its subjective rating. Furthermore, data provides initial insight into players' emotional experiences during each of the practice conditions.<br><br>DISCUSSION: These noteworthy findings on players' abilities to accurately judge their performances based on selfmonitoring and intrinsic feedback are discussed from an Ecological Dynamics perspective, linked to a Nonlinear Pedagogy for coaching. Here, representative and affective learning designs for skill learning and performance preparation are presented. Finally, a hypothetical catalyst effect of auditory stadium noise on subjective performance rating is proposed.},
}
@article {pmid38741150,
year = {2024},
author = {Sõukand, R},
title = {Dark local knowledge: the yet-to-be scientifically discovered and locally acknowledged aspects of local knowledge systems.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {20},
number = {1},
pages = {50},
pmid = {38741150},
issn = {1746-4269},
mesh = {*Knowledge ; Humans ; Science ; },
abstract = {This essay brings forward the idea that there is more than meets the eye in local knowledge systems than what science can show us now. To comprehend this, we need to make a conceptual jump and look for the "dark matter" (the notion borrowed from astronomy that refers to a hypothetical form of matter that does not interact with light or electromagnetic fields) that can potentially sustain local knowledge. Considering that it is a complex of knowledge, practices, and beliefs contained in TEK, knowledge in LEK does not correspond to the notion of knowledge in science. Therefore, in order to map LEK-science interactions, we will refer to the concept of peoples' knowledge of LEK as acknowledgement and the scientific recognition and awareness of information, facts, and principles as knowledge. Applying this to a Johari Window, we can observe four categories of LEK in a known-unknown/acknowledged-unacknowledged matrix. We can refer to unknown and unacknowledged as dark local knowledge. Indeed, local knowledge systems contain many aspects that modern science cannot yet explain, as a major part of its components are not even considered in scholarly research. Dark local knowledge can potentially provide us with the invaluable touch of experience of countless generations, opening different ways of seeing reality.},
}
@article {pmid38739654,
year = {2024},
author = {Bloxham, B and Lee, H and Gore, J},
title = {Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012049},
pmid = {38739654},
issn = {1553-7358},
mesh = {*Biodiversity ; *Models, Biological ; *Ecosystem ; Computational Biology ; Animals ; },
abstract = {How natural communities maintain their remarkable biodiversity and which species survive in complex communities are central questions in ecology. Resource competition models successfully explain many phenomena but typically predict only as many species as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles can support many more species than resources. We explore how communities modify their own environments by sequentially depleting resources to form sequences of temporal niches, or intermediately depleted environments. Biodiversity is enhanced when community-driven or environmental fluctuations modulate the resource depletion order and produce different temporal niches on each growth cycle. Community-driven fluctuations under constant environmental conditions are rare, but exploring them illuminates the temporal niche structure that emerges from sequential resource utilization. With environmental fluctuations, we find most communities have more stably coexisting species than resources with survivors accurately predicted by the same temporal niche structure and each following a distinct optimal strategy. Our results thus present a new niche-based approach to understanding highly diverse fluctuating communities.},
}
@article {pmid38729378,
year = {2024},
author = {Yu, H and Yin, D and Yang, B and Yang, Y and Chen, F},
title = {Challenges for sustainable development goal of land degradation neutrality in drylands: Evidence from the Northern Slope of the Tianshan Mountains, China.},
journal = {The Science of the total environment},
volume = {932},
number = {},
pages = {173094},
doi = {10.1016/j.scitotenv.2024.173094},
pmid = {38729378},
issn = {1879-1026},
abstract = {The SDG 15.3.1 target of Land Degradation Neutrality (LDN) only has 15 years from conception (in 2015) to realization (in 2030). Therefore, investigating the effectiveness and challenges of LDN has become a priority, especially in drylands, where fragile ecosystems intersect with multiple disturbances. In this study, solutions are proposed and validated based on the challenges of LDN. We chose the Northern Slope of the Tianshan Mountains as a case study and set baselines in 2005 and 2010. The region and degree of land change (including degraded, stable, and improved) were depicted at the pixel scale (100 × 100 m), and LDN realization was assessed at the regional scale (including administrative districts and 5000 × 5000 m grids). The results showed a significant disparity between the two baselines. The number of areas that realized the LDN target was rare, regardless of the scale of the administrative districts or grids. Chord plots, Spearman's correlation, and curve estimation were employed to reveal the relationship between LDN and seven natural or socioeconomic factors. We found that substantial degradation was closely related to the expansion of unused, urban, and mining land and reduction in water, glaciers, and forests. Further evidence suggests that agricultural development both positively and negatively affects LDN, whereas urbanization and mining activities are undesirable for LDN. Notably, the adverse effects of glacier melting require additional attention. Therefore, we consider the easy-to-achieve and hard-to-achieve baselines as the mandatory and desirable targets of LDN, respectively, and focus further efforts in three aspects: preventing agricultural exploitation from occupying ecological resources, defining reasonable zones for urbanization and mining, and reducing greenhouse gas emissions to mitigate warming. Overall, this study is expected to be a beneficial addition to existing LDN theoretical systems and serve as a case validation of the challenges of LDN in drylands.},
}
@article {pmid38729197,
year = {2024},
author = {Caini, S and Meijer, A and Nunes, MC and Henaff, L and Zounon, M and Boudewijns, B and Del Riccio, M and Paget, J},
title = {Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance databases.},
journal = {The Lancet. Microbe},
volume = {5},
number = {8},
pages = {100851},
doi = {10.1016/S2666-5247(24)00066-1},
pmid = {38729197},
issn = {2666-5247},
mesh = {Humans ; *Influenza, Human/epidemiology/virology ; *Influenza B virus/genetics/isolation &amp; purification ; *Public Health ; Global Health ; COVID-19/epidemiology/prevention &amp; control ; Databases, Factual ; SARS-CoV-2 ; Pandemics ; },
abstract = {Early after the start of the COVID-19 pandemic, the detection of influenza B/Yamagata cases decreased globally. Given the potential public health implications of this decline, in this Review, we systematically analysed data on influenza B/Yamagata virus circulation (for 2020-23) from multiple complementary sources of information. We identified relevant articles published in PubMed and Embase, and data from the FluNet, Global Initiative on Sharing All Influenza Data, and GenBank databases, webpages of respiratory virus surveillance systems from countries worldwide, and the Global Influenza Hospital Surveillance Network. A progressive decline of influenza B/Yamagata detections was reported across all sources, in absolute terms (total number of cases), as positivity rate, and as a proportion of influenza B detections. Sporadically reported influenza B/Yamagata cases since March, 2020 were mostly vaccine-derived, attributed to data entry errors, or have yet to be definitively confirmed. The likelihood of extinction necessitates a rapid response in terms of reassessing the composition of influenza vaccines, enhanced surveillance for B/Yamagata, and a possible change in the biosafety level when handling B/Yamagata viruses in laboratories.},
}
@article {pmid38724591,
year = {2024},
author = {Bhandari, N and Bald, L and Wraase, L and Zeuss, D},
title = {Multispectral analysis-ready satellite data for three East African mountain ecosystems.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {473},
pmid = {38724591},
issn = {2052-4463},
support = {5064//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 2358//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Climate Change ; *Ecosystem ; Environmental Monitoring/methods ; Ethiopia ; Remote Sensing Technology ; *Satellite Imagery ; Tanzania ; },
abstract = {The East African mountain ecosystems are facing increasing threats due to global change, putting their unique socio-ecological systems at risk. To monitor and understand these changes, researchers and stakeholders require accessible analysis-ready remote sensing data. Although satellite data is available for many applications, it often lacks accurate geometric orientation and has extensive cloud cover. This can generate misleading results and make it unreliable for time-series analysis. Therefore, it needs comprehensive processing before usage, which encompasses multi-step operations, requiring large computational and storage capacities, as well as expert knowledge. Here, we provide high-quality, atmospherically corrected, and cloud-free analysis-ready Sentinel-2 imagery for the Bale Mountains (Ethiopia), Mounts Kilimanjaro and Meru (Tanzania) ecosystems in East Africa. Our dataset ranges from 2017 to 2021 and is provided as monthly and annual aggregated products together with 24 spectral indices. Our dataset enables researchers and stakeholders to conduct immediate and impactful analyses. These applications can include vegetation mapping, wildlife habitat assessment, land cover change detection, ecosystem monitoring, and climate change research.},
}
@article {pmid38724027,
year = {2024},
author = {Dar, FA and Hamid, M and Malik, RA and Wani, SA and Singh, CP and Shah, MA and Khuroo, AA},
title = {ToTE: A global database on trees of the treeline ecotone.},
journal = {Ecology},
volume = {105},
number = {6},
pages = {e4309},
doi = {10.1002/ecy.4309},
pmid = {38724027},
issn = {1939-9170},
support = {923/CSIR-UGC NET JUNE 2019//University Grants Commission/ ; SR/FST/LS-II/2017/103(C)//Department of Science &amp; Technology, Govt. of India, New Delhi/ ; SAC/EPSA/ALPINE/SHRESTI/10/2019//Space Applications Centre (SAC) ISRO, Ahmedabad/ ; },
mesh = {*Trees ; *Databases, Factual ; Biodiversity ; Forests ; Ecosystem ; },
abstract = {Globally, treelines form a transition zone between tree-dominated forest downslope and treeless alpine vegetation upslope. Treelines represent the highest boundary of "tree" life form in high-elevation mountains and at high latitudes. Recently, treelines have been shifting upslope in response to climate warming, so it has become important to understand global tree diversity and treeline distributions. However, to the best of our knowledge, no global database on tree flora of treelines exists, which limits our capacity to undertake macroecological analyses. Here, for the first time, we present a global data set on the trees of the treeline ecotone, supported by an online ToTE database. We synthesized the database from 1202 studies published over the last 60 years (1962 to 2022) following the Preferred Reporting Items in Systematic Reviews and Meta-Analysis (PRISMA) protocol. We classified the tree species in the database into three categories: treeline tree (TL) species, near to treeline (NTL) tree species, and tree species with an upper montane range limit (TUMR). The ToTE Version-1 presents a total of 208 tree taxa, including 189 species, five subspecies, and 14 varieties, belonging to 54 genera and 26 families distributed across 34 mountain regions worldwide that either grow exactly at the treeline or have a range limit below the treeline. Of the total taxa, 155, 14, and 39 belong to TL, NTL, and TUMR, respectively. Genera such as Abies, Picea, Pinus, Larix, and Juniperus are more represented in the treeline tree category. On the other hand, Acer, Prunus, Populus, and Quercus have more representatives in the near to treeline category, whereas Erica, Nothofagus, and Polylepis contribute more tree species with an upper montane range limit. Furthermore, families such as Rosaceae and Pinaceae include trees that occur both at the treeline and with an upper montane range limit, whereas Sapindaceae includes trees that occur exclusively near to treeline. Our database also includes information on the global distribution patterns of treeline tree species richness across mountains and biomes. The mountains with the highest number of tree species are the Andes (39) followed by the Himalaya (37). Close to 67% of tree species show restricted distributions in different mountains, with the highest endemism in the Andes and the Himalaya. In terms of tree species distribution, Pinus sylvestris was widespread, with a distribution across nine mountain regions, followed by Picea glauca and Fagus sylvatica, both distributed across five mountain regions. In terms of species' distribution across biomes, the temperate biome harbors the highest treeline tree species richness (152 species), which may reflect the fact that the majority of studies are available from the temperate regions of the world. The remaining 56 species are distributed within five other biomes, with the least in dry tropical and subarctic (four species each). Furthermore, currently 40 treeline tree species fall under different International Union for Conservation of Nature threat categories. We anticipate that our database will help advance research on macroecological, biogeographic, evolutionary, climate-change, and conservation aspects of the treeline on a global scale. The data are released under a Creative Commons Attribution 4.0 international license. Please cite this data paper when the data are reused.},
}
@article {pmid38723067,
year = {2024},
author = {Holstad, A and Voje, KL and Opedal, &#xd8;H and Bolstad, GH and Bourg, S and Hansen, TF and Pélabon, C},
title = {Evolvability predicts macroevolution under fluctuating selection.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6696},
pages = {688-693},
doi = {10.1126/science.adi8722},
pmid = {38723067},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; *Fossils ; Genetic Variation ; *Selection, Genetic ; Datasets as Topic ; },
abstract = {Heritable variation is a prerequisite for evolutionary change, but the relevance of genetic constraints on macroevolutionary timescales is debated. By using two datasets on fossil and contemporary taxa, we show that evolutionary divergence among populations, and to a lesser extent among species, increases with microevolutionary evolvability. We evaluate and reject several hypotheses to explain this relationship and propose that an effect of evolvability on population and species divergence can be explained by the influence of genetic constraints on the ability of populations to track rapid, stationary environmental fluctuations.},
}
@article {pmid38721834,
year = {2024},
author = {Freedman, AH and Sackton, TB},
title = {Rethinking eco-evo studies of gene expression for non-model organisms in the genomic era.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17378},
doi = {10.1111/mec.17378},
pmid = {38721834},
issn = {1365-294X},
abstract = {Recent advances in genomic technology, including the rapid development of long-read sequencing technology and single-cell RNA-sequencing methods, are poised to significantly expand the kinds of studies that are feasible in ecological genomics. In this perspective, we review these new technologies and discuss their potential impact on gene expression studies in non-model organisms. Although traditional RNA-sequencing methods have been an extraordinarily powerful tool to apply functional genomics in an ecological context, bulk RNA-seq approaches often rely on de novo transcriptome assembly, and cannot capture expression changes in rare cell populations or distinguish shifts in cell type abundance. Advancements in genome assembly technology, particularly long-read sequencing, and improvements in the scalability of single-cell RNA-sequencing (scRNA-seq) offer unprecedented resolution in understanding cellular heterogeneity and gene regulation. We discuss the potential of these technologies to enable disentangling differential gene regulation from cell type composition differences and uncovering subtle expression patterns masked by bulk RNA-seq. The integration of these approaches provides a more nuanced understanding of the ecological and evolutionary dynamics of gene expression, paving the way for refined models and deeper insights into the generation of biodiversity.},
}
@article {pmid38721398,
year = {2024},
author = {Ross, KE and Bastian, FB and Buys, M and Cook, CE and D'Eustachio, P and Harrison, M and Hermjakob, H and Li, D and Lord, P and Natale, DA and Peters, B and Sternberg, PW and Su, AI and Thakur, M and Thomas, PD and Bateman, A and , },
title = {Perspectives on tracking data reuse across biodata resources.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbae057},
pmid = {38721398},
issn = {2635-0041},
support = {R35 GM141873/GM/NIGMS NIH HHS/United States ; },
abstract = {MOTIVATION: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge.<br><br>RESULTS: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use.&#xa0;Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources.<br><br>Summaries of survey results are available at: https://docs.google.com/forms/d/1j-VU2ifEKb9C-sW6l3ATB79dgHdRk5v_lESv2hawnso/viewanalytics (survey of data providers) and https://docs.google.com/forms/d/18WbJFutUd7qiZoEzbOytFYXSfWFT61hVce0vjvIwIjk/viewanalytics (survey of users).},
}
@article {pmid38720068,
year = {2024},
author = {Mahon, MB and Sack, A and Aleuy, OA and Barbera, C and Brown, E and Buelow, H and Civitello, DJ and Cohen, JM and de Wit, LA and Forstchen, M and Halliday, FW and Heffernan, P and Knutie, SA and Korotasz, A and Larson, JG and Rumschlag, SL and Selland, E and Shepack, A and Vincent, N and Rohr, JR},
title = {A meta-analysis on global change drivers and the risk of infectious disease.},
journal = {Nature},
volume = {629},
number = {8013},
pages = {830-836},
pmid = {38720068},
issn = {1476-4687},
mesh = {Animals ; Humans ; Anthropogenic Effects ; *Biodiversity ; *Climate Change/statistics &amp; numerical data ; *Communicable Diseases/epidemiology/etiology ; Conservation of Natural Resources/trends ; Datasets as Topic ; *Environmental Pollution/adverse effects ; Forestry ; Forests ; *Introduced Species/statistics &amp; numerical data ; Plant Diseases/etiology ; Risk Assessment ; Urbanization ; },
abstract = {Anthropogenic change is contributing to the rise in emerging infectious diseases, which are significantly correlated with socioeconomic, environmental and ecological factors[1]. Studies have shown that infectious disease risk is modified by changes to biodiversity[2-6], climate change[7-11], chemical pollution[12-14], landscape transformations[15-20] and species introductions[21]. However, it remains unclear which global change drivers most increase disease and under what contexts. Here we amassed a dataset from the literature that contains 2,938 observations of infectious disease responses to global change drivers across 1,497 host-parasite combinations, including plant, animal and human hosts. We found that biodiversity loss, chemical pollution, climate change and introduced species are associated with increases in disease-related end points or harm, whereas urbanization is associated with decreases in disease end points. Natural biodiversity gradients, deforestation and forest fragmentation are comparatively unimportant or idiosyncratic as drivers of disease. Overall, these results are consistent across human and non-human diseases. Nevertheless, context-dependent effects of the global change drivers on disease were found to be common. The findings uncovered by this meta-analysis should help target disease management and surveillance efforts towards global change drivers that increase disease. Specifically, reducing greenhouse gas emissions, managing ecosystem health, and preventing biological invasions and biodiversity loss could help to reduce the burden of plant, animal and human diseases, especially when coupled with improvements to social and economic determinants of health.},
}
@article {pmid38718196,
year = {2024},
author = {Leroux, A and Crainiceanu, C and Zeger, S and Taub, M and Ansari, B and Wager, TD and Bayman, E and Coffey, C and Langefeld, C and McCarthy, R and Tsodikov, A and Brummet, C and Clauw, DJ and Edwards, RR and Lindquist, MA and , },
title = {Statistical modeling of acute and chronic pain patient-reported outcomes obtained from ecological momentary assessment.},
journal = {Pain},
volume = {165},
number = {9},
pages = {1955-1965},
doi = {10.1097/j.pain.0000000000003214},
pmid = {38718196},
issn = {1872-6623},
support = {U54 DA049113/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; *Chronic Pain/diagnosis ; *Patient Reported Outcome Measures ; *Ecological Momentary Assessment ; *Models, Statistical ; *Pain Measurement/methods ; *Acute Pain/diagnosis ; Male ; Female ; },
abstract = {Ecological momentary assessment (EMA) allows for the collection of participant-reported outcomes (PROs), including pain, in the normal environment at high resolution and with reduced recall bias. Ecological momentary assessment is an important component in studies of pain, providing detailed information about the frequency, intensity, and degree of interference of individuals' pain. However, there is no universally agreed on standard for summarizing pain measures from repeated PRO assessment using EMA into a single, clinically meaningful measure of pain. Here, we quantify the accuracy of summaries (eg, mean and median) of pain outcomes obtained from EMA and the effect of thresholding these summaries to obtain binary clinical end points of chronic pain status (yes/no). Data applications and simulations indicate that binarizing empirical estimators (eg, sample mean, random intercept linear mixed model) can perform well. However, linear mixed-effect modeling estimators that account for the nonlinear relationship between average and variability of pain scores perform better for quantifying the true average pain and reduce estimation error by up to 50%, with larger improvements for individuals with more variable pain scores. We also show that binarizing pain scores (eg, <3 and ≥3) can lead to a substantial loss of statistical power (40%-50%). Thus, when examining pain outcomes using EMA, the use of linear mixed models using the entire scale (0-10) is superior to splitting the outcomes into 2 groups (<3 and ≥3) providing greater statistical power and sensitivity.},
}
@article {pmid38717702,
year = {2024},
author = {Zhou, Q and Song, Y and Zhang, Y and Ping, Z and Zheng, Y and Chen, H and Liu, P and Hong, P and Zheng, Z},
title = {Land use transition and its effect on ecosystem service value with introducing "three wastes" factor in the industrial county, China.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {24},
pages = {34962-34980},
pmid = {38717702},
issn = {1614-7499},
support = {ZR2023MD033//Natural Science Foundation of Shandong Province/ ; LJNY202103//Key Technology Research and Development Program of Shandong Province/ ; },
mesh = {China ; *Ecosystem ; Conservation of Natural Resources ; Urbanization ; Forests ; Environmental Monitoring ; },
abstract = {Land use transition and its impact on ecosystem service value (ESV) are the foundation for optimizing the layout of territorial space and ecological civilization construction. With the acceleration of industrialization and urbanization, the area of construction land expands in China. To accurately estimate the ESV in industrial counties, the impact of construction land on the ecological environment should be fully considered. This paper took Gangcheng District, Jinan City, a steel base in the Shandong Province of China as an example, then the value coefficients of "three wastes" factors (waste gas, wastewater, and waste) were introduced, and an improved calculation method of ESV was put forward for industrial counties in combination with remote sensing and land use data. Finally, the land use transition and its ESV effect in typical industrial counties were analyzed using geo-informatic Tupu and grid method. The results showed that the most important land use transitions were from grassland and forestland to cultivated land, from cultivated land and forestland to construction land in 1990-2010, and from cultivated land transformed to forestland in 2010-2021. The types of land use transition were mainly repetitive and continuous. The ESV first decreased and then increased, with a slight overall decline for more than 30 years, showing a spatial distribution characteristic of "low in the south-central and high around." Land use transition had the impact on ESV with the negative contribution rate of 68.28% in 1990-2000 and 73.16% in 2000-2010, mainly caused by the transition from forestland and grassland to cultivated land and construction land, and the positive contribution rate of 81.72% in 2010-2021, mainly caused by the transition from cultivated land to forestland. Compared with the ESV calculation method without introducing the "three wastes" factor and Xie Gaodi's method, the improved method in this paper considered the inevitable impact of construction land on ESV in industrial counties and made the ESV calculated more accurate according to the regional nature. This paper cannot only enrich the theories and technical methods of land use transition and its effects, and provide a case reference for similar industrial counties, but also provide data and decision-making support for the spatial layout and ecological protection in the study area.},
}
@article {pmid38716048,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Ruddy Flat-body, Agonopterix subpropinquella (Stainton, 1849).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {487},
pmid = {38716048},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Agonopterix subpropinquella (the Ruddy Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 667.9 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,796 protein coding genes.},
}
@article {pmid38714914,
year = {2024},
author = {Zhang, L and Zhang, Y and Liu, Y and Miao, W and Ai, J and Li, J and Peng, S and Li, S and Ye, L and Zeng, R and Shi, X and Ma, J and Lin, Y and Kuang, W and Cui, R},
title = {Multi-omics analysis revealed that the protein kinase MoKin1 affected the cellular response to endoplasmic reticulum stress in the rice blast fungus, Magnaporthe oryzae.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {449},
pmid = {38714914},
issn = {1471-2164},
mesh = {*Endoplasmic Reticulum Stress ; *Oryza/microbiology/genetics ; *Fungal Proteins/metabolism/genetics ; *Proteomics ; Plant Diseases/microbiology ; Gene Expression Regulation, Fungal ; Protein Kinases/metabolism/genetics ; Mutation ; Multiomics ; Ascomycota ; },
abstract = {BACKGROUND: Previous studies have shown that protein kinase MoKin1 played an important role in the growth, conidiation, germination and pathogenicity in rice blast fungus, Magnaporthe oryzae. ΔMokin1 mutant showed significant phenotypic defects and significantly reduced pathogenicity. However, the internal mechanism of how MoKin1 affected the development of physiology and biochemistry remained unclear in M. oryzae.<br><br>RESULT: This study adopted a multi-omics approach to comprehensively analyze MoKin1 function, and the results showed that MoKin1 affected the cellular response to endoplasmic reticulum stress (ER stress). Proteomic analysis revealed that the downregulated proteins in &#x394;Mokin1 mutant were enriched mainly in the response to ER stress triggered by the unfolded protein. Loss of MoKin1 prevented the ER stress signal from reaching the nucleus. Therefore, the phosphorylation of various proteins regulating the transcription of ER stress-related genes and mRNA translation was significantly downregulated. The insensitivity to ER stress led to metabolic disorders, resulting in a significant shortage of carbohydrates and a low energy supply, which also resulted in severe phenotypic defects in &#x394;Mokin1 mutant. Analysis of MoKin1-interacting proteins indicated that MoKin1 really took participate in the response to ER stress.<br><br>CONCLUSION: Our results showed the important role of protein kinase MoKin1 in regulating cellular response to ER stress, providing a new research direction to reveal the mechanism of MoKin1 affecting pathogenic formation, and to provide theoretical support for the new biological target sites searching and bio-pesticides developing.},
}
@article {pmid38714759,
year = {2024},
author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R},
title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.},
journal = {Nature microbiology},
volume = {9},
number = {5},
pages = {1152-1156},
pmid = {38714759},
issn = {2058-5276},
support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; },
mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; },
}
@article {pmid38714055,
year = {2024},
author = {Li, Z and Wang, J and Yue, H and Rehman, A and Yousaf, M and Du, M and Zhang, X},
title = {Applying metabolic modeling and multi-omics to elucidate the biotransformation mechanisms of marine algal toxin domoic acid (DA) in sediments.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134541},
doi = {10.1016/j.jhazmat.2024.134541},
pmid = {38714055},
issn = {1873-3336},
mesh = {*Kainic Acid/analogs &amp; derivatives/metabolism ; *Geologic Sediments/microbiology ; *Biotransformation ; *Marine Toxins/metabolism ; Microbiota ; Metabolome ; Biodegradation, Environmental ; Metagenome ; Water Pollutants, Chemical/metabolism ; Multiomics ; },
abstract = {Domoic acid (DA)-producing algal blooms are a global marine environmental issue. However, there has been no previous research addressing the question regarding the fate of DA in marine benthic environments. In this work, we investigated the DA fate in the water-sediment microcosm via the integrative analysis of a top-down metabolic model, metagenome, and metabolome. Results demonstrated that biodegradation is the leading mechanism for the nonconservative attenuation of DA. Specifically, DA degradation was prominently completed by the sediment aerobic community, with a degradation rate of 0.0681 ± 0.00954 d[-1]. The DA degradation pathway included hydration, dehydrogenation, hydrolysis, decarboxylation, automatic ring opening of hydration, and β oxidation reactions. Moreover, the reverse ecological analysis demonstrated that the microbial community transitioned from nutrient competition to metabolic cross-feeding during DA degradation, further enhancing the cooperation between DA degraders and other taxa. Finally, we reconstructed the metabolic process of microbial communities during DA degradation and confirmed that the metabolism of amino acid and organic acid drove the degradation of DA. Overall, our work not only elucidated the fate of DA in marine environments but also provided crucial insights for applying metabolic models and multi-omics to investigate the biotransformation of other contaminants.},
}
@article {pmid38713735,
year = {2024},
author = {Oszoli, I and Zachar, I},
title = {Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012107},
pmid = {38713735},
issn = {1553-7358},
mesh = {*Models, Biological ; *Biological Evolution ; Computational Biology ; Ecosystem ; Animals ; Predatory Behavior/physiology ; Selection, Genetic ; Computer Simulation ; },
abstract = {The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection instead other mechanisms maintain cooperation against cheater phenotypes that benefit from cooperators but do not contribute to groups. Spatiality with limited diffusion can facilitate group selection, as interactions among individuals are restricted to local neighbourhoods only. Selection for larger size (e.g. avoiding predation) may facilitate the emergence of aggregation, though it is unknown, whether and how much role such selection played during the evolution of aggregative multicellularity. We have investigated the effect of spatiality and the necessity of predation on the stability of aggregative multicellularity via individual-based modelling on the ecological timescale. We have examined whether aggregation facilitates the survival of cooperators in a temporally heterogeneous environment against cheaters, where only a subset of the population is allowed to periodically colonize a new, resource-rich habitat. Cooperators constitutively produce adhesive molecules to promote aggregation and propagule-formation while cheaters spare this expense to grow faster but cannot aggregate on their own, hence depending on cooperators for long-term survival. We have compared different population-level reproduction modes with and without individual selection (predation) to evaluate the different hypotheses. In a temporally homogeneous environment without propagule-based colonization, cheaters always win. Predation can benefit cooperators, but it is not enough to maintain the necessary cooperator amount in successive dispersals, either randomly or by fragmentation. Aggregation-based propagation however can ensure the adequate ratio of cooperators-to-cheaters in the propagule and is sufficient to do so even without predation. Spatiality combined with temporal heterogeneity helps cooperators via group selection, thus facilitating aggregative multicellularity. External stress selecting for larger size (e.g. predation) may facilitate aggregation, however, according to our results, it is neither necessary nor sufficient for aggregative multicellularity to be maintained when there is effective group-selection.},
}
@article {pmid38711355,
year = {2024},
author = {Tsutsui, K and Tanaka, R and Takeda, K and Fujii, K},
title = {Collaborative hunting in artificial agents with deep reinforcement learning.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {38711355},
issn = {2050-084X},
support = {20H04075//Japan Society for the Promotion of Science/ ; 21H04892//Japan Society for the Promotion of Science/ ; 21H05300//Japan Society for the Promotion of Science/ ; 22K17673//Japan Society for the Promotion of Science/ ; JPMJPR20CA//Japan Science and Technology Agency/ ; },
mesh = {Animals ; *Deep Learning ; *Predatory Behavior ; *Reinforcement, Psychology ; Cooperative Behavior ; Humans ; Computer Simulation ; Decision Making ; },
abstract = {Collaborative hunting, in which predators play different and complementary roles to capture prey, has been traditionally believed to be an advanced hunting strategy requiring large brains that involve high-level cognition. However, recent findings that collaborative hunting has also been documented in smaller-brained vertebrates have placed this previous belief under strain. Here, using computational multi-agent simulations based on deep reinforcement learning, we demonstrate that decisions underlying collaborative hunts do not necessarily rely on sophisticated cognitive processes. We found that apparently elaborate coordination can be achieved through a relatively simple decision process of mapping between states and actions related to distance-dependent internal representations formed by prior experience. Furthermore, we confirmed that this decision rule of predators is robust against unknown prey controlled by humans. Our computational ecological results emphasize that collaborative hunting can emerge in various intra- and inter-specific interactions in nature, and provide insights into the evolution of sociality.},
}
@article {pmid38709778,
year = {2024},
author = {Xu, N and Zeng, P and Guo, Y and Siddique, MA and Li, J and Ren, X and Tang, F and Zhang, R},
title = {The spatiotemporal evolution of rural landscape patterns in Chinese metropolises under rapid urbanization.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0301754},
pmid = {38709778},
issn = {1932-6203},
mesh = {China ; Cities ; Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; Rural Population ; Spatio-Temporal Analysis ; *Urbanization ; },
abstract = {Understanding the evolution of rural landscapes in metropolises during rapid urbanization is crucial for formulating policies to protect the rural ecological environment. In this study, remote sensing and geographical information system data, as well as applied landscape index analysis, are used to examine the spatiotemporal evolution of rural landscape patterns in the Beijing-Tianjin region of China, which has experienced rapid urbanization. The relationships between land use/land cover changes and changes in rural landscape patterns are explored. The results revealed significant spatial differences in the rural landscapes in the Beijing-Tianjin region; farmland and forestland were the main types of landscapes, creating a "mountain-field-sea" natural landscape pattern. The conversion of rural landscapes in the Beijing-Tianjin region involved mainly the conversion of farmland to urban areas, with few exchanges between other landscape types. The urban areas in the Beijing-Tianjin region increased by 3% per decade; farmland decreased at the same rate. Additionally, the rural landscape patterns in the Beijing-Tianjin region were dominated by fragmentation, dispersion, and heterogeneity and moved from complex to regular. Water bodies displayed the most fragmented natural landscape; their number of patches increased by 36%, though their network characteristics were maintained. Forestland was the most concentrated natural landscape. In this study, theoretical support and a scientific reference for the optimization of rural landscape patterns and the improvement in rural living environments in rapidly urbanizing areas are provided.},
}
@article {pmid38708866,
year = {2024},
author = {Villarreal-Rosas, J and Brown, CJ and Andradi-Brown, DA and Domínguez, R and Jacobo, P and Martínez, A and Mascote, C and Najera, E and Paiz, Y and Vázquez Moran, VH and Villarreal, J and Adame, MF},
title = {Integrating socioeconomic and ecological data into restoration practice.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {38},
number = {4},
pages = {e14286},
doi = {10.1111/cobi.14286},
pmid = {38708866},
issn = {1523-1739},
support = {//Advance Queensland Industry Research Fellowship/ ; //Jeremy and Hannelore Grantham Environmental Trust/ ; FT210100792//Australian Research Council/ ; },
mesh = {*Conservation of Natural Resources/methods/economics ; Mexico ; *Socioeconomic Factors ; Environmental Restoration and Remediation/economics ; Ecosystem ; Decision Support Techniques ; },
abstract = {Driven by the United Nations Decade on Restoration and international funding initiatives, such as the Mangrove Breakthrough, investment in mangrove restoration is expected to increase. Yet, mangrove restoration efforts frequently fail, usually because of ad hoc site-selection processes that do not consider mangrove ecology and the socioeconomic context. Using decision analysis, we developed an approach that accounts for socioeconomic and ecological data to identify sites with the highest likelihood of mangrove restoration success. We applied our approach in the Biosphere Reserve Marismas Nacionales Nayarit, Mexico, an area that recently received funding for implementing mangrove restoration actions. We identified 468 potential restoration sites, assessed their restorability potential based on socioeconomic and ecological metrics, and ranked sites for implementation with spatial optimization. The metrics we used included favorable conditions for propagules to establish and survive under sea-level rise, provision of ecosystem services, and community dynamics. Sites that were selected based on socioeconomic or ecological metrics alone had lower likelihood of mangrove restoration success than sites that were selected based on integrated socioeconomic and ecological metrics. For example, selecting sites based on only socioeconomic metrics captured 16% of the maximum attainable value of functioning mangroves able to provide propagules to potential restoration sites, whereas selecting sites based on ecological and socioeconomic metrics captured 46% of functioning mangroves. Our approach was developed as part of a collaboration between nongovernmental organizations, local government, and academics under rapid delivery time lines given preexisting mangrove restoration implementation commitments. The systematic decision process we used integrated socioeconomic and ecological considerations even under short delivery deadlines, and our approach can be adapted to help mangrove restoration site-selection decisions elsewhere.},
}
@article {pmid38707490,
year = {2023},
author = {Boyes, D and Phillips, D and , and , and , and , and , and , },
title = {The genome sequence of the Early Thorn, Selenia dentaria (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {485},
pmid = {38707490},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Selenia dentaria (the Early Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 1,030.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,390 protein coding genes.},
}
@article {pmid38705187,
year = {2024},
author = {Meier, R and Hartop, E and Pylatiuk, C and Srivathsan, A},
title = {Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230120},
pmid = {38705187},
issn = {1471-2970},
mesh = {*Insecta/physiology/classification/genetics ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; },
abstract = {Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}
@article {pmid38704010,
year = {2024},
author = {Song, X and Li, C and Qiu, Z and Wang, C and Zeng, Q},
title = {Ecotoxicological effects of polyethylene microplastics and lead (Pb) on the biomass, activity, and community diversity of soil microbes.},
journal = {Environmental research},
volume = {252},
number = {Pt 3},
pages = {119012},
doi = {10.1016/j.envres.2024.119012},
pmid = {38704010},
issn = {1096-0953},
mesh = {*Soil Microbiology ; *Lead/toxicity ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Biomass ; *Polyethylene/toxicity ; Soil/chemistry ; Ecotoxicology ; },
abstract = {Microplastics and heavy metals are ubiquitous and persistent contaminants that are widely distributed worldwide, yet little is known about the effects of their interaction on soil ecosystems. A soil incubation experiment was conducted to investigate the individual and combined effects of polyethylene microplastics (PE-MPs) and lead (Pb) on soil enzymatic activities, microbial biomass, respiration rate, and community diversity. The results indicate that the presence of PE-MPs notably reduced soil pH and elevated soil Pb bioavailability, potentially exacerbated the combined toxicity on the biogeochemical cycles of soil nutrients, microbial biomass carbon and nitrogen, and the activities of soil urease, sucrase, and alkaline phosphatase. Soil CO2 emissions increased by 7.9% with PE-MPs alone, decreased by 46.3% with single Pb, and reduced by 69.4% with PE-MPs and Pb co-exposure, compared to uncontaminated soils. Specifically, the presence of PE-MPs and Pb, individually and in combination, facilitated the soil metabolic quotient, leading to reduced microbial metabolic efficiency. Moreover, the addition of Pb and PE-MPs modified the composition of the microbial community, leading to the enrichment of specific taxa. Tax4Fun analysis showed the effects of Pb, PE-MPs and their combination on the biogeochemical processes and ecological functions of microbes were mainly by altering amino acid metabolism, carbohydrate metabolism, membrane transport, and signal transduction. These findings offer valuable insights into the ecotoxicological effects of combined PE-MPs and Pb on soil microbial dynamics, reveals key assembly mechanisms and environmental drivers, and highlights the potential threat of MPs and heavy metals to the multifunctionality of soil ecosystems.},
}
@article {pmid38703986,
year = {2024},
author = {Li, JY and Yao, S and Mo, Z and Miao, Y and Chen, Y and He, W and Jin, L and Tang, W},
title = {Submerged plant-biochar composite system exhibits effective control over residual organic pollutants in the benthic organisms of aquaculture ponds.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {351},
number = {},
pages = {124078},
doi = {10.1016/j.envpol.2024.124078},
pmid = {38703986},
issn = {1873-6424},
mesh = {*Aquaculture ; *Water Pollutants, Chemical/analysis/metabolism ; *Charcoal/chemistry ; *Ponds/chemistry ; *Geologic Sediments/chemistry ; Corbicula ; Biodegradation, Environmental ; Hydrocharitaceae/metabolism ; Animals ; },
abstract = {As of now, submerged plants and biochar have demonstrated significant benefits in aquaculture pond sediment remediation. However, there is limited research on the synergistic effects of biochar and submerged plants in mitigating hydrophobic organic contaminant (HOC) accumulation in aquaculture benthic organisms and in controlling the nutrient (nitrogen and phosphorus) levels in aquaculture water. This study assesses a submerged plant-biochar system's efficacy in removing HOCs from simulated freshwater aquaculture ponds. Vallisneria natans was planted in sediment with varying levels of wheat straw biochar, while Corbicula fluminea served as the targeted benthic organism. The bioaccumulation experiment identified the optimal biochar ratio for the Vallisneria natans-biochar system in controlling HOCs in aquaculture products. Analyses included final accumulation concentrations in benthic organisms, changes in freely-dissolved concentrations in aquaculture sediment, and a mass balance calculation to explore key factors in their removal from the system. Results indicated that the Vallisneria natans-1.5% biochar composite system achieved optimal control of HOCs in sediment and aquaculture products. Biochar addition to the sediment in the composite system demonstrated a "promotion with low addition, inhibition with high addition" effect on Vallisneria natans growth. Notably, the addition of 1.5% biochar (VN1.5 group) significantly promoted the growth of Vallisneria natans leaves and roots. Comparing the final pollutant proportions in different environmental media, concentrations in water (0.20%-1.8%), clam accumulation (0.032%-0.11%), and plant absorption (0.10%-0.44%) constituted a minimal portion of the overall pollutant load in the system. The majority of pollutants (24%-65%) were degraded in the aquaculture environment, with microbial degradation likely playing a predominant role. Bacterial phyla, particularly Proteobacteria and Firmicutes, were identified as potential direct contributors to pollutant degradation in the Vallisneria natans-biochar system.},
}
@article {pmid38696025,
year = {2024},
author = {Xiao, Y and Luan, H and Lu, S and Xing, M and Guo, C and Qian, R and Xiao, X},
title = {Correction: Toxic effects of atmospheric deposition in mining areas on wheat seedlings.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {6},
pages = {199},
doi = {10.1007/s10653-024-01986-5},
pmid = {38696025},
issn = {1573-2983},
}
@article {pmid38689759,
year = {2024},
author = {Falk, S and Poole, O and , and , and , and , and , and , and , },
title = {The genome sequence of a conopid fly, Myopa testacea (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {99},
pmid = {38689759},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Myopa testacea (conopid fly; Arthropoda; Insecta; Diptera; Conopidae). The genome sequence is 243.3 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,472 protein coding genes.},
}
@article {pmid38688803,
year = {2024},
author = {Binion, KE and Perreira, KM and Villa Torres, L and White, JT and Hernandez, GC and Kaefer, M and Misseri, R and Ross, S and Chan, KH},
title = {A multi-site cultural and linguistic adaptation of a hypospadias decision aid for Latinx communities.},
journal = {Journal of pediatric urology},
volume = {20},
number = {4},
pages = {674.e1-674.e9},
pmid = {38688803},
issn = {1873-4898},
support = {UL1 TR002489/TR/NCATS NIH HHS/United States ; UM1 TR004406/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Male ; *Hispanic or Latino/psychology ; *Hypospadias/ethnology/surgery/psychology ; *Decision Support Techniques ; Focus Groups ; Parents/psychology ; Child, Preschool ; Female ; Language ; Linguistics ; Cultural Characteristics ; },
abstract = {INTRODUCTION: Latinx, Spanish-speaking (LSS) patients are more likely to experience decisional conflict and regret about healthcare decisions than non-Hispanic, white, English-speaking patients.<br><br>OBJECTIVE: To adapt the Hypospadias Hub (Hub), a rigorously developed and tested web-based decision aid (DA), for LSS parents.<br><br>METHODS: Guided by the Ecological Validity Model (EVM), a heuristic framework was followed to culturally adapt the Hub (see Extended Summary Figure). In stage 1, recommendations were obtained from a focus group with members of the institution's Latinx Community Review Board (Latinx CRB) and semi-structured interviews with pediatricians with Latinx-focused practices. In stage 2, preliminary cultural modifications were made, the Hub was translated into Spanish, and a second focus group with the Latinx CRB was convened to review the revised Hub. In stage 3, semi-structured interviews with LSS parents of healthy boys (i.e., without hypospadias)&#xa0;&#x2264;&#xa0;5 years old were conducted to identify any cultural adaptations and/or usability issues regarding the revised Hub. In stage 4, based on parents' feedback, final revisions to the Hub were made. The focus groups and parent interviews were conducted in Spanish; then, the recordings were professionally transcribed in Spanish and translated into English. Interviews with pediatricians were conducted in English; then, the recordings were professionally transcribed. Three coders conducted a qualitative content analysis to identify areas for revision. Changes were applied iteratively.<br><br>RESULTS: Participants included 3 Latinx CRB members (2 women, 1 did not disclose gender; mean age&#xa0;=&#xa0;48.3, SD&#xa0;=&#xa0;21.2), 3 non-Latinx pediatricians (2 women, 1 man; mean age&#xa0;=&#xa0;49.6, SD&#xa0;=&#xa0;9.1), and 5 Latinx mothers (mean age&#xa0;=&#xa0;34.0, SD&#xa0;=&#xa0;1.26). Participants recommended: 1) featuring video testimonials from Latinx families or including Spanish voice-overs/subtitles; 2) diversifying racial/ethnic/geographic representation and including extended families in photographs/illustrations; 3) adding information about health insurance coverage and circumcision, 4) reassuring parents that the condition is not their fault, 5) considering cultural values (e.g., reliance on expert advice), and 6) clarifying medical terminology. Feedback related to seven EVM dimensions: concepts, content, context, goals, language, metaphors, and methods.<br><br>DISCUSSION: Participants perceived the Hub to be informative in guiding parents' treatment decisions. Revisions were reasonable and acceptable for a linguistic and cultural adaptation for LSS parents.<br><br>CONCLUSIONS: We identified and implemented preliminary cultural modifications to the Hub and applied user-centered design methods to test and revise the website. The product is a culturally appropriate DA for LSS parents. Next, English and Spanish-versions of the Hub will be tested in a randomized controlled trial.},
}
@article {pmid38688387,
year = {2024},
author = {Hu, YL and Liu, Y and Fu, W and Yang, H},
title = {Efficiency and mechanism of enhanced norfloxacin removal using amorphous TiO2-modified biochar.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {351},
number = {},
pages = {124027},
doi = {10.1016/j.envpol.2024.124027},
pmid = {38688387},
issn = {1873-6424},
mesh = {*Charcoal/chemistry ; *Titanium/chemistry ; *Norfloxacin/chemistry ; Adsorption ; *Water Pollutants, Chemical/chemistry ; Anti-Bacterial Agents/chemistry ; Wastewater/chemistry ; Waste Disposal, Fluid/methods ; },
abstract = {Inadequate treatment of antibiotic-contaminated wastewater, including compounds such as norfloxacin (NOR), poses a substantial treat to both ecological safety and human well-being. An innovative approach was devised to address NOR pollution using amorphous TiO2 modified biochar (A-TiO2/BC) prepared via sol-gel impregnation. The resultant had a commendably specific surface area of 131.8 m[2]/g[-1], which was 1.91 times more than the original surface area of unmodified BC. A-TiO2/BC also exhibited abundant hydroxyl and oxygen-containing functional groups, thereby provided adequately active sites for NOR adsorption. R[2] values obtained from NOR isotherm adsorption models descended in order of Freundlich < Temkin < Sips < Langmuir, which indicated that the NOR removal by A-TiO2/BC mainly complied with monolayer adsorption accompanied by heterogeneous surface adsorption. Under weakly acidic conditions, NOR adsorption benefits from the synergistic physicochemical interactions of A-TiO2 and BC. Notably, A-TiO2/BC demonstrated an impressive NOR adsorption capacity of up to 78.14 mg g[-1], with a dosage of 20 mg L[-1] at 25 °C under pH 6. Such A-TiO2 modified biochar thus presents a promising alternative for NOR removal.},
}
@article {pmid38688113,
year = {2024},
author = {Ghani, MI and Yi, B and Rehmani, MS and Wei, X and Siddiqui, JA and Fan, R and Liu, Y and El-Sheikh, MA and Chen, X and Ahmad, P},
title = {Potential of melatonin and Trichoderma harzianum inoculation in ameliorating salt toxicity in watermelon: Insights into antioxidant system, leaf ultrastructure, and gene regulation.},
journal = {Plant physiology and biochemistry : PPB},
volume = {211},
number = {},
pages = {108639},
doi = {10.1016/j.plaphy.2024.108639},
pmid = {38688113},
issn = {1873-2690},
mesh = {*Citrullus/microbiology/drug effects/metabolism ; *Melatonin/pharmacology ; *Antioxidants/metabolism ; *Plant Leaves/drug effects/metabolism ; *Gene Expression Regulation, Plant/drug effects ; Salt Stress ; Hypocreales ; Photosynthesis/drug effects ; Oxidative Stress/drug effects ; },
abstract = {Melatonin (MT) is an extensively studied biomolecule with dual functions, serving as an antioxidant and a signaling molecule. Trichoderma Harzianum (TH) is widely recognized for its effectiveness as a biocontrol agent against many plant pathogens. However, the interplay between seed priming and MT (150 μm) in response to NaCl (100 mM) and its interaction with TH have rarely been investigated. This study aimed to evaluate the potential of MT and TH, alone and in combination, to mitigate salt stress (SS) in watermelon plants. The findings of this study revealed a significant decline in the morphological, physiological, and biochemical indices of watermelon seedlings exposed to SS. However, MT and TH treatments reduced the negative impact of salt stress. The combined application of MT and TH exerted a remarkable positive effect by increasing the growth, photosynthetic and gas exchange parameters, chlorophyll fluorescence indices, and ion balance (decreasing Na[+] and enhancing K[+]). MT and TH effectively alleviated oxidative injury by inhibiting hydrogen peroxide formation in saline and non-saline environments, as established by reduced lipid peroxidation and electrolyte leakage. Moreover, oxidative injury induced by SS on the cells was significantly mitigated by regulation of the antioxidant system, AsA-GSH-related enzymes, the glyoxalase system, augmentation of osmolytes, and activation of several genes involved in the defense system. Additionally, the reduction in oxidative damage was examined by chloroplast integrity via transmission electron microscopy (TEM). Overall, the results of this study provide a promising contribution of MT and TH in safeguarding the watermelon crop from oxidative damage induced by salt stress.},
}
@article {pmid38686023,
year = {2024},
author = {Boyes, D and Blaxter, ML and , and , and , and , and , and , },
title = {The genome sequence of the Tipped Oak Case-bearer, Coleophora flavipennella (Duponchel 1843).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {3},
pmid = {38686023},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Coleophora flavipennella (the Tipped Oak Case-bearer; Arthropoda; Insecta; Lepidoptera; Coleophoridae). The genome sequence is 989.3 megabases in span. Most of the assembly is scaffolded into 57 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.77 kilobases in length.},
}
@article {pmid38684755,
year = {2024},
author = {Yang, P and Huang, G and Li, Y and Yu, L and Yin, Z and Li, Q},
title = {Identification of PANoptosis-related biomarkers and analysis of prognostic values in head and neck squamous cell carcinoma.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9824},
pmid = {38684755},
issn = {2045-2322},
mesh = {Humans ; *Squamous Cell Carcinoma of Head and Neck/genetics/pathology/metabolism/mortality ; *Biomarkers, Tumor/metabolism/genetics ; Prognosis ; *Head and Neck Neoplasms/genetics/pathology/metabolism ; *Gene Expression Regulation, Neoplastic ; Female ; Male ; Computational Biology/methods ; Gene Expression Profiling ; Fas-Associated Death Domain Protein/metabolism/genetics ; Lymphatic Metastasis ; },
abstract = {PANoptosis plays a crucial role in cancer initiation and progression. However, the roles of PANoptosis-related genes (PARGs) in the prognosis and immune landscape of head and neck squamous cell carcinoma (HNSCC) remain unclear. Integrated bioinformatics analyses based on the data of HNSCC patients in the TCGA database were conducted. We extracted 48 PARGs expression profile and then conducted differentially expressed analysis, following building a Cox model to predict the survival of HNSCC patients. Subsequently, the relationships between the risk score, immune landscape, chemo-, and immune-therapy responses were analyzed, respectively. Moreover, we investigated the prognostic value, and further predicted the pathways influenced by PARGs. Finally, we identified the biological function of crucial PARGs. A total of 18 differentially expressed PARGs were identified in HNSCC, and a Cox model including CASP8, FADD, NLRP1, TNF, and ZBP1 was constructed, which showed that the risk score was associated with the prognosis as well as immune infiltration of HNSCC patients, and the risk score could be regarded as an independent biomarker. Additionally, patients with high-risk score might be an indicator of lymph node metastasis and advanced clinical stage. High-risk scores also contributed to the chemotherapy resistance and immune escape of HNSCC patients. In addition, FADD and ZBP1 played a crucial role in various cancer-related pathways, such as the MAPK, WNT, and MTOR signaling pathways. On the other hand, we suggested that FADD facilitated the progression and 5-fluorouracil (5-FU) resistance of HNSCC cells. A signature based on PANoptosis showed great predictive power for lymph node metastasis and advanced stage, suggesting that the risk score might be an independent prognostic biomarker for HNSCC. Meanwhile, FADD, identified as a prognostic biomarker, may represent an effective therapeutic target for HNSCC.},
}
@article {pmid38684726,
year = {2024},
author = {Poquérusse, J and Brown, CL and Gaillard, C and Doughty, C and Dalén, L and Gallagher, AJ and Wooller, M and Zimov, N and Church, GM and Lamm, B and Hysolli, E},
title = {Assessing contemporary Arctic habitat availability for a woolly mammoth proxy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9804},
pmid = {38684726},
issn = {2045-2322},
mesh = {Arctic Regions ; *Ecosystem ; Animals ; *Mammoths ; *Biomass ; Alaska ; Carbon/analysis/metabolism ; },
abstract = {Interest continues to grow in Arctic megafaunal ecological engineering, but, since the mass extinction of megafauna ~ 12-15 ka, key physiographic variables and available forage continue to change. Here we sought to assess the extent to which contemporary Arctic ecosystems are conducive to the rewilding of megaherbivores, using a woolly mammoth (M. primigenius) proxy as a model species. We first perform a literature review on woolly mammoth dietary habits. We then leverage Oak Ridge National Laboratories Distributive Active Archive Center Global Aboveground and Belowground Biomass Carbon Density Maps to generate aboveground biomass carbon density estimates in plant functional types consumed by the woolly mammoth at 300 m resolution on Alaska's North Slope. We supplement these analyses with a NASA Arctic Boreal Vulnerability Experiment dataset to downgrade overall biomass estimates to digestible levels. We further downgrade available forage by using a conversion factor representing the relationship between total biomass and net primary productivity (NPP) for arctic vegetation types. Integrating these estimates with the forage needs of woolly mammoths, we conservatively estimate Alaska's North Slope could support densities of 0.0-0.38 woolly mammoth km[-2] (mean 0.13) across a variety of habitats. These results may inform innovative rewilding strategies.},
}
@article {pmid38683839,
year = {2024},
author = {Ma, R and Li, C and Gao, A and Jiang, N and Li, J and Hu, W and Feng, X},
title = {Tick species diversity and potential distribution alternation of dominant ticks under different climate scenarios in Xinjiang, China.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {4},
pages = {e0012108},
pmid = {38683839},
issn = {1935-2735},
mesh = {*Ticks/classification ; *Tick-Borne Diseases/epidemiology/parasitology ; China/epidemiology ; *Datasets as Topic ; Biodiversity ; Animal Distribution ; Humans ; Animals ; Climate Change ; },
abstract = {Ticks are a hematophagous parasite and a vector of pathogens for numerous human and animal diseases of significant importance. The expansion of tick distribution and the increased risk of tick-borne diseases due to global climate change necessitates further study of the spatial distribution trend of ticks and their potential influencing factors. This study constructed a dataset of tick species distribution in Xinjiang for 60 years based on literature database retrieval and historical data collection (January 1963-January 2023). The distribution data were extracted, corrected, and deduplicated. The dominant tick species were selected for analysis using the MaxEnt model to assess their potential distribution in different periods under the current and BCC-CSM2.MR mode scenarios. The results indicated that there are eight genera and 48 species of ticks in 108 cities and counties of Xinjiang, with Hyalomma asiaticum, Rhipicephalus turanicus, Dermacentor marginatus, and Haemaphysalis punctatus being the top four dominant species. The MaxEnt model analysis revealed that the suitability areas of the four dominant ticks were mainly distributed in the north of Xinjiang, in areas such as Altay and Tacheng Prefecture. Over the next four periods, the medium and high suitable areas within the potential distribution range of the four tick species will expand towards the northwest. Additionally, new suitability areas will emerge in Altay, Changji Hui Autonomous Prefecture, and other local areas. The 60-year tick dataset in this study provides a map of preliminary tick distribution in Xinjiang, with a diverse array of tick species and distribution patterns throughout the area. In addition, the MaxEnt model revealed the spatial change characteristics and future distribution trend of ticks in Xinjiang, which can provide an instrumental data reference for tick monitoring and tick-borne disease risk prediction not only in the region but also in other countries participating in the Belt and Road Initiative.},
}
@article {pmid38683244,
year = {2024},
author = {Bai, Y and Song, K and Gao, M and Ma, J and Zhou, Y and Liu, H and Zeng, H and Wang, J and Zheng, X},
title = {Using multi-omics to explore the effect of Bacillus velezensis SAAS-63 on resisting nutrient stress in lettuce.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {313},
pmid = {38683244},
issn = {1432-0614},
mesh = {*Bacillus/metabolism/genetics ; *Lactuca/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Nutrients/metabolism ; *Stress, Physiological ; Plant Roots/microbiology ; Microbiota ; Multiomics ; },
abstract = {To avoid the unreasonable use of chemical fertilizer, an environmentally friendly means of improving soil fertility is required. This study explored the role of the plant growth-promoting rhizosphere bacteria (PGPR) strain Bacillus velezensis SAAS-63 in improving nutrient stress in lettuce. Compared with no inoculation, B. velezensis SAAS-63 inoculants exhibited significantly increased fresh weight, root length, and shoot height under nutrient deficiency, as well as improved antioxidant activities and proline contents. The exogenous addition of B. velezensis SAAS-63 also significantly increased the accumulation of macroelements and micronutrients in lettuce. To elucidate the resistance mechanisms induced by B. velezensis SAAS-63 under nutrient stress, high-throughput sequencing and multi-omics analysis were performed. Inoculation with B. velezensis SAAS-63 altered the microbial community of the rhizosphere and increased the relative abundances of Streptomyces, Actinoallomurus, Verrucomicrobia, and Chloroflexi. It is worth noting that the inoculant SAAS-63 can affect plant rhizosphere metabolism. The inoculant changed the metabolic flow of phenylpropanoid metabolic pathway under nutrient deficiency and promoted phenylalanine to participate more in the synthesis of lignin precursors and coumarin substances by inhibiting the synthesis of flavone and isoflavone, thus improving plant resistance. This study showed that the addition of inoculant SAAS-63 could help plants recruit microorganisms to decompose and utilize trehalose and re-established the carbon metabolism of the plant rhizosphere. Additionally, microbes were found to be closely related to the accumulation of metabolites based on correlation analysis. The results indicated that the addition of PGPRs has an important role in regulating soil rhizosphere microbes and metabolism, providing valuable information for understanding how PGPRs affect complex biological processes and enhance plant adaptation to nutrient deficiency. KEY POINTS: • Inoculation with SAAS-63 significantly promoted plant growth under nutrient-deficient conditions • Inoculation with SAAS-63 affected rhizosphere microbial diversity and community structure • Inoculation with SAAS-63 affected plant rhizosphere metabolism and induced plants to synthesize substances that resist stress.},
}
@article {pmid38680650,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Crescent Bell, Epinotia bilunana (Haworth, 1811).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {163},
pmid = {38680650},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Epinotia bilunana (the Crescent Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 659.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.},
}
@article {pmid38677227,
year = {2024},
author = {Alves, RA and Santos, MMD and Rudke, AP and Francisquetti Venturin, PR and Martins, JA},
title = {Site selection for nature-based solutions for stormwater management in urban areas: An approach combining GIS and multi-criteria analysis.},
journal = {Journal of environmental management},
volume = {359},
number = {},
pages = {120999},
doi = {10.1016/j.jenvman.2024.120999},
pmid = {38677227},
issn = {1095-8630},
mesh = {*Geographic Information Systems ; Brazil ; *Conservation of Natural Resources/methods ; *Rain ; Ecosystem ; Sustainable Development ; },
abstract = {In recent years, particularly following the definition of the UN Sustainable Development Goals (SDGs) for 2030, Nature-Based Solutions (NBS) have gained considerable attention, capturing the interest of both the scientific community and policymakers committed to addressing urban environmental issues. However, the need for studies to guide decision-makers in identifying suitable locations for NBS implementation within urban stormwater management is evident. To address this gap, the present study employs a methodological approach grounded in multi-criteria analysis integrated with Geographic Information Systems (GIS) to identify areas with potential for NBS implementation. In this process, ten NBS were proposed and tested in the drainage area of a shallow tropical urban lake in Londrina, southern Brazil. Additionally, the study investigates areas hosting lower-income populations, a relevant aspect for public managers given the diverse economic subsidies required to implement NBS. Furthermore, the study incorporates a preliminary analysis that evaluates the potential ecosystem benefits to determine the most suitable NBS for a specific site. The result shows that all the ten analyzed NBS were deemed suitable for the study area. Rain barrels had the highest percentage coverage in the study area (37.1%), followed by tree pits (27.9%), and rain gardens (25.4%). Despite having the highest distribution in the basin area, rain barrels exhibited only moderate ecosystem benefits, prompting the prioritization of other NBS with more significant ecological advantages in the final integrated map. In summary, the methodology proposed showed to be a robust approach to selecting optimal solutions in densely populated urban areas.},
}
@article {pmid38672746,
year = {2024},
author = {Bakacsy, L and Kardos, LV and Szepesi, &#xc1; and Nagy, KN and Vasas, A and Feigl, G},
title = {Investigation of the Allelopathic Effect of Two Invasive Plant Species in Rhizotron System.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {38672746},
issn = {2075-1729},
support = {FK129061//National Research, Development and Innovation Office (Hungary)/ ; },
abstract = {A key question in plant invasion biology is why invasive plants are more competitive in their introduced habitat than in their native habitat. Studies show that invasive species exhibit allelopathy, influencing other plants by releasing chemicals. Research on allelopathy uses in vitro tests, investigating effects on seed germination and seedling development. Although soil plays a role in modifying allelopathic effects, observations with soil are rare and almost nothing is known about the root development of test plants developing in soil and the effects of allelopathic compounds on root architecture. Our study evaluates the allelopathic effects of false indigo-bush (Amorpha fruticosa L.) and common milkweed (Asclepias syriaca L.) on oilseed rape growth as a model plant. The rhizotron system was used to study the effect of morphology and root architecture. Leaf-soil mixtures at 0.5%, 1%, and 5% concentrations were used. Shoot and root development was strongly inhibited at 5%. But there was no difference between the allelopathy of the two species, and the application of lower concentrations did not show any effect, demonstrating that soil has a significant modifying effect on their allelopathy. Our results highlight that the development of roots growing in the soil is also worth investigating in connection with allelopathy, which can strengthen the ecological importance of allelochemicals during successful invasions.},
}
@article {pmid38670119,
year = {2024},
author = {Atağ, G and Kaptan, D and Yüncü, E and Başak Vural, K and Mereu, P and Pirastru, M and Barbato, M and Leoni, GG and Güler, MN and Er, T and Eker, E and Yazıcı, TD and Kılıç, MS and Altınışık, NE and Çelik, EA and Morell Miranda, P and Dehasque, M and Floridia, V and Götherström, A and Bilgin, CC and Togan, &#x130; and Günther, T and Özer, F and Hadjisterkotis, E and Somel, M},
title = {Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages.},
journal = {Genome biology and evolution},
volume = {16},
number = {5},
pages = {},
pmid = {38670119},
issn = {1759-6653},
support = {/ERC_/European Research Council/International ; 772390//European Union's Horizon 2020 research and innovation programme/ ; //Scientific and Technological Research Council of Turkey/ ; //National Scholarship Programme/ ; //Swedish Research Council Vetenskapsr&#xe5;det/ ; //Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 772390/ERC_/European Research Council/International ; },
mesh = {Animals ; *Endangered Species ; Sheep/genetics ; *Sheep, Domestic/genetics ; Genome ; Genetic Variation ; },
abstract = {Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.},
}
@article {pmid38668970,
year = {2024},
author = {Muthye, V and Lavrov, DV},
title = {Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2757},
number = {},
pages = {239-257},
pmid = {38668970},
issn = {1940-6029},
mesh = {Animals ; *Ctenophora/metabolism/genetics ; *Proteome ; *Mitochondrial Proteins/metabolism/genetics ; Computational Biology/methods ; Mitochondria/metabolism ; Proteomics/methods ; Software ; },
abstract = {Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.},
}
@article {pmid38668514,
year = {2024},
author = {Li, Q and Yao, S and Wen, H and Li, W and Jin, L and Huang, X},
title = {Improving Lead Phytoremediation Using Endophytic Bacteria Isolated from the Pioneer Plant Ageratina adenophora (Spreng.) from a Mining Area.},
journal = {Toxics},
volume = {12},
number = {4},
pages = {},
pmid = {38668514},
issn = {2305-6304},
support = {2020KY15017//Project for Enhancing Young and Middle-aged Teacher's Research Basis Ability in Colleges of Guangxi/ ; },
abstract = {This study aimed to isolate and characterise endophytic bacteria from the pioneer plant Ageratina adenophora in a mining area. Seven strains of metal-resistant endophytic bacteria that belong to five genera were isolated from the roots of A. adenophora. These strains exhibited various plant growth-promoting (PGP) capabilities. Sphingomonas sp. ZYG-4, which exhibited the ability to secrete indoleacetic acid (IAA; 53.2 ± 8.3 mg·L[-1]), solubilize insoluble inorganic phosphates (Phosphate solubilization; 11.2 ± 2.9 mg·L[-1]), and regulate root ethylene levels (1-aminocyclopropane-1-carboxylic acid deaminase activity; 2.87 ± 0.19 µM α-KB·mg[-1]·h[-1]), had the highest PGP potential. Therefore, Sphingomonas sp. ZYG-4 was used in a pot experiment to study its effect on the biomass and Pb uptake of both host (Ageratina adenophora) and non-host (Dysphania ambrosioides) plants. Compared to the uninoculated control, Sphingomonas sp. ZYG-4 inoculation increased the biomass of shoots and roots by 59.4% and 144.4% for A. adenophora and by 56.2% and 57.1% for D. ambrosioides, respectively. In addition, Sphingomonas sp. ZYG-4 inoculation enhanced Pb accumulation in the shoot and root by 268.9% and 1187.3% for A. adenophora, and by 163.1% and 343.8% for D. ambrosioides, respectively, compared to plants without bacterial inoculation. Our research indicates that endophytic bacteria are promising candidates for enhancing plant growth and facilitating microbe-assisted phytoremediation in heavy metal-contaminated soil.},
}
@article {pmid38668506,
year = {2024},
author = {Li, S and Yang, J and Zheng, K and He, S and Liu, Z and Song, S and Zeng, T},
title = {Effective Activation of Peroxymonosulfate by Oxygen Vacancy Induced Musa Basjoo Biochar to Degrade Sulfamethoxazole: Efficiency and Mechanism.},
journal = {Toxics},
volume = {12},
number = {4},
pages = {},
pmid = {38668506},
issn = {2305-6304},
support = {2023M743772//China Postdoctoral Science Foundation/ ; 22276172//National Natural Science Foundation of China/ ; 22076168//National Natural Science Foundation of China/ ; LR21E080001//Zhejiang Provincial Natural Science Foundation of China/ ; RF-B2022005//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; 2023C03132//"Leading Goose" R&amp;D Program of Zhejiang/ ; },
abstract = {Biochar materials have garnered attention as potential catalysts for peroxymonosulfate (PMS) activation due to their cost-effectiveness, notable specific surface area, and advantageous structural properties. In this study, a suite of plantain-derived biochar (MBB-400, MBB-600, and MBB-800), possessing a well-defined pore structure and a substantial number of uniformly distributed active sites (oxygen vacancy, OVs), was synthesized through a facile calcination process at varying temperatures (400, 600, and 800 °C). These materials were designed for the activation of PMS in the degradation of sulfamethoxazole (SMX). Experimental investigations revealed that OVs not only functioned as enriched sites for pollutants, enhancing the opportunities for free radicals ([•]OH/SO4[•-]) and surface-bound radicals (SBRs) to attack pollutants, but also served as channels for intramolecular charge transfer leaps. This role contributed to a reduction in interfacial charge transfer resistance, expediting electron transfer rates with PMS, thereby accelerating the decomposition of pollutants. Capitalizing on these merits, the MBB-800/PMS system displayed a 61-fold enhancement in the conversion rate for SMX degradation compared to inactivated MBB/PMS system. Furthermore, the MBB-800 exhibited less cytotoxicity towards rat pheochromocytoma (PC12) cells. Hence, the straightforward calcination synthesis of MBB-800 emerges as a promising biochar catalyst with vast potential for sustainable and efficient wastewater treatment and environmental remediation.},
}
@article {pmid38666081,
year = {2024},
author = {Omar, KM and Kitundu, GL and Jimoh, AO and Namikelwa, DN and Lisso, FM and Babajide, AA and Olufemi, SE and Awe, OI},
title = {Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17181},
pmid = {38666081},
issn = {2167-8359},
mesh = {Animals ; Cattle ; *Metagenomics ; Kenya/epidemiology ; Uganda/epidemiology ; Tanzania ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genes, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.},
}
@article {pmid38662943,
year = {2024},
author = {Lu, XY and Wu, HP and Ma, H and Li, H and Li, J and Liu, YT and Pan, ZY and Xie, Y and Wang, L and Ren, B and Liu, GK},
title = {Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives.},
journal = {Analytical chemistry},
volume = {96},
number = {20},
pages = {7959-7975},
doi = {10.1021/acs.analchem.4c01639},
pmid = {38662943},
issn = {1520-6882},
abstract = {Spectrum-structure correlation is playing an increasingly crucial role in spectral analysis and has undergone significant development in recent decades. With the advancement of spectrometers, the high-throughput detection triggers the explosive growth of spectral data, and the research extension from small molecules to biomolecules accompanies massive chemical space. Facing the evolving landscape of spectrum-structure correlation, conventional chemometrics becomes ill-equipped, and deep learning assisted chemometrics rapidly emerges as a flourishing approach with superior ability of extracting latent features and making precise predictions. In this review, the molecular and spectral representations and fundamental knowledge of deep learning are first introduced. We then summarize the development of how deep learning assist to establish the correlation between spectrum and molecular structure in the recent 5 years, by empowering spectral prediction (i.e., forward structure-spectrum correlation) and further enabling library matching and de novo molecular generation (i.e., inverse spectrum-structure correlation). Finally, we highlight the most important open issues persisted with corresponding potential solutions. With the fast development of deep learning, it is expected to see ultimate solution of establishing spectrum-structure correlation soon, which would trigger substantial development of various disciplines.},
}
@article {pmid38658779,
year = {2024},
author = {Andrianova, MA and Seplyarskiy, VB and Terradas, M and Sánchez-Heras, AB and Mur, P and Soto, JL and Aiza, G and Borràs, E and Kondrashov, FA and Kondrashov, AS and Bazykin, GA and Valle, L},
title = {Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells.},
journal = {European journal of human genetics : EJHG},
volume = {32},
number = {7},
pages = {837-845},
pmid = {38658779},
issn = {1476-5438},
support = {PID2020-112595RB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&#xf3;n (Spanish Agencia Estatal de Investigaci&#xf3;n)/ ; AGAUR 2017SGR1282; CERCA Program//Government of Catalonia | Departament de Salut, Generalitat de Catalunya/ ; ISCIII-AES-2017 PI17/01082//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; I5127-B//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 429960716//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC Consolidator (771209)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *DNA Polymerase III/genetics/metabolism ; Female ; Male ; Pedigree ; Heterozygote ; Genes, Recessive ; Neoplasms/genetics/pathology ; Mutation ; Germ-Line Mutation ; Adult ; },
abstract = {Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.},
}
@article {pmid38656485,
year = {2024},
author = {Jiménez-Madrigal, JP and Till, BJ and Gatica-Arias, A},
title = {Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2787},
number = {},
pages = {107-122},
pmid = {38656485},
issn = {1940-6029},
mesh = {*Genetic Variation ; *Plants/genetics ; *Genome, Plant ; Software ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Genomics/methods ; },
abstract = {Genetic diversity refers to the variety of genetic traits within a population or a species. It is an essential aspect of both plant ecology and plant breeding because it contributes to the adaptability, survival, and resilience of populations in changing environments. This chapter outlines a pipeline for estimating genetic diversity statistics from reduced representation or whole genome sequencing data. The pipeline involves obtaining DNA sequence reads, mapping the corresponding reads to a reference genome, calling variants from the alignments, and generating an unbiased estimation of nucleotide diversity and divergence between populations. The pipeline is suitable for single-end Illumina reads and can be adjusted for paired-end reads. The resulting pipeline provides a comprehensive approach for aligning and analyzing sequencing data to estimate genetic diversity.},
}
@article {pmid38655208,
year = {2023},
author = {Wu, SH and Ko, JC and Lin, RS and Chang-Yang, CH and Chang, HW},
title = {Evaluating community-wide temporal sampling in passive acoustic monitoring: A comprehensive study of avian vocal patterns in subtropical montane forests.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {1299},
pmid = {38655208},
issn = {2046-1402},
mesh = {Animals ; *Vocalization, Animal/physiology ; *Acoustics ; *Birds/physiology ; *Forests ; Environmental Monitoring/methods ; },
abstract = {BACKGROUND: From passive acoustic monitoring (PAM) recordings, the vocal activity rate (VAR), vocalizations per unit of time, can be calculated and is essential for assessing bird population abundance. However, VAR is subject to influences from a range of factors, including species and environmental conditions. Identifying the optimal sampling design to obtain representative acoustic data for VAR estimation is crucial for research objectives. PAM commonly uses temporal sampling strategies to decrease the volume of recordings and the resources needed for audio data management. Yet, the comprehensive impact of this sampling approach on VAR estimation remains insufficiently explored.<br><br>METHODS: In this study, we used vocalizations extracted from recordings of 12 bird species, taken at 14 PAM stations situated in subtropical montane forests over a four-month period, to assess the impact of temporal sampling on VAR across three distinct scales: short-term periodic, diel, and hourly. For short-term periodic sampling analysis, we employed hierarchical clustering analysis (HCA) and the coefficient of variation (CV). Generalized additive models (GAMs) were utilized for diel sampling analysis, and we determined the average difference in VAR values per minute for the hourly sampling analysis.<br><br>RESULTS: We identified significant day and species-specific VAR fluctuations. The survey season was divided into five segments; the earliest two showed high variability and are best avoided for surveys. Data from days with heavy rain and strong winds showed reduced VAR values and should be excluded from analysis. Continuous recordings spanning at least seven days, extending to 14 days is optimal for minimizing sampling variance. Morning chorus recordings effectively capture the majority of bird vocalizations, and hourly sampling with frequent, shorter intervals aligns closely with continuous recording outcomes.<br><br>CONCLUSIONS: While our findings are context-specific, they highlight the significance of strategic sampling in avian monitoring, optimizing resource utilization and enhancing the breadth of monitoring efforts.},
}
@article {pmid38654647,
year = {2024},
author = {Spake, L and Hassan, A and Schaffnit, SB and Alam, N and Amoah, AS and Badjie, J and Cerami, C and Crampin, A and Dube, A and Kaye, MP and Kotch, R and Liew, F and McLean, E and Munthali-Mkandawire, S and Mwalwanda, L and Petersen, AC and Prentice, AM and Zohora, FT and Watts, J and Sear, R and Shenk, MK and Sosis, R and Shaver, JH},
title = {A practical guide to cross-cultural and multi-sited data collection in the biological and behavioural sciences.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2021},
pages = {20231422},
pmid = {38654647},
issn = {1471-2954},
mesh = {Humans ; *Behavioral Sciences ; *Data Collection/methods ; Cross-Cultural Comparison ; Research Design ; Ecology/methods ; },
abstract = {Researchers in the biological and behavioural sciences are increasingly conducting collaborative, multi-sited projects to address how phenomena vary across ecologies. These types of projects, however, pose additional workflow challenges beyond those typically encountered in single-sited projects. Through specific attention to cross-cultural research projects, we highlight four key aspects of multi-sited projects that must be considered during the design phase to ensure success: (1) project and team management; (2) protocol and instrument development; (3) data management and documentation; and (4) equitable and collaborative practices. Our recommendations are supported by examples from our experiences collaborating on the Evolutionary Demography of Religion project, a mixed-methods project collecting data across five countries in collaboration with research partners in each host country. To existing discourse, we contribute new recommendations around team and project management, introduce practical recommendations for exploring the validity of instruments through qualitative techniques during piloting, highlight the importance of good documentation at all steps of the project, and demonstrate how data management workflows can be strengthened through open science practices. While this project was rooted in cross-cultural human behavioural ecology and evolutionary anthropology, lessons learned from this project are applicable to multi-sited research across the biological and behavioural sciences.},
}
@article {pmid38649162,
year = {2024},
author = {Niimura, Y and Biswa, BB and Kishida, T and Toyoda, A and Fujiwara, K and Ito, M and Touhara, K and Inoue-Murayama, M and Jenkins, SH and Adenyo, C and Kayang, BB and Koide, T},
title = {Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents.},
journal = {Molecular biology and evolution},
volume = {41},
number = {4},
pages = {},
pmid = {38649162},
issn = {1537-1719},
support = {18K06359//JSPS KAKENHI/ ; JPMJAS2017//JST aXis/ ; 1B2020//National Institute of Genetics, NIG-Joint/ ; },
mesh = {Animals ; *Evolution, Molecular ; *Multigene Family ; *Phylogeny ; Receptors, G-Protein-Coupled/genetics ; *Receptors, Odorant/genetics ; Receptors, Pheromone/genetics/metabolism ; *Rodentia/genetics ; Smell/genetics ; Taste/genetics ; *Vomeronasal Organ/metabolism ; },
abstract = {Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.},
}
@article {pmid38648741,
year = {2024},
author = {Crauwels, C and Heidig, SL and Díaz, A and Vranken, WF},
title = {Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {5},
pages = {},
pmid = {38648741},
issn = {1367-4811},
support = {1SE5923N//Research Foundation Flanders/ ; },
mesh = {*Software ; *Proteins/chemistry ; *Sequence Alignment/methods ; *Sequence Analysis, Protein/methods ; Algorithms ; Amino Acid Sequence ; Computational Biology/methods ; Databases, Protein ; },
abstract = {SUMMARY: SIMSApiper is a Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences faster than standard structure-based alignment methods. Structural information can be provided by the user or collected by the pipeline from online resources. Parallelization with sequence identity-based subsets can be activated to significantly speed up the alignment process. Finally, the number of gaps in the final alignment can be reduced by leveraging the position of conserved secondary structure elements.<br><br>The pipeline is implemented using Nextflow, Python3, and Bash. It is publicly available on github.com/Bio2Byte/simsapiper.},
}
@article {pmid38648214,
year = {2024},
author = {Lauber, C and Zhang, X and Vaas, J and Klingler, F and Mutz, P and Dubin, A and Pietschmann, T and Roth, O and Neuman, BW and Gorbalenya, AE and Bartenschlager, R and Seitz, S},
title = {Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.},
journal = {PLoS pathogens},
volume = {20},
number = {4},
pages = {e1012163},
pmid = {38648214},
issn = {1553-7374},
mesh = {Animals ; *Nidovirales/genetics ; *Genome, Viral ; *Coronavirus/genetics/classification ; *Phylogeny ; Vertebrates/virology/genetics ; Fishes/virology ; Evolution, Molecular ; Data Mining ; Nidovirales Infections/virology/genetics ; },
abstract = {Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.},
}
@article {pmid38646766,
year = {2024},
author = {Hu, JY and Liu, LY and Dai, QL and Yang, B and Zhou, WJ},
title = {Evaluation of ecotourism suitability based on AHP-GIS: Taking Xiaoxiangling area of the Giant Panda National Park and the surrounding communities as an example.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {3},
pages = {780-788},
doi = {10.13287/j.1001-9332.202403.020},
pmid = {38646766},
issn = {1001-9332},
mesh = {Animals ; *Conservation of Natural Resources ; China ; *Parks, Recreational ; *Ecosystem ; *Ursidae ; *Geographic Information Systems ; Recreation ; },
abstract = {The primary goal of national parks is to protect ecological environment, but also with the functions of scientific research, education, and recreation. Aiming for the realization of universal sharing, we used the analytic hierarchy process (AHP) to construct an ecotourism suitability evaluation system by selecting four factors, including landscape resources, ecological environment carrying capacity, recreation utilization capacity and social condition, taking Xiaoxiangling area of Giant Panda National Park and the surrounding communities as an example. We evaluated the ecotourism suitability based on GIS, and conducted a questionnaire survey of tourists, to propose suggestions on the functional zoning in terms of ecotourism suitability and subjective choice preferences of tourists. The results showed that the ecotourism suitability of the evaluation area could be classified into five levels. The most suitable areas were located nearby the natural landscape resources and far away from the core conservation area, and the least suitable areas distributed at the edge of the core conservation area. According to the results of suitability analysis, the evaluation area was divided into suitable development area, moderate development area, and restricted development area. Combined with the tourist preferences, we divided the recreational activities in the evaluation area into seven activities, namely, ecotourism, eco-camping, science education, leisure vacation, agricultural and animal husbandry culture experience, eco-education, and mountain adventure. These findings could help provide suitable services for different tourists and offer reference for the ecotourism developmental planning of the Xiaoxiangling area of the Giant Panda National Park.},
}
@article {pmid38646687,
year = {2024},
author = {Filatov, DA},
title = {ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13962},
pmid = {38646687},
issn = {1755-0998},
support = {BB/P009808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Software ; *Polymorphism, Genetic ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)-a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.},
}
@article {pmid38644930,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Scalloped Oak, Crocallis elinguaria (Linneas, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {426},
pmid = {38644930},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Crocallis elinguaria (the Scalloped Oak; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 430.4 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,741 protein coding genes.},
}
@article {pmid38644519,
year = {2024},
author = {Chen, J and Lin, JJ and Wang, W and Huang, H and Pan, Z and Ye, G and Dong, S and Lin, Y and Lin, C and Huang, Q},
title = {EV-COMM: A database of interspecies and intercellular interactions mediated by extracellular vesicles.},
journal = {Journal of extracellular vesicles},
volume = {13},
number = {4},
pages = {e12442},
pmid = {38644519},
issn = {2001-3078},
support = {2021J06037//Fujian Provincial Department of Science and Technology/ ; 2022T3063//Fujian Provincial Department of Science and Technology/ ; 32161143016//National Natural Science Foundation of China/ ; 42177362//National Natural Science Foundation of China/ ; 42250410328//National Natural Science Foundation of China/ ; CAS-WX2021SF-0302//Chinese Academy of Sciences/ ; NO. NBSDC-DB-21//National Basic Science Data Center "Environment Health DataBase"/ ; },
mesh = {Animals ; Humans ; *Cell Communication ; Databases, Factual ; *Extracellular Vesicles/metabolism ; MicroRNAs/metabolism/genetics ; },
abstract = {Intra- and inter-organismal interactions play a crucial role in the maintenance and function of individuals, as well as communities. Extracellular vesicles (EVs) have been identified as effective mediators for the communication both within and between species. They can carry and transport molecular cargoes to transmit biological messages. Several databases (ExoBCD, ExoCarta, EVpedia, EV-TRACK, Vesiclepedia) complied the cargoes information including DNA, RNA, protein, lipid and metabolite associated with EVs. Databases that refer to the complete records on both donor and recipient information are warranted to facilitate the understanding of the interaction across cells and species. In this study, we developed a database that compiled the records equipped with a structured process of EV-mediated interaction. The sources of donor and recipient were classified by cell type, tissues/organs and species, thus providing an extended knowledge of cell-cell, species-species interaction. The isolation and identification methods were presented for assessing the quality of EVs. Information on functional cargoes was included, where microRNA was linked to a prediction server to broaden its potential effects. Physiological and pathological context was marked to show the environment where EVs functioned. At present, a total of 1481 data records in our database, including 971 cell-cell interactions belonging to more than 40 different tissues/organs, and 510 cross-species records. The database provides a web interface to browse, search, visualize and download the interaction records. Users can search for interactions by selecting the context of interest or specific cells/species types, as well as functional cargoes. To the best of our knowledge, the database is the first comprehensive database focusing on interactions between donor and recipient cells or species mediated by EVs, serving as a convenient tool to explore and validate interactions. The Database, shorten as EV-COMM (EV mediated communication) is freely available at http://sdc.iue.ac.cn/evs/list/ and will be continuously updated.},
}
@article {pmid38643978,
year = {2024},
author = {Rosbakh, S and Carta, A and Fernández-Pascual, E and Phartyal, SS and Dayrell, RLC and Mattana, E and Saatkamp, A and Vandelook, F and Baskin, JM and Baskin, CC},
title = {Large dataset analyses advance knowledge of seed ecology and evolutionary biology.},
journal = {The New phytologist},
volume = {242},
number = {6},
pages = {2399-2400},
doi = {10.1111/nph.19752},
pmid = {38643978},
issn = {1469-8137},
support = {//Novo Nordisk Foundation/ ; },
mesh = {*Biological Evolution ; *Seeds/physiology/genetics ; *Ecology ; Datasets as Topic ; },
}
@article {pmid38643126,
year = {2024},
author = {Xiao, W and Chen, YL and Du, LY and Wu, J and Wang, Z and Mao, B and Wen, FQ and Gibson, PG and McDonald, VM and Yu, H and Fu, JJ},
title = {Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations.},
journal = {Respiratory research},
volume = {25},
number = {1},
pages = {173},
pmid = {38643126},
issn = {1465-993X},
support = {No.82100046//National Natural Science Foundation of China/ ; No.81870014//National Natural Science Foundation of China/ ; 2023NSFSC1460//Sichuan Science and Technology Program of China/ ; 2020YFS0145//Sichuan Science and Technology Program of China/ ; },
mesh = {Humans ; *Dysbiosis ; *Pulmonary Disease, Chronic Obstructive/drug therapy ; Lung ; Haemophilus ; Sputum/microbiology ; Disease Progression ; },
abstract = {RATIONALE: Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome.<br><br>OBJECTIVES: To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes.<br><br>METHODS: We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data.<br><br>RESULTS: Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (&#x2265;&#x2009;2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota.<br><br>CONCLUSIONS: Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.},
}
@article {pmid38632407,
year = {2024},
author = {Maes, SL and Dietrich, J and Midolo, G and Schwieger, S and Kummu, M and Vandvik, V and Aerts, R and Althuizen, IHJ and Biasi, C and Björk, RG and Böhner, H and Carbognani, M and Chiari, G and Christiansen, CT and Clemmensen, KE and Cooper, EJ and Cornelissen, JHC and Elberling, B and Faubert, P and Fetcher, N and Forte, TGW and Gaudard, J and Gavazov, K and Guan, Z and Guðmundsson, J and Gya, R and Hallin, S and Hansen, BB and Haugum, SV and He, JS and Hicks Pries, C and Hovenden, MJ and Jalava, M and Jónsdóttir, IS and Juhanson, J and Jung, JY and Kaarlejärvi, E and Kwon, MJ and Lamprecht, RE and Le Moullec, M and Lee, H and Marushchak, ME and Michelsen, A and Munir, TM and Myrsky, EM and Nielsen, CS and Nyberg, M and Olofsson, J and Óskarsson, H and Parker, TC and Pedersen, EP and Petit Bon, M and Petraglia, A and Raundrup, K and Ravn, NMR and Rinnan, R and Rodenhizer, H and Ryde, I and Schmidt, NM and Schuur, EAG and Sjögersten, S and Stark, S and Strack, M and Tang, J and Tolvanen, A and Töpper, JP and Väisänen, MK and van Logtestijn, RSP and Voigt, C and Walz, J and Weedon, JT and Yang, Y and Ylänne, H and Björkman, MP and Sarneel, JM and Dorrepaal, E},
title = {Environmental drivers of increased ecosystem respiration in a warming tundra.},
journal = {Nature},
volume = {629},
number = {8010},
pages = {105-113},
pmid = {38632407},
issn = {1476-4687},
mesh = {Arctic Regions ; Carbon/metabolism/analysis ; Carbon Cycle ; Datasets as Topic ; *Ecosystem ; *Global Warming ; Hydrogen-Ion Concentration ; Nitrogen/metabolism/analysis ; Plants/metabolism ; Seasons ; Soil/chemistry ; Soil Microbiology ; Temperature ; *Tundra ; Time Factors ; *Cell Respiration ; },
abstract = {Arctic and alpine tundra ecosystems are large reservoirs of organic carbon[1,2]. Climate warming may stimulate ecosystem respiration and release carbon into the atmosphere[3,4]. The magnitude and persistency of this stimulation and the environmental mechanisms that drive its variation remain uncertain[5-7]. This hampers the accuracy of global land carbon-climate feedback projections[7,8]. Here we synthesize 136 datasets from 56 open-top chamber in situ warming experiments located at 28 arctic and alpine tundra sites which have been running for less than 1 year up to 25 years. We show that a mean rise of 1.4 °C [confidence interval (CI) 0.9-2.0 °C] in air and 0.4 °C [CI 0.2-0.7 °C] in soil temperature results in an increase in growing season ecosystem respiration by 30% [CI 22-38%] (n = 136). Our findings indicate that the stimulation of ecosystem respiration was due to increases in both plant-related and microbial respiration (n = 9) and continued for at least 25 years (n = 136). The magnitude of the warming effects on respiration was driven by variation in warming-induced changes in local soil conditions, that is, changes in total nitrogen concentration and pH and by context-dependent spatial variation in these conditions, in particular total nitrogen concentration and the carbon:nitrogen ratio. Tundra sites with stronger nitrogen limitations and sites in which warming had stimulated plant and microbial nutrient turnover seemed particularly sensitive in their respiration response to warming. The results highlight the importance of local soil conditions and warming-induced changes therein for future climatic impacts on respiration.},
}
@article {pmid38632405,
year = {2024},
author = {Swain, A and Woodhouse, A and Fagan, WF and Fraass, AJ and Lowery, CM},
title = {Biogeographic response of marine plankton to Cenozoic environmental changes.},
journal = {Nature},
volume = {629},
number = {8012},
pages = {616-623},
pmid = {38632405},
issn = {1476-4687},
mesh = {Animals ; *Aquatic Organisms/physiology/classification ; Biodiversity ; Biological Evolution ; *Climate Change/history ; Datasets as Topic ; Extinction, Biological ; *Foraminifera/classification/physiology ; History, Ancient ; *Phylogeography ; *Plankton/classification/physiology ; Spatio-Temporal Analysis ; },
abstract = {In palaeontological studies, groups with consistent ecological and morphological traits across a clade's history (functional groups)[1] afford different perspectives on biodiversity dynamics than do species and genera[2,3], which are evolutionarily ephemeral. Here we analyse Triton, a global dataset of Cenozoic macroperforate planktonic foraminiferal occurrences[4], to contextualize changes in latitudinal equitability gradients[1], functional diversity, palaeolatitudinal specialization and community equitability. We identify: global morphological communities becoming less specialized preceding the richness increase after the Cretaceous-Palaeogene extinction; ecological specialization during the Early Eocene Climatic Optimum, suggesting inhibitive equatorial temperatures during the peak of the Cenozoic hothouse; increased specialization due to circulation changes across the Eocene-Oligocene transition, preceding the loss of morphological diversity; changes in morphological specialization and richness about 19 million years ago, coeval with pelagic shark extinctions[5]; delayed onset of changing functional group richness and specialization between hemispheres during the mid-Miocene plankton diversification. The detailed nature of the Triton dataset permits a unique spatiotemporal view of Cenozoic pelagic macroevolution, in which global biogeographic responses of functional communities and richness are decoupled during Cenozoic climate events. The global response of functional groups to similar abiotic selection pressures may depend on the background climatic state (greenhouse or icehouse) to which a group is adapted.},
}
@article {pmid38632210,
year = {2024},
author = {Griesberger, P and Kunz, F and Hackländer, K and Mattsson, B},
title = {Building a decision-support tool to inform sustainability approaches under complexity: Case study on managing wild ruminants.},
journal = {Ambio},
volume = {53},
number = {9},
pages = {1307-1322},
pmid = {38632210},
issn = {1654-7209},
mesh = {Animals ; *Conservation of Natural Resources/methods ; *Animals, Wild ; *Decision Support Techniques ; *Bayes Theorem ; *Ruminants ; Austria ; Decision Making ; },
abstract = {In wildlife management, differing perspectives among stakeholders generate conflicts about how to achieve disparate sustainability goals that include ecological, economic, and sociocultural dimensions. To mitigate such conflicts, decisions regarding wildlife management must be taken thoughtfully. To our knowledge, there exists no integrative modeling framework to inform these decisions, considering all dimensions of sustainability. We constructed a decision-support tool based on stakeholder workshops and a Bayesian decision network to inform management of wild ruminants in the federal state of Lower Austria. We use collaborative decision analysis to compare resource allocations while accounting for trade-offs among dimensions of sustainability. The tool is designed for application by non-technical users across diverse decision-making contexts with particular sets of wildlife management actions, objectives, and uncertainties. Our tool represents an important step toward developing and evaluating a transparent and replicable approach for mitigating wildlife-based conflicts in Europe and beyond.},
}
@article {pmid38630866,
year = {2024},
author = {Ma, L and Hu, Z and Shen, W and Zhang, Y and Wang, G and Chang, B and Lu, J and Cui, Y and Xu, H and Feng, Y and Jin, B and Zhang, X and Wang, L and Lin, J},
title = {Three-dimensional reconstruction and multiomics analysis reveal a unique pattern of embryogenesis in Ginkgo biloba.},
journal = {Plant physiology},
volume = {196},
number = {1},
pages = {95-111},
doi = {10.1093/plphys/kiae219},
pmid = {38630866},
issn = {1532-2548},
support = {5232016//Beijing Municipal Natural Science Foundation/ ; 32000558//National Natural Science Foundation of China/ ; BLX202116//Fundamental Research Funds for the Central Universities/ ; B13007//Program of Introducing Talents of Discipline to Universities/ ; },
mesh = {*Ginkgo biloba/genetics/embryology ; *Seeds/genetics/growth &amp; development ; Imaging, Three-Dimensional/methods ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism/genetics ; X-Ray Microtomography ; Cotyledon/genetics ; Multiomics ; },
abstract = {Ginkgo (Ginkgo biloba L.) is one of the earliest extant species in seed plant phylogeny. Embryo development patterns can provide fundamental evidence for the origin, evolution, and adaptation of seeds. However, the architectural and morphological dynamics during embryogenesis in G. biloba remain elusive. Herein, we obtained over 2,200 visual slices from 3 stages of embryo development using micro-computed tomography imaging with improved staining methods. Based on 3-dimensional (3D) spatiotemporal pattern analysis, we found that a shoot apical meristem with 7 highly differentiated leaf primordia, including apical and axillary leaf buds, is present in mature Ginkgo embryos. 3D rendering from the front, top, and side views showed 2 separate transport systems of tracheids located in the hypocotyl and cotyledon, representing a unique pattern of embryogenesis. Furthermore, the morphological dynamic analysis of secretory cavities indicated their strong association with cotyledons during development. In addition, we identified genes GbLBD25a (lateral organ boundaries domain 25a), GbCESA2a (cellulose synthase 2a), GbMYB74c (myeloblastosis 74c), GbPIN2 (PIN-FORMED 2) associated with vascular development regulation, and GbWRKY1 (WRKYGOK 1), GbbHLH12a (basic helix-loop-helix 12a), and GbJAZ4 (jasmonate zim-domain 4) potentially involved in the formation of secretory cavities. Moreover, we found that flavonoid accumulation in mature embryos could enhance postgerminative growth and seedling establishment in harsh environments. Our 3D spatial reconstruction technique combined with multiomics analysis opens avenues for investigating developmental architecture and molecular mechanisms during embryogenesis and lays the foundation for evolutionary studies of embryo development and maturation.},
}
@article {pmid38629556,
year = {2024},
author = {Dai, WT and Zhang, H and Wu, X and Zhong, M and Duan, GL and Dong, JH and Zhang, PP and Fan, HM},
title = {[Pollution Characteristics and Source Analysis of Soil Heavy Metal in Coal Mine Area near the Yellow River in Shandong].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {5},
pages = {2952-2961},
doi = {10.13227/j.hjkx.202306029},
pmid = {38629556},
issn = {0250-3301},
abstract = {To explore the pollution characteristics and source of soil heavy metal in a coal mine area near the Yellow River in Shandong, the geo-accumulation index method and improved Nemerow pollution index method were used to evaluate the pollution characteristics of soil heavy metal. The absolute principal component-multiple linear regression model (APCS-MLR) was used to quantitatively analyze the source of soil heavy metal, and the spatial distribution of Hg and Cd were analyzed using the Kriging spatial difference method in ArcGIS. The result accuracy of the APCS-MLR model was further verified. The results showed that:The measured contents of soil heavy metal Cu, Zn, Pb, Cr, Cd, Ni, As, and Hg all exceeded the normal site, among which, Hg and Cd exceeded the background values of soil elements in Shandong. The coefficient of variation (CV) of Hg was higher than 0.500, indicating significant spatial heterogeneity. Moreover, the correlation between Hg and other heavy metals was generally low, and the possibility of the same pollution source was small. The results of the geo-accumulation index and improved Nemerow pollution index showed that the overall soil heavy metal pollution was at a moderate level, among which the Hg pollution level was the highest, and its maximum value was at a slanted-heavy pollution level; Cu, Cd, and As in soil caused local pollution, which were at a slanted-light pollution level. Soil heavy metal pollution was closely related to mining activities, rehabilitation, and engineering construction in the coal mine area. The two major pollution sources of soil heavy metal in the research area were the compound source of the parent material and industrial and mining transportation sources (known source 1) and the compound source of atmospheric sedimentation and coal production (known source 2), the contribution rates of which were 76.705% and 16.171%, respectively. The results of the APCS-MLR model were shown to be reliable by analyzing the content distribution of Hg and Cd using the Kriging space difference mode. This research can provide scientific basis for the precise control and improvement of soil heavy metal pollution, ensuring the safety of food and agricultural products and improving the quality of the ecological environment in the coal mine area in the Shandong section of the Yellow River Basin.},
}
@article {pmid38629131,
year = {2024},
author = {Reginato, M and Ordónez-Parra, CA and Messeder, JVS and Brito, VLG and Dellinger, A and Kriebel, R and Marra, C and Melo, L and Cornelissen, T and Fuzessy, L and Sperotto, P and Calderón-Hernández, M and Guerra, TJ and Kopper, C and Mancipe-Murillo, C and Pizo, MA and Posada-Herrera, JM and Hasui, &#xc9; and Silva, WR and Silveira, FAO},
title = {MelastomaTRAITs 1.0: A database of functional traits in Melastomataceae, a large pantropical angiosperm family.},
journal = {Ecology},
volume = {105},
number = {6},
pages = {e4308},
doi = {10.1002/ecy.4308},
pmid = {38629131},
issn = {1939-9170},
support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; FWF P-30669 T-1186//Austrian Science Fund/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Fulbright Association/ ; },
mesh = {*Databases, Factual ; Ecosystem ; *Melastomataceae/physiology/genetics ; },
abstract = {The recent availability of open-access repositories of functional traits has revolutionized trait-based approaches in ecology and evolution. Nevertheless, the underrepresentation of tropical regions and lineages remains a pervasive bias in plant functional trait databases, which constrains large-scale assessments of plant ecology, evolution, and biogeography. Here, we present MelastomaTRAITs 1.0, a comprehensive and updatable database of functional traits for the pantropical Melastomataceae, the ninth-largest angiosperm family with 177 genera and more than 5800 species. Melastomataceae encompass species with a wide diversity of growth forms (herbs, shrubs, trees, epiphytes, and woody climbers), habitats (including tropical forests, savannas, grasslands, and wetlands from sea level to montane areas above the treeline), ecological strategies (from pioneer, edge-adapted and invasive species to shade-tolerant understory species), geographic distribution (from microendemic to continental-wide distribution), reproductive, pollination, and seed dispersal systems. MelastomaTRAITs builds on 581 references, such as taxonomic monographs, ecological research, and unpublished data, and includes four whole-plant traits, six leaf traits, 11 flower traits, 18 fruit traits, and 27 seed traits for 2520 species distributed in 144 genera across all 21 tribes. Most data come from the Neotropics where the family is most species-rich. Miconieae (the largest tribe) contains the highest number of trait records (49.6%) and species (41.1%) records. The trait types with the most information in the database were whole-plant traits, flowers, and leaf traits. With the breadth of functional traits recorded, our database helps to fill a gap in information for tropical plants and will significantly improve our capacity for large-scale trait-based syntheses across levels of organization, plant-animal interactions, regeneration ecology, and thereby support conservation and restoration programs. There are no copyright restrictions on the dataset; please cite this data paper when reusing the data.},
}
@article {pmid38627476,
year = {2024},
author = {Ridley, RS and Conrad, RE and Lindner, BG and Woo, S and Konstantinidis, KT},
title = {Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8798},
pmid = {38627476},
issn = {2045-2322},
support = {2136146//National Science Foundation/ ; },
mesh = {Humans ; *Multiomics ; *Plastics ; Polymers ; Biotransformation ; Biodegradation, Environmental ; },
abstract = {Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.},
}
@article {pmid38627422,
year = {2024},
author = {Hammoud, R and Tognin, S and Smythe, M and Gibbons, J and Davidson, N and Bakolis, I and Mechelli, A},
title = {Smartphone-based ecological momentary assessment reveals an incremental association between natural diversity and mental wellbeing.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7051},
pmid = {38627422},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Smartphone ; *Ecological Momentary Assessment ; Mental Health ; Trees ; Biodiversity ; },
abstract = {Using smartphone-based ecological momentary assessment, this study investigated an association between natural diversity on mental wellbeing. A sample of 1,998 participants completed 41,448 assessments between April 2018 and September 2023. Environments which included a larger range of natural features, such as trees, plants and birdlife (high natural diversity) were associated with greater mental wellbeing than environments including a smaller range of natural features (low natural diversity). There was evidence of a mediating effect of natural diversity on the association between natural environments and mental wellbeing. These results highlight the importance of policies and practices that support richness of biodiversity for public mental health.},
}
@article {pmid38625737,
year = {2024},
author = {Jonathan, J and Barakabitze, AA and Fast, CD and Cox, C},
title = {Machine Learning for Prediction of Tuberculosis Detection: Case Study of Trained African Giant Pouched Rats.},
journal = {Online journal of public health informatics},
volume = {16},
number = {},
pages = {e50771},
pmid = {38625737},
issn = {1947-2579},
abstract = {BACKGROUND: Technological advancement has led to the growth and rapid increase of tuberculosis (TB) medical data generated from different health care areas, including diagnosis. Prioritizing better adoption and acceptance of innovative diagnostic technology to reduce the spread of TB significantly benefits developing countries. Trained TB-detection rats are used in Tanzania and Ethiopia for operational research to complement other TB diagnostic tools. This technology has increased new TB case detection owing to its speed, cost-effectiveness, and sensitivity.<br><br>OBJECTIVE: During the TB detection process, rats produce vast amounts of data, providing an opportunity to identify interesting patterns that influence TB detection performance. This study aimed to develop models that predict if the rat will hit (indicate the presence of TB within) the sample or not using machine learning (ML) techniques. The goal was to improve the diagnostic accuracy and performance of TB detection involving rats.<br><br>METHODS: APOPO (Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling) Center in Morogoro provided data for this study from 2012 to 2019, and 366,441 observations were used to build predictive models using ML techniques, including decision tree, random forest, na&#xef;ve Bayes, support vector machine, and k-nearest neighbor, by incorporating a variety of variables, such as the diagnostic results from partner health clinics using methods endorsed by the World Health Organization (WHO).<br><br>RESULTS: The support vector machine technique yielded the highest accuracy of 83.39% for prediction compared to other ML techniques used. Furthermore, this study found that the inclusion of variables related to whether the sample contained TB or not increased the performance accuracy of the predictive model.<br><br>CONCLUSIONS: The inclusion of variables related to the diagnostic results of TB samples may improve the detection performance of the trained rats. The study results may be of importance to TB-detection rat trainers and TB decision-makers as the results may prompt them to take action to maintain the usefulness of the technology and increase the TB detection performance of trained rats.},
}
@article {pmid38622188,
year = {2024},
author = {Liu, X and Chen, J and Tang, BH and He, L and Xu, Y and Yang, C},
title = {Eco-environmental changes due to human activities in the Erhai Lake Basin from 1990 to 2020.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8646},
pmid = {38622188},
issn = {2045-2322},
support = {42301454//National Natural Science Foundation of China/ ; 42230109//National Natural Science Foundation of China/ ; 42201319//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Lakes ; *Sustainable Development ; Human Activities ; China ; Environmental Monitoring/methods ; },
abstract = {Human activities have increased with urbanisation in the Erhai Lake Basin, considerably impacting its eco-environmental quality (EEQ). This study aims to reveal the evolution and driving forces of the EEQ using water benefit-based ecological index (WBEI) in response to human activities and policy variations in the Erhai Lake Basin from 1990 to 2020. Results show that (1) the EEQ exhibited a pattern of initial degradation, subsequent improvement, further degradation and a rebound from 1990 to 2020, and the areas with poor and fair EEQ levels mainly concentrated around the Erhai Lake Basin with a high level of urbanisation and relatively flat terrain; (2) the EEQ levels were not optimistic in 1990, 1995 and 2015, and areas with poor and fair EEQ levels accounted for 43.41%, 47.01% and 40.05% of the total area, respectively; and (3) an overall improvement in the EEQ was observed in 1995-2000, 2000-2005, 2005-2009 and 2015-2020, and the improvement was most significant in 1995-2000, covering an area of 823.95 km[2] and accounting for 31.79% of the total area. Results also confirmed that the EEQ changes in the Erhai Lake Basin were primarily influenced by human activities and policy variations. Moreover, these results can provide a scientific basis for the formulation and planning of sustainable development policy in the Erhai Lake Basin.},
}
@article {pmid38621404,
year = {2024},
author = {Turtle, L and Elliot, S and Drake, TM and Thorpe, M and Khoury, EG and Greenhalf, W and Hardwick, HE and Leeming, G and Law, A and Oosthuyzen, W and Pius, R and Shaw, CA and Baillie, JK and Openshaw, PJM and Docherty, AB and Semple, MG and Harrison, EM and Palmieri, C and , },
title = {Changes in hospital mortality in patients with cancer during the COVID-19 pandemic (ISARIC-CCP-UK): a prospective, multicentre cohort study.},
journal = {The Lancet. Oncology},
volume = {25},
number = {5},
pages = {636-648},
doi = {10.1016/S1470-2045(24)00107-4},
pmid = {38621404},
issn = {1474-5488},
mesh = {Humans ; *COVID-19/mortality/epidemiology ; *Neoplasms/mortality/therapy ; Male ; Female ; Prospective Studies ; Aged ; Middle Aged ; *Hospital Mortality ; United Kingdom/epidemiology ; *SARS-CoV-2 ; Adult ; Aged, 80 and over ; Pandemics ; },
abstract = {BACKGROUND: Patients with cancer are at greater risk of dying from COVID-19 than many other patient groups. However, how this risk evolved during the pandemic remains unclear. We aimed to determine, on the basis of the UK national pandemic protocol, how factors influencing hospital mortality from COVID-19 could differentially affect patients undergoing cancer treatment. We also examined changes in hospital mortality and escalation of care in patients on cancer treatment during the first 2 years of the COVID-19 pandemic in the UK.<br><br>METHODS: We conducted a prospective cohort study of patients aged older than 19 years and admitted to 306 health-care facilities in the UK with confirmed SARS-CoV-2 infection, who were enrolled in the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol (CCP) across the UK from April 23, 2020, to Feb 28, 2022; this analysis included all patients in the complete dataset when the study closed. The primary outcome was 30-day in-hospital mortality, comparing patients on cancer treatment and those without cancer. The study was approved by the South Central-Oxford C Research Ethics Committee in England (Ref: 13/SC/0149) and the Scotland A Research Ethics Committee (Ref 20/SS/0028), and is registered on the ISRCTN Registry (ISRCTN66726260).<br><br>FINDINGS: 177&#x2008;871 eligible adult patients either with no history of cancer (n=171&#x2008;303) or on cancer treatment (n=6568) were enrolled; 93&#x2008;205 (52&#xb7;4%) were male, 84&#x2008;418 (47&#xb7;5%) were female, and in 248 (13&#xb7;9%) sex or gender details were not specified or data were missing. Patients were followed up for a median of 13 (IQR 6-21) days. Of the 6568 patients receiving cancer treatment, 2080 (31&#xb7;7%) died at 30 days, compared with 30&#x2008;901 (18&#xb7;0%) of 171&#x2008;303 patients without cancer. Patients aged younger than 50 years on cancer treatment had the highest age-adjusted relative risk (hazard ratio [HR] 5&#xb7;2 [95% CI 4&#xb7;0-6&#xb7;6], p<0&#xb7;0001; vs 50-69 years 2&#xb7;4 [2&#xb7;2-2&#xb7;6], p<0&#xb7;0001; 70-79 years 1&#xb7;8 [1&#xb7;6-2&#xb7;0], p<0&#xb7;0001; and >80 years 1&#xb7;5 [1&#xb7;3-1&#xb7;6], p<0&#xb7;0001) but a lower absolute risk (51 [6&#xb7;7%] of 763 patients <50 years died compared with 459 [30&#xb7;2%] of 1522 patients aged >80 years). In-hospital mortality decreased for all patients during the pandemic but was higher for patients on cancer treatment than for those without cancer throughout the study period.<br><br>INTERPRETATION: People with cancer have a higher risk of mortality from COVID-19 than those without cancer. Patients younger than 50 years with cancer treatment have the highest relative risk of death. Continued action is needed to mitigate the poor outcomes in patients with cancer, such as through optimising vaccination, long-acting passive immunisation, and early access to therapeutics. These findings underscore the importance of the ISARIC-WHO pandemic preparedness initiative.<br><br>FUNDING: National Institute for Health Research and the Medical Research Council.},
}
@article {pmid38618197,
year = {2023},
author = {Short, S and Green Etxabe, A and Robinson, A and Spurgeon, D and Kille, P and , and , and , and , },
title = {The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {354},
pmid = {38618197},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lumbricus rubellus (the red compost earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 787.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 33,426 protein coding genes.},
}
@article {pmid38617028,
year = {2024},
author = {Liu, J and He, C and Si, Y and Li, B and Wu, Q and Ni, J and Zhao, Y and Hu, Q and Du, S and Lu, Z and Jin, J and Xu, C},
title = {Toward Better and Healthier Air Quality: Global PM2.5 and O3 Pollution Status and Risk Assessment Based on the New WHO Air Quality Guidelines for 2021.},
journal = {Global challenges (Hoboken, NJ)},
volume = {8},
number = {4},
pages = {2300258},
pmid = {38617028},
issn = {2056-6646},
abstract = {To reduce the high burden of disease caused by air pollution, the World Health Organization (WHO) released new Air Quality Guidelines (AQG) on September 22, 2021. In this study, the daily fine particulate matter (PM2.5) and surface ozone (O3) data of 618 cities around the world is collected from 2019 to 2022. Based on the new AQG, the number of attainment days for daily average concentrations of PM2.5 (≤ 15 µg m[-3]) and O3 (≤ 100 µg m[-3]) is approximately 10% and 90%, respectively. China and India exhibit a decreasing trend in the number of highly polluted days (> 75 µg m[-3]) for PM. Every year over 68% and 27% of cities in the world are exposed to harmful PM2.5 (> 35 µg m[-3]) and O3 (> 100 µg m[-3]) pollution, respectively. Combined with the United Nations Sustainable Development Goals (SDGs), it is found that more than 35% of the world's cities face PM2.5-O3 compound pollution. Furthermore, the exposure risks in these cities (China, India, etc.) are mainly categorized as "High Risk", "Risk", and "Stabilization". In contrast, economically developed cities are mainly categorized as "High Safety", "Safety", and "Deep Stabilization." These findings indicate that global implementation of the WHO's new AQG will minimize the inequitable exposure risk from air pollution.},
}
@article {pmid38616489,
year = {2024},
author = {Bleker, C and Ramšak, &#x17d; and Bittner, A and Podpečan, V and Zagorščak, M and Wurzinger, B and Baebler, &#x160; and Petek, M and Križnik, M and van Dieren, A and Gruber, J and Afjehi-Sadat, L and Weckwerth, W and Županič, A and Teige, M and Vothknecht, UC and Gruden, K},
title = {Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses.},
journal = {Plant communications},
volume = {5},
number = {6},
pages = {100920},
pmid = {38616489},
issn = {2590-3462},
mesh = {*Systems Biology ; *Stress, Physiological ; *Plants/genetics/metabolism ; Plant Physiological Phenomena/genetics ; Signal Transduction/genetics ; Databases, Factual ; },
abstract = {Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.},
}
@article {pmid38616247,
year = {2024},
author = {Kibet, CK and Entfellner, JD and Jjingo, D and de Villiers, EP and de Villiers, S and Wambui, K and Kinyanjui, S and Masiga, D},
title = {Designing and delivering bioinformatics project-based learning in East Africa.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {150},
pmid = {38616247},
issn = {1471-2105},
support = {U2R TW010677/TW/FIC NIH HHS/United States ; U2RTW010677/TW/FIC NIH HHS/United States ; },
mesh = {Humans ; *Learning ; Africa, Eastern ; *COVID-19/epidemiology ; Computational Biology ; Pandemics ; },
abstract = {BACKGROUND: The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its goals and how experiential learning through mini projects enhances the acquisition of skills and collaboration. We continued to learn and grow through honest feedback and evaluation of the program, trainers, and modules, enabling us to provide robust training even during the Coronavirus disease 2019 (COVID-19) pandemic, when we had to redesign the program due to restricted travel and in person group meetings.<br><br>RESULTS: In response to the pandemic, we developed a program to maintain "residential" training experiences and benefits remotely. We had to answer the following questions: What must change to still achieve the RT goals? What optimal platforms should be used? How would we manage connectivity and data challenges? How could we avoid online fatigue? Going virtual presented an opportunity to reflect on the essence and uniqueness of the program and its ability to meet the objective of strengthening bioinformatics skills among the cohorts of students using different delivery approaches. It allowed an increase in the number of participants. Evaluating each program component is critical for improvement, primarily when feedback feeds into the program's continuous amendment. Initially, the participants noted that there were too many modules, insufficient time, and a lack of hands-on training as a result of too much focus on theory. In the subsequent iterations, we reduced the number of modules from 27 to five, created a harmonized repository for the materials on GitHub, and introduced project-based learning through the mini projects.<br><br>CONCLUSION: We demonstrate that implementing a program design through detailed monitoring and evaluation leads to success, especially when participants who are the best fit for the program are selected on an appropriate level of skills, motivation, and commitment.},
}
@article {pmid38614075,
year = {2024},
author = {Breeyear, JH and Mautz, BS and Keaton, JM and Hellwege, JN and Torstenson, ES and Liang, J and Bray, MJ and Giri, A and Warren, HR and Munroe, PB and Velez Edwards, DR and Zhu, X and Li, C and Edwards, TL},
title = {A new test for trait mean and variance detects unreported loci for blood-pressure variation.},
journal = {American journal of human genetics},
volume = {111},
number = {5},
pages = {954-965},
pmid = {38614075},
issn = {1537-6605},
support = {U01 HG006378/HG/NHGRI NIH HHS/United States ; U19 HL065962/HL/NHLBI NIH HHS/United States ; S10 RR025141/RR/NCRR NIH HHS/United States ; R01 HG004517/HG/NHGRI NIH HHS/United States ; TL1 TR002244/TR/NCATS NIH HHS/United States ; U01 HG008672/HG/NHGRI NIH HHS/United States ; U01 HG008684/HG/NHGRI NIH HHS/United States ; U01 HG008679/HG/NHGRI NIH HHS/United States ; RC2 GM092618/GM/NIGMS NIH HHS/United States ; P50 GM115305/GM/NIGMS NIH HHS/United States ; U01 HG006379/HG/NHGRI NIH HHS/United States ; U01 HG008664/HG/NHGRI NIH HHS/United States ; U01 HG008701/HG/NHGRI NIH HHS/United States ; U01 HG008676/HG/NHGRI NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; F31 EY033663/EY/NEI NIH HHS/United States ; K12 HD043483/HD/NICHD NIH HHS/United States ; R01 HD074711/HD/NICHD NIH HHS/United States ; U01 HG008657/HG/NHGRI NIH HHS/United States ; U19 HL065962/HL/NHLBI NIH HHS/United States ; R01 HG004517/HG/NHGRI NIH HHS/United States ; U01 HG008666/HG/NHGRI NIH HHS/United States ; R01 HD074711/HD/NICHD NIH HHS/United States ; U01 HG004798/HG/NHGRI NIH HHS/United States ; K12 HD043483/HD/NICHD NIH HHS/United States ; U01 HG008680/HG/NHGRI NIH HHS/United States ; U01 HG006378/HG/NHGRI NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; R01 AI093234/AI/NIAID NIH HHS/United States ; U01 HG008673/HG/NHGRI NIH HHS/United States ; R01 NS032830/NS/NINDS NIH HHS/United States ; U01 HG004798/HG/NHGRI NIH HHS/United States ; R21 HL121429/HL/NHLBI NIH HHS/United States ; R21 HL121429/HL/NHLBI NIH HHS/United States ; R01 NS032830/NS/NINDS NIH HHS/United States ; UL1 TR002243/TR/NCATS NIH HHS/United States ; U01 HG008685/HG/NHGRI NIH HHS/United States ; RC2 GM092618/GM/NIGMS NIH HHS/United States ; F31 EY033663/EY/NEI NIH HHS/United States ; },
mesh = {Humans ; *Blood Pressure/genetics ; *Quantitative Trait Loci ; *Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Models, Genetic ; Genotype ; Genetic Variation ; Computer Simulation ; Phenotype ; },
abstract = {Variability in quantitative traits has clinical, ecological, and evolutionary significance. Most genetic variants identified for complex quantitative traits have only a detectable effect on the mean of trait. We have developed the mean-variance test (MVtest) to simultaneously model the mean and log-variance of a quantitative trait as functions of genotypes and covariates by using estimating equations. The advantages of MVtest include the facts that it can detect effect modification, that multiple testing can follow conventional thresholds, that it is robust to non-normal outcomes, and that association statistics can be meta-analyzed. In simulations, we show control of type I error of MVtest over several alternatives. We identified 51 and 37 previously unreported associations for effects on blood-pressure variance and mean, respectively, in the UK Biobank. Transcriptome-wide association studies revealed 633 significant unique gene associations with blood-pressure mean variance. MVtest is broadly applicable to studies of complex quantitative traits and provides an important opportunity to detect novel loci.},
}
@article {pmid38613584,
year = {2024},
author = {Kredics, L and Büchner, R and Balázs, D and Allaga, H and Kedves, O and Racić, G and Varga, A and Nagy, VD and Vágvölgyi, C and Sipos, G},
title = {Recent advances in the use of Trichoderma-containing multicomponent microbial inoculants for pathogen control and plant growth promotion.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {5},
pages = {162},
pmid = {38613584},
issn = {1573-0972},
mesh = {Humans ; *Agricultural Inoculants ; *Trichoderma ; Fertilizers ; *Pesticides ; Soil ; },
abstract = {Chemical pesticides and fertilizers are used in agricultural production worldwide to prevent damage from plant pathogenic microorganisms, insects, and nematodes, to minimize crop losses and to preserve crop quality. However, the use of chemical pesticides and fertilizers can severely pollute soil, water, and air, posing risks to the environment and human health. Consequently, developing new, alternative, environment-friendly microbial soil treatment interventions for plant protection and crop yield increase has become indispensable. Members of the filamentous fungal genus Trichoderma (Ascomycota, Sordariomycetes, Hypocreales) have long been known as efficient antagonists of plant pathogenic microorganisms based on various beneficial traits and abilities of these fungi. This minireview aims to discuss the advances in the field of Trichoderma-containing multicomponent microbiological inoculants based on recent experimental updates. Trichoderma strains can be combined with each other, with other fungi and/or with beneficial bacteria. The development and field performance of such inoculants will be addressed, focusing on the complementarity, synergy, and compatibility of their microbial components.},
}
@article {pmid38613177,
year = {2024},
author = {Wan, JSH and Bonser, SP and Pang, CK and Fazlioglu, F and Rutherford, S},
title = {Adaptive responses to living in stressful habitats: Do invasive and native plant populations use different strategies?.},
journal = {Ecology letters},
volume = {27},
number = {4},
pages = {e14419},
doi = {10.1111/ele.14419},
pmid = {38613177},
issn = {1461-0248},
mesh = {Reproduction ; *Plant Physiological Phenomena ; *Stress, Physiological ; },
abstract = {Plants inhabit stressful environments characterized by a variety of stressors, including mine sites, mountains, deserts, and high latitudes. Populations from stressful and reference (non-stressful) sites often have performance differences. However, while invasive and native species may respond differently to stressful environments, there is limited understanding of the patterns in reaction norms of populations from these sites. Here, we use phylogenetically controlled meta-analysis to assess the performance of populations under stress and non-stress conditions. We ask whether stress populations of natives and invasives differ in the magnitude of lowered performance under non-stress conditions and if they vary in the degree of performance advantage under stress. We also assessed whether these distinctions differ with stress intensity. Our findings revealed that natives not only have greater adaptive advantages but also more performance reductions than invasives. Populations from very stressful sites had more efficient adaptations, and performance costs increased with stress intensity in natives only. Overall, the results support the notion that adaptation is frequently costless. Reproductive output was most closely associated with adaptive costs and benefits. Our study characterized the adaptive strategies used by invasive and native plants under stressful conditions, thereby providing important insights into the limitations of adaptation to extreme sites.},
}
@article {pmid38613081,
year = {2024},
author = {Jeong, S and Choi, YJ},
title = {Association between Socioecological Status, Nutrient Intake, and Cancer Screening Behaviors in Adults Aged 40 and Over: Insights from the Eighth Korea National Health and Nutrition Examination Survey (KNHANES, 2019).},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613081},
issn = {2072-6643},
mesh = {Adult ; Humans ; Middle Aged ; *Early Detection of Cancer ; Nutrition Surveys ; Eating ; Energy Intake ; Republic of Korea ; *Neoplasms ; },
abstract = {Cancer screening is pivotal for early detection and improved survival rates. While socio-ecological factors are known to influence screening uptake, the role of lifestyle, dietary habits, and general health in shaping these decisions remains underexplored. Utilizing the 2019 Korea National Health and Nutrition Examination Survey (KNHANES), this study examined the myriad of factors impacting cancer screening utilization. Data from 274,872 adults aged 40 years or older were scrutinized, highlighting demographics, income, lifestyle behaviors, health-related variables, nutrient intake, and dietary quality. A combination of descriptive statistics and logistic regression helped us ascertain influential determinants. Higher educational attainment and income quartiles were positively correlated with cancer screening rates. Regular walkers, those engaged in moderate physical activity, and individuals with a previous cancer diagnosis were more likely to get screened. High-risk drinkers and smokers were less inclined towards screening. Dietary habits also influenced screening decisions. Notably, participants with healthier eating behaviors, indicated by factors such as regular breakfasts and fewer meals out, were more likely to undergo screening. Additionally, nutrient intake analysis revealed that those who had undergone screening consumed greater quantities of most nutrients, bar a few exceptions. For individuals aged 50-64, nutritional assessment indicators highlighted a higher mean adequacy ratio (MAR) and index of nutritional quality (INQ) value among those who participated in screening, suggesting better nutritional quality. This study elucidates the complex socio-ecological and nutritional landscape influencing cancer screening decisions. The results underscore the importance of a holistic approach, emphasizing lifestyle, dietary habits, and socio-economic considerations. It provides a roadmap for policymakers to craft more inclusive screening programs, ensuring equal access and promoting early detection.},
}
@article {pmid38612552,
year = {2024},
author = {Jankovic, M and Knezevic, T and Tomic, A and Milicevic, O and Jovanovic, T and Djunic, I and Mihaljevic, B and Knezevic, A and Todorovic-Balint, M},
title = {Human Cytomegalovirus Oncoprotection across Diverse Populations, Tumor Histologies, and Age Groups: The Relevance for Prospective Vaccinal Therapy.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612552},
issn = {1422-0067},
support = {200110/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Cytomegalovirus ; Prospective Studies ; Seroepidemiologic Studies ; *Neoplasms/epidemiology ; *Cytomegalovirus Infections/epidemiology ; },
abstract = {The oncogenicity of the human cytomegalovirus (CMV) is currently being widely debated. Most recently, mounting clinical evidence suggests an anti-cancer effect via CMV-induced T cell-mediated tumor destruction. However, the data were mostly obtained from single-center studies and in vitro experiments. Broad geographic coverage is required to offer a global perspective. Our study examined the correlation between country-specific CMV seroprevalence (across 73 countries) and the age-standardized incidence rate (of 34 invasive tumors). The populations studied were stratified according to decadal age periods as the immunologic effects of CMV seropositivity may depend upon age at initial infection. The International Agency for Research on Cancer of the World Health Organization (IARC WHO) database was used. The multivariate linear regression analysis revealed a worldwide inverse correlation between CMV seroprevalence and the incidences of 62.8% tumors. Notably, this inverse link persists for all cancers combined (Spearman's ρ = -0.732, p < 0.001; β = -0.482, p < 0.001, adjusted R[2] = 0.737). An antithetical and significant correlation was also observed in particular age groups for the vast majority of tumors. Our results corroborate the conclusions of previous studies and indicate that this oncopreventive phenomenon holds true on a global scale. It applies to a wide spectrum of cancer histologies, additionally supporting the idea of a common underlying mechanism-CMV-stimulated T cell tumor targeting. Although these results further advance the notion of CMV-based therapies, in-depth investigation of host-virus interactions is still warranted.},
}
@article {pmid38611576,
year = {2024},
author = {Sulaiman, N and Salehi, F and Prakofjewa, J and Cavalleri, SAE and Ahmed, HM and Mattalia, G and Rastegar, A and Maghsudi, M and Amin, HM and Rasti, A and Hosseini, SH and Ghorbani, A and Pieroni, A and Sõukand, R},
title = {Cultural vs. State Borders: Plant Foraging by Hawraman and Mukriyan Kurds in Western Iran.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611576},
issn = {2223-7747},
abstract = {Plant foraging is a millennia-old activity still practiced by many people in the Middle East, particularly in the Fertile Crescent region, where several socioeconomic, ecological, and cultural factors shape this practice. This study seeks to understand the drivers of plant foraging in this complex region characterized by highly diverse linguistic, religious, and cultural groups. Our study aims to document the wild plants used by Kurds in Western Iran, identify similarities and differences among Hawraman and Mukriyan Kurdish groups in Iran, and compare our findings with a previous study on the Hawramani in Iraq. Forty-three semi-structured in-depth interviews were conducted in Kurdish villages of Western Iran. The results revealed the use of 44 wild food plant taxa, their preparation, and culinary uses. Among the reported taxa, 28 plant taxa were used by Mukriyani, and 33 by Hawramani. The study revealed a significant difference between the Hawraman and Mukriyan regions in Iran, whereas there is a high similarity between Hawramani Kurds in Iran and Iraq. We found that the invisible cultural border carries more weight than political divisions, and this calls for a paradigm shift in how we perceive and map the distribution of ethnobotanical knowledge.},
}
@article {pmid38609485,
year = {2024},
author = {Kazlou, A and Bornukova, K and Wickham, A and Slaykovskiy, V and Peven, K and Klepchukova, A and Ponzo, S and Garfinkel, S},
title = {Effects of stress on pain in females using a mobile health app in the Russia-Ukraine conflict.},
journal = {Npj mental health research},
volume = {3},
number = {1},
pages = {2},
pmid = {38609485},
issn = {2731-4251},
support = {MR/V037676/1//MRC/NIHR/ ; },
abstract = {The chronic and acute effects of stress can have divergent effects on health; long-term effects are associated with detrimental physical and mental health sequelae, while acute effects may be advantageous in the short-term. Stress-induced analgesia, the attenuation of pain perception due to stress, is a well-known phenomenon that has yet to be systematically investigated under ecological conditions. Using Flo, a women's health and wellbeing app and menstrual cycle tracker, with a world-wide monthly active usership of more than 57 million, women in Ukraine were monitored for their reporting of stress, pain and affective symptoms before, and immediately after, the onset of the Russian-Ukrainian conflict. To avoid potential selection (attrition) or collider bias, we rely on a sample of 87,315 users who were actively logging multiple symptoms before and after the start of the war. We found an inverse relationship between stress and pain, whereby higher reports of stress predicted lower rates of pain. Stress did not influence any other physiological symptoms with a similar magnitude, nor did any other symptom have a similar effect on pain. This relationship generally decreased in magnitude in countries neighbouring and surrounding Ukraine, with Ukraine serving as the epicentre. These findings help characterise the relationship between stress and health in a real-world setting.},
}
@article {pmid38605417,
year = {2024},
author = {Roder, T and Pimentel, G and Fuchsmann, P and Stern, MT and von Ah, U and Vergères, G and Peischl, S and Brynildsrud, O and Bruggmann, R and Bär, C},
title = {Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {93},
pmid = {38605417},
issn = {1474-760X},
support = {GRS-070/17//Gebert R&#xfc;f Stiftung/ ; },
mesh = {*Genome-Wide Association Study ; *Multiomics ; Phenotype ; Genes, Bacterial ; Genomics ; },
abstract = {Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40-60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.},
}
@article {pmid38604487,
year = {2024},
author = {Zhang, Y and Huang, C and Zhao, J and Hu, L and Yang, L and Zhang, Y and Sang, W},
title = {Insights into tolerance mechanisms of earthworms (Eisenia fetida) in copper-contaminated soils by integrating multi-omics analyses.},
journal = {Environmental research},
volume = {252},
number = {Pt 2},
pages = {118910},
doi = {10.1016/j.envres.2024.118910},
pmid = {38604487},
issn = {1096-0953},
mesh = {*Oligochaeta/metabolism/drug effects ; Animals ; *Soil Pollutants/toxicity/metabolism ; *Copper/toxicity/metabolism ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {Earthworms can resist high levels of soil copper (Cu) contamination and play an essential role in absorbing them effectively. However, the molecular mechanisms underlying Cu tolerance in earthworms are poorly understood. To address this research gap, we studied alterations of Eisenia fetida in antioxidant enzymes, gut microbiota, metabolites, and genes under varying levels of Cu exposure soils (0, 67.58, 168.96, 337.92 mg/kg). Our results revealed a reduction in antioxidant enzyme activities across all treatment groups, indicating an adaptive response to alleviate Cu-induced oxidative stress. Analysis of gut microbiota revealed a significant increase in the abundance of bacteria associated with nutrient uptake and Cu[2+] excretion under Cu stress. Furthermore, metabolomic analysis discovered an increase in certain metabolites associated with energy metabolism, such as pyruvic acid, L-malic acid, and fumaric acid, as Cu concentration escalated. These results suggested that enhanced energy supply contributes to the elevated tolerance of E. fetida towards Cu. Additionally, transcriptome analysis not only identified crucial detoxification genes (Hsp70, CTSL, GST, CHAC, and GCLC), but also confirmed the critical role of glutathione metabolism as a key pathway in E. fetida Cu detoxification processes. These findings provide a new perspective on the molecular mechanisms of Cu tolerance in earthworms.},
}
@article {pmid38602562,
year = {2024},
author = {Nurkassimova, M and Omarova, N and Zinicovscaia, I and Yushin, N and Chaligava, O},
title = {Mosses as bioindicators of air pollution with potentially toxic elements in the Burabay State National Natural Park, Kazakhstan.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {5},
pages = {442},
pmid = {38602562},
issn = {1573-2959},
mesh = {Humans ; Environmental Biomarkers ; Parks, Recreational ; Kazakhstan ; Environmental Monitoring ; *Air Pollution ; *Bryophyta ; },
abstract = {The Burabay State National Natural Park is a national park of the great natural and historical values located in the north of Kazakhstan, which has been exposed in recent years to significant anthropogenic impact. The moss biomonitoring was performed in the Borovoye resort community, an important tourist destination in the national park, to identify the level of air pollution. Mosses collected at 29 locations were subjected to neutron activation analysis to determine 36 elements and additionally to ICP-OES to detect the level of Cu and Pb. Factor analysis was applied to check if there are any associations between identified elements and to link them with possible emission sources. According to contamination factor and pollution load indices the investigated area belongs to three classes of pollution: unpolluted, suspected and moderate. Potential ecological risk index calculated for selected elements revealed harmless risk to human health. The level of element obtained in Burabay State National Natural Park was compared with the data available for other national parks.},
}
@article {pmid38598963,
year = {2024},
author = {Shen, C and Feng, G and Zhao, F and Huang, X and Li, X},
title = {The multi-omics analysis in the hepatopancreas of Eriocheir sinensis provides novel insights into the response mechanism of heat stress.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {50},
number = {},
pages = {101232},
doi = {10.1016/j.cbd.2024.101232},
pmid = {38598963},
issn = {1878-0407},
mesh = {Animals ; *Hepatopancreas/metabolism ; *Brachyura/physiology/genetics/metabolism ; *Heat-Shock Response ; *Arthropod Proteins/genetics/metabolism ; *Proteomics ; Transcriptome ; Energy Metabolism ; Heat-Shock Proteins/genetics/metabolism ; Proteome ; Multiomics ; },
abstract = {Under global warming, heat stress can induce the excessive production of reactive oxygen species, causing irreversible damage to aquatic animals. It is essential to predict potentially harmful impacts on aquatic organisms under heat stress. Eriocheir sinensis, a typical crustacean crab, is widely distributed in China, American and Europe. Parent E. sinensis need migrate to the estuaries to reproduce in winter, and temperature is a key environmental factor. Herein, we performed a comprehensive transcriptomic and proteomic analysis in the hepatopancreas of E. sinensis under heat stress (20 °C and 30 °C), focusing on heat shock protein family, antioxidant system, energy metabolism and immune defense. The results revealed that parent E. sinensis generated adaptative responses to maintain physiological function under 20 °C stress via the transcriptional up-regulation of energy metabolism enzymes, mRNA synthesis and heat shock proteins. The transcriptional inhibition of key enzymes related to energy metabolism implied that 30 °C stress may lead to the dysfunction of energy metabolism in parent E. sinensis. Meanwhile, parent E. sinensis also enhanced the expression of ferritin and phospholipase D at translational level, and the glutathione s-transferase and heat shock protein 70 at both transcriptional and translational levels, speculating that parent E. sinensis can strengthen antioxidant and immune capacity to resist oxidative stress under 30 °C stress. This study elucidated the potential molecular mechanism in response to heat stress of parent E. sinensis hepatopancreas. The preliminary selection of heat tolerance genes or proteins in E. sinensis can provide a reference for the population prediction and the study of evolutionary mechanism under heat stress in crabs.},
}
@article {pmid38598334,
year = {2024},
author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C},
title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114078},
doi = {10.1016/j.celrep.2024.114078},
pmid = {38598334},
issn = {2211-1247},
mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota/genetics ; *Lactobacillus/genetics ; Adhesins, Bacterial/genetics ; Ethnicity/genetics ; Adult ; Evolution, Molecular ; Pregnancy ; Selection, Genetic ; Biological Evolution ; },
abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.},
}
@article {pmid38597343,
year = {2024},
author = {Schwartz, LC and González, VL and Strong, EE and Truebano, M and Hilbish, TJ},
title = {Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone.},
journal = {Molecular ecology},
volume = {33},
number = {9},
pages = {e17333},
doi = {10.1111/mec.17333},
pmid = {38597343},
issn = {1365-294X},
support = {//National Museum of Natural History/ ; //University of South Carolina/ ; },
mesh = {Animals ; *Hybridization, Genetic ; Temperature ; Climate Change ; Stress, Physiological/genetics ; Gene Expression/genetics ; Phenotype ; Mytilus/genetics ; Transcriptome ; },
abstract = {Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.},
}
@article {pmid38594342,
year = {2024},
author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS},
title = {Author Correction: Landscape-scale benefits of protected areas for tropical biodiversity.},
journal = {Nature},
volume = {628},
number = {8009},
pages = {E5},
doi = {10.1038/s41586-024-07333-z},
pmid = {38594342},
issn = {1476-4687},
}
@article {pmid38594221,
year = {2024},
author = {Mujica, MI and Silva-Flores, P and Bueno, CG and Duchicela, J},
title = {Integrating perspectives in developing mycorrhizal trait databases: a call for inclusive and collaborative continental efforts.},
journal = {The New phytologist},
volume = {242},
number = {4},
pages = {1436-1440},
doi = {10.1111/nph.19754},
pmid = {38594221},
issn = {1469-8137},
support = {Ram&#xf3;n y Cajal fellowship #RYC2021-032533-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 11230870//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 3200774//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; },
mesh = {Biodiversity ; Databases, Factual ; *Mycorrhizae/physiology ; Quantitative Trait, Heritable ; *Symbiosis ; },
abstract = {Global assessments of mycorrhizal symbiosis present large sampling gaps in rich biodiversity regions. Filling these gaps is necessary to build large-scale, unbiased mycorrhizal databases to obtain reliable analyses and prevent misleading generalizations. Underrepresented regions in mycorrhizal research are mainly in Africa, Asia, and South America. Despite the high biodiversity and endemism in these regions, many groups of organisms remain understudied, especially mycorrhizal fungi. In this Viewpoint, we emphasize the importance of inclusive and collaborative continental efforts in integrating perspectives for comprehensive trait database development and propose a conceptual framework that can help build large mycorrhizal databases in underrepresented regions. Based on the four Vs of big data (volume, variety, veracity, and velocity), we identify the main challenges of constructing a large mycorrhizal dataset and propose solutions for each challenge. We share our collaborative methodology, which involves employing open calls and working groups to engage all mycorrhizal researchers in the region to build a South American Mycorrhizal Database. By fostering interdisciplinary collaborations and embracing a continental-scale approach, we can create robust mycorrhizal trait databases that provide valuable insights into the evolution, ecology, and functioning of mycorrhizal associations, reducing the geographical biases that are so common in large-scale ecological studies.},
}
@article {pmid38589621,
year = {2024},
author = {Liew, F and Efstathiou, C and Fontanella, S and Richardson, M and Saunders, R and Swieboda, D and Sidhu, JK and Ascough, S and Moore, SC and Mohamed, N and Nunag, J and King, C and Leavy, OC and Elneima, O and McAuley, HJC and Shikotra, A and Singapuri, A and Sereno, M and Harris, VC and Houchen-Wolloff, L and Greening, NJ and Lone, NI and Thorpe, M and Thompson, AAR and Rowland-Jones, SL and Docherty, AB and Chalmers, JD and Ho, LP and Horsley, A and Raman, B and Poinasamy, K and Marks, M and Kon, OM and Howard, LS and Wootton, DG and Quint, JK and de Silva, TI and Ho, A and Chiu, C and Harrison, EM and Greenhalf, W and Baillie, JK and Semple, MG and Turtle, L and Evans, RA and Wain, LV and Brightling, C and Thwaites, RS and Openshaw, PJM and , and , },
title = {Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease.},
journal = {Nature immunology},
volume = {25},
number = {4},
pages = {607-621},
pmid = {38589621},
issn = {1529-2916},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Biomedical Research ; Hospitalization ; Immunoglobulin G ; },
abstract = {One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood[1]. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.},
}
@article {pmid38587202,
year = {2024},
author = {Montfort, J and Hervas-Sotomayor, F and Le Cam, A and Murat, F},
title = {FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes.},
journal = {Nucleic acids research},
volume = {52},
number = {W1},
pages = {W65-W69},
pmid = {38587202},
issn = {1362-4962},
support = {ANR-23-CE13-0008//ANR/ ; },
mesh = {Animals ; *Fishes/genetics ; *Evolution, Molecular ; *Transcriptome/genetics ; *Internet ; Gene Expression Profiling/methods ; Databases, Genetic ; Phylogeny ; Genomics/methods ; Software ; Genome/genetics ; },
abstract = {Teleost fish represent one of the largest and most diverse clades of vertebrates, which makes them great models in various research areas such as ecology and evolution. Recent sequencing endeavors provided high-quality genomes for species covering the main fish evolutionary lineages, opening up large-scale comparative genomics studies. However, transcriptomic data across fish species and organs are heterogenous and have not been integrated with newly sequenced genomes making gene expression quantification and comparative analyses particularly challenging. Thus, resources integrating genomic and transcriptomic data across fish species and organs are still lacking. Here, we present FEVER, a web-based resource allowing evolutionary transcriptomics across species and tissues. First, based on query genes FEVER reconstructs gene trees providing orthologous and paralogous relationships as well as their evolutionary dynamics across 13 species covering the major fish lineages, and 4 model species as evolutionary outgroups. Second, it provides unbiased gene expression across 11 tissues using up-to-date fish genomes. Finally, genomic and transcriptomic data are combined together allowing the exploration of gene expression evolution following speciation and duplication events. FEVER is freely accessible at https://fever.sk8.inrae.fr/.},
}
@article {pmid38584951,
year = {2024},
author = {Badiyal, A and Mahajan, R and Rana, RS and Sood, R and Walia, A and Rana, T and Manhas, S and Jayswal, DK},
title = {Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1280846},
pmid = {38584951},
issn = {1664-462X},
abstract = {The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.},
}
@article {pmid38583934,
year = {2024},
author = {Swanson, SA and Miller, M},
title = {Toward a clearer understanding of what works to reduce gun violence: the role of falsification strategies.},
journal = {American journal of epidemiology},
volume = {193},
number = {8},
pages = {1061-1065},
doi = {10.1093/aje/kwae036},
pmid = {38583934},
issn = {1476-6256},
mesh = {Humans ; *Gun Violence/prevention &amp; control/statistics &amp; numerical data ; United States ; *Firearms/legislation &amp; jurisprudence ; Data Interpretation, Statistical ; Homicide/prevention &amp; control/statistics &amp; numerical data ; Wounds, Gunshot/prevention &amp; control/epidemiology ; },
abstract = {Strong epidemiologic evidence from ecological and individual-level studies in the United States supports the claim that access to firearms substantially increases the risk of dying by suicide, homicide, and firearm accidents. Less certain is how well particular interventions work to prevent these deaths and other firearm-related harms. Given the limits of existing data to study firearm violence and the infeasibility of conducting randomized trials of firearm access, it is important to do the best we can with the data we already have. We argue that falsification strategies are a critical-yet underutilized-component of any such analytical approach. The falsification strategies we focus on are versions of "negative controls" analyses in which we expect that an analysis should yield a null causal effect, and thus where not obtaining a null effect estimate raises questions about the assumptions underlying causal interpretation of a study's findings. We illustrate the saliency of this issue today with examples drawn from studies published in leading peer-reviewed journals within the last 5 years. Collecting rich, high-quality data always takes time, urgent as the need may be. On the other hand, doing better with the data we already have can start right now.},
}
@article {pmid38581683,
year = {2024},
author = {Loos, D and Filho, APDC and Dutilh, BE and Barber, AE and Panagiotou, G},
title = {A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114046},
doi = {10.1016/j.celrep.2024.114046},
pmid = {38581683},
issn = {2211-1247},
mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Humans ; Biodiversity ; Genomics/methods ; Phylogeny ; },
abstract = {Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.},
}
@article {pmid38581418,
year = {2024},
author = {Chen, Z and Ain, NU and Zhao, Q and Zhang, X},
title = {From tradition to innovation: conventional and deep learning frameworks in genome annotation.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {3},
pages = {},
pmid = {38581418},
issn = {1477-4054},
support = {2021YFF1000900//National Key Research and Development Program of China/ ; RCYX20210706092103024//Shenzhen Science and Technology Program/ ; 32222019//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Deep Learning ; Genome ; Algorithms ; Software ; Computational Biology/methods ; Molecular Sequence Annotation ; },
abstract = {Following the milestone success of the Human Genome Project, the 'Encyclopedia of DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularly in annotating and predicting the functions of unknown genes. The core idea behind genome annotation is to identify genes and various functional elements within the genome sequence and infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for functional verification. However, early bioinformatics algorithms and software primarily employed shallow learning techniques; thus, the ability to characterize data and features learning was limited. With the widespread adoption of RNA-Seq technology, scientists from the biological community began to harness the potential of machine learning and deep learning approaches for gene structure prediction and functional annotation. In this context, we reviewed both conventional methods and contemporary deep learning frameworks, and highlighted novel perspectives on the challenges arising during annotation underscoring the dynamic nature of this evolving scientific landscape.},
}
@article {pmid38578160,
year = {2024},
author = {Zhang, T and Peng, W and Xiao, H and Cao, S and Chen, Z and Su, X and Luo, Y and Liu, Z and Peng, Y and Yang, X and Jiang, GF and Xu, X and Ma, Z and Zhou, Y},
title = {Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape.},
journal = {Journal of integrative plant biology},
volume = {66},
number = {7},
pages = {1408-1426},
doi = {10.1111/jipb.13653},
pmid = {38578160},
issn = {1744-7909},
support = {20210020//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 20210039//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 2023YFF1000100//the National Key Research and Development Program of China/ ; 2023YFD2200700//the National Key Research and Development Program of China/ ; 32300191//National Natural Science Foundation of China/ ; 32372662//National Natural Science Foundation of China/ ; No.20210020;No.20210039//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 2023YFF1000100;2023YFD2200700;//the National Key Research and Development Program of China/ ; No.32300191;No.32372662//National Natural Science Foundation of China/ ; },
mesh = {*Vitis/genetics ; Adaptation, Physiological/genetics ; Genome, Plant/genetics ; Genetics, Population ; Polymorphism, Single Nucleotide/genetics ; Salt Tolerance/genetics ; Genomic Structural Variation/genetics ; Genomics ; Genes, Plant ; },
abstract = {Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.},
}
@article {pmid38577785,
year = {2024},
author = {Baril, T and Galbraith, J and Hayward, A},
title = {Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline.},
journal = {Molecular biology and evolution},
volume = {41},
number = {4},
pages = {},
pmid = {38577785},
issn = {1537-1719},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *DNA Transposable Elements/genetics ; Molecular Sequence Annotation ; *Drosophila melanogaster/genetics ; Genomics/methods ; Computational Biology ; },
abstract = {Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage, and (ii) repeat models represented by short sections of total TE length, with poor capture of 5' and 3' ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above while scoring highly in benchmarking for TE annotation and classification and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focused on further quality control and tailored analyses in future releases.},
}
@article {pmid38569653,
year = {2024},
author = {Augustijn, HE and Roseboom, AM and Medema, MH and van Wezel, GP},
title = {Harnessing regulatory networks in Actinobacteria for natural product discovery.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {51},
number = {},
pages = {},
pmid = {38569653},
issn = {1476-5535},
support = {948770/ERC_/European Research Council/International ; },
mesh = {*Actinobacteria/metabolism/genetics ; *Biological Products/metabolism ; Biosynthetic Pathways ; Computational Biology/methods ; *Drug Discovery ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Multigene Family ; Transcription Factors/metabolism/genetics ; },
abstract = {UNLABELLED: Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches.<br><br>ONE-SENTENCE SUMMARY: This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.},
}
@article {pmid38560995,
year = {2024},
author = {Stiller, J and Feng, S and Chowdhury, AA and Rivas-González, I and Duchêne, DA and Fang, Q and Deng, Y and Kozlov, A and Stamatakis, A and Claramunt, S and Nguyen, JMT and Ho, SYW and Faircloth, BC and Haag, J and Houde, P and Cracraft, J and Balaban, M and Mai, U and Chen, G and Gao, R and Zhou, C and Xie, Y and Huang, Z and Cao, Z and Yan, Z and Ogilvie, HA and Nakhleh, L and Lindow, B and Morel, B and Fjeldså, J and Hosner, PA and da Fonseca, RR and Petersen, B and Tobias, JA and Székely, T and Kennedy, JD and Reeve, AH and Liker, A and Stervander, M and Antunes, A and Tietze, DT and Bertelsen, MF and Lei, F and Rahbek, C and Graves, GR and Schierup, MH and Warnow, T and Braun, EL and Gilbert, MTP and Jarvis, ED and Mirarab, S and Zhang, G},
title = {Complexity of avian evolution revealed by family-level genomes.},
journal = {Nature},
volume = {629},
number = {8013},
pages = {851-860},
pmid = {38560995},
issn = {1476-4687},
mesh = {Animals ; *Birds/genetics/classification/anatomy &amp; histology ; Brain/anatomy &amp; histology ; *Evolution, Molecular ; Extinction, Biological ; *Genome/genetics ; Genomics ; *Phylogeny ; Population Density ; Male ; Female ; },
abstract = {Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions[1-3]. Here we address these issues by analysing the genomes of 363 bird species[4] (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.},
}
@article {pmid38560613,
year = {2024},
author = {Boyes, D and Gibbs, M and , and , and , and , and , and , },
title = {The genome sequence of the Brown Oak Tortrix, Archips crataeganus (Hübner, 1796).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {9},
pmid = {38560613},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Archips crataeganus (the Brown Oak Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 626.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,596 protein coding genes.},
}
@article {pmid38554963,
year = {2024},
author = {Li, W and Feng, Q and Li, Z and Jin, T and Zhang, Y and Southam, G},
title = {Inhibition of iron oxidation in Acidithiobacillus ferrooxidans by low-molecular-weight organic acids: Evaluation of performance and elucidation of mechanisms.},
journal = {The Science of the total environment},
volume = {927},
number = {},
pages = {171919},
doi = {10.1016/j.scitotenv.2024.171919},
pmid = {38554963},
issn = {1879-1026},
mesh = {*Acidithiobacillus/metabolism/drug effects ; *Iron/metabolism ; *Oxidation-Reduction ; Mining ; Formates/metabolism ; Acetic Acid/metabolism ; *Propionates ; },
abstract = {The catalytic role of Acidithiobacillus ferrooxidans (A. ferrooxidans) in iron biooxidation is pivotal in the formation of Acid Mine Drainage (AMD), which poses a significant threat to the environment. To control AMD generation, treatments with low-molecular-weight organic acids are being studied, yet their exact mechanisms are unclear. In this study, AMD materials, organic acids, and molecular methods were employed to gain a deeper understanding of the inhibitory effects of low-molecular-weight organic acids on the biooxidation of iron by A. ferrooxidans. The inhibition experiments of A. ferrooxidans on the oxidation of Fe[2+] showed that to attain a 90 % inhibition efficacy within 72 h, the minimum concentrations required for formic acid, acetic acid, propionic acid, and lactic acid are 0.5, 6, 4, and 10 mmol/L, respectively. Bacterial imaging illustrated the detrimental effects of these organic acids on the cell envelope structure. This includes severe damage to the outer membrane, particularly from formic and acetic acids, which also caused cell wall damage. Coupled with alterations in the types and quantities of protein, carbohydrate, and nucleic acid content in extracellular polymeric substances (EPS), indicate the mechanisms underlying these inhibitory treatments. Transcriptomic analysis revealed interference of these organic acids with crucial metabolic pathways, particularly those related to energy metabolism. These findings establish a comprehensive theoretical basis for understanding the inhibition of A. ferrooxidans' biooxidation by low-molecular-weight organic acids, offering a novel opportunity to effectively mitigate the generation of AMD at its source.},
}
@article {pmid38554685,
year = {2024},
author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Sfriso, A and Rizzolio, F and Adeel, M and Wahsha, M and Munari, C and Mistri, M},
title = {Microplastic accumulation and ecological impacts on benthic invertebrates: Insights from a microcosm experiment.},
journal = {Marine pollution bulletin},
volume = {202},
number = {},
pages = {116231},
doi = {10.1016/j.marpolbul.2024.116231},
pmid = {38554685},
issn = {1879-3363},
mesh = {Animals ; *Water Pollutants, Chemical/analysis ; *Invertebrates ; *Environmental Monitoring ; *Microplastics ; Aquatic Organisms ; Ecosystem ; },
abstract = {Microplastic (MP) pollution poses a global concern, especially for benthic invertebrates. This one-month study investigated the accumulation of small MP polymers (polypropylene and polyester resin, 3-500 μm, 250 μg L[-1]) in benthic invertebrates and on one alga species. Results revealed species-specific preferences for MP size and type, driven by ingestion, adhesion, or avoidance behaviours. Polyester resin accumulated in Mytilus galloprovincialis, Chamelea gallina, Hexaplex trunculus, and Paranemonia cinerea, while polypropylene accumulated on Ulva rigida. Over time, MP accumulation decreased in count but not size, averaging 6.2 ± 5.0 particles per individual after a month. MP were mainly found inside of the organisms, especially in the gut, gills, and gonads and externally adherent MP ranged from 11 to 35 % of the total. Biochemical energy assessments after two weeks of MP exposure indicated energy gains for water column species but energy loss for sediment-associated species, highlighting the susceptibility of infaunal benthic communities to MP contamination.},
}
@article {pmid38552719,
year = {2024},
author = {Martin, NG and Defres, S and Willis, L and Beckley, R and Hardwick, H and Coxon, A and Kadambari, S and Yu, LM and Liu, X and Galal, U and Conlin, K and Griffiths, MJ and Kneen, R and Nadel, S and Heath, PT and Kelly, DE and Solomon, T and Sadarangani, M and Pollard, AJ and , },
title = {Paediatric meningitis in the conjugate vaccine era and a novel clinical decision model to predict bacterial aetiology.},
journal = {The Journal of infection},
volume = {88},
number = {5},
pages = {106145},
doi = {10.1016/j.jinf.2024.106145},
pmid = {38552719},
issn = {1532-2742},
mesh = {Humans ; Child ; Infant ; *Meningitis, Bacterial/diagnosis/cerebrospinal fluid/microbiology ; Child, Preschool ; Adolescent ; Female ; Male ; Prospective Studies ; *Vaccines, Conjugate ; *Meningitis, Viral/diagnosis/cerebrospinal fluid ; Clinical Decision Rules ; United Kingdom/epidemiology ; Neisseria meningitidis/isolation &amp; purification ; Streptococcus pneumoniae/isolation &amp; purification ; Decision Support Techniques ; },
abstract = {OBJECTIVES: The aims of this study were to assess aetiology and clinical characteristics in childhood meningitis, and develop clinical decision rules to distinguish bacterial meningitis from other similar clinical syndromes.<br><br>METHODS: Children aged <16 years hospitalised with suspected meningitis/encephalitis were included, and prospectively recruited at 31 UK hospitals. Meningitis was defined as identification of bacteria/viruses from cerebrospinal fluid (CSF) and/or a raised CSF white blood cell count. New clinical decision rules were developed to distinguish bacterial from viral meningitis and those of alternative aetiology.<br><br>RESULTS: The cohort included 3002 children (median age 2&#xb7;4 months); 1101/3002 (36&#xb7;7%) had meningitis, including 180 bacterial, 423 viral and 280 with no pathogen identified. Enterovirus was the most common pathogen in those aged <6 months and 10-16 years, with Neisseria meningitidis and/or Streptococcus pneumoniae commonest at age 6 months to 9 years. The Bacterial Meningitis Score had a negative predictive value of 95&#xb7;3%. We developed two clinical decision rules, that could be used either before (sensitivity 82%, specificity 71%) or after lumbar puncture (sensitivity 84%, specificity 93%), to determine risk of bacterial meningitis.<br><br>CONCLUSIONS: Bacterial meningitis comprised 6% of children with suspected meningitis/encephalitis. Our clinical decision rules provide potential novel approaches to assist with identifying children with bacterial meningitis.<br><br>FUNDING: This study was funded by the Meningitis Research Foundation, Pfizer and the NIHR Programme Grants for Applied Research.},
}
@article {pmid38552245,
year = {2024},
author = {Han, B and Tian, D and Li, X and Liu, S and Tian, F and Liu, D and Wang, S and Zhao, K},
title = {Multiomics Analyses Provide New Insight into Genetic Variation of Reproductive Adaptability in Tibetan Sheep.},
journal = {Molecular biology and evolution},
volume = {41},
number = {3},
pages = {},
pmid = {38552245},
issn = {1537-1719},
support = {No. 2022-ZJ-901//Natural Science Foundation of Qinghai Province/ ; },
mesh = {Humans ; Female ; Sheep/genetics ; Animals ; Tibet ; *Genome-Wide Association Study ; *Multiomics ; Proteomics ; Reproduction ; Mutation ; },
abstract = {Domestication and artificial selection during production-oriented breeding have greatly shaped the level of genomic variability in sheep. However, the genetic variation associated with increased reproduction remains elusive. Here, two groups of samples from consecutively monotocous and polytocous sheep were collected for genome-wide association, transcriptomic, proteomic, and metabolomic analyses to explore the genetic variation in fecundity in Tibetan sheep. Genome-wide association study revealed strong associations between BMPR1B (p.Q249R) and litter size, as well as between PAPPA and lambing interval; these findings were validated in 1,130 individuals. Furthermore, we constructed the first single-cell atlas of Tibetan sheep ovary tissues and identified a specific mural granulosa cell subtype with PAPPA-specific expression and differential expression of BMPR1B between the two groups. Bulk RNA-seq indicated that BMPR1B and PAPPA expressions were similar between the two groups of sheep. 3D protein structure prediction and coimmunoprecipitation analysis indicated that mutation and mutually exclusive exons of BMPR1B are the main mechanisms for prolific Tibetan sheep. We propose that PAPPA is a key gene for stimulating ovarian follicular growth and development, and steroidogenesis. Our work reveals the genetic variation in reproductive performance in Tibetan sheep, providing insights and valuable genetic resources for the discovery of genes and regulatory mechanisms that improve reproductive success.},
}
@article {pmid38552150,
year = {2024},
author = {Howard-Varona, C and Lindback, MM and Fudyma, JD and Krongauz, A and Solonenko, NE and Zayed, AA and Andreopoulos, WB and Olson, HM and Kim, YM and Kyle, JE and Glavina Del Rio, T and Adkins, JN and Tfaily, MM and Paul, S and Sullivan, MB and Duhaime, MB},
title = {Environment-specific virocell metabolic reprogramming.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38552150},
issn = {1751-7370},
support = {2149505//NSF Advances in Biological Informatics/ ; DE-AC05-76RL0-1830//U.S. Department of Energy/ ; //Joint Genome Institute/ ; //U.S. Department of Energy/ ; 1536989//National Science Foundation/ ; //University of Michigan/ ; 034//C-CoMP/ ; //Department of Energy/ ; T32 AI112542/AI/NIAID NIH HHS/United States ; 2055455//NSF Polar Programs/ ; 1-T32-AI-112542//National Institutes of Health (NIH)/National Institute of Allergy and Infectious Diseases (NIAID)/ ; //Facilities Integrating Collaborations for User Science/ ; 3790//Gordon and Betty Moore Foundation/ ; //EMSL/ ; //Office of Science/ ; DGE1256260//NSF Graduate Research Fellowship/ ; DE-AC02-05CH11231//Biological and Environmental Research/ ; C-CoMP NSF-STC 2019589//NSF Center for Chemical Currencies of a Microbial Planet/ ; //Environmental Molecular Sciences Laboratory/ ; DE-SC0020173//Office of Biological and Environmental Research/ ; },
mesh = {*Bacteriophages/genetics/physiology ; Proteomics ; Phosphates/metabolism ; Metabolomics ; Systems Biology ; Transcriptome ; Metabolic Reprogramming ; },
abstract = {Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.},
}
@article {pmid38551211,
year = {2024},
author = {Groote-Woortmann, W and Korbel, K and Hose, GC},
title = {STYGOTOX: A Quality-Assessed Database of (Eco)Toxicological Data on Stygofauna and Other Aquatic Subterranean Organisms.},
journal = {Environmental toxicology and chemistry},
volume = {43},
number = {12},
pages = {2492-2500},
pmid = {38551211},
issn = {1552-8618},
support = {LP190100927//Australian Research Council/ ; },
mesh = {Animals ; *Water Pollutants, Chemical/toxicity ; *Aquatic Organisms/drug effects ; *Databases, Factual ; Environmental Monitoring ; Risk Assessment ; },
abstract = {We have compiled the toxicity data on stygofauna and other aquatic subterranean organisms in one (eco)toxicological database. A total of 46 studies were found, containing 472 toxic endpoints covering 43 different stressors. These compounds were tested on subterranean organisms from four phyla, 12 orders, 24 genera, and 55 species. The studies included were published between 1976 and December 2023 using fauna collected in 13 different countries. The suitability of the studies was assessed to indicate the completeness of reporting and their suitability for use in hazard and risk assessment. This compilation provides a valuable source of data for future development of toxicity testing protocols for groundwater organisms, and to support decision-making, ecological risk assessments and the derivation of water quality criteria for the protection of groundwater ecosystems. Environ Toxicol Chem 2024;43:2492-2500. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.},
}
@article {pmid38547306,
year = {2024},
author = {Milić, D and Rat, M and Bokić, B and Mudri-Stojnić, S and Milošević, N and Sukur, N and Jakovetić, D and Radak, B and Tot, T and Vujanović, D and Anačkov, G and Radišić, D},
title = {Exploring the effects of habitat management on grassland biodiversity: A case study from northern Serbia.},
journal = {PloS one},
volume = {19},
number = {3},
pages = {e0301391},
pmid = {38547306},
issn = {1932-6203},
mesh = {Animals ; *Grassland ; Serbia ; *Ecosystem ; Biodiversity ; Agriculture ; Insecta ; Plants ; Birds/physiology ; },
abstract = {Grasslands represent a biodiversity hotspot in the European agricultural landscape, their restoration is necessary and offers a great opportunity to mitigate or halt harmful processes. These measures require a comprehensive knowledge of historical landscape changes, but also adequate management strategies. The required data was gathered from the sand grasslands of northern Serbia, as this habitat is of high conservation priority. This area also has a long history of different habitat management approaches (grazing and mowing versus unmanaged), which has been documented over of the last two decades. This dataset enabled us to quantify the effects of different measures across multiple taxa (plants, insect pollinators, and birds). We linked the gathered data on plants, pollinators, and birds with habitat management measures. Our results show that, at the taxon level, the adopted management strategies were beneficial for species richness, abundance, and composition, as the highest diversity of plant, insect pollinator, and bird species was found in managed areas. Thus, an innovative modelling approach was adopted in this work to identify and explain the effects of management practices on changes in habitat communities. The findings yielded can be used in the decision making as well as development of new management programmes. We thus posit that, when restoring and establishing particular communities, priority needs to be given to species with a broad ecological response. We recommend using the decision tree as a suitable machine learning model for this purpose.},
}
@article {pmid38540697,
year = {2024},
author = {Giordano, D and Bonora, S and D'Orsi, I and D'Alelio, D and Facchiano, A},
title = {Structural and Functional Characterization of Lipoxygenases from Diatoms by Bioinformatics and Modelling Studies.},
journal = {Biomolecules},
volume = {14},
number = {3},
pages = {},
pmid = {38540697},
issn = {2218-273X},
mesh = {*Lipoxygenases/chemistry/genetics ; *Diatoms/genetics ; Oxylipins ; Phylogeny ; Molecular Docking Simulation ; Ecosystem ; Computational Biology ; },
abstract = {Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of oxylipins, which are involved in many physiological and pathological processes in marine organisms. The interest in diatoms' lipoxygenases and oxylipins has increased due to their possible biotechnological applications, ranging from ecology to medicine. We investigated using bioinformatics and molecular docking tools the lipoxygenases of diatoms and the possible interaction with substrates. A large-scale analysis of sequence resources allowed us to retrieve 45 sequences of lipoxygenases from diatoms. We compared and analyzed the sequences by multiple alignments and phylogenetic trees, suggesting the possible clustering in phylogenetic groups. Then, we modelled the 3D structure of representative enzymes from the different groups and investigated in detail the structural and functional properties by docking simulations with possible substrates. The results allowed us to propose a classification of the lipoxygenases from diatoms based on their sequence features, which may be reflected in specific structural differences and possible substrate specificity.},
}
@article {pmid38540627,
year = {2024},
author = {Santric-Milicevic, M and Pavlekic, K and Bukumiric, Z and Stevanovic, A and Nikolic, D and Matejic, B and Matanovic, D and Backovic, D and Tulic, G and Lukic, R and Zivanovic, D and Radosavljevic, S and Milovanovic, V and Zdujic, M and Stankovic, S and Asanin, M and Zdravkovic, M and Tomasevic, R},
title = {Nurses' Perception of Tension, Stress, and Pressure before and during the COVID-19 Pandemic: A Multicenter Serbian Study.},
journal = {Healthcare (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
pmid = {38540627},
issn = {2227-9032},
abstract = {The mental health of healthcare workers, especially the nursing staff in intensive care units, is crucial for the optimal functioning of healthcare systems during medical emergencies. This study implements a cross-sectional design to investigate the associations between nurses' personal characteristics, workplace challenges, and job satisfaction with the increased perception of tension, stress, and pressure at the workplace (TSPW) before and during the COVID-19 pandemic. In 2021, we surveyed 4210 nurses from 19 intensive healthcare facilities in the capital of Serbia, Belgrade, and, at that time, collected data about their perceived TSPW before and during the COVID-19 pandemic. Our study identified six predictors of the increase in TSPW, as perceived by nurses: their work in COVID-19 infectious zones (OR = 1.446), exhaustion due to work under protective equipment (OR = 1.413), uncertainty and fear of infection (OR = 1.481), a high degree of superiors' appreciation and respect (OR = 1.147), a high degree of patients' attitudes (OR = 1.111), and a low degree of work autonomy (OR = 0.889). The study's findings suggest that a solution to this issue is necessary to ensure that nurses are safe and able to alleviate the physical and mental strain that comes with prolonged use of protective equipment. Nurses on the frontline of the pandemic require better health protection, better conditions, and respect for their role. Strategies to promote mental health would help reduce nurses' stress and increase job satisfaction.},
}
@article {pmid38538788,
year = {2024},
author = {Johnson, TF and Beckerman, AP and Childs, DZ and Webb, TJ and Evans, KL and Griffiths, CA and Capdevila, P and Clements, CF and Besson, M and Gregory, RD and Thomas, GH and Delmas, E and Freckleton, RP},
title = {Revealing uncertainty in the status of biodiversity change.},
journal = {Nature},
volume = {628},
number = {8009},
pages = {788-794},
pmid = {38538788},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources/methods/trends ; Datasets as Topic ; Phylogeny ; Spatio-Temporal Analysis ; Time Factors ; *Uncertainty ; },
abstract = {Biodiversity faces unprecedented threats from rapid global change[1]. Signals of biodiversity change come from time-series abundance datasets for thousands of species over large geographic and temporal scales. Analyses of these biodiversity datasets have pointed to varied trends in abundance, including increases and decreases. However, these analyses have not fully accounted for spatial, temporal and phylogenetic structures in the data. Here, using a new statistical framework, we show across ten high-profile biodiversity datasets[2-11] that increases and decreases under existing approaches vanish once spatial, temporal and phylogenetic structures are accounted for. This is a consequence of existing approaches severely underestimating trend uncertainty and sometimes misestimating the trend direction. Under our revised average abundance trends that appropriately recognize uncertainty, we failed to observe a single increasing or decreasing trend at 95% credible intervals in our ten datasets. This emphasizes how little is known about biodiversity change across vast spatial and taxonomic scales. Despite this uncertainty at vast scales, we reveal improved local-scale prediction accuracy by accounting for spatial, temporal and phylogenetic structures. Improved prediction offers hope of estimating biodiversity change at policy-relevant scales, guiding adaptive conservation responses.},
}
@article {pmid38532952,
year = {2024},
author = {Feutz, E and Biswas, PK and Ndeketa, L and Ogwel, B and Onwuchekwa, U and Sarwar, G and Sultana, S and Peñataro Yori, P and Acebedo, A and Ahmed, N and Ahmed, I and Atlas, HE and Awuor, AO and Bhuiyan, MAI and Conteh, B and Diawara, O and Elwood, S and Fane, M and Hossen, MI and Ireen, M and Jallow, AF and Karim, M and Kosek, MN and Kotloff, KL and Lefu, C and Liu, J and Maguire, R and Qamar, FN and Ndalama, M and Ochieng, JB and Okonji, C and Paredes, LFZ and Pavlinac, PB and Perez, K and Qureshi, S and Schiaffino, F and Traore, M and Tickell, KD and Wachepa, R and Witte, D and Cornick, J and Jahangir Hossain, M and Khanam, F and Olortegui, MP and Omore, R and Sow, SO and Yousafzai, MT and Galagan, SR},
title = {Data Management in Multicountry Consortium Studies: The Enterics For Global Health (EFGH) Shigella Surveillance Study Example.},
journal = {Open forum infectious diseases},
volume = {11},
number = {Suppl 1},
pages = {S48-S57},
pmid = {38532952},
issn = {2328-8957},
support = {D43 TW010913/TW/FIC NIH HHS/United States ; K43 TW012298/TW/FIC NIH HHS/United States ; UL1 TR002319/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Rigorous data management systems and planning are essential to successful research projects, especially for large, multicountry consortium studies involving partnerships across multiple institutions. Here we describe the development and implementation of data management systems and procedures for the Enterics For Global Health (EFGH) Shigella surveillance study-a 7-country diarrhea surveillance study that will conduct facility-based surveillance concurrent with population-based enumeration and a health care utilization survey to estimate the incidence of Shigella--associated diarrhea in children 6 to 35 months old.<br><br>METHODS: The goals of EFGH data management are to utilize the knowledge and experience of consortium members to collect high-quality data and ensure equity in access and decision-making. During the planning phase before study initiation, a working group of representatives from each EFGH country site, the coordination team, and other partners met regularly to develop the data management systems for the study.<br><br>RESULTS: This resulted in the Data Management Plan, which included selecting REDCap and SurveyCTO as the primary database systems. Consequently, we laid out procedures for data processing and storage, study monitoring and reporting, data quality control and assurance activities, and data access. The data management system and associated real-time visualizations allow for rapid data cleaning activities and progress monitoring and will enable quicker time to analysis.<br><br>CONCLUSIONS: Experiences from this study will contribute toward enriching the sparse landscape of data management methods publications and serve as a case study for future studies seeking to collect and manage data consistently and rigorously while maintaining equitable access to and control of data.},
}
@article {pmid38531865,
year = {2024},
author = {Corponi, F and Li, BM and Anmella, G and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A},
title = {Automated mood disorder symptoms monitoring from multivariate time-series sensory data: getting the full picture beyond a single number.},
journal = {Translational psychiatry},
volume = {14},
number = {1},
pages = {161},
pmid = {38531865},
issn = {2158-3188},
mesh = {Humans ; *Mood Disorders/diagnosis ; *Affect ; Machine Learning ; Sleep ; },
abstract = {Mood disorders (MDs) are among the leading causes of disease burden worldwide. Limited specialized care availability remains a major bottleneck thus hindering pre-emptive interventions. MDs manifest with changes in mood, sleep, and motor activity, observable in ecological physiological recordings thanks to recent advances in wearable technology. Therefore, near-continuous and passive collection of physiological data from wearables in daily life, analyzable with machine learning (ML), could mitigate this problem, bringing MDs monitoring outside the clinician's office. Previous works predict a single label, either the disease state or a psychometric scale total score. However, clinical practice suggests that the same label may underlie different symptom profiles, requiring specific treatments. Here we bridge this gap by proposing a new task: inferring all items in HDRS and YMRS, the two most widely used standardized scales for assessing MDs symptoms, using physiological data from wearables. To that end, we develop a deep learning pipeline to score the symptoms of a large cohort of MD patients and show that agreement between predictions and assessments by an expert clinician is clinically significant (quadratic Cohen's κ and macro-average F1 score both of 0.609). While doing so, we investigate several solutions to the ML challenges associated with this task, including multi-task learning, class imbalance, ordinal target variables, and subject-invariant representations. Lastly, we illustrate the importance of testing on out-of-distribution samples.},
}
@article {pmid38531495,
year = {2024},
author = {Yuan, Q and Yao, LF and Tang, JW and Ma, ZW and Mou, JY and Wen, XR and Usman, M and Wu, X and Wang, L},
title = {Rapid discrimination and ratio quantification of mixed antibiotics in aqueous solution through integrative analysis of SERS spectra via CNN combined with NN-EN model.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.03.016},
pmid = {38531495},
issn = {2090-1224},
abstract = {INTRODUCTION: Abusing antibiotic residues in the natural environment has become a severe public health and ecological environmental problem. The side effects of its biochemical and physiological consequences are severe. To avoid antibiotic contamination in water, implementing universal and rapid antibiotic residue detection technology is critical to maintaining antibiotic safety in aquatic environments. Surface-enhanced Raman spectroscopy (SERS) provides a powerful tool for identifying small molecular components with high sensitivity and selectivity. However, it remains a challenge to identify pure antibiotics from SERS spectra due to coexisting components in the mixture.<br><br>OBJECTIVES: In this study, an intelligent analysis model for the SERS spectrum based on a deep learning algorithm was proposed for rapid identification of the antibiotic components in the mixture and quantitative determination of the ratios of these components.<br><br>METHODS: We established a water environment system containing three antibiotic residues of ciprofloxacin, doxycycline, and levofloxacin. To facilitate qualitative and quantitative analysis of the SERS spectra antibiotic mixture datasets, we developed a computational framework integrating a convolutional neural network (CNN) and a non-negative elastic network (NN-EN) method.<br><br>RESULTS: The experimental results demonstrate that the CNN model has a recognition accuracy of 98.68%, and the interpretation analysis of Shapley Additive exPlanations (SHAP) shows that our model can specifically focus on the characteristic peak distribution. In contrast, the NN-EN model can accurately quantify each component's ratio in the mixture.<br><br>CONCLUSION: Integrating the SERS technique assisted by the CNN combined with the NN-EN model exhibits great potential for rapid identification and high-precision quantification of antibiotic residues in aquatic environments.},
}
@article {pmid38531460,
year = {2024},
author = {Enjavinejad, SM and Zahedifar, M and Moosavi, AA and Khosravani, P},
title = {Integrated application of multiple indicators and geographic information system-based approaches for comprehensive assessment of environmental impacts of toxic metals-contaminated agricultural soils and vegetables.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {171747},
doi = {10.1016/j.scitotenv.2024.171747},
pmid = {38531460},
issn = {1879-1026},
mesh = {Adult ; Child ; Humans ; Vegetables ; Geographic Information Systems ; Environmental Monitoring ; Cadmium/analysis ; Copper/analysis ; Lead/analysis ; Risk Assessment ; *Metals, Heavy/analysis ; Soil/chemistry ; Carcinogens/analysis ; Receptors, Antigen, T-Cell ; *Soil Pollutants/analysis ; China ; },
abstract = {Conventional monitoring and mapping approaches are laborious, expensive, and time-consuming because they need a large number of data and consequently extensive sampling and experimental operations. Therefore, due to the growing concern about the potential of contamination of soils and agricultural products with heavy metals (HMs), a field experiment was conducted on 77 farm lands in an area of 2300 ha in the southeast of Shiraz (Iran) to investigate the source of metal contamination in the soils and vegetables and to model spatial distribution of HMs (iron, Fe; manganese, Mn; copper, Cu; zinc, Zn; cadmium, Cd; nickel, Ni, and lead, Pb) over the region using geographic information system (GIS) and geostatistical (Ordinary Kriging, OK) approaches and compare the results with deterministic approaches (Inverse Distance Weighting, IDW with different weighting power). Furthermore, some ecological and health risks indices including Pollution index (PI), Nemerow integrated pollution index (NIPI), pollution load index (PLI), degree of contamination (Cdeg), modified contamination degree (mCd), PIaverage and PIvector for soil quality, multi-element contamination (MEC), the probability of toxicity (MERMQ), the potential ecological index (RI), total hazard index (THI) and total carcinogenic risk index (TCR) based on ingestion, inhalation, and dermal exposure pathways for adults and children respectively for analyzing the noncarcinogenic and carcinogenic risks were calculated. Experimental semivariogram of the mentioned HMs were calculated and theoretical models (i.e., exponential, spherical, Gaussian, and linear models) were fitted in order to model their spatial structures and to investigate the most representative models. Moreover, principal component analysis (PCA) and cluster analysis (CA) were used to identify sources of HMs in the soils. Results showed that IDW method was more efficient than the OK approach to estimate the properties and HMs contents in the soils and plants. The estimated daily intake of metals (DIM) values of Pb and Ni exceeded their safe limits. In addition, Cd was the main element responsible for ecological risk. The PIave and PIvector indices showed that soil quality in the study area is not suitable. According to mCd values, the soils classified as ultra-high contaminated for Cu and Cd, extremely high for Zn and Pb, very high, high, and very low degree of contamination for Ni, Mn, and Fe, respectively. 36, 60, and 4 % of the sampling sites had high, medium, and low risk levels with 49, 21, and 9 % probability of toxicity, respectively. The maximum health risk index (HRI) value of 20.42 with extremely high risk for children was obtained for Ni and the HI for adults and children were 0.22 and 1.55, respectively. The THI values of Pb and Cd were the highest compared to the other HMs studied, revealing a possible non-cancer risk in children associated with exposure to these metals. The routes of exposure with the greatest influence on the THI and TCR indices were in the order of ingestion > inhalation > dermal. Therefore, ingestion, as the main route of exposure, is the route of greatest contribution to health risks. PCA analysis revealed that Fe, Mn, Cu, and Ni may originate from natural sources, while Fe was appeared to be controlled by fertilizer, and Cu primarily coming from pesticide, while Cd and Pb were mainly associated with the anthropogenic contamination, atmospheric depositions, and terrific in the urban soils. While, Zn mainly originated from fertilization. Findings are vital for developing remediation approaches for controlling the contaminants distribution as well as for monitoring and mapping the quality and health of soil resources.},
}
@article {pmid38528816,
year = {2024},
author = {Del Bianco, T and Haartsen, R and Mason, L and Leno, VC and Springer, C and Potter, M and Mackay, W and Smit, P and Plessis, CD and Brink, L and Johnson, MH and Murphy, D and Loth, E and Odendaal, H and Jones, EJH},
title = {The importance of decomposing periodic and aperiodic EEG signals for assessment of brain function in a global context.},
journal = {Developmental psychobiology},
volume = {66},
number = {4},
pages = {e22484},
doi = {10.1002/dev.22484},
pmid = {38528816},
issn = {1098-2302},
support = {777394//EU/EFPIA/SFARI/Autistica/AUTISM SPEAKS Innovative Medicines Initiative 2 Joint Undertaking (AIMS-2-TRIALS)/ ; 115300//Innovative Medicines Initiative 1 Joint Undertaking (AIMS-2-TRIALS)/ ; MR/K021389/1//the Medical Research Council for the projects "The Development of Social Attention and Perception Abilities in Typical and At-risk Infants"/ ; MR/T003057/1//"Human neurocognitive development: Early-stage processing, modifiers, and outcomes"/ ; 213608/Z/18/Z//Sir Henry Wellcome Postdoctoral Fellowship/ ; MR/S036423/1//UK&#xa0;Research&#xa0;and Innovation/ ; },
mesh = {Child ; Humans ; Female ; *Electroencephalography ; *Brain ; Brain Mapping ; Cognition ; },
abstract = {Measures of early neuro-cognitive development that are suitable for use in low-resource settings are needed to enable studies of the effects of early adversity on the developing brain in a global context. These measures should have high acquisition rates and good face and construct validity. Here, we investigated the feasibility of a naturalistic electroencephalography (EEG) paradigm in a low-resource context during childhood. Additionally, we examined the sensitivity of periodic and aperiodic EEG metrics to social and non-social stimuli. We recorded simultaneous 20-channel EEG and eye-tracking in 72 children aged 4-12 years (45 females) while they watched videos of women singing nursery rhymes and moving toys, selected to represent familiar childhood experiences. These measures were part of a feasibility study that assessed the feasibility and acceptability of a follow-up data collection of the South African Safe Passage Study, which tracks environmental adversity and brain and cognitive development from before birth up until childhood. We examined whether data quantity and quality varied with child characteristics and the sensitivity of varying EEG metrics (canonical band power in the theta and alpha band and periodic and aperiodic features of the power spectra). We found that children who completed the EEG and eye-tracking assessment were, in general, representative of the full cohort. Data quantity was higher in children with greater visual attention to the stimuli. Out of the tested EEG metrics, periodic measures in the theta frequency range were most sensitive to condition differences, compared to alpha range measures and canonical and aperiodic EEG measures. Our results show that measuring EEG during ecologically valid social and non-social stimuli is feasible in low-resource settings, is feasible for most children, and produces robust indices of social brain function. This work provides preliminary support for testing longitudinal links between social brain function, environmental factors, and emerging behaviors.},
}
@article {pmid38527064,
year = {2024},
author = {Barrett, C and Chiphwanya, J and Mkwanda, S and Matipula, DE and Ndhlovu, P and Chaponda, L and Turner, JD and Giorgi, E and Betts, H and Martindale, S and Taylor, MJ and Read, JM and Kelly-Hope, LA},
title = {The national distribution of lymphatic filariasis cases in Malawi using patient mapping and geostatistical modelling.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {3},
pages = {e0012056},
pmid = {38527064},
issn = {1935-2735},
mesh = {Humans ; *Elephantiasis, Filarial/epidemiology ; Malawi/epidemiology ; Prevalence ; Data Management ; Surveys and Questionnaires ; },
abstract = {BACKGROUND: In 2020 the World Health Organization (WHO) declared that Malawi had successfully eliminated lymphatic filariasis (LF) as a public health problem. Understanding clinical case distributions at a national and sub-national level is important, so essential care packages can be provided to individuals living with LF symptoms. This study aimed to develop a national database and map of LF clinical cases across Malawi using geostatistical modelling approaches, programme-identified clinical cases, antigenaemia prevalence and climate information.<br><br>METHODOLOGY: LF clinical cases identified through programme house-to-house surveys across 90 sub-district administrative boundaries (Traditional Authority (TA)) and antigenaemia prevalence from 57 sampled villages in Malawi were used in a two-step geostatistical modelling process to predict LF clinical cases across all TAs of the country. First, we modelled antigenaemia prevalence in relation to climate covariates to predict nationwide antigenaemia prevalence. Second, we modelled clinical cases for unmapped TAs based on our antigenaemia prevalence spatial estimates.<br><br>PRINCIPLE FINDINGS: The models estimated 20,938 (95% CrI 18,091 to 24,071) clinical cases in unmapped TAs (70.3%) in addition to the 8,856 (29.7%), programme-identified cases in mapped TAs. In total, the overall national number of LF clinical cases was estimated to be 29,794 (95% CrI 26,957 to 32,927). The antigenaemia prevalence and clinical case mapping and modelling found the highest burden of disease in Chikwawa and Nsanje districts in the Southern Region and Karonga district in the Northern Region of the country.<br><br>CONCLUSIONS: The models presented in this study have facilitated the development of the first national LF clinical case database and map in Malawi, the first endemic country in sub-Saharan Africa. It highlights the value of using existing LF antigenaemia prevalence and clinical case data together with modelling approaches to produce estimates that may be used for the WHO dossier requirements, to help target limited resources and implement long-term health strategies.},
}
@article {pmid38523092,
year = {2024},
author = {Ouyang, YY and Su, ZW and Li, CH and Zeng, AC and Guo, FT},
title = {Forest fire risk zoning based on fuzzy logic and analytical network process.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {2},
pages = {354-362},
doi = {10.13287/j.1001-9332.202402.024},
pmid = {38523092},
issn = {1001-9332},
mesh = {Humans ; Fires/prevention &amp; control ; Forests ; *Fuzzy Logic ; Geographic Information Systems ; Trees ; *Wildfires/statistics &amp; numerical data ; },
abstract = {Forest fires have a significant impact on human life, property safety, and ecological environment. Deve-loping high-quality forest fire risk maps is beneficial for preventing forest fires, guiding resource allocation for firefighting, assisting in fire suppression efforts, and supporting decision-making. With a multi-criteria decision analysis (MCDA) method based on geographic information systems (GIS) and literature review, we assessed the main factors influencing the occurrences of forest fires in Youxi County, Fujian Province. We analyzed the importance of each fire risk factor using the analytic network process (ANP) and assigned weights, and evaluated the sub-standard weights using fuzzy logic assessment. Using ArcGIS aggregation functions, we generated a forest fire risk map and validated it with satellite fire points. The results showed that the areas classified as level 4 or higher fire risk accounted for a considerable proportion in Youxi County, and that the central and northern regions were at higher risk. The overall fire risk situation in the county was severe. The fuzzy ANP model demonstrated a high accuracy of 85.8%. The introduction of this novel MCDA method could effectively improve the accuracy of forest fire risk mapping at a small scale, providing a basis for early fire warning and the planning and allocation of firefighting resources.},
}
@article {pmid38521905,
year = {2024},
author = {Wu, J and Lv, Y and Hao, P and Zhang, Z and Zheng, Y and Chen, E and Fan, Y},
title = {Immunological profile of lactylation-related genes in Crohn's disease: a comprehensive analysis based on bulk and single-cell RNA sequencing data.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {300},
pmid = {38521905},
issn = {1479-5876},
support = {82300630//National Natural Science Foundation of China/ ; 2022GGB011//Project of Young and Middle-aged Backbone Talents Cultivation/ ; 2021J011329//Fujian Provincial Natural Science Foundation/ ; 2021QNB017//Health Science Foundation of Fujian Youth Program/ ; },
mesh = {Humans ; *Crohn Disease/genetics ; Databases, Factual ; Lactic Acid ; Sequence Analysis, RNA ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a disease characterized by intestinal immune dysfunction, often accompanied by metabolic abnormalities. Disturbances in lactate metabolism have been found in the intestine of patients with CD, but studies on the role of lactate and related Lactylation in the pathogenesis of CD are still unknown.<br><br>METHODS: We identified the core genes associated with Lactylation by downloading and merging three CD-related datasets (GSE16879, GSE75214, and GSE112366) from the GEO database, and analyzed the functions associated with the hub genes and the correlation between their expression levels and immune infiltration through comprehensive analysis. We explored the Lactylation levels of different immune cells using single-cell data and further analyzed the differences in Lactylation levels between inflammatory and non-inflammatory sites.<br><br>RESULTS: We identified six Lactylation-related hub genes that are highly associated with CD. Further analysis revealed that these six hub genes were highly correlated with the level of immune cell infiltration. To further clarify the effect of Lactylation on immune cells, we analyzed single-cell sequencing data of immune cells from inflammatory and non-inflammatory sites in CD patients and found that there were significant differences in the levels of Lactylation between different types of immune cells, and that the levels of Lactylation were significantly higher in immune cells from inflammatory sites.<br><br>CONCLUSIONS: These results suggest that Lactylation-related genes and their functions are closely associated with changes in inflammatory cells in CD patients.},
}
@article {pmid38514998,
year = {2024},
author = {Alari, A and Ranzani, O and Olmos, S and Milà, C and Rico, A and Ballester, J and Basagaña, X and Dadvand, P and Duarte-Salles, T and Nieuwenhuijsen, M and Vivanco-Hidalgo, RM and Tonne, C},
title = {Short-term exposure to air pollution and hospital admission after COVID-19 in Catalonia: the COVAIR-CAT study.},
journal = {International journal of epidemiology},
volume = {53},
number = {2},
pages = {},
doi = {10.1093/ije/dyae041},
pmid = {38514998},
issn = {1464-3685},
support = {//Health Effects Institute/ ; },
mesh = {Humans ; Spain/epidemiology ; Cohort Studies ; Nitrogen Dioxide/adverse effects/analysis ; COVID-19 Testing ; *COVID-19/epidemiology ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Particulate Matter/adverse effects/analysis ; *Ozone/adverse effects/analysis ; Hospitalization ; Hospitals ; Environmental Exposure/adverse effects/analysis ; },
abstract = {BACKGROUND: A growing body of evidence has reported positive associations between long-term exposure to air pollution and poor COVID-19 outcomes. Inconsistent findings have been reported for short-term air pollution, mostly from ecological study designs. Using individual-level data, we studied the association between short-term variation in air pollutants [nitrogen dioxide (NO2), particulate matter with a diameter of <2.5 µm (PM2.5) and a diameter of <10 µm (PM10) and ozone (O3)] and hospital admission among individuals diagnosed with COVID-19.<br><br>METHODS: The COVAIR-CAT (Air pollution in relation to COVID-19 morbidity and mortality: a large population-based cohort study in Catalonia, Spain) cohort is a large population-based cohort in Catalonia, Spain including 240&#xa0;902 individuals diagnosed with COVID-19 in the primary care system from 1 March until 31 December 2020. Our outcome was hospitalization within 30&#x2009;days of COVID-19 diagnosis. We used individual residential address to assign daily air-pollution exposure, estimated using machine-learning methods for spatiotemporal prediction. For each pandemic wave, we fitted Cox proportional-hazards models accounting for non-linear-distributed lagged exposure over the previous 7&#xa0;days.<br><br>RESULTS: Results differed considerably by pandemic wave. During the second wave, an interquartile-range increase in cumulative weekly exposure to air pollution (lag0_7) was associated with a 12% increase (95% CI: 4% to 20%) in COVID-19 hospitalizations for NO2, 8% (95% CI: 1% to 16%) for PM2.5 and 9% (95% CI: 3% to 15%) for PM10. We observed consistent positive associations for same-day (lag0) exposure, whereas lag-specific associations beyond lag0 were generally not statistically significant.<br><br>CONCLUSIONS: Our study suggests positive associations between NO2, PM2.5 and PM10 and hospitalization risk among individuals diagnosed with COVID-19 during the second wave. Cumulative hazard ratios were largely driven by exposure on the same day as hospitalization.},
}
@article {pmid38514747,
year = {2024},
author = {Chanda, MM and Purse, BV and Hemadri, D and Patil, SS and Yogisharadhya, R and Prajapati, A and Shivachandra, SB},
title = {Spatial and temporal analysis of haemorrhagic septicaemia outbreaks in India over three decades (1987-2016).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6773},
pmid = {38514747},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Hemorrhagic Septicemia/epidemiology/veterinary/microbiology ; *Pasteurella multocida ; Buffaloes/microbiology ; Disease Outbreaks ; India/epidemiology ; *Cattle Diseases/microbiology ; },
abstract = {Haemorrhagic septicaemia (HS) is an economically important disease affecting cattle and buffaloes and the livelihoods of small-holder farmers that depend upon them. The disease is caused by Gram-negative bacterium, Pasteurella multocida, and is considered to be endemic in many states of India with more than 25,000 outbreaks in the past three decades. Currently, there is no national policy for control of HS in India. In this study, we analysed thirty year (1987-2016) monthly data on HS outbreaks using different statistical and mathematical methods to identify spatial variability and temporal patterns (seasonality, periodicity). There was zonal variation in the trend and seasonality of HS outbreaks. Overall, South zone reported maximum proportion of the outbreaks (70.2%), followed by East zone (7.2%), Central zone (6.4%), North zone (5.6%), West zone (5.5%) and North-East zone (4.9%). Annual state level analysis indicated that the reporting of HS outbreaks started at different years independently and there was no apparent transmission between the states. The results of the current study are useful for the policy makers to design national control programme on HS in India and implement state specific strategies. Further, our study and strategies could aid in implementation of similar approaches in HS endemic tropical countries around the world.},
}
@article {pmid38514421,
year = {2024},
author = {Morel, B and Williams, TA and Stamatakis, A and Szöllősi, GJ},
title = {AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {4},
pages = {},
pmid = {38514421},
issn = {1367-4811},
support = {//Klaus Tschira Foundation/ ; /ERC_/European Research Council/International ; },
mesh = {Phylogeny ; *Gene Duplication ; *Algorithms ; Software ; Models, Statistical ; Evolution, Molecular ; },
abstract = {MOTIVATION: Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree.<br><br>RESULTS: We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a simple, yet powerful, probabilistic model of gene duplication, transfer, and loss. A key feature of AleRax is its ability to account for uncertainty in the gene tree and its reconciliation by using an efficient approximation to calculate the joint phylogenetic-reconciliation likelihood and sample reconciled gene trees accordingly. Simulations and analyses of empirical data show that AleRax is one order of magnitude faster than competing gene tree inference tools while attaining the same accuracy. It is consistently more robust than species tree inference methods such as SpeciesRax and ASTRAL-Pro 2 under gene tree uncertainty. Finally, AleRax can process multiple gene families in parallel thereby allowing users to compare competing phylogenetic hypotheses and estimate model parameters, such as duplication, transfer, and loss probabilities for genome-scale datasets with hundreds of taxa.<br><br>GNU GPL at https://github.com/BenoitMorel/AleRax and data are made available at https://cme.h-its.org/exelixis/material/alerax_data.tar.gz.},
}
@article {pmid38512945,
year = {2024},
author = {Scalabrin, E and Radaelli, M and Capodaglio, G and Pierobon, M and Del Vecchio, S and Buffa, G},
title = {Hemp cultivation opportunities for marginal lands development.},
journal = {PloS one},
volume = {19},
number = {3},
pages = {e0299981},
pmid = {38512945},
issn = {1932-6203},
mesh = {*Cannabis ; Flowers ; Inflorescence ; Dietary Supplements ; Plant Leaves ; },
abstract = {Agricultural diversification and high-quality products deriving from sustainable crops such as hemp can represent a solution to revitalize marginal areas and reverse land abandonment. This study aimed at comparing four different hemp cultivars (Carmagnola Selezionata, "CS"; Futura 75, "FUT"; Felina 32, "FEL"; Secuieni Jubileu, "JUB") to provide information to select the best suited cultivar for cultivation in mountain marginal areas and for specific end-use applications. Hemp cultivars were cultivated in a single experimental field to compare their ecological and agronomic behavior (duration of life cycle phases, plant size and biomass allocation, and plant resource-use strategies). Through metabolomic analysis of both vegetative and reproductive parts of the plants we tested the presence of substances of nutraceutical interest and traced seed nutritional profile. The four cultivars had different ecological and agronomic behavior, and nutritional profile. We found several compounds with potential pharmaceutical and nutraceutical values in all parts of the plant (leaves, inflorescences, and stems). JUB resulted the most suitable for seed production while CS showed the highest content of bioactive compounds in flowers and leaves. FUT, showed the best suitability for multi-purpose cultivation, while FEL seemed to be not appropriate for the cultivation in mountain area. The multi-disciplinary approach we adopted was effective in distinguish across hemp cultivars and provided information to farmers for the selection of the best hemp cultivar to select. Hemp had a high potential for cultivation in marginal lands, demonstrating to be an economic resource due to its multi-purpose use and to the possibility to generate high-added values products. Our results could serve as a stimulus for the reintroduction of this culture in the study area and in other similar environments.},
}
@article {pmid38509110,
year = {2024},
author = {Berner, LT and Orndahl, KM and Rose, M and Tamstorf, M and Arndal, MF and Alexander, HD and Humphreys, ER and Loranty, MM and Ludwig, SM and Nyman, J and Juutinen, S and Aurela, M and Happonen, K and Mikola, J and Mack, MC and Vankoughnett, MR and Iversen, CM and Salmon, VG and Yang, D and Kumar, J and Grogan, P and Danby, RK and Scott, NA and Olofsson, J and Siewert, MB and Deschamps, L and Lévesque, E and Maire, V and Morneault, A and Gauthier, G and Gignac, C and Boudreau, S and Gaspard, A and Kholodov, A and Bret-Harte, MS and Greaves, HE and Walker, D and Gregory, FM and Michelsen, A and Kumpula, T and Villoslada, M and Ylänne, H and Luoto, M and Virtanen, T and Forbes, BC and Hölzel, N and Epstein, H and Heim, RJ and Bunn, A and Holmes, RM and Hung, JKY and Natali, SM and Virkkala, AM and Goetz, SJ},
title = {The Arctic Plant Aboveground Biomass Synthesis Dataset.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {305},
pmid = {38509110},
issn = {2052-4463},
support = {80NSSC21K1364//National Aeronautics and Space Administration (NASA)/ ; 80NSSC22K1247//National Aeronautics and Space Administration (NASA)/ ; 80NSSC22K1247//National Aeronautics and Space Administration (NASA)/ ; NNX12AK83G//National Aeronautics and Space Administration (NASA)/ ; NNX15AP04H//National Aeronautics and Space Administration (NASA)/ ; 2127273//National Science Foundation (NSF)/ ; 1417745//National Science Foundation (NSF)/ ; 1636476//National Science Foundation (NSF)/ ; 2224776//National Science Foundation (NSF)/ ; 2127273//National Science Foundation (NSF)/ ; 330319//Academy of Finland (Suomen Akatemia)/ ; 330319//Academy of Finland (Suomen Akatemia)/ ; 330845//Academy of Finland (Suomen Akatemia)/ ; 1342890//Academy of Finland (Suomen Akatemia)/ ; 256991//Academy of Finland (Suomen Akatemia)/ ; 2021-05767//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; FRQNT-2018-PR-208107//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; FRQNT-2018-PR-208107//Fonds de Recherche du Qu&#xe9;bec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; },
mesh = {Arctic Regions ; Biomass ; *Ecosystem ; *Trees ; *Plants ; },
abstract = {Plant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m[-2]) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.},
}
@article {pmid38507308,
year = {2024},
author = {Sánchez Reyes, LL and McTavish, EJ and O'Meara, B},
title = {DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life.},
journal = {Systematic biology},
volume = {73},
number = {2},
pages = {470-485},
pmid = {38507308},
issn = {1076-836X},
support = {ABI-1458603//National Science Foundation/ ; DBI-0905606//National Evolutionary Synthesis Center/ ; ABI-1759846//Open Tree of Life project/ ; ABI-1458572//Phylotastic project/ ; },
mesh = {*Phylogeny ; *Classification/methods ; *Software ; Databases, Factual ; },
abstract = {Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.},
}
@article {pmid38506735,
year = {2024},
author = {Stefanovic, M and Takano, K and Wittekind, CE and Ehring, T},
title = {Dynamic symptom associations in posttraumatic stress disorder: a network approach.},
journal = {European journal of psychotraumatology},
volume = {15},
number = {1},
pages = {2317675},
pmid = {38506735},
issn = {2000-8066},
mesh = {Humans ; *Stress Disorders, Post-Traumatic/diagnosis ; Anxiety ; Checklist ; Diagnostic and Statistical Manual of Mental Disorders ; Ecological Momentary Assessment ; },
abstract = {Background and objective: The current study aimed to investigate the within-day symptom dynamics in PTSD patients, specifically focusing on symptoms that most predict changes in other symptoms. The study included a baseline diagnostic assessment, followed by an assessment using the experience sampling method (ESM) via a smartphone.Method: Participants answered questions related to their PTSD symptoms four times per day for 15 consecutive days (compliance rate 75%). The clinical sample consisted of 48 treatment-seeking individuals: 44 with PTSD as a primary diagnosis, and four patients with subsyndromal PTSD, all of whom had not yet begun trauma-focused treatment. The ESM assessment included the 20 items from the PTSD Checklist for DSM-5, five items from the International Trauma Questionnaire (ITQ) assessing disturbances in relationships and functional impairment, and two items from the Clinician-Administered PTSD Scale for DSM-5 assessing symptoms of depersonalization and derealization.Results: Temporal networks (prospective associations between symptoms) showed that changes in hypervigilance predicted changes in the greatest number of symptoms at the next time point. Furthermore, hypervigilance showed temporal connections with at least one additional symptom from each of the DSM-5 PTSD symptom clusters.Conclusions: Results show that the contemporaneous network (representing the relationship between given symptoms within the same assessment occasion) and the temporal network (representing prospective associations between symptoms) differ and that it is important to estimate both. Some findings from earlier research are replicated, but heterogeneity across studies remains. Future studies should include potential moderators.},
}
@article {pmid38505831,
year = {2023},
author = {Clifton-Brown, J and Hastings, A and von Cossel, M and Murphy-Bokern, D and McCalmont, J and Whitaker, J and Alexopoulou, E and Amaducci, S and Andronic, L and Ashman, C and Awty-Carroll, D and Bhatia, R and Breuer, L and Cosentino, S and Cracroft-Eley, W and Donnison, I and Elbersen, B and Ferrarini, A and Ford, J and Greef, J and Ingram, J and Lewandowski, I and Magenau, E and Mos, M and Petrick, M and Pogrzeba, M and Robson, P and Rowe, RL and Sandu, A and Schwarz, KU and Scordia, D and Scurlock, J and Shepherd, A and Thornton, J and Trindade, LM and Vetter, S and Wagner, M and Wu, PC and Yamada, T and Kiesel, A},
title = {Perennial biomass cropping and use: Shaping the policy ecosystem in European countries.},
journal = {Global change biology. Bioenergy},
volume = {15},
number = {5},
pages = {538-558},
pmid = {38505831},
issn = {1757-1693},
abstract = {Demand for sustainably produced biomass is expected to increase with the need to provide renewable commodities, improve resource security and reduce greenhouse gas emissions in line with COP26 commitments. Studies have demonstrated additional environmental benefits of using perennial biomass crops (PBCs), when produced appropriately, as a feedstock for the growing bioeconomy, including utilisation for bioenergy (with or without carbon capture and storage). PBCs can potentially contribute to Common Agricultural Policy (CAP) (2023-27) objectives provided they are carefully integrated into farming systems and landscapes. Despite significant research and development (R&amp;D) investment over decades in herbaceous and coppiced woody PBCs, deployment has largely stagnated due to social, economic and policy uncertainties. This paper identifies the challenges in creating policies that are acceptable to all actors. Development will need to be informed by measurement, reporting and verification (MRV) of greenhouse gas emissions reductions and other environmental, economic and social metrics. It discusses interlinked issues that must be considered in the expansion of PBC production: (i) available land; (ii) yield potential; (iii) integration into farming systems; (iv) R&amp;D requirements; (v) utilisation options; and (vi) market systems and the socio-economic environment. It makes policy recommendations that would enable greater PBC deployment: (1) incentivise farmers and land managers through specific policy measures, including carbon pricing, to allocate their less productive and less profitable land for uses which deliver demonstrable greenhouse gas reductions; (2) enable greenhouse gas mitigation markets to develop and offer secure contracts for commercial developers of verifiable low-carbon bioenergy and bioproducts; (3) support innovation in biomass utilisation value chains; and (4) continue long-term, strategic R&amp;D and education for positive environmental, economic and social sustainability impacts.},
}
@article {pmid38493394,
year = {2024},
author = {Ketterer, T and Sieke, E and Min, J and Quidgley-Martin, M and Barral, RL and Akers, A and Adams, A and Miller, E and Miller, MK and Mollen, C},
title = {Contraception Initiation in the Emergency Department: Adolescent Perspectives.},
journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine},
volume = {75},
number = {1},
pages = {147-154},
pmid = {38493394},
issn = {1879-1972},
support = {K23 HD109464/HD/NICHD NIH HHS/United States ; R21 HD095096/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Adolescent ; Female ; *Emergency Service, Hospital ; Pregnancy ; *Pregnancy in Adolescence/prevention &amp; control ; *Contraception Behavior/psychology ; Health Knowledge, Attitudes, Practice ; Qualitative Research ; Prospective Studies ; Adolescent Behavior/psychology ; Interviews as Topic ; Contraception/psychology ; Counseling ; },
abstract = {PURPOSE: The purpose of this study was to identify factors affecting contraceptive intention and behavior among adolescent females in the pediatric Emergency Department.<br><br>METHODS: We conducted a qualitative interview study nested within a larger prospective cohort study examining adolescent contraceptive counseling for females ages 15-18&#xa0;years at-risk of unintended pregnancy presenting to the pediatric Emergency Department. Interviews were conducted in a subset of participants. The ecologically expanded Theory of Planned Behavior, expert opinion, and literature review informed the interview guide. Interviews were recorded, transcribed, coded and monitored for thematic saturation.<br><br>RESULTS: Twenty-eight interviews were analyzed. Mean age was 17.1&#xa0;years. Themes were mapped to ecologically expanded Theory of Planned Behavior constructs. Within health system influences, prior contraceptive experiences and patient-clinician interactions were described. Within community influences, contraceptive education, knowledge and misinformation, teen pregnancy norms, and social media impacts were described. Within attitudes influences, side-effect and safety concerns, contraceptive motivations and teen pregnancy beliefs were described. Within subjective norm influences, peer and family impacts were described. Within perceived behavioral control, Emergency Department (ED) counseling intervention impacts were described.<br><br>DISCUSSION: We identified factors affecting contraceptive initiation/behavior among an ED adolescent population that otherwise may not have received contraceptive education in similar detail as provided by study clinicians. Adolescents' prior contraceptive and clinician interactions, limited access to contraceptive education, knowledge and misinformation, and side-effect and safety concerns affected initiation. Peer/family sharing and social media were leading contraceptive information sources. Future studies should incorporate insights into adolescent ED intervention design to make optimal use of resources while maximizing potential benefit.},
}
@article {pmid38493360,
year = {2024},
author = {Wen, F and Liu, R and Garcia Y Garcia, A and Ye, H and Lu, L and Qimuge, E and Sun, Z and Nie, C and Han, X and Zhang, Y},
title = {Study on the prediction method of grasshopper occurrence risk in Inner Mongolia based on the maximum entropy model during the growing period.},
journal = {Journal of economic entomology},
volume = {117},
number = {3},
pages = {843-857},
doi = {10.1093/jee/toae036},
pmid = {38493360},
issn = {1938-291X},
support = {CBAS2022 DF001//Director of the International Research Center for Big Data for Sustainable SDG/ ; 420QN293//Hainan Provincial Natural Science Foundation of China/ ; 2021119//Youth Innovation Promotion Association CAS/ ; 2020 KTYWLZX08//Future Star Talent Program of Aerospace Information Research Institute, Chinese Academy of Sciences/ ; },
mesh = {*Grasshoppers/growth &amp; development/physiology ; Animals ; Entropy ; *Models, Statistical ; Animal Husbandry ; Herbivory ; Population Dynamics ; Animal Migration ; Ecosystem ; Agriculture ; Ecological Momentary Assessment ; Geographic Information Systems ; Surveys and Questionnaires ; Remote Sensing Technology ; },
abstract = {Grasshoppers represent a significant biological challenge in Inner Mongolia's grasslands, severely affecting the region's animal husbandry. Thus, dynamic monitoring of grasshopper infestation risk is crucial for sustainable livestock farming. This study employed the Maxent model, along with remote sensing data, to forecast Oedaleus decorus asiaticus occurrence during the growing season, using grasshopper suitability habitats as a base. The Maxent model's predictive accuracy was high, with an AUC of 0.966. The most influential environmental variables for grasshopper distribution were suitable habitat data (34.27%), the temperature-vegetation dryness index during the spawning period (18.81%), and various other meteorological and vegetation factors. The risk index model was applied to calculate the grasshopper distribution across different risk levels for the years 2019-2022. The data indicated that the level 1 risk area primarily spans central, eastern, and southwestern Inner Mongolia. By examining the variable weights, the primary drivers of risk level fluctuation from 2019 to 2022 were identified as accumulated precipitation and land surface temperature anomalies during the overwintering period. This study offers valuable insights for future O. decorus asiaticus monitoring in Inner Mongolia.},
}
@article {pmid38486028,
year = {2024},
author = {Arslan, D and Akdağ, B and Yaşar, &#xc7; and Olivier, A and Benedetti, Y and Morelli, F and Çiçek, K},
title = {An extensive database on the traits and occurrences of amphibian species in Turkey.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {292},
pmid = {38486028},
issn = {2052-4463},
mesh = {Animals ; *Amphibians ; Biodiversity ; *Ecosystem ; Turkey ; Databases, Factual ; },
abstract = {Amphibians are the most endangered taxa among vertebrates, and they face many threats during their complex life cycles. The species' life history traits and occurrence database help understand species responses against ecological factors. Consequently, the species-level-trait database has gained more prominence in recent years as a useful tool for understanding the dimensions of communities, assembly processes of communities, and conserving biodiversity at the ecosystem level against environmental changes. However, in Turkey, there are deficiencies in the knowledge of the ecological traits of amphibians compared to other vertebrate taxa, as most studies have focused on their distribution or taxonomic status. Consequently, there is a need to create such a database for future research on all known extant amphibians in Turkey. We compiled a species-level data set of species traits and occurrences for all amphibians in Turkey using 436 literature sources. We completed 36 trait categories with 5611 occurrence data for 37 amphibian species in Turkey. This study provides an open, useful, and comprehensive database for macroecological and conservation studies on amphibians in Turkey.},
}
@article {pmid38483685,
year = {2024},
author = {Guo, Y and Li, X and Li, Q and Hu, Z},
title = {Environmental impact assessment of acidic coal gangue leaching solution on groundwater: a coal gangue pile in Shanxi, China.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {4},
pages = {120},
pmid = {38483685},
issn = {1573-2983},
mesh = {Coal/analysis ; Environmental Pollution ; Soil ; *Environmental Pollutants ; Ions ; China ; *Soil Pollutants/analysis ; *Coal Mining ; },
abstract = {With the continual advancement of coal resource development, the comprehensive utilization of coal gangue as a by-product encounters certain constraints. A substantial amount of untreated coal gangue is openly stored, particularly acidic gangue exposed to rainfall. The leaching effect of acidic solutions, containing heavy metal ions and other pollutants, results in environmental challenges such as local soil or groundwater pollution, presenting a significant concern in the current ecological landscape of mining areas. Investigating the migration patterns of pollutants in the soil-groundwater system and elucidating the characteristics of polluted solute migration are imperative. To understand the migration dynamics of pollutants and unveil the features of solute migration, this study focuses on a coal gangue dump in a mining area in Shanxi. Utilizing indoor leaching experiments and soil column migration experiments, a two-dimensional soil-groundwater model is established using the finite element method of COMSOL. This model quantitatively delineates the migration patterns of key pollutant components leached from coal gangue into the groundwater. The findings reveal that sulfate ions can migrate and infiltrate groundwater within a mere 7 years in the vadose zone of aeration. Moreover, the average concentration of iron ions in groundwater can reach approximately 58.3 mg/L. Convection, hydrodynamic dispersion, and adsorption emerge as the primary factors influencing pollution transport. Understanding the leaching patterns and environmental impacts of major pollutants in acidic coal gangue is crucial for predicting soil-groundwater pollution and implementing effective protective measures.},
}
@article {pmid38483497,
year = {2024},
author = {Yang, R and Feng, J and Tang, J and Sun, Y},
title = {Risk assessment and classification prediction for water environment treatment PPP projects.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {89},
number = {5},
pages = {1264-1281},
doi = {10.2166/wst.2024.052},
pmid = {38483497},
issn = {0273-1223},
mesh = {*Environment ; Risk Assessment ; *Risk Management ; },
abstract = {Water treatment public-private partnership (PPP) projects are pivotal for sustainable water management but are often challenged by complex risk factors. Efficient risk management in these projects is crucial, yet traditional methodologies often fall short of addressing the dynamic and intricate nature of these risks. Addressing this gap, this comprehensive study introduces an advanced risk classification prediction model tailored for water treatment PPP projects, aimed at enhancing risk management capabilities. The proposed model encompasses an intricate evaluation of crucial risk areas: the natural and ecological environments, socio-economic factors, and engineering entities. It delves into the complex relationships between these risk elements and the overall risk profile of projects. Grounded in a sophisticated ensemble learning framework employing stacking, our model is further refined through a weighted voting mechanism, significantly elevating its predictive accuracy. Rigorous validation using data from the Jiujiang City water environment system project Phase I confirms the model's superiority over standard machine learning models. The development of this model marks a significant stride in risk classification for water treatment PPP projects, offering a powerful tool for enhancing risk management practices. Beyond accurately predicting project risks, this model also aids in developing effective government risk management strategies.},
}
@article {pmid38483377,
year = {2024},
author = {Browning, CR and Pinchak, NP and Calder, CA and Boettner, B},
title = {Racial Differences in Activity Space Exposures and Everyday Perceptions of Safety Among Urban Youth.},
journal = {The Journal of adolescent health : official publication of the Society for Adolescent Medicine},
volume = {74},
number = {6},
pages = {1156-1163},
pmid = {38483377},
issn = {1879-1972},
support = {P2C HD042849/HD/NICHD NIH HHS/United States ; P2C HD058484/HD/NICHD NIH HHS/United States ; R01 DA032371/DA/NIDA NIH HHS/United States ; R01 HD088545/HD/NICHD NIH HHS/United States ; },
mesh = {Adolescent ; Child ; Female ; Humans ; Male ; *Black or African American/psychology ; Geographic Information Systems ; Ohio ; Perception ; *Residence Characteristics ; *Safety ; *Urban Population ; Violence/ethnology ; *White ; },
abstract = {PURPOSE: The everyday experience of safety promotes health and successful development during adolescence. To date, few studies have examined racial variation in the spatial determinants of in-the-moment perceived safety.<br><br>METHODS: Drawing on data from the Columbus, Ohio-based Adolescent Health and Development in Context study (N&#xa0;= 1,405), we consider the influence of intraindividual variability in Global Positioning System-based exposure to both high-proportion White urban neighborhoods and neighborhood violence for the everyday location-based safety perceptions of Black and White youth (ages 11-17) as captured by ecological momentary assessment.<br><br>RESULTS: Exposure to higher area-level violence reduces youths' safety perceptions. Momentary exposure to residentially White-dominated neighborhoods also reduces perceived safety, but only for Black youth who spend more time, on average, in White areas. In contrast, we observe some limited evidence that White youth perceive greater safety when in White neighborhoods if they spend more time in white neighborhoods on average.<br><br>DISCUSSION: These findings point to the need for greater attention to in situ experiences in understanding the origins of racial disparities in health and wellbeing. For Black youth, a restricted focus on the consequences of residing in Black segregated neighborhoods may obscure potentially health consequential exposures beyond these areas.},
}
@article {pmid38482998,
year = {2024},
author = {Furuya, S and Zheng, F and Lu, Q and Fletcher, JM},
title = {Separating Scarring Effect and Selection of Early-Life Exposures With Genetic Data.},
journal = {Demography},
volume = {61},
number = {2},
pages = {363-392},
doi = {10.1215/00703370-11239766},
pmid = {38482998},
issn = {1533-7790},
mesh = {Humans ; Infant ; Educational Status ; *Environmental Exposure ; Infant Mortality ; Life Change Events ; Prenatal Exposure Delayed Effects ; Gene-Environment Interaction ; },
abstract = {Causal life course research examining consequences of early-life exposures has largely relied on associations between early-life environments and later-life outcomes using exogenous environmental shocks. Nonetheless, even with (quasi-)randomized early-life exposures, these associations may reflect not only causation ("scarring") but also selection (i.e., which members are included in data assessing later life). Investigating this selection and its impacts on estimated effects of early-life conditions has, however, often been ignored because of a lack of pre-exposure data. This study proposes an approach for assessing and correcting selection, separately from scarring, using genetic measurements. Because genetic measurements are determined at the time of conception, any associations with early-life exposures should be interpreted as selection. Using data from the UK Biobank, we find that in utero exposure to a higher area-level infant mortality rate is associated with genetic predispositions correlated with better educational attainment and health. These findings point to the direction and magnitude of selection from this exposure. Corrections for this selection in examinations of effects of exposure on later educational attainment suggest underestimates of 26-74%; effects on other life course outcomes also vary across selection correction methods.},
}
@article {pmid38479865,
year = {2024},
author = {Kekalih, A and Adi, NP and Soemarko, DS},
title = {Preparation and Challenges in Developing a Big Data Analysis Framework in Occupational Medicine in Indonesia.},
journal = {Journal of UOEH},
volume = {46},
number = {1},
pages = {113-118},
doi = {10.7888/juoeh.46.113},
pmid = {38479865},
issn = {0387-821X},
mesh = {Humans ; *Artificial Intelligence ; *Occupational Medicine ; Big Data ; Indonesia ; Pandemics ; },
abstract = {This mini review explores the transformative potential of big data analysis and artificial intelligence (AI) in reforming occupational medicine in Indonesia. Emphasizing the preconditions, case studies, and benefits, it underscores the role of big data in enhancing worker well-being. The review highlights the importance of informative health big data, especially in high-risk industries, with examples of case studies of AI implementation in occupational medicine during the COVID-19 pandemic and other relevant scenarios. While acknowledging the challenges of AI implementation, the essay identifies the role of academic and professional organizations as pioneers in big data utilization. Six potential benefits that are identified, including improved patient care and efficient resource allocation, demonstrate the transformative impact of big data analysis. The proposed pathway of preparation underscores the need for awareness, skill enhancement, and collaboration, addressing challenges in data management and stakeholder engagement. The conclusion emphasizes continuous assessment, feasibility studies, and commitment as essential steps in advancing occupational medicine through big data analysis.},
}
@article {pmid38476212,
year = {2024},
author = {Kearsley, E and Verbeeck, H and Stoffelen, P and Janssens, SB and Yakusu, EK and Kosmala, M and De Mil, T and Bauters, M and Kitima, ER and Ndiapo, JM and Chuda, AL and Richardson, AD and Wingate, L and Ilondea, BA and Beeckman, H and van den Bulcke, J and Boeckx, P and Hufkens, K},
title = {Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest.},
journal = {Plant-environment interactions (Hoboken, N.J.)},
volume = {5},
number = {2},
pages = {e10136},
pmid = {38476212},
issn = {2575-6265},
abstract = {Tropical forest phenology directly affects regional carbon cycles, but the relation between species-specific and whole-canopy phenology remains largely uncharacterized. We present a unique analysis of historical tropical tree phenology collected in the central Congo Basin, before large-scale impacts of human-induced climate change. Ground-based long-term (1937-1956) phenological observations of 140 tropical tree species are recovered, species-specific phenological patterns analyzed and related to historical meteorological records, and scaled to characterize stand-level canopy dynamics. High phenological variability within and across species and in climate-phenology relationships is observed. The onset of leaf phenophases in deciduous species was triggered by drought and light availability for a subset of species and showed a species-specific decoupling in time along a bi-modal seasonality. The majority of the species remain evergreen, although central African forests experience relatively low rainfall. Annually a maximum of 1.5% of the canopy is in leaf senescence or leaf turnover, with overall phenological variability dominated by a few deciduous species, while substantial variability is attributed to asynchronous events of large and/or abundant trees. Our results underscore the importance of accounting for constituent signals in canopy-wide scaling and the interpretation of remotely sensed phenology signals.},
}
@article {pmid38474911,
year = {2024},
author = {Omega, RL and Ishigaki, Y and Permana, S and Matsumoto, Y and Yamamoto, K and Shozugawa, K and Hori, M},
title = {Low-Cost Sensor Deployment on a Public Minibus in Fukushima Prefecture.},
journal = {Sensors (Basel, Switzerland)},
volume = {24},
number = {5},
pages = {},
pmid = {38474911},
issn = {1424-8220},
support = {20KK0231//JSPS KAKENHI/ ; },
mesh = {*Radiation Monitoring ; *Fukushima Nuclear Accident ; Motor Vehicles ; Geographic Information Systems ; Electrocardiography ; Japan ; Radiation Dosage ; },
abstract = {This study analyzed radiation dose data to observe the annual decline in ambient radiation doses and assess the factors contributing to fluctuations in reconstructed areas of the Fukushima prefecture. Utilizing a novel mobile monitoring system installed on a community minibus, the study employed a cost-effective sensor, namely, Pocket Geiger which was integrated with a microcontroller and telecommunication system for data transfer, access, visualization, and accumulation. The study area included the region between Okuma and Tomioka towns. The ambient dose rate recorded along the minibus route was depicted on a map, averaged within a 1 × 1 km mesh created with the Quantum Geographic Information System. To ensure accuracy, the shielding factor of the minibus material is determined to adjust the dose readings. A significant decrease (p < 0.001) in the radiation dose ranges from 2022 to 2023 was observed. The land use classification by the Advanced Land Observation Satellite revealed an ecological half-life ranging from 2.41 years to 1 year, suggesting a rapid radiation decay across all land types. This underscores the close connection between radiation attenuation and environmental factors, as well as decontamination efforts across diverse land categories.},
}
@article {pmid38474163,
year = {2024},
author = {Kozicki, M and Sąsiadek-Andrzejczak, E and Wach, R and Maras, P},
title = {Flexible Cotton Fabric-Based Ionizing Radiation Dosimeter for 2D Dose Distribution Measurements over a Wide Dose Range at High Dose Rates.},
journal = {International journal of molecular sciences},
volume = {25},
number = {5},
pages = {},
pmid = {38474163},
issn = {1422-0067},
mesh = {*Radiation Dosimeters ; *Radiation, Ionizing ; Cellulose ; Radiometry/methods ; },
abstract = {This work presents an ecological, flexible 2D radiochromic dosimeter for measuring ionizing radiation in the kilogray dose range. Cotton woven fabric made of cellulose was volume-modified with nitrotetrazolium blue chloride as a radiation-sensitive compound. Its features include a color change during exposure from yellowish to purple-brown and flexibility that allows it to adapt to various shapes. It was found that (i) the dose response is up to ~80 kGy, (ii) it is independent of the dose rate for 1.1-73.1 kGy/min, (iii) it can be measured in 2D using a flatbed scanner, (iv) the acquired images can be filtered using a mean filter, which improves its dose resolution, (v) the dose resolution is -0.07 to -0.4 kGy for ~0.6 to ~75.7 kGy for filtered images, and (vi) two linear dose subranges can be distinguished: ~0.6 to ~7.6 kGy and ~9.9 to ~62.0 kGy. The dosimeter combined with flatbed scanner reading and data processing using dedicated software packages constitutes a comprehensive system for measuring dose distributions for objects with complex shapes.},
}
@article {pmid38473771,
year = {2024},
author = {Li, Z and Fan, H and Yang, L and Wang, S and Hong, D and Cui, W and Wang, T and Wei, C and Sun, Y and Wang, K and Liu, Y},
title = {Multi-Omics Analysis of the Effects of Soil Amendment on Rapeseed (Brassica napus L.) Photosynthesis under Drip Irrigation with Brackish Water.},
journal = {International journal of molecular sciences},
volume = {25},
number = {5},
pages = {},
pmid = {38473771},
issn = {1422-0067},
support = {2022B02021-3-1//The research was funded by the Major Science and Technology Project and Key Research and Development of Autonomous region, Xinjiang, China/ ; (Title: Research and demonstration on the key technologies of soil improvement and ecological prevention and control in the desert desert belt of Southern Xinjiang)//The Central Government Guides Local Science and Technology Development Fund Projects/ ; CXFZ202207//Shihezi University Innovative Development Special Projectand, China/ ; },
mesh = {*Brassica napus ; Antioxidants ; Multiomics ; *Brassica rapa ; Photosynthesis ; Crops, Agricultural ; Water ; },
abstract = {Drip irrigation with brackish water increases the risk of soil salinization while alleviating water shortage in arid areas. In order to alleviate soil salinity stress on crops, polymer soil amendments are increasingly used. But the regulation mechanism of a polymer soil amendment composed of polyacrylamide polyvinyl alcohol, and manganese sulfate (PPM) on rapeseed photosynthesis under drip irrigation with different types of brackish water is still unclear. In this field study, PPM was applied to study the responses of the rapeseed (Brassica napus L.) phenotype, photosynthetic physiology, transcriptomics, and metabolomics at the peak flowering stage under drip irrigation with water containing 6 g·L[-1] NaCl (S) and Na2CO3 (A). The results showed that the inhibitory effect of the A treatment on rapeseed photosynthesis was greater than that of the S treatment, which was reflected in the higher Na[+] content (73.30%) and lower photosynthetic-fluorescence parameters (6.30-61.54%) and antioxidant enzyme activity (53.13-77.10%) of the A-treated plants. The application of PPM increased the biomass (63.03-75.91%), photosynthetic parameters (10.55-34.06%), chlorophyll fluorescence parameters (33.83-62.52%), leaf pigment content (10.30-187.73%), and antioxidant enzyme activity (28.37-198.57%) under S and A treatments. However, the difference is that under the S treatment, PPM regulated the sulfur metabolism, carbon fixation and carbon metabolism pathways in rapeseed leaves. And it also regulated the photosynthesis-, oxidative phosphorylation-, and TCA cycle-related metabolic pathways in rapeseed leaves under A treatment. This study will provide new insights for the application of polymer materials to tackle the salinity stress on crops caused by drip irrigation with brackish water, and solve the difficulty in brackish water utilization.},
}
@article {pmid38467837,
year = {2024},
author = {Bhosle, A and Bae, S and Zhang, Y and Chun, E and Avila-Pacheco, J and Geistlinger, L and Pishchany, G and Glickman, JN and Michaud, M and Waldron, L and Clish, CB and Xavier, RJ and Vlamakis, H and Franzosa, EA and Garrett, WS and Huttenhower, C},
title = {Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease.},
journal = {Molecular systems biology},
volume = {20},
number = {4},
pages = {338-361},
pmid = {38467837},
issn = {1744-4292},
support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 CA230551/CA/NCI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Inflammatory Bowel Diseases/drug therapy/metabolism ; *Colitis ; Metabolome ; Bile Acids and Salts ; },
abstract = {Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates.},
}
@article {pmid38465958,
year = {2024},
author = {Rivero-Marcos, M and Lasa, B and Neves, T and Zamarreño, &#xc1;M and García-Mina, JM and García-Olaverri, C and Aparicio-Tejo, PM and Cruz, C and Ariz, I},
title = {Plant ammonium sensitivity is associated with external pH adaptation, repertoire of nitrogen transporters, and nitrogen requirement.},
journal = {Journal of experimental botany},
volume = {75},
number = {11},
pages = {3557-3578},
pmid = {38465958},
issn = {1460-2431},
support = {RYC2021-032345-I//European Union Next Generation EU/PRTR/ ; },
mesh = {*Nitrogen/metabolism ; Hydrogen-Ion Concentration ; *Ammonium Compounds/metabolism ; Nitrates/metabolism ; Plant Proteins/metabolism/genetics ; Plants/metabolism ; Adaptation, Physiological ; },
abstract = {Modern crops exhibit diverse sensitivities to ammonium as the primary nitrogen source, influenced by environmental factors such as external pH and nutrient availability. Despite its significance, there is currently no systematic classification of plant species based on their ammonium sensitivity. We conducted a meta-analysis of 50 plant species and present a new classification method based on the comparison of fresh biomass obtained under ammonium and nitrate nutrition. The classification uses the natural logarithm of the biomass ratio as the size effect indicator of ammonium sensitivity. This numerical parameter is associated with critical factors for nitrogen demand and form preference, such as Ellenberg indicators and the repertoire of nitrogen transporters for ammonium and nitrate uptake. Finally, a comparative analysis of the developmental and metabolic responses, including hormonal balance, is conducted in two species with divergent ammonium sensitivity values in the classification. Results indicate that nitrate has a key role in counteracting ammonium toxicity in species with a higher abundance of genes encoding NRT2-type proteins and fewer of those encoding the AMT2-type proteins. Additionally, the study demonstrates the reliability of the phytohormone balance and methylglyoxal content as indicators for anticipating ammonium toxicity.},
}
@article {pmid38461307,
year = {2024},
author = {Zhang, L and Li, H and Shi, M and Ren, K and Zhang, W and Cheng, Y and Wang, Y and Xia, XQ},
title = {FishSNP: a high quality cross-species SNP database of fishes.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {286},
pmid = {38461307},
issn = {2052-4463},
mesh = {Animals ; *Fishes/genetics ; Genome ; *Genomics ; *Polymorphism, Single Nucleotide ; Reproducibility of Results ; *Databases, Genetic ; },
abstract = {The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP (http://bioinfo.ihb.ac.cn/fishsnp), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.},
}
@article {pmid38452667,
year = {2024},
author = {Chen, X and Zhu, Y and Zheng, W and Yan, S and Li, Y and Xie, S},
title = {Elucidating doxycycline biotransformation mechanism by Chryseobacterium sp. WX1: Multi-omics insights.},
journal = {Journal of hazardous materials},
volume = {469},
number = {},
pages = {133975},
doi = {10.1016/j.jhazmat.2024.133975},
pmid = {38452667},
issn = {1873-3336},
mesh = {*Doxycycline ; *Chryseobacterium/genetics ; Multiomics ; Proteomics ; Biotransformation ; },
abstract = {Doxycycline (DOX) represents a second-generation tetracycline antibiotic that persists as a challenging-to-degrade contaminant in environmental compartments. Despite its ubiquity, scant literature exists on bacteria proficient in DOX degradation. This study marked a substantial advancement in this field by isolating Chryseobacterium sp. WX1 from an activated sludge enrichment culture, showcasing its unprecedented ability to completely degrade 50 mg/L of DOX within 44 h. Throughout the degradation process, seven biotransformation products were identified, revealing a complex pathway that began with the hydroxylation of DOX, followed by a series of transformations. Employing an integrated multi-omics approach alongside in vitro heterologous expression assays, our study distinctly identified the tetX gene as a critical facilitator of DOX hydroxylation. Proteomic analyses further pinpointed the enzymes postulated to mediate the downstream modifications of DOX hydroxylation derivatives. The elucidated degradation pathway encompassed several key biological processes, such as the microbial transmembrane transport of DOX and its intermediates, the orchestration of enzyme synthesis for transformation, energy metabolism, and other gene-regulated biological directives. This study provides the first insight into the adaptive biotransformation strategies of Chryseobacterium under DOX-induced stress, highlighting the potential applications of this strain to augment DOX removal in wastewater treatment systems containing high concentrations of DOX.},
}
@article {pmid38451645,
year = {2024},
author = {Souza, IM and Araújo, EM and Silva Filho, AMD},
title = {Incomplete recording of race/colour in health information systems in Brazil: time trend, 2009-2018.},
journal = {Ciencia &amp; saude coletiva},
volume = {29},
number = {3},
pages = {e05092023},
doi = {10.1590/1413-81232024293.05092023},
pmid = {38451645},
issn = {1678-4561},
mesh = {Humans ; Black People ; Brazil/epidemiology ; *Health Information Systems ; *Hospital Information Systems ; Racial Groups ; Ethnicity ; },
abstract = {This ecological study of time trends and multiple groups evaluated incompleteness in the race/colour field of Brazilian health information system records and the related time trend, 2009-2018, for the diseases and disorders most prevalent in the black population. The Romero and Cunha (2006) classification was applied in order to examine incompleteness using secondary data from Brazil's National Notifiable Diseases System, Hospital Information System and Mortality Information System, by administrative regions of Brazil, while percentage underreporting and time trend were calculated using simple linear regression models with Prais-Winsten correction (p-value<0.05). All records scored poorly except those for mortality from external causes (excellent), tuberculosis (good) and infant mortality (fair). An overall downward trend was observed in percentage incompleteness. Analysis by region found highest mean incompleteness in the North (30.5%), Northeast (33.3%) and Midwest (33.0%) regions. The Southeast and Northeast regions showed the strongest downward trends. The findings intended to increase visibility on the implications of the race/color field for health equity.},
}
@article {pmid38448699,
year = {2024},
author = {Tao, F and Houlton, BZ and Frey, SD and Lehmann, J and Manzoni, S and Huang, Y and Jiang, L and Mishra, U and Hungate, BA and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Wang, YP and Ahrens, B and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y},
title = {Reply to: Model uncertainty obscures major driver of soil carbon.},
journal = {Nature},
volume = {627},
number = {8002},
pages = {E4-E6},
pmid = {38448699},
issn = {1476-4687},
mesh = {*Uncertainty ; },
}
@article {pmid38447714,
year = {2024},
author = {Liu, Y and You, S and Ding, L and Yuan, F and Sun, Y},
title = {Hepatotoxic effects of chronic exposure to environmentally relevant concentrations of Di-(2-ethylhexyl) phthalate (DEHP) on crucian carp: Insights from multi-omics analyses.},
journal = {The Science of the total environment},
volume = {923},
number = {},
pages = {171447},
doi = {10.1016/j.scitotenv.2024.171447},
pmid = {38447714},
issn = {1879-1026},
mesh = {Animals ; *Diethylhexyl Phthalate/metabolism ; Ecosystem ; *Carps/metabolism ; Multiomics ; *Phthalic Acids/toxicity/analysis ; },
abstract = {Di-(2-ethylhexyl) phthalate (DEHP) is an extensively used phthalate esters (PAEs) that raise growing ecotoxicological concerns due to detrimental effects on living organisms and ecosystems. This study performed hepatotoxic investigations on crucian carp under chronic low-dosage (CLD) exposure to DEHP at environmentally relevant concentrations (20-500 μg/L). The results demonstrated that the CLD exposure induced irreversible damage to the liver tissue. Multi-omics (transcriptomics and metabolomics) analyses revealed the predominant toxicological mechanisms underlying DEHP-induced hepatotoxicity by inhibiting energy production pathways and the up-regulation of the purine metabolism. Disruption of metabolic pathways led to excessive reactive oxygen species (ROS) production and subsequent oxidative stress. The adverse metabolic effects were exacerbated by an interplay between oxidative stress and endoplasmic reticulum stress. This study not only provides new mechanistic insights into the ecotoxicological effects of DEHP under chronic low-dosage exposure, but also suggests a potential strategy for further ecological risk assessment of PAEs.},
}
@article {pmid38447388,
year = {2024},
author = {van der Feltz-Cornelis, C and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A},
title = {Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis.},
journal = {General hospital psychiatry},
volume = {88},
number = {},
pages = {10-22},
doi = {10.1016/j.genhosppsych.2024.02.009},
pmid = {38447388},
issn = {1873-7714},
mesh = {Humans ; *COVID-19/epidemiology ; Prevalence ; *Post-Acute COVID-19 Syndrome ; Cognitive Dysfunction/epidemiology/etiology ; Mental Disorders/epidemiology ; },
abstract = {OBJECTIVE: Long COVID can include impaired cognition ('brain fog'; a term encompassing multiple symptoms) and mental health conditions. We performed a systematic review and meta-analysis to estimate their prevalence and to explore relevant factors associated with the incidence of impaired cognition and mental health conditions.<br><br>METHODS: Searches were conducted in Medline and PsycINFO to cover the start of the pandemic until August 2023. Included studies reported prevalence of mental health conditions and brain fog in adults with long COVID after clinically-diagnosed or PCR-confirmed SARS-CoV-2 infection.<br><br>FINDINGS: 17 studies were included, reporting 41,249 long COVID patients. Across all timepoints (3-24&#xa0;months), the combined prevalence of mental health conditions and brain fog was 20&#xb7;4% (95% CI 11&#xb7;1%-34&#xb7;4%), being lower among those previously hospitalised than in community-managed patients(19&#xb7;5 vs 29&#xb7;7% respectively; p&#xa0;=&#xa0;0&#xb7;047). The odds of mental health conditions and brain fog increased over time and when validated instruments were used. Odds of brain fog significantly decreased with increasing vaccination rates (p&#xa0;=&#xa0;&#xb7;000).<br><br>CONCLUSIONS: Given the increasing prevalence of mental health conditions and brain fog over time, preventive interventions and treatments are needed. Research is needed to explore underlying mechanisms that could inform further research in development of effective treatments. The reduced risk of brain fog associated with vaccination emphasizes the need for ongoing vaccination programs.},
}
@article {pmid38445504,
year = {2024},
author = {Kudamba, A and Kasolo, JN and Bbosa, GS and Lugaajju, A and Wabinga, H and Kafeero, HM and Ssenku, JE and Alemu, SO and Walusansa, A and Niyonzima, N and Muwonge, H},
title = {Review of Herbal Medicinal Plants Used in the Management of Cancers in the East Africa Region from 2019 to 2023.},
journal = {Integrative cancer therapies},
volume = {23},
number = {},
pages = {15347354241235583},
pmid = {38445504},
issn = {1552-695X},
mesh = {Male ; Humans ; *Plants, Medicinal ; Africa, Eastern ; *Prostatic Neoplasms ; *Apocynaceae ; Databases, Factual ; },
abstract = {BACKGROUND: In the East African region, herbal plants are essential in the treatment and control of cancer. Given the diverse ecological and cultural makeup of the regional states, it is likely that different ethnic groups will use the same or different plants for the same or different diseases. However, since 2019, this has not been compiled into a single study.<br><br>PURPOSE: The study aimed to compile and record the medicinal plants utilized in East Africa from April 2019 to June 2023 to treat various cancer types.<br><br>MATERIALS AND METHODS: The study examined 13 original studies that included ethnobotanical research conducted in East Africa. They were retrieved from several internet databases, including Google Scholar, Scopus, PubMed/Medline, Science Direct, and Research for Life. The study retrieved databases on plant families and species, plant parts used, preparation methods and routes of administration, and the country where the ethnobotanical field surveys were conducted. Graphs were produced using the GraphPad Prism 8.125 program (GraphPad Software, Inc., San Diego, CA). Tables and figures were used to present the data, which had been condensed into percentages and frequencies.<br><br>RESULTS: A total of 105 different plant species from 45 different plant families were identified, including Asteraceae (14), Euphorbiaceae (12), Musaceae (8), and Apocynaceae (7). Uganda registered the highest proportion (46% of the medicinal plants used). The most commonly mentioned medicinal plant species in cancer management was Prunus africana. Herbs (32%), trees and shrubs (28%), and leaves (45%) constituted the majority of herbal remedies. Most herbal remedies were prepared by boiling (decoction) and taken orally (57%).<br><br>CONCLUSION: East Africa is home to a wide variety of medicinal plant species that local populations and herbalists, or TMP, frequently use in the treatment of various types of cancer. The most frequently used families are Asteraceae and Euphorbiaceae, with the majority of species being found in Uganda. The most frequently utilized plant species is Prunus africana. Studies on the effectiveness of Prunus africana against other malignancies besides prostate cancer are required.},
}
@article {pmid38444395,
year = {2024},
author = {Liu, Y and Li, L and Feng, J and Wan, B and Tu, Q and Cai, W and Jin, F and Tang, G and Rodrigues, LR and Zhang, X and Yin, J and Zhang, Y},
title = {Modulation of chronic obstructive pulmonary disease progression by antioxidant metabolites from Pediococcus pentosaceus: enhancing gut probiotics abundance and the tryptophan-melatonin pathway.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2320283},
pmid = {38444395},
issn = {1949-0984},
mesh = {Animals ; Mice ; Antioxidants ; Pediococcus pentosaceus ; *Melatonin/pharmacology ; Tryptophan ; *Gastrointestinal Microbiome ; *Probiotics ; *Pulmonary Disease, Chronic Obstructive ; },
abstract = {Chronic obstructive pulmonary disease (COPD), a condition primarily linked to oxidative stress, poses significant health burdens worldwide. Recent evidence has shed light on the association between the dysbiosis of gut microbiota and COPD, and their metabolites have emerged as potential modulators of disease progression through the intricate gut-lung axis. Here, we demonstrate the efficacy of oral administration of the probiotic Pediococcus pentosaceus SMM914 (SMM914) in delaying the progression of COPD by attenuating pulmonary oxidative stress. Specially, SMM914 induces a notable shift in the gut microbiota toward a community structure characterized by an augmented abundance of probiotics producing short-chain fatty acids and antioxidant metabolisms. Concurrently, SMM914 synthesizes L-tryptophanamide, 5-hydroxy-L-tryptophan, and 3-sulfino-L-alanine, thereby enhancing the tryptophan-melatonin pathway and elevating 6-hydroxymelatonin and hypotaurine in the lung environment. This modulation amplifies the secretion of endogenous anti-inflammatory factors, diminishes macrophage polarization toward the M1 phenotype, and ultimately mitigates the oxidative stress in mice with COPD. The demonstrated efficacy of the probiotic intervention, specifically with SMM914, not only highlights the modulation of intestine microbiota but also emphasizes the consequential impact on the intricate interplay between the gastrointestinal system and respiratory health.},
}
@article {pmid38443441,
year = {2024},
author = {Zhang, Z and Xu, H and Zhu, G},
title = {Incorporating high-frequency information into edge convolution for link prediction in complex networks.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {5437},
pmid = {38443441},
issn = {2045-2322},
support = {1908085QF283//Natural Science Foundation of Anhui Province/ ; 2019jb08//Doctoral Startup Research Fund of Suzhou University/ ; 2021bsk016//Doctoral Startup Research Fund of Suzhou University/ ; GXXT-2022-047//University Synergy Innovation Program of Anhui Province/ ; 2021XJPT50, 2022xhx004, 2022xhx099//Scientific Research Projects Funded by Suzhou University/ ; AE202201//Open Research Fund of National Engineering Research Center for Agro-Ecological Big Data Analysis &amp; Application, Anhui University/ ; },
abstract = {Link prediction in complex networks aims to mine hidden or to-be-generated links between network nodes, which plays a significant role in fields such as the cold start of recommendation systems, knowledge graph completion and biomedical experiments. The existing link prediction models based on graph neural networks, such as graph convolution neural networks, often only learn the low-frequency information reflecting the common characteristics of nodes while ignoring the high-frequency information reflecting the differences between nodes when learning node representation, which makes the corresponding link prediction models show over smoothness and poor performance. Focusing on links in complex networks, this paper proposes an edge convolutional graph neural network EdgeConvHiF that fuses high-frequency node information to achieve the representation learning of links so that link prediction can be realized by implementing the classification of links. EdgeConvHiF can also be employed as a baseline, and extensive experiments on real-world benchmarks validate that EdgeConvHiF not only has high stability but also has more advantages than the existing representative baselines.},
}
@article {pmid38443432,
year = {2024},
author = {Ge, X and Peng, L and Deng, Z and Du, J and Sun, C and Wang, B},
title = {Chromosome-scale genome assemblies of Himalopsyche anomala and Eubasilissa splendida (Insecta: Trichoptera).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {267},
pmid = {38443432},
issn = {2052-4463},
support = {32271631//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Comparative Genomic Hybridization ; Ecology ; *Insecta/genetics ; *Genome, Insect ; *Databases, Genetic ; },
abstract = {Trichoptera is one of the most evolutionarily successful aquatic insect lineages and is highly valued value in adaptive evolution research. This study presents the chromosome-level genome assemblies of Himalopsyche anomala and Eubasilissa splendida achieved using PacBio, Illumina, and Hi-C sequencing. For H. anomala and E. splendida, assembly sizes were 663.43 and 859.28 Mb, with scaffold N50 lengths of 28.44 and 31.17 Mb, respectively. In H. anomala and E. splendida, we anchored 24 and 29 pseudochromosomes, and identified 11,469 and 10,554 protein-coding genes, respectively. The high-quality genomes of H. anomala and E. splendida provide critical genomic resources for understanding the evolution and ecology of Trichoptera and performing comparative genomics analyses.},
}
@article {pmid38443357,
year = {2024},
author = {Zhou, H and Zhang, X and Liu, H and Ma, J and Hao, F and Ye, H and Wang, Y and Zhang, S and Yue, M and Zhao, P},
title = {Chromosome-level genome assembly of Platycarya strobilacea.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {269},
pmid = {38443357},
issn = {2052-4463},
support = {32370386, 32070372, and 32200295//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Asia, Eastern ; Biological Evolution ; Chromosomes ; *Juglandaceae/genetics ; Phylogeny ; *Genome, Plant ; *Databases, Genetic ; },
abstract = {Platycarya strobilacea belongs to the walnut family (Juglandaceae), is commonly known as species endemic to East Asia, and is an ecologically important, wind pollinated, woody deciduous tree. To facilitate this ancient tree for the ecological value and conservation of this ancient tree, we report a new high-quality genome assembly of P. strobilacea. The genome size was 677.30 Mb, with a scaffold N50 size of 45,791,698 bp, and 98.43% of the assembly was anchored to 15 chromosomes. We annotated 32,246 protein-coding genes in the genome, of which 96.30% were functionally annotated in six databases. This new high-quality assembly of P. strobilacea provide valuable resource for the phylogenetic and evolutionary analysis of the walnut family and angiosperm.},
}
@article {pmid38442095,
year = {2024},
author = {Tamosiunaite, M and Tetzlaff, C and Wörgötter, F},
title = {Unsupervised learning of perceptual feature combinations.},
journal = {PLoS computational biology},
volume = {20},
number = {3},
pages = {e1011926},
pmid = {38442095},
issn = {1553-7358},
mesh = {Animals ; *Unsupervised Machine Learning ; *Models, Neurological ; Neurons/physiology ; },
abstract = {In many situations it is behaviorally relevant for an animal to respond to co-occurrences of perceptual, possibly polymodal features, while these features alone may have no importance. Thus, it is crucial for animals to learn such feature combinations in spite of the fact that they may occur with variable intensity and occurrence frequency. Here, we present a novel unsupervised learning mechanism that is largely independent of these contingencies and allows neurons in a network to achieve specificity for different feature combinations. This is achieved by a novel correlation-based (Hebbian) learning rule, which allows for linear weight growth and which is combined with a mechanism for gradually reducing the learning rate as soon as the neuron's response becomes feature combination specific. In a set of control experiments, we show that other existing advanced learning rules cannot satisfactorily form ordered multi-feature representations. In addition, we show that networks, which use this type of learning always stabilize and converge to subsets of neurons with different feature-combination specificity. Neurons with this property may, thus, serve as an initial stage for the processing of ecologically relevant real world situations for an animal.},
}
@article {pmid38441325,
year = {2024},
author = {Davies, H and Blackwell, E and Fins, IS and Noble, PJM and Pinchbeck, G and Pirmohamed, M and Killick, DR},
title = {Recording of suspected adverse drug reaction reporting in veterinary free-text clinical narratives.},
journal = {The Journal of small animal practice},
volume = {65},
number = {6},
pages = {361-367},
doi = {10.1111/jsap.13721},
pmid = {38441325},
issn = {1748-5827},
support = {VM0541//Veterinary Medicines Directorate/ ; SRP 02.21//British Small Animal Veterinary Association/ ; 204822/z/16/z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Adverse Drug Reaction Reporting Systems/statistics &amp; numerical data ; Animals ; *Drug-Related Side Effects and Adverse Reactions/veterinary ; Data Mining ; Veterinary Drugs/adverse effects ; Electronic Health Records ; Veterinary Medicine ; Pharmacovigilance ; },
abstract = {OBJECTIVES: To use text mining approaches to identify instances of suspected adverse drug reactions recorded in first opinion veterinary free-text clinical narratives, and to evaluate whether these were also reported to either the Veterinary Medicines Directorate or the relevant Marketing Authorisation holder in order to derive an estimate of the suspected adverse drug reaction (sADR) minimum under-reporting rate. To characterise sADR reports and explore whether particular features are associated with report submission.<br><br>MATERIALS AND METHODS: Two regular expressions were developed to identify mentions of "adverse drug reactions" and "side effects" in the free-text clinical narratives of electronic health records contained within the Small Animal Veterinary Surveillance Network database. Consultations containing a match for the developed regular expressions were manually reviewed for inclusion and further classified to determine the suspected product, seriousness and expectedness of the event, and an indication of whether the event had been reported. The associations between event characteristics and reporting were explored using Fisher's exact tests.<br><br>RESULTS: A total of 10,565 records were manually reviewed from which 827 sADRs were identified. Approximately 90% of these sADRs were not recorded as reported. Suspected adverse drug reactions that were not considered "expected" were recorded as reported more frequently than "expected" sADRs. However, clinical severity did not appear to impact on whether there was a record of reporting.<br><br>CLINICAL SIGNIFICANCE: This is the first estimate of under reporting sADRs based on real world evidence from veterinary clinical records. The under-reporting rate implied by this study highlights that further interventions are required to improve reporting rate within the veterinary profession in order to support pharmacovigilance activities and improve drug safety.},
}
@article {pmid38438998,
year = {2024},
author = {Wu, LF and Zhu, WG and Yu, EP and Cao, HL and Wang, ZF},
title = {Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant.},
journal = {BMC genomic data},
volume = {25},
number = {1},
pages = {24},
pmid = {38438998},
issn = {2730-6844},
mesh = {*Seeds ; *Plant Weeds ; Allelopathy ; China ; Databases, Factual ; },
abstract = {OBJECTIVES: Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant, it can also be used in the management of aquatic weeds. Here, we present its assembled and annotated genome to help shed light on medial and allelopathic substrates and facilitate their conservation.<br><br>DATA DESCRIPTION: Genomic DNA and RNA extracted from B. schreberi leaf tissues were used for whole genome and RNA sequencing using a Nanopore and/or MGI sequencer. The assembly was 1,055,148,839&#xa0;bp in length, with 92 contigs and an N50 of 22,379,495&#xa0;bp. The repetitive elements in the assembly were 555,442,205&#xa0;bp. A completeness assessment of the assembly with BUSCO and compleasm indicated 88.4 and 90.9% completeness in the Eudicots database and 95.4 and 96.6% completeness in the Embryphyta database. Gene annotation revealed 67,747 genes that coded for 73,344 proteins.},
}
@article {pmid38436579,
year = {2024},
author = {Qian, J and Qian, L and Pu, N and Bi, Y and Wilhelms, A and Norra, S},
title = {An Intelligent Early Warning System for Harmful Algal Blooms: Harnessing the Power of Big Data and Deep Learning.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {35},
pages = {15607-15618},
doi = {10.1021/acs.est.3c03906},
pmid = {38436579},
issn = {1520-5851},
mesh = {*Deep Learning ; *Harmful Algal Bloom ; *Big Data ; *Environmental Monitoring/methods ; Lakes ; },
abstract = {Harmful algal blooms (HABs) pose a significant ecological threat and economic detriment to freshwater environments. In order to develop an intelligent early warning system for HABs, big data and deep learning models were harnessed in this study. Data collection was achieved utilizing the vertical aquatic monitoring system (VAMS). Subsequently, the analysis and stratification of the vertical aquatic layer were conducted employing the "DeepDPM-Spectral Clustering" method. This approach drastically reduced the number of predictive models and enhanced the adaptability of the system. The Bloomformer-2 model was developed to conduct both single-step and multistep predictions of Chl-a, integrating the " Alert Level Framework" issued by the World Health Organization to accomplish early warning for HABs. The case study conducted in Taihu Lake revealed that during the winter of 2018, the water column could be partitioned into four clusters (Groups W1-W4), while in the summer of 2019, the water column could be partitioned into five clusters (Groups S1-S5). Moreover, in a subsequent predictive task, Bloomformer-2 exhibited superiority in performance across all clusters for both the winter of 2018 and the summer of 2019 (MAE: 0.175-0.394, MSE: 0.042-0.305, and MAPE: 0.228-2.279 for single-step prediction; MAE: 0.184-0.505, MSE: 0.101-0.378, and MAPE: 0.243-4.011 for multistep prediction). The prediction for the 3 days indicated that Group W1 was in a Level I alert state at all times. Conversely, Group S1 was mainly under an Level I alert, with seven specific time points escalating to a Level II alert. Furthermore, the end-to-end architecture of this system, coupled with the automation of its various processes, minimized human intervention, endowing it with intelligent characteristics. This research highlights the transformative potential of integrating big data and artificial intelligence in environmental management and emphasizes the importance of model interpretability in machine learning applications.},
}
@article {pmid38436026,
year = {2024},
author = {Specker, F and Paz, A and Crowther, TW and Maynard, DS},
title = {Treemendous: an R package for integrating taxonomic information across backbones.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16896},
pmid = {38436026},
issn = {2167-8359},
mesh = {*Biodiversity ; Databases, Factual ; *Ecology ; Forests ; Software ; Trees ; },
abstract = {Standardizing and translating species names from different databases is key to the successful integration of data sources in biodiversity research. There are numerous taxonomic name-resolution applications that implement increasingly powerful name-cleaning and matching approaches, allowing the user to resolve species relative to multiple backbones simultaneously. Yet there remains no principled approach for combining information across these underlying taxonomic backbones, complicating efforts to combine and merge species lists with inconsistent and conflicting taxonomic information. Here, we present Treemendous, an open-source software package for the R programming environment that integrates taxonomic relationships across four publicly available backbones to improve the name resolution of tree species. By mapping relationships across the backbones, this package can be used to resolve datasets with conflicting and inconsistent taxonomic origins, while ensuring the resulting species are accepted and consistent with a single reference backbone. The user can chain together different functionalities ranging from simple matching to a single backbone, to graph-based iterative matching using synonym-accepted relations across all backbones in the database. In addition, the package allows users to 'translate' one tree species list into another, streamlining the assimilation of new data into preexisting datasets or models. The package provides a flexible workflow depending on the use case, and can either be used as a stand-alone name-resolution package or in conjunction with existing packages as a final step in the name-resolution pipeline. The Treemendous package is fast and easy to use, allowing users to quickly merge different data sources by standardizing their species names according to the regularly updated database. By combining taxonomic information across multiple backbones, the package increases matching rates and minimizes data loss, allowing for more efficient translation of tree species datasets to aid research into forest biodiversity and tree ecology.},
}
@article {pmid38434748,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Diamond-back Marble, Eudemis profundana (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {184},
pmid = {38434748},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Eudemis profundana (the Diamond-back Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.},
}
@article {pmid38434745,
year = {2023},
author = {Boyes, D and Lees, DC and Hammond, J and , and , and , and , and , and , and , },
title = {The genome sequence of the Ashy Button, Acleris sparsana (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {241},
pmid = {38434745},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Acleris sparsana (the Ashy Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 589.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,123 protein coding genes.},
}
@article {pmid38434742,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Minor Shoulder-knot, Brachylomia viminalis (Fabricius, 1777).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {245},
pmid = {38434742},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Brachylomia viminalis (the Minor Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 782.2 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,191 protein coding genes.},
}
@article {pmid38434736,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Orange Footman, Eilema sororcula (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {282},
pmid = {38434736},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Eilema sororcula (the Orange Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 729.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,093 protein coding genes.},
}
@article {pmid38434623,
year = {2023},
author = {Thiébaut, A and Altenhoff, AM and Campli, G and Glover, N and Dessimoz, C and Waterhouse, RM},
title = {DrosOMA: the Drosophila Orthologous Matrix browser.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {936},
pmid = {38434623},
issn = {2046-1402},
mesh = {Animals ; *Drosophila/genetics ; Comparative Genomic Hybridization ; Databases, Factual ; *Evolution, Molecular ; Genomics ; },
abstract = {BACKGROUND: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking.<br><br>METHODS: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results.<br><br>RESULTS: DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation.<br><br>CONCLUSIONS: The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.},
}
@article {pmid38433952,
year = {2024},
author = {Mallinson, DC and Elwert, F and Ehrenthal, DB},
title = {Spillover effects of gestational age on sibling's literacy.},
journal = {Early child development and care},
volume = {194},
number = {2},
pages = {244-259},
pmid = {38433952},
issn = {0300-4430},
support = {R01 HD102125/HD/NICHD NIH HHS/United States ; T32 HD007014/HD/NICHD NIH HHS/United States ; },
abstract = {Adverse health events within families can harm children's development, including their early literacy. Using data from a longitudinal Wisconsin birth cohort, we estimated the spillover effect of younger siblings' gestational ages on older siblings' kindergarten-level literacy. We sampled 20,014 sibling pairs born during 2007-2010 who took Phonological Awareness Literacy Screening-Kindergarten tests during 2012-2016. Exposures were gestational age (completed weeks), preterm birth (gestational age <37 weeks), and very preterm birth (gestational age <32 weeks). We used gain-score regression-a fixed effects strategy-to estimate spillover effect. A one-week increase in younger siblings' gestational age improved the older siblings' test score by 0.011 SD (95% confidence interval: 0.001, 0.021 SD). The estimated spillover effect was larger among siblings whose mothers reported having a high school diploma/equivalent only (0.024 SD; 95% CI: 0.004, 0.044 SD). The finding underscores the networked effects of one individual's early-life health shocks on their family members.},
}
@article {pmid38432384,
year = {2024},
author = {Baima Ferreira Freitas, I and Duarte-Neto, PJ and Sorigotto, LR and Cardoso Yoshii, MP and de Palma Lopes, LF and de Almeida Pereira, MM and Girotto, L and Badolato Athayde, D and Veloso Goulart, B and Montagner, CC and Schiesari, LC and Martinelli, LA and Gaeta Espíndola, EL},
title = {Effects of pasture intensification and sugarcane cultivation on non-target species: A realistic evaluation in pesticide-contaminated mesocosms.},
journal = {The Science of the total environment},
volume = {922},
number = {},
pages = {171425},
doi = {10.1016/j.scitotenv.2024.171425},
pmid = {38432384},
issn = {1879-1026},
mesh = {Female ; Animals ; Cattle ; *Pesticides/toxicity ; *Saccharum ; Environmental Biomarkers ; Soil ; Water/chemistry ; 2,4-Dichlorophenoxyacetic Acid/toxicity ; *Water Pollutants, Chemical/toxicity ; },
abstract = {Conventional soil management in agricultural areas may expose non-target organisms living nearby to several types of contaminants. In this study, the effects of soil management in extensive pasture (EP), intensive pasture (IP), and sugarcane crops (C) were evaluated in a realistic-field-scale study. Thirteen aquatic mesocosms embedded in EP, IP, and C treatments were monitored over 392 days. The recommended management for each of the areas was simulated, such as tillage, fertilizer, pesticides (i.e. 2,4-D, fipronil) and vinasse application, and cattle pasture. To access the potential toxic effects that the different steps of soil management in these areas may cause, the cladoceran Ceriophania silvestrii was used as aquatic bioindicator, the dicot Eruca sativa as phytotoxicity bioindicator in water, and the dipteran Chironomus sancticaroli as sediment bioindicator. Generalized linear mixed models were used to identify differences between the treatments. Low concentrations of 2,4-D (<97 μg L[-1]) and fipronil (<0.21 μg L[-1]) in water were able to alter fecundity, female survival, and the intrinsic rate of population increase of C. silvestrii in IP and C treatments. Similarly, the dicot E. sativa had germination, shoot and root growth affected mainly by 2,4-D concentrations in the water. For C. sancticarolli, larval development was affected by the presence of fipronil (<402.6 ng g[-1]). The acidic pH (below 5) reduced the fecundity and female survival of C. silvestrii and affected the germination and growth of E. sativa. Fecundity and female survival of C. silvestrii decrease in the presence of phosphorus-containing elements. The outcomes of this study may improve our understanding of the consequences of exposure of freshwater biota to complex stressors in an environment that is rapidly and constantly changing.},
}
@article {pmid38430051,
year = {2024},
author = {Rillig, MC and Mansour, I and Hempel, S and Bi, M and König-Ries, B and Kasirzadeh, A},
title = {How widespread use of generative AI for images and video can affect the environment and the science of ecology.},
journal = {Ecology letters},
volume = {27},
number = {3},
pages = {e14397},
doi = {10.1111/ele.14397},
pmid = {38430051},
issn = {1461-0248},
mesh = {*Artificial Intelligence ; *Biodiversity ; },
abstract = {Generative artificial intelligence (AI) models will have broad impacts on society including the scientific enterprise; ecology and environmental science will be no exception. Here, we discuss the potential opportunities and risks of advanced generative AI for visual material (images and video) for the science of ecology and the environment itself. There are clearly opportunities for positive impacts, related to improved communication, for example; we also see possibilities for ecological research to benefit from generative AI (e.g., image gap filling, biodiversity surveys, and improved citizen science). However, there are also risks, threatening to undermine the credibility of our science, mostly related to actions of bad actors, for example in terms of spreading fake information or committing fraud. Risks need to be mitigated at the level of government regulatory measures, but we also highlight what can be done right now, including discussing issues with the next generation of ecologists and transforming towards radically open science workflows.},
}
@article {pmid38429902,
year = {2024},
author = {Chen, C and He, Y and Ni, Y and Tang, Z and Zhang, W},
title = {Identification of crosstalk genes relating to ECM-receptor interaction genes in MASH and DN using bioinformatics and machine learning.},
journal = {Journal of cellular and molecular medicine},
volume = {28},
number = {6},
pages = {e18156},
pmid = {38429902},
issn = {1582-4934},
support = {81771152//National Nature Science Foundation of China/ ; },
mesh = {Humans ; *Interleukin-17 ; *Diabetic Nephropathies ; Phosphatidylinositol 3-Kinases ; Computational Biology ; Machine Learning ; },
abstract = {This study aimed to identify genes shared by metabolic dysfunction-associated fatty liver disease (MASH) and diabetic nephropathy (DN) and the effect of extracellular matrix (ECM) receptor interaction genes on them. Datasets with MASH and DN were downloaded from the Gene Expression Omnibus (GEO) database. Pearson's coefficients assessed the correlation between ECM-receptor interaction genes and cross talk genes. The coexpression network of co-expression pairs (CP) genes was integrated with its protein-protein interaction (PPI) network, and machine learning was employed to identify essential disease-representing genes. Finally, immuno-penetration analysis was performed on the MASH and DN gene datasets using the CIBERSORT algorithm to evaluate the plausibility of these genes in diseases. We found 19 key CP genes. Fos proto-oncogene (FOS), belonging to the IL-17 signalling pathway, showed greater centrality PPI network; Hyaluronan Mediated Motility Receptor (HMMR), belonging to ECM-receptor interaction genes, showed most critical in the co-expression network map of 19 CP genes; Forkhead Box C1 (FOXC1), like FOS, showed a high ability to predict disease in XGBoost analysis. Further immune infiltration showed a clear positive correlation between FOS/FOXC1 and mast cells that secrete IL-17 during inflammation. Combining the results of previous studies, we suggest a FOS/FOXC1/HMMR regulatory axis in MASH and DN may be associated with mast cells in the acting IL-17 signalling pathway. Extracellular HMMR may regulate the IL-17 pathway represented by FOS through the Mitogen-Activated Protein Kinase 1 (ERK) or PI3K-Akt-mTOR pathway. HMMR may serve as a signalling carrier between MASH and DN and could be targeted for therapeutic development.},
}
@article {pmid38426108,
year = {2024},
author = {Huo, J and Li, X and Hu, X and Lv, A},
title = {Multi-omics analysis of miRNA-mediated intestinal microflora changes in crucian carp Carassius auratus infected with Rahnella aquatilis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1335602},
pmid = {38426108},
issn = {1664-3224},
mesh = {Animals ; Goldfish/genetics ; *Carps/genetics ; *Rahnella/genetics ; NF-kappa B ; Multiomics ; *Gastrointestinal Microbiome ; Tumor Necrosis Factor-alpha ; Inflammation ; *Enteritis ; Transforming Growth Factor beta ; *MicroRNAs/genetics ; },
abstract = {Infection by an emerging bacterial pathogen Rahnella aquatilis caused enteritis and septicemia in fish. However, the molecular pathogenesis of enteritis induced by R. aquatilis infection and its interacting mechanism of the intestinal microflora associated with microRNA (miRNA) immune regulation in crucian carp Carassius auratus are still unclear. In this study, C. auratus intraperitoneally injected with R. aquatilis KCL-5 was used as an experimental animal model, and the intestinal pathological changes, microflora, and differentially expressed miRNAs (DEMs) were investigated by multi-omics analysis. The significant changes in histopathological features, apoptotic cells, and enzyme activities (e.g., lysozyme (LYS), alkaline phosphatase (AKP), alanine aminotransferase (ALT), aspartate transaminase (AST), and glutathione peroxidase (GSH-Px)) in the intestine were examined after infection. Diversity and composition analysis of the intestinal microflora clearly demonstrated four dominant bacteria: Proteobacteria, Fusobacteria, Bacteroidetes, and Firmicutes. A total of 87 DEMs were significantly screened, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes were mainly involved in the regulation of lipid, glutathione, cytosine, and purine metabolism, which participated in the local immune response through the intestinal immune network for IgA production, lysosome, and Toll-like receptor (TLR) pathways. Moreover, the expression levels of 11 target genes (e.g., TLR3, MyD88, NF-κB, TGF-β, TNF-α, MHC II, IL-22, LysC, F2, F5, and C3) related to inflammation and immunity were verified by qRT-PCR detection. The correlation analysis indicated that the abundance of intestinal Firmicutes and Proteobacteria was significantly associated with the high local expression of miR-203/NF-κB, miR-129/TNF-α, and miR-205/TGF-β. These findings will help to elucidate the molecular regulation mechanism of the intestinal microflora, inflammation, and immune response-mediated miRNA-target gene axis in cyprinid fish.},
}
@article {pmid38423780,
year = {2024},
author = {Hitchings, L and Fleet, B and Smith, DT and Read, JM and Melville, C and Sedda, L},
title = {Determining the distance patterns in the movements of future doctors in UK between 2002 and 2015: a retrospective cohort study.},
journal = {BMJ open},
volume = {14},
number = {3},
pages = {e077635},
pmid = {38423780},
issn = {2044-6055},
mesh = {Humans ; Retrospective Studies ; *Career Choice ; Gender Identity ; Social Class ; *Students, Medical ; Schools, Medical ; United Kingdom ; },
abstract = {OBJECTIVE: To determine and identify distance patterns in the movements of medical students and junior doctors between their training locations.<br><br>DESIGN: A retrospective cohort study of UK medical students from 2002 to 2015 (UKMED data).<br><br>SETTING: All UK medical schools, foundations and specialty training organisation.<br><br>PARTICIPANTS: All UK medical students from 2002 to 2015, for a total of 97&#x2009;932 participants.<br><br>OUTCOME MEASURES: Individual movements and number of movements by county of students from family home to medical school training, from medical school to foundation training and from foundation to specialty training.<br><br>METHODS: Leslie matrix, principal components analysis, Gini coefficient, &#x3c7;[2] test, generalised linear models and variable selection methods were employed to explore the different facets of students' and junior doctors' movements from the family home to medical school and for the full pathway (from family home to specialty training).<br><br>RESULTS: The majority of the movements between the different stages of the full pathway were restricted to a distance of up to 50&#x2009;km; although the proportion of movements changed from year-to-year, with longer movements during 2007-2008. At the individual level, ethnicity, socioeconomic class of the parent(s) and the deprivation score of the family home region were found to be the most important factors associated with the length of the movements from the family home to medical school. Similar results were found when movements were aggregated at the county level, with the addition of factors such as gender and qualification at entry (to medical school) being statistically associated with the number of new entrant students moving between counties.<br><br>CONCLUSION: Our findings show that while future doctors do not move far from their family home or training location, this pattern is not homogeneous over time. Distances are influenced by demographics, socioeconomic status and deprivation. These results may contribute in designing interventions aimed at solving the chronic problems of maldistribution and underdoctoring in the UK.},
}
@article {pmid38422100,
year = {2024},
author = {Barrenechea Angeles, I and Nguyen, NL and Greco, M and Tan, KS and Pawlowski, J},
title = {Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity.},
journal = {PloS one},
volume = {19},
number = {2},
pages = {e0298440},
pmid = {38422100},
issn = {1932-6203},
mesh = {Phylogeny ; *DNA, Environmental ; DNA, Ribosomal ; Databases, Factual ; *Foraminifera/genetics ; Water ; },
abstract = {Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.},
}
@article {pmid38418873,
year = {2024},
author = {Delavaux, CS and Crowther, TW and Bever, JD and Weigelt, P and Gora, EM},
title = {Mutualisms weaken the latitudinal diversity gradient among oceanic islands.},
journal = {Nature},
volume = {627},
number = {8003},
pages = {335-339},
pmid = {38418873},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; Datasets as Topic ; *Geographic Mapping ; *Islands ; Mycorrhizae/physiology ; *Plants/microbiology ; Pollination ; *Symbiosis ; Tropical Climate ; Oceans and Seas ; Phylogeography ; },
abstract = {The latitudinal diversity gradient (LDG) dominates global patterns of diversity[1,2], but the factors that underlie the LDG remain elusive. Here we use a unique global dataset[3] to show that vascular plants on oceanic islands exhibit a weakened LDG and explore potential mechanisms for this effect. Our results show that traditional physical drivers of island biogeography[4]-namely area and isolation-contribute to the difference between island and mainland diversity at a given latitude (that is, the island species deficit), as smaller and more distant islands experience reduced colonization. However, plant species with mutualists are underrepresented on islands, and we find that this plant mutualism filter explains more variation in the island species deficit than abiotic factors. In particular, plant species that require animal pollinators or microbial mutualists such as arbuscular mycorrhizal fungi contribute disproportionately to the island species deficit near the Equator, with contributions decreasing with distance from the Equator. Plant mutualist filters on species richness are particularly strong at low absolute latitudes where mainland richness is highest, weakening the LDG of oceanic islands. These results provide empirical evidence that mutualisms, habitat heterogeneity and dispersal are key to the maintenance of high tropical plant diversity and mediate the biogeographic patterns of plant diversity on Earth.},
}
@article {pmid38416313,
year = {2024},
author = {Vigna-Taglianti, FD and Martorana, M and Viola, E and Renna, M and Vadrucci, S and Sciutto, A and Andrà, C and Mehanović, E and Ginechesi, M and Vullo, C and Ceccano, A and Casella, P and Faggiano, F and , },
title = {Evaluation of Effectiveness of the Unplugged Program on Gambling Behaviours among Adolescents: Study Protocol of the Experimental Controlled Study "GAPUnplugged".},
journal = {Journal of prevention (2022)},
volume = {45},
number = {3},
pages = {405-429},
pmid = {38416313},
issn = {2731-5541},
support = {0005406//ASLRoma1/ ; },
mesh = {Humans ; *Gambling/prevention &amp; control/psychology ; Adolescent ; Female ; Male ; Surveys and Questionnaires ; Adolescent Behavior/psychology ; Program Evaluation ; Risk-Taking ; Students/psychology ; Italy ; },
abstract = {Gambling risk behaviour is an emerging problem among adolescents. "Unplugged" is an effective Social Influence curriculum for preventing substance use among students. This study aims to develop and test a new component focused on gambling added to the Unplugged program. Schools of Piedmont region and Rome city were invited to participate in the study. A self-completed anonymous questionnaire including questions on socio-demographic characteristics, addictive behaviours, beliefs, attitudes and risk perceptions about gambling, normative perceptions, parental practices, school climate, refusal skills, impulsiveness, self-esteem, antisocial behaviours and sensation seeking was prepared for baseline and follow-up surveys. The protocol of the study was submitted and approved by the Novara Ethical Committee and registered in ClinicalTrials.gov (NCT05630157, Protocol ID: 080.742, 11/17/2022). Twenty-nine schools accepted to participate in the study. Sixty-three classes (1325 students) satisfied the eligibility criteria for intervention and were allocated to the intervention arm, and the other 61 (1269 students) were allocated to the control arm. Because of drop-out, absentees, refusals, and invalid questionnaires, data on 1874 students (998 in the intervention and 876 in the control arm), were available for the analysis at baseline. Data management of follow-up questionnaires is in progress. Results of the present study will be useful to clarify the effectiveness of prevention interventions in reducing gambling behaviours among adolescents. Moreover, this will be the first experience of evaluating a new component focused on a different risk behaviour, added to a curriculum previously shown as effective on other risk behaviours.},
}
@article {pmid38415798,
year = {2024},
author = {Jager, T},
title = {Identifying and Predicting Delayed Mortality with Toxicokinetic-Toxicodynamic Models.},
journal = {Environmental toxicology and chemistry},
volume = {43},
number = {5},
pages = {1030-1035},
doi = {10.1002/etc.5833},
pmid = {38415798},
issn = {1552-8618},
mesh = {Animals ; Humans ; Daphnia magna/drug effects ; Datasets as Topic ; Death ; *Ecotoxicology/methods ; Fluoroquinolones/toxicity ; *Mortality ; Pesticides/toxicity ; *Pharmacokinetics ; Risk Assessment ; Stochastic Processes ; Time Factors ; *Toxicity Tests, Acute/methods/standards ; },
abstract = {The prevalence of standardized toxicity testing in ecotoxicology has largely obscured the notion that toxicity is a function of time as well. The necessity of considering time is vividly demonstrated by observations of delayed mortality, that is, deaths continue to occur even when animals are no longer exposed to a toxicant. In this contribution, I explore to what extent toxicokinetic-toxicodynamic (TKTD) models from the framework of the General Unified Threshold model for Survival (GUTS) can capture delayed mortality, and to what extent this phenomenon can be predicted from short-term standard tests. I use a previously published data set for fluoroquinolones in Daphnia magna that shows strongly delayed mortality (using immobilization as a proxy for death). The model analysis shows that the GUTS stochastic death models can capture delayed mortality in the complete data set with a long recovery phase, but that the delayed effects would not have been predicted from a 2-day standard test. The study underlines the limited information content of standard acute test designs. Toxicokinetic-toxicodynamic modeling offers a handle on the time aspects of toxicity but cannot always be relied on to provide accurate extrapolations based on severely limited standard tests. The phenomenon of delayed toxicity requires more structured study to clarify its prevalence and impact; I discuss several avenues for further investigation. Environ Toxicol Chem 2024;43:1030-1035. © 2024 SETAC.},
}
@article {pmid38413777,
year = {2024},
author = {Lemane, T and Lezzoche, N and Lecubin, J and Pelletier, E and Lescot, M and Chikhi, R and Peterlongo, P},
title = {Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.},
journal = {Nature computational science},
volume = {4},
number = {2},
pages = {104-109},
pmid = {38413777},
issn = {2662-8457},
support = {ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-CE45-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; PIA/ANR16-CONV-0005//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-P3IA-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; 956229//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 872539//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; },
mesh = {*Genomics ; Oceans and Seas ; *Seawater ; Metagenome/genetics ; Databases, Nucleic Acid ; },
abstract = {Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex, an approach that can index thousands of metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. Here we demonstrate the scalability of kmindex by successfully indexing 1,393 marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server Ocean Read Atlas, which enables real-time queries on the Tara Oceans dataset.},
}
@article {pmid38413616,
year = {2024},
author = {Xu, W and Pan, Z and Wu, Y and An, XL and Wang, W and Adamovich, B and Zhu, YG and Su, JQ and Huang, Q},
title = {A database on the abundance of environmental antibiotic resistance genes.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {250},
pmid = {38413616},
issn = {2052-4463},
support = {32161143016//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177362//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42250410328//National Natural Science Foundation of China (National Science Foundation of China)/ ; GPNI GR no. 20212317//Belarusian Republican Foundation for Fundamental Research (BRFFR)/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; China ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; *Databases, Genetic ; },
abstract = {Antimicrobial resistance (AMR) poses a severe threat to global health. The wide distribution of environmental antibiotic resistance genes (ARGs), which can be transferred between microbiota, especially clinical pathogens and human commensals, contributed significantly to AMR. However, few databases on the spatiotemporal distribution, abundance, and health risk of ARGs from multiple environments have been developed, especially on the absolute level. In this study, we compiled the ARG occurrence data generated by a high-throughput quantitative PCR platform from 1,403 samples in 653 sampling sites across 18 provinces in China. The database possessed 291,870 records from five types of habitats on the abundance of 290 ARGs, as well as 8,057 records on the abundance of 30 mobile genetic elements (MGEs) from 2013 to 2020. These ARGs conferred resistance to major common types of antibiotics (a total of 15 types) and represented five major resistance mechanisms, as well as four risk ranks. The database can provide information for studies on the dynamics of ARGs and is useful for the health risk assessment of AMR.},
}
@article {pmid38407293,
year = {2024},
author = {Dai, Y and Chen, H and Yu, J and Cai, J and Lu, B and Dai, M and Zhu, L},
title = {Global and regional trends in the incidence and prevalence of uterine fibroids and attributable risk factors at the national level from 2010 to 2019: A worldwide database study.},
journal = {Chinese medical journal},
volume = {137},
number = {21},
pages = {2583-2589},
pmid = {38407293},
issn = {2542-5641},
mesh = {Humans ; Female ; *Leiomyoma/epidemiology ; Incidence ; Risk Factors ; Prevalence ; Adult ; Middle Aged ; Uterine Neoplasms/epidemiology ; Disability-Adjusted Life Years ; Databases, Factual ; },
abstract = {BACKGROUND: Uterine fibroids (UFs), the most common tumors in women worldwide, may reduce quality of life and daily activities and even lead to adverse fertility and general health events in patients, causing significant societal health and financial burdens. The objective of this study was to evaluate the global burden through epidemiological trends and examine the potential risk factors for UFs at the national level.<br><br>METHODS: Data on the incidence, prevalence, disability-adjusted life years (DALYs), age-standardized incidence rates (ASIRs), age-standardized prevalence rates (ASPRs), and age-standardized DALY rates for UFs were collected, and the associations with the Human Development Index (HDI) and fertility were evaluated. The age trends in the average annual percent change (AAPC) of the incidence and prevalence rates of UFs were evaluated by joinpoint regression analysis. The associations between lifestyle, metabolic, and socioeconomic factors and the ASIRs of UFs were examined using multivariable linear regression analysis.<br><br>RESULTS: The worldwide incidence and prevalence of UFs have been increasing in the past decade, with AAPCs of 0.27% in the incidence rate and 0.078% in the prevalence rate. During 2010-2019, significant increasing trends in UF ASIR were observed in 52 of 88 countries. The age-specific incidence and prevalence of UFs in most age groups showed increasing trends except for 45-54-year-old women which showed no significant trend. Ecological analysis demonstrated no relationship between the incidence of UFs and the HDI but an inverse association with fertility. The incidence of UFs was positively correlated with alcohol intake, hypertension, overweight, and obesity and negatively correlated with smoking.<br><br>CONCLUSION: With the increasing incidence and prevalence worldwide, effective targeted prevention and control of relevant risk factors at the national level should be encouraged to reduce the disease burden of UFs.},
}
@article {pmid38405013,
year = {2024},
author = {Boyes, D and Sims, I and Lees, DC and Eagles, M and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Chequered Fruit-tree Tortrix, Pandemis corylana (Fabricius, 1794).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {6},
pmid = {38405013},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Pandemis corylana (the Chequered Fruit-tree Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 441.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.53 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,608 protein coding genes.},
}
@article {pmid38404638,
year = {2023},
author = {Boyes, D and Eagles, M and , and , and , and , and , and , },
title = {The genome sequence of the Light Emerald, Campaea margaritaria (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {476},
pmid = {38404638},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Campaea margaritaria (the Light Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 335.2 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,403 protein coding genes.},
}
@article {pmid38404637,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Phoenix, Eulithis prunata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {185},
pmid = {38404637},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eulithis prunata (the Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 263.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,023 protein coding genes.},
}
@article {pmid38404636,
year = {2023},
author = {Boyes, D and Eagles, M and , and , and , and , and , and , },
title = {The genome sequence of the Flame Shoulder, Ochropleura plecta (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {506},
pmid = {38404636},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Ochropleura plecta (the Flame Shoulder; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 643.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,016 protein coding genes.},
}
@article {pmid38404635,
year = {2023},
author = {Hayward, A and Lohse, K and Vila, R and Laetsch, DR and Hedlund, JSU and , and , and , and , },
title = {The genome sequence of the Brown Argus, Aricia agestis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {336},
pmid = {38404635},
issn = {2398-502X},
abstract = {We present genome assemblies from two male Aricia agestis specimens (the Brown Argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequences are 435.3 and 437.4 megabases in span. Each assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genomes were assembled and are 15.47 and 15.45 kilobases in length. Gene annotation of these assemblies on Ensembl identified 12,688 and 12,654 protein coding genes.},
}
@article {pmid38402992,
year = {2024},
author = {Zhu, Y and Wang, L and Ma, J and Hua, Z and Yang, Y and Chen, F},
title = {Assessment of carbon sequestration potential of mining areas under ecological restoration in China.},
journal = {The Science of the total environment},
volume = {921},
number = {},
pages = {171179},
doi = {10.1016/j.scitotenv.2024.171179},
pmid = {38402992},
issn = {1879-1026},
abstract = {Mining activities aggravate the ecological degradation and emission of greenhouse gases throughout the world, thereby affecting the global climate and posing a serious threat to the ecological safety. Vegetation restoration is considered to be an effective and sustainable strategy to improve the post-mining soil quality and functions. However, we still have a limited knowledge of the impact of vegetation restoration on carbon sequestration potential in mining areas. In this pursuit, the present study was envisaged to integrate the findings from studies on soil organic carbon (SOC) sequestration in mining areas under vegetation restoration with field monitoring data. The carbon sequestration potential under vegetation restoration in China's mining areas was estimated by using a machine learning model. The results showed that (1) Vegetation restoration exhibited a consistently positive impact on the changes in the SOC reserves. The carbon sequestration potential was the highest in mixed forests, followed by broad-leaved forests, coniferous forests, grassland, shrubland, and farmland; (2) The number of years of vegetation restoration and mean annual precipitation were found to be the important moderating variables affecting the SOC reserves in reclaimed soils in mining areas; (3) There were significant differences in the SOC sequestration potential under different vegetation restoration scenarios in mining areas in China. The SOC sequestration potential reached up to 9.86 million t C a[-1], when the soil was restored to the initial state. Based on the meta-analysis, the maximal attainable SOC sequestration potential was found to be 4.26 million t C a[-1]. The SOC sequestration potential reached the highest level of 12.86 million t C a[-1], when the optimal vegetation type in a given climate was restored. The results indicated the importance of vegetation restoration for improving the soil sequestration potential in mining areas. The time lag in carbon sequestration potential for different vegetation types in mining areas was also revealed. Our findings can assist the development of ecological restoration regimens in mining areas to mitigate the global climate change.},
}
@article {pmid38402941,
year = {2024},
author = {Ulanova, A and Mansfeldt, C},
title = {EcoGenoRisk: Developing a computational ecological risk assessment tool for synthetic biology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {346},
number = {},
pages = {123647},
doi = {10.1016/j.envpol.2024.123647},
pmid = {38402941},
issn = {1873-6424},
mesh = {*Synthetic Biology ; *Software ; Risk Assessment ; Computational Biology ; Genome, Bacterial ; },
abstract = {The expanding field of synthetic biology (synbio) supports new opportunities in the design of targeted bioproducts or modified microorganisms. However, this rapid development of synbio products raises concerns surrounding the potential risks of modified microorganisms contaminating unintended environments. These potential invasion risks require new bioinformatic tools to inform the design phase. EcoGenoRisk is a newly constructed computational risk assessment tool for invasiveness that aims to predict where synbio microorganisms may establish a population by screening for habitats of genetically similar microorganisms. The first module of the tool identifies genetically similar microorganisms and potential ecological relationships such as competition, mutualism, and inhibition. In total, 520 archaeal and 32,828 bacterial complete assembly genomes were analyzed to test the specificity and accuracy of the tool as well as to characterize the enzymatic profiles of different taxonomic lineages. Additionally, ecological relationships were analyzed to determine which would result in the greatest potential overlap between shared functional profiles. Notably, competition displayed the significantly highest overlap of shared functions between compared genomes. Overall, EcoGenoRisk is a flexible software pipeline that assists environmental risk assessors to query large databases of known microorganisms and prioritize follow-up bench scale studies.},
}
@article {pmid38402789,
year = {2024},
author = {Gonyo, SB and Burkart, H and Regan, S},
title = {Leveraging big data for outdoor recreation management: A case study from the York river in Virginia.},
journal = {Journal of environmental management},
volume = {354},
number = {},
pages = {120482},
doi = {10.1016/j.jenvman.2024.120482},
pmid = {38402789},
issn = {1095-8630},
mesh = {Child ; Humans ; Child, Preschool ; Middle Aged ; *Recreation ; Virginia ; *Rivers ; Big Data ; Quality of Life ; },
abstract = {Outdoor recreation is important for improving quality of life, well-being, and local economies, but quantifying its value without direct monetary transactions can be challenging. This study explores combining non-market valuation techniques with emerging big data sources to estimate the value of recreation for the York River and surrounding parks in Virginia. By applying the travel cost method to anonymous human mobility data, we gain deeper insights into the significance of recreational experiences for visitors and the local economy. Results of a zero-inflated Negative Binomial model show a mean consumer surplus value of $26.91 per trip, totaling $15.5 million across nearly 600,000 trips observed in 2022. Further, weekends, holidays, and the summer and fall months are found to be peak visitation times, whereas those with young children and who are Hispanic or over 64 years old are less likely to visit. These findings shed light on various factors influencing visitation patterns and recreation values, including temporal effects and socio-demographics, revealing disparities that warrant targeted efforts for inclusivity and accessibility. Policymakers can use these insights to make informed and sustainable choices in outdoor recreation management, fostering the preservation of natural resources for the benefit of both visitors and the environment.},
}
@article {pmid38398847,
year = {2024},
author = {Navratilova, HF and Lanham-New, S and Whetton, AD and Geifman, N},
title = {Associations of Diet with Health Outcomes in the UK Biobank: A Systematic Review.},
journal = {Nutrients},
volume = {16},
number = {4},
pages = {},
pmid = {38398847},
issn = {2072-6643},
mesh = {Female ; Humans ; Male ; Middle Aged ; *Cardiovascular Diseases/epidemiology/etiology ; Colorectal Neoplasms/epidemiology/etiology/prevention &amp; control ; *Diabetes Mellitus, Type 2/epidemiology/etiology ; *Diet/statistics &amp; numerical data/adverse effects ; Diet, Healthy/statistics &amp; numerical data ; Neoplasms/epidemiology/etiology ; Risk Factors ; UK Biobank/statistics &amp; numerical data ; United Kingdom/epidemiology ; },
abstract = {The UK Biobank is a cohort study that collects data on diet, lifestyle, biomarkers, and health to examine diet-disease associations. Based on the UK Biobank, we reviewed 36 studies on diet and three health conditions: type 2 diabetes (T2DM), cardiovascular disease (CVD), and cancer. Most studies used one-time dietary data instead of repeated 24 h recalls, which may lead to measurement errors and bias in estimating diet-disease associations. We also found that most studies focused on single food groups or macronutrients, while few studies adopted a dietary pattern approach. Several studies consistently showed that eating more red and processed meat led to a higher risk of lung and colorectal cancer. The results suggest that high adherence to "healthy" dietary patterns (consuming various food types, with at least three servings/day of whole grain, fruits, and vegetables, and meat and processed meat less than twice a week) slightly lowers the risk of T2DM, CVD, and colorectal cancer. Future research should use multi-omics data and machine learning models to account for the complexity and interactions of dietary components and their effects on disease risk.},
}
@article {pmid38396178,
year = {2024},
author = {Wang, F and Sun, N and Zhang, C and Fan, C and Xiong, J and Wei, X and Hao, W},
title = {Experimental study on mine water purification mechanism for broken coal and rock masses in the underground reservoir of ecologically vulnerable mining area.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {14},
pages = {21442-21457},
pmid = {38396178},
issn = {1614-7499},
support = {52104155//National Natural Science Foundation of China/ ; 51974297//National Natural Science Foundation of China/ ; },
mesh = {*Coal ; *Mining ; Water Quality ; Minerals ; },
abstract = {Water-rock interaction mechanism and water purification capacity of broken coal and rock masses are very important for the efficient operation of the underground reservoir. In this paper, a water purification simulation device for an underground mine reservoir was designed. The experimental study on the dynamic interaction between broken coal and rock masses and mine water was carried out. The water purification mechanism is analyzed from the changes in rock mineral composition and mine water quality before and after the test. The results show that after the broken coal and rock mass purification, the water turbidity and the concentration of chlorides and suspended solids decreased obviously. The water purification capacities of mudstone and sandstone are stronger than that of coal samples. After 60 days of reaction between the working face sewage and the broken samples (mudstone, sandstone, and coal), the turbidity, chromaticity, and residual chlorine decreased by > 90%, 90%, and 60%, respectively; and COD decreased by 35.29%, 30.59%, and 28.99%, respectively. While the TDS and the total hardness increased by about 40%, 30%, and 10% for the mudstone, sandstone, and coal, respectively. It shows that coal also has the worst degradation performance. The water purification effect of broken coal and rock masses has a significant time effect. The early stage of water-rock interaction is dominated by mineral dissolution, and the middle stage is dominated by precipitation and adsorption. The pH value of the solution has a certain influence on the ion change. In the later stage, the water-rock interaction is weak in a dynamic equilibrium state, and the change in the mine water quality index is not obvious. Considering the influence of rock lithology on water quality and the law of water-rock interaction time, the construction site selection and water storage time optimization of underground reservoirs in Jinjie Coal Mine were carried out, respectively.},
}
@article {pmid38396055,
year = {2024},
author = {Gauzens, B and Kalinkat, G and Antunes, AC and Boy, T and O'Gorman, EJ and Jacob, U and Jochum, M and Kortsch, S and Rosenbaum, B and Figueiredo, L and Brose, U},
title = {Quantitative description of six fish species' gut contents and prey abundances in the Baltic Sea (1968-1978).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {236},
pmid = {38396055},
issn = {2052-4463},
support = {DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DAAD, 57070483//Deutscher Akademischer Austauschdienst (German Academic Exchange Service)/ ; },
mesh = {Animals ; Baltic States ; *Fishes ; *Gastrointestinal Contents ; Oceans and Seas ; },
abstract = {The dataset presents a compilation of stomach contents from six demersal fish species from two functional groups inhabiting the Baltic Sea. It includes detailed information on prey identities, body masses, and biomasses recovered from both the fish's digestive systems and their surrounding environment. Environmental parameters, such as salinity and temperature levels, have been integrated to enrich this dataset. The juxtaposition of information on prey found in stomachs and in the environment provides an opportunity to quantify trophic interactions across different environmental contexts and investigate how fish foraging behaviour adapts to changes in their environment, such as an increase in temperature. The compilation of body mass and taxonomic information for all species allows approaching these new questions using either a taxonomic (based on species identity) or functional trait (based on body mass) approach.},
}
@article {pmid38395906,
year = {2024},
author = {Ou, AH and Rosenthal, SB and Adli, M and Akiyama, K and Akula, N and Alda, M and Amare, AT and Ardau, R and Arias, B and Aubry, JM and Backlund, L and Bauer, M and Baune, BT and Bellivier, F and Benabarre, A and Bengesser, S and Bhattacharjee, AK and Biernacka, JM and Cervantes, P and Chen, GB and Chen, HC and Chillotti, C and Cichon, S and Clark, SR and Colom, F and Cousins, DA and Cruceanu, C and Czerski, PM and Dantas, CR and Dayer, A and Del Zompo, M and Degenhardt, F and DePaulo, JR and Étain, B and Falkai, P and Fellendorf, FT and Ferensztajn-Rochowiak, E and Forstner, AJ and Frisén, L and Frye, MA and Fullerton, JM and Gard, S and Garnham, JS and Goes, FS and Grigoroiu-Serbanescu, M and Grof, P and Gruber, O and Hashimoto, R and Hauser, J and Heilbronner, U and Herms, S and Hoffmann, P and Hofmann, A and Hou, L and Jamain, S and Jiménez, E and Kahn, JP and Kassem, L and Kato, T and Kittel-Schneider, S and König, B and Kuo, PH and Kusumi, I and Lackner, N and Laje, G and Landén, M and Lavebratt, C and Leboyer, M and Leckband, SG and Jaramillo, CAL and MacQueen, G and Maj, M and Manchia, M and Marie-Claire, C and Martinsson, L and Mattheisen, M and McCarthy, MJ and McElroy, SL and McMahon, FJ and Mitchell, PB and Mitjans, M and Mondimore, FM and Monteleone, P and Nievergelt, CM and Nöthen, MM and Novák, T and Ösby, U and Ozaki, N and Papiol, S and Perlis, RH and Pisanu, C and Potash, JB and Pfennig, A and Reich-Erkelenz, D and Reif, A and Reininghaus, EZ and Rietschel, M and Rouleau, GA and Rybakowski, JK and Schalling, M and Schofield, PR and Schubert, KO and Schulze, TG and Schweizer, BW and Seemüller, F and Severino, G and Shekhtman, T and Shilling, PD and Shimoda, K and Simhandl, C and Slaney, CM and Squassina, A and Stamm, T and Stopkova, P and Tighe, SK and Tortorella, A and Turecki, G and Vieta, E and Volkert, J and Witt, S and Wray, NR and Wright, A and Young, LT and Zandi, PP and Kelsoe, JR},
title = {Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study.},
journal = {Translational psychiatry},
volume = {14},
number = {1},
pages = {109},
pmid = {38395906},
issn = {2158-3188},
support = {R01 MH059556/MH/NIMH NIH HHS/United States ; Z01 MH002810/ImNIH/Intramural NIH HHS/United States ; R01 MH059535/MH/NIMH NIH HHS/United States ; R01 MH059567/MH/NIMH NIH HHS/United States ; R01 MH059545/MH/NIMH NIH HHS/United States ; P01 CA089392/CA/NCI NIH HHS/United States ; R01 MH059548/MH/NIMH NIH HHS/United States ; R01 MH059534/MH/NIMH NIH HHS/United States ; R01 MH059533/MH/NIMH NIH HHS/United States ; U01 MH092758/MH/NIMH NIH HHS/United States ; K02 DA021237/DA/NIDA NIH HHS/United States ; MR/L006642/1/MRC_/Medical Research Council/United Kingdom ; R01 MH059553/MH/NIMH NIH HHS/United States ; R01 MH060068/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Lithium/pharmacology/therapeutic use ; *Bipolar Disorder/drug therapy/genetics ; Proto-Oncogene Proteins c-akt/genetics ; Phosphatidylinositol 3-Kinases/genetics ; Genome-Wide Association Study ; Multiomics ; Focal Adhesions ; },
abstract = {Lithium is the gold standard treatment for bipolar disorder (BD). However, its mechanism of action is incompletely understood, and prediction of treatment outcomes is limited. In our previous multi-omics study of the Pharmacogenomics of Bipolar Disorder (PGBD) sample combining transcriptomic and genomic data, we found that focal adhesion, the extracellular matrix (ECM), and PI3K-Akt signaling networks were associated with response to lithium. In this study, we replicated the results of our previous study using network propagation methods in a genome-wide association study of an independent sample of 2039 patients from the International Consortium on Lithium Genetics (ConLiGen) study. We identified functional enrichment in focal adhesion and PI3K-Akt pathways, but we did not find an association with the ECM pathway. Our results suggest that deficits in the neuronal growth cone and PI3K-Akt signaling, but not in ECM proteins, may influence response to lithium in BD.},
}
@article {pmid38395161,
year = {2024},
author = {Brunelli, A and Cazzagon, V and Faraggiana, E and Bettiol, C and Picone, M and Marcomini, A and Badetti, E},
title = {An overview on dispersion procedures and testing methods for the ecotoxicity testing of nanomaterials in the marine environment.},
journal = {The Science of the total environment},
volume = {921},
number = {},
pages = {171132},
doi = {10.1016/j.scitotenv.2024.171132},
pmid = {38395161},
issn = {1879-1026},
mesh = {*Nanostructures/toxicity/chemistry ; Oxides/chemistry ; Research Design ; Ecotoxicology ; },
abstract = {Considerable efforts have been devoted to develop or adapt existing guidelines and protocols, to obtain robust and reproducible results from (eco)toxicological assays on engineered nanomaterials (NMs). However, while many studies investigated adverse effects of NMs on freshwater species, less attention was posed to the marine environment, a major sink for these contaminants. This review discusses the procedures used to assess the ecotoxicity of NMs in the marine environment, focusing on the use of protocols and methods for preparing NMs dispersions and on the NMs physicochemical characterization in exposure media. To this purpose, a critical analysis of the literature since 2010 was carried out, based on the publication of the first NMs dispersion protocols. Among the 89 selected studies, only <5 % followed a standardized dispersion protocol combined with NMs characterization in ecotoxicological media, while more than half used a non-standardized dispersion method but performed NMs characterization. In the remaining studies, only partial or no information on dispersion procedures or on physicochemical characterization was provided. This literature review also highlighted that metal oxides NMs were the most studied (42 %), but with an increasing interest in last years towards nanoplastics (14 %) and multicomponent nanomaterials (MCNMs, 7 %), in line with the growing attention on these emerging contaminants. For all these NMs, primary producers as algae and bacteria were the most studied groups of marine species, in addition to mollusca, while organisms at higher trophic levels were less represented, likely due to challenges in evaluating adverse effects on more complex organisms. Thus, despite the wide use of NMs in different applications, standard dispersion protocols are not often used for ecotoxicity testing with marine species. However, the efforts to characterize NMs in ecotoxicological media recognize the importance of following conditions that are as standardized as possible to support the ecological hazard assessment of NMs.},
}
@article {pmid38390626,
year = {2024},
author = {Kumar, A and Ojha, PK and Roy, K},
title = {First report on pesticide sub-chronic and chronic toxicities against dogs using QSAR and chemical read-across.},
journal = {SAR and QSAR in environmental research},
volume = {35},
number = {3},
pages = {241-263},
doi = {10.1080/1062936X.2024.2320143},
pmid = {38390626},
issn = {1029-046X},
mesh = {Dogs ; Animals ; *Pesticides/toxicity ; Quantitative Structure-Activity Relationship ; Reproducibility of Results ; Databases, Factual ; },
abstract = {Excessive use of chemicals is the outcome of the industrialization of agricultural sectors which leads to disturbance of ecological balance. Various agrochemicals are widely used in agricultural fields, urban green areas, and to protect from various pest-associated diseases. Due to their long-term health and environmental hazards, chronic toxicity assessment is crucial. Since in vivo and in vitro toxicity assessments are costly, lengthy, and require a large number of animal experiments, in silico toxicity approaches are better alternatives to save time, cost, and animal experimentation. We have developed the first regression-based 2D-QSAR models using different sub-chronic and chronic toxicity data of pesticides against dogs employing 2D descriptors. From the statistical results (ntrain=53-62, r2 = 0.614 to 0.754, QLOO2 = 0.501 to 0.703 and QF12 = 0.531 to 0.718, QF22=0.523-0.713), it was concluded that the models are robust, reliable, interpretable, and predictive. Similarity-based read-across algorithm was also used to improve the predictivity (QF12=0.595-0.813,QF22=0.573-0.809) of the models. 5132 chemicals obtained from the CPDat and 1694 pesticides obtained from the PPDB database were also screened using the developed models, and their predictivity and reliability were checked. Thus, these models will be helpful for eco-toxicological data-gap filling, toxicity prediction of untested pesticides, and development of novel, safer &amp; eco-friendly pesticides.},
}
@article {pmid38389111,
year = {2024},
author = {Messer, LF and Lee, CE and Wattiez, R and Matallana-Surget, S},
title = {Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {36},
pmid = {38389111},
issn = {2049-2618},
support = {NE/V009621/1//Natural Environment Research Council/ ; NE/V009621/1//Natural Environment Research Council/ ; NE/V009621/1//Natural Environment Research Council/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership/ ; },
mesh = {*Plastics ; Bacteria/genetics ; Multiomics ; Biofilms ; Biodegradation, Environmental ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment.<br><br>RESULTS: For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community.<br><br>CONCLUSION: Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.},
}
@article {pmid38386279,
year = {2024},
author = {Ambrosini, E and Giangregorio, C and Lomurno, E and Moccia, S and Milis, M and Loizou, C and Azzolino, D and Cesari, M and Cid Gala, M and Galán de Isla, C and Gomez-Raja, J and Borghese, NA and Matteucci, M and Ferrante, S},
title = {Automatic Spontaneous Speech Analysis for the Detection of Cognitive Functional Decline in Older Adults: Multilanguage Cross-Sectional Study.},
journal = {JMIR aging},
volume = {7},
number = {},
pages = {e50537},
pmid = {38386279},
issn = {2561-7605},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Humans ; Aged ; Female ; Male ; *Cognitive Dysfunction/diagnosis ; Cross-Sectional Studies ; Italy/epidemiology ; Aged, 80 and over ; *Speech/physiology ; Spain/epidemiology ; Mental Status and Dementia Tests ; Machine Learning ; Algorithms ; },
abstract = {BACKGROUND: The rise in life expectancy is associated with an increase in long-term and gradual cognitive decline. Treatment effectiveness is enhanced at the early stage of the disease. Therefore, there is a need to find low-cost and ecological solutions for mass screening of community-dwelling older adults.<br><br>OBJECTIVE: This work aims to exploit automatic analysis of free speech to identify signs of cognitive function decline.<br><br>METHODS: A sample of 266 participants older than 65 years were recruited in Italy and Spain and were divided into 3 groups according to their Mini-Mental Status Examination (MMSE) scores. People were asked to tell a story and describe a picture, and voice recordings were used to extract high-level features on different time scales automatically. Based on these features, machine learning algorithms were trained to solve binary and multiclass classification problems by using both mono- and cross-lingual approaches. The algorithms were enriched using Shapley Additive Explanations for model explainability.<br><br>RESULTS: In the Italian data set, healthy participants (MMSE score&#x2265;27) were automatically discriminated from participants with mildly impaired cognitive function (20&#x2264;MMSE score&#x2264;26) and from those with moderate to severe impairment of cognitive function (11&#x2264;MMSE score&#x2264;19) with accuracy of 80% and 86%, respectively. Slightly lower performance was achieved in the Spanish and multilanguage data sets.<br><br>CONCLUSIONS: This work proposes a transparent and unobtrusive assessment method, which might be included in a mobile app for large-scale monitoring of cognitive functionality in older adults. Voice is confirmed to be an important biomarker of cognitive decline due to its noninvasive and easily accessible nature.},
}
@article {pmid38385125,
year = {2023},
author = {Boyes, D and Turnbull, L and , and , and , and , and , and , },
title = {The genome sequence of the Hornet Moth, Sesia apiformis (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {499},
pmid = {38385125},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Sesia apiformis (the Hornet Moth; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 546.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,358 protein coding genes.},
}
@article {pmid38385124,
year = {2023},
author = {Boyes, D and Broad, GR and , and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Shuttle-shaped Dart, Agrotis puta (Hübner, 1803).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {84},
pmid = {38385124},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agrotis puta (the Shuttle-shaped Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 522 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,136 protein coding genes.},
}
@article {pmid38383691,
year = {2024},
author = {Yu, D and Zhang, Y and Dang, H and Zhang, Q},
title = {Multiomics analyses reveal the mechanisms of the responses of subalpine treeline trees to phenology and winter low-temperature stress.},
journal = {Physiologia plantarum},
volume = {176},
number = {1},
pages = {e14218},
doi = {10.1111/ppl.14218},
pmid = {38383691},
issn = {1399-3054},
support = {31971491//National Natural Science Foundation of China/ ; 32201371//National Natural Science Foundation of China/ ; },
mesh = {*Trees/genetics ; Temperature ; *Multiomics ; Cold Temperature ; Seasons ; },
abstract = {Withstanding extreme cold stress is a prerequisite for alpine treeline trees to persist and survive. However, the underlying mechanism by which treeline trees sense phenological changes and survive hard winters has not been fully elucidated. Here, we investigated the physiology, transcriptome, and metabolome of the subalpine treeline species Larix chinensis to identify the molecular mechanism of phenological and cold resistance. Calcium and antioxidant enzyme activities (e.g., superoxide dismutase and glutathione peroxidase) are essential for coping with winter cold stress in L. chinensis. Transcriptome analysis revealed that circadian rhythm and phytohormone signalling transduction played important roles in regulating L. chinensis phenological changes and cold stress responses. The variations in the transcriptome identified were accompanied by the specific accumulation of flavones, flavonols, and monosaccharides. The flavonoid biosynthesis and phenylpropanoid biosynthesis pathways played important roles in the adaptation of L. chinensis to the extreme winter environment, and flavone and flavonol biosynthesis was an important pathway involved in bud burst. In addition, temperature and photoperiod had synergistic influences on the formation and release of bud dormancy. Thus, our findings provided new insights into the mechanism of subalpine treeline formation.},
}
@article {pmid38379958,
year = {2024},
author = {Tran, T and Xie, S},
title = {Mitigating Wildlife Spillover in the Clinical Setting: How Physicians and Veterinarians Can Help Prevent Future Disease Outbreaks.},
journal = {AJPM focus},
volume = {3},
number = {2},
pages = {100193},
pmid = {38379958},
issn = {2773-0654},
abstract = {INTRODUCTION: The transmission of pathogens from wildlife to humans is a major global health threat that has been highlighted by the proposed origins of the COVID-19 pandemic. Numerous barriers impede pathogen spillover events from ensuing widespread human transmission, but human activity has accelerated the frequency of spillovers and subsequent disease outbreaks, in part through a booming wildlife trade whose impacts on health are not well understood.<br><br>METHODS: A literature review was conducted to examine the risk that the wildlife trade poses to public health and the degree to which these risks are recognized and addressed in clinical practice and medical and veterinary education.<br><br>RESULTS: The illicit aspects of the wildlife trade challenge efforts to understand its impacts on health. The U.S. and Europe play a leading role in the global wildlife trade that often goes unacknowledged. In particular, the consumption of wild meat and ownership of exotic pets poses public health risks. The potential role of clinicians is underutilized, both in the clinical setting and in clinical education.<br><br>DISCUSSION: Physicians and veterinarians have the unique opportunity to utilize their clinical roles to address these knowledge gaps and mitigate future outbreaks. We outline a multifaceted approach that includes increasing clinical knowledge about the ecology of zoonotic diseases, leveraging opportunities for mitigation during patient/client-clinician interactions, and incorporating One Health core competencies into medical and veterinary school curricula.},
}
@article {pmid38379504,
year = {2024},
author = {Castro-Alvarez, S and Sinharay, S and Bringmann, LF and Meijer, RR and Tendeiro, JN},
title = {Assessment of fit of the time-varying dynamic partial credit model using the posterior predictive model checking method.},
journal = {The British journal of mathematical and statistical psychology},
volume = {77},
number = {3},
pages = {532-552},
doi = {10.1111/bmsp.12339},
pmid = {38379504},
issn = {2044-8317},
mesh = {Humans ; *Psychometrics/methods/statistics &amp; numerical data ; *Models, Statistical ; *Computer Simulation ; Longitudinal Studies ; Time Factors ; Bayes Theorem ; Data Interpretation, Statistical ; Regression Analysis ; },
abstract = {Several new models based on item response theory have recently been suggested to analyse intensive longitudinal data. One of these new models is the time-varying dynamic partial credit model (TV-DPCM; Castro-Alvarez et al., Multivariate Behavioral Research, 2023, 1), which is a combination of the partial credit model and the time-varying autoregressive model. The model allows the study of the psychometric properties of the items and the modelling of nonlinear trends at the latent state level. However, there is a severe lack of tools to assess the fit of the TV-DPCM. In this paper, we propose and develop several test statistics and discrepancy measures based on the posterior predictive model checking (PPMC) method (PPMC; Rubin, The Annals of Statistics, 1984, 12, 1151) to assess the fit of the TV-DPCM. Simulated and empirical data are used to study the performance of and illustrate the effectiveness of the PPMC method.},
}
@article {pmid38376945,
year = {2024},
author = {Townley, B and Akin, D and Dimaguila, GL and Sawires, R and Sepulveda Kattan, G and King, S and Bines, J and Wood, N and Lambert, S and Buttery, J},
title = {Exploring the Infectious Contribution to Intussusception Causality Using the Effects of COVID-19 Lockdowns in Australia: An Ecological Study.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {79},
number = {1},
pages = {255-262},
doi = {10.1093/cid/ciae084},
pmid = {38376945},
issn = {1537-6591},
support = {//Murdoch Children's/ ; //Research Institute/ ; //Child Health Analytics and Informatics Research/ ; },
mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control ; *Intussusception/epidemiology/etiology ; Infant ; Retrospective Studies ; Child, Preschool ; Child ; Male ; Female ; Australia/epidemiology ; Adolescent ; *SARS-CoV-2 ; Infant, Newborn ; Adult ; Hospitalization/statistics &amp; numerical data ; Middle Aged ; Young Adult ; Aged ; New South Wales/epidemiology ; Queensland/epidemiology ; Victoria/epidemiology ; },
abstract = {BACKGROUND: Intussusception is the primary cause of acute bowel obstruction in infants. The majority of cases <2 years of age are classed as idiopathic, with viral infection implicated as one of the causes. Coronavirus disease 2019 (COVID-19) public health measures led to significant decreases in communicable disease prevalence. During these times, reductions in intussusception frequency were greater than would be expected with our previous understanding of its infectious etiology.<br><br>METHODS: We conducted a retrospective, multistate, ecological study over a 12-year period. Monthly case numbers of "intussusception"-coded admissions (code K56.1; International Classification of Diseases and Related Health Problems, Tenth Revision, Australian Modification) were acquired from state-wide admissions data sets from New South Wales, Victoria, and Queensland, representing 77.62% of the eligible Australian population. These counts within differing jurisdictional lockdowns were compared with non-lockdown periods in order to investigate a correlation between intussusception frequency and lockdown periods.<br><br>RESULTS: We found a negative association between intussusception frequency and lockdown periods in both eligible states. The largest reductions were seen in the <2-year age groups, with Victoria experiencing a 62.7% reduction (rate ratio, 0.37; P < .001) and New South Wales a 40.1% reduction (0.599; P = .006) during lockdown times. Controls for variations in lockdown restrictions between both regional and metropolitan areas also showed expected decreases.<br><br>CONCLUSIONS: Our ecological study demonstrates significant decreases in the frequency of pediatric intussusception admissions during the COVID-19 lockdown periods. The unexpected magnitude of the reductions suggests that the true proportion of infectious disease-caused idiopathic intussusception is greatly underestimated.},
}
@article {pmid38376180,
year = {2024},
author = {Schaan, AP and Vidal, A and Zhang, A-N and Poyet, M and Alm, EJ and Groussin, M and Ribeiro-Dos-Santos, &#xc2;},
title = {Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.},
journal = {mSystems},
volume = {9},
number = {3},
pages = {e0070723},
pmid = {38376180},
issn = {2379-5077},
support = {88882.160155/2017-01//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior (CAPES)/ ; 304413/2015-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Brazil ; *Microbiota ; Bacteria ; Urbanization ; },
abstract = {Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.},
}
@article {pmid38376167,
year = {2024},
author = {Hegarty, B and Riddell V, J and Bastien, E and Langenfeld, K and Lindback, M and Saini, JS and Wing, A and Zhang, J and Duhaime, M},
title = {Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.},
journal = {mSystems},
volume = {9},
number = {3},
pages = {e0110523},
pmid = {38376167},
issn = {2379-5077},
support = {DGE1256260, 2055455, DGE134012//National Science Foundation (NSF)/ ; NA17OAR4320152//DOC | National Oceanic and Atmospheric Administration (NOAA)/ ; Blue Sky Initiative//College of Engineering, University of Michigan/ ; },
mesh = {*Benchmarking ; Ecosystem ; *Viruses ; Metagenomics/methods ; Databases, Nucleic Acid ; },
abstract = {UNLABELLED: Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.<br><br>IMPORTANCE: The identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.},
}
@article {pmid38371853,
year = {2024},
author = {Meyer, F and Sandbakk, &#xd8; and Millet, GP},
title = {Editorial: Sport performance analysis: from the laboratory to the field.},
journal = {Frontiers in sports and active living},
volume = {6},
number = {},
pages = {1372080},
pmid = {38371853},
issn = {2624-9367},
}
@article {pmid38368650,
year = {2024},
author = {Shchepin, ON and López Villalba, &#xc1; and Inoue, M and Prikhodko, IS and Erastova, DA and Okun, MV and Woyzichovski, J and Yajima, Y and Gmoshinskiy, VI and Moreno, G and Novozhilov, YK and Schnittler, M},
title = {DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia.},
journal = {Protist},
volume = {175},
number = {2},
pages = {126023},
doi = {10.1016/j.protis.2024.126023},
pmid = {38368650},
issn = {1618-0941},
mesh = {*Myxomycetes ; DNA Barcoding, Taxonomic/methods ; Bayes Theorem ; Phylogeny ; DNA, Ribosomal/genetics ; },
abstract = {The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.},
}
@article {pmid38366261,
year = {2024},
author = {Jensen, PM and Danielsen, F and Jacobsen, SK and Vikstrøm, T},
title = {Fair concordance between Google Trends and Danish ornithologists in the assessment of temporal trends in Danish bird populations highlights the informational value of big data.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {3},
pages = {276},
pmid = {38366261},
issn = {1573-2959},
support = {869673//CAPARDUS/ ; 862731//FRAMEwork/ ; 101058509//ECS/ ; 101096887//BestLife2030/ ; 5228-00001B//UArctic/ ; },
mesh = {Animals ; Humans ; *Ecosystem ; *Search Engine ; Big Data ; Environmental Monitoring ; Birds ; Denmark ; },
abstract = {The ongoing depletion of natural systems and associated biodiversity decline is of growing international concern. Climate change is expected to exacerbate anthropogenic impacts on wild populations. The scale of impact on ecosystems and ecosystem services will be determined by the impact on a multitude of species and functional groups, which due to their biology and numbers are difficult to monitor. The IPCC has argued that surveillance or monitoring is critical and proposed that monitoring systems should be developed, which not only track developments but also function as "early warning systems." Human populations are already generating large continuous datasets on multiple taxonomic groups through internet searches. These time series could in principle add substantially to current monitoring if they reflect true changes in the natural world. We here examined whether information on internet search frequencies delivered by the Danish population and captured by Google Trends (GT) appropriately informs on population trends in 106 common Danish bird species. We compared the internet search activity with independent equivalent population trend assessments from the Danish Ornithological Society (BirdLife Denmark/DOF). We find a fair concordance between the GT trends and the assessments by DOF. A substantial agreement can be obtained by omitting species without clear temporal trends. Our findings suggest that population trend proxies from internet search frequencies can be used to supplement existing wildlife population monitoring and to ask questions about an array of ecological phenomena, which potentially can be integrated into an early warning system for biodiversity under climate change.},
}
@article {pmid38365244,
year = {2024},
author = {Yu, XA and McLean, C and Hehemann, JH and Angeles-Albores, D and Wu, F and Muszyński, A and Corzett, CH and Azadi, P and Kujawinski, EB and Alm, EJ and Polz, MF},
title = {Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38365244},
issn = {1751-7370},
support = {DE-SC0008743//United States Department of Energy/ ; DE-SC0015662//United States Department of Energy/ ; },
mesh = {Bacteria/genetics ; *Seaweed ; *Microbiota ; },
abstract = {Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.},
}
@article {pmid38365075,
year = {2024},
author = {Lyu, Y and Gao, Y and Pang, X and Sun, S and Luo, P and Cai, D and Qin, K and Wu, Z and Wang, B},
title = {Elucidating contributions of volatile organic compounds to ozone formation using random forest during COVID-19 pandemic: A case study in China.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {346},
number = {},
pages = {123532},
doi = {10.1016/j.envpol.2024.123532},
pmid = {38365075},
issn = {1873-6424},
mesh = {Humans ; *Air Pollutants/analysis ; *Volatile Organic Compounds/analysis ; Pandemics ; *Ozone/analysis ; Random Forest ; Nitrogen Dioxide ; *COVID-19 ; Toluene ; Alkenes ; China ; Environmental Monitoring ; *Xylenes ; },
abstract = {Ozone has been reported to increase despite nitrogen oxides reductions during the COVID-19 pandemic, and ozone formation needs to be revisited using volatile organic compounds (VOCs), which are rarely measured during the pandemic. Here, a total of 98 VOCs species were monitored in an economy-active city in China from January 2021 to August 2022 to assess contributions to ozone formation during the pandemic. Total VOCs concentrations were 35.55 ± 21.47 ppb during the entire period, among which alkanes account for the largest fraction (13.78 ppb, 38.0%), followed by aromatics (6.16 ppb, 16.8%) and oxygenated VOCs (OVOCs, 5.69 ppb, 15.7%). Most VOCs groups (e.g., alkenes, OVOCs) and individual species (e.g., isoprene, methyl vinyl ketone) display obvious seasonal and diurnal variations, which are related to their sources and reactivities. No weekend effects of VOCs suggest limited influences from traffic emissions during pandemic. Aromatics and alkenes are the major contributors (39% and 33%) to ozone formation potential, largely driven by o/m/p-xylene (21%), ethylene (15%), toluene (9%). Secondary organic aerosol formation potential is dominated by toluene (>50%) despite its low proportion (5%). Further inclusion of VOCs and meteorology in the Random Forest model shows good ozone prediction performance (R[2] = 0.77-0.86, RMSE = 11.95-19.91 μg/m[3], MAE = 8.89-14.58 μg/m[3]). VOCs and NO2 contribute >50% of total importance with the largest difference in importance ratio of VOCs/NO2 in the summer and winter, implying ozone formation regime may vary. No seasonal variations in importance of meteorology are observed, while importance of other variables (e.g., PM2.5) is highest in the summer. This work identifies critical VOCs groups and species for ozone formation during the pandemic, and demonstrates the feasibility of machine learning algorithms in elucidation of ozone formation mechanisms.},
}
@article {pmid38360168,
year = {2024},
author = {Ko, CY and Lee, YC and Wang, YC and Hsu, HH and Chow, CH and Chen, RG and Liu, TH and Chen, CS and Chiu, TS and Chiang, DH and Wu, RF and Tseng, WL},
title = {Modulations of ocean-atmosphere interactions on squid abundance over Southwest Atlantic.},
journal = {Environmental research},
volume = {250},
number = {},
pages = {118444},
doi = {10.1016/j.envres.2024.118444},
pmid = {38360168},
issn = {1096-0953},
mesh = {*Decapodiformes/physiology ; Animals ; Atlantic Ocean ; *Atmosphere ; Temperature ; Seasons ; Climate Change ; },
abstract = {Anthropogenic shifts in seas are reshaping fishing trends, with significant implications for aquatic food sources throughout this century. Examining a 21-year abundance dataset of Argentine shortfin squids Illex argentinus paired with a regional oceanic analysis, we noted strong correlations between squid annual abundance and sea surface temperature (SST) in January and February and eddy kinetic energy (EKE) from March to May in the Southwest Atlantic. A deeper analysis revealed combined ocean-atmosphere interactions, pinpointed as the primary mode in a rotated empirical orthogonal function analysis of SST. This pattern produced colder SST and amplified EKE in the surrounding seas, factors crucial for the unique life stages of squids. Future projections from the CMIP6 archive indicated that this ocean-atmosphere pattern, referred to as the Atlantic symmetric pattern, would persist in its cold SST phase, promoting increased squid abundance. However, rising SSTs due to global warming might counteract the abundance gains. Our findings uncover a previously unrecognized link between squids and specific environmental conditions governed by broader ocean-atmosphere interactions in the Southwest Atlantic. Integrating these insights with seasonal and decadal projections can offer invaluable information to stakeholders in squid fisheries and marine conservation under a changing climate.},
}
@article {pmid38358627,
year = {2024},
author = {Akar, AU and Sisman, S and Ulku, H and Yel, E and Yalpir, S},
title = {Evaluating lake water quality with a GIS-based MCDA integrated approach: a case in Konya/Karapınar.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {13},
pages = {19478-19499},
pmid = {38358627},
issn = {1614-7499},
mesh = {Humans ; *Water Quality ; *Geographic Information Systems ; Lakes ; Environmental Monitoring/methods ; Decision Support Techniques ; },
abstract = {Considering water quality is an essential requirement in terms of environmental planning and management. To protect and manage water resources effectively, it is necessary to develop an analytical decision-support system. In this study, a systematic approach was suggested to evaluate the lake water quality. The methodology includes the prediction of the values in different locations of the lakes from experimental data through inverse distance weighting (IDW) method, creation of maps by using Geographic Information System (GIS) integrated with analytic hierarchy process (AHP) from multi-criteria decision analysis (MCDA), reclassification into five class, combining the time-related spatial data into a single map to predict the whole lake water quality from the data of sampling points, and finally overlapping the final maps with topography/geology and land use. The proposed approach was verified and presented as case study for Meke and Acigol Lakes in Konya/Turkey which were affected by human and natural factors although they have ecological, hydromorphological, and socio-economic importance. In the proposed approach, categorizing water quality parameters as "hardness and minerals," "substrates and nutrients," "solids content," "metals," and "oil-grease" groups was helpful for AHP with the determined group weights of 0.484, 0.310, 0.029, and 0.046, respectively. Assigning weights within each group and then assigning weights between groups resulted in creating accurate final map. The proposed approach is flexible and applicable to any lake water quality data; even with a limited number of data, the whole lake water quality maps could be created for assessment.},
}
@article {pmid38358505,
year = {2024},
author = {Zhang, J and Wu, Z and Dong, B and Ge, S and He, S},
title = {Effective degradation of quinoline by catalytic ozonation with MnCexOy catalysts: performance and mechanism.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {89},
number = {3},
pages = {823-837},
doi = {10.2166/wst.2024.027},
pmid = {38358505},
issn = {0273-1223},
mesh = {Humans ; Manganese Compounds ; Oxides ; Catalysis ; *Quinolines ; *Cocaine ; *Coke ; Oxygen ; *Ozone ; },
abstract = {Quinoline inevitably remains in the effluent of coking wastewater treatment plants due to its bio-refractory nature, which might cause unfavorable effects on human and ecological environments. In this study, MnCexOy was consciously synthesized by α-MnO2 doped with Ce[3+] (Ce:Mn = 1:10) and employed as the ozonation catalyst for quinoline degradation. After that, the removal efficiency and mechanism of quinoline were systematically analyzed by characterizing the physicochemical properties of MnCexOy, investigating free radicals and monitoring the solution pH. Results indicated that the removal rate of quinoline was greatly improved by the prepared MnCexOy catalyst. Specifically, the removal efficiencies of quinoline could be 93.73, 62.57 and 43.76%, corresponding to MnCexOy, α-MnO2 and single ozonation systems, respectively. The radical scavenging tests demonstrated that [•]OH and [•]O2[-] were the dominant reactive oxygen species in the MnCexOy ozonation system. Meanwhile, the contribution levels of [•]OH and [•]O2[-] to quinoline degradation were about 42 and 35%, respectively. The abundant surface hydroxyl groups and oxygen vacancies of the MnCexOy catalyst were two important factors for decomposing molecular O3 into more [•]OH and [•]O2[-]. This study could provide scientific support for the application of the MnCexOy/O3 system in degrading quinoline in bio-treated coking wastewater.},
}
@article {pmid38357349,
year = {2024},
author = {Moore, LR and Caspi, R and Campbell, DA and Casey, JR and Crevecoeur, S and Lea-Smith, DJ and Long, B and Omar, NM and Paley, SM and Schmelling, NM and Torrado, A and Zehr, JP and Karp, PD},
title = {CyanoCyc cyanobacterial web portal.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1340413},
pmid = {38357349},
issn = {1664-302X},
abstract = {CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists' work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.},
}
@article {pmid38356288,
year = {2024},
author = {Speyer, LG and Murray, AL and Kievit, R},
title = {Investigating Moderation Effects at the Within-Person Level Using Intensive Longitudinal Data: A Two-Level Dynamic Structural Equation Modelling Approach in Mplus.},
journal = {Multivariate behavioral research},
volume = {59},
number = {3},
pages = {620-637},
doi = {10.1080/00273171.2023.2288575},
pmid = {38356288},
issn = {1532-7906},
mesh = {Humans ; Longitudinal Studies ; *Latent Class Analysis ; Depression/psychology ; Social Media/statistics &amp; numerical data ; Software ; Loneliness/psychology ; Models, Statistical ; Female ; Male ; Data Interpretation, Statistical ; },
abstract = {Recent technological advances have provided new opportunities for the collection of intensive longitudinal data. Using methods such as dynamic structural equation modeling, these data can provide new insights into moment-to-moment dynamics of psychological and behavioral processes. In intensive longitudinal data (t > 20), researchers often have theories that imply that factors that change from moment to moment within individuals act as moderators. For instance, a person's level of sleep deprivation may affect how much an external stressor affects mood. Here, we describe how researchers can implement, test, and interpret dynamically changing within-person moderation effects using two-level dynamic structural equation modeling as implemented in the structural equation modeling software Mplus. We illustrate the analysis of within-person moderation effects using an empirical example investigating whether changes in spending time online using social media affect the moment-to-moment effect of loneliness on depressive symptoms, and highlight avenues for future methodological development. We provide annotated Mplus code, enabling researchers to better isolate, estimate, and interpret the complexities of within-person interaction effects.},
}
@article {pmid38355478,
year = {2024},
author = {Zhang, M and Qiao, L and Sun, P and Jiang, H and Shi, Y and Zhang, W and Mei, Y and Yu, M and Wang, H},
title = {Spatiotemporal pattern of leprosy in southwest China from 2010 to 2020: an ecological study.},
journal = {BMC public health},
volume = {24},
number = {1},
pages = {465},
pmid = {38355478},
issn = {1471-2458},
support = {2019YFE0113300//The National Key R&amp;D Program of China/ ; 81972950, 82173431, 82103748//National Natural Science Foundation of China/ ; ZDXYS202204//Jiangsu Provincial Medical Key Laboratory, Jiangsu Province Capability Improvement Project through Science, Technology and Education/ ; 2019060001//The Nanjing Incubation Program for National Clinical Research Center/ ; 2022-I2M-C&amp;T-B-094//Chinese Academy of Medical Sciences Innovation Fund for Medical Science/ ; },
mesh = {Humans ; China/epidemiology ; *Leprosy/epidemiology ; Spatial Analysis ; Cluster Analysis ; Databases, Factual ; Spatio-Temporal Analysis ; },
abstract = {BACKGROUND: Despite many efforts to control leprosy worldwide, it is still a significant public health problem in low- and middle-income regions. It has been endemic in China for thousands of years, and southwest China has the highest leprosy burden in the country.<br><br>METHODS: This observational study was conducted with all newly detected leprosy cases in southwest China from 2010 to 2020. Data were extracted from the Leprosy Management Information System (LEPMIS) database in China. The Joinpoint model was used to determine the time trends in the study area. Spatial autocorrelation statistics was performed to understand spatial distribution of leprosy cases. Spatial scan statistics was applied to identify significant clusters with high rate.<br><br>RESULTS: A total of 4801 newly detected leprosy cases were reported in southwest China over 11 years. The temporal trends declined stably. The new case detection rate (NCDR) dropped from 4.38/1,000,000 population in 2010 to 1.25/1,000,000 population in 2020, with an average decrease of 12.24% (95% CI: -14.0 to -&#x2009;10.5; P&#x2009;<&#x2009;0.001). Results of global spatial autocorrelation showed that leprosy cases presented clustering distribution in the study area. Most likely clusters were identified during the study period and were frequently located at Yunnan or the border areas between Yunnan and Guizhou Provinces. Secondary clusters were always located in the western counties, the border areas between Yunnan and Sichuan Provinces.<br><br>CONCLUSIONS: Geographic regions characterized by clusters with high rates were considered as leprosy high-risk areas. The findings of this study could be used to design leprosy control measures and provide indications to strengthen the surveillance of high-risk areas. These areas should be prioritized in the allocation of resources.},
}
@article {pmid38355366,
year = {2024},
author = {Jones, CB and Stock, K and Perkins, SE},
title = {AI-based discovery of habitats from museum collections.},
journal = {Trends in ecology &amp; evolution},
volume = {39},
number = {4},
pages = {323-327},
doi = {10.1016/j.tree.2024.01.006},
pmid = {38355366},
issn = {1872-8383},
mesh = {*Museums ; *Artificial Intelligence ; Ecosystem ; Biological Evolution ; },
abstract = {Museum collection records are a source of historic data for species occurrence, but little attention is paid to the associated descriptions of habitat at the sample locations. We propose that artificial intelligence methods have potential to use these descriptions for reconstructing past habitat, to address ecological and evolutionary questions.},
}
@article {pmid38353941,
year = {2024},
author = {Iyamu, I and McKee, G and Haag, D and Gilbert, M},
title = {Defining the role of digital public health in the evolving digital health landscape: policy and practice implications in Canada.},
journal = {Health promotion and chronic disease prevention in Canada : research, policy and practice},
volume = {44},
number = {2},
pages = {66-69},
pmid = {38353941},
issn = {2368-738X},
mesh = {Humans ; *Digital Health ; *Public Health ; Canada ; Policy ; },
}
@article {pmid38350096,
year = {2024},
author = {Krys, K and Kostoula, O and van Tilburg, WAP and Mosca, O and Lee, JH and Maricchiolo, F and Kosiarczyk, A and Kocimska-Bortnowska, A and Torres, C and Hitokoto, H and Liew, K and Bond, MH and Lun, VM and Vignoles, VL and Zelenski, JM and Haas, BW and Park, J and Vauclair, CM and Kwiatkowska, A and Roczniewska, M and Witoszek, N and Işık, &#x130; and Kosakowska-Berezecka, N and Domínguez-Espinosa, A and Yeung, JC and Górski, M and Adamovic, M and Albert, I and Pavlopoulos, V and Fülöp, M and Sirlopu, D and Okvitawanli, A and Boer, D and Teyssier, J and Malyonova, A and Gavreliuc, A and Serdarevich, U and Akotia, CS and Appoh, L and Mira, DMA and Baltin, A and Denoux, P and Esteves, CS and Gamsakhurdia, V and Garðarsdóttir, RB and Igbokwe, DO and Igou, ER and Kascakova, N and Klůzová Kracˇmárová, L and Kronberger, N and Barrientos, PE and Mohoricć, T and Murdock, E and Mustaffa, NF and Nader, M and Nadi, A and van Osch, Y and Pavlović, Z and Polácˇková Šolcová, I and Rizwan, M and Romashov, V and Røysamb, E and Sargautyte, R and Schwarz, B and Selecká, L and Selim, HA and Stogianni, M and Sun, CR and Wojtczuk-Turek, A and Xing, C and Uchida, Y},
title = {Happiness Maximization Is a WEIRD Way of Living.},
journal = {Perspectives on psychological science : a journal of the Association for Psychological Science},
volume = {},
number = {},
pages = {17456916231208367},
doi = {10.1177/17456916231208367},
pmid = {38350096},
issn = {1745-6924},
abstract = {Psychological science tends to treat subjective well-being and happiness synonymously. We start from the assumption that subjective well-being is more than being happy to ask the fundamental question: What is the ideal level of happiness? From a cross-cultural perspective, we propose that the idealization of attaining maximum levels of happiness may be especially characteristic of Western, educated, industrial, rich, and democratic (WEIRD) societies but less so for others. Searching for an explanation for why "happiness maximization" might have emerged in these societies, we turn to studies linking cultures to their eco-environmental habitat. We discuss the premise that WEIRD cultures emerged in an exceptionally benign ecological habitat (i.e., faced relatively light existential pressures compared with other regions). We review the influence of the Gulf Stream on the Northwestern European climate as a source of these comparatively benign geographical conditions. We propose that the ecological conditions in which WEIRD societies emerged afforded them a basis to endorse happiness as a value and to idealize attaining its maximum level. To provide a nomological network for happiness maximization, we also studied some of its potential side effects, namely alcohol and drug consumption and abuse and the prevalence of mania. To evaluate our hypothesis, we reanalyze data from two large-scale studies on ideal levels of personal life satisfaction-the most common operationalization of happiness in psychology-involving respondents from 61 countries. We conclude that societies whose members seek to maximize happiness tend to be characterized as WEIRD, and generalizing this across societies can prove problematic if adopted at the ideological and policy level.},
}
@article {pmid38344693,
year = {2023},
author = {Boyes, D and Gibbs, M and , and , and , and , and , and , },
title = {The genome sequence of the Variegated Golden Tortrix, Archips xylosteana (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {538},
pmid = {38344693},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Archips xylosteana (the Variegated Golden Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 650.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,861 protein coding genes.},
}
@article {pmid38343945,
year = {2024},
author = {Kwon, H and Jin, BR and Kim, HJ and Kwon, J and Park, K and Kim, C and Kim, JG and Hwang, BY and Kwon, SL and Kim, JJ and Shim, SH and Guo, Y and An, HJ and Lee, D},
title = {New Pimarane Diterpenoids Isolated from EtOAc-Extract of Apiospora arundinis Culture Medium Show Antibenign Prostatic Hyperplasia Potential.},
journal = {ACS omega},
volume = {9},
number = {5},
pages = {5616-5623},
pmid = {38343945},
issn = {2470-1343},
abstract = {Three new pimarane diterpenoids, libertellenones U-W (1-3), together with libertellenone C (4) and myrocin A (5) were isolated from an EtOAc-extract of Apiospora arundinis culture medium. The chemical structures of the new compounds were elucidated using MS, NMR, and CD spectroscopic data. Benign prostatic hyperplasia (BPH), the abnormal and pathological proliferation of epithelial and stromal cells in prostatic tissues, is a common disease in middle-aged and elderly men. In this study, the anti-BPH effects of myrocin A (5) were evaluated using BPH-1 and WPMY-1 cells. Treatment with myrocin A (5) exerted antiproliferative effects in BPH-1 and dihydrotestosterone (DHT)-stimulated WPMY-1 cells. In BPH, treatment with myrocin A (5) significantly suppressed the mRNA levels of androgen receptor (AR) and its downstream targets nuclear receptor coactivator 1 (NCOA1), proliferating cell nuclear antigen (PCNA) and kallikrein-related peptidase 3 (KLK3). Additionally, DHT-stimulated WPMY-1 cells demonstrated an upregulated mRNA levels of AR, NCOA1, PCNA, and KLK3. However, treatment with myrocin A (5) resulted in suppression of the mRNA levels. Moreover, myrocin A (5) docked computationally into the binding site of the androgen receptor (-5.5 kcal/mol).},
}
@article {pmid38342840,
year = {2024},
author = {Xiao, Y and Luan, H and Lu, S and Xing, M and Guo, C and Qian, R and Xiao, X},
title = {Toxic effects of atmospheric deposition in mining areas on wheat seedlings.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {2},
pages = {69},
pmid = {38342840},
issn = {1573-2983},
support = {52130402//the Key Program of the National Natural Science Foundation of China/ ; DYGX-2023-035//2023 China University of Mining and Technology Large Instrument and Equipment Open Sharing Fund Project/ ; },
mesh = {Triticum ; Seedlings ; Soil ; Cadmium ; Lead ; *Soil Pollutants/toxicity/analysis ; *Metals, Heavy/analysis ; Coal ; Environmental Monitoring/methods ; China ; Risk Assessment ; },
abstract = {Storage and transportation of coal, as well as operation of coal-fired power plants, produce amounts of metallic exhaust that may lead to different atmospheric environment in the overlapped areas of farmland and coal resource (OAFCR) environment. To investigate the effects of different atmospheric environment in the OAFCR region (north of Xuzhou) on wheat seedlings (AK-58), a box experiment was conducted and compared to an area far from the OAFCR (south of Xuzhou). The study revealed that (1) compared to the southern suburb of Xuzhou, the fresh and dry weight, activities of photosynthetic enzymes and POD of wheat seedlings in the OAFCR reduced obviously. (2) Significantly higher levels of Cr, Cd, Pb, Zn, and Cu were found in the shoots and roots of wheat seedlings in the OAFCR, with lower transfer factor for heavy metals (except Cd and As) in comparison to those in the southern suburb. And the bioconcentration factors of heavy metals (except As) in wheat seedlings in the OAFCR were significantly higher. (3) Nearly 90% of heavy metals (Pb, Cu, Cd, Zn, and Cr) absorbed by wheat were stored in cell walls and soluble fractions, with significantly higher contents of Cu and Cr in wheat seedlings' cell walls and higher contents of Pb, Zn, and Cd in soluble components found in the OAFCR. Our results showed that atmospheric deposition in the mining area has a certain toxic effect on wheat seedlings, and this study provides a theoretical basis for OAFCR crop toxicity management.},
}
@article {pmid38342219,
year = {2024},
author = {Lausch, A and Selsam, P and Pause, M and Bumberger, J},
title = {Monitoring vegetation- and geodiversity with remote sensing and traits.},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
volume = {382},
number = {2269},
pages = {20230058},
pmid = {38342219},
issn = {1471-2962},
mesh = {*Ecosystem ; *Remote Sensing Technology ; Phylogeny ; Biodiversity ; Phenotype ; },
abstract = {Geodiversity has shaped and structured the Earth's surface at all spatio-temporal scales, not only through long-term processes but also through medium- and short-term processes. Geodiversity is, therefore, a key control and regulating variable in the overall development of landscapes and biodiversity. However, climate change and land use intensity are leading to major changes and disturbances in bio- and geodiversity. For sustainable ecosystem management, temporal, economically viable and standardized monitoring is needed to monitor and model the effects and changes in vegetation- and geodiversity. RS approaches have been used for this purpose for decades. However, to understand in detail how RS approaches capture vegetation- and geodiversity, the aim of this paper is to describe how five features of vegetation- and geodiversity are captured using RS technologies, namely: (i) trait diversity, (ii) phylogenetic/genese diversity, (iii) structural diversity, (iv) taxonomic diversity and (v) functional diversity. Trait diversity is essential for establishing the other four. Traits provide a crucial interface between in situ, close-range, aerial and space-based RS monitoring approaches. The trait approach allows complex data of different types and formats to be linked using the latest semantic data integration techniques, which will enable ecosystem integrity monitoring and modelling in the future. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.},
}
@article {pmid38339498,
year = {2024},
author = {Li, J and Xing, Q and Li, X and Arif, M and Li, J},
title = {Monitoring Off-Shore Fishing in the Northern Indian Ocean Based on Satellite Automatic Identification System and Remote Sensing Data.},
journal = {Sensors (Basel, Switzerland)},
volume = {24},
number = {3},
pages = {},
pmid = {38339498},
issn = {1424-8220},
support = {CAS-WX2021SF-0408//Informatization Plan of Chinese Academy of Sciences/ ; XDA19060501//International Partnership Program of Chinese Academy of Sciences, the Strategic Priority Research Program of the Chinese Academy of Sciences (Class A)/ ; },
abstract = {Satellite-derived Sea Surface Temperature (SST) and sea-surface Chlorophyll a concentration (Chl-a), along with Automatic Identification System (AIS) data of fishing vessels, were used in the examination of the correlation between fishing operations and oceanographic factors within the northern Indian Ocean from March 2020 to February 2023. Frequency analysis and the empirical cumulative distribution function (ECDF) were used to calculate the optimum ranges of two oceanographic factors for fishing operations. The results revealed a substantial influence of the northeast and southwest monsoons significantly impacting fishing operations in the northern Indian Ocean, with extensive and active operations during the period from October to March and a notable reduction from April to September. Spatially, fishing vessels were mainly concentrated between 20° N and 6° S, extending from west of 90° E to the eastern coast of Africa. Observable seasonal variations in the distribution of fishing vessels were observed in the central and southeastern Arabian Sea, along with its adjacent high sea of the Indian Ocean. Concerning the marine environment, it was observed that during the northeast monsoon, the suitable SST contributed to high CPUEs in fishing operation areas. Fishing vessels were widely distributed in the areas with both mid-range and low-range Chl-a concentrations, with a small part distributed in high-concentration areas. Moreover, the monthly numbers of fishing vessels showed seasonal fluctuations between March 2020 and February 2023, displaying a periodic pattern with an overall increasing trend. The total number of fishing vessels decreased due to the impact of the COVID-19 pandemic in 2020, but this was followed by a gradual recovery in the subsequent two years. For fishing operations in the northern Indian Ocean, the optimum ranges for SST and Chl-a concentration were 27.96 to 29.47 °C and 0.03 to 1.81 mg/m[3], respectively. The preliminary findings of this study revealed the spatial-temporal distribution characteristics of fishing vessels in the northern Indian Ocean and the suitable ranges of SST and Chl-a concentration for fishing operations. These results can serve as theoretical references for the production and resource management of off-shore fishing operations in the northern Indian Ocean.},
}
@article {pmid38337048,
year = {2024},
author = {Trepel, J and le Roux, E and Abraham, AJ and Buitenwerf, R and Kamp, J and Kristensen, JA and Tietje, M and Lundgren, EJ and Svenning, JC},
title = {Meta-analysis shows that wild large herbivores shape ecosystem properties and promote spatial heterogeneity.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {4},
pages = {705-716},
pmid = {38337048},
issn = {2397-334X},
support = {1131-00006B//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; 0135-00225B//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; 101062339//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CF20-0238//Carlsbergfondet (Carlsberg Foundation)/ ; DNRF173//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; 16549//Villum Fonden (Villum Foundation)/ ; },
mesh = {Animals ; *Ecosystem ; *Herbivory ; Biodiversity ; Soil ; Biological Evolution ; },
abstract = {Megafauna (animals ≥45 kg) have probably shaped the Earth's terrestrial ecosystems for millions of years with pronounced impacts on biogeochemistry, vegetation, ecological communities and evolutionary processes. However, a quantitative global synthesis on the generality of megafauna effects on ecosystems is lacking. Here we conducted a meta-analysis of 297 studies and 5,990 individual observations across six continents to determine how wild herbivorous megafauna influence ecosystem structure, ecological processes and spatial heterogeneity, and whether these impacts depend on body size and environmental factors. Despite large variability in megafauna effects, we show that megafauna significantly alter soil nutrient availability, promote open vegetation structure and reduce the abundance of smaller animals. Other responses (14 out of 26), including, for example, soil carbon, were not significantly affected. Further, megafauna significantly increase ecosystem heterogeneity by affecting spatial heterogeneity in vegetation structure and the abundance and diversity of smaller animals. Given that spatial heterogeneity is considered an important driver of biodiversity across taxonomic groups and scales, these results support the hypothesis that megafauna may promote biodiversity at large scales. Megafauna declined precipitously in diversity and abundance since the late Pleistocene, and our results indicate that their restoration would substantially influence Earth's terrestrial ecosystems.},
}
@article {pmid38333733,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Ingrailed Clay, Diarsia mendica (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {448},
pmid = {38333733},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Diarsia mendica (the Ingrailed Clay; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 727.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 14,077 protein coding genes.},
}
@article {pmid38332565,
year = {2024},
author = {Hou, Z and Qiang, W and Wang, X and Chen, X and Hu, X and Han, X and Shen, W and Zhang, B and Xing, P and Shi, W and Dai, J and Huang, X and Zhao, G},
title = {"Cell Disk" DNA Storage System Capable of Random Reading and Rewriting.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {11},
number = {15},
pages = {e2305921},
pmid = {38332565},
issn = {2198-3844},
support = {2021YFF1201700//National Key Research and Development Program of China/ ; 2018YFA0900100//National Key Research and Development Program of China/ ; 31971340//National Natural Science Foundation of China/ ; 31800080//National Natural Science Foundation of China/ ; 32030004//National Natural Science Foundation of China/ ; 32150025//National Natural Science Foundation of China/ ; XDB0480000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2021M692645//China Postdoctoral Science Foundation/ ; 172644KYSB20180022//Bureau of International Co-operation, Chinese Academy of Sciences/ ; KQTD20180413181837372//Shenzhen Science and Technology Innovation Program/ ; RCYX20221008092950122//Shenzhen Science and Technology Innovation Program/ ; //Shenzhen Outstanding Talents Training Fund/ ; },
mesh = {*Reading ; Reproducibility of Results ; *Saccharomyces cerevisiae/genetics ; DNA/genetics ; Information Storage and Retrieval ; },
abstract = {DNA has emerged as an appealing material for information storage due to its great storage density and durability. Random reading and rewriting are essential tasks for practical large-scale data storage. However, they are currently difficult to implement simultaneously in a single DNA-based storage system, strongly limiting their practicability. Here, a "Cell Disk" storage system is presented, achieving high-density in vivo DNA data storage that enables both random reading and rewriting. In this system, each yeast cell is used as a chamber to store information, similar to a "disk block" but with the ability to self-replicate. Specifically, each genome of yeast cell has a customized CRISPR/Cas9-based "lock-and-key" module inserted, which allows selective retrieval, erasure, or rewriting of the targeted cell "block" from a pool of cells ("disk"). Additionally, a codec algorithm with lossless compression ability is developed to improve the information density of each cell "block". As a proof of concept, target-specific reading and rewriting of the compressed data from a mimic cell "disk" comprising up to 10[5] "blocks" are demonstrated and achieve high specificity and reliability. The "Cell Disk" system described here concurrently supports random reading and rewriting, and it should have great scalability for practical data storage use.},
}
@article {pmid38331396,
year = {2024},
author = {Li, C and Li, X and Bank, MS and Dong, T and Fang, JK and Leusch, FDL and Rillig, MC and Wang, J and Wang, L and Xia, Y and Xu, EG and Yang, Y and Zhang, C and Zhu, D and Liu, J and Jin, L},
title = {The "Microplastome" - A Holistic Perspective to Capture the Real-World Ecology of Microplastics.},
journal = {Environmental science &amp; technology},
volume = {58},
number = {9},
pages = {4060-4069},
pmid = {38331396},
issn = {1520-5851},
mesh = {*Microplastics ; Plastics/toxicity ; Ecosystem ; Prospective Studies ; Environmental Monitoring ; *Water Pollutants, Chemical/toxicity ; },
abstract = {Microplastic pollution, an emerging pollution issue, has become a significant environmental concern globally due to its ubiquitous, persistent, complex, toxic, and ever-increasing nature. As a multifaceted and diverse suite of small plastic particles with different physicochemical properties and associated matters such as absorbed chemicals and microbes, future research on microplastics will need to comprehensively consider their multidimensional attributes. Here, we introduce a novel, conceptual framework of the "microplastome", defined as the entirety of various plastic particles (<5 mm), and their associated matters such as chemicals and microbes, found within a sample and its overall environmental and toxicological impacts. As a novel concept, this paper aims to emphasize and call for a collective quantification and characterization of microplastics and for a more holistic understanding regarding the differences, connections, and effects of microplastics in different biotic and abiotic ecosystem compartments. Deriving from this lens, we present our insights and prospective trajectories for characterization, risk assessment, and source apportionment of microplastics. We hope this new paradigm can guide and propel microplastic research toward a more holistic era and contribute to an informed strategy for combating this globally important environmental pollution issue.},
}
@article {pmid38330650,
year = {2024},
author = {Li, X and Cheng, X and Wu, J and Cai, Z and Wang, Z and Zhou, J},
title = {Multi-omics reveals different impact patterns of conventional and biodegradable microplastics on the crop rhizosphere in a biofertilizer environment.},
journal = {Journal of hazardous materials},
volume = {467},
number = {},
pages = {133709},
doi = {10.1016/j.jhazmat.2024.133709},
pmid = {38330650},
issn = {1873-3336},
mesh = {*Microplastics ; *Multiomics ; Plastics ; Rhizosphere ; Polyethylene ; Crops, Agricultural ; Polyesters ; },
abstract = {Microplastics (MPs) from the incomplete degradation of agricultural mulch can stress the effectiveness of biofertilizers and ultimately affect the rhizosphere environment of crops. Yet, the involved mechanisms are poorly known and robust empirical data is generally lacking. Here, conventional polyethylene (PE) MPs and poly(butylene adipate-co-butylene terephthalate) (PBAT) / poly(lactic acid) (PLA) biodegradable MPs (PBAT-PLA BioMPs) were investigated to assess their potential impact on the rhizosphere environment of Brassica parachinensis in the presence of Bacillus amyloliquefaciens biofertilizer. The results revealed that both MPs caused different levels of inhibited crop both above- and belowground crop biomass (up to 50.11% and 57.09%, respectively), as well as a significant decrease in plant height (up to 48.63% and 25.95%, respectively), along with an imbalance of microbial communities. Transcriptomic analyses showed that PE MPs mainly affected root's vitamin metabolism, whereas PBAT-PLA BioMPs mainly interfered with the lipid's enrichment. Metabolomic analyses further indicated that PE MPs interfered with amino acid synthesis that involved in crops' oxidative stress, and that PBAT-PLA BioMPs mainly affected the pathways associated with root growth. Additionally, PBAT-PLA BioMPs had a bigger ecological negative impact than did PE MPs, as evidenced by more pronounced alterations in root antioxidant abilities, a higher count of identified differential metabolites, more robust interrelationships among rhizosphere parameters, and a more intricate pattern of impacts on rhizosphere metrics. This study highlights the MPs' impact on crop rhizosphere in a biofertilizer environment from a rhizosphere multi-omics perspective, and has theoretical implications for scientific application of biofertilizers.},
}
@article {pmid38322859,
year = {2024},
author = {Mahmoudzadeh, H and Abedini, A and Aram, F and Mosavi, A},
title = {Evaluating urban environmental quality using multi criteria decision making.},
journal = {Heliyon},
volume = {10},
number = {3},
pages = {e24921},
pmid = {38322859},
issn = {2405-8440},
abstract = {In the urban environment, the quality refers to the capacity that provides and fulfills the material and spiritual needs of inhabitants. In order to improve the quality of urban life and standard of living for their citizens, planners and managers strive to raise Urban Environmental Quality. The objective of this study is to evaluate the quality of urban environment through the spatial analysis of a multi-criteria decision making (MCDM) method utilizing CRITIC. This research is conducted in district 4 and district 2 of the Tabriz Metropolis Municipality. In order to determine the quality of an urban environment, air pollution, vegetation coverage, land surface temperature, production of waste, population density, noise pollution, health care per capita, green spaces per capita, recreational spaces per capita, and distance from fault lines are used. After evaluating and producing environmental quality maps in two separate districts, 10 indicators were tested for significance and a comparative evaluation of two districts was conducted in order to determine which district was in better condition based on a statistical analysis of the T-test results. In accordance with the CRITIC method, there are significant differences between averages of waste production, population density, noise pollution, distance from fault lines, Land Surface Temperature, Normalized difference vegetation index, and distance from fault lines between the two districts. It appears that recreational space, air pollution, health care per capita, and green space per capita are not meaningfully different on averages. The preparation of environmental quality maps reveals the importance of meaningful indicators at the neighborhood level in two urban districts. In both districts by strengthening the continuity of the landscape through the development of ecological corridors and an increase in per capita can contribute to the improvement of the quality of the urban environment.},
}
@article {pmid38322797,
year = {2023},
author = {Faria, AL and Almeida, Y and Branco, D and Câmara, J and Cameirão, M and Ferreira, L and Moreira, A and Paulino, T and Rodrigues, P and Spinola, M and Vilar, M and Bermúdez I Badia, S and Simões, M and Fermé, E},
title = {NeuroAIreh@b: an artificial intelligence-based methodology for personalized and adaptive neurorehabilitation.},
journal = {Frontiers in neurology},
volume = {14},
number = {},
pages = {1258323},
pmid = {38322797},
issn = {1664-2295},
abstract = {Cognitive impairments are a prevalent consequence of acquired brain injury, dementia, and age-related cognitive decline, hampering individuals' daily functioning and independence, with significant societal and economic implications. While neurorehabilitation represents a promising avenue for addressing these deficits, traditional rehabilitation approaches face notable limitations. First, they lack adaptability, offering one-size-fits-all solutions that may not effectively meet each patient's unique needs. Furthermore, the resource-intensive nature of these interventions, often confined to clinical settings, poses barriers to widespread, cost-effective, and sustained implementation, resulting in suboptimal outcomes in terms of intervention adaptability, intensity, and duration. In response to these challenges, this paper introduces NeuroAIreh@b, an innovative cognitive profiling and training methodology that uses an AI-driven framework to optimize neurorehabilitation prescription. NeuroAIreh@b effectively bridges the gap between neuropsychological assessment and computational modeling, thereby affording highly personalized and adaptive neurorehabilitation sessions. This approach also leverages virtual reality-based simulations of daily living activities to enhance ecological validity and efficacy. The feasibility of NeuroAIreh@b has already been demonstrated through a clinical study with stroke patients employing a tablet-based intervention. The NeuroAIreh@b methodology holds the potential for efficacy studies in large randomized controlled trials in the future.},
}
@article {pmid38316926,
year = {2024},
author = {Zuffa, S and Schmid, R and Bauermeister, A and P Gomes, PW and Caraballo-Rodriguez, AM and El Abiead, Y and Aron, AT and Gentry, EC and Zemlin, J and Meehan, MJ and Avalon, NE and Cichewicz, RH and Buzun, E and Terrazas, MC and Hsu, CY and Oles, R and Ayala, AV and Zhao, J and Chu, H and Kuijpers, MCM and Jackrel, SL and Tugizimana, F and Nephali, LP and Dubery, IA and Madala, NE and Moreira, EA and Costa-Lotufo, LV and Lopes, NP and Rezende-Teixeira, P and Jimenez, PC and Rimal, B and Patterson, AD and Traxler, MF and Pessotti, RC and Alvarado-Villalobos, D and Tamayo-Castillo, G and Chaverri, P and Escudero-Leyva, E and Quiros-Guerrero, LM and Bory, AJ and Joubert, J and Rutz, A and Wolfender, JL and Allard, PM and Sichert, A and Pontrelli, S and Pullman, BS and Bandeira, N and Gerwick, WH and Gindro, K and Massana-Codina, J and Wagner, BC and Forchhammer, K and Petras, D and Aiosa, N and Garg, N and Liebeke, M and Bourceau, P and Kang, KB and Gadhavi, H and de Carvalho, LPS and Silva Dos Santos, M and Pérez-Lorente, AI and Molina-Santiago, C and Romero, D and Franke, R and Brönstrup, M and Vera Ponce de León, A and Pope, PB and La Rosa, SL and La Barbera, G and Roager, HM and Laursen, MF and Hammerle, F and Siewert, B and Peintner, U and Licona-Cassani, C and Rodriguez-Orduña, L and Rampler, E and Hildebrand, F and Koellensperger, G and Schoeny, H and Hohenwallner, K and Panzenboeck, L and Gregor, R and O'Neill, EC and Roxborough, ET and Odoi, J and Bale, NJ and Ding, S and Sinninghe Damsté, JS and Guan, XL and Cui, JJ and Ju, KS and Silva, DB and Silva, FMR and da Silva, GF and Koolen, HHF and Grundmann, C and Clement, JA and Mohimani, H and Broders, K and McPhail, KL and Ober-Singleton, SE and Rath, CM and McDonald, D and Knight, R and Wang, M and Dorrestein, PC},
title = {microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data.},
journal = {Nature microbiology},
volume = {9},
number = {2},
pages = {336-345},
pmid = {38316926},
issn = {2058-5276},
support = {R01 GM107550/GM/NIGMS NIH HHS/United States ; U01 DK119702/DK/NIDDK NIH HHS/United States ; R01 AI167860/AI/NIAID NIH HHS/United States ; R01 LM013115/LM/NLM NIH HHS/United States ; R35 GM142938/GM/NIGMS NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; R01 GM132649/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; R01 GM137135/GM/NIGMS NIH HHS/United States ; S10 OD021750/OD/NIH HHS/United States ; F32 AT011475/AT/NCCIH NIH HHS/United States ; U24 DK133658/DK/NIDDK NIH HHS/United States ; T32 AR064194/AR/NIAMS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; P 31915/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Humans ; *Tandem Mass Spectrometry ; *Metabolomics/methods ; Databases, Factual ; },
abstract = {microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms' role in ecology and human health.},
}
@article {pmid38296495,
year = {2024},
author = {Haga, Y and Manabe, S and Tsujino, H and Asahara, H and Higashisaka, K and Tsutsumi, Y},
title = {[Mechanisms of Cell Toxicity Caused by Degraded Microplastics].},
journal = {Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan},
volume = {144},
number = {2},
pages = {177-181},
doi = {10.1248/yakushi.23-00152-3},
pmid = {38296495},
issn = {1347-5231},
mesh = {Animals ; Humans ; *Microplastics/toxicity ; Plastics/toxicity ; Ultraviolet Rays ; *Water Pollutants, Chemical/toxicity/analysis ; Fishes ; },
abstract = {Microplastics (MPs), defined as plastic particles less than 5 mm in size, are ubiquitous in the environment. The accumulation of MPs in various environmental compartments, such as the ocean, soil, and air, has raised considerable concerns regarding their impact on ecological systems, including marine life and human health. Notably, MPs have been detected in marine organisms such as shellfish and fish, and have even been found in the human body, including in the blood and placenta. Moreover, considering that MPs have been detected in drinking water, human exposure to these particles in daily life is inevitable. To assess the risk posed by MPs to human health, it is essential to consider their physiological and chemical properties, including size, shape, surface modification, and material composition. However, current risk analyses focus primarily on spherical MPs with smooth surfaces, which differ substantially from most of the MPs detected in the environment. Environmental factors, such as ocean waves and ultraviolet radiation, alter the properties of MPs, including size, shape, and surface characteristics. In this review, we summarize current research on MPs, with a particular emphasis on the effects of MP degradation on human health. Furthermore, we generated MPs with surface degradation and evaluated their impact on cell toxicity, along with the underlying biological mechanisms.},
}
@article {pmid38315121,
year = {2024},
author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C},
title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.},
journal = {Microbiology spectrum},
volume = {12},
number = {3},
pages = {e0360223},
pmid = {38315121},
issn = {2165-0497},
support = {2021YFF0703805//MOST | National Key Research and Development Program of China (NKPs)/ ; 82102447//MOST | National Natural Science Foundation of China (NSFC)/ ; DFL20191801//Beijing Hospital Authority/ ; Z201100005520040//Beijing Municipal Science and Technology Commission, Adminitrative Commission of Zhongguancun Science Park/ ; QML20230701//Beijing Hospitals Authority Youth Programme/ ; },
mesh = {Animals ; Humans ; Mice ; *Gene Transfer, Horizontal ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Bacteria/genetics ; DNA ; },
abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.},
}
@article {pmid38315112,
year = {2024},
author = {Chandel, AS},
title = {Geo-spatial technology based on a multi-criteria evaluation technique used to find potential landfill sites in the town of Bule Hora in southern Ethiopia.},
journal = {Journal of the Air &amp; Waste Management Association (1995)},
volume = {74},
number = {4},
pages = {207-239},
doi = {10.1080/10962247.2024.2312889},
pmid = {38315112},
issn = {2162-2906},
mesh = {Humans ; *Solid Waste ; Ethiopia ; Prospective Studies ; Quality of Life ; Geographic Information Systems ; Decision Support Techniques ; *Refuse Disposal/methods ; Waste Disposal Facilities ; Technology ; },
abstract = {Solid waste has surfaced as an eminent and critical concern of environmental and social significance on a global scale, and Ethiopia, a developing country with limited income, has also encountered unfavorable outcomes due to substandard waste management practices. When pinpointing a fitting landfill location in the town of Bule Hora, various ecological, economic, and societal aspects must be considered; these may result in discord and exacerbate a multifaceted and lengthy process. Hence, this research aims to identify prospective landfill sites within the town and utilize geospatial methods, such as Multi-Criteria Evaluation and Analytic Hierarchy Process, to accomplish its objectives. The utilization of geospatial technology and multi-criteria evaluation provides an efficient manner to simultaneously address all bottlenecks involved in the selection of an appropriate landfill location. Geospatial technology evaluates and manages environmental constraints, whereas multi-criteria assessment categorizes choices based on their desirability. Furthermore, by employing a restriction map adhering to established standards, seven landfill sites have successfully been identified within the town. The Land Suitability Index assesses site suitability based on ecological factors, while the Total Hauling Distance evaluates sites within an economic framework. AHP determines weightings through 25.4 pairwise comparisons, resulting in a consistency ratio of 1.95%. The cartographic analysis is conducted using ESRI ArcGIS version 10.8 software. The findings of this study reveal that 98.69% of the area under study is subject to restrictions. The study recommends the implementation of geospatial methods for identifying suitable landfill sites, which would aid in the decision-making process and prevent hasty decisions from triggering environmental degradation. Proper waste disposal would augment the quality of life for residents by diminishing health hazards. The study endeavors to serve as a reference for other developing countries in selecting appropriate landfill sites.Implications: The town of Bule Hora also faces the problem of waste disposal; there is no scientifically selected suitable landfill. Residents of the town of Bule Hora practice waste disposal in open fields, near settlements, water bodies, roads, agricultural land, and other places. The main sources of solid waste in the town are homes, shops, hotels, restaurants, open markets, hospitals, educational institutions, private clinics, etc. Water pollution can potentially lead to the spread of waterborne diseases. According to reports from the Bule Horas Health Department, many people are affected by water-related diseases every year. These open landfill systems with no regard for settlement, topography, geology, surface, or groundwater conditions are the consequences of these unsuitable habitats and health problems. To reduce these problems, this study plays an important role in determining the suitability of landfills for the town and proposing alternative measures that can minimize negative environmental impacts from waste. This study aims to apply geospatial-based technology to a multi-criteria assessment technique to select perfectly suitable landfill sites that are environmentally friendly, economically cost-effective, and socially responsible; examine the town's current waste management system; calculate the selected parameter weights for feature ranking; and delineate solid waste landfills.},
}
@article {pmid38312217,
year = {2024},
author = {Ogawa, T and Tsuzuki, S and Ohbe, H and Matsui, H and Fushimi, K and Yasunaga, H and Kutsuna, S},
title = {Analysis of Differences in Characteristics of High-Risk Endemic Areas for Contracting Japanese Spotted Fever, Tsutsugamushi Disease, and Severe Fever With Thrombocytopenia Syndrome.},
journal = {Open forum infectious diseases},
volume = {11},
number = {2},
pages = {ofae025},
pmid = {38312217},
issn = {2328-8957},
abstract = {BACKGROUND: Tick-borne infections, including tsutsugamushi disease, Japanese spotted fever, and severe fever with thrombocytopenia syndrome (SFTS), are prevalent in East Asia with varying geographic distribution and seasonality. This study aimed to investigate the differences in the characteristics among endemic areas for contracting each infection.<br><br>METHODS: We conducted an ecologic study in Japan, using data from a nationwide inpatient database and publicly available geospatial data. We identified 4493 patients who were hospitalized for tick-borne infections between July 2010 and March 2021. Mixed-effects modified Poisson regression analysis was used to identify factors associated with a higher risk of contracting each tick-borne disease (Tsutsugamushi, Japanese spotted fever, and SFTS).<br><br>RESULTS: Mixed-effects modified Poisson regression analysis revealed that environmental factors, such as temperature, sunlight duration, elevation, precipitation, and vegetation, were associated with the risk of contracting these diseases. Tsutsugamushi disease was positively associated with higher temperatures, farms, and forests, whereas Japanese spotted fever and SFTS were positively associated with higher solar radiation and forests.<br><br>CONCLUSIONS: Our findings from this ecologic study indicate that different environmental factors play a significant role in the risk of transmission of tick-borne infections. Understanding the differences can aid in identifying high-risk areas and developing public health strategies for infection prevention. Further research is needed to address causal relationships.},
}
@article {pmid38311099,
year = {2024},
author = {Stanic, B and Sukur, N and Milošević, N and Markovic Filipovic, J and Pogrmic-Majkic, K and Andric, N},
title = {Differential eigengene network analysis reveals benzo[a]pyrene and 2,3,7,8-tetrachlorodibenzo-p-dioxin consensus regulatory network in human liver cell line HepG2.},
journal = {Toxicology},
volume = {502},
number = {},
pages = {153737},
doi = {10.1016/j.tox.2024.153737},
pmid = {38311099},
issn = {1879-3185},
mesh = {Humans ; *Benzo(a)pyrene/toxicity ; *Polychlorinated Dibenzodioxins/toxicity ; Consensus ; Liver/metabolism ; Cell Line, Tumor ; Receptors, Aryl Hydrocarbon/genetics/metabolism ; },
abstract = {Aryl hydrocarbon receptor (AHR) is one of the main mediators of the toxic effects of benzo[a]pyrene (BaP) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). However, a vast number of BaP- and TCDD-affected genes may suggest a more complex transcriptional regulatory network driving common adverse effects of these two chemicals. Unlike TCDD, BaP is rapidly metabolized in the liver, yielding products with a questionable ability to bind and activate AHR. In this study, we used transcriptomics data from the BaP- and TCCD-exposed human liver cell line HepG2, and performed differential eigengene network analysis to understand the correlation among genes and to untangle the common regulatory mechanism in the action of BaP and TCDD. The genes were grouped into 11 meta-modules with an overall preservation of 0.72 and were also segregated into three consensus time clusters: 12, 24, and 48 h. The analysis showed that the consensus genes in each time cluster were either directly regulated by the AHR or the AHR-TF interactions. Some TFs form a direct physical interaction with AHR such as ESR1, FOXA1, and E2F1, whereas others, including CTCF, RXRA, FOXO1, CEBPA, CEBPB, and TP53 show an indirect interaction with AHR. The analysis of biological processes (BPs) identified unique and common BPs in BaP and TCDD samples, with DNA damage response detected in all three time points. In summary, we identified a consensus transcriptional regulatory network common for BaP and TCDD consisting of direct AHR targets and AHR-TF targets. This analysis sheds new light on the common mechanism of action of a genotoxic (BaP) and non-genotoxic (TCDD) chemical in liver cells.},
}
@article {pmid38308167,
year = {2024},
author = {Wang, Y and Chen, Y and Lu, S and Guo, X},
title = {Development and trends of constructed wetland substrates over the past 30 years: a literature visualization analysis based on CiteSpace.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {10},
pages = {14537-14552},
pmid = {38308167},
issn = {1614-7499},
mesh = {Humans ; *Wetlands ; Cluster Analysis ; Databases, Factual ; *Environmental Pollutants ; Sewage ; },
abstract = {Constructed wetland substrates (CWSs) have received considerable attention owing to their importance in adsorbing and degrading pollutants, providing growth attachment points for microorganisms, and supporting wetland plants. There are differences in the configurations and functions of constructed wetlands (CWs) for treating different water bodies and sewage, resulting in a wide variety of substrates. Research on the application and mechanism of CWSs is not sufficiently systematic. Therefore, the current research advancements and hotspots must be identified. Hence, we used CiteSpace to analyze 1955 English publications from the core collection database of the Web of Science to assess the current state of the CWS research field. Based on the cooperative network analysis, the roles of various countries, institutions, and authors in research on CWSs were reviewed. Keyword co-occurrence and cluster analyses were used to discuss the transformation of CWSs from removing traditional pollutants to emerging pollutants and the transition from incorporating natural substrates to artificial substrates. Finally, we underscored the need for more emphasis to be placed on the collocation and application of the CWSs at different latitudes. Furthermore, the substrate micro-interface process and its effects on the interaction patterns of pollutants and microorganisms should be thoroughly investigated to provide theoretical guidance for the development of wetland applications and mechanisms.},
}
@article {pmid38307178,
year = {2024},
author = {Fu, Y and He, Y and Chen, W and Xiao, W and Ren, H and Shi, Y and Hu, Z},
title = {Dynamics of carbon storage driven by land use/land cover transformation in coal mining areas with a high groundwater table: A case study of Yanzhou Coal Mine, China.},
journal = {Environmental research},
volume = {247},
number = {},
pages = {118392},
doi = {10.1016/j.envres.2024.118392},
pmid = {38307178},
issn = {1096-0953},
mesh = {Humans ; *Coal Mining ; Carbon ; China ; *Groundwater ; Coal ; Ecosystem ; Conservation of Natural Resources ; },
abstract = {Intensive anthropogenic activities have led to drastic changes in land use/land cover (LULC) and impacted the carbon storage in high-groundwater coal basins. In this paper, we conduct a case study on the Yanzhou Coalfield in Shandong Province of China. We further classify waterbodies by using the Google Earth Engine (GEE) to better investigate the process of LULC transformation and the forces driving it in four periods from 1985 to 2020 (i.e., 1985-1995, 1995-2005, 2005-2015, and 2015-2020). We modeled the spatiotemporal dynamics of carbon storage by using InVEST based on the transformation in LULC and its drivers, including mining (M), reclamation (R), urbanization and village relocation (U), and ecological restoration (E). The results indicate that carbon storage had depleted by 19.69 % (321099.06 Mg) owing to intensive transformations in LULC. The area of cropland shrank with the expansion of built-up land and waterbodies, and 56.31 % of the study area underwent transitions in land use in the study period. U was the primary driver of carbon loss while E was the leading driver of carbon gain. While the direct impact of M on carbon loss accounted for only 5.23 % of the total, it affected urbanization and led to village relocation. R led to the recovery of cropland and the reclamation of water for aquaculture, which in turn improved the efficiency of land use. However, it contributed only 2.09 % to the total increase in carbon storage. Numerous complicated and intertwined processes (211) drove the changes in carbon storage in the study area. The work here provides valuable information for decision-makers as well as people involved in reclamation and ecological restoration to better understand the link between carbon storage and the forces influencing it. The results can be used to integrate the goals of carbon sequestration into measures for land management.},
}
@article {pmid38305922,
year = {2024},
author = {Eshetu, SB and Kipkulei, HK and Koepke, J and Kächele, H and Sieber, S and Löhr, K},
title = {Impact of forest landscape restoration in combating soil erosion in the Lake Abaya catchment, Southern Ethiopia.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {3},
pages = {228},
pmid = {38305922},
issn = {1573-2959},
mesh = {*Soil Erosion ; *Ecosystem ; Ethiopia ; Lakes ; Environmental Monitoring/methods ; Conservation of Natural Resources ; Soil ; Geographic Information Systems ; Forests ; },
abstract = {As an effect of forest degradation, soil erosion is among Ethiopia's most pressing environmental challenges and a major threat to food security where it could potentially compromise the ecosystem functions and services. As the effects of soil erosion intensify, the landscape's capacity to support ecosystem functions and services is compromised. Exploring the ecological implications of soil erosion is crucial. This study investigated the soil loss and land degradation in the Lake Abaya catchment to explore forest landscape restoration (FLR) implementation as a possible countermeasure to the effects. The study used a geographic information system (GIS)-based approach of the Revised Universal Soil Loss Equation (RUSLE) to determine the potential annual soil loss and develop an erosion risk map. Results show that 13% of the catchment, which accounts for approximately 110,000 ha, is under high erosion risk of exceeding the average annual tolerable soil loss of 10 t/ha/year. Allocation of land on steep slopes to crop production is the major reason for the calculated high erosion risk in the catchment. A scenario-based analysis was implemented following the slope-based land-use allocation proposal indicated in the Rural Land Use Proclamation 456/2005 of Ethiopia. The scenario analysis resulted in a reversal erosion effect whereby an estimated 3000 t/ha/year of soil loss in the catchment. Thus, FLR activities hold great potential for minimizing soil loss and contributing to supporting functioning and providing ecosystem services. Tree-based agroforestry systems are among the key FLR measures championed in highly degraded landscapes in Ethiopia. This study helps policymakers and FLR implementors identify erosion risk areas for future FLR activities. Thereby, it contributes to achieving the country's restoration commitment.},
}
@article {pmid38305133,
year = {2024},
author = {Ramakodi, MP},
title = {Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.},
journal = {FEMS microbiology letters},
volume = {371},
number = {},
pages = {},
doi = {10.1093/femsle/fnae009},
pmid = {38305133},
issn = {1574-6968},
mesh = {RNA, Ribosomal, 18S/genetics ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor = 0.950; P-value = 4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.},
}
@article {pmid38302634,
year = {2024},
author = {Rajan, SC and M, V and Mitra, A and N P, S and K, A and Pillai, MS and R, J},
title = {Threshold of anthropogenic sound levels within protected landscapes in Kerala, India, for avian habitat quality and conservation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {2701},
pmid = {38302634},
issn = {2045-2322},
mesh = {Animals ; Acoustics ; *Birds ; Conservation of Natural Resources/methods ; *Ecosystem ; India ; *Anthropogenic Effects ; *Sound ; },
abstract = {Anthrophony is an important determinant of habitat quality in the Anthropocene. Acoustic adaptation of birds at lower levels of anthrophony is known. However, threshold anthrophony, beyond which biophony starts decreasing, is less explored. Here, we present empirical results of the relationship between anthrophony and biophony in four terrestrial soundscapes. The constancy of the predicted threshold vector normalised anthropogenic power spectral density (~ 0.40 Watts/Hz) at all the study sites is intriguing. We propose the threshold value of anthropogenic power spectral density as an indicator of the avian acoustic tolerance level in the study sites. The findings pave the way to determine permissible sound levels within protected landscapes and directly contribute to conservation planning.},
}
@article {pmid38301473,
year = {2024},
author = {Huang, Y and Qin, R and Wei, H and Chai, N and Yang, Y and Li, Y and Wan, P and Li, Y and Zhao, W and Lawawirojwong, S and Suepa, T and Zhang, F},
title = {Plastic film mulching application improves potato yields, reduces ammonia emissions, but boosts the greenhouse gas emissions in China.},
journal = {Journal of environmental management},
volume = {353},
number = {},
pages = {120241},
doi = {10.1016/j.jenvman.2024.120241},
pmid = {38301473},
issn = {1095-8630},
mesh = {*Greenhouse Gases/analysis ; *Solanum tuberosum ; Ammonia ; Carbon Dioxide/analysis ; Agriculture ; Soil ; China ; Methane/analysis ; Nitrous Oxide/analysis ; Fertilizers/analysis ; },
abstract = {With global population growth and climate change, food security and global warming have emerged as two major challenges to agricultural development. Plastic film mulching (PM) has long been used to improve yields in rain-fed agricultural systems, but few studies have focused on soil gas emissions from mulched rainfed potatoes on a long-term and regional scale. This study integrated field data with the Denitrification-Decomposition (DNDC) model to evaluate the impacts of PM on potato yields, greenhouse gas (GHG) and ammonia (NH3) emissions in rainfed agricultural systems in China. We found that PM increased potato yield by 39.7 % (1505 kg ha[-1]), carbon dioxide (CO2) emissions by 15.4 % (123 kg CO2 eq ha[-1]), nitrous oxide (N2O) emissions by 47.8 % (1016 kg CO2 eq ha[-1]), and global warming potential (GWP) by 38.9 % (1030 kg CO2 eq ha[-1]), while NH3 volatilization decreased by 33.9 % (8.4 kg NH3 ha[-1]), and methane (CH4) emissions were little changed compared to CK. Specifically, the yield after PM significantly increased in South China (SC), North China (NC), and Northwest China (NWC), with increases of 66.1 % (2429 kg ha[-1]), 44.1 % (1173 kg ha[-1]), and 43.6 % (956 kg ha[-1]) compared to CK, respectively. The increase in GWP and greenhouse gas emission intensity (GHGI) under PM was more pronounced in the Northeast China (NEC) and NWC regions, with respective increases of 57.1 % and 60.2 % in GWP, 16.9 % and 10.3 % in GHGI. While in the Middle and Lower reaches of the Yangtze River (MLYR) and SC, PM decreased GHGI with 10.2 % and 31.1 %, respectively. PM significantly reduced NH3 emissions in all regions and these reductions were most significant in Southwest China (SWC), SCand MLYR, which were 41 %, 38.0 %, and 38.0 % lower than CK, respectively. In addition, climatic and edaphic variables were the main contributors to GHG and NH3 emissions. In conclusion, it is appropriate to promote the use of PM in the MLYR and SC regions, because of the ability to increase yields while reducing environmental impacts (lower GHGI and NH3 emissions). The findings provide a theoretical basis for sustainable agricultural production of PM potatoes.},
}
@article {pmid38297840,
year = {2024},
author = {Tian, C and Li, J and Wu, Y and Wang, G and Zhang, Y and Zhang, X and Sun, Y and Wang, Y},
title = {An integrative database and its application for plant synthetic biology research.},
journal = {Plant communications},
volume = {5},
number = {5},
pages = {100827},
pmid = {38297840},
issn = {2590-3462},
mesh = {*Synthetic Biology/methods ; Plants/genetics ; Databases, Genetic ; Nicotiana/genetics ; Computational Biology/methods ; },
abstract = {Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants. Limited by few well-characterized bioparts for plant chassis, the development of plant synthetic biology lags behind that of its microbial counterpart. Here, we constructed a web-based Plant Synthetic BioDatabase (PSBD), which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals. Online bioinformatics tools including local BLAST, chem similarity, phylogenetic analysis, and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta. We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quantitative regulation in tobacco leaves. More powerful synthetic devices were then assembled to amplify the transcriptional signals, enabling enhanced expression of flavivirus non-structure 1 proteins in plants. The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.},
}
@article {pmid38297125,
year = {2024},
author = {Xu, P and Li, G and Zheng, Y and Fung, JCH and Chen, A and Zeng, Z and Shen, H and Hu, M and Mao, J and Zheng, Y and Cui, X and Guo, Z and Chen, Y and Feng, L and He, S and Zhang, X and Lau, AKH and Tao, S and Houlton, BZ},
title = {Fertilizer management for global ammonia emission reduction.},
journal = {Nature},
volume = {626},
number = {8000},
pages = {792-798},
pmid = {38297125},
issn = {1476-4687},
mesh = {*Ammonia/analysis/metabolism ; *Crop Production/methods/statistics &amp; numerical data/trends ; Datasets as Topic ; Ecosystem ; *Fertilizers/adverse effects/analysis/statistics &amp; numerical data ; Machine Learning ; Nitrogen/analysis/metabolism ; Oryza/metabolism ; Soil/chemistry ; Triticum/metabolism ; Zea mays/metabolism ; Climate Change/statistics &amp; numerical data ; },
abstract = {Crop production is a large source of atmospheric ammonia (NH3), which poses risks to air quality, human health and ecosystems[1-5]. However, estimating global NH3 emissions from croplands is subject to uncertainties because of data limitations, thereby limiting the accurate identification of mitigation options and efficacy[4,5]. Here we develop a machine learning model for generating crop-specific and spatially explicit NH3 emission factors globally (5-arcmin resolution) based on a compiled dataset of field observations. We show that global NH3 emissions from rice, wheat and maize fields in 2018 were 4.3 ± 1.0 Tg N yr[-1], lower than previous estimates that did not fully consider fertilizer management practices[6-9]. Furthermore, spatially optimizing fertilizer management, as guided by the machine learning model, has the potential to reduce the NH3 emissions by about 38% (1.6 ± 0.4 Tg N yr[-1]) without altering total fertilizer nitrogen inputs. Specifically, we estimate potential NH3 emissions reductions of 47% (44-56%) for rice, 27% (24-28%) for maize and 26% (20-28%) for wheat cultivation, respectively. Under future climate change scenarios, we estimate that NH3 emissions could increase by 4.0 ± 2.7% under SSP1-2.6 and 5.5 ± 5.7% under SSP5-8.5 by 2030-2060. However, targeted fertilizer management has the potential to mitigate these increases.},
}
@article {pmid38294243,
year = {2024},
author = {Omondi, VO and Bosire, GO and Onyari, JM and Kibet, C and Mwasya, S and Onyonyi, VN and Getahun, MN},
title = {Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species.},
journal = {mSystems},
volume = {9},
number = {2},
pages = {e0122823},
pmid = {38294243},
issn = {2379-5077},
support = {B1126A-185//Max Planck Institute for Chemical Ecology/ ; B1126A-185//International Centre of Insect Physiology and Ecology (ICIPE)/ ; },
mesh = {Cattle ; Humans ; Sheep ; Animals ; *Livestock/microbiology ; Rumen/metabolism ; Camelus ; Multiomics ; Ruminants/microbiology ; *Microbiota/genetics ; Goats/physiology ; Animal Feed/analysis ; },
abstract = {Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.},
}
@article {pmid38292065,
year = {2023},
author = {Macgregor, CJ and Saccheri, IJ and , and , and , and , },
title = {The genome sequence of the Rock Grayling, Hipparchia semele (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {495},
pmid = {38292065},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Hipparchia semele (the Rock Grayling; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 403.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,540 protein coding genes.},
}
@article {pmid38285940,
year = {2024},
author = {Long, C and Deng, J and Nguyen, J and Liu, YY and Alm, EJ and Solé, R and Saavedra, S},
title = {Structured community transitions explain the switching capacity of microbial systems.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {6},
pages = {e2312521121},
pmid = {38285940},
issn = {1091-6490},
support = {R01 AI141529/AI/NIAID NIH HHS/United States ; },
mesh = {*Microbiota ; *Environment ; *Ecology ; },
abstract = {Microbial systems appear to exhibit a relatively high switching capacity of moving back and forth among few dominant communities (taxon memberships). While this switching behavior has been mainly attributed to random environmental factors, it remains unclear the extent to which internal community dynamics affect the switching capacity of microbial systems. Here, we integrate ecological theory and empirical data to demonstrate that structured community transitions increase the dependency of future communities on the current taxon membership, enhancing the switching capacity of microbial systems. Following a structuralist approach, we propose that each community is feasible within a unique domain in environmental parameter space. Then, structured transitions between any two communities can happen with probability proportional to the size of their feasibility domains and inversely proportional to their distance in environmental parameter space-which can be treated as a special case of the gravity model. We detect two broad classes of systems with structured transitions: one class where switching capacity is high across a wide range of community sizes and another class where switching capacity is high only inside a narrow size range. We corroborate our theory using temporal data of gut and oral microbiota (belonging to class 1) as well as vaginal and ocean microbiota (belonging to class 2). These results reveal that the topology of feasibility domains in environmental parameter space is a relevant property to understand the changing behavior of microbial systems. This knowledge can be potentially used to understand the relevant community size at which internal dynamics can be operating in microbial systems.},
}
@article {pmid38284174,
year = {2024},
author = {Challa, A and Maras, JS and Nagpal, S and Tripathi, G and Taneja, B and Kachhawa, G and Sood, S and Dhawan, B and Acharya, P and Upadhyay, AD and Yadav, M and Sharma, R and Bajpai, M and Gupta, S},
title = {Multi-omics analysis identifies potential microbial and metabolite diagnostic biomarkers of bacterial vaginosis.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {38},
number = {6},
pages = {1152-1165},
doi = {10.1111/jdv.19805},
pmid = {38284174},
issn = {1468-3083},
support = {8-06/AC-06/2018-RS//All India Institute of Medical Sciences/ ; },
mesh = {Humans ; Female ; *Vaginosis, Bacterial/diagnosis/microbiology ; *Biomarkers/metabolism ; Adult ; *Machine Learning ; *Microbiota ; Metabolomics/methods ; Young Adult ; Vagina/microbiology ; Metabolome ; RNA, Ribosomal, 16S/genetics ; Multiomics ; },
abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common clinical manifestation of a perturbed vaginal ecology associated with adverse sexual and reproductive health outcomes if left untreated. The existing diagnostic modalities are either cumbersome or require skilled expertise, warranting alternate tests. Application of machine-learning tools to heterogeneous and high-dimensional multi-omics datasets finds promising potential in data integration and may aid biomarker discovery.<br><br>OBJECTIVES: The present study aimed to evaluate the potential of the microbiome and metabolome-derived biomarkers in BV diagnosis. Interpretable machine-learning algorithms were used to evaluate the utility of an integrated-omics-derived classification model.<br><br>METHODS: Vaginal samples obtained from reproductive-age group women with (n&#x2009;=&#x2009;40) and without BV (n&#x2009;=&#x2009;40) were subjected to 16S rRNA amplicon sequencing and LC-MS-based metabolomics. The vaginal microbiome and metabolome were characterized, and machine-learning analysis was performed to build a classification model using biomarkers with the highest diagnostic accuracy.<br><br>RESULTS: Microbiome-based diagnostic model exhibited a ROC-AUC (10-fold CV) of 0.84&#x2009;&#xb1;&#x2009;0.21 and accuracy of 0.79&#x2009;&#xb1;&#x2009;0.18, and important features were Aerococcus spp., Mycoplasma hominis, Sneathia spp., Lactobacillus spp., Prevotella spp., Gardnerella spp. and Fannyhessea vaginae. The metabolome-derived model displayed superior performance with a ROC-AUC of 0.97&#x2009;&#xb1;&#x2009;0.07 and an accuracy of 0.92&#x2009;&#xb1;&#x2009;0.08. Beta-leucine, methylimidazole acetaldehyde, dimethylethanolamine, L-arginine and beta cortol were among key predictive metabolites for BV. A predictive model combining both microbial and metabolite features exhibited a high ROC-AUC of 0.97&#x2009;&#xb1;&#x2009;0.07 and accuracy of 0.94&#x2009;&#xb1;&#x2009;0.08 with diagnostic performance only slightly superior to the metabolite-based model.<br><br>CONCLUSION: Application of machine-learning tools to multi-omics datasets aid biomarker discovery with high predictive performance. Metabolome-derived classification models were observed to have superior diagnostic performance in predicting BV than microbiome-based biomarkers.},
}
@article {pmid38283543,
year = {2024},
author = {Wang, H and Chen, Z and Li, Z and He, X and Subramanian, SV},
title = {How economic development affects healthcare access for people with disabilities: A multilevel study in China.},
journal = {SSM - population health},
volume = {25},
number = {},
pages = {101594},
pmid = {38283543},
issn = {2352-8273},
abstract = {Meeting the healthcare needs of people with disabilities is an important challenge in achieving the central promise of "leave no one behind" during the Sustainable Development Goals era. In this study, we describe the accessibility of healthcare for people living with disabilities, as well as the potential influences of individuals' socioeconomic status and regional economic development. Our data covered 324 prefectural cities in China in 2019 and captured the access to healthcare services for people with disabilities. First, we used linear probability regression models to investigate the association between individual socioeconomic status, including residence, poverty status, education, and healthcare access. Second, we conducted an ecological analysis to test the association between prefectural economic indicators, including GDP (gross domestic product) per capita, urbanization ratio, average years of education, Engel's coefficient, and the overall prevalence of access to healthcare for people with disabilities within prefectures. Third, we used multilevel regression models to explore the association between the individual's socio-economic status, prefectural economic indicators, and access to healthcare at the individual level for people with disabilities. The results showed, first, that higher individual socioeconomic status (urban residence or higher educational level) was associated with better access to healthcare for people with disabilities. Second, regional economic indicators were positively associated with access to healthcare at the aggregate and individual levels. This study suggests that local governments, particularly in low- and middle-income countries, should promote economic development and conduct poverty alleviation policies to improve healthcare access for disadvantaged groups.},
}
@article {pmid38279205,
year = {2024},
author = {Reuber, VM and Westbury, MV and Rey-Iglesia, A and Asefa, A and Farwig, N and Miehe, G and Opgenoorth, L and Šumbera, R and Wraase, L and Wube, T and Lorenzen, ED and Schabo, DG},
title = {Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent.},
journal = {Molecular ecology},
volume = {33},
number = {5},
pages = {e17271},
doi = {10.1111/mec.17271},
pmid = {38279205},
issn = {1365-294X},
support = {FOR 2358//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Ecosystem ; *Rodentia/genetics ; Ethiopia ; Gene Flow ; Microsatellite Repeats ; Genetic Variation/genetics ; Genetics, Population ; },
abstract = {Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high-elevation systems in Africa, we studied the giant root-rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro-alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low-coverage nuclear genomes, we investigated 77 giant root-rat individuals sampled from nine localities across its entire ~1000 km[2] range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000-16,000 years ago). Despite this landscape-scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local-scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies.},
}
@article {pmid38278971,
year = {2024},
author = {Larivière, D and Abueg, L and Brajuka, N and Gallardo-Alba, C and Grüning, B and Ko, BJ and Ostrovsky, A and Palmada-Flores, M and Pickett, BD and Rabbani, K and Antunes, A and Balacco, JR and Chaisson, MJP and Cheng, H and Collins, J and Couture, M and Denisova, A and Fedrigo, O and Gallo, GR and Giani, AM and Gooder, GM and Horan, K and Jain, N and Johnson, C and Kim, H and Lee, C and Marques-Bonet, T and O'Toole, B and Rhie, A and Secomandi, S and Sozzoni, M and Tilley, T and Uliano-Silva, M and van den Beek, M and Williams, RW and Waterhouse, RM and Phillippy, AM and Jarvis, ED and Schatz, MC and Nekrutenko, A and Formenti, G},
title = {Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.},
journal = {Nature biotechnology},
volume = {42},
number = {3},
pages = {367-370},
pmid = {38278971},
issn = {1546-1696},
support = {U24 HG010263/HG/NHGRI NIH HHS/United States ; U24 CA231877/CA/NCI NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; U01 CA253481/CA/NCI NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; },
mesh = {*Computational Biology ; *Software ; },
}
@article {pmid38278172,
year = {2024},
author = {, },
title = {Effects of education on adult mortality: a global systematic review and meta-analysis.},
journal = {The Lancet. Public health},
volume = {9},
number = {3},
pages = {e155-e165},
pmid = {38278172},
issn = {2468-2667},
mesh = {Adult ; Humans ; Databases, Factual ; Educational Status ; *Life Expectancy ; Norway ; *Mortality ; },
abstract = {BACKGROUND: The positive effect of education on reducing all-cause adult mortality is known; however, the relative magnitude of this effect has not been systematically quantified. The aim of our study was to estimate the reduction in all-cause adult mortality associated with each year of schooling at a global level.<br><br>METHODS: In this systematic review and meta-analysis, we assessed the effect of education on all-cause adult mortality. We searched PubMed, Web of Science, Scopus, Embase, Global Health (CAB), EconLit, and Sociology Source Ultimate databases from Jan 1, 1980, to May 31, 2023. Reviewers (LD, TM, HDV, CW, IG, AG, CD, DS, KB, KE, and AA) assessed each record for individual-level data on educational attainment and mortality. Data were extracted by a single reviewer into a standard template from the Global Burden of Diseases, Injuries, and Risk Factors Study. We excluded studies that relied on case-crossover or ecological study designs to reduce the risk of bias from unlinked data and studies that did not report key measures of interest (all-cause adult mortality). Mixed-effects meta-regression models were implemented to address heterogeneity in referent and exposure measures among studies and to adjust for study-level covariates. This study was registered with PROSPERO (CRD42020183923).<br><br>FINDINGS: 17&#x2009;094 unique records were identified, 603 of which were eligible for analysis and included data from 70 locations in 59 countries, producing a final dataset of 10&#x2009;355 observations. Education showed a dose-response relationship with all-cause adult mortality, with an average reduction in mortality risk of 1&#xb7;9% (95% uncertainty interval 1&#xb7;8-2&#xb7;0) per additional year of education. The effect was greater in younger age groups than in older age groups, with an average reduction in mortality risk of 2&#xb7;9% (2&#xb7;8-3&#xb7;0) associated with each additional year of education for adults aged 18-49 years, compared with a 0&#xb7;8% (0&#xb7;6-1&#xb7;0) reduction for adults older than 70 years. We found no differential effect of education on all-cause mortality by sex or Socio-demographic Index level. We identified publication bias (p<0&#xb7;0001) and identified and reported estimates of between-study heterogeneity.<br><br>INTERPRETATION: To our knowledge, this is the first systematic review and meta-analysis to quantify the importance of years of schooling in reducing adult mortality, the benefits of which extend into older age and are substantial across sexes and economic contexts. This work provides compelling evidence of the importance of education in improving life expectancy and supports calls for increased investment in education as a crucial pathway for reducing global inequities in mortality.<br><br>FUNDING: Research Council of Norway and the Bill &amp; Melinda Gates Foundation.},
}
@article {pmid38277106,
year = {2024},
author = {Shen, Z and Shi, H and Jiang, Y and Sun, Z},
title = {Diurnal variation in the urban thermal environment and its relationship to human activities in China: a Tencent location-based service geographic big data perspective.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {9},
pages = {14218-14228},
pmid = {38277106},
issn = {1614-7499},
mesh = {Humans ; *Hot Temperature ; Cities ; *Big Data ; Environmental Monitoring/methods ; Temperature ; China ; },
abstract = {The main factor of the formation and deterioration in China's urban thermal environment is human activity, which is difficult to describe and measure. A new perspective on the effect of human activity on the urban thermal environment can be obtained by examining the interaction between location-based service (LBS) data and the urban thermal environment in China. However, relevant research is still limited. In this study, we used Tencent LBS data, Terra/Aqua MODIS land surface temperature (LST) data, and land use data to investigate the relationship between LBS and the urban thermal environment, specifically the LST and surface urban heat island intensity (SUHII) across China and its provinces. Our results showed that (1) in summer, the heat island effect was an issue in 94% of the urban areas in China, which was worse during the day. The high- and low-value periods of LBS data on a given day coincided with the acquisition times of MODIS LST products during the day and at night, respectively. (2) During both the day and at night, there was a significant connection between LBS data and the urban thermal environment in China. The highest correlation coefficient (r) between LBS data and the LST could reach 0.55 (p < 0.01) at the provincial level, and the highest correlation coefficient (r) between LBS data and the SUHII could reach 0.78 (p < 0.01) at the provincial level. (3) The urban thermal environment diurnal difference and LBS data exhibited a significant relationship. The ΔLBS diurnal differences were significantly positively related to the SUHII diurnal differences in China. The overall study findings revealed that LBS data constitute an important parameter to represent the human activity intensity when investigating the formation of the urban thermal environment in China.},
}
@article {pmid38274410,
year = {2023},
author = {Boyes, D and Mulley, JF and , and , and , and , and , and , },
title = {The genome sequence of the Common Pug, Eupithecia vulgata (Haworth, 1809).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {129},
pmid = {38274410},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Eupithecia vulgata (the Common Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 454.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.1 kilobases in length.},
}
@article {pmid38273575,
year = {2024},
author = {Augustine, SP and Bailey-Marren, I and Charton, KT and Kiel, NG and Peyton, MS},
title = {Improper data practices erode the quality of global ecological databases and impede the progress of ecological research.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17116},
doi = {10.1111/gcb.17116},
pmid = {38273575},
issn = {1365-2486},
mesh = {*Plant Leaves ; *Plants ; Big Data ; Databases, Factual ; Phenotype ; },
abstract = {The scientific community has entered an era of big data. However, with big data comes big responsibilities, and best practices for how data are contributed to databases have not kept pace with the collection, aggregation, and analysis of big data. Here, we rigorously assess the quantity of data for specific leaf area (SLA) available within the largest and most frequently used global plant trait database, the TRY Plant Trait Database, exploring how much of the data were applicable (i.e., original, representative, logical, and comparable) and traceable (i.e., published, cited, and consistent). Over three-quarters of the SLA data in TRY either lacked applicability or traceability, leaving only 22.9% of the original data usable compared with the 64.9% typically deemed usable by standard data cleaning protocols. The remaining usable data differed markedly from the original for many species, which led to altered interpretation of ecological analyses. Though the data we consider here make up only 4.5% of SLA data within TRY, similar issues of applicability and traceability likely apply to SLA data for other species as well as other commonly measured, uploaded, and downloaded plant traits. We end with suggested steps forward for global ecological databases, including suggestions for both uploaders to and curators of databases with the hope that, through addressing the issues raised here, we can increase data quality and integrity within the ecological community.},
}
@article {pmid38273562,
year = {2024},
author = {Ross, SRP and Friedman, NR and Dudley, KL and Yoshida, T and Yoshimura, M and Economo, EP and Armitage, DW and Donohue, I},
title = {Divergent ecological responses to typhoon disturbance revealed via landscape-scale acoustic monitoring.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17067},
doi = {10.1111/gcb.17067},
pmid = {38273562},
issn = {1365-2486},
support = {//Canon Foundation in Europe/ ; GOIPG/2018/3023//Irish Research Council/ ; //Okinawa Institute of Science and Technology Graduate University/ ; },
mesh = {Animals ; *Cyclonic Storms ; Ecosystem ; Climate Change ; Birds/physiology ; Acoustics ; },
abstract = {Climate change is increasing the frequency, intensity, and duration of extreme weather events across the globe. Understanding the capacity for ecological communities to withstand and recover from such events is critical. Typhoons are extreme weather events that are expected to broadly homogenize ecological dynamics through structural damage to vegetation and longer-term effects of salinization. Given their unpredictable nature, monitoring ecological responses to typhoons is challenging, particularly for mobile animals such as birds. Here, we report spatially variable ecological responses to typhoons across terrestrial landscapes. Using a high temporal resolution passive acoustic monitoring network across 24 sites on the subtropical island of Okinawa, Japan, we found that typhoons elicit divergent ecological responses among Okinawa's diverse terrestrial habitats, as indicated by increased spatial variability of biological sound production (biophony) and individual species detections. This suggests that soniferous communities are capable of a diversity of different responses to typhoons. That is, spatial insurance effects among local ecological communities provide resilience to typhoons at the landscape scale. Even though site-level typhoon impacts on soundscapes and bird detections were not particularly strong, monitoring at scale with high temporal resolution across a broad spatial extent nevertheless enabled detection of spatial heterogeneity in typhoon responses. Further, species-level responses mirrored those of acoustic indices, underscoring the utility of such indices for revealing insight into fundamental questions concerning disturbance and stability. Our findings demonstrate the significant potential of landscape-scale acoustic sensor networks to capture the understudied ecological impacts of unpredictable extreme weather events.},
}
@article {pmid38273542,
year = {2024},
author = {Zeuss, D and Bald, L and Gottwald, J and Becker, M and Bellafkir, H and Bendix, J and Bengel, P and Beumer, LT and Brandl, R and Brändle, M and Dahlke, S and Farwig, N and Freisleben, B and Friess, N and Heidrich, L and Heuer, S and Höchst, J and Holzmann, H and Lampe, P and Leberecht, M and Lindner, K and Masello, JF and Mielke Möglich, J and Mühling, M and Müller, T and Noskov, A and Opgenoorth, L and Peter, C and Quillfeldt, P and Rösner, S and Royauté, R and Mestre-Runge, C and Schabo, D and Schneider, D and Seeger, B and Shayle, E and Steinmetz, R and Tafo, P and Vogelbacher, M and Wöllauer, S and Younis, S and Zobel, J and Nauss, T},
title = {Nature 4.0: A networked sensor system for integrated biodiversity monitoring.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17056},
doi = {10.1111/gcb.17056},
pmid = {38273542},
issn = {1365-2486},
support = {519/03/04.001 - (0006)//Hessian state research programme for the development of scientific-economic excellence (LOEWE, Germany)/ ; },
mesh = {Animals ; *Ecosystem ; *Conservation of Natural Resources ; Biodiversity ; Plants ; },
abstract = {Ecosystem functions and services are severely threatened by unprecedented global loss in biodiversity. To counteract these trends, it is essential to develop systems to monitor changes in biodiversity for planning, evaluating, and implementing conservation and mitigation actions. However, the implementation of monitoring systems suffers from a trade-off between grain (i.e., the level of detail), extent (i.e., the number of study sites), and temporal repetition. Here, we present an applied and realized networked sensor system for integrated biodiversity monitoring in the Nature 4.0 project as a solution to these challenges, which considers plants and animals not only as targets of investigation, but also as parts of the modular sensor network by carrying sensors. Our networked sensor system consists of three main closely interlinked components with a modular structure: sensors, data transmission, and data storage, which are integrated into pipelines for automated biodiversity monitoring. We present our own real-world examples of applications, share our experiences in operating them, and provide our collected open data. Our flexible, low-cost, and open-source solutions can be applied for monitoring individual and multiple terrestrial plants and animals as well as their interactions. Ultimately, our system can also be applied to area-wide ecosystem mapping tasks, thereby providing an exemplary cost-efficient and powerful solution for biodiversity monitoring. Building upon our experiences in the Nature 4.0 project, we identified ten key challenges that need to be addressed to better understand and counteract the ongoing loss of biodiversity using networked sensor systems. To tackle these challenges, interdisciplinary collaboration, additional research, and practical solutions are necessary to enhance the capability and applicability of networked sensor systems for researchers and practitioners, ultimately further helping to ensure the sustainable management of ecosystems and the provision of ecosystem services.},
}
@article {pmid38273499,
year = {2024},
author = {Liang, C and Zhang, M and Wang, Z and Xiang, X and Gong, H and Wang, K and Liu, H},
title = {The strengthened impact of water availability at interannual and decadal time scales on vegetation GPP.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17138},
doi = {10.1111/gcb.17138},
pmid = {38273499},
issn = {1365-2486},
support = {164320H116//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; CAS-WX2021SF-0305//Special application demonstration project of network security and informatization of Chinese Academy of Sciences/ ; 41971382//National Natural Science Foundation of China/ ; 32271663//National Natural Science Foundation of China/ ; 41930652//National Natural Science Foundation of China/ ; U19A2051//National Natural Science Foundation of China/ ; U20A2048//National Natural Science Foundation of China/ ; KYCX22_1593//Postgraduate Research amp; Practice Innovation Program of Jiangsu Province/ ; KYCX23_1712//Postgraduate Research amp; Practice Innovation Program of Jiangsu Province/ ; },
mesh = {*Ecosystem ; *Water ; Forests ; Carbon Cycle ; Climate Change ; },
abstract = {Water availability (WA) is a key factor influencing the carbon cycle of terrestrial ecosystems under climate warming, but its effects on gross primary production (EWA-GPP) at multiple time scales are poorly understood. We used ensemble empirical mode decomposition (EEMD) and partial correlation analysis to assess the WA-GPP relationship (RWA-GPP) at different time scales, and geographically weighted regression (GWR) to analyze their temporal dynamics from 1982 to 2018 with multiple GPP datasets, including near-infrared radiance of vegetation GPP, FLUXCOM GPP, and eddy covariance-light-use efficiency GPP. We found that the 3- and 7-year time scales dominated global WA variability (61.18% and 11.95%), followed by the 17- and 40-year time scales (7.28% and 8.23%). The long-term trend also influenced 10.83% of the regions, mainly in humid areas. We found consistent spatiotemporal patterns of the EWA-GPP and RWA-GPP with different source products: In high-latitude regions, RWA-GPP changed from negative to positive as the time scale increased, while the opposite occurred in mid-low latitudes. Forests had weak RWA-GPP at all time scales, shrublands showed negative RWA-GPP at long time scales, and grassland (GL) showed a positive RWA-GPP at short time scales. Globally, the EWA-GPP , whether positive or negative, enhanced significantly at 3-, 7-, and 17-year time scales. For arid and humid zones, the semi-arid and sub-humid zones experienced a faster increase in the positive EWA-GPP , whereas the humid zones experienced a faster increase in the negative EWA-GPP . At the ecosystem types, the positive EWA-GPP at a 3-year time scale increased faster in GL, deciduous broadleaf forest, and savanna (SA), whereas the negative EWA-GPP at other time scales increased faster in evergreen needleleaf forest, woody savannas, and SA. Our study reveals the complex and dynamic EWA-GPP at multiple time scales, which provides a new perspective for understanding the responses of terrestrial ecosystems to climate change.},
}
@article {pmid38272936,
year = {2024},
author = {Gnacek, M and Quintero, L and Mavridou, I and Balaguer-Ballester, E and Kostoulas, T and Nduka, C and Seiss, E},
title = {AVDOS-VR: Affective Video Database with Physiological Signals and Continuous Ratings Collected Remotely in VR.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {132},
pmid = {38272936},
issn = {2052-4463},
support = {EP/L016540/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; },
abstract = {Investigating emotions relies on pre-validated stimuli to evaluate induced responses through subjective self-ratings and physiological changes. The creation of precise affect models necessitates extensive datasets. While datasets related to pictures, words, and sounds are abundant, those associated with videos are comparatively scarce. To overcome this challenge, we present the first virtual reality (VR) database with continuous self-ratings and physiological measures, including facial EMG. Videos were rated online using a head-mounted VR device (HMD) with attached emteqPRO mask and a cinema VR environment in remote home and laboratory settings with minimal setup requirements. This led to an affective video database with continuous valence and arousal self-rating measures and physiological responses (PPG, facial-EMG (7x), IMU). The AVDOS-VR database includes data from 37 participants who watched 30 randomly ordered videos (10 positive, neutral, and negative). Each 30-second video was assessed with two-minute relaxation between categories. Validation results suggest that remote data collection is ecologically valid, providing an effective strategy for future affective study designs. All data can be accessed via: www.gnacek.com/affective-video-database-online-study .},
}
@article {pmid38272335,
year = {2024},
author = {Chen, Y and Shi, Y and Liang, C and Min, Z and Deng, Q and Yu, R and Zhang, J and Chang, K and Chen, L and Yan, K and Wang, C and Tan, Y and Wang, X and Chen, J and Hua, Q},
title = {MicrobeTCM: A comprehensive platform for the interactions of microbiota and traditional Chinese medicine.},
journal = {Pharmacological research},
volume = {201},
number = {},
pages = {107080},
doi = {10.1016/j.phrs.2024.107080},
pmid = {38272335},
issn = {1096-1186},
mesh = {*Medicine, Chinese Traditional ; Medicine, Traditional ; *Microbiota ; Computational Biology ; Databases, Factual ; },
abstract = {Thanks to the advancements in bioinformatics, drugs, and other interventions that modulate microbes to treat diseases have been emerging continuously. In recent years, an increasing number of databases related to traditional Chinese medicine (TCM) or gut microbes have been established. However, a database combining the two has not yet been developed. To accelerate TCM research and address the traditional medicine and micro ecological system connection between short board, we have developed the most comprehensive micro-ecological database of TCM. This initiative includes the standardization of the following advantages: (1) A repeatable process achieved through the standardization of a retrieval strategy to identify literature. This involved identifying 419 experiment articles from PubMed and six authoritative databases; (2) High-quality data integration achieved through double-entry extraction of literature, mitigating uncertainties associated with natural language extraction; (3) Implementation of a similar strategy aiding in the prediction of mechanisms of action. Leveraging drug similarity, target entity similarity, and known drug-target entity association, our platform enables the prediction of the effects of a new herb or acupoint formulas using the existing data. In total, MicrobeTCM includes 171 diseases, 725 microbes, 1468 herb-formulas, 1032 herbs, 15780 chemical compositions, 35 acupoint-formulas, and 77 acupoints. For further exploration, please visit https://www.microbetcm.com.},
}
@article {pmid38271874,
year = {2024},
author = {Ren, XY and Zheng, YL and Liu, ZL and Duan, GL and Zhu, D and Ding, LJ},
title = {Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR.},
journal = {Journal of hazardous materials},
volume = {466},
number = {},
pages = {133567},
doi = {10.1016/j.jhazmat.2024.133567},
pmid = {38271874},
issn = {1873-3336},
mesh = {Cadmium/metabolism ; *Arsenic/toxicity/analysis ; Soil ; Multiomics ; *Microbiota/genetics ; *Environmental Pollutants/analysis ; Crops, Agricultural/metabolism ; Polymerase Chain Reaction ; *Soil Pollutants/metabolism ; },
abstract = {Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.},
}
@article {pmid38271521,
year = {2024},
author = {Couce, A and Limdi, A and Magnan, M and Owen, SV and Herren, CM and Lenski, RE and Tenaillon, O and Baym, M},
title = {Changing fitness effects of mutations through long-term bacterial evolution.},
journal = {Science (New York, N.Y.)},
volume = {383},
number = {6681},
pages = {eadd1417},
doi = {10.1126/science.add1417},
pmid = {38271521},
issn = {1095-9203},
support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; },
mesh = {Adaptation, Physiological/genetics ; *Escherichia coli/genetics ; *Evolution, Molecular ; *Genetic Fitness ; Mutagenesis, Insertional ; Mutation ; Selection, Genetic ; },
abstract = {The distribution of fitness effects of new mutations shapes evolution, but it is challenging to observe how it changes as organisms adapt. Using Escherichia coli lineages spanning 50,000 generations of evolution, we quantify the fitness effects of insertion mutations in every gene. Macroscopically, the fraction of deleterious mutations changed little over time whereas the beneficial tail declined sharply, approaching an exponential distribution. Microscopically, changes in individual gene essentiality and deleterious effects often occurred in parallel; altered essentiality is only partly explained by structural variation. The identity and effect sizes of beneficial mutations changed rapidly over time, but many targets of selection remained predictable because of the importance of loss-of-function mutations. Taken together, these results reveal the dynamic-but statistically predictable-nature of mutational fitness effects.},
}
@article {pmid38269820,
year = {2024},
author = {Andison, M},
title = {Digital Health Safety Matters: A Promising Practice Study into the Adoption of Patient Safety Guidelines in Australia.},
journal = {Studies in health technology and informatics},
volume = {310},
number = {},
pages = {334-338},
doi = {10.3233/SHTI230982},
pmid = {38269820},
issn = {1879-8365},
mesh = {Humans ; *Digital Health ; *Patient Safety ; Australia ; Artifacts ; Data Mining ; },
abstract = {A foundation for digitally enabling healthier living is the safe development and use of technology. The practice of digital health safety has emerged from patient harm attributed to failing technologies. The study aimed to investigate how to adopt and implement digital health safety guidelines at scale. Data was collected through an online survey, semi-structured interviews, focus groups, document review, and data mining of artefacts. The findings of this study capture the emerging practice from Australia in a way that offers insights into the problem of practice, patient safety practice, safety culture, and socio-technical factors. The research findings contribute to better understanding of the complexities of balancing digital innovation with patient safety. The four recommendations from the study and the provision of a logic model will support the audience to implement actions toward a safer digital health ecology.},
}
@article {pmid38268612,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Muslin moth, Diaphora mendica (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {257},
pmid = {38268612},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Diaphora mendica (the Muslin moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 748.7 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length.},
}
@article {pmid38263406,
year = {2024},
author = {Ismaeel, A and Tai, APK and Santos, EG and Maraia, H and Aalto, I and Altman, J and Doležal, J and Lembrechts, JJ and Camargo, JL and Aalto, J and Sam, K and Avelino do Nascimento, LC and Kopecký, M and Svátek, M and Nunes, MH and Matula, R and Plichta, R and Abera, T and Maeda, EE},
title = {Patterns of tropical forest understory temperatures.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {549},
pmid = {38263406},
issn = {2041-1723},
support = {319905//Academy of Finland (Suomen Akatemia)/ ; 345472//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {*Ecosystem ; Temperature ; *Forests ; Climate Change ; Computer Systems ; },
abstract = {Temperature is a fundamental driver of species distribution and ecosystem functioning. Yet, our knowledge of the microclimatic conditions experienced by organisms inside tropical forests remains limited. This is because ecological studies often rely on coarse-gridded temperature estimates representing the conditions at 2 m height in an open-air environment (i.e., macroclimate). In this study, we present a high-resolution pantropical estimate of near-ground (15 cm above the surface) temperatures inside forests. We quantify diurnal and seasonal variability, thus revealing both spatial and temporal microclimate patterns. We find that on average, understory near-ground temperatures are 1.6 °C cooler than the open-air temperatures. The diurnal temperature range is on average 1.7 °C lower inside the forests, in comparison to open-air conditions. More importantly, we demonstrate a substantial spatial variability in the microclimate characteristics of tropical forests. This variability is regulated by a combination of large-scale climate conditions, vegetation structure and topography, and hence could not be captured by existing macroclimate grids. Our results thus contribute to quantifying the actual thermal ranges experienced by organisms inside tropical forests and provide new insights into how these limits may be affected by climate change and ecosystem disturbances.},
}
@article {pmid38262510,
year = {2024},
author = {Sajjad, W and Ilahi, N and Haq, A and Shang, Z and Nabi, G and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S},
title = {Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes.},
journal = {Environmental research},
volume = {247},
number = {},
pages = {118288},
doi = {10.1016/j.envres.2024.118288},
pmid = {38262510},
issn = {1096-0953},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Metals ; },
abstract = {Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.},
}
@article {pmid38259099,
year = {2024},
author = {Caesar, L and Rice, DW and McAfee, A and Underwood, R and Ganote, C and Tarpy, DR and Foster, LJ and Newton, ILG},
title = {Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phages.},
journal = {mSystems},
volume = {9},
number = {2},
pages = {e0118223},
pmid = {38259099},
issn = {2379-5077},
support = {2005306//National Science Foundation (NSF)/ ; 2022049//National Science Foundation (NSF)/ ; //L'Oreal USA (L'Or&#xe9;al)/ ; //Project Apis m. (PAm)/ ; 2017-51300-26814//U.S. Department of Agriculture (USDA)/ ; },
mesh = {Bees ; Female ; Animals ; *Bacteriophages/genetics ; *Microbiota/genetics ; Reproduction ; Metagenome ; },
abstract = {In eusocial insects, the health of the queens-the colony founders and sole reproductive females-is a primary determinant for colony success. Queen failure in the honey bee Apis mellifera, for example, is a major concern of beekeepers who annually suffer colony losses, necessitating a greater knowledge of queen health. Several studies on the microbiome of honey bees have characterized its diversity and shown its importance for the health of worker bees, the female non-reproductive caste. However, the microbiome of workers differs from that of queens, which, in comparison, is still poorly studied. Thus, direct investigations of the queen microbiome are required to understand colony-level microbiome assembly, functional roles, and evolution. Here, we used metagenomics to comprehensively characterize the honey bee queen microbiome. Comparing samples from different geographic locations and breeder sources, we show that the microbiome of queens is mostly shaped by the environment experienced since early life and is predicted to play roles in the breakdown of the diet and protection from pathogens and xenobiotics. We also reveal that the microbiome of queens comprises only four candidate core bacterial species, Apilactobacillus kunkeei, Lactobacillus apis, Bombella apis, and Commensalibacter sp. Interestingly, in addition to bacteria, we show that bacteriophages infect the queen microbiome, for which Lactobacillaceae are predicted to be the main reservoirs. Together, our results provide the basis to understand the honey bee colony microbiome assemblage, can guide improvements in queen-rearing processes, and highlight the importance of considering bacteriophages for queen microbiome health and microbiome homeostasis in eusocial insects.IMPORTANCEThe queen caste plays a central role in colony success in eusocial insects, as queens lay eggs and regulate colony behavior and development. Queen failure can cause colonies to collapse, which is one of the major concerns of beekeepers. Thus, understanding the biology behind the queen's health is a pressing issue. Previous studies have shown that the bee microbiome plays an important role in worker bee health, but little is known about the queen microbiome and its function in vivo. Here, we characterized the queen microbiome, identifying for the first time the present species and their putative functions. We show that the queen microbiome has predicted nutritional and protective roles in queen association and comprises only four consistently present bacterial species. Additionally, we bring to attention the spread of phages in the queen microbiome, which increased in abundance in failing queens and may impact the fate of the colony.},
}
@article {pmid38259095,
year = {2024},
author = {Wang, C and Ma, A and Li, Y and McNutt, ME and Zhang, S and Zhu, J and Hoyd, R and Wheeler, CE and Robinson, LA and Chan, CHF and Zakharia, Y and Dodd, RD and Ulrich, CM and Hardikar, S and Churchman, ML and Tarhini, AA and Singer, EA and Ikeguchi, AP and McCarter, MD and Denko, N and Tinoco, G and Husain, M and Jin, N and Osman, AEG and Eljilany, I and Tan, AC and Coleman, SS and Denko, L and Riedlinger, G and Schneider, BP and Spakowicz, D and Ma, Q and , },
title = {A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset.},
journal = {Cancer research communications},
volume = {4},
number = {2},
pages = {293-302},
pmid = {38259095},
issn = {2767-9764},
support = {UL1 TR000090/TR/NCATS NIH HHS/United States ; U01 CA206110/CA/NCI NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; AS1695/AS/Autism Speaks/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Phylogeny ; *Microbiota/genetics ; Computational Biology ; High-Throughput Nucleotide Sequencing ; },
abstract = {UNLABELLED: Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10%-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, microbial graph attention (MEGA), to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of nine cancer centers in the Oncology Research Information Exchange Network. This package has three unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2,704 tumor RNA sequencing samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.<br><br>SIGNIFICANCE: Studying the tumor microbiome in high-throughput sequencing data is challenging because of the extremely sparse data matrices, heterogeneity, and high likelihood of contamination. We present a new deep learning tool, MEGA, to refine the organisms that interact with tumors.},
}
@article {pmid38258939,
year = {2024},
author = {Mori, K and Odagami, K and Inagaki, M and Moriya, K and Fujiwara, H and Eguchi, H},
title = {Work engagement among older workers: a systematic review.},
journal = {Journal of occupational health},
volume = {66},
number = {1},
pages = {},
doi = {10.1093/joccuh/uiad008},
pmid = {38258939},
issn = {1348-9585},
mesh = {Humans ; Adult ; Middle Aged ; *Work Engagement ; *Aging ; Databases, Factual ; Employment ; Europe ; Observational Studies as Topic ; },
abstract = {OBJECTIVES: Given current labor force conditions, including population aging, keeping older workers engaged in work and motivated is important. Aging may alter the effects that psychological and environmental factors have on work engagement. We conducted a systematic review to understand the features of work engagement among older workers.<br><br>METHODS: A systematic search was conducted in July 2022 using 4 databases. The review included relevant articles that focused on participants aged 40&#xa0;years and older.<br><br>RESULTS: Fifty articles were selected for our review, which were grouped into 5 categories: (1) studies examining the relationship between chronological age and work engagement, (2) studies investigating the moderating effects of age on the relationship between job-related psychological factors and work environment factors and work engagement, (3) studies comparing the relationship of job-related psychological factors and work environment factors with work engagement across different age groups, (4) studies exploring the relationship between work engagement and retirement intentions or continued employment beyond retirement age, and (5) other studies discussing work engagement in the context of older workers. Most articles focused on workers in Europe and the United States and used observational study designs.<br><br>CONCLUSIONS: Work engagement increases with age, and is mainly mediated by increased emotional regulation. In addition, age moderates the relationships between various job-related psychological and work-environmental factors and work engagement. Work engagement is associated with working beyond retirement age. Organizations should understand the characteristics of work engagement among older workers and make age-conscious efforts to support them in adapting to social changes.},
}
@article {pmid38258936,
year = {2024},
author = {Tani, N and Fujihara, H and Ishii, K and Kamakura, Y and Tsunemi, M and Yamaguchi, C and Eguchi, H and Imamura, K and Kanamori, S and Kojimahara, N and Ebara, T},
title = {What digital health technology types are used in mental health prevention and intervention? Review of systematic reviews for systematization of technologies.},
journal = {Journal of occupational health},
volume = {66},
number = {1},
pages = {},
pmid = {38258936},
issn = {1348-9585},
support = {JP22rea522006//Japan Agency for Medical Research and Development (AMED)/ ; },
mesh = {Humans ; *Digital Health ; *Mental Health ; Systematic Reviews as Topic ; Technology ; Avatar ; },
abstract = {Digital health technology has been widely applied to mental health interventions worldwide. Using digital phenotyping to identify an individual's mental health status has become particularly important. However, many technologies other than digital phenotyping are expected to become more prevalent in the future. The systematization of these technologies is necessary to accurately identify trends in mental health interventions. However, no consensus on the technical classification of digital health technologies for mental health interventions has emerged. Thus, we conducted a review of systematic review articles on the application of digital health technologies in mental health while attempting to systematize the technology using the Delphi method. To identify technologies used in digital phenotyping and other digital technologies, we included 4 systematic review articles that met the inclusion criteria, and an additional 8 review articles, using a snowballing approach, were incorporated into the comprehensive review. Based on the review results, experts from various disciplines participated in the Delphi process and agreed on the following 11 technical categories for mental health interventions: heart rate estimation, exercise or physical activity, sleep estimation, contactless heart rate/pulse wave estimation, voice and emotion analysis, self-care/cognitive behavioral therapy/mindfulness, dietary management, psychological safety, communication robots, avatar/metaverse devices, and brain wave devices. The categories we defined intentionally included technologies that are expected to become widely used in the future. Therefore, we believe these 11 categories are socially implementable and useful for mental health interventions.},
}
@article {pmid38258809,
year = {2024},
author = {Viera, A and Ondrusek, A and Tengatenga, C and McBurney, E and Lauckner, J and Tran, E and Muilenburg, J and Kershaw, T and Lauckner, C},
title = {A Qualitative Exploration of Attitudes Toward Global Positioning System Tracking and Ecological Momentary Assessment Among Individuals in Substance Use Treatment.},
journal = {Substance use &amp; addiction journal},
volume = {45},
number = {2},
pages = {260-267},
doi = {10.1177/29767342231218514},
pmid = {38258809},
issn = {2976-7350},
mesh = {Humans ; *Ecological Momentary Assessment ; Geographic Information Systems ; *Substance-Related Disorders ; Craving ; Georgia ; },
abstract = {BACKGROUND: The use of tracking technology in substance use research can uncover the role of contextual factors, such as social networks and environmental cues, in triggering cravings and precipitating return to use. Few studies have explored the opinions of individuals in substance use treatment related to tracking technology.<br><br>METHODS: We conducted 30 semi-structured interviews with individuals in substance use treatment facilities in Connecticut and Georgia. Interviews were not limited to individuals with any specific substance use disorder. Interviewers described a hypothetical study involving ecological momentary assessment and global positioning system tracking to examine place-based predictors of substance use. Participants were invited to share reactions to this description. We used thematic analysis to identify themes in participant perceptions of this hypothetical research study.<br><br>RESULTS: Most participants shared positive opinions about study participation and expressed little to no concern about the tracking components. Participant concerns focused on the security of their information and the potential burden of responding to study questions. Participants largely understood the importance of study participation for promoting greater understanding of substance use and identified potential therapeutic effects of study participation on their own recovery.<br><br>CONCLUSIONS: Individuals in substance use treatment expressed little concern with research studies or interventions incorporating mobile-tracking elements. Future studies should explore the responsible use of tracking elements in recovery support interventions.},
}
@article {pmid38257567,
year = {2024},
author = {Kraft, R and Reichert, M and Pryss, R},
title = {Mobile Crowdsensing in Ecological Momentary Assessment mHealth Studies: A Systematic Review and Analysis.},
journal = {Sensors (Basel, Switzerland)},
volume = {24},
number = {2},
pages = {},
pmid = {38257567},
issn = {1424-8220},
mesh = {Humans ; *Ecological Momentary Assessment ; Computers, Handheld ; Data Collection ; Databases, Factual ; *Telemedicine ; },
abstract = {As mobile devices have become a central part of our daily lives, they are also becoming increasingly important in research. In the medical context, for example, smartphones are used to collect ecologically valid and longitudinal data using Ecological Momentary Assessment (EMA), which is mostly implemented through questionnaires delivered via smart notifications. This type of data collection is intended to capture a patient's condition on a moment-to-moment and longer-term basis. To collect more objective and contextual data and to understand patients even better, researchers can not only use patients' input via EMA, but also use sensors as part of the Mobile Crowdsensing (MCS) approach. In this paper, we examine how researchers have embraced the topic of MCS in the context of EMA through a systematic literature review. This PRISMA-guided review is based on the databases PubMed, Web of Science, and EBSCOhost. It is shown through the results that both EMA research in general and the use of sensors in EMA research are steadily increasing. In addition, most of the studies reviewed used mobile apps to deliver EMA to participants, used a fixed-time prompting strategy, and used signal-contingent or interval-contingent self-assessment as sampling/assessment strategies. The most commonly used sensors in EMA studies are the accelerometer and GPS. In most studies, these sensors are used for simple data collection, but sensor data are also commonly used to verify study participant responses and, less commonly, to trigger EMA prompts. Security and privacy aspects are addressed in only a subset of mHealth EMA publications. Moreover, we found that EMA adherence was negatively correlated with the total number of prompts and was higher in studies using a microinteraction-based EMA (μEMA) approach as well as in studies utilizing sensors. Overall, we envision that the potential of the technological capabilities of smartphones and sensors could be better exploited in future, more automated approaches.},
}
@article {pmid38256741,
year = {2024},
author = {Hanazaki, N},
title = {Brazilian Environment and Plants as Seen by Japanese Eyes Two Hundred and Twenty Years Ago.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
pmid = {38256741},
issn = {2223-7747},
support = {305789/2022-1//National Council for Scientific and Technological Development/ ; },
abstract = {In 2023, the Japanese migration to Brazil completed 115 years. However, the first time Japanese people arrived in Brazil and left a testimony of their experience was about two centuries ago. Their reports were registered in a historical document, handwritten during the Edo period when Japan was adopting a closed-door policy. The episode of their visit to Brazil is only a small part of the odyssey of these four Japanese sailors who departed from Ishinomiya to Tokyo at the end of the 18th century, but unexpectedly traveled around the globe. After a storm, they were adrift for six months until shipwrecking on the Aleutian Islands; from the Russian Aleutian Islands, they crossed the whole of Russia and boarded, in Saint Petersburg, on the first Russian expedition to circumnavigate the world. Their only stop in South America was at Santa Catarina Island, southern Brazil, and this is the first analysis of this episode from an ethnobiological perspective. Their reports described both the forest environment and the plants they observed and included at least 23 taxa of plants, mostly cultivated. These descriptions of plants and the environment are in contrast with other reports from the same period and to the current environment found in Santa Catarina Island, inspiring reflections on the construction of Brazil's image in Japan before the 20th century.},
}
@article {pmid38256002,
year = {2024},
author = {Han, S and Han, X and Qi, C and Guo, F and Yin, J and Liu, Y and Zhu, Y},
title = {Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale.},
journal = {International journal of molecular sciences},
volume = {25},
number = {2},
pages = {},
pmid = {38256002},
issn = {1422-0067},
support = {CARS-24-G-17//Fengling Guo/ ; },
mesh = {*Zingiber officinale/genetics ; Amino Acid Sequence ; Cold-Shock Response/genetics ; Computational Biology ; *Fusariosis ; *MicroRNAs/genetics ; },
abstract = {The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.},
}
@article {pmid38254931,
year = {2023},
author = {Yang, D and Zhang, X and Cao, M and Yin, L and Gao, A and An, K and Gao, S and Guo, S and Yin, H},
title = {Genome-Wide Identification, Expression and Interaction Analyses of PP2C Family Genes in Chenopodium quinoa.},
journal = {Genes},
volume = {15},
number = {1},
pages = {},
pmid = {38254931},
issn = {2073-4425},
support = {2022SZX17//Science &amp; Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta/ ; 2019BHLC001//the "Bohai Sea Granary" Science and Technology Demonstration Project of Shandong Provincial/ ; },
mesh = {Humans ; *Chenopodium quinoa/genetics ; Genome-Wide Association Study ; Phylogeny ; Biological Evolution ; Data Interpretation, Statistical ; Phosphoric Monoester Hydrolases ; },
abstract = {Plant protein phosphatase 2Cs (PP2Cs) function as inhibitors in protein kinase cascades involved in various processes and are crucial participants in both plant development and signaling pathways activated by abiotic stress. In this study, a genome-wide study was conducted on the CqPP2C gene family. A total of putative 117 CqPP2C genes were identified. Comprehensive analyses of physicochemical properties, chromosome localization and subcellular localization were conducted. According to phylogenetic analysis, CqPP2Cs were divided into 13 subfamilies. CqPP2Cs in the same subfamily had similar gene structures, and conserved motifs and all the CqPP2C proteins had the type 2C phosphatase domains. The expansion of CqPP2Cs through gene duplication was primarily driven by segmental duplication, and all duplicated CqPP2Cs underwent evolutionary changes guided by purifying selection. The expression of CqPP2Cs in various tissues under different abiotic stresses was analyzed using RNA-seq data. The findings indicated that CqPP2C genes played a role in regulating both the developmental processes and stress responses of quinoa. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis of six CqPP2C genes in subfamily A revealed that they were up-regulated or down-regulated under salt and drought treatments. Furthermore, the results of yeast two-hybrid assays revealed that subfamily A CqPP2Cs interacted not only with subclass III CqSnRK2s but also with subclass II CqSnRK2s. Subfamily A CqPP2Cs could interact with CqSnRK2s in different combinations and intensities in a variety of biological processes and biological threats. Overall, our results will be useful for understanding the functions of CqPP2C in regulating ABA signals and responding to abiotic stress.},
}
@article {pmid38251877,
year = {2024},
author = {Schloss, PD},
title = {Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses.},
journal = {mSphere},
volume = {9},
number = {2},
pages = {e0035423},
pmid = {38251877},
issn = {2379-5042},
support = {R01 CA215574/CA/NCI NIH HHS/United States ; U01 CA264071/CA/NCI NIH HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; P30 DK034933/DK/NIDDK NIH HHS/United States ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; },
abstract = {UNLABELLED: Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses.<br><br>IMPORTANCE: Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.},
}
@article {pmid38250723,
year = {2024},
author = {Abdullah, NI and Elias, NA and Ohte, N and Vincenot, C},
title = {Resource partitioning among bat species in Peninsular Malaysia rice fields.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16657},
pmid = {38250723},
issn = {2167-8359},
mesh = {Humans ; Pregnancy ; Animals ; Female ; Male ; *Oryza ; *Chiroptera ; Lactation ; Malaysia ; *Coleoptera ; *Lepidoptera ; },
abstract = {Resource partitioning among tropical bats in agricultural areas of Peninsular Malaysia remains unclear. This study was conducted to evaluate resource partitioning among bats by examining their fecal samples. The main bat species sampled included: Rhinolophus coelophyllus, Rhinolophus malayanus, Rhinolophus pusillus, Rhinolophus refulgens, Taphozous melanopogon and Hipposideros larvatus. Two harp traps were set at different elevations on a hilltop (Gunung Keriang) and two high nets were used in neighboring rice fields at three sites, for three consecutive nights per sampling from April 2021 to February 2022. A total of 301 bats and 1,505 pellets were analyzed using a conventional approach which examined the fecal sample under the microscope. All of the bat species within the study had insects from the order Coleoptera, Lepidoptera, Diptera and Hemiptera in their diet. Larger bats exhibited a greater variety of prey consumption. Male individuals were observed to be generalists while female individuals were specialists, particularly during pregnancy and lactating reproductive stages. Bat species and insect order had a significant impact on the percentage fragment frequency of the insects consumed. Rhinolophus coelophyllus specialized in feeding on Coleoptera and Diptera, H. larvatus fed on Coleoptera, R. malayanus fed on Hemiptera, R. pusillus and T. melanopogon fed on Lepidoptera. Future molecular analysis can be carried out to further identify the insect pests consumed by these bats up to species level. These findings enhance our understanding of bats' ecological roles in agricultural landscapes and contribute to conservation and pest management strategies.},
}
@article {pmid38249959,
year = {2023},
author = {Blaxter, ML and Spurgeon, D and Kille, P and , and , and , and , },
title = {The genome sequence of the common earthworm, Lumbricus terrestris (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {500},
pmid = {38249959},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Lumbricus terrestris (the common earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 1,056.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.93 kilobases in length.},
}
@article {pmid38249957,
year = {2023},
author = {Boyes, D and Eagles, M and Holland, PWH and , and , and , and , and , },
title = {The genome sequence of the Willow Beauty, Peribatodes rhomboidaria (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {233},
pmid = {38249957},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Peribatodes rhomboidaria (the Willow Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 499.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,486 protein coding genes.},
}
@article {pmid38248287,
year = {2024},
author = {Sokołowska, B},
title = {Being in Virtual Reality and Its Influence on Brain Health-An Overview of Benefits, Limitations and Prospects.},
journal = {Brain sciences},
volume = {14},
number = {1},
pages = {},
pmid = {38248287},
issn = {2076-3425},
abstract = {BACKGROUND: Dynamic technological development and its enormous impact on modern societies are posing new challenges for 21st-century neuroscience. A special place is occupied by technologies based on virtual reality (VR). VR tools have already played a significant role in both basic and clinical neuroscience due to their high accuracy, sensitivity and specificity and, above all, high ecological value.<br><br>OBJECTIVE: Being in a digital world affects the functioning of the body as a whole and its individual systems. The data obtained so far, both from experimental and modeling studies, as well as (clinical) observations, indicate their great and promising potential, but apart from the benefits, there are also losses and negative consequences for users.<br><br>METHODS: This review was conducted according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework across electronic databases (such as Web of Science Core Collection; PubMed; and Scopus, Taylor &amp; Francis Online and Wiley Online Library) to identify beneficial effects and applications, as well as adverse impacts, especially on brain health in human neuroscience.<br><br>RESULTS: More than half of these articles were published within the last five years and represent state-of-the-art approaches and results (e.g., 54.7% in Web of Sciences and 63.4% in PubMed), with review papers accounting for approximately 16%. The results show that in addition to proposed novel devices and systems, various methods or procedures for testing, validation and standardization are presented (about 1% of articles). Also included are virtual developers and experts, (bio)(neuro)informatics specialists, neuroscientists and medical professionals.<br><br>CONCLUSIONS: VR environments allow for expanding the field of research on perception and cognitive and motor imagery, both in healthy and patient populations. In this context, research on neuroplasticity phenomena, including mirror neuron networks and the effects of applied virtual (mirror) tasks and training, is of interest in virtual prevention and neurogeriatrics, especially in neurotherapy and neurorehabilitation in basic/clinical and digital neuroscience.},
}
@article {pmid38247366,
year = {2024},
author = {Erickson, BA and Griffith, JW and Wensheng, G and Mengying, Y and Herman, T and Bradley, CS and Quentin Clemens, J and Farrar, JT and Gupta, P and Kreder, KJ and Henry Lai, H and Naliboff, BD and Newman, DK and Rodriguez, LV and Spitznagle, T and Sutcliffe, S and Sutherland, SE and Taple, BJ and Richard Landis, J},
title = {Ecological momentary assessment of pelvic pain and urinary urgency variability in urologic chronic pelvic pain syndrome and their association with illness impact and quality of life: Findings from the multidisciplinary approach to the study of chronic pelvic pain symptom patterns study.},
journal = {Neurourology and urodynamics},
volume = {43},
number = {4},
pages = {893-901},
pmid = {38247366},
issn = {1520-6777},
support = {U01 DK082345/DK/NIDDK NIH HHS/United States ; U01 DK082315/DK/NIDDK NIH HHS/United States ; U01 DK082344/DK/NIDDK NIH HHS/United States ; U01 DK082333/DK/NIDDK NIH HHS/United States ; R01 DK117208/DK/NIDDK NIH HHS/United States ; U24 DK082333/DK/NIDDK NIH HHS/United States ; U01 DK082325/DK/NIDDK NIH HHS/United States ; U01 DK082342/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; *Quality of Life ; Ecological Momentary Assessment ; *Chronic Pain/diagnosis ; Pelvic Pain/diagnosis ; Pain Measurement ; },
abstract = {PURPOSE: This study tested the hypothesis that ecological momentary assessment (EMA) of pelvic pain (PP) and urinary urgency (UU) would reveal unique Urologic Chronic Pelvic Pain Syndrome (UCPPS) phenotypes that would be associated with disease specific quality of life (QOL) and illness impact metrics (IIM).<br><br>MATERIALS AND METHODS: A previously validated smart phone app (M-app) was provided to willing Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP) participants. M-app notifications were sent 4-times daily for 14 days inquiring about PP and UU severity. A clustering algorithm that accounted for variance placed participants into PP and UU variability? clusters. Associations between clusters and QOL and IIM were then determined.<br><br>RESULTS: A total of 204 participants enrolled in the M-app study (64% female). M-app compliance was high (median 63% of surveys). Cluster analysis revealed k&#x2009;=&#x2009;3 (high, low, none) PP clusters and k&#x2009;=&#x2009;2 (high, low) UU clusters. When adjusting for baseline pain severity, high PP variability, but not UU variability, was strongly associated with QOL and IIM; specifically worse mood, worse sleep and higher anxiety. UU and PP clusters were associated with each other (p&#x2009;<&#x2009;0.0001), but a large percentage (33%) of patients with high PP variability had low UU variability.<br><br>CONCLUSIONS: PP variability is an independent predictor of worse QOL and more severe IIM in UCPPS participants after controlling for baseline pain severity and UU. These findings suggest alternative pain indices, such as pain variability and unpredictability, may be useful adjuncts to traditional measures of worst and average pain when assessing UCPPS treatment responses.},
}
@article {pmid38246154,
year = {2024},
author = {McConnell, RJ and Kamysh, O and O'Kane, PL and Greenebaum, E and Rozhko, AV and Yauseyenka, VV and Minenko, VF and Drozdovitch, V and Yarets, Y and Kukhta, T and Mabuchi, K and Little, MP and Cahoon, EK and Zablotska, LB},
title = {Radiation Dose Does Not Affect the Predictive Value of Thyroid Biopsy for Diagnosing Papillary Thyroid Cancer in a Belarusian Cohort Exposed to Chernobyl Fallout.},
journal = {Acta cytologica},
volume = {68},
number = {1},
pages = {34-44},
pmid = {38246154},
issn = {1938-2650},
support = {N01CP21178/CP/NCI NIH HHS/United States ; ZIA CP010132/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Adolescent ; Child ; Humans ; Biopsy ; *Carcinoma, Papillary/pathology ; *Chernobyl Nuclear Accident ; *Eastern European People ; Radiation Dosage ; Thyroid Cancer, Papillary/diagnosis ; *Thyroid Neoplasms/diagnosis/epidemiology/pathology ; Adult ; },
abstract = {INTRODUCTION: The Chernobyl nuclear accident exposed residents of contaminated territories to substantial quantities of radioiodines and was followed by an increase in thyroid cancer, primarily papillary thyroid cancer (PTC), among exposed children and adolescents. Although thyroid biopsy is an essential component of screening programs following accidental exposure to radioiodines, it is unknown whether the predictive value of biopsy is affected by different levels of environmental exposure.<br><br>METHODS: A cohort of 11,732 Belarusians aged &#x2264;18 years at the time of the Chernobyl accident with individual thyroid radiation dose estimates was screened at least once 11-22 years later. Paired cytologic conclusions and histopathologic diagnoses were possible for 258 thyroid nodules from 238 cohort members. Cytologic conclusions were divided into five reporting categories, with all follicular lesion aspirates combined into a single indeterminate category. Standard performance indicators, risk of malignancy (ROM), and odds ratios for a correct cytologic conclusion were calculated, both overall and according to quintile of thyroid radiation dose.<br><br>RESULTS: The arithmetic mean thyroid dose estimate for the study group was 1.73 Gy (range: 0.00-23.64 Gy). The final histopathologic diagnosis was cancer for 136 of 258 biopsies (52.7%; 135 papillary and 1 follicular). The overall ROM was 96.7% for cytologies definite for PTC, 83.7% for suspicious for PTC, 33.0% for indeterminate, 8.1% for benign, and 31.0% for non-diagnostic. The ROM showed little change according to level of radiation exposure. Overall, there was no association between thyroid radiation dose and the odds ratio for a correct cytologic conclusion (p = 0.24). When analyzed according to dose quintile, the odds ratio for a correct conclusion increased two-fold at 0.10-0.29 Gy compared to a dose of 0.00-0.09 Gy and decreased at doses of 0.3-24 Gy (p value for linear trend = 0.99).<br><br>CONCLUSIONS: At radiation doses received by a cohort of young Belarusians exposed to radioiodines by the Chernobyl accident, the predictive value of thyroid biopsy for diagnosing PTC was not significantly affected by level of radiation exposure.},
}
@article {pmid38246125,
year = {2024},
author = {Mahony, J},
title = {Biological and bioinformatic tools for the discovery of unknown phage-host combinations.},
journal = {Current opinion in microbiology},
volume = {77},
number = {},
pages = {102426},
doi = {10.1016/j.mib.2024.102426},
pmid = {38246125},
issn = {1879-0364},
mesh = {*Bacteriophages/genetics ; Artificial Intelligence ; Computational Biology ; *Microbiota ; Metagenomics ; },
abstract = {The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.},
}
@article {pmid38245889,
year = {2024},
author = {Schlapbach, LJ and Watson, RS and Sorce, LR and Argent, AC and Menon, K and Hall, MW and Akech, S and Albers, DJ and Alpern, ER and Balamuth, F and Bembea, M and Biban, P and Carrol, ED and Chiotos, K and Chisti, MJ and DeWitt, PE and Evans, I and Flauzino de Oliveira, C and Horvat, CM and Inwald, D and Ishimine, P and Jaramillo-Bustamante, JC and Levin, M and Lodha, R and Martin, B and Nadel, S and Nakagawa, S and Peters, MJ and Randolph, AG and Ranjit, S and Rebull, MN and Russell, S and Scott, HF and de Souza, DC and Tissieres, P and Weiss, SL and Wiens, MO and Wynn, JL and Kissoon, N and Zimmerman, JJ and Sanchez-Pinto, LN and Bennett, TD and , },
title = {International Consensus Criteria for Pediatric Sepsis and Septic Shock.},
journal = {JAMA},
volume = {331},
number = {8},
pages = {665-674},
pmid = {38245889},
issn = {1538-3598},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 HD105939/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Child ; *Shock, Septic/mortality ; Multiple Organ Failure/diagnosis/etiology ; Consensus ; *Sepsis/mortality ; Systemic Inflammatory Response Syndrome/diagnosis ; Organ Dysfunction Scores ; },
abstract = {IMPORTANCE: Sepsis is a leading cause of death among children worldwide. Current pediatric-specific criteria for sepsis were published in 2005 based on expert opinion. In 2016, the Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) defined sepsis as life-threatening organ dysfunction caused by a dysregulated host response to infection, but it excluded children.<br><br>OBJECTIVE: To update and evaluate criteria for sepsis and septic shock in children.<br><br>EVIDENCE REVIEW: The Society of Critical Care Medicine (SCCM) convened a task force of 35 pediatric experts in critical care, emergency medicine, infectious diseases, general pediatrics, nursing, public health, and neonatology from 6 continents. Using evidence from an international survey, systematic review and meta-analysis, and a new organ dysfunction score developed based on more than 3 million electronic health record encounters from 10 sites on 4 continents, a modified Delphi consensus process was employed to develop criteria.<br><br>FINDINGS: Based on survey data, most pediatric clinicians used sepsis to refer to infection with life-threatening organ dysfunction, which differed from prior pediatric sepsis criteria that used systemic inflammatory response syndrome (SIRS) criteria, which have poor predictive properties, and included the redundant term, severe sepsis. The SCCM task force recommends that sepsis in children be identified by a Phoenix Sepsis Score of at least 2 points in children with suspected infection, which indicates potentially life-threatening dysfunction of the respiratory, cardiovascular, coagulation, and/or neurological systems. Children with a Phoenix Sepsis Score of at least 2 points had in-hospital mortality of 7.1% in higher-resource settings and 28.5% in lower-resource settings, more than 8 times that of children with suspected infection not meeting these criteria. Mortality was higher in children who had organ dysfunction in at least 1 of 4-respiratory, cardiovascular, coagulation, and/or neurological-organ systems that was not the primary site of infection. Septic shock was defined as children with sepsis who had cardiovascular dysfunction, indicated by at least 1 cardiovascular point in the Phoenix Sepsis Score, which included severe hypotension for age, blood lactate exceeding 5 mmol/L, or need for vasoactive medication. Children with septic shock had an in-hospital mortality rate of 10.8% and 33.5% in higher- and lower-resource settings, respectively.<br><br>CONCLUSIONS AND RELEVANCE: The Phoenix sepsis criteria for sepsis and septic shock in children were derived and validated by the international SCCM Pediatric Sepsis Definition Task Force using a large international database and survey, systematic review and meta-analysis, and modified Delphi consensus approach. A Phoenix Sepsis Score of at least 2 identified potentially life-threatening organ dysfunction in children younger than 18 years with infection, and its use has the potential to improve clinical care, epidemiological assessment, and research in pediatric sepsis and septic shock around the world.},
}
@article {pmid38244396,
year = {2024},
author = {Sakamoto, Y and Miyoshi, K},
title = {A confidence framing effect: Flexible use of evidence in metacognitive monitoring.},
journal = {Consciousness and cognition},
volume = {118},
number = {},
pages = {103636},
doi = {10.1016/j.concog.2024.103636},
pmid = {38244396},
issn = {1090-2376},
mesh = {Humans ; *Decision Making ; Choice Behavior ; *Metacognition ; },
abstract = {Human behavior is flexibly regulated by specific goals of cognitive tasks. One notable example is goal-directed modulation of metacognitive behavior, where logically equivalent decision-making problems can yield different patterns of introspective confidence depending on the frame in which they are presented. While this observation highlights the important heuristic nature of metacognitive monitoring, computational mechanisms underlying this phenomenon remain elusive. We confirmed the confidence framing effect in two-alternative dot-number discrimination and in previously published preference-choice data, demonstrating distinctive confidence patterns between "choose more" or "choose less" frames. Formal model comparisons revealed a simple confidence heuristic behind this phenomenon, which assigns greater weight to chosen than unchosen stimulus evidence. This computation appears to be based on internal evidence constituted under specific task demands rather than physical stimulus intensity itself, a view justified in terms of ecological rationality. These results shed light on the adaptive nature of human decision-making and metacognitive monitoring.},
}
@article {pmid38243062,
year = {2024},
author = {Kwon, H and Ann, HW and Park, S and Kwon, J and Park, K and Ryu, SM and Guo, Y and Kim, JJ and Yim, JH and Kim, IC and Shim, SH and Lee, S and Lee, D},
title = {Mass spectrometry-guided isolation of thiodiketopiperazines from an EtOAc-extract of Setosphaeria rostrata culture medium and their anti-skin aging effects on TNF-α-induced human dermal fibroblasts.},
journal = {The Journal of antibiotics},
volume = {77},
number = {4},
pages = {257-263},
pmid = {38243062},
issn = {1881-1469},
support = {PE23150//Korea Polar Research Institute (KOPRI)/ ; NRF-2022R1A4A3022401//National Research Foundation of Korea (NRF)/ ; NRF-2019R1A2C1006226//National Research Foundation of Korea (NRF)/ ; },
mesh = {Humans ; *Tumor Necrosis Factor-alpha ; *Matrix Metalloproteinase 1/pharmacology ; Reactive Oxygen Species ; Fibroblasts ; *Ascomycota ; },
abstract = {Using mass spectrometry (MS)-guided isolation methods, a new thiodiketopiperazine derivative (1) and exserohilone (2) were isolated from an EtOAc-extract of Setosphaeria rostrata culture medium. The chemical structure of the new compound was elucidated by MS and NMR spectroscopy, and the absolute configurations were established by the quantum mechanical calculations of electronic circular dichroism. All isolated compounds were examined for their effects on reactive oxygen species (ROS) production, matrix metalloproteinase 1 (MMP-1) secretion, and procollagen type I α1 secretion in tumor necrosis factor (TNF)-α-induced human dermal fibroblasts. Compound 1 and exserohilone (2) exhibited the inhibition of TNF-α-induced ROS generation and MMP-1 secretion. Additionally, compound 1 and exserohilone (2) increased the procollagen type I α1 secretion. Compound 1 docked computationally into the active site of MMP-1 (-6.0 kcal/mol).},
}
@article {pmid38242303,
year = {2024},
author = {Rojo, J and Cervigón, P and Ferencova, Z and Cascón, &#xc1; and Galán Díaz, J and Romero-Morte, J and Sabariego, S and Torres, M and Gutiérrez-Bustillo, AM},
title = {Assessment of environmental risk areas based on airborne pollen patterns as a response to land use and land cover distribution.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {344},
number = {},
pages = {123385},
doi = {10.1016/j.envpol.2024.123385},
pmid = {38242303},
issn = {1873-6424},
mesh = {Cluster Analysis ; Databases, Factual ; *Pollen ; Public Health ; *Respiratory Tract Diseases ; },
abstract = {Allergic respiratory diseases are considered to be among the most important public health concerns, and pollen is the main cause of allergic respiratory diseases worldwide. However, the biological component of air quality is largely underestimated, and there is an important gap in the legislation in this area. The aims of this study were to characterise the occurrence and incidence of pollen exposure in relation to potential pollen sources and to delineate the main areas of aerobiological risk in the Madrid Autonomous Region based on homogeneous patterns of pollen exposure. This study uses the historical aerobiological database of the Madrid Region Palynological Network (central Spain) from ten pollen stations from 1994 to 2022, and the land-use information from the Corine Land Cover. Multiple clustering approaches were followed to group the sampling stations and subsequently all the 1 × 1km pixels for the Madrid Autonomous Region. The clustering dendrogram for land-use distribution was compared to the dendrogram for historical airborne pollen data. The two dendrograms showed a good alignment with a very high correlation (0.95) and very low entanglement (0.15), which indicates a close correspondence between the distribution of the potential pollen sources and the airborne pollen dynamics. Based on this knowledge, the Madrid Autonomous Region was divided into six aerobiological risk areas following a clear anthropogenic gradient in terms of the potential pollen sources that determine pollen exposure in the Madrid Region. Spatial regionalisation is a common practice in environmental risk assessment to improve the application of management plans and optimise the air quality monitoring networks. The risk areas proposed by scientific criteria in the Madrid Autonomous Region can be adjusted to other operational criteria following a framework equivalent to other air quality networks.},
}
@article {pmid38236268,
year = {2024},
author = {Rogoza, R and Krammer, G and Jauk, E and Flakus, M and Baran, L and Di Sarno, M and Di Pierro, R and Zajenkowski, M and Dufner, M and Fatfouta, R},
title = {The peaks and valleys of narcissism: The factor structure of narcissistic states and their relations to trait measures.},
journal = {Psychological assessment},
volume = {36},
number = {2},
pages = {147-161},
doi = {10.1037/pas0001295},
pmid = {38236268},
issn = {1939-134X},
support = {//National Science Centre/ ; //Austrian Science Fund (FWF)/ ; },
mesh = {Humans ; *Narcissism ; Databases, Factual ; *Ecological Momentary Assessment ; Phenotype ; },
abstract = {Although interindividual differences in narcissism are well studied, little is known about assessing narcissism at the within-person level. To fill this research gap, we investigated whether the narcissism construct is represented in the same way at the between- and within-person levels. We analyzed four established narcissism measures across multiple studies. In each of the studies, participants completed narcissism measures in ecological momentary assessment or daily diary studies. Equivalent construct representation across between- and within-person narcissism (i.e., cross-level measurement invariance) was found. State narcissism measures showed convergent validities for the trait narcissism scales. Moreover, we also found that antagonistic narcissism was most strongly related to within-person variability in narcissism. Our investigation sheds new light on the structure and assessment of narcissism on the within-person level by providing a comprehensive examination of its measurement. (PsycInfo Database Record (c) 2024 APA, all rights reserved).},
}
@article {pmid38235411,
year = {2024},
author = {Coury, SM and López, V and Bajwa, Z and Garcia, JM and Teresi, GI and Kuhlman, KR and Li, Y and Cole, S and Miklowitz, DJ and Pappas, I and Ho, TC},
title = {Protocol for teen inflammation glutamate emotion research (TIGER): Toward predictors of treatment response and clinical course in depressed adolescents.},
journal = {Brain, behavior, &amp; immunity - health},
volume = {35},
number = {},
pages = {100718},
pmid = {38235411},
issn = {2666-3546},
support = {K01 MH117442/MH/NIMH NIH HHS/United States ; P30 AG066530/AG/NIA NIH HHS/United States ; R01 MH127176/MH/NIMH NIH HHS/United States ; },
abstract = {Adolescent-onset depression is a prevalent and debilitating condition commonly associated with treatment refractory depression and non-response to first-line antidepressants. There are, however, no objective tests to determine who may or may not respond to antidepressants. As depressed adolescents are especially vulnerable to the lifelong consequences of ineffectively-treated depression, it is critical to identify neurobiological predictors of treatment non-response in this population. Here, we describe the scientific rationale and protocol for the Teen Inflammation Glutamate Emotion Research (TIGER) study, a prospective 18-month investigation of 160 depressed adolescents who will be assessed before and after treatment with selective serotonin reuptake inhibitors. TIGER will be using ultra-high field imaging to test the effects of acute stress and antidepressant treatment on inflammatory and glutamatergic processes hypothesized to underlie depression maintenance. Results from this work will motivate future studies testing alternative therapeutics for depressed adolescents at risk for treatment resistant depression. ClinicalTrials.gov Identifier: NCT05329441.},
}
@article {pmid38232851,
year = {2024},
author = {Liu, YE and Luo, XJ and Huang, CC and Lu, Q and Wang, S and Mai, BX},
title = {Insights into the occurrence, spatial distribution, and ecological implications of organophosphate triesters in surface sediments from polluted urban rivers across China.},
journal = {The Science of the total environment},
volume = {915},
number = {},
pages = {170108},
doi = {10.1016/j.scitotenv.2024.170108},
pmid = {38232851},
issn = {1879-1026},
abstract = {Organophosphate triesters (tri-OPEs) are a kind of widespread contaminants in the world, particularly in China, which is a major producer and user of tri-OPEs. However, tri-OPE pollution in urban river sediments in China remains unclear. In current work, we carried out the first nationwide investigation to comprehensively monitor 10 conventional and five emerging tri-OPEs in sediments of 173 black-odorous urban rivers throughout China. Concentrations of 10 conventional and five emerging tri-OPEs were 3.8-1240 ng/g dw (mean: 253 ng/g dw) and 0.21-1107 ng/g dw (68 ng/g dw), respectively, and significantly differed among the cities sampled but generally decreased from Northeast and East China to Central and West China. These spatial patterns suggest that tri-OPE pollution was mainly from local sources and was controlled by the industrial and economic development levels in these four areas, as indicated by the significant correlations between tri-OPE concentrations and gross domestic production, gross industrial output, and daily wastewater treatment capacity. Although the tri-OPE composition varied spatially at different sites, which indicated different tri-OPE input patterns, it was commonly dominated by tris(2-chloroethyl) phosphate, tris(2-ethylhexyl) phosphate, and tris(1-chloro-2-propyl) phosphate (conventional tri-OPEs) and bisphenol A-bis(diphenyl phosphate) and isodecyl diphenyl phosphate (emerging tri-OPEs). A risk assessment indicated that tri-OPEs in most sampling sediments had a low to moderate risk to aquatic organisms.},
}
@article {pmid38231860,
year = {2024},
author = {Grones, C and Eekhout, T and Shi, D and Neumann, M and Berg, LS and Ke, Y and Shahan, R and Cox, KL and Gomez-Cano, F and Nelissen, H and Lohmann, JU and Giacomello, S and Martin, OC and Cole, B and Wang, JW and Kaufmann, K and Raissig, MT and Palfalvi, G and Greb, T and Libault, M and De Rybel, B},
title = {Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.},
journal = {The Plant cell},
volume = {36},
number = {4},
pages = {812-828},
pmid = {38231860},
issn = {1532-298X},
support = {F32 GM136030/GM/NIGMS NIH HHS/United States ; /ERC_/European Research Council/International ; },
mesh = {Reproducibility of Results ; *Gene Expression Profiling ; *Plants/genetics ; Stress, Physiological/genetics ; Information Storage and Retrieval ; },
abstract = {Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.},
}
@article {pmid38229583,
year = {2024},
author = {Devine, K and Russell, CD and Blanco, GR and Walker, BR and Homer, NZM and Denham, SG and Simpson, JP and Leavy, OC and Elneima, O and McAuley, HJC and Shikotra, A and Singapuri, A and Sereno, M and Saunders, RM and Harris, VC and Houchen-Wolloff, L and Greening, NJ and Lone, NI and Thorpe, M and Greenhalf, W and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Raman, B and Moore, SC and Dunning, J and Semple, MG and Andrew, R and Wain, LV and Evans, RA and Brightling, CE and Kenneth Baillie, J and Reynolds, RM and , },
title = {Plasma steroid concentrations reflect acute disease severity and normalise during recovery in people hospitalised with COVID-19.},
journal = {Clinical endocrinology},
volume = {100},
number = {4},
pages = {317-327},
doi = {10.1111/cen.15012},
pmid = {38229583},
issn = {1365-2265},
support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Male ; Female ; *COVID-19 ; Hydrocortisone ; Acute Disease ; Aftercare ; Patient Discharge ; Glucocorticoids/therapeutic use ; Steroids/therapeutic use ; Patient Acuity ; Testosterone ; },
abstract = {OBJECTIVE: Endocrine systems are disrupted in acute illness, and symptoms reported following coronavirus disease 2019 (COVID-19) are similar to those found with clinical hormone deficiencies. We hypothesised that people with severe acute COVID-19 and with post-COVID symptoms have glucocorticoid and sex hormone deficiencies.<br><br>DESIGN/PATIENTS: Samples were obtained for analysis from two UK multicentre cohorts during hospitalisation with COVID-19 (International Severe Acute Respiratory Infection Consortium/World Health Organisation [WHO] Clinical Characterization Protocol for Severe Emerging Infections in the UK study), and at follow-up 5 months after hospitalisation (Post-hospitalisation COVID-19 study).<br><br>MEASUREMENTS: Plasma steroids were quantified by liquid chromatography-mass spectrometry. Steroid concentrations were compared against disease severity (WHO ordinal scale) and validated symptom scores. Data are presented as geometric mean (SD).<br><br>RESULTS: In the acute cohort (n&#x2009;=&#x2009;239, 66.5% male), plasma cortisol concentration increased with disease severity (cortisol 753.3 [1.6] vs. 429.2 [1.7]&#x2009;nmol/L in fatal vs. least severe, p&#x2009;<&#x2009;.001). In males, testosterone concentrations decreased with severity (testosterone 1.2 [2.2] vs. 6.9 [1.9]&#x2009;nmol/L in fatal vs. least severe, p&#x2009;<&#x2009;.001). In the follow-up cohort (n&#x2009;=&#x2009;198, 62.1% male, 68.9% ongoing symptoms, 165 [121-192] days postdischarge), plasma cortisol concentrations (275.6 [1.5]&#x2009;nmol/L) did not differ with in-hospital severity, perception of recovery, or patient-reported symptoms. Male testosterone concentrations (12.6 [1.5]&#x2009;nmol/L) were not related to in-hospital severity, perception of recovery or symptom scores.<br><br>CONCLUSIONS: Circulating glucocorticoids in patients hospitalised with COVID-19 reflect acute illness, with a marked rise in cortisol and fall in male testosterone. These findings are not observed 5 months from discharge. The lack of association between hormone concentrations and common post-COVID symptoms suggests steroid insufficiency does not play a causal role in this condition.},
}
@article {pmid38229470,
year = {2024},
author = {Wondimagegnehu, A and Assefa, M and Teferra, S and Kantelhardt, EJ and Zebrack, B and Addissie, A},
title = {A Qualitative Study on Psychosocial Challenges of Patients With Cancer in Ethiopia Using the Social-Ecological Model.},
journal = {Qualitative health research},
volume = {34},
number = {8-9},
pages = {828-841},
doi = {10.1177/10497323231219409},
pmid = {38229470},
issn = {1049-7323},
mesh = {Humans ; Ethiopia ; *Neoplasms/psychology/therapy ; *Qualitative Research ; Female ; Male ; Adult ; *Social Support ; Middle Aged ; *Focus Groups ; Interviews as Topic ; Young Adult ; Family/psychology ; Aged ; Stress, Psychological/psychology ; Depression/psychology/therapy ; },
abstract = {Cancer diagnosis and treatment can be physically arduous, disrupting patients' social and work lives. Understanding the extent of these problems is key to addressing patients' needs, but specific psychosocial challenges have not yet been well studied in resource-limited settings. A qualitative study was conducted in the capital and two regions of Ethiopia with the aim of exploring psychosocial challenges among cancer patients. A total of 14 in-depth interviews (IDIs) and 16 focus group discussions (FGDs) were done with cancer patients, health professionals, community representatives, and religious leaders. Four separate interview guides were used to facilitate the interviews and discussions. All transcribed documents, field notes, and reflexive memos were entered into NVivo 12 software, and deductive thematic analysis using the social-ecological model was applied to summarize the main findings. At an individual level, emotional distress, suicidal risk, denial, and refusal of treatment were identified immediately after diagnosis while hopelessness, feeling depressed, and fear of death were commonly reported psychosocial challenges during the course of treatment. Involvement of family members in major treatment decisions was recognized at an interpersonal level. Our result also revealed that cancer patients had strong social support from family members and close friends. In the community, traditional medicine and religious rituals were considered an alternative treatment for cancer. The findings indicate that counselling and psychoeducation are crucial for cancer patients, family members, and close friends. Awareness creation programmes should be delivered through collaboration with religious leaders and traditional healers.},
}
@article {pmid38225503,
year = {2024},
author = {Gubó, E and Plutzer, J and Molnár, T and Pordán-Háber, D and Szabó, L and Szalai, Z and Gubó, R and Szakál, P and Szakál, T and Környei, L and Bede-Fazekas, &#xc1; and Kalocsai, R},
title = {Correction to: A 4‑year study of bovine reproductive hormones that are induced by pharmaceuticals and appear as steroid estrogenic pollutants in the resulting slurry, using in vitro and instrumental analytical methods.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {6},
pages = {9868},
doi = {10.1007/s11356-024-31992-0},
pmid = {38225503},
issn = {1614-7499},
}
@article {pmid38218164,
year = {2024},
author = {Pérez, G and O'Leary, BC and Allegri, E and Casal, G and Cornet, CC and de Juan, S and Failler, P and Fredriksen, S and Fonseca, C and Furlan, E and Gil, A and Hawkins, JP and Maréchal, JP and McCarthy, T and Roberts, CM and Trégarot, E and van der Geest, M and Simide, R},
title = {A conceptual framework to help choose appropriate blue nature-based solutions.},
journal = {Journal of environmental management},
volume = {352},
number = {},
pages = {119936},
doi = {10.1016/j.jenvman.2023.119936},
pmid = {38218164},
issn = {1095-8630},
mesh = {Humans ; *Ecosystem ; *Biodiversity ; Climate Change ; },
abstract = {Biodiversity loss and climate change have severely impacted ecosystems and livelihoods worldwide, compromising access to food and water, increasing disaster risk, and affecting human health globally. Nature-based Solutions (NbS) have gained interest in addressing these global societal challenges. Although much effort has been directed to NbS in urban and terrestrial environments, the implementation of NbS in marine and coastal environments (blue NbS) lags. The lack of a framework to guide decision-makers and practitioners through the initial planning stages appears to be one of the main obstacles to the slow implementation of blue NbS. To address this, we propose an integrated conceptual framework, built from expert knowledge, to inform the selection of the most appropriate blue NbS based on desired intervention objectives and social-ecological context. Our conceptual framework follows a four incremental steps structure: Step 1 aims to identify the societal challenge(s) to address; Step 2 highlights ecosystem services and the underlying biodiversity and ecological functions that could contribute to confronting the societal challenge(s); Step 3 identify the specific environmental context the intervention needs to be set within (e.g. the spatial scale the intervention will operate within, the ecosystem's vulnerability to stressors, and its ecological condition); and Step 4 provides a selection of potential blue NbS interventions that would help address the targeted societal challenge(s) considering the context defined through Step 3. Designed to maintain, enhance, recover, rehabilitate, or create ecosystem services by supporting biodiversity, the blue NbS intervention portfolio includes marine protection (i.e., fully, highly, lightly, and minimally protected areas), restorative activities (i.e., active, passive, and partial restoration; rehabilitation of ecological function and ecosystem creation), and other management measures (i.e., implementation and enforcement of regulation). Ultimately, our conceptual framework guides decision-makers toward a versatile portfolio of interventions that cater to the specific needs of each ecosystem rather than imposing a rigid, one-size-fits-all model. In the future, this framework needs to integrate socio-economic considerations more comprehensively and be kept up-to-date by including the latest scientific information.},
}
@article {pmid38215805,
year = {2024},
author = {Lacson, R and Pianykh, O and Hartmann, S and Johnston, H and Daye, D and Flores, E and Kapoor, N and Khorasani, R},
title = {Factors Associated With Timeliness and Equity of Access to Outpatient MRI Examinations.},
journal = {Journal of the American College of Radiology : JACR},
volume = {21},
number = {7},
pages = {1049-1057},
doi = {10.1016/j.jacr.2023.12.028},
pmid = {38215805},
issn = {1558-349X},
mesh = {Humans ; Female ; Male ; *Magnetic Resonance Imaging ; *Health Services Accessibility ; Middle Aged ; Adult ; Time Factors ; Aged ; Ambulatory Care/statistics &amp; numerical data ; Outpatients ; },
abstract = {OBJECTIVE: The role of MRI in guiding patients' diagnosis and treatment is increasing. Therefore, timely MRI performance prevents delays that can impact patient care. We assessed the timeliness of performing outpatient MRIs using the socio-ecological model approach and evaluated multilevel factors associated with delays.<br><br>METHODS: This institutional review board-approved study included outpatient MRI examinations ordered between October 1, 2021, and December 31, 2022, for performance at a large quaternary care health system. Mean order-to-performed (OtoP) interval (in days) and prolonged OtoP interval (defined as >10 days) for MRI orders with an expected date of 1 day to examination performance were measured. Logistic regression was used to assess patient-level (demographic and social determinants of health), radiology practice-level, and community-level factors associated with prolonged OtoP interval.<br><br>RESULTS: There were 126,079 MRI examination orders with expected performance within 1 day placed during the study period (56% of all MRI orders placed). After excluding duplicates, there were 97,160 orders for unique patients. Of the MRI orders, 48% had a prolonged OtoP interval, and mean OtoP interval was 18.5 days. Factors significantly associated with delay in MRI performance included public insurance (odds ratio [OR]&#xa0;= 1.11, P < .001), female gender (OR&#xa0;= 1.11, P < .001), radiology subspecialty (ie, cardiac, OR&#xa0;= 1.71, P < .001), and patients from areas that are most deprived (ie, highest Area Deprivation Index quintile, OR&#xa0;= 1.70, P < .001).<br><br>DISCUSSION: Nearly half of outpatient MRI orders were delayed, performed >10 days from the expected date selected by the ordering provider. Addressing multilevel factors associated with such delays may help enhance timeliness and equity of access to MRI examinations, potentially reducing diagnostic errors and treatment delays.},
}
@article {pmid38215053,
year = {2024},
author = {Ho, PC and Yu, WH and Tee, BL and Lee, WP and Li, C and Gu, Y and Yokoyama, JS and Reyes-Dumeyer, D and Choi, YB and Yang, HS and Vardarajan, BN and Tzuang, M and Lieu, K and Lu, A and Faber, KM and Potter, ZD and Revta, C and Kirsch, M and McCallum, J and Mei, D and Booth, B and Cantwell, LB and Chen, F and Chou, S and Clark, D and Deng, M and Hong, TH and Hwang, LJ and Jiang, L and Joo, Y and Kang, Y and Kim, ES and Kim, H and Kim, K and Kuzma, AB and Lam, E and Lanata, SC and Lee, K and Li, D and Li, M and Li, X and Liu, CL and Liu, C and Liu, L and Lupo, JL and Nguyen, K and Pfleuger, SE and Qian, J and Qian, W and Ramirez, V and Russ, KA and Seo, EH and Song, YE and Tartaglia, MC and Tian, L and Torres, M and Vo, N and Wong, EC and Xie, Y and Yau, EB and Yi, I and Yu, V and Zeng, X and St George-Hyslop, P and Au, R and Schellenberg, GD and Dage, JL and Varma, R and Hsiung, GR and Rosen, H and Henderson, VW and Foroud, T and Kukull, WA and Peavy, GM and Lee, H and Feldman, HH and Mayeux, R and Chui, H and Jun, GR and Ta Park, VM and Chow, TW and Wang, LS},
title = {Asian Cohort for Alzheimer's Disease (ACAD) pilot study on genetic and non-genetic risk factors for Alzheimer's disease among Asian Americans and Canadians.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {20},
number = {3},
pages = {2058-2071},
pmid = {38215053},
issn = {1552-5279},
support = {R01 AG080469/AG/NIA NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; U19AG068753/AG/NIA NIH HHS/United States ; K23AG062750/AG/NIA NIH HHS/United States ; UH2 AG083258/AG/NIA NIH HHS/United States ; U19 AG068753/AG/NIA NIH HHS/United States ; R21 AG068757/AG/NIA NIH HHS/United States ; P30AG062422/AG/NIA NIH HHS/United States ; K24 AG045333/AG/NIA NIH HHS/United States ; R56 AG069130/AG/NIA NIH HHS/United States ; R24 AG063718/AG/NIA NIH HHS/United States ; R01 AG062588/AG/NIA NIH HHS/United States ; U19 AG079774/AG/NIA NIH HHS/United States ; ALZ-NAN-22-928181/ALZ/Alzheimer's Association/United States ; R01AG080469/AG/NIA NIH HHS/United States ; P30 AG062422/AG/NIA NIH HHS/United States ; R01 AG083840/AG/NIA NIH HHS/United States ; P01 AG019724/AG/NIA NIH HHS/United States ; P30 AG066462/AG/NIA NIH HHS/United States ; R24AG063718/AG/NIA NIH HHS/United States ; UH2AG083258/AG/NIA NIH HHS/United States ; P30 AG066530/AG/NIA NIH HHS/United States ; R01 AG083926/AG/NIA NIH HHS/United States ; AACSFD-22-972143/ALZ/Alzheimer's Association/United States ; R61 AG083582/AG/NIA NIH HHS/United States ; U19AG079774/AG/NIA NIH HHS/United States ; R01AG083926/AG/NIA NIH HHS/United States ; K23 AG062750/AG/NIA NIH HHS/United States ; U10EY017337/EY/NEI NIH HHS/United States ; R01AG083840/AG/NIA NIH HHS/United States ; R21AG077649/AG/NIA NIH HHS/United States ; R21 AG077649/AG/NIA NIH HHS/United States ; R21AG068757/AG/NIA NIH HHS/United States ; R61AG083582/AG/NIA NIH HHS/United States ; U10 EY017337/EY/NEI NIH HHS/United States ; U24AG021886/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Alzheimer Disease/genetics ; Pilot Projects ; Asian/genetics ; Canada ; Risk Factors ; *North American People ; },
abstract = {INTRODUCTION: Clinical research in Alzheimer's disease (AD) lacks cohort diversity despite being a global health crisis. The Asian Cohort for Alzheimer's Disease (ACAD) was formed to address underrepresentation of Asians in research, and limited understanding of how genetics and non-genetic/lifestyle factors impact this multi-ethnic population.<br><br>METHODS: The ACAD started fully recruiting in October 2021 with one central coordination site, eight recruitment sites, and two analysis sites. We developed a comprehensive study protocol for outreach and recruitment, an extensive data collection packet, and a centralized data management system, in English, Chinese, Korean, and Vietnamese.<br><br>RESULTS: ACAD has recruited 606 participants with an additional 900 expressing interest in enrollment since program inception.<br><br>DISCUSSION: ACAD's traction indicates the feasibility of recruiting Asians for clinical research to enhance understanding of AD risk factors. ACAD will recruit&#xa0;>&#xa0;5000 participants to identify genetic and non-genetic/lifestyle AD risk factors, establish blood biomarker levels for AD diagnosis, and facilitate clinical trial readiness.<br><br>HIGHLIGHTS: The Asian Cohort for Alzheimer's Disease (ACAD) promotes awareness of under-investment in clinical research for Asians. We are recruiting Asian Americans and Canadians for novel insights into Alzheimer's disease. We describe culturally appropriate recruitment strategies and data collection protocol. ACAD addresses challenges of recruitment from heterogeneous Asian subcommunities. We aim to implement a successful recruitment program that enrolls across three Asian subcommunities.},
}
@article {pmid38212658,
year = {2024},
author = {Ning, D and Wang, Y and Fan, Y and Wang, J and Van Nostrand, JD and Wu, L and Zhang, P and Curtis, DJ and Tian, R and Lui, L and Hazen, TC and Alm, EJ and Fields, MW and Poole, F and Adams, MWW and Chakraborty, R and Stahl, DA and Adams, PD and Arkin, AP and He, Z and Zhou, J},
title = {Environmental stress mediates groundwater microbial community assembly.},
journal = {Nature microbiology},
volume = {9},
number = {2},
pages = {490-501},
pmid = {38212658},
issn = {2058-5276},
support = {DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; },
mesh = {Phylogeny ; *Microbiota ; *Groundwater ; Stochastic Processes ; },
abstract = {Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.},
}
@article {pmid38204360,
year = {2024},
author = {Kiran, A and Hanachi, M and Alsayed, N and Fassatoui, M and Oduaran, OH and Allali, I and Maslamoney, S and Meintjes, A and Zass, L and Rocha, JD and Kefi, R and Benkahla, A and Ghedira, K and Panji, S and Mulder, N and Fadlelmola, FM and Souiai, O},
title = {The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38204360},
issn = {1758-0463},
support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Metadata ; Metagenome ; Databases, Factual ; Metagenomics ; *Microbiota/genetics ; },
abstract = {There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet.org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user's applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet.org/.},
}
@article {pmid38203410,
year = {2023},
author = {Di Martino, J and Arcieri, M and Madeddu, F and Pieroni, M and Carotenuto, G and Bottoni, P and Botta, L and Castrignanò, T and Gabellone, S and Saladino, R},
title = {Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity.},
journal = {International journal of molecular sciences},
volume = {25},
number = {1},
pages = {},
pmid = {38203410},
issn = {1422-0067},
mesh = {Humans ; *Molecular Dynamics Simulation ; *DNA Topoisomerases, Type I ; Biomimetics ; DNA Adducts ; Data Interpretation, Statistical ; Pyrimidine Dimers ; },
abstract = {Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of DNA photo-adducts, including cyclobutane pyrimidine dimers (CPDs) and Dewar valence derivatives (DVs). While CPDs usually occur at higher frequency than DVs, recent studies have shown that the latter display superior selectivity and significant stability in interaction with the human DNA/topoisomerase 1 complex (TOP1). With the aim to deeply investigate the mechanism of interaction of DVs with TOP1, we report here four all-atom molecular dynamic simulations spanning one microsecond. These simulations are focused on the stability and conformational changes of two DNA/TOP1-DV complexes in solution, the data being compared with the biomimetic thymine dimer counterparts. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, and hydrophobic interactions, as well as pinpointing the non-covalent interactions within the complexes, enabled the identification of specific TOP1 residues involved in the interactions over time and suggested a potential TOP1 inhibition mechanism in action.},
}
@article {pmid38196369,
year = {2024},
author = {Hauber, ME and Nagy, J and Sheard, C and Antonson, ND and Street, SE and Healy, SD and Lala, KN and Mainwaring, MC},
title = {Nest architecture influences host use by avian brood parasites and is shaped by coevolutionary dynamics.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2014},
pages = {20231734},
pmid = {38196369},
issn = {1471-2954},
mesh = {Animals ; Biological Evolution ; *Birds ; Databases, Factual ; Host Specificity ; *Nesting Behavior ; },
abstract = {Brood (social) parasites and their hosts exhibit a wide range of adaptations and counter-adaptations as part of their ongoing coevolutionary arms races. Obligate avian brood parasites are expected to use potential host species with more easily accessible nests, while potential hosts are expected to evade parasitism by building more concealed nests that are difficult for parasites to enter and in which to lay eggs. We used phylogenetically informed comparative analyses, a global database of the world's brood parasites, their host species, and the design of avian host and non-host nests (approx. 6200 bird species) to examine first, whether parasites preferentially target host species that build open nests and, second, whether host species that build enclosed nests are more likely to be targeted by specialist parasites. We found that species building more accessible nests are more likely to serve as hosts, while host species with some of the more inaccessible nests are targeted by more specialist brood parasites. Furthermore, evolutionary-transition analyses demonstrate that host species building enclosed nests frequently evolve to become non-hosts. We conclude that nest architecture and the accessibility of nests for parasitism represent a critical stage of the ongoing coevolutionary arms race between avian brood parasites and their hosts.},
}
@article {pmid38195441,
year = {2024},
author = {Rádai, Z and Váradi, A and Takács, P and Nagy, NA and Schmitt, N and Prépost, E and Kardos, G and Laczkó, L},
title = {An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {45},
pmid = {38195441},
issn = {1471-2164},
support = {GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; },
mesh = {*Research Design ; *Genome, Bacterial ; Benchmarking ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described. However, past studies generally focused on their additive effects, overlooking their potential interactions possibly exacerbating one another's effects in a multiplicative manner. To investigate whether or not they act interactively on de novo genome assembly quality, we simulated sequencing data for 13 bacterial reference genomes, with varying levels of error rate, sequencing depth, PCR and optical duplicate ratios.<br><br>RESULTS: We assessed the quality of assemblies from the simulated sequencing data with a number of contiguity and accuracy metrics, which we used to quantify both additive and multiplicative effects of the four parameters. We found that the tested parameters are engaged in complex interactions, exerting multiplicative, rather than additive, effects on assembly quality. Also, the ratio of non-repeated regions and GC% of the original genomes can shape how the four parameters affect assembly quality.<br><br>CONCLUSIONS: We provide a framework for consideration in future studies using de novo genome assembly of bacterial genomes, e.g. in choosing the optimal sequencing depth, balancing between its positive effect on contiguity and negative effect on accuracy due to its interaction with error rate. Furthermore, the properties of the genomes to be sequenced also should be taken into account, as they might influence the effects of error sources themselves.},
}
@article {pmid38194414,
year = {2024},
author = {Terpstra, S and Marquitti, FMD and Vasconcelos, VV},
title = {Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change.},
journal = {PLoS computational biology},
volume = {20},
number = {1},
pages = {e1011762},
pmid = {38194414},
issn = {1553-7358},
mesh = {Humans ; *Pollination/physiology ; *Models, Biological ; Models, Theoretical ; Plants ; Food Chain ; },
abstract = {Plant and pollinator communities are vital for transnational food chains. Like many natural systems, they are affected by global change: rapidly deteriorating conditions threaten their numbers. Previous theoretical studies identified the potential for community-wide collapse above critical levels of environmental stressors-so-called bifurcation-induced tipping points. Fortunately, even as conditions deteriorate, individuals have some adaptive capacity, potentially increasing the boundary for a safe operating space where changes in ecological processes are reversible. Our study considers this adaptive capacity of pollinators to resource availability and identifies a new threat to disturbed pollinator communities. We model the adaptive foraging of pollinators in changing environments. Pollinator's adaptive foraging alters the dynamical responses of species, to the advantage of some-typically generalists-and the disadvantage of others, with systematic non-linear and non-monotonic effects on the abundance of particular species. We show that, in addition to the extent of environmental stress, the pace of change of environmental stress can also lead to the early collapse of both adaptive and nonadaptive pollinator communities. Specifically, perturbed communities exhibit rate-induced tipping points at stress levels within the safe boundary defined for constant stressors. With adaptive foraging, tipping is a more asynchronous collapse of species compared to nonadaptive pollinator communities, meaning that not all pollinator species reach a tipping event simultaneously. These results suggest that it is essential to consider the adaptive capacity of pollinator communities for monitoring and conservation. Both the extent and the rate of stress change relative to the ability of communities to recover are critical environmental boundaries.},
}
@article {pmid38188173,
year = {2024},
author = {Lizardo, V and García Trejo, EA and Morrone, JJ},
title = {Niche conservatism and convergence in birds of three cenocrons in the Mexican Transition Zone.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16664},
pmid = {38188173},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; *Biological Evolution ; *Biota ; Birds ; },
abstract = {BACKGROUND: The niche conservatism hypothesis postulates that physiological and phylogenetic factors constrain species distributions, creating richness hotspots with older lineages in ancestral climatic conditions. Conversely, niche convergence occurs when species successfully disperse to novel environments, diversifying and resulting in areas with high phylogenetic clustering and endemism, low diversity, and lower clade age. The Mexican Transition Zone exhibits both patterns as its biotic assembly resulted from successive dispersal events of different biotic elements called cenocrons. We test the hypothesis that biogeographic transitionallity in the area is a product of niche conservatism in the Nearctic and Typical Neotropical cenocrons and niche convergence in the Mountain Mesoamerican cenocron.<br><br>METHODS: We split the avifauna into three species sets representing cenocrons (sets of taxa that share the same biogeographic history, constituting an identifiable subset within a biota by their common biotic origin and evolutionary history). Then, we correlated richness, endemism, phylogenetic diversity, number of nodes, and crowning age with environmental and topographic variables. These correlations were then compared with the predictions of niche conservatism versus niche convergence. We also detected areas of higher species density in environmental space and interpreted them as an environmental transition zone where birds' niches converge.<br><br>RESULTS: Our findings support the expected predictions on how niches evolved. Nearctic and Typical Neotropical species behaved as predicted by niche conservatism, whereas Mountain Mesoamerican species and the total of species correlations indicated niche convergence. We also detected distinct ecological and evolutionary characteristics of the cenocrons on a macroecological scale and the environmental conditions where the three cenocrons overlap in the Mesoamerican region.},
}
@article {pmid38184954,
year = {2024},
author = {Loo, SL and Howerton, E and Contamin, L and Smith, CP and Borchering, RK and Mullany, LC and Bents, S and Carcelen, E and Jung, SM and Bogich, T and van Panhuis, WG and Kerr, J and Espino, J and Yan, K and Hochheiser, H and Runge, MC and Shea, K and Lessler, J and Viboud, C and Truelove, S},
title = {The US COVID-19 and Influenza Scenario Modeling Hubs: Delivering long-term projections to guide policy.},
journal = {Epidemics},
volume = {46},
number = {},
pages = {100738},
doi = {10.1016/j.epidem.2023.100738},
pmid = {38184954},
issn = {1878-0067},
support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/epidemiology ; *Influenza, Human/epidemiology ; Pandemics ; Policy ; Public Health ; },
abstract = {Between December 2020 and April 2023, the COVID-19 Scenario Modeling Hub (SMH) generated operational multi-month projections of COVID-19 burden in the US to guide pandemic planning and decision-making in the context of high uncertainty. This effort was born out of an attempt to coordinate, synthesize and effectively use the unprecedented amount of predictive modeling that emerged throughout the COVID-19 pandemic. Here we describe the history of this massive collective research effort, the process of convening and maintaining an open modeling hub active over multiple years, and attempt to provide a blueprint for future efforts. We detail the process of generating 17 rounds of scenarios and projections at different stages of the COVID-19 pandemic, and disseminating results to the public health community and lay public. We also highlight how SMH was expanded to generate influenza projections during the 2022-23 season. We identify key impacts of SMH results on public health and draw lessons to improve future collaborative modeling efforts, research on scenario projections, and the interface between models and policy.},
}
@article {pmid38182924,
year = {2024},
author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS},
title = {Publisher Correction: Landscape-scale benefits of protected areas for tropical biodiversity.},
journal = {Nature},
volume = {625},
number = {7996},
pages = {E28},
doi = {10.1038/s41586-023-07007-2},
pmid = {38182924},
issn = {1476-4687},
}
@article {pmid38182741,
year = {2024},
author = {Ryu, H and Kinoshita, K and Joo, S and Choi, YS and Kim, SS},
title = {Increased urinary creatinine during hibernation and day roosting in the Eastern bent-winged bat (Miniopterus fuliginosus) in Korea.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {42},
pmid = {38182741},
issn = {2399-3642},
mesh = {Animals ; *Hibernation ; *Chiroptera ; Creatinine ; *Torpor ; Republic of Korea ; },
abstract = {Torpor and arousal cycles, both daily and seasonal (e.g. hibernation), are crucial for small mammals, including bats, to maintain the energy and water balance. The alternation between torpor and arousal leads to metabolic changes, leaving traceable evidence of metabolic wastes in urine. In this study we investigated urinary creatinine and acetoacetate (a ketone body) in the Eastern bent-wing bat (Miniopterus fuliginosus) in Mungyeong, South Korea. We found an increase in urinary creatinine during torpor in summer, indicating changes in renal water reabsorption rates during the active season. Although we could not confirm ketonuria in hibernating bats due to a methodological limitation caused by the small amount of urine, we verified an increase in urinary creatinine concentration during hibernation. This finding suggests that managing water stress resulting from evaporative water loss is one of key reasons for arousal during hibernation in Eastern bent-wing bats.},
}
@article {pmid38175682,
year = {2024},
author = {Henry, LM and Hansen, E and Chimoff, J and Pokstis, K and Kiderman, M and Naim, R and Kossowsky, J and Byrne, ME and Lopez-Guzman, S and Kircanski, K and Pine, DS and Brotman, MA},
title = {Selecting an Ecological Momentary Assessment Platform: Tutorial for Researchers.},
journal = {Journal of medical Internet research},
volume = {26},
number = {},
pages = {e51125},
pmid = {38175682},
issn = {1438-8871},
support = {K01 DA057374/DA/NIDA NIH HHS/United States ; ZIA MH002969/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Adolescent ; Child ; Humans ; *Ecological Momentary Assessment ; Data Management ; Digital Technology ; Laboratories ; *Medicine ; },
abstract = {BACKGROUND: Although ecological momentary assessment (EMA) has been applied in psychological research for decades, delivery methods have evolved with the proliferation of digital technology. Technological advances have engendered opportunities for enhanced accessibility, convenience, measurement precision, and integration with wearable sensors. Notwithstanding, researchers must navigate novel complexities in EMA research design and implementation.<br><br>OBJECTIVE: In this paper, we aimed to provide guidance on platform selection for clinical scientists launching EMA studies.<br><br>METHODS: Our team includes diverse specialties in child and adolescent behavioral and mental health with varying expertise on EMA platforms (eg, users and developers). We (2 research sites) evaluated EMA platforms with the goal of identifying the platform or platforms with the best fit for our research. We created a list of extant EMA platforms; conducted a web-based review; considered institutional security, privacy, and data management requirements; met with developers; and evaluated each of the candidate EMA platforms for 1 week.<br><br>RESULTS: We selected 2 different EMA platforms, rather than a single platform, for use at our 2 research sites. Our results underscore the importance of platform selection driven by individualized and prioritized laboratory needs; there is no single, ideal platform for EMA researchers. In addition, our project generated 11 considerations for researchers in selecting an EMA platform: (1) location; (2) developer involvement; (3) sample characteristics; (4) onboarding; (5) survey design features; (6) sampling scheme and scheduling; (7) viewing results; (8) dashboards; (9) security, privacy, and data management; (10) pricing and cost structure; and (11) future directions. Furthermore, our project yielded a suggested timeline for the EMA platform selection process.<br><br>CONCLUSIONS: This study will guide scientists initiating studies using EMA, an in vivo, real-time research tool with tremendous promise for facilitating advances in psychological assessment and intervention.},
}
@article {pmid38173562,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Pine Hawkmoth, Sphinx pinastri (Linneaus 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {312},
pmid = {38173562},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Sphinx pinastri (the Pine Hawkmoth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 509.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.},
}
@article {pmid38172362,
year = {2024},
author = {Paolo, FS and Kroodsma, D and Raynor, J and Hochberg, T and Davis, P and Cleary, J and Marsaglia, L and Orofino, S and Thomas, C and Halpin, P},
title = {Satellite mapping reveals extensive industrial activity at sea.},
journal = {Nature},
volume = {625},
number = {7993},
pages = {85-91},
pmid = {38172362},
issn = {1476-4687},
mesh = {Humans ; COVID-19/epidemiology ; Deep Learning ; Energy-Generating Resources/statistics &amp; numerical data ; Food Supply/statistics &amp; numerical data ; Geographic Information Systems ; Geographic Mapping ; *Human Activities/economics/statistics &amp; numerical data ; Hunting/statistics &amp; numerical data ; *Industry/economics/statistics &amp; numerical data ; *Oceans and Seas ; *Satellite Imagery ; Ships/statistics &amp; numerical data ; Wind ; },
abstract = {The world's population increasingly relies on the ocean for food, energy production and global trade[1-3], yet human activities at sea are not well quantified[4,5]. We combine satellite imagery, vessel GPS data and deep-learning models to map industrial vessel activities and offshore energy infrastructure across the world's coastal waters from 2017 to 2021. We find that 72-76% of the world's industrial fishing vessels are not publicly tracked, with much of that fishing taking place around South Asia, Southeast Asia and Africa. We also find that 21-30% of transport and energy vessel activity is missing from public tracking systems. Globally, fishing decreased by 12 ± 1% at the onset of the COVID-19 pandemic in 2020 and had not recovered to pre-pandemic levels by 2021. By contrast, transport and energy vessel activities were relatively unaffected during the same period. Offshore wind is growing rapidly, with most wind turbines confined to small areas of the ocean but surpassing the number of oil structures in 2021. Our map of ocean industrialization reveals changes in some of the most extensive and economically important human activities at sea.},
}
@article {pmid38172330,
year = {2024},
author = {Gong, Y and Zha, J and Guo, Q and Guo, G},
title = {A new indicator for estimating the degree of mining-induced land subsidence: the overburden's average GSI value.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {332},
pmid = {38172330},
issn = {2045-2322},
support = {2023YFC3804200//National Key Research and Development Program of China/ ; 2023YFC3804200//National Key Research and Development Program of China/ ; 2023YFC3804200//National Key Research and Development Program of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; U21A20109, 4227040173, 52274164, 42174048//National Natural Science Foundation of China/ ; },
abstract = {Underground coal mining leads to land subsidence, which, in turn, results in damage to buildings and infrastructure, disturbs the original ecological environment, and hinders the sustainable development of coal mining cities. A reasonable estimation of land subsidence, on the other hand, is the foundation for building protection, land reclamation, and ecological environment reconstruction. However, when we applied the existing land subsidence estimation theory to the deep mining areas of the Ordos coalfield in western China, there was a significant deviation between the estimations and the measurements. To explain such unusual case, we propose using the overburden's average GSI (Geological Strength Index) value instead of the compressive strength (UCS) of rock specimens for a better representation of the overburden's overall properties. By using on-site subsidence monitoring results and historical data, we provided evidence which supports that the overburden's average GSI value has a much greater impact on subsidence rates than the UCS. Subsequently, we investigated the relationship between three typical overburden's GSI values and the subsidence rates via a calibrated numerical model, revealing the variation patterns of maximum surface subsidence when the overburden's average GSI value is set at 30, 50, and 75, respectively. Finally, on the basis of the measured and simulated results, we discussed a non-conventional strip mining method for mining subsidence control in the deep mining areas of the Ordos coalfield in western China, and explained why it is possible and what are the significant advantages behind. The proposed methods, findings, and suggestions in this paper are therefore quite helpful for researchers and engineers who wish to estimate and control the mining-induced land subsidence, as well as for those who are particularly interested in the study of environment science related to land subsidence.},
}
@article {pmid38172116,
year = {2024},
author = {Külling, N and Adde, A and Fopp, F and Schweiger, AK and Broennimann, O and Rey, PL and Giuliani, G and Goicolea, T and Petitpierre, B and Zimmermann, NE and Pellissier, L and Altermatt, F and Lehmann, A and Guisan, A},
title = {SWECO25: a cross-thematic raster database for ecological research in Switzerland.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {21},
pmid = {38172116},
issn = {2052-4463},
abstract = {Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventions). Consequently, their joint use can require heavy data management and geomatic operations. Here, we introduce SWECO25, a Swiss-wide raster database at 25-meter resolution gathering 5,265 layers. The 10 environmental categories included in SWECO25 are: geologic, topographic, bioclimatic, hydrologic, edaphic, land use and cover, population, transportation, vegetation, and remote sensing. SWECO25 layers were standardized to a common grid sharing the same resolution, extent, and geographic coordinate system. SWECO25 includes the standardized source data and newly calculated layers, such as those obtained by computing focal or distance statistics. SWECO25 layers were validated by a data integrity check, and we verified that the standardization procedure had a negligible effect on the output values. SWECO25 is available on Zenodo and is intended to be updated and extended regularly.},
}
@article {pmid38167330,
year = {2024},
author = {Li, M and Liang, H and Yang, H and Ding, Q and Xia, R and Chen, J and Zhou, W and Yang, Y and Zhang, Z and Yao, Y and Ran, C and Zhou, Z},
title = {Deciphering the gut microbiome of grass carp through multi-omics approach.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {2},
pmid = {38167330},
issn = {2049-2618},
support = {31925038//National Natural Science Foundation of China/ ; 31925038//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Carps ; Multiomics ; *Microbiota ; Proteobacteria/genetics ; Fusobacteria/genetics ; Bacteroidetes/genetics ; Firmicutes/genetics ; Fusobacterium/genetics ; RNA, Ribosomal, 16S/genetics ; Mammals/genetics ; },
abstract = {BACKGROUND: Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking.<br><br>RESULTS: We identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and the liver was consistently opposite to that of Fusobacteria, Firmicutes, and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were considered as two functional groups, i.e., Functional Group 1: Proteobacteria and Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp.<br><br>CONCLUSIONS: The gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota and shed lights on targets for microbiota regulation. Video Abstract.},
}
@article {pmid38166118,
year = {2024},
author = {Muraleedharan, V and Rajan, SC and R, J},
title = {Geometric entropy of plant leaves: A measure of morphological complexity.},
journal = {PloS one},
volume = {19},
number = {1},
pages = {e0293596},
pmid = {38166118},
issn = {1932-6203},
mesh = {Entropy ; *Plants ; *Biological Evolution ; Physical Phenomena ; Plant Leaves/anatomy &amp; histology ; },
abstract = {Shape is an objective characteristic of an object. A boundary separates a physical object from its surroundings. It defines the shape and regulates energy flux into and from an object. Visual perception of a definite shape (geometry) of physical objects is an abstraction. While the perceived geometry at an object's sharp interface (macro) creates a Euclidian illusion of actual shape, the notion of diffuse interfaces (micro) allows an understanding of the realistic form of objects. Here, we formulate a dimensionless geometric entropy of plant leaves (SL) by a 2-D description of a phase-field function. We applied this method to 112 tropical plant leaf images. SL was estimated from the leaf perimeter (P) and leaf area (A). It correlates positively with a fractal dimensional measure of leaf complexity, viz., segmental fractal complexity. Leaves with a higher P: A ratio have higher SL and possess complex morphology. The univariate cluster analysis of SL reveals the taxonomic relationship among the leaf shapes at the genus level. An increase in SL of plant leaves could be an evolutionary strategy. The results of morphological complexity presented in this paper will trigger discussion on the causal links between leaf adaptive stability/efficiency and complexity. We present SL as a derived plant trait to describe plant leaf complexity and adaptive stability. Integrating SL into other leaf physiological measures will help to understand the dynamics of energy flow between plants and their environment.},
}
@article {pmid38160970,
year = {2024},
author = {Thenmozhi, M and Sujatha, M and Kavitha, M and Senthilraja, S and Babu, M and Priya, V},
title = {Assessment of cyclone risk and case study of Gaja cyclone using GIS techniques and machine learning algorithms in coastal zone of Tamil Nadu, India.},
journal = {Environmental research},
volume = {246},
number = {},
pages = {118089},
doi = {10.1016/j.envres.2023.118089},
pmid = {38160970},
issn = {1096-0953},
mesh = {*Cyclonic Storms ; India ; Geographic Information Systems ; *Disasters ; Algorithms ; },
abstract = {Cyclones can cause devastating impacts, including strong winds, heavy rainfall, storm surges, and flooding. The aftermath includes infrastructure damage, loss of life, displacement of communities, and ecological disruptions. Timely response and recovery efforts are crucial to minimize the socio-economic and environmental consequences of cyclones. To accelerate the time-consuming risk assessment process, particularly in geographically diverse regions, a blend of multi-criteria decision-making and machine learning models was utilized. This novel approach swiftly assessed cyclone risk and the impact of the Gaja cyclone in Nagapattinam, India. The method involved assigning weights to distinct criteria, unveiling notable vulnerability aspects like elevation, slope, proximity to the coast, distance from cyclone tracts, Lu/Lc, population density, proximity to cyclone shelters, household density, accessibility to healthcare facilities, NDVI, and levels of awareness. Daddavari, Ettugudi, Kodikarai, Vedharanyam, Velankanni, and Thirupoondi face high/extreme cyclone risk. Nagore, Nagapattinam, Pillai, Enangudi, and Sannanllur have low/no threat. To further enhance the precision of the study, machine learning algorithms like SVM, SAM, and MLC were deployed. These models were instrumental in generating pre- and post-cyclone land use maps. The influence of Gaja cyclones effects shows decreasing of agriculture land from 34% to 30%, aquaculture increase 1%, barren land decrease from 8% to 6%, Built-up land decrease from 15% to 13%, land with scrub and salt pan also decrease from 21% to 17% and 10%-8%. Mostly effect of Gaja cyclone is dramatic increase of water body from 8% to 21%. Conducting cyclone risk zone analysis and pre/post-cyclone Land Use Land Cover (LULC) detection in Nagapattinam offers valuable insights for disaster preparedness, infrastructure planning, and climate resilience. This study can enhance understanding of vulnerability and aid in formulating strategies to mitigate cyclone impacts, ensuring sustainable development in the region.},
}
@article {pmid38160816,
year = {2024},
author = {Jevšenak, J and Klisz, M and Mašek, J and Čada, V and Janda, P and Svoboda, M and Vostarek, O and Treml, V and van der Maaten, E and Popa, A and Popa, I and van der Maaten-Theunissen, M and Zlatanov, T and Scharnweber, T and Ahlgrimm, S and Stolz, J and Sochová, I and Roibu, CC and Pretzsch, H and Schmied, G and Uhl, E and Kaczka, R and Wrzesiński, P and Šenfeldr, M and Jakubowski, M and Tumajer, J and Wilmking, M and Obojes, N and Rybníček, M and Lévesque, M and Potapov, A and Basu, S and Stojanović, M and Stjepanović, S and Vitas, A and Arnič, D and Metslaid, S and Neycken, A and Prislan, P and Hartl, C and Ziche, D and Horáček, P and Krejza, J and Mikhailov, S and Světlík, J and Kalisty, A and Kolář, T and Lavnyy, V and Hordo, M and Oberhuber, W and Levanič, T and Mészáros, I and Schneider, L and Lehejček, J and Shetti, R and Bošeľa, M and Copini, P and Koprowski, M and Sass-Klaassen, U and Izmir, &#x15e;C and Bakys, R and Entner, H and Esper, J and Janecka, K and Martinez Del Castillo, E and Verbylaite, R and Árvai, M and de Sauvage, JC and Čufar, K and Finner, M and Hilmers, T and Kern, Z and Novak, K and Ponjarac, R and Puchałka, R and Schuldt, B and Škrk Dolar, N and Tanovski, V and Zang, C and Žmegač, A and Kuithan, C and Metslaid, M and Thurm, E and Hafner, P and Krajnc, L and Bernabei, M and Bojić, S and Brus, R and Burger, A and D'Andrea, E and Đorem, T and Gławęda, M and Gričar, J and Gutalj, M and Horváth, E and Kostić, S and Matović, B and Merela, M and Miletić, B and Morgós, A and Paluch, R and Pilch, K and Rezaie, N and Rieder, J and Schwab, N and Sewerniak, P and Stojanović, D and Ullmann, T and Waszak, N and Zin, E and Skudnik, M and Oštir, K and Rammig, A and Buras, A},
title = {Incorporating high-resolution climate, remote sensing and topographic data to map annual forest growth in central and eastern Europe.},
journal = {The Science of the total environment},
volume = {913},
number = {},
pages = {169692},
doi = {10.1016/j.scitotenv.2023.169692},
pmid = {38160816},
issn = {1879-1026},
mesh = {*Ecosystem ; *Remote Sensing Technology ; Forests ; Trees ; Climate Change ; Europe, Eastern ; Europe ; },
abstract = {To enhance our understanding of forest carbon sequestration, climate change mitigation and drought impact on forest ecosystems, the availability of high-resolution annual forest growth maps based on tree-ring width (TRW) would provide a significant advancement to the field. Site-specific characteristics, which can be approximated by high-resolution Earth observation by satellites (EOS), emerge as crucial drivers of forest growth, influencing how climate translates into tree growth. EOS provides information on surface reflectance related to forest characteristics and thus can potentially improve the accuracy of forest growth models based on TRW. Through the modelling of TRW using EOS, climate and topography data, we showed that species-specific models can explain up to 52 % of model variance (Quercus petraea), while combining different species results in relatively poor model performance (R[2] = 13 %). The integration of EOS into models based solely on climate and elevation data improved the explained variance by 6 % on average. Leveraging these insights, we successfully generated a map of annual TRW for the year 2021. We employed the area of applicability (AOA) approach to delineate the range in which our models are deemed valid. The calculated AOA for the established forest-type models was 73 % of the study region, indicating robust spatial applicability. Notably, unreliable predictions predominantly occurred in the climate margins of our dataset. In conclusion, our large-scale assessment underscores the efficacy of combining climate, EOS and topographic data to develop robust models for mapping annual TRW. This research not only fills a critical void in the current understanding of forest growth dynamics but also highlights the potential of integrated data sources for comprehensive ecosystem assessments.},
}
@article {pmid38159778,
year = {2024},
author = {Kelly, MG and Mann, DG and Taylor, JD and Juggins, S and Walsh, K and Pitt, JA and Read, DS},
title = {Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers.},
journal = {The Science of the total environment},
volume = {914},
number = {},
pages = {169445},
doi = {10.1016/j.scitotenv.2023.169445},
pmid = {38159778},
issn = {1879-1026},
mesh = {*Rivers ; *Diatoms ; Fresh Water ; Biodiversity ; Databases, Factual ; Environmental Monitoring ; Ecosystem ; },
abstract = {DNA metabarcoding has been performed on a large number of river phytobenthos samples collected from the UK, using rbcL primers optimised for diatoms. Within this dataset the composition of non-diatom sequence reads was studied and the effect of including these in models for evaluating the nutrient gradient was assessed. Whilst many non-diatom taxonomic groups were detected, few contained the full diversity expected in riverine environments. This may be due to the performance of the current primers in characterising the wider phytobenthic community and influenced by the sampling method employed, as both were developed specifically for diatoms. Nevertheless, the study identified considerable diversity in some groups, e.g. Eustigmatophyceae and a wider distribution than previously thought for freshwater Phaeophyceae. These results offer a strong case for the benefits of metabarcoding for expanding knowledge of aquatic biodiversity in the UK and elsewhere. Many of the ASVs associated with non-diatoms showed significant pressure responses; however, models that included non-diatoms had similar predictive strength to those based on diatoms alone. Whilst limitations of the primers for assessing non-diatoms may play a role in explaining these results, the diatoms provide a strong signal along the nutrient gradient and other algae, therefore, add little unique information. We recommend that future developments should use ASVs to calculate metrics, with links to reference databases made as a final step to generate lists of taxa to support interpretation. Any further exploration of the potential of non-diatoms would benefit from access to a well-curated reference database, similar to diat.barcode. Such a database does not yet exist, and we caution against the indiscriminate use of NCBI GenBank as a taxonomic resource as many rbcL sequences deposited have not been curated.},
}
@article {pmid38155557,
year = {2024},
author = {Forbes, VE and Accolla, C and Banitz, T and Crouse, K and Galic, N and Grimm, V and Raimondo, S and Schmolke, A and Vaugeois, M},
title = {Mechanistic population models for ecological risk assessment and decision support: The importance of good conceptual model diagrams.},
journal = {Integrated environmental assessment and management},
volume = {20},
number = {5},
pages = {1566-1574},
doi = {10.1002/ieam.4886},
pmid = {38155557},
issn = {1551-3793},
support = {//Helmholtz/ ; 2018-06139//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {Risk Assessment/methods ; *Ecology ; *Decision Support Techniques ; Models, Theoretical ; Environmental Monitoring/methods ; },
abstract = {The use of mechanistic population models as research and decision-support tools in ecology and ecological risk assessment (ERA) is increasing. This growth has been facilitated by advances in technology, allowing the simulation of more complex systems, as well as by standardized approaches for model development, documentation, and evaluation. Mechanistic population models are particularly useful for simulating complex systems, but the required model complexity can make them challenging to communicate. Conceptual diagrams that summarize key model elements, as well as elements that were considered but not included, can facilitate communication and understanding of models and increase their acceptance as decision-support tools. Currently, however, there are no consistent standards for creating or presenting conceptual model diagrams (CMDs), and both terminology and content vary widely. Here, we argue that greater consistency in CMD development and presentation is an important component of good modeling practice, and we provide recommendations, examples, and a free web app (pop-cmd.com) for achieving this for population models used for decision support in ERAs. Integr Environ Assess Manag 2024;20:1566-1574. © 2023 SETAC.},
}
@article {pmid38149298,
year = {2023},
author = {Fins, IS and Singleton, DA and Radford, AD and Sánchez-Vizcaíno, F and Pinchbeck, GL},
title = {A mixed-methods approach utilising electronic health records to examine antimicrobial prescription surrounding gastrointestinal clinical presentations in dogs and cats.},
journal = {Frontiers in veterinary science},
volume = {10},
number = {},
pages = {1166114},
pmid = {38149298},
issn = {2297-1769},
abstract = {INTRODUCTION: Systemically-administered antimicrobials are often prescribed in canine and feline gastrointestinal clinical presentations. Responsible use of antimicrobials, particularly those considered Highest Priority Critically Important Antimicrobials (HPCIAs) is vital to tackle antimicrobial resistance. Although practice-level prescription guidance is available, further strategies based on a greater understanding of antimicrobial prescription at the population-level are needed. Here, we used a mixed-methods approach, harnessing veterinary electronic health records (EHRs) to characterise the use of antimicrobials in canine and feline gastrointestinal presentations, and to explore justification and reasoning around antimicrobial prescribing, particularly of HPCIAs.<br><br>METHODS: This observational study used 23,337 EHRs complemented with veterinary practitioner-completed questionnaires, from canine and feline gastrointestinal consultations from 225 volunteer UK veterinary practices between April 2014 and September 2018.<br><br>RESULTS: A total of 83.4% (95% confidence interval (CI) 82.6-84.3) gastrointestinal presentations were reported as mild, with non-haemorrhagic diarrhoea and vomiting the most frequently reported clinical signs. Systemically-administered antimicrobials occurred in 28.6% of canine (95% CI 26.9-30.3) and 22.4% of feline (95% CI 20.4-24.4) gastrointestinal consultations, with HPCIA prescription occurring more frequently in cats. Results of multivariable analysis showed the presence of non-haemorrhagic diarrhoea (canine Odds Ratio (OR) 2.1, 95% CI 1.9-2.3; feline OR 1.8, 95% CI 1.5-2.1), haemorrhagic diarrhoea (canine OR 4.2, 95% CI 3.8-4.7; feline OR 3.1, 95% CI 2.4-3.8), and moderate/severe presentations (canine OR 1.9, 95% CI 1.7-2.8; feline OR 2.0, 95% CI 1.7-2.5) were positively associated with receiving a systemically-administered antimicrobial. Thematic analysis of clinical narrative content of 516 gastrointestinal consultations where HPCIAs were prescribed allowed the identification of ten factors underpinning reasoning or decision-making for HPCIA prescription: perceived animal/owner compliance; owner's expectations; perceived risk of infection; clinical signs; recent clinical history; perceived positive previous response to antimicrobial therapy; geriatric patients and euthanasia; concomitant conditions; diagnostic testing and the behavioral trend to trial antimicrobial therapy empirically in gastrointestinal cases. No explicit justification for HPCIA prescription was recorded in 77% of cases.<br><br>DISCUSSION: Improving recorded justification represents a clear target for stewardship programmes. By utilising a complementary mixed-methods approach to EHRs, this study unlocks previously untapped data recorded within EHRs. These results can help inform targeted interventions, contributing towards enhanced antimicrobial stewardship.},
}
@article {pmid38149262,
year = {2023},
author = {Wang, Y and Shojaie, A and Randolph, T and Knight, P and Ma, J},
title = {GENERALIZED MATRIX DECOMPOSITION REGRESSION: ESTIMATION AND INFERENCE FOR TWO-WAY STRUCTURED DATA.},
journal = {The annals of applied statistics},
volume = {17},
number = {4},
pages = {2944-2969},
pmid = {38149262},
issn = {1932-6157},
support = {R01 GM129512/GM/NIGMS NIH HHS/United States ; U19 CA203654/CA/NCI NIH HHS/United States ; T32 GM135117/GM/NIGMS NIH HHS/United States ; R01 GM145772/GM/NIGMS NIH HHS/United States ; P50 CA228944/CA/NCI NIH HHS/United States ; R01 HL155417/HL/NHLBI NIH HHS/United States ; R01 GM133848/GM/NIGMS NIH HHS/United States ; },
abstract = {Motivated by emerging applications in ecology, microbiology, and neuroscience, this paper studies high-dimensional regression with two-way structured data. To estimate the high-dimensional coefficient vector, we propose the generalized matrix decomposition regression (GMDR) to efficiently leverage auxiliary information on row and column structures. GMDR extends the principal component regression (PCR) to two-way structured data, but unlike PCR, GMDR selects the components that are most predictive of the outcome, leading to more accurate prediction. For inference on regression coefficients of individual variables, we propose the generalized matrix decomposition inference (GMDI), a general high-dimensional inferential framework for a large family of estimators that include the proposed GMDR estimator. GMDI provides more flexibility for incorporating relevant auxiliary row and column structures. As a result, GMDI does not require the true regression coefficients to be sparse, but constrains the coordinate system representing the regression coefficients according to the column structure. GMDI also allows dependent and heteroscedastic observations. We study the theoretical properties of GMDI in terms of both the type-I error rate and power and demonstrate the effectiveness of GMDR and GMDI in simulation studies and an application to human microbiome data.},
}
@article {pmid38147867,
year = {2023},
author = {He, Z and Pfaff, E and Guo, SJ and Guo, Y and Wu, Y and Tao, C and Stiglic, G and Bian, J},
title = {Enriching Real-world Data with Social Determinants of Health for Health Outcomes and Health Equity: Successes, Challenges, and Opportunities.},
journal = {Yearbook of medical informatics},
volume = {32},
number = {1},
pages = {253-263},
pmid = {38147867},
issn = {2364-0502},
support = {U2C ES026555/ES/NIEHS NIH HHS/United States ; R21 LM013911/LM/NLM NIH HHS/United States ; R21 ES032762/ES/NIEHS NIH HHS/United States ; R01 AG080624/AG/NIA NIH HHS/United States ; R21 CA245858/CA/NCI NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; R01 DK133465/DK/NIDDK NIH HHS/United States ; R01 CA246418/CA/NCI NIH HHS/United States ; U18DP006512/ACL/ACL HHS/United States ; P01 AA029547/AA/NIAAA NIH HHS/United States ; UL1 TR002489/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *Health Equity ; Social Determinants of Health ; Electronic Health Records ; *Population Health ; Outcome Assessment, Health Care ; },
abstract = {OBJECTIVE: To summarize the recent methods and applications that leverage real-world data such as electronic health records (EHRs) with social determinants of health (SDoH) for public and population health and health equity and identify successes, challenges, and possible solutions.<br><br>METHODS: In this opinion review, grounded on a social-ecological-model-based conceptual framework, we surveyed data sources and recent informatics approaches that enable leveraging SDoH along with real-world data to support public health and clinical health applications including helping design public health intervention, enhancing risk stratification, and enabling the prediction of unmet social needs.<br><br>RESULTS: Besides summarizing data sources, we identified gaps in capturing SDoH data in existing EHR systems and opportunities to leverage informatics approaches to collect SDoH information either from structured and unstructured EHR data or through linking with public surveys and environmental data. We also surveyed recently developed ontologies for standardizing SDoH information and approaches that incorporate SDoH for disease risk stratification, public health crisis prediction, and development of tailored interventions.<br><br>CONCLUSIONS: To enable effective public health and clinical applications using real-world data with SDoH, it is necessary to develop both non-technical solutions involving incentives, policies, and training as well as technical solutions such as novel social risk management tools that are integrated into clinical workflow. Ultimately, SDoH-powered social risk management, disease risk prediction, and development of SDoH tailored interventions for disease prevention and management have the potential to improve population health, reduce disparities, and improve health equity.},
}
@article {pmid38147769,
year = {2024},
author = {Wang, M and Ji, L and Xie, Y and Huang, G},
title = {Regional bioethanol supply chain optimization with the integration of GIS-MCDM method and quantile-based scenario analysis.},
journal = {Journal of environmental management},
volume = {351},
number = {},
pages = {119883},
doi = {10.1016/j.jenvman.2023.119883},
pmid = {38147769},
issn = {1095-8630},
mesh = {*Geographic Information Systems ; Biomass ; Uncertainty ; *Agriculture ; China ; },
abstract = {This study presents a novel decision-support framework for the bioethanol supply chain network planning and management under uncertainties. Under the holistic framework, the most suitable sites for biorefineries are first screened out by adopting a GIS-based multi-criteria decision-making approach. Then, a mixed-integer linear programming model combined with quantile-based scenario analysis is developed to determine the strategic planning (i.e. locations and size of biorefineries) and tactical management (i.e. biomass purchasing, feedstock transportation, bioethanol production, and product delivery) under uncertainties. The model can effectively search for reliable solutions under uncertainties and achieve tradeoff solutions with the consideration of decision makers' risk tolerance. The proposed framework is demonstrated through a case study in China. It is suggested to build seven biorefineries with a capacity of 100 million liters in Zhumadian city. Utilizing 41% of local agricultural residues could satisfy the bioethanol requirement in the transportation sector under the E20 policy. However, the estimated production cost of bioethanol in Zhumadian is very high, about 1.11 $/L, which makes it lose cost advantage in the fuel market. Thus, currently, effective subsidies, mandatory energy substitution policies, along other environmental regulatory measures are desired to promote the bioethanol industry development.},
}
@article {pmid38147054,
year = {2024},
author = {Cusack, CE and Vanzhula, IA and Sandoval-Araujo, LE and Pennesi, JL and Kelley, SW and Levinson, CA},
title = {Are central eating disorder network symptoms sensitive to item selection and sample? Implications for conceptualization of eating disorder psychopathology from a network perspective.},
journal = {Journal of psychopathology and clinical science},
volume = {133},
number = {1},
pages = {48-60},
pmid = {38147054},
issn = {2769-755X},
support = {R15 MH121445/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Concept Formation ; *Feeding and Eating Disorders/diagnosis ; Databases, Factual ; Ecological Momentary Assessment ; Fear ; },
abstract = {Item selection is a critical decision in modeling psychological networks. The current preregistered two-study research used random selections of 1,000 symptom networks to examine which eating disorder (ED) and co-occurring symptoms are most central in longitudinal networks among individuals with EDs (N = 71, total observations = 6,060) and tested whether centrality changed based on which items were included in the network. Participants completed 2 weeks of ecological momentary assessment (five surveys/day). In Study 1, we obtained initial strength centrality values by estimating an a priori network using eight items with the highest means. We then estimated 1,000 networks and their centrality from a random selection of unique eight-item symptom combinations. We compared the strength centrality from the a priori network to the distribution of strength centrality estimates from the random-item networks. In Study 2, we repeated this procedure in an independent longitudinal dataset (N = 41, total observations = 4,575) to determine if our results generalized across samples. Shame, guilt, worry, and fear of losing control were consistently central across networks, regardless of items included in the network or sample. Results suggest that these symptoms may be important to the structure of ED psychopathology and have implications for how we understand the structure of ED psychopathology. Existing methods for item inclusion in psychological networks may distort the structure of ED symptom networks by either under- or overestimating strength centrality, or by omitting consistently central symptoms that are nontraditional ED symptoms. Future research should consider including these symptoms in models of ED psychopathology. (PsycInfo Database Record (c) 2023 APA, all rights reserved).},
}
@article {pmid38144190,
year = {2023},
author = {Graves, SJ and Marconi, S and Stewart, D and Harmon, I and Weinstein, B and Kanazawa, Y and Scholl, VM and Joseph, MB and McGlinchy, J and Browne, L and Sullivan, MK and Estrada-Villegas, S and Wang, DZ and Singh, A and Bohlman, S and Zare, A and White, EP},
title = {Data science competition for cross-site individual tree species identification from airborne remote sensing data.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16578},
pmid = {38144190},
issn = {2167-8359},
mesh = {Humans ; *Remote Sensing Technology ; *Data Science ; Neural Networks, Computer ; Ecosystem ; },
abstract = {Data on individual tree crowns from remote sensing have the potential to advance forest ecology by providing information about forest composition and structure with a continuous spatial coverage over large spatial extents. Classifying individual trees to their taxonomic species over large regions from remote sensing data is challenging. Methods to classify individual species are often accurate for common species, but perform poorly for less common species and when applied to new sites. We ran a data science competition to help identify effective methods for the task of classification of individual crowns to species identity. The competition included data from three sites to assess each methods' ability to generalize patterns across two sites simultaneously and apply methods to an untrained site. Three different metrics were used to assess and compare model performance. Six teams participated, representing four countries and nine individuals. The highest performing method from a previous competition in 2017 was applied and used as a baseline to understand advancements and changes in successful methods. The best species classification method was based on a two-stage fully connected neural network that significantly outperformed the baseline random forest and gradient boosting ensemble methods. All methods generalized well by showing relatively strong performance on the trained sites (accuracy = 0.46-0.55, macro F1 = 0.09-0.32, cross entropy loss = 2.4-9.2), but generally failed to transfer effectively to the untrained site (accuracy = 0.07-0.32, macro F1 = 0.02-0.18, cross entropy loss = 2.8-16.3). Classification performance was influenced by the number of samples with species labels available for training, with most methods predicting common species at the training sites well (maximum F1 score of 0.86) relative to the uncommon species where none were predicted. Classification errors were most common between species in the same genus and different species that occur in the same habitat. Most methods performed better than the baseline in detecting if a species was not in the training data by predicting an untrained mixed-species class, especially in the untrained site. This work has highlighted that data science competitions can encourage advancement of methods, particularly by bringing in new people from outside the focal discipline, and by providing an open dataset and evaluation criteria from which participants can learn.},
}
@article {pmid38140503,
year = {2023},
author = {Tunklová, B and Šerá, B and Šrámková, P and Ďurčányová, S and Šerý, M and Kováčik, D and Zahoranová, A and Hnilička, F},
title = {Growth Stimulation of Durum Wheat and Common Buckwheat by Non-Thermal Atmospheric Pressure Plasma.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {24},
pages = {},
pmid = {38140503},
issn = {2223-7747},
support = {APVV-21-147//Slovak Research and Development Agency/ ; },
abstract = {The grains of durum wheat (Triticum durum Desf.) and achenes of common buckwheat (Fagopyrum esculentum Moench) were tested after treatment with two sources of non-thermal atmospheric pressure plasma (DCSBD, MSDBD) with different treatment times (0, 3, 5, 10, 20, 30, and 40 s). The effect of these treatments was monitored with regard to the seed surface diagnostics (water contact angle-WCA, chemical changes by Fourier transform infrared spectroscopy-FTIR); twenty parameters associated with germination and initial seed growth were monitored. A study of the wettability confirmed a decrease in WCA values indicating an increase in surface energy and hydrophilicity depending on the type of seed, plasma source, and treatment time. Surface analysis by attenuated total reflectance FTIR (ATR-FTIR) showed no obvious changes in the chemical bonds on the surface of the plasma-treated seeds, which confirms the non-destructive effect of the plasma on the chemical composition of the seed shell. A multivariate analysis of the data showed many positive trends (not statistically significant) in germination and initial growth parameters. The repeated results for germination rate and root/shoot dry matter ratio indicate the tendency of plants to invest in underground organs. Durum wheat required longer treatment times with non-thermal plasma (10 s, 20 s) for germination and early growth, whereas buckwheat required shorter times (5 s, 10 s). The responses of durum wheat grains to the two non-thermal plasma sources used were equal. In contrast, the responses of buckwheat achenes were more favorable to MSDBD treatment than to DCSBD.},
}
@article {pmid38138669,
year = {2023},
author = {Abramovskis, V and Drunka, R and Csáki, &#x160; and Lukáč, F and Veverka, J and Illkova, K and Gavrilovs, P and Shishkin, A},
title = {Preparation and Characteristics of High-Performance, Low-Density Metallo-Ceramics Composite.},
journal = {Materials (Basel, Switzerland)},
volume = {16},
number = {24},
pages = {},
pmid = {38138669},
issn = {1996-1944},
support = {VPP-AIPP-2021/1-0015//Latvian research council/ ; ZM-2023/10//B57 RTU internal scientific research, ZM-2023/10/ ; },
abstract = {By applying the physical vapour deposition method, hollow ceramic microspheres were coated with titanium, and subsequently, they were sintered using the spark plasma sintering technique to create a porous ceramic material that is lightweight and devoid of a matrix. The sintering process was carried out at temperatures ranging from 1050 to 1200 °C, with a holding time of 2 min. The samples were subjected to conventional thermal analyses (differential scanning calorimetry, thermogravimetry, dilatometry), oxidation resistance tests, and thermal diffusivity measurements. Phase analysis of the samples was performed using the XRD and the microstructure of the prepared specimens was examined using electron microscopy. The titanium coating on the microspheres increased the compressive strength and density of the resulting ceramic material as the sintering temperature increased. The morphology of the samples was carefully examined, and phase transitions were also identified during the analysis of the samples.},
}
@article {pmid38138064,
year = {2023},
author = {Bedard, DL and Van Slyke, G and Nübel, U and Bateson, MM and Brumfield, S and An, YJ and Becraft, ED and Wood, JM and Thiel, V and Ward, DM},
title = {Geographic and Ecological Diversity of Green Sulfur Bacteria in Hot Spring Mat Communities.},
journal = {Microorganisms},
volume = {11},
number = {12},
pages = {},
pmid = {38138064},
issn = {2076-2607},
support = {CAN-97-01-055-004/NASA/NASA/United States ; NCC2-1073/NASA/NASA/United States ; NAG5-8824/NASA/NASA/United States ; NNX16AJ62G/NASA/NASA/United States ; },
abstract = {Three strains of thermophilic green sulfur bacteria (GSB) are known; all are from microbial mats in hot springs in Rotorua, New Zealand (NZ) and belong to the species Chlorobaculum tepidum. Here, we describe diverse populations of GSB inhabiting Travel Lodge Spring (TLS) (NZ) and hot springs ranging from 36.1 °C to 51.1 °C in the Republic of the Philippines (PHL) and Yellowstone National Park (YNP), Wyoming, USA. Using targeted amplification and restriction fragment length polymorphism analysis, GSB 16S rRNA sequences were detected in mats in TLS, one PHL site, and three regions of YNP. GSB enrichments from YNP and PHL mats contained small, green, nonmotile rods possessing chlorosomes, chlorobactene, and bacteriochlorophyll c. Partial 16S rRNA gene sequences from YNP, NZ, and PHL mats and enrichments from YNP and PHL samples formed distinct phylogenetic clades, suggesting geographic isolation, and were associated with samples differing in temperature and pH, suggesting adaptations to these parameters. Sequences from enrichments and corresponding mats formed clades that were sometimes distinct, increasing the diversity detected. Sequence differences, monophyly, distribution patterns, and evolutionary simulation modeling support our discovery of at least four new putative moderately thermophilic Chlorobaculum species that grew rapidly at 40 °C to 44 °C.},
}
@article {pmid38129780,
year = {2023},
author = {Duan, L and Wang, F and Shen, H and Xie, S and Chen, X and Xie, Q and Li, R and Cao, A and Li, H},
title = {Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {795},
pmid = {38129780},
issn = {1471-2164},
support = {31960413//National Natural Science Foundation of China/ ; 2016AC017, 2020BC002//Science and Technology Project of Bingtuan/ ; },
mesh = {*Esterases/genetics/metabolism ; *Lipase/genetics/metabolism ; Gossypium/metabolism ; Genome, Plant ; Gene Duplication ; Computational Biology ; Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism.<br><br>RESULTS: A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner.<br><br>CONCLUSIONS: Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.},
}
@article {pmid38128801,
year = {2024},
author = {Wang, G and Jiang, G and Peng, R and Wang, Y and Li, J and Sima, Y and Xu, S},
title = {Multi-omics integrative analysis revealed characteristic changes in blood cell immunity and amino acid metabolism in a silkworm model of hyperproteinemia.},
journal = {International journal of biological macromolecules},
volume = {258},
number = {Pt 1},
pages = {128809},
doi = {10.1016/j.ijbiomac.2023.128809},
pmid = {38128801},
issn = {1879-0003},
mesh = {Humans ; Animals ; Histones/metabolism ; *Bombyx/metabolism ; Lysine/metabolism ; Multiomics ; Chromatin ; Blood Proteins/metabolism ; Blood Cells/metabolism ; *Metabolic Diseases ; Acetylation ; },
abstract = {Hyperproteinemia is a serious metabolic disease of both humans and animals characterized by an abnormally high plasma protein concentration (HPPC). Although hyperproteinemia can cause an imbalance in blood cell homeostasis, the functional changes to blood cells remain unclear. Here, a HPPC silkworm model was used to assess changes to the chromatin accessibility and transcript levels of genes related to blood cell metabolism and immune function. The results showed that HPPC enhanced phagocytosis of blood cells, increased chromatin accessibility and transcript levels of genes involved in cell phagocytosis, proliferation, stress, and programmed death, while genes associated with aromatic amino acid metabolism, and antibacterial peptide synthesis were inhibited in blood cells. Further analysis of the chromatin accessibility of the promoter region found that the high chromatin accessibility of genes sensitive to HPPC, was related to histone modifications, including tri-methylation of lysine residue 4 of histone H3 and acetylation of lysine residue 27 of histone H3. Changes to the chromatin accessibility and transcript levels of genes related to immune function and amino acid metabolism in the blood cells of the HPPC silkworm model provided useful references for future studies of the mechanisms underlying epigenomic regulation mediated by hyperproteinemia.},
}
@article {pmid38125713,
year = {2023},
author = {Tamburro, G and Fiedler, P and De Fano, A and Raeisi, K and Khazaei, M and Vaquero, L and Bruña, R and Oppermann, H and Bertollo, M and Filho, E and Zappasodi, F and Comani, S},
title = {An ecological study protocol for the multimodal investigation of the neurophysiological underpinnings of dyadic joint action.},
journal = {Frontiers in human neuroscience},
volume = {17},
number = {},
pages = {1305331},
pmid = {38125713},
issn = {1662-5161},
abstract = {A novel multimodal experimental setup and dyadic study protocol were designed to investigate the neurophysiological underpinnings of joint action through the synchronous acquisition of EEG, ECG, EMG, respiration and kinematic data from two individuals engaged in ecologic and naturalistic cooperative and competitive joint actions involving face-to-face real-time and real-space coordinated full body movements. Such studies are still missing because of difficulties encountered in recording reliable neurophysiological signals during gross body movements, in synchronizing multiple devices, and in defining suitable study protocols. The multimodal experimental setup includes the synchronous recording of EEG, ECG, EMG, respiration and kinematic signals of both individuals via two EEG amplifiers and a motion capture system that are synchronized via a single-board microcomputer and custom Python scripts. EEG is recorded using new dry sports electrode caps. The novel study protocol is designed to best exploit the multimodal data acquisitions. Table tennis is the dyadic motor task: it allows naturalistic and face-to-face interpersonal interactions, free in-time and in-space full body movement coordination, cooperative and competitive joint actions, and two task difficulty levels to mimic changing external conditions. Recording conditions-including minimum table tennis rally duration, sampling rate of kinematic data, total duration of neurophysiological recordings-were defined according to the requirements of a multilevel analytical approach including a neural level (hyperbrain functional connectivity, Graph Theoretical measures and Microstate analysis), a cognitive-behavioral level (integrated analysis of neural and kinematic data), and a social level (extending Network Physiology to neurophysiological data recorded from two interacting individuals). Four practical tests for table tennis skills were defined to select the study population, permitting to skill-match the dyad members and to form two groups of higher and lower skilled dyads to explore the influence of skill level on joint action performance. Psychometric instruments are included to assess personality traits and support interpretation of results. Studying joint action with our proposed protocol can advance the understanding of the neurophysiological mechanisms sustaining daily life joint actions and could help defining systems to predict cooperative or competitive behaviors before being overtly expressed, particularly useful in real-life contexts where social behavior is a main feature.},
}
@article {pmid38116500,
year = {2023},
author = {Ji, JS and Xia, Y and Liu, L and Zhou, W and Chen, R and Dong, G and Hu, Q and Jiang, J and Kan, H and Li, T and Li, Y and Liu, Q and Liu, Y and Long, Y and Lv, Y and Ma, J and Ma, Y and Pelin, K and Shi, X and Tong, S and Xie, Y and Xu, L and Yuan, C and Zeng, H and Zhao, B and Zheng, G and Liang, W and Chan, M and Huang, C},
title = {China's public health initiatives for climate change adaptation.},
journal = {The Lancet regional health. Western Pacific},
volume = {40},
number = {},
pages = {100965},
pmid = {38116500},
issn = {2666-6065},
abstract = {China's health gains over the past decades face potential reversals if climate change adaptation is not prioritized. China's temperature rise surpasses the global average due to urban heat islands and ecological changes, and demands urgent actions to safeguard public health. Effective adaptation need to consider China's urbanization trends, underlying non-communicable diseases, an aging population, and future pandemic threats. Climate change adaptation initiatives and strategies include urban green space, healthy indoor environments, spatial planning for cities, advance location-specific early warning systems for extreme weather events, and a holistic approach for linking carbon neutrality to health co-benefits. Innovation and technology uptake is a crucial opportunity. China's successful climate adaptation can foster international collaboration regionally and beyond.},
}
@article {pmid38114459,
year = {2023},
author = {Novella-Fernandez, R and Brandl, R and Pinkert, S and Zeuss, D and Hof, C},
title = {Seasonal variation in dragonfly assemblage colouration suggests a link between thermal melanism and phenology.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {8427},
pmid = {38114459},
issn = {2041-1723},
mesh = {Animals ; Seasons ; *Odonata ; Climate ; Temperature ; Insecta ; Climate Change ; },
abstract = {Phenology, the seasonal timing of life events, is an essential component of diversity patterns. However, the mechanisms involved are complex and understudied. Body colour may be an important factor, because dark-bodied species absorb more solar radiation, which is predicted by the Thermal Melanism Hypothesis to enable them to thermoregulate successfully in cooler temperatures. Here we show that colour lightness of dragonfly assemblages varies in response to seasonal changes in solar radiation, with darker early- and late-season assemblages and lighter mid-season assemblages. This finding suggests a link between colour-based thermoregulation and insect phenology. We also show that the phenological pattern of dragonfly colour lightness advanced over the last decades. We suggest that changing seasonal temperature patterns due to global warming together with the static nature of solar radiation may drive dragonfly flight periods to suboptimal seasonal conditions. Our findings open a research avenue for a more mechanistic understanding of phenology and spatio-phenological impacts of climate warming on insects.},
}
@article {pmid38114230,
year = {2023},
author = {Wu, TF and Deng, J and Wang, X and Liu, HQ and Teng, YX and Ma, ZG and Wu, MH and Huang, WZ and Cao, H and Zhang, Y},
title = {[Textual research on Bungarus Parvus].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {22},
pages = {6234-6248},
doi = {10.19540/j.cnki.cjcmm.20230708.101},
pmid = {38114230},
issn = {1001-5302},
mesh = {Animals ; *Bungarus ; Snakes ; China ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal ; },
abstract = {Bungarus Parvus, a precious animal Chinese medicinal material used in clinical practice, is believed to be first recorded in Ying Pian Xin Can published in 1936. This study was carried out to analyze the names, geographical distribution, morphological characteristics, ecological habits, poisonousness, and medicinal parts by consulting ancient Chinese medical books and local chronicles, Chinese Pharmacopeia, different processing standards of trditional Chinese medicine(TCM) decoction pieces, and modern literatures. The results showed that the earliest medicinal record of Bungarus Parvus was traced to 1894. In 1930, this medicinal material was used in the formulation of Annao Pills. The original animal, Bungarus multicinctus, was recorded by the name of "Bojijia" in 1521. The morphological characteristics, ecological habits, and poisonousness of the original animal are the same in ancient and modern records. The geographical distribution is similar between the ancient records and modern documents such as China Medicinal Animal Fauna. The dried body of young B. multicinctus is used as Bungarus Parvus, which lack detailed references. As a matter of fact, it is still inconclusive whether there are differences between young snakes and adult snakes in terms of active ingredients, pharmacological effects, and clinical applications. This study clarified the medicinal history and present situation of Bungarus Parvus. On the basis of the results, it is suggested that systematic comparison on young and adult B. multicinctus should be carried out to provide references for revising the medicinal parts of B. multicinctus.},
}
@article {pmid38113992,
year = {2024},
author = {Hussain, A and Maitra, J and Saifi, A and Ahmed, S and Ahmed, J and Shrestha, NK and Qureshi, F and Kamyab, H and Chelliapan, S and Yusuf, M},
title = {A sustainable approach for fluoride treatment using coconut fiber cellulose as an adsorbent.},
journal = {Environmental research},
volume = {244},
number = {},
pages = {117952},
doi = {10.1016/j.envres.2023.117952},
pmid = {38113992},
issn = {1096-0953},
mesh = {Fluorides ; Cellulose ; *Drinking Water ; Cocos ; Fluoride Treatment ; Kinetics ; *Water Pollutants, Chemical/analysis ; *Water Purification/methods ; Hydrogen-Ion Concentration ; Adsorption ; },
abstract = {In developing countries like India, an economically viable and ecologically approachable strategy is required to safeguard the drinking water. Excessive fluoride intake through drinking water can lead to dental fluorosis, skeletal fluorosis, or both. The present study has been under with an objective to investigate the feasibility of using cellulose derived from coconut fiber as an adsorbent under varying pH conditions for fluoride elimination from water. The assessment of equilibrium concentration of metal ions using adsorption isotherms is an integral part of the study. This present finding indicates the considerable effect of variation of adsorbent dosages on the fluoride removal efficiency under constant temperature conditions of 25 ± 2 °C with a contact period of 24 h. It is pertinent to mention that maximum adsorption of 88% has been observed with a pH value of 6 with 6 h time duration with fluoride dosage of 50 mg/L. The equilibrium concentration dwindled to 0.4 mg/L at fluoride concentration of 20 mg/L. The Langmuir model designates the adsorption capacity value of 2.15 mg/L with initial fluoride concentration of 0.21 mg/g with R[2] value of 0.660. Similarly, the adsorption capacity using Freundlich isotherms is found to be 0.58 L/g and 0.59 L/g with fluoride concentration of 1.84 mg/L and 2.15 mg/L respectively. The results from the present study confirm that coconut fiber possesses appropriate sorption capabilities of fluoride ion but is a pH dependent phenomenon. The outcomes of the study indicate the possible use of cellulose extracted from waste coconut fiber as a low-cost fluoride adsorbent. The present study can be well implemented on real scale systems as it will be beneficial economically as well as environmentally.},
}
@article {pmid38111463,
year = {2024},
author = {Li, C and Gillings, MR and Zhang, C and Chen, Q and Zhu, D and Wang, J and Zhao, K and Xu, Q and Leung, PH and Li, X and Liu, J and Jin, L},
title = {Ecology and risks of the global plastisphere as a newly expanding microbial habitat.},
journal = {Innovation (Cambridge (Mass.))},
volume = {5},
number = {1},
pages = {100543},
pmid = {38111463},
issn = {2666-6758},
abstract = {Plastic offers a new niche for microorganisms, the plastisphere. The ever-increasing emission of plastic waste makes it critical to understand the microbial ecology of the plastisphere and associated effects. Here, we present a global fingerprint of the plastisphere, analyzing samples collected from freshwater, seawater, and terrestrial ecosystems. The plastisphere assembles a distinct microbial community that has a clearly higher heterogeneity and a more deterministically dominated assembly compared to natural habitats. New coexistence patterns-loose and fragile networks with mostly specialist linkages among microorganisms that are rarely found in natural habitats-are seen in the plastisphere. Plastisphere microbiomes generally have a great potential to metabolize organic compounds, which could accelerate carbon turnover. Microorganisms involved in the nitrogen cycle are also altered in the plastisphere, especially in freshwater plastispheres, where a high abundance of denitrifiers may increase the release of nitrite (aquatic toxicant) and nitrous oxide (greenhouse gas). Enrichment of animal, plant, and human pathogens means that the plastisphere could become an increasingly mobile reservoir of harmful microorganisms. Our findings highlight that if the trajectory of plastic emissions is not reversed, the expanding plastisphere could pose critical planetary health challenges.},
}
@article {pmid38111050,
year = {2023},
author = {Cochetel, N and Minio, A and Guarracino, A and Garcia, JF and Figueroa-Balderas, R and Massonnet, M and Kasuga, T and Londo, JP and Garrison, E and Gaut, BS and Cantu, D},
title = {A super-pangenome of the North American wild grape species.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {290},
pmid = {38111050},
issn = {1474-760X},
support = {1741627//National Science Foundation/ ; },
mesh = {*Genome, Plant ; *Vitis/genetics ; Plant Breeding ; Genomics ; North America ; },
abstract = {BACKGROUND: Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations.<br><br>RESULTS: Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes.<br><br>CONCLUSIONS: This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.},
}
@article {pmid38110096,
year = {2024},
author = {Chatterjee, D and Singh, PK and Singh, D and Singh, VP},
title = {A novel partitioning of gross primary production and water use efficiency for sustaining water and food security using Budyko hypothesis.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {169283},
doi = {10.1016/j.scitotenv.2023.169283},
pmid = {38110096},
issn = {1879-1026},
mesh = {*Water ; *Hydrology ; Agriculture ; Rivers ; Food Security ; },
abstract = {This study coupled the green water and blue water accounting with the existing standard Budyko framework and Fu's 1-parameter Budyko framework to diagnose the basin hydrological behavior. Both Budyko frameworks were employed to determine green water consumption (ETGreen) and blue water consumption (ETBlue) which, in turn, were used to map the blue water index (BWI) hotspots and green water index (GWI) bright spots. The relative contributions of green water and blue water were quantified for sustaining water and food security. A new methodology is proposed using BWI and GWI for partitioning the Gross Primary Production (GPP) and Water Use Efficiency (WUE) into GPPBlue, GPPGreen and WUEBlue and WUEGreen. The methodology was applied to five sub-basins of the Central Godavari River Basin (CGRB): Purna, Dhalegaon, GR Bridge, Yeli and Delta. Results showed that all five basins exhibited larger deviations from the theoretical Budyko curve of Fu's 1-parameter Budyko framework than did the standard Budyko framework and the Dhalegaon basin showed the largest deviations. The partitioning of GPP and WUE by the proposed methodology showed that the proportion of GPPGreen to the total GPP was much higher than that of the GPPBlue. Similarly, the proportion of WUEGreen to WUE was more than that of WUEBlue. The mapping of GPPBlue and GPPGreen, and WUEBlue and WUEGreen showed that the Delta and Yeli basins had the highest values of both GPPGreen &amp; GPPBlue and WUEBlue and WUEGreen (bright spot basins) and the Dhalegaon and parts of GR Bridge basin had the lowest values (hot spot basins). The proposed partitioning of GPP and WUE will help identify the relative contributions of green water and blue water (for managing agricultural waters) and formulate agronomical and engineering practices for stakeholders and policy makers for increasing the overall WUE and GPP to sustain water and food security.},
}
@article {pmid38108929,
year = {2024},
author = {Liu, M and Wang, L and Yu, Q and Song, J and Zhu, L and Jia, KH and Qin, X},
title = {The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii.},
journal = {Photosynthesis research},
volume = {161},
number = {1-2},
pages = {65-78},
pmid = {38108929},
issn = {1573-5079},
mesh = {*Chlamydomonas reinhardtii/genetics/metabolism/radiation effects ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Gene Regulatory Networks ; *Green Light ; *Photosynthesis/genetics ; Pigments, Biological/metabolism ; *RNA, Long Noncoding/genetics/metabolism ; Transcriptome ; },
abstract = {The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear. In this study, we exposed the unicellular green alga Chlamydomonas reinhardtii to green light and analyzed the dynamics of transcriptome changes. Based on the whole transcriptome data from C. reinhardtii, a total of 9974 differentially expressed genes (DEGs) were identified under green light. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were mainly related to "carboxylic acid metabolic process," "enzyme activity," "carbon metabolism," and "photosynthesis and other processes." At the same time, 253 differentially expressed long non-coding RNAs (DELs) were characterized as green light responsive. We also made a detailed analysis of the responses of photosynthesis- and pigment synthesis-related genes in C. reinhardtii to green light and found that these genes exhibited obvious dynamic expression. Lastly, we constructed a co-expression regulatory network, comprising 49 long non-coding RNAs (lncRNAs) and 20 photosynthesis and pigment related genes, of which 9 mRNAs were also the predicted trans/cis-targets of 8 lncRNAs, these results suggested that lncRNAs may affect the expression of mRNAs related to photosynthesis and pigment synthesis. Our findings give a preliminary explanation of the response mechanism of C. reinhardtii to green light at the transcriptional level.},
}
@article {pmid38105177,
year = {2023},
author = {Aziz, MA and Hassan, M and Ullah, A and Ullah, Z and Sõukand, R and Pieroni, A},
title = {Keeping their own and integrating the other: medicinal plant use among Ormurs and Pathans in South Waziristan, Pakistan.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {19},
number = {1},
pages = {62},
pmid = {38105177},
issn = {1746-4269},
mesh = {Phytotherapy ; *Plants, Medicinal ; South Asian People ; Medicine, Traditional/methods ; Ethnobotany ; Humans ; Pakistan ; },
abstract = {BACKGROUND: In multicultural societies, traditional knowledge among minorities faces several challenges. Minority groups often face difficult situations living in specific peripheral geographies and striving to retain their biocultural heritage, including medicinal plant knowledge and practices. Folk medicinal plant knowledge is a dynamic eco-cultural complex influenced by various environmental, socio-cultural, and political factors. Examining medicinal plant knowledge among minorities has been an increasingly popular topic in cross-cultural ethnobiology. It also helps understand the dynamics of local/traditional ecological knowledge (LEK/TEK) change within a given community. The current study was designed to investigate the status of medicinal plant knowledge among two linguistic groups, i.e. Ormurs and Pathans, living in a remote valley of West Pakistan.<br><br>METHODS: We recruited 70 male study participants from the studied groups for semi-structured interviews to record the medicinal plant use of their communities. Data were compared among the two studied communities using the stacked charts employing the presence or absence of data with Past 4.03 and Venn diagrams. Use reports (URs) were counted for each recorded taxon.<br><br>RESULTS AND DISCUSSION: A total of seventy-four medicinal plants were quoted as used as ethnomedicines by the researched communities. Most of the reported plants were used to treat digestive and liver problems. The cross-cultural comparison revealed a considerable homogeneity of medicinal plant knowledge (the two groups commonly used more than seventy plants); however, comparing uses recorded for the widely utilised medicinal plants showed numerous idiosyncratic uses among Ormurs but very few among Pathans. Ormurs reported a higher number of cultivated, wild, and imported plant uses than did Pathans. These results indicate that, compared to Pathans, the Ormur linguistic minority retain more folk medicinal plant knowledge, which may be explained by the fact that they have incorporated different folk remedies: their "own knowledge" plus that of Pathans, with whom they have lived together for centuries. Moreover, the local plant nomenclature among Ormurs was highly affected by the plant nomenclature of Pathans.<br><br>CONCLUSION: The current study revealed that living together for a few centuries has not implied sharing plant knowledge (as the Pathans do not seem to have learnt from the Ormurs) or, in other words, that plant knowledge exchanges have been unidirectional. The findings show that the Pashto dominant culture may have possibly put pressure on the minority groups and affected local plant-centred cultural practices, as we see in the case of local plant nomenclature hybridisation among Omuri speakers. Hence, it is imperative to employ diverse educational strategies to revitalise the decline of medicinal plant knowledge in the studied communities, especially among Ormurs, who need more attention as they face more challenges than the other group. Locally based strategies should be devised to restore the fading connection with nature, which will be advantageous for revitalising plant knowledge.},
}
@article {pmid38105079,
year = {2024},
author = {Liu, C and How, ZT and Ju, Y and Feng, L and Ren, X and Gamal El-Din, M},
title = {Experimental and theoretical insight into carbamazepine degradation by chlorine-based advanced oxidation processes: Efficiency, energy consumption, mechanism and DBPs formation.},
journal = {Journal of environmental sciences (China)},
volume = {139},
number = {},
pages = {72-83},
doi = {10.1016/j.jes.2023.05.012},
pmid = {38105079},
issn = {1001-0742},
mesh = {Chlorine ; Disinfection ; *Water Purification ; *Water Pollutants, Chemical/analysis ; Carbamazepine ; Oxidation-Reduction ; Halogenation ; Chlorides ; Ultraviolet Rays ; },
abstract = {Chlorine has been widely used in different advanced oxidation processes (AOPs) for micropollutants removal. In this study, different chlorine-based AOPs, namely medium pressure (MP) UV/chlorine, low pressure (LP) UV/chlorine, and in-situ chlorination, were compared for carbamazepine (CBZ) removal efficiency, energy consumption, and disinfection by-products (DBPs) formation. All three processes could achieve nearly 100% CBZ removal, while the reaction time needed by in-situ chlorination was double the time required by UV/chlorine processes. The energy consumed per magnitude of CBZ removed (EE/O) of MP UV/chlorine was 13 times higher than that of LP UV/chlorine, and relative to that of in-situ chlorination process. Accordingly, MP and LP UV/chlorine processes generated one to two orders of magnitude more hydroxyl radicals ([•]OH) and reactive chlorine species (RCS) than in-situ chlorination. Besides, RCS were the dominant reactive species, contributing to 78.3%, 75.6%, and 71.6% of CBZ removal in MP, LP UV/chlorine, and in-situ chlorination, respectively. According to the Gibbs free energy barriers between CBZ and RCS/[•]OH calculated based on density functional theory (DFT), RCS had more reaction routes with CBZ and showed lower energy barrier in the main CBZ degradation pathways like epoxidation and formation of iminostilbene. When applied to secondary wastewater effluent, UV/chlorine and in-situ chlorination produced overall DBPs ranging from 104.77 to 135.41 µg/L. However, the production of chlorate during UV/chlorine processes was 15 times higher than that during in-situ chlorination.},
}
@article {pmid38104847,
year = {2024},
author = {Khatri-Chhetri, U and Banerjee, S and Thompson, KA and Quideau, SA and Boyce, MS and Bork, EW and Carlyle, CN},
title = {Cattle grazing management affects soil microbial diversity and community network complexity in the Northern Great Plains.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {169353},
doi = {10.1016/j.scitotenv.2023.169353},
pmid = {38104847},
issn = {1879-1026},
mesh = {Animals ; Cattle ; Humans ; *Ecosystem ; Soil ; Grassland ; Soil Microbiology ; Community Networks ; Canada ; *Microbiota ; Bacteria ; },
abstract = {Soil microbial communities play a vital role in the biogeochemical cycling and ecological functioning of grassland, but may be affected by common land uses such as cattle grazing. Changes in microbial diversity and network complexity can affect key ecosystem functions such as nutrient cycling. However, it is not well known how microbial diversity and network complexity respond to grazing in the Northern Great Plains. Consequently, it is important to understand whether variation in grazing management alters the diversity and complexity of grassland microbial communities. We compared the effect of intensive adaptive multi-paddock (AMP) grazing and conventional grazing practices on soil microbial communities using 16S/ITS amplicon sequencing. Samples were collected from grasslands in 13 AMP ranches and 13 neighboring, conventional ranches located across the Canadian prairies. We found that AMP grazing increased fungal diversity and evenness, and led to more complex microbial associations. Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes were keystone taxa associated with AMP grazing, while Actinobacteria, Acidobacteria, Proteobacteria, and Armatimonadetes were keystone taxa under conventional grazing. Besides overall grazing treatment effects, specific grazing metrics like cattle stocking rate and rest-to-grazing ratio affected microbial richness and diversity. Bacterial and fungal richness increased with elevated stocking rate, and fungal richness and diversity increased directly with the rest-to-grazing ratio. These results suggest that AMP grazing may improve ecosystem by enhancing fungal diversity and increasing microbial network complexity and connectivity.},
}
@article {pmid38102035,
year = {2024},
author = {Del Campo, J and Carlos-Oliveira, M and Čepička, I and Hehenberger, E and Horák, A and Karnkowska, A and Kolisko, M and Lara, E and Lukeš, J and Pánek, T and Piwosz, K and Richter, DJ and Škaloud, P and Sutak, R and Tachezy, J and Hampl, V},
title = {The protist cultural renaissance.},
journal = {Trends in microbiology},
volume = {32},
number = {2},
pages = {128-131},
doi = {10.1016/j.tim.2023.11.010},
pmid = {38102035},
issn = {1878-4380},
mesh = {*Eukaryota/genetics ; Multiomics ; },
abstract = {Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.},
}
@article {pmid38100404,
year = {2023},
author = {Biswas, A and Kumari, A and Gaikwad, DS and Pandey, DK},
title = {Revolutionizing Biological Science: The Synergy of Genomics in Health, Bioinformatics, Agriculture, and Artificial Intelligence.},
journal = {Omics : a journal of integrative biology},
volume = {27},
number = {12},
pages = {550-569},
doi = {10.1089/omi.2023.0197},
pmid = {38100404},
issn = {1557-8100},
mesh = {Animals ; Humans ; *Artificial Intelligence ; *Ecosystem ; Genomics ; Computational Biology ; Agriculture ; },
abstract = {With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary of human and ecosystem health has been deeply challenged. The interdependence of human and nonhuman animal health is increasingly acknowledged and paving the way for new frontiers in integrative biology. The convergence of genomics in health, bioinformatics, agriculture, and artificial intelligence (AI) has ushered in a new era of possibilities and applications. However, the sheer volume of genomic/multiomics big data generated also presents formidable sociotechnical challenges in extracting meaningful biological, planetary health and ecological insights. Over the past few years, AI-guided bioinformatics has emerged as a powerful tool for managing, analyzing, and interpreting complex biological datasets. The advances in AI, particularly in machine learning and deep learning, have been transforming the fields of genomics, planetary health, and agriculture. This article aims to unpack and explore the formidable range of possibilities and challenges that result from such transdisciplinary integration, and emphasizes its radically transformative potential for human and ecosystem health. The integration of these disciplines is also driving significant advancements in precision medicine and personalized health care. This presents an unprecedented opportunity to deepen our understanding of complex biological systems and advance the well-being of all life in planetary ecosystems. Notwithstanding in mind its sociotechnical, ethical, and critical policy challenges, the integration of genomics, multiomics, planetary health, and agriculture with AI-guided bioinformatics opens up vast opportunities for transnational collaborative efforts, data sharing, analysis, valorization, and interdisciplinary innovations in life sciences and integrative biology.},
}
@article {pmid38095449,
year = {2024},
author = {Arehart, CH and Sterrett, JD and Garris, RL and Quispe-Pilco, RE and Gignoux, CR and Evans, LM and Stanislawski, MA},
title = {Poly-omic risk scores predict inflammatory bowel disease diagnosis.},
journal = {mSystems},
volume = {9},
number = {1},
pages = {e0067723},
pmid = {38095449},
issn = {2379-5077},
support = {K01 HL157658/HL/NHLBI NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/diagnosis ; Metagenomics/methods ; Phenotype ; *Microbiota ; Risk Factors ; },
abstract = {Inflammatory bowel disease (IBD) is characterized by complex etiology and a disrupted colonic ecosystem. We provide a framework for the analysis of multi-omic data, which we apply to study the gut ecosystem in IBD. Specifically, we train and validate models using data on the metagenome, metatranscriptome, virome, and metabolome from the Human Microbiome Project 2 IBD multi-omic database, with 1,785 repeated samples from 130 individuals (103 cases and 27 controls). After splitting the participants into training and testing groups, we used mixed-effects least absolute shrinkage and selection operator regression to select features for each omic. These features, with demographic covariates, were used to generate separate single-omic prediction scores. All four single-omic scores were then combined into a final regression to assess the relative importance of the individual omics and the predictive benefits when considered together. We identified several species, pathways, and metabolites known to be associated with IBD risk, and we explored the connections between data sets. Individually, metabolomic and viromic scores were more predictive than metagenomics or metatranscriptomics, and when all four scores were combined, we predicted disease diagnosis with a Nagelkerke's R[2] of 0.46 and an area under the curve of 0.80 (95% confidence interval: 0.63, 0.98). Our work supports that some single-omic models for complex traits are more predictive than others, that incorporating multiple omic data sets may improve prediction, and that each omic data type provides a combination of unique and redundant information. This modeling framework can be extended to other complex traits and multi-omic data sets.IMPORTANCEComplex traits are characterized by many biological and environmental factors, such that multi-omic data sets are well-positioned to help us understand their underlying etiologies. We applied a prediction framework across multiple omics (metagenomics, metatranscriptomics, metabolomics, and viromics) from the gut ecosystem to predict inflammatory bowel disease (IBD) diagnosis. The predicted scores from our models highlighted key features and allowed us to compare the relative utility of each omic data set in single-omic versus multi-omic models. Our results emphasized the importance of metabolomics and viromics over metagenomics and metatranscriptomics for predicting IBD status. The greater predictive capability of metabolomics and viromics is likely because these omics serve as markers of lifestyle factors such as diet. This study provides a modeling framework for multi-omic data, and our results show the utility of combining multiple omic data types to disentangle complex disease etiologies and biological signatures.},
}
@article {pmid38093346,
year = {2023},
author = {Masroni, MSB and Lee, KW and Lee, VKM and Ng, SB and Law, CT and Poon, KS and Lee, BT and Liu, Z and Tan, YP and Chng, WL and Tucker, S and Ngo, LS and Yip, GWC and Nga, ME and Hue, SSS and Putti, TC and Bay, BH and Lin, Q and Zhou, L and Hartman, M and Loh, TP and Lakshmanan, M and Lee, SY and Tergaonkar, V and Chua, H and Lee, AVH and Yeo, EYM and Li, MH and Chang, CF and Kee, Z and Tan, KM and Tan, SY and Koay, ES and Archetti, M and Leong, SM},
title = {Dynamic altruistic cooperation within breast tumors.},
journal = {Molecular cancer},
volume = {22},
number = {1},
pages = {206},
pmid = {38093346},
issn = {1476-4598},
support = {NUS Postgraduate Research Scholarships//National University of Singapore/ ; NUS Postgraduate Research Scholarships//National University of Singapore/ ; Department of Pathology Startup Grants//National University of Singapore/ ; Department of Pathology Startup Grants//National University of Singapore/ ; T1- NUHS Joint Grant Call FY17 - 2nd call-10//Ministry of Education - Singapore/ ; NMRC-NIG NMRC/CNIG/1119/2014//National Medical Research Council/ ; A*STAR-SERC Public Service Fund 1121202021//Agency for Science, Technology and Research/ ; NUHS Bridging fund//National University Health System/ ; },
mesh = {Humans ; Female ; Altruism ; Phosphatidylinositol 3-Kinases ; *MicroRNAs/genetics ; *Breast Neoplasms/genetics ; },
abstract = {BACKGROUND: Social behaviors such as altruism, where one self-sacrifices for collective benefits, critically influence an organism's survival and responses to the environment. Such behaviors are widely exemplified in nature but have been underexplored in cancer cells which are conventionally seen as selfish competitive players. This multidisciplinary study explores altruism and its mechanism in breast cancer cells and its contribution to chemoresistance.<br><br>METHODS: MicroRNA profiling was performed on circulating tumor cells collected from the blood of treated breast cancer patients. Cancer cell lines ectopically expressing candidate miRNA were used in co-culture experiments and treated with docetaxel. Ecological parameters like relative survival and relative fitness were assessed using flow cytometry. Functional studies and characterization performed in vitro and in vivo include proliferation, iTRAQ-mass spectrometry, RNA sequencing, inhibition by small molecules and antibodies, siRNA knockdown, CRISPR/dCas9 inhibition and fluorescence imaging of promoter reporter-expressing cells. Mathematical modeling based on evolutionary game theory was performed to simulate spatial organization of cancer cells.<br><br>RESULTS: Opposing cancer processes underlie altruism: an oncogenic process involving secretion of IGFBP2 and CCL28 by the altruists to induce survival benefits in neighboring cells under taxane exposure, and a self-sacrificial tumor suppressive process impeding proliferation of altruists via cell cycle arrest. Both processes are regulated concurrently in the altruists by miR-125b, via differential NF-&#x3ba;B signaling specifically through IKK&#x3b2;. Altruistic cells persist in the tumor despite their self-sacrifice, as they can regenerate epigenetically from non-altruists via a KLF2/PCAF-mediated mechanism. The altruists maintain a sparse spatial organization by inhibiting surrounding cells from adopting the altruistic fate via a lateral inhibition mechanism involving a GAB1-PI3K-AKT-miR-125b signaling circuit.<br><br>CONCLUSIONS: Our data reveal molecular mechanisms underlying manifestation, persistence and spatial spread of cancer cell altruism. A minor population behave altruistically at a cost to itself producing a collective benefit for the tumor, suggesting tumors to be dynamic social systems governed by the same rules of cooperation in social organisms. Understanding cancer cell altruism may lead to more holistic models of tumor evolution and drug response, as well as therapeutic paradigms that account for social interactions. Cancer cells constitute tractable experimental models for fields beyond oncology, like evolutionary ecology and game theory.},
}
@article {pmid38093003,
year = {2023},
author = {Reis, ALM and Rapadas, M and Hammond, JM and Gamaarachchi, H and Stevanovski, I and Ayuputeri Kumaheri, M and Chintalaphani, SR and Dissanayake, DSB and Siggs, OM and Hewitt, AW and Llamas, B and Brown, A and Baynam, G and Mann, GJ and McMorran, BJ and Easteal, S and Hermes, A and Jenkins, MR and , and Patel, HR and Deveson, IW},
title = {The landscape of genomic structural variation in Indigenous Australians.},
journal = {Nature},
volume = {624},
number = {7992},
pages = {602-610},
pmid = {38093003},
issn = {1476-4687},
mesh = {Microsatellite Repeats/genetics ; *Australian Aboriginal and Torres Strait Islander Peoples/genetics ; DNA Copy Number Variations/genetics ; *Genomic Structural Variation/genetics ; *Genome, Human/genetics ; Datasets as Topic ; Genetics, Medical ; Australia/ethnology ; Interspersed Repetitive Sequences/genetics ; Australasian People ; Genetic Loci/genetics ; Alleles ; INDEL Mutation/genetics ; Humans ; Genomics ; },
abstract = {Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets[1-3]. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing[4] to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci[5], uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.},
}
@article {pmid38085368,
year = {2023},
author = {Ilyas, MZ and Sa, KJ and Ali, MW and Lee, JK},
title = {Toxic effects of lead on plants: integrating multi-omics with bioinformatics to develop Pb-tolerant crops.},
journal = {Planta},
volume = {259},
number = {1},
pages = {18},
pmid = {38085368},
issn = {1432-2048},
mesh = {*Lead/toxicity ; Multiomics ; *Soil Pollutants/metabolism ; Crops, Agricultural/genetics/metabolism ; Computational Biology ; },
abstract = {Lead disrupts plant metabolic homeostasis and key structural elements. Utilizing modern biotechnology tools, it's feasible to develop Pb-tolerant varieties by discovering biological players regulating plant metabolic pathways under stress. Lead (Pb) has been used for a variety of purposes since antiquity despite its toxic nature. After arsenic, lead is the most hazardous heavy metal without any known beneficial role in the biological system. It is a crucial inorganic pollutant that affects plant biochemical and morpho-physiological attributes. Lead toxicity harms plants throughout their life cycle and the extent of damage depends on the concentration and duration of exposure. Higher levels of lead exposure disrupt numerous key metabolic activities of plants including oxygen-evolving complex, organelles integrity, photosystem II connectivity, and electron transport chain. This review summarizes the detrimental effects of lead toxicity on seed germination, crop growth, and yield, oxidative and ultra-structural alterations, as well as nutrient absorption, transport, and assimilation. Further, it discusses the Pb-induced toxic modulation of stomatal conductance, photosynthesis, respiration, metabolic-enzymatic activity, osmolytes accumulation, and antioxidant activity. It is a comprehensive review that reports on omics-based studies along with morpho-physiological and biochemical modifications caused by lead stress. With advances in DNA sequencing technologies, genomics and transcriptomics are gradually becoming popular for studying Pb stress effects in plants. Proteomics and metabolomics are still underrated and there is a scarcity of published data, and this review highlights both their technical and research gaps. Besides, there is also a discussion on how the integration of omics with bioinformatics and the use of the latest biotechnological tools can aid in developing Pb-tolerant crops. The review concludes with core challenges and research directions that need to be addressed soon.},
}
@article {pmid38085351,
year = {2024},
author = {Paul, T and Aggarwal, A and Behera, SK and Meher, SK and Gupta, S and Baskaran, D and Rene, ER and Pakshirajan, K and Pugazhenthi, G},
title = {Neuro-fuzzy modelling of a continuous stirred tank bioreactor with ceramic membrane technology for treating petroleum refinery effluent: a case study from Assam, India.},
journal = {Bioprocess and biosystems engineering},
volume = {47},
number = {1},
pages = {91-103},
pmid = {38085351},
issn = {1615-7605},
mesh = {*Artificial Intelligence ; Waste Disposal, Fluid/methods ; *Petroleum ; Bayes Theorem ; Bioreactors ; Ceramics ; Lipids ; },
abstract = {A continuous stirred tank bioreactor (CSTB) with cell recycling combined with ceramic membrane technology and inoculated with Rhodococcus opacus PD630 was employed to treat petroleum refinery wastewater for simultaneous chemical oxygen demand (COD) removal and lipid production from the retentate obtained during wastewater treatment. In the present study, the COD removal efficiency (CODRE) (%) and lipid concentration (g/L) were predicted using two artificial intelligence models, i.e., an artificial neural network (ANN) and a neuro-fuzzy neural network (NF-NN) with a network topology of 6-25-2 being the best for NF-NN. The results revealed the superiority of NF-NN over ANN in terms of determination coefficient (R[2]), root mean square error (RMSE), and mean absolute percentage error (MAPE). Three learning algorithms were tested with NF-NN; among them, the Bayesian regularization backpropagation (BR-BP) outperformed others. The sensitivity analysis revealed that, if solid retention time and biomass concentrations were maintained between 35 and 75 h and 3.0 g/L and 3.5 g/L, respectively, high CODRE (93%) and lipid concentration (2.8 g/L) could be obtained consistently.},
}
@article {pmid38084497,
year = {2024},
author = {Dalla Costa, G and Nos, C and Zabalza, A and Buron, M and Magyari, M and Sellebjerg, F and Guerrero, AI and Roselli, L and La Porta, ML and Martinis, M and Bailon, R and Kontaxis, S and Laporta, E and Garcia, E and Pokorny, FB and Schuller, BW and Folarin, A and Stewart, C and Leocani, L and Vairavan, S and Cummins, N and Dobson, R and Hotopf, M and Narayan, V and Montalban, X and Sorensen, PS and Comi, G},
title = {A wearable device perspective on the standard definitions of disability progression in multiple sclerosis.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {30},
number = {1},
pages = {103-112},
doi = {10.1177/13524585231214362},
pmid = {38084497},
issn = {1477-0970},
mesh = {Female ; Humans ; Male ; Middle Aged ; Disability Evaluation ; *Disabled Persons ; *Multiple Sclerosis/diagnosis ; Walk Test ; Walking/physiology ; *Wearable Electronic Devices ; Adult ; },
abstract = {INTRODUCTION: Multiple sclerosis (MS) is a leading cause of disability among young adults, but standard clinical scales may not accurately detect subtle changes in disability occurring between visits. This study aims to explore whether wearable device data provides more granular and objective measures of disability progression in MS.<br><br>METHODS: Remote Assessment of Disease and Relapse in Central Nervous System Disorders (RADAR-CNS) is a longitudinal multicenter observational study in which 400 MS patients have been recruited since June 2018 and prospectively followed up for 24 months. Monitoring of patients included standard clinical visits with assessment of disability through use of the Expanded Disability Status Scale (EDSS), 6-minute walking test (6MWT) and timed 25-foot walk (T25FW), as well as remote monitoring through the use of a Fitbit.<br><br>RESULTS: Among the 306 patients who completed the study (mean age, 45.6 years; females 67%), confirmed disability progression defined by the EDSS was observed in 74 patients, who had approximately 1392 fewer daily steps than patients without disability progression. However, the decrease in the number of steps experienced over time by patients with EDSS progression and stable patients was not significantly different. Similar results were obtained with disability progression defined by the 6MWT and the T25FW.<br><br>CONCLUSION: The use of continuous activity monitoring holds great promise as a sensitive and ecologically valid measure of disability progression in MS.},
}
@article {pmid38079567,
year = {2023},
author = {Deng, CH and Naithani, S and Kumari, S and Cobo-Simón, I and Quezada-Rodríguez, EH and Skrabisova, M and Gladman, N and Correll, MJ and Sikiru, AB and Afuwape, OO and Marrano, A and Rebollo, I and Zhang, W and Jung, S},
title = {Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.},
journal = {Database : the journal of biological databases and curation},
volume = {2023},
number = {},
pages = {},
pmid = {38079567},
issn = {1758-0463},
support = {//National Science Foundation (NSF)/ ; 2126334//Research Coordination Network (RCN)/ ; //National Science Foundation (NSF)/ ; 2126334//Research Coordination Network (RCN)/ ; },
mesh = {*Big Data ; *Databases, Genetic ; Genotype ; Phenotype ; Plant Breeding ; },
abstract = {Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.},
}
@article {pmid38078767,
year = {2024},
author = {Smith, AB and Specker, JT and Hewlett, KK and Scoggins, TR and Knight, M and Lustig, AM and Li, Y and Evans, KM and Guo, Y and She, Q and Christopher, MW and Garrett, TJ and Moustafa, AM and Van Tyne, D and Prentice, BM and Zackular, JP},
title = {Liberation of host heme by Clostridioides difficile-mediated damage enhances Enterococcus faecalis fitness during infection.},
journal = {mBio},
volume = {15},
number = {1},
pages = {e0165623},
pmid = {38078767},
issn = {2150-7511},
support = {K22 AI137220/AI/NIAID NIH HHS/United States ; R21 AI164018/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; R03 AI168491/AI/NIAID NIH HHS/United States ; L40 AI147162/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Clostridioides difficile ; Enterococcus faecalis ; *Clostridium Infections/microbiology ; Bacteria ; *Gastrointestinal Microbiome ; },
abstract = {Clostridioides difficile and Enterococcus faecalis are two pathogens of great public health importance. Both bacteria colonize the human gastrointestinal tract where they are known to interact in ways that worsen disease outcomes. We show that the damage associated with C. difficile infection (CDI) releases nutrients that benefit E. faecalis. One particular nutrient, heme, allows E. faecalis to use oxygen to generate energy and grow better in the gut. Understanding the mechanisms of these interspecies interactions could inform therapeutic strategies for CDI.},
}
@article {pmid38078294,
year = {2023},
author = {Groom, Q and Dillen, M and Addink, W and Ariño, AHH and Bölling, C and Bonnet, P and Cecchi, L and Ellwood, ER and Figueira, R and Gagnier, PY and Grace, OM and Güntsch, A and Hardy, H and Huybrechts, P and Hyam, R and Joly, AAJ and Kommineni, VK and Larridon, I and Livermore, L and Lopes, RJ and Meeus, S and Miller, JA and Milleville, K and Panda, R and Pignal, M and Poelen, J and Ristevski, B and Robertson, T and Rufino, AC and Santos, J and Schermer, M and Scott, B and Seltmann, KC and Teixeira, H and Trekels, M and Gaikwad, J},
title = {Envisaging a global infrastructure to exploit the potential of digitised collections.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e109439},
pmid = {38078294},
issn = {1314-2828},
abstract = {Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in.},
}
@article {pmid38075858,
year = {2023},
author = {Marcos-Zambrano, LJ and López-Molina, VM and Bakir-Gungor, B and Frohme, M and Karaduzovic-Hadziabdic, K and Klammsteiner, T and Ibrahimi, E and Lahti, L and Loncar-Turukalo, T and Dhamo, X and Simeon, A and Nechyporenko, A and Pio, G and Przymus, P and Sampri, A and Trajkovik, V and Lacruz-Pleguezuelos, B and Aasmets, O and Araujo, R and Anagnostopoulos, I and Aydemir, &#xd6; and Berland, M and Calle, ML and Ceci, M and Duman, H and Gündoğdu, A and Havulinna, AS and Kaka Bra, KHN and Kalluci, E and Karav, S and Lode, D and Lopes, MB and May, P and Nap, B and Nedyalkova, M and Paciência, I and Pasic, L and Pujolassos, M and Shigdel, R and Susín, A and Thiele, I and Truică, CO and Wilmes, P and Yilmaz, E and Yousef, M and Claesson, MJ and Truu, J and Carrillo de Santa Pau, E},
title = {A toolbox of machine learning software to support microbiome analysis.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1250806},
pmid = {38075858},
issn = {1664-302X},
abstract = {The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis.},
}
@article {pmid38069903,
year = {2024},
author = {Mirchandani, CD and Shultz, AJ and Thomas, GWC and Smith, SJ and Baylis, M and Arnold, B and Corbett-Detig, R and Enbody, E and Sackton, TB},
title = {A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.},
journal = {Molecular biology and evolution},
volume = {41},
number = {1},
pages = {},
pmid = {38069903},
issn = {1537-1719},
mesh = {Animals ; *Software ; *Metagenomics ; Workflow ; Genomics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; },
abstract = {The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.},
}
@article {pmid38069227,
year = {2023},
author = {Wang, Z and Yadav, V and Chen, X and Zhang, S and Yuan, X and Li, H and Ma, J and Zhang, Y and Yang, J and Zhang, X and Wei, C},
title = {Multi-Omics Analysis Reveals Intricate Gene Networks Involved in Female Development in Melon.},
journal = {International journal of molecular sciences},
volume = {24},
number = {23},
pages = {},
pmid = {38069227},
issn = {1422-0067},
support = {No. 2023-JC-YB-199//National Natural Science Foundation of Shaanxi Province, China/ ; 2452022116//Northwest A&amp;F University/ ; Ylzy-sc-01//Key Research and Development Project of Yangling Seed Industry Innovation Center/ ; NGSB-2021-7//High-quality Development and Ecological Protection Science and Technology Innovation Project of Ningxia Academy of Agriculture and Forestry Sciences/ ; },
mesh = {*Cucurbitaceae ; Gene Regulatory Networks ; Multiomics ; Ethylenes/metabolism ; Indoleacetic Acids ; Gene Expression Regulation, Plant ; Fruit/metabolism ; },
abstract = {Sexual differentiation is an important developmental phenomenon in cucurbits that directly affects fruit yield. The natural existence of multiple flower types in melon offers an inclusive structure for studying the molecular basis of sexual differentiation. The current study aimed to identify and characterize the molecular network involved in sex determination and female development in melon. Male and female pools separated by the F2 segregated generation were used for sequencing. The comparative multi-omics data revealed 551 DAPs and 594 DEGs involved in multiple pathways of melon growth and development, and based on functional annotation and enrichment analysis, we summarized four biological process modules, including ethylene biosynthesis, flower organ development, plant hormone signaling, and ubiquitinated protein metabolism, that are related to female development. Furthermore, the detailed analysis of the female developmental regulatory pathway model of ethylene biosynthesis, signal transduction, and target gene regulation identified some important candidates that might have a crucial role in female development. Two CMTs ((cytosine-5)-methyltransferase), one AdoHS (adenosylhomocysteinase), four ACSs (1-aminocyclopropane-1-carboxylic acid synthase), three ACOs (ACC oxidase), two ARFs (auxin response factor), four ARPs (auxin-responsive protein), and six ERFs (Ethylene responsive factor) were identified based on various female developmental regulatory models. Our data offer new and valuable insights into female development and hold the potential to offer a deeper comprehension of sex differentiation mechanisms in melon.},
}
@article {pmid38061019,
year = {2024},
author = {Ganasegeran, K and Abdul Manaf, MR and Safian, N and Waller, LA and Abdul Maulud, KN and Mustapha, FI},
title = {GIS-Based Assessments of Neighborhood Food Environments and Chronic Conditions: An Overview of Methodologies.},
journal = {Annual review of public health},
volume = {45},
number = {1},
pages = {109-132},
doi = {10.1146/annurev-publhealth-101322-031206},
pmid = {38061019},
issn = {1545-2093},
mesh = {Humans ; *Geographic Information Systems ; *Residence Characteristics/statistics &amp; numerical data ; Chronic Disease/epidemiology ; Food Supply/statistics &amp; numerical data ; Spatial Analysis ; },
abstract = {The industrial revolution and urbanization fundamentally restructured populations' living circumstances, often with poor impacts on health. As an example, unhealthy food establishments may concentrate in some neighborhoods and, mediated by social and commercial drivers, increase local health risks. To understand the connections between neighborhood food environments and public health, researchers often use geographic information systems (GIS) and spatial statistics to analyze place-based evidence, but such tools require careful application and interpretation. In this article, we summarize the factors shaping neighborhood health in relation to local food environments and outline the use of GIS methodologies to assess associations between the two. We provide an overview of available data sources, analytical approaches, and their strengths and weaknesses. We postulate next steps in GIS integration with forecasting, prediction, and simulation measures to frame implications for local health policies.},
}
@article {pmid38060123,
year = {2024},
author = {Brusati, A and Agostinetto, G and Bruno, A and Casiraghi, M and Pescini, D and Sandionigi, A and Balech, B},
title = {Exploration and Retrieval of Virus-Related Molecular Data Using ExTaxsI: The Monkeypox Use Case.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2732},
number = {},
pages = {145-154},
pmid = {38060123},
issn = {1940-6029},
mesh = {Humans ; *Mpox (monkeypox) ; Biodiversity ; Databases, Factual ; Bacteria ; *Viruses/genetics ; },
abstract = {Retrieval and visualization of biological data are essential for understanding complex systems. With the increasing volume of data generated from high-throughput sequencing technologies, effective and optimized data visualization tools have become indispensable. This is particularly relevant in the COVID-19 postpandemic period, where understanding the diversity and interactions of microbial communities (i.e., viral and bacterial) constitutes an important asset to develop and plan suitable interventions.In this chapter, we show the usage and the potentials of ExTaxsI (Exploring Taxonomy Information) tool to retrieve viral biodiversity data stored in National Center for Biotechnology Information (NCBI) databases and create the related visualization. In addition, by integrating different functions and modules, the tool generates relevant types of visualization plots to facilitate the exploration of microbial biodiversity communities useful to deep dive into ecological and taxonomic relationships among different species and identify potential significant targets.Using the Monkeypox virus as a case study, this work points out significant perspectives on biological data visualization, which can be used to gain insights into the ecology, evolution, and pathogenesis of viruses. Accordingly, we show the potentiality of ExTaxsI to organize and describe the available/downloaded data in an easy, simple, and interpretable way allowing the user to interact dynamically with the visualization plots through specific filters, zoom, and explore functions.},
}
@article {pmid38059267,
year = {2023},
author = {Massey, R and Rogers, BM and Berner, LT and Cooperdock, S and Mack, MC and Walker, XJ and Goetz, SJ},
title = {Forest composition change and biophysical climate feedbacks across boreal North America.},
journal = {Nature climate change},
volume = {13},
number = {12},
pages = {1368-1375},
pmid = {38059267},
issn = {1758-678X},
abstract = {Deciduous tree cover is expected to increase in North American boreal forests with climate warming and wildfire. This shift in composition has the potential to generate biophysical cooling via increased land surface albedo. Here we use Landsat-derived maps of continuous tree canopy cover and deciduous fractional composition to assess albedo change over recent decades. We find, on average, a small net decrease in deciduous fraction from 2000 to 2015 across boreal North America and from 1992 to 2015 across Canada, despite extensive fire disturbance that locally increased deciduous vegetation. We further find near-neutral net biophysical change in radiative forcing associated with albedo when aggregated across the domain. Thus, while there have been widespread changes in forest composition over the past several decades, the net changes in composition and associated post-fire radiative forcing have not induced systematic negative feedbacks to climate warming over the spatial and temporal scope of our study.},
}
@article {pmid38058223,
year = {2024},
author = {Fins, IS and Davies, H and Farrell, S and Torres, JR and Pinchbeck, G and Radford, AD and Noble, PJ},
title = {Evaluating ChatGPT text mining of clinical records for companion animal obesity monitoring.},
journal = {The Veterinary record},
volume = {194},
number = {3},
pages = {e3669},
pmid = {38058223},
issn = {2042-7670},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Pets ; *Data Mining ; Language ; Narration ; Obesity/veterinary ; },
abstract = {BACKGROUND: Veterinary clinical narratives remain a largely untapped resource for addressing complex diseases. Here we compare the ability of a large language model (ChatGPT) and a previously developed regular expression (RegexT) to identify overweight body condition scores (BCS) in veterinary narratives pertaining to companion animals.<br><br>METHODS: BCS values were extracted from 4415 anonymised clinical narratives using either RegexT or by appending the narrative to a prompt sent to ChatGPT, prompting the model to return the BCS information. Data were manually reviewed for comparison.<br><br>RESULTS: The precision of RegexT was higher (100%, 95% confidence interval [CI] 94.81%-100%) than that of ChatGPT (89.3%, 95% CI 82.75%-93.64%). However, the recall of ChatGPT (100%, 95% CI 96.18%-100%) was considerably higher than that of RegexT (72.6%, 95% CI 63.92%-79.94%).<br><br>LIMITATIONS: Prior anonymisation and subtle prompt engineering are needed to improve ChatGPT output.<br><br>CONCLUSIONS: Large language models create diverse opportunities and, while complex, present an intuitive interface to information. However, they require careful implementation to avoid unpredictable errors.},
}
@article {pmid38055593,
year = {2023},
author = {Silva, ABDS and Costa, LS and Frias, PG and Araújo, ACM and Bonfim, CVD},
title = {Temporal analysis of mortality from preventable causes in the first 24 hours of life, 2000-2021.},
journal = {Revista latino-americana de enfermagem},
volume = {31},
number = {},
pages = {e4079},
pmid = {38055593},
issn = {1518-8345},
mesh = {Humans ; Cause of Death ; *Information Systems ; Brazil ; *Mortality ; },
abstract = {OBJECTIVE: to analyze the temporal pattern and estimate mortality rates in the first 24 hours of life and from preventable causes in the state of Pernambuco from 2000 to 2021.<br><br>METHOD: an ecological study, using the quarter as the unit of analysis. The data source was made up of the Mortality Information System and the Live Birth Information System. The time series modeling was conducted according to the Autoregressive Integrated Moving Average Model.<br><br>RESULTS: 14,462 deaths were recorded in the first 24 hours of life, 11,110 (76.8%) of which being preventable. It is observed from the forecasts that the mortality rate in the first 24 hours of life ranged from 3.3 to 2.4 per 1,000 live births, and the mortality rate from preventable causes ranged from 2.3 to 1.8 per 1,000 live births.<br><br>CONCLUSION: the prediction suggested progress in reducing mortality in the first 24 hours of life in the state and from preventable causes. The ARIMA models presented satisfactory estimates for mortality rates and preventable causes in the first 24 hours of life.},
}
@article {pmid38053578,
year = {2023},
author = {Esterhuizen, M and Park, CB and Kim, YJ and Kim, TY and Yoon, H and Andres, F and Rodriguez-Rodriguez, R and Tanabe, S},
title = {A perspective on the role of physiological stresses in cancer, diabetes and cognitive disease as environmental diseases.},
journal = {Frontiers in molecular biosciences},
volume = {10},
number = {},
pages = {1274221},
pmid = {38053578},
issn = {2296-889X},
abstract = {With rapid industrialization, urbanization, and climate change, the impact of environmental factors on human health is becoming increasingly evident and understanding the complex mechanisms involved is vital from a healthcare perspective. Nevertheless, the relationship between physiological stress resulting from environmental stressors and environmental disease is complex and not well understood. Chronic exposure to environmental stressors, such as air and water contaminants, pesticides, and toxic metals, has been recognized as a potent elicitor of physiological responses ranging from systemic inflammation to immune system dysregulation causing or progressing environmental diseases. Conversely, physiological stress can exacerbate susceptibility to environmental diseases. Stress-induced alterations in immune function and hormonal balance may impair the ability to detoxify harmful substances and combat pathogens. Additionally, prolonged stress can impact lifestyle choices, leading to harmful behaviors. Understanding the link between physiological stress and environmental disease requires a systematic, multidisciplinary approach. Addressing this complex relationship necessitates the establishment of a global research network. This perspective discusses the intricate interplay between physiological stress and environmental disease, focusing on common environmental diseases, cancer, diabetes, and cognitive degeneration. Furthermore, we highlight the intricate and reciprocal nature of the connection between physiological stress and these environmental diseases giving a perspective on the current state of knowledge as well as identifying where further information is necessary. Recognizing the role of physiological stress in environmental health outcomes will aid in the development of comprehensive strategies to safeguard public health and promote ecological balance.},
}
@article {pmid38052982,
year = {2024},
author = {Choudhary, P and Monasso, GS and Karhunen, V and Ronkainen, J and Mancano, G and Howe, CG and Niu, Z and Zeng, X and Guan, W and Dou, J and Feinberg, JI and Mordaunt, C and Pesce, G and Baïz, N and Alfano, R and Martens, DS and Wang, C and Isaevska, E and Keikkala, E and Mustaniemi, S and Thio, CHL and Fraszczyk, E and Tobi, EW and Starling, AP and Cosin-Tomas, M and Urquiza, J and Röder, S and Hoang, TT and Page, C and Jima, DD and House, JS and Maguire, RL and Ott, R and Pawlow, X and Sirignano, L and Zillich, L and Malmberg, A and Rauschert, S and Melton, P and Gong, T and Karlsson, R and Fore, R and Perng, W and Laubach, ZM and Czamara, D and Sharp, G and Breton, CV and Schisterman, E and Yeung, E and Mumford, SL and Fallin, MD and LaSalle, JM and Schmidt, RJ and Bakulski, KM and Annesi-Maesano, I and Heude, B and Nawrot, TS and Plusquin, M and Ghantous, A and Herceg, Z and Nisticò, L and Vafeiadi, M and Kogevinas, M and Vääräsmäki, M and Kajantie, E and Snieder, H and Corpeleijn, E and Steegers-Theunissen, RPM and Yang, IV and Dabelea, D and Fossati, S and Zenclussen, AC and Herberth, G and Magnus, M and Håberg, SE and London, SJ and Munthe-Kaas, MC and Murphy, SK and Hoyo, C and Ziegler, AG and Hummel, S and Witt, SH and Streit, F and Frank, J and Räikkönen, K and Lahti, J and Huang, RC and Almqvist, C and Hivert, MF and Jaddoe, VWV and Järvelin, MR and Kantomaa, M and Felix, JF and Sebert, S},
title = {Maternal educational attainment in pregnancy and epigenome-wide DNA methylation changes in the offspring from birth until adolescence.},
journal = {Molecular psychiatry},
volume = {29},
number = {2},
pages = {348-358},
pmid = {38052982},
issn = {1476-5578},
support = {P30 ES025128/ES/NIEHS NIH HHS/United States ; R00 ES030400/ES/NIEHS NIH HHS/United States ; MC_PC_19009/MRC_/Medical Research Council/United Kingdom ; U24 ES028533/ES/NIEHS NIH HHS/United States ; MC_PC_15018/MRC_/Medical Research Council/United Kingdom ; 873749//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 733206//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; R24 ES028531/ES/NIEHS NIH HHS/United States ; G9815508/MRC_/Medical Research Council/United Kingdom ; 848158//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 001/WHO_/World Health Organization/International ; R01 ES025531/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *DNA Methylation/genetics ; Female ; Pregnancy ; Adolescent ; *Epigenome/genetics ; Child ; *Educational Status ; Male ; *Genome-Wide Association Study/methods ; *Epigenesis, Genetic/genetics ; Prenatal Exposure Delayed Effects/genetics ; Child, Preschool ; Infant ; Mothers ; Infant, Newborn ; Adult ; Academic Success ; },
abstract = {Maternal educational attainment (MEA) shapes offspring health through multiple potential pathways. Differential DNA methylation may provide a mechanistic understanding of these long-term associations. We aimed to quantify the associations of MEA with offspring DNA methylation levels at birth, in childhood and in adolescence. Using 37 studies from high-income countries, we performed meta-analysis of epigenome-wide association studies (EWAS) to quantify the associations of completed years of MEA at the time of pregnancy with offspring DNA methylation levels at birth (n = 9 881), in childhood (n = 2 017), and adolescence (n = 2 740), adjusting for relevant covariates. MEA was found to be associated with DNA methylation at 473 cytosine-phosphate-guanine sites at birth, one in childhood, and four in adolescence. We observed enrichment for findings from previous EWAS on maternal folate, vitamin-B12 concentrations, maternal smoking, and pre-pregnancy BMI. The associations were directionally consistent with MEA being inversely associated with behaviours including smoking and BMI. Our findings form a bridge between socio-economic factors and biology and highlight potential pathways underlying effects of maternal education. The results broaden our understanding of bio-social associations linked to differential DNA methylation in multiple early stages of life. The data generated also offers an important resource to help a more precise understanding of the social determinants of health.},
}
@article {pmid38052241,
year = {2023},
author = {Cribb, AT and Formoso, KK and Woolley, CH and Beech, J and Brophy, S and Byrne, P and Cassady, VC and Godbold, AL and Larina, E and Maxeiner, PP and Wu, YH and Corsetti, FA and Bottjer, DJ},
title = {Contrasting terrestrial and marine ecospace dynamics after the end-Triassic mass extinction event.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2012},
pages = {20232232},
pmid = {38052241},
issn = {1471-2954},
mesh = {*Ecosystem ; *Extinction, Biological ; Fossils ; Databases, Factual ; Biodiversity ; },
abstract = {Mass extinctions have fundamentally altered the structure of the biosphere throughout Earth's history. The ecological severity of mass extinctions is well studied in marine ecosystems by categorizing marine taxa into functional groups based on 'ecospace' approaches, but the ecological response of terrestrial ecosystems to mass extinctions is less well understood due to the lack of a comparable methodology. Here, we present a new terrestrial ecospace framework that categorizes fauna into functional groups as defined by tiering, motility and feeding traits. We applied the new terrestrial and traditional marine ecospace analyses to data from the Paleobiology Database across the end-Triassic mass extinction-a time of catastrophic global warming-to compare changes between the marine and terrestrial biospheres. We found that terrestrial functional groups experienced higher extinction severity, that taxonomic and functional richness are more tightly coupled in the terrestrial, and that the terrestrial realm continued to experience high ecological dissimilarity in the wake of the extinction. Although signals of extinction severity and ecological turnover are sensitive to the quality of the terrestrial fossil record, our findings suggest greater ecological pressure from the end-Triassic mass extinction on terrestrial ecosystems than marine ecosystems, contributing to more prolonged terrestrial ecological flux.},
}
@article {pmid38051947,
year = {2023},
author = {Wroblewski, TH and Witt, KE and Lee, SB and Malhi, RS and Peede, D and Huerta-Sánchez, E and Villanea, FA and Claw, KG},
title = {Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications.},
journal = {Genome biology and evolution},
volume = {15},
number = {12},
pages = {},
pmid = {38051947},
issn = {1759-6653},
support = {1R35GM128946-01/NH/NIH HHS/United States ; R35 HG011319/HG/NHGRI NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; R35HG011319/HG/NHGRI NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Neanderthals/genetics ; Pharmacogenetics ; Genome, Human ; *Hominidae/genetics ; Biological Evolution ; },
abstract = {Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.},
}
@article {pmid38051448,
year = {2023},
author = {Urbano, F and Viterbi, R and Pedrotti, L and Vettorazzo, E and Movalli, C and Corlatti, L},
title = {Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {1},
pages = {12},
pmid = {38051448},
issn = {1573-2959},
mesh = {Humans ; *Ecosystem ; *Conservation of Natural Resources/methods ; Data Management ; Environmental Monitoring ; Biodiversity ; },
abstract = {A scientifically informed approach to decision-making is key to ensuring the sustainable management of ecosystems, especially in the light of increasing human pressure on habitats and species. Protected areas, with their long-term institutional mandate for biodiversity conservation, play an important role as data providers, for example, through the long-term monitoring of natural resources. However, poor data management often limits the use and reuse of this wealth of information. In this paper, we share lessons learned in managing long-term data from the Italian Alpine national parks. Our analysis and examples focus on specific issues faced by managers of protected areas, which partially differ from those faced by academic researchers, predominantly owing to different mission, governance, and temporal perspectives. Rigorous data quality control, the use of appropriate data management tools, and acquisition of the necessary skills remain the main obstacles. Common protocols for data collection offer great opportunities for the future, and complete recovery and documentation of time series is an urgent priority. Notably, before data can be shared, protected areas should improve their data management systems, a task that can be achieved only with adequate resources and a long-term vision. We suggest strategies that protected areas, funding agencies, and the scientific community can embrace to address these problems. The added value of our work lies in promoting engagement with managers of protected areas and in reporting and analysing their concrete requirements and problems, thereby contributing to the ongoing discussion on data management and sharing through a bottom-up approach.},
}
@article {pmid38046930,
year = {2023},
author = {Tschernosterová, K and Trávníčková, E and Grattarola, F and Rosse, C and Keil, P},
title = {SPARSE 1.0: a template for databases of species inventories, with an open example of Czech birds.},
journal = {Biodiversity data journal},
volume = {11},
number = {},
pages = {e108731},
pmid = {38046930},
issn = {1314-2828},
abstract = {Here, we introduce SPARSE (acronym for "SPecies AcRoss ScalEs"), a simple and portable template for databases that can store data on species composition derived from ecological inventories, surveys and checklists, with emphasis on metadata describing sampling effort and methods. SPARSE can accommodate resurveys and time series and data from different spatial scales, as well as complex sampling designs. SPARSE focuses on inventories that report multiple species for a given site, together with sampling methods and effort, which can be used in statistical models of true probability of occurrence of species. SPARSE is spatially explicit and can accommodate nested spatial structures from multiple spatial scales, including sampling designs where multiple sites within a larger area have been surveyed and the larger area can again be nested in an even larger region. Each site in SPARSE is represented either by a point, line (for transects) or polygon, stored in an ESRI shapefile. SPARSE implements a new combination of our own field definitions with Darwin Core biodiversity data standard and its Humboldt core extension. The use of Humboldt core also makes SPARSE suitable for biodiversity data with temporal replication. We provide an example use of the SPARSE framework by digitising data on birds from the Czech Republic, from 348 sites and 524 sampling events, with 15,969 unique species-per-event observations of presence, abundance or population density. To facilitate use without the need for a high-level database expertise, the Czech bird example is implemented as MS Access .accdb file, but can be ported to other database engines. The example of Czech birds complements other bird datasets from the Czech Republic, specifically the four gridded national atlases and the breeding bird survey which cover a similar temporal extent, but different locations and spatial scales.},
}
@article {pmid38046192,
year = {2023},
author = {Boyes, D and Sims, I and Lees, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Black-tipped Ermine, Yponomeuta plumbella (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {246},
pmid = {38046192},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Yponomeuta plumbella (the Black-tipped Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 636.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.},
}
@article {pmid38046063,
year = {2023},
author = {Suresh, KP and Barman, NN and Bari, T and Jagadish, D and Sushma, B and Darshan, HV and Patil, SS and Bora, M and Deka, A},
title = {Application of machine learning models for risk estimation and risk prediction of classical swine fever in Assam, India.},
journal = {Virusdisease},
volume = {34},
number = {4},
pages = {514-525},
pmid = {38046063},
issn = {2347-3584},
abstract = {UNLABELLED: The present study is aimed to develop an early warning system of Classical swine fever (CSF) disease by applying machine learning models and to study the climate-disease relationship with respect to the spatial occurrence and outbreaks of the disease in the north-eastern state of Assam, India. The disease incidence data from the year 2005 to 2021 was used. The linear discriminant analysis (LDA) revealed that significant environmental and remote sensing risk factors like air temperature, enhanced vegetation index, land surface temperature, potential evaporation rate and wind speed were significantly contributing to CSF incidences in Assam. Furthermore, the climate-based disease modelling was applied to relevant ecological and environmental risk factors determined using LDA and risk maps were generated. The western and eastern regions of the state were predicted to be at high risk of CSF with presence of significant hotspots. For the districts that are significantly clustered, the Basic reproduction number (R0) was calculated after the predicted results were superimposed onto the risk maps. The R0 value ranged from 1.04 to 2.07, implying that the eastern and western regions of Assam are more susceptible to CSF. Machine learning models were implemented using R statistical software version 3.1.3. The random forest, classification tree analysis and gradient boosting machine were found to be the best-fitted models for the study group. The models' performance was measured using the Receiving Operating Characteristic (ROC) curve, Cohen's Kappa, True Skill Statistics, Area Under ROC Curve, ACCURACY, ERROR RATE, F1 SCORE, and Logistic Loss. As a part of the suggested study, these models will help us to understand the disease transmission dynamics, risk factors and spatio-temporal pattern of spread and evaluate the efficacy of control measures to battle the economic losses caused by CSF outbreaks.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13337-023-00847-6.},
}
@article {pmid38045543,
year = {2023},
author = {Lin, B and Shi, W and Lu, Q and Shito, TT and Yu, H and Dong, B},
title = {Establishment of a developmental atlas and transgenetic tools in the ascidian Styela clava.},
journal = {Marine life science &amp; technology},
volume = {5},
number = {4},
pages = {435-454},
pmid = {38045543},
issn = {2662-1746},
abstract = {UNLABELLED: The ascidian Styela clava is an ecologically important species that is distributed along coastal regions worldwide. It has a long history as a model animal for evolutionary and developmental biology research owing to its phylogenetic position between vertebrates and invertebrates, and its classical mosaic expression patterns. However, the standard developmental atlas and protocols and tools for molecular manipulation of this organism are inadequate. In this study, we established a standard developmental table and provided a web-based digital image resource for S. clava embryogenesis at each developmental stage from fertilized eggs to hatching larvae by utilizing confocal laser microscopy and 3D reconstruction images. It takes around 10 h for fertilized eggs to develop into swimming larvae and 20-30 min to complete the tail regression processes at the metamorphic stage. We observed that the notochord cells in S. clava embryos did not produce an extracellular lumen like Ciona robusta, but showed polarized elongation behaviors, providing us an ideal comparative model to study tissue morphogenesis. In addition, we established a chemical-washing procedure to remove the chorion easily from the fertilized eggs. Based on the dechorionation technique, we further realized transgenic manipulation by electroporation and successfully applied tissue-specific fluorescent labeling in S. clava embryos. Our work provides a standard imaging atlas and powerful genetic tools for investigating embryogenesis and evolution using S. clava as a model organism.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-023-00200-2.},
}
@article {pmid39268176,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the White Satin, Leucoma salicis (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {323},
pmid = {39268176},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Leucoma salicis (the White Satin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 733.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,222 protein coding genes.},
}
@article {pmid39114813,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Thicket Knot-horn, Acrobasis suavella (Zincken, 1818).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {252},
pmid = {39114813},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Acrobasis suavella (the Thicket Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 647.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,101 protein coding genes.},
}
@article {pmid39430045,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Olive Pearl, Udea olivalis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {238},
pmid = {39430045},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Udea olivalis (the Olive Pearl; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 624.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.},
}
@article {pmid39242656,
year = {2023},
author = {Hui, C and Pyšek, P and Richardson, DM},
title = {Disentangling the relationships among abundance, invasiveness and invasibility in trait space.},
journal = {npj biodiversity},
volume = {2},
number = {1},
pages = {13},
pmid = {39242656},
issn = {2731-4243},
support = {89967//National Research Foundation/ ; NE/V007548/1//Natural Environment Research Council/ ; DP200101680//Australian Research Council/ ; 101059592//HORIZON EUROPE European Research Council/ ; EXPRO 19-28807X//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; RVO 67985939//Czech Academy of Sciences/ ; CZ.02.2.69/0.0/0.0/18_053/0017850//Ministry of Education, Youth, and Sports of the Czech Republic/ ; },
abstract = {Identifying conditions and traits that allow an introduced species to grow and spread, from being initially rare to becoming abundant (defined as invasiveness), is the crux of invasion ecology. Invasiveness and abundance are related but not the same, and we need to differentiate these concepts. Predicting both species abundance and invasiveness and their relationship in an invaded community is highly contextual, being contingent on the community trait profile and its invasibility. We operationalised a three-pronged invasion framework that considers traits, environmental context, and propagule pressure. Specifically, we measure the invasiveness of an alien species by combining three components (performance reflecting environmental suitability, product of species richness and the covariance between interaction strength and species abundance, and community-level interaction pressure); the expected population growth rate of alien species simply reflects the total effect of propagule pressure and the product of their population size and invasiveness. The invasibility of a community reflects the size of opportunity niches (the integral of positive invasiveness in the trait space) under the given abiotic conditions of the environment. Both species abundance and the surface of invasiveness over the trait space can be dynamic and variable. Whether an introduced species with functional traits similar to those of an abundant species in the community exhibits high or low invasiveness depends largely on the kernel functions of performance and interaction strength with respect to traits and environmental conditions. Knowledge of the covariance between interaction strength and species abundance and these kernel functions, thus, holds the key to accurate prediction of invasion dynamics.},
}
@article {pmid38903245,
year = {2023},
author = {Boyes, D and Goate, Z and , and , and , and , and , and , },
title = {The genome sequence of the White-backed Marble, Hedya salicella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {219},
pmid = {38903245},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Hedya salicella (the White-backed Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 742.3 megabases in span. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,961 protein coding genes.},
}
@article {pmid39262678,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brindled Flat-body, Agonopterix arenella (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {214},
pmid = {39262678},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agonopterix arenella (the Brindled Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 545.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.},
}
@article {pmid39502585,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Small Phoenix, Ecliptopera silaceata (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {209},
pmid = {39502585},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Ecliptopera silaceata (the Small Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 316.5 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,770 protein coding genes.},
}
@article {pmid39211527,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Small Square-spot, Diarsia rubi (Vieweg, 1790).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {210},
pmid = {39211527},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Diarsia rubi (the Small Square-spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 624.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,173 protein coding genes.},
}
@article {pmid38817338,
year = {2022},
author = {Cocker, D and Sammarro, M and Chidziwisano, K and Elviss, N and Jacob, ST and Kajumbula, H and Mugisha, L and Musoke, D and Musicha, P and Roberts, AP and Rowlingson, B and Singer, AC and Byrne, RL and Edwards, T and Lester, R and Wilson, CN and Hollihead, B and Thomson, NR and Jewell, CP and Morse, T and Feasey, NA},
title = {Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {55},
pmid = {38817338},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/R015074/1/MRC_/Medical Research Council/United Kingdom ; MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.},
}
@article {pmid38779052,
year = {2023},
author = {Lohse, K and Hayward, A and Laetsch, DR and Marques, V and Vila, R and Tyler-Smith, C and , and , and , and , },
title = {The genome sequence of the Mazarine Blue, Cyaniris semiargus (Rottemburg, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {181},
pmid = {38779052},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Cyaniris semiargus (the Mazarine Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 441.5 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,408 protein coding genes.},
}
@article {pmid38798993,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Lilac Beauty, Apeira syringaria (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {159},
pmid = {38798993},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Apeira syringaria (the Lilac Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 544.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,426 protein coding genes.},
}
@article {pmid38770266,
year = {2023},
author = {Vila, R and Lohse, K and Hayward, A and Laetsch, DR and Wright, C and , and , and , and , },
title = {The genome sequence of the Chalkhill Blue, Lysandra coridon (Poda, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {162},
pmid = {38770266},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Lysandra coridon (the Chalkhill Blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 541 megabases in span. Most of the assembly is scaffolded into 90 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,334 protein coding genes.},
}
@article {pmid38764974,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Sycamore Piercer, Pammene aurita (Razowski, 1991).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {160},
pmid = {38764974},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Pammene aurita (the Sycamore Piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 1,041.8 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length.},
}
@article {pmid39219859,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Ruby Tiger, Phragmatobia fuliginosa (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {124},
pmid = {39219859},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Phragmatobia fuliginosa (the Ruby Tiger; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 629.4 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,338 protein coding genes.},
}
@article {pmid38707488,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Boyes, C and , },
title = {The genome sequence of the Fulvous Clothes Moth, Tinea semifulvella (Haworth, 1828).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {104},
pmid = {38707488},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Tinea semifulvella (the Fulvous Clothes Moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 596.6 megabases in span. The whole assembly is scaffolded into 45 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 16.8 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,516 protein coding genes.},
}
@article {pmid39129913,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Mulley, JF and , },
title = {The genome sequence of the Dark Arches Apamea monoglypha (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {63},
pmid = {39129913},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Apamea monoglypha (the Dark Arches, Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,963 protein coding genes.},
}
@article {pmid39148947,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Green-brindled Crescent, Allophyes oxyacanthae (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {53},
pmid = {39148947},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Allophyes oxyacanthae (the Green-brindled Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 458 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,301 protein coding genes.},
}
@article {pmid38868331,
year = {2023},
author = {Li, C and Jin, L and Zhang, C and Li, S and Zhou, T and Hua, Z and Wang, L and Ji, S and Wang, Y and Gan, Y and Liu, J},
title = {Destabilized microbial networks with distinct performances of abundant and rare biospheres in maintaining networks under increasing salinity stress.},
journal = {iMeta},
volume = {2},
number = {1},
pages = {e79},
pmid = {38868331},
issn = {2770-596X},
abstract = {Global changes such as seawater intrusion and freshwater resource salinization increase environmental stress imposed on the aquatic microbiome. A strong predictive understanding of the responses of the aquatic microbiome to environmental stress will help in coping with the "gray rhino" events in the environment, thereby contributing to an ecologically sustainable future. Considering that microbial ecological networks are tied to the stability of ecosystem functioning and that abundant and rare biospheres with different biogeographic patterns are important drivers of ecosystem functioning, the roles of abundant and rare biospheres in maintaining ecological networks need to be clarified. Here we showed that, with the increasing salinity stress induced by the freshwater-to-seawater transition, the microbial diversity reduced significantly and the taxonomic structure experienced a strong succession. The complexity and stability of microbial ecological networks were diminished by the increasing stress. The composition of the microorganisms supporting the networks underwent sharp turnovers during the freshwater-to-seawater transition, with the abundant biosphere behaving more robustly than the rare biosphere. Notably, the abundant biosphere played a much more important role than the rare biosphere in stabilizing ecological networks under low-stress environments, but the difference between their relative importance narrowed significantly with the increasing stress, suggesting that the environmental stress weakened the "Matthew effect" in the microbial world. With in-depth insights into the aquatic microbial ecology under stress, our findings highlight the importance of adjusting conservation strategies for the abundant and rare biospheres to maintain ecosystem functions and services in response to rising environmental stress.},
}
@article {pmid39328383,
year = {2023},
author = {Catalàn, N and Campo, RD and Talluto, L and Mendoza-Lera, C and Grandi, G and Bernal, S and Schiller, DV and Singer, G and Bertuzzo, E},
title = {Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks.},
journal = {Ecosystems (New York, N.Y.)},
volume = {26},
number = {4},
pages = {873-892},
pmid = {39328383},
issn = {1432-9840},
abstract = {UNLABELLED: Streams and rivers act as landscape-scale bioreactors processing large quantities of terrestrial particulate organic matter (POM). This function is linked to their flow regime, which governs residence times, shapes organic matter reactivity and controls the amount of carbon (C) exported to the atmosphere and coastal oceans. Climate change impacts flow regimes by increasing both flash floods and droughts. Here, we used a modelling approach to explore the consequences of lateral hydrological contraction, that is, the reduction of the wet portion of the streambed, for POM decomposition and transport at the river network scale. Our model integrates seasonal leaf litter input as generator of POM, transient storage of POM on wet and dry streambed portions with associated decomposition and ensuing changes in reactivity, and transport dynamics through a dendritic river network. Simulations showed that the amount of POM exported from the river network and its average reactivity increased with lateral hydrological contraction, due to the combination of (1) low processing of POM while stored on dry streambeds, and (2) large shunting during flashy events. The sensitivity analysis further supported that high lateral hydrological contraction leads to higher export of higher reactivity POM, regardless of transport coefficient values, average reactivity of fresh leaf litter and differences between POM reactivity under wet and dry conditions. Our study incorporates storage in dry streambed areas into the pulse-shunt concept (Raymond and others in Ecology 97(1):5-16, 2016. 10.1890/14-1684.1), providing a mechanistic framework and testable predictions about leaf litter storage, transport and decomposition in fluvial networks.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10021-022-00802-4.},
}
@article {pmid38799509,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Parkerson, L and , },
title = {The genome sequence of the common grass-veneer, Agriphila tristella (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {304},
pmid = {38799509},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Agriphila tristella (the common grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 802 megabases in span. Most of the assembly (99.83%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.},
}
@article {pmid38867895,
year = {2022},
author = {Wu, D and Liu, L and Jiao, N and Zhang, Y and Yang, L and Tian, C and Lan, P and Zhu, L and Loomba, R and Zhu, R},
title = {Targeting keystone species helps restore the dysbiosis of butyrate-producing bacteria in nonalcoholic fatty liver disease.},
journal = {iMeta},
volume = {1},
number = {4},
pages = {e61},
pmid = {38867895},
issn = {2770-596X},
support = {P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; },
abstract = {The dysbiosis of the gut microbiome is one of the pathogenic factors of nonalcoholic fatty liver disease (NAFLD) and also affects the treatment and intervention of NAFLD. Among gut microbiomes, keystone species that regulate the integrity and stability of an ecological community have become the potential intervention targets for NAFLD. Here, we collected stool samples from 22 patients with nonalcoholic steatohepatitis (NASH), 25 obese patients, and 16 healthy individuals from New York for 16S rRNA gene sequencing. An algorithm was implemented to identify keystone species based on causal inference theories and dynamic intervention simulation. External validation was performed in an independent cohort from California. Eight keystone species in the gut of NAFLD, represented by Porphyromonas loveana, Alistipes indistinctus, and Dialister pneumosintes, were identified, which could efficiently restore the microbial composition of the NAFLD toward a normal gut microbiome with 92.3% recovery. These keystone species regulate intestinal amino acid metabolism and acid-base environment to promote the growth of the butyrate-producing Lachnospiraceae and Ruminococcaceae species that are significantly reduced in NAFLD patients. Our findings demonstrate the importance of keystone species in restoring the microbial composition toward a normal gut microbiome, suggesting a novel potential microbial treatment for NAFLD.},
}
@article {pmid39144291,
year = {2022},
author = {Fitzhugh, B and Brown, WA and Misarti, N and Takase, K and Tremayne, AH},
title = {Human Paleodemography and Paleoecology of the North Pacific Rim from the Mid to Late Holocene.},
journal = {Quaternary research},
volume = {108},
number = {PESAS},
pages = {123-149},
pmid = {39144291},
issn = {0033-5894},
support = {P2C HD042828/HD/NICHD NIH HHS/United States ; },
abstract = {Using 14 proxy human population time series from around the North Pacific (Alaska, Hokkaido and the Kuril Islands), we evaluate the possibility that the North Pacific climate and marine ecosystem includes a millennial-scale regime shift cycle affecting subsistence and migration. We develop both visual and statistical methods for addressing questions about relative population growth and movement in the past. We introduce and explore the use of a Time Iterative Moran I (TIMI) spatial autocorrelation method to compare time series trends quantitatively - a method that could prove useful in other paleoecological analyses. Results reveal considerable population dynamism around the North Pacific in the last 5000 years and strengthen a previously reported inverse correlation between Northeast and Northwest Pacific proxy population indices. Visual and TIMI analyses suggest multiple, overlapping explanations for the variability, including the potential that oscillating ecological regime shifts affect the North Pacific basin. These results provide an opening for coordinated research to unpack the interrelated social, cultural and environmental dynamics around the subarctic and arctic North Pacific at different spatial and temporal scales by international teams of archaeologists, historians, paleoecologists, paleoceanographers, paleoclimatologists, modelers and data management specialists.},
}
@article {pmid38235459,
year = {2022},
author = {De Castro Martins, C and Chaminade, T and Cavazza, M},
title = {Causal Analysis of Activity in Social Brain Areas During Human-Agent Conversation.},
journal = {Frontiers in neuroergonomics},
volume = {3},
number = {},
pages = {843005},
pmid = {38235459},
issn = {2673-6195},
abstract = {This article investigates the differences in cognitive and neural mechanisms between human-human and human-virtual agent interaction using a dataset recorded in an ecologically realistic environment. We use Convergent Cross Mapping (CCM) to investigate functional connectivity between pairs of regions involved in the framework of social cognitive neuroscience, namely the fusiform gyrus, superior temporal sulcus (STS), temporoparietal junction (TPJ), and the dorsolateral prefrontal cortex (DLPFC)-taken as prefrontal asymmetry. Our approach is a compromise between investigating local activation in specific regions and investigating connectivity networks that may form part of larger networks. In addition to concording with previous studies, our results suggest that the right TPJ is one of the most reliable areas for assessing processes occurring during human-virtual agent interactions, both in a static and dynamic sense.},
}
@article {pmid38799510,
year = {2022},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the silver Y moth, Autographa gamma (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {100},
pmid = {38799510},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Autographa gamma (the silver Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 373 megabases in span. The majority of the assembly (99.65%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled and is 15.2 kilobases in length.},
}
@article {pmid39175988,
year = {2021},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the bramble shoot moth, Notocelia uddmanniana (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {348},
pmid = {39175988},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Notocelia uddmanniana (the bramble shoot moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 794 megabases in span. The majority of the assembly, 99.96%, is scaffolded into 28 chromosomal pseudomolecules, with the Z sex chromosome assembled.},
}
@article {pmid38912275,
year = {2021},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the iron prominent, Notodonta dromedarius (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {341},
pmid = {38912275},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Notodonta dromedarius (iron prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 342 megabases in span. The majority of the assembly, 99.35%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.},
}
@article {pmid39449730,
year = {2021},
author = {Boyes, D and Crowley, LM and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of Svensson's copper underwing, Amphipyra berbera Rungs, 1949.},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {314},
pmid = {39449730},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Amphipyra berbera (Svensson's copper underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 582 megabases in span. The majority (99.97%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.},
}
@article {pmid38044542,
year = {2024},
author = {Cains, MG and Desrousseaux, AOS and Boxall, ABA and Molander, S and Molina-Navarro, E and Sussams, J and Critto, A and Stahl, RG and Rother, HA},
title = {Environmental management cycles for chemicals and climate change, EMC[4] : A new conceptual framework contextualizing climate and chemical risk assessment and management.},
journal = {Integrated environmental assessment and management},
volume = {20},
number = {2},
pages = {433-453},
doi = {10.1002/ieam.4872},
pmid = {38044542},
issn = {1551-3793},
mesh = {Humans ; *Climate Change ; *Conservation of Natural Resources ; Risk Assessment ; Risk Management ; Ecotoxicology ; },
abstract = {The environmental management cycles for chemicals and climate change (EMC[4]) is a suggested conceptual framework for integrating climate change aspects into chemical risk management. The interaction of climate change and chemical risk brings together complex systems that are imperfectly understood by science. Making management decisions in this context is therefore difficult and often exacerbated by a lack of data. The consequences of poor decision-making can be significant for both environmental and human health. This article reflects on the ways in which existing chemicals management systems consider climate change and proposes the EMC[4] conceptual framework, which is a tool for decision-makers operating at different spatial scales. Also presented are key questions raised by the tool to help the decision-maker identify chemical risks from climate change, management options, and, importantly, the different types of actors that are instrumental in managing that risk. Case studies showing decision-making at different spatial scales are also presented highlighting the conceptual framework's applicability to multiple scales. The United Nations Environment Programme's development of an intergovernmental Science Policy Panel on Chemicals and Waste has presented an opportunity to promote and generate research highlighting the impacts of chemicals and climate change interlinkages. Integr Environ Assess Manag 2024;20:433-453. © 2023 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology &amp; Chemistry (SETAC).},
}
@article {pmid38043132,
year = {2024},
author = {Golden, E and Allen, D and Amberg, A and Anger, LT and Baker, E and Baran, SW and Bringezu, F and Clark, M and Duchateau-Nguyen, G and Escher, SE and Giri, V and Grevot, A and Hartung, T and Li, D and Lotfi, L and Muster, W and Snyder, K and Wange, R and Steger-Hartmann, T},
title = {Toward implementing virtual control groups in nonclinical safety studies.},
journal = {ALTEX},
volume = {41},
number = {2},
pages = {282-301},
doi = {10.14573/altex.2310041},
pmid = {38043132},
issn = {1868-8551},
mesh = {Animals ; Control Groups ; Pharmaceutical Preparations ; *Research ; },
abstract = {Historical data from control groups in animal toxicity studies are currently mainly used for comparative purposes to assess validity and robustness of study results. Due to the highly controlled environment in which the studies are performed and the homogeneity of the animal collectives it has been proposed to use the historical data to build so-called virtual control groups, which could partly or entirely replace the concurrent control group. This would constitute a substantial contribution to the reduction of animal use in safety studies. Before the concept can be implemented, the prerequisites regarding data collection, curation, and statistical evaluation together with a validation strategy need to be identified to avoid any impairment of the study outcome and subsequent consequences for human risk assessment. To further assess and develop the concept of virtual control groups, the transatlantic think tank for toxicology (t4) sponsored a workshop with stakeholders from the phar­maceutical and chemical industry, academia, FDA, contract research organizations (CROs), and non-governmental organizations in Washington, which took place in March 2023. This report sum­marizes the current efforts of a European initiative to share, collect, and curate animal control data in a centralized database and the first approaches to identify optimal matching criteria between virtual controls and the treatment arms of a study as well as first reflections about strategies for a qualifi­cation procedure and potential pitfalls of the concept.},
}
@article {pmid38042774,
year = {2023},
author = {Mendoza, JN and Hanazaki, N and Prūse, B and Martini, A and Bittner, MV and Kochalski, S and Macusi, E and Ciriaco, A and Mattalia, G and Sõukand, R},
title = {Ethnobotanical contributions to global fishing communities: a review.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {19},
number = {1},
pages = {57},
pmid = {38042774},
issn = {1746-4269},
mesh = {Humans ; *Ecosystem ; *Conservation of Natural Resources/methods ; Hunting ; Ethnobotany ; Fisheries ; },
abstract = {BACKGROUND: Ethnobotanical knowledge about the role of plants in fisheries provides valuable ecological information vital for sustainable management of local resources; however, it is diluted and understudied globally. This literature review aims to map the knowledge of plant use within traditional fishing communities.<br><br>METHODS: Through the PRISMA method, we identified and selected 34 articles reporting the use of plants in fisheries, and including 344 taxa of plants and algae. Uses of plants and algae were grouped into different categories.<br><br>RESULTS: In the novel categorization of fishery-related uses we proposed, the most mentioned were for fishing and building/repair of fishing artifacts and habitat-related uses, while the records of plants related to fiber uses, providing aid in fishing management and species causing problems, were among the least mentioned. Semi-structured interview is most commonly used with local resource users, especially fishery experts, in exploring perceptions on plant use within traditional fishing communities. Diversity was high in all the recorded families, but most were reported locally.<br><br>CONCLUSION: Ethnobotanical studies with fishers are not common in the documented literature but they provide a large number of use reports. On the basis this review, in most of the world, the information is of a casual and sporadic nature. Fishers can provide information on aquatic plants and algae that create problems and aid in fishing management, which are crucial in understanding the ecosystem of a region experiencing environmental challenges. This knowledge is greatly understudied globally and undergoing a rapid decline, as highlighted in several of the reviewed articles. Thus, further systematic research on fishery-related uses of plants by fisherfolk is needed considering its potential contribution to the sustainable management of fishery resources.},
}
@article {pmid38042196,
year = {2024},
author = {Zhang, Y and Cai, L and Chen, L and Zhang, H and Li, G and Wang, G and Cui, J and Filatova, I and Liu, Y},
title = {Effect of micro-nano bubbles on the remediation of saline-alkali soil with microbial agent.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {168940},
doi = {10.1016/j.scitotenv.2023.168940},
pmid = {38042196},
issn = {1879-1026},
mesh = {*Alkalies ; *Soil/chemistry ; Plants ; Environmental Pollution ; *Benzenesulfonates ; },
abstract = {The widespread distribution of saline-alkali soil around the world affects the health of ecological systems and the development of the national economy by limiting the growth of plants. However, the commonly used remediation technologies have the drawbacks of low efficiency, high cost, and secondary pollution. This study investigated the feasibility and efficacy of novel combined micro-nanobubbles (MNBs) and microbial agent (MA) technology for the remediation of saline-alkali soil. The results demonstrated that the combined MA-MNBs method greatly renovated the properties of saline-alkali soil compared with the technologies of single utilization of MA or MNBs process in the laboratory. The method resulted in a reduction of soil electrical conductivity and pH levels, an improvement in soil fertility, and the formation of soil aggregates. Moreover, the method significantly impacted the growth of plants, particularly in plant length, dry weight, and rhizome elongation. Further high-throughput sequencing and gene expression analysis revealed that the MA-MNBs method enhanced the abundance of soil microbial community compared with single MA and MNBs treatment. Gene enrichment analysis revealed that the MA-MNBs method could compensate for the shortcomings of single MA treatment and enhance the expression of energy metabolism and salt stress-related genes attributed to MNBs treatment, thereby significantly improving the growth and development of plants. Consistently, 6115 kg/ha of rice was yielded in the field for the saline-alkali soils using this MA-MNBs method, with zero crops before remediation. This study provided a novel, efficient, and green strategy for the remediation of saline-alkali soil without adding any chemicals.},
}
@article {pmid38042080,
year = {2024},
author = {Xiao, L and Leng, M and Greenwood, P and Zhao, R and Xie, Z and You, Z and Liu, J},
title = {Temporal and vertical dynamics of carbon accumulation potential under grazing-excluded grasslands in China: The role of soil bulk density.},
journal = {Journal of environmental management},
volume = {351},
number = {},
pages = {119696},
doi = {10.1016/j.jenvman.2023.119696},
pmid = {38042080},
issn = {1095-8630},
mesh = {*Soil ; *Carbon/analysis ; Grassland ; Biomass ; China ; Carbon Sequestration ; },
abstract = {Despite the progress made in understanding relevant carbon dynamics under grazing exclusion, previous studies have underestimated the role of soil bulk density (BD), and its implications for potential accumulation of soil organic carbon (SOC), especially at regional scale over long term. In this study, we first constructed a database covering a vast majority of the grasslands in northwestern China based on 131 published literatures. A synthesis was then conducted by analyzing the experimental data to comprehensively investigate the mechanisms of vegetation recovery, carbon-nitrogen coupling, and the importance of changed soil BD in evaluating SOC sequestration potential. The results showed that although the recovery of vegetation height and cover were both critical for improving vegetation biomass, vegetation height required a longer recovery period. While the SOC accumulation was found to be greater in surface layers than deeper ones, it exhibited a reduced capacity for carbon sequestration and an increased risk of SOC loss. Grazing exclusion significantly reduced soil BD across different soil profiles, with the rate of change influenced by soil depth, time, geographical and climatic conditions. The potential for SOC accumulation in the top 30 cm of soil based on data of 2003-2022 was 0.78 Mg ha[-1] yr[-1] without considering BD effects, which was significantly underestimated compared to that of 1.16 Mg ha[-1] yr[-1] when BD changes were considered properly. This suggests that the efficiency of grazing exclusion in carbon sequestration and climate mitigation may have been previously underreported. Furthermore, mean annual precipitation represented the most relevant environmental factor that positively correlated to SOC accumulation, and a wetter climate may offer greater potential for carbon accumulation. Overall, this study implies grazing exclusion may play an even more critical role in carbon sequestration and climate change mitigation over long-term than previously recognized, which provides essential scientific evidence for implementing stepwise ecological restoration in grasslands.},
}
@article {pmid38042076,
year = {2024},
author = {Parent, JR and Gold, AJ and Vogler, E and Lowder, KA},
title = {Guiding decisions on the future of dams: A GIS database characterizing ecological and social considerations of Dam decisions.},
journal = {Journal of environmental management},
volume = {351},
number = {},
pages = {119683},
doi = {10.1016/j.jenvman.2023.119683},
pmid = {38042076},
issn = {1095-8630},
mesh = {Animals ; *Conservation of Natural Resources ; *Geographic Information Systems ; New England ; Rivers ; Fishes ; Ecosystem ; },
abstract = {In the United States and elsewhere, there are a growing number of dams which have exceeded their design life and will need to be repaired or removed in the coming decades. Most of these dams no longer serve their original purpose and removal can provide ecological benefits and eliminate future maintenance costs and hazards. However, many decision-makers have been ill-prepared by community resistance to proposals to remove dams. Given the number of dam removal initiatives that have failed or been delayed due to community resistance, both ecological and social attributes of dams need to be better mapped and conveyed in understandable ways. The goal of this study was to support future decisions regarding dams by 1) developing a set of metrics to assess the social and ecological dimensions of dams, and 2) using these metrics to develop a GIS database, for the 1000+ dams in the Narragansett Bay/Rhode Island area of southern New England. The database characterizes the ecological benefits of dam removal or modification, in terms of fish passage, and the social dimensions that may need to be considered when engaging a community in discussions about the future of a dam. Our emphasis was on small-head dams (i.e. <5 m tall) which comprise most dams in the study area. We created social value metrics that used GIS data to assess dams and their impoundments for potential benefits to waterfront properties, history, sense-of-place, and recreation. We modeled our ecological metrics and ranking system after the Nature Conservancy's Northeast Aquatic Connectivity study which considered factors relating to river connectivity and watershed quality. We evaluated our social and ecological metrics using case studies of dams in the study area that had been previously removed or modified. We assumed that both sets of dams were ecologically important, but the modified dams had higher social value that prohibited their removal. Dams that had been removed or modified were both ranked as high priority in terms of value for fish passage, particularly for diadromous fish. Dams that were modified to include fish passage had substantially larger impoundments, more waterfront properties, and more features associated with recreational or cultural value (e.g. boating opportunity, visibility, etc.). Our social metrics were consistent with expectations based on the limited case studies (7 removals, 19 modifications) available in the study area. We made the dam assessment metrics readily accessible to stakeholders through an interactive ArcGIS Online web map.},
}
@article {pmid38037645,
year = {2022},
author = {Lees, D and Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the early grey, Xylocampa areola (Esper, 1789).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {312},
pmid = {38037645},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Xylocampa areola (the early grey; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 565 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,869 protein coding genes.},
}
@article {pmid38037560,
year = {2023},
author = {Boyes, D and , and , and , and , and Hammond, J and , },
title = {The genome sequence of the Gold Triangle, Hypsopygia costalis (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {15},
pmid = {38037560},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Hypsopygia costalis (the Gold Triangle; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 818 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,248 protein coding genes.},
}
@article {pmid38037477,
year = {2023},
author = {Turk, F and Sweetman, J and Allsopp, G and Crooks, M and Cuthbertson, DJ and Gabbay, M and Hishmeh, L and Lip, GYH and Strain, WD and Williams, N and Wootton, D and Banerjee, A and van der Feltz-Cornelis, C and , },
title = {Pathways to care for Long COVID and for long-term conditions from patients' and clinicians' perspective.},
journal = {Journal of evidence-based medicine},
volume = {16},
number = {4},
pages = {435-437},
doi = {10.1111/jebm.12563},
pmid = {38037477},
issn = {1756-5391},
support = {COV-LT2-0043//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Post-Acute COVID-19 Syndrome ; *COVID-19 ; Attitude of Health Personnel ; },
}
@article {pmid38036774,
year = {2023},
author = {Belho, K and Rawat, MS and Rawat, PK},
title = {GIS modeling to investigate environmental change and degradation in Kohima district, North East Hill (NEH) region of India.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {12},
pages = {1553},
pmid = {38036774},
issn = {1573-2959},
support = {202021-NFST-NAG-00170//Ministry of Tribal Affairs/ ; },
mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; Forests ; India ; Water ; },
abstract = {As a part of the Himalayan mountains, the North East Hill (NEH) region of India is geophysically dynamic and seismotectonically active since its formation about 55 million years ago with a head-on collision of the Indian plate and the Eurasian plate. The region still has been underthrusting at a rate of 4.5-5 cm/year causing the reshaping and changing of its geophysical characteristics (geology, geomorphology, relief, slope gradient, drainage system, etc.), whereas anthropogenic activities, particularly shifting cultivation and technological intervention, have caused changes or degradation of the ecological environment (air, land, water, vegetation, crop pattern, climate, wildlife, etc.). Addressing this burning geoecological problem, a geospatial technology-based case study from the Kohima district of Nagaland in the North East Hill region of India is presented here. Through the development and integration of multiple GIS modules, this reconnaissance study suggests that continuous seismic activities (about 27 seismic events/year) along tectonic faults, thrusts, and lithological shear zones have been reshaping and changing the geophysical environment, whereas the ecological environment has been changing or degrading due to decreasing natural landscape and habitats (forest area, water bodies, and shrubs) at an annual rate of 5.91 km[2] (0.60%), increasing built-up area, agricultural land, and wasteland at an annual rate of 2.73 km[2] (0.28%), 2.69 km[2] (0.27%), and 0.49 km[2] (0.05%) respectively. Results also suggest that environmental degradation results in accelerated trends of climate change (rising temperature at the rate of 0.13 °C/year, decreasing annual rainy days at the rate of 2 days/year, decreasing annual rainfall at the rate of 9.55 cm/year, mounting climatic zones at the rate of 175 m/year) and its adverse impacts (increasing extreme rainfall events at the rate of 3 events/year and causing cloud burst, erosion, landslides, and floods) in the region.},
}
@article {pmid38031900,
year = {2024},
author = {Mori, Y and Okawara, M and Shibao, K and Kohi, S and Tamura, T and Sato, N and Fujino, Y and Fushimi, K and Matsuda, S and Hirata, K},
title = {Short-term outcomes of pancreatoduodenectomy in older individuals over a 9-year period using real-world data: A multilevel analysis based on a nationwide administrative database in Japan.},
journal = {Journal of hepato-biliary-pancreatic sciences},
volume = {31},
number = {4},
pages = {262-272},
doi = {10.1002/jhbp.1396},
pmid = {38031900},
issn = {1868-6982},
support = {20AA2005//Ministry of Health, Labour and Welfare/ ; },
mesh = {Humans ; *Pancreaticoduodenectomy/mortality ; Japan/epidemiology ; Aged ; Male ; Female ; Aged, 80 and over ; *Hospital Mortality ; *Databases, Factual ; *Length of Stay/statistics &amp; numerical data ; Postoperative Complications/epidemiology ; Age Factors ; Multilevel Analysis ; Middle Aged ; Retrospective Studies ; Treatment Outcome ; },
abstract = {BACKGROUND: We aimed to evaluate the short-term outcomes of pancreatoduodenectomy (PD) in older individuals.<br><br>METHODS: Data from the Japanese Diagnosis Procedure Combination database on 62&#x2009;275 patients who underwent PD from 1 April 2012 to 31 March 2020 were analyzed. Patients were divided into five age groups: <70, 70-74, 75-79, 80-84, and&#x2009;&#x2265;85&#x2009;years. The associations between postoperative outcomes and age were investigated using multilevel analysis. The mean differences in length of hospital stay and cost were also compared.<br><br>RESULTS: The rate of PD in older individuals increased annually. Compared with the youngest age group (<&#x2009;70&#x2009;years), the incidence rate ratios for in-hospital mortality were 1.52 (95% confidence interval [CI]: 1.30-1.76), 2.07 (1.82-2.37), 2.29 (1.94-2.71), and 2.92 (2.20-3.87) in the 70-74, 75-79, 80-84, and&#x2009;&#x2265;&#x2009;85-year-old age groups, respectively (all p&#x2009;<&#x2009;.001). Postoperative complications, length of postoperative hospital stay, and cost increased significantly with increasing age.<br><br>CONCLUSIONS: These real-world data emphasize the higher levels of morbidity, mortality, and cost in older patients. Careful attention should be paid when considering the indication for PD in older individuals.},
}
@article {pmid38029580,
year = {2024},
author = {Díaz Alarcón, JA and Fonseca Alfonso, PM and Vergara Gómez, I and Díaz Lagos, M and Videira-Quintela, D and Montalvo, G},
title = {Assessment of potentially hazardous elements in soils of the Boyacá industrial corridor (Colombia) using GIS, multivariate statistical analysis, and geochemical indexes.},
journal = {Ecotoxicology and environmental safety},
volume = {269},
number = {},
pages = {115725},
doi = {10.1016/j.ecoenv.2023.115725},
pmid = {38029580},
issn = {1090-2414},
mesh = {Soil ; *Metals, Heavy/analysis ; Geographic Information Systems ; Colombia ; Cadmium/analysis ; Lead/analysis ; *Soil Pollutants/analysis ; Environmental Monitoring/methods ; *Mercury/analysis ; Risk Assessment ; China ; },
abstract = {In the industrial corridor of Boyacá, Colombia, population growth is accompanied by anthropogenic activities such as industrial operations, vehicle exhaust fumes, mining, smelting, atmospheric deposition, and excessive use of chemical products to promote crop growth. These activities are known to have a significant impact on urban and rural soils, contributing significantly to elevated concentrations of potentially hazardous elements in the environment. This industrial corridor is an area of economic and social development that needs to provide reference information that will allow us to know the state of soil quality to preserve and manage the public and geoenvironmental health of this region. Anthropogenic activities have contributed to the accumulation of potentially hazardous elements in the environment, affecting various levels of life and creating risks with economic and social implications. However, igneous activity or detrital deposition also enriches soils and creates geochemical anomalies in specific locations. In these cases, the identification of potentially hazardous elements involves the determination of likely sources of contamination and their relationship to the geological setting. In this study, the concentrations of As, Cd, Pb, Mn, Fe, Zn, Hg, Cu and Ni were determined in eighty-one soil samples from the Boyacá industrial corridor (Colombia). The sequential trend of the concentrations of potentially hazardous elements was as follows: Fe > Mn > Zn > Ni > Cu> Pb > As > Cd > Hg. Furthermore, the application of spatial analysis criteria in GIS software with multivariate statistical tools and geochemical indices allowed the identification of anthropogenic and geogenic sources. Most of the potentially hazardous elements were found in soils exposed to industrial and agricultural activities, except for iron. This element showed low variability in all samples, regardless of the geological formations. Due to the lack of reference values for potentially hazardous elements in Colombia, the concentrations were compared with the environmental standards of the Environmental Protection Agency (EPA) and the Ecuadorian Ministry of Environment, Water and Ecological Transition (MAE). The results demonstrate the complexity of the soil and represent the first exploratory study of potentially hazardous elements in this industrial corridor. These results are the starting point for the establishment of geochemical background lines in Colombia and for inspection policies for areas where productive activities converge.},
}
@article {pmid38023870,
year = {2023},
author = {Engloner, AI and Németh, K and Kós, PB and Meglécz, E and Bereczki, J},
title = {Genetic diversity of the submerged macrophyte Ceratophyllum demersum depends on habitat hydrology and habitat fragmentation.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1277916},
pmid = {38023870},
issn = {1664-462X},
abstract = {The adaptability of plant populations to a changing environment depends on their genetic diversity, which in turn is influenced by the degree of sexual reproduction and gene flow from distant areas. Aquatic macrophytes can reproduce both sexually and asexually, and their reproductive fragments are spread in various ways (e.g. by water). Although these plants are obviously exposed to hydrological changes, the degree of vulnerability may depend on the types of their reproduction and distribution, as well as the hydrological differences of habitats. The aim of this study was to investigate the genetic diversity of the cosmopolitan macrophyte Ceratophyllum demersum in hydrologically different aquatic habitats, i.e. rivers and backwaters separated from the main river bed to a different extent. For this purpose, the first microsatellite primer set was developed for this species. Using 10 developed primer pairs, a high level of genetic variation was explored in C. demersum populations. Overall, more than 80% of the loci were found to be polymorphic, a total of 46 different multilocus genotypes and 18 private alleles were detected in the 63 individuals examined. The results demonstrated that microsatellite polymorphism in this species depends on habitat hydrology. The greatest genetic variability was revealed in populations of rivers, where flowing water provides constant longitudinal connections with distant habitats. The populations of the hydrologically isolated backwaters showed the lowest microsatellite polymorphism, while plants from an oxbow occasionally flooded by the main river had medium genetic diversity. The results highlight that in contrast to species that spread independently of water flow or among hydrologically isolated water bodies, macrophytes with exclusive or dominant hydrochory may be most severely affected by habitat fragmentation, for example due to climate change.},
}
@article {pmid38020677,
year = {2023},
author = {Horvatić, S and Parmentier, E and Malavasi, S and Amorim, MPC and Fonseca, PJ and Zanella, D},
title = {Endemic fish calling: Acoustics and reproductive behaviour of the Neretva dwarf goby Orsinigobius croaticus.},
journal = {Ecology and evolution},
volume = {13},
number = {11},
pages = {e10673},
pmid = {38020677},
issn = {2045-7758},
abstract = {The Neretva dwarf goby Orsinigobius croaticus (Gobiiformes, Gobionellidae) is an endemic fish native to the freshwaters of the Adriatic Basin in Croatia and Bosnia and Herzegovina, a Mediterranean Biodiversity Hotspot. Due to its limited distribution range, specific karst habitat and endangered status, laboratory studies on reproductive biology are scarce but crucial. Herein, we investigated the sound production and acoustic behaviour of the endangered O. croaticus during reproductive intersexual laboratory encounters, utilising an interdisciplinary approach. We also performed dissections and micro-computed tomography (μCT) scanning of the pectoral girdle to explore its potential involvement in sound production. Finally, comparative acoustic analysis was conducted on sounds produced by previously recorded soniferous sand gobies to investigate whether acoustic features are species-specific. The endemic O. croaticus is a soniferous species. Males of this species emit pulsatile sounds composed of a variable number of short (~15 ms) consecutive pulses when interacting with females, usually during the pre-spawning phase in the nest, but also during courtship outside the nest. Pulsatile sounds were low-frequency and short pulse trains (~140 Hz, <1000 ms). Male visual behaviour rate was higher when co-occurring with sounds and females entered the male's nest significantly more frequently when sounds were present. Characteristic body movements accompanied male sound production, such as head thrust and fin spreading. Furthermore, μCT scans and dissections suggest that O. croaticus shares certain anatomical similarities of the pectoral girdle (i.e. osseous elements and arrangement of levator pectoralis muscles) to previously studied sand gobies that could be involved in sound production. Multivariate comparisons, using sounds produced by eight soniferous European sand gobies, effectively distinguished soniferous (and sympatric) species based on their acoustic properties. However, the discrimination success decreased when temperature-dependent features (sound duration and pulse repetition rate) were excluded from the analysis. Therefore, we suggest both spectral and temporal features are important for the acoustic differentiation of sand gobies.},
}
@article {pmid38019786,
year = {2023},
author = {Lu, Z and Zhong, H and Tang, L and Luo, J and Zhou, W and Liu, L},
title = {Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network.},
journal = {PLoS computational biology},
volume = {19},
number = {11},
pages = {e1011634},
pmid = {38019786},
issn = {1553-7358},
mesh = {Humans ; *RNA, Long Noncoding/genetics ; Computational Biology/methods ; *Neoplasms/genetics ; *MicroRNAs ; Neural Networks, Computer ; Algorithms ; },
abstract = {There is a growing body of evidence indicating the crucial roles that long non-coding RNAs (lncRNAs) play in the development and progression of various diseases, including cancers, cardiovascular diseases, and neurological disorders. However, accurately predicting potential lncRNA-disease associations remains a challenge, as existing methods have limitations in extracting heterogeneous association information and handling sparse and unbalanced data. To address these issues, we propose a novel computational method, called HGC-GAN, which combines heterogeneous graph convolutional neural networks (GCN) and generative adversarial networks (GAN) to predict potential lncRNA-disease associations. Specifically, we construct a lncRNA-miRNA-disease heterogeneous network by integrating multiple association data and sequence information. The GCN-based generator is then employed to aggregate neighbor information of nodes and obtain node embeddings, which are used to predict lncRNA-disease associations. Meanwhile, the GAN-based discriminator is trained to distinguish between real and fake lncRNA-disease associations generated by the generator, enabling the generator to improve its ability to generate accurate lncRNA-disease associations gradually. Our experimental results demonstrate that HGC-GAN performs better in predicting potential lncRNA-disease associations, with AUC and AUPR values of 0.9591 and 0.9606, respectively, under 10-fold cross-validation. Moreover, our case study further confirms the effectiveness of HGC-GAN in predicting potential lncRNA-disease associations, even for novel lncRNAs without any known lncRNA-disease associations. Overall, our proposed method HGC-GAN provides a promising approach to predict potential lncRNA-disease associations and may have important implications for disease diagnosis, treatment, and drug development.},
}
@article {pmid38018647,
year = {2023},
author = {Gouvêa, ECDP and Ribeiro, AM and Aquino, EC and Stopa, SR},
title = {Mortality trend due to chronic kidney disease in Brazil: an ecological study.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {32},
number = {3},
pages = {e2023313},
pmid = {38018647},
issn = {2237-9622},
mesh = {Female ; Humans ; Male ; Brazil/epidemiology ; Information Systems ; *Renal Insufficiency, Chronic/mortality ; *Mortality/trends ; },
abstract = {OBJECTIVE: To analyze chronic kidney disease mortality in Brazil according to sex, age group and region of residence, from 2009 to 2020.<br><br>METHODS: This was a time series study having deaths as its unit of analysis, based on Mortality Information System data. The mortality rate was standardized using the direct method and the temporal trend was analyzed using the Prais-Winsten method.<br><br>RESULTS: There was a rising trend in chronic kidney disease mortality, ranging from 2.82, in 2009, to 3.24 in 2020 (average annual increase 1.29%; 95%CI 0.73;1.85), with a greater increase in males (1.14% per year; 95%CI 0.52;1.76), those aged 75 years and over (2.23% per year; 95%CI 1.87; 2.60) and in the Northern Region (3.86% per year; 95%CI 1.86;5.90) and Northeast Region (3.36% per year; 95%CI 2.24;4.50).<br><br>CONCLUSION: Chronic kidney disease mortality showed a rising trend in the period, with sociodemographic disparities.<br><br>MAIN RESULTS: A rising mortality trend was found for both sexes, with a greater increase in males, those aged over 75 years and in the North and Northeast regions of Brazil; mortality was highest in the Midwest region throughout the entire period.<br><br>IMPLICATIONS FOR SERVICES: The results point to the need to implement public policies with guidelines for addressing chronic kidney disease, focused on strengthening Primary Health Care (PHC).<br><br>PERSPECTIVES: Expanding access to health services, health education and integration between PHC, health surveillance and specialized care are strategies that would possibly prove to be efficient in managing this chronic health condition.},
}
@article {pmid38017684,
year = {2023},
author = {Yin, FF and Shi, X and Guo, HF and Shen, YR},
title = {Performance evaluation of rural water environment governance based on AHP: a case study of the Beitang River Basin.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {88},
number = {10},
pages = {2661-2676},
doi = {10.2166/wst.2023.354},
pmid = {38017684},
issn = {0273-1223},
mesh = {*Rivers ; *Analytic Hierarchy Process ; Water Quality ; Conservation of Natural Resources ; China ; },
abstract = {Rural water environment governance in China still lacks a systematic and comprehensive assessment protocol to help analyze and improve such governance performance. The Analytic Hierarchy Process (AHP) method was employed in this study to build a governance assessment system that integrates ecological conditions, water pollution control, and public satisfaction. To cover these topics, the assessment system is composed of an indicator layer that is customized to rural water environment governance in China. The Beitang River, located in the rural region of Hangzhou, Zhejiang, China, was presented as a case study. Field investigation provided raw data for this assessment. A questionnaire survey was conducted to interview local residents on the governance performance. An additional survey with executives who played major roles in the governance was performed to reconstruct a water environment assessment on the Beitang River prior to the governance, in order to highlight the effects of the governance through contrast. The results showed consistency in the questionnaire survey and the assessment system. The AHP assessment system was able to reflect the improvement in the water quality, river ecology, and residential welfare after the governance, and suggested limits and future directions in the following upgrade programs for the river basin.},
}
@article {pmid38017319,
year = {2023},
author = {Lawler, T and Warren Andersen, S and Trentham-Dietz, A and Sethi, AK and Tevaarwerk, AJ and Malecki, KMC and Litzelman, K and Pophali, PA and Gangnon, RE and Hampton, JM and Kwekkeboom, K and LoConte, NK},
title = {Change in alcohol consumption during the Covid-19 pandemic and associations with mental health and financial hardship: results from a survey of Wisconsin patients with cancer.},
journal = {Journal of cancer survivorship : research and practice},
volume = {},
number = {},
pages = {},
pmid = {38017319},
issn = {1932-2267},
support = {P30 CA014520/CA/NCI NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; P30CA014520/CA/NCI NIH HHS/United States ; UL1TR002373/NH/NIH HHS/United States ; },
abstract = {PURPOSE: Alcohol consumption increases health risks for patients with cancer. The Covid-19 pandemic may have affected drinking habits for these individuals. We surveyed patients with cancer to examine whether changes in drinking habits were related to mental health or financial effects of the pandemic.<br><br>METHODS: From October 2020 to April 2021, adult patients (age 18-80 years at diagnosis) treated for cancer in southcentral Wisconsin were invited to complete a survey. Age-adjusted percentages for history of anxiety or depression, emotional distress, and financial impacts of Covid-19 overall and by change in alcohol consumption (non-drinker, stable, decreased, or increased) were obtained via logistic regression.<br><br>RESULTS: In total, 1,875 patients were included in the analysis (median age 64, range 19-87 years), including 9% who increased and 23% who decreased drinking. Compared to stable drinkers (32% of sample), a higher proportion of participants who increased drinking alcohol also reported anxiety or depression (45% vs. 26%), moderate to severe emotional distress (61% vs. 37%) and viewing Covid-19 as a threat to their community (67% vs. 55%). Decreased (vs. stable) drinking was associated with higher prevalence of depression or anxiety diagnosis, emotional distress, and negative financial impacts of the pandemic. Compared to non-drinkers (36% of sample), participants who increased drinking were more likely to report emotional distress (61% vs. 48%).<br><br>CONCLUSIONS: Patients with cancer from Wisconsin who changed their alcohol consumption during the Covid-19 pandemic were more likely to report poor mental health including anxiety, depression, and emotional distress than persons whose alcohol consumption was stable.<br><br>Clinicians working with cancer survivors should be aware of the link between poor mental health and increased alcohol consumption and be prepared to offer guidance or referrals to counseling, as needed.},
}
@article {pmid38017016,
year = {2023},
author = {Adhurya, S and Lee, DY and Lee, DS and Park, YS},
title = {Functional trait dataset of benthic macroinvertebrates in South Korean streams.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {838},
pmid = {38017016},
issn = {2052-4463},
support = {NRF-2019R1A2C1087099//National Research Foundation of Korea (NRF)/ ; 2020003050003//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; },
mesh = {Animals ; Biodiversity ; *Ecosystem ; Environmental Monitoring ; *Invertebrates ; Rivers ; Republic of Korea ; },
abstract = {Functional traits are the result of evolution and adaptation, providing important ecological insights into how organisms interact with their environment. Benthic macroinvertebrates, in particular, have garnered attention as biomonitoring indicators for freshwater ecosystems. This study presents a functional trait dataset for benthic macroinvertebrates, comprising 447 taxa (393 at genus level, 53 at family level and one at class level) from five phyla (Annelida, Arthropoda, Mollusca, Nematomorpha, and Platyhelmenthes), categorized into nine traits related to life history, morphology, and habit. To account for variation in available trait information, we assigned confidence levels to each taxon and functional trait based on the level of evidence using fuzzy coding. Our dataset provides an important resource for understanding the ecology of benthic macroinvertebrates in South Korea, serving as a valuable baseline dataset for studying their biodiversity, conservation, and biomonitoring in freshwater ecosystems.},
}
@article {pmid38014157,
year = {2023},
author = {Warren, WC and Rice, ES and Maggs, X and Roback, E and Keene, A and Martin, F and Ogeh, D and Haggerty, L and Carroll, RA and McGaugh, S and Rohner, N},
title = {Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38014157},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 GM127872/GM/NIGMS NIH HHS/United States ; R24 OD011198/OD/NIH HHS/United States ; },
abstract = {The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and non-coding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared to other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared to a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.},
}
@article {pmid38013951,
year = {2022},
author = {Wang, Z and Yang, W and Ryan, K and Garai, S and Auerbach, BM and Shen, L},
title = {Using Optimal Transport to Improve Spherical Harmonic Quantification of Complex Biological Shapes.},
journal = {Proceedings. IEEE International Conference on Bioinformatics and Biomedicine},
volume = {2022},
number = {},
pages = {1255-1261},
pmid = {38013951},
issn = {2156-1125},
support = {RF1 AG068191/AG/NIA NIH HHS/United States ; U01 AG068057/AG/NIA NIH HHS/United States ; },
abstract = {The knowledge of the anatomical shape of both gross and microscopic structures is the key to understanding the effects of disease processes on cellular structure. Geometric morphometric methods, such as Procrustes superimposition, and Spherical Harmonics (SPHARM), have been used to capture the biological shape variation and group differences in morphology. Previous SPHARM-MAT techniques use the CALD algorithm to parameterize the mesh surface. It starts from initial mapping and performs local and global smoothing methods alternately to control the area and length distortions simultaneously. However, this parameterization may not be sufficient in complex morphological cases. To bridge this gap, we propose SPHARM-OT, an enhanced SPHARM surface modeling method using optimal transport (OT) for spherical parameterization. First, the genus 0 3D objects are conformally mapped onto a sphere. Then the optimal transport theory via spherical power diagram is introduced to minimize the area distortion. This new algorithm can effectively reduce the area distortion and lead to a better reconstruction result. We demonstrate the effectiveness of the method by applying it to the human sphenoidal paranasal sinuses.},
}
@article {pmid38011826,
year = {2024},
author = {Wilson, J and Sokhansanj, BA and Chong, WC and Chandraghatgi, R and Rosen, GL and Ji, HF},
title = {Fragment databases from screened ligands for drug discovery (FDSL-DD).},
journal = {Journal of molecular graphics &amp; modelling},
volume = {127},
number = {},
pages = {108669},
doi = {10.1016/j.jmgm.2023.108669},
pmid = {38011826},
issn = {1873-4243},
mesh = {Ligands ; *Drug Discovery/methods ; *Drug Design ; High-Throughput Screening Assays ; Databases, Factual ; },
abstract = {Fragment-based drug design (FBDD) is one major drug discovery method employed in computer-aided drug discovery. Due to its inherent limitations, this process experiences long processing times and limited success rates. Here we present a new Fragment Databases from Screened Ligands Drug Design method (FDSL-DD) that intelligently incorporates information about fragment characteristics into a fragment-based design approach to the drug development process. The initial step of the FDSL-DD is the creation of a fragment database from a library of docked, drug-like ligands for a specific target, which deviates from the traditional in silico FBDD strategy, incorporating structure-based design screening techniques to combine the advantages of both approaches. Three different protein targets have been tested in this study to demonstrate the potential of the created fragment library and FDSL-DD. Utilizing the FDSL-DD led to an increase in binding affinity for each protein target. The most substantial increase was exhibited by the ligand designed for TIPE2, with a 3.6 kcalmol[-1] difference between the top ligand from the FDSL-DD and top ligand from the high throughput virtual screening (HTVS). Using drug-like ligands in the initial HTVS allows for a greater search of chemical space, with higher efficiency in fragments selection, less grid boxes, and potentially identifying more interactions.},
}
@article {pmid38010780,
year = {2024},
author = {Jovanović, V and Rudnev, M and Abdelrahman, M and Abdul Kadir, NB and Adebayo, DF and Akaliyski, P and Alaseel, R and Alkamali, YA and Alonso Palacio, LM and Amin, A and Andres, A and Ansari-Moghaddam, A and Aruta, JJB and Avanesyan, HM and Ayub, N and Bacikova-Sleskova, M and Baikanova, R and Bakkar, B and Bartoluci, S and Benitez, D and Bodnar, I and Bolatov, A and Borchet, J and Bosnar, K and Broche-Pérez, Y and Buzea, C and Cassibba, R and Del Pilar Grazioso, M and Dhakal, S and Dimitrova, R and Dominguez, A and Duong, CD and Dutra Thome, L and Estavela, AJ and Fayankinnu, EA and Ferenczi, N and Fernández-Morales, R and Friehs, MT and Gaete, J and Gharz Edine, W and Gindi, S and Giordani, RCF and Gjoneska, B and Godoy, JC and Hancheva, CD and Hapunda, G and Hihara, S and Islam, MS and Janovská, A and Javakhishvili, N and Kabir, RS and Kabunga, A and Karakulak, A and Karl, JA and Katović, D and Kauyzbay, Z and Kaźmierczak, M and Khanna, R and Khosla, M and Kisaakye, P and Klicperova-Baker, M and Kokera, R and Kozina, A and Krauss, SE and Landabur, R and Lefringhausen, K and Lewandowska-Walter, A and Liang, YH and Lizarzaburu-Aguinaga, D and López Steinmetz, LC and Makashvili, A and Malik, S and Manrique-Millones, D and Martín-Carbonell, M and Mattar Yunes, MA and McGrath, B and Mechili, EA and Mejía Alvarez, M and Mhizha, S and Michałek-Kwiecień, J and Mishra, SK and Mohammadi, M and Mohsen, F and Moreta-Herrera, R and Muradyan, MD and Musso, P and Naterer, A and Nemat, A and Neto, F and Neto, J and Okati-Aliabad, H and Orellana, CI and Orellana, L and Park, J and Pavlova, I and Peralta, EA and Petrytsa, P and Pilkauskaite Valickiene, R and Et Al, },
title = {The Coronavirus Anxiety Scale: Cross-national measurement invariance and convergent validity evidence.},
journal = {Psychological assessment},
volume = {36},
number = {1},
pages = {14-29},
doi = {10.1037/pas0001270},
pmid = {38010780},
issn = {1939-134X},
support = {//Cooperative University of Colombia/ ; //Agencia Nacional de Investigaci&#xf3;n y Desarrollo; Millennium Science Initiative Program/ ; //GESIS-Leibniz Institute for the Social Sciences/ ; //Ministry of Education, Youth, and Sports; European Union-Next Generation European Union/ ; //RA Science Committee/ ; //American Psychological Association; Division 48/ ; //Foundation for Polish Science/ ; //Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Humans ; Reproducibility of Results ; Psychometrics/methods ; *Anxiety/diagnosis ; *COVID-19/diagnosis ; Fear ; },
abstract = {Coronavirus Anxiety Scale (CAS) is a widely used measure that captures somatic symptoms of coronavirus-related anxiety. In a large-scale collaboration spanning 60 countries (Ntotal = 21,513), we examined the CAS's measurement invariance and assessed the convergent validity of CAS scores in relation to the fear of COVID-19 (FCV-19S) and the satisfaction with life (SWLS-3) scales. We utilized both conventional exact invariance tests and alignment procedures, with results revealing that the single-factor model fit the data well in almost all countries. Partial scalar invariance was supported in a subset of 56 countries. To ensure the robustness of results, given the unbalanced samples, we employed resampling techniques both with and without replacement and found the results were more stable in larger samples. The alignment procedure demonstrated a high degree of measurement invariance with 9% of the parameters exhibiting noninvariance. We also conducted simulations of alignment using the parameters estimated in the current model. Findings demonstrated reliability of the means but indicated challenges in estimating the latent variances. Strong positive correlations between CAS and FCV-19S estimated with all three different approaches were found in most countries. Correlations of CAS and SWLS-3 were weak and negative but significantly differed from zero in several countries. Overall, the study provided support for the measurement invariance of the CAS and offered evidence of its convergent validity while also highlighting issues with variance estimation. (PsycInfo Database Record (c) 2024 APA, all rights reserved).},
}
@article {pmid38007505,
year = {2023},
author = {Wang, Z and Jia, Y and Li, P and Tang, Z and Guo, Y and Wen, L and Yu, H and Cui, F and Hu, F},
title = {Study on environmental factors affecting the quality of codonopsis radix based on MaxEnt model and all-in-one functional factor.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20726},
pmid = {38007505},
issn = {2045-2322},
support = {81972018//National Natural Science Foundation of China/ ; 21ZD4FA013//Major science and technology project of Gansu Province/ ; 20CX4FK014//People's Livelihood Special Project from Technical Innovation Guide Plan of Gansu Province/ ; [2022] Gan-71//Key Talent Project of Organization Department of Gansu Provincial Party Committee/ ; 22ZY1QA012//Central Government Guiding Local Science and Technology Development Fund Project/ ; 22CX8GA009//Special Project of Science and Technology Commissioner of Gansu Province/ ; 2017-RC-115, 2020-RC-41//Talent Innovation and Entrepreneurship Project of Lanzhou/ ; },
mesh = {*Codonopsis/chemistry ; Geographic Information Systems ; Plant Roots/chemistry ; Altitude ; },
abstract = {Owing to the increasing market demand of Codonopsis Radix, the cropper blindly cultivates to expand planting area for economic benefits, which seriously affects the quality of Codonopsis Radix. Therefore, this study synthesized 207 batches of Codonopsis Radix and 115 ecological factors, and analyzed the suitable planting areas of Codonopsis pilosula under current and future climate change based on Geographic Information System (GIS) and MaxEnt model. Secondly, we evaluated the quality of Codonopsis Radix based on the all-in-one functional factor including chromatographic fingerprint, the index components, the effective compounds groups, the nutritional components, and the nutritional elements, and the quality regionalization of Codonopsis Radix was analyzed. Finally, the ecological factors affecting the accumulation of effective components of Codonopsis Radix were analyzed. This study found for the first time that the highly suitable area of Codonopsis pilosula was mainly distributed in the Weihe River system and the Bailongjiang River system in Gansu Province. There were differences in the quality of Codonopsis Radix from different ecologically suitable areas based on the all-in-one functional factors, and the comprehensive high-quality area of Codonopsis Radix was mainly distributed in Longnan and Longxi district of Gansu Province. The precipitation, temperature and altitude play a key role in the accumulation of chemical components in the 10 ecological factors affecting the distribution of Codonopsis pilosula. Under future climatic conditions, the highly suitable area of Codonopsis pilosula is decreased.},
}
@article {pmid38005973,
year = {2023},
author = {Klee, B and Diexer, S and Sarajan, MH and Glaser, N and Binder, M and Frese, T and Girndt, M and Sedding, D and Hoell, JI and Moor, I and Gekle, M and Mikolajczyk, R and Gottschick, C},
title = {Regional Differences in Uptake of Vaccination against COVID-19 and Influenza in Germany: Results from the DigiHero Cohort.},
journal = {Vaccines},
volume = {11},
number = {11},
pages = {},
pmid = {38005973},
issn = {2076-393X},
abstract = {During the COVID-19 pandemic in Germany, vaccination uptake exhibited considerable regional disparities. To assess the factors contributing to this variation, we examined the association of sociodemographic variables with COVID-19, COVID-19 booster, and influenza vaccination status within a cohort of 37,078 participants from 13 German federal states in the digital health cohort study commonly known as DigiHero. Our findings revealed variations in vaccination rates based on sociodemographic factors. However, these factors had limited explanatory power regarding regional differences in vaccine uptake. In contrast, we found substantial correlations between regional support of specific parties during the last local elections and the vaccination uptake at the level of each administrative district. In conclusion, sociodemographic factors alone did not suffice to explain the regional disparities in vaccine uptake. Political stances can play a major role, although the current investigation did not assess individual political orientations but rather used only an ecological approach.},
}
@article {pmid38005880,
year = {2023},
author = {Barnes, M and Price, DC},
title = {Endogenous Viral Elements in Ixodid Tick Genomes.},
journal = {Viruses},
volume = {15},
number = {11},
pages = {},
pmid = {38005880},
issn = {1999-4915},
support = {Capacity Project NE1943: "Biology, Ecology &amp; Management of Emerging Disease Vectors"//United States Department of Agriculture/ ; },
mesh = {Animals ; Humans ; *Ixodidae/genetics ; *Arthropods ; *Ixodes ; *RNA Viruses ; *Viruses ; },
abstract = {The documentation of endogenous viral elements (EVEs; virus-derived genetic material integrated into the genome of a nonviral host) has offered insights into how arthropods respond to viral infection via RNA interference pathways. Small non-coding RNAs derived from EVE loci serve to direct RNAi pathways in limiting replication and infection from cognate viruses, thus benefiting the host's fitness and, potentially, vectorial capacity. Here we use informatic approaches to analyze nine available genome sequences of hard ticks (Acari: Ixodidae; Rhipicephalus sanguineus, R. microplus, R. annulatus, Ixodes ricinus, I. persulcatus, I. scapularis, Hyalomma asiaticum, Haemaphysalis longicornis, and Dermacentor silvarum) to identify endogenous viral elements and to illustrate the shared ancestry of all elements identified. Our results highlight a broad diversity of viral taxa as having given rise to 1234 identified EVEs in ticks, with Mononegavirales (specifically Rhabdoviridae) well-represented in this subset of hard ticks. Further investigation revealed extensive adintovirus integrations in several Ixodes species, the prevalence of Bunyavirales EVEs (notably not observed in mosquitoes), and the presence of several elements similar to known emerging human and veterinary pathogens. These results will inform subsequent work on current and past associations with tick species with regard to the viruses from which their "viral fossils" are derived and may serve as a reference for quality control of various tick-omics data that may suffer from misidentification of EVEs as viral genetic material.},
}
@article {pmid38004638,
year = {2023},
author = {Zhu, Q and Ruan, M and Hu, Z and Miao, K and Ye, C},
title = {The Relationship between Acid Production and the Microbial Community of Newly Produced Coal Gangue in the Early Oxidation Stage.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004638},
issn = {2076-2607},
support = {grant number 2019YFC1805003//National Key Research and Development Program/ ; },
abstract = {Coal gangue is a solid waste formed during coal production, and the acid mine drainage it generates during open-pit storage severely pollutes the ecological environment of mining areas. Microorganisms play a crucial catalytic role in acidification, and their species and gene functions change during the oxidation process of coal gangue. In this study, the changes in microbial community structure were investigated during the initial acidification process for newly produced gangue exposed to moisture by monitoring the changes in pH, EC, sulfate ion concentration, and the iron oxidation rate of gangue leaching solutions. Moreover, the composition and functional abundance of microbial communities on the surface of the gangue were analyzed with rainfall simulation experiments and 16S rRNA sequencing. The study yielded the following findings: (1) The critical period for newly produced gangue oxidation spanned from 0~15 d after its exposure to water; the pH of leaching solutions decreased from 4.65 to 4.09 during this time, and the concentration and oxidation rate of iron in the leaching solutions remained at low levels, indicating that iron oxidation was not the main driver for acidification during this stage. (2) When the gangue was kept dry, Burkholderia spp. dominated the gangue microbial community. When the gangue was exposed to moisture, the rate of acidification accelerated, and Pseudomonas replaced Burkholderia as the dominant genus in the community. (3) In terms of gene function, the microbial community of the acidified gangue had stronger nitrogen cycling functions, and an increase in the abundance of microorganisms related to the sulfur cycle occurred after day 15 of the experiment. The microbial community in the acidified gangue had more stress resistance than the community of the newly formed gangue, but its potential to decompose environmental pollutants decreased.},
}
@article {pmid38001289,
year = {2023},
author = {Zhou, L and Wang, Y and Li, D and Zhang, J and Zhu, X},
title = {Efficient degradation of phenanthrene by biochar-supported nano zero-valent iron activated persulfate: performance evaluation and mechanism insights.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {60},
pages = {125731-125740},
pmid = {38001289},
issn = {1614-7499},
mesh = {Iron/chemistry ; *Water Pollutants, Chemical/analysis ; Charcoal/chemistry ; *Phenanthrenes ; },
abstract = {Biochar-supported nano zero-valent iron (BC@nZVI) is a novel and efficient non-homogeneous activator for persulfate (PS). This study aimed to identify the primary pathways, the degradation mechanism and the performance of phenanthrene (PHE) with PS activated by BC@nZVI (BC@nZVI/PS). BC@nZVI as an activator for PS was prepared by liquid phase reduction method. BC@nZVI was characterized using scanning electron microscopy, transmission electron microscopy, X-ray diffractometer and Fourier transform infrared spectroscopy. The effects of the iron-carbon mass ratio and BC@nZVI dosage were investigated, and a pseudo-first-order kinetic model was used to evaluate the PHE degradation. The results showed that BC supported nZVI and inhibited the agglomeration of nZVI, improving PS's activation efficiency. The optimal iron-carbon mass ratio was determined to be 1:4, accompanied by a dosage of 0.6 g/L of BC@nZVI. During PS activation, nZVI was transformed to Fe[2+] and Fe[3+], with the majority being Fe[3+]. The reducibility of nZVI in BC@nZVI enabled the reduction of Fe[3+] to Fe[2+] to activate PS. Radical quenching and electron paramagnetic resonance (EPR) revealed that the oxidative radicals in the BC@nZVI/PS system were mainly SO4[-]· and ·OH, where SO4[-]· was the primary free radical under acidic and neutral conditions and ·OH in alkaline conditions. Additionally, BC@nZVI adsorption had a limited role in PHE removal. This study can provide mechanism insights of PHE degradation in water with BC@nZVI activation of the Na2S2O8 system.},
}
@article {pmid37999540,
year = {2023},
author = {Tan, M and Dong, J and Qu, J and Hao, M},
title = {The Patterns of Migration of Potentially Toxic Elements from Coal Mining Subsidence Areas and Associated Soils to Waterlogged Areas.},
journal = {Toxics},
volume = {11},
number = {11},
pages = {},
pmid = {37999540},
issn = {2305-6304},
support = {52204190//National Natural Science Foundation of China/ ; 42271368//National Natural Science Foundation of China/ ; 2021YCPY0113//Fundamental Research Funds for the Central Universities/ ; 2019ZD03//Xuzhou Ecological Civilization Construction research project/ ; },
abstract = {It is crucial for effectively controlling potentially toxic element (PTE) pollution to understand the pollution situation, ecological risks, health risks, and migration patterns of PTEs. However, currently, no research has been conducted on the migration patterns of soil PTEs from coal mining subsidence areas to waterlogged areas under different restoration modes. In this study, a total of 15 sediment samples and 60 soil samples were collected from landscaped wetlands, aquaculture wetland, fish-photovoltaic complementary wetland, photovoltaic wetland, and waterlogged areas with untreated coal mining subsidence. The PTE pollution status, ecological risks, health risks, migration patterns, and the important factors influencing the migration were analyzed. The results indicated that the comprehensive pollution level of PTEs in waterlogged areas with coal mining subsidence can be reduced by developing them into landscaped wetlands, aquaculture wetlands, fish-photovoltaic complementary wetlands, and photovoltaic wetlands. Additionally, the closer to the waterlogged area, the higher the Cu content in the subsidence area soil is, reaching its peak in the waterlogged area. The Cd was influenced positively by SOC and pH. The research results were of great significance for formulating reclamation plans for waterlogged areas and controlling PTE pollution.},
}
@article {pmid37996937,
year = {2023},
author = {Dougan, KE and Deng, ZL and Wöhlbrand, L and Reuse, C and Bunk, B and Chen, Y and Hartlich, J and Hiller, K and John, U and Kalvelage, J and Mansky, J and Neumann-Schaal, M and Overmann, J and Petersen, J and Sanchez-Garcia, S and Schmidt-Hohagen, K and Shah, S and Spröer, C and Sztajer, H and Wang, H and Bhattacharya, D and Rabus, R and Jahn, D and Chan, CX and Wagner-Döbler, I},
title = {Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {265},
pmid = {37996937},
issn = {1474-760X},
support = {Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; Transregio SFB TRR-52 Roseobacter//Deutsche Forschungsgemeinschaft/ ; DP190102474//Australian Research Council/ ; DP190102474//Australian Research Council/ ; Thomas Davies Research Grant for Marine//Australian Academy of Science/ ; Soil//Australian Academy of Science/ ; Plant Biology//Australian Academy of Science/ ; },
mesh = {Humans ; *Harmful Algal Bloom ; *Dinoflagellida/genetics ; Multiomics ; Genomics ; Heat-Shock Response ; },
abstract = {BACKGROUND: "Red tides" are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters, and are increasingly frequent. The molecular, regulatory, and evolutionary mechanisms that underlie the heat stress response in these harmful bloom-forming algal species remain little understood, due in part to the limited genomic resources from dinoflagellates, complicated by the large sizes of genomes, exhibiting features atypical of eukaryotes.<br><br>RESULTS: We present the de novo assembled genome (~&#x2009;4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we study the molecular mechanisms that underpin the algal response to heat stress, which is relevant to current ocean warming trends. We present the first evidence of a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. These results reveal genomic signatures and post-transcriptional regulation for the first time in a pelagic dinoflagellate.<br><br>CONCLUSIONS: Our multi-omics analyses uncover the molecular response to heat stress in an important bloom-forming algal species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation. The dynamics and interplay of molecular regulatory mechanisms may explain in part how dinoflagellates diversified to become some of the most ecologically successful organisms on Earth.},
}
@article {pmid37994954,
year = {2023},
author = {Aksoy, H},
title = {Determination of landslide susceptibility with Analytic Hierarchy Process (AHP) and the role of forest ecosystem services on landslide susceptibility.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {12},
pages = {1525},
pmid = {37994954},
issn = {1573-2959},
mesh = {*Ecosystem ; *Landslides ; Analytic Hierarchy Process ; Environmental Monitoring/methods ; Geographic Information Systems ; Forests ; },
abstract = {The analysis of landslide susceptibility is a crucial tool in the mitigation and management of ecological and economic hazards. The number of studies examining how the form and durability of forest areas affect landslide susceptibility is very limited. This study was conducted in the Marmara region of northwestern Türkiye, where forested areas and industrial zones are intertwined and dense. The landslide susceptibility map was produced by Analytic Hierarchy Process (AHP) method. In the context of AHP, a total of 12 different variables were employed, namely lithology, slope, curvatures, precipitations, aspect, distance to fault lines, distance to streams, distance to roads, land use, soil, elevation, and Normalized Difference Vegetation Index (NDVI). The performance analysis of the landslide susceptibility map was conducted using the Receiver Operating Characteristics (ROC) curve method. The AUC value was computed (0.809) for the landslide susceptibility map generated by using the AHP technique. Forest type maps were used to analyze the impact of forests on landslide susceptibility. In terms of forest structure, 4 main criteria were determined: stand structure, development stage, crown closure, and stand age. Each criterion was analyzed with Geographic Information Systems (GIS) by overlaying it with the landslide susceptibility map of the study area. The results showed that the risk of landslides was lowest in forests with more than one tree species, mature, development stage and of (e) > 52 cm, and crown closure of 41%-70% (2).},
}
@article {pmid37994909,
year = {2023},
author = {Jiahui, G and Feilong, M and Nastase, SA and Haxby, JV and Gobbini, MI},
title = {Cross-movie prediction of individualized functional topography.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {37994909},
issn = {2050-084X},
support = {R01 MH127199/MH/NIMH NIH HHS/United States ; MH127199/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Motion Pictures ; *Academies and Institutes ; Brain ; Cognition ; Databases, Factual ; },
abstract = {Participant-specific, functionally defined brain areas are usually mapped with functional localizers and estimated by making contrasts between responses to single categories of input. Naturalistic stimuli engage multiple brain systems in parallel, provide more ecologically plausible estimates of real-world statistics, and are friendly to special populations. The current study shows that cortical functional topographies in individual participants can be estimated with high fidelity from naturalistic stimuli. Importantly, we demonstrate that robust, individualized estimates can be obtained even when participants watched different movies, were scanned with different parameters/scanners, and were sampled from different institutes across the world. Our results create a foundation for future studies that allow researchers to estimate a broad range of functional topographies based on naturalistic movies and a normative database, making it possible to integrate high-level cognitive functions across datasets from laboratories worldwide.},
}
@article {pmid37994038,
year = {2024},
author = {Nahas, C and Gandit, M and Quillion-Dupré, L and Monfort, E},
title = {How to engage patients in computerized cognitive training: a cognitive rehabilitation expert's perspective.},
journal = {Disability and rehabilitation. Assistive technology},
volume = {19},
number = {6},
pages = {2306-2318},
doi = {10.1080/17483107.2023.2284879},
pmid = {37994038},
issn = {1748-3115},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Cognitive Training/methods ; Interviews as Topic ; Patient Participation ; Qualitative Research ; *Software ; Therapy, Computer-Assisted ; },
abstract = {PURPOSE: The relationship between a patient and their therapist plays a crucial role in patient engagement. While Computerized Cognitive Training (CCT) may assist in preserving cognitive skills in cases of aging, dementia or acquired brain injuries, its effectiveness has not been definitively proven. Improving user engagement, acceptance, and software usability could aid in addressing this issue. The present study aims to identify potential obstacles and facilitators by examining the perspectives of rehabilitation professionals on the current usage of CCT software.<br><br>METHODS: Semi-structured interviews were conducted with 16 rehabilitation professionals, familiar with a CCT software. The data were transcribed and followed by an independent iterative thematic analysis.<br><br>RESULTS: Two major themes were identified: (1) facilitating factors and (2) difficulties related to use. The main obstacles were difficulties related to the computerized nature of the exercises, technology use, understanding the software and general learning difficulties. The main facilitators were the ecological and novel nature of the exercises, and the adaptability of the difficulty levels.<br><br>CONCLUSION: The complexity of the CCT presents challenges for its usage by rehabilitation professionals, which in turn can impede patient utilization as well. To address this issue and promote sustainable use of the software, providing instruction delivery to facilitate learning and understanding of the CCT is essential. Additionally, creating a standardized foundation that therapists can refer to for guidance may also aid in optimizing the software's usage. It is recommended to utilize a model for CCT acceptability and acceptance in developing these solutions to enhance patient engagement.},
}
@article {pmid37985899,
year = {2023},
author = {Gonzalez, A and Vihervaara, P and Balvanera, P and Bates, AE and Bayraktarov, E and Bellingham, PJ and Bruder, A and Campbell, J and Catchen, MD and Cavender-Bares, J and Chase, J and Coops, N and Costello, MJ and Czúcz, B and Delavaud, A and Dornelas, M and Dubois, G and Duffy, EJ and Eggermont, H and Fernandez, M and Fernandez, N and Ferrier, S and Geller, GN and Gill, M and Gravel, D and Guerra, CA and Guralnick, R and Harfoot, M and Hirsch, T and Hoban, S and Hughes, AC and Hugo, W and Hunter, ME and Isbell, F and Jetz, W and Juergens, N and Kissling, WD and Krug, CB and Kullberg, P and Le Bras, Y and Leung, B and Londoño-Murcia, MC and Lord, JM and Loreau, M and Luers, A and Ma, K and MacDonald, AJ and Maes, J and McGeoch, M and Mihoub, JB and Millette, KL and Molnar, Z and Montes, E and Mori, AS and Muller-Karger, FE and Muraoka, H and Nakaoka, M and Navarro, L and Newbold, T and Niamir, A and Obura, D and O'Connor, M and Paganini, M and Pelletier, D and Pereira, H and Poisot, T and Pollock, LJ and Purvis, A and Radulovici, A and Rocchini, D and Roeoesli, C and Schaepman, M and Schaepman-Strub, G and Schmeller, DS and Schmiedel, U and Schneider, FD and Shakya, MM and Skidmore, A and Skowno, AL and Takeuchi, Y and Tuanmu, MN and Turak, E and Turner, W and Urban, MC and Urbina-Cardona, N and Valbuena, R and Van de Putte, A and van Havre, B and Wingate, VR and Wright, E and Torrelio, CZ},
title = {Author Correction: A global biodiversity observing system to unite monitoring and guide action.},
journal = {Nature ecology &amp; evolution},
volume = {7},
number = {12},
pages = {2173},
doi = {10.1038/s41559-023-02263-x},
pmid = {37985899},
issn = {2397-334X},
}
@article {pmid37985664,
year = {2023},
author = {Howerton, E and Contamin, L and Mullany, LC and Qin, M and Reich, NG and Bents, S and Borchering, RK and Jung, SM and Loo, SL and Smith, CP and Levander, J and Kerr, J and Espino, J and van Panhuis, WG and Hochheiser, H and Galanti, M and Yamana, T and Pei, S and Shaman, J and Rainwater-Lovett, K and Kinsey, M and Tallaksen, K and Wilson, S and Shin, L and Lemaitre, JC and Kaminsky, J and Hulse, JD and Lee, EC and McKee, CD and Hill, A and Karlen, D and Chinazzi, M and Davis, JT and Mu, K and Xiong, X and Pastore Y Piontti, A and Vespignani, A and Rosenstrom, ET and Ivy, JS and Mayorga, ME and Swann, JL and España, G and Cavany, S and Moore, S and Perkins, A and Hladish, T and Pillai, A and Ben Toh, K and Longini, I and Chen, S and Paul, R and Janies, D and Thill, JC and Bouchnita, A and Bi, K and Lachmann, M and Fox, SJ and Meyers, LA and Srivastava, A and Porebski, P and Venkatramanan, S and Adiga, A and Lewis, B and Klahn, B and Outten, J and Hurt, B and Chen, J and Mortveit, H and Wilson, A and Marathe, M and Hoops, S and Bhattacharya, P and Machi, D and Cadwell, BL and Healy, JM and Slayton, RB and Johansson, MA and Biggerstaff, M and Truelove, S and Runge, MC and Shea, K and Viboud, C and Lessler, J},
title = {Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7260},
pmid = {37985664},
issn = {2041-1723},
support = {U01IP001137/ACL/ACL HHS/United States ; R01 GM140564/GM/NIGMS NIH HHS/United States ; UL1 TR002489/TR/NCATS NIH HHS/United States ; U01 IP001137/IP/NCIRD CDC HHS/United States ; NU38OT000297/CC/CDC HHS/United States ; U01IP001136/ACL/ACL HHS/United States ; R01 AI151176/AI/NIAID NIH HHS/United States ; UM1 TR004406/TR/NCATS NIH HHS/United States ; U24 GM132013/GM/NIGMS NIH HHS/United States ; R35 GM119582/GM/NIGMS NIH HHS/United States ; R01 GM109718/GM/NIGMS NIH HHS/United States ; U01 IP001136/IP/NCIRD CDC HHS/United States ; R21 AI164391/AI/NIAID NIH HHS/United States ; U01 IP001122/IP/NCIRD CDC HHS/United States ; R01 AI102939/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/epidemiology ; Pandemics/prevention &amp; control ; SARS-CoV-2 ; Uncertainty ; },
abstract = {Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections.},
}
@article {pmid37981161,
year = {2024},
author = {Sajjad, W and Ilahi, N and Kang, S and Bahadur, A and Banerjee, A and Zada, S and Ali, B and Rafiq, M and Zheng, G},
title = {Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals.},
journal = {The Science of the total environment},
volume = {909},
number = {},
pages = {168635},
doi = {10.1016/j.scitotenv.2023.168635},
pmid = {37981161},
issn = {1879-1026},
mesh = {*Ecosystem ; Phylogeny ; *Metals, Heavy/analysis ; Environmental Pollution ; Archaea ; },
abstract = {Acid mine drainage (AMD) is one of the leading causes of environmental pollution and is linked to public health and ecological consequences. Microbes-mineral interaction generates AMD, but microorganisms can also remedy AMD pollution. Exploring the microbial response to AMD effluents may reveal survival strategies in extreme ecosystems. Three distinct sites across a mine (inside the mine, the entrance of the mine, and outside) were selected to study their heavy metal concentrations due to significant variations in pH and physicochemical characteristics, and high-throughput sequencing was carried out to investigate the microbial diversity. The metal and ion concentrations followed the order SO4[2-], Fe, Cu, Zn, Mg, Pb, Co, Cr, and Ni from highest to lowest, respectively. Maximum sequences were allocated to Proteobacteria and Firmicutes. Among archaea, the abundance of Thaumarchaeota and Euryarchaeota was higher outside of mine. Most of the genera (23.12 %) were unclassified and unknown. The average OTUs (operational taxonomic units) were significantly higher outside the mine; however, diversity indices were not significantly different across the mine sites. Hierarchical clustering of selective genera and nMDS ordination of OTUs displayed greater segregation resolution inside and outside of mine, whereas the entrance samples clustered with greater similarity. Heterogeneous selection might be the main driver of community composition outside the mine, whereas stochastic processes became prominent inside the mine. However, the ANOSIM test shows a relatively even distribution of community composition within and between the groups. Microbial phyla showed both positive and negative correlations with physicochemical factors. A greater number of biomarkers were reported outside of the mine. Predictive functional investigation revealed the existence of putative degradative, metabolic, and biosynthetic pathways. This study presents a rare dataset in our understanding of microbial diversity and distribution as shaped by the ecological gradient and potential novelty in phylogenetic/taxonomic diversity in AMD, with potential biotechnological applications.},
}
@article {pmid37980986,
year = {2024},
author = {Iqbal, A and Maqsood Ur Rehman, M and Sajjad, W and Degen, AA and Rafiq, M and Jiahuan, N and Khan, S and Shang, Z},
title = {Patterns of bacterial communities in the rhizosphere and rhizoplane of alpine wet meadows.},
journal = {Environmental research},
volume = {241},
number = {},
pages = {117672},
doi = {10.1016/j.envres.2023.117672},
pmid = {37980986},
issn = {1096-0953},
mesh = {Humans ; *Rhizosphere ; *Ecosystem ; Carbon ; Grassland ; Soil/chemistry ; Soil Microbiology ; Bacteria/genetics ; Plants ; Nitrogen ; },
abstract = {Wet meadows, a type of wetland, are vulnerable to climate change and human activity, impacting soil properties and microorganisms that are crucial to the ecosystem processes of wet meadows. To decipher the ecological mechanisms and processes involved in wet meadows, it is necessary to examine the bacterial communities associated with plant roots. To gain valuable insight into the microbial dynamics of alpine wet meadows, we used Illumina MiSeq sequencing to investigate how environmental factors shape the bacterial communities thriving in the rhizosphere and rhizoplane of three plant species: Cremanthodium ellisii, Caltha scaposa, and Cremanthodium lineare. The most abundant bacterial phyla in rhizosphere and rhizoplane were Proteobacteria > Firmicutes > Actinobacteria, while Macrococcus, Lactococcus, and Exiguobacterium were the most abundant bacterial genera between rhizosphere and rhizoplane. The mantel test, network, and structure equation models revealed that bacterial communities of rhizosphere were shaped by total nitrogen (TN), soil water content (SWC), soil organic carbon (SOC), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), pH, however, rhizoplane bacterial communities exhibited varying results. The bacterial communities exhibited significant heterogeneity, with stochastic process predominating in both the rhizosphere and rhizoplane. PICRUSt2 and FAPROTAX analysis revealed substantial differences in key biogeochemical cycles and metabolic functional predictions. It was concluded that root compartments significantly influenced the bacterial communities, although plant species and elevation asserted varying effects. This study portrays how physicochemical properties, plant species, and elevations can shift the overall structure and functional repertoire of bacterial communities in alpine wet meadows.},
}
@article {pmid37979845,
year = {2024},
author = {Henke, AN and Chilukuri, S and Langan, LM and Brooks, BW},
title = {Reporting and reproducibility: Proteomics of fish models in environmental toxicology and ecotoxicology.},
journal = {The Science of the total environment},
volume = {912},
number = {},
pages = {168455},
doi = {10.1016/j.scitotenv.2023.168455},
pmid = {37979845},
issn = {1879-1026},
mesh = {Animals ; *Ecotoxicology/methods ; *Proteomics/methods ; Reproducibility of Results ; Fishes ; Computational Biology ; },
abstract = {Environmental toxicology and ecotoxicology research efforts are employing proteomics with fish models as New Approach Methodologies, along with in silico, in vitro and other omics techniques to elucidate hazards of toxicants and toxins. We performed a critical review of toxicology studies with fish models using proteomics and reported fundamental parameters across experimental design, sample preparation, mass spectrometry, and bioinformatics of fish, which represent alternative vertebrate models in environmental toxicology, and routinely studied animals in ecotoxicology. We observed inconsistencies in reporting and methodologies among experimental designs, sample preparations, data acquisitions and bioinformatics, which can affect reproducibility of experimental results. We identified a distinct need to develop reporting guidelines for proteomics use in environmental toxicology and ecotoxicology, increased QA/QC throughout studies, and method optimization with an emphasis on reducing inconsistencies among studies. Several recommendations are offered as logical steps to advance development and application of this emerging research area to understand chemical hazards to public health and the environment.},
}
@article {pmid37978186,
year = {2023},
author = {Clark, MS and Hoffman, JI and Peck, LS and Bargelloni, L and Gande, D and Havermans, C and Meyer, B and Patarnello, T and Phillips, T and Stoof-Leichsenring, KR and Vendrami, DLJ and Beck, A and Collins, G and Friedrich, MW and Halanych, KM and Masello, JF and Nagel, R and Norén, K and Printzen, C and Ruiz, MB and Wohlrab, S and Becker, B and Dumack, K and Ghaderiardakani, F and Glaser, K and Heesch, S and Held, C and John, U and Karsten, U and Kempf, S and Lucassen, M and Paijmans, A and Schimani, K and Wallberg, A and Wunder, LC and Mock, T},
title = {Multi-omics for studying and understanding polar life.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7451},
pmid = {37978186},
issn = {2041-1723},
mesh = {*Ecosystem ; *Multiomics ; Biodiversity ; Forecasting ; },
abstract = {Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.},
}
@article {pmid37977539,
year = {2024},
author = {Chen, F and Mao, P and Wang, M and Li, Y and Li, Y and Xia, K and Chen, J and Mo, H and Wang, F and Li, Z and Zhuang, P},
title = {Benefit evaluation of in-situ Cd immobilization with naturally occurring minerals using an analytical hierarchy process.},
journal = {Chemosphere},
volume = {347},
number = {},
pages = {140720},
doi = {10.1016/j.chemosphere.2023.140720},
pmid = {37977539},
issn = {1879-1298},
mesh = {Cadmium/analysis ; Analytic Hierarchy Process ; Calcium Carbonate ; *Metals, Heavy/analysis ; Soil ; *Oryza ; *Soil Pollutants/analysis ; },
abstract = {Immobilization has a wide range of applications in heavy metal-contaminated soil remediation, and immobilization agents serve as the key to the successful application of this technology. In this study, we designed a comprehensive and efficient scoring system based on an analytic hierarchy process (AHP) to evaluate the feasibility and effectiveness of three immobilization agents (wollastonite, dolomite, and calcite) in remediating Cd-polluted soil. The scoring system comprised four criteria and 11 indicators, and the results showed that all three immobilization agents significantly reduced the accumulation of Cd in rice. The Cd reduction rates of early rice with a single application of wollastonite, dolomite, and calcite were 67.6%, 46.9%, and 83.8%, respectively. Single or combined application of dolomite and calcite decreased the available Cd concentration in early rice soil, and the application of calcite resulted in an excellent rating of both early and late rice, demonstrating its highest immobilization and stability performance. Therefore, the immobilization efficiency of the three materials in descending order followed calcite > dolomite + thioglycols > wollastonite. In summary, this comprehensive evaluation system offers new insight into assessing the efficiency of soil remediation, serving as a valuable reference for selecting immobilization agents and making decisions regarding remediation plans for heavy metal-contaminated soil.},
}
@article {pmid37976789,
year = {2024},
author = {Karimian, H and Zou, W and Chen, Y and Xia, J and Wang, Z},
title = {Corrigendum to 'Landscape ecological risk assessment and driving factor analysis in Dongjiang river watershed' [Chemosphere 307 (2022)135835].},
journal = {Chemosphere},
volume = {346},
number = {},
pages = {140599},
doi = {10.1016/j.chemosphere.2023.140599},
pmid = {37976789},
issn = {1879-1298},
}
@article {pmid37971111,
year = {2023},
author = {Stahnke, DN and Nied, C and Oliveira, MLG and Costa, JSDD},
title = {Trends in hospital admissions and mortality from diabetes mellitus in Rio Grande do Sul: historical series 2000-2020.},
journal = {Revista gaucha de enfermagem},
volume = {44},
number = {},
pages = {e20230103},
doi = {10.1590/1983-1447.2023.20230103.en},
pmid = {37971111},
issn = {1983-1447},
mesh = {Humans ; Brazil/epidemiology ; *Information Systems ; Hospitalization ; *Diabetes Mellitus/epidemiology ; Hospitals ; },
abstract = {OBJECTIVE: To analyze the trends of hospital admissions and deaths from diabetes mellitus in the 18 host municipalities of the 19 regional health coordination offices and in Rio Grande do Sul, 2000-2020.<br><br>METHOD: Ecological study with secondary data collected in the Hospital Information System, the Mortality Information System, and the Brazilian Institute of Geography and Statistics, from 2000-2020. Coefficients were standardized using the direct method and Prais-Winsten regression analysis.<br><br>RESULTS: A downward trend wasfound in the coefficients of hospitalizations for diabetes mellitus in most cities and states. In 2020, for both areas, hospitalizations for diabetes mellitus were below the average of the period. The mortality trend remained stationary in almost all municipalities and in the state.<br><br>CONCLUSION: There was evidence of a decrease in hospitalizations and stationary mortality by DM in most municipalities analyzed, possibly due to the policies and actions implemented in the period, despite the aging of the population.},
}
@article {pmid37968269,
year = {2023},
author = {Swets, MC and Kerr, S and Scott-Brown, J and Brown, AB and Gupta, R and Millar, JE and Spata, E and McCurrach, F and Bretherick, AD and Docherty, A and Harrison, D and Rowan, K and Young, N and , and Groeneveld, GH and Dunning, J and Nguyen-Van-Tam, JS and Openshaw, P and Horby, PW and Harrison, E and Staplin, N and Semple, MG and Lone, N and Baillie, JK},
title = {Evaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7374},
pmid = {37968269},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; Reproducibility of Results ; *COVID-19/diagnosis ; Lung ; Sample Size ; },
abstract = {Choosing optimal outcome measures maximizes statistical power, accelerates discovery and improves reliability in early-phase trials. We devised and evaluated a modification to a pragmatic measure of oxygenation function, the [Formula: see text] ratio. Because of the ceiling effect in oxyhaemoglobin saturation, [Formula: see text] ratio ceases to reflect pulmonary oxygenation function at high [Formula: see text] values. We found that the correlation of [Formula: see text] with the reference standard ([Formula: see text]/[Formula: see text] ratio) improves substantially when excluding [Formula: see text] and refer to this measure as [Formula: see text]. Using observational data from 39,765 hospitalised COVID-19 patients, we demonstrate that [Formula: see text] is predictive of mortality, and compare the sample sizes required for trials using four different outcome measures. We show that a significant difference in outcome could be detected with the smallest sample size using [Formula: see text]. We demonstrate that [Formula: see text] is an effective intermediate outcome measure in COVID-19. It is a non-invasive measurement, representative of disease severity and provides greater statistical power.},
}
@article {pmid37967264,
year = {2023},
author = {Yuan, Y and Li, X and Li, L and Jiang, FJ and Tang, X and Zhang, F and Goncalves, J and Voss, HU and Ding, H and Kurths, J},
title = {Machine discovery of partial differential equations from spatiotemporal data: A sparse Bayesian learning framework.},
journal = {Chaos (Woodbury, N.Y.)},
volume = {33},
number = {11},
pages = {},
doi = {10.1063/5.0160900},
pmid = {37967264},
issn = {1089-7682},
abstract = {This study presents a general framework, namely, Sparse Spatiotemporal System Discovery (S3d), for discovering dynamical models given by Partial Differential Equations (PDEs) from spatiotemporal data. S3d is built on the recent development of sparse Bayesian learning, which enforces sparsity in the estimated PDEs. This approach enables a balance between model complexity and fitting error with theoretical guarantees. The proposed framework integrates Bayesian inference and a sparse priori distribution with the sparse regression method. It also introduces a principled iterative re-weighted algorithm to select dominant features in PDEs and solve for the sparse coefficients. We have demonstrated the discovery of the complex Ginzburg-Landau equation from a traveling-wave convection experiment, as well as several other PDEs, including the important cases of Navier-Stokes and sine-Gordon equations, from simulated data.},
}
@article {pmid37967119,
year = {2023},
author = {Xue, J and Zhu, J and Hu, L and Yang, J and Lv, Y and Zhao, F and Liu, Y and Zhang, T and Cai, Y and Fang, M},
title = {EISA-EXPOSOME: One Highly Sensitive and Autonomous Exposomic Platform with Enhanced in-Source Fragmentation/Annotation.},
journal = {Analytical chemistry},
volume = {95},
number = {47},
pages = {17228-17237},
doi = {10.1021/acs.analchem.3c02697},
pmid = {37967119},
issn = {1520-6882},
mesh = {Tandem Mass Spectrometry/methods ; *Exposome ; *Pesticides/analysis ; Metabolomics/methods ; Ions ; Dust ; },
abstract = {Lacking a highly sensitive exposome screening technique is one of the biggest challenges in moving exposomic research forward. Enhanced in-source fragmentation/annotation (EISA) has been developed to facilitate molecular identification in untargeted metabolomics and proteomics. In this work, with a mixture of 50 pesticides at three concentration levels (20, 4, and 0.8 ppb), we investigated the analytical performance of the EISA technique over the well-accepted targeted MS/MS mode (TMM) in the detection and identification of chemicals at low levels using a quadrupole time-of-flight (qTOF) instrument. Compared with the TMM method, the EISA technique can recognize additional 1, 20, and 23 chemicals, respectively, at the three concentration levels (20, 4, and 0.8 ppb, respectively) investigated. At the 0.8 ppb level, intensities of precursor ions and fragments observed using the EISA technique are 30-1,154 and 3-80 times higher, respectively, than those observed at the TMM mode. A higher matched fragment ratio (MFR) between the EISA technique and the TMM method was recognized for most chemicals. We further developed a chemical annotation informatics algorithm, EISA-EXPOSOME, which can automatically search each precursor ion (m/z) in the MS/MS library against the EISA MS1 spectra. This algorithm then calculated a weighted score to rank the candidate features by comparing the experimental fragment spectra to those in the library. The peak intensity, zigzag index, and retention time prediction model as well as the peak correlation coefficient were further adopted in the algorithm to filter false positives. The performance of EISA-EXPOSOME was demonstrated using a pooled dust extract with a pesticide mixture (n = 200) spiked at 5 ppb. One urine sample spiked with a contaminant mixture (n = 50) at the 5 ppb level was also used for the validation of the pipeline. Proof-of-principal application of EISA-EXPOSOME in the real sample was further evaluated on the pooled dust sample with a modified T3DB database (n = 1650). Our results show that the EISA-EXPOSOME algorithm can remarkably improve the detection and annotation coverage at trace levels beyond the traditional approach as well as facilitate the high throughput screening of suspected chemicals.},
}
@article {pmid37967108,
year = {2023},
author = {Zhao, H and Zheng, J and Ma, S and Zhao, L and Xu, P and Li, J},
title = {Spatial distribution and influencing factors analysis of national key rural tourism villages in the Yangtze River Delta region based on geographically weighted regression.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0291614},
pmid = {37967108},
issn = {1932-6203},
mesh = {Humans ; China ; *Spatial Regression ; *Tourism ; Spatial Analysis ; Cities ; },
abstract = {National key rural tourism villages (NKRTVs) can lead to the high-quality development of rural tourism, and their spatial distribution is influenced by a variety of factors. However, existing studies have neglected the fact that influencing factors can have different directions and effects in different geographic spaces. This study investigates 156 NKRTVs in the Yangtze River Delta region of China as the research object and employs ArcGIS spatial analysis technology to examine their spatial distribution characteristics. Additionally, two new indicators of land and culture are introduced to enhance the index system of influencing factors. A geographically weighted regression model is utilized to identify the spatial heterogeneity of various factors that affect the spatial distribution of NKRTVs. The results of this study indicate the following: (1) The spatial distribution of NKRTVs in the Yangtze River Delta region is characterized by "small clustering and large dispersion." The spatial distribution exhibits strong spatial correlation, with Shanghai serving as the primary spatial clustering core and Huangshan city forming a secondary spatial clustering subcore. The distribution of NKRTVs is relatively scattered in other areas, with obvious differences in the spatial distribution of cold and hot spots. (2) The results of the geographically weighted regression model show that with the change in spatial location, the influence effect of each influencing factor on the spatial distribution of NKRTVs has obvious spatial differences. Based on the spatial heterogeneity of the influencing factors, this study proposes targeted suggestions for the development of rural tourism in different regions.},
}
@article {pmid37967091,
year = {2023},
author = {Radovic, I and Krdzic, I and Jovanovic, A and Vukasinovic, D and Soldatovic, I and Petrovic, M and Tomic, A and Jesic-Petrovic, T and Matejic, A and Salovic, B and Jelena, IZ},
title = {Transcultural adaptation and validation of the Serbian version of Functional Assessment of Chronic Illness Therapy-Treatment Satisfaction-Patient Satisfaction (FACIT-TS-PS) questionnaire.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0294339},
pmid = {37967091},
issn = {1932-6203},
mesh = {Humans ; *Patient Satisfaction ; Reproducibility of Results ; Serbia ; Quality of Life ; Language ; Surveys and Questionnaires ; *Neoplasms/therapy ; Chronic Disease ; Personal Satisfaction ; Psychometrics/methods ; },
abstract = {OBJECTIVE: Transcultural adaptation and validation of FACIT-TS-PS questionnaire to Serbian language.<br><br>METHODS: Standard forward and backward translation from English to Serbian language was performed. Pilot testing of FACIT-TS-PS was conducted on 12 patients with a confirmed diagnosis of malignant tumor. The study included 154 patients with malignant disease. The Questionnaire of Patient Satisfaction was used as a validated tool to evaluate concurrent validity of FACIT-TS-PS questionnaire. Reproducibility was tested on 30 subjects who answered the questionnaire for the second time two weeks later.<br><br>RESULTS: Three FACIT-TS-PS subscales (Physician Communication, Treatment Staff Communication and Nurse Communication) demonstrated satisfactory construct validity using Cronbach's alpha, the remaining two subscales (Technical Competence and Confidence &amp; Trust) showed high ceiling effect. Treatment Staff Communication subscale showed large floor effect. Concurrent validity was demonstrated by correlation with the two dimensions of the Questionnaire of Patient Satisfaction. Satisfactory reproducibility was demonstrated on 30 patients who filled the questionnaire for the second time two weeks after initial interview.<br><br>CONCLUSION: The Serbian version of FACIT-TS-PS with the omission of Treatment Staff Communication subscale could be used as a valid instrument to assess patient and treatment satisfaction in chronically ill patients in the Serbian population. Omission of Treatment Staff Communication subscale is necessary because it contains questions not relevant for patients in Serbian healthcare system.},
}
@article {pmid37966364,
year = {2023},
author = {Hutt Vater, C and Biederman, J and DiSalvo, M and O'Connor, H and Parker, H and Woodworth, KY and Wozniak, J and Faraone, SV},
title = {Growth Trajectories in Stimulant Treated Children and Adolescents: A Qualitative Review of the Literature from Comprehensive Datasets and Registries.},
journal = {Journal of child and adolescent psychopharmacology},
volume = {33},
number = {9},
pages = {344-355},
pmid = {37966364},
issn = {1557-8992},
support = {U01 AR076092/AR/NIAMS NIH HHS/United States ; R21 MH126494/MH/NIMH NIH HHS/United States ; R01 MH116037/MH/NIMH NIH HHS/United States ; R01 NS128535/NS/NINDS NIH HHS/United States ; },
mesh = {Adult ; Adolescent ; Humans ; Child ; *Central Nervous System Stimulants/adverse effects ; Registries ; Body Mass Index ; Databases, Factual ; *Drug-Related Side Effects and Adverse Reactions ; },
abstract = {Objective: Attention-deficit/hyperactivity disorder (ADHD) treatment with stimulant products has been shown to be safe and effective; however, there are remaining concerns about their possible adverse effects on growth trajectories. We conducted a systematic review of the extant literature derived from ecologically valid databases and registries to assess the body of knowledge about the effects of stimulants on growth trajectories in naturalistic samples. Methods: Using PubMed and PsycINFO, we searched for articles published before February 8, 2023 that focused on growth findings associated with stimulant treatment in pediatric ADHD from comprehensive datasets derived from naturalistic population studies. Results: Of the 1070 articles initially identified, 12 met all inclusion criteria. Sample sizes ranged from 157 to 163,820 youths. Seven of 10 articles examining height found significant decreases in height associated with chronic stimulant treatment that normalized over time in 2 studies. Three articles found no significant association between stimulant treatment and height. No clear associations were identified between cumulative duration and dose of stimulant treatment and adult height. All articles examining weight and six of eight articles examining body mass index (BMI) found significant initial decreases that tended to normalize then increase over time. Longer duration of stimulant medication use was predominantly associated with significant weight and BMI reductions. The effects of stimulant dose on weight and BMI were mostly weak and clinically insignificant. Most studies found no significant association between age at start of stimulant treatment and change in height, weight, or BMI. Most studies did not find significant sex effects in relation to growth parameters. Conclusions: This review of ecologically informative samples revealed that the effects of stimulant treatment on growth trajectories are mainly small and transient. These effects seem to be clinically insignificant for most youth with ADHD who receive stimulant treatment from childhood onto adolescence and adulthood.},
}
@article {pmid37966259,
year = {2024},
author = {Schiebelhut, LM and Guillaume, AS and Kuhn, A and Schweizer, RM and Armstrong, EE and Beaumont, MA and Byrne, M and Cosart, T and Hand, BK and Howard, L and Mussmann, SM and Narum, SR and Rasteiro, R and Rivera-Colón, AG and Saarman, N and Sethuraman, A and Taylor, HR and Thomas, GWC and Wellenreuther, M and Luikart, G},
title = {Genomics and conservation: Guidance from training to analyses and applications.},
journal = {Molecular ecology resources},
volume = {24},
number = {2},
pages = {e13893},
doi = {10.1111/1755-0998.13893},
pmid = {37966259},
issn = {1755-0998},
support = {80NSSC19K0185/NASA/NASA/United States ; 80NSSC19K0185/NASA/NASA/United States ; },
mesh = {Humans ; *Conservation of Natural Resources/methods ; *Genomics ; Biodiversity ; Genome ; },
abstract = {Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.},
}
@article {pmid37966155,
year = {2024},
author = {Amendola, S and Hengartner, MP},
title = {Antidepressants use in Italy: an ecological study of national and regional trends and associated factors.},
journal = {International clinical psychopharmacology},
volume = {39},
number = {2},
pages = {93-105},
doi = {10.1097/YIC.0000000000000522},
pmid = {37966155},
issn = {1473-5857},
mesh = {Humans ; Italy/epidemiology ; *Antidepressive Agents/therapeutic use ; *Patient Discharge ; Mood Disorders/drug therapy ; Data Management ; },
abstract = {The present study aimed to (1) provide an update on trends in AD consumption both at the national and regional unit of analysis for the period 2000-2020 in Italy and (2) analyze sociodemographic and healthcare system-related factors associated with AD prescribing at the regional-population level between 2000 and 2019. Data were extracted from reports of the Italian Medicines Agency and databases of the Italian National Institute of Statistics. Linear regression and mixed models were applied to analyze trends in AD use (DDD/1000/day) and ecological factors associated with AD prescribing. Between 2000 and 2010 AD prescription rates constantly increased. Thereafter they stabilized until 2017 when a positive trend began again. There was a positive ecological association between AD prescribing and rates of hospital discharge due to affective disorders, antibiotics prescribing, public non-drug healthcare spending per capita, and Northern regions compared to Southern regions. AD consumption increased massively during the 2000s, flattened during the 2010s but thereafter increased again until 2020. The ecological correlation between healthcare provision/spending and AD consumption suggests that health-economic factors may play an important role.},
}
@article {pmid37965283,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Leopard Moth, Zeuzera pyrina (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {94},
pmid = {37965283},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Zeuzera pyrina (the Leopard Moth, Arthropoda; Insecta; Lepidoptera; Cossidae). The genome sequence is 687 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,738 protein coding genes.},
}
@article {pmid37964699,
year = {2024},
author = {Knoch, D and Meyer, RC and Heuermann, MC and Riewe, D and Peleke, FF and Szymański, J and Abbadi, A and Snowdon, RJ and Altmann, T},
title = {Integrated multi-omics analyses and genome-wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola.},
journal = {The Plant journal : for cell and molecular biology},
volume = {117},
number = {3},
pages = {713-728},
doi = {10.1111/tpj.16524},
pmid = {37964699},
issn = {1365-313X},
support = {234585441//Deutsche Forschungsgemeinschaft/ ; 491250510//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Genome-Wide Association Study ; *Multiomics ; Quantitative Trait Loci/genetics ; Genomics ; Phenotype ; },
abstract = {Genome-wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High-throughput omics technologies, such as genomics, transcriptomics, proteomics and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalise on a diverse canola population with 477 spring-type lines which was previously analysed by high-throughput phenotyping of growth-related traits and by RNA sequencing and metabolite profiling for multi-omics-based hybrid performance prediction. We deepened the phenotypic data analysis, now providing 123 time-resolved image-based traits, to gain insight into the complex relations during early vegetative growth and reanalysed the transcriptome data based on the latest Darmor-bzh v10 genome assembly. Genome-wide association testing revealed 61 298 robust quantitative trait loci (QTL) including 187 metabolite QTL, 56814 expression QTL and 4297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritised candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1) and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the Brassica A and C subgenomes on early biomass production.},
}
@article {pmid37962866,
year = {2023},
author = {Zang, Z and Zhang, Y and Zuo, C and Chen, J and He, B and Luo, N and Zou, J and Zhao, W and Shi, W and Yan, X},
title = {Exploring Global Land Coarse-Mode Aerosol Changes from 2001-2021 Using a New Spatiotemporal Coaction Deep-Learning Model.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {48},
pages = {19881-19890},
doi = {10.1021/acs.est.3c07982},
pmid = {37962866},
issn = {1520-5851},
mesh = {*Air Pollutants/analysis ; *Deep Learning ; Environmental Monitoring/methods ; Dust/analysis ; Aerosols/analysis ; },
abstract = {Coarse-mode aerosol optical depths (cAODs) are critical for understanding the impact of coarse particle sizes, especially dust aerosols, on climate. Currently, the limited data length and high uncertainty of satellite products diminish the applicability of cAOD for climate research. Here, we propose a spatiotemporal coaction deep-learning model (SCAM) for the retrieval of global land cAOD (500 nm) from 2001-2021. In contrast to conventional deep-learning models, the SCAM considers the impacts of spatiotemporal feature interactions and can simultaneously describe linear and nonlinear relationships for retrievals. Based on these unique characteristics, the SCAM considerably improved global daily cAOD accuracies and coverages (R = 0.82, root-mean-square error [RMSE] = 0.04). Compared to official products from the multiangle imaging spectroradiometer (MISR), the moderate resolution imaging spectroradiometer (MODIS), and the polarization and directionality of Earth's reflectances (POLDER) instrument, as well as the physical-deep learning (Phy-DL) derived cAOD, the SCAM cAOD improved the monthly R from 0.44 to 0.88 and more accurately captured over the desert regions. Based on the SCAM cAOD, daily dust cases decreased over the Sahara, Thar Desert, Gobi Desert, and Middle East during 2001-2021 (>3 × 10[-3]/year). The SCAM-retrieved cAOD can contribute considerably to resolving the climate change uncertainty related to coarse-mode aerosols. Our proposed method is highly valuable for reducing uncertainties regarding coarse aerosols and climate interactions.},
}
@article {pmid37961949,
year = {2024},
author = {O'Brien, MJ and Valverde, S and Duran-Nebreda, S and Vidiella, B and Bentley, RA},
title = {Punctuated equilibrium at 50: Anything there for evolutionary anthropology? Yes; definitely.},
journal = {Evolutionary anthropology},
volume = {33},
number = {1},
pages = {e22009},
doi = {10.1002/evan.22009},
pmid = {37961949},
issn = {1520-6505},
support = {2019 BP 00206//Beatriu de Pin&#xf3;s postdoctoral programme in the Office of the General Secretary of Research and Universities and the Ministry of Research and Univertisites/ ; 801370//Marie Sklodowska-Curie COFUND/ ; //2020-2021 Biodiversa and Water JPI/ ; 101003777//BiodivRestore ERA-NET Cofund/ ; //Innovation Fund Denmark (IFD)/ ; //Agence Nationale de la Recherche (ANR)/ ; //Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; //Swedish Environmental Protection Agency (SEPA)/ ; PCI2022-132936//MCIN/AEI/10.13039/501100011033/ ; //European Union NextGenerationEU/PRTR/ ; PID2020-117822GB-I00/AEI/10.13039/501100011033//Spanish Ministry of Science and Innovation through the State Research Agency (AEI)/ ; },
mesh = {Humans ; *Biological Evolution ; *Fossils ; Cultural Diversity ; Databases, Factual ; },
abstract = {The theory of punctuated equilibrium (PE) was developed a little over 50 years ago to explain long-term, large-scale appearance and disappearance of species in the fossil record. A theory designed specifically for that purpose cannot be expected, out of the box, to be directly applicable to biocultural evolution, but in revised form, PE offers a promising approach to incorporating not only a wealth of recent empirical research on genetic, linguistic, and technological evolution but also large databases that document human biological and cultural diversity across time and space. Here we isolate the fundamental components of PE and propose which pieces, when reassembled or renamed, can be highly useful in evolutionary anthropology, especially as humanity faces abrupt ecological challenges on an increasingly larger scale.},
}
@article {pmid37960453,
year = {2023},
author = {Abbas, Q and Ahmad, G and Alyas, T and Alghamdi, T and Alsaawy, Y and Alzahrani, A},
title = {Revolutionizing Urban Mobility: IoT-Enhanced Autonomous Parking Solutions with Transfer Learning for Smart Cities.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {21},
pages = {},
pmid = {37960453},
issn = {1424-8220},
abstract = {Smart cities have emerged as a specialized domain encompassing various technologies, transitioning from civil engineering to technology-driven solutions. The accelerated development of technologies, such as the Internet of Things (IoT), software-defined networks (SDN), 5G, artificial intelligence, cognitive science, and analytics, has played a crucial role in providing solutions for smart cities. Smart cities heavily rely on devices, ad hoc networks, and cloud computing to integrate and streamline various activities towards common goals. However, the complexity arising from multiple cloud service providers offering myriad services necessitates a stable and coherent platform for sustainable operations. The Smart City Operational Platform Ecology (SCOPE) model has been developed to address the growing demands, and incorporates machine learning, cognitive correlates, ecosystem management, and security. SCOPE provides an ecosystem that establishes a balance for achieving sustainability and progress. In the context of smart cities, Internet of Things (IoT) devices play a significant role in enabling automation and data capture. This research paper focuses on a specific module of SCOPE, which deals with data processing and learning mechanisms for object identification in smart cities. Specifically, it presents a car parking system that utilizes smart identification techniques to identify vacant slots. The learning controller in SCOPE employs a two-tier approach, and utilizes two different models, namely Alex Net and YOLO, to ensure procedural stability and improvement.},
}
@article {pmid37954922,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Miller, Acronicta leporina (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {49},
pmid = {37954922},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Acronicta leporina (the Miller; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.},
}
@article {pmid37953792,
year = {2023},
author = {Furtado, DP and Vieira, EA and Nascimento, WF and Inagaki, KY and Bleuel, J and Alves, MAZ and Longo, GO and Oliveira, LS},
title = {#DeOlhoNosCorais: a polygonal annotated dataset to optimize coral monitoring.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16219},
pmid = {37953792},
issn = {2167-8359},
mesh = {Humans ; Animals ; *Anthozoa/physiology ; Coral Reefs ; Ecosystem ; Crustacea ; Fishes ; },
abstract = {Corals are colonial animals within the Phylum Cnidaria that form coral reefs, playing a significant role in marine environments by providing habitat for fish, mollusks, crustaceans, sponges, algae, and other organisms. Global climate changes are causing more intense and frequent thermal stress events, leading to corals losing their color due to the disruption of a symbiotic relationship with photosynthetic endosymbionts. Given the importance of corals to the marine environment, monitoring coral reefs is critical to understanding their response to anthropogenic impacts. Most coral monitoring activities involve underwater photographs, which can be costly to generate on large spatial scales and require processing and analysis that may be time-consuming. The Marine Ecology Laboratory (LECOM) at the Federal University of Rio Grande do Norte (UFRN) developed the project "#DeOlhoNosCorais" which encourages users to post photos of coral reefs on their social media (Instagram) using this hashtag, enabling people without previous scientific training to contribute to coral monitoring. The laboratory team identifies the species and gathers information on coral health along the Brazilian coast by analyzing each picture posted on social media. To optimize this process, we conducted baseline experiments for image classification and semantic segmentation. We analyzed the classification results of three different machine learning models using the Local Interpretable Model-agnostic Explanations (LIME) algorithm. The best results were achieved by combining EfficientNet for feature extraction and Logistic Regression for classification. Regarding semantic segmentation, the U-Net Pix2Pix model produced a pixel-level accuracy of 86%. Our results indicate that this tool can enhance image selection for coral monitoring purposes and open several perspectives for improving classification performance. Furthermore, our findings can be expanded by incorporating other datasets to create a tool that streamlines the time and cost associated with analyzing coral reef images across various regions.},
}
@article {pmid37953409,
year = {2024},
author = {Abarenkov, K and Nilsson, RH and Larsson, KH and Taylor, AFS and May, TW and Frøslev, TG and Pawlowska, J and Lindahl, B and Põldmaa, K and Truong, C and Vu, D and Hosoya, T and Niskanen, T and Piirmann, T and Ivanov, F and Zirk, A and Peterson, M and Cheeke, TE and Ishigami, Y and Jansson, AT and Jeppesen, TS and Kristiansson, E and Mikryukov, V and Miller, JT and Oono, R and Ossandon, FJ and Paupério, J and Saar, I and Schigel, D and Suija, A and Tedersoo, L and Kõljalg, U},
title = {The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered.},
journal = {Nucleic acids research},
volume = {52},
number = {D1},
pages = {D791-D797},
pmid = {37953409},
issn = {1362-4962},
support = {PRG1170//Estonian Research Council/ ; 101059492//Horizon 2020/ ; //Estonian Research Infrastructure/ ; //UNITE Community/ ; },
mesh = {DNA, Ribosomal Spacer ; *Fungi/genetics ; *Databases, Nucleic Acid ; Biodiversity ; DNA, Fungal ; Phylogeny ; },
abstract = {UNITE (https://unite.ut.ee) is a web-based database and sequence management environment for molecular identification of eukaryotes. It targets the nuclear ribosomal internal transcribed spacer (ITS) region and offers nearly 10 million such sequences for reference. These are clustered into ∼2.4M species hypotheses (SHs), each assigned a unique digital object identifier (DOI) to promote unambiguous referencing across studies. UNITE users have contributed over 600 000 third-party sequence annotations, which are shared with a range of databases and other community resources. Recent improvements facilitate the detection of cross-kingdom biological associations and the integration of undescribed groups of organisms into everyday biological pursuits. Serving as a digital twin for eukaryotic biodiversity and communities worldwide, the latest release of UNITE offers improved avenues for biodiversity discovery, precise taxonomic communication and integration of biological knowledge across platforms.},
}
@article {pmid37953341,
year = {2024},
author = {Shi, H and Wu, X and Zhu, Y and Jiang, T and Wang, Z and Li, X and Liu, J and Zhang, Y and Chen, F and Gao, J and Xu, X and Zhang, G and Xiao, N and Feng, X and Zhang, P and Wu, Y and Li, A and Chen, P and Li, X},
title = {RefMetaPlant: a reference metabolome database for plants across five major phyla.},
journal = {Nucleic acids research},
volume = {52},
number = {D1},
pages = {D1614-D1628},
pmid = {37953341},
issn = {1362-4962},
support = {XDA24010400//Strategic Priority Research Program of Chinese Academy of Sciences/ ; 32270719//National Natural Science Foundation of China/ ; CARS-11//Earmarked Fund for China Agriculture Research System/ ; BK20220307//Natural Science Foundation of Jiangsu Province/ ; 2021387//Shanghai Post-doctoral Excellence Program/ ; SJ(22)107//Special funds for scientific research and development of Institute of Agricultural Sciences for Lixiahe Region in Jiangsu/ ; },
mesh = {Chromatography, Liquid ; *Databases, Factual ; *Metabolome/genetics ; Metabolomics/methods ; Plants/metabolism ; Tandem Mass Spectrometry ; },
abstract = {Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC-MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A 'Reference Metabolome Database for Plants' (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like 'LC-MS/MS Query', 'RefMetaBlast' and 'CompoundLibBlast' for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.},
}
@article {pmid37952420,
year = {2024},
author = {Hao, W and Shan, YF and Kimura, T and Ukawa, S and Ohira, H and Okabayashi, S and Wakai, K and Ando, M and Tamakoshi, A},
title = {Dual decline in subjective gait speed and domain-specific cognition is associated with higher risk of incident dementia in older Japanese adults: A 15-year age-specific cohort study.},
journal = {Archives of gerontology and geriatrics},
volume = {117},
number = {},
pages = {105254},
doi = {10.1016/j.archger.2023.105254},
pmid = {37952420},
issn = {1872-6976},
mesh = {Male ; Humans ; Aged ; Aged, 80 and over ; Walking Speed ; Cohort Studies ; East Asian People ; Gait ; Cognition ; *Dementia/epidemiology ; Age Factors ; *Cognitive Dysfunction ; },
abstract = {OBJECTIVES: Dual decline in gait speed and cognition has been found to have higher dementia risk than no decline or pure decline. However, evidence from the Asian population is lacking. Therefore, we aimed to investigate the association of dual decline from age 65 to 70 years with late-life dementia in older Japanese adults with different personal characteristics.<br><br>METHODS: Data were collected from an age-specific cohort study conducted in 482 Japanese 65-year-old adults. We investigated participant demographics, medical histories, lifestyles, subjective gait speed, and cognition at both 64/65 and 70/71 years old, and confirmed dementia until age of 85 years. Cox proportion hazard models were used to estimate the risk of dementia, with adjustments for covariates, and death was treated as a competing risk.<br><br>RESULTS: After a mean follow-up period of 12.5-years, 111 participants developed dementia. Older adults with dual decline are more likely to have hyperlipidemia, diabetes, and smoking habits. And we found that dual decline in gait speed and domain-specific cognition was associated with a higher risk of dementia compared with no decline in most cognitive tests, with the highest risk observed for gait speed combined with memory (sub-distribution hazard ratio:3.89, 95&#xa0;%, confidence intervals: [1.68-9.01]). However, significant differences only existed in men after stratification by sex.<br><br>CONCLUSIONS: A dual decline in subjective gait speed and cognition may serve as a robust predictor of dementia over a decade prior to its onset, particularly in men. These findings highlighted the importance of screening for dual decline at an early age.},
}
@article {pmid37951122,
year = {2023},
author = {Waqas, M and Wong, MS and Stocchino, A and Abbas, S and Hafeez, S and Zhu, R},
title = {Marine plastic pollution detection and identification by using remote sensing-meta analysis.},
journal = {Marine pollution bulletin},
volume = {197},
number = {},
pages = {115746},
doi = {10.1016/j.marpolbul.2023.115746},
pmid = {37951122},
issn = {1879-3363},
mesh = {*Ecosystem ; *Remote Sensing Technology ; Environmental Monitoring/methods ; Plastics/analysis ; Oceans and Seas ; Waste Products/analysis ; },
abstract = {The persistent plastic litter, originating from different sources and transported from rivers to oceans, has posed serious biological, ecological, and chemical effects on the marine ecosystem, and is considered a global issue. In the past decade, many studies have identified, monitored, and tracked marine plastic debris in coastal and open ocean areas using remote sensing technologies. Compared to traditional surveying methods, high-resolution (spatial and temporal) multispectral or hyperspectral remote sensing data have been substantially used to monitor floating marine macro litter (FMML). In this systematic review, we present an overview of remote sensing data and techniques for detecting FMML, as well as their challenges and opportunities. We reviewed the studies based on different sensors and platforms, spatial and spectral resolution, ground sampling data, plastic detection methods, and accuracy obtained in detecting marine litter. In addition, this study elaborates the usefulness of high-resolution remote sensing data in Visible (VIS), Near-infrared (NIR), and Short-Wave InfraRed (SWIR) range, along with spectral signatures of plastic, in-situ samples, and spectral indices for automatic detection of FMML. Moreover, the Thermal Infrared (TIR), Synthetic aperture radar (SAR), and Light Detection and Ranging (LiDAR) data were introduced and these were demonstrated that could be used as a supplement dataset for the identification and quantification of FMML.},
}
@article {pmid37950741,
year = {2024},
author = {Kimotho, RN and Maina, S},
title = {Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?.},
journal = {Journal of experimental botany},
volume = {75},
number = {5},
pages = {1289-1313},
pmid = {37950741},
issn = {1460-2431},
support = {//Chinese Government Scholarship/ ; //University of Chinese Academy of Sciences/ ; },
mesh = {*Multiomics ; *Microbiota ; Plants/genetics ; Symbiosis ; },
abstract = {Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.},
}
@article {pmid37947402,
year = {2023},
author = {Alexander, H and Hu, SK and Krinos, AI and Pachiadaki, M and Tully, BJ and Neely, CJ and Reiter, T},
title = {Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0167623},
pmid = {37947402},
issn = {2150-7511},
support = {OCE-1948025//National Science Foundation (NSF)/ ; OCE-0939564, OCE-194777, OCE-2327203//National Science Foundation (NSF)/ ; 931886//Simons Foundation (SF)/ ; DE-SC0020347//U.S. Department of Energy (DOE)/ ; OCE-1924492//National Science Foundation (NSF)/ ; OCE-0939654//National Science Foundation (NSF)/ ; },
mesh = {*Metagenomics/methods ; *Plankton/genetics/classification ; *Eukaryota/genetics/classification ; *Oceans and Seas ; *Metagenome ; Biodiversity ; Computational Biology/methods ; Phylogeny ; Seawater/microbiology ; Phylogeography ; },
abstract = {Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.},
}
@article {pmid37943735,
year = {2023},
author = {Skoric, D and Rakic, JG and Jovanovic, V and Backovic, D and Soldatovic, I and Zivojinovic, JI},
title = {Psychosocial school factors and mental health of first grade secondary school students-Results of the Health Behaviour in School-aged Children Survey in Serbia.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0293179},
pmid = {37943735},
issn = {1932-6203},
mesh = {Female ; Humans ; Child ; Adolescent ; Male ; *Mental Health ; Serbia/epidemiology ; Cross-Sectional Studies ; *Schools ; Psychophysiologic Disorders ; Students/psychology ; Health Behavior ; },
abstract = {This cross-sectional study aimed to investigate the association between psychosocial school factors and life satisfaction, symptoms of depression and psychosomatic health complaints among first grade secondary school students in Serbia. We analysed data from the 2018 Health Behaviour in School-aged Children (HBSC) study in the Republic of Serbia. Analyzed psychosocial school factors included satisfaction with school, schoolwork pressure, teacher support, classmate support and being bullied at school. Life satisfaction was assessed by the 11-step Cantril's ladder (cutoff >5). Symptoms of depression were measured by the Center for Epidemiologic Studies Depression Scale (CESD-10) and psychosomatic health complaints by using the HBSC symptom checklist. Univariable and multivariable binary logistic regression was used to determine independent predictors of students' life satisfaction, symptoms of depression and psychosomatic health complaints in the school environment, while also considering their socio-demographic characteristics and perceived family and friend support. The study included 1605 students (average age 15.26 ±0.44 years), of whom 50.3% were females. Results from the binary logistic regression analyses showed that life satisfaction was positively related to school satisfaction and classmate support, and negatively to being bullied at school. Symptoms of depression were positively associated with schoolwork pressure and being bullied at school, and negatively with teacher and classmate support. All analyzed factors of the school environment were significantly related to psychosomatic health complaints, whereby schoolwork pressure and being bullied at school were positively associated, while teacher and classmate support and satisfaction with school were negatively associated. Given the established association of psychosocial school factors with mental health, there is a need for targeted measures both at school and community level with the aim of improving social support in the school environment, reducing schoolwork burden and preventing bullying at school, potentially resulting in the overall improvement of mental health of the first grade secondary school students.},
}
@article {pmid37942709,
year = {2023},
author = {Furuya, S and Liu, J and Sun, Z and Lu, Q and Fletcher, JM},
title = {The Big (Genetic) Sort? A Research Note on Migration Patterns and Their Genetic Imprint in the United Kingdom.},
journal = {Demography},
volume = {60},
number = {6},
pages = {1649-1664},
doi = {10.1215/00703370-11054960},
pmid = {37942709},
issn = {1533-7790},
mesh = {Humans ; United Kingdom ; *Transients and Migrants ; Educational Status ; },
abstract = {This research note reinvestigates Abdellaoui et al.'s (2019) findings that genetically selective migration may lead to persistent and accumulating socioeconomic and health inequalities between types (coal mining or non-coal mining) of places in the United Kingdom. Their migration measure classified migrants who moved to the same type of place (coal mining to coal mining or non-coal mining to non-coal mining) into "stay" categories, preventing them from distinguishing migrants from nonmigrants. We reinvestigate the question of genetically selective migration by examining migration patterns between places rather than place types and find genetic selectivity in whether people migrate and where. For example, we find evidence of positive selection: people with genetic variants correlated with better education moved from non-coal mining to coal mining places with our measure of migration. Such findings were obscured in earlier work that could not distinguish nonmigrants from migrants.},
}
@article {pmid37942213,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Palmada-Flores, M and , },
title = {The genome sequence of the lesser treble-bar moth, Aplocera efformata (Guenée, 1857).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {303},
pmid = {37942213},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Aplocera efformata (the lesser treble-bar; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 350 megabases in span. Most of the assembly (99.97%) is scaffolded into 32 chromosomal pseudomolecules, with W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,393 protein coding genes.},
}
@article {pmid37939139,
year = {2023},
author = {Conte, L and Gonella, F and Giansanti, A and Kleidon, A and Romano, A},
title = {Modeling cell populations metabolism and competition under maximum power constraints.},
journal = {PLoS computational biology},
volume = {19},
number = {11},
pages = {e1011607},
pmid = {37939139},
issn = {1553-7358},
mesh = {Humans ; *Ecosystem ; *Multiple Myeloma/pathology ; Bone Marrow/metabolism ; Models, Theoretical ; Tumor Microenvironment/physiology ; },
abstract = {Ecological interactions are fundamental at the cellular scale, addressing the possibility of a description of cellular systems that uses language and principles of ecology. In this work, we use a minimal ecological approach that encompasses growth, adaptation and survival of cell populations to model cell metabolisms and competition under energetic constraints. As a proof-of-concept, we apply this general formulation to study the dynamics of the onset of a specific blood cancer-called Multiple Myeloma. We show that a minimal model describing antagonist cell populations competing for limited resources, as regulated by microenvironmental factors and internal cellular structures, reproduces patterns of Multiple Myeloma evolution, due to the uncontrolled proliferation of cancerous plasma cells within the bone marrow. The model is characterized by a class of regime shifts to more dissipative states for selectively advantaged malignant plasma cells, reflecting a breakdown of self-regulation in the bone marrow. The transition times obtained from the simulations range from years to decades consistently with clinical observations of survival times of patients. This irreversible dynamical behavior represents a possible description of the incurable nature of myelomas based on the ecological interactions between plasma cells and the microenvironment, embedded in a larger complex system. The use of ATP equivalent energy units in defining stocks and flows is a key to constructing an ecological model which reproduces the onset of myelomas as transitions between states of a system which reflects the energetics of plasma cells. This work provides a basis to construct more complex models representing myelomas, which can be compared with model ecosystems.},
}
@article {pmid37939092,
year = {2023},
author = {Suire, A and Kunita, I and Harel, R and Crofoot, M and Mutinda, M and Kamau, M and Hassel, JM and Murray, S and Kawamura, S and Matsumoto-Oda, A},
title = {Estimating individual exposure to predation risk in group-living baboons, Papio anubis.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0287357},
pmid = {37939092},
issn = {1932-6203},
mesh = {Humans ; Animals ; Male ; *Papio anubis ; Papio ; *Predatory Behavior ; Geographic Information Systems ; },
abstract = {In environments with multiple predators, vulnerabilities associated with the spatial positions of group-living prey are non-uniform and depend on the hunting styles of the predators. Theoretically, coursing predators follow their prey over long distances and attack open areas, exposing individuals at the edge of the group to predation risk more than those at the center (marginal predation). In contrast, ambush predators lurk unnoticed by their prey and appear randomly anywhere in the group; therefore, isolated individuals in the group would be more vulnerable to predators. These positions of vulnerability to predation are expected to be taken by larger-bodied males. Moreover, dominant males presumably occupy the center of the safe group. However, identifying individuals at higher predation risk requires both simultaneous recording of predator location and direct observation of predation events; empirical observations leave ambiguity as to who is at risk. Instead, several theoretical methods (predation risk proxies) have been proposed to assess predation risk: (1) the size of the individual 'unlimited domain of danger' based on Voronoi tessellation, (2) the size of the 'limited domain of danger' based on predator detection distance, (3) peripheral/center position in the group (minimum convex polygon), (4) the number and direction of others in the vicinity (surroundedness), and (5) dyadic distances. We explored the age-sex distribution of individuals in at-risk positions within a wild baboon group facing predation risk from leopards, lions, and hyenas, using Global Positioning System collars. Our analysis of the location data from 26 baboons revealed that adult males were consistently isolated at the edge of the group in all predation risk proxies. Empirical evidence from previous studies indicates that adult male baboons are the most frequently preyed upon, and our results highlights the importance of spatial positioning in this.},
}
@article {pmid37937916,
year = {2023},
author = {Furuya, S and Liu, J and Sun, Z and Lu, Q and Fletcher, JM},
title = {Understanding Internal Migration: A Research Note Providing an Assessment of Migration Selection With Genetic Data.},
journal = {Demography},
volume = {60},
number = {6},
pages = {1631-1648},
doi = {10.1215/00703370-11053145},
pmid = {37937916},
issn = {1533-7790},
mesh = {Humans ; *Emigration and Immigration ; Cross-Sectional Studies ; Genome-Wide Association Study ; *Transients and Migrants ; Social Class ; },
abstract = {Migration is selective, resulting in inequalities between migrants and nonmigrants. However, investigating migration selection is empirically challenging because combined pre- and post-migration data are rarely available. We propose an alternative approach to assessing internal migration selection by integrating genetic data, enabling an investigation of migration selection with cross-sectional data collected post-migration. Using data from the UK Biobank, we utilized standard tools from statistical genetics to conduct a genome-wide association study (GWAS) for migration distance. We then calculated genetic correlations to compare GWAS results for migration with those for other characteristics. Given that individual genetics are determined at conception, these analyses allow a unique exploration of the association between pre-migration characteristics and migration. Results are generally consistent with the healthy migrant literature: genetics correlated with longer migration distance are associated with higher socioeconomic status and better health. We also extended the analysis to 53 traits and found novel correlations between migration and several physical health, mental health, personality, and sociodemographic traits.},
}
@article {pmid37934751,
year = {2024},
author = {Laporte, C and Fortin, F and Dupouy, J and Darmon, D and Pereira, B and Authier, N and Delorme, J and Chenaf, C and Maisonneuve, H and Schuers, M},
title = {The French ecology of medical care. A nationwide population-based cross sectional study.},
journal = {Family practice},
volume = {41},
number = {2},
pages = {92-98},
doi = {10.1093/fampra/cmad098},
pmid = {37934751},
issn = {1460-2229},
mesh = {Male ; Humans ; Female ; Adolescent ; Young Adult ; Adult ; Cross-Sectional Studies ; *General Practitioners ; Referral and Consultation ; Hospitalization ; Ambulatory Care ; },
abstract = {PURPOSE: Studies in the United States, Canada, Belgium, and Switzerland showed that the majority of health problems are managed within primary health care; however, the ecology of French medical care has not yet been described.<br><br>METHODS: Nationwide, population-based, cross sectional study. In 2018, we included data from 576,125 beneficiaries from the General Sample of Beneficiaries database. We analysed the reimbursement of consultations with (i) a general practitioner (GP), (ii) an outpatient doctor other than a GP, (iii) a doctor from a university or non-university hospital; and the reimbursement of (iv) hospitalization in a private establishment, (v) general hospital, and (vi) university hospital. For each criterion, we calculated the average monthly number of reimbursements reported on 1,000 beneficiaries. For categorical variables, we used the &#x3c7;2 test, and to compare means we used the z test. All tests were 2-tailed with a P-value&#x2005;<&#x2005;5% considered significant.<br><br>RESULTS: Each month, on average, 454 (out of 1,000) beneficiaries received at least 1 reimbursement, 235 consulted a GP, 74 consulted other outpatient doctors in ambulatory care and 24 in a hospital, 13 were hospitalized in a public non-university hospital and 10 in the private sector, and 5 were admitted to a university hospital. Independently of age, people consulted GPs twice as much as other specialists. The 13-25-year-old group consulted the least. Women consulted more than men. Individuals covered by complementary universal health insurance had more care.<br><br>CONCLUSIONS: Our study on reimbursement data confirmed that, like in other countries, in France the majority of health problems are managed within primary health care.},
}
@article {pmid37934729,
year = {2023},
author = {Vasileiou, D and Karapiperis, C and Baltsavia, I and Chasapi, A and Ahrén, D and Janssen, PJ and Iliopoulos, I and Promponas, VJ and Enright, AJ and Ouzounis, CA},
title = {CGG toolkit: Software components for computational genomics.},
journal = {PLoS computational biology},
volume = {19},
number = {11},
pages = {e1011498},
pmid = {37934729},
issn = {1553-7358},
mesh = {Reproducibility of Results ; *Genomics/methods ; *Software ; Computational Biology/methods ; Genome ; },
abstract = {Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.},
}
@article {pmid37933857,
year = {2024},
author = {Yang, S and Zong, W and Shi, L and Li, R and Ma, Z and Ma, S and Si, J and Wu, Z and Zhai, J and Ma, Y and Fan, Z and Chen, S and Huang, H and Zhang, D and Bao, Y and Li, R and Xie, J},
title = {PPGR: a comprehensive perennial plant genomes and regulation database.},
journal = {Nucleic acids research},
volume = {52},
number = {D1},
pages = {D1588-D1596},
pmid = {37933857},
issn = {1362-4962},
support = {QNTD202305//Central Universities/ ; 32371906//National Natural Science Foundation of China/ ; 2022YFD2201600//National Key R&amp;D Program of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; XDB38030200//Chinese Academy of Sciences/ ; WX145XQ07-04//Genomics Data Center Construction of Chinese Academy of Sciences/ ; ANSO-PA-2020-07//Alliance of International Science Organizations/ ; //Open Biodiversity and Health Big Data Programme of IUBS/ ; },
mesh = {*Databases, Genetic ; *Genome, Plant ; *Genomics ; Plants/genetics ; Transcriptome ; },
abstract = {Perennial woody plants hold vital ecological significance, distinguished by their unique traits. While significant progress has been made in their genomic and functional studies, a major challenge persists: the absence of a comprehensive reference platform for collection, integration and in-depth analysis of the vast amount of data. Here, we present PPGR (Resource for Perennial Plant Genomes and Regulation; https://ngdc.cncb.ac.cn/ppgr/) to address this critical gap, by collecting, integrating, analyzing and visualizing genomic, gene regulation and functional data of perennial plants. PPGR currently includes 60 species, 847 million protein-protein/TF (transcription factor)-target interactions, 9016 transcriptome samples under various environmental conditions and genetic backgrounds. Noteworthy is the focus on genes that regulate wood production, seasonal dormancy, terpene biosynthesis and leaf senescence representing a wealth of information derived from experimental data, literature mining, public databases and genomic predictions. Furthermore, PPGR incorporates a range of multi-omics search and analysis tools to facilitate browsing and application of these extensive datasets. PPGR represents a comprehensive and high-quality resource for perennial plants, substantiated by an illustrative case study that demonstrates its capacity in unraveling gene functions and shedding light on potential regulatory processes.},
}
@article {pmid37933429,
year = {2023},
author = {Hofmeister, NR and Stuart, KC and Warren, WC and Werner, SJ and Bateson, M and Ball, GF and Buchanan, KL and Burt, DW and Cardilini, APA and Cassey, P and De Meyer, T and George, J and Meddle, SL and Rowland, HM and Sherman, CDH and Sherwin, WB and Vanden Berghe, W and Rollins, LA and Clayton, DF},
title = {Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17195},
pmid = {37933429},
issn = {1365-294X},
support = {//Newnham College, Cambridge/ ; //The Winston Churchill Memorial Trust/ ; BB/P013759/1//UK Biotechnology and Biological Sciences Research Council/ ; //University of New South Wales/ ; },
abstract = {A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.},
}
@article {pmid37930866,
year = {2024},
author = {Camargo, AP and Call, L and Roux, S and Nayfach, S and Huntemann, M and Palaniappan, K and Ratner, A and Chu, K and Mukherjeep, S and Reddy, TBK and Chen, IA and Ivanova, NN and Eloe-Fadrosh, EA and Woyke, T and Baltrus, DA and Castañeda-Barba, S and de la Cruz, F and Funnell, BE and Hall, JPJ and Mukhopadhyay, A and Rocha, EPC and Stalder, T and Top, E and Kyrpides, NC},
title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.},
journal = {Nucleic acids research},
volume = {52},
number = {D1},
pages = {D164-D173},
pmid = {37930866},
issn = {1362-4962},
support = {MR/W02666X/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Metagenome ; Metadata ; Software ; Databases, Genetic ; Plasmids/genetics ; *Microbiota ; },
abstract = {Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.},
}
@article {pmid37928210,
year = {2023},
author = {Crowley, LM and Mitchell, R and , and , and , and , and , and , and Weston, ST and Wotton, KR and , },
title = {The genome sequence of the Lesser Hornet Hoverfly, Volucella inanis (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {69},
pmid = {37928210},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Volucella inanis (the Lesser Hornet Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 961 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, including the assembled X sex chromosome. The mitochondrial genome has also been assembled and is 16.0 kilobases in length. Gene annotation of this assembly on Ensembl has identified 11,616 protein coding genes.},
}
@article {pmid37926802,
year = {2024},
author = {Šiljeg, A and Šiljeg, S and Milošević, R and Marić, I and Domazetović, F and Panđa, L},
title = {Multi-hazard susceptibility model based on high spatial resolution data-a case study of Sali settlement (Dugi otok, Croatia).},
journal = {Environmental science and pollution research international},
volume = {31},
number = {28},
pages = {40732-40747},
pmid = {37926802},
issn = {1614-7499},
mesh = {Croatia ; *Models, Theoretical ; Floods ; Geographic Information Systems ; Climate Change ; Wildfires ; Ecosystem ; },
abstract = {The world has been facing an increase in various natural hazards. The coastal regions are recognized as one of the most vulnerable due to high population pressure and climate change intensity. Mediterranean countries have one of the most burnable ecosystems in the world, one of the most exposed to pluvial floods, and have the highest erosion rates within the EU. Therefore, the aim of this study was to develop the first multihazard susceptibility model in Croatia for the Sali settlement (island of Dugi otok). The creation of a multi-hazard susceptibility model (MHSM) combined the application of geospatial technology (GST) with a local perception survey. The methodology consisted of two main steps: (1) creating individual hazard susceptibility models (soil erosion, wildfires, pluvial floods), and (2) overall hazard susceptibility modeling. Multicriterial GIS analyses and the Analytical Hierarchy Process were used to create individual hazard models. Criteria used (32) to create models are derived from very-high-resolution (VHR) models. Two versions of MHSM are created: 1) all criteria with equal weighting coefficients and 2) weight coefficients determined based on public perception. According to MHSM 1, most of the research (58%) area is moderately susceptible to multiple hazards. Highly and very highly susceptible areas are 27% of the drainage basin and are mostly located near roads and houses. MHSM 2 reveals similar results to MHSM 1. The public perceives that the research area is the most susceptible to wildfires. The wildfire ignition risk is ranked as moderate (3.00) with a standard deviation of 1.16. Pluvial flood risk is ranked low (2.78), with a standard deviation of 1.15. The risk of soil is most inferior (2.24) with a standard deviation of 0.91. The the most significant difference between public perception and the GIS-MCDA model of hazard susceptibility is related to soil erosion. However, the accuracy of the soil erosion model was confirmed by ROC curves based on recent traces of soil erosion in the research area. The proposed methodological framework of multi-hazard susceptibility modeling can be applied, with minor modifications, to other Mediterranean countries.},
}
@article {pmid37925458,
year = {2023},
author = {Srivastava, A and De Corte, D and Garcia, JAL and Swan, BK and Stepanauskas, R and Herndl, GJ and Sintes, E},
title = {Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {239},
pmid = {37925458},
issn = {2049-2618},
support = {I 486/FWF_/Austrian Science Fund FWF/Austria ; P 23234/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Heterotrophic Processes ; *Thiosulfates/metabolism ; Carbon/metabolism ; *Gammaproteobacteria/genetics ; Sulfur/metabolism ; Carbon Cycle ; },
abstract = {BACKGROUND: Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.<br><br>METHODS: Seawater samples were collected from Labrador Sea Water (LSW,&#x2009;~&#x2009;2000&#xa0;m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1&#xa0;&#xb5;M thiosulfate, or with 1&#xa0;&#xb5;M thiosulfate plus 10&#xa0;&#xb5;M glucose and 10&#xa0;&#xb5;M acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1&#xa0;h and 72&#xa0;h of incubation.<br><br>RESULTS: Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).<br><br>CONCLUSIONS: The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.},
}
@article {pmid37914135,
year = {2024},
author = {Hulme, PE and Ahmed, DA and Haubrock, PJ and Kaiser, BA and Kourantidou, M and Leroy, B and McDermott, SM},
title = {Widespread imprecision in estimates of the economic costs of invasive alien species worldwide.},
journal = {The Science of the total environment},
volume = {909},
number = {},
pages = {167997},
doi = {10.1016/j.scitotenv.2023.167997},
pmid = {37914135},
issn = {1879-1026},
mesh = {*Introduced Species ; Reproducibility of Results ; Databases, Factual ; *Research Design ; },
abstract = {Several hundred studies have attempted to estimate the monetary cost arising from the management and/or impacts of invasive alien species. However, the diversity of methods used to estimate the monetary costs of invasive alien species, the types of costs that have been reported, and the spatial scales at which they have been assessed raise important questions as to the precision of these reported monetary costs. Benford's Law has been increasingly used as a diagnostic tool to assess the accuracy and reliability of estimates reported in financial accounts but has rarely been applied to audit data on environmental costs. Therefore, the distributions of first, second- and leading double-digits of the monetary costs arising from biological invasions, as reported in the InvaCost database, were compared with the null expectations under Benford's Law. There was strong evidence that the reported monetary costs of biological invasions departed considerably from Benford's Law and the departures were of a scale equal to that found in global macroeconomic data. The rounding upwards of costs appears to be widespread. Furthermore, numerical heaping, where values cluster around specific numbers was evident with only 901 unique cost values accounting for half of the 13,553 cost estimates within the InvaCost database. Irrespective of the currency, the value of 1,000,000 was the most common cost estimate. An investigation of anomalous data entries concluded that non-peer reviewed official government reports need to provide greater detail regarding how costs are estimated. Despite the undeniably high economic cost of biological invasions worldwide, individual records of costs were often found to be imprecise and possibly inflated and this emphasises the need for greater transparency and rigour when reporting the costs of biological invasions. Identifying whether the irregularities found for the costs of biological invasions are general for other types of environmental costs should be a research priority.},
}
@article {pmid37907108,
year = {2024},
author = {Zhao, Y and Jia, H and Deng, H and Ge, C and Xing, W and Yu, H and Li, J},
title = {Integrated microbiota and multi-omics analysis reveal the differential responses of earthworm to conventional and biodegradable microplastics in soil under biogas slurry irrigation.},
journal = {The Science of the total environment},
volume = {907},
number = {},
pages = {168191},
doi = {10.1016/j.scitotenv.2023.168191},
pmid = {37907108},
issn = {1879-1026},
mesh = {Animals ; Soil ; *Oligochaeta ; Biofuels ; Microplastics ; Multiomics ; Plastics ; Polyethylene ; *Biodegradable Plastics ; *Microbiota ; Polyesters ; *Soil Pollutants/toxicity ; },
abstract = {As one of the promising alternatives of conventional plastic mulching film (C-PMF), biodegradable plastic mulching films (B-PMF) were employed in agronomy production to alleviate the environmental burden of C-PMF. However, information regarding the potential toxicity effects of biodegradable microplastics (MPs) in soil still in scarcity, and the available findings were found to be controversial. Additionally, little is known about the molecular toxicity effects of conventional and biodegradable MPs on terrestrial organisms. Thus, 5 % (w/w) biodegradable (polylactic acid, PLA) and conventional (polyvinylchloride, PVC; low-density polyvinylchloride, LDPE) MPs were employed to assess the toxicity effects on Eisenia fetida in agricultural soil with biogas slurry irrigation. In the present study, transcriptomic, metabolomic profiles and individual indexes were selected to reveal the toxicity mechanisms from molecular level to the individual response. Furthermore, dysbiosis of bacterial community in gut was also investigated for obtaining comprehensive knowledge on the MPs toxicity. At the end of the exposure, the number of survival earthworms after MPs exposure was significantly reduced. Compared with the initial body weight, PLA and LDPE increased the biomass of earthworms after MPs exposure, while no significant influence on the biomass was observed in PVC treatment. Microbacterium, Klebsiella and Chryseobacterium were significantly enriched in earthworm gut after PLA, PVC and LDPE exposure, respectively (p < 0.05). Transcriptomic and metabolomic analysis revealed that PLA exposure induced neurotransmission disorder and high energetic expenditure in earthworms. However, PVC and LDPE inhibited the nutrient absorption efficiency and activated the innate immunity responses of earthworms. The PLS-SEM results showed that the effects of MPs were dominated by the polymer types, and hence, significantly and directly influence the gut bacterial community of earthworms. This study provides a better understanding of the similarities and discrepancies in toxicity effects of biodegradable and conventional MPs from the perspectives of individual, gut bacterial community, transcriptome and metabolome.},
}
@article {pmid37905937,
year = {2023},
author = {Rihacek, M and Kosaristanova, L and Fialova, T and Kuthanova, M and Eichmeier, A and Hakalova, E and Cerny, M and Berka, M and Palkovicova, J and Dolejska, M and Svec, P and Adam, V and Zurek, L and Cihalova, K},
title = {Zinc effects on bacteria: insights from Escherichia coli by multi-omics approach.},
journal = {mSystems},
volume = {8},
number = {6},
pages = {e0073323},
pmid = {37905937},
issn = {2379-5077},
support = {CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; CZ.02.2.69/0.0/0.0/19_073/0016670//EC | EU Social | European Social Fund (ESF)/ ; },
mesh = {Humans ; Animals ; *Zinc/pharmacology ; *Zinc Oxide/chemistry ; Escherichia coli/genetics ; Multiomics ; Proteomics ; },
abstract = {A long-term exposure of bacteria to zinc oxide and zinc oxide nanoparticles leads to major alterations in bacterial morphology and physiology. These included biochemical and physiological processes promoting the emergence of strains with multi-drug resistance and virulence traits. After the removal of zinc pressure, bacterial phenotype reversed back to the original state; however, certain changes at the genomic, transcriptomic, and proteomic level remained. Why is this important? The extensive and intensive use of supplements in animal feed effects the intestinal microbiota of livestock and this may negatively impact the health of animals and people. Therefore, it is crucial to understand and monitor the impact of feed supplements on intestinal microorganisms in order to adequately assess and prevent potential health risks.},
}
@article {pmid37905717,
year = {2024},
author = {Liu, L and Chen, J and Shen, M and Chen, X and Cao, R and Cao, X and Cui, X and Yang, W and Zhu, X and Li, L and Tang, Y},
title = {A remote sensing method for mapping alpine grasslines based on graph-cut.},
journal = {Global change biology},
volume = {30},
number = {1},
pages = {e17005},
doi = {10.1111/gcb.17005},
pmid = {37905717},
issn = {1365-2486},
support = {//Fundamental Research Funds for the Central Universities/ ; 2019QZKK0405//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0106//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 20190ZKK0307//Second Tibetan Plateau Scientific Expedition and Research Program/ ; //Top-Notch Young Talents Program of China/ ; 23K18517//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; },
mesh = {*Remote Sensing Technology ; *Climate Change ; Tibet ; Grassland ; Ecosystem ; },
abstract = {Climate change has induced substantial shifts in vegetation boundaries such as alpine treelines and shrublines, with widespread ecological and climatic influences. However, spatial and temporal changes in the upper elevational limit of alpine grasslands ("alpine grasslines") are still poorly understood due to lack of field observations and remote sensing estimates. In this study, taking the Tibetan Plateau as an example, we propose a novel method for automatically identifying alpine grasslines from multi-source remote sensing data and determining their positions at 30-m spatial resolution. We first identified 2895 mountains potentially having alpine grasslines. On each mountain, we identified a narrow area around the upper elevational limit of alpine grasslands where the alpine grassline was potentially located. Then, we used linear discriminant analysis to adaptively generate from Landsat reflectance features a synthetic feature that maximized the difference between vegetated and unvegetated pixels in each of these areas. After that, we designed a graph-cut algorithm to integrate the advantages of the Otsu and Canny approaches, which was used to determine the precise position of the alpine grassline from the synthetic feature image. Validation against alpine grasslines visually interpreted from a large number of high-spatial-resolution images showed a high level of accuracy (R[2] , .99 and .98; mean absolute error, 22.6 and 36.2 m, vs. drone and PlanetScope images, respectively). Across the Tibetan Plateau, the alpine grassline elevation ranged from 4038 to 5380 m (5th-95th percentile), lower in the northeast and southeast and higher in the southwest. This study provides a method for remotely sensing alpine grasslines for the first-time at large scale and lays a foundation for investigating their responses to climate change.},
}
@article {pmid37903262,
year = {2023},
author = {Lien, AM and Banki, O and Barik, SK and Buckeridge, JS and Christidis, L and Cigliano, MM and Conix, S and Costello, MJ and Hobern, D and Kirk, PM and Kroh, A and Montgomery, N and Nikolaeva, S and Orrell, TM and Pyle, RL and Raz, L and Thiele, K and Thomson, SA and van Dijk, PP and Wambiji, N and Whalen, A and Zachos, FE and Zhang, ZQ and Garnett, ST},
title = {Widespread support for a global species list with a formal governance system.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {45},
pages = {e2306899120},
pmid = {37903262},
issn = {1091-6490},
support = {IUBS//International Union of Biological Sciences/ ; DP230102933//Australian Research Council/ ; T.0177.21//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; },
mesh = {Humans ; *Commerce ; Internationality ; *Physicians ; },
abstract = {Taxonomic data are a scientific common. Unlike nomenclature, which has strong governance institutions, there are currently no generally accepted governance institutions for the compilation of taxonomic data into an accepted global list. This gap results in challenges for conservation, ecological research, policymaking, international trade, and other areas of scientific and societal importance. Consensus on a global list and its management requires effective governance and standards, including agreed mechanisms for choosing among competing taxonomies and partial lists. However, governance frameworks are currently lacking, and a call for governance in 2017 generated critical responses. Any governance system to which compliance is voluntary requires a high level of legitimacy and credibility among those by and for whom it is created. Legitimacy and credibility, in turn, require adequate and credible consultation. Here, we report on the results of a global survey of taxonomists, scientists from other disciplines, and users of taxonomy designed to assess views and test ideas for a new system of taxonomic list governance. We found a surprisingly high degree of agreement on the need for a global list of accepted species and their names, and consistent views on what such a list should provide to users and how it should be governed. The survey suggests that consensus on a mechanism to create, manage, and govern a single widely accepted list of all the world's species is achievable. This finding was unexpected given past controversies about the merits of list governance.},
}
@article {pmid37898720,
year = {2023},
author = {Jin, Q and Gheeya, J and Nepal, S and Shi, N and Folefac, E and Webb, MZ and Grainger, EM and Wei, L and Prosek, JM and Focht, BC and Gong, M and Clinton, SK and Tabung, FK},
title = {Associations of dietary patterns with kidney cancer risk, kidney cancer-specific mortality and all-cause mortality among postmenopausal women.},
journal = {British journal of cancer},
volume = {129},
number = {12},
pages = {1978-1987},
pmid = {37898720},
issn = {1532-1827},
support = {T32 CA247815/CA/NCI NIH HHS/United States ; 75N92021D00002/HL/NHLBI NIH HHS/United States ; 75N92021D00005/WH/WHI NIH HHS/United States ; 75N92021D00001/HL/NHLBI NIH HHS/United States ; 75N92021D00003/WH/WHI NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; 75N92021D00004/WH/WHI NIH HHS/United States ; },
mesh = {Humans ; Female ; Postmenopause ; Prospective Studies ; Diet/adverse effects ; *Carcinoma, Renal Cell ; *Kidney Neoplasms ; Risk Factors ; },
abstract = {BACKGROUND: The empirical dietary index for hyperinsulinemia (EDIH) and empirical dietary inflammatory pattern (EDIP) are novel measures of dietary quality associated with insulin hypersecretion or chronic inflammation, respectively, whereas the Healthy Eating Index (HEI-2015) measures adherence to the Dietary Guidelines for Americans (DGA). We evaluated associations of EDIH, EDIP and HEI-2015 on the risk of both kidney cancer development and mortality.<br><br>METHODS: We calculated the dietary scores from baseline food frequency questionnaires among 115,830 participants aged 50-79 years in the Women's Health Initiative. Multivariable-adjusted Cox regression was used to estimate hazard ratios (HR) and 95% confidence intervals (95%CI) for kidney cancer risk, kidney cancer-specific mortality and all-cause mortality, per 1-standard deviation increment in dietary pattern scores.<br><br>RESULTS: Higher EDIH was associated with greater risk of kidney cancer development [HR, 1.12; 95%CI, (1.01,1.23)], kidney cancer-specific death [1.22(0.99,1.48)], and all-cause mortality, [1.05(1.02,1.08)]. Higher HEI-2015 was associated with lower risk of kidney cancer development, [0.85(0.77, 0.94)], kidney cancer-specific death, [0.84(0.69,1.03)] and all-cause mortality, [0.97(0.95,1.00)]. However, EDIP was not significantly associated with outcomes. Associations did not differ by BMI categories.<br><br>CONCLUSIONS: Low-insulinemic dietary patterns and higher quality diets, are worthy of testing in dietary pattern intervention trials for kidney cancer prevention and improved survivorship.},
}
@article {pmid37898190,
year = {2024},
author = {Huang, C and Guan, K and Qi, X and Liu, YE and Lu, Q and Zeng, Y and Wang, S and Luo, X and Mai, B},
title = {Spatial distribution, conversion, and ecological risk assessment of hexabromocyclododecanes in the sediments of black-odorous urban rivers nationwide in China.},
journal = {The Science of the total environment},
volume = {907},
number = {},
pages = {168057},
doi = {10.1016/j.scitotenv.2023.168057},
pmid = {37898190},
issn = {1879-1026},
mesh = {Rivers ; Environmental Monitoring/methods ; Geologic Sediments ; *Hydrocarbons, Brominated/analysis ; China ; Risk Assessment ; *Flame Retardants/analysis ; },
abstract = {Hexabromocyclododecanes (HBCDs) have become a global pollution problem, particularly in China-a major producer and user of HBCDs. However, little is known about the HBCD pollution status in urban rivers nationwide in China. In this study, we comprehensively investigated the pollution characteristics of HBCDs in 173 sediment samples from black-odorous urban rivers across China. Total HBCD concentrations ranged from not-detected to 848 ng/g dw, showing significant differences among the various sampling cities, but generally increasing from west to east China. This distribution pattern of HBCDs was strongly associated with the local industrial output, gross domestic product, and daily wastewater treatment capacity. α-HBCD was the predominant diastereoisomer in most sediments, with an average proportion of 63.8 ± 18.8 %, followed by γ-HBCD (23.8 ± 19.5 %) and β-HBCD (12.4 ± 6.49 %), showing a significant increase of the α-HBCD proportions relative to those in HBCD commercial mixtures and an opposite trend for that of γ-HBCD. These results suggested that HBCDs might undergo isomerization from γ- to α-HBCD and biotic/abiotic degradation with preference for γ-HBCD. Of these conversions, the microbial degradation of HBCDs was further verified by the preferential transformation of (-)-α-, (+)-β-, and (-)-γ-HBCDs and the detection of HBCD-degrading bacteria, including Dehalococcoides, Bacillus, Sphingobium, and Pseudomonas. A risk assessment indicated that HBCDs pose low to moderate risks to aquatic organisms in most black-odorous urban river sediments.},
}
@article {pmid37898004,
year = {2023},
author = {Karakurt-Fischer, S and Johnson, DR and Fenner, K and Hafner, J},
title = {Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia.},
journal = {Water research},
volume = {247},
number = {},
pages = {120756},
doi = {10.1016/j.watres.2023.120756},
pmid = {37898004},
issn = {1879-2448},
mesh = {Microbial Consortia ; *Environmental Pollutants/metabolism ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Soil/chemistry ; *Soil Pollutants/metabolism ; Soil Microbiology ; },
abstract = {Biodegradation holds promise as an effective and sustainable process for the removal of synthetic chemical pollutants. Nevertheless, rational engineering of biodegradation for pollutant remediation remains an unfulfilled goal, while chemical pollution of waters and soils continues to advance. Efforts to (i) identify functional bacteria from aquatic and soil microbiomes, (ii) assemble them into biodegrading consortia, and (iii) identify maintenance and performance determinants, are challenged by large number of pollutants and the complexity in the enzymology and ecology of pollutant biodegradation. To overcome these challenges, approaches that leverage knowledge from environmental bio-chem-informatics and metabolic engineering are crucial. Here, we propose a novel high-throughput bio-chem-informatics pipeline, to link chemicals and their predicted biotransformation pathways with potential enzymes and bacterial strains. Our framework systematically selects the most promising candidates for the degradation of chemicals with unknown biotransformation pathways and associated enzymes from the vast array of aquatic and soil bacteria. We substantiated our perspective by validating the pipeline for two chemicals with known or predicted pathways and show that our predicted strains are consistent with strains known to biotransform those chemicals. Such pipelines can be integrated with metabolic network analysis built upon genome-scale models and ecological principles to rationally design fit-for-purpose bacterial communities for augmenting deficient biotransformation functions and study operational and design parameters that influence their structure and function. We believe that research in this direction can pave the way for achieving our long-term goal of enhancing pollutant biodegradation.},
}
@article {pmid37897291,
year = {2023},
author = {Zhang, HS and Zhong, XM and Xiong, Y and Wu, XR},
title = {[Big data analysis of coastal illegal fishing from the perspective of compensation of ecological and environmental damage].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {34},
number = {10},
pages = {2827-2834},
doi = {10.13287/j.1001-9332.202310.032},
pmid = {37897291},
issn = {1001-9332},
mesh = {Big Data ; China ; Conservation of Natural Resources/methods ; *Ecosystem ; *Hunting ; },
abstract = {Illegal fishing is one of the sources of marine ecological damage. The implementation of compensation of ecological and environmental damage in this field is poorly understood. In this study, we examined data pertaining to coastal illegal fishing cases during 2018-2022 using the big data publicly made available by China Judgement Online. The main results included: 1) there are numerous types of illegal fishing, and more efforts should focus on the nature and extent of illegal fishing, with electrofishing and trawl being suitable entry points; 2) Special attention should be paid to the variation characteristics of rakes in the range of high illegal catch weight and value. It was suggested to optimize and adjust its management mode to avoid the frequent occurrence of such illegal fishing cases of rake; 3) The varieties of assessment models increased the uncertainty of damages computation, which might be reduced by establishing strong criteria for value quantification and damage assessment; 4) There is limited scientific support for the compensation for releasing the most popular ecological restoration technique for illegal fishing. As a result, the "compensation" design for "restoration" should be implemented, while the potential for additional restoration methods should be investigated.},
}
@article {pmid37895673,
year = {2023},
author = {Dudek, M and Sąsiadek-Andrzejczak, E and Jaszczak-Kuligowska, M and Rokita, B and Kozicki, M},
title = {The Surface Modification of Papers Using Laser Processing towards Applications.},
journal = {Materials (Basel, Switzerland)},
volume = {16},
number = {20},
pages = {},
pmid = {37895673},
issn = {1996-1944},
abstract = {This work presents the results of paper laser processing. It begins with the selection and examination of the processing parameters, then an examination of the properties of the modified papers and examples of applications of the developed modification method. The properties of laser-modified paper were studied using reflectance spectrophotometry to examine the colour aspects of the modified papers, scanning electron microscopy (SEM) and confocal microscopy for a morphological analysis, and Raman spectroscopy to analyse the papers under the influence of laser light. The influence of laser processing on the wettability of paper and the evenness of unprinted and printed paper was also investigated. The knowledge gained on paper surface modification with laser light was used to propose several applications, such as methods of marking, tactile detection, the controlled removal of optical brightener, ink, and metallised coatings from paper packaging, highlighting the design and aesthetics of paper. The developed laser-assisted method shows a promising, ecological approach to the design of many value-added paper products.},
}
@article {pmid37892395,
year = {2023},
author = {Gutiérrez-Hellín, J and Del Coso, J and Espada, MC and Hernández-Beltrán, V and Ferreira, CC and Varillas-Delgado, D and Mendoza Laiz, N and Roberts, JD and Gamonales, JM},
title = {Research Trends in the Effect of Caffeine Intake on Fat Oxidation: A Bibliometric and Visual Analysis.},
journal = {Nutrients},
volume = {15},
number = {20},
pages = {},
pmid = {37892395},
issn = {2072-6643},
support = {UID04045/2020//Portuguese Foundation for Science and Technology/ ; GR21149//University of Extremadura/ ; },
mesh = {Humans ; United States ; Aged ; *Caffeine ; *Bibliometrics ; Netherlands ; Authorship ; Databases, Factual ; },
abstract = {In the last few decades, numerous studies pertaining to research groups worldwide have investigated the effects of oral caffeine intake on fat oxidation at rest, during exercise, and after exercise. However, there is no bibliometric analysis to assess the large volume of scientific output associated with this topic. A bibliometric analysis of this topic may be used by researchers to assess the current scientific interest in the application of caffeine as a nutritional strategy to augment fat oxidation, the journals with more interest in this type of publication, and to draw international collaborations between groups working in the same area. For these reasons, the purpose of this study was to assess the research activity regarding oral caffeine intake and fat oxidation rate in the last few decades by conducting a bibliometric and visual analysis. Relevant publications from 1992 to 2022 were retrieved from the Web of Science (WoS) Core Collection database. Quantitative and qualitative variables were collected, including the number of publications and citations, H-indexes, journals of citation reports, co-authorship, co-citation, and the co-occurrence of keywords. There were 182 total publications, while the number of annual publications is saw-shaped with a modest increase of 11.3% from 2000 to 2009 to 2010 to 2019. The United States was the country with the highest number of publications (24.17% of the total number of articles), followed by the Netherlands (17.03%). According to citation analyses, the average number of citations per document is 130, although there are 21 documents that have received more than 100 citations; the most cited document reached 644 citations. These citation data support the overall relevance of this topic in the fields of nutrition and dietetics and sport sciences that when combined harbored 85.71% of all articles published in the WoS. The most productive author was Westerterp-Plantenga with 16 articles (8.79% of the total number of articles). Nutrients was the journal that published the largest number of articles on this topic (6.59% of the total number of articles). Last, there is a tendency to include keywords such as "performance", "carbohydrate", and "ergogenic aid" in the newer articles, while "obesity", "thermogenic", and "tea" are the keywords more commonly included in older documents. Although research into the role of caffeine on fat oxidation has existed since the 1970s, our analysis suggests that the scientific output associated with this topic has progressively increased since 1992, demonstrating that this is a nutritional research area with a strong foundational base of scientific evidence. Based on the findings of this bibliometric analysis, future investigation may consider focusing on the effects of sex and tolerance to caffeine to widen the assessment of the effectiveness of oral caffeine intake as a nutritional strategy to augment the use of fat as a fuel, as these terms rarely appear in the studies included in this analysis. Additionally, more translational research is necessary as the studies that investigate the effect of oral caffeine intake in ecologically valid contexts (i.e., exercise training programs for individuals with excessive adiposity) are only a minor part of the studies on this topic.},
}
@article {pmid37889410,
year = {2023},
author = {Jalil, F and Yang, J and Rehman, SU and Khan, MM},
title = {Post-COVID-19's impact on green supply chain management and sustainable E-commerce performance: the moderating role of big data analytics.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {54},
pages = {115683-115698},
pmid = {37889410},
issn = {1614-7499},
mesh = {*Commerce ; COVID-19 ; Data Science ; *Industry ; *Big Data ; Data Analysis ; *Sustainable Development ; Internet ; Pakistan ; },
abstract = {This study investigates the relationship between COVID-19 and the adoption of green supply chain management practices (GSCM) in the Pakistani e-commerce industry. It also assesses the impact of these practices on ecological sustainability across three dimensions and explores the role of big data analytics (BDA) in enhancing them after the pandemic. The research utilized partial least squares structural equation modeling to evaluate data and test hypotheses. The research sample was composed of 390 managers operating within Pakistan's e-commerce industry. The study's preliminary findings reveal that COVID-19 has positively influenced the adoption of GSCM practices, which are moderated by BDA. Implementing GSCM has a positive impact on the perceived environmental and social resilience of e-commerce enterprises, but no significant effect on their perceived economic resilience. Additionally, GSCM acts as a mediator in the relationship between the impact of COVID-19 and the perceived environmental and social resilience of e-commerce firms, but not for economic resilience. This research focuses on Pakistan's e-commerce industry and investigates how COVID-19 affects the adoption of eco-friendly supply chain practices. It measures the impact of these practices on ecological sustainability using three dimensions. The study also examines how BDA can improve the adoption of GSCM in e-commerce, offering new insights into sustainability during and post-pandemic. The results recommend that the e-commerce industry can use BDA and GSCM practices to improve e-commerce sustainable performance. This is initial research that integrates COVID-19 impact, BDA, GSCM practices, and e-commerce sustainability in a single framework that was overlooked previously.},
}
@article {pmid37888680,
year = {2023},
author = {Zhu, X and Ji, H and Hua, G and Zhou, L},
title = {Dynamic Release Characteristics and Kinetics of a Persulfate Sustained-Release Material.},
journal = {Toxics},
volume = {11},
number = {10},
pages = {},
pmid = {37888680},
issn = {2305-6304},
support = {2020YFC1806502//The National Key Research and Development Project of China/ ; },
abstract = {Sustained-release materials are increasingly being used in the delivery of oxidants for in situ chemical oxidation (ISCO) for groundwater remediation. Successful implementation of sustained-release materials depends on a clear understanding of the mechanism and kinetics of sustained release. In this research, a columnar sustained-release material (PS@PW) was prepared with paraffin wax and sodium persulfate (PS), and column experiments were performed to investigate the impacts of the PS@PW diameter and PS/PW mass ratio on PS release. The results demonstrated that a reduction in diameter led to an increase in both the rate and proportion of PS release, as well as a diminished lifespan of release. The release process followed the second-order kinetics, and the release rate constant was positively correlated with the PS@PW diameter. A matrix boundary diffusion model was utilized to determine the PS@PW diffusion coefficient of the PS release process, and the release lifespan of a material with a length of 500 mm and a diameter of 80 mm was predicted to be more than 280 days. In general, this research provided a better understanding of the release characteristics and kinetics of persulfate from a sustained-release system and could lead to the development of columnar PS@PW as a practical oxidant for in situ chemical oxidation of contaminated aquifers.},
}
@article {pmid37885811,
year = {2023},
author = {Boyes, D and Chua, P and , and , and , and , and , and , },
title = {The genome sequence of the Oak Hook-tip, Watsonalla binaria (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {324},
pmid = {37885811},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Watsonalla binaria (the Oak Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 333.0 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.24 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,002 protein coding genes.},
}
@article {pmid37883444,
year = {2024},
author = {Kinkade, JA and Seetharam, AS and Sachdev, S and Bivens, NJ and Phinney, BS and Grigorean, G and Roberts, RM and Tuteja, G and Rosenfeld, CS},
title = {Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta-brain axis†.},
journal = {Biology of reproduction},
volume = {110},
number = {2},
pages = {310-328},
pmid = {37883444},
issn = {1529-7268},
support = {R01 ES025547/ES/NIEHS NIH HHS/United States ; R01 HD096083/HD/NICHD NIH HHS/United States ; S10 OD021801/OD/NIH HHS/United States ; R01HD096083/GF/NIH HHS/United States ; },
mesh = {Humans ; Pregnancy ; Female ; Animals ; Mice ; Serotonin/metabolism ; Placenta/metabolism ; *MicroRNAs/genetics/metabolism ; *Extracellular Vesicles/metabolism ; Brain/metabolism ; Trophoblasts/metabolism ; Stem Cells/metabolism ; },
abstract = {The fetal brain of the mouse is thought to be dependent upon the placenta as a source of serotonin (5-hydroxytryptamine; 5-HT) and other factors. How factors reach the developing brain remains uncertain but are postulated here to be part of the cargo carried by placental extracellular vesicles (EV). We have analyzed the protein, catecholamine, and small RNA content of EV from mouse trophoblast stem cells (TSC) and TSC differentiated into parietal trophoblast giant cells (pTGC), potential primary purveyors of 5-HT. Current studies examined how exposure of mouse neural progenitor cells (NPC) to EV from either TSC or pTGC affect their transcriptome profiles. The EV from trophoblast cells contained relatively high amounts of 5-HT, as well as dopamine and norepinephrine, but there were no significant differences between EV derived from pTGC and from TSC. Content of miRNA and small nucleolar (sno)RNA, however, did differ according to EV source, and snoRNA were upregulated in EV from pTGC. The primary inferred targets of the microRNA (miRNA) from both pTGC and TSC were mRNA enriched in the fetal brain. NPC readily internalized EV, leading to changes in their transcriptome profiles. Transcripts regulated were mainly ones enriched in neural tissues. The transcripts in EV-treated NPC that demonstrated a likely complementarity with miRNA in EV were mainly up- rather than downregulated, with functions linked to neuronal processes. Our results are consistent with placenta-derived EV providing direct support for fetal brain development and being an integral part of the placenta-brain axis.},
}
@article {pmid37881861,
year = {2024},
author = {Rick, JA and Brock, CD and Lewanski, AL and Golcher-Benavides, J and Wagner, CE},
title = {Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.},
journal = {Systematic biology},
volume = {73},
number = {1},
pages = {76-101},
doi = {10.1093/sysbio/syad065},
pmid = {37881861},
issn = {1076-836X},
support = {DEB-1556963//National Science Foundation/ ; },
mesh = {*Phylogeny ; *Genome/genetics ; *Classification/methods ; Genomics/methods ; Computational Biology/methods ; },
abstract = {Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference.},
}
@article {pmid37881225,
year = {2023},
author = {Bald, L and Gottwald, J and Zeuss, D},
title = {spatialMaxent: Adapting species distribution modeling to spatial data.},
journal = {Ecology and evolution},
volume = {13},
number = {10},
pages = {e10635},
pmid = {37881225},
issn = {2045-7758},
abstract = {Conventional practices in species distribution modeling lack predictive power when the spatial structure of data is not taken into account. However, choosing a modeling approach that accounts for overfitting during model training can improve predictive performance on spatially separated test data, leading to more reliable models. This study introduces spatialMaxent (https://github.com/envima/spatialMaxent), a software that combines state-of-the-art spatial modeling techniques with the popular species distribution modeling software Maxent. It includes forward-variable-selection, forward-feature-selection, and regularization-multiplier tuning based on spatial cross-validation, which enables addressing overfitting during model training by considering the impact of spatial dependency in the training data. We assessed the performance of spatialMaxent using the National Center for Ecological Analysis and Synthesis dataset, which contains over 200 anonymized species across six regions worldwide. Our results show that spatialMaxent outperforms both conventional Maxent and models optimized according to literature recommendations without using a spatial tuning strategy in 80 percent of the cases. spatialMaxent is user-friendly and easily accessible to researchers, government authorities, and conservation practitioners. Therefore, it has the potential to play an important role in addressing pressing challenges of biodiversity conservation.},
}
@article {pmid37881092,
year = {2024},
author = {Wang, S and Ye, H and Shang, S and Li, Z and Peng, Y and Zhou, P},
title = {A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.},
journal = {Current medicinal chemistry},
volume = {31},
number = {26},
pages = {4127-4137},
pmid = {37881092},
issn = {1875-533X},
mesh = {*Peptides/chemistry/metabolism ; *Databases, Protein ; *Proteins/chemistry/metabolism ; Protein Binding ; Molecular Docking Simulation ; Ligands ; Humans ; Protein Conformation ; },
abstract = {BACKGROUND: Peptides play crucial roles in diverse cellular functions and participate in many biological processes by interacting with a variety of proteins, which have also been exploited as a promising class of therapeutic agents to target druggable proteins over the past decades. Understanding the intrinsic association between the structure and affinity of protein-peptide interactions (PpIs) should be considerably valuable for the computational peptidology area, such as guiding protein-peptide docking calculations, developing protein-peptide affinity scoring functions, and designing peptide ligands for specific protein receptors.<br><br>OBJECTIVE: We attempted to create a data source for relating PpI structure to affinity.<br><br>METHODS: By exhaustively surveying the whole protein data bank (PDB) database as well as the ontologically enriched literature information, we manually curated a structure- based data set of protein-peptide affinities, PpI[S/A]DS, which assembled over 350 PpI complex samples with both the experimentally measured structure and affinity data. The data set was further reduced to a nonredundant benchmark consisting of 102 culled samples, PpI[S/A]BM, which only selected those of structurally reliable, functionally diverse and evolutionarily nonhomologous.<br><br>RESULTS: The collected structures were resolved at a high-resolution level with either Xray crystallography or solution NMR, while the deposited affinities were characterized by dissociation constant, i.e. Kd value, which is a direct biophysical measure of the intermolecular interaction strength between protein and peptide, ranging from subnanomolar to millimolar levels. The PpI samples in the set/benchmark were arbitrarily classified into &#x3b1;-helix, partial &#x3b1;-helix, &#x3b2;-sheet formed through binding, &#x3b2;-strand formed through selffolding, mixed, and other irregular ones, totally resulting in six classes according to the secondary structure of their peptide ligands. In addition, we also categorized these PpIs in terms of their biological function and binding behavior.<br><br>CONCLUSION: The PpI[S/A]DS set and PpI[S/A]BM benchmark can be considered a valuable data source in the computational peptidology community, aiming to relate the affinity to structure for PpIs.},
}
@article {pmid37880625,
year = {2023},
author = {Bernardini, I and Quagliariello, A and Peruzza, L and Martino, ME and Dalla Rovere, G and Iori, S and Asnicar, D and Ciscato, M and Fabrello, J and Corami, F and Cecchetto, M and Giubilato, E and Carrer, C and Bettiol, C and Semenzin, E and Marcomini, A and Matozzo, V and Bargelloni, L and Milan, M and Patarnello, T},
title = {Contaminants from dredged sediments alter the transcriptome of Manila clam and induce shifts in microbiota composition.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {234},
pmid = {37880625},
issn = {1741-7007},
mesh = {Animals ; Geologic Sediments/chemistry ; Transcriptome ; Dibenzofurans/metabolism ; *Water Pollutants, Chemical/toxicity/analysis/metabolism ; *Polychlorinated Dibenzodioxins/analysis/metabolism/toxicity ; *Bivalvia/genetics/chemistry/metabolism ; *Microbiota ; },
abstract = {BACKGROUND: The reuse of dredged sediments in ports and lagoons is a big issue as it should not affect the quality and the equilibrium of ecosystems. In the lagoon of Venice, sediment management is of crucial importance as sediments are often utilized to built-up structures necessary to limit erosion. However, the impact of sediment reuse on organisms inhabiting this delicate area is poorly known. The Manila clam is a filter-feeding species of high economic and ecological value for the Venice lagoon experiencing a drastic decline in the last decades. In order to define the molecular mechanisms behind sediment toxicity, we exposed clams to sediments sampled from different sites within one of the Venice lagoon navigable canals close to the industrial area. Moreover, we investigated the impacts of dredged sediments on clam's microbial communities.<br><br>RESULTS: Concentrations of the trace elements and organic chemicals showed increasing concentrations from the city of Venice to sites close to the industrial area of Porto Marghera, where PCDD/Fs and PCBs concentrations were up to 120 times higher than the southern lagoon. While bioaccumulation of organic contaminants of industrial origin reflected sediments' chemical concentrations, metal bioaccumulation was not consistent with metal concentrations measured in sediments probably due to the activation of ABC transporters. At the transcriptional level, we found a persistent activation of the mTORC1 signalling pathway, which is central in the coordination of cellular responses to chemical stress. Microbiota characterization showed the over-representation of potential opportunistic pathogens following exposure to the most contaminated sediments, leading to host immune response activation. Despite the limited acquisition of new microbial species from sediments, the latter play an important role in shaping Manila clam microbial communities.<br><br>CONCLUSIONS: Sediment management in the Venice lagoon will increase in the next years to maintain and create new canals as well as to allow the operation of the new mobile gates at the three Venice lagoon inlets. Our data reveal important transcriptional and microbial changes of Manila clams after exposure to sediments, therefore reuse of dredged sediments represents a potential risk for the conservation of this species and possibly for other organisms inhabiting the Venice lagoon.},
}
@article {pmid37880359,
year = {2023},
author = {Liang, D and Giam, X and Hu, S and Ma, L and Wilcove, DS},
title = {Assessing the illegal hunting of native wildlife in China.},
journal = {Nature},
volume = {623},
number = {7985},
pages = {100-105},
pmid = {37880359},
issn = {1476-4687},
mesh = {Animals ; Amphibians ; *Animals, Wild ; *Biodiversity ; Birds ; China ; Databases, Factual ; Endangered Species/economics/legislation &amp; jurisprudence/statistics &amp; numerical data ; *Hunting/economics/legislation &amp; jurisprudence/statistics &amp; numerical data ; Mammals ; Reptiles ; },
abstract = {Illegal harvesting and trading of wildlife have become major threats to global biodiversity and public health[1-3]. Although China is widely recognized as an important destination for wildlife illegally obtained abroad[4], little attention has been given to illegal hunting within its borders. Here we extracted 9,256 convictions for illegal hunting from a nationwide database of trial verdicts in China spanning January 2014 to March 2020. These convictions involved illegal hunting of 21% (n = 673) of China's amphibian, reptile, bird and mammal species, including 25% of imperilled species in these groups. Sample-based extrapolation indicates that many more species were taken illegally during this period. Larger body mass and range size (for all groups), and proximity to urban markets (for amphibians and birds) increase the probability of a species appearing in the convictions database. Convictions pertained overwhelmingly to illegal hunting for commercial purposes and involved all major habitats across China. A small number of convictions represented most of the animals taken, indicating the existence of large commercial poaching operations. Prefectures closer to urban markets show higher densities of convictions and more individual animals taken. Our results suggest that illegal hunting is a major, overlooked threat to biodiversity throughout China.},
}
@article {pmid37880224,
year = {2023},
author = {Sonkoly, J and Tóth, E and Balogh, N and Balogh, L and Bartha, D and Csendesné Bata, K and Bátori, Z and Békefi, N and Botta-Dukát, Z and Bölöni, J and Csecserits, A and Csiky, J and Csontos, P and Dancza, I and Deák, B and Dobolyi, ZK and E-Vojtkó, A and Gyulai, F and Hábenczyus, AA and Henn, T and Horváth, F and Höhn, M and Jakab, G and Kelemen, A and Király, G and Kis, S and Kovacsics-Vári, G and Kun, A and Lehoczky, &#xc9; and Lengyel, A and Lhotsky, B and Löki, V and Lukács, BA and Matus, G and McIntosh-Buday, A and Mesterházy, A and Miglécz, T and Molnár V, A and Molnár, Z and Morschhauser, T and Papp, L and Pósa, P and Rédei, T and Schmidt, D and Szmorad, F and Takács, A and Tamás, J and Tiborcz, V and Tölgyesi, C and Tóth, K and Tóthmérész, B and Valkó, O and Virók, V and Wirth, T and Török, P},
title = {PADAPT 1.0 - the Pannonian Dataset of Plant Traits.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {742},
pmid = {37880224},
issn = {2052-4463},
support = {K 119225//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; K 137573//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; KKP 144068//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; PD 137747//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; KH 130320//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; PD 138859//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; PD 138715//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; PD 137828//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; BO/00587/23/8//Magyar Tudom&#xe1;nyos Akad&#xe9;mia (Hungarian Academy of Sciences)/ ; },
mesh = {Databases, Factual ; Europe ; Geography ; *Plants ; },
abstract = {The existing plant trait databases' applicability is limited for studies dealing with the flora and vegetation of the eastern and central part of Europe and for large-scale comparisons across regions, mostly because their geographical data coverage is limited and they incorporate records from several different sources, often from regions with markedly different climatic conditions. These problems motivated the compilation of a regional dataset for the flora of the Pannonian region (Eastern Central Europe). PADAPT, the Pannonian Dataset of Plant Traits relies on regional data sources and collates data on 54 traits and attributes of the plant species of the Pannonian region. The current version covers approximately 90% of the species of the region and consists of 126,337 records on 2745 taxa. By including species of the eastern part of Europe not covered by other databases, PADAPT can facilitate studying the flora and vegetation of the eastern part of the continent. Although data coverage is far from complete, PADAPT meets the longstanding need for a regional database of the Pannonian flora.},
}
@article {pmid37879178,
year = {2023},
author = {Li, D and Guan, X and Tang, T and Zhao, L and Tong, W and Wang, Z},
title = {The clean energy development path and sustainable development of the ecological environment driven by big data for mining projects.},
journal = {Journal of environmental management},
volume = {348},
number = {},
pages = {119426},
doi = {10.1016/j.jenvman.2023.119426},
pmid = {37879178},
issn = {1095-8630},
mesh = {*Sustainable Development ; *Carbon Dioxide ; Big Data ; Mining ; Economic Development ; Renewable Energy ; },
abstract = {Clean energy is urgently needed to realize mining projects' sustainable development (SD). This study aims to discuss the clean energy development path and the related issues of SD in the ecological environment driven by big data for mining projects. This study adopts a comprehensive research approach, including a literature review, case analysis, and model construction. Firstly, an in-depth literature review of the development status of clean energy is carried out, and the existing research results and technology applications are explored. Secondly, some typical mining projects are selected as cases to discuss the practice and effect of their clean energy application. Finally, the corresponding clean energy development path and the SD analysis model of the ecological environment are constructed based on big data technology to evaluate the feasibility and potential benefits of promoting and applying clean energy in mining projects. (1) It is observed that under different Gross Domestic Product (GDP) growth rates, the new and cumulative installed capacities of wind energy show an increasing trend. In 2022, under the low GDP growth rate, the cumulative installed capacity of global wind energy was 370.60 Gigawatt (GW), and the new installed capacity was 45 GW. With the high GDP growth rate, the cumulative and new installed capacities were 367.83 GW and 46 GW. As the economy grows, new wind energy capacity is expected to increase significantly by 2030. In 2046, 2047, and 2050, carbon dioxide (CO2) emissions reductions are projected to be 8183.35, 8539.22, and 9842.73 Million tons (Mt) (low scenario), 8750.68, 9087.16, and 10,468.75 Mt (medium scenario), and 9083.03, 9458.86, and 10,879.58 Mt (high scenario). By 2060, it is expected that CO2 emissions reduction will continue to increase. (2) The proposed clean energy development path model has achieved a good effect. Through this study, it is hoped to provide empirical support and decision-making reference for the development of mining projects in clean energy, and promote the SD of the mining industry, thus achieving a win-win situation of economic and ecological benefits. This is of great significance for protecting the ecological environment and realizing the sustainable utilization of resources.},
}
@article {pmid37877166,
year = {2024},
author = {Santos, CAQ and Tseng, M and Martinez, AI and Shankaran, S and Hodgson, HA and Ahmad, FS and Zhang, H and Sievert, DM and Trick, WE},
title = {Comparative antimicrobial use in coronavirus disease 2019 (COVID-19) and non-COVID-19 inpatients from 2019 to 2020: A multicenter ecological study.},
journal = {Infection control and hospital epidemiology},
volume = {45},
number = {3},
pages = {335-342},
doi = {10.1017/ice.2023.180},
pmid = {37877166},
issn = {1559-6834},
mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; Retrospective Studies ; Inpatients ; Anti-Bacterial Agents/therapeutic use ; *Cross Infection ; },
abstract = {OBJECTIVE: We sought to determine whether increased antimicrobial use (AU) at the onset of the coronavirus disease 2019 (COVID-19) pandemic was driven by greater AU in COVID-19 patients only, or whether AU also increased in non-COVID-19 patients.<br><br>DESIGN: In this retrospective observational ecological study from 2019 to 2020, we stratified inpatients by COVID-19 status and determined relative percentage differences in median monthly AU in COVID-19 patients versus non-COVID-19 patients during the COVID-19 period (March-December 2020) and the pre-COVID-19 period (March-December 2019). We also determined relative percentage differences in median monthly AU in non-COVID-19 patients during the COVID-19 period versus the pre-COVID-19 period. Statistical significance was assessed using Wilcoxon signed-rank tests.<br><br>SETTING: The study was conducted in 3 acute-care hospitals in Chicago, Illinois.<br><br>PATIENTS: Hospitalized patients.<br><br>RESULTS: Facility-wide AU for broad-spectrum antibacterial agents predominantly used for hospital-onset infections was significantly greater in COVID-19 patients versus non-COVID-19 patients during the COVID-19 period (with relative increases of 73%, 66%, and 91% for hospitals A, B, and C, respectively), and during the pre-COVID-19 period (with relative increases of 52%, 64%, and 66% for hospitals A, B, and C, respectively). In contrast, facility-wide AU for all antibacterial agents was significantly lower in non-COVID-19 patients during the COVID-19 period versus the pre-COVID-19 period (with relative decreases of 8%, 7%, and 8% in hospitals A, B, and C, respectively).<br><br>CONCLUSIONS: AU for broad-spectrum antimicrobials was greater in COVID-19 patients compared to non-COVID-19 patients at the onset of the pandemic. AU for all antibacterial agents in non-COVID-19 patients decreased in the COVID-19 period compared to the pre-COVID-19 period.},
}
@article {pmid37874849,
year = {2023},
author = {Mwangungulu, SP and Dorothea, D and Ngereja, ZR and Kaindoa, EW},
title = {Geospatial based model for malaria risk prediction in Kilombero valley, South-eastern, Tanzania.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0293201},
pmid = {37874849},
issn = {1932-6203},
support = {/WT_/Wellcome Trust/United Kingdom ; 216448/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 107768/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; },
mesh = {Humans ; Tanzania/epidemiology ; *Malaria/epidemiology/prevention &amp; control ; Environment ; Geographic Information Systems ; Public Health ; },
abstract = {BACKGROUND: Malaria continues to pose a major public health challenge in tropical regions. Despite significant efforts to control malaria in Tanzania, there are still residual transmission cases. Unfortunately, little is known about where these residual malaria transmission cases occur and how they spread. In Tanzania for example, the transmission is heterogeneously distributed. In order to effectively control and prevent the spread of malaria, it is essential to understand the spatial distribution and transmission patterns of the disease. This study seeks to predict areas that are at high risk of malaria transmission so that intervention measures can be developed to accelerate malaria elimination efforts.<br><br>METHODS: This study employs a geospatial based model to predict and map out malaria risk area in Kilombero Valley. Environmental factors related to malaria transmission were considered and assigned valuable weights in the Analytic Hierarchy Process (AHP), an online system using a pairwise comparison technique. The malaria hazard map was generated by a weighted overlay of the altitude, slope, curvature, aspect, rainfall distribution, and distance to streams in Geographic Information Systems (GIS). Finally, the risk map was created by overlaying components of malaria risk including hazards, elements at risk, and vulnerability.<br><br>RESULTS: The study demonstrates that the majority of the study area falls under moderate risk level (61%), followed by the low risk level (31%), while the high malaria risk area covers a small area, which occupies only 8% of the total area.<br><br>CONCLUSION: The findings of this study are crucial for developing spatially targeted interventions against malaria transmission in residual transmission settings. Predicted areas prone to malaria risk provide information that will inform decision-makers and policymakers for proper planning, monitoring, and deployment of interventions.},
}
@article {pmid37872949,
year = {2023},
author = {Ahmad, K and Shankar Pacha, A and Yahya Naqash, R and Kumar Peddamma, S and Yellapu, S and Hudson, S and Singh Baghel, D and Nigam, P and Mondol, S},
title = {Evolutionary insights on critically endangered Kashmir red deer or hangul (Cervus hanglu hanglu) through a mitogenomic lens.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15746},
pmid = {37872949},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; Bayes Theorem ; *Deer/genetics ; Biological Evolution ; Phylogeography ; },
abstract = {BACKGROUND: The Kashmir red deer or Hangul (Cervus hanglu hanglu) is the only Tarim red deer species endemic to India. With a current estimated population size of fewer than 200 individuals, this critically endangered species is confined to the greater Dachigam landscape in Jammu and Kashmir. Poaching, habitat loss and fragmentation, resource competition with livestock, and small population size are the major conservation challenges for this species.<br><br>METHODS: Blood sampling was conducted from two wild Hangul individuals during radio-collaring operations at Dachigam National Park, Kashmir in 2013 and 2020, respectively. Using next-generation sequencing approach, we sequenced the 16,351 bp long mitogenome of two wild-caught Hangul individuals (1 M:1 F at ~14&#xd7; and ~10&#xd7; coverage, respectively) from Dachigam National Park.<br><br>RESULTS: The annotated sequences were identical with an AT-rich composition, including 13 protein-coding genes (11,354 bp), 22 tRNA genes (1,515 bp), two ribosomal genes (2,526 bp) and a non-coding control region (917 bp) in a conserved order like other red deer species. Bayesian phylogenetic reconstruction of the red deer complex revealed two major groups: the elaphoid and the wapitoid clades. Hangul formed a distinct clade with its other subspecies C. hanglu yarkandensis and is sister to the Hungarian red deer (C. elaphus hippelaphus). Divergence time analyses suggested that the Tarim deer species group separated ~1.55 Mya from their common ancestors and Hangul diverged ~0.75 Mya from closely related C. yarkandensis, corroborating with the known paleobiogeographic events related to refugia during glaciations in the Pleistocene era. This study provides baseline information on Hangul mitogenome for further research on phylogeography and other population parameters and helps in developing suitable conservation plans for this species.},
}
@article {pmid37869838,
year = {2023},
author = {Marceglia, S and Manzelli, V and Caruso, A and Prenassi, M and Prandin, R and Savino, C and Tacconi, D and Ferrucci, R and Conti, C and Candiani, G and Toraldo, C and Judica, E and Corbo, M and Masiero, M and Pravettoni, G},
title = {PainRE-Life: A FHIR Based Telemonitoring Ecosystem for the Management of Patients with Chronic Pain.},
journal = {Studies in health technology and informatics},
volume = {309},
number = {},
pages = {183-184},
doi = {10.3233/SHTI230773},
pmid = {37869838},
issn = {1879-8365},
mesh = {Humans ; *Chronic Pain/diagnosis/therapy ; Data Management ; *Electronic Health Records ; Italy ; },
abstract = {Chronic pain is a condition in which the use of digital health technologies, ecological momentary assessments, and digital communication tools may boost patient's engagement and coping. Here we present the results of the PainRE-Life a project, financed by the Lombardy Region (Italy), aimed to develop a dynamic and integrated technology ecosystem based on big data management and analysis to allow care continuity in patients with pain, and able to act as a decision aid for patients and caregivers.},
}
@article {pmid37867198,
year = {2023},
author = {Koludarov, I and Velasque, M and Senoner, T and Timm, T and Greve, C and Hamadou, AB and Gupta, DK and Lochnit, G and Heinzinger, M and Vilcinskas, A and Gloag, R and Harpur, BA and Podsiadlowski, L and Rost, B and Jackson, TNW and Dutertre, S and Stolle, E and von Reumont, BM},
title = {Prevalent bee venom genes evolved before the aculeate stinger and eusociality.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {229},
pmid = {37867198},
issn = {1741-7007},
mesh = {Bees/genetics ; Animals ; *Bee Venoms ; Gene Expression Profiling ; Transcriptome ; Genomics ; Gene Duplication ; },
abstract = {BACKGROUND: Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected.<br><br>RESULTS: Utilizing a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification.<br><br>CONCLUSIONS: Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.},
}
@article {pmid37865683,
year = {2023},
author = {Farrell, S and Appleton, C and Noble, PM and Al Moubayed, N},
title = {PetBERT: automated ICD-11 syndromic disease coding for outbreak detection in first opinion veterinary electronic health records.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {18015},
pmid = {37865683},
issn = {2045-2322},
mesh = {Animals ; *International Classification of Diseases ; *Electronic Health Records ; Disease Outbreaks/veterinary ; Public Health Surveillance ; },
abstract = {Effective public health surveillance requires consistent monitoring of disease signals such that researchers and decision-makers can react dynamically to changes in disease occurrence. However, whilst surveillance initiatives exist in production animal veterinary medicine, comparable frameworks for companion animals are lacking. First-opinion veterinary electronic health records (EHRs) have the potential to reveal disease signals and often represent the initial reporting of clinical syndromes in animals presenting for medical attention, highlighting their possible significance in early disease detection. Yet despite their availability, there are limitations surrounding their free text-based nature, inhibiting the ability for national-level mortality and morbidity statistics to occur. This paper presents PetBERT, a large language model trained on over 500 million words from 5.1 million EHRs across the UK. PetBERT-ICD is the additional training of PetBERT as a multi-label classifier for the automated coding of veterinary clinical EHRs with the International Classification of Disease 11 framework, achieving F1 scores exceeding 83% across 20 disease codings with minimal annotations. PetBERT-ICD effectively identifies disease outbreaks, outperforming current clinician-assigned point-of-care labelling strategies up to 3 weeks earlier. The potential for PetBERT-ICD to enhance disease surveillance in veterinary medicine represents a promising avenue for advancing animal health and improving public health outcomes.},
}
@article {pmid37865347,
year = {2024},
author = {Anmella, G and Mas, A and Sanabra, M and Valenzuela-Pascual, C and Valentí, M and Pacchiarotti, I and Benabarre, A and Grande, I and De Prisco, M and Oliva, V and Fico, G and Giménez-Palomo, A and Bastidas, A and Agasi, I and Young, AH and Garriga, M and Corponi, F and Li, BM and de Looff, P and Vieta, E and Hidalgo-Mazzei, D},
title = {Electrodermal activity in bipolar disorder: Differences between mood episodes and clinical remission using a wearable device in a real-world clinical setting.},
journal = {Journal of affective disorders},
volume = {345},
number = {},
pages = {43-50},
doi = {10.1016/j.jad.2023.10.125},
pmid = {37865347},
issn = {1573-2517},
mesh = {Humans ; *Bipolar Disorder/diagnosis/drug therapy ; Galvanic Skin Response ; Cyclothymic Disorder ; Affect ; Mania ; *Wearable Electronic Devices ; },
abstract = {BACKGROUND: Bipolar disorder (BD) lacks objective measures for illness activity and treatment response. Electrodermal activity (EDA) is a quantitative measure of autonomic function, which is altered in manic and depressive episodes. We aimed to explore differences in EDA (1) inter-individually: between patients with BD on acute mood episodes, euthymic states and healthy controls (HC), and (2) intra-individually: longitudinally within patients during acute mood episodes of BD and after clinical remission.<br><br>METHODS: A longitudinal observational study. EDA was recorded using a research-grade wearable in patients with BD during acute manic and depressive episodes and at clinical remission. Euthymic BD patients and HC were recorded during a single session. We compared EDA parameters derived from the tonic (mean EDA, mEDA) and phasic components (EDA peaks per minute, pmEDA, and EDA peaks mean amplitude, pmaEDA). Inter- and intra-individual comparisons were computed respectively with ANOVA and paired t-tests.<br><br>RESULTS: 49 patients with BD (15 manic, 9 depressed, and 25 euthymic), and 19 HC were included. Patients with bipolar depression showed significantly reduced mEDA (p&#xa0;=&#xa0;0.003) and pmEDA (p&#xa0;=&#xa0;0.001), which increased to levels similar to euthymia or HC after clinical remission (mEDA, p&#xa0;=&#xa0;0.011; pmEDA, p&#xa0;<&#xa0;0.001; pmaEDA, p&#xa0;<&#xa0;0.001). Manic patients showed no differences compared to euthymic patients and HCs, but a significant reduction of tonic and phasic EDA parameters after clinical remission (mEDA, p&#xa0;=&#xa0;0.035; pmEDA, p&#xa0;=&#xa0;0.004).<br><br>LIMITATIONS: Limited sample size, high inter-individual variability of EDA parameters, limited comparability to previous studies and non-adjustment for medication.<br><br>CONCLUSION: EDA ecological monitoring might provide several opportunities for early detection of depressive symptoms, and might aid at assessing early response to treatments in mania and bipolar depression.},
}
@article {pmid37858689,
year = {2023},
author = {Sajjad, W and Ali, B and Niu, H and Ilahi, N and Rafiq, M and Bahadur, A and Banerjee, A and Kang, S},
title = {High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment.},
journal = {Environmental research},
volume = {239},
number = {Pt 2},
pages = {117444},
doi = {10.1016/j.envres.2023.117444},
pmid = {37858689},
issn = {1096-0953},
mesh = {*Genes, Bacterial ; *Ice Cover/microbiology ; Prevalence ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria ; Anti-Bacterial Agents/pharmacology/analysis ; Metals/analysis ; Gram-Negative Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.},
}
@article {pmid37857132,
year = {2023},
author = {Hassan, L and Eisner, E and Berry, K and Emsley, R and Ainsworth, J and Lewis, S and Haddock, G and Edge, D and Bucci, S},
title = {User engagement in a randomised controlled trial for a digital health intervention for early psychosis (Actissist 2.0 trial).},
journal = {Psychiatry research},
volume = {329},
number = {},
pages = {115536},
doi = {10.1016/j.psychres.2023.115536},
pmid = {37857132},
issn = {1872-7123},
support = {MR/P026664/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Psychotic Disorders/therapy ; *Cognitive Behavioral Therapy ; *Mobile Applications ; Smartphone ; Patient Participation ; },
abstract = {Digital Health Interventions (DHIs) can help support people with mental health problems. Achieving satisfactory levels of patient engagement is a crucial, yet often underexplored, pre-requisite for health improvement. Actissist is a co-produced DHI delivered via a smartphone app for people with early psychosis, based on Cognitive Behaviour Therapy principles. This study describes and compares engagement patterns among participants in the two arms of the Actissist 2.0 randomised controlled trial. Engagement frequency and duration were measured among participants using the Actissist app in the intervention arm (n = 87) and the ClinTouch symptom monitoring only app used as the control condition (n = 81). Overall, 47.1 % of Actissist and 45.7 % of ClinTouch users completed at least a third of scheduled alerts while active in the study. The mean frequency (77.1 versus 60.2 total responses) and the median duration (80 versus 75 days until last response) of engagement were not significantly higher among Actissist users compared to ClinTouch users. Older age, White ethnicity, using their own smartphone device and, among Actissist users, an increased sense of therapeutic alliance were significantly associated with increased engagement. Through exploiting detailed usage data, this study identifies possible participant-level and DHI-level predictors of engagement to inform the practical implementation of future DHIs.},
}
@article {pmid37855447,
year = {2024},
author = {Gorijala, P and Aslam, MM and Dang, LT and Xicota, L and Fernandez, MV and Sung, YJ and Fan, KH and Feingold, E and Surace, EI and Chhatwal, JP and Hom, CL and , and , and Hartley, SL and Hassenstab, J and Perrin, RJ and Mapstone, M and Zaman, SH and Ances, BM and Kamboh, MI and Lee, JH and Cruchaga, C},
title = {Alzheimer's polygenic risk scores are associated with cognitive phenotypes in Down syndrome.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {20},
number = {2},
pages = {1038-1049},
pmid = {37855447},
issn = {1552-5279},
support = {P30 AG066444/AG/NIA NIH HHS/United States ; R01 AG064877/AG/NIA NIH HHS/United States ; RF1 AG071706/AG/NIA NIH HHS/United States ; RF1 AG053303/AG/NIA NIH HHS/United States ; RF1AG053303/NH/NIH HHS/United States ; U54 HD087011/HD/NICHD NIH HHS/United States ; RF1 AG074007/AG/NIA NIH HHS/United States ; P50 HD105353/HD/NICHD NIH HHS/United States ; U01 AG051412/AG/NIA NIH HHS/United States ; P50 AG005133/AG/NIA NIH HHS/United States ; /EB/NIBIB NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; P01AG003991/NH/NIH HHS/United States ; P30 AG062715/AG/NIA NIH HHS/United States ; U19 AG032438/AG/NIA NIH HHS/United States ; U01 AG058922/AG/NIA NIH HHS/United States ; UL1 TR001857/TR/NCATS NIH HHS/United States ; R01 AG044546/AG/NIA NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; SG-20-690363-DIAN/ALZ/Alzheimer's Association/United States ; P30 AG062421/AG/NIA NIH HHS/United States ; U01 AG024904/AG/NIA NIH HHS/United States ; P50 AG008702/AG/NIA NIH HHS/United States ; P01 AG003991/AG/NIA NIH HHS/United States ; P50 AG005681/AG/NIA NIH HHS/United States ; RF1AG074007/NH/NIH HHS/United States ; P01 AG026276/AG/NIA NIH HHS/United States ; RF1 AG058501/AG/NIA NIH HHS/United States ; P30 AG066519/AG/NIA NIH HHS/United States ; U19 AG068054/AG/NIA NIH HHS/United States ; U01 AG024904/NH/NIH HHS/United States ; R01 AG064614/AG/NIA NIH HHS/United States ; UL1 TR001414/TR/NCATS NIH HHS/United States ; RF1AG058501/NH/NIH HHS/United States ; RF1 AG044546/AG/NIA NIH HHS/United States ; U54 HD090256/HD/NICHD NIH HHS/United States ; R01AG064877/NH/NIH HHS/United States ; U01 AG051406/AG/NIA NIH HHS/United States ; UL1 TR001873/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; U01AG058922/NH/NIH HHS/United States ; },
mesh = {Adult ; Humans ; *Alzheimer Disease/diagnosis ; *Down Syndrome/genetics ; Genetic Risk Score ; Apolipoproteins E/genetics ; Phenotype ; *Cognitive Dysfunction/diagnosis ; Biomarkers/cerebrospinal fluid ; Cognition ; Memory Disorders ; Amyloid beta-Peptides/cerebrospinal fluid ; },
abstract = {INTRODUCTION: This study aimed to investigate the influence of the overall Alzheimer's disease (AD) genetic architecture on Down syndrome (DS) status, cognitive measures, and cerebrospinal fluid (CSF) biomarkers.<br><br>METHODS: AD polygenic risk scores (PRS) were tested for association with DS-related traits.<br><br>RESULTS: The AD risk PRS was associated with disease status in several cohorts of sporadic late- and early-onset and familial late-onset AD, but not in familial early-onset AD or DS. On the other hand, lower DS Mental Status Examination memory scores were associated with higher PRS, independent of intellectual disability and APOE (PRS including APOE, PRSAPOE , p&#xa0;=&#xa0;2.84&#xa0;&#xd7;&#xa0;10[-4] ; PRS excluding APOE, PRSnonAPOE , p&#xa0;=&#xa0;1.60&#xa0;&#xd7;&#xa0;10[-2]). PRSAPOE exhibited significant associations with A&#x3b2;42, tTau, pTau, and A&#x3b2;42/40 ratio in DS.<br><br>DISCUSSION: These data indicate that the AD genetic architecture influences cognitive and CSF phenotypes in DS adults, supporting common pathways that influence memory decline in both traits.<br><br>HIGHLIGHTS: Examination of the polygenic risk of AD in DS presented here is the first of its kind. AD PRS influences memory aspects in DS individuals, independently of APOE genotype. These results point to an overlap between the genes and pathways that leads to AD and those that influence dementia and memory decline in the DS population. APOE &#x3b5;4 is linked to DS cognitive decline, expanding cognitive insights in adults.},
}
@article {pmid37853225,
year = {2023},
author = {Jin, T and Li, D and Liu, Y and Li, K and Wang, L},
title = {Microbe combined with Fe[2+]-heat activated persulfate to decompose phenanthrene in red soil: comparison of acid-resistant degrading microflora and indigenous bacteria.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {53},
pages = {113932-113947},
pmid = {37853225},
issn = {1614-7499},
support = {No. 51974314//National Natural Science Foundation of China/ ; No. 52270171//National Natural Science Foundation of China/ ; },
mesh = {Soil/chemistry ; Hot Temperature ; *Phenanthrenes/analysis ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/analysis ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Soil Microbiology ; },
abstract = {This work is designed to counteract the deficiency of targeted research on the PAHs polluted specific soil, especially when the chemicals extremely denatured it. Phenanthrene-contaminated red soil was treated through two-stage process: persulfate oxidation (on dosages of 3.48%, 5.21%, and 6.94%, combined with Fe[2+] and β-cyclodextrin, then heated) followed by biodegradation (indigenous bacteria vs. acid-resistant PAHs-degrading microflora (named ADM)) for 90 days. The dosage of oxidant greatly affected the removal efficiencies, which ranged from 46.78 to 85.34% under different treatment. After undergoing oxidation, the soil pH dropped below 3.0 synchronously and retained relatively strong oxidation state. The indigenous bacteria in red soil showed considerable degradation potential that will not vanish upon the sudden change of soil properties, whose average combined removal reached 95.43%, even higher than subgroups of bioaugmentation, but the population structure showed extremely simplex (Proteobacteria as superior occupied proportion of 91.77% after 90-day rehabilitation). The ADM screened from the coking wastewater was dominated by Klebsiella (75.4%) and Pseudomonas (23.6%), whose cooperation with 6.94% persulfate made the residual PHE reduced to less than 50 mg·kg[-1] in about 28 days. High-throughput sequencing analysis showed that the microbial community composition of the ADM applied-group was more abundant in the later stage of remediation. ADM inoculation has the advantages of shortening the restoration period and having a positive impact on the soil micro-ecology.},
}
@article {pmid37853050,
year = {2023},
author = {Qiao, Q and Shi, G and Yang, D and Wang, L and Zhang, X and Li, S and Bai, XE},
title = {Study on the destruction law of physical and shear properties of soil in mining disturbance.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {17751},
pmid = {37853050},
issn = {2045-2322},
support = {No. U2003103//the Key Project of Joint Funds of the National Natural Science Foundation of China/ ; S202210755006//2022 autonomous region level college students innovative training program project/ ; 2021B03004//the Special Program for Key Research and Development Tasks of Xinjiang Uygur Autonomous Region/ ; KC22075//special fund for promoting scientific and technological innovation in Xuzhou in 2022 (key research and development plan (modern agriculture) - general project/ ; },
abstract = {Underground mining activities can easily trigger surface subsidence and cause damage to surface soil. However, there is still a lack of studies on damaged soil, restricting ecological remediation in mining-induced subsidence regions to a certain degree. Focusing on the particular example of No. 4 Mine in Yili, Xinjiang, China, this study comprehensively combined field sampling, laboratory experiments, and data analysis to investigate the variation rules of basic physical properties and shear characteristics of soil samples. The latter had different subsidence degrees (0, 0-20, 20-40, and above 40 cm) and various depths (0- 10, 10-20, 20- 40, 40-60, and 60-80 cm). The experimental results show that: First, the natural density and dry unit weight of shallow soil in the serious-subsidence region were more significantly affected by mining-induced subsidence than the conditions in the deep layer, which also dropped with the increase in subsidence degree (with a mean drop rate of 7%). Second, serious subsidence could greatly counteract the positive effect of slight and moderate subsidence on the soil shear strength, with a drop rate of up to 30.7%. Third, compared with soil physical indices, mining-induced subsidence more easily affected shear strength indices. In particular, the soil samples taken from 0 to 10 cm depth in the slight subsidence area and 60-80 cm depth in the moderate subsidence area were most significantly affected by mining-induced subsidence, with PCA comprehensive scores of over 1.5. The present study can con-tribute to gaining in-depth knowledge of the damage characteristics of surface soil under mining-induced subsidence and provide a theoretical foundation for formulating reasonable coal mining strategies and ecological protection measures.},
}
@article {pmid37852461,
year = {2024},
author = {Ghiotto, G and Zampieri, G and Campanaro, S and Treu, L},
title = {Strain-resolved metagenomics approaches applied to biogas upgrading.},
journal = {Environmental research},
volume = {240},
number = {Pt 2},
pages = {117414},
doi = {10.1016/j.envres.2023.117414},
pmid = {37852461},
issn = {1096-0953},
mesh = {*Biofuels ; *Computational Biology ; Hydrogen ; Metagenomics ; Nucleotides ; },
abstract = {Genetic heterogeneity is a common trait in microbial populations, caused by de novo mutations and changes in variant frequencies over time. Microbes can thus differ genetically within the same species and acquire different phenotypes. For instance, performance and stability of anaerobic reactors are linked to the composition of the microbiome involved in the digestion process and to the environmental parameters imposing selective pressure on the metagenome, shaping its evolution. Changes at the strain level have the potential to determine variations in microbial functions, and their characterization could provide new insight into ecological and evolutionary processes driving anaerobic digestion. In this work, single nucleotide variant dynamics were studied in two time-course biogas upgrading experiments, testing alternative carbon sources and the response to exogenous hydrogen addition. A cumulative total of 76,229 and 64,289 high-confidence single nucleotide variants were discerned in the experiments related to carbon substrate availability and hydrogen addition, respectively. By combining complementary bioinformatic approaches, the study reconstructed the precise strain count-two for both hydrogenotrophic archaea-and tracked their abundance over time, while also characterizing tens of genes under strong selection. Results in the dominant archaea revealed the presence of nearly 100 variants within genes encoding enzymes involved in hydrogenotrophic methanogenesis. In the bacterial counterparts, 119 mutations were identified across 23 genes associated with the Wood-Ljungdahl pathway, suggesting a possible impact on the syntrophic acetate-oxidation process. Strain replacement events took place in both experiments, confirming the trends suggested by the variants trajectories and providing a comprehensive understanding of the biogas upgrading microbiome at the strain level. Overall, this resolution level allowed us to reveal fine-scale evolutionary mechanisms, functional dynamics, and strain-level metabolic variation that could contribute to the selection of key species actively involved in the carbon dioxide fixation process.},
}
@article {pmid37851996,
year = {2023},
author = {Alsamara, I and Ogilvie, L and Sudbrak, R and Brand, A},
title = {One Health Lens for Antimicrobial Resistance Research and Funding: A Systematic Review.},
journal = {Omics : a journal of integrative biology},
volume = {27},
number = {12},
pages = {570-580},
doi = {10.1089/omi.2023.0049},
pmid = {37851996},
issn = {1557-8100},
mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial ; *One Health ; Databases, Factual ; },
abstract = {One Health (OH) offers conceptual and applied prospects to advance planetary health and integrative biology in the 21st century. For example, The World Health Organization (WHO) has declared antimicrobial resistance (AMR) one of humanity's top 10 health threats worldwide (AMR). The AMR research, as seen through the OH lens, recognizes the interdependence and the coproduction of the health of humans, nonhuman animals, and the environment (the OH triad). Moreover, research and development (R&amp;D) is required to generate potential solutions to prevent, diagnose, and treat infections and control the spread and emergence of AMR. However, it is still unclear how well the OH approach is integrated into current AMR R&amp;D. In this study, we present a systematic review on the OH funding landscape for cross-sectoral AMR R&amp;D, and its alignment/gaps with the current global strategic agenda on AMR. A systematic literature review was conducted using public databases covering the period between January 2015 and May 2022. We included the studies and reviews on AMR encompassing more than one sector of the OH triad. Out of the 777 included studies, 475 (61%) encompassed the three OH sectors. A key finding of the present systematic review is that the environment was the most neglected sector in the OH triad. AMR surveillance, transmission, and interventions are the most commonly studied priority topics. In addition, both cross-sectoral AMR literature and investments have been increasing since 2017. The operational aspect of AMR is the most researched and funded area. However, certain priority topics in the strategic research and innovation agenda of the Joint Programming Initiative on AMR are underrepresented in OH AMR research, such as diagnosis and therapeutics. To the best of authors' knowledge, this is the first study that systematically reviews the cross-sectoral literature on AMR, classifies it, and aligns and contextualizes it in regard to the funding landscape of AMR. This systematic review identifies neglected areas in AMR R&amp;D and could serve as critical information for policymaking so as to realize the objectives of the Global Action Plan on AMR. Going forward, more cross-sectoral AMR research and funding are needed. As integrative biology and omics systems science are poised to benefit from a rapprochement with the OH lens, the present article highlights the AMR research and funding landscapes.},
}
@article {pmid37849397,
year = {2023},
author = {Hartman, AL and Myler, PJ},
title = {Bunyavirales: Scientific Gaps and Prototype Pathogens for a Large and Diverse Group of Zoonotic Viruses.},
journal = {The Journal of infectious diseases},
volume = {228},
number = {Suppl 6},
pages = {S376-S389},
pmid = {37849397},
issn = {1537-6613},
support = {HHSN272201700059C/AI/NIAID NIH HHS/United States ; R01 NS101100/NS/NINDS NIH HHS/United States ; R21 AI163603/AI/NIAID NIH HHS/United States ; HHSN272201700059C/NH/NIH HHS/United States ; },
mesh = {Animals ; Humans ; *RNA Viruses ; },
abstract = {Research directed at select prototype pathogens is part of the approach put forth by the National Institute of Allergy and Infectious Disease (NIAID) to prepare for future pandemics caused by emerging viruses. We were tasked with identifying suitable prototypes for four virus families of the Bunyavirales order (Phenuiviridae, Peribunyaviridae, Nairoviridae, and Hantaviridae). This is a challenge due to the breadth and diversity of these viral groups. While there are many differences among the Bunyavirales, they generally have complex ecological life cycles, segmented genomes, and cause a range of human clinical outcomes from mild to severe and even death. Here, we delineate potential prototype species that encompass the breadth of clinical outcomes of a given family, have existing reverse genetics tools or animal disease models, and can be amenable to a platform approach to vaccine testing. Suggested prototype pathogens outlined here can serve as a starting point for further discussions.},
}
@article {pmid37847320,
year = {2023},
author = {Li, J and Yu, Q and Qian, R and Xiao, X and Liang, Y and Luo, P and Wang, H and Lu, Y and Xu, L and Liu, Q and Xiao, Y},
title = {Distribution and transformation of potentially toxic elements in crack under coal mining disturbance.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {11},
pages = {1327},
pmid = {37847320},
issn = {1573-2959},
mesh = {*Coal Mining ; *Metals, Heavy/analysis ; Environmental Monitoring/methods ; *Soil Pollutants/analysis ; Mining ; Soil/chemistry ; China ; Coal ; Risk Assessment ; },
abstract = {In China, coal provides about 56.8% of the energy. Most of China's coal mines are shaft mines, which cause the surface to collapse and crack during the mining process. The soil near the cracks changes its physicochemical properties due to the altered stress conditions. This will affect the distribution of PTEs in the soil. We collected 18 samples from a selected crack in the abandoned land. The pH, Eh, and PTE and their fractions of the samples were determined. With the test results, we understand the distribution characteristics of pH, Eh, PTEs, and their fractions at the cracks. Meanwhile, we explored the key factors that contribute to this distribution. It was determined that crack decreases surface soil pH while increasing Eh. The total amount of 7 PTEs is higher in the bottom soil of the main crack and 2 m away from the main crack. The content of reducible fractions of PTEs increases with the increase of soil Eh. The oxidizable and residual fractions of PTEs adsorbed to the clay particles migrate to and enrich the deeper layers of the main crack. This study emphasizes the effect of crack generation on the distribution of PTEs in soil. It provides insights to describe the distribution of PTE throughout the full life cycle of crack.},
}
@article {pmid37844141,
year = {2023},
author = {Wu, D and Xie, J and Liu, Y and Jin, L and Li, G and An, T},
title = {Metagenomic and Machine Learning Meta-Analyses Characterize Airborne Resistome Features and Their Hosts in China Megacities.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {43},
pages = {16414-16423},
doi = {10.1021/acs.est.3c02593},
pmid = {37844141},
issn = {1520-5851},
mesh = {*Genes, Bacterial ; *Metagenome ; Cities ; Anti-Bacterial Agents/pharmacology ; China ; },
abstract = {Urban ambient air contains a cocktail of antibiotic resistance genes (ARGs) emitted from various anthropogenic sites. However, what is largely unknown is whether the airborne ARGs exhibit site-specificity or their pathogenic hosts persistently exist in the air. Here, by retrieving 1.2 Tb metagenomic sequences (n = 136), we examined the airborne ARGs from hospitals, municipal wastewater treatment plants (WWTPs) and landfills, public transit centers, and urban sites located in seven of China's megacities. As validated by the multiple machine learning-based classification and optimization, ARGs' site-specificity was found to be the most apparent in hospital air, with featured resistances to clinical-used rifamycin and (glyco)peptides, whereas the more environmentally prevalent ARGs (e.g., resistance to sulfonamide and tetracycline) were identified being more specific to the nonclinical ambient air settings. Nearly all metagenome-assembled genomes (MAGs) that possessed the site-featured resistances were identified as pathogenic taxa, which occupied the upper-representative niches in all the neutrally distributed airborne microbial community (P < 0.01, m = 0.22-0.50, R[2] = 0.41-0.86). These niche-favored putative resistant pathogens highlighted the enduring antibiotic resistance hazards in the studied urban air. These findings are critical, albeit the least appreciated until our study, to gauge the airborne dimension of resistomes' features and fates in urban atmospheric environments.},
}
@article {pmid37842337,
year = {2021},
author = {Martens, M and Stierum, R and Schymanski, EL and Evelo, CT and Aalizadeh, R and Aladjov, H and Arturi, K and Audouze, K and Babica, P and Berka, K and Bessems, J and Blaha, L and Bolton, EE and Cases, M and Damalas, D&#x395; and Dave, K and Dilger, M and Exner, T and Geerke, DP and Grafström, R and Gray, A and Hancock, JM and Hollert, H and Jeliazkova, N and Jennen, D and Jourdan, F and Kahlem, P and Klanova, J and Kleinjans, J and Kondic, T and Kone, B and Lynch, I and Maran, U and Martinez Cuesta, S and Ménager, H and Neumann, S and Nymark, P and Oberacher, H and Ramirez, N and Remy, S and Rocca-Serra, P and Salek, RM and Sallach, B and Sansone, SA and Sanz, F and Sarimveis, H and Sarntivijai, S and Schulze, T and Slobodnik, J and Spjuth, O and Tedds, J and Thomaidis, N and Weber, RJM and van Westen, GJP and Wheelock, CE and Williams, AJ and Witters, H and Zdrazil, B and Županič, A and Willighagen, EL},
title = {ELIXIR and Toxicology: a community in development.},
journal = {F1000Research},
volume = {10},
number = {},
pages = {},
pmid = {37842337},
issn = {2046-1402},
support = {/WT_/Wellcome Trust/United Kingdom ; 001/WHO_/World Health Organization/International ; },
mesh = {*Biological Science Disciplines ; Europe ; Risk Assessment ; },
abstract = {Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.},
}
@article {pmid37841229,
year = {2023},
author = {Turner, TF and Bart, HL and McCormick, F and Besser, AC and Bowes, RE and Capps, KA and DeArmon, ES and Dillman, CB and Driscoll, KP and Dugger, A and Hamilton, GL and Harris, PM and Hendrickson, DA and Hoffman, J and Knouft, JH and Lepak, RF and López-Fernández, H and Montaña, CG and Newsome, SD and Pease, AA and Smith, WL and Taylor, CA and Welicky, RL},
title = {Long-term ecological research in freshwaters enabled by regional biodiversity collections, stable isotope analysis, and environmental informatics.},
journal = {Bioscience},
volume = {73},
number = {7},
pages = {479-493},
pmid = {37841229},
issn = {0006-3568},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {Biodiversity collections are experiencing a renaissance fueled by the intersection of informatics, emerging technologies, and the extended use and interpretation of specimens and archived databases. In this article, we explore the potential for transformative research in ecology integrating biodiversity collections, stable isotope analysis (SIA), and environmental informatics. Like genomic DNA, SIA provides a common currency interpreted in the context of biogeochemical principles. Integration of SIA data across collections allows for evaluation of long-term ecological change at local to continental scales. Challenges including the analysis of sparse samples, a lack of information about baseline isotopic composition, and the effects of preservation remain, but none of these challenges is insurmountable. The proposed research framework interfaces with existing databases and observatories to provide benchmarks for retrospective studies and ecological forecasting. Collections and SIA add historical context to fundamental questions in freshwater ecological research, reference points for ecosystem monitoring, and a means of quantitative assessment for ecosystem restoration.},
}
@article {pmid37840885,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Lesser Broad-bordered Yellow Underwing, Noctua janthe (Borkhausen, 1792).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {189},
pmid = {37840885},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Noctua janthe (the Lesser Broad-bordered Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 532.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,653 protein coding genes.},
}
@article {pmid37840882,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Langdon, WBV and , },
title = {The genome sequence of the Lunar Hornet, Sesia bembeciformis (Hübner 1806).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {109},
pmid = {37840882},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Sesia bembeciformis (the Lunar Hornet; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 477.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,843 protein coding genes.},
}
@article {pmid37838199,
year = {2023},
author = {Zhao, X and Xie, Y and Sun, B and Liu, Y and Zhu, S and Li, W and Zhao, M and Liu, D},
title = {Unraveling microbial characteristics of simultaneous nitrification, denitrification and phosphorus removal in a membrane-aerated biofilm reactor.},
journal = {Environmental research},
volume = {239},
number = {Pt 1},
pages = {117402},
doi = {10.1016/j.envres.2023.117402},
pmid = {37838199},
issn = {1096-0953},
mesh = {*Phosphorus ; Denitrification ; Nitrification ; Phylogeny ; Wastewater ; Phosphates ; Biofilms ; Carbon ; Nitrogen ; *Ammonium Compounds ; Sulfur ; },
abstract = {This study describes the simultaneous removal of carbon, ammonium, and phosphate from domestic wastewater by a membrane-aerated biofilm reactor (MABR) which was operated for 360 days. During the operation, the maximum removal efficiencies of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) reached 93.1%, 83.98%, and 96.41%, respectively. Statistical analysis showed that the MABR could potentially treat wastewater with a high ammonium concentration and a relatively low C/N ratio. Dissolved oxygen and multiple pollutants, including ammonium, carbon, phosphate, and sulfate, shaped the structure of the microbial community in the MABR. High throughput sequencing uncovered the crucial microbiome in ammonium transformation in MABR. Phylogenetic analysis of the ammonia monooxygenase (amoA) genes revealed an important role for comammox Nitrospira in the nitrification process. Diverse novel phosphate-accumulating organisms (Thauera, Bacillus, and Pseudomonas) and sulfur-oxidizing bacteria (Thiobacillus, Thiothrix and Sulfurimonas) were potentially involved in denitrification in MABR. The results from this study suggested that MABR could be a feasible system for the simultaneous removal of nitrogen, carbon, phosphorus, and sulfur from sewage water.},
}
@article {pmid37833155,
year = {2023},
author = {Munley, JA and Kelly, LS and Park, G and Gillies, GS and Pons, EE and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM},
title = {Sex-specific intestinal dysbiosis persists after multicompartmental injury.},
journal = {Surgery},
volume = {174},
number = {6},
pages = {1453-1462},
doi = {10.1016/j.surg.2023.08.023},
pmid = {37833155},
issn = {1532-7361},
support = {R01 GM105893/GM/NIGMS NIH HHS/United States ; },
mesh = {Female ; Male ; Rats ; Animals ; Rats, Sprague-Dawley ; *Dysbiosis/etiology ; RNA, Ribosomal, 16S ; *Multiple Trauma ; Computational Biology ; },
abstract = {BACKGROUND: Preclinical studies of the gut microbiome after severe traumatic injury have demonstrated severe dysbiosis in males, with sex-specific microbial differences up to 2 days after injury. However, the impact of host sex on injury-driven dysbiosis over time remains unknown. We hypothesized that sex-specific differences in intestinal microbiome diversity and composition after traumatic injury with and without stress would persist after 7 days.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n&#xa0;= 8/group) were subjected to either polytrauma (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), polytrauma plus chronic restraint stress, or na&#xef;ve controls. The fecal microbiome was measured on days 0, 3, and 7 using 16S rRNA sequencing and Quantitative Insights into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity (Chao1 and Shannon indices) and beta-diversity were assessed. Analyses were performed in GraphPad and "R," with significance defined as P < .05.<br><br>RESULTS: Polytrauma and polytrauma plus chronic restraint stress reduced alpha-diversity (Chao1, Shannon) within 3 days postinjury, which persisted up to day 7 in both sexes; polytrauma and polytrauma plus chronic restraint stress females had significantly decreased Chao1 compared to male counterparts at day 7 (P&#xa0;= .02). At day 7, the microbiome composition in polytrauma females had higher proportion of Mucispirillum, whereas polytrauma plus chronic restraint stress males demonstrated elevated abundance of Ruminococcus and Akkermansia.<br><br>CONCLUSION: Multicompartmental trauma induces intestinal dysbiosis that is sex-specific with persistence of decreased diversity and unique "pathobiome" signatures in females after 1 week. These findings underline sex as an important biological variable that may influence variable host-specific responses and outcomes after severe trauma and critical illness. This underscores the need to consider precision medicine strategies to ameliorate these outcomes.},
}
@article {pmid37831234,
year = {2023},
author = {Li, Z and Li, X and Li, S and Yang, Y and Yan, W and Xu, H},
title = {Bibliometric analysis of electrochemical disinfection: current status and development trend from 2002 to 2022.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {52},
pages = {111714-111731},
pmid = {37831234},
issn = {1614-7499},
support = {52270078//National Natural Science Foundation of China/ ; LZY21E080003//Welfare Technology Research Plan of Zhejiang Province/ ; 2021KFKT-7//Open Research Fund of the State Key Laboratory of Ecological Water Conservancy in the Arid area of Northwest China (Xi'an University of Technology)/ ; },
mesh = {*Disinfection ; *Bibliometrics ; Databases, Factual ; Electrochemical Techniques ; Electrodes ; },
abstract = {The removal of waterborne pathogens from water is critical in preventing the spread of waterborne diseases. Electrochemical methods have been extensively researched and implemented for disinfection, primarily owing to their simplicity, efficiency, and eco-friendliness. Thus, it is essential to conduct a review about the research progress and hotspots on this promising technique. In this paper, we provided a comprehensive bibliometric analysis to systematically study and analyze the current status, hotspots, and trends in electrochemical disinfection research from 2002 to 2022. This study analyzed literature related to electrochemical disinfection or electrochemical sterilization published in the Web of Science database from 2002 to 2022 using CiteSpace and Biblioshiny R language software packages. The analysis focused on the visualization and assessment of annual publication volume, discipline and journal distribution, collaborative networks, highly cited papers, and keywords to systematically understand the current status and trends of electrochemical disinfection. The results showed that between 2002 and 2022, 1171 publications related to electrochemical disinfection were published, with an exponential increase in the cumulative number of publications (y=17.518e[0.2147x], R[2]= 0.9788). The publications covered 76 disciplines with many articles published in high-impact journals. However, the research power was characterized by a large number of scattered research efforts and insufficient cooperation, indicating the need for further innovative collaboration. The citation analysis and keyword analysis suggest that future development in this field may focus on optimizing electrode materials, investigating the disinfection performance of ·OH based systems, optimizing conditions for actual wastewater treatment, and reducing energy consumption to promote practical applications.},
}
@article {pmid37828216,
year = {2023},
author = {Oza, A},
title = {Reproducibility trial: 246 biologists get different results from same data sets.},
journal = {Nature},
volume = {622},
number = {7984},
pages = {677-678},
doi = {10.1038/d41586-023-03177-1},
pmid = {37828216},
issn = {1476-4687},
mesh = {*Biology/methods/standards ; *Data Analysis ; *Datasets as Topic ; Ecology/methods/standards ; *Reproducibility of Results ; Research Personnel ; },
}
@article {pmid37824826,
year = {2024},
author = {Mabry, ME and Abrahams, RS and Al-Shehbaz, IA and Baker, WJ and Barak, S and Barker, MS and Barrett, RL and Beric, A and Bhattacharya, S and Carey, SB and Conant, GC and Conran, JG and Dassanayake, M and Edger, PP and Hall, JC and Hao, Y and Hendriks, KP and Hibberd, JM and King, GJ and Kliebenstein, DJ and Koch, MA and Leitch, IJ and Lens, F and Lysak, MA and McAlvay, AC and McKibben, MTW and Mercati, F and Moore, RC and Mummenhoff, K and Murphy, DJ and Nikolov, LA and Pisias, M and Roalson, EH and Schranz, ME and Thomas, SK and Yu, Q and Yocca, A and Pires, JC and Harkess, AE},
title = {Complementing model species with model clades.},
journal = {The Plant cell},
volume = {36},
number = {5},
pages = {1205-1226},
pmid = {37824826},
issn = {1532-298X},
support = {1923589/2019610//National Science Foundation, USA, and The United States-Israel Binational Science Foundation/ ; //The Goldinger Trust Jewish Fund/ ; BER-DE-SC0020358//US Department of Energy/ ; },
mesh = {*Phylogeny ; *Arabidopsis/genetics ; *Brassicaceae/genetics/classification ; Genomics/methods ; Genome, Plant/genetics ; },
abstract = {Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.},
}
@article {pmid37822564,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Langdon, WBV and , },
title = {The genome sequence of the Pied Smudge, Ypsolopha sequella (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {32},
pmid = {37822564},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Ypsolopha sequella (the Pied Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 867 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,394 protein coding genes.},
}
@article {pmid37821698,
year = {2023},
author = {Pavlopoulos, GA and Baltoumas, FA and Liu, S and Selvitopi, O and Camargo, AP and Nayfach, S and Azad, A and Roux, S and Call, L and Ivanova, NN and Chen, IM and Paez-Espino, D and Karatzas, E and , and Iliopoulos, I and Konstantinidis, K and Tiedje, JM and Pett-Ridge, J and Baker, D and Visel, A and Ouzounis, CA and Ovchinnikov, S and Buluç, A and Kyrpides, NC},
title = {Unraveling the functional dark matter through global metagenomics.},
journal = {Nature},
volume = {622},
number = {7983},
pages = {594-602},
pmid = {37821698},
issn = {1476-4687},
support = {DP5 OD026389/OD/NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; },
mesh = {Cluster Analysis ; *Metagenome/genetics ; *Metagenomics/methods ; *Proteins/chemistry/classification/genetics ; Databases, Protein ; Protein Conformation ; *Microbiology ; },
abstract = {Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities[1,2]. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database[3]. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.},
}
@article {pmid37819593,
year = {2023},
author = {Baňas, M and Šofranková, L and Kurimský, J and Pavlík, M and Pikalík, M and Majláthová, V and Cimbala, R and Pipová, N and Wurfl, L and Majláth, I},
title = {Interspecific differences in the behavioral response of ticks exposed to radiofrequency electromagnetic radiation.},
journal = {Experimental &amp; applied acarology},
volume = {91},
number = {3},
pages = {477-485},
pmid = {37819593},
issn = {1572-9702},
mesh = {Humans ; Male ; Female ; Animals ; *Dermacentor/physiology ; *Ixodes/physiology ; *Ixodidae ; Radio Waves/adverse effects ; Electromagnetic Fields ; },
abstract = {Artificial electromagnetic radiation is a new environmental factor that affects animals. Experiments with the effect of radio frequency electromagnetic radiation were focused on both vertebrates and invertebrates. Ticks showed a significant affinity to radiation. Our study is a continuation of this research and its aim was to monitor the effect of radiation on the behavior of four tick species: Ixodes ricinus, Dermacentor reticulatus, Dermacentor marginatus and Haemaphysalis inermis. In total 1,200 ticks, 300 of each species, were tested in modules allowing the choice of an exposed or shielded area. During the test, the ticks were exposed to electro-magnetic radiation of 900 MHz for 24 h. The position of the individuals was recorded and we evaluated the obtained data statistically. We observed a significant preference to the exposed area in both sexes of I. ricinus. Males of D. reticulatus and D. marginatus also showed an affinity to radiation, but not females of both species, nor females and males of H. inermis. The results of the study support the assumption that ticks perceive the electromagnetic field and the observed differences in their response have the potential to help understand the mechanism of perception.},
}
@article {pmid37815079,
year = {2023},
author = {Ilić Živojinović, J and Soldatović, I and Backović, D and Vukašinović, D and Babić, S and Tomanić, M and Ilić, B and Vlaisavljević, &#x17d;},
title = {Personal Listening Device Use and Attitude to Noise in Relation to Depression and Anxiety among Medical Students.},
journal = {Noise &amp; health},
volume = {25},
number = {118},
pages = {176-182},
pmid = {37815079},
issn = {1998-4030},
mesh = {Female ; Adolescent ; Humans ; Male ; *Students, Medical ; Cross-Sectional Studies ; Depression/epidemiology/etiology ; Anxiety/epidemiology/etiology ; Anxiety Disorders ; },
abstract = {BACKGROUND: High levels of environmental noise may lead to psychological symptoms. The present study has hypothesized that personal listening device (PLD) use and a negative attitude to noise are significantly related to anxiety and/or depression.<br><br>METHODS: This is a cross-sectional study conducted on 431 six-grade students (35% male) at the Faculty of Medicine, University of Belgrade. All students completed the questionnaires related to socio-demographic data, noise/music exposure habits, behaviors related to PLD use, tinnitus, headaches, consumption of alcohol, coffee, energy drinks and cigarettes, YANS (Youth Attitude to Noise Scale), CES-D (The Center for Epidemiologic Studies Depression), and GAD-7 (Generalised Anxiety Disorder Assessment - 7 item scale) questionnaires.<br><br>RESULTS: There were 396 (91.9%) of investigated students who used PLD, with more frequent use among girls compared to boys (95.0% and 86.8%, respectively; p&#x2009;=&#x2009;0.002). We found no significant relationship between the frequency of PLD use and depression and anxiety. However, continuous daily PLD use longer than 1 hour was significantly and positively related to depression (p&#x2009;=&#x2009;0.006). Students with depression had a lower total YANS score compared to those without depression, indicating a more negative attitude toward noise (p&#x2009;=&#x2009;0.042). Students with no difficulties to concentrate in noise and with a positive attitude to daily noises had about 37% lower chance to suffer from depression and anxiety, respectively.<br><br>CONCLUSIONS: PLD use is common among medical students and may be associated with their mental health. Longer than 1 hour of continuous daily use of PLD may be positively related to depression. We also found a significant relationship between difficulties concentrating in noisy environments and depression, and between negative attitudes to daily noises and anxiety.},
}
@article {pmid37808390,
year = {2023},
author = {Sivell, D and Sivell, O and , and , and , and , and , and Hawkes, WL and Wotton, KR and , },
title = {The genome sequence of the Vagrant Hoverfly, Eupeodes corollae (Fabricius, 1794).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {112},
pmid = {37808390},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Eupeodes corollae (the Vagrant Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 648.2 megabases in span. Most of the assembly is scaffolded into four chromosomal pseudomolecules, including with the X sex chromosome. The mitochondrial genome has also been assembled and is 18.3 kilobases in length.},
}
@article {pmid37807043,
year = {2023},
author = {Hayes, MG and Langille, MGI and Gu, H},
title = {Cross-study analyses of microbial abundance using generalized common factor methods.},
journal = {BMC bioinformatics},
volume = {24},
number = {1},
pages = {380},
pmid = {37807043},
issn = {1471-2105},
support = {CGS-M Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/05108-2017//Natural Sciences and Engineering Research Council of Canada/ ; Scotia Scholars Award//Nova Scotia Health Research Foundation/ ; },
mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Genomics ; Computational Biology/methods ; },
abstract = {BACKGROUND: By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results.<br><br>RESULTS: We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space.<br><br>CONCLUSIONS: By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.},
}
@article {pmid37802837,
year = {2023},
author = {Zhang, HH and Meng, XX and Lin, YL and Chen, SL and Huang, LF},
title = {[Prediction of global potential growth areas for Panax ginseng based on GMPGIS system and MaxEnt model].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {18},
pages = {4959-4966},
doi = {10.19540/j.cnki.cjcmm.20230514.102},
pmid = {37802837},
issn = {1001-5302},
mesh = {*Panax ; Ecosystem ; China ; Geographic Information Systems ; Temperature ; *Plants, Medicinal ; },
abstract = {The suitable habitat for the endangered and valuable medicinal herb Panax ginseng is gradually decreasing. It is crucial to investigate its suitable growing areas in China for global protection and sustainable utilization of P. ginseng. In this study, 371 distribution points of P. ginseng were collected, and 21 environmental factors were used as ecological indicators. The geographic information system for global medicinal plants(GMPGIS) system, MaxEnt model, and Thiessen polygon method were used to analyze the potential suitable areas for P. ginseng globally. The results showed that the key environmental variables affecting P. ginseng were precipitation in the hottest quarter(Bio18) and the coefficient of temperature seasonality(Bio4). The suitable habitats for P. ginseng were mostly located in the "One Belt, One Road" countries such as China, Japan, South Korea, North Korea, and Russia. The highly suitable habitats were mainly distributed along mountain ranges in southeastern Shandong, southern Shanxi and Shaanxi, northern Jiangsu, and northwestern Henan of China. Data analysis indicated that the current P. ginseng planting sites were all in high suitability zones, and the Thiessen polygon results showed that the geographic locations of P. ginseng production companies were unbalanced and urgently needed optimization. This study provides data support for P. ginseng planting site selection, scientific introduction, production layout, and long-term development planning.},
}
@article {pmid37802618,
year = {2023},
author = {Middleton, J and Colthart, G and Dem, F and Elkins, A and Fairhead, J and Hazell, RJ and Head, MG and Inacio, J and Jimbudo, M and Jones, CI and Laman, M and MacGregor, H and Novotny, V and Peck, M and Philip, J and Paliau, J and Pomat, W and Stockdale, JA and Sui, S and Stewart, AJ and Umari, R and Walker, SL and Cassell, JA},
title = {Health service needs and perspectives of a rainforest conserving community in Papua New Guinea's Ramu lowlands: a combined clinical and rapid anthropological assessment with parallel treatment of urgent cases.},
journal = {BMJ open},
volume = {13},
number = {10},
pages = {e075946},
pmid = {37802618},
issn = {2044-6055},
mesh = {Male ; Female ; Humans ; Adult ; Papua New Guinea ; *Rainforest ; *Health Services ; },
abstract = {OBJECTIVES: Determine community needs and perspectives as part of planning health service incorporation into Wanang Conservation Area, in support of locally driven sustainable development.<br><br>DESIGN: Clinical and rapid anthropological assessment (individual primary care assessments, key informant (KI) interviews, focus groups (FGs), ethnography) with treatment of urgent cases.<br><br>SETTING: Wanang (pop. c189), a rainforest community in Madang province, Papua New Guinea.<br><br>PARTICIPANTS: 129 villagers provided medical histories (54 females (f), 75 males (m); median 19 years, range 1 month to 73 years), 113 had clinical assessments (51f, 62m; median 18 years, range 1 month to 73 years). 26 &#x2265;18&#x2009;years participated in sex-stratified and age-stratified FGs (f<40&#x2009;years; m<40&#x2009;years; f>40&#x2009;years; m>40&#x2009;years). Five KIs were interviewed (1f, 4m). Daily ethnographic fieldnotes were recorded.<br><br>RESULTS: Of 113 examined, 11 were 'well' (a clinical impression based on declarations of no current illness, medical histories, conversation, no observed disease signs), 62 (30f, 32m) were treated urgently, 31 referred (15f, 16m), indicating considerable unmet need. FGs top-4 ranked health issues concorded with KI views, medical histories and clinical examinations. For example, ethnoclassifications of three ((A) 'malaria', (B) 'sotwin', (C) 'grile') translated to the five biomedical conditions diagnosed most ((A) malaria, 9 villagers; (B) upper respiratory infection, 25; lower respiratory infection, 10; tuberculosis, 9; (C) tinea imbricata, 15) and were highly represented in declared medical histories ((A) 75 participants, (B) 23, (C) 35). However, 29.2% of diagnoses (49/168) were limited to one or two people. Treatment approaches included plant medicines, stored pharmaceuticals, occasionally rituals. Travel to hospital/pharmacy was sometimes undertaken for severe/refractory disease. Service barriers included: no health patrols/accessible aid post, remote hospital, unfamiliarity with institutions and medicine costs. Service introduction priorities were: aid post, vaccinations, transport, perinatal/birth care and family planning.<br><br>CONCLUSIONS: This study enabled service planning and demonstrated a need sufficient to acquire funding to establish primary care. In doing so, it aided Wanang's community to develop sustainably, without sacrificing their forest home.},
}
@article {pmid37798344,
year = {2023},
author = {Shim, T and Kim, Z and Jung, J},
title = {A Benford's law-based framework to determine the threshold of occurrence sites for species distribution modelling from ecological monitoring databases.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {16777},
pmid = {37798344},
issn = {2045-2322},
mesh = {*Reproducibility of Results ; Databases, Factual ; },
abstract = {The use of data-based species distribution models (SDMs) has increased significantly in recent years. However, studies of determining the minimum requirements of occurrence sites from ecological monitoring datasets used in species distribution modelling remain insufficient. Therefore, this study proposed a framework to determine the threshold of minimum occurrence sites for SDMs by assessing compliance with Benford's law. The compliance test verified that the national-scale freshwater fish monitoring dataset was natural and reliable. Results derived from true skill statistics (TSS) determined the minimum number of occurrence sites for reliable species distribution modelling was 20 with a TSS value of 0.793 and an overall accuracy of 0.804. The Benford compliance test has shown to be a useful tool for swift and efficient evaluation of the reliability of species occurrence datasets, or the determination of the threshold of occurrence sites before species distribution modelling. Further studies regarding the evaluation of this method's transferability to other species and validation using SDM performance are required. Overall, the framework proposed in this study demonstrates that Benford compliance test applied to species monitoring datasets can be used to derive a universal and model-independent minimum occurrence threshold for SDMs.},
}
@article {pmid37796561,
year = {2023},
author = {Jordan, EJ and Shih, PC and Nelson, EJ and Carter, SJ and Schootman, M and Prather, AA and Yao, X and Peters, CD and Perry, CSE},
title = {Ecological Momentary Assessment of Midlife Adults' Daily Stress: Protocol for the Stress Reports in Variable Environments (STRIVE) App Study.},
journal = {JMIR research protocols},
volume = {12},
number = {},
pages = {e51845},
pmid = {37796561},
issn = {1929-0748},
support = {R21 AG077333/AG/NIA NIH HHS/United States ; },
abstract = {BACKGROUND: Daily stressors are associated with cognitive decline and increased risk of heart disease, depression, and other debilitating chronic illnesses in midlife adults. Daily stressors tend to occur at home or at work and are more frequent in urban versus rural settings. Conversely, spending time in natural environments such as parks or forests, or even viewing nature-themed images in a lab setting, is associated with lower levels of perceived stress and is hypothesized to be a strong stress "buffer," reducing perceived stress even after leaving the natural setting. However, many studies of daily stress have not captured environmental contexts and relied on end-of-day recall instead of in-the-moment data capture. With new technology, these limitations can be addressed to enhance knowledge of the daily stress experience.<br><br>OBJECTIVE: We propose to use our novel custom-built Stress Reports in Variable Environments (STRIVE) ecological momentary assessment mobile phone app to measure the experience of daily stress of midlife adults in free-living conditions. Using our app to capture data in real time will allow us to determine (1) where and when daily stress occurs for midlife adults, (2) whether midlife adults' daily stressors are linked to certain elements of the built and natural environment, and (3) how ecological momentary assessment measurement of daily stress is similar to and different from a modified version of the popular Daily Inventory of Stressful Events measurement tool that captures end-of-day stress reports (used in the Midlife in the United States [MIDUS] survey).<br><br>METHODS: We will enroll a total of 150 midlife adults living in greater Indianapolis, Indiana, in this study on a rolling basis for 3-week periods. As those in underrepresented minority groups and low-income areas have previously been found to experience greater levels of stress, we will use stratified sampling to ensure that half of our study sample is composed of underrepresented minorities (eg, Black, American Indian, Hispanic, or Native Pacific Islanders) and approximately one-third of our sample falls within low-, middle-, and high-income brackets.<br><br>RESULTS: This project is funded by the National Institute on Aging from December 2022 to November 2024. Participant enrollment began in August 2023 and is expected to finish in July 2024. Data will be spatiotemporally analyzed to determine where and when stress occurs for midlife adults. Pictures of stressful environments will be qualitatively analyzed to determine the common elements of stressful environments. Data collected by the STRIVE app will be compared with retrospective Daily Inventory of Stressful Events data.<br><br>CONCLUSIONS: Completing this study will expand our understanding of midlife adults' experience of stress in free-living conditions and pave the way for data-driven individual and community-based intervention designs to promote health and well-being in midlife adults.<br><br>DERR1-10.2196/51845.},
}
@article {pmid37794496,
year = {2023},
author = {Lühken, R and Becker, N and Dyczko, D and Sauer, FG and Kliemke, K and Schmidt-Chanasit, J and Rydzanicz, K},
title = {First record of Anopheles (Anopheles) hyrcanus (Pallas 1771) (Diptera: Culicidae) in Poland.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {345},
pmid = {37794496},
issn = {1756-3305},
support = {BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; BMBF//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {Animals ; *Culicidae ; *Anopheles/parasitology ; Poland ; Mosquito Vectors ; Climate ; Europe ; },
abstract = {The spatial distribution of mosquito species in the course of globalization and climate warming is highly dynamic. Different studies have demonstrated the spread and establishment of thermophilic mosquito species, potentially increasing the prevalence of 'nuisance' mosquitoes and the local transmission of pathogens. Here we report the first recorded sampling of Anopheles hyrcanus in Wrocław, southwest Poland. This is the most northern detection of this species to date in Europe. Future spread and population development of this potential vector of malaria parasites, viruses or zoonotic helminths, such as Dirofilaria spp., must be monitored carefully. Potential factors underlying the spread of this species are discussed.},
}
@article {pmid37793967,
year = {2023},
author = {Brehm, AM and Orrock, JL},
title = {Extensive behavioral data contained within existing ecological datasets.},
journal = {Trends in ecology &amp; evolution},
volume = {38},
number = {12},
pages = {1129-1133},
doi = {10.1016/j.tree.2023.08.016},
pmid = {37793967},
issn = {1872-8383},
mesh = {*Ecology ; *Datasets as Topic ; },
abstract = {Long-term ecological datasets contain vast behavioral data, enabling the quantification of among-individual behavioral variation at unprecedented spatiotemporal scales. We detail how behaviors can be extracted and describe how such data can be used to test new hypotheses, inform population and community ecology, and address pressing conservation needs.},
}
@article {pmid37789481,
year = {2022},
author = {Cao, J and Zhang, Y and Tan, S and Yang, Q and Wang, HL and Xia, X and Luo, J and Guo, H and Zhang, Z and Li, Z},
title = {LSD 4.0: an improved database for comparative studies of leaf senescence.},
journal = {Molecular horticulture},
volume = {2},
number = {1},
pages = {24},
pmid = {37789481},
issn = {2730-9401},
support = {32170345//National Natural Science Foundation of China/ ; 31970196//National Natural Science Foundation of China/ ; XDA19050302//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDB13040500//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2017YFC0907502//National Key Research and Development Program of China, Startup Funding/ ; XXH13505-05//13th Five-year Informatization Plan of Chinese Academy of Sciences/ ; 153F11KYSB20160008//International Partnership Program of the Chinese Academy of Sciences/ ; 2019YFA0903904//National Key Research and Development Program of China/ ; },
}
@article {pmid37789366,
year = {2023},
author = {Reinar, WB and Tørresen, OK and Nederbragt, AJ and Matschiner, M and Jentoft, S and Jakobsen, KS},
title = {Teleost genomic repeat landscapes in light of diversification rates and ecology.},
journal = {Mobile DNA},
volume = {14},
number = {1},
pages = {14},
pmid = {37789366},
issn = {1759-8753},
support = {222378/WT_/Wellcome Trust/United Kingdom ; 222378/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring.},
}
@article {pmid37787405,
year = {2024},
author = {Brooks, BW and van den Berg, S and Dreier, DA and LaLone, CA and Owen, SF and Raimondo, S and Zhang, X},
title = {Towards Precision Ecotoxicology: Leveraging Evolutionary Conservation of Pharmaceutical and Personal Care Product Targets to Understand Adverse Outcomes Across Species and Life Stages.},
journal = {Environmental toxicology and chemistry},
volume = {43},
number = {3},
pages = {526-536},
pmid = {37787405},
issn = {1552-8618},
support = {EPA999999/ImEPA/Intramural EPA/United States ; P01 ES028942/ES/NIEHS NIH HHS/United States ; 1P01ES028942/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; Ecotoxicology ; Ecosystem ; Environmental Monitoring ; Risk Assessment ; *Cosmetics/toxicity/analysis ; Pharmaceutical Preparations ; *Water Pollutants, Chemical/analysis ; },
abstract = {Translation of environmental science to the practice aims to protect biodiversity and ecosystem services, and our future ability to do so relies on the development of a precision ecotoxicology approach wherein we leverage the genetics and informatics of species to better understand and manage the risks of global pollution. A little over a decade ago, a workshop focusing on the risks of pharmaceuticals and personal care products (PPCPs) in the environment identified a priority research question, "What can be learned about the evolutionary conservation of PPCP targets across species and life stages in the context of potential adverse outcomes and effects?" We review the activities in this area over the past decade, consider prospects of more recent developments, and identify future research needs to develop next-generation approaches for PPCPs and other global chemicals and waste challenges. Environ Toxicol Chem 2024;43:526-536. © 2023 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.},
}
@article {pmid37781634,
year = {2022},
author = {Vila, R and Lohse, K and Hayward, A and Laetsch, DR and , and , and , and Wahlberg, N and , },
title = {The genome sequence of the white admiral, Limenitis camilla (Linnaeus, 1764).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {301},
pmid = {37781634},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Limenitis camilla (the white admiral; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 435 megabases in span. Most of the assembly (99.97%) is scaffolded into 31 chromosomal pseudomolecules, corresponding to 29 autosomes plus the W and Z sex chromosomes. The complete mitochondrial genome was also assembled and is 15.2 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,489 protein coding genes.},
}
@article {pmid37781318,
year = {2023},
author = {Petza, D and Amorim, E and Ben Lamine, E and Colloca, F and Dominguez Crisóstomo, E and Fabbrizzi, E and Fraschetti, S and Galparsoro, I and Giakoumi, S and Kruse, M and Stelzenmüller, V and Katsanevakis, S},
title = {Assessing the potential of Other Effective area-based Conservation Measures (OECMs) for contributing to conservation targets: A global scoping review protocol.},
journal = {Open research Europe},
volume = {3},
number = {},
pages = {118},
pmid = {37781318},
issn = {2732-5121},
abstract = {This scoping review (ScR) protocol aims to establish the methodological approach for identifying and mapping the evidence regarding the actual contribution of Other Effective area-based Conservation Measures (OECMs) to spatial conservation targets. Emphasis will be placed on examining the research conducted, including the methodologies applied. OECMs, introduced by the Convention on Biological Diversity (CBD) in 2010, refer to areas outside of protected areas, such as fisheries restricted areas, archaeological sites, and military areas, that effectively conserve biodiversity in-situ over the long term. OECMs are recognized rather than designated. Many countries currently endeavor to identify, recognize and report OECMs to the CBD for formal acceptance to support the implementation of spatial conservation targets. Studies that assess the contribution of OECMs to spatial conservation targets will be considered. Potential OECMs with primary, secondary or ancillary conservation objectives established by all sectors in the terrestrial, freshwater and marine realm worldwide will be considered. Peer-reviewed and grey literature will be considered without imposing limitations based on publication year, stage, subject area and source type. Both experimental and observational studies in English, French, German, Greek, Italian, and Spanish will be reviewed. The ScR will follow the Joanna Briggs Institute (JBI) methodology. The protocol will be guided by the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) extension for scoping reviews. The search will encompass bibliographic databases such as Scopus, Web of Science and Google Scholar. Grey literature sources will include databases, pre-print archives and organizational websites. The Covidence platform will be utilized for data management and extraction.},
}
@article {pmid37777307,
year = {2023},
author = {Strobl, MAR and Gallaher, J and Robertson-Tessi, M and West, J and Anderson, ARA},
title = {Treatment of evolving cancers will require dynamic decision support.},
journal = {Annals of oncology : official journal of the European Society for Medical Oncology},
volume = {34},
number = {10},
pages = {867-884},
pmid = {37777307},
issn = {1569-8041},
support = {U01 CA232382/CA/NCI NIH HHS/United States ; U54 CA193489/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Neoplasms/drug therapy ; *Decision Support Systems, Clinical ; Precision Medicine ; Models, Theoretical ; },
abstract = {Cancer research has traditionally focused on developing new agents, but an underexplored question is that of the dose and frequency of existing drugs. Based on the modus operandi established in the early days of chemotherapies, most drugs are administered according to predetermined schedules that seek to deliver the maximum tolerated dose and are only adjusted for toxicity. However, we believe that the complex, evolving nature of cancer requires a more dynamic and personalized approach. Chronicling the milestones of the field, we show that the impact of schedule choice crucially depends on processes driving treatment response and failure. As such, cancer heterogeneity and evolution dictate that a one-size-fits-all solution is unlikely-instead, each patient should be mapped to the strategy that best matches their current disease characteristics and treatment objectives (i.e. their 'tumorscape'). To achieve this level of personalization, we need mathematical modeling. In this perspective, we propose a five-step 'Adaptive Dosing Adjusted for Personalized Tumorscapes (ADAPT)' paradigm to integrate data and understanding across scales and derive dynamic and personalized schedules. We conclude with promising examples of model-guided schedule personalization and a call to action to address key outstanding challenges surrounding data collection, model development, and integration.},
}
@article {pmid37776607,
year = {2023},
author = {Brant, LCC and Pinheiro, PC and Passaglia, LG and de Souza, MFM and Malta, DC and Banerjee, A and Ribeiro, ALP and Nascimento, BR},
title = {Cardiovascular mortality in Brazil during the COVID-19 pandemic: a comparison between underlying and multiple causes of death.},
journal = {Public health},
volume = {224},
number = {},
pages = {131-139},
doi = {10.1016/j.puhe.2023.08.027},
pmid = {37776607},
issn = {1476-5616},
mesh = {Humans ; *COVID-19/mortality/epidemiology ; Brazil/epidemiology ; *Cardiovascular Diseases/mortality/epidemiology ; *Cause of Death ; Male ; Female ; Middle Aged ; Aged ; Adult ; Aged, 80 and over ; SARS-CoV-2 ; Pandemics ; },
abstract = {OBJECTIVES: The COVID-19 pandemic has differentially impacted cardiovascular disease (CVD) mortality worldwide. Causes of death misclassification may be one of the reasons. We evaluated the impact of the pandemic on CVD mortality in Brazil, comparing underlying causes (UCs) and multiple causes (MCs) of death.<br><br>STUDY DESIGN: Ecological time-series study.<br><br>METHODS: An ecological, time-series study was conducted analysing age-standardised death rates for CVD, from epidemiological week (EW) 10/2020 to 39/2021, using data from the Mortality Information System, Brazil. CVD was defined using the International Classification of Diseases (ICD-10) coding, if reported as UC or MC of death. Observed and expected data (mean for the same EW, 2017-2019) were compared. Risk ratios (RiRs) were analysed, and 95% confidence intervals (CIs) were calculated.<br><br>RESULTS: Age-standardised mortality rate for CVD as UC of death was 165.8 (95%CI: 165.4-166.3) per 100,000 inhabitants, similar to what was expected (165.6/100,000, 95%CI: 165.2-166.1, RiR&#xa0;=&#xa0;1.00). There was increased out-of-hospital mortality (RiR&#xa0;=&#xa0;1.18; 95%CI: 1.17-1.19) and deaths of ill-defined causes (RiR&#xa0;=&#xa0;1.43; 95%CI: 1.42-1.44). The increase in out-of-hospital deaths was more pronounced in the North (RiR&#xa0;=&#xa0;1.33; 95%CI 1.30-1.36) region, with a less resilient health system. Conversely, as MCs of death, there was a 10% increase in CVD mortality (observed: 243.2 [95%CI: 242.7-243.7], expected: 221.6 [95%CI: 221.1-222.1] per 100,000). An increase also occurred in the North and Central West regions (RiR&#xa0;=&#xa0;1.16; 95%CI: 1.15-1.18), among men (RiR&#xa0;=&#xa0;1.11; 95%CI: 1.11-1.12) and individuals aged &#x2265;60 years (RiR&#xa0;=&#xa0;1.11; 95%CI: 1.10-1.11).<br><br>CONCLUSIONS: During the pandemic, mortality rates for CVD as MCs of death increased in Brazil, whereas as UC mortality rates did not change. Higher out-of-hospital mortality, misclassification, and competing causes of death may explain this pattern.},
}
@article {pmid37775284,
year = {2023},
author = {Murray, A and Speyer, L and Thye, M and Stewart, T and Obsuth, I and Kane, J and Whyte, K and Devaney, J and Rohde, LA and Ushakova, A and Rhodes, S},
title = {Illuminating the daily life experiences of adolescents with and without ADHD: protocol for an ecological momentary assessment study.},
journal = {BMJ open},
volume = {13},
number = {9},
pages = {e077222},
pmid = {37775284},
issn = {2044-6055},
support = {/WT_/Wellcome Trust/United Kingdom ; 225364/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Adolescent ; *Attention Deficit Disorder with Hyperactivity/diagnosis ; Ecological Momentary Assessment ; Life Change Events ; State Medicine ; Mental Health ; },
abstract = {INTRODUCTION: Adolescents with attention-deficit/hyperactivity disorder (ADHD) are at elevated risk of a range of difficulties, among which emotion regulation, peer and co-occurring mental health problems are prominent challenges. To better support adolescents with ADHD, ecologically valid interventions that can be embedded in daily life to target the most proximal antecedents of these challenges are needed. Ecological momentary assessment (EMA) designs are ideally suited to meeting this need.<br><br>METHODS AND ANALYSES: In the mental health in the moment ADHD study, we will use an EMA design to capture the daily life experiences of approximately 120 adolescents aged 11-14 years with a clinical diagnosis of ADHD and the same number of age-matched and gender-matched peers without a diagnosis of ADHD. We will combine this with comprehensive information gathered from online surveys. Analysing the data using techniques such as dynamic structural equation modelling, we will examine, among other research questions, the role of emotion regulation and peer problems in mediating the links between characteristics of ADHD and commonly co-occurring outcomes such as anxiety, depression and conduct problems. The results can help inform interventions to support improved peer functioning and emotion regulation for adolescents with ADHD.<br><br>ETHICS AND DISSEMINATION: This study received a favourable ethical opinion through the National Health Service ethical review board and the University of Edinburgh PPLS Research Ethics panel. The results will be disseminated through journal publications, conferences and seminar presentations and to relevant stakeholders, such as those with ADHD, their families and clinicians.},
}
@article {pmid37771003,
year = {2023},
author = {Gautam, A and Bhowmik, D and Basu, S and Zeng, W and Lahiri, A and Huson, DH and Paul, S},
title = {Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.},
journal = {Briefings in bioinformatics},
volume = {24},
number = {6},
pages = {},
doi = {10.1093/bib/bbad325},
pmid = {37771003},
issn = {1477-4054},
mesh = {*Metabolome ; *Microbiota ; Metabolomics/methods ; Internet ; },
abstract = {A microbial community maintains its ecological dynamics via metabolite crosstalk. Hence, knowledge of the metabolome, alongside its populace, would help us understand the functionality of a community and also predict how it will change in atypical conditions. Methods that employ low-cost metagenomic sequencing data can predict the metabolic potential of a community, that is, its ability to produce or utilize specific metabolites. These, in turn, can potentially serve as markers of biochemical pathways that are associated with different communities. We developed MMIP (Microbiome Metabolome Integration Platform), a web-based analytical and predictive tool that can be used to compare the taxonomic content, diversity variation and the metabolic potential between two sets of microbial communities from targeted amplicon sequencing data. MMIP is capable of highlighting statistically significant taxonomic, enzymatic and metabolic attributes as well as learning-based features associated with one group in comparison with another. Furthermore, MMIP can predict linkages among species or groups of microbes in the community, specific enzyme profiles, compounds or metabolites associated with such a group of organisms. With MMIP, we aim to provide a user-friendly, online web server for performing key microbiome-associated analyses of targeted amplicon sequencing data, predicting metabolite signature, and using learning-based linkage analysis, without the need for initial metabolomic analysis, and thereby helping in hypothesis generation.},
}
@article {pmid37767299,
year = {2023},
author = {Cai, J and Pan, R and Lin, J and Liu, J and Zhang, L and Wen, X and Chen, X and Zhang, X},
title = {Improved EfficientNet for corn disease identification.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1224385},
pmid = {37767299},
issn = {1664-462X},
abstract = {INTRODUCTION: Corn is one of the world's essential crops, and the presence of corn diseases significantly affects both the yield and quality of corn. Accurate identification of corn diseases in real time is crucial to increasing crop yield and improving farmers' income. However, in real-world environments, the complexity of the background, irregularity of the disease region, large intraclass variation, and small interclass variation make it difficult for most convolutional neural network models to achieve disease recognition under such conditions. Additionally, the low accuracy of existing lightweight models forces farmers to compromise between accuracy and real-time.<br><br>METHODS: To address these challenges, we propose FCA-EfficientNet. Building upon EfficientNet, the fully-convolution-based coordinate attention module allows the network to acquire spatial information through convolutional structures. This enhances the network's ability to focus on disease regions while mitigating interference from complex backgrounds. Furthermore, the adaptive fusion module is employed to fuse image information from different scales, reducing interference from the background in disease recognition. Finally, through multiple experiments, we have determined the network structure that achieves optimal performance.<br><br>RESULTS: Compared to other widely used deep learning models, this proposed model exhibits outstanding performance in terms of accuracy, precision, recall, and F1 score. Furthermore, the model has a parameter count of 3.44M and Flops of 339.74M, which is lower than most lightweight network models. We designed and implemented a corn disease recognition application and deployed the model on an Android device with an average recognition speed of 92.88ms, which meets the user's needs.<br><br>DISCUSSION: Overall, our model can accurately identify corn diseases in realistic environments, contributing to timely and effective disease prevention and control.},
}
@article {pmid37767015,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Couch, C and Plotkin, D and Kawahara, AY and , },
title = {The genome sequence of the peacock moth, Macaria notata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {228},
pmid = {37767015},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Macaria notata (the peacock moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 394 megabases in span. The majority of the assembly (99.98%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.},
}
@article {pmid37766852,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Broken-barred Carpet, Electrophaes corylata (Thunberg, 1792).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {283},
pmid = {37766852},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Electrophaes corylata (the Broken-barred Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 347.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,031 protein coding genes.},
}
@article {pmid37766851,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Dark Spectacle, Abrostola triplasia (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {278},
pmid = {37766851},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Abrostola triplasia (the Dark Spectacle; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 362.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,532 protein coding genes.},
}
@article {pmid37759063,
year = {2023},
author = {Ha, LT},
title = {Scrutinizing the nexus between green innovations and the sustainability of environmental system: novel insights from European database.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {50},
pages = {109087-109109},
pmid = {37759063},
issn = {1614-7499},
mesh = {*Ecosystem ; *Agriculture ; Biodiversity ; Databases, Factual ; Europe ; Economic Development ; Carbon Dioxide ; },
abstract = {A study is presented in this paper that examines the effect of environmental innovation (EI) on environmental performance (EP). Six measures are used to reflect environmental innovation, including the percentage of enterprises that invest in environmental innovation, the percentage of enterprises implementing environmental innovation activities, the number of ISO 14001 certificates, patents related to environmental innovation, the total R&amp;D personnel and researchers, and the amount of green early-stage investments. The estimation results show that EI positively impacts EP in 21 European countries using different econometric techniques during the 2011-2019 period. By using various econometric techniques (namely a panel-corrected standard errors (PCSE) model, a feasible generalized least square estimates (FGLS) model, and the two-step general method of moment (the two-step GMM), our research demonstrates how environmental innovation impacts on environmental quality. The short- and long-term effects of autoregressive distributed lag (ARDL) methods were also investigated using pooled mean groups (PMGs) to distinguish the short-run and long-run influences of EI. The relationship between EI and EP is explored by demonstrating how EI affects EP short- and long-term and comparing its influence on EP across many component measures of EI: air quality, sanitation, drinking water, heavy metals, waste management, biodiversity, habitat, ecosystem services, water resources, and agriculture. Notably, we find that the influences of EI become more pronounced in a country characterized by a well-developed institutional system. Our findings suggest policy implications to help countries invest in research and development with concerns about environmental damage mitigations more effectively. These findings are critical to suggest a way to help countries pursue ecological sustainability.},
}
@article {pmid37755898,
year = {2023},
author = {Bekele, D and Aragie, S and Alene, KA and Dejene, T and Warkaye, S and Mezemir, M and Abdena, D and Kebebew, T and Botore, A and Mekonen, G and Gutema, G and Dufera, B and Gemede, K and Kenate, B and Gobena, D and Alemu, B and Hailemariam, D and Muleta, D and Siu, GKH and Tafess, K},
title = {Spatiotemporal Distribution of Tuberculosis in the Oromia Region of Ethiopia: A Hotspot Analysis.},
journal = {Tropical medicine and infectious disease},
volume = {8},
number = {9},
pages = {},
pmid = {37755898},
issn = {2414-6366},
abstract = {Tuberculosis (TB) is a major public health concern in low- and middle-income countries including Ethiopia. This study aimed to assess the spatiotemporal distribution of TB and identify TB risk factors in Ethiopia's Oromia region. Descriptive and spatiotemporal analyses were conducted. Bayesian spatiotemporal modeling was used to identify covariates that accounted for variability in TB and its spatiotemporal distribution. A total of 206,278 new pulmonary TB cases were reported in the Oromia region between 2018 and 2022, with the lowest annual TB case notification (96.93 per 100,000 population) reported in 2020 (i.e., during the COVID-19 pandemic) and the highest TB case notification (106.19 per 100,000 population) reported in 2019. Substantial spatiotemporal variations in the distribution of notified TB case notifications were observed at zonal and district levels with most of the hotspot areas detected in the northern and southern parts of the region. The spatiotemporal distribution of notified TB incidence was positively associated with different ecological variables including temperature (β = 0.142; 95% credible interval (CrI): 0.070, 0.215), wind speed (β = -0.140; 95% CrI: -0.212, -0.068), health service coverage (β = 0.426; 95% CrI: 0.347, 0.505), and population density (β = 0.491; 95% CrI: 0.390, 0.594). The findings of this study indicated that preventive measures considering socio-demographic and health system factors can be targeted to high-risk areas for effective control of TB in the Oromia region. Further studies are needed to develop effective strategies for reducing the burden of TB in hotspot areas.},
}
@article {pmid37754785,
year = {2023},
author = {Leo, P and Onofri, S and Zucconi, L and Selbmann, L and Turchetti, B and Buzzini, P and Chander, AM and Simpson, A and Singh, N and Vellone, D and Tighe, S and Venkateswaran, K},
title = {Draft genome sequencing of Naganishia species isolated from the polar environments.},
journal = {Microbiology resource announcements},
volume = {12},
number = {10},
pages = {e0038823},
pmid = {37754785},
issn = {2576-098X},
support = {18-PPR18-0011//National Aeronautics and Space Administration (NASA)/ ; },
abstract = {The draft genomes of five Naganishia strains were sequenced using MinION and annotated using Funannotate pipeline. Phylogenetic and genomic analyses were performed to provide their genetic relationships, diversity, and potential functional capabilities. This approach will aid in understanding their potential to survive under microgravity and their resilience to extreme environments.},
}
@article {pmid37754733,
year = {2023},
author = {Ježová, Z and Prokop, P and Zvaríková, M and Zvarík, M},
title = {Unraveling the Significance of Draglines: Female Sexual Signalization in the Nursery-Web Spider, Pisaura mirabilis.},
journal = {Insects},
volume = {14},
number = {9},
pages = {},
pmid = {37754733},
issn = {2075-4450},
support = {20-0081//Slovak Research and Development Agency/ ; },
abstract = {Chemical signals used by animals to attract the opposite sex are well known in insects, but heavily understudied in spiders. We investigated the role of chemical signals in female draglines in a gift-giving spider, Pisaura mirabilis, using combined data from behavioral tests and high-performance liquid chromatography (HPLC). We also investigated whether the quality of sexual signalization is influenced by crucial factors, such as female spider ontogeny, nutritional status, and mating status. We found that draglines of adult (versus subadult) and hungry (versus fed) females stimulated male motivation to produce nuptial gift, and highly sexually excited males invested more silk in gift production than less sexually excited males. Unexpectedly, chemical signals of eggsac-carrying females were similarly sexually attractive to draglines of adult females not carrying eggsac. HPLC identified significant chemical differences in female draglines, but these differences did not always correspond to male behavior. The integration of behavioral and chemical approaches is required to better understand animal behavior in future research.},
}
@article {pmid37753602,
year = {2023},
author = {Aguiar, A and Gebremariam, MK and Romanenko, E and Önal, F and Kopainsky, B and Savona, N and Brown, A and Allender, S and Lien, N},
title = {System dynamics simulation models on overweight and obesity in children and adolescents: A systematic review.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {24 Suppl 2},
number = {},
pages = {e13632},
doi = {10.1111/obr.13632},
pmid = {37753602},
issn = {1467-789X},
mesh = {Child ; Adolescent ; Humans ; *Overweight/epidemiology ; *Pediatric Obesity/epidemiology/prevention &amp; control ; Databases, Factual ; Pandemics ; Policy ; },
abstract = {It has increasingly been recognized that developing successful obesity prevention policies and interventions requires understanding of the complex mechanisms driving the obesity pandemic and that models could be useful tools for simulating policies. This paper reviews system dynamics simulation models of mechanisms driving childhood overweight and obesity and/or testing of preventive interventions. A systematic literature search was conducted in six databases from inception to January 2023 using terms related to overweight/obesity, children, and system dynamics. Study descriptives, mechanisms, and where to intervene (the leverage points), as well as quality assessments of the simulation models were extracted by two researchers into a predetermined template and narratively synthesized. Seventeen papers describing 15 models were included. Models describing the mechanisms ranged from only intrapersonal factors to models cutting across multiple levels of the ecological model, but mechanisms across levels were lacking. The majority of interventions tested in the simulation models were changes to existing model parameters with less emphasis on models that alter system structure. In conclusion, existing models included mechanisms driving youth obesity at multiple levels of the ecological model. This is useful for developing an integrated simulation model combining mechanisms at multiple levels and allowing for testing fundamental system changes.},
}
@article {pmid37749493,
year = {2023},
author = {Smith, SK and Frazel, PW and Khodadadi-Jamayran, A and Zappile, P and Marier, C and Okhovat, M and Brown, S and Long, MA and Heguy, A and Phelps, SM},
title = {De novo assembly and annotation of the singing mouse genome.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {569},
pmid = {37749493},
issn = {1471-2164},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 NS113071/NS/NINDS NIH HHS/United States ; R01 NS113071/GF/NIH HHS/United States ; },
mesh = {Male ; Animals ; Mice ; *Genomics ; *Biological Evolution ; Multifactorial Inheritance ; Phenotype ; Reproduction ; },
abstract = {BACKGROUND: Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston's singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions.<br><br>RESULTS: Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types.<br><br>CONCLUSIONS: These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.},
}
@article {pmid37748067,
year = {2023},
author = {Stenseth, NC and Schlatte, R and Liu, X and Pielke, R and Chen, B and Bjørnstad, ON and Kusnezov, D and Gao, GF and Fraser, C and Whittington, JD and Gong, P and Guan, D and Johnsen, EB},
title = {Reply to Ekström and Ottersen: Real-time access to data during outbreaks is a key to avoid a local epidemic becoming a global pandemic.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {40},
pages = {e2312649120},
pmid = {37748067},
issn = {1091-6490},
mesh = {*Pandemics/prevention &amp; control ; *Disease Outbreaks/prevention &amp; control ; },
}
@article {pmid37745602,
year = {2023},
author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F},
title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37745602},
issn = {2692-8205},
support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; },
abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.},
}
@article {pmid37741542,
year = {2023},
author = {Chen, H and Zhang, X and Ji, C and Deng, W and Yang, G and Hao, Z and Chen, B},
title = {Physicochemical properties of environmental media can affect the adsorption of arsenic (As) by microplastics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {338},
number = {},
pages = {122592},
doi = {10.1016/j.envpol.2023.122592},
pmid = {37741542},
issn = {1873-6424},
mesh = {Humans ; Microplastics/chemistry ; Plastics ; *Arsenic/analysis ; Adsorption ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil/chemistry ; },
abstract = {Microplastics are emerging pollutants that can adsorb heavy metals and threaten human health through food chain. Recently, there has been increasing interest in understanding the adsorption behavior of heavy metals by microplastics in farmland soil. In particular, arsenic (As), as a carcinogen, has the potential to be adsorbed by soil microplastics. However, the mechanisms and controlling factors of As adsorption by microplastics in farmland soil under natural conditions are still unknown. Here, microplastics and As were respectively added to farmland soils with different physicochemical properties from twelve provinces of China for adsorption experiment. We performed surface analysis of microplastics, quantified As accumulation through quasi-first-order kinetic equation and developed regression models to screen the factors controlling As adsorption. The results showed that the adsorption of As by soil microplastics was a chemical process accompanied by the loss of electrons from oxygen-containing functional groups. Soil cation exchange capacity (CEC) was the main factor controlling the adsorption rate, while soil organic matter (SOM), total nitrogen (TN) and CEC mainly influenced the equilibrium adsorption capacity. This is the first report on microplastic-As adsorption in natural soil, which allows deeper insights into risk assessment, prediction and control of microplastic-As pollution in agricultural soil.},
}
@article {pmid37737917,
year = {2023},
author = {Miletić, S and Beloica, J and Perović, V and Miljković, P and Lukić, S and Obradović, S and Čakmak, D and Belanović-Simić, S},
title = {Environmental sensitivity assessment and land degradation in southeastern Serbia: application of modified MEDALUS model.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {10},
pages = {1241},
pmid = {37737917},
issn = {1573-2959},
mesh = {*Environmental Monitoring ; Serbia ; *Benchmarking ; Databases, Factual ; Droughts ; },
abstract = {This paper aims to improve the methodology and results accuracy of MEDALUS model for assessing land degradation sensitivity through the application of different data detail levels and by introducing the application of Ellenberg indices in metrics related to vegetation drought sensitivity assessment. For that purpose, the MEDALUS model was applied at 2 levels of detail. Level I (municipality level) implied the use of available large-scale databases and level II (watershed) contains more detailed information about vegetation used in the calculation of the VQI and MQI factors (Fig. S6). The comparison was made using data based on CORINE Land Cover (2012) and forest inventory data, complemented with object-based classification. Results showed that data based on forest inventory data with the application of Ellenberg's indices and object-based classification have one class more, critical (C1 and C2) and that the percentage distribution of classes is different in both quantitative (area size of class sensitivity) and qualitative (aggregation and dispersion of sensitivity classes). The use of data from Forest Management Plans and the application of Ellenberg's indices affect the quality of the results and find its application in the model, especially if these results are used for monitoring and land area management on fine scales. Remote sensed data images (Sentinel-2B) were introduced into the methodology as a very important environmental monitoring tool and model results validation.},
}
@article {pmid37736012,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Rustic Shoulder-knot, Apamea sordens (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {51},
pmid = {37736012},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Apamea sordens (the Rustic Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 614 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length.},
}
@article {pmid37735266,
year = {2024},
author = {Camargo, AP and Roux, S and Schulz, F and Babinski, M and Xu, Y and Hu, B and Chain, PSG and Nayfach, S and Kyrpides, NC},
title = {Identification of mobile genetic elements with geNomad.},
journal = {Nature biotechnology},
volume = {42},
number = {8},
pages = {1303-1312},
pmid = {37735266},
issn = {1546-1696},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Plasmids/genetics ; Software ; Databases, Genetic ; Molecular Sequence Annotation ; Genome, Viral/genetics ; Viruses/genetics ; Neural Networks, Computer ; Computational Biology/methods ; },
abstract = {Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad .},
}
@article {pmid37733803,
year = {2023},
author = {Engloner, AI and Vargha, M and Kós, P and Borsodi, AK},
title = {Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts.},
journal = {PloS one},
volume = {18},
number = {9},
pages = {e0292057},
pmid = {37733803},
issn = {1932-6203},
mesh = {*Plankton/genetics ; Climate Change ; Seasons ; Rivers ; Global Warming ; *Gammaproteobacteria ; },
abstract = {In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.},
}
@article {pmid37731848,
year = {2023},
author = {Ohashi, K and Osanai, T and Fujiwara, K and Tanikawa, T and Tani, Y and Takamiya, S and Sato, H and Morii, Y and Ogasawara, K},
title = {Access to mechanical thrombectomy and ischemic stroke mortality in Japan: a spatial ecological study.},
journal = {Frontiers in neurology},
volume = {14},
number = {},
pages = {1209446},
pmid = {37731848},
issn = {1664-2295},
abstract = {BACKGROUND: Advances in stroke treatment have greatly improved outcomes; however, disparities in access to treatment might increase. Achieving equitable access to stroke treatment is a health policy challenge, as rapid treatment is essential for positive outcomes. This ecological cross-sectional study aimed to determine the relationship between the disparities in spatial accessibility to mechanical thrombectomy (SAMT) and stroke mortality rates in Japan, hypothesizing that disparities in SAMT may increase the differences in stroke mortality between regions.<br><br>METHODS: We used the average number of ischemic stroke (IS) deaths between 2020 and 2021 as the response variable; and SAMT, medical resources, and socioeconomic characteristics of each municipality as explanatory variables. A conditional autoregressive model was used to examine the association between the risk of stroke mortality and SAMT. The standardized mortality ratio (SMR) was mapped to understand the nationwide disparities in stroke mortality risk.<br><br>RESULTS: The median number of IS deaths was 17.5 persons per year in the municipalities (2020 to 2021). The study also found that municipalities with low SAMT were located in the northern part of Japan. The non-spatial regression model results indicated that poor accessibility, a small proportion of bachelor's degrees or higher, and a high proportion of workers in secondary industries were related to high IS mortality. Three models were evaluated using spatial analysis; Model 1 with accessibility indicators alone, Model 2 with medical resources added to Model 1, and Model 3 with socioeconomic characteristics added to Model 2. In Models 1 and 2, the population-weighted spatial accessibility index (PWSAI) showed a significant negative relationship with stroke mortality. However, this was not evident in Model 3. Mapping using Model 3 showed that the high-risk areas were predominantly located in northern Japan, excluding Hokkaido.<br><br>CONCLUSION: Access to mechanical thrombectomy was estimated, and regional differences were observed. The relationship between accessibility and IS mortality is unknown; however, regardless of accessibility, municipalities with a high proportion of workers in secondary industries and a small proportion with bachelor's degrees or above are at risk of death from stroke.},
}
@article {pmid37731597,
year = {2023},
author = {Molina, MA and Melchers, WJG and Andralojc, KM and Leenders, WPJ and Huynen, MA},
title = {Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {4424-4431},
pmid = {37731597},
issn = {2001-0370},
abstract = {The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health. Lactobacillus-depleted communities particularly associate with an increased susceptibility for persistence of high-risk human papillomavirus (hrHPV) infections and progression of disease, but the long-term ecological dynamics of CSTs after hrHPV infection diagnosis remain poorly understood. To determine such dynamics, we examined the CVM of our longitudinal cohort of 141 women diagnosed with hrHPV infection at baseline with collected cervical smears at two timepoints six-months apart. Here we describe that the long-term microbiome dissimilarity has a positive correlation with microbial diversity at both visits and that women with high abundance and dominance for Lactobacillus iners at baseline exhibit more similar microbiome composition at second visit than women with Lactobacillus-depleted communities at baseline. We further show that the species Lactobacillus acidophilus and Megasphaera genomosp type 1 associate with CST changes between both visits. Lastly, we also observe that Gardnerella vaginalis is associated with the stability of Lactobacillus-depleted communities while L. iners is associated with the instability of Megasphaera genomosp type 1-dominated communities. Our data suggest dynamic patterns of cervicovaginal CSTs during hrHPV infection, which could be potentially used to develop microbiome-based therapies against infection progression towards disease.},
}
@article {pmid37731336,
year = {2024},
author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A},
title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.},
journal = {Critical reviews in biotechnology},
volume = {44},
number = {6},
pages = {1164-1182},
doi = {10.1080/07388551.2023.2254933},
pmid = {37731336},
issn = {1549-7801},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Bacteria/genetics/classification ; Guidelines as Topic ; Microbiota/genetics ; Humans ; Data Interpretation, Statistical ; Reproducibility of Results ; },
abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.},
}
@article {pmid37731274,
year = {2023},
author = {Kazemi, A and Racil, G and Ahmadi Hekmatikar, AH and Behnam Moghadam, M and Karami, P and Henselmans, M},
title = {Improved physical performance of elite soccer players based on GPS results after 4 days of carbohydrate loading followed by 3 days of low carbohydrate diet.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {20},
number = {1},
pages = {2258837},
pmid = {37731274},
issn = {1550-2783},
mesh = {Adult ; Humans ; *Diet, Carbohydrate Loading ; Geographic Information Systems ; *Soccer ; Diet, Carbohydrate-Restricted ; Physical Functional Performance ; Carbohydrates ; },
abstract = {BACKGROUND: Carbohydrate loading is an established sports nutrition strategy for endur- 16 ance exercise performance. We tested if carbohydrate loading could improve the performance of 17 elite soccer players under ecologically valid circumstances using Global Positioning System (GPS) data.<br><br>METHODS: Twenty-two adult Iran Premier league soccer players were divided into a carbohydrate-loading group (CLG) and Control group (CG). The carbohydrate loading group restricted carbohydrate intake for three days to 1.5&#x2009;g/kg/d while increasing exercise intensity. From days four to seven, exercise intensity was decreased and carbohydrate intake was considerably increased up to 7.5&#x2009;g/kg/d on the day of the match, during which performance was analyzed using GPS data. The control group performed the same exercise training but maintained their habitual carbohydrate intake of 5-6&#x2009;g/kg/d. The data were analyzed using a univariate ANCOVA with baseline data from a pre-intervention match as the control variable.<br><br>RESULTS: The carbohydrate loading team scored significantly higher on running distance, maximum speed and the number of top and repeated sprints; the carbohydrate loading group scored significantly lower on player load, metabolic power and running imbalance compared to the control team during their match.<br><br>CONCLUSIONS: Our findings suggest carbohydrate loading enabled elite soccer players to achieve greater running outputs with greater metabolic efficiency and lower fatigue compared to their habitual diets.},
}
@article {pmid37725327,
year = {2023},
author = {Liao, PJ and Lee, CH and Wang, SL and Chiou, HY and Chen, CJ and Seak, CJ and Wu, IW and Hsu, KH},
title = {Low-to-Moderate Arsenic Exposure and Urothelial Tract Cancers with a Long Latent Period of Follow-Up in an Arseniasis Area.},
journal = {Journal of epidemiology and global health},
volume = {13},
number = {4},
pages = {807-815},
pmid = {37725327},
issn = {2210-6014},
support = {110-2410-H-182-013-MY3//Ministry of Science and Technology, Taiwan/ ; EMRPD1L0401//Health Aging Research Center of Chang Gung University/ ; EMRPD1L0451//Health Aging Research Center of Chang Gung University/ ; CMRPD3L0021//Chang Gung Medical Foundation/ ; CMRPD3L0022//Chang Gung Medical Foundation/ ; CMRPD1M0281//Chang Gung Medical Foundation/ ; CMRPD1M0281, CMRPD1M0282//Chang Gung Medical Foundation/ ; WJY 2020-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; WJY 2021-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; WJY 2022-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; },
mesh = {Humans ; *Arsenic/toxicity ; Follow-Up Studies ; *Urinary Bladder Neoplasms/chemically induced/epidemiology ; *Arsenicals/adverse effects ; Water ; },
abstract = {BACKGROUND: Arsenic exposure can cause adverse health effects. The effects of long-term low-to-moderate exposure and methylations remain unclear.<br><br>OBJECTIVE: This study aims to examine the association between low-to-moderate arsenic exposure and urothelial tract cancers while considering the effects of methylation capacity.<br><br>METHODS: In this study, 5,811 participants were recruited from an arseniasis area in Taiwan for inorganic arsenic metabolite analysis. This follow-up study was conducted between August 1995 and&#xa0;December 2017. We identified 85 urothelial tract cancers in these participants, including 49 bladder and 36 upper urothelial tract cancer cases. A Cox proportional hazards model was employed.<br><br>RESULTS: The analyses revealed a significant association between concentrations of inorganic arsenic in water&#x2009;>&#x2009;100 ug/L and bladder cancer occurrence, with a hazard ratio (HR) of 4.88 (95% CI 1.35-17.61). A monotonic trend was observed between concentrations of inorganic arsenic in water (from 0 to&#x2009;>&#x2009;100 ug/L) and the incidence of urothelial tract cancer, including bladder cancer (p&#x2009;<&#x2009;0.05) and upper urothelial tract cancers (p&#x2009;<&#x2009;0.05). Participants with a lower primary methylation index or higher secondary methylation index had a prominent effect.<br><br>CONCLUSIONS: Rigorous regulations and active interventions should be considered for populations with susceptible characteristics.},
}
@article {pmid37721104,
year = {2023},
author = {Lu, YR and Fang, CC and He, SP},
title = {cnfishbase: A cyber Chinese fish database.},
journal = {Zoological research},
volume = {44},
number = {5},
pages = {950-953},
pmid = {37721104},
issn = {2095-8137},
mesh = {Animals ; *Databases, Factual ; *Fishes ; Internet ; },
}
@article {pmid37718603,
year = {2023},
author = {Hoyer, D and Bennett, JS and Reddish, J and Holder, S and Howard, R and Benam, M and Levine, J and Ludlow, F and Feinman, G and Turchin, P},
title = {Navigating polycrisis: long-run socio-cultural factors shape response to changing climate.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {378},
number = {1889},
pages = {20220402},
pmid = {37718603},
issn = {1471-2970},
mesh = {Humans ; *Climate Change ; Databases, Factual ; *Floods ; Head ; Social Interaction ; },
abstract = {Climate variability and natural hazards like floods and earthquakes can act as environmental shocks or socioecological stressors leading to instability and suffering throughout human history. Yet, societies experience a wide range of outcomes when facing such challenges: some suffer from social unrest, civil violence or complete collapse; others prove more resilient and maintain key social functions. We currently lack a clear, generally agreed-upon conceptual framework and evidentiary base to explore what causes these divergent outcomes. Here, we discuss efforts to develop such a framework through the Crisis Database (CrisisDB) programme. We illustrate that the impact of environmental stressors is mediated through extant cultural, political and economic structures that evolve over extended timescales (decades to centuries). These structures can generate high resilience to major shocks, facilitate positive adaptation, or, alternatively, undermine collective action and lead to unrest, violence and even societal collapse. By exposing the ways that different societies have reacted to crises over their lifetime, this framework can help identify the factors and complex social-ecological interactions that either bolster or undermine resilience to contemporary climate shocks. This article is part of the theme issue 'Climate change adaptation needs a science of culture'.},
}
@article {pmid37714749,
year = {2023},
author = {Reid, MC and Mittler, JE and Murphy, JT and Stansfield, SE and Goodreau, SM and Abernethy, N and Herbeck, JT},
title = {Evolution of HIV virulence in response to disease-modifying vaccines: A modeling study.},
journal = {Vaccine},
volume = {41},
number = {43},
pages = {6461-6469},
pmid = {37714749},
issn = {1873-2518},
support = {P2C HD042828/HD/NICHD NIH HHS/United States ; R01 AI108490/AI/NIAID NIH HHS/United States ; R01 GM125440/GM/NIGMS NIH HHS/United States ; },
mesh = {Male ; Humans ; Virulence ; Homosexuality, Male ; *HIV-1/genetics ; *HIV Infections/prevention &amp; control/epidemiology ; *Sexual and Gender Minorities ; *AIDS Vaccines ; },
abstract = {Pathogens face a tradeoff with respect to virulence; while more virulent strains often have higher per-contact transmission rates, they are also more likely to kill their hosts earlier. Because virulence is a heritable trait, there is concern that a disease-modifying vaccine, which reduces the disease severity of an infected vaccinee without changing the underlying pathogen genotype, may result in the evolution of higher pathogen virulence. We explored the potential for such virulence evolution with a disease-modifying HIV-1 vaccine in an agent-based stochastic epidemic model of HIV in United States men who have sex with men (MSM). In the model, vaccinated agents received no protection against infection, but experienced lower viral loads and slower disease progression. We compared the genotypic set point viral load (SPVL), a measure of HIV virulence, in populations given vaccines that varied in the degree of SPVL reduction they induce. Sensitivity analyses were conducted under varying vaccine coverage scenarios. With continual vaccination rollout under ideal circumstances of 90 % coverage over thirty years, the genotypic SPVL of vaccinated individuals evolved to become greater than the genotypic SPVL of unvaccinated individuals. This virulence evolution in turn diminished the public health benefit of the vaccine, and in some scenarios resulted in an accelerated epidemic. These findings demonstrate the complexity of viral evolution and have important implications for the design and development of HIV vaccines.},
}
@article {pmid37711328,
year = {2023},
author = {Faria, AL and Latorre, J and Silva Cameirão, M and Bermúdez I Badia, S and Llorens, R},
title = {Ecologically valid virtual reality-based technologies for assessment and rehabilitation of acquired brain injury: a systematic review.},
journal = {Frontiers in psychology},
volume = {14},
number = {},
pages = {1233346},
pmid = {37711328},
issn = {1664-1078},
abstract = {PURPOSE: A systematic review was conducted to examine the state of the literature regarding using ecologically valid virtual environments and related technologies to assess and rehabilitate people with Acquired Brain Injury (ABI).<br><br>MATERIALS AND METHODS: A literature search was performed following the PRISMA guidelines using PubMed, Web of Science, ACM and IEEE databases. The focus was on assessment and intervention studies using ecologically valid virtual environments (VE). All studies were included if they involved individuals with ABI and simulated environments of the real world or Activities of Daily Living (ADL).<br><br>RESULTS: Seventy out of 363 studies were included in this review and grouped and analyzed according to the nature of its simulation, prefacing a total of 12 kitchens, 11 supermarkets, 10 shopping malls, 16 streets, 11 cities, and 10 other everyday life scenarios. These VE were mostly presented on computer screens, HMD's and laptops and patients interacted with them primarily via mouse, keyboard, and joystick. Twenty-five out of 70 studies had a non-experimental design.<br><br>CONCLUSION: Evidence about the clinical impact of ecologically valid VE is still modest, and further research with more extensive samples is needed. It is important to standardize neuropsychological and motor outcome measures to strengthen conclusions between studies.<br><br>identifier CRD42022301560, https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=301560.},
}
@article {pmid37709808,
year = {2023},
author = {Cosentino, F and Castiello, G and Maiorano, L},
title = {A dataset on African bats' functional traits.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {623},
pmid = {37709808},
issn = {2052-4463},
support = {AR12117A5D86252A//Sapienza Universit&#xe0; di Roma (Sapienza University of Rome)/ ; },
mesh = {Animals ; *Chiroptera ; Databases, Factual ; Machine Learning ; Nutritional Status ; },
abstract = {Trait-based approaches are becoming extremely common in ecological modeling and the availability of traits databases is increasing. However, data availability is often biased towards particular regions and taxa, with many taxa (e.g., bats) often under-represented. Here, we present the AfroBaT dataset, a compilation of trait data on 320 African bat species containing 76,914 values for 86 traits focusing on morphology, reproduction, life-history, trophic ecology, and species distributions. All data were gathered from published literature following the ecological trait-data standard procedure. Missing data for both numerical and categorical traits were imputed with a machine learning approach including species phylogeny. Trophic ecology traits showed the highest coverage in the literature (72% of the species averaged over all traits), while reproductive traits the lowest. Our data imputation improved the coverage of AfroBaT especially for reproductive traits, going from 27% to 58% of the species covered. AfroBaT has a range of potential applications in macroecology and community ecology, and the availability of open-access data on African bats will enable collaboration and data-sharing among researchers.},
}
@article {pmid37707483,
year = {2024},
author = {Guevara Beltran, D and Shiota, MN and Aktipis, A},
title = {Empathic concern motivates willingness to help in the absence of interdependence.},
journal = {Emotion (Washington, D.C.)},
volume = {24},
number = {3},
pages = {628-647},
doi = {10.1037/emo0001288},
pmid = {37707483},
issn = {1931-1516},
support = {//ASU; President's Office; Interdisciplinary Cooperation Initiative/ ; //Cooperation Science Network/ ; //Charles Koch Foundation/ ; //John Templeton Foundation/ ; },
mesh = {Humans ; *Empathy ; *Friends ; Motivation ; Data Management ; },
abstract = {Previous research suggests that empathic concern selectively promotes motivation to help those with whom we typically have interdependent relationships, such as friends or siblings, rather than strangers or acquaintances. In a sample of U.S. participants (collected between 2018 and 2020), our studies not only confirmed the finding that empathic concern is directed somewhat more strongly toward interdependent relationship partners, but also showed cross-sectionally (Studies 1a-1b), and when manipulating target distress experimentally (Study 2), that empathic concern predicts higher willingness to help only when people perceive low interdependence in their relationship with the target. In Study 3, we manipulated perceived interdependence with an acquaintance via shared fate, and found that empathic concern only predicted helping motivation when we reduced shared fate, but not when we increased shared fate. These results suggest that when people perceive high interdependence in their relationships, shared fate is the driving force behind their desire to help, whereas when people perceive low interdependence with someone in need, empathic concern motivates them to help. A relationship-building perspective on empathic concern provides avenues for testing additional moderators, including those related to target-specific characteristics and culture and ecology. (PsycInfo Database Record (c) 2024 APA, all rights reserved).},
}
@article {pmid37705614,
year = {2023},
author = {Mora-Rubio, A and Bravo-Ortíz, MA and Quiñones Arredondo, S and Saborit Torres, JM and Ruz, GA and Tabares-Soto, R},
title = {Classification of Alzheimer's disease stages from magnetic resonance images using deep learning.},
journal = {PeerJ. Computer science},
volume = {9},
number = {},
pages = {e1490},
pmid = {37705614},
issn = {2376-5992},
support = {P30 AG066444/AG/NIA NIH HHS/United States ; R01 AG043434/AG/NIA NIH HHS/United States ; U01 AG024904/AG/NIA NIH HHS/United States ; P01 AG003991/AG/NIA NIH HHS/United States ; P01 AG026276/AG/NIA NIH HHS/United States ; R01 EB009352/EB/NIBIB NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; },
abstract = {Alzheimer's disease (AD) is a progressive type of dementia characterized by loss of memory and other cognitive abilities, including speech. Since AD is a progressive disease, detection in the early stages is essential for the appropriate care of the patient throughout its development, going from asymptomatic to a stage known as mild cognitive impairment (MCI), and then progressing to dementia and severe dementia; is worth mentioning that everyone suffers from cognitive impairment to some degree as we age, but the relevant task here is to identify which people are most likely to develop AD. Along with cognitive tests, evaluation of the brain morphology is the primary tool for AD diagnosis, where atrophy and loss of volume of the frontotemporal lobe are common features in patients who suffer from the disease. Regarding medical imaging techniques, magnetic resonance imaging (MRI) scans are one of the methods used by specialists to assess brain morphology. Recently, with the rise of deep learning (DL) and its successful implementation in medical imaging applications, it is of growing interest in the research community to develop computer-aided diagnosis systems that can help physicians to detect this disease, especially in the early stages where macroscopic changes are not so easily identified. This article presents a DL-based approach to classifying MRI scans in the different stages of AD, using a curated set of images from Alzheimer's Disease Neuroimaging Initiative and Open Access Series of Imaging Studies databases. Our methodology involves image pre-processing using FreeSurfer, spatial data-augmentation operations, such as rotation, flip, and random zoom during training, and state-of-the-art 3D convolutional neural networks such as EfficientNet, DenseNet, and a custom siamese network, as well as the relatively new approach of vision transformer architecture. With this approach, the best detection percentage among all four architectures was around 89% for AD vs. Control, 80% for Late MCI vs. Control, 66% for MCI vs. Control, and 67% for Early MCI vs. Control.},
}
@article {pmid37701708,
year = {2023},
author = {Paudel, S and Mueller, K and Ovando-Montejo, G and Tango, L and Rushforth, R and Lant, C},
title = {A dataset cataloging product-specific human appropriation of net primary production (HANPP) in US counties.},
journal = {Data in brief},
volume = {50},
number = {},
pages = {109530},
pmid = {37701708},
issn = {2352-3409},
abstract = {This paper describes the dataset associated with the paper "Product-Specific Human Appropriation of Net Primary Production (HANPP) in US Counties" (Paudel et al., 2023). This dataset comprises human appropriation of net primary production (HANPP) values for 3101 counties in the conterminous US for the years 1997, 2002, 2007, and 2012. For this dataset, HANPP is the carbon content of specific crop, timber, and livestock grazing products appropriated by humans in a county in a year. To calculate HANPP, raw agricultural data were downloaded from public databases such as USDA-National Agricultural Statistics Service Quick Stats and Cropland Data Layer, US Forest Service Timber Product Output, and NPP data from MODIS. These data were processed in Microsoft Excel using stoichiometry derived from established scientific literature. HANPP was partitioned by year, county, product, used and unused and above- and below-ground. This complete dataset is published in Mendeley Data and the methods used to compile them are included to make our research well documented, reproducible, and useful for future studies.},
}
@article {pmid37700122,
year = {2023},
author = {Yang, L and Wu, S and Li, G and Yuan, Y},
title = {Explore public concerns about environmental protection on Sina Weibo: evidence from text mining.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {47},
pages = {104067-104085},
pmid = {37700122},
issn = {1614-7499},
mesh = {Male ; Humans ; Female ; *COVID-19 ; Conservation of Natural Resources ; Data Mining ; *Social Media ; Environmental Pollution ; China ; },
abstract = {The increasingly serious problem of ecological environmental pollution warns the importance of human environmental protection behavior. However, public attention to environmental protection plays an important role in solving environmental problems. Therefore, in order to explore the environmental concerns of Chinese residents, the trends in time and space, the relationship between online retweets, and the extraction of environmental concerns, this study analyzed the data of Sina Weibo users and their comments on related posts. At the same time, we used the text mining analysis method to analyze the social media text data, and the results are as follows. In that analysis of concern about environmental protection, women show a stronger attitude and willingness to protect the environment than men, and the public in economically developed areas is more concerned. In order to further investigate the public's environmental concerns, this study also utilized the PageRank algorithm to further study the forwarding relationships between users. The study found that celebrities and some good media organizations can attract environmental attention. Finally, we use pyLDAvis technology to visualize and analyze popular environmental themes and propose reasonable countermeasures and suggestions to enhance public environmental awareness based on the research results.},
}
@article {pmid37699986,
year = {2023},
author = {Sharaf, A and Ndiribe, CC and Omotoriogun, TC and Abueg, L and Badaoui, B and Badiane Markey, FJ and Beedessee, G and Diouf, D and Duru, VC and Ebuzome, C and Eziuzor, SC and Jaufeerally Fakim, Y and Formenti, G and Ghanmi, N and Guerfali, FZ and Houaga, I and Ideozu, JE and Katee, SM and Khayi, S and Kuja, JO and Kwon-Ndung, EH and Marks, RA and Moila, AM and Mungloo-Dilmohamud, Z and Muzemil, S and Nigussie, H and Osuji, JO and Ras, V and Tchiechoua, YH and Zoclanclounon, YAB and Tolley, KA and Ziyomo, C and Mapholi, N and Muigai, AWT and Djikeng, A and Ebenezer, TE},
title = {Bridging the gap in African biodiversity genomics and bioinformatics.},
journal = {Nature biotechnology},
volume = {41},
number = {9},
pages = {1348-1354},
pmid = {37699986},
issn = {1546-1696},
mesh = {*Computational Biology ; *Genomics ; },
}
@article {pmid37697042,
year = {2023},
author = {Mullowney, MW and Duncan, KR and Elsayed, SS and Garg, N and van der Hooft, JJJ and Martin, NI and Meijer, D and Terlouw, BR and Biermann, F and Blin, K and Durairaj, J and Gorostiola González, M and Helfrich, EJN and Huber, F and Leopold-Messer, S and Rajan, K and de Rond, T and van Santen, JA and Sorokina, M and Balunas, MJ and Beniddir, MA and van Bergeijk, DA and Carroll, LM and Clark, CM and Clevert, DA and Dejong, CA and Du, C and Ferrinho, S and Grisoni, F and Hofstetter, A and Jespers, W and Kalinina, OV and Kautsar, SA and Kim, H and Leao, TF and Masschelein, J and Rees, ER and Reher, R and Reker, D and Schwaller, P and Segler, M and Skinnider, MA and Walker, AS and Willighagen, EL and Zdrazil, B and Ziemert, N and Goss, RJM and Guyomard, P and Volkamer, A and Gerwick, WH and Kim, HU and Müller, R and van Wezel, GP and van Westen, GJP and Hirsch, AKH and Linington, RG and Robinson, SL and Medema, MH},
title = {Artificial intelligence for natural product drug discovery.},
journal = {Nature reviews. Drug discovery},
volume = {22},
number = {11},
pages = {895-916},
pmid = {37697042},
issn = {1474-1784},
support = {P30 CA014236/CA/NCI NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; U24 AT010811/AT/NCCIH NIH HHS/United States ; },
mesh = {Humans ; *Artificial Intelligence ; Algorithms ; Machine Learning ; Drug Discovery ; Drug Design ; *Biological Products/pharmacology ; },
abstract = {Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.},
}
@article {pmid37697020,
year = {2023},
author = {Chen, L and Qin, L and Zhang, Y and Xu, H and Bu, Y and Wu, R and Liu, H and Hao, Q and Hu, H and Zhou, Y and Feng, J and Jing, Y and Han, J and Wang, X},
title = {Insights from multi-omics integration into seed germination of Taxus chinensis var mairei.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {931},
pmid = {37697020},
issn = {2399-3642},
mesh = {*Taxus/genetics ; Germination ; Multiomics ; Seeds ; Cycadopsida ; },
abstract = {The transition from deep dormancy to seed germination is essential for the life cycle of plants, but how this process occurs in the gymnosperm Chinese yew (Taxus chinensis var mairei), the natural source of the anticancer drug paclitaxel, remains unclear. Herein, we analyse the transcriptome, proteome, spatial metabolome, and spatial lipidome of the Chinese yew and present the multi-omics profiles of dormant and germinating seeds. Our results show that abscisic acid and gibberellic acid 12 homoeostasis is closely associated with gene transcription and protein translation, and the balance between these phytohormones thereby determines if seeds remain dormant or germinate. We find that an energy supply of carbohydrates from glycolysis and the TCA cycle feed into the pentose phosphate pathway during seed germination, and energy supplied from lipids are mainly derived from the lipolysis of triacylglycerols. Using mass spectrometry imaging, we demonstrate that the spatial distribution of plant hormones and phospholipids has a remarkable influence on embryo development. We also provide an atlas of the spatial distribution of paclitaxel C in Chinese yew seeds for the first time. The data from this study enable exploration of the germination mechanism of Chinese yew seeds across several omics levels.},
}
@article {pmid37694423,
year = {2023},
author = {Jiang, BY and Zhang, YL and Li, S and Li, JJ and Zheng, ZH and Wang, HG},
title = {Spatio-temporal dynamics and sensitive distance of nighttime light environment in Pearl River Delta Protected Areas, China.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {34},
number = {6},
pages = {1601-1609},
doi = {10.13287/j.1001-9332.202306.020},
pmid = {37694423},
issn = {1001-9332},
mesh = {Humans ; *Rivers ; China ; *Big Data ; Light ; },
abstract = {Protected areas (PAs) are important barriers to ensure the ecological security of territory. Light pollution is a threat to PAs, which is particularly obvious in the urban agglomeration environment. We used multi-source big data (satellite remote sensing light data, land cover types and points of interest) to quantitatively analyze the temporal and spatial dynamics of nighttime light in the PAs of the Pearl River Delta (PRD) urban agglomeration from 2000 to 2018, the correlation between the night light environment within the PAs and human activity intensity outside, as well as the sensitive distance of the PAs to artificial light interference. The results showed that the total value of nighttime light data of PAs in the PRD increased from 71107 nanoW·cm[-2]·sr[-1] to 127682 nanoW·cm[-2]·sr[-1] from 2000 to 2018, the mean value per pixel increased from 15.3 nanoW·cm[-2]·sr[-1] to 23.7 nanoW·cm[-2]·sr[-1], and the lighted ratio increased from 73.3% to 86.4%, indicating that the nighttime light environment of PAs in the region were facing cumulative deterioration risks and serious challenges. The nighttime light intensity of the PAs in the core area of the PRD was much higher than that in the peripheral areas such as Zhaoqing and Huizhou, whereas the expansion degree of the PAs in the peripheral areas was higher than that in the core area. The nighttime light environment inside the PAs was positively correlated with the intensity of human activities around it. The most sensitive distance of the PAs to the artificial light interference around it was 10 km, and the interference degree tended to be stable after 30 km. We proposed that 0-10 km area outside the boundary of the PAs should be the light control core zone and 10-20 km area as the control buffer zone.},
}
@article {pmid37693498,
year = {2023},
author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Nordgren, CE and Lampson, M and Levine, M and Searle, JB and Good, JM},
title = {The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37693498},
issn = {2692-8205},
support = {R01 HD094787/HD/NICHD NIH HHS/United States ; S10 OD016290/OD/NIH HHS/United States ; },
abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.},
}
@article {pmid37692385,
year = {2023},
author = {Fan, R and Liu, Y and Bin, Y and Huang, J and Yi, B and Tang, X and Li, Y and Cai, Y and Yang, Z and Yang, M and Song, J and Pan, Q and Liu, Z and Ghani, MI and Hu, X and Chen, X},
title = {Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1222844},
pmid = {37692385},
issn = {1664-302X},
abstract = {Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.},
}
@article {pmid37688324,
year = {2023},
author = {Zhao, D and Zhang, Y and Ren, H and Shi, Y and Dong, D and Li, Z and Cui, G and Shen, Y and Mou, Z and Kennelly, EJ and Huang, L and Ruan, J and Chen, S and Yu, D and Cun, Y},
title = {Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum.},
journal = {Journal of integrative plant biology},
volume = {65},
number = {10},
pages = {2320-2335},
doi = {10.1111/jipb.13565},
pmid = {37688324},
issn = {1744-7909},
support = {31960082//National Natural Science Foundation of China/ ; 32270395//National Natural Science Foundation of China/ ; and 31960096//National Natural Science Foundation of China/ ; },
mesh = {*Aconitum/genetics/metabolism ; Multiomics ; *Diterpenes/metabolism ; *Alkaloids/metabolism ; Transcriptome/genetics ; Plant Roots ; },
abstract = {Diterpenoid alkaloids (DAs) have been often utilized in clinical practice due to their analgesic and anti-inflammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains unknown. In this study, we successfully assembled a high-quality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum (A. vilmorinianum) (5.76 Gb). An A. vilmorinianum-specific whole-genome duplication event was discovered using comparative genomic analysis, which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in A. vilmorinianum as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs.},
}
@article {pmid37685932,
year = {2023},
author = {Milicevic, O and Loncar, A and Abazovic, D and Vukcevic, M and Despot, D and Djukic, T and Djukic, V and Milovanovic, A and Panic, N and Plecic, N and Banko, A},
title = {Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization.},
journal = {International journal of molecular sciences},
volume = {24},
number = {17},
pages = {},
pmid = {37685932},
issn = {1422-0067},
mesh = {Humans ; *SARS-CoV-2/genetics ; Transcriptome ; *COVID-19/genetics ; Gene Expression Profiling ; Computational Biology ; },
abstract = {Previous transcriptome profiling studies showed significantly upregulated genes and altered biological pathways in acute COVID-19. However, changes in the transcriptional signatures during a defined time frame are not yet examined and described. The aims of this study included viral metagenomics and evaluation of the total expression in time-matched and tissue-matched paired COVID-19 samples with the analysis of the host splicing profile to reveal potential therapeutic targets. Prospective analysis of paired nasopharyngeal swabs (NPS) and blood (BL) samples from 18 COVID-19 patients with acute and resolved infection performed using Kallisto, Suppa2, Centrifuge, EdgeR, PantherDB, and L1000CDS2 tools. In NPS, we discovered 6 genes with changed splicing and 40 differentially expressed genes (DEG) that yielded 88 altered pathways. Blood samples yielded 15 alternatively spliced genes. Although the unpaired DEG analysis failed, pairing identified 78 genes and 242 altered pathways with meaningful clinical interpretation and new candidate drug combinations with up to 65% overlap. Metagenomics analyses showed SARS-CoV-2 dominance during and after the acute infection, with a significant reduction in NPS (0.008 vs. 0.002, p = 0.019). Even though both NPS and BL give meaningful insights into expression changes, this is the first demonstration of how the power of blood analysis is vastly maximized by pairing. The obtained results essentially showed that pairing is a determinant between a failed and a comprehensive study. Finally, the bioinformatics results prove to be a comprehensive tool for full-action insights, drug development, and infectious disease research when designed properly.},
}
@article {pmid37683992,
year = {2023},
author = {Sukur, N and Milošević, N and Pogrmic-Majkic, K and Stanic, B and Andric, N},
title = {Predicting chemicals' toxicity pathway of female reproductive disorders using AOP7 and deep neural networks.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {180},
number = {},
pages = {114013},
doi = {10.1016/j.fct.2023.114013},
pmid = {37683992},
issn = {1873-6351},
abstract = {Experimental evidence shows that certain chemicals, particularly endocrine disrupting chemicals, may negatively affect the female reproductive system, thereby lowering women's fertility. However, humans are constantly exposed to a number of different chemicals with limited or no experimental data regarding their effect and the mechanism of action in the female reproductive system. To predict chemical hazards to the female reproductive system, we used a previously defined adverse outcome pathway (AOP) that links activation of the peroxisome proliferator-activated receptor γ to the reproductive toxicity in adult females (AOP7) and the Convolutional Deep Neural Network models that produce meaningful predictions when trained on a significant amount of data. The models trained using CompTox assays with intended molecular and biological targets corresponding to AOP7 achieved high performance (over 90% validation accuracy). The integration of AOP7 and Deep Neural Network identified chemicals that could negatively affect female reproduction through the mechanism described in AOP7. We provide a solution to quickly analyze the data and produce machine learning models to identify potentially active chemicals in the female reproductive system. Although we focused on the female reproductive system, this approach could be valid for a number of other chemicals and AOPs if the right data exist.},
}
@article {pmid37681394,
year = {2023},
author = {Xie, X and Wu, TC and Cao, BL and Li, JZ and Xue, B},
title = {Virtual ecological technology: Concepts, systems, and application perspectives.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {34},
number = {8},
pages = {2297-2304},
doi = {10.13287/j.1001-9332.202308.022},
pmid = {37681394},
issn = {1001-9332},
mesh = {Humans ; *Ecosystem ; *Air Pollution ; Environment ; Geography ; Sustainable Development ; },
abstract = {Virtual ecological technology is a new technology that builds the foundation of a digital ecological system, simulates the process of ecological evolution, and establishes a global knowledge analysis system based on a unified spatio-temporal benchmark. It is a new direction for the interdisciplinary integration and development of eco-logy, geographic information science, computer science and other subjects towards modernization, informatization, and intelligence. Research, development, and application of virtual ecological technology is of great significance for the development of ecology as a discipline, ecosystem management, and regional sustainable development. Curren-tly, research on virtual ecological technology is still in its infancy and lacks a complete and clearly defined framework, making it difficult to support systematic iterative development and scientific analysis. In this paper, starting from the main theories and objectives of modern ecology, we summarized the main contents and technical requirements of virtual ecological construction, and proposed a key technical system of virtual ecology that integrated vir-tual geography and digital twin technology. From the perspective of application scenarios, we analyzed the application capabilities of virtual ecological technology in air pollution and energy analysis. Finally, we summarized the deve-lopment potential of virtual ecological technology in the digital construction of the ecological environment, intelligent computing, and realistic expression of different levels of ecological space resources transformation under the background of new generation of information technology, both at the local computing point breakthrough and the global technology point fusion aspects. This would enrich and advance the technical capabilities that support China's ecological space resource transformation.},
}
@article {pmid37680963,
year = {2023},
author = {Tóth, F and Zsuga, K and Kerepeczki, &#xc9; and Kovács, B and Magura, T and Körmöczi, L and Lövei, GL},
title = {Discordant spatiotemporal dynamics of functional and phylogenetic diversity of rotiferan communities exposed to aquaculture effluent.},
journal = {Ecology and evolution},
volume = {13},
number = {9},
pages = {e10503},
pmid = {37680963},
issn = {2045-7758},
abstract = {The growth of the human population brought about the global intensification of aquacultural production, and aquaculture became the fastest growing animal husbandry sector. Effluent from aquaculture is an anthropogenic environmental burden, containing organic matter, nutrients and suspended solids that affect water quality especially in the water bodies of high biodiversity and conservation value. Water quality assessment often relies on bioindicators, analysing changes in taxonomic diversity of various freshwater organismal groups. Stepping beyond taxon diversity, we used functional and phylogenetic diversities of rotifers to identify factors affecting their community organization in response to an aquaculture effluent gradient in the largest oxbow lake in the Carpathian Basin, Hungary. Sampling was carried out three times per season at five points along a 3.5 km section of the oxbow lake, including the point of effluent inflow. We used eight traits to evaluate functional diversity: body size, trophi type, feeding mode, protection type, body wall type, corona type, habitat preference and tolerance level. Functional and phylogenetic distances among the 24 species identified indicated trait conservatism. Rotiferan diversity increased with increasing distance from the point of influx in spring and summer. Among the factors affecting community organization in spring and summer, we find examples of environmental filtering, while in autumn the role of biotic interaction is more frequent. Under nutrient-rich conditions in spring and summer, organisms belonging to the same functional group were dominant, whereas under oligotrophic conditions, more diverse but less abundant groups were present. Considering functional and phylogenetic traits allowed us to identify organising forces of rotifer communities in the largest oxbow lake of the Hungarian Lowland.},
}
@article {pmid37680030,
year = {2023},
author = {Moran, ME and Aparecido, LMT and Koepke, DF and Cooper, HF and Doughty, CE and Gehring, CA and Throop, HL and Whitham, TG and Allan, GJ and Hultine, KR},
title = {Limits of thermal and hydrological tolerance in a foundation tree species (Populus fremontii) in the desert southwestern United States.},
journal = {The New phytologist},
volume = {240},
number = {6},
pages = {2298-2311},
doi = {10.1111/nph.19247},
pmid = {37680030},
issn = {1469-8137},
support = {DEB-1340852//National Science Foundation/ ; DEB-1340856//National Science Foundation/ ; DEB-2017895//National Science Foundation/ ; },
mesh = {*Trees/physiology ; *Populus/physiology ; Plant Leaves/physiology ; Southwestern United States ; Temperature ; },
abstract = {Populus fremontii is among the most dominant, and ecologically important riparian tree species in the western United States and can thrive in hyper-arid riparian corridors. Yet, P. fremontii forests have rapidly declined over the last decade, particularly in places where temperatures sometimes exceed 50°C. We evaluated high temperature tolerance of leaf metabolism, leaf thermoregulation, and leaf hydraulic function in eight P. fremontii populations spanning a 5.3°C mean annual temperature gradient in a well-watered common garden, and at source locations throughout the lower Colorado River Basin. Two major results emerged. First, despite having an exceptionally high Tcrit (the temperature at which Photosystem II is disrupted) relative to other tree taxa, recent heat waves exceeded Tcrit , requiring evaporative leaf cooling to maintain leaf-to-air thermal safety margins. Second, in midsummer, genotypes from the warmest locations maintained lower midday leaf temperatures, a higher midday stomatal conductance, and maintained turgor pressure at lower water potentials than genotypes from more temperate locations. Taken together, results suggest that under well-watered conditions, P. fremontii can regulate leaf temperature below Tcrit along the warm edge of its distribution. Nevertheless, reduced Colorado River flows threaten to lower water tables below levels needed for evaporative cooling during episodic heat waves.},
}
@article {pmid37678709,
year = {2023},
author = {Green Ii, DA},
title = {Tracking technologies: advances driving new insights into monarch migration.},
journal = {Current opinion in insect science},
volume = {60},
number = {},
pages = {101111},
doi = {10.1016/j.cois.2023.101111},
pmid = {37678709},
issn = {2214-5753},
mesh = {Humans ; Animals ; *Butterflies ; Animal Migration ; Ecology ; Seasons ; },
abstract = {Understanding the rules of how monarch butterflies complete their annual North American migration will be clarified by studying them within a movement ecology framework. Insect movement ecology is growing at a rapid pace due to the development of novel monitoring systems that allow ever-smaller animals to be tracked at higher spatiotemporal resolution for longer periods of time. New innovations in tracking hardware and associated software, including miniaturization, energy autonomy, data management, and wireless communication, are reducing the size and increasing the capability of next-generation tracking technologies, bringing the goal of tracking monarchs over their entire migration closer within reach. These tools are beginning to be leveraged to provide insight into different aspects of monarch biology and ecology, and to contribute to a growing capacity to understand insect movement ecology more broadly and its impact on human life.},
}
@article {pmid37674876,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Feathered Gothic, Tholera decimalis (Poda, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {200},
pmid = {37674876},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Tholera decimalis (the Feathered Gothic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,334.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,771 protein coding genes.},
}
@article {pmid37674686,
year = {2023},
author = {Asaaga, FA and Sriram, A and Chanda, MM and Hoti, SL and Young, JC and Purse, BV},
title = {'It doesn't happen how you think, it is very complex!' Reconciling stakeholder priorities, evidence, and processes for zoonoses prioritisation in India.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1228950},
pmid = {37674686},
issn = {2296-2565},
support = {MR/S012893/1/MRC_/Medical Research Council/United Kingdom ; MR/S012893/2/MRC_/Medical Research Council/United Kingdom ; MR/T029846/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Humans ; *Administrative Personnel ; *Cost of Illness ; Health Policy ; India ; Zoonoses/prevention &amp; control ; },
abstract = {BACKGROUND: Why do some zoonotic diseases receive priority from health policy decision-makers and planners whereas others receive little attention? By leveraging Shiffman and Smith's political prioritisation framework, our paper advances a political economy of disease prioritisation focusing on four key components: the strength of the actors involved in the prioritisation, the power of the ideas they use to portray the issue, the political contexts in which they operate, and the characteristics of the issue itself (e.g., overall burdens, severity, cost-effective interventions). These components afford a nuanced characterisation of how zoonotic diseases are prioritised for intervention and highlight the associated knowledge gaps affecting prioritisation outcomes. We apply this framework to the case of zoonoses management in India, specifically to identify the factors that shape disease prioritisation decision-making and outcomes.<br><br>METHODS: We conducted 26 semi-structured interviews with national, state and district level health policymakers, disease managers and technical experts involved in disease surveillance and control in India.<br><br>RESULTS: Our results show pluralistic interpretation of risks, exemplified by a disconnect between state and district level actors on priority diseases. The main factors identified as shaping prioritisation outcomes were related to the nature of the zoonoses problem (the complexity of the zoonotic disease, insufficient awareness and lack of evidence on disease burdens and impacts) as well as political, social, cultural and institutional environments (isolated departmental priorities, limited institutional authority, opaque funding mechanisms), and challenges in organisation leadership for cross-sectoral engagement.<br><br>CONCLUSION: The findings highlight a compartmentalised regulatory system for zoonoses where political, social, cultural, and media factors can influence disease management and prioritisation. A major policy window is the institutionalisation of One Health to increase the political priority for strengthening cross-sectoral engagement to address several challenges, including the creation of effective institutions to reconcile stakeholder priorities and prioritisation processes.},
}
@article {pmid37674040,
year = {2023},
author = {Lu, AT and Fei, Z and Haghani, A and Robeck, TR and Zoller, JA and Li, CZ and Lowe, R and Yan, Q and Zhang, J and Vu, H and Ablaeva, J and Acosta-Rodriguez, VA and Adams, DM and Almunia, J and Aloysius, A and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, GG and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, SM and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and DiRocco, S and Dold, C and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Gorbunova, V and Goya, RG and Grant, MJ and Green, CB and Hales, EN and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaitre, JF and Levine, AJ and Li, C and Li, X and Lim, AR and Lin, DTS and Lindemann, DM and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and O'Brien, JK and O'Tierney Ginn, P and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pellegrini, M and Peters, KJ and Pedersen, AB and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Seluanov, A and Shafer, ABA and Shanmuganayagam, D and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmaohammadi, E and Spangler, ML and Spriggs, MC and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Wallingford, MC and Wang, N and Wayne, RK and Wilkinson, GS and Williams, CK and Williams, RW and Yang, XW and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, P and Zhao, Y and Zhou, W and Zimmermann, J and Ernst, J and Raj, K and Horvath, S},
title = {Author Correction: Universal DNA methylation age across mammalian tissues.},
journal = {Nature aging},
volume = {3},
number = {11},
pages = {1462},
doi = {10.1038/s43587-023-00499-7},
pmid = {37674040},
issn = {2662-8465},
support = {P01 AG047200/AG/NIA NIH HHS/United States ; P01 AG051449/AG/NIA NIH HHS/United States ; R01 AG027237/AG/NIA NIH HHS/United States ; },
}
@article {pmid37673539,
year = {2023},
author = {Pinho-Gomes, AC and Roaf, E and Fuller, G and Fowler, D and Lewis, A and ApSimon, H and Noakes, C and Johnstone, P and Holgate, S},
title = {Air pollution and climate change.},
journal = {The Lancet. Planetary health},
volume = {7},
number = {9},
pages = {e727-e728},
doi = {10.1016/S2542-5196(23)00189-4},
pmid = {37673539},
issn = {2542-5196},
mesh = {*Climate Change ; *Air Pollution/adverse effects ; },
}
@article {pmid37673174,
year = {2024},
author = {Lei, T and Chang, Y and Yao, C and Zhang, H},
title = {A systematic evaluation of computational methods for predicting translated non-canonical ORFs from ribosome profiling data.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {51},
number = {1},
pages = {105-108},
doi = {10.1016/j.jgg.2023.08.010},
pmid = {37673174},
issn = {1673-8527},
mesh = {*Ribosome Profiling ; Open Reading Frames ; *Protein Biosynthesis ; Ribosomes/genetics/metabolism ; Computational Biology ; },
}
@article {pmid37670833,
year = {2023},
author = {Zhylkybekova, A and Turlayev, A and Grjibovski, AM and Koshmaganbetova, GK},
title = {Measures to support informal care for the older adults in Kazakhstan: a review of the current status.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1247684},
pmid = {37670833},
issn = {2296-2565},
mesh = {Child ; Humans ; Aged ; Kazakhstan ; *Quality of Life ; *Patient Care ; Long-Term Care ; Databases, Factual ; },
abstract = {The demand for informal caregivers to support the older adults has grown worldwide in recent decades. However, informal caregivers themselves require support. This article aims to examine existing support measures for caregivers of the older adults in the Republic of Kazakhstan. Relevant articles and grey literature were identified through manual searches on Google and Google Scholar, as well as electronic searches using indexed databases like PubMed, Web of Science, and Scopus. Moreover, the reference lists of identified sources and government ministry websites were meticulously scrutinized. This review highlights the scarcity of research on caregiver support measures in Kazakhstan, supported by the lack of peer-reviewed articles on this subject. A comprehensive analysis of the literature shows that in Kazakhstan's legislative framework, "caregivers" exclusively refers to individuals providing care for a first-degree disability. The responsibility of caring for older adults parents lies with able-bodied children. However, there is a lack of registration and assessment procedures to evaluate the burden and quality of life of caregivers. As a result, the medical and social support provided to caregivers is standardized, failing to adequately address their unique needs and requirements. The analysis of current support measures for informal caregivers highlights the need to develop support mechanisms and recognize individuals providing informal care as key figures in the long-term care system.},
}
@article {pmid37667004,
year = {2023},
author = {Li, Y and Niu, Z and Zhu, M and Wang, Z and Xu, R and Li, M and Zheng, Z and Lu, Z and Dong, C and Hu, H and Yang, Y and Wu, Y and Wang, D and Yang, J and Zhang, J and Wan, D and Abbott, R and Liu, J and Yang, Y},
title = {Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {906},
pmid = {37667004},
issn = {2399-3642},
mesh = {*Rheum/genetics ; Multiomics ; Acclimatization/genetics ; Comparative Genomic Hybridization ; Down-Regulation ; },
abstract = {Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.},
}
@article {pmid37665528,
year = {2023},
author = {Omang, BO and Omeka, ME and Asinya, EA and Oko, PE and Aluma, VC},
title = {Application of GIS and feedforward back-propagated ANN models for predicting the ecological and health risk of potentially toxic elements in soils in Northwestern Nigeria.},
journal = {Environmental geochemistry and health},
volume = {45},
number = {11},
pages = {8599-8631},
pmid = {37665528},
issn = {1573-2983},
mesh = {Child ; Humans ; *Metals, Heavy/analysis ; Soil ; Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Nigeria/epidemiology ; *Neoplasms ; Risk Assessment ; *Soil Pollutants/toxicity/analysis ; China ; },
abstract = {Potentially toxic elements (PTEs) occur naturally in most geologic materials. However, recent anthropogenic disturbances such as ore mining have contributed significantly to their enrichment in soils. Their occurrence in soil may portend a myriad of related risks to the environment and biota. Most traditional soil quality evaluation methods involve comparing the background values of the elements to the established guideline values, which is often time-consuming and fraught with computational errors. As a result, to conduct a comprehensive and unbiased evaluation of soil quality and its effects on the ecosystem and human health, this research combined geochemical, numerical, and GIS data for a composite health risk zonation of the entire study area. Furthermore, the multilayer perceptron artificial neural network (MLP-NN) was used to forecast the most important toxic components influencing soil quality. Geochemical, statistical, and quantitative soil pollution evaluation (pollution index and ecological risk index) showed that apart from mining, the spread and association of trace elements and oxides occur as a consequence of surface environmental conditions (e.g., leaching, weathering, and organo-metallic complexation). The hazard quotients (HQs) and hazard index (HI) of all PTEs were greater than one. This indicates that residents (particularly children) are more susceptible to risks from toxic element ingestion than dermal exposure and inhalation. Ingestion of As and Cr resulted in higher cancer risks and lifetime cancer risk levels (> 1.0E 04), with risk levels increasing toward the northeastern, western, and southeastern directions of the study area. The low modeling errors observed from the sum of square errors, relative errors, and coefficient of determination confirmed the efficiency of the MLP-NN in pollution load prediction. Based on the sensitivity analysis, Hg, Sr, Zn, Ba, As, and Zr showed the greatest influence on soil quality. Focus on remediation should therefore be placed on the removal of these elements from the soil.},
}
@article {pmid37665400,
year = {2023},
author = {Bayer, JM and Scully, RA and Dlabola, EK and Courtwright, JL and Hirsch, CL and Hockman-Wert, D and Miller, SW and Roper, BB and Saunders, WC and Snyder, MN},
title = {Sharing FAIR monitoring program data improves discoverability and reuse.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {10},
pages = {1141},
pmid = {37665400},
issn = {1573-2959},
mesh = {*Environmental Monitoring ; *Natural Resources ; },
abstract = {Data resulting from environmental monitoring programs are valuable assets for natural resource managers, decision-makers, and researchers. These data are often collected to inform specific reporting needs or decisions with a specific timeframe. While program-oriented data and related publications are effective for meeting program goals, sharing well-documented data and metadata allows users to research aspects outside initial program intentions. As part of an effort to integrate data from four long-term large-scale US aquatic monitoring programs, we evaluated the original datasets against the FAIR (Findable, Accessible, Interoperable, Reusable) data principles and offer recommendations and lessons learned. Differences in data governance across these programs resulted in considerable effort to access and reuse the original datasets. Requirements, guidance, and resources available to support data publishing and documentation are inconsistent across agencies and monitoring programs, resulting in various data formats and storage locations that are not easily found, accessed, or reused. Making monitoring data FAIR will reduce barriers to data discovery and reuse. Programs are continuously striving to improve data management, data products, and metadata; however, provision of related tools, consistent guidelines and standards, and more resources to do this work is needed. Given the value of these data and the significant effort required to access and reuse them, actions and steps intended on improving data documentation and accessibility are described.},
}
@article {pmid37663792,
year = {2023},
author = {Boyes, D and Sims, I and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Round-winged Muslin, Thumatha senex (Hübner, 1804).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {298},
pmid = {37663792},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Thumatha senex (the Round-winged Muslin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 810.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.},
}
@article {pmid37663789,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Light Brocade, Lacanobia w-latinum (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {299},
pmid = {37663789},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Lacanobia w-latinum (the Light Brocade; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 903.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,592 protein coding genes.},
}
@article {pmid37663407,
year = {2023},
author = {Günther, F and Wong, D and Elison-Davies, S and Yau, C},
title = {Identifying factors associated with user retention and outcomes of a digital intervention for substance use disorder: a retrospective analysis of real-world data.},
journal = {JAMIA open},
volume = {6},
number = {3},
pages = {ooad072},
pmid = {37663407},
issn = {2574-2531},
abstract = {OBJECTIVES: Successful delivery of digital health interventions is affected by multiple real-world factors. These factors may be identified in routinely collected, ecologically valid data from these interventions. We propose ideas for exploring these data, focusing on interventions targeting complex, comorbid conditions.<br><br>MATERIALS AND METHODS: This study retrospectively explores pre-post data collected between 2016 and 2019 from users of digital cognitive behavioral therapy (CBT)-containing psychoeducation and practical exercises-for substance use disorder (SUD) at UK addiction services. To identify factors associated with heterogenous user responses to the technology, we employed multivariable and multivariate regressions and random forest models of user-reported questionnaire data.<br><br>RESULTS: The dataset contained information from 14&#x200a;078 individuals of which 12&#x200a;529 reported complete data at baseline and 2925 did so again after engagement with the CBT. Ninety-three percent screened positive for dependence on 1 of 43 substances at baseline, and 73% screened positive for anxiety or depression. Despite pre-post improvements independent of user sociodemographics, women reported more frequent and persistent symptoms of SUD, anxiety, and depression. Retention-minimum 2 use events recorded-was associated more with deployment environment than user characteristics. Prediction accuracy of post-engagement outcomes was acceptable (Area Under Curve [AUC]: 0.74-0.79), depending non-trivially on user characteristics.<br><br>DISCUSSION: Traditionally, performance of digital health interventions is determined in controlled trials. Our analysis showcases multivariate models with which real-world data from these interventions can be explored and sources of user heterogeneity in retention and symptom reduction uncovered.<br><br>CONCLUSION: Real-world data from digital health interventions contain information on natural user-technology interactions which could enrich results from controlled trials.},
}
@article {pmid37660507,
year = {2023},
author = {Isoyama, K and Matsuura, M and Hayasaka, M and Nagao, S and Nishimura, Y and Yoshioka, T and Imai, Y and Miyagi, E and Suzuki, Y and Saito, T},
title = {Nationwide trends in and regional factors associated with minimally invasive hysterectomy for benign indications in Japan.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {289},
number = {},
pages = {129-135},
doi = {10.1016/j.ejogrb.2023.08.388},
pmid = {37660507},
issn = {1872-7654},
mesh = {Female ; Humans ; Japan/epidemiology ; Retrospective Studies ; *Laparoscopy ; Databases, Factual ; Hysterectomy ; },
abstract = {OBJECTIVE: To examine the prevalence trends of minimally invasive hysterectomy for benign indications in Japan and investigate regional disparities.<br><br>STUDY DESIGN: A retrospective cohort and ecological study using "The National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) Open Data".<br><br>SETTING: Nationwide Japan.<br><br>PATIENTS: Individuals who underwent hysterectomy for benign indications from 2014 to 2020.<br><br>INTERVENTIONS: Trend analysis of minimally invasive surgery (MIS) rates through laparoscopic hysterectomies (LH) and robotic-assisted laparoscopic hysterectomies (RA-LH) at the national and prefecture levels. Examination of regional factors contributing to the disparity in MIS implementation rates by second medical service area (SMSA).<br><br>RESULTS: The number of LH has increased from 16,016 in 2014 to 27,755 in 2020. The nationwide MIS hysterectomy rate increased from 29% in 2014 to 55% in 2020 (p&#xa0;less than&#xa0;0.001). More than 50% of hysterectomies have been performed as MIS since 2019. There was an increasing trend in MIS rates in all age groups. All prefectures except one showed a significant upward trend (p&#xa0;less than&#xa0;0.05) in the MIS rates, but MIS rates varied widely (23-84%). In a multivariable model, the MIS was more likely to be performed in the SMSAs in western Japan (p&#xa0;=&#xa0;0.011), in the SMSAs where the number of laparoscopy-qualified gynecologists is 5-10 (p&#xa0;=&#xa0;0.013), and 11 or higher (p&#xa0;less than&#xa0;0.001).<br><br>CONCLUSIONS: This study reveals a shift towards minimally invasive surgery (MIS) in total hysterectomy procedures in Japan. However, significant disparities in the prevalence of MIS hysterectomy exist, potentially influenced by the number of laparoscopy-qualified gynecologists.},
}
@article {pmid37659520,
year = {2023},
author = {Schulz, G and van Beusekom, JEE and Jacob, J and Bold, S and Schöl, A and Ankele, M and Sanders, T and Dähnke, K},
title = {Low discharge intensifies nitrogen retention in rivers - A case study in the Elbe River.},
journal = {The Science of the total environment},
volume = {904},
number = {},
pages = {166740},
doi = {10.1016/j.scitotenv.2023.166740},
pmid = {37659520},
issn = {1879-1026},
mesh = {*Rivers ; *Nitrates/analysis ; Ecosystem ; Environmental Monitoring/methods ; Nitrogen/analysis ; Eutrophication ; Harmful Algal Bloom ; Water ; },
abstract = {Eutrophication due to excessive nutrient inputs is a major threat to coastal ecosystems worldwide, causing harmful algae blooms, seagrass loss and hypoxia. Decisions to combat eutrophication in the North Sea were made in the 1980s. Despite significant improvements during recent decades, high nitrogen loads and resulting eutrophication problems remain. In this study, long-term changes in nitrogen inputs to the Elbe Estuary (Germany) were characterized based on nitrogen data provided by the Elbe River Basin Community from 1985 to 2019. Additionally, surface water samples were taken at the weir separating the river from the estuary from 2011 to 2021 to characterize dissolved inorganic nitrogen concentrations and nitrate stable isotope composition. The findings suggest a close coupling of river discharge with the riverine nitrogen cycle. Nitrogen loads decreased disproportionately with decreasing discharge. This decrease is due to intensified nitrogen retention in the Elbe catchment, which can double nitrogen retention compared to average discharge conditions. Phytoplankton growth was enhanced by long residence times and high light availability at low water levels. This suggests that the recent decreases in nitrogen loads in the Elbe River were not only a result of management measures in the catchment but were also amplified by a recent long-lasting drought in the catchment. Based on projections from the Intergovernmental Panel on Climate Change, more frequent and extensive droughts are anticipated, which may lead to future seasonal shifts to nitrate limitation in the lower Elbe River.},
}
@article {pmid37658362,
year = {2023},
author = {Bezerra, ALL and de Almeida, PRB and Reis, RK and Ferreira, GRON and Sousa, FJD and Gir, E and Botelho, EP},
title = {Human immunodeficiency virus epidemic scenery among brazilian women: a spatial analysis study.},
journal = {BMC women's health},
volume = {23},
number = {1},
pages = {463},
pmid = {37658362},
issn = {1472-6874},
mesh = {Humans ; Female ; Adolescent ; *HIV ; Brazil/epidemiology ; Spatial Analysis ; Databases, Factual ; *HIV Infections/epidemiology ; },
abstract = {BACKGROUND: Approximately 37.7 million people worldwide are infected with human immunodeficiency virus (HIV). Although HIV detection among women, they still representing 53% of population living with the virus. Spatial analysis techniques are powerful tools for combating HIV allowing the association of the phenomenon with socioeconomic and political factors. Therefore, the main goal of this study was to spatially analyze HIV prevalence among Brazilian women from 2007 to 2020.<br><br>METHODS: ecological study was conducted using secondary databases of the Notifiable Diseases Information System (SINAN) for HIV and Acquired Immunodeficiency Syndrom (AIDS) in Brazilian women 15 years old and over. Age-adjusted HIV/AIDS incidence rates were analyzed using spatial distribution, autocorrelation, and spatiotemporal risk analysis techniques.<br><br>RESULTS: During the study period, 119,890 cases of HIV/AIDS were reported among Brazilian women. The southeastern region had a higher age-adjusted HIV/AIDS incidence than other Brazilian regions. Hotspot HIV/AIDS incidence rates decreased in all Brazil. Piau&#xed;, Paran&#xe1;, and Minas Gerais were the only states with an increased number of cold spots. Previous spatiotemporal risk zones were observed in the states of S&#xe3;o Paulo, Rio Grande do Sul, and Rio de Janeiro. Bel&#xe9;m was a risk zone with a later spatiotemporal risk.<br><br>CONCLUSIONS: The efficiency of public policies fighting HIV has not been uniform among municipalities, although HIV/AIDS cases have decreased among Brazilian women. The social determinants of health in each municipality should be considered when local health authorities implement policies. Women empowerment should be promoted, and access to preventive, diagnostic, and treatment healthcare places should be expanded and guaranteed.},
}
@article {pmid37657322,
year = {2023},
author = {Jia, H and Zhao, Y and Deng, H and Yu, H and Ge, C and Li, J},
title = {Integrated microbiome and multi-omics analysis reveal the molecular mechanisms of Eisenia fetida in response to biochar-derived dissolved and particulate matters.},
journal = {Journal of hazardous materials},
volume = {460},
number = {},
pages = {132422},
doi = {10.1016/j.jhazmat.2023.132422},
pmid = {37657322},
issn = {1873-3336},
mesh = {Animals ; *Oligochaeta ; Multiomics ; *Microbiota ; Particulate Matter/toxicity ; Soil ; },
abstract = {At present, most ecotoxicological studies are still confined to focusing on the harmful effects of biochar itself on soil fauna. However, the potential ecotoxicity of different components separated from biochar to terrestrial invertebrates remains poorly understood. In this study, the dissolved matter (DM) and particulate matter (PM) were separated from biochar (BC) and then introduced into the soil-earthworm system to investigate the response mechanism of earthworms at the molecular level. The results showed that BC and DM exposure caused an increase in the abundance of Proteobacteria in the cast bacterial community, suggesting the dysbiosis of intestinal microbiota. It was also observed that the cast bacterial communities were more sensitive to DM exposure than PM exposure. Transcriptomic analysis showed that BC and DM exposure induced significant enrichment of functional pathways related to infectious and neuropathic diseases. Metabolomic profiling manifested that DM exposure caused metabolic dysfunction, antioxidant and detoxification abilities recession. Furthermore, significant differences in the responses of earthworms at transcriptomic and metabolic levels confirmed that DM exhibited greater ecotoxicity than PM. This study highlighted the significant contributions of dissolved matter to the ecotoxicity of biochar from the perspective of transcriptomic and metabolomic profiles.},
}
@article {pmid37654707,
year = {2023},
author = {LeBaron, V and Homdee, N and Ogunjirin, E and Patel, N and Blackhall, L and Lach, J},
title = {Describing and visualizing the patient and caregiver experience of cancer pain in the home context using ecological momentary assessments.},
journal = {Digital health},
volume = {9},
number = {},
pages = {20552076231194936},
pmid = {37654707},
issn = {2055-2076},
support = {R01 NR019639/NR/NINR NIH HHS/United States ; },
abstract = {BACKGROUND: Pain continues to be a difficult and pervasive problem for patients with cancer, and those who care for them. Remote health monitoring systems (RHMS), such as the Behavioral and Environmental Sensing and Intervention for Cancer (BESI-C), can utilize Ecological Momentary Assessments (EMAs) to provide a more holistic understanding of the patient and family experience of cancer pain within the home context.<br><br>METHODS: Participants used the BESI-C system for 2-weeks which collected data via EMAs deployed on wearable devices (smartwatches) worn by both patients with cancer and their primary family caregiver. We developed three unique EMA schemas that allowed patients and caregivers to describe patient pain events and perceived impact on quality of life from their own perspective. EMA data were analyzed to provide a descriptive summary of pain events and explore different types of data visualizations.<br><br>RESULTS: Data were collected from five (n&#x2009;=&#x2009;5) patient-caregiver dyads (total 10 individual participants, 5 patients, 5 caregivers). A total of 283 user-initiated pain event EMAs were recorded (198 by patients; 85 by caregivers) over all 5 deployments with an average severity score of 5.4/10 for patients and 4.6/10 for caregivers' assessments of patient pain. Average self-reported overall distress and pain interference levels (1&#x2009;=&#x2009;least distress; 4&#x2009;=&#x2009;most distress) were higher for caregivers (x&#xaf; 3.02, x&#xaf;2.60,respectively) compared to patients (x&#xaf; 2.82, x&#xaf; 2.25, respectively) while perceived burden of partner distress was higher for patients (i.e., patients perceived caregivers to be more distressed, x&#xaf; 3.21, than caregivers perceived patients to be distressed, x&#xaf;2.55). Data visualizations were created using time wheels, bubble charts, box plots and line graphs to graphically represent EMA findings.<br><br>CONCLUSION: Collecting data via EMAs is a viable RHMS strategy to capture longitudinal cancer pain event data from patients and caregivers that can inform personalized pain management and distress-alleviating interventions.},
}
@article {pmid37654007,
year = {2024},
author = {Papadopoulos, NG and Akdis, CA and Akdis, M and Damialis, A and Esposito, G and Fergadiotou, I and Goroncy, C and Guitton, P and Gotua, M and Erotokritou, K and Jartti, T and Murray, C and Nenes, A and Nikoletseas, S and Finotto, S and Pandis, SN and Ramiconi, V and Simpson, A and Soudunsaari, A and Stårbröst, A and Staiano, M and Varriale, A and Xepapadaki, P and Zuberbier, T and Annesi-Maesano, I and , },
title = {Addressing adverse synergies between chemical and biological pollutants at schools-The 'SynAir-G' hypothesis.},
journal = {Allergy},
volume = {79},
number = {2},
pages = {294-301},
doi = {10.1111/all.15857},
pmid = {37654007},
issn = {1398-9995},
support = {101057271//HORIZON EUROPE Health/ ; },
mesh = {Child ; Humans ; *Air Pollution, Indoor/adverse effects ; *Environmental Pollutants ; *Air Pollutants/adverse effects/analysis ; Particulate Matter ; *Asthma/epidemiology/etiology ; Environmental Monitoring ; },
abstract = {While the number and types of indoor air pollutants is rising, much is suspected but little is known about the impact of their potentially synergistic interactions, upon human health. Gases, particulate matter, organic compounds but also allergens and viruses, fall within the 'pollutant' definition. Distinct populations, such as children and allergy and asthma sufferers are highly susceptible, while a low socioeconomic background is a further susceptibility factor; however, no specific guidance is available. We spend most of our time indoors; for children, the school environment is of paramount importance and potentially amenable to intervention. The interactions between some pollutant classes have been studied. However, a lot is missing with respect to understanding interactions between specific pollutants of different classes in terms of concentrations, timing and sequence, to improve targeting and upgrade standards. SynAir-G is a European Commission-funded project aiming to reveal and quantify synergistic interactions between different pollutants affecting health, from mechanisms to real life, focusing on the school setting. It will develop a comprehensive and responsive multipollutant monitoring system, advance environmentally friendly interventions, and disseminate the generated knowledge to relevant stakeholders in accessible and actionable formats. The aim of this article it to put forward the SynAir-G hypothesis, and describe its background and objectives.},
}
@article {pmid37651934,
year = {2023},
author = {Fang, R and Chen, T and Han, Z and Ji, W and Bai, Y and Zheng, Z and Su, Y and Jin, L and Xie, B and Wu, D},
title = {From air to airway: Dynamics and risk of inhalable bacteria in municipal solid waste treatment systems.},
journal = {Journal of hazardous materials},
volume = {460},
number = {},
pages = {132407},
doi = {10.1016/j.jhazmat.2023.132407},
pmid = {37651934},
issn = {1873-3336},
mesh = {Humans ; *Solid Waste ; China ; *Bacteria ; Dust ; Machine Learning ; },
abstract = {Municipal solid waste treatment (MSWT) system emits a cocktail of microorganisms that jeopardize environmental and public health. However, the dynamics and risks of airborne microbiota associated with MSWT are poorly understood. Here, we analyzed the bacterial community of inhalable air particulates (PM10, n = 71) and the potentially exposed on-site workers' throat swabs (n = 30) along with waste treatment chain in Shanghai, the largest city of China. Overall, the airborne bacteria varied largely in composition and abundance during the treatment (P < 0.05), especially in winter. Compared to the air conditions, MSWT-sources that contributed to 15 ∼ 70% of airborne bacteria more heavily influenced the PM10-laden bacterial communities (PLS-SEM, β = 0.40, P < 0.05). Moreover, our year-span analysis found PM10 as an important media spreading pathogens (10[4] ∼ 10[8] copies/day) into on-site workers. The machine-learning identified Lactobacillus and Streptococcus as pharynx-niched featured biomarker in summer and Rhodococcus and Capnocytophaga in winter (RandomForest, ntree = 500, mtry = 10, cross = 10, OOB = 0%), which closely related to their airborne counterparts (Procrustes test, P < 0.05), suggesting that MSWT a dynamic hotspot of airborne bacteria with the pronounced inhalable risks to the neighboring communities.},
}
@article {pmid37650794,
year = {2023},
author = {Roma, P and Giromini, L and Sellbom, M and Cardinale, A and Ferracuti, S and Mazza, C},
title = {The ecological validity of the IOP-29: A follow-up study using the MMPI-2-RF and the SIMS as criterion variables.},
journal = {Psychological assessment},
volume = {35},
number = {10},
pages = {868-879},
doi = {10.1037/pas0001273},
pmid = {37650794},
issn = {1939-134X},
mesh = {Humans ; Follow-Up Studies ; *MMPI ; Databases, Factual ; Malingering ; *Psychological Trauma ; },
abstract = {Current guidelines for conducting symptom validity assessments require that professionals administer multiple symptom validity tests (SVTs) and that the SVTs selected for their evaluations provide nonredundant information. However, not many SVTs are currently available, and most of them rely on the same, (in)frequency-based, feigning detection strategy. In this context, the Inventory of Problems (IOP-29) could be a valuable addition to the assessor's toolbox because of its brevity (29 items) and its different approach to assessing the credibility of presented symptoms. As its ecological validity has been poorly investigated, the present study used a criterion groups design to examine the classification accuracy of the IOP-29 in a data set of 174 court-ordered psychological evaluations focused on psychological injury. The validity scales of the Minnesota Multiphasic Personality Inventory-2 Restructured Form and the total score of the Structured Inventory of Malingered Symptoms were used as criterion variables. Overall, the results of this study confirm that the IOP-29 is an effective measure (1.70 ≤ d ≤ 2.67) that provides valuable information when added to the multimethod assessment of symptom validity in civil forensic contexts. (PsycInfo Database Record (c) 2023 APA, all rights reserved).},
}
@article {pmid37648185,
year = {2023},
author = {Tan, M and Bian, Z and Dong, J and Hao, M and Qu, J},
title = {Comparing the variation and influencing factors of CO2 emission from subsidence waterbodies under different restoration modes in coal mining area.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {116936},
doi = {10.1016/j.envres.2023.116936},
pmid = {37648185},
issn = {1096-0953},
abstract = {Subsidence waterbodies play an important role in carbon cycle in coal mining area. However, little effort has been made to explore the carbon dioxide (CO2) release characteristics and influencing factors in subsidence waterbodies, especially under different restoration modes. Here, we measured CO2 release fluxes (F(CO2)) across Anguo wetland (AW), louts pond (LP), fishpond (FP), fishery-floating photovoltaic wetland (FFPV), floating photovoltaic wetland (FPV) in coal mining subsidence area, with unrestored subsidence waterbodies (SW) and unaffected normal Dasha river (DR) as the control area. We sampled each waterbody and tested which physical, chemical, and biological characteristics of water and sediment related to variability in CO2. The results indicated that F(CO2) exhibited the following patterns: FFPV > FPV > FP > SW > DR > LP > AW. Trophic lake index (TLI) and microbial biomass carbon content (MBC) in sediment had a positive impact on F(CO2). The dominant archaea Euryarchaeota and Thaumarchaeota, and dominant bacteria Proteobacteria promoted F(CO2). This study can help more accurately quantify CO2 emissions and guide CO2 future emission reduction and subsidence waterbodies estoration.},
}
@article {pmid37646945,
year = {2023},
author = {Bosch, M and López-Pujol, J and Blanché, C and Simon, J},
title = {DCDB: Chromosome Database of Tribe Delphinieae (Ranunculaceae): Structure, Exploitation, and Recent Development.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2703},
number = {},
pages = {173-192},
pmid = {37646945},
issn = {1940-6029},
mesh = {*Ranunculaceae ; Phylogeny ; Cytogenetic Analysis ; Databases, Factual ; Internet ; },
abstract = {An updated (and now online) version of the former chromosome database of tribe Delphinieae (Ranunculaceae) is presented (http://www.delphinieae.online). This new version is the result of an accurate, exhaustive literature and Internet research, by adding chromosome counts and all related karyological information for the genera Aconitum L., Gymnaconitum (Stapf) Wei Wang &amp; Z. D. Chen, Delphinium L. (including Staphisagria Spach), Consolida (DC.) S. F. Gray and Aconitella Spach, accumulated during the approximately last 25 years and that comprise worldwide published data from 1889 to 2021. The Delphinieae Chromosome Database (DCDB) (last updated 31.12.2021) contains a total number of 3435 reports belonging to 425 species (503 taxa), which represents 48.6% of the total species of the tribe (an increase of c. 213% and 32% compared with the 1097 and 2598 reports gathered in the 1999 and 2016 versions, respectively). This increase is due both to chromosome research progress and to improved information capture system. Moreover, recent taxonomic advances, synonymization, and new phylogenetic criteria have also been considered.The DCDB database provides the most complete currently available information on published chromosome numbers, ploidy-level estimates, and other karyological data of Delphinieae, and it is aimed to be useful for the building of cytotaxonomical databases and for specific research ongoing projects of systematics and evolution of Ranunculaceae. DCDB includes two levels of taxonomic resolution, published name (original and standardized form) and database accepted name (based on either Plants of the World - POWO or expert specialist criteria), as well as the geographic origin of each count (country, locality, geographic coordinates, elevation, or ecological information when reported in the original publication), associated karyological data if originally provided (studied material type, graphic information, chromosome measures and formulas, satellites, B chromosomes, other cytogenetic techniques used, etc.), voucher information and reference (with DOI and other links to access the original document). An effort to check the original sources and to search in grey literature allowed to indicate the counts that appear to be registered twice.},
}
@article {pmid37646941,
year = {2023},
author = {Henniges, MC and Johnston, E and Pellicer, J and Hidalgo, O and Bennett, MD and Leitch, IJ},
title = {The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2703},
number = {},
pages = {111-122},
pmid = {37646941},
issn = {1940-6029},
mesh = {Genome Size ; *Genome, Plant ; Cytogenetics ; DNA, Plant/genetics ; *Databases, Nucleic Acid ; },
abstract = {Genome size is a plant character with far-reaching implications, ranging from impacts on the financial and computing feasibility of sequencing and assembling genomes all the way to influencing the very ecology and evolution of species. The increasing recognition of the role of genome size in plant science has led to a rising demand for comprehensive and easily accessible sources of genome size data. The Plant DNA C-values database has established itself as a trusted and widely used central hub for users needing to access available plant genome size data, complemented with related cytogenetic (ploidy level) and karyological (chromosome number) information where available. Since its inception in 2001, the database has undergone six major updates to incorporate newly available genome size information, leading to the most recent release (Release 7.1), which comprises data for 12,273 species across all the major land plant and some algal lineages. Here we describe how to use the database efficiently, making use of its different query and filtering settings.},
}
@article {pmid37645296,
year = {2022},
author = {Anegg, M and Prakofjewa, J and Kalle, R and Sõukand, R},
title = {Local ecological knowledge and folk medicine in historical Estonia, Livonia, Courland and Galicia in Northeastern Europe, 1805-1905.},
journal = {Open research Europe},
volume = {2},
number = {},
pages = {30},
pmid = {37645296},
issn = {2732-5121},
abstract = {Background: Historical ethnobotanical data can provide valuable information about past human-nature relationships as well as serve as a basis for diachronic analysis. This data note aims to present a dataset which documented medicinal plant uses, mentioned in a selection of German-language sources from the 19 [th] century covering the historical regions of Estonia, Livonia, Courland, and Galicia. Methods: Data was mainly entered by systematic manual search in various ethnobotanical historical German-language works focused on the medicinal use of plants. Data about plant and non-plant constituents, their usage, the mode of administration, used plant parts, and their German and local names was extracted and collected into a database in the form of Use Reports.},
}
@article {pmid37644145,
year = {2023},
author = {Zhao, W and Zhang, P and Chen, D and Wang, H and Gu, B and Zhang, J},
title = {Data mining from process monitoring of typical polluting enterprise.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {9},
pages = {1109},
pmid = {37644145},
issn = {1573-2959},
support = {2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 2021C03178//Science and Technology Program of Zhejiang Province/ ; 2021C03178//Science and Technology Program of Zhejiang Province/ ; },
mesh = {*Environmental Monitoring ; *Wastewater ; Data Mining ; China ; Electric Conductivity ; Vehicle Emissions ; },
abstract = {With the increasing volume of environmental monitoring data, extracting valuable insights from multivariate time series sensor data can facilitate comprehensive information utilization and support informed decision-making in environmental management. However, there is a dearth of comprehensive research on multivariate data analysis for process monitoring in typical polluting enterprises. In this study, an artificial neural network model based on back-propagation algorithm (BP-ANN) was developed to predict the wastewater and exhaust gas emissions using IoT data obtained from process monitoring of a typical polluting enterprise located in Taizhou, Zhejiang Province, China. The results indicate that the model constructed has a high predictive coefficient of determination (R[2]) with values of 0.8510, 0.9565, 0.9561, 0.9677, and 0.9061 for chemical oxygen demand (COD), potential of hydrogen (pH), electrical conductivity (EC), flue gas emission (FGE), and non-methane hydrocarbon concentration (NMHC) respectively. For the first time, the variable importance measure (VIM)-assisted BP-ANN was employed to investigate the internal and external correlations between wastewater and exhaust gas treatment, thereby enhancing the interpretability of mapping features in the BP-ANN model. The predicted errors for pH and FGE have been demonstrated to fall within the range of - 0.62 ~ 0.30 and - 0.21 ~ 0.15 m[3]/s, respectively, with average relative errors of 1.05% and 9.60%, which is advantageous in detecting anomalous data and forecasting pollution indicator values. Our approach successfully addresses the challenge of segregating data analysis for wastewater disposal and exhaust gas disposal in the process monitoring of polluting enterprises, while also unearthing potential variables that significantly contribute to the BP-ANN model, thereby facilitating the selection and extraction of characteristic variables.},
}
@article {pmid37642912,
year = {2023},
author = {Goparaju, L and Pillutla, RCP and Venkata, SBK},
title = {Assessment of forest fire emissions in Uttarakhand State, India, using Open Geospatial data and Google Earth Engine.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {45},
pages = {100873-100891},
pmid = {37642912},
issn = {1614-7499},
mesh = {*Carbon Monoxide/analysis ; *Wildfires ; Nitrogen Dioxide/analysis ; Search Engine ; Gases/analysis ; Aerosols ; },
abstract = {In the recent past, forest fires have increased due to the changing climate pattern. It is necessary to analyse and quantify various gaseous emissions so as to mitigate their harmful effects on air pollution. Satellite remote sensing data provides an opportunity to study the greenhouse gases in the atmosphere. The multispectral sensor of the Tropospheric Monitoring Instrument (Sentinel-5) is capable of recording the reflectance of wavelengths vital for measuring the atmospheric concentrations of methane, formaldehyde, aerosol, carbon monoxide, etc., at a spatial resolution of 0.01°. The present study utilized the Google Earth Engine (GEE) platform to study the emissions caused by forest fires in four districts of Uttarakhand State of India, which witnessed unprecedented fires in April-May 2021. All the datasets were ingested in GEE, which has the capability to analyse large datasets without the need to download them. The pre-fire period chosen was September 2020; the fire period was February-May 2021, and the post-fire period was June 2021. The variables chosen were aerosol absorbing index (AAI), carbon monoxide (CO) and nitrogen dioxide (NO2). The climate parameter temperature (Moderate Resolution Imaging Spectroradiometer Land Surface Temperature) and precipitation (from Climate Hazards Group InfraRed Precipitation (CHIRPS) Pentad) were also studied for the period mentioned. The results indicate a different trend for emissions in each district. For AAI, maximum emissions were noted in district Nainital followed by Almora, Tehri Garhwal and Garhwal. For CO emissions, the most affected district was Almora followed by Nainital, Garhwal and Tehri Garhwal. For NO2 emissions, the most affected district was Garhwal, followed by Nainital, Tehri Garhwal and Almora. Delta Normalized Burn Ratio was computed from Sentinel data (difference of pre-fire and post-fire images) to assess the burnt area severity. The Delta Normalized Burn Ratio values observed that the district with the most burnt area is Garhwal, followed by Nainital, Almora and Tehri Garhwal. The elevated temperatures and scanty rainfall patterns regulated the intensity and duration of forest fire. Monitoring the gaseous emissions as a consequence of forest fire in the GEE platform is much easier and more convenient at a regional level. Such data is much needed for mitigation measures to be implemented in time.},
}
@article {pmid37640770,
year = {2023},
author = {Mudge, L and Bruno, JF},
title = {Disturbance intensification is altering the trait composition of Caribbean reefs, locking them into a low functioning state.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {14022},
pmid = {37640770},
issn = {2045-2322},
mesh = {Animals ; Caribbean Region ; *Anthozoa ; Climate Change ; *Cyclonic Storms ; Databases, Factual ; *Marijuana Abuse ; Plant Weeds ; },
abstract = {Anthropogenic climate change is intensifying natural disturbance regimes, which negatively affects some species, while benefiting others. This could alter the trait composition of ecological communities and influence resilience to disturbance. We investigated how the frequency and intensification of the regional storm regime (and likely other disturbances) is altering coral species composition and in turn resistance and recovery. We developed regional databases of coral cover and composition (3144 reef locations from 1970 to 2017) and of the path and strength of cyclonic storms in the region (including 10,058 unique storm-reef intersections). We found that total living coral cover declined steadily through 2017 (the median annual loss rate was ~ 0.25% per year). Our results also indicate that despite the observed increase in the intensity of Atlantic cyclonic storms, their effect on coral cover has decreased markedly. This could be due in part to selection for disturbance-resistant taxa in response to the intensifying disturbance regime. We found that storms accelerated the loss of threatened acroporid corals but had no measurable effect on the cover of more resilient "weedy" corals, thereby increasing their relative cover. Although resistance to disturbance has increased, recovery rates have slowed due to the dominance of small, slow-growing species. This feedback loop is locking coral communities into a low-functioning state dominated by weedy species with limited ecological or societal value.},
}
@article {pmid37636281,
year = {2023},
author = {Wang, F and Liu, J and Qin, G and Zhang, J and Zhou, J and Wu, J and Zhang, L and Thapa, P and Sanders, CJ and Santos, IR and Li, X and Lin, G and Weng, Q and Tang, J and Jiao, N and Ren, H},
title = {Coastal blue carbon in China as a nature-based solution toward carbon neutrality.},
journal = {Innovation (Cambridge (Mass.))},
volume = {4},
number = {5},
pages = {100481},
pmid = {37636281},
issn = {2666-6758},
abstract = {To achieve the Paris Agreement, China pledged to become "Carbon Neutral" by the 2060s. In addition to massive decarbonization, this would require significant changes in ecosystems toward negative CO2 emissions. The ability of coastal blue carbon ecosystems (BCEs), including mangrove, salt marsh, and seagrass meadows, to sequester large amounts of CO2 makes their conservation and restoration an important "nature-based solution (NbS)" for climate adaptation and mitigation. In this review, we examine how BCEs in China can contribute to climate mitigation. On the national scale, the BCEs in China store up to 118 Tg C across a total area of 1,440,377 ha, including over 75% as unvegetated tidal flats. The annual sedimental C burial of these BCEs reaches up to 2.06 Tg C year[-1], of which most occurs in salt marshes and tidal flats. The lateral C flux of mangroves and salt marshes contributes to 1.17 Tg C year[-1] along the Chinese coastline. Conservation and restoration of BCEs benefit climate change mitigation and provide other ecological services with a value of $32,000 ha[-1] year[-1]. The potential practices and technologies that can be implemented in China to improve BCE C sequestration, including their constraints and feasibility, are also outlined. Future directions are suggested to improve blue carbon estimates on aerial extent, carbon stocks, sequestration, and mitigation potential. Restoring and preserving BCEs would be a cost-effective step to achieve Carbon Neutral by 2060 in China despite various barriers that should be removed.},
}
@article {pmid37635752,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Powdered Quaker, Orthosia gracilis (Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {290},
pmid = {37635752},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Orthosia gracilis (the powdered quaker; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 715.5 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.43 kilobases in length.},
}
@article {pmid37634178,
year = {2023},
author = {Zhou, L and Ye, T and Zheng, S and Zhu, X and Chen, Z and Wu, Y},
title = {Experimental and modeling investigation of dual-source iron release in water-solid-gas interaction of abandoned coal mine drainage.},
journal = {Environmental geochemistry and health},
volume = {45},
number = {11},
pages = {8433-8449},
pmid = {37634178},
issn = {1573-2983},
support = {2022YFC3702203//the National Key R&amp;D Program of China/ ; 2020ZDPYMS07//the Fundamental Research Funds for the Central Universities, China/ ; },
mesh = {*Water ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; Iron/analysis ; Minerals ; Coal ; Steel ; },
abstract = {After mine closure and flooding, abandoned iron-prone devices and equipment (e.g., steel bolts and ground support meshes) and iron-bearing minerals (e.g., pyrite) form a dual-source iron pollution system in mine groundwater. Dual-source iron contributes to the water-solid-gas interaction in abandoned coal mines and the release of iron at different periods after mine closure, posing environmental risks in groundwater and discharging acid mine drainage, which contains large amounts of iron. In this study, a series of hydrochemical experiments were conducted to simulate the iron release process of the dual-source system, and electrochemical experiments were carried out to reveal the reaction mechanism, characterize the dual-source iron pollution release mode and quantify the release rate ratio. PHREEQC package was used to simulate the long-term hydrogeochemistry reactions of the water-solid-gas interaction to determine the key factors and suitable conditions that inhibit dual-source iron release. The results show that the dual-source system of iron-bearing minerals (pyrite) and steel bolts promote iron release from each other. The resulting calculated annual iron release indicated that the overall iron release rate ratio is: dual-source > bolt > pyrite, indicating that mine water would remain acidic for a long time due to the continuous release of iron from the system. Numerical modeling results show that maintaining the environment temperature below 25 °C and the pH above 3.5 is an effective way to reduce the iron release rate.},
}
@article {pmid37634023,
year = {2023},
author = {Medo, A and Ohte, N and Kajitani, H and Nose, T and Manabe, Y and Sugawara, T and Onishi, Y and Goto, AS and Koba, K and Arai, N and Mitsunaga, Y and Kume, M and Nishizawa, H and Kojima, D and Yokoyama, A and Yamanaka, T and Viputhanumas, T and Mitamura, H},
title = {Striped catfish (Pangasianodon hypophthalmus) exploit food sources across anaerobic decomposition- and primary photosynthetic production-based food chains.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13992},
pmid = {37634023},
issn = {2045-2322},
mesh = {*Catfishes/growth &amp; development/physiology ; Animals ; Food Chain ; Ecosystem ; Thailand ; Geologic Sediments ; },
abstract = {Dietary information from aquatic organisms is instrumental in predicting biological interactions and understanding ecosystem functionality. In freshwater habitats, generalist fish species can access a diverse array of food sources from multiple food chains. These may include primary photosynthetic production and detritus derived from both oxic and anoxic decomposition. However, the exploitation of anoxic decomposition products by fish remains insufficiently explored. This study examines feeding habits of striped catfish (Pangasianodon hypophthalmus) at both adult and juvenile stages within a tropical reservoir, using stable carbon, nitrogen, and sulfur isotope ratios (δ[13]C, δ[15]N, and δ[34]S, respectively) and fatty acid (FA) analyses. The adult catfish exhibited higher δ[15]N values compared to primary consumers that feed on primary photosynthetic producers, which suggests ingestion of food sources originating from primary photosynthetic production-based food chains. On the other hand, juvenile catfish demonstrated lower δ[15]N values than primary consumers, correlating with low δ[34]S value and large proportions of bacterial FA but contained small proportions of polyunsaturated FA. This implies that juveniles utilize food sources from both anoxic decomposition and primary photosynthetic production-based food chains. Our results indicate that food chains based on anoxic decomposition can indeed contribute to the dietary sources of tropical fish species.},
}
@article {pmid37633161,
year = {2024},
author = {Shan, Y and Zhao, W and Hao, W and Kimura, T and Ukawa, S and Ohira, H and Kawamura, T and Wakai, K and Ando, M and Tamakoshi, A and Wang, C},
title = {Five-year changes of social activity and incident long-term care needs among depressed older adults: A 15-year follow up.},
journal = {Archives of gerontology and geriatrics},
volume = {116},
number = {},
pages = {105163},
doi = {10.1016/j.archger.2023.105163},
pmid = {37633161},
issn = {1872-6976},
mesh = {Humans ; Aged ; *Long-Term Care ; Follow-Up Studies ; Prospective Studies ; *Insurance, Long-Term Care ; },
abstract = {OBJECTIVES: To examine the effects of changes in individual/multiple social activities between 65 and 70 years of age on incident long-term care (LTC) needs between 70 and 80 in older adults with depressive symptoms.<br><br>METHODS: Participants were recruited from the New Integrated Suburban Seniority Investigation Project, an ongoing prospective cohort study. A total of 525 older adults with depressive symptoms were included. The validated 15-item Geriatric Depression Scale was used to assess depressive symptoms. A self-report questionnaire was used to measure social activities (social-related, learning, and personal). LTC needs was defined according to Japan's Long-term Care Insurance System. A competing risk model and a Laplace regression model were used to estimate the hazard ratios of LTC needs incidence and the 25th percentile difference in LTC-needs-free survival time and their 95% confidence intervals.<br><br>RESULTS: Out of 4314 person-years of mild LTC needs, 108 individuals developed it. Participants who increased their frequency of learning activities have a lower risk of developing mild LTC needs. Increasing the frequency could also prolong LTC-needs-free survival time by approximately 2.61 years. Out of 4535 person-years for severe LTC needs, 54 individuals developed it. Participants with a continuous regular frequency of learning activities had a lower risk of developing severe LTC needs. However, the association between this frequency and LTC-needs-free survival time for severe LTC needs was insignificant in the multivariable models.<br><br>CONCLUSIONS: Increased frequency of learning activities reduced the risk of LTC needs among older adults with depressive symptoms and prolonged their LTC-needs-free survival time.},
}
@article {pmid37632753,
year = {2022},
author = {Meyer, R and Davies, N and Pitz, KJ and Meyer, C and Samuel, R and Anderson, J and Appeltans, W and Barker, K and Chavez, FP and Duffy, JE and Goodwin, KD and Hudson, M and Hunter, ME and Karstensen, J and Laney, CM and Leinen, M and Mabee, P and Macklin, JA and Muller-Karger, F and Pade, N and Pearlman, J and Phillips, L and Provoost, P and Santi, I and Schigel, D and Schriml, LM and Soccodato, A and Suominen, S and Thibault, KM and Ung, V and van de Kamp, J and Wallis, E and Walls, R and Buttigieg, PL},
title = {The founding charter of the Omic Biodiversity Observation Network (Omic BON).},
journal = {GigaScience},
volume = {12},
number = {},
pages = {},
pmid = {37632753},
issn = {2047-217X},
mesh = {*Biodiversity ; *Knowledge ; },
abstract = {Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.},
}
@article {pmid37630465,
year = {2023},
author = {Koga, S and Takazono, T and Kido, T and Muramatsu, K and Tokutsu, K and Tokito, T and Okuno, D and Ito, Y and Yura, H and Takeda, K and Iwanaga, N and Ishimoto, H and Sakamoto, N and Yatera, K and Izumikawa, K and Yanagihara, K and Fujino, Y and Fushimi, K and Matsuda, S and Mukae, H},
title = {Evaluation of the Effectiveness and Use of Anti-Methicillin-Resistant Staphylococcus aureus Agents for Aspiration Pneumonia in Older Patients Using a Nationwide Japanese Administrative Database.},
journal = {Microorganisms},
volume = {11},
number = {8},
pages = {},
pmid = {37630465},
issn = {2076-2607},
abstract = {Studies indicated potential harm from empirical broad-spectrum therapy. A recent study of hospitalizations for community-acquired pneumonia suggested that empirical anti-methicillin-resistant Staphylococcus aureus (MRSA) therapy was associated with an increased risk of death and other complications. However, limited evidence supports empirical anti-MRSA therapy for older patients with aspiration pneumonia. In a nationwide Japanese database, patients aged ≥65 years on admission with aspiration pneumonia were analyzed. Patients were divided based on presence of respiratory failure and further sub-categorized based on their condition within 3 days of hospital admission, either receiving a combination of anti-MRSA agents and other antibiotics, or not using MRSA agents. An inverse probability weighting method with estimated propensity scores was used. Out of 81,306 eligible patients, 55,098 had respiratory failure, and 26,208 did not. In the group with and without respiratory failure, 0.93% and 0.42% of the patients, respectively, received anti-MRSA agents. In patients with respiratory failure, in-hospital mortality (31.38% vs. 19.03%, p < 0.001), 30-day mortality, and 90-day mortality were significantly higher, and oxygen administration length was significantly longer in the anti-MRSA agent combination group. Anti-MRSA agent combination use did not improve the outcomes in older patients with aspiration pneumonia and respiratory failure, and should be carefully and comprehensively considered.},
}
@article {pmid37626975,
year = {2023},
author = {Irwin, G and Rogatzki, MJ and Wiltshire, HD and Williams, GKR and Gu, Y and Ash, GI and Tao, D and Baker, JS},
title = {Sports-Related Concussion Assessment: A New Physiological, Biomechanical, and Cognitive Methodology Incorporating a Randomized Controlled Trial Study Protocol.},
journal = {Biology},
volume = {12},
number = {8},
pages = {},
pmid = {37626975},
issn = {2079-7737},
support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Taking part in moderate-to-vigorous exercise in contact sports on a regular basis may be linked to an increase in cerebrovascular injury and head trauma. Validated objective measures are lacking in the initial post-event diagnosis of head injury. The exercise style, duration, and intensity may also confound diagnostic indicators. As a result, we propose that the new Interdisciplinary Group in Movement &amp; Performance from Acute &amp; Chronic Head Trauma (IMPACT) analyze a variety of functional (biomechanical and motor control) tests as well as related biochemistry to see how they are affected by contact in sports and head injury. The study's goal will be to look into the performance and physiological changes in rugby players after a game for head trauma and injury.<br><br>METHODS: This one-of-a-kind study will use a randomized controlled trial (RCT) utilizing a sport participation group and a non-participation control group. Forty male rugby 7 s players will be recruited for the study and allocated randomly to the experimental groups. The intervention group will participate in three straight rugby matches during a local 7 s rugby event. At the pre-match baseline, demographic and anthropometric data will be collected. This will be followed by the pre-match baseline collection of biochemical, biomechanical, and cognitive-motor task data. After three consecutive matches, the same measures will be taken. During each match, a notational analysis will be undertaken to obtain contact information. All measurements will be taken again 24, 48, and 72 h after the third match.<br><br>DISCUSSION: When the number of games increases owing to weariness and/or stressful circumstances, we expect a decline in body movement, coordination, and cognitive-motor tasks. Changes in blood biochemistry are expected to correspond to changes in biomechanics and cognitive-motor processes. This research proposal will generate considerable, ecologically valid data on the occurrence of head trauma events under game conditions, as well as the influence of these events on the biological systems of the performers. This will lead to a greater understanding of how sports participants react to exercise-induced injuries. This study's scope will have far-reaching ramifications for doctors, coaches, managers, scientists, and sports regulatory bodies concerned with the health and well-being of athletic populations at all levels of competition, including all genders and ages.},
}
@article {pmid37626434,
year = {2023},
author = {Kelliher, JM and Robinson, AJ and Longley, R and Johnson, LYD and Hanson, BT and Morales, DP and Cailleau, G and Junier, P and Bonito, G and Chain, PSG},
title = {The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {192},
pmid = {37626434},
issn = {2049-2618},
mesh = {*Multiomics ; Data Analysis ; Eukaryota ; *Microbiota/genetics ; Prokaryotic Cells ; },
abstract = {As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.},
}
@article {pmid37624884,
year = {2023},
author = {Elser, D and Pflieger, D and Villette, C and Moegle, B and Miesch, L and Gaquerel, E},
title = {Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations.},
journal = {Science advances},
volume = {9},
number = {34},
pages = {eade8984},
pmid = {37624884},
issn = {2375-2548},
mesh = {*Nicotiana/genetics ; *Metabolomics ; Acclimatization ; Consensus ; Databases, Factual ; },
abstract = {Specialized metabolite (SM) diversification is a core process to plants' adaptation to diverse ecological niches. Here, we implemented a computational mass spectrometry-based metabolomics approach to exploring SM diversification in tissues of 20 species covering Nicotiana phylogenetics sections. To markedly increase metabolite annotation, we created a large in silico fragmentation database, comprising >1 million structures, and scripts for connecting class prediction to consensus substructures. Together, the approach provides an unprecedented cartography of SM diversity and section-specific innovations in this genus. As a case study and in combination with nuclear magnetic resonance and mass spectrometry imaging, we explored the distribution of N-acylnornicotines, alkaloids predicted to be specific to Repandae allopolyploids, and revealed their prevalence in the genus, albeit at much lower magnitude, as well as a greater structural diversity than previously thought. Together, the data integration approaches provided here should act as a resource for future research in plant SM evolution.},
}
@article {pmid37621575,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Buff Ermine, Spilarctia lutea (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {92},
pmid = {37621575},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Spilarctia lutea (the Buff Ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 584.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the assembled Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,304 protein coding genes.},
}
@article {pmid37620553,
year = {2023},
author = {Gonzalez, A and Vihervaara, P and Balvanera, P and Bates, AE and Bayraktarov, E and Bellingham, PJ and Bruder, A and Campbell, J and Catchen, MD and Cavender-Bares, J and Chase, J and Coops, N and Costello, MJ and Czúcz, B and Delavaud, A and Dornelas, M and Dubois, G and Duffy, EJ and Eggermont, H and Fernandez, M and Fernandez, N and Ferrier, S and Geller, GN and Gill, M and Gravel, D and Guerra, CA and Guralnick, R and Harfoot, M and Hirsch, T and Hoban, S and Hughes, AC and Hugo, W and Hunter, ME and Isbell, F and Jetz, W and Juergens, N and Kissling, WD and Krug, CB and Kullberg, P and Le Bras, Y and Leung, B and Londoño-Murcia, MC and Lord, JM and Loreau, M and Luers, A and Ma, K and MacDonald, AJ and Maes, J and McGeoch, M and Mihoub, JB and Millette, KL and Molnar, Z and Montes, E and Mori, AS and Muller-Karger, FE and Muraoka, H and Nakaoka, M and Navarro, L and Newbold, T and Niamir, A and Obura, D and O'Connor, M and Paganini, M and Pelletier, D and Pereira, H and Poisot, T and Pollock, LJ and Purvis, A and Radulovici, A and Rocchini, D and Roeoesli, C and Schaepman, M and Schaepman-Strub, G and Schmeller, DS and Schmiedel, U and Schneider, FD and Shakya, MM and Skidmore, A and Skowno, AL and Takeuchi, Y and Tuanmu, MN and Turak, E and Turner, W and Urban, MC and Urbina-Cardona, N and Valbuena, R and Van de Putte, A and van Havre, B and Wingate, VR and Wright, E and Torrelio, CZ},
title = {A global biodiversity observing system to unite monitoring and guide action.},
journal = {Nature ecology &amp; evolution},
volume = {7},
number = {12},
pages = {1947-1952},
pmid = {37620553},
issn = {2397-334X},
mesh = {*Biodiversity ; *Ecosystem ; },
}
@article {pmid37619239,
year = {2023},
author = {Qiu, S and Yang, A and Zeng, H},
title = {Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.},
journal = {PLoS computational biology},
volume = {19},
number = {8},
pages = {e1011391},
pmid = {37619239},
issn = {1553-7358},
mesh = {Secondary Metabolism ; Cell Cycle ; Cell Proliferation ; *Computational Biology ; *Engineering ; },
abstract = {In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.},
}
@article {pmid37614677,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the White-shouldered Marble, Apotomis turbidana (Hübner, 1825).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {127},
pmid = {37614677},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Apotomis turbidana (the White-shouldered Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 720.5 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,646 protein coding genes.},
}
@article {pmid37614458,
year = {2023},
author = {Gavurova, B and Kelemen, M and Polishchuk, V and Mudarri, T and Smolanka, V},
title = {A fuzzy decision support model for the evaluation and selection of healthcare projects in the framework of competition.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1222125},
pmid = {37614458},
issn = {2296-2565},
mesh = {European Union ; *Policy ; *Delivery of Health Care ; Decision Support Techniques ; },
abstract = {Our research aims to support decision-making regarding the financing of healthcare projects by structural funds with policies targeting reduction of the development gap among different regions and countries of the European Union as well as the achievement of economic and social cohesion. A fuzzy decision support model for the evaluation and selection of healthcare projects should rank the project applications for the selected region, accounting for the investor's wishes in the form of a regional coefficient in order to reduce the development gap between regions. On the one hand, our proposed model evaluates project applications based on selected criteria, which may be structured, weakly structured, or unstructured. On the other hand, it also incorporates information on the level of healthcare development in the region. The obtained ranking increases the degree of validity of the decision regarding the selection of projects for financing by investors, considering the level of development of the region where the project will be implemented. At the expense of European Union (EU) structural funds, a village, city, region, or state can receive funds for modernization and development of the healthcare sector and all related processes. To minimize risks, it is necessary to implement adequate support systems for decision-making in the assessment of project applications, as well as regional policy in the region where the project will be implemented. The primary goal of this study was to develop a complex fuzzy decision support model for the evaluation and selection of projects in the field of healthcare with the aim of reducing the development gap between regions. Based on the above description, we formed the following scientific hypothesis for this research: if the project selected for financing can successfully achieve its stated goals and increase the level of development of its region, it should be evaluated positively. This evaluation can be obtained using a complex fuzzy model constructed to account for the region's level of development in terms of the availability and quality of healthcare services in the region where the project will be implemented.},
}
@article {pmid37612675,
year = {2023},
author = {Sentamu, DN and Kungu, J and Dione, M and Thomas, LF},
title = {Prevention of human exposure to livestock faecal waste in the household: a scoping study of interventions conducted in sub-Saharan Africa.},
journal = {BMC public health},
volume = {23},
number = {1},
pages = {1613},
pmid = {37612675},
issn = {1471-2458},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Humans ; *Livestock ; Databases, Factual ; Europe ; Feces ; *Hygiene ; },
abstract = {BACKGROUND: Poorly managed animal faecal waste can result in detrimental environmental and public health implications. Limiting human exposure to animal waste through Animal inclusive Water Sanitation and Hygiene (A-WASH) strategies is imperative to improve public health in livestock keeping households but has received little attention to date. A small number of A-WASH interventions have previously been identified through a systematic review by another research team, and published in 2017. To inform intervention design with the most up-to-date information, a scoping study was conducted to map the existing evidence for A-WASH in sub-Saharan Africa (SSA) emerging since the previous review.<br><br>METHODS: This review followed PRISMA guidelines to identify interventions in SSA published between January 2016 to October 2022. Databases searched included PubMed, PMC Europe, CabDirect and Web of Science. Studies were eligible for inclusion if they were written in English and documented interventions limiting human contact with animal faecal material in the SSA context. Key data extracted included: the intervention itself,&#xa0;its target population, cost, measure of effectiveness, quantification of effect, assessment of success, acceptability and limitations. These data were synthesized into a narrative, structured around the intervention type.<br><br>FINDINGS: Eight eligible articles were identified. Interventions to reduce human exposure to animal faecal matter were conducted in combination with 'standard' human-centric WASH practices. Identified interventions included the management of human-animal co-habitation, educational programs and the creation of child-safe spaces. No novel A-WASH interventions were identified in this review, beyond those identified by the review in 2017. Randomised Controlled Trials (RCTs) were used to evaluate six of the eight identified interventions, but as effect was evaluated through various measures, the ability to formally compare efficacy of interventions is lacking.<br><br>CONCLUSION: This study indicates that the number of A-WASH studies in SSA is increasing and the use of RCTs suggests a strong desire to create high-quality evidence within this field. There is a need for standardisation of effect measures to enable meta-analyses to be conducted to better understand intervention effectiveness. Evaluation of scalability and sustainability of interventions is still lacking in A - WASH research.},
}
@article {pmid37612513,
year = {2023},
author = {Delavaux, CS and Crowther, TW and Zohner, CM and Robmann, NM and Lauber, T and van den Hoogen, J and Kuebbing, S and Liang, J and de-Miguel, S and Nabuurs, GJ and Reich, PB and Abegg, M and Adou Yao, YC and Alberti, G and Almeyda Zambrano, AM and Alvarado, BV and Alvarez-Dávila, E and Alvarez-Loayza, P and Alves, LF and Ammer, C and Antón-Fernández, C and Araujo-Murakami, A and Arroyo, L and Avitabile, V and Aymard, GA and Baker, TR and Bałazy, R and Banki, O and Barroso, JG and Bastian, ML and Bastin, JF and Birigazzi, L and Birnbaum, P and Bitariho, R and Boeckx, P and Bongers, F and Bouriaud, O and Brancalion, PHS and Brandl, S and Brienen, R and Broadbent, EN and Bruelheide, H and Bussotti, F and Gatti, RC and César, RG and Cesljar, G and Chazdon, R and Chen, HYH and Chisholm, C and Cho, H and Cienciala, E and Clark, C and Clark, D and Colletta, GD and Coomes, DA and Cornejo Valverde, F and Corral-Rivas, JJ and Crim, PM and Cumming, JR and Dayanandan, S and de Gasper, AL and Decuyper, M and Derroire, G and DeVries, B and Djordjevic, I and Dolezal, J and Dourdain, A and Engone Obiang, NL and Enquist, BJ and Eyre, TJ and Fandohan, AB and Fayle, TM and Feldpausch, TR and Ferreira, LV and Fischer, M and Fletcher, C and Frizzera, L and Gamarra, JGP and Gianelle, D and Glick, HB and Harris, DJ and Hector, A and Hemp, A and Hengeveld, G and Hérault, B and Herbohn, JL and Herold, M and Hillers, A and Honorio Coronado, EN and Hui, C and Ibanez, TT and Amaral, I and Imai, N and Jagodziński, AM and Jaroszewicz, B and Johannsen, VK and Joly, CA and Jucker, T and Jung, I and Karminov, V and Kartawinata, K and Kearsley, E and Kenfack, D and Kennard, DK and Kepfer-Rojas, S and Keppel, G and Khan, ML and Killeen, TJ and Kim, HS and Kitayama, K and Köhl, M and Korjus, H and Kraxner, F and Laarmann, D and Lang, M and Lewis, SL and Lu, H and Lukina, NV and Maitner, BS and Malhi, Y and Marcon, E and Marimon, BS and Marimon-Junior, BH and Marshall, AR and Martin, EH and Martynenko, O and Meave, JA and Melo-Cruz, O and Mendoza, C and Merow, C and Mendoza, AM and Moreno, VS and Mukul, SA and Mundhenk, P and Nava-Miranda, MG and Neill, D and Neldner, VJ and Nevenic, RV and Ngugi, MR and Niklaus, PA and Oleksyn, J and Ontikov, P and Ortiz-Malavasi, E and Pan, Y and Paquette, A and Parada-Gutierrez, A and Parfenova, EI and Park, M and Parren, M and Parthasarathy, N and Peri, PL and Pfautsch, S and Phillips, OL and Picard, N and Piedade, MTTF and Piotto, D and Pitman, NCA and Polo, I and Poorter, L and Poulsen, AD and Pretzsch, H and Ramirez Arevalo, F and Restrepo-Correa, Z and Rodeghiero, M and Rolim, SG and Roopsind, A and Rovero, F and Rutishauser, E and Saikia, P and Salas-Eljatib, C and Saner, P and Schall, P and Schepaschenko, D and Scherer-Lorenzen, M and Schmid, B and Schöngart, J and Searle, EB and Seben, V and Serra-Diaz, JM and Sheil, D and Shvidenko, AZ and Silva-Espejo, JE and Silveira, M and Singh, J and Sist, P and Slik, F and Sonké, B and Souza, AF and Miscicki, S and Stereńczak, KJ and Svenning, JC and Svoboda, M and Swanepoel, B and Targhetta, N and Tchebakova, N and Ter Steege, H and Thomas, R and Tikhonova, E and Umunay, PM and Usoltsev, VA and Valencia, R and Valladares, F and van der Plas, F and Do, TV and van Nuland, ME and Vasquez, RM and Verbeeck, H and Viana, H and Vibrans, AC and Vieira, S and von Gadow, K and Wang, HF and Watson, JV and Werner, GDA and Wiser, SK and Wittmann, F and Woell, H and Wortel, V and Zagt, R and Zawiła-Niedźwiecki, T and Zhang, C and Zhao, X and Zhou, M and Zhu, ZX and Zo-Bi, IC and Maynard, DS},
title = {Native diversity buffers against severity of non-native tree invasions.},
journal = {Nature},
volume = {621},
number = {7980},
pages = {773-781},
pmid = {37612513},
issn = {1476-4687},
mesh = {*Biodiversity ; Databases, Factual ; Human Activities ; *Introduced Species/statistics &amp; numerical data/trends ; Phylogeny ; Rain ; Temperature ; *Trees/classification/physiology ; *Environment ; },
abstract = {Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species[1,2]. Tree invasions in particular have been relatively overlooked, even though they have the potential to transform ecosystems and economies[3,4]. Here, leveraging global tree databases[5-7], we explore how the phylogenetic and functional diversity of native tree communities, human pressure and the environment influence the establishment of non-native tree species and the subsequent invasion severity. We find that anthropogenic factors are key to predicting whether a location is invaded, but that invasion severity is underpinned by native diversity, with higher diversity predicting lower invasion severity. Temperature and precipitation emerge as strong predictors of invasion strategy, with non-native species invading successfully when they are similar to the native community in cold or dry extremes. Yet, despite the influence of these ecological forces in determining invasion strategy, we find evidence that these patterns can be obscured by human activity, with lower ecological signal in areas with higher proximity to shipping ports. Our global perspective of non-native tree invasion highlights that human drivers influence non-native tree presence, and that native phylogenetic and functional diversity have a critical role in the establishment and spread of subsequent invasions.},
}
@article {pmid37612396,
year = {2023},
author = {Dethier, EN and Silman, M and Leiva, JD and Alqahtani, S and Fernandez, LE and Pauca, P and Çamalan, S and Tomhave, P and Magilligan, FJ and Renshaw, CE and Lutz, DA},
title = {A global rise in alluvial mining increases sediment load in tropical rivers.},
journal = {Nature},
volume = {620},
number = {7975},
pages = {787-793},
pmid = {37612396},
issn = {1476-4687},
mesh = {Animals ; Humans ; Databases, Factual ; *Ecosystem ; Gold ; Hydrology ; *Rivers ; *Mining/statistics &amp; numerical data/trends ; Fishes ; *Tropical Climate ; *Geologic Sediments/analysis ; },
abstract = {Increasing gold and mineral mining activity in rivers across the global tropics has degraded ecosystems and threatened human health[1,2]. Such river mineral mining involves intensive excavation and sediment processing in river corridors, altering river form and releasing excess sediment downstream[2]. Increased suspended sediment loads can reduce water clarity and cause siltation to levels that may result in disease and mortality in fish[3,4], poor water quality[5] and damage to human infrastructure[6]. Although river mining has been investigated at local scales, no global synthesis of its physical footprint and impacts on hydrologic systems exists, leaving its full environmental consequences unknown. We assemble and analyse a 37-year satellite database showing pervasive, increasing river mineral mining worldwide. We identify 396 mining districts in 49 countries, concentrated in tropical waterways that are almost universally altered by mining-derived sediment. Of 173 mining-affected rivers, 80% have suspended sediment concentrations (SSCs) more than double pre-mining levels. In 30 countries in which mining affects large (>50 m wide) rivers, 23 ± 19% of large river length is altered by mining-derived sediment, a globe-spanning effect representing 35,000 river kilometres, 6% (±1% s.e.) of all large tropical river reaches. Our findings highlight the ubiquity and intensity of mining-associated degradation in tropical river systems.},
}
@article {pmid37612395,
year = {2023},
author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS},
title = {Landscape-scale benefits of protected areas for tropical biodiversity.},
journal = {Nature},
volume = {620},
number = {7975},
pages = {807-812},
pmid = {37612395},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources/legislation &amp; jurisprudence/methods/trends ; Mammals ; *Tropical Climate ; *Goals ; *United Nations ; Forestry/legislation &amp; jurisprudence/methods/trends ; },
abstract = {The United Nations recently agreed to major expansions of global protected areas (PAs) to slow biodiversity declines[1]. However, although reserves often reduce habitat loss, their efficacy at preserving animal diversity and their influence on biodiversity in surrounding unprotected areas remain unclear[2-5]. Unregulated hunting can empty PAs of large animals[6], illegal tree felling can degrade habitat quality[7], and parks can simply displace disturbances such as logging and hunting to unprotected areas of the landscape[8] (a phenomenon called leakage). Alternatively, well-functioning PAs could enhance animal diversity within reserves as well as in nearby unprotected sites[9] (an effect called spillover). Here we test whether PAs across mega-diverse Southeast Asia contribute to vertebrate conservation inside and outside their boundaries. Reserves increased all facets of bird diversity. Large reserves were also associated with substantially enhanced mammal diversity in the adjacent unprotected landscape. Rather than PAs generating leakage that deteriorated ecological conditions elsewhere, our results are consistent with PAs inducing spillover that benefits biodiversity in surrounding areas. These findings support the United Nations goal of achieving 30% PA coverage by 2030 by demonstrating that PAs are associated with higher vertebrate diversity both inside their boundaries and in the broader landscape.},
}
@article {pmid37611791,
year = {2023},
author = {Sarkar, DJ and Das Sarkar, S and V, SK and Chanu, TN and Banerjee, T and Chakraborty, L and Bhor, M and Nag, SK and Samanta, S and Das, BK},
title = {Ameliorative effect of natural floating island as fish aggregating devices on heavy metals distribution in a freshwater wetland.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {336},
number = {},
pages = {122428},
doi = {10.1016/j.envpol.2023.122428},
pmid = {37611791},
issn = {1873-6424},
mesh = {Animals ; Humans ; Wetlands ; Geologic Sediments ; Environmental Monitoring ; *Metals, Heavy/analysis ; Fresh Water ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; China ; },
abstract = {Growing human population and climate change are leading reasons for water quality deterioration globally; and ecologically important waterbodies including freshwater wetlands are in a vulnerable state due to increasing concentrations of pollutants like heavy metals. Given the declining health of these valuable resources, the present study was conducted to evaluate the effect of natural floating island in the form of fish aggregating devices (FADs) made of native weed mass on the distribution of heavy metals in the abiotic and bio compartments of a freshwater wetland. Lower concentrations of surface water heavy metals were observed inside the FADs with a reduction of 73.91%, 65.22% and 40.57-49.16% for Cd, Pb and other metals (viz. Co, Cr, Cu, Ni and Zn), respectively as compared to outside FAD. These led to 14.72-55.39% reduction in the heavy metal pollution indices inside the FAD surface water. The fish species inside the FADs were also found less contaminated (24.07-25.07% reduction) with lower health risk indices. The study signifies the valuable contribution of natural floating island as FADs in ameliorating the effect of heavy metals pollution emphasizing the tremendous role of the natural floating islands in sustainable maintenance of freshwater wetlands for better human health and livelihood.},
}
@article {pmid37601214,
year = {2023},
author = {Rocha, AFBM and Freitas-Junior, R and Soares, LR and Ferreira, GLR},
title = {Breast cancer screening and diagnosis in older adults women in Brazil: why it is time to reconsider the recommendations.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1232668},
pmid = {37601214},
issn = {2296-2565},
mesh = {Aged ; Female ; Humans ; Brazil/epidemiology ; *Breast Neoplasms/diagnosis ; Databases, Factual ; *Early Detection of Cancer ; State Medicine ; Mammography ; Neoplasm Staging ; Middle Aged ; },
abstract = {INTRODUCTION: Breast cancer screening in women of 70 years of age or older remains controversial due to a lack of studies that include women of this age.<br><br>METHODS: This ecological study evaluated data from the Brazilian National Health Service (SUS) on breast cancer screening and staging in this age group compared to 50-69-year olds, for Brazil as a whole and for its geographical regions, between 2013 and 2019. A secondary database was obtained from the outpatient data system of the SUS's Informatics Department, the Brazil Oncology Panel, the Brazilian Institute of Geography and Statistics, the Supplementary Health Agency and the Online Mortality Atlas.<br><br>RESULTS: There was a marked reduction in screening in women &#x2265;70&#x2009;years of age (annual percent change [APC] -3.5; p&#x2009;<&#x2009;0.001) compared to those of 50-69&#x2009;years of age (APC-2.2; p&#x2009;=&#x2009;0.010). There was a trend towards an increase in clinical staging, with a greater occurrence of stages III and IV in the &#x2265;70 group (44.3%) compared to the women of 50-69&#x2009;years of age (40.8%; p&#x2009;<&#x2009;0.001).<br><br>CONCLUSION: Considering the increasing age of the Brazilian population and the heterogeneity among older adults women, screening for the over-70s within the SUS merits greater debate insofar as the implementation of public policies is concerned.},
}
@article {pmid37600587,
year = {2023},
author = {Saccheri, IJ and , and , and , and , },
title = {The genome sequence of the Squinting Bush Brown, Bicyclus anynana (Butler, 1879).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {280},
pmid = {37600587},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Bicyclus anynana (the Squinting Bush Brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 457.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length.},
}
@article {pmid37600586,
year = {2023},
author = {Lohse, K and Hayward, A and Vila, R and , and , and , and Carvalho, APS and Kawahara, AY and , },
title = {The genome sequence of the Large Skipper, Ochlodes sylvanus, (Esper, 1777).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {75},
pmid = {37600586},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Ochlodes sylvanus, the Large Skipper (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 380 megabases in span. Most of the assembly (99.97%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,451 protein coding genes.},
}
@article {pmid37600582,
year = {2023},
author = {Lees, D and Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the Dotted Border, Agriopis marginaria (Fabricius, 1776).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {152},
pmid = {37600582},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agriopis marginaria (the Dotted Border, Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 500.9 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,443 protein coding genes.},
}
@article {pmid37598535,
year = {2023},
author = {Tokatlı, C and Uğurluoğlu, A and Muhammad, S},
title = {Ecotoxicological evaluation of organic contamination in the world's two significant gateways to the Black Sea using GIS techniques: Turkish Straits.},
journal = {Marine pollution bulletin},
volume = {194},
number = {Pt A},
pages = {115405},
doi = {10.1016/j.marpolbul.2023.115405},
pmid = {37598535},
issn = {1879-3363},
mesh = {Child ; Humans ; Black Sea ; *Ecosystem ; *Geographic Information Systems ; Ecotoxicology ; Lakes ; },
abstract = {This study was carried out to determine the spatial-temporal distributions of limnological parameters of Çanakkale Strait (ÇS) and İstanbul Strait (İS), Turkiye. Fluvial (n = 11) and lacustrine (n = 4) habitats water samples were collected in the dry and rainy seasons of 2022-2023. Among limnological parameters, the highest mean electrical conductivity values of 6063 μS/cm were noted in the İS basin during the rainy season and the lowest was 0.04 mg/L for nitrite in the ÇS basin. Generally, the levels of organic contaminants and ecological risk indices were as follows: rivers of İS > rivers of ÇS > Alibey Dam Lake (İS) > Atikhisar Dam Lake (ÇS). The highest non-carcinogenic health risks of 0.88 were noted for children in the ÇS basin during the dry season and the lowest of <0.01 in Atikhisar Dam Lake during the rainy season. Multivariate statistical techniques were applied to data to categorize investigated ecosystems and sources apportionment of contaminants and geospatial distribution.},
}
@article {pmid37598281,
year = {2023},
author = {Nazari Ashani, M and Alesheikh, AA and Neisani Samani, Z and Lotfata, A and Bayat, S and Alipour, S and Hoseini, B},
title = {Socioeconomic and environmental determinants of foot and mouth disease incidence: an ecological, cross-sectional study across Iran using spatial modeling.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13526},
pmid = {37598281},
issn = {2045-2322},
mesh = {Animals ; Sheep ; Iran/epidemiology ; *Foot-and-Mouth Disease/epidemiology ; Cross-Sectional Studies ; Asia ; Goats ; Socioeconomic Factors ; },
abstract = {Foot-and-mouth disease (FMD) is a highly contagious animal disease caused by a ribonucleic acid (RNA) virus, with significant economic costs and uneven distribution across Asia, Africa, and South America. While spatial analysis and modeling of FMD are still in their early stages, this research aimed to identify socio-environmental determinants of FMD incidence in Iran at the provincial level by studying 135 outbreaks reported between March 21, 2017, and March 21, 2018. We obtained 46 potential socio-environmental determinants and selected four variables, including percentage of population, precipitation in January, percentage of sheep, and percentage of goats, to be used in spatial regression models to estimate variation in spatial heterogeneity. In our analysis, we employed global models, namely ordinary least squares (OLS), spatial error model (SEM), and spatial lag model (SLM), as well as local models, including geographically weighted regression (GWR) and multiscale geographically weighted regression (MGWR). The MGWR model yielded the highest adjusted [Formula: see text] of 90%, outperforming the other local and global models. Using local models to map the effects of environmental determinants (such as the percentage of sheep and precipitation) on the spatial variability of FMD incidence provides decision-makers with helpful information for targeted interventions. Our findings advocate for multiscale and multidisciplinary policies to reduce FMD incidence.},
}
@article {pmid37598114,
year = {2023},
author = {Tom, M and Lubinevsky, H and Kanari, M},
title = {Integrative data system for monitoring biota and natural habitats in the Israeli Eastern Mediterranean marine environment.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {9},
pages = {1068},
pmid = {37598114},
issn = {1573-2959},
mesh = {Humans ; Israel ; *Environmental Monitoring ; *Biota ; Databases, Factual ; Environmental Policy ; },
abstract = {An integrative data system for monitoring the biota of the Mediterranean waters of Israel as well as selected records from adjacent Levantine basin regions is presented here, aimed at providing data and research tools for long-term bio-geographic and ecological studies and more important, providing background data for assisting governmental regulators to establish educated habitat-oriented environmental policy. The system relies on the geographic information system (GIS) online map-based platform and contains at present the following components: biotic database of ~ 170,000 recorded sampling events; uniform habitat maps of 63 benthic habitats and 2 pelagic ones, constructed using relevant bathymetric features and biotic community compositions; bathymetric hill-shade map; depth contours; raster depth grid and human interference map. Other informative auxiliary maps are planned to be added (e.g., map of potential pockmark sites, detailed maps of tiny carbonate crust nolls and more). A number of 883 cited documents were listed by us for potential extraction of sampling efforts, most of them are available to us as PDFs and are available also to the users, excluding copyright-protected ones. Forty-three major projects were depicted in addition to a variety of small studies (e.g., university theses). Thirty-five sampling devices were documented and described, and 3187 species-level identifications were already recorded. In addition, the system provides access to description of sampling devices and pictures of species and seascapes. New data is continuously deposited to the system and the system is flexible, allowing future addition of new types of information. The system site is accessible through the link: https://experience.arcgis.com/experience/40e86605ff4d4e5096ed2c901fec2a2f .},
}
@article {pmid37596254,
year = {2023},
author = {Szymura, TH and Kassa, H and Swacha, G and Szymura, M and Zając, A and Kącki, Z},
title = {Spatial patterns of vascular plant species richness in Poland - a data set.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {542},
pmid = {37596254},
issn = {2052-4463},
mesh = {Checklist ; Computer Systems ; Databases, Factual ; Poland ; *Tracheophyta ; },
abstract = {Recognition of species richness spatial patterns is important for nature conservation and theoretical studies. Inventorying species richness, especially at a larger spatial extent is challenging, thus different data sources are joined and harmonized to obtain a comprehensive data set. Here we present a new data set showing vascular plant species richness in Poland based on a grid of 10 × 10 km squares. The data set was created using data from two sources: the Atlas of Distribution of Vascular Plants in Poland and the Polish Vegetation Database. Using this data set, we analysed 2,160 species with taxonomical nomenclature according to the Euro + Med PlantBase checklist in 3,283 squares covering the entire territory of Poland (ca. 312,000 km[2]). The species were divided into groups according to their status and frequency of distribution, and the statistics for each square were obtained. For purposes of analysis, sampling bias was assessed. The data set promotes theoretical analysis on species richness and reinforces the planning of nature conservations.},
}
@article {pmid37593568,
year = {2023},
author = {Jaron, KS and Berg, MP and Ellers, J and Hodson, CN and Ross, L and , and , and , and , and , },
title = {The genome sequence of the springtail Allacma fusca (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {319},
pmid = {37593568},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Allacma fusca (the springtail; Arthropoda; Collembola; Symphypleona; Sminthuridae). The genome sequence is 392.8 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 14.94 kilobases in length.},
}
@article {pmid37593439,
year = {2023},
author = {Santarius, T and Bieser, JCT and Frick, V and Höjer, M and Gossen, M and Hilty, LM and Kern, E and Pohl, J and Rohde, F and Lange, S},
title = {Digital sufficiency: conceptual considerations for ICTs on a finite planet.},
journal = {Annales des telecommunications},
volume = {78},
number = {5-6},
pages = {277-295},
pmid = {37593439},
issn = {1958-9395},
abstract = {ICT hold significant potential to increase resource and energy efficiencies and contribute to a circular economy. Yet unresolved is whether the aggregated net effect of ICT overall mitigates or aggravates environmental burdens. While the savings potentials have been explored, drivers that prevent these and possible counter measures have not been researched thoroughly. The concept digital sufficiency constitutes a basis to understand how ICT can become part of the essential environmental transformation. Digital sufficiency consists of four dimensions, each suggesting a set of strategies and policy proposals: (a) hardware sufficiency, which aims for fewer devices needing to be produced and their absolute energy demand being kept to the lowest level possible to perform the desired tasks; (b) software sufficiency, which covers ensuring that data traffic and hardware utilization during application are kept as low as possible; (c) user sufficiency, which strives for users applying digital devices frugally and using ICT in a way that promotes sustainable lifestyles; and (d) economic sufficiency, which aspires to digitalization supporting a transition to an economy characterized not by economic growth as the primary goal but by sufficient production and consumption within planetary boundaries. The policies for hardware and software sufficiency are relatively easily conceivable and executable. Policies for user and economic sufficiency are politically more difficult to implement and relate strongly to policies for environmental transformation in general. This article argues for comprehensive policies for digital sufficiency, which are indispensible if ICT are to play a beneficial role in overall environmental transformation.},
}
@article {pmid37590347,
year = {2023},
author = {O'Keefe, FR and Dunn, RE and Weitzel, EM and Waters, MR and Martinez, LN and Binder, WJ and Southon, JR and Cohen, JE and Meachen, JA and DeSantis, LRG and Kirby, ME and Ghezzo, E and Coltrain, JB and Fuller, BT and Farrell, AB and Takeuchi, GT and MacDonald, G and Davis, EB and Lindsey, EL},
title = {Pre-Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift.},
journal = {Science (New York, N.Y.)},
volume = {381},
number = {6659},
pages = {eabo3594},
doi = {10.1126/science.abo3594},
pmid = {37590347},
issn = {1095-9203},
mesh = {Humans ; Archaeology ; Desiccation ; *Ecosystem ; *Fires ; *Fossils ; California ; *Extinction, Biological ; Animals ; },
abstract = {The cause, or causes, of the Pleistocene megafaunal extinctions have been difficult to establish, in part because poor spatiotemporal resolution in the fossil record hinders alignment of species disappearances with archeological and environmental data. We obtained 172 new radiocarbon dates on megafauna from Rancho La Brea in California spanning 15.6 to 10.0 thousand calendar years before present (ka). Seven species of extinct megafauna disappeared by 12.9 ka, before the onset of the Younger Dryas. Comparison with high-resolution regional datasets revealed that these disappearances coincided with an ecological state shift that followed aridification and vegetation changes during the Bølling-Allerød (14.69 to 12.89 ka). Time-series modeling implicates large-scale fires as the primary cause of the extirpations, and the catalyst of this state shift may have been mounting human impacts in a drying, warming, and increasingly fire-prone ecosystem.},
}
@article {pmid37589308,
year = {2022},
author = {Mendes de Farias, T and Wollbrett, J and Robinson-Rechavi, M and Bastian, F},
title = {Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience.},
journal = {GigaScience},
volume = {12},
number = {},
pages = {},
pmid = {37589308},
issn = {2047-217X},
support = {U01 CA215010/CA/NCI NIH HHS/United States ; },
mesh = {*Biomedical Research ; Computational Biology ; Knowledge Bases ; },
abstract = {BACKGROUND: Enhancing interoperability of bioinformatics knowledge bases is a high-priority requirement to maximize data reusability and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange value once the knowledge base is (re)used, and without interoperability, the utility lies dormant.<br><br>RESULTS: In this article, we discuss several approaches to boost interoperability depending on the interoperable parts. The findings are driven by several real-world scenario examples that were mostly implemented by Bgee, a well-established gene expression knowledge base. To better justify the findings are transferable, for each Bgee interoperability experience, we also highlight similar implementations by major bioinformatics knowledge bases. Moreover, we discuss ten general main lessons learned. These lessons can be applied in the context of any bioinformatics knowledge base to foster data reusability.<br><br>CONCLUSIONS: This work provides pragmatic methods and transferable skills to promote reusability of bioinformatics knowledge bases by focusing on interoperability.},
}
@article {pmid37587525,
year = {2023},
author = {Ma, R and Li, C and Tian, H and Zhang, Y and Feng, X and Li, J and Hu, W},
title = {The current distribution of tick species in Inner Mongolia and inferring potential suitability areas for dominant tick species based on the MaxEnt model.},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {286},
pmid = {37587525},
issn = {1756-3305},
support = {U22A20526//Study on pathogen spectrum, temporal and spatial distribution and transmission features of the important emerging and re-emerging zoonosis in Inner Mongolia Autonomous Region/ ; },
mesh = {Humans ; Animals ; *Ixodes ; China/epidemiology ; *Ixodidae ; Databases, Factual ; Global Warming ; },
abstract = {BACKGROUND: Ticks are known to transmit a wide range of diseases, including those caused by bacteria, viruses, and protozoa. The expansion of tick habitats has been intensified in recent years due to various factors such as global warming, alterations in microclimate, and human activities. Consequently, the probability of human exposure to diseases transmitted by ticks has increased, leading to a higher degree of risk associated with such diseases.<br><br>METHODS: In this study, we conducted a comprehensive review of domestic and international literature databases to determine the current distribution of tick species in Inner Mongolia. Next, we employed the MaxEnt model to analyze vital climatic and environmental factors influencing dominant tick distribution. Subsequently, we predicted the potential suitability areas of these dominant tick species under the near current conditions and the BCC-CSM2.MR model SSP245 scenario for the future periods of 2021-2040, 2041-2060, 2061-2080, and 2081-2100.<br><br>RESULTS: Our study revealed the presence of 23 tick species from six genera in Inner Mongolia, including four dominant tick species (Dermacentor nuttalli, Ixodes persulcatus, Dermacentor silvarum, and Hyalomma asiaticum). Dermacentor nuttalli, D. silvarum, and I. persulcatus are predominantly found in regions such as Xilin Gol and Hulunbuir. Temperature seasonality (Bio4), elevation (elev), and precipitation seasonality (Bio15) were the primary variables impacting the distribution of three tick species. In contrast, H. asiaticum is mainly distributed in Alxa and Bayannur and demonstrates heightened sensitivity to precipitation and other climatic factors. Our modeling results suggested that the potential suitability areas of these tick species would experience fluctuations over the four future periods (2021-2040, 2041-2060, 2061-2080, and 2081-2100). Specifically, by 2081-2100, the centroid of suitable habitat for D. nuttalli, H. asiaticum, and I. persulcatus was predicted to shift westward, with new suitability areas emerging in regions such as Chifeng and Xilin Gol. The centroid of suitable habitat for H. asiaticum will move northeastward, and new suitability areas are likely to appear in areas such as Ordos and Bayannur.<br><br>CONCLUSIONS: This study provided a comprehensive overview of the tick species distribution patterns in Inner Mongolia. Our research has revealed a significant diversity of tick species in the region, exhibiting a wide distribution but with notable regional disparities. Our modeling results suggested that the dominant tick species' suitable habitats will significantly expand in the future compared to their existing distribution under the near current conditions. Temperature and precipitation are the primary variables influencing these shifts in distribution. These findings can provide a valuable reference for future research on tick distribution and the surveillance of tick-borne diseases in the region.},
}
@article {pmid37586008,
year = {2023},
author = {Garces, TS and Damasceno, LLV and Sousa, GJB and Cestari, VRF and Pereira, MLD and Moreira, TMM},
title = {Relationship between social development indicators and mortality due to Diabetes Mellitus in Brazil: a space-time analysis.},
journal = {Revista latino-americana de enfermagem},
volume = {31},
number = {},
pages = {e3971},
pmid = {37586008},
issn = {1518-8345},
mesh = {Humans ; *Diabetes Mellitus/mortality ; Social Factors ; Brazil/epidemiology ; Spatio-Temporal Analysis ; Income ; },
abstract = {OBJECTIVE: to identify the space-time pattern of mortality due to Diabetes Mellitus in Brazil, as well as its relationship with social development indicators.<br><br>METHOD: an ecological and time series nationwide study based on secondary data from the Unified Health System Informatics Department, with space-time analysis and inclusion of indicators in non-spatial and spatial regression models. The following was performed: overall mortality rate calculation; characterization of the sociodemographic and regional profiles of the death cases by means of descriptive and time analysis; and elaboration of thematic maps.<br><br>RESULTS: a total of 601,521&#xa0;deaths related to Diabetes Mellitus were recorded in Brazil, representing a mean mortality rate of 29.5/100,000&#xa0;inhabitants. The states of Rio Grande do Norte, Para&#xed;ba, Pernambuco, Alagoas and Sergipe, Rio de Janeiro, Paran&#xe1; and Rio Grande do Sul presented high-high clusters. By using regression models, it was verified that the Gini index (&#x3b2;=11.7) and the Family Health Strategy coverage (&#x3b2;=3.9) were the indicators that most influenced mortality due to Diabetes Mellitus in Brazil.<br><br>CONCLUSION: in Brazil, mortality due to Diabetes presents an overall increasing trend, revealing itself as strongly associated with places that have worse social indicators.<br><br>HIGHLIGHTS: (1) The time-space pattern of mortality due to Diabetes presents an increasing trend. (2) The Northeast and South regions present high rates of mortality due to Diabetes. (3) Mortality due to Diabetes is associated with worse sociodemographic indicators. (4) A relationship is observed between income, access to health and mortality due to&#xa0;Diabetes.},
}
@article {pmid37577540,
year = {2023},
author = {Liu, C and Downey, RJ and Salminen, JS and Rojas, SA and Richer, N and Pliner, EM and Hwang, J and Cruz-Almeida, Y and Manini, TM and Hass, CJ and Seidler, RD and Clark, DJ and Ferris, DP},
title = {Electrical Brain Activity during Human Walking with Parametric Variations in Terrain Unevenness and Walking Speed.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37577540},
issn = {2692-8205},
support = {R01 NS104772/NS/NINDS NIH HHS/United States ; F32 AG072808/AG/NIA NIH HHS/United States ; P30 AG028740/AG/NIA NIH HHS/United States ; U01 AG061389/AG/NIA NIH HHS/United States ; T32 AG062728/AG/NIA NIH HHS/United States ; },
abstract = {Mobile brain imaging with high-density electroencephalography (EEG) can provide insight into the cortical processes involved in complex human walking tasks. While uneven terrain is common in the natural environment and poses challenges to human balance control, there is limited understanding of the supraspinal processes involved with traversing uneven terrain. The primary objective of this study was to quantify electrocortical activity related to parametric variations in terrain unevenness for neurotypical young adults. We used high-density EEG to measure brain activity when thirty-two young adults walked on a novel custom-made uneven terrain treadmill surface with four levels of difficulty at a walking speed tailored to each participant. We identified multiple brain regions associated with uneven terrain walking. Alpha (8 - 13 Hz) and beta (13 - 30 Hz) spectral power decreased in the sensorimotor and posterior parietal areas with increasing terrain unevenness while theta (4 - 8 Hz) power increased in the mid/posterior cingulate area with terrain unevenness. We also found that within stride spectral power fluctuations increased with terrain unevenness. Our secondary goal was to investigate the effect of parametric changes in walking speed (0.25 m/s, 0.5m/s, 0.75 m/s, 1.0 m/s) to differentiate the effects of walking speed from uneven terrain. Our results revealed that electrocortical activities only changed substantially with speed within the sensorimotor area but not in other brain areas. Together, these results indicate there are distinct cortical processes contributing to the control of walking over uneven terrain versus modulation of walking speed on smooth, flat terrain. Our findings increase our understanding of cortical involvement in an ecologically valid walking task and could serve as a benchmark for identifying deficits in cortical dynamics that occur in people with mobility deficits.},
}
@article {pmid37574463,
year = {2023},
author = {Stapp, EK and Zipunnikov, V and Leroux, A and Cui, L and Husky, MM and Dey, D and Merikangas, KR},
title = {Specificity of affective dynamics of bipolar and major depressive disorder.},
journal = {Brain and behavior},
volume = {13},
number = {9},
pages = {e3134},
pmid = {37574463},
issn = {2162-3279},
support = {Z01 MH002804/ImNIH/Intramural NIH HHS/United States ; ZIA MH002804/ImNIH/Intramural NIH HHS/United States ; ZIA MH002804/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Depressive Disorder, Major/psychology ; *Bipolar Disorder/psychology ; Anxiety ; Anxiety Disorders ; },
abstract = {OBJECTIVE: Here, we examine whether the dynamics of the four dimensions of the circumplex model of affect assessed by ecological momentary assessment (EMA) differ among those with bipolar disorder (BD) and major depressive disorder (MDD).<br><br>METHODS: Participants aged 11-85&#xa0;years (n&#xa0;=&#xa0;362) reported momentary sad, anxious, active, and energetic dimensional states four times per day for 2&#xa0;weeks. Individuals with lifetime mood disorder subtypes of bipolar-I, bipolar-II, and MDD derived from a semistructured clinical interview were compared to each other and to controls without a lifetime history of psychiatric disorders. Random effects from individual means, inertias, innovation (residual) variances, and cross-lags across the four affective dimensions simultaneously were derived from multivariate dynamic structural equation models.<br><br>RESULTS: All mood disorder subtypes were associated with higher levels of sad and anxious mood and lower energy than controls. Those with bipolar-I had lower average activation, and lower energy that was independent of activation, compared to MDD or controls. However, increases in activation were more likely to perpetuate in those with bipolar-I. Bipolar-II was characterized by higher lability of sad and anxious mood compared to bipolar-I and controls but not MDD. Compared to BD and controls, those with MDD exhibited cross-augmentation of sadness and anxiety, and sadness blunted energy.<br><br>CONCLUSION: Bipolar-I is more strongly characterized by activation and energy than sad and anxious mood. This distinction has potential implications for both specificity of intervention targets and differential pathways underlying these dynamic affective systems. Confirmation of the longer term stability and generalizability of these findings in future studies is necessary.},
}
@article {pmid37572835,
year = {2023},
author = {Chaemsaithong, P and Jenjaroenpun, P and Pongchaikul, P and Singsaneh, A and Thaipisuttikul, I and Romero, R and Wongsurawat, T},
title = {Rapid detection of bacteria and antimicrobial resistant genes in intraamniotic infection using nanopore adaptive sampling.},
journal = {American journal of obstetrics and gynecology},
volume = {229},
number = {6},
pages = {690-693.e1},
pmid = {37572835},
issn = {1097-6868},
support = {Z01 HD002400/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Humans ; Female ; *Nanopores ; Bacteria ; *Chorioamnionitis/microbiology ; *Anti-Infective Agents ; Amniotic Fluid/microbiology ; },
abstract = {Nanopore adaptive sampling to diagnose intraamniotic infection},
}
@article {pmid37568226,
year = {2023},
author = {Leo, P and de Melo Texeira, M and Chander, AM and Singh, NK and Simpson, AC and Yurkov, A and Karouia, F and Stajich, JE and Mason, CE and Venkateswaran, K},
title = {Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities.},
journal = {IMA fungus},
volume = {14},
number = {1},
pages = {15},
pmid = {37568226},
issn = {2210-6340},
support = {18-PPR18-0011//NNH18ZDA001N-PPR/ ; },
abstract = {During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3[T], isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1[T], isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3[T] = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1[T] = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.},
}
@article {pmid37567881,
year = {2023},
author = {Koludarov, I and Senoner, T and Jackson, TNW and Dashevsky, D and Heinzinger, M and Aird, SD and Rost, B},
title = {Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {4861},
pmid = {37567881},
issn = {2041-1723},
mesh = {Animals ; *Three Finger Toxins ; Phylogeny ; Snakes/genetics ; *Toxins, Biological/genetics ; Reptiles ; Elapid Venoms/genetics ; Evolution, Molecular ; },
abstract = {Three-finger toxins (3FTXs) are a functionally diverse family of toxins, apparently unique to venoms of caenophidian snakes. Although the ancestral function of 3FTXs is antagonism of nicotinic acetylcholine receptors, redundancy conferred by the accumulation of duplicate genes has facilitated extensive neofunctionalization, such that derived members of the family interact with a range of targets. 3FTXs are members of the LY6/UPAR family, but their non-toxin ancestor remains unknown. Combining traditional phylogenetic approaches, manual synteny analysis, and machine learning techniques (including AlphaFold2 and ProtT5), we have reconstructed a detailed evolutionary history of 3FTXs. We identify their immediate ancestor as a non-secretory LY6, unique to squamate reptiles, and propose that changes in molecular ecology resulting from loss of a membrane-anchoring domain and changes in gene expression, paved the way for the evolution of one of the most important families of snake toxins.},
}
@article {pmid37567871,
year = {2023},
author = {Tonin, R and Wilhelmi, S and Gültas, M and Gerdol, R and Paun, O and Trucchi, E and Schmitt, AO and Wellstein, C},
title = {Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae).},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {13055},
pmid = {37567871},
issn = {2045-2322},
mesh = {Humans ; *Ericaceae ; *Vaccinium vitis-idaea/genetics ; Ice ; Seasons ; Polymorphism, Single Nucleotide ; },
abstract = {In the mountain terrain, ice holes are little depressions between rock boulders that are characterized by the exit of cold air able to cool down the rock surface even in summer. This cold air creates cold microrefugia in warmer surroundings that preserve plant species probably over thousands of years under extra-zonal climatic conditions. We hypothesized that ice hole populations of the model species Vaccinium vitis-idaea (Ericaceae) show genetic differentiation from nearby zonal subalpine populations, and high functional trait distinctiveness, in agreement with genetic patterns. We genotyped almost 30,000 single nucleotide polymorphisms using restriction site-associated DNA sequencing and measured eight functional traits indicative of individual performance and ecological strategies. Genetic results showed high differentiation among the six populations suggesting isolation. On siliceous bedrock, ice hole individuals exhibited higher levels of admixture than those from subalpine populations which could have experienced more bottlenecks during demographic fluctuations related to glacial cycles. Ice hole and subalpine calcareous populations clearly separated from siliceous populations, indicating a possible effect of bedrock in shaping genetic patterns. Trait analysis reflected the bedrock effect on populations' differentiation. The significant correlation between trait and genetic distances suggests the genetic contribution in shaping intraspecific functional differentiation. In conclusion, extra-zonal populations reveal a prominent genetic and phenotypic differentiation determined by history and ecological contingency. Therefore, microrefugia populations can contribute to the overall variability of the species and lead to intraspecific-driven responses to upcoming environmental changes.},
}
@article {pmid37564020,
year = {2023},
author = {Xu, P and Zhang, W and Wang, X and Zhu, Y and Liang, W and He, Y and Yu, X},
title = {Multiomics analysis reveals a link between Brassica-specific miR1885 and rapeseed tolerance to low temperature.},
journal = {Plant, cell &amp; environment},
volume = {46},
number = {11},
pages = {3405-3419},
doi = {10.1111/pce.14690},
pmid = {37564020},
issn = {1365-3040},
support = {2016YFD0101900//National Programs for Science and Technology Development of China/ ; 2019NY-038//Science and Technology Program of Shaanxi Province/ ; 2022M72211//China Postdoctoral Science Foundation/ ; 21PJ1407600//Shanghai Pujiang Program/ ; 32170581//National Natural Science Foundation of China/ ; 31471883//National Natural Science Foundation of China/ ; 31571261//National Natural Science Foundation of China/ ; },
mesh = {*Brassica napus/genetics ; *Brassica rapa/genetics ; *Brassica/genetics ; Genome-Wide Association Study ; Multiomics ; Temperature ; *MicroRNAs/genetics ; RNA, Messenger ; Gene Expression Regulation, Plant ; },
abstract = {Brassica crops include various edible vegetable and plant oil crops, and their production is limited by low temperature beyond their tolerant capability. The key regulators of low-temperature resistance in Brassica remain largely unexplored. To identify posttranscriptional regulators of plant response to low temperature, we performed small RNA profiling, and found that 16 known miRNAs responded to cold treatment in Brassica rapa. The cold response of seven of those miRNAs were further confirmed by qRT-PCR and/or northern blot analyses. In parallel, a genome-wide association study of 220 accessions of Brassica napus identified four candidate MIRNA genes, all of which were cold-responsive, at the loci associated with low-temperature resistance. Specifically, these large-scale data analyses revealed a link between miR1885 and the plant response to low temperature in both B. rapa and B. napus. Using 5' rapid amplification of cDNA ends approach, we validated that miR1885 can cleave its putative target gene transcripts, Bn.TIR.A09 and Bn.TNL.A03, in B. napus. Furthermore, overexpression of miR1885 in Semiwinter type B. napus decreased the mRNA abundance of Bn.TIR.A09 and Bn.TNL.A03 and resulted in increased sensitivity to low temperature. Knocking down of miR1885 in Spring type B. napus led to increased mRNA abundance of its targets and improved rapeseed tolerance to low temperature. Together, our results suggested that the loci of miR1885 and its targets could be potential candidates for the molecular breeding of low temperature-tolerant Spring type Brassica crops.},
}
@article {pmid37563691,
year = {2023},
author = {Lotfata, A and Moosazadeh, M and Helbich, M and Hoseini, B},
title = {Socioeconomic and environmental determinants of asthma prevalence: a cross-sectional study at the U.S. County level using geographically weighted random forests.},
journal = {International journal of health geographics},
volume = {22},
number = {1},
pages = {18},
pmid = {37563691},
issn = {1476-072X},
mesh = {Adult ; Humans ; *Asthma/diagnosis/epidemiology ; Cross-Sectional Studies ; Environment ; Prevalence ; *Random Forest ; Socioeconomic Factors ; United States/epidemiology ; Artificial Intelligence ; },
abstract = {BACKGROUND: Some studies have established associations between the prevalence of new-onset asthma and asthma exacerbation and socioeconomic and environmental determinants. However, research remains limited concerning the shape of these associations, the importance of the risk factors, and how these factors vary geographically.<br><br>OBJECTIVE: We aimed (1) to examine ecological associations between asthma prevalence and multiple socio-physical determinants in the United States; and (2) to assess geographic variations in their relative importance.<br><br>METHODS: Our study design is cross sectional based on county-level data for 2020 across the United States. We obtained self-reported asthma prevalence data of adults aged 18&#xa0;years or older for each county. We applied conventional and geographically weighted random forest (GWRF) to investigate the associations between asthma prevalence and socioeconomic (e.g., poverty) and environmental determinants (e.g., air pollution and green space). To enhance the interpretability of the GWRF, we (1) assessed the shape of the associations through partial dependence plots, (2) ranked the determinants according to their global importance scores, and (3) mapped the local variable importance spatially.<br><br>RESULTS: Of the 3059 counties, the average asthma prevalence was 9.9 (standard deviation&#x2009;&#xb1;&#x2009;0.99). The GWRF outperformed the conventional random forest. We found an indication, for example, that temperature was inversely associated with asthma prevalence, while poverty showed positive associations. The partial dependence plots showed that these associations had a non-linear shape. Ranking the socio-physical environmental factors concerning their global importance showed that smoking prevalence and depression prevalence were most relevant, while green space and limited language were of minor relevance. The local variable importance measures showed striking geographical differences.<br><br>CONCLUSION: Our findings strengthen the evidence that socio-physical environments play a role in explaining asthma prevalence, but their relevance seems to vary geographically. The results are vital for implementing future asthma prevention programs that should be tailor-made for specific areas.},
}
@article {pmid37563227,
year = {2023},
author = {Lu, AT and Fei, Z and Haghani, A and Robeck, TR and Zoller, JA and Li, CZ and Lowe, R and Yan, Q and Zhang, J and Vu, H and Ablaeva, J and Acosta-Rodriguez, VA and Adams, DM and Almunia, J and Aloysius, A and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, GG and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, SM and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and DiRocco, S and Dold, C and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Gorbunova, V and Goya, RG and Grant, MJ and Green, CB and Hales, EN and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaitre, JF and Levine, AJ and Li, C and Li, X and Lim, AR and Lin, DTS and Lindemann, DM and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and O'Brien, JK and O'Tierney Ginn, P and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pellegrini, M and Peters, KJ and Pedersen, AB and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Seluanov, A and Shafer, ABA and Shanmuganayagam, D and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmaohammadi, E and Spangler, ML and Spriggs, MC and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Wallingford, MC and Wang, N and Wayne, RK and Wilkinson, GS and Williams, CK and Williams, RW and Yang, XW and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, P and Zhao, Y and Zhou, W and Zimmermann, J and Ernst, J and Raj, K and Horvath, S},
title = {Universal DNA methylation age across mammalian tissues.},
journal = {Nature aging},
volume = {3},
number = {9},
pages = {1144-1166},
pmid = {37563227},
issn = {2662-8465},
support = {K00 CA234840/CA/NCI NIH HHS/United States ; R01 AG065403/AG/NIA NIH HHS/United States ; U34 AG068482/AG/NIA NIH HHS/United States ; R21 AG055841/AG/NIA NIH HHS/United States ; P30 AG013319/AG/NIA NIH HHS/United States ; MR/T021985/1/MRC_/Medical Research Council/United Kingdom ; R01 AG050797/AG/NIA NIH HHS/United States ; HHSN268201600003C/HL/NHLBI NIH HHS/United States ; HHSN268201500001I/HL/NHLBI NIH HHS/United States ; HHSN268201600004C/HL/NHLBI NIH HHS/United States ; P51 OD011133/OD/NIH HHS/United States ; U01 AG060908/AG/NIA NIH HHS/United States ; HHSN268201600002C/HL/NHLBI NIH HHS/United States ; HHSN268201500001C/HL/NHLBI NIH HHS/United States ; HHSN268201600018C/HL/NHLBI NIH HHS/United States ; P30 AG044271/AG/NIA NIH HHS/United States ; HHSN268201600001C/HL/NHLBI NIH HHS/United States ; P01 AG051449/AG/NIA NIH HHS/United States ; N01HC25195/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Mice ; Animals ; *DNA Methylation/genetics ; *Epigenesis, Genetic ; Aging/genetics ; Longevity/genetics ; Mammals/genetics ; },
abstract = {Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.},
}
@article {pmid37561875,
year = {2023},
author = {Haghani, A and Li, CZ and Robeck, TR and Zhang, J and Lu, AT and Ablaeva, J and Acosta-Rodríguez, VA and Adams, DM and Alagaili, AN and Almunia, J and Aloysius, A and Amor, NMS and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, G and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chavez, AS and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, S and Cook, JA and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and Dirocco, S and Dold, C and Dunnum, JL and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Fei, Z and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Goya, RG and Grant, MJ and Green, CB and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaître, JF and Levine, AJ and Li, X and Li, C and Lim, AR and Lin, DTS and Lindemann, DM and Liphardt, SW and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Murphy, WJ and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and Nyamsuren, B and O'Brien, JK and Ginn, PO and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pedersen, AB and Pellegrini, M and Peters, KJ and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Shafer, ABA and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmohammadi, E and Spangler, ML and Spriggs, M and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Vu, H and Wallingford, MC and Wang, N and Wilkinson, GS and Williams, RW and Yan, Q and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, Y and Zhao, P and Zhou, W and Zoller, JA and Ernst, J and Seluanov, A and Gorbunova, V and Yang, XW and Raj, K and Horvath, S},
title = {DNA methylation networks underlying mammalian traits.},
journal = {Science (New York, N.Y.)},
volume = {381},
number = {6658},
pages = {eabq5693},
pmid = {37561875},
issn = {1095-9203},
support = {R01 AG065403/AG/NIA NIH HHS/United States ; R01 AG043930/AG/NIA NIH HHS/United States ; R21 AG055841/AG/NIA NIH HHS/United States ; 20412/CRUK_/Cancer Research UK/United Kingdom ; R56 AG072736/AG/NIA NIH HHS/United States ; R01 AG050797/AG/NIA NIH HHS/United States ; P30 AG044271/AG/NIA NIH HHS/United States ; R56 AG076607/AG/NIA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R21 ES024356/ES/NIEHS NIH HHS/United States ; U01 AG060908/AG/NIA NIH HHS/United States ; R01 AG045795/AG/NIA NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; U34 AG068482/AG/NIA NIH HHS/United States ; R21 DE028271/DE/NIDCR NIH HHS/United States ; R01 AG067782/AG/NIA NIH HHS/United States ; P30 AG013319/AG/NIA NIH HHS/United States ; R21 OD022988/OD/NIH HHS/United States ; R01 AG072736/AG/NIA NIH HHS/United States ; },
mesh = {Adult ; Animals ; Humans ; *DNA Methylation ; *Epigenesis, Genetic ; Epigenome ; Genome ; *Mammals/genetics ; Phylogeny ; },
abstract = {Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.},
}
@article {pmid37558860,
year = {2023},
author = {Béchade, B and Cabuslay, CS and Hu, Y and Mendonca, CM and Hassanpour, B and Lin, JY and Su, Y and Fiers, VJ and Anandarajan, D and Lu, R and Olson, CJ and Duplais, C and Rosen, GL and Moreau, CS and Aristilde, L and Wertz, JT and Russell, JA},
title = {Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants.},
journal = {The ISME journal},
volume = {17},
number = {10},
pages = {1751-1764},
pmid = {37558860},
issn = {1751-7370},
mesh = {Animals ; *Nitrogen ; *Ants/physiology ; Phylogeny ; Symbiosis/genetics ; Urea ; },
abstract = {While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.},
}
@article {pmid37556975,
year = {2023},
author = {Song, L and Chen, Y and Liu, S and Xu, M and Cui, J},
title = {SLWE-Net: An improved lightweight U-Net for Sargassum extraction from GOCI images.},
journal = {Marine pollution bulletin},
volume = {194},
number = {Pt B},
pages = {115349},
doi = {10.1016/j.marpolbul.2023.115349},
pmid = {37556975},
issn = {1879-3363},
mesh = {*Sargassum ; China ; Environment ; },
abstract = {The Sargassum bloom has severely impacted the ecological environment of the East China Sea and the Yellow Sea, causing significant economic losses. In recent years, deep learning has seen extensive development due to its outstanding feature extraction capabilities. However, the deep learning process typically involves a large number of parameters and computations. To address this issue, this paper proposes a lightweight deep learning network based on the U-Net framework, called SLWE-NET, which uses lightweight modules to replace the feature extraction modules in U-Net. In this experiment, SLWE-Net performed the best in both extraction accuracy and model lightweight. Compared to the formal U-Net, the number of parameters decreased by 65.83 %, the model size reduced from 94.97 MB to 32.51 MB, and the mIoU increased to 93.81 %. Therefore, the method proposed in this paper is beneficial for Sargassum extraction and provides a basis for operational monitoring.},
}
@article {pmid37556709,
year = {2023},
author = {Pavinati, G and Lima, LV and Palmieri, IGS and Magnabosco, GT},
title = {Distribution and spatial autocorrelation of viral hepatitis B and C in Paraná, Brazil: an ecological study, 2011-2019.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {32},
number = {2},
pages = {e2022888},
pmid = {37556709},
issn = {2237-9622},
mesh = {Humans ; Brazil/epidemiology ; *Hepatitis B/epidemiology ; Spatial Analysis ; *Hepatitis C/epidemiology ; Information Systems ; },
abstract = {OBJECTIVE: to analyze the distribution and spatial autocorrelation of hepatitis B and C detection rates in the state of Paraná, Brazil.<br><br>METHODS: this was an ecological study of hepatitis B and C notifications held on the Notifiable Health Conditions Information System, between 2011 and 2019. Percentage change in detection rates between the first and last three-year periods was estimated. Spatial autocorrelation was analyzed using Moran's index.<br><br>RESULTS: there were 16,699 notifications of hepatitis B, with a greater reduction in detection in the North (-30.0%) and Northwest (-25.9%) macro-regions. There were clusters of high occurrence in the Foz do Igua&#xe7;u, Francisco Beltr&#xe3;o and Cascavel regions between 2011 and 2019. There were 10,920 notifications of hepatitis C, with a greater reduction in detection in the Northwest macro-region (-18.9%) and an increase in the West (51.1%). The Paranagu&#xe1; region recorded a high detection cluster between 2011 and 2016.<br><br>CONCLUSION: hepatitis B and C showed heterogeneous distribution between health regions.},
}
@article {pmid37554800,
year = {2023},
author = {Motuziuk, O and Nozdrenko, D and Prylutska, S and Vareniuk, I and Bogutska, K and Braniuk, S and Korotkyi, O and Prylutskyy, Y and Ritter, U and Piosik, J},
title = {The effect of C60 fullerene on the mechanokinetics of muscle gastrocnemius contraction in chronically alcoholized rats.},
journal = {Heliyon},
volume = {9},
number = {8},
pages = {e18745},
pmid = {37554800},
issn = {2405-8440},
abstract = {The C60 fullerene effect (oral administration at a dose of 1 mg kg[-1]) on the selected biomechanical parameters of muscle gastrocnemius contraction, biochemical indicators of blood and muscle tissue as well as histological changes in rat muscle tissue after chronic alcoholization for 3, 6 and 9 months was studied in detail. Water-soluble C60 fullerenes were shown to reduce the pathological processes development in the muscle apparatus by an average of (35-40)%. In particular, they reduced the time occurrence of fatigue processes in muscle during the long-term development of alcoholic myopathy and inhibited oxidative processes in muscle, thereby preventing its degradation. These findings open up the possibility of using C60 fullerenes as potent antioxidants for the correction of the pathological conditions of the muscle system arising from alcohol intoxication.},
}
@article {pmid37554074,
year = {2023},
author = {Mpinga, K and Rukundo, T and Mwale, O and Kamwiyo, M and Thengo, L and Ruderman, T and Matanje, B and Munyaneza, F and Connolly, E and Kulisewa, K and Udedi, M and Kachimanga, C and Dullie, L and McBain, R},
title = {Depressive disorder at the household level: prevalence and correlates of depressive symptoms among household members.},
journal = {Global health action},
volume = {16},
number = {1},
pages = {2241808},
pmid = {37554074},
issn = {1654-9880},
support = {R01 MH117760/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; Male ; Female ; Adult ; *Depressive Disorder, Major/epidemiology ; *Depression/epidemiology ; Prevalence ; Family Characteristics ; Social Determinants of Health ; Social Environment ; Adolescent ; Middle Aged ; Aged ; Aged, 80 and over ; },
abstract = {BACKGROUND: Globally, an estimated five percent of adults have major depressive disorder. However, little is known about the relationship between these individuals' depressive symptoms and their household members' mental health and well-being.<br><br>OBJECTIVES: We aimed to investigate the prevalence and predictors of depressive symptoms among adult household members of patients living with major depressive disorder in Neno District, Malawi.<br><br>METHODS: As part of a cluster randomized controlled trial providing depression care to adults with major depressive disorder, we conducted surveys with patients' household members (n&#x2009;=&#x2009;236) and inquired about their overall health, depressive symptoms, disability, and social support. We calculated prevalence rates of depressive disorder and conducted multivariable linear regression and multivariable logistic regression analyses to assess correlates of depressive symptom severity and predictors of having depressive disorder (PHQ-9), respectively, among household members.<br><br>RESULTS: We observed that roughly one in five household members (19%) screened positive for a depressive disorder (PHQ-9&#x2009;>&#x2009;9). More than half of household members endorsed six or more of the nine symptoms, with 68% reporting feeling 'down, depressed, or hopeless' in the prior two weeks. Elevated depression symptom severity was associated with greater disability (&#x3b2;&#x2009;=&#x2009;0.17, p&#x2009;<&#x2009;0.001), less social support (&#x3b2;&#x2009;= -0.04, p&#x2009;=&#x2009;0.016), and lower self-reported overall health (&#x3b2;&#x2009;=&#x2009;0.54, p&#x2009;=&#x2009;0.001). Having depressive disorder was also associated with greater disability (adjusted Odds Ratio [aOR]&#x2009;=&#x2009;1.12, p&#x2009;=&#x2009;0.001) and less social support (aOR&#x2009;=&#x2009;0.97, p&#x2009;=&#x2009;0.024).<br><br>CONCLUSIONS: In the Malawian context, we find that depressive disorder and depression symptoms are shared attributes among household members. This has implications for both screening and treatment, and it suggests that mental health should be approached from the vantage point of the broader social ecology of the household and family unit.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT04777006) - March 2, 2021.},
}
@article {pmid37552473,
year = {2023},
author = {Jiang, Z and Liu, S and Zhang, D and Sha, Z},
title = {The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2781-2789},
pmid = {37552473},
issn = {1432-184X},
mesh = {*Nitrates ; Pacific Ocean ; Chlorophyll A ; *Thiosulfates ; Seawater/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Carbon ; Chitin ; Phylogeny ; },
abstract = {To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.},
}
@article {pmid37550506,
year = {2023},
author = {Sahu, N and Indic, B and Wong-Bajracharya, J and Merényi, Z and Ke, HM and Ahrendt, S and Monk, TL and Kocsubé, S and Drula, E and Lipzen, A and Bálint, B and Henrissat, B and Andreopoulos, B and Martin, FM and Bugge Harder, C and Rigling, D and Ford, KL and Foster, GD and Pangilinan, J and Papanicolaou, A and Barry, K and LaButti, K and Virágh, M and Koriabine, M and Yan, M and Riley, R and Champramary, S and Plett, KL and Grigoriev, IV and Tsai, IJ and Slot, J and Sipos, G and Plett, J and Nagy, LG},
title = {Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.},
journal = {Nature microbiology},
volume = {8},
number = {9},
pages = {1668-1681},
pmid = {37550506},
issn = {2058-5276},
support = {758161/ERC_/European Research Council/International ; },
mesh = {*Armillaria/genetics/metabolism ; Biomass ; Gene Transfer, Horizontal ; Ecosystem ; Plants ; },
abstract = {The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.},
}
@article {pmid37549500,
year = {2023},
author = {Keat-Chuan Ng, C and Linus-Lojikip, S and Mohamed, K and Hss, AS},
title = {Application of medical information system to identify dengue outbreak factors: Insights from a hyperendemic city in Malaysia.},
journal = {International journal of medical informatics},
volume = {177},
number = {},
pages = {105162},
doi = {10.1016/j.ijmedinf.2023.105162},
pmid = {37549500},
issn = {1872-8243},
mesh = {Animals ; Humans ; Cities/epidemiology ; *Dengue/epidemiology ; Malaysia/epidemiology ; Disease Outbreaks ; Information Systems ; *Zika Virus ; *Zika Virus Infection/epidemiology ; },
abstract = {BACKGROUND: Dengue is widespread globally, but it is more severe in hyperendemic regions where the virus, its vectors, and its human hosts naturally occur. The problem is particularly acute in cities, where outbreaks affect a large human population living in a wide array of socio-environmental conditions. Controlling outbreaks will rely largely on systematic data collection and analysis approaches to uncover nuances on a city-by-city basis due to the diversity of factors.<br><br>OBJECTIVE: The main objective of this study is to consolidate and analyse the dengue case dataset amassed by the e-Dengue web-based information system, developed by the Ministry of Health Malaysia, to improve our epidemiological understanding.<br><br>METHODS: We retrieved data from the e-Dengue system and integrated a total of 18,812 cases from 2012 to 2019 (8&#xa0;years) with meteorological data, geoinformatics techniques, and socio-environmental observations to identify plausible factors that could have caused dengue outbreaks in Ipoh, a hyperendemic city in Malaysia.<br><br>RESULTS: The rainfall trend characterised by a linearity of R[2]&#xa0;>&#xa0;0.99, termed the "wet-dry steps", may be the unifying factor for triggering dengue outbreaks, though it is still a hypothesis that needs further validation. Successful mapping of the dengue "reservoir" contact zones and spill-over diffusion revealed socio-environmental factors that may be controlled through preventive measures. Age is another factor to consider, as the platelet and white blood cell counts in the "below 5" age group are much greater than in other age groups.<br><br>CONCLUSIONS: Our work demonstrates the novelty of the e-Dengue system, which can identify outbreak factors at high resolution when integrated with non-medical fields. Besides dengue, the techniques and insights laid out in this paper are valuable, at large, for advancing control strategies for other mosquito-borne diseases such as malaria, chikungunya, and zika in other hyperendemic cities elsewhere globally.},
}
@article {pmid37548802,
year = {2023},
author = {Dong, H and Liu, Y and Cui, J and Zhu, M and Ji, W},
title = {Spatial and temporal variations of vegetation cover and its influencing factors in Shandong Province based on GEE.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {9},
pages = {1023},
pmid = {37548802},
issn = {1573-2959},
support = {42201077 and 42177453//National Natural Science Foundation of China/ ; ZR2021QD074//Natural Science Foundation of Shandong Province/ ; 17YJAZH013//the MOE Layout Foundation of Humanities and Social Sciences/ ; },
mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Soil ; Sustainable Development ; },
abstract = {Economic development has rapidly progressed since the implementation of reform and opening up policies, posing significant challenges to sustainable development, especially to vegetation, which plays a crucial role in maintaining ecosystem service functions and promoting green low-carbon transformations. In this study, we estimated the fractional vegetation cover (FVC) in Shandong Province from 2000 to 2020 using the Google Earth Engine (GEE) platform. The spatial and temporal changes in FVC were analyzed using gravity center migration analysis, trend analysis, and geographic detector, and the vegetation changes of different land use types were analyzed to reveal the internal driving mechanism of FVC changes. Our results indicate that vegetation cover in Shandong Province was in good condition during the period 2000 to 2020. The high vegetation cover classes dominated, and overall changes were relatively small, with the center of gravity of vegetation cover generally shifting towards the southwest. Land use type, soil type, population density, and GDP factors had the most significant impact on vegetation cover change in Shandong Province. The interaction of these factors enhanced the effect on vegetation cover change, with land use type and soil type having the highest degree of influence. The observational results of this study can provide data support for the policy makers to formulate new ecological restoration strategies, and the findings would help facilitate the sustainability management of regional ecosystem and natural resource planning.},
}
@article {pmid37548515,
year = {2024},
author = {Hakimzadeh, A and Abdala Asbun, A and Albanese, D and Bernard, M and Buchner, D and Callahan, B and Caporaso, JG and Curd, E and Djemiel, C and Brandström Durling, M and Elbrecht, V and Gold, Z and Gweon, HS and Hajibabaei, M and Hildebrand, F and Mikryukov, V and Normandeau, E and Özkurt, E and M Palmer, J and Pascal, G and Porter, TM and Straub, D and Vasar, M and Větrovský, T and Zafeiropoulos, H and Anslan, S},
title = {A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13847},
pmid = {37548515},
issn = {1755-0998},
support = {P20 GM103449/GM/NIGMS NIH HHS/United States ; EXC2124//Deutsche Forschungsgemeinschaft (DFG)/ ; MOBTP198//European Regional Development Fund and the programme Mobilitas Pluss/ ; //Genome Canada and Ontario Genomics/ ; U24 CA248454/CA/NCI NIH HHS/United States ; P20GM103449/GM/NIGMS NIH HHS/United States ; 21-17749S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Software ; High-Throughput Nucleotide Sequencing/methods ; Archaea/genetics/classification ; DNA, Environmental/genetics ; Metagenomics/methods ; Data Analysis ; Bacteria/genetics/classification ; Eukaryota/genetics/classification ; },
abstract = {Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty-two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.},
}
@article {pmid37548100,
year = {2023},
author = {Anderson, LM and Lim, KO and Kummerfeld, E and Crosby, RD and Crow, SJ and Engel, SG and Forrest, L and Wonderlich, SA and Peterson, CB},
title = {Causal discovery analysis: A promising tool in advancing precision medicine for eating disorders.},
journal = {The International journal of eating disorders},
volume = {56},
number = {11},
pages = {2012-2021},
doi = {10.1002/eat.24040},
pmid = {37548100},
issn = {1098-108X},
support = {K23MH123910/MH/NIMH NIH HHS/United States ; 1P20GM134969/GM/NIGMS NIH HHS/United States ; R34 MH077571/MH/NIMH NIH HHS/United States ; R34MH077571/MH/NIMH NIH HHS/United States ; K23 MH123910/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Precision Medicine ; *Feeding and Eating Disorders/diagnosis/therapy ; Psychopathology ; },
abstract = {OBJECTIVE: Precision medicine (i.e., individually tailored treatments) represents an optimal goal for treating complex psychiatric disorders, including eating disorders. Within the eating disorders field, most treatment development efforts have been limited in their ability to identify individual-level models of eating disorder psychopathology and to develop and apply an individually tailored treatment for a given individual's personalized model of psychopathology. In addition, research is still needed to identify causal relationships within a given individual's model of eating disorder psychopathology. Addressing this limitation of the current state of precision medicine-related research in the field will allow us to progress toward advancing research and practice for eating disorders treatment.<br><br>METHOD: We present a novel set of analytic tools, causal discovery analysis (CDA) methods, which can facilitate increasingly fine-grained, person-specific models of causal relations among cognitive, behavioral, and affective symptoms.<br><br>RESULTS: CDA can advance the identification of an individual's causal model that maintains that individuals' eating disorder psychopathology.<br><br>DISCUSSION: In the current article, we (1) introduce CDA methods as a set of promising analytic tools for developing precision medicine methods for eating disorders including the potential strengths and weaknesses of CDA, (2) provide recommendations for future studies utilizing this approach, and (3) outline the potential clinical implications of using CDA to generate personalized models of eating disorder psychopathology.<br><br>PUBLIC SIGNIFICANCE STATEMENT: CDA provides a novel statistical approach for identifying causal relationships among variables of interest for a given individual. Person-specific causal models may offer a promising approach to individualized treatment planning and inform future personalized treatment development efforts for eating disorders.},
}
@article {pmid37543705,
year = {2023},
author = {Pakulnicka, J and Kruk, M},
title = {Regional differences in water beetle communities networks settling in dystrophic lakes in northern Poland.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {12699},
pmid = {37543705},
issn = {2045-2322},
mesh = {Humans ; *Ecosystem ; *Lakes ; Water ; Poland ; Community Networks ; },
abstract = {The relationships between the species that form the networks in small dystrophic lakes remain poorly recognised. To investigate and better understand the functioning of beetle communities in different ecosystems, we created three network models that we subjected to graph network analysis. This approach displays correlation-based networks of connections (edges) between objects (nodes) by evaluating the features of the whole network and the attributes of nodes and edges in the context of their roles, expressed by centrality metrics. We used this method to determine the importance of specific species in the networks and the interspecific relationships. Our analyses are based on faunal material collected from 25 dystrophic lakes in three regions of northern Poland. We found a total of 104 species representing different ecological elements and functional trophic groups. We have shown that the network of relationships between the biomass of species differs considerably in the three study regions. The Kashubian Lakeland had the highest cohesion and density, while the network in the Suwalki Lakeland was the thinnest and most heterogeneous, which might be related to the fractal structure and the degree of development of the studied lakes. Small-bodied predators that congregated in different clusters with species with similar ecological preferences dominated all networks. We found the highest correlations in the Masurian Lakeland, where we obtained the highest centralisation of the network. Small tyrphophiles typically occupied the central places in the network, while the periphery of the network consisted of clusters with different habitat preferences, including large predators. The species that were most important for network cohesion and density were mainly tyrphophilous species, such as Anacaena lutescens, Hygrotus decoratus, Enochrus melanocephalus and Hydroporus neglectus. The values of attributes determining the role of species in community networks were influenced by both biotic and environmental factors.},
}
@article {pmid37543634,
year = {2023},
author = {Fu, Y and Mason, AS and Song, M and Ni, X and Liu, L and Shi, J and Wang, T and Xiao, M and Zhang, Y and Fu, D and Yu, H},
title = {Multi-omics strategies uncover the molecular mechanisms of nitrogen, phosphorus and potassium deficiency responses in Brassica napus.},
journal = {Cellular &amp; molecular biology letters},
volume = {28},
number = {1},
pages = {63},
pmid = {37543634},
issn = {1689-1392},
support = {LY23C130007//Zhejiang Provincial Natural Science Foundation of China/ ; 2021C02064-2//Medical Technology and Education of Zhejiang Province of China/ ; No. 2022E10012//Key Laboratory of Digital Upland Crops of Zhejiang Province/ ; },
mesh = {*Brassica napus/genetics/metabolism ; Phosphorus ; *Potassium Deficiency/genetics ; Nitrogen/metabolism ; Multiomics ; Transcriptome ; Potassium/metabolism ; *MicroRNAs/genetics/metabolism ; Gene Expression Regulation, Plant ; },
abstract = {BACKGROUND: Nitrogen (N), phosphorus (P) and potassium (K) are critical macronutrients in crops, such that deficiency in any of N, P or K has substantial effects on crop growth. However, the specific commonalities of plant responses to different macronutrient deficiencies remain largely unknown.<br><br>METHODS: Here, we assessed the phenotypic and physiological performances along with whole transcriptome and metabolomic profiles of rapeseed seedlings exposed to N, P and K deficiency stresses.<br><br>RESULTS: Quantities of reactive oxygen species were significantly increased by all macronutrient deficiencies. N and K deficiencies resulted in more severe root development responses than P deficiency, as well as greater chlorophyll content reduction in leaves (associated with disrupted chloroplast structure). Transcriptome and metabolome analyses validated the macronutrient-specific responses, with more pronounced effects of N and P deficiencies on mRNAs, microRNAs (miRNAs), circular RNAs (circRNAs) and metabolites relative to K deficiency. Tissue-specific responses also occurred, with greater effects of macronutrient deficiencies on roots compared with shoots. We further uncovered a set of common responders with simultaneous roles in all three macronutrient deficiencies, including 112 mRNAs and 10 miRNAs involved in hormonal signaling, ion transport and oxidative stress in the root, and 33 mRNAs and 6 miRNAs with roles in abiotic stress response and photosynthesis in the shoot. 27 and seven common miRNA-mRNA pairs with role in miRNA-mediated regulation of oxidoreduction processes and ion transmembrane transport were identified in all three macronutrient deficiencies. No circRNA was responsive to three macronutrient deficiency stresses, but two common circRNAs were identified for two macronutrient deficiencies. Combined analysis of circRNAs, miRNAs and mRNAs suggested that two circRNAs act as decoys for miR156 and participate in oxidoreduction processes and transmembrane transport in both N- and P-deprived roots. Simultaneously, dramatic alterations of metabolites also occurred. Associations of RNAs with metabolites were observed, and suggested potential positive regulatory roles for tricarboxylic acids, azoles, carbohydrates, sterols and auxins, and negative regulatory roles for aromatic and aspartate amino acids, glucosamine-containing compounds, cinnamic acid, and nicotianamine in plant adaptation to macronutrient deficiency.<br><br>CONCLUSIONS: Our findings revealed strategies to rescue rapeseed from macronutrient deficiency stress, including reducing the expression of non-essential genes and activating or enhancing the expression of anti-stress genes, aided by plant hormones, ion transporters and stress responders. The common responders to different macronutrient deficiencies identified could be targeted to enhance nutrient use efficiency in rapeseed.},
}
@article {pmid37541986,
year = {2023},
author = {Drozdovitch, V and Kukhta, T and Minenko, V and Trofimik, S and Veyalkin, I and Yauseyenka, V and Mabuchi, K and Rozhko, A},
title = {Recall of residential history and dietary habits during pregnancy and lactation in the distant past: reliability of questionnaire-based radiation doses for persons exposed in utero and early life.},
journal = {Radiation and environmental biophysics},
volume = {62},
number = {4},
pages = {465-481},
pmid = {37541986},
issn = {1432-2099},
support = {HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; },
mesh = {Female ; Pregnancy ; Humans ; Animals ; Cattle ; Radiation Dosage ; Reproducibility of Results ; *Chernobyl Nuclear Accident ; Iodine Radioisotopes ; Surveys and Questionnaires ; Lactation ; Feeding Behavior ; },
abstract = {This study evaluates the reliability of information obtained by standardized questionnaires used in by personal interviews for estimation of radiation thyroid doses of 1065 individuals in the Belarusian cohort of individuals who were exposed in utero and early life following the Chernobyl accident in April 1986. Data from two interviews conducted in 2012-2017 and in 2018-2022 with mothers, who were pregnant or gave birth shortly after the Chernobyl accident, were analysed. The most reliable answers dealt with various attributes related to residential history. In contrast, the reliability of answers regarding consumption rates of milk from privately owned cows or trade network was moderate, while the agreement in responses for consumption of milk products and leafy vegetables was fair. Information from the two interviews was used to calculate thyroid doses received by the cohort members. Specifically, 'model-based' thyroid doses due to [131]I were estimated using input data on individual residential history and food consumption reported during the personal interviews and ecological data ([131]I ground deposition in the corresponding settlements). In addition, for a subset of cohort subjects (n = 205) whose mothers were measured for [131]I thyroid activity, 'measurement-based' thyroid doses were calculated by adjusting the model-based dose using a scaling factor that is defined as the ratio of measured [131]I thyroid activity to model-based [131]I thyroid activity calculated for the date of measurement. A moderate agreement was observed for total (prenatal and postnatal) model-based thyroid doses due to [131]I intake, the arithmetic mean ± standard deviation for the Jaccard similarity coefficient ([Formula: see text]) was 0.45 ± 0.34 (median = 0.39), while measurement-based doses showed a much better agreement with a [Formula: see text] of 0.78 ± 0.29 (median = 0.93). For model-based thyroid doses from external irradiation and from ingestion of [134]Cs and [137]Cs, [Formula: see text] was 0.82 ± 0.23 (median = 0.90) and 0.84 ± 0.24 (median = 0.96), respectively. Measurement-based doses due to ingestion of radiocaesium isotopes resulted in an almost perfect agreement, [Formula: see text] was 0.91 ± 0.19 (median = 1.0). The present findings suggest that long-term memory recall can be reliable, if a person is asked about unique or important life events, such as pregnancy and childbirth occurring around the time of a nuclear reactor accident. However, the substantial difference (more than 10 times) observed for model-bases doses calculated using the two questionnaires represents an important source of human factor uncertainties that needs to be considered in any dose response analyses. Other lessons learned from this study are that (i) individual measurements of radionuclides in the human body are the most valuable source of information for estimating radiation doses, and (ii) whenever a radiation accident occurs, a sample of affected people should be asked to keep a diary, if at all possible.},
}
@article {pmid37536963,
year = {2023},
author = {Tobin, K and Heidari, O and Volpi, C and Sodder, S and Duncan, D},
title = {Use of geofencing interventions in population health research: a scoping review.},
journal = {BMJ open},
volume = {13},
number = {8},
pages = {e069374},
pmid = {37536963},
issn = {2044-6055},
support = {KL2 TR002317/TR/NCATS NIH HHS/United States ; R34 MH118178/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Population Health ; *Geographic Information Systems ; },
abstract = {OBJECTIVES: Technological advancements that use global positioning system (GPS), such as geofencing, provide the opportunity to examine place-based context in population health research. This review aimed to systematically identify, assess and synthesise the existing evidence on geofencing intervention design, acceptability, feasibility and/or impact.<br><br>DESIGN: Scoping review, using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guidance for reporting.<br><br>DATA SOURCES: PubMed, CINAHL, EMBASE, Web of Science, Cochrane and PsycINFO for articles in English published up to 31 December 2021.<br><br>ELIGIBILITY CRITERIA: Articles were included if geofencing was used as a mechanism for intervention delivery.<br><br>EXCLUSION CRITERIA: (1) a component or combination of GPS, geographical information system or ecological momentary assessment was used without delivery of an intervention; (2) did not include a health or health-related outcome from the geofencing intervention; or (3) was not a peer-reviewed study.<br><br>DATA EXTRACTION AND SYNTHESIS: Several researchers independently reviewed all abstracts and full-text articles for final inclusion.<br><br>RESULTS: A total of 2171 articles were found; after exclusions, nine studies were included in the review. The majority were published in 5 years preceding the search (89%). Geofences in most studies (n=5) were fixed and programmed in the mobile application carried by participants without their input. Mechanisms of geofencing interventions were classified as direct or indirect, with five studies (56%) using direct interventions. There were several different health outcomes (from smoking to problematic alcohol use) across the five studies that used a direct geofencing intervention.<br><br>CONCLUSIONS: This scoping review found geofencing to be an emerging technology that is an acceptable and feasible intervention applied to several different populations and health outcomes. Future studies should specify the rationale for the locations that are geofenced and user input. Moreover, attention to mechanisms of actions will enable scientists to understand not only whether geofencing is an appropriate and effective intervention but why it works to achieve the outcomes observed.},
}
@article {pmid37533557,
year = {2023},
author = {Wang, TY and Goh, KS and Wang, LJ and Wu, LL and Wang, FY and Wu, YW},
title = {Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the Endemic Firefly of Taiwan.},
journal = {Zoological studies},
volume = {62},
number = {},
pages = {e25},
pmid = {37533557},
issn = {1810-522X},
abstract = {Abscondita cerata is the most abundant and widely distributed endemic firefly species in Taiwan and is considered a key environmental and ecological indicator organism. In this study, we report the first long-read genome sequencing of Abs. cerata sequenced by Nanopore technology. The draft genome size, 967 Mb, was measured through a hybrid approach that consisted of assembling using 11.25-Gb Nanopore long reads and polishing using 9.47-Gb BGI PE100 short reads. The drafted genome was assembled into 4,855 contigs, with the N50 reaching 325.269 kb length. The assembled genome was predicted to possess 55,206 protein-coding genes, of which 20,862 (37.78%) were functionally annotated with public databases. 47.11% of the genome sequences consisted of repeat elements; among them DNA transposons accounted for the largest proportion (26.79%). A BUSCO (Benchmarking Universal Single Copy Orthologs) evaluation demonstrated that the genome and gene completeness were 84.8% and 79%, respectively. The phylogeny constructed using 1,792 single copy genes was consistent with previous studies. The comparative transcriptome between adult male head and lantern tissues revealed (1) the vision of Abs. cerata is primarily UV-sensitive to environmental twilight, which determines when it begins its nocturnal activity, (2) the major expressed OR56d receptor may be correlated to suitable humidity sensing, and (3) Luc1-type luciferase is responsible for Abs. cerata's luminescent spectrum.},
}
@article {pmid37531569,
year = {2023},
author = {Beer, RD},
title = {On the Proper Treatment of Dynamics in Cognitive Science.},
journal = {Topics in cognitive science},
volume = {},
number = {},
pages = {},
doi = {10.1111/tops.12686},
pmid = {37531569},
issn = {1756-8765},
abstract = {This essay examines the relevance of dynamical ideas for cognitive science. On its own, the mere mathematical idea of a dynamical system is too weak to serve as a scientific theory of anything, and dynamical approaches within cognitive science are too rich and varied to be subsumed under a single "dynamical hypothesis." Instead, after first attempting to dissect the different notions of "dynamics" and "cognition" at play, a more specific theoretical framework for cognitive science broadly construed is sketched. This framework draws upon not only dynamical ideas, but also such contemporaneous perspectives as situatedness, embodiment, ecological psychology, enaction, neuroethology/neuroscience, artificial life, and biogenic approaches. The paper ends with some methodological suggestions for pursuing this theoretical framework.},
}
@article {pmid37531181,
year = {2023},
author = {Murray, A and Ushakova, A and Zhu, X and Yang, Y and Xiao, Z and Brown, R and Speyer, L and Ribeaud, D and Eisner, M},
title = {Predicting Participation Willingness in Ecological Momentary Assessment of General Population Health and Behavior: Machine Learning Study.},
journal = {Journal of medical Internet research},
volume = {25},
number = {},
pages = {e41412},
pmid = {37531181},
issn = {1438-8871},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Young Adult ; Humans ; *Ecological Momentary Assessment ; *Tobacco Use ; Machine Learning ; Research Design ; Health Behavior ; },
abstract = {BACKGROUND: Ecological momentary assessment (EMA) is widely used in health research to capture individuals' experiences in the flow of daily life. The majority of EMA studies, however, rely on nonprobability sampling approaches, leaving open the possibility of nonrandom participation concerning the individual characteristics of interest in EMA research. Knowledge of the factors that predict participation in EMA research is required to evaluate this possibility and can also inform optimal recruitment strategies.<br><br>OBJECTIVE: This study aimed to examine the extent to which being willing to participate in EMA research is related to respondent characteristics and to identify the most critical predictors of participation.<br><br>METHODS: We leveraged the availability of comprehensive data on a general young adult population pool of potential EMA participants and used and compared logistic regression, classification and regression trees, and random forest approaches to evaluate respondents' characteristic predictors of willingness to participate in the Decades-to-Minutes EMA study.<br><br>RESULTS: In unadjusted logistic regression models, gender, migration background, anxiety, attention deficit hyperactivity disorder symptoms, stress, and prosociality were significant predictors of participation willingness; in logistic regression models, mutually adjusting for all predictors, migration background, tobacco use, and social exclusion were significant predictors. Tree-based approaches also identified migration status, tobacco use, and prosociality as prominent predictors. However, overall, willingness to participate in the Decades-to-Minutes EMA study was only weakly predictable from respondent characteristics. Cross-validation areas under the curve for the best models were only in the range of 0.56 to 0.57.<br><br>CONCLUSIONS: Results suggest that migration background is the single most promising target for improving EMA participation and sample representativeness; however, more research is needed to improve prediction of participation in EMA studies in health.},
}
@article {pmid37530223,
year = {2023},
author = {Sun, M and Yan, H and Zhang, A and Jin, Y and Lin, C and Luo, L and Wu, B and Fan, Y and Tian, S and Cao, X and Wang, Z and Luo, J and Yang, Y and Jia, J and Zhou, P and Tang, Q and Jones, CS and Varshney, RK and Srivastava, RK and He, M and Xie, Z and Wang, X and Feng, G and Nie, G and Huang, D and Zhang, X and Zhu, F and Huang, L},
title = {Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets.},
journal = {Plant biotechnology journal},
volume = {21},
number = {11},
pages = {2348-2357},
pmid = {37530223},
issn = {1467-7652},
mesh = {Humans ; *Millets/genetics ; *DNA Shuffling ; Genome-Wide Association Study ; Multiomics ; Genomics/methods ; },
abstract = {Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.},
}
@article {pmid37529296,
year = {2023},
author = {Kumar, V and Goyal, N and Prasad, A and Babu, S and Khare, K and Yadav, G},
title = {Quantification of pollen viability in Lantana camara by digital holographic microscopy.},
journal = {Quantitative plant biology},
volume = {4},
number = {},
pages = {e7},
pmid = {37529296},
issn = {2632-8828},
abstract = {Pollen grains represent the male gametes of seed plants and their viability is critical for sexual reproduction in the plant life cycle. Palynology and viability studies have traditionally been used to address a range of botanical, ecological and geological questions, but recent work has revealed the importance of pollen viability in invasion biology as well. Here, we report an efficient visual method for assessing the viability of pollen using digital holographic microscopy (DHM). Imaging data reveal that quantitative phase information provided by the technique can be correlated with viability as indicated by the outcome of the colorimetric test. We successfully test this method on pollen grains of Lantana camara, a well-known alien invasive plant in the tropical world. Our results show that pollen viability may be assessed accurately without the usual staining procedure and suggest potential applications of the DHM methodology to a number of emerging areas in plant science.},
}
@article {pmid37527270,
year = {2023},
author = {Kandel, AW and Sommer, C and Kanaeva, Z and Bolus, M and Bruch, AA and Groth, C and Haidle, MN and Hertler, C and Heß, J and Malina, M and Märker, M and Hochschild, V and Mosbrugger, V and Schrenk, F and Conard, NJ},
title = {The ROCEEH Out of Africa Database (ROAD): A large-scale research database serves as an indispensable tool for human evolutionary studies.},
journal = {PloS one},
volume = {18},
number = {8},
pages = {e0289513},
pmid = {37527270},
issn = {1932-6203},
mesh = {Humans ; *Artificial Intelligence ; Databases, Factual ; *Geographic Information Systems ; Software ; Africa ; },
abstract = {Large scale databases are critical for helping scientists decipher long-term patterns in human evolution. This paper describes the conception and development of such a research database and illustrates how big data can be harnessed to formulate new ideas about the past. The Role of Culture in Early Expansions of Humans (ROCEEH) is a transdisciplinary research center whose aim is to study the origins of culture and the multifaceted aspects of human expansions across Africa and Eurasia over the last three million years. To support its research, the ROCEEH team developed an online tool named the ROCEEH Out of Africa Database (ROAD) and implemented its web-based applications. ROAD integrates geographical data as well as archaeological, paleoanthropological, paleontological and paleobotanical content within a robust chronological framework. In fact, a unique feature of ROAD is its ability to dynamically link scientific data both spatially and temporally, thereby allowing its reuse in ways that were not originally conceived. The data stem from published sources spanning the last 150 years, including those generated by the research team. Descriptions of these data rely on the development of a standardized vocabulary and profit from online explanations of each table and attribute. By synthesizing legacy data, ROAD facilitates the reuse of heritage data in novel ways. Database queries yield structured information in a variety of interoperable formats. By visualizing data on maps, users can explore this vast dataset and develop their own theories. By downloading data, users can conduct further quantitative analyses, for example with Geographic Information Systems, modeling programs and artificial intelligence. In this paper, we demonstrate the innovative nature of ROAD and show how it helps scientists studying human evolution to access datasets from different fields, thereby connecting the social and natural sciences. Because it permits the reuse of "old" data in new ways, ROAD is now an indispensable tool for researchers of human evolution and paleogeography.},
}
@article {pmid37526960,
year = {2023},
author = {Parfitt, KM and Green, AE and Connor, TR and Neill, DR and Mahenthiralingam, E},
title = {Identification of two distinct phylogenomic lineages and model strains for the understudied cystic fibrosis lung pathogen Burkholderia multivorans.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {8},
pages = {},
pmid = {37526960},
issn = {1465-2080},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; 204457/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Mice ; *Burkholderia/classification/genetics ; *Burkholderia Infections/complications/microbiology ; *Cystic Fibrosis/complications/microbiology ; Multilocus Sequence Typing ; *Phylogeny ; Genome, Bacterial/genetics ; Mice, Inbred BALB C ; Female ; },
abstract = {Burkholderia multivorans is the dominant Burkholderia pathogen recovered from lung infection in people with cystic fibrosis. However, as an understudied pathogen there are knowledge gaps in relation to its population biology, phenotypic traits and useful model strains. A phylogenomic study of B. multivorans was undertaken using a total of 283 genomes, of which 73 were sequenced and 49 phenotypically characterized as part of this study. Average nucleotide identity analysis (ANI) and phylogenetic alignment of core genes demonstrated that the B. multivorans population separated into two distinct evolutionary clades, defined as lineage 1 (n=58 genomes) and lineage 2 (n=221 genomes). To examine the population biology of B. multivorans, a representative subgroup of 77 B. multivorans genomes (28 from the reference databases and the 49 novel short-read genome sequences) were selected based on multilocus sequence typing (MLST), isolation source and phylogenetic placement criteria. Comparative genomics was used to identify B. multivorans lineage-specific genes - ghrB_1 in lineage 1 and glnM_2 in lineage 2 - and diagnostic PCRs targeting them were successfully developed. Phenotypic analysis of 49 representative B. multivorans strains showed considerable inter-strain variance, but the majority of the isolates tested were motile and capable of biofilm formation. A striking absence of B. multivorans protease activity in vitro was observed, but no lineage-specific phenotypic differences were demonstrated. Using phylogenomic and phenotypic criteria, three model B. multivorans CF strains were identified, BCC0084 (lineage 1), BCC1272 (lineage 2a) and BCC0033 lineage 2b, and their complete genome sequences determined. B. multivorans CF strains BCC0033 and BCC0084, and the environmental reference strain, ATCC 17616, were all capable of short-term survival within a murine lung infection model. By mapping the population biology, identifying lineage-specific PCRs and model strains, we provide much needed baseline resources for future studies of B. multivorans.},
}
@article {pmid37524975,
year = {2023},
author = {Honeker, LK and Pugliese, G and Ingrisch, J and Fudyma, J and Gil-Loaiza, J and Carpenter, E and Singer, E and Hildebrand, G and Shi, L and Hoyt, DW and Chu, RK and Toyoda, J and Krechmer, JE and Claflin, MS and Ayala-Ortiz, C and Freire-Zapata, V and Pfannerstill, EY and Daber, LE and Meeran, K and Dippold, MA and Kreuzwieser, J and Williams, J and Ladd, SN and Werner, C and Tfaily, MM and Meredith, LK},
title = {Drought re-routes soil microbial carbon metabolism towards emission of volatile metabolites in an artificial tropical rainforest.},
journal = {Nature microbiology},
volume = {8},
number = {8},
pages = {1480-1494},
pmid = {37524975},
issn = {2058-5276},
mesh = {*Carbon/metabolism ; Carbon Dioxide/metabolism ; *Droughts ; *Rainforest ; Soil/chemistry ; *Soil Microbiology ; Tropical Climate ; *Bacteria/classification/genetics/metabolism ; Biodiversity ; Multiomics ; Gene Expression Regulation, Bacterial ; },
abstract = {Drought impacts on microbial activity can alter soil carbon fate and lead to the loss of stored carbon to the atmosphere as CO2 and volatile organic compounds (VOCs). Here we examined drought impacts on carbon allocation by soil microbes in the Biosphere 2 artificial tropical rainforest by tracking [13]C from position-specific [13]C-pyruvate into CO2 and VOCs in parallel with multi-omics. During drought, efflux of [13]C-enriched acetate, acetone and C4H6O2 (diacetyl) increased. These changes represent increased production and buildup of intermediate metabolites driven by decreased carbon cycling efficiency. Simultaneously,[13]C-CO2 efflux decreased, driven by a decrease in microbial activity. However, the microbial carbon allocation to energy gain relative to biosynthesis was unchanged, signifying maintained energy demand for biosynthesis of VOCs and other drought-stress-induced pathways. Overall, while carbon loss to the atmosphere via CO2 decreased during drought, carbon loss via efflux of VOCs increased, indicating microbially induced shifts in soil carbon fate.},
}
@article {pmid37518859,
year = {2024},
author = {Mueller, HM and Franzisky, BL and Messerer, M and Du, B and Lux, T and White, PJ and Carpentier, SC and Winkler, JB and Schnitzler, JP and El-Serehy, HA and Al-Rasheid, KAS and Al-Harbi, N and Alfarraj, S and Kudla, J and Kangasjärvi, J and Reichelt, M and Mithöfer, A and Mayer, KFX and Rennenberg, H and Ache, P and Hedrich, R and Geilfus, CM},
title = {Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water.},
journal = {The plant genome},
volume = {17},
number = {1},
pages = {e20372},
doi = {10.1002/tpg2.20372},
pmid = {37518859},
issn = {1940-3372},
support = {//King Saud University/ ; (471624304;GZ: GE 3111/5-1)//German Research Foundation (German: Deutsche Forschungsgemeinschaft)/ ; },
mesh = {*Phoeniceae/genetics ; Salt-Tolerant Plants/genetics ; Multiomics ; Proteomics ; Seawater ; },
abstract = {Date palm (Phoenix dactylifera L.) is able to grow and complete its life cycle while being rooted in highly saline soils. Which of the many well-known salt-tolerance strategies are combined to fine-tune this remarkable resilience is unknown. The precise location, whether in the shoot or the root, where these strategies are employed remains uncertain, leaving us unaware of how the various known salt-tolerance mechanisms are integrated to fine-tune this remarkable resilience. To address this shortcoming, we exposed date palm to a salt stress dose equivalent to seawater for up to 4 weeks and applied integrative multi-omics analyses followed by targeted metabolomics, hormone, and ion analyses. Integration of proteomic into transcriptomic data allowed a view beyond simple correlation, revealing a remarkably high degree of convergence between gene expression and protein abundance. This sheds a clear light on the acclimatization mechanisms employed, which depend on reprogramming of protein biosynthesis. For growth in highly saline habitats, date palm effectively combines various salt-tolerance mechanisms found in both halophytes and glycophytes: "avoidance" by efficient sodium and chloride exclusion at the roots, and "acclimation" by osmotic adjustment, reactive oxygen species scavenging in leaves, and remodeling of the ribosome-associated proteome in salt-exposed root cells. Combined efficiently as in P. dactylifera L., these sets of mechanisms seem to explain the palm's excellent salt stress tolerance.},
}
@article {pmid37518126,
year = {2023},
author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM},
title = {Fauna and taxonomy of Diamesinae (Diptera, Chironomidae) from the Caucasus, with a morphological description and DNA barcoding of new taxa and a discussion of diagnostic problems for Diamesa Meigen and Pseudodiamesa Goetghebuer.},
journal = {Zootaxa},
volume = {5271},
number = {2},
pages = {313-328},
doi = {10.11646/zootaxa.5271.2.6},
pmid = {37518126},
issn = {1175-5334},
mesh = {Male ; Animals ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA ; Databases, Nucleic Acid ; },
abstract = {As a result of the revision of adult males as well as available literature data, 26 species of the subfamily Diamesinae are registered for the Caucasus, belonging to 5 genera. Four species are recorded for the first time for this region, one species, D. elbrusica sp. nov., and one subspecies, D. sakartvella gidanica subsp. nov., are new to science and are described. Six species are classified as endemics of the Caucasus. Distribution of other species of Caucasian Diamesinae is discussed. DNA barcodes of 102 specimens and 20 species of four genera, Boreoheptagyia Brundin, Diamesa Meigen, Pseudodiamesa Goetghebuer and Syndiamesa Kieffer were obtained in this study. Of these, 12 species were deposed in the GenBank and BOLD systems for the first time. We have established that D. cinerella group includes D. kasymovi and probably D. lavillei whereas D. zernyi group includes D. vaillanti and D. valentinae. Highly supported phylogeny and results of species delimitation suggest the description of D. elbrusica sp. nov. and D. sakartvella gidanica subsp. nov. Ps. aff. branickii and Ps. aff. nivosa are new species based on DNA barcoding. The results of species delimitation show that genus Pseudodiamesa includes 10 (ASAP, GMYC), 14 (mPTP) or 21 (BOLD) distinct molecular taxonomic units (mOTUs) among which only Ps. stackelbergi have an undoubted species status that requires a large revision using both morphological and molecular approaches.},
}
@article {pmid37517987,
year = {2023},
author = {Wang, Y and Xue, K and Hu, R and Ding, B and Zeng, H and Li, R and Xu, B and Pang, Z and Song, X and Li, C and Du, J and Yang, X and Zhang, Z and Hao, Y and Cui, X and Guo, K and Gao, Q and Zhang, Y and Zhu, J and Sun, J and Li, Y and Jiang, L and Zhou, H and Luo, C and Zhang, Z and Gao, Q and Chen, S and Ji, B and Xu, X and Chen, H and Li, Q and Zhao, L and Xu, S and Liu, Y and Hu, L and Wu, J and Yang, Q and Dong, S and He, J and Zhao, X and Wang, S and Piao, S and Yu, G and Fu, B},
title = {Vegetation structural shift tells environmental changes on the Tibetan Plateau over 40 years.},
journal = {Science bulletin},
volume = {68},
number = {17},
pages = {1928-1937},
doi = {10.1016/j.scib.2023.07.035},
pmid = {37517987},
issn = {2095-9281},
mesh = {Humans ; *Ecosystem ; Tibet ; *Grassland ; Climate Change ; China ; },
abstract = {Structural information of grassland changes on the Tibetan Plateau is essential for understanding alterations in critical ecosystem functioning and their underlying drivers that may reflect environmental changes. However, such information at the regional scale is still lacking due to methodological limitations. Beyond remote sensing indicators only recognizing vegetation productivity, we utilized multivariate data fusion and deep learning to characterize formation-based plant community structure in alpine grasslands at the regional scale of the Tibetan Plateau for the first time and compared it with the earlier version of Vegetation Map of China for historical changes. Over the past 40 years, we revealed that (1) the proportion of alpine meadows in alpine grasslands increased from 50% to 69%, well-reflecting the warming and wetting trend; (2) dominances of Kobresia pygmaea and Stipa purpurea formations in alpine meadows and steppes were strengthened to 76% and 92%, respectively; (3) the climate factor mainly drove the distribution of Stipa purpurea formation, but not the recent distribution of Kobresia pygmaea formation that was likely shaped by human activities. Therefore, the underlying mechanisms of grassland changes over the past 40 years were considered to be formation dependent. Overall, the first exploration for structural information of plant community changes in this study not only provides a new perspective to understand drivers of grassland changes and their spatial heterogeneity at the regional scale of the Tibetan Plateau, but also innovates large-scale vegetation study paradigm.},
}
@article {pmid37511196,
year = {2023},
author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T},
title = {Multi-Drug Resistance in Bacterial Genomes-A Comprehensive Bioinformatic Analysis.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511196},
issn = {1422-0067},
support = {UI/BD/153078/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BD/04631/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UIDP/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; },
mesh = {*Genome, Bacterial ; Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Computational Biology ; Drug Resistance, Multiple ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistance is presently one of the greatest threats to public health. The excessive and indiscriminate use of antibiotics imposes a continuous selective pressure that triggers the emergence of multi-drug resistance. We performed a large-scale analysis of closed bacterial genomes to identify multi-drug resistance considering the ResFinder antimicrobial classes. We found that more than 95% of the genomes harbor genes associated with resistance to disinfectants, glycopeptides, macrolides, and tetracyclines. On average, each genome encodes resistance to more than nine different classes of antimicrobial drugs. We found higher-than-expected co-occurrences of resistance genes in both plasmids and chromosomes for several classes of antibiotic resistance, including classes categorized as critical according to the World Health Organization (WHO). As a result of antibiotic-resistant priority pathogens, higher-than-expected co-occurrences appear in plasmids, increasing the potential for resistance dissemination. For the first time, co-occurrences of antibiotic resistance have been investigated for priority pathogens as defined by the WHO. For critically important pathogens, co-occurrences appear in plasmids, not in chromosomes, suggesting that the resistances may be epidemic and probably recent. These results hint at the need for new approaches to treating infections caused by critically important bacteria.},
}
@article {pmid37508724,
year = {2023},
author = {Pinto Pereira, SM and Nugawela, MD and McOwat, K and Dalrymple, E and Xu, L and Ladhani, SN and Simmons, R and Chalder, T and Swann, O and Ford, T and Heyman, I and Segal, T and Semple, MG and Rojas, NK and CLoCk Consortium, and Shafran, R and Stephenson, T},
title = {Symptom Profiles of Children and Young People 12 Months after SARS-CoV-2 Testing: A National Matched Cohort Study (The CLoCk Study).},
journal = {Children (Basel, Switzerland)},
volume = {10},
number = {7},
pages = {},
pmid = {37508724},
issn = {2227-9067},
support = {MR/P020372/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: Although 99% of children and young people have been exposed to SARS-CoV-2, the long-term prevalence of post-COVID-19 symptoms in young people is unclear. The aim of this study is to describe symptom profiles 12 months after SARS-CoV-2 testing.<br><br>METHOD: A matched cohort study of a national sample of 20,202 children and young people who took a SARS-CoV-2 PCR test between September 2020 and March 2021.<br><br>RESULTS: 12 months post-index-test, there was a difference in the number of symptoms reported by initial negatives who never tested positive (NN) compared to the other three groups who had at least one positive test (p < 0.001). Similarly, 10.2% of the NN group described five-plus symptoms at 12 months compared to 15.9-24.0% in the other three groups who had at least one positive test. The most common symptoms were tiredness, sleeping difficulties, shortness of breath, and headaches for all four groups. For all these symptoms, the initial test positives with subsequent reports of re-infection had higher prevalences than other positive groups (p < 0.001). Symptom profiles, mental health, well-being, fatigue, and quality of life did not vary by vaccination status.<br><br>CONCLUSIONS: Following the pandemic, many young people, particularly those that have had multiple SARS-CoV-2 positive tests, experience a range of symptoms that warrant consideration and potential investigation and intervention.},
}
@article {pmid37508342,
year = {2023},
author = {Oravec, P and Wittlinger, L and Máliš, F},
title = {Endangered Forest Communities in Central Europe: Mapping Current and Potential Distributions of Euro-Siberian Steppic Woods with Quercus spp. in South Slovak Basin.},
journal = {Biology},
volume = {12},
number = {7},
pages = {},
pmid = {37508342},
issn = {2079-7737},
support = {1/0706/20//Constantine the Philosopher University in Nitra/ ; APVV-19-0319//Technical University in Zvolen/ ; },
abstract = {In this article we focus on the issue of determining the presence and status of the priority habitat 91I0* Euro-Siberian steppic woods with Quercus spp. in the South Slovak basin. As part of the issue, we try to verify the correctness of the procedure of the State Nature Conservancy of the Slovak Republic in the search for potential habitats and areas of European importance by converting the typological map to a map of habitats. Habitat 91I0* occurs in Slovakia in the form of three subtypes, namely Thermophilous and supra-Mediterranean oak woods (Carpineto-Quercetum and Betuleto-Quercetum), Acidophilous oak forests (Quercetum), while the last-named subtype is divided into two subunits: Medio-European acidophilous oak forests-part A and Pannonic hairy greenweed sessile oak woods-part B. Due to the current unsatisfactory state of the mentioned habitats, the requirement of the State Nature Conservancy of the Slovak Republic is to find and add new areas with the occurrence of habitat 91I0* in the south of Central Slovakia. During the mapping in the Lučenecká and Rimavská basins, greater emphasis was placed on the occurrence of the subtype Thermophilic Pontic-Pannonian oak forests on loess and sand, but its presence has not been confirmed. Subsequently, we focused on the search and identification of habitats in the model area, which is the area of European importance SKUEV0957 Uderinky. The result is a map of habitats in this area, which we then compare with a typological map, which determines the reliability of the converter used by the State Nature Conservancy of the Slovak Republic.},
}
@article {pmid37504804,
year = {2023},
author = {Gaboutchian, AV and Knyaz, VA and Maschenko, EN and Dac, LX and Maksimov, AA and Emelyanov, AV and Korost, DV and Stepanov, NV},
title = {Measuring Dental Enamel Thickness: Morphological and Functional Relevance of Topographic Mapping.},
journal = {Journal of imaging},
volume = {9},
number = {7},
pages = {},
pmid = {37504804},
issn = {2313-433X},
abstract = {The interest in the development of dental enamel thickness measurement techniques is connected to the importance of metric data in taxonomic assessments and evolutionary research as well as in other directions of dental studies. At the same time, advances in non-destructive imaging techniques and the application of scanning methods, such as micro-focus-computed X-ray tomography, has enabled researchers to study the internal morpho-histological layers of teeth with a greater degree of accuracy and detail. These tendencies have contributed to changes in established views in different areas of dental research, ranging from the interpretation of morphology to metric assessments. In fact, a significant amount of data have been obtained using traditional metric techniques, which now should be critically reassessed using current technologies and methodologies. Hence, we propose new approaches for measuring dental enamel thickness using palaeontological material from the territories of northern Vietnam by means of automated and manually operated techniques. We also discuss method improvements, taking into account their relevance for dental morphology and occlusion. As we have shown, our approaches demonstrate the potential to form closer links between the metric data and dental morphology and provide the possibility for objective and replicable studies on dental enamel thickness through the application of automated techniques. These features are likely to be effective in more profound taxonomic research and for the development of metric and analytical systems. Our technique provides scope for its targeted application in clinical methods, which could help to reveal functional changes in the masticatory system. However, this will likely require improvements in clinically applicable imaging techniques.},
}
@article {pmid37502985,
year = {2023},
author = {Pekar, JE and Lytras, S and Ghafari, M and Magee, AF and Parker, E and Havens, JL and Katzourakis, A and Vasylyeva, TI and Suchard, MA and Hughes, AC and Hughes, J and Robertson, DL and Dellicour, S and Worobey, M and Wertheim, JO and Lemey, P},
title = {The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37502985},
issn = {2692-8205},
support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI135992/AI/NIAID NIH HHS/United States ; },
abstract = {The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 has led to increased sampling of related sarbecoviruses circulating primarily in horseshoe bats. These viruses undergo frequent recombination and exhibit spatial structuring across Asia. Employing recombination-aware phylogenetic inference on bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed just ~1-3 years prior to their emergence in humans. Phylogeographic analyses examining the movement of related sarbecoviruses demonstrate that they traveled at similar rates to their horseshoe bat hosts and have been circulating for thousands of years in Asia. The closest-inferred bat virus ancestor of SARS-CoV likely circulated in western China, and that of SARS-CoV-2 likely circulated in a region comprising southwest China and northern Laos, both a substantial distance from where they emerged. This distance and recency indicate that the direct ancestors of SARS-CoV and SARS-CoV-2 could not have reached their respective sites of emergence via the bat reservoir alone. Our recombination-aware dating and phylogeographic analyses reveal a more accurate inference of evolutionary history than performing only whole-genome or single gene analyses. These results can guide future sampling efforts and demonstrate that viral genomic fragments extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.},
}
@article {pmid37499537,
year = {2023},
author = {Wu, M and Liu, X and Tu, W and Xia, J and Zou, Y and Gong, X and Yu, P and Huang, WE and Wang, H},
title = {Deep insight into oriented propionate production from food waste: Microbiological interpretation and design practice.},
journal = {Water research},
volume = {243},
number = {},
pages = {120399},
doi = {10.1016/j.watres.2023.120399},
pmid = {37499537},
issn = {1879-2448},
mesh = {*Propionates ; Food ; *Refuse Disposal ; Fermentation ; Fatty Acids, Volatile ; Lactic Acid ; Butyrates ; Hydrogen-Ion Concentration ; Bioreactors ; Sewage ; Anaerobiosis ; },
abstract = {Using mixed microbial cultures (MMCs) for oriented volatile fatty acids (VFAs) refining in an open environment is a typical challenge due to the microbial diversiform and the process complexity. Especially for carbohydrate-rich waste (such as food waste), butyrate-type fermentation is usually dominant in a single-stage MMCs anaerobic process, while the production of odd-carbon VFAs (such as propionate) is difficult although it plays a significant role in chemicals industries. In this study, firstly, we gave a new perspective on the rationality of the oriented propionate production using MMCs with lactate as feedstock by conducting in-depth microbial informatics and reaction analysis. Secondly, we verified the feasibility of the "food waste-lactate-propionate" route to reverse the original butyrate-type fermentation situation and explore mechanisms for maintaining stability. In the first stage, a defined lactate fermentation microbiome was used to produce lactate-containing broth (80% of total chemical oxygen demand) at pH=4. In the second stage, an undomesticated undefined anaerobic microbiome was used to drive propionate production (45.26% ± 2.23% of total VFAs) under optimized conditions (C/N = 100:1-200:1 and pH=5.0). The low pH environment in the first stage enhanced the lactic acid bacteria to resist the invasion of non-functional flanking bacteria, making the community stable. In the second stage, the system maintained the propionate-type fermentation due to the absence of the ecological niche of the invasive lactic acid bacteria; The selection of propionate-producing specialists was a necessary but not sufficient condition for propionate-type fermentation. At last, this study proposed an enhanced engineering strategy framework for understanding elaborate MMCs fermentation.},
}
@article {pmid37495700,
year = {2023},
author = {Hughes, LJ and Massam, MR and Morton, O and Edwards, FA and Scheffers, BR and Edwards, DP},
title = {Global hotspots of traded phylogenetic and functional diversity.},
journal = {Nature},
volume = {620},
number = {7973},
pages = {351-357},
pmid = {37495700},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; *Birds ; *Conservation of Natural Resources/methods/trends ; Datasets as Topic ; Endangered Species ; Europe ; Extinction, Biological ; Geographic Mapping ; *Mammals ; *Phylogeny ; Tropical Climate ; United States ; *Commerce/statistics &amp; numerical data ; },
abstract = {Wildlife trade is a multibillion-dollar industry[1] targeting a hyperdiversity of species[2] and can contribute to major declines in abundance[3]. A key question is understanding the global hotspots of wildlife trade for phylogenetic (PD) and functional (FD) diversity, which underpin the conservation of evolutionary history[4], ecological functions[5] and ecosystem services benefiting humankind[6]. Using a global dataset of traded bird and mammal species, we identify that the highest levels of traded PD and FD are from tropical regions, where high numbers of evolutionary distinct and globally endangered species in trade occur. The standardized effect size (ses) of traded PD and FD also shows strong tropical epicentres, with additional hotspots of mammalian ses.PD in the eastern United States and ses.FD in Europe. Large-bodied, frugivorous and canopy-dwelling birds and large-bodied mammals are more likely to be traded whereas insectivorous birds and diurnally foraging mammals are less likely. Where trade drives localized extinctions[3], our results suggest substantial losses of unique evolutionary lineages and functional traits, with possible cascading effects for communities and ecosystems[5,7]. Avoiding unsustainable exploitation and lost community integrity requires targeted conservation efforts, especially in hotspots of traded phylogenetic and functional diversity.},
}
@article {pmid37495016,
year = {2023},
author = {Regmi, PR and Adhikaree, A and Bhattarai, U and Chhetri, S and Shakya, U and Uranw, S and Lamichhane, P and Sharma, SK},
title = {Rheumatic heart disease in school-attending Nepalese children: A descriptive analysis of the national heart screening database.},
journal = {Indian heart journal},
volume = {75},
number = {5},
pages = {363-369},
pmid = {37495016},
issn = {2213-3763},
mesh = {Humans ; *Rheumatic Heart Disease/epidemiology/diagnosis ; Nepal/epidemiology ; Cross-Sectional Studies ; Child ; Male ; Female ; Prevalence ; Adolescent ; *Mass Screening/methods ; Child, Preschool ; Echocardiography ; Databases, Factual ; Schools ; Retrospective Studies ; },
abstract = {OBJECTIVE: Rheumatic Heart Disease (RHD) remains a significant public health problem with high morbidity and mortality in children and young adults from lower-middle income countries like Nepal. However, a nation-wide database of the disease is lacking for designing effective future prevention and control programmes and strategies. The aim of our study is to estimate the prevalence of RHD in school-attending Nepalese children.<br><br>METHODS: We performed a cross-sectional descriptive analysis of a nationally representative database of Nepal Heart Foundation (NHF) national RHD screening programme which included school-attending Nepalese children between five and sixteen years of age. The screening was conducted between May 2015 and March 2020 in 236 schools, representing all seven provinces, across all three ecological zones of Nepal. Transthoracic two-dimensional echocardiography was performed in all eligible children with more than grade one murmur on cardiac auscultation. We estimated the prevalence of RHD among school-attending children as the number of RHD cases per 1000 school-attending children with a 95% confidence interval.<br><br>RESULTS: The database included a total of 107,340 children who were screened clinically, of whom 10,600 (9&#xb7;9%) underwent transthoracic two-dimensional echocardiography. The overall prevalence of RHD was 2.22 cases per 1000 school-attending children (95% CI:1&#xb7;94 - 2&#xb7;50). The highest prevalence was observed among children living in the southern Terai ecological zone (2&#xb7;89 per 1000, 95% CI (2&#xb7;32-3&#xb7;46)) of Nepal. Among the provinces, Karnali had the highest prevalence of RHD (3&#xb7;45 per 1000, 95% CI (2&#xb7;42-4&#xb7;48)). Among the districts screened, Kalikot had the highest RHD prevalence (5.47 per 1000, 95% CI (3.02-7.92)).<br><br>CONCLUSION: Primordial, primary and secondary prevention programmes should pay special attention to southern Terai zone, particularly the under-privileged children from remote districts.},
}
@article {pmid37494338,
year = {2023},
author = {Kiyingi, M and Nankabirwa, JI and Wiltshire, CS and Nangendo, J and Kiweewa, JM and Katahoire, AR and Semitala, FC},
title = {Perspectives of people living with HIV on barriers to timely ART initiation following referral for antiretroviral therapy: A qualitative study at an urban HIV clinic in Kampala, Uganda.},
journal = {PLOS global public health},
volume = {3},
number = {7},
pages = {e0001483},
pmid = {37494338},
issn = {2767-3375},
support = {D43 TW011304/TW/FIC NIH HHS/United States ; },
abstract = {Early initiation of antiretroviral therapy (ART) after HIV diagnosis prevents HIV transmission, progression of HIV to AIDS and improves quality of life. However, little is known about the barriers to timely ART initiation among patients who test HIV positive in settings different from where they will receive HIV treatment, hence are referred in the routine setting. Therefore, we explored the perspectives of people living with HIV on barriers faced to initiate ART following HIV testing and referral for treatment. In this qualitative study, we purposively sampled and enrolled 17 patients attending the Mulago ISS clinic. We selected patients (≥18 years) who previously were received as referrals for HIV treatment and had delayed ART initiation, as ascertained from their records. We conducted in-depth interviews, which were audio recorded, transcribed and translated. We used Atlas.ti version 9 software for data management. Data analysis followed thematic and framework analysis techniques and we adopted the socio-ecological model to categorize final themes. Key themes were found at organizational level including; negative experiences at the place of HIV diagnosis attributed to inadequate counselling and support, unclear communication of HIV-positive results and ambiguous referral procedures; and, long waiting time when patients reached the HIV clinic. At individual level, the themes identified were; immediate denial with late acceptance of HIV-positive results attributed to severe emotional and psychological distress at receiving results, fear of perceived side effects and long duration on ART. At interpersonal level, we found that anticipated and enacted stigma after HIV diagnosis resulted in non-disclosure, discrimination and lack of social support. We found that challenges at entry (during HIV test) and navigation of the HIV care system in addition to individual and interpersonal factors contributed to delayed ART initiation. Interventions during HIV testing would facilitate early ART initiation among patients referred for HIV care.},
}
@article {pmid37491491,
year = {2023},
author = {Ma, Y and Zheng, M and Xu, F and Qian, Y and Liu, M and Zheng, X and Liu, J},
title = {Modeling and exploring the coordination relationship between green infrastructure and land use eco-efficiency: an urban agglomeration perspective.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {40},
pages = {92537-92554},
pmid = {37491491},
issn = {1614-7499},
support = {42201471//National Natural Science Foundation of China/ ; 72033005//National Natural Science Foundation of China/ ; 42171113//National Natural Science Foundation of China/ ; KF-2020-05-063//Ministry of Natural Resources/ ; },
mesh = {Humans ; *Urbanization ; Cities ; Beijing ; *Sustainable Development ; Efficiency ; China ; Economic Development ; },
abstract = {In limited land space, improving the construction of infrastructure with ecological services can help to achieve the goal of promoting land use eco-efficiency (LUEE). In view of this, this study constructed interactive coordination relationship model of green infrastructure (GI) and LUEE that involves entropy method model, super-efficiency slack-based measure (SBM) model with undesirable outputs, and coupling coordination degree model. The interactive coordination relationship model can help to study and reveal the mechanisms of interaction and the coordination relationship between GI and LUEE from a land benefit and ecological perspective. We took the Beijing-Tianjin-Hebei urban agglomeration as the study area. The results showed that the assessment results of GI showed a decreasing trend from 2000 to 2020. LUEE in different cities displayed obvious variability with efficiency values ranging from 0.5666 to 2.4437. The relationship between GI and LUEE is in the stage of uncoordinated development in 53.8% of cities, mainly concentrated in the eastern and southern parts of the study area. The unnatural human activities are the critical factors affecting interactive coupling coordination degree of LUEE and GI. It is clarified that the level of coordination relationship of the two can be used as an important indicator to judge the sustainable development of urban agglomerations. Intensive use of land, optimal connection of geographic information, and localization of policies would help improve the balance and coordination between the two. This study provides interesting research ideas and novel modeling approaches for the study of green and sustainable development of urban agglomerations.},
}
@article {pmid37490521,
year = {2023},
author = {Schaupp, CM and Maloney, EM and Mattingly, KZ and Olker, JH and Villeneuve, DL},
title = {Comparison of in silico, in vitro, and in vivo toxicity benchmarks suggests a role for ToxCast data in ecological hazard assessment.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {195},
number = {2},
pages = {145-154},
pmid = {37490521},
issn = {1096-0929},
support = {EPA999999/ImEPA/Intramural EPA/United States ; //United States Environmental Protection Agency Office of Research and Development/ ; //Chemical Safety for Sustainability National Research Program/ ; },
mesh = {Risk Assessment ; Animals ; *Quantitative Structure-Activity Relationship ; *Benchmarking ; Humans ; Computer Simulation ; Databases, Factual ; Toxicity Tests ; United States Environmental Protection Agency ; Ecotoxicology ; Hazardous Substances/toxicity ; United States ; },
abstract = {Large repositories of in vitro bioactivity data such as US EPA's Toxicity Forecaster (ToxCast) provide a wealth of publicly accessible toxicity information for thousands of chemicals. These data can be used to calculate point-of-departure (POD) estimates via concentration-response modeling that may serve as lower bound, protective estimates of in vivo effects. However, the data are predominantly based on mammalian models and discussions to date about their utility have largely focused on potential integration into human hazard assessment, rather than application to ecological risk assessment. The goal of the present study was to compare PODs based on (1) quantitative structure-activity relationships (QSARs), (2) the 5th centile of the activity concentration at cutoff (ACC), and (3) lower-bound cytotoxic burst (LCB) from ToxCast, with the distribution of in vivo PODs compiled in the Ecotoxicology Knowledgebase (ECOTOX). While overall correlation between ToxCast ACC5 and ECOTOX PODs for 649 chemicals was weak, there were significant associations among PODs based on LCB and ECOTOX, LCB and QSARs, and ECOTOX and QSARs. Certain classes of compounds showed moderate correlation across datasets (eg, antimicrobials/disinfectants), while others, such as organophosphate insecticides, did not. Unsurprisingly, more precise classifications of the data based on ECOTOX effect and endpoint type (eg, apical vs biochemical; acute vs chronic) had a significant effect on overall relationships. Results of this research help to define appropriate roles for data from new approach methodologies in chemical prioritization and screening of ecological hazards.},
}
@article {pmid37488464,
year = {2024},
author = {Andrade, M&#xc2; and Cipriano, M and Raposo, A},
title = {ObScene database: Semantic congruency norms for 898 pairs of object-scene pictures.},
journal = {Behavior research methods},
volume = {56},
number = {4},
pages = {3058-3071},
pmid = {37488464},
issn = {1554-3528},
mesh = {Humans ; *Semantics ; Female ; Male ; Young Adult ; Adult ; *Recognition, Psychology/physiology ; Databases, Factual ; Photic Stimulation ; Pattern Recognition, Visual/physiology ; Visual Perception/physiology ; Adolescent ; },
abstract = {Research on the interaction between object and scene processing has a long history in the fields of perception and visual memory. Most databases have established norms for pictures where the object is embedded in the scene. In this study, we provide a diverse and controlled stimulus set comprising real-world pictures of 375 objects (e.g., suitcase), 245 scenes (e.g., airport), and 898 object-scene pairs (e.g., suitcase-airport), with object and scene presented separately. Our goal was twofold. First, to create a database of object and scene pictures, normed for the same variables to have comparable measures for both types of pictures. Second, to acquire normative data for the semantic relationships between objects and scenes presented separately, which offers more flexibility in the use of the pictures and allows disentangling the processing of the object and its context (the scene). Along three experiments, participants evaluated each object or scene picture on name agreement, familiarity, and visual complexity, and rated object-scene pairs on semantic congruency. A total of 125 septuplets of one scene and six objects (three congruent, three incongruent), and 120 triplets of one object and two scenes (in congruent and incongruent pairings) were built. In future studies, these objects and scenes can be used separately or combined, while controlling for their key features. Additionally, as object-scene pairs received semantic congruency ratings along the entire scale, researchers may select among a wide range of congruency values. ObScene is a comprehensive and ecologically valid database, useful for psychology and neuroscience studies of visual object and scene processing.},
}
@article {pmid37484483,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Mulley, JF and , },
title = {The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {45},
pmid = {37484483},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Idaea aversata (the Riband Wave; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,165 protein coding genes.},
}
@article {pmid37484482,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Burnished Brass, Diachrysia chrysitis (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {82},
pmid = {37484482},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Diachrysia chrysitis (the Burnished Brass; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 386 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,320 protein coding genes.},
}
@article {pmid37476650,
year = {2023},
author = {Crowley, LM and Barclay, M and Roy, HE and Brown, PMJ and , and , and , and , and , and , and , },
title = {The genome sequence of the orange ladybird, Halyzia sedecimguttata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {186},
pmid = {37476650},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Halyzia sedecimguttata (the orange ladybird, Arthropoda; Insecta; Coleoptera, Coccinellidae). The genome sequence is 919.1 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 27,547 protein coding genes.},
}
@article {pmid37475130,
year = {2023},
author = {Yang, G and Cao, JM and Cui, HL and Zhan, XM and Duan, G and Zhu, YG},
title = {Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {30},
pages = {10919-10928},
doi = {10.1021/acs.est.2c08673},
pmid = {37475130},
issn = {1520-5851},
mesh = {*Sweetening Agents/pharmacology ; Drug Resistance, Microbial/drug effects/genetics ; Anaerobiosis/drug effects ; Genes, Bacterial ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; },
abstract = {Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.},
}
@article {pmid37471436,
year = {2023},
author = {Zhong, X and Xu, M and Li, T and Sun, R},
title = {Development of EST-SSRs based on the transcriptome of Castanopsis carlesii and cross-species transferability in other Castanopsis species.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0288999},
pmid = {37471436},
issn = {1932-6203},
mesh = {Humans ; *Transcriptome/genetics ; Expressed Sequence Tags ; Genetic Markers/genetics ; *Polymorphism, Genetic ; Microsatellite Repeats/genetics ; Databases, Protein ; },
abstract = {Castanopsis carlesii (Hemsl.) Hay. is a widely distributed and dominant tree species native to subtropical China with significant ecological and economic value. Due to serious human-related disturbance, its wild resources have been increasingly reduced, and whether may result in the loss of genetic diversity. However, no population genetics studies of natural C. carlesii have been reported to date. Microsatellite markers have been a useful tool in population genetics. Therefore, we developed EST-SSR markers based on the transcriptome sequencing of C. carlesii leaves. A total of 149,380,224 clean reads were obtained, and 63,012 nonredundant unigenes with a mean length of 1,034 bp were assembled and annotated based on sequence similarity searches in the Nr, Nt, KO, SwissProt, PFAM, KOG, and GO databases. The results showed that only 5,559 (8.82%) unigenes were annotated in all seven databases, but 46,338 (73.53%) could be annotated in at least one database. A total of 31,459 potential EST-SSRs were identified in 18,690 unigenes, with an average frequency of one SSR approximately 2 kb. Among the 100 EST-SSR primer pairs designed, 49 primer pairs successfully produced the expected product by amplification, with a success rate of 49%, but only 20 primer pairs showed abundant polymorphisms. Polymorphisms were verified using 25 samples from C. carlesii in Qimen, Anhui. A total of 119 alleles were detected, with a mean number of alleles (Na) of 5.95 per locus and a mean polymorphism information content (PIC) of 0.6125. All the 20 newly developed EST-SSR markers were verified in other Castanopsis species (C. sclerophylla, C. lamontii, C. fargesii, C. eyrei and C. jucunda). Sixteen primer pairs showed successful amplification in all five Castanopsis species (80%), and the transferability ratios ranged from 90% to 100%. These developed EST-SSR markers can be applied to population genetic and germplasm evaluations of C. carlesii and related species.},
}
@article {pmid37471432,
year = {2023},
author = {Alwan, NA and Clutterbuck, D and Pantelic, M and Hayer, J and Fisher, L and Hishmeh, L and Heightman, M and Allsopp, G and Wootton, D and Khan, A and Hastie, C and Jackson, M and Rayner, C and Brown, D and Parrett, E and Jones, G and Smith, K and Clarke, R and Mcfarland, S and Gabbay, M and Banerjee, A and , },
title = {Long Covid active case finding study protocol: A co-produced community-based pilot within the STIMULATE-ICP study (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0284297},
pmid = {37471432},
issn = {1932-6203},
mesh = {Humans ; *COVID-19/epidemiology ; Post-Acute COVID-19 Syndrome ; Pilot Projects ; *Delivery of Health Care, Integrated ; United Kingdom ; },
abstract = {BACKGROUND AND AIM: Long Covid is a significant public health concern with potentially negative implications for health inequalities. We know that those who are already socially disadvantaged in society are more exposed to COVID-19, experience the worst health outcomes and are more likely to suffer economically. We also know that these groups are more likely to experience stigma and have negative healthcare experiences even before the pandemic. However, little is known about disadvantaged groups' experiences of Long Covid, and preliminary evidence suggests they may be under-represented in those who access formal care. We will conduct a pilot study in a defined geographical area in London, United Kingdom to test the feasibility of a community-based approach of identifying Long Covid cases that have not been clinically diagnosed and have not been referred to Long Covid specialist services. We will explore the barriers to accessing recognition, care, and support, as well as experiences of stigma and perceived discrimination.<br><br>METHODS: This protocol and study materials were co-produced with a Community Advisory Board (CAB) made up primarily of people living with Long Covid. Working with voluntary organisations, a study leaflet will be distributed in the local community to highlight Long Covid symptoms and invite those experiencing them to participate in the study if they are not formally diagnosed. Potential participants will be assessed according to the study's inclusion criteria and offered the opportunity to participate if they fit them. Awareness of Long Covid and associated symptoms, experiences of trying to access care, as well as stigma and discrimination will be explored through qualitative interviews with participants. Upon completion of the interviews, participants will be offered a referral to the local social prescribing team to receive support that is personalised to them potentially including, but not restricted to, liaising with their primary care provider and the regional Long Covid clinic.},
}
@article {pmid37469857,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Oak-tree Pug, Eupithecia dodoneata (Guenée, 1858).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {133},
pmid = {37469857},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eupithecia dodoneata (the Oak-tree Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 353.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.},
}
@article {pmid37468639,
year = {2023},
author = {Caglayan, E and Ayhan, F and Liu, Y and Vollmer, RM and Oh, E and Sherwood, CC and Preuss, TM and Yi, SV and Konopka, G},
title = {Molecular features driving cellular complexity of human brain evolution.},
journal = {Nature},
volume = {620},
number = {7972},
pages = {145-153},
pmid = {37468639},
issn = {1476-4687},
support = {R24 NS092988/NS/NINDS NIH HHS/United States ; R01 MH103517/MH/NIMH NIH HHS/United States ; R01 MH126481/MH/NIMH NIH HHS/United States ; R01 HG011641/HG/NHGRI NIH HHS/United States ; T32 HL139438/HL/NHLBI NIH HHS/United States ; P51 OD011132/OD/NIH HHS/United States ; },
mesh = {Animals ; Humans ; Cell Nucleus/metabolism ; Chromatin/genetics/metabolism ; Datasets as Topic ; *Evolution, Molecular ; Genome, Human/genetics ; Genomics ; *Gyrus Cinguli/cytology/metabolism ; Macaca mulatta/genetics ; Neurons/classification/cytology ; Oligodendroglia/cytology/metabolism ; Pan troglodytes/genetics ; Single-Cell Gene Expression Analysis ; Stem Cells/cytology ; Transposases/metabolism ; Chromatin Assembly and Disassembly ; },
abstract = {Human-specific genomic changes contribute to the unique functionalities of the human brain[1-5]. The cellular heterogeneity of the human brain[6,7] and the complex regulation of gene expression highlight the need to characterize human-specific molecular features at cellular resolution. Here we analysed single-nucleus RNA-sequencing and single-nucleus assay for transposase-accessible chromatin with sequencing datasets for human, chimpanzee and rhesus macaque brain tissue from posterior cingulate cortex. We show a human-specific increase of oligodendrocyte progenitor cells and a decrease of mature oligodendrocytes across cortical tissues. Human-specific regulatory changes were accelerated in oligodendrocyte progenitor cells, and we highlight key biological pathways that may be associated with the proportional changes. We also identify human-specific regulatory changes in neuronal subtypes, which reveal human-specific upregulation of FOXP2 in only two of the neuronal subtypes. We additionally identify hundreds of new human accelerated genomic regions associated with human-specific chromatin accessibility changes. Our data also reveal that FOS::JUN and FOX motifs are enriched in the human-specifically accessible chromatin regions of excitatory neuronal subtypes. Together, our results reveal several new mechanisms underlying the evolutionary innovation of human brain at cell-type resolution.},
}
@article {pmid37467926,
year = {2023},
author = {Otálora, P and Guzmán, JL and Acién, FG and Berenguel, M and Reul, A},
title = {An artificial intelligence approach for identification of microalgae cultures.},
journal = {New biotechnology},
volume = {77},
number = {},
pages = {58-67},
doi = {10.1016/j.nbt.2023.07.003},
pmid = {37467926},
issn = {1876-4347},
mesh = {*Artificial Intelligence ; *Microalgae ; Neural Networks, Computer ; Biomass ; },
abstract = {In this work, a model for the characterization of microalgae cultures based on artificial neural networks has been developed. The characterization of microalgae cultures is essential to guarantee the quality of the biomass, and the objective of this work is to achieve a simple and fast method to address this issue. Data acquisition was performed using FlowCam, a device capable of capturing images of the cells detected in a culture sample, which are used as inputs by the model. The model can distinguish between 6 different genera of microalgae, having been trained with several species of each genus. It was further complemented with a classification threshold to discard unwanted objects while improving the overall accuracy of the model. The model achieved an accuracy of up to 97.27% when classifying a culture. The results demonstrate the effectiveness of the Deep Learning models for the characterization of microalgae cultures, it being a useful tool for the monitoring of microalgae cultures in large-scale production facilities while providing accurate characterization over a wide range of genera.},
}
@article {pmid37467038,
year = {2023},
author = {Sommerhoff, A and Ehring, T and Takano, K},
title = {Effects of Induced Mindfulness at Night on Repetitive Negative Thinking: Ecological Momentary Assessment Study.},
journal = {JMIR mental health},
volume = {10},
number = {},
pages = {e44365},
pmid = {37467038},
issn = {2368-7959},
abstract = {BACKGROUND: Repetitive negative thinking (RNT) is a cognitive risk factor for various disorders. Although brief mindfulness-based interventions (MBIs; lasting 20-30 minutes or shorter) are effective tools to reduce RNT, the effect of a minimal (5-minute) MBI remains largely unknown.<br><br>OBJECTIVE: We investigated the acute changes in RNT induced by a 10-day minimal MBI (body scan before sleeping) using an ecological momentary assessment (EMA) administered during the MBI training phase. In addition, we examined longer-term effects on the postintervention and 2-month follow-up assessments for questionnaire-based RNT and psychological distress.<br><br>METHODS: A total of 68 participants (community sample, aged 18-55 years; n=58, 85% women) were randomly allocated to either the intervention group (n=35, 51%) or the no-training control group (n=33, 49%). Both groups completed a 10-day EMA phase of RNT, during which only the intervention group performed a daily 5-minute body scan before sleeping.<br><br>RESULTS: The intervention group showed a significantly larger reduction in questionnaire-based RNT than the control group at the follow-up assessment (for growth-curve modeling analysis [GMA], dGMA=-0.91; P<.001), but this effect was not observed during the EMA phase or at the postintervention assessment. Furthermore, the intervention group showed significantly larger decreases in stress both at the postintervention (dGMA=-0.78; P<.001) and follow-up (dGMA=-0.60; P<.001) assessments than the control group. We found no intervention effects on depressive and anxiety symptoms.<br><br>CONCLUSIONS: A 5-minute body scan before sleeping reduces RNT and stress when continued for at least 10 days; however, the results suggest that this effect only appears with some time lag because no acute changes during and immediately after the intervention emerged for RNT.},
}
@article {pmid37466563,
year = {2023},
author = {Xavier, DR and Albuquerque, MP and Sousa-Carmo, SVT and Pinter, A},
title = {Evaluation of completeness and timeliness of data in the National Information System for Notifiable Diseases for spotted fever in the state of São Paulo, Brazil, 2007-2017.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {32},
number = {2},
pages = {e2022416},
pmid = {37466563},
issn = {2237-9622},
mesh = {Humans ; *Population Surveillance/methods ; Brazil/epidemiology ; Disease Notification ; *Spotted Fever Group Rickettsiosis ; Information Systems ; },
abstract = {OBJECTIVE: to evaluate the completeness and timeliness of notifications of cases of spotted fever (SF) held on the Notifiable Health Conditions Information System (SINAN) in São Paulo State, Brazil, from 2007 to 2017.<br><br>METHODS: this was a descriptive and ecological study of confirmed human cases of SF regarding completeness and timeliness of ten fields of the notification form (good if &#x2265; 90% for most variables); time series analysis was performed using the Prais-Winsten technique.<br><br>RESULTS: we analyzed 736 records; among essential fields, only "Discharge date" showed poor completeness (68.5%). Timeliness was good for the "Investigation" and "Closure" fields; other time lapses were not adequate.<br><br>CONCLUSION: in S&#xe3;o Paulo state, data completeness was good for most variables, whereas timeliness was not adequate (except for "Closure" and "Investigation"), pointing to the need for health education and communication actions about SF.},
}
@article {pmid37466561,
year = {2023},
author = {Barbosa, JS and Tartaro, L and Vasconcelos, LDR and Nedel, M and Serafini, JF and Svirski, SGS and Souza, LS and Agranonik, M},
title = {Assessment of incompleteness of Mortality Information System records on deaths from external causes in the state of Rio Grande do Sul, Brazil, 2000-2019.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {32},
number = {2},
pages = {e2022301},
pmid = {37466561},
issn = {2237-9622},
mesh = {Humans ; Brazil/epidemiology ; *Suicide ; Information Systems ; Skin Pigmentation ; },
abstract = {OBJECTIVE: to evaluate the incompleteness of Mortality Information System (Sistema de Informações sobre Mortalidade - SIM) data on deaths from external causes (ECs) in the state of Rio Grande do Sul, Brazil, 2000-2019.<br><br>METHODS: This was an ecological study, using SIM data on all deaths from external causes and, specifically, from transport accident, homicides, suicides and falls; the analysis of the trend of incompleteness was performed by means of Prais-Winsten regression, with a 5% significance level.<br><br>RESULTS: A total of 146,882 deaths were evaluated; sex (0.1%), place of death (0.1%) and age (0.4%) showed the lowest incompleteness in 2019; the proportion of incompleteness showed a decreasing trend for the place of death and schooling, an increasing trend for marital status and a stable trend for age and race/skin color, among all types of death evaluated.<br><br>CONCLUSION: the variables analyzed reached a high degree of completion; with the exception of marital status and schooling, for which unsatisfactory scores persisted for deaths from ECs, both total and by subgroups.},
}
@article {pmid37465614,
year = {2023},
author = {Asefa, A and Reuber, V and Miehe, G and Wraase, L and Wube, T and Schabo, DG and Farwig, N},
title = {Human activities modulate reciprocal effects of a subterranean ecological engineer rodent, Tachyoryctes macrocephalus, on Afroalpine vegetation cover.},
journal = {Ecology and evolution},
volume = {13},
number = {7},
pages = {e10337},
pmid = {37465614},
issn = {2045-7758},
abstract = {Human activities, directly and indirectly, impact ecological engineering activities of subterranean rodents. As engineering activities of burrowing rodents are affected by, and reciprocally affect vegetation cover via feeding, burrowing and mound building, human influence such as settlements and livestock grazing, could have cascading effects on biodiversity and ecosystem processes such as bioturbation. However, there is limited understanding of the relationship between human activities and burrowing rodents. The aim of this study was therefore to understand how human activities influence the ecological engineering activity of the giant root-rat (Tachyoryctes macrocephalus), a subterranean rodent species endemic to the Afroalpine ecosystem of the Bale Mountains of Ethiopia. We collected data on human impact, burrowing activity and vegetation during February and March of 2021. Using path analysis, we tested (1) direct effects of human settlement on the patterns of livestock grazing intensity, (2) direct and indirect impacts of humans and livestock grazing intensity on the root-rat burrow density and (3) whether human settlement and livestock grazing influence the effects of giant root-rat burrow density on vegetation and vice versa. We found lower levels of livestock grazing intensity further from human settlement than in its proximity. We also found a significantly increased giant root-rat burrow density with increasing livestock grazing intensity. Seasonal settlement and livestock grazing intensity had an indirect negative and positive effect on giant root-rat burrow density, respectively, both via vegetation cover. Analysing the reciprocal effects of giant root-rat on vegetation, we found a significantly decreased vegetation cover with increasing density of giant root-rat burrows, and indirectly with increasing livestock grazing intensity via giant root-rat burrow density. Our results demonstrate that giant root-rats play a synanthropic engineering role that affects vegetation structure and ecosystem processes.},
}
@article {pmid37463417,
year = {2023},
author = {Williams, TA and Davín, AA and Morel, B and Szánthó, LL and Spang, A and Stamatakis, A and Hugenholtz, P and Szöllősi, GJ},
title = {Parameter Estimation and Species Tree Rooting Using ALE and GeneRax.},
journal = {Genome biology and evolution},
volume = {15},
number = {7},
pages = {},
pmid = {37463417},
issn = {1759-6653},
mesh = {Phylogeny ; *Algorithms ; *Evolution, Molecular ; Gene Duplication ; Bacteria/genetics ; Eukaryota ; Models, Genetic ; },
abstract = {ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene vs. species tree discordance to infer gene duplication, transfer, and loss events, map gene family origins, and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria, and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria-where there is less certainty about the root position-ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.},
}
@article {pmid37461608,
year = {2023},
author = {Compton, ZT and Harris, V and Mellon, W and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, L and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Zehnder, A and Graham, TA and Troan, B and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, A and Abegglen, LM and Maley, CC and Boddy, AM},
title = {Cancer Prevalence Across Vertebrates.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37461608},
issn = {2693-5015},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; U2C CA233254/CA/NCI NIH HHS/United States ; P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; },
abstract = {Cancer is pervasive across multicellular species, but what explains differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades (amphibians, sauropsids and mammals) we found that neoplasia and malignancy prevalence increases with adult weight (contrary to Peto's Paradox) and somatic mutation rate, but decreases with gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%) the black-footed penguin (<0.4%), ferrets (63%) and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer.},
}
@article {pmid37455607,
year = {2023},
author = {Hutchins, L and Mc Cartney, A and Graham, N and Gillespie, R and Guzman, A},
title = {Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13822},
pmid = {37455607},
issn = {1755-0998},
support = {//Berkeley Food Institute Faculty Seed Grant/ ; //National Science Foundation Innovations at the Nexus of Food, Energy, and Water Systems/ ; },
abstract = {Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as farm sites near a natural habitat had higher OTU richness than those farther away. We also provide evidence that management factors such as the number of Polynesian crops cultivated may drive arthropod community composition. Through this case study, we emphasize the context-dependent opportunities and challenges for operationalizing IDS by utilizing participatory research methods, expanding novel data management tools through the Local Contexts Hub, and developing and nurturing community partnerships-all while highlighting the potential of agroecosystems for arthropod conservation. Overall, the workflow and the example presented here can help researchers take tangible steps to achieve IDS, which often seems elusive with the expanding use of genomic data.},
}
@article {pmid37454924,
year = {2023},
author = {Le, DH and Nguyen, TH and Takasu, F},
title = {Spatial metapopulation dynamics with local and global colonization.},
journal = {Journal of theoretical biology},
volume = {572},
number = {},
pages = {111579},
doi = {10.1016/j.jtbi.2023.111579},
pmid = {37454924},
issn = {1095-8541},
abstract = {We revisit a spatial metapopulation model on continuous space as a stochastic point pattern dynamics. In the model, local patches as points are distributed with a certain spatial configuration and status of each patch changes stochastically between occupied and empty: an occupied patch becomes empty by local extinction and an empty patch becomes occupied both by local and global colonization. We carry out simulation analysis and derive an analytical model in terms of singlet, pair and triplet probabilities that describe the stochastic dynamics. Using a simple closure that approximates triplet probabilities by singlet and pair probabilities, we show that equilibrium singlet and pair probabilities can be analytically derived. The derived equilibrium properties successfully describe simulation results under a certain condition where the range of local colonization and the proportion of global colonization play key roles. Our model is an extension of the classical non-spatial Levins model to a spatially explicit metapopulation model. We appeal the advantage of point pattern approach to study spatial dynamics in general ecology and call for the need to deepen our understanding of mathematical tools to explore point pattern dynamics.},
}
@article {pmid37454795,
year = {2023},
author = {Đokić, M and Manić, M and Đorđević, M and Gocić, M and Čupić, A and Jović, M and Dragović, R and Gajić, B and Smičiklas, I and Dragović, S},
title = {Remote sensing and nuclear techniques for high-resolution mapping and quantification of gully erosion in the highly erodible area of the Malčanska River Basin, Eastern Serbia.},
journal = {Environmental research},
volume = {235},
number = {},
pages = {116679},
doi = {10.1016/j.envres.2023.116679},
pmid = {37454795},
issn = {1096-0953},
mesh = {*Remote Sensing Technology ; *Ecosystem ; Geographic Information Systems ; Conservation of Natural Resources/methods ; Rivers ; Serbia ; Soil ; },
abstract = {Gully erosion leads to the formation of deep and wide channels that increase the risk of soil loss, flooding, and water pollution. In addition, this process reduces the productivity and viability of agricultural land and natural ecosystems. Preventing gully erosion is critical for maintaining ecological balance and preserving natural resources in certain areas. This paper presents a methodology integrating remote sensing and nuclear techniques to study gully erosion. The morphometric characterization of gullies using 360-degree camera photogrammetry was introduced as a new method in erosion research. This approach aims to investigate the suitability of unmanned aerial vehicle and terrestrial photogrammetry for modeling gullies, to study the variability of erosion processes in gullies at a small scale, and to compare the differences in erosion intensity between nearby gullies. The study's objectives include identifying the effective and economical method for gullies monitoring and providing a starting point for controlling and safeguarding gullies. Mainly erosion process was detected in the studied gullies, while deposition was identified at only 2 out of 39 sampling locations. The results showed an average soil redistribution rate of 16.2 t ha[-1] yr[-1] and coefficients of variation of 32%, 59%, and 91% for three investigated gullies. It was determined that aerial photogrammetry methods were not practical under the conditions prevailing in the study area. Highly detailed 3D models of the gullies were created using 360-degree photogrammetry. It was confirmed that the micro-relief obtained by photogrammetric modeling is an essential contribution to erosion research. The 360-degree camera photogrammetry serves as a reliable tool for analyzing the morphology of gullies and, in perspective, tracking changes in gully systems over time or monitoring the effectiveness of the applied protection measures.},
}
@article {pmid37454715,
year = {2023},
author = {Wu, X and Zhang, X and Chen, X and Ye, A and Cao, J and Hu, X and Zhou, W},
title = {The effects of polylactic acid bioplastic exposure on midgut microbiota and metabolite profiles in silkworm (Bombyx mori): An integrated multi-omics analysis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {334},
number = {},
pages = {122210},
doi = {10.1016/j.envpol.2023.122210},
pmid = {37454715},
issn = {1873-6424},
mesh = {Animals ; *Bombyx ; Multiomics ; Prospective Studies ; Polyesters/toxicity/metabolism ; Biopolymers/metabolism ; *Microbiota ; Larva ; },
abstract = {Polylactic acid (PLA) is a highly common biodegradable plastic and a potential threat to health and the environment. However, limited data are available on the effects of PLA exposure in the silkworm (Bombyx mori), a model organism used in toxicity studies. In this study, silkworms with or without PLA exposure (P1: 1 mg/L, P5: 5 mg/L, P25: 25 mg/L, and P0: 0 mg/L) for the entire 5th instar period were used to investigate the impact of PLA exposure on midgut morphology, larvae growth, and survival. Mitochondrial damage was observed in the P5 and P25 groups. The weights of the P25 posterior silk gland (5th day in the 5th instar), mature larvae and pupae were all significantly lower than those of the controls (P < 0.05). Dead worm cocoon rates and larva-pupa to 5th instar larvae ratios showed a positive and negative dose-dependent manner with respect to PLA concentrations, respectively. Additionally, reactive oxygen species levels and superoxide dismutase activity of the P25 midgut were significantly higher and lower when compared with controls, respectively (P < 0.05). The molecular mechanisms underlying the effects of PLA and associated physiological responses were also investigated. In the midgut metabolome, 127 significantly different metabolites (variable importance projection >1 and P < 0.05) were identified between the P0 and P25 groups and were mainly enriched for amino acid metabolism and energy supply pathways. The 16 S rDNA data showed that PLA altered microbial richness and structural composition. Microbiota, classified into 34 genera and 63 species, were significantly altered after 25 mg/L PLA exposure (P < 0.05). Spearman's correlation results showed that Bifidobacterium catenulatum and Schaalia odontolytica played potentially vital roles during exposure, as they demonstrated stronger correlations with the significantly different metabolites than other bacterial species. In sum, PLA induced toxic effects on silkworms, especially on energy- and protein-relevant metabolism, but at high concentrations (25 mg/L). This prospective mechanistic investigation on the effects of PLA on larval toxicity provides novel insight regarding the ecological risks of biodegradable plastics in the environment.},
}
@article {pmid37448139,
year = {2023},
author = {Ewers, I and Rajter, L and Czech, L and Mahé, F and Stamatakis, A and Dunthorn, M},
title = {Interpreting phylogenetic placements for taxonomic assignment of environmental DNA.},
journal = {The Journal of eukaryotic microbiology},
volume = {70},
number = {5},
pages = {e12990},
doi = {10.1111/jeu.12990},
pmid = {37448139},
issn = {1550-7408},
mesh = {*DNA, Environmental ; Phylogeny ; },
abstract = {Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA-ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA-ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA-ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.},
}
@article {pmid37447657,
year = {2023},
author = {Li, J and Cai, Y and Gong, X and Jiang, J and Lu, Y and Meng, X and Zhang, L},
title = {Semantic Retrieval of Remote Sensing Images Based on the Bag-of-Words Association Mapping Method.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {13},
pages = {},
pmid = {37447657},
issn = {1424-8220},
support = {41961063//National Natural Science Foundation of China/ ; },
mesh = {*Algorithms ; *Semantics ; Remote Sensing Technology ; Information Storage and Retrieval ; Pattern Recognition, Automated/methods ; },
abstract = {With the increasing demand for remote sensing image applications, extracting the required images from a huge set of remote sensing images has become a hot topic. The previous retrieval methods cannot guarantee the efficiency, accuracy, and interpretability in the retrieval process. Therefore, we propose a bag-of-words association mapping method that can explain the semantic derivation process of remote sensing images. The method constructs associations between low-level features and high-level semantics through visual feature word packets. An improved FP-Growth method is proposed to achieve the construction of strong association rules to semantics. A feedback mechanism is established to improve the accuracy of subsequent retrievals by reducing the semantic probability of incorrect retrieval results. The public datasets AID and NWPU-RESISC45 were used to validate these experiments. The experimental results show that the average accuracies of the two datasets reach 87.5% and 90.8%, which are 22.5% and 20.3% higher than VGG16, and 17.6% and 15.6% higher than ResNet18, respectively. The experimental results were able to validate the effectiveness of our proposed method.},
}
@article {pmid37443081,
year = {2023},
author = {Sharo, AG and Zou, Y and Adhikari, AN and Brenner, SE},
title = {ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden.},
journal = {Genome medicine},
volume = {15},
number = {1},
pages = {51},
pmid = {37443081},
issn = {1756-994X},
support = {T32 GM008295/GM/NIGMS NIH HHS/United States ; U19 HD077627/HD/NICHD NIH HHS/United States ; HD077627/NH/NIH HHS/United States ; U41 HG007346/HG/NHGRI NIH HHS/United States ; U24 HG007346/HG/NHGRI NIH HHS/United States ; },
mesh = {*Genetic Variation ; *Databases, Genetic ; Gene Frequency ; Genotype ; Genomics ; },
abstract = {BACKGROUND: Curated databases of genetic variants assist clinicians and researchers in interpreting genetic variation. Yet, these databases contain some misclassified variants. It is unclear whether variant misclassification is abating as these databases rapidly grow and implement new guidelines.<br><br>METHODS: Using archives of ClinVar and HGMD, we investigated how variant misclassification has changed over 6&#xa0;years, across different ancestry groups. We considered inborn errors of metabolism (IEMs) screened in newborns as a model system because these disorders are often highly penetrant with neonatal phenotypes. We used samples from the 1000 Genomes Project (1KGP) to identify individuals with genotypes that were classified by the databases as pathogenic. Due to the rarity of IEMs, nearly all such classified pathogenic genotypes indicate likely variant misclassification in ClinVar or HGMD.<br><br>RESULTS: While the false-positive rates of both ClinVar and HGMD have improved over time, HGMD variants currently imply two orders of magnitude more affected individuals in 1KGP than ClinVar variants. We observed that African ancestry individuals have a significantly increased chance of being incorrectly indicated to be affected by a screened IEM when HGMD variants are used. However, this bias affecting genomes of African ancestry was no longer significant once common variants were removed in accordance with recent variant classification guidelines. We discovered that ClinVar variants classified as Pathogenic or Likely Pathogenic are reclassified sixfold more often than DM or DM? variants in HGMD, which has likely resulted in ClinVar's lower false-positive rate.<br><br>CONCLUSIONS: Considering misclassified variants that have since been reclassified reveals our increasing understanding of rare genetic variation. We found that variant classification guidelines and allele frequency databases comprising genetically diverse samples are important factors in reclassification. We also discovered that ClinVar variants common in European and South Asian individuals were more likely to be reclassified to a lower confidence category, perhaps due to an increased chance of these variants being classified by multiple submitters. We discuss features for variant classification databases that would support their continued improvement.},
}
@article {pmid37440444,
year = {2023},
author = {Pokolm, M and Kirchhain, M and Müller, D and Jordet, G and Memmert, D},
title = {Head movement direction in football - a field study on visual scanning activity during the UEFA-U17 and -U21 European Championship 2019.},
journal = {Journal of sports sciences},
volume = {41},
number = {7},
pages = {695-705},
doi = {10.1080/02640414.2023.2235160},
pmid = {37440444},
issn = {1466-447X},
mesh = {Humans ; *Soccer ; Head Movements ; Visual Perception ; Foot ; },
abstract = {Visual exploration (scanning) of one's environment is a key aspect in team sports. Based on Gibson's (1979) ecological approach of visual perception, this study aims to advance the understanding of scanning by focusing on the direction of head movements in football and its implications for subsequent on-ball actions. The video-based data analysis consisted of nine selected matches and 162 players of the Union of European Football Associations (UEFA) U17 and U21 European Championship 2019. The results indicate that the direction of the last scan prior to receiving the ball is related to the foot used for the first ball contact. This relationship was further analysed in view of the game context (direction of play and opponent pressure) and with information about the player's dominant foot. The findings reveal a relationship between the direction of the last scan before receiving the ball and the direction the game is proceeded in. Further, when a player performs the last scan to the side of their dominant foot, the probability increases that their dominant foot is used for the subsequent first ball contact. Depending on the direction of the last scan, opponent pressure had various effects on the foot used for the first contact.},
}
@article {pmid37438069,
year = {2023},
author = {Yao, L and Yang, Y and Wang, Z and Pan, X and Xu, L},
title = {Compliance with ecological momentary assessment programmes in the elderly: a systematic review and meta-analysis.},
journal = {BMJ open},
volume = {13},
number = {7},
pages = {e069523},
pmid = {37438069},
issn = {2044-6055},
mesh = {Aged ; Humans ; *Ecological Momentary Assessment ; *Health Status ; PubMed ; Publication Bias ; Research Personnel ; },
abstract = {OBJECTIVE: Ecological momentary assessment (EMA) refers to the repeated sampling of information about an individual's symptoms and behaviours, enabling the capture of ecologically meaningful real-time information in a timely manner. Compliance with EMA is critical in determining the validity of an assessment. However, there is limited evidence related to how the elderly comply with EMA programmes or the factors that are associated with compliance.<br><br>DESIGN: Systematic review and meta-analysis.<br><br>DATA SOURCES: PubMed, Embase, the Cochrane Library and Web of Science were searched up to 17 July 2022.<br><br>ELIGIBILITY CRITERIA: We included observational studies on EMA in the elderly reported in English.<br><br>DATA EXTRACTION AND SYNTHESIS: Two investigators independently performed screening and data extraction. Discrepancies were resolved by discussion or a third investigator. A systematic review was carried out to characterise the basic characteristics of the participants and EMA programmes. Random-effects meta-analysis was conducted to assess overall compliance and to explore factors associated with differences in compliance among the elderly.<br><br>RESULTS: A total of 20 studies with 2047 participants were included in the systematic review and meta-analysis. Meta-analysis showed that the combined compliance rate was 86.41% (95% CI: 77.38% to 92.20%; I[2]=96.4%; p<0.001). Subgroup analysis revealed high levels of heterogeneity in terms of the methods used to assess population classification, assessment method and assessment frequency, although these may not be the sources of heterogeneity. Meta-regression analysis showed that population classification and assessment period might have a significant impact on heterogeneity (p<0.05). Egger's test indicated significant publication bias (p<0.001).<br><br>CONCLUSIONS: Compliance with EMA programmes is high in the elderly. It is recommended that scholars design reasonable EMA programmes according to the health status of the elderly in the future.},
}
@article {pmid37437086,
year = {2023},
author = {Hua, QQH and Young, C and Pukala, TL and Martino, JC and Hoffmann, P and Gillanders, BM and Doubleday, ZA},
title = {Better late than never: Optimising the proteomic analysis of field-collected octopus.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0288084},
pmid = {37437086},
issn = {1932-6203},
mesh = {Animals ; *Octopodiformes ; Proteomics ; Chromatography, Liquid ; Computational Biology ; Electrophoresis, Polyacrylamide Gel ; Fixatives ; },
abstract = {Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to inadequate protocols for the sampling and preparation of animal tissues from the field. Although RNAlater is an ideal alternative to freezing for tissue preservation in transcriptomics studies, its suitability for the field could be more broadly examined. Moreover, existing protocols require samples to be preserved immediately to maintain protein integrity, yet the effects of delays in preservation on proteomic analyses have not been thoroughly tested. Hence, we optimised a proteomic workflow for wild-caught samples. First, we conducted a preliminary in-lab test using SDS-PAGE analysis on aquaria-reared Octopus berrima confirming that RNAlater can effectively preserve proteins up to 6 h after incubation, supporting its use in the field. Subsequently, we collected arm tips from wild-caught Octopus berrima and preserved them in homemade RNAlater immediately, 3 h, and 6 h after euthanasia. Processed tissue samples were analysed by liquid chromatography tandem mass spectrometry to ascertain protein differences between time delay in tissue preservation, as well as the influence of sex, tissue type, and tissue homogenisation methods. Over 3500 proteins were identified from all tissues, with bioinformatic analysis revealing protein abundances were largely consistent regardless of sample treatment. However, nearly 10% additional proteins were detected from tissues homogenised with metal beads compared to liquid nitrogen methods, indicating the beads were more efficient at extracting proteins. Our optimised workflow demonstrates that sampling non-model organisms from remote field sites is achievable and can facilitate extensive proteomic coverage without compromising protein integrity.},
}
@article {pmid37436329,
year = {2023},
author = {Barros, ZDS and Rodrigues, BGM and Frota, KMG and Penha, JCD and Nascimento, FFD and Rodrigues, MTP and Mascarenhas, MDM},
title = {Syphilis detection rate trend in aged people: Brazil, 2011-2019.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {26},
number = {},
pages = {e230033},
pmid = {37436329},
issn = {1980-5497},
mesh = {Aged ; Humans ; Male ; Female ; *Syphilis/diagnosis/epidemiology ; Brazil/epidemiology ; Regression Analysis ; Linear Models ; Information Systems ; },
abstract = {OBJECTIVE: To analyze the trend in the detection rate of syphilis in elderly people in Brazil from 2011 to 2019.<br><br>METHODS: An ecological, time-series study with data from the Notifiable Diseases Information System. The temporal trend of syphilis detection rates was analyzed according to the Prais-Winsten linear regression method.<br><br>RESULTS: 62,765 cases of syphilis in aged people were reported. There was a growing trend in the rate of syphilis detection in aged people in Brazil. The increase was of approximately six times, with a mean increase of 25% each year (annual percent change [APC]: 25.0; 95%CI 22.1-28.1). The increase in the detection rate was identified in both genders and for all age groups, with emphasis on the increase in females (APC: 49.1; 95%CI 21.9-26.8) and in the group aged 70 to 79 years old (APC: 25.8; 95%CI 23.3-28.3). All macro-regions of the country showed an increasing trend, with emphasis on the Northeast (APC: 51.2; 95%CI 43.0-59.8) and South (APC: 49.2; 95%CI 32.3-68.3).<br><br>CONCLUSION: The growing trend in the detection rate of syphilis in aged people throughout Brazil highlights the need for planning and developing effective and multidisciplinary prevention actions and assistance adapted to this public.},
}
@article {pmid37433877,
year = {2023},
author = {Pairo-Castineira, E and Rawlik, K and Bretherick, AD and Qi, T and Wu, Y and Nassiri, I and McConkey, GA and Zechner, M and Klaric, L and Griffiths, F and Oosthuyzen, W and Kousathanas, A and Richmond, A and Millar, J and Russell, CD and Malinauskas, T and Thwaites, R and Morrice, K and Keating, S and Maslove, D and Nichol, A and Semple, MG and Knight, J and Shankar-Hari, M and Summers, C and Hinds, C and Horby, P and Ling, L and McAuley, D and Montgomery, H and Openshaw, PJM and Begg, C and Walsh, T and Tenesa, A and Flores, C and Riancho, JA and Rojas-Martinez, A and Lapunzina, P and , and , and , and , and Yang, J and Ponting, CP and Wilson, JF and Vitart, V and Abedalthagafi, M and Luchessi, AD and Parra, EJ and Cruz, R and Carracedo, A and Fawkes, A and Murphy, L and Rowan, K and Pereira, AC and Law, A and Fairfax, B and Hendry, SC and Baillie, JK},
title = {Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.},
journal = {Nature},
volume = {619},
number = {7971},
pages = {E61},
doi = {10.1038/s41586-023-06383-z},
pmid = {37433877},
issn = {1476-4687},
support = {MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; MR/S01165X/1/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MR/V001329/1/MRC_/Medical Research Council/United Kingdom ; },
}
@article {pmid37432953,
year = {2023},
author = {Medina, P and Russell, SL and Corbett-Detig, R},
title = {Deep data mining reveals variable abundance and distribution of microbial reproductive manipulators within and among diverse host species.},
journal = {PloS one},
volume = {18},
number = {7},
pages = {e0288261},
pmid = {37432953},
issn = {1932-6203},
support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Drosophila melanogaster/genetics ; *Arthropods ; Data Mining ; Ecology ; Reproduction ; *Wolbachia/genetics ; },
abstract = {Bacterial symbionts that manipulate the reproduction of their hosts are important factors in invertebrate ecology and evolution, and are being leveraged for host biological control. Infection prevalence restricts which biological control strategies are possible and is thought to be strongly influenced by the density of symbiont infection within hosts, termed titer. Current methods to estimate infection prevalence and symbiont titers are low-throughput, biased towards sampling infected species, and rarely measure titer. Here we develop a data mining approach to estimate symbiont infection frequencies within host species and titers within host tissues. We applied this approach to screen ~32,000 publicly available sequence samples from the most common symbiont host taxa, discovering 2,083 arthropod and 119 nematode infected samples. From these data, we estimated that Wolbachia infects approximately 44% of all arthropod and 34% of all nematode species, while other reproductive manipulators only infect 1-8% of arthropod and nematode species. Although relative titers within hosts were highly variable within and between arthropod species, a combination of arthropod host species and Wolbachia strain explained approximately 36% of variation in Wolbachia titer across the dataset. To explore potential mechanisms for host control of symbiont titer, we leveraged population genomic data from the model system Drosophila melanogaster. In this host, we found a number of SNPs associated with titer in candidate genes potentially relevant to host interactions with Wolbachia. Our study demonstrates that data mining is a powerful tool to detect bacterial infections and quantify infection intensities, thus opening an array of previously inaccessible data for further analysis in host-symbiont evolution.},
}
@article {pmid37430538,
year = {2023},
author = {Zhang, R and Zou, X and Deng, X and Wang, Z and Chen, Y and Lin, C and Xing, H and Dai, F},
title = {Fast and Accurate ROI Extraction for Non-Contact Dorsal Hand Vein Detection in Complex Backgrounds Based on Improved U-Net.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {10},
pages = {},
pmid = {37430538},
issn = {1424-8220},
support = {IEC\NSFC\191320//International Exchanges 2019 Cost Share (NSFC)/ ; },
mesh = {*Hand/diagnostic imaging ; *Veins/diagnostic imaging ; Image Processing, Computer-Assisted ; Information Storage and Retrieval ; Normal Distribution ; },
abstract = {In response to the difficulty of traditional image processing methods to quickly and accurately extract regions of interest from non-contact dorsal hand vein images in complex backgrounds, this study proposes a model based on an improved U-Net for dorsal hand keypoint detection. The residual module was added to the downsampling path of the U-Net network to solve the model degradation problem and improve the feature information extraction ability of the network; the Jensen-Shannon (JS) divergence loss function was used to supervise the final feature map distribution so that the output feature map tended to Gaussian distribution and improved the feature map multi-peak problem; and Soft-argmax is used to calculate the keypoint coordinates of the final feature map to realize end-to-end training. The experimental results showed that the accuracy of the improved U-Net network model reached 98.6%, which was 1% better than the original U-Net network model; the improved U-Net network model file was only 1.16 M, which achieved a higher accuracy than the original U-Net network model with significantly reduced model parameters. Therefore, the improved U-Net model in this study can realize dorsal hand keypoint detection (for region of interest extraction) for non-contact dorsal hand vein images and is suitable for practical deployment in low-resource platforms such as edge-embedded systems.},
}
@article {pmid37430467,
year = {2023},
author = {Peltier, DMP and Carbone, MS and McIntire, CD and Robertson, N and Thompson, RA and Malone, S and LeMoine, J and Richardson, AD and McDowell, NG and Adams, HD and Pockman, WT and Trowbridge, AM},
title = {Carbon starvation following a decade of experimental drought consumes old reserves in Pinus edulis.},
journal = {The New phytologist},
volume = {240},
number = {1},
pages = {92-104},
doi = {10.1111/nph.19119},
pmid = {37430467},
issn = {1469-8137},
mesh = {*Carbon/metabolism ; *Pinus/physiology ; Droughts ; Carbohydrates/chemistry ; Starch/metabolism ; Trees/physiology ; Carbohydrate Metabolism ; },
abstract = {Shifts in the age or turnover time of non-structural carbohydrates (NSC) may underlie changes in tree growth under long-term increases in drought stress associated with climate change. But NSC responses to drought are challenging to quantify, due in part to large NSC stores in trees and subsequently long response times of NSC to climate variation. We measured NSC age (Δ[14] C) along with a suite of ecophysiological metrics in Pinus edulis trees experiencing either extreme short-term drought (-90% ambient precipitation plot, 2020-2021) or a decade of severe drought (-45% plot, 2010-2021). We tested the hypothesis that carbon starvation - consumption exceeding synthesis and storage - increases the age of sapwood NSC. One year of extreme drought had no impact on NSC pool size or age, despite significant reductions in predawn water potential, photosynthetic rates/capacity, and twig and needle growth. By contrast, long-term drought halved the age of the sapwood NSC pool, coupled with reductions in sapwood starch concentrations (-75%), basal area increment (-39%), and bole respiration rates (-28%). Our results suggest carbon starvation takes time, as tree carbon reserves appear resilient to extreme disturbance in the short term. However, after a decade of drought, trees apparently consumed old stored NSC to support metabolism.},
}
@article {pmid37430226,
year = {2023},
author = {Demidova, EV and Serebriiskii, IG and Vlasenkova, R and Kelow, S and Andrake, MD and Hartman, TR and Kent, T and Virtucio, J and Rosen, GL and Pomerantz, RT and Dunbrack, RL and Golemis, EA and Hall, MJ and Chen, DYT and Daly, MB and Arora, S},
title = {Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {388},
pmid = {37430226},
issn = {1471-2164},
}
@article {pmid37428511,
year = {2023},
author = {Minich, M and Zhao, Q and Eickhoff, J and Moreno, MA},
title = {In the Mood for Music: Listening to Music and Other Smartphone Uses Improve Adolescent Mood.},
journal = {Cyberpsychology, behavior and social networking},
volume = {26},
number = {11},
pages = {869-873},
doi = {10.1089/cyber.2022.0344},
pmid = {37428511},
issn = {2152-2723},
mesh = {Humans ; Adolescent ; *Smartphone ; *Music ; Affect ; Ecological Momentary Assessment ; },
abstract = {Rates of adolescent mood disorders and adolescent smartphone use have risen in parallel, leading some to suggest that smartphone use might have detrimental effects on adolescents' moods. Alternatively, it is possible that adolescents turn to smartphone use when experiencing negative mood. Past experimental study suggests that certain smartphone activities can reduce adolescents' negative moods or induce more positive moods, but little is known about the effects of real-world smartphone use, which can involve many different activities. A sample of N = 253 adolescents participated in an Ecological Momentary Assessment (EMA) procedure, which assessed which smartphone activities they were engaged in at random moments throughout the day. This procedure also prompted adolescents to rate their moods before and during smartphone use. Adolescents reported mood improvements during almost all smartphone activities and did not report that moods became more negative during any smartphone activity. Mood improvements were the largest when adolescents said they were listening to music, podcasts, or audiobooks. This may suggest some adolescent smartphone use is driven by a desire to alleviate negative mood.},
}
@article {pmid37427807,
year = {2024},
author = {Liu, S and Gates, KM and Ferrer, E},
title = {Homogeneity Assumptions in the Analysis of Dynamic Processes.},
journal = {Multivariate behavioral research},
volume = {59},
number = {6},
pages = {1166-1176},
doi = {10.1080/00273171.2023.2225172},
pmid = {37427807},
issn = {1532-7906},
mesh = {Humans ; *Emotions ; Data Interpretation, Statistical ; Models, Statistical ; Female ; },
abstract = {With the increased use of time series data in human research, ranging from ecological momentary assessments to data passively obtained, researchers can explore dynamic processes more than ever before. An important question researchers must ask themselves is, do I think all individuals have similar processes? If not, how different, and in what ways? Dr. Peter Molenaar's work set the foundation to answer these questions by providing insight into individual-level analysis for processes that are assumed to differ across individuals in at least some aspects. Currently, such assumptions do not have a clear taxonomy regarding the degree of homogeneity in the patterns of relations among variables and the corresponding parameter values. This paper provides the language with which researchers can discuss assumptions inherent in their analyses. We define strict homogeneity as the assumption that all individuals have an identical pattern of relations as well as parameter values; pattern homogeneity assumes the same pattern of relations but parameter values can differ; weak homogeneity assumes there are some (but not all) generalizable aspects of the process; and no homogeneity explicitly assumes no population-level similarities in dynamic processes across individuals. We demonstrate these assumptions with an empirical data set of daily emotions in couples.},
}
@article {pmid37425881,
year = {2023},
author = {Larivière, D and Abueg, L and Brajuka, N and Gallardo-Alba, C and Grüning, B and Ko, BJ and Ostrovsky, A and Palmada-Flores, M and Pickett, BD and Rabbani, K and Balacco, JR and Chaisson, M and Cheng, H and Collins, J and Denisova, A and Fedrigo, O and Gallo, GR and Giani, AM and Gooder, GM and Jain, N and Johnson, C and Kim, H and Lee, C and Marques-Bonet, T and O'Toole, B and Rhie, A and Secomandi, S and Sozzoni, M and Tilley, T and Uliano-Silva, M and van den Beek, M and Waterhouse, RM and Phillippy, AM and Jarvis, ED and Schatz, MC and Nekrutenko, A and Formenti, G},
title = {Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37425881},
issn = {2692-8205},
support = {U01 CA253481/CA/NCI NIH HHS/United States ; U24 CA231877/CA/NCI NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; },
abstract = {Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).},
}
@article {pmid37415394,
year = {2023},
author = {Serra, A and Mozgunov, P and Davies, G and Jaki, T},
title = {Determining the minimum duration of treatment in tuberculosis: An order restricted non-inferiority trial design.},
journal = {Pharmaceutical statistics},
volume = {22},
number = {5},
pages = {938-962},
doi = {10.1002/pst.2320},
pmid = {37415394},
issn = {1539-1612},
support = {MC_UU_00002/14/MRC_/Medical Research Council/United Kingdom ; MC_UU_00002/19/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Duration of Therapy ; Research Design ; *Tuberculosis/drug therapy ; Equivalence Trials as Topic ; },
abstract = {Tuberculosis (TB) is one of the biggest killers among infectious diseases worldwide. Together with the identification of drugs that can provide benefits to patients, the challenge in TB is also the optimisation of the duration of these treatments. While conventional duration of treatment in TB is 6 months, there is evidence that shorter durations might be as effective but could be associated with fewer side effects and may be associated with better adherence. Based on a recent proposal of an adaptive order-restricted superiority design that employs the ordering assumptions within various duration of the same drug, we propose a non-inferiority (typically used in TB trials) adaptive design that effectively uses the order assumption. Together with the general construction of the hypothesis testing and expression for type I and type II errors, we focus on how the novel design was proposed for a TB trial concept. We consider a number of practical aspects such as choice of the design parameters, randomisation ratios, and timings of the interim analyses, and how these were discussed with the clinical team.},
}
@article {pmid37413727,
year = {2023},
author = {Xing, Z and Chen, S and Xu, F and Su, X and Gou, F and Shi, Y and Chen, H and Xiang, J and Li, J and Zhao, T},
title = {Quantitative analysis of TCE biodegradation pathway in landfill cover utilizing continuous monitoring, droplet digital PCR and multi-omics sequencing technology.},
journal = {Journal of environmental management},
volume = {344},
number = {},
pages = {118509},
doi = {10.1016/j.jenvman.2023.118509},
pmid = {37413727},
issn = {1095-8630},
mesh = {*Trichloroethylene/chemistry ; Multiomics ; Biodegradation, Environmental ; Waste Disposal Facilities ; Bacteria/genetics/metabolism ; Soil ; Polymerase Chain Reaction ; Technology ; },
abstract = {The remediation of volatile chlorinated hydrocarbons in the quasi-vadose zone has become a significant challenge. We applied an integrated approach to assess the biodegradability of trichloroethylene to identify the biotransformation mechanism. The formation of the functional zone biochemical layer was assessed by analyzing the distribution of landfill gas, physical and chemical properties of cover soil, spatial-temporal variations of micro-ecology, biodegradability of landfill cover soil and distributional difference metabolic pathway. Real-time online monitoring showed that trichloroethylene continuously undergoes anaerobic dichlorination and simultaneous aerobic/anaerobic conversion-aerobic co-metabolic degradation on the vertical gradient of the landfill cover system and reduction in trans-1,2-dichloroethylene in the anoxic zone but not 1,1-dichloroethylene. PCR and diversity sequencing revealed the abundance and spatial distribution of known dichlorination-related genes within the landfill cover, with 6.61 ± 0.25 × 10[4]-6.78 ± 0.09 × 10[6] and 1.17 ± 0.78 × 10[3]-7.82 ± 0.07 × 10[5] copies per g/soil of pmoA and tceA, respectively. In addition, dominant bacteria and diversity were significantly linked with physicochemical factors, and Mesorhizobium, Pseudoxanthomonas and Gemmatimonas were responsible for biodegradation in the aerobic, anoxic and anaerobic zones. Metagenome sequencing identified 6 degradation pathways of trichloroethylene that may occur in the landfill cover; the main pathway was incomplete dechlorination accompanied by cometabolic degradation. These results indicate that the anoxic zone is important for trichloroethylene degradation.},
}
@article {pmid37408609,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Spruce Carpet Moth, Thera britannica (Turner, 1925).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {114},
pmid = {37408609},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Thera britannica (the Spruce Carpet Moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 381 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,457 protein coding genes.},
}
@article {pmid37407490,
year = {2023},
author = {Shinohara, N and Zhao, W and Shan, Y and Ukawa, S and Ohira, H and Kawamura, T and Okabayashi, S and Wakai, K and Ando, M and Tsushita, K and Tamakoshi, A},
title = {Temporal change in the association between life satisfaction and functional decline with gender differences: an age-specific prospective cohort study.},
journal = {Environmental health and preventive medicine},
volume = {28},
number = {},
pages = {42},
pmid = {37407490},
issn = {1347-4715},
mesh = {Male ; Adult ; Humans ; Female ; Aged ; Cohort Studies ; Prospective Studies ; Sex Factors ; *Personal Satisfaction ; Age Factors ; },
abstract = {BACKGROUND: Although life satisfaction (LS) has been shown to predict mortality, research studying the relationship between LS and functional decline is scarce. This study examined the association between LS and functional decline across four time points in young-old Japanese adults.<br><br>METHODS: We analysed 1,899 community-dwelling 65-year-olds in this age-specific cohort study conducted between 2000 and 2005. The Life Satisfaction Index K was used to evaluate LS and was classified into quartiles. Functional decline was determined using the Japanese Long-Term Care Insurance (LTCI) system: 1) mild disability; 2) severe disability; 3) all-cause mortality; 4) mild or severe disability; 5) severe disability or death; 6) mild or severe disability, or death. Adjusted hazard ratios (HR) with 95% confidence intervals (CI) were calculated using the Cox proportional hazard model. The analyses were conducted in the 8[th], 10[th], 12[th], and 14[th] years to assess the effect of LS on functional decline across time points.<br><br>RESULTS: The impact of LS gradually weakened over time. In the 8[th] year (aged 72-73), a higher LS was associated with a lower risk of mild or severe disability among the women participants (adjusted HR [95% CI] = 0.30 [0.11-0.81]). However, the effect disappeared gradually (adjusted HR [95% CI] = 0.55 [0.27-1.14]) in the 10[th] year (aged 74-75), 0.72 (0.41-1.26) in the 12[th] year (aged 76-77), and 0.68 (0.41-1.14) in the 14[th] year (aged 78-79). This trend continued in severe disability or death (adjusted HR [95% CI] = 0.24 [0.06-0.70], 0.31 [0.11-0.76], 0.57 [0.28-1.14], and 0.60 [0.32-1.12]) and mild or severe disability, or death (adjusted HR [95% CI] = 0.30 [0.14-0.68], 0.46 [0.24-0.87], 0.67 [0.41-1.10], and 0.65 [0.42-1.02]) in the 8[th], 10[th], 12[th], and 14[th] years, respectively. No statistically significant association was found among men at any time points or in any classification of outcomes.<br><br>CONCLUSIONS: Higher LS scores in 65-year-old women were associated with a lower risk for functional decline in any combination of mild disability, severe disability, or death. Additionally, the effect of LS was observed to weaken over time.<br><br>TRIAL REGISTRATION: This is not an intervention survey and does not require registration.},
}
@article {pmid37402922,
year = {2024},
author = {Li, K and Zhou, Y and Huang, X and Xiao, H and Shan, Y},
title = {Low-carbon development pathways for resource-based cities in China under the carbon peaking and carbon neutrality goals.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {7},
pages = {10213-10233},
pmid = {37402922},
issn = {1614-7499},
mesh = {*Carbon/analysis ; Cities ; *Carbon Dioxide/analysis ; Goals ; China ; Economic Development ; },
abstract = {Resource-based cities are important strategic bases for securing resources in China and have made great contributions to the country's economic development. Long-term extensive resource development has made resource-based cities an important region constraining China from achieving comprehensive low-carbon development. Therefore, it is of great significance to explore the low-carbon transition path of resource-based cities for their energy greening, industrial transformation, and high-quality economic development. This study compiled the CO2 emission inventory of resource-based cities in China from 2005 to 2017, explored the contribution to CO2 emissions from three perspectives (driver, industry, and city), and predicted the peak of CO2 emissions in resource-based cities. The results show that resource-based cities contribute 18.4% of the country's GDP and emit 44.4% of the country's CO2 and that economic growth and CO2 emissions have not yet been decoupled. The per capita CO2 emissions and emission intensity of resource-based cities are 1.8 times and 2.4 times higher than the national average, respectively. Economic growth and energy intensity are the biggest drivers and main inhibitors of CO2 emissions growth. Industrial restructuring has become the biggest inhibitor of CO2 emissions growth. Based on the different resource endowments, industrial structures, and socio-economic development levels of resource-based cities, we propose differentiated low-carbon transition pathways. This study can provide references for cities to develop differentiated low-carbon development paths under the "double carbon" target.},
}
@article {pmid37396199,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Northern Deep-brown Dart, Aporophyla lueneburgensis (Freyer, 1848).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {149},
pmid = {37396199},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Aporophyla lueneburgensis (the Northern Deep-brown Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 978.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,580 protein coding genes.},
}
@article {pmid37394173,
year = {2023},
author = {Fan, W and Song, X and Liu, M and Shan, B and Ma, M and Liu, Y},
title = {Spatio-temporal evolution of resources and environmental carrying capacity and its influencing factors: A case study of Shandong Peninsula urban agglomeration.},
journal = {Environmental research},
volume = {234},
number = {},
pages = {116469},
doi = {10.1016/j.envres.2023.116469},
pmid = {37394173},
issn = {1096-0953},
mesh = {*Conservation of Natural Resources ; Cities ; Spatial Analysis ; *Economic Development ; Industry ; China ; Rivers ; Urbanization ; },
abstract = {Promoting ecological conservation and high-quality development in the Yellow River basin is an important objective in China's 14th Five-Year Plan. Understanding the spatio-temporal evolution of and factors affecting the resources and environmental carrying capacity (RECC) of the urban agglomerations is critical for boosting high-quality green-oriented development. We first combined the Driver-Pressure-State-Impact-Response (DPSIR) framework and the improved Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) model to evaluate the RECC of Shandong Peninsula urban agglomeration in 2000, 2010 and 2020; we then used trend analysis and spatial autocorrelation analysis to understand the spatio-temporal evolution and distribution pattern of RECC. Furthermore, we employed Geodetector to detect the influencing factors and classified the urban agglomeration into six zones based on the weighted Voronoi diagram of RECC as well as specific conditions of the study area. The results show that the RECC of Shandong Peninsula urban agglomeration increased consistently over time, from 0.3887 in 2000 to 0.4952 in 2010 and 0.6097 in 2020, respectively. Geographically, RECC decreased gradually from the northeast coast to the southwest inland. Globally, only in 2010 the RECC presented a significant spatial positive correlation, and that in the other years were not significant. The high-high cluster was mainly located in Weifang, while the low-low cluster in Jining. Furthermore, our study reveals three key factors-advancement of industrial structure, resident consumption level, and water consumption per ten thousand yuan of industrial added value-that affected the distribution of RECC. Other factors, including the interactions between residents' consumption level and environmental regulation, residents' consumption level and advancement of industrial structure, as well as between the proportion of R&amp;D expenditure in GDP and resident consumption level also played important roles resulting in the variation of RECC among different cities within the urban agglomeration. Accordingly, we proposed suggestions for achieving high-quality development for different zones.},
}
@article {pmid37391265,
year = {2023},
author = {Docherty, AB and Farrell, J and Thorpe, M and Egan, C and Dunn, S and Norman, L and Shaw, CA and Law, A and Leeming, G and Norris, L and Brooks, A and Prodan, B and MacLeod, R and Baxter, R and Morris, C and Rennie, D and Oosthuyzen, W and Semple, MG and Baillie, JK and Pius, R and Seth, S and Harrison, EM and Lone, NI},
title = {Patient emergency health-care use before hospital admission for COVID-19 and long-term outcomes in Scotland: a national cohort study.},
journal = {The Lancet. Digital health},
volume = {5},
number = {7},
pages = {e446-e457},
pmid = {37391265},
issn = {2589-7500},
support = {MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; /CSO_/Chief Scientist Office/United Kingdom ; },
mesh = {Adult ; Humans ; Cohort Studies ; Retrospective Studies ; *COVID-19 Vaccines ; *COVID-19/epidemiology/therapy ; Hospitals ; },
abstract = {BACKGROUND: It is unclear what effect the pattern of health-care use before admission to hospital with COVID-19 (index admission) has on the long-term outcomes for patients. We sought to describe mortality and emergency readmission to hospital after discharge following the index admission (index discharge), and to assess associations between these outcomes and patterns of health-care use before such admissions.<br><br>METHODS: We did a national, retrospective, complete cohort study by extracting data from several national databases and linking the databases for all adult patients admitted to hospital in Scotland with COVID-19. We used latent class trajectory modelling to identify distinct clusters of patients on the basis of their emergency admissions to hospital in the 2 years before the index admission. The primary outcomes were mortality and emergency readmission up to 1 year after index admission. We used multivariable regression models to explore associations between these outcomes and patient demographics, vaccination status, level of care received in hospital, and previous emergency hospital use.<br><br>FINDINGS: Between March 1, 2020, and Oct 25, 2021, 33&#x2008;580 patients were admitted to hospital with COVID-19 in Scotland. Overall, the Kaplan-Meier estimate of mortality within 1 year of index admission was 29&#xb7;6% (95% CI 29&#xb7;1-30&#xb7;2). The cumulative incidence of emergency hospital readmission within 30 days of index discharge was 14&#xb7;4% (95% CI 14&#xb7;0-14&#xb7;8), with the number increasing to 35&#xb7;6% (34&#xb7;9-36&#xb7;3) patients at 1 year. Among the 33&#x2008;580 patients, we identified four distinct patterns of previous emergency hospital use: no admissions (n=18&#x2008;772 [55&#xb7;9%]); minimal admissions (n=12&#x2008;057 [35&#xb7;9%]); recently high admissions (n=1931 [5&#xb7;8%]), and persistently high admissions (n=820 [2&#xb7;4%]). Patients with recently or persistently high admissions were older, more multimorbid, and more likely to have hospital-acquired COVID-19 than patients with no or minimal admissions. People in the minimal, recently high, and persistently high admissions groups had an increased risk of mortality and hospital readmission compared with those in the no admissions group. Compared with the no admissions group, mortality was highest in the recently high admissions group (post-hospital mortality HR 2&#xb7;70 [95% CI 2&#xb7;35-2&#xb7;81]; p<0&#xb7;0001) and the risk of readmission was highest in the persistently high admissions group (3&#xb7;23 [2&#xb7;89-3&#xb7;61]; p<0&#xb7;0001).<br><br>INTERPRETATION: Long-term mortality and readmission rates for patients hospitalised with COVID-19 were high; within 1 year, one in three patients had died and a third had been readmitted as an emergency. Patterns of hospital use before index admission were strongly predictive of mortality and readmission risk, independent of age, pre-existing comorbidities, and COVID-19 vaccination status. This increasingly precise identification of individuals at high risk of poor outcomes from COVID-19 will enable targeted support.<br><br>FUNDING: Chief Scientist Office Scotland, UK National Institute for Health Research, and UK Research and Innovation.},
}
@article {pmid37389324,
year = {2022},
author = {Ebdon, S and Lohse, K and , and , and , and Jansen Van Rensburg, A and , },
title = {The genome sequence of the northern brown argus, Aricia artaxerxes (Fabricius, 1793).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {314},
pmid = {37389324},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Aricia artaxerxes (the northern brown argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 458 megabases in span. Most of the assembly (99.99%) is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,688 protein coding genes.},
}
@article {pmid37387279,
year = {2023},
author = {Wang, QX and Feng, QY and Zhu, XQ},
title = {[Determination of bisphenols in sediment by accelerated solvent extraction and solid-phase extraction purification coupled with ultra performance liquid chromatography-tandem mass spectrometry].},
journal = {Se pu = Chinese journal of chromatography},
volume = {41},
number = {7},
pages = {582-590},
pmid = {37387279},
issn = {1872-2059},
mesh = {Humans ; *Tandem Mass Spectrometry ; Chromatography, Liquid ; Acetonitriles ; },
abstract = {Bisphenols are endocrine disruptors that are characterized with bioaccumulation, persistence, and estrogenic activity. Even low contents of bisphenols can exert adverse effects on human health and the ecological environment. Herein, a method combining accelerated solvent extraction and solid-phase extraction purification with ultra performance liquid chromatography-tandem mass spectrometry was developed for the accurate detection of bisphenol A (BPA), bisphenol B (BPB), bisphenol F (BPF), bisphenol S (BPS), bisphenol Z (BPZ), bisphenol AF (BPAF), and bisphenol AP (BPAP) in sediments. The mass spectrometric parameters of the seven bisphenols were optimized, and the response values, separation effects, and chromatographic peak shapes of the target compounds were compared under three different mobile phase conditions. The sediment samples were pretreated by accelerated solvent extraction, and orthogonal tests were used to optimize the extraction solvent, extraction temperature, and cycle number. The results showed that the use of 0.05% (v/v) ammonia and acetonitrile as the mobile phase for gradient elution could rapidly separate the seven bisphenols on an Acquity UPLC BEH C18 column (100 mm×2.1 mm, 1.7 μm). The gradient program was as follows: 0-2 min, 60%A; 2-6 min, 60%A-40%A; 6-6.5 min, 40%A; 6.5-7 min, 40%A-60%A; 7-8 min, 60%A. Orthogonal experiments indicated that the optimal extraction conditions were as follows: extraction solvent of acetonitrile, extraction temperature of 100 ℃, and cycle number of three. The seven bisphenols showed good linearity in the range of 1.0-200 μg/L, with correlation coefficients (r[2]) greater than 0.999, and the limits of detection were 0.01-0.3 ng/g. The recoveries for the seven bisphenols ranged from 74.9% to 102.8% at three spiking levels (2.0, 10, 20 ng/g), with relative standard deviations ranging from 6.2% to 10.3%. The established method was applied to detect the seven bisphenols in sediment samples collected from Luoma Lake and its inflow rivers. BPA, BPB, BPF, BPS, and BPAF were detected in the sediments of the lake, and BPA, BPF, and BPS were detected in the sediments of its inflow rivers. The detection frequency of BPA and BPF was 100%, and the contents of these bisphenols in the sediment were 11.9-38.0 ng/g and 11.0-27.3 ng/g, respectively. The developed method is simple, rapid with high accuracy and precision, and is suitable for the determination of the seven bisphenols in sediment.},
}
@article {pmid37387086,
year = {2023},
author = {Sijm-Eeken, M and Marcilly, R and Jaspers, M and Peute, L},
title = {Organizational and Human Factors in Green Medical Informatics - A Case Study in Dutch Hospitals.},
journal = {Studies in health technology and informatics},
volume = {305},
number = {},
pages = {537-540},
doi = {10.3233/SHTI230552},
pmid = {37387086},
issn = {1879-8365},
mesh = {Humans ; *Ethnicity ; Hospitals ; Health Facilities ; *Medical Informatics ; Organizations ; },
abstract = {Medical Informatics brings methods and solutions that could support reducing healthcare's ecological footprint. Initial frameworks for Green Medical Informatics solutions are available, however these do not address organizational and human factors. Including these factors in evaluation or analysis of (technical) interventions aimed at making healthcare more sustainable, is essential for improving usability as well as effectiveness of these interventions. Interviews with healthcare professionals from Dutch hospitals led to preliminary insights into which organizational and human factors impact the implementation and adoption of sustainable solutions. Results indicate that forming multi-disciplinary teams is considered an important factor for realizing intended outcomes in terms of reducing carbon emissions and waste. Some other key factors mentioned are formalizing tasks, allocating budget and time, creating awareness and changing protocols to promote sustainable diagnosis and treatment procedures.},
}
@article {pmid37379842,
year = {2023},
author = {Talley, J and Pusdekar, S and Feltenberger, A and Ketner, N and Evers, J and Liu, M and Gosh, A and Palmer, SE and Wardill, TJ and Gonzalez-Bellido, PT},
title = {Predictive saccades and decision making in the beetle-predating saffron robber fly.},
journal = {Current biology : CB},
volume = {33},
number = {14},
pages = {2912-2924.e5},
doi = {10.1016/j.cub.2023.06.019},
pmid = {37379842},
issn = {1879-0445},
mesh = {Humans ; Animals ; Saccades ; *Coleoptera ; *Crocus ; *Odonata ; Decision Making ; },
abstract = {Internal predictions about the sensory consequences of self-motion, encoded by corollary discharge, are ubiquitous in the animal kingdom, including for fruit flies, dragonflies, and humans. In contrast, predicting the future location of an independently moving external target requires an internal model. With the use of internal models for predictive gaze control, vertebrate predatory species compensate for their sluggish visual systems and long sensorimotor latencies. This ability is crucial for the timely and accurate decisions that underpin a successful attack. Here, we directly demonstrate that the robber fly Laphria saffrana, a specialized beetle predator, also uses predictive gaze control when head tracking potential prey. Laphria uses this predictive ability to perform the difficult categorization and perceptual decision task of differentiating a beetle from other flying insects with a low spatial resolution retina. Specifically, we show that (1) this predictive behavior is part of a saccade-and-fixate strategy, (2) the relative target angular position and velocity, acquired during fixation, inform the subsequent predictive saccade, and (3) the predictive saccade provides Laphria with additional fixation time to sample the frequency of the prey's specular wing reflections. We also demonstrate that Laphria uses such wing reflections as a proxy for the wingbeat frequency of the potential prey and that consecutively flashing LEDs to produce apparent motion elicits attacks when the LED flicker frequency matches that of the beetle's wingbeat cycle.},
}
@article {pmid37377567,
year = {2023},
author = {Schwienhorst-Stich, EM and Wabnitz, K and Geck, E and Gepp, S and Jung, L and Mumm, A and Schmid, J and Simmenroth, A and Simon, J and Eichinger, M},
title = {Initiatives promoting planetary health education in Germany: An overview.},
journal = {GMS journal for medical education},
volume = {40},
number = {3},
pages = {Doc38},
pmid = {37377567},
issn = {2366-5017},
mesh = {Germany ; *Education, Medical ; Health Education ; Curriculum ; Schools, Medical ; },
abstract = {Planetary health education focuses on the climate and ecological crises and their adverse health effects. Given the acceleration of these crises, nationwide integration of planetary health education into undergraduate and graduate education, postgraduate training and continuing education for all health professionals has repeatedly been called for. Since 2019, planetary health education has been promoted by several national initiatives in Germany that are summarized in this commentary: 1. National Working Group Planetary Health Education, 2. Manual for planetary health education, 3. Catalog of National Planetary Health Learning Objectives in the National Competency-Based Catalog of Learning Objectives for Medical Education, 4. Working Group Climate, Environment and Health Impact Assessment at the Institute for Medical and Pharmaceutical Examinations, 5. Planetary Health Report Card, and 6. PlanetMedEd study: planetary health education in medical schools in Germany. We hope these initiatives promote collaboration across institutions involved in educating and training health professionals, inter-professional cooperation as well as rapid implementation of planetary health education.},
}
@article {pmid37375921,
year = {2023},
author = {Qi, Y and Ma, L and Ghani, MI and Peng, Q and Fan, R and Hu, X and Chen, X},
title = {Effects of Drought Stress Induced by Hypertonic Polyethylene Glycol (PEG-6000) on Passiflora edulis Sims Physiological Properties.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {12},
pages = {},
pmid = {37375921},
issn = {2223-7747},
support = {2021-229, HZJD [2022]001//Guizhou Provincial Science and Technology Program/ ; Guike AA21196003//Science and Technology Base &amp; Talent Project of Guangxi Province/ ; 2021YFD1100303-3//National Key Research and Development Program of China/ ; 2019-04//Guizhou University Cultivation Project/ ; },
abstract = {Passion fruit is known to be sensitive to drought, and in order to study the physiological and biochemical changes that occur in passion fruit seedlings under drought stress, a hypertonic polyethylene glycol (PEG) solution (5%, 10%, 15%, and 20%) was used to simulate drought stress in passion fruit seedlings. We explored the physiological changes in passion fruit seedlings under drought stress induced by PEG to elucidate their response to drought stress and provide a theoretical basis for drought-resistant cultivation of passion fruit seedlings. The results show that drought stress induced by PEG had a significant effect on the growth and physiological indices of passion fruit. Drought stress significantly decreased fresh weight, chlorophyll content, and root vitality. Conversely, the contents of soluble protein (SP), proline (Pro), and malondialdehyde (MDA) increased gradually with the increasing PEG concentration and prolonged stress duration. After nine days, the SP, Pro and MDA contents were higher in passion fruit leaves and roots under 20% PEG treatments compared with the control. Additionally, with the increase in drought time, the activities of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) showed an increasing trend and then a decreasing trend, and they reached the highest value at the sixth day of drought stress. After rehydration, SP, Pro and MDA contents in the leaves and roots of passion fruit seedlings was reduced. Among all the stress treatments, 20% PEG had the most significant effect on passion fruit seedlings. Therefore, our study demonstrated sensitive concentrations of PEG to simulate drought stress on passion fruit and revealed the physiological adaptability of passion fruit to drought stress.},
}
@article {pmid37372376,
year = {2023},
author = {Cheng, CC and Rivera-Colón, AG and Minhas, BF and Wilson, L and Rayamajhi, N and Vargas-Chacoff, L and Catchen, JM},
title = {Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus-The Closest Ancestral Proxy of Antarctic Cryonotothenioids.},
journal = {Genes},
volume = {14},
number = {6},
pages = {},
pmid = {37372376},
issn = {2073-4425},
mesh = {Humans ; Animals ; Phylogeny ; Antarctic Regions ; *Perciformes/genetics ; Fishes/genetics ; Chromosomes ; },
abstract = {The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of the E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We also reconstructed a notothenioid phylogeny using 2918 proteins of single-copy orthologous genes from these genomes that reaffirmed E. maclovinus' phylogenetic position. We additionally curated E. maclovinus' repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Through reconstructing circadian gene trees, we also assessed the potential role of the retained genes in cryonotothenioids by referencing to the functions of the human orthologs. Our results found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as the direct sister and best suited ancestral proxy of cryonotothenioids. The high-quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, and conversely on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses.},
}
@article {pmid37368895,
year = {2023},
author = {Aceves-Bueno, E and Nenadovic, M and Dove, I and Atkins-Davis, C and Aceves-Bueno, JS and Trejo-Ramirez, A and Rivas-Ochoa, C and Rodriguez-Van Dyck, S and Weaver, AH},
title = {Sustaining small-scale fisheries through a nation-wide Territorial Use Rights in Fisheries system.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0286739},
pmid = {37368895},
issn = {1932-6203},
mesh = {*Fisheries ; *Conservation of Natural Resources ; Territoriality ; Mexico ; Data Management ; Ecosystem ; },
abstract = {Territorial Use rights in Fisheries (TURFs) are used around the world to manage small-scale fisheries and they've shown varying levels of success. Our understanding of what leads to different performance levels is limited due to several reasons. Firstly, these systems are often present in areas with low monitoring capacity where data is scarce. Secondly, past research has centered on the analysis of successful cases, with little attention paid to entire systems. Thirdly, research has been ahistorical, disconnected from the development process of TURF systems. Fourthly, TURFs are often viewed as homogenous ignoring the socio-ecological conditions under which they develop. To address these gaps, the study focuses on Mexico as a case study and context. The research first presents a historical overview of the development of TURF systems in Mexico, including the institutional and legal frameworks that have shaped their evolution. The paper then presents a TURF database that maps all TURF systems in Mexico, including their geographical locations and characteristics. In addition, the study presents case studies based on identified archetypes that showcase the diversity of TURF systems in Mexico, highlighting the different types of systems and the challenges they face. By presenting a comprehensive map of all TURF systems in Mexico, this research paper aims to make an important addition to the case studies in the global literature on TURF systems and provide a valuable resource for marine resource management policymakers, researchers, and practitioners.},
}
@article {pmid37366114,
year = {2023},
author = {Sahoo, P and Jana, P and Kundu, S and Mishra, S and Chattopadhyay, K and Mukherjee, A and Ghosh, CK},
title = {Quercetin@Gd[3+] doped Prussian blue nanocubes induce the pyroptotic death of MDA-MB-231 cells: combinational targeted multimodal therapy, dual modal MRI, intuitive modelling of r1-r2 relaxivities.},
journal = {Journal of materials chemistry. B},
volume = {11},
number = {28},
pages = {6646-6663},
doi = {10.1039/d3tb00316g},
pmid = {37366114},
issn = {2050-7518},
mesh = {Humans ; *Quercetin/pharmacology ; MDA-MB-231 Cells ; *Triple Negative Breast Neoplasms/pathology ; Magnetic Resonance Imaging/methods ; Water ; Caspases ; },
abstract = {Quercetin (Qu), a potential bioflavonoid has gained considerable interest as a promising chemotherapeutic drug which can inhibit the proliferation of triple-negative breast cancer (TNBC) cells due to its regulation of the expression of tumor-suppressor gene metastasis and antioxidant property. Notably, Qu exhibits a very negligible cytotoxic effect on normal cells, even with high-dose treatment, while it is shows high affinity to TNBC. However, the efficiency of Qu is limited clinically due to its poor bioavailability, caused by its low aqueous solubility (2.15 μg mL[-1] at 25 °C), rapid gastrointestinal digestion and chemical instability in alkaline and neutral media. Herein, polydopamine (PDA)-coated, NH2-PEG-NH2 and hyaluronic acid (HA)-functionalized Gd[3+]-doped Prussian blue nanocubes (GPBNC) are reported as a multifunctional platform for the codelivery of Qu as a chemotherapeutic agent and GPBNC as a photodynamic (PDT) and photothermal (PTT) agent with improved therapeutic efficiency to overcome theses barriers. PDA, NH2-PEG-NH2 and HA stabilize GPBNC@Qu and facilitate bioavailability and active-targeting, while absorption of near infrared (NIR) (808 nm; 1 W cm[-2]) induces PDT and PTT activities and dual T1-T2-weighted magnetic resonance imaging (MRI) with high relaxometric parameters (r1 10.06 mM[-1] s[-1] and r2 24.96 mM[-1] s[-1] at a magnetic field of 3 T). The designed platform shows a pH-responsive Qu release profile and NIR-induced therapeutic efficiency of ∼79% in 20 minutes of irradiation, wherein N-terminal gardermin D (N-GSDMD) and a P2X7-receptor-mediated pyroptosis pathway induces cell death, corroborating the up-regulation of NLRP3, caspase-1, caspase-5, N-GSDMD, IL-1β, cleaved Pannexin-1 and P2X7 proteins. More interestingly, the increasing relaxivity values of Prussian blue nanocubes with Gd[3+] doping have been explained on the basis of Solomon-Bloembergen-Morgan theory, considering inner- and outer-sphere relaxivity, wherein crystal defects, coordinated water molecules, tumbling rate, metal to water proton distance, correlation time, magnetisation value etc. play a significant role. In summary, our study suggests that GPBNC could be a beneficial nanocarrier for theranostic purposes against TNBC, while our conceptual study clearly demonstrates the role of various factors in increasing relaxometric parameters.},
}
@article {pmid37365013,
year = {2023},
author = {Azzouz, DF and Chen, Z and Izmirly, PM and Chen, LA and Li, Z and Zhang, C and Mieles, D and Trujillo, K and Heguy, A and Pironti, A and Putzel, GG and Schwudke, D and Fenyo, D and Buyon, JP and Alekseyenko, AV and Gisch, N and Silverman, GJ},
title = {Longitudinal gut microbiome analyses and blooms of pathogenic strains during lupus disease flares.},
journal = {Annals of the rheumatic diseases},
volume = {82},
number = {10},
pages = {1315-1327},
pmid = {37365013},
issn = {1468-2060},
support = {R01 AR042455/AR/NIAMS NIH HHS/United States ; R24 GM137763/GM/NIGMS NIH HHS/United States ; HHSN272201400019C/AI/NIAID NIH HHS/United States ; P50 AR070591/AR/NIAMS NIH HHS/United States ; UL1 TR000038/TR/NCATS NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; UM1 AI109565/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Symptom Flare Up ; *Lupus Erythematosus, Systemic ; *Microbiota ; Feces ; *Lupus Nephritis/genetics ; },
abstract = {OBJECTIVE: Whereas genetic susceptibility for systemic lupus erythematosus (SLE) has been well explored, the triggers for clinical disease flares remain elusive. To investigate relationships between microbiota community resilience and disease activity, we performed the first longitudinal analyses of lupus gut-microbiota communities.<br><br>METHODS: In an observational study, taxononomic analyses, including multivariate analysis of &#xdf;-diversity, assessed time-dependent alterations in faecal communities from patients and healthy controls. From gut blooms, strains were isolated, with genomes and associated glycans analysed.<br><br>RESULTS: Multivariate analyses documented that, unlike healthy controls, significant temporal community-wide ecological microbiota instability was common in SLE patients, and transient intestinal growth spikes of several pathogenic species were documented. Expansions of only the anaerobic commensal, Ruminococcus (blautia) gnavus (RG) occurred at times of high-disease activity, and were detected in almost half of patients during lupus nephritis (LN) disease flares. Whole genome sequence analysis of RG strains isolated during these flares documented 34 genes postulated to aid adaptation and expansion within a host with an inflammatory condition. Yet, the most specific feature of strains found during lupus flares was the common expression of a novel type of cell membrane-associated lipoglycan. These lipoglycans share conserved structural features documented by mass spectroscopy, and highly immunogenic repetitive antigenic-determinants, recognised by high-level serum IgG2 antibodies, that spontaneously arose, concurrent with RG blooms and lupus flares.<br><br>CONCLUSIONS: Our findings rationalise how blooms of the RG pathobiont may be common drivers of clinical flares of often remitting-relapsing lupus disease, and highlight the potential pathogenic properties of specific strains isolated from active LN patients.},
}
@article {pmid37363228,
year = {2023},
author = {Sauer, FG and Lange, U and Schmidt-Chanasit, J and Kiel, E and Wiatrowska, B and Myczko, &#x141; and Lühken, R},
title = {Overwintering Culex torrentium in abandoned animal burrows as a reservoir for arboviruses in Central Europe.},
journal = {One health (Amsterdam, Netherlands)},
volume = {16},
number = {},
pages = {100572},
pmid = {37363228},
issn = {2352-7714},
abstract = {Culex pipiens s.s./Culex torrentium belong to the most widespread mosquito taxa in Europe and are the main vectors of Sindbis, West Nile and Usutu virus. The adult overwintering females can act as reservoir for these arthropod-borne viruses (arboviruses), thus contributing to their local persistence when transmission cycles are interrupted during the winter. However, the main overwintering sites of Cx. torrentium are unknown. In a study from 2017, 3455 Cx. pipiens s.s./Cx. torrentium specimens were collected from abandoned animal burrows in Poznan, Poland. These specimens were retrospectively identified to species-level with a PCR assay, which revealed Cx. torrentium as dominant species (> 60%). Motivated by these results, we conducted a field study from February to July 2022 to systematically analyse the overwintering site patterns of Cx. pipiens s.s./Cx. torrentium. Mosquitoes were sampled using pipe traps in abandoned animal burrows (n = 20) and with aspirators in nearby anthropogenic overwintering sites (n = 23). All Cx. pipiens s.s./Cx. torrentium were screened for Flaviviridae RNA. In total, 4710 mosquitoes of five different taxa were collected from anthropogenic sites. 3977 of them were identified as Cx. p. pipiens/Cx. torrentium (Cx. p. pipiens: 85%, Cx torrentium: 1%, pools with both species: 14%). In contrast, only Cx. p. pipiens/Cx. torrentium (1688 specimens) were collected from animal burrows dominated by Cx. torrentium (52%), followed by pools with both species (40%) and Cx. p pipiens (8%). A single pool of 10 Cx. torrentium specimens collected from an animal burrow was positive for Usutu virus. The detection of Usutu virus demonstrates that Cx. torrentium can act as winter reservoir for arboviruses. Abandoned animal burrows may by the primary overwintering site for the species and should be considered in future surveillance programmes, when sampling overwintering mosquitoes.},
}
@article {pmid37363059,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Mouse Moth, Amphipyra tragopoginis (Clerck 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {54},
pmid = {37363059},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Amphipyra tragopoginis (the Mouse Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 806 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 13,359 protein coding genes.},
}
@article {pmid37359433,
year = {2023},
author = {Fu, D and Abawi, F and Carneiro, H and Kerzel, M and Chen, Z and Strahl, E and Liu, X and Wermter, S},
title = {A Trained Humanoid Robot can Perform Human-Like Crossmodal Social Attention and Conflict Resolution.},
journal = {International journal of social robotics},
volume = {},
number = {},
pages = {1-16},
pmid = {37359433},
issn = {1875-4791},
abstract = {To enhance human-robot social interaction, it is essential for robots to process multiple social cues in a complex real-world environment. However, incongruency of input information across modalities is inevitable and could be challenging for robots to process. To tackle this challenge, our study adopted the neurorobotic paradigm of crossmodal conflict resolution to make a robot express human-like social attention. A behavioural experiment was conducted on 37 participants for the human study. We designed a round-table meeting scenario with three animated avatars to improve ecological validity. Each avatar wore a medical mask to obscure the facial cues of the nose, mouth, and jaw. The central avatar shifted its eye gaze while the peripheral avatars generated sound. Gaze direction and sound locations were either spatially congruent or incongruent. We observed that the central avatar's dynamic gaze could trigger crossmodal social attention responses. In particular, human performance was better under the congruent audio-visual condition than the incongruent condition. Our saliency prediction model was trained to detect social cues, predict audio-visual saliency, and attend selectively for the robot study. After mounting the trained model on the iCub, the robot was exposed to laboratory conditions similar to the human experiment. While the human performance was overall superior, our trained model demonstrated that it could replicate attention responses similar to humans.},
}
@article {pmid37352503,
year = {2023},
author = {Park, Y and Shimada, T and Son, SW and Park, HJ},
title = {Invasion and interaction determine population composition in an open evolving ecological system.},
journal = {Chaos (Woodbury, N.Y.)},
volume = {33},
number = {6},
pages = {},
doi = {10.1063/5.0142978},
pmid = {37352503},
issn = {1089-7682},
mesh = {*Ecosystem ; Population Dynamics ; *Models, Biological ; },
abstract = {It is well-known that interactions between species determine the population composition in an ecosystem. Conventional studies have focused on fixed population structures to reveal how interactions shape population compositions. However, interaction structures are not fixed but change over time due to invasions. Thus, invasion and interaction play an important role in shaping communities. Despite its importance, however, the interplay between invasion and interaction has not been well explored. Here, we investigate how invasion affects the population composition with interactions in open evolving ecological systems considering generalized Lotka-Volterra-type dynamics. Our results show that the system has two distinct regimes. One is characterized by low diversity with abrupt changes of dominant species in time, appearing when the interaction between species is strong and invasion slowly occurs. On the other hand, frequent invasions can induce higher diversity with slow changes in abundances despite strong interactions. It is because invasion happens before the system reaches its equilibrium, which drags the system from its equilibrium all the time. All species have similar abundances in this regime, which implies that fast invasion induces regime shift. Therefore, whether invasion or interaction dominates determines the population composition.},
}
@article {pmid37352137,
year = {2023},
author = {Dias Marques, V and Massago, M and da Silva, MT and Roskowski, I and de Lima, DAN and Dos Santos, L and Louro, E and Gonçalves, ST and Pedroso, RB and Obale, AM and Pelloso, SM and Vissoci, JRN and Staton, CA and Nihei, OK and Carvalho, MDB and Dutra, AC and de Andrade, L},
title = {Exploring regional disparities in lung cancer mortality in a Brazilian state: A cross-sectional ecological study.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0287371},
pmid = {37352137},
issn = {1932-6203},
mesh = {Humans ; Adult ; Brazil/epidemiology ; Cross-Sectional Studies ; Socioeconomic Factors ; Cities ; *Lung Neoplasms/epidemiology ; },
abstract = {BACKGROUND: Lung cancer (LC) is one of the main causes of mortality in Brazil; geographic, cultural, socioeconomic and health access factors can affect the development of the disease. We explored the geospatial distribution of LC mortality, and associated factors, between 2015 and 2019, in Parana state, Brazil.<br><br>METHODS AND FINDINGS: We obtained mortality (from the Brazilian Health Informatics Department) and population rates (from the Brazilian Institute of Geography and Statistics [IBGE]) in people over 40 years old, accessibility of oncology centers by municipality, disease diagnosis rate (from Brazilian Ministry of Health), the tobacco production rate (IBGE) and Parana Municipal Performance Index (IPDM) (from Parana Institute for Economic and Social Development). Global Moran's Index and Local Indicators of Spatial Association were performed to evaluate the spatial distribution of LC mortality in Parana state. Ordinary Least Squares Regression and Geographically Weighted Regression were used to verify spatial association between LC mortality and socioeconomic indicators and health service coverage. A strong spatial autocorrelation of LC mortality was observed, with the detection of a large cluster of high LC mortality in the South of Parana state. Spatial regression analysis showed that all independent variables analyzed were directly related to LC mortality by municipality in Paran&#xe1;.<br><br>CONCLUSIONS: There is a disparity in the LC mortality in Parana state, and inequality of socioeconomic and accessibility to health care services could be associated with it. Our findings may help health managers to intensify actions in regions with vulnerability in the detection and treatment of LC.},
}
@article {pmid37351546,
year = {2023},
author = {Boyes, D and Goate, Z and , and , and , and , and , },
title = {The genome sequence of the Lesser Swallow Prominent, Pheosia gnoma (Fabricius, 1777).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {192},
pmid = {37351546},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Pheosia gnoma (the Lesser Swallow Prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 271.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,628 protein coding genes.},
}
@article {pmid37346819,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Mother Shipton moth , Euclidia mi (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {108},
pmid = {37346819},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Euclidia mi (the Mother Shipton moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 2,320 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,454 protein coding genes.},
}
@article {pmid37346773,
year = {2022},
author = {Boyes, D and Sims, I and Lees, D and , and , and , and , and , and , and Dove, A and , },
title = {The genome sequence of the Kent black arches, Meganola albula (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {310},
pmid = {37346773},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Meganola albula (the Kent black arches; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 405 megabases in span. Most of the assembly (99.95%) is scaffolded into 30 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.},
}
@article {pmid37344755,
year = {2023},
author = {Adelisardou, F and Mederly, P and Minkina, T},
title = {Assessment of soil- and water-related ecosystem services with coupling the factors of climate and land-use change (Example of the Nitra region, Slovakia).},
journal = {Environmental geochemistry and health},
volume = {45},
number = {8},
pages = {6605-6620},
pmid = {37344755},
issn = {1573-2983},
mesh = {Humans ; *Ecosystem ; *Soil ; Water ; Slovakia ; Conservation of Natural Resources ; China ; },
abstract = {Climate and land use change can profoundly impact the provision of ecosystem services (ES) over time, particularly in the landscape of open fields along with growing urbanization and rising demand for space, food and energy. Policymakers are keen on knowing the combined effects of climate and land use change on ESs as a critical issue in human well-being. However, deep knowledge of how to identify these relationships is still lacking. This research aims to undertake a comprehensive assessment of soil- and water-related ES, and improvement in understanding how they are affected by climate and land use change. We applied the Integrated Valuation of Ecosystem Services and Trade-offs model for four ES (soil retention, nutrient delivery ratio, carbon storage, and water yield) for the years 2000 and 2018 in the Nitra region, Slovakia. We investigated the spatial and temporal changes in ES provision and determined the hotspots and coldspots of multiple ES. We found that soil retention, water yield, and carbon storage display a rising trend while the nutrient delivery ratio showed a decreasing trend over the past 18 years. Although all the mentioned services mainly attributed to land use change, the relative contribution of climate change was not deniable. Forests in the north and east and distributed urbanization and agriculture are the hotspots and coldspots for all ESs, respectively. Our results, in terms of determining the relative importance of land use and climate change and identifying the sensitive areas of ES provision, provide a scientific basis for ecosystem conservation and management priority setting at the local and regional levels.},
}
@article {pmid37343095,
year = {2023},
author = {Riva, F and Graco-Roza, C and Daskalova, GN and Hudgins, EJ and Lewthwaite, JMM and Newman, EA and Ryo, M and Mammola, S},
title = {Toward a cohesive understanding of ecological complexity.},
journal = {Science advances},
volume = {9},
number = {25},
pages = {eabq4207},
pmid = {37343095},
issn = {2375-2548},
mesh = {*Ecology/methods ; *Ecosystem ; Data Mining ; Bibliometrics ; Animals ; Human Activities ; },
abstract = {Ecological systems are quintessentially complex systems. Understanding and being able to predict phenomena typical of complex systems is, therefore, critical to progress in ecology and conservation amidst escalating global environmental change. However, myriad definitions of complexity and excessive reliance on conventional scientific approaches hamper conceptual advances and synthesis. Ecological complexity may be better understood by following the solid theoretical basis of complex system science (CSS). We review features of ecological systems described within CSS and conduct bibliometric and text mining analyses to characterize articles that refer to ecological complexity. Our analyses demonstrate that the study of complexity in ecology is a highly heterogeneous, global endeavor that is only weakly related to CSS. Current research trends are typically organized around basic theory, scaling, and macroecology. We leverage our review and the generalities identified in our analyses to suggest a more coherent and cohesive way forward in the study of complexity in ecology.},
}
@article {pmid37343007,
year = {2023},
author = {Isaacson, JE and Ye, JJ and Silva, LL and Hernandes Rocha, TA and de Andrade, L and Scheidt, JFHC and Wen, FH and Sachett, J and Monteiro, WM and Staton, CA and Vissoci, JRN and Gerardo, CJ},
title = {Antivenom access impacts severity of Brazilian snakebite envenoming: A geographic information system analysis.},
journal = {PLoS neglected tropical diseases},
volume = {17},
number = {6},
pages = {e0011305},
pmid = {37343007},
issn = {1935-2735},
support = {R21 TW011944/TW/FIC NIH HHS/United States ; },
mesh = {Humans ; *Snake Bites/epidemiology/therapy ; Antivenins/therapeutic use ; Brazil/epidemiology ; Geographic Information Systems ; Cross-Sectional Studies ; },
abstract = {BACKGROUND: Snakebite envenoming (SBE) is a neglected tropical disease capable of causing both significant disability and death. The burden of SBE is especially high in low- and middle-income countries. The aim of this study was to perform a geospatial analysis evaluating the association of sociodemographics and access to care indicators on moderate and severe cases of SBE in Brazil.<br><br>METHODS: We conducted an ecological, cross-sectional study of SBE in Brazil from 2014 to 2019 using the open access National System Identification of Notifiable Diseases (SINAN) database. We then collected a set of indicators from the Brazil Census of 2010 and performed a Principal Component Analysis to create variables related to health, economics, occupation, education, infrastructure, and access to care. Next, a descriptive and exploratory spatial analysis was conducted to evaluate the geospatial association of moderate and severe events. These variables related to events were evaluated using Geographically Weighted Poisson Regression. T-values were plotted in choropleth maps and considered statistically significant when values were <-1.96 or >+1.96.<br><br>RESULTS: We found that the North region had the highest number of SBE cases by population (47.83/100,000), death rates (0.18/100,000), moderate and severe rates (22.96/100,000), and proportion of cases that took more than three hours to reach healthcare assistance (44.11%). The Northeast and Midwest had the next poorest indicators. Life expectancy, young population structure, inequality, electricity, occupation, and more than three hours to reach healthcare were positively associated with greater cases of moderate and severe events, while income, illiteracy, sanitation, and access to care were negatively associated. The remaining indicators showed a positive association in some areas of the country and a negative association in other areas.<br><br>CONCLUSION: Regional disparities in SBE incidence and rates of poor outcomes exist in Brazil, with the North region disproportionately affected. Multiple indicators were associated with rates of moderate and severe events, such as sociodemographic and health care indicators. Any approach to improving snakebite care must work to ensure the timeliness of antivenom administration.},
}
@article {pmid37340013,
year = {2023},
author = {Tulis, F and Ševčík, M and Jánošíková, R and Baláž, I and Ambros, M and Zvaríková, L and Horváth, G},
title = {Author Correction: The impact of the striped field mouse's range expansion on communities of native small mammals.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {10006},
doi = {10.1038/s41598-023-36731-y},
pmid = {37340013},
issn = {2045-2322},
}
@article {pmid37336403,
year = {2023},
author = {Li, W and Feng, Q and Southam, G and Jin, T and Li, Z},
title = {Changes in microbial community structure during the biooxidation of iron and inorganic/organic sulfur provide prediction of acid mine drainage from coal spoil.},
journal = {The Science of the total environment},
volume = {894},
number = {},
pages = {164945},
doi = {10.1016/j.scitotenv.2023.164945},
pmid = {37336403},
issn = {1879-1026},
mesh = {*Coal ; Sulfur ; Mining ; Bacteria ; Iron ; Acids ; Oxidation-Reduction ; *Microbiota ; },
abstract = {To thoroughly investigate the formation mechanism of acid mine drainage (AMD) from coal mine spoil, this study conducted microbial shake flask experiments on gangue possessing inorganic and organic sulfur to predict the future generation of AMD. The results revealed that microbial-mediated sulfur oxidation effectively lowered the pH of leachate and increased metal ion and sulfate concentrations. The oxidation of pyrite sulfur and thiophene sulfur contributed to 70 % and 30 % of the total acid production, respectively, highlighting the importance of both processes in coal mine acidification. The abundance and diversity of the microbial community increased, with "new" iron and sulfur oxidizing bacterial species during acidification, with "new" iron and sulfur oxidizing bacterial species, such as Sulfobacillus sp. and Acidibacillus sp., emerging and constituting approximately one-third of the bacterial population. These bacteria survived desiccation and proliferated faster than A. ferrooxidans YQ-N3 when conditions favored growth.},
}
@article {pmid37335075,
year = {2023},
author = {Burger, J and Gochfeld, M and Giffen, N and Brown, KG and Cortes, M and Ng, K and Kosson, DS},
title = {Comparing land cover and interior forests on contaminated land and the surrounding region: Oak Ridge Reservation as a case study.},
journal = {Journal of toxicology and environmental health. Part A},
volume = {86},
number = {15},
pages = {501-517},
doi = {10.1080/15287394.2023.2223231},
pmid = {37335075},
issn = {1528-7394},
support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; },
mesh = {*Conservation of Natural Resources/methods ; *Forests ; Databases, Factual ; Ecosystem ; },
abstract = {Pressure from expanding populations has resulted in a need for protection, reclamation, and restoration of damaged land to productive, beneficial health uses. The objective of this investigation was to 1) compare land cover on the Department of Energy (DOE) Oak Ridge Reservation (ORR) with the surrounding region, 2) select an indicator to evaluate ORR's protection of ecological resources, and 3) develop and implement a method to compare the amount of the indicator on ORR with the regions using National Land Cover Database (NLCD). Data demonstrated that ORR has a higher % of forests (deciduous, coniferous, mixed) than the 10 km and 30 km areas surrounding ORR, suggesting that obligations are being met to protect the ecology and environment. The findings also indicate that the interior forest at ORR is fragmented more than is the interior forest in the 30 km buffer zone, suggesting a need for DOE and managers of other lands to take into consideration the importance of intact interior forest when developing land or planning roads. The study describes the basis for specific ecological parameters such as interior forest that are important to consider when planning and executing remediation, restoration, and other management actions.},
}
@article {pmid37331314,
year = {2023},
author = {Liu, J and Xu, X and Zou, C and Lin, N and Zhang, K and Shan, N and Zhang, H and Liu, R},
title = {A Bayesian network-GIS probabilistic model for addressing human disturbance risk to ecological conservation redline areas.},
journal = {Journal of environmental management},
volume = {344},
number = {},
pages = {118400},
doi = {10.1016/j.jenvman.2023.118400},
pmid = {37331314},
issn = {1095-8630},
mesh = {Humans ; *Geographic Information Systems ; *Conservation of Natural Resources/methods ; Bayes Theorem ; Forests ; Models, Statistical ; China ; Ecosystem ; },
abstract = {Population growth and associated ecological space occupation are posing great risks to regional ecological security and social stability. In China, "Ecological Conservation Redline" (ECR) that prohibited urbanization and industrial construction has been proposed as a national policy to resolve spatial mismatches and management contradictions. However, unfriendly human disturbance activities (e.g., cultivation, mining, and infrastructure construction) still exist within the ECR, posing a great threat to ecological stability and safety. In this article, a Bayesian network (BN)-GIS probabilistic model is proposed to spatially and quantitatively address the human disturbance risk to the ECR at the regional scale. The Bayesian models integrate multiple human activities, ecological receptors of the ECR, and their exposure relationships for calculating the human disturbance risk. The case learning method geographic information systems (GIS) is then introduced to train BN models based on the spatial attribute of variables to evaluate the spatial distribution and correlation of risks. This approach was applied to the human disturbance risk assessment for the ECR that was delineated in 2018 in Jiangsu Province, China. The results indicated that most of the ECRs were at a low or medium human disturbance risk level, while some drinking water sources and forest parks in Lianyungang City possessed the highest risk. The sensitivity analysis result showed the ECR vulnerability, especially for cropland, that contributed most to the human disturbance risk. This spatially probabilistic method can not only enhance model's prediction precision, but also help decision-makers to determine how to establish priorities for policy design and conservation interventions. Overall, it presents a foundation for later ECR adjustments as well as for human disturbance risk supervision and management at the regional scale.},
}
@article {pmid37325324,
year = {2023},
author = {Douet Vannucci, V and Marchand, T and Hennequin, A and Caci, H and Staccini, P},
title = {The EPIDIA4Kids protocol for a digital epidemiology study on brain functioning in children, based on a multimodality biometry tool running on an unmodified tablet.},
journal = {Frontiers in public health},
volume = {11},
number = {},
pages = {1185565},
pmid = {37325324},
issn = {2296-2565},
mesh = {Humans ; Child ; *Mental Disorders ; Brain/diagnostic imaging ; Biometry ; },
abstract = {INTRODUCTION: Neurodevelopment and related mental disorders (NDDs) are one of the most frequent disabilities among young people. They have complex clinical phenotypes often associated with transnosographic dimensions, such as emotion dysregulation and executive dysfunction, that lead to adverse impacts in personal, social, academic, and occupational functioning. Strong overlap exists then across NDDs phenotypes that are challenging for diagnosis and therapeutic intervention. Recently, digital epidemiology uses the rapidly growing data streams from various devices to advance our understanding of health's and disorders' dynamics, both in individuals and the general population, once coupled with computational science. An alternative transdiagnostic approach using digital epidemiology may thus better help understanding brain functioning and hereby NDDs in the general population.<br><br>OBJECTIVE: The EPIDIA4Kids study aims to propose and evaluate in children, a new transdiagnostic approach for brain functioning examination, combining AI-based multimodality biometry and clinical e-assessments on an unmodified tablet. We will examine this digital epidemiology approach in an ecological context through data-driven methods to characterize cognition, emotion, and behavior, and ultimately the potential of transdiagnostic models of NDDs for children in real-life practice.<br><br>METHODS AND ANALYSIS: The EPIDIA4Kids is an uncontrolled open-label study. 786 participants will be recruited and enrolled if eligible: they are (1) aged 7 to 12&#x2009;years and (2) are French speaker/reader; (3) have no severe intellectual deficiencies. Legal representative and children will complete online demographic, psychosocial and health assessments. During the same visit, children will perform additionally a paper/pencil neuro-assessments followed by a 30-min gamified assessment on a touch-screen tablet. Multi-stream data including questionnaires, video, audio, digit-tracking, will be collected, and the resulting multimodality biometrics will be generated using machine- and deep-learning algorithms. The trial will start in March 2023 and is expected to end by December 2024.<br><br>DISCUSSION: We hypothesize that the biometrics and digital biomarkers will be capable of detecting early onset symptoms of neurodevelopment compared to paper-based screening while as or more accessible in real-life practice.},
}
@article {pmid37316182,
year = {2023},
author = {Eliason, PH and Galarneau, JM and Kolstad, AT and Pankow, MP and West, SW and Bailey, S and Miutz, L and Black, AM and Broglio, SP and Davis, GA and Hagel, BE and Smirl, JD and Stokes, KA and Takagi, M and Tucker, R and Webborn, N and Zemek, R and Hayden, A and Schneider, KJ and Emery, CA},
title = {Prevention strategies and modifiable risk factors for sport-related concussions and head impacts: a systematic review and meta-analysis.},
journal = {British journal of sports medicine},
volume = {57},
number = {12},
pages = {749-761},
doi = {10.1136/bjsports-2022-106656},
pmid = {37316182},
issn = {1473-0480},
mesh = {Adolescent ; Child ; Humans ; *Brain Concussion/prevention &amp; control ; *Football ; Rugby ; *Hockey ; Databases, Factual ; },
abstract = {OBJECTIVES: To evaluate prevention strategies, their unintended consequences and modifiable risk factors for sport-related concussion (SRC) and/or head impact risk.<br><br>DESIGN: This systematic review and meta-analysis was registered on PROSPERO (CRD42019152982) and conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.<br><br>DATA SOURCES: Eight databases (MEDLINE, CINAHL, APA PsycINFO, Cochrane (Systematic Review and Controlled Trails Registry), SPORTDiscus, EMBASE, ERIC0 were searched in October 2019 and updated in March 2022, and references searched from any identified systematic review.<br><br>ELIGIBILITY CRITERIA: Study inclusion criteria were as follows: (1) original data human research studies, (2) investigated SRC or head impacts, (3) evaluated an SRC prevention intervention, unintended consequence or modifiable risk factor, (4) participants competing in any sport, (5) analytic study design, (6) systematic reviews and meta-analyses were included to identify original data manuscripts in reference search and (7) peer-reviewed. Exclusion criteria were as follows: (1) review articles, pre-experimental, ecological, case series or case studies and (2) not written in English.<br><br>RESULTS: In total, 220 studies were eligible for inclusion and 192 studies were included in the results based on methodological criteria as assessed through the Scottish Intercollegiate Guidelines Network high ('++') or acceptable ('+') quality. Evidence was available examining protective gear (eg, helmets, headgear, mouthguards) (n=39), policy and rule changes (n=38), training strategies (n=34), SRC management strategies (n=12), unintended consequences (n=5) and modifiable risk factors (n=64). Meta-analyses demonstrated a protective effect of mouthguards in collision sports (incidence rate ratio, IRR 0.74; 95%&#x2009;CI 0.64 to 0.89). Policy disallowing bodychecking in child and adolescent ice hockey was associated with a 58% lower concussion rate compared with bodychecking leagues (IRR 0.42; 95%&#x2009;CI 0.33 to 0.53), and evidence supports no unintended injury consequences of policy disallowing bodychecking. In American football, strategies limiting contact in practices were associated with a 64% lower practice-related concussion rate (IRR 0.36; 95%&#x2009;CI 0.16 to 0.80). Some evidence also supports up to 60% lower concussion rates with implementation of a neuromuscular training warm-up programme in rugby. More research examining potentially modifiable risk factors (eg, neck strength, optimal tackle technique) are needed to inform concussion prevention strategies.<br><br>CONCLUSIONS: Policy and rule modifications, personal protective equipment, and neuromuscular training strategies may help to prevent SRC.<br><br>PROSPERO REGISTRATION NUMBER: CRD42019152982.},
}
@article {pmid37311775,
year = {2023},
author = {Nemesházi, E and Bókony, V},
title = {HerpSexDet: the herpetological database of sex determination and sex reversal.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {377},
pmid = {37311775},
issn = {2052-4463},
support = {ESP 239-B//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; NKFIH K-135016//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; },
mesh = {Animals ; *Animals, Wild ; Databases, Factual ; *Ecology ; Phenotype ; Species Specificity ; Sex Determination Processes ; },
abstract = {Wildlife exhibits various sex-determination systems where sex chromosomes and environmental temperatures may both contribute to individual sexual development. The causes and consequences of this variability are important questions for evolutionary ecology, especially in light of ongoing environmental change. Amphibians and reptiles are emerging as a key group for studying these questions, with new data accumulating acceleratingly. We collected empirical data from earlier databases, reviews and primary literature to create the most up-to-date database on herpetological sex determination. We named our database HerpSexDet, which currently features data on genetic and temperature-dependent sex determination as well as reports on sex reversal for a total of 192 amphibian and 697 reptile species. This dataset, which we will regularly update in the future, facilitates interspecific comparative studies on the evolution of sex determination and its consequences for species-specific traits such as life history and conservation status, and may also help guiding future research by identifying species or higher taxa that are potentially most enlightening for the study of environmentally driven sex reversal.},
}
@article {pmid37307237,
year = {2023},
author = {Tardelli, VS and Bianco, MCM and Patel, R and Areco, KCN and Bandiera-Paiva, P and Tardelli, AO and Segura, LE and Castaldelli-Maia, JM and Fidalgo, TM and Martins, SS},
title = {Overdose death rates in Brazil: an ecological analysis by region.},
journal = {Revista brasileira de psiquiatria (Sao Paulo, Brazil : 1999)},
volume = {45},
number = {4},
pages = {381-382},
pmid = {37307237},
issn = {1809-452X},
}
@article {pmid37306048,
year = {2023},
author = {Mumme, S and Middleton, AD and Ciucci, P and De Groeve, J and Corradini, A and Aikens, EO and Ossi, F and Atwood, P and Balkenhol, N and Cole, EK and Debeffe, L and Dewey, SR and Fischer, C and Gude, J and Heurich, M and Hurley, MA and Jarnemo, A and Kauffman, MJ and Licoppe, A and van Loon, E and McWhirter, D and Mong, TW and Pedrotti, L and Morellet, N and Mysterud, A and Peters, W and Proffitt, K and Saïd, S and Signer, J and Sunde, P and Starý, M and Cagnacci, F},
title = {Wherever I may roam-Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents.},
journal = {Global change biology},
volume = {29},
number = {20},
pages = {5788-5801},
doi = {10.1111/gcb.16769},
pmid = {37306048},
issn = {1365-2486},
support = {//&#xc5;gerups &amp; Elsag&#xe5;rdens S&#xe4;teri AB/ ; //Assm&#xe5;sa Gods AB/ ; //Carl Piper/ ; Wildlife &amp; Landscape Research Package-project 2B//Danish Forest and Nature Agency/ ; //Ersaf Lombardia and Trento/ ; //Fondazione Edmund Mach/ ; //Grand Teton Association/ ; //Halmstad University/ ; //H&#xf6;gestad &amp; Christinehofs F&#xf6;rvaltnings AB/ ; //Holmen Skog AB/ ; //International Research School of Applied Ecology/ ; //Ittur AB/ ; //Karl-Erik &#xd6;nnesj&#xf6;s Stiftelse f&#xf6;r Vetenskaplig forskning och Utveckling/ ; //Kolm&#xe5;rdens insamlingsstiftelse/T&#xe5;by Allm&#xe4;nning/ ; //Marie-Claire Cronstedts Stiftelse/ ; //Office Fran&#xe7;ais de la Biodiversit&#xe9;/ ; //Public Service of Wallonia/ ; //Region Sk&#xe5;ne / Stiftelsen Sk&#xe5;nska Landskap/ ; //Stelvio National Park/ ; //Stiftelsen Oscar och Lili Lamms Minne/ ; //Sveaskog/ ; 5871/2005//Swedish Association for Hunting and Wildlife Management/ ; 802-0092-11//Swedish Environmental Protection Agency/ ; //Swedish University of Agricultural Sciences/ ; //Universit&#xe0; degli Studi di Trento/ ; //University of California Berkeley/ ; //Vectronic Aerospace GmbH/ ; //Vir&#xe5; Bruk AB/ ; },
mesh = {Humans ; Animals ; *Ecosystem ; *Deer/physiology ; Human Activities ; North America ; Geographic Information Systems ; },
abstract = {Human activity and associated landscape modifications alter the movements of animals with consequences for populations and ecosystems worldwide. Species performing long-distance movements are thought to be particularly sensitive to human impact. Despite the increasing anthropogenic pressure, it remains challenging to understand and predict animals' responses to human activity. Here we address this knowledge gap using 1206 Global Positioning System movement trajectories of 815 individuals from 14 red deer (Cervus elaphus) and 14 elk (Cervus canadensis) populations spanning wide environmental gradients, namely the latitudinal range from the Alps to Scandinavia in Europe, and the Greater Yellowstone Ecosystem in North America. We measured individual-level movements relative to the environmental context, or movement expression, using the standardized metric Intensity of Use, reflecting both the directionality and extent of movements. We expected movement expression to be affected by resource (Normalized Difference Vegetation Index, NDVI) predictability and topography, but those factors to be superseded by human impact. Red deer and elk movement expression varied along a continuum, from highly segmented trajectories over relatively small areas (high intensity of use), to directed transitions through restricted corridors (low intensity of use). Human activity (Human Footprint Index, HFI) was the strongest driver of movement expression, with a steep increase in Intensity of Use as HFI increased, but only until a threshold was reached. After exceeding this level of impact, the Intensity of Use remained unchanged. These results indicate the overall sensitivity of Cervus movement expression to human activity and suggest a limitation of plastic responses under high human pressure, despite the species also occurring in human-dominated landscapes. Our work represents the first comparison of metric-based movement expression across widely distributed populations of a deer genus, contributing to the understanding and prediction of animals' responses to human activity.},
}
@article {pmid37302594,
year = {2023},
author = {Haas, D and Ilieva, M and Fritz, T and Galler, H and Habib, J and Kriso, A and Kropsch, M and Ofner-Kopeinig, P and Reinthaler, FF and Strasser, A and Zentner, E and Schalli, M},
title = {Background concentrations of airborne, culturable fungi and dust particles in urban, rural and mountain regions.},
journal = {The Science of the total environment},
volume = {892},
number = {},
pages = {164700},
doi = {10.1016/j.scitotenv.2023.164700},
pmid = {37302594},
issn = {1879-1026},
mesh = {Humans ; *Dust ; *Environmental Monitoring/methods ; Air Microbiology ; Fungi ; Spores, Fungal ; Seasons ; },
abstract = {Geographic location and meteorological factors can affect the content of bioaerosol concentrations. This study was conducted to determine the natural background concentrations of culturable fungal spores and dust particles in three different geographical areas. Focus was given to the dominant airborne genera Cladosporium, Penicillium, Aspergillus and the species Aspergillus fumigatus. The influence of weather conditions on the microorganism concentrations in urban, rural and mountain regions were examined. Possible correlations between particle counts and culturable fungal spore concentrations were investigated. 125 measurements of the air were conducted using the air sampler MAS-100NT® and the particle counter Alphasense OPC-N3. The analyses of the collected samples were based on culture methods using different media. The highest median of fungal spore concentrations was detected in the urban region and was of 2.0 × 10[3] CFU/m[3] for xerophilic fungi and 1.7 × 10[3] CFU/m[3] for the genus Cladosporium. The concentrations of fine and coarse particles in rural and urban regions were the highest of 1.9 × 10[7] pa/m[3] and 1.3 × 10[7] pa/m[3], respectively. Little cloud cover and slight wind had a positive influence on the concentration of fungal spores. Furthermore, correlations were observed between air temperature and the concentrations of xerophilic fungi as well as the genera Cladosporium. In contrast, relative humidity correlated negatively with total fungi and Cladosporium and no correlation was found with the other fungi. For the region of Styria in summer and early autumn, the natural background concentration for xerophilic fungi ranged between 3.5 × 10[2] and 4.7 × 10[3] CFU/m[3] air. No significant differences were detected between the fungal spore concentrations in urban, rural and mountainous regions. The data of this study could be used as a reference to compare the natural background concentrations of airborne culturable fungi in further studies concerning air quality assessment.},
}
@article {pmid37301186,
year = {2023},
author = {Yin, Q and Wu, T and Gao, R and Wu, L and Shi, Y and Wang, X and Wang, M and Xu, Z and Zhao, Y and Su, X and Su, Y and Han, X and Yuan, L and Xiang, L and Chen, S},
title = {Multi-omics reveal key enzymes involved in the formation of phenylpropanoid glucosides in Artemisia annua.},
journal = {Plant physiology and biochemistry : PPB},
volume = {201},
number = {},
pages = {107795},
doi = {10.1016/j.plaphy.2023.107795},
pmid = {37301186},
issn = {1873-2690},
mesh = {*Artemisia annua/metabolism ; Scopoletin/chemistry/metabolism/pharmacology ; Esculin/metabolism ; Multiomics ; Molecular Docking Simulation ; *Artemisinins/metabolism ; Glucosides/metabolism ; Glucose/metabolism ; Uridine Diphosphate/metabolism ; },
abstract = {Although mainly known for producing artemisinin, Artemisia annua is enriched in phenylpropanoid glucosides (PGs) with significant bioactivities. However, the biosynthesis of A. annua PGs is insufficiently investigated. Different A. annua ecotypes from distinct growing environments accumulate varying amounts of metabolites, including artemisinin and PGs such as scopolin. UDP-glucose:phenylpropanoid glucosyltransferases (UGTs) transfers glucose from UDP-glucose in PG biosynthesis. Here, we found that the low-artemisinin ecotype GS produces a higher amount of scopolin, compared to the high-artemisinin ecotype HN. By combining transcriptome and proteome analyses, we selected 28 candidate AaUGTs from 177 annotated AaUGTs. Using AlphaFold structural prediction and molecular docking, we determined the binding affinities of 16 AaUGTs. Seven of the AaUGTs enzymatically glycosylated phenylpropanoids. AaUGT25 converted scopoletin to scopolin and esculetin to esculin. The lack of accumulation of esculin in the leaf and the high catalytic efficiency of AaUGT25 on esculetin suggest that esculetin is methylated to scopoletin, the precursor of scopolin. We also discovered that AaOMT1, a previously uncharacterized O-methyltransferase, converts esculetin to scopoletin, suggesting an alternative route for producing scopoletin, which contributes to the high-level accumulation of scopolin in A. annua leaves. AaUGT1 and AaUGT25 responded to induction of stress-related phytohormones, implying the involvement of PGs in stress responses.},
}
@article {pmid37297635,
year = {2023},
author = {Ojukwu, EN and Okoye, HU and Saewyc, E},
title = {Social Correlates of HIV-Risky Behaviours among African Canadian Adolescents Living in British Columbia, Canada: A Secondary Data Analysis.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {11},
pages = {},
pmid = {37297635},
issn = {1660-4601},
mesh = {Humans ; Adolescent ; British Columbia/epidemiology ; *Secondary Data Analysis ; Black or African American ; Sexual Behavior ; *HIV Infections/epidemiology ; Risk-Taking ; },
abstract = {Studies have linked HIV-risky behaviours among young people to several socio-contextual factors. However, the social factors that might increase African Canadian adolescents' exposure to HIV-risky behaviours, including unprotected sex and forced or multiple-sexual partnerships, have received little or no attention in the literature. Using data from the British Columbia Adolescent Health Surveys (2003-2018) and guided by intersectionality and socio-ecological frameworks, we examined the social determinants of HIV-risky behaviours (HRB) among African Canadian adolescents in British Columbia. We observed a general decline in HRB from 2008 to 2018. However, more than half (54.5%) of the 1042 who were sexually experienced in 2018 reported having 2 or more sexual partners, and nearly half reported condom-less sex. Our results demonstrate an important need to evaluate the impacts of several social factors on health outcomes for a unique, marginalized population.},
}
@article {pmid37289204,
year = {2023},
author = {Brown, MJM and Walker, BE and Black, N and Govaerts, RHA and Ondo, I and Turner, R and Nic Lughadha, E},
title = {rWCVP: a companion R package for the World Checklist of Vascular Plants.},
journal = {The New phytologist},
volume = {240},
number = {4},
pages = {1355-1365},
doi = {10.1111/nph.18919},
pmid = {37289204},
issn = {1469-8137},
mesh = {*Software ; Checklist ; *Tracheophyta ; Plants ; Databases, Factual ; },
abstract = {The World Checklist of Vascular Plants (WCVP) is an extremely valuable resource that is being used to address many fundamental and applied questions in plant science, conservation, ecology and evolution. However, databases of this size require data manipulation skills that pose a barrier to many potential users. Here, we present rWCVP, an open-source R package that aims to facilitate the use of the WCVP by providing clear, intuitive functions to execute many common tasks. These functions include taxonomic name reconciliation, geospatial integration, mapping and generation of multiple different summaries of the WCVP in both data and report format. We have included extensive documentation and tutorials, providing step-by-step guides that are accessible even to users with minimal programming experience. rWCVP is available on cran and GitHub.},
}
@article {pmid37278908,
year = {2023},
author = {Gao, H and Wu, M and Liu, H and Ou, Y and Zhang, T and Duan, X},
title = {Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics.},
journal = {Microbial ecology},
volume = {86},
number = {4},
pages = {2436-2446},
pmid = {37278908},
issn = {1432-184X},
mesh = {*Petroleum ; Soil/chemistry ; *Soil Pollutants/analysis ; Soil Microbiology ; Biodegradation, Environmental ; Hydrocarbons/metabolism ; Bacteria/genetics/metabolism ; Computational Biology ; },
abstract = {Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.},
}
@article {pmid37277721,
year = {2023},
author = {Zhong, H and Luo, J and Tang, L and Liao, S and Lu, Z and Lin, G and Murphy, RW and Liu, L},
title = {Association filtering and generative adversarial networks for predicting lncRNA-associated disease.},
journal = {BMC bioinformatics},
volume = {24},
number = {1},
pages = {234},
pmid = {37277721},
issn = {1471-2105},
support = {grant no. 2019FY003027//Yunnan Provincial Science and Technology Department-Yunnan University Double First-Class Joint Fund Key Projects/ ; grant no. 2022YFC2602500//National Key R&amp;D Program of China/ ; grant no. 61862067, U1902201//National Natural Science Foundation of China/ ; grant no. 202201AT070042//Applied Basic Research Project in Yunnan Province/ ; },
mesh = {*RNA, Long Noncoding/genetics ; Algorithms ; Computational Biology/methods ; },
abstract = {BACKGROUND: Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and understand pathogenesis, and thus better diagnose preventable diseases.<br><br>RESULTS: Herein, we offer the LDAF_GAN method for predicting lncRNA-associated disease based on association filtering and generative adversarial networks. Experimentation used two types of data: lncRNA-disease associated data without lncRNA sequence features, and fused lncRNA sequence features. LDAF_GAN uses a generator and discriminator, and differs from the original GAN by the addition of a filtering operation and negative sampling. Filtering allows the generator output to filter out unassociated diseases before being fed into the discriminator. Thus, the results generated by the model focuses only on lncRNAs associated with disease. Negative sampling takes a portion of disease terms with 0 from the association matrix as negative samples, which are assumed to be unassociated with lncRNA. A regular term is added to the loss function to avoid producing a vector with all values of 1, which can fool the discriminator. Thus, the model requires that generated positive samples are close to 1, and negative samples are close to 0. The model achieved a superior fitting effect; LDAF_GAN had superior performance in predicting fivefold cross-validations on the two datasets with AUC values of 0.9265 and 0.9278, respectively. In the case study, LDAF_GAN predicted disease association for six lncRNAs-H19, MALAT1, XIST, ZFAS1, UCA1, and ZEB1-AS1-and with the top ten predictions of 100%, 80%, 90%, 90%, 100%, and 90%, respectively, which were reported by previous studies.<br><br>CONCLUSION: LDAF_GAN efficiently predicts the potential association of existing lncRNAs and the potential association of new lncRNAs with diseases. The results of fivefold cross-validation, tenfold cross-validation, and case studies suggest that the model has great predictive potential for lncRNA-disease association prediction.},
}
@article {pmid37273367,
year = {2023},
author = {Ekram, R and Nazer, MS},
title = {Hospital Admission Profile Due to Osteoarthritis: An Ecological Study.},
journal = {Cureus},
volume = {15},
number = {5},
pages = {e38435},
pmid = {37273367},
issn = {2168-8184},
abstract = {Background Osteoarthritis (OA) is also known as degenerative joint disease and is considered the major cause of joint pain and disability. Furthermore, OA is the most common, costly, and disabling form of joint diseases. The objective of this study is to explore the hospital admission profile due to OA between the period 1999 and 2019 in England and Wales. Method This is an ecological study that used health care data in the United Kingdom. Patients who were hospitalized for OA in England and Wales between 1999 and 2019 formed the study population. The Hospital Episode Statistics in England and the Patient Episode Database for Wales databases were used in this study. The difference in the admission rate during the study period was estimated using the chi-squared test. Results The admission rate during the study period increased by 112.1% for all hospital admission related to OA. The most common type of admission was related to gonarthrosis, which accounted for 46.7% of the total number of admissions for OA. The increase in admission rate across different types of admissions related to OA was not consistent. The highest increase in the admission rate was observed for polyarthrosis (604.6%). Admission rates related to OA were observed to be directly related to age. The highest increase in the admission rate during the study period was for the age group of 15-59 years (102.1%). Admission rate due to OA was higher among females compared to males. Conclusion The increase in admission rates for the various OA-related admissions was not consistent. This study found that the age range of 15 to 59 years experienced the greatest increase in admission rates. Female gender is a high risk factor for OA, especially in women around menopause.},
}
@article {pmid37270983,
year = {2023},
author = {Vo, HT and Vrachioli, M and Frick, F and Sauer, J and Brucet Balmana, S and Benejam Vidal, L and Mehner, T and Lemmens, P and Oertli, B and Boissezon, A and Beklioğlu, M and Dolcerocca, A and Meerhoff, M},
title = {Socio-economic or environmental benefits from pondscapes? Deriving stakeholder preferences using analytic hierarchy process and compositional data analysis.},
journal = {Journal of environmental management},
volume = {342},
number = {},
pages = {118298},
doi = {10.1016/j.jenvman.2023.118298},
pmid = {37270983},
issn = {1095-8630},
mesh = {Humans ; *Ecosystem ; *Analytic Hierarchy Process ; Biodiversity ; Ponds ; Socioeconomic Factors ; Conservation of Natural Resources ; },
abstract = {Ponds occupy a large share of standing water worldwide and play an important role in providing various ecosystem services. There are concerted efforts of the European Union either to create new ponds, or to restore and preserve existing ponds as nature-based solutions to provide benefits to ecosystem and human well-being. As part of the EU PONDERFUL project, selected pondscapes (i.e. landscapes of ponds) in eight different countries - hereafter "demo-sites", are studied to comprehensively understand their characteristics and their efficiency to provide ecosystem services. In addition, the needs and knowledge of stakeholders who own, work, research, or benefit from the pondscapes are also important, because of their capabilities to create, manage and develop the pondscapes. Therefore, we established connection with stakeholders to study their preferences and visions on the pondscapes. Using the analytic hierarchy process, this study shows that in general stakeholders in the European and Turkish demo-sites prefer environmental benefits to economic benefits, while stakeholders in the Uruguayan demo-sites rank the economic benefits higher. More specifically, in the European and Turkish demo-sites, the biodiversity benefits, i.e. life-cycle maintenance, habitat and gene pool protection, receive the highest ranking among all groups. On the other hand, stakeholders at the Uruguayan demo-sites rank provisioning benefits as the most important, because many ponds in Uruguayan demo-sites are being used for agricultural purposes. Understanding those preferences helps policy makers to address the needs of stakeholders more correctly, when considering any action or policy for the pondscapes.},
}
@article {pmid37267326,
year = {2023},
author = {Spencer, N and Łukasik, P and Meyer, M and Veloso, C and McCutcheon, JP},
title = {No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas.},
journal = {Genome biology and evolution},
volume = {15},
number = {6},
pages = {},
pmid = {37267326},
issn = {1759-6653},
mesh = {Animals ; Phylogeny ; *Hemiptera/microbiology ; Symbiosis/genetics ; *Flavobacteriaceae/genetics ; *Alphaproteobacteria/genetics ; Genome, Bacterial ; Gene Dosage ; Evolution, Molecular ; },
abstract = {Bacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and stable genomes. Paradoxically, the some of the same evolutionary processes that drive genome reduction and simplification may also cause genome expansion and complexification. A bacterial endosymbiont of cicadas, Hodgkinia cicadicola, exemplifies this paradox. In many cicada species, a single Hodgkinia lineage with a tiny, gene-dense genome has split into several interdependent cell and genome lineages. Each new Hodgkinia lineage encodes a unique subset of the ancestral unsplit genome in a complementary way, such that the collective gene contents of all lineages match the total found in the ancestral single genome. This splitting creates genetically distinct Hodgkinia cells that must function together to carry out basic cellular processes. It also creates a gene dosage problem where some genes are encoded by only a small fraction of cells while others are much more abundant. Here, by sequencing DNA and RNA of Hodgkinia from different cicada species with different amounts of splitting-along with its structurally stable, unsplit partner endosymbiont Sulcia muelleri-we show that Hodgkinia does not transcriptionally compensate to rescue the wildly unbalanced gene and genome ratios that result from lineage splitting. We also find that Hodgkinia has a reduced capacity for basic transcriptional control independent of the splitting process. Our findings reveal another layer of degeneration further pushing the limits of canonical molecular and cell biology in Hodgkinia and may partially explain its propensity to go extinct through symbiont replacement.},
}
@article {pmid37265476,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Hammond, J and , },
title = {The genome sequence of the Elbow-stripe Grass-veneer, Agriphila geniculea (Haworth, 1811).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {86},
pmid = {37265476},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Agriphila geniculea (the Elbow-stripe Grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 781.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,132 protein coding genes.},
}
@article {pmid37263997,
year = {2023},
author = {Duncanson, L and Liang, M and Leitold, V and Armston, J and Krishna Moorthy, SM and Dubayah, R and Costedoat, S and Enquist, BJ and Fatoyinbo, L and Goetz, SJ and Gonzalez-Roglich, M and Merow, C and Roehrdanz, PR and Tabor, K and Zvoleff, A},
title = {The effectiveness of global protected areas for climate change mitigation.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2908},
pmid = {37263997},
issn = {2041-1723},
support = {80NSSC21K0196//National Aeronautics and Space Administration (NASA)/ ; 80NSSC21K0196//National Aeronautics and Space Administration (NASA)/ ; NNL 15AA03C//National Aeronautics and Space Administration (NASA)/ ; NNL 15AA03C//National Aeronautics and Space Administration (NASA)/ ; 80NSSC21K0189//National Aeronautics and Space Administration (NASA)/ ; OAC1934389//National Science Foundation (NSF)/ ; OAC1934389//National Science Foundation (NSF)/ ; 80NSSC19K0186//National Science Foundation (NSF)/ ; OAC1934389//National Science Foundation (NSF)/ ; OAC1934389//National Science Foundation (NSF)/ ; },
abstract = {Forests play a critical role in stabilizing Earth's climate. Establishing protected areas (PAs) represents one approach to forest conservation, but PAs were rarely created to mitigate climate change. The global impact of PAs on the carbon cycle has not previously been quantified due to a lack of accurate global-scale carbon stock maps. Here we used ~412 million lidar samples from NASA's GEDI mission to estimate a total PA aboveground carbon (C) stock of 61.43 Gt (+/- 0.31), 26% of all mapped terrestrial woody C. Of this total, 9.65 + /- 0.88 Gt of additional carbon was attributed to PA status. These higher C stocks are primarily from avoided emissions from deforestation and degradation in PAs compared to unprotected forests. This total is roughly equivalent to one year of annual global fossil fuel emissions. These results underscore the importance of conservation of high biomass forests for avoiding carbon emissions and preserving future sequestration.},
}
@article {pmid37263027,
year = {2023},
author = {Mokarram, M and Mokarram, MJ and Najafi, A},
title = {Thermal power plants pollution assessment based on deep neural networks, remote sensing, and GIS: A real case study in Iran.},
journal = {Marine pollution bulletin},
volume = {192},
number = {},
pages = {115069},
doi = {10.1016/j.marpolbul.2023.115069},
pmid = {37263027},
issn = {1879-3363},
mesh = {Environmental Monitoring/methods ; Geographic Information Systems ; Iran ; Carbon Dioxide/analysis ; Remote Sensing Technology ; *Air Pollution/analysis ; Neural Networks, Computer ; Water/analysis ; Power Plants ; *Air Pollutants/analysis ; },
abstract = {To investigate the impact of the Bandar Abbas thermal power plant on the waters of the Persian Gulf coast, a combination of satellite images and ground data was utilized to determine the Sea Surface Temperature (SST) as a thermal index, Total Organic Carbon (TOC) and Chemical Oxygen Demand (COD) as biological indices. Additionally, measurements of SO2, O3, NO2, CO2, CO, and CH4 values in the atmosphere were taken to determine the plant's impact on air pollution. Temperature values of the water for different months were predicted using Long Short-Term Memory (LSTM), Support Vector Regression (SVR), and Cascade neural networks. The results indicate that the waters near thermal power plants exhibit the highest temperatures in July and September, with temperatures reaching approximately 50 °C. Furthermore, the SST values were found to be strongly correlated with ecological indices. The Multiple Linear Regression (MLR) analysis revealed a strong correlation between the temperature and TOC, COD, and O2 in water (RTOC[2]=0.98), [Formula: see text] , RCOD[2]=0.87 and O3, NO3, CO2, and CO in the air ([Formula: see text]). Finally, the results demonstrate that the LSTM method exhibited high accuracy in predicting the water temperature (R[2] = 0.98).},
}
@article {pmid37262156,
year = {2023},
author = {Gao, H and Hamp, T and Ede, J and Schraiber, JG and McRae, J and Singer-Berk, M and Yang, Y and Dietrich, ASD and Fiziev, PP and Kuderna, LFK and Sundaram, L and Wu, Y and Adhikari, A and Field, Y and Chen, C and Batzoglou, S and Aguet, F and Lemire, G and Reimers, R and Balick, D and Janiak, MC and Kuhlwilm, M and Orkin, JD and Manu, S and Valenzuela, A and Bergman, J and Rousselle, M and Silva, FE and Agueda, L and Blanc, J and Gut, M and de Vries, D and Goodhead, I and Harris, RA and Raveendran, M and Jensen, A and Chuma, IS and Horvath, JE and Hvilsom, C and Juan, D and Frandsen, P and de Melo, FR and Bertuol, F and Byrne, H and Sampaio, I and Farias, I and do Amaral, JV and Messias, M and da Silva, MNF and Trivedi, M and Rossi, R and Hrbek, T and Andriaholinirina, N and Rabarivola, CJ and Zaramody, A and Jolly, CJ and Phillips-Conroy, J and Wilkerson, G and Abee, C and Simmons, JH and Fernandez-Duque, E and Kanthaswamy, S and Shiferaw, F and Wu, D and Zhou, L and Shao, Y and Zhang, G and Keyyu, JD and Knauf, S and Le, MD and Lizano, E and Merker, S and Navarro, A and Bataillon, T and Nadler, T and Khor, CC and Lee, J and Tan, P and Lim, WK and Kitchener, AC and Zinner, D and Gut, I and Melin, A and Guschanski, K and Schierup, MH and Beck, RMD and Umapathy, G and Roos, C and Boubli, JP and Lek, M and Sunyaev, S and O'Donnell-Luria, A and Rehm, HL and Xu, J and Rogers, J and Marques-Bonet, T and Farh, KK},
title = {The landscape of tolerated genetic variation in humans and primates.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6648},
pages = {eabn8153},
pmid = {37262156},
issn = {1095-9203},
support = {P30 AG012836/AG/NIA NIH HHS/United States ; R24 HD044964/HD/NICHD NIH HHS/United States ; R01 GM089753/GM/NIGMS NIH HHS/United States ; T32 GM007748/GM/NIGMS NIH HHS/United States ; P40 OD024628/OD/NIH HHS/United States ; },
mesh = {Animals ; Humans ; Base Sequence ; Gene Frequency ; *Genetic Variation ; *Primates/genetics ; Whole Genome Sequencing ; },
abstract = {Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.},
}
@article {pmid37259063,
year = {2023},
author = {Ormaasen, I and Rudi, K and Diep, DB and Snipen, L},
title = {Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {295},
pmid = {37259063},
issn = {1471-2164},
mesh = {*Metagenome ; Humans ; Child, Preschool ; Child ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Data Mining ; *Gastrointestinal Microbiome/drug effects ; Bacteriocins/pharmacology ; Genome ; },
abstract = {BACKGROUND: Our knowledge about the ecological role of bacterial antimicrobial peptides (bacteriocins) in the human gut is limited, particularly in relation to their role in the diversification of the gut microbiota during early life. The aim of this paper was therefore to address associations between bacteriocins and bacterial diversity in the human gut microbiota. To investigate this, we did an extensive screening of 2564 healthy human gut metagenomes for the presence of predicted bacteriocin-encoding genes, comparing bacteriocin gene presence to strain diversity and age.<br><br>RESULTS: We found that the abundance of bacteriocin genes was significantly higher in infant-like metagenomes (<&#x2009;2&#xa0;years) compared to adult-like metagenomes (2-107&#xa0;years). By comparing infant-like metagenomes with and without a given bacteriocin, we found that bacteriocin presence was associated with increased strain diversities.<br><br>CONCLUSIONS: Our findings indicate that bacteriocins may play a role in the strain diversification during the infant gut microbiota establishment.},
}
@article {pmid37258861,
year = {2023},
author = {Abdelsalam, NA and Elshora, H and El-Hadidi, M},
title = {Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {133-174},
pmid = {37258861},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Ecology ; Computational Biology/methods ; Data Analysis ; },
abstract = {Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the potential of a myriad of ecosystems and biomes. Metagenomics studies the composition and functions of microbial communities and paves the way to multiple applications in medicine, industry, and ecology. Nonetheless, the immense amount of sequencing data of metagenomics research and the few user-friendly analysis tools and pipelines carry a new challenge to the data analysis.Web-based bioinformatics tools are now being developed to facilitate the analysis of complex metagenomic data without prior knowledge of any programming languages or special installation. Specialized web tools help answer researchers' main questions on the taxonomic classification, functional capabilities, discrepancies between two ecosystems, and the probable functional correlations between the members of a specific microbial community. With an Internet connection and a few clicks, researchers can conveniently and efficiently analyze the metagenomic datasets, summarize results, and visualize key information on the composition and the functional potential of metagenomic samples under study. This chapter provides a simple guide to a few of the fundamental web-based services used for metagenomic data analyses, such as BV-BRC, RDP, MG-RAST, MicrobiomeAnalyst, METAGENassist, and MGnify.},
}
@article {pmid37258857,
year = {2023},
author = {Wang, D},
title = {Metagenomics Databases for Bacteria.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {55-67},
pmid = {37258857},
issn = {1940-6029},
mesh = {Phylogeny ; *Metagenomics ; Bacteria/genetics ; Databases, Genetic ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).},
}
@article {pmid37255989,
year = {2023},
author = {Pauley, E and Drake, TM and Griffith, DM and Sigfrid, L and Lone, NI and Harrison, EM and Baillie, JK and Scott, JT and Walsh, TS and Semple, MG and Docherty, AB and , },
title = {Recovery from Covid-19 critical illness: A secondary analysis of the ISARIC4C CCP-UK cohort study and the RECOVER trial.},
journal = {Journal of the Intensive Care Society},
volume = {24},
number = {2},
pages = {162-169},
pmid = {37255989},
issn = {1751-1437},
support = {MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: We aimed to compare the prevalence and severity of fatigue in survivors of Covid-19 versus non-Covid-19 critical illness, and to explore potential associations between baseline characteristics and worse recovery.<br><br>METHODS: We conducted a secondary analysis of two prospectively collected datasets. The population included was 92 patients who received invasive mechanical ventilation (IMV) with Covid-19, and 240 patients who received IMV with non-Covid-19 illness before the pandemic. Follow-up data were collected post-hospital discharge using self-reported questionnaires. The main outcome measures were self-reported fatigue severity and the prevalence of severe fatigue (severity >7/10) 3 and 12-months post-hospital discharge.<br><br>RESULTS: Covid-19 IMV-patients were significantly younger with less prior comorbidity, and more males, than pre-pandemic IMV-patients. At 3-months, the prevalence (38.9% [7/18] vs. 27.1% [51/188]) and severity (median 5.5/10 vs 5.0/10) of fatigue were similar between the Covid-19 and pre-pandemic populations, respectively. At 6-months, the prevalence (10.3% [3/29] vs. 32.5% [54/166]) and severity (median 2.0/10 vs. 5.7/10) of fatigue were less in the Covid-19 cohort. In the total sample of IMV-patients included (i.e. all Covid-19 and pre-pandemic patients), having Covid-19 was significantly associated with less severe fatigue (severity <7/10) after adjusting for age, sex and prior comorbidity (adjusted OR 0.35 (95%CI 0.15-0.76, p=0.01).<br><br>CONCLUSION: Fatigue may be less severe after Covid-19 than after other critical illness.},
}
@article {pmid37253577,
year = {2023},
author = {Lee, K and McMorris, BJ and Chi, CL and Looman, WS and Burns, MK and Delaney, CW},
title = {Using data-driven analytics and ecological systems theory to identify risk and protective factors for school absenteeism among secondary students.},
journal = {Journal of school psychology},
volume = {98},
number = {},
pages = {148-180},
doi = {10.1016/j.jsp.2023.03.002},
pmid = {37253577},
issn = {1873-3506},
mesh = {Adolescent ; Humans ; Protective Factors ; *Absenteeism ; *Students ; Schools ; Forecasting ; },
abstract = {Chronic absenteeism is an administrative term defining extreme failure for students to be present at school, which can have devastating long-term impacts on students. Although numerous prior studies have investigated associated variables and interventions, there are few studies that utilize both theory-driven and data-informed approaches to investigate absenteeism. The current study applied data-driven machine learning techniques, grounded in "The Kids and Teens at School" (KiTeS) theoretical framework, to student-level data (N = 121,005) to identify risk and protective variables that are highly associated with school absences. A total of 18 risk and protective variables were identified; all 18 variables were characteristics of the microsystem or mesosystem, emphasizing school absences' proximity to variables within inner ecological systems rather than the exosystem or macrosystem. Implications for future studies and health infrastructure are discussed.},
}
@article {pmid37253238,
year = {2024},
author = {Borg, JM and Buskell, A and Kapitany, R and Powers, ST and Reindl, E and Tennie, C},
title = {Evolved Open-Endedness in Cultural Evolution: A New Dimension in Open-Ended Evolution Research.},
journal = {Artificial life},
volume = {30},
number = {3},
pages = {417-438},
doi = {10.1162/artl_a_00406},
pmid = {37253238},
issn = {1530-9185},
mesh = {*Cultural Evolution ; Humans ; *Biological Evolution ; },
abstract = {The goal of Artificial Life research, as articulated by Chris Langton, is "to contribute to theoretical biology by locating life-as-we-know-it within the larger picture of life-as-it-could-be." The study and pursuit of open-ended evolution in artificial evolutionary systems exemplify this goal. However, open-ended evolution research is hampered by two fundamental issues: the struggle to replicate open-endedness in an artificial evolutionary system and our assumption that we only have one system (genetic evolution) from which to draw inspiration. We argue not only that cultural evolution should be seen as another real-world example of an open-ended evolutionary system but that the unique qualities seen in cultural evolution provide us with a new perspective from which we can assess the fundamental properties of, and ask new questions about, open-ended evolutionary systems, especially with regard to evolved open-endedness and transitions from bounded to unbounded evolution. Here we provide an overview of culture as an evolutionary system, highlight the interesting case of human cultural evolution as an open-ended evolutionary system, and contextualize cultural evolution by developing a new framework of (evolved) open-ended evolution. We go on to provide a set of new questions that can be asked once we consider cultural evolution within the framework of open-ended evolution and introduce new insights that we may be able to gain about evolved open-endedness as a result of asking these questions.},
}
@article {pmid37252922,
year = {2023},
author = {Hassard, F and Vu, M and Rahimzadeh, S and Castro-Gutierrez, V and Stanton, I and Burczynska, B and Wildeboer, D and Baio, G and Brown, MR and Garelick, H and Hofman, J and Kasprzyk-Hordern, B and Majeed, A and Priest, S and Denise, H and Khalifa, M and Bassano, I and Wade, MJ and Grimsley, J and Lundy, L and Singer, AC and Di Cesare, M},
title = {Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0286259},
pmid = {37252922},
issn = {1932-6203},
mesh = {Humans ; *COVID-19/epidemiology ; SARS-CoV-2/genetics ; Wastewater ; Public Health ; Pandemics ; Wastewater-Based Epidemiological Monitoring ; England/epidemiology ; RNA, Viral ; },
abstract = {BACKGROUND: Schools are high-risk settings for infectious disease transmission. Wastewater monitoring for infectious diseases has been used to identify and mitigate outbreaks in many near-source settings during the COVID-19 pandemic, including universities and hospitals but less is known about the technology when applied for school health protection. This study aimed to implement a wastewater surveillance system to detect SARS-CoV-2 and other public health markers from wastewater in schools in England.<br><br>METHODS: A total of 855 wastewater samples were collected from 16 schools (10 primary, 5 secondary and 1 post-16 and further education) over 10 months of school term time. Wastewater was analysed for SARS-CoV-2 genomic copies of N1 and E genes by RT-qPCR. A subset of wastewater samples was sent for genomic sequencing, enabling determination of the presence of SARS-CoV-2 and emergence of variant(s) contributing to COVID-19 infections within schools. In total, >280 microbial pathogens and >1200 AMR genes were screened using RT-qPCR and metagenomics to consider the utility of these additional targets to further inform on health threats within the schools.<br><br>RESULTS: We report on wastewater-based surveillance for COVID-19 within English primary, secondary and further education schools over a full academic year (October 2020 to July 2021). The highest positivity rate (80.4%) was observed in the week commencing 30th November 2020 during the emergence of the Alpha variant, indicating most schools contained people who were shedding the virus. There was high SARS-CoV-2 amplicon concentration (up to 9.2x106 GC/L) detected over the summer term (8th June - 6th July 2021) during Delta variant prevalence. The summer increase of SARS-CoV-2 in school wastewater was reflected in age-specific clinical COVID-19 cases. Alpha variant and Delta variant were identified in the wastewater by sequencing of samples collected from December to March and June to July, respectively. Lead/lag analysis between SARS-CoV-2 concentrations in school and WWTP data sets show a maximum correlation between the two-time series when school data are lagged by two weeks. Furthermore, wastewater sample enrichment coupled with metagenomic sequencing and rapid informatics enabled the detection of other clinically relevant viral and bacterial pathogens and AMR.<br><br>CONCLUSIONS: Passive wastewater monitoring surveillance in schools can identify cases of COVID-19. Samples can be sequenced to monitor for emerging and current variants of concern at the resolution of school catchments. Wastewater based monitoring for SARS-CoV-2 is a useful tool for SARS-CoV-2 passive surveillance and could be applied for case identification and containment, and mitigation in schools and other congregate settings with high risks of transmission. Wastewater monitoring enables public health authorities to develop targeted prevention and education programmes for hygiene measures within undertested communities across a broad range of use cases.},
}
@article {pmid37251658,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Lees, D and , },
title = {The genome sequence of the long-horned flat-body, Carcina quercana (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {16},
pmid = {37251658},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Carcina quercana (the long-horned flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 409 megabases in span. Most of the assembly (99.96%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,108 protein coding genes.},
}
@article {pmid37251651,
year = {2023},
author = {Dhellemmes, F and Aspillaga, E and Monk, CT},
title = {ATfiltR: A solution for managing and filtering detections from passive acoustic telemetry data.},
journal = {MethodsX},
volume = {10},
number = {},
pages = {102222},
pmid = {37251651},
issn = {2215-0161},
abstract = {Acoustic telemetry is a popular and cost-efficient method for tracking the movements of animals in the aquatic ecosystem. But data acquired via acoustic telemetry often contains spurious detections that must be identified and excluded by researchers to ensure valid results. Such data management is difficult as the amount of data collected often surpasses the capabilities of simple spreadsheet applications. ATfiltR is an open-source package programmed in R that allows users to integrate all telemetry data collected into a single file, to conditionally attribute animal data and location data to detections and to filter spurious detections based on customizable rules. Such tool will likely be useful to new researchers in acoustic telemetry and enhance results reproducibility.•ATfiltR compiles telemetry files and identifies and stores all data that was collected outside of your study period (e.g. when your receivers were on land for servicing) elsewhere.•As spurious detections are unlikely to appear sequentially in the data, ATfiltR finds all detections that occurred only once (per receiver or in the whole array) within a user-designated time period and stores them elsewhere.•ATfiltR identifies detections that are impossible given the animals' swimming speeds and the receivers detection range and stores them elsewhere.},
}
@article {pmid37247155,
year = {2023},
author = {Wang, Y and Lin, C and Wang, H and Wang, W and Wang, S and Zheng, R},
title = {Implementation of pollution source assessment and treatment strategy for plateau railway construction in China: an AHP-cloud model approach.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {6},
pages = {749},
pmid = {37247155},
issn = {1573-2959},
mesh = {*Analytic Hierarchy Process ; *Sewage ; Environmental Monitoring ; Environmental Pollution ; China ; },
abstract = {During the construction process of railways in the plateau region, various types of pollution sources can have serious or even irreversible impacts on the plateau ecology. To address pollution source treatment during the construction process, protect the ecological environment along the railway, and maintain the ecological balance, we collected geological and environmental data and analyzed the influencing factors of pollution sources. Taking sewage as the main research subject, we propose a new method based on the Analytic Hierarchy Process (AHP)-cloud model to classify the pollution source treatment level, establish an index system, and select the ecological environment level, sewage rate, and pollutant characteristics as the three main influencing factors. Finally, we divide the pollution source treatment level into I, II, and III, corresponding to V1 = {I-level}
= {high impact},
V2 = {II-level}
= {moderate impact},
and V3 = {III-level}
= {low impact}
. Based on the comprehensive factor weight analysis and the field engineering conditions of the studied railway in the western plateau of China, we classify the pollution source treatment level of six tunnels and propose treatment suggestions for each level. To advance the efficient implementation of environmental protection during the construction of the plateau railway, we propose three policy recommendations that can positively contribute to environmental protection and green development. This work provides theoretical and technical guidance for the treatment of pollution sources in the construction of the plateau railway, which also serves as a significant reference for other similar projects.},
}
@article {pmid37244965,
year = {2023},
author = {Mattalia, G and Svanberg, I and Ståhlberg, S and Kuznetsova, N and Prūse, B and Kolosova, V and Aziz, MA and Kalle, R and Sõukand, R},
title = {Outdoor activities foster local plant knowledge in Karelia, NE Europe.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8627},
pmid = {37244965},
issn = {2045-2322},
support = {714874/ERC_/European Research Council/International ; },
mesh = {Humans ; Adult ; Child ; Europe ; Finland/epidemiology ; *Plants, Edible ; *Allergens ; Food ; },
abstract = {Wild edible plants, particularly berries, are relevant nutritional elements in the Nordic countries. In contrast to decreasing global trends, approximately 60% of the Finnish population is actively involved in (berry) foraging. We conducted 67 interviews with Finns and Karelians living in Finnish Karelia to: (a) detect the use of wild edible plants, (b) compare those results with the published data about neighbouring Russian Karelians, and (c) document the sources of local plant knowledge. The results revealed three main findings. First, we observed a similarity in wild food plant knowledge among Karelians and Finns from Karelia. Second, we detected divergences in wild food plant knowledge among Karelians living on both sides of the Finnish-Russian border. Third, the sources of local plant knowledge include vertical transmission, acquisition through literary sources, acquisition from "green" nature shops promoting healthy lifestyles, childhood foraging activities performed during the famine period following WWII, and outdoor recreational activities. We argue that the last two types of activities in particular may have influenced knowledge and connectedness with the surrounding environment and its resources at a stage of life that is crucial for shaping adult environmental behaviours. Future research should address the role of outdoor activities in maintaining (and possibly enhancing) local ecological knowledge in the Nordic countries.},
}
@article {pmid37243840,
year = {2024},
author = {Chaves, T and Azevedo, &#xc1; and Caldas, IM},
title = {Cheiloscopy in sex estimation: a systematic review.},
journal = {Forensic science, medicine, and pathology},
volume = {20},
number = {1},
pages = {280-292},
pmid = {37243840},
issn = {1556-2891},
support = {UIDB/04004/2020//FCT-MCTES/ ; },
mesh = {Humans ; Databases, Factual ; *Sex Determination Analysis/methods ; },
abstract = {This study aimed to conduct a systematic review to gather evidence to clarify if cheiloscopy can be used in sex estimation and identify the reasons behind the lack of consensus in the scientific community. The systematic review was performed following the PRISMA guidelines. A bibliographic survey was conducted in PubMed, Scopus, and Web of Science databases, restricted to articles published between 2010 and 2020. Studies were selected according to eligibility criteria, and then the study data were collected. The risk of bias in each study was assessed and applied as additional inclusion or exclusion criteria. The results of the articles eligible for analysis were synthesized using a descriptive approach. In the 41 included studies, several methodological flaws and variations between studies that contribute to the discrepancy in results were identified. The data gathered allowed us to conclude that there is no strong scientific evidence to support the use of cheiloscopy in sex estimation, as there is no specific pattern for each sex, which reduces the criminalistic interest of cheiloscopy in estimating this parameter.},
}
@article {pmid37243228,
year = {2023},
author = {Tokito, T and Kido, T and Muramatsu, K and Tokutsu, K and Okuno, D and Yura, H and Takemoto, S and Ishimoto, H and Takazono, T and Sakamoto, N and Obase, Y and Ishimatsu, Y and Fujino, Y and Yatera, K and Fushimi, K and Matsuda, S and Mukae, H},
title = {Impact of Administering Intravenous Azithromycin within 7 Days of Hospitalization for Influenza Virus Pneumonia: A Propensity Score Analysis Using a Nationwide Administrative Database.},
journal = {Viruses},
volume = {15},
number = {5},
pages = {},
pmid = {37243228},
issn = {1999-4915},
mesh = {Humans ; Azithromycin/therapeutic use ; *Influenza, Human/drug therapy ; Propensity Score ; Retrospective Studies ; *Pneumonia/drug therapy ; Hospitalization ; *Respiratory Insufficiency ; *Orthomyxoviridae ; },
abstract = {The potential antimicrobial and anti-inflammatory effectiveness of azithromycin against severe influenza is yet unclear. We retrospectively investigated the effect of intravenous azithromycin administration within 7 days of hospitalization in patients with influenza virus pneumonia and respiratory failure. Using Japan's national administrative database, we enrolled and classified 5066 patients with influenza virus pneumonia into severe, moderate, and mild groups based on their respiratory status within 7 days of hospitalization. The primary endpoints were total, 30-day, and 90-day mortality rates. The secondary endpoints were the duration of intensive-care unit management, invasive mechanical ventilation, and hospital stay. The inverse probability of the treatment weighting method with estimated propensity scores was used to minimize data collection bias. Use of intravenous azithromycin was proportional to the severity of respiratory failure (mild: 1.0%, moderate: 3.1%, severe: 14.8%). In the severe group, the 30-day mortality rate was significantly lower with azithromycin (26.49% vs. 36.65%, p = 0.038). In the moderate group, the mean duration of invasive mechanical ventilation after day 8 was shorter with azithromycin; there were no significant differences in other endpoints between the severe and moderate groups. These results suggest that intravenous azithromycin has favorable effects in patients with influenza virus pneumonia using mechanical ventilation or oxygen.},
}
@article {pmid37240180,
year = {2023},
author = {Lafleur, S and Bodein, A and Mbuya Malaïka Mutombo, J and Mathieu, A and Joly Beauparlant, C and Minne, X and Chandad, F and Droit, A and Houde, VP},
title = {Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.},
journal = {International journal of molecular sciences},
volume = {24},
number = {10},
pages = {},
pmid = {37240180},
issn = {1422-0067},
support = {Biocodex Microbiota Foundation//Biocodex (France)/ ; },
mesh = {Humans ; Multiomics ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; U937 Cells ; *Periodontitis/microbiology ; *Microbiota/genetics ; Bacteria/metabolism ; Cytokines/metabolism ; RNA-Binding Proteins ; },
abstract = {Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.},
}
@article {pmid37232406,
year = {2023},
author = {Watson, SJ and Aguirre, BA and Wright, AJ},
title = {Soil versus atmospheric drought: A test case of plant functional trait responses.},
journal = {Ecology},
volume = {104},
number = {8},
pages = {e4109},
doi = {10.1002/ecy.4109},
pmid = {37232406},
issn = {1939-9170},
mesh = {*Soil ; *Ecosystem ; Droughts ; Plants ; Plant Leaves/physiology ; },
abstract = {Climate change alters mean global surface temperatures, precipitation regimes, and atmospheric moisture. Resultant drought affects the composition and diversity of terrestrial ecosystems worldwide. To date, there have been no assessments of the combined impacts of reduced precipitation and atmospheric drying on functional trait distributions of any species in an outdoor experiment. Here, we examined whether soil and atmospheric drought affected the functional traits of a focal grass species (Poa secunda) growing in monoculture and eight-species grass communities in outdoor mesocosms. We focused on specific leaf area (SLA), leaf area, stomatal density, root:shoot ratio, and fine root:coarse root ratio responses. Leaf area and overall growth were reduced with soil drying. Root:shoot ratio only increased for P. secunda growing in monoculture under combined atmospheric and soil drought. Plant energy allocation strategy (measured using principal components) differed when P. secunda was grown in combined soil and atmospheric drought conditions compared with soil drought alone. Given a lack of outdoor manipulations of this kind, our results emphasize the importance of atmospheric drying on functional trait responses more broadly. We suggest that drought methods focused purely on soil water inputs may be imprecisely predicting drought effects on other terrestrial organisms as well (other plants, arthropods, and higher trophic levels).},
}
@article {pmid37230884,
year = {2023},
author = {Williams, JW and Spanbauer, TL and Heintzman, PD and Blois, J and Capo, E and Goring, SJ and Monchamp, ME and Parducci, L and Von Eggers, JM and , },
title = {Strengthening global-change science by integrating aeDNA with paleoecoinformatics.},
journal = {Trends in ecology &amp; evolution},
volume = {38},
number = {10},
pages = {946-960},
doi = {10.1016/j.tree.2023.04.016},
pmid = {37230884},
issn = {1872-8383},
mesh = {*Biodiversity ; *DNA, Ancient ; Computational Biology ; DNA Barcoding, Taxonomic ; },
abstract = {Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.},
}
@article {pmid37226845,
year = {2023},
author = {Bizzotto, E and Bonetto, A and Marcomini, A and Vighi, M},
title = {Environmental exposure and ecotoxicological properties of a new-generation fluorosurfactant (cC6 O4): A comparison with selected legacy perfluoroalkyl acids.},
journal = {Integrated environmental assessment and management},
volume = {19},
number = {6},
pages = {1636-1648},
doi = {10.1002/ieam.4794},
pmid = {37226845},
issn = {1551-3793},
support = {//Solvay Specialty Polymers Italy S.p.A./ ; },
mesh = {Ecosystem ; Ecotoxicology ; Environmental Exposure ; *Fluorocarbons/toxicity ; Water ; *Water Pollutants, Chemical/toxicity/analysis ; },
abstract = {Cyclic C6 O4 (cC6 O4 , CAS number 1190931-27-1) is a new-generation polyfluorinated alkyl substance (PFAS) used as a polymerization aid in the synthesis of fluoropolymers, which has been produced in Italy since 2011. A review of the properties of cC6 O4 , focused on environmental distribution and ecotoxicology, was conducted. The EQuilibrium Criterion model was applied, using default environmental scenarios, to estimate environmental distribution and fate. In a situation of static thermodynamic equilibrium in a closed system (Level I), cC6 O4 distributes mainly to water (97.6%) and in a minimal amount to soil (2.3%). In a more realistic scenario (Level III), with dynamic conditions in an open system, with advection in air and water and with equal emissions in air and water, the major amount of the compound is transported through water advection. Monitoring data, mainly referring to surface and groundwater, are available for water bodies close to the production sites (maximum measured concentration 52 μg/L) as well as for a wider area in the river Po watershed with concentrations generally lower than 1 μg/L. Few values are also available for concentration in biota. Effect data indicate low toxicity on all tested organisms with no observed effect concentration (NOEC) values always higher than the maximum concentrations tested (100 mg/L for acute tests). Bioaccumulation potential is also very low. A comparison with selected widely used PFAS with five to eight C atoms indicates that cC6 O4 is substantially less dangerous to aquatic organisms. For the time being, an ecological risk for the aquatic ecosystem may be excluded even in directly exposed ecosystems. However, for a complete assessment of the suitability of cC6 O4 as a substitute for other PFAS (namely, perfluorooctanoic acid), more comprehensive chronic experiments are necessary, to produce realistic NOEC, as well as higher tier experiments (e.g., mesocosms) capable of providing ecologically relevant endpoints. Moreover, a more accurate evaluation of the environmental persistence would be necessary. Integr Environ Assess Manag 2023;19:1636-1648. © 2023 SETAC.},
}
@article {pmid37226152,
year = {2023},
author = {Bakó, C and Balázs, VL and Kerekes, E and Kocsis, B and Nagy, DU and Szabó, P and Micalizzi, G and Mondello, L and Krisch, J and Pethő, D and Horváth, G},
title = {Flowering phenophases influence the antibacterial and anti-biofilm effects of Thymus vulgaris L. essential oil.},
journal = {BMC complementary medicine and therapies},
volume = {23},
number = {1},
pages = {168},
pmid = {37226152},
issn = {2662-7671},
mesh = {*Oils, Volatile/pharmacology ; *Thymus Plant ; Gas Chromatography-Mass Spectrometry ; Anti-Bacterial Agents/pharmacology ; },
abstract = {BACKGROUND: Essential oils are becoming increasingly popular in medicinal applications because of their antimicrobial effect. Thymus vulgaris L. (Lamiaceae) is a well-known and widely cultivated medicinal plant, which is used as a remedy for cold, cough and gastrointestinal symptoms. Essential oil content of thyme is responsible for its antimicrobial activity, however, it has been reported that the chemical composition of essential oils influences its biological activity. In order to explore flowering phenophases influence on the chemical composition of thyme essential oil and its antibacterial and anti-biofilm activity, plant materials were collected at the beginning of flowering, in full bloom and at the end of flowering periods in 2019.<br><br>METHODS: Essential oils from fresh and dried plant materials were distilled and analyzed with gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detection (GC-FID). The antibacterial activity was performed by broth microdilution and thin layer chromatography-direct bioautography (TLC-DB) assays and the anti-biofilm effect by crystal violet assay, respectively. Scanning electron microscopy was applied to illustrate the cellular changes of bacterial cells after essential oil treatment.<br><br>RESULTS: Thymol (52.33-62.46%) was the main component in the thyme essential oils. Thyme oil distilled from fresh plant material and collected at the beginning of flowering period exerted the highest antibacterial and anti-biofilm activity against Haemophilus influenzae, H. parainfluenzae and Pseudomonas aeruginosa.<br><br>CONCLUSION: The different flowering periods of Thymus vulgaris influence the antibacterial and anti-biofilm activity of its essential oils, therefore, the collection time has to be taken into consideration and not only the full bloom, but the beginning of flowering period may provide biological active thyme essential oil.},
}
@article {pmid37225998,
year = {2023},
author = {Tao, F and Huang, Y and Hungate, BA and Manzoni, S and Frey, SD and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Jiang, L and Lehmann, J and Wang, YP and Houlton, BZ and Ahrens, B and Mishra, U and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y},
title = {Microbial carbon use efficiency promotes global soil carbon storage.},
journal = {Nature},
volume = {618},
number = {7967},
pages = {981-985},
pmid = {37225998},
issn = {1476-4687},
mesh = {*Carbon/analysis/metabolism ; *Carbon Sequestration ; Climate Change ; *Ecosystem ; Plants ; *Soil/chemistry ; *Soil Microbiology ; Datasets as Topic ; Deep Learning ; },
abstract = {Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.},
}
@article {pmid37225767,
year = {2023},
author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Lacombe, B and Le Roux, X and Perrier, L and Sales-Mabily, L and Laumond, M and Vinyeta, M and Moulin, P and Beurier, G and Rouan, L and Cornet, D and Vasseur, F},
title = {AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {314},
pmid = {37225767},
issn = {2052-4463},
support = {ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0018-01//Agence Nationale de la Recherche (French National Research Agency)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SCHE 1899/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Adaptation, Physiological ; *Arabidopsis/genetics ; Biological Evolution ; Databases, Factual ; Plant Leaves ; },
abstract = {Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.},
}
@article {pmid37224319,
year = {2022},
author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and , and , and , and Wahlberg, N and , },
title = {The genome sequence of the high brown fritillary, Fabriciana adippe (Dennis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {298},
pmid = {37224319},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Fabriciana adippe (the high brown fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 485 megabases in span. Most of the assembly (99.98%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.1 kilobases in length. Gene annotation of this assembly in Ensembl identified 13,536 protein coding genes.},
}
@article {pmid37224178,
year = {2023},
author = {Passmore, S and Barth, W and Greenhill, SJ and Quinn, K and Sheard, C and Argyriou, P and Birchall, J and Bowern, C and Calladine, J and Deb, A and Diederen, A and Metsäranta, NP and Araujo, LH and Schembri, R and Hickey-Hall, J and Honkola, T and Mitchell, A and Poole, L and Rácz, PM and Roberts, SG and Ross, RM and Thomas-Colquhoun, E and Evans, N and Jordan, FM},
title = {Kinbank: A global database of kinship terminology.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0283218},
pmid = {37224178},
issn = {1932-6203},
mesh = {Humans ; Female ; Male ; *Sexism ; *Anthropology ; Databases, Factual ; Family ; Interdisciplinary Studies ; },
abstract = {For a single species, human kinship organization is both remarkably diverse and strikingly organized. Kinship terminology is the structured vocabulary used to classify, refer to, and address relatives and family. Diversity in kinship terminology has been analyzed by anthropologists for over 150 years, although recurrent patterning across cultures remains incompletely explained. Despite the wealth of kinship data in the anthropological record, comparative studies of kinship terminology are hindered by data accessibility. Here we present Kinbank, a new database of 210,903 kinterms from a global sample of 1,229 spoken languages. Using open-access and transparent data provenance, Kinbank offers an extensible resource for kinship terminology, enabling researchers to explore the rich diversity of human family organization and to test longstanding hypotheses about the origins and drivers of recurrent patterns. We illustrate our contribution with two examples. We demonstrate strong gender bias in the phonological structure of parent terms across 1,022 languages, and we show that there is no evidence for a coevolutionary relationship between cross-cousin marriage and bifurcate-merging terminology in Bantu languages. Analysing kinship data is notoriously challenging; Kinbank aims to eliminate data accessibility issues from that challenge and provide a platform to build an interdisciplinary understanding of kinship.},
}
@article {pmid37221394,
year = {2023},
author = {Drott, MT and Park, SC and Wang, YW and Harrow, L and Keller, NP and Pringle, A},
title = {Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range.},
journal = {The ISME journal},
volume = {17},
number = {8},
pages = {1236-1246},
pmid = {37221394},
issn = {1751-7370},
support = {R01 GM112739/GM/NIGMS NIH HHS/United States ; T32 ES007015/ES/NIEHS NIH HHS/United States ; },
mesh = {*Amanita/genetics ; *Agaricales/genetics ; Computational Biology ; },
abstract = {The poisonous European mushroom Amanita phalloides (the "death cap") is invading California. Whether the death caps' toxic secondary metabolites are evolving as it invades is unknown. We developed a bioinformatic pipeline to identify the MSDIN genes underpinning toxicity and probed 88 death cap genomes from an invasive Californian population and from the European range, discovering a previously unsuspected diversity of MSDINs made up of both core and accessory elements. Each death cap individual possesses a unique suite of MSDINs, and toxin genes are significantly differentiated between Californian and European samples. MSDIN genes are maintained by strong natural selection, and chemical profiling confirms MSDIN genes are expressed and result in distinct phenotypes; our chemical profiling also identified a new MSDIN peptide. Toxin genes are physically clustered within genomes. We contextualize our discoveries by probing for MSDINs in genomes from across the order Agaricales, revealing MSDIN diversity originated in independent gene family expansions among genera. We also report the discovery of an MSDIN in an Amanita outside the "lethal Amanitas" clade. Finally, the identification of an MSDIN gene and its associated processing gene (POPB) in Clavaria fumosa suggest the origin of MSDINs is older than previously suspected. The dynamic evolution of MSDINs underscores their potential to mediate ecological interactions, implicating MSDINs in the ongoing invasion. Our data change the understanding of the evolutionary history of poisonous mushrooms, emphasizing striking parallels to convergently evolved animal toxins. Our pipeline provides a roadmap for exploring secondary metabolites in other basidiomycetes and will enable drug prospecting.},
}
@article {pmid37221042,
year = {2023},
author = {Chaudhary, S and Wu, Y and Strongman, D and Wang, Y},
title = {CIGAF-a database and interactive platform for insect-associated trichomycete fungi.},
journal = {Database : the journal of biological databases and curation},
volume = {2023},
number = {},
pages = {},
pmid = {37221042},
issn = {1758-0463},
mesh = {Animals ; *Insecta ; Databases, Factual ; *Fungi ; Metadata ; Software ; },
abstract = {Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.},
}
@article {pmid37216923,
year = {2023},
author = {Ma, Y and Liu, L and Ma, Y and Zhang, S},
title = {HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {6},
pages = {},
pmid = {37216923},
issn = {1367-4811},
mesh = {*Multiomics ; Software ; Algorithms ; *Microbiota ; Cluster Analysis ; },
abstract = {MOTIVATION: The accumulation of multi-omics microbiome data provides an unprecedented opportunity to understand the diversity of bacterial, fungal, and viral components from different conditions. The changes in the composition of viruses, bacteria, and fungi communities have been associated with environments and critical illness. However, identifying and dissecting the heterogeneity of microbial samples and cross-kingdom interactions remains challenging.<br><br>RESULTS: We propose HONMF for the integrative analysis of multi-modal microbiome data, including bacterial, fungal, and viral composition profiles. HONMF enables identification of microbial samples and data visualization, and also facilitates downstream analysis, including feature selection and cross-kingdom association analysis between species. HONMF is an unsupervised method based on hypergraph induced orthogonal non-negative matrix factorization, where it assumes that latent variables are specific for each composition profile and integrates the distinct sets of latent variables through graph fusion strategy, which better tackles the distinct characteristics in bacterial, fungal, and viral microbiome. We implemented HONMF on several multi-omics microbiome datasets from different environments and tissues. The experimental results demonstrate the superior performance of HONMF in data visualization and clustering. HONMF also provides rich biological insights by implementing discriminative microbial feature selection and bacterium-fungus-virus association analysis, which improves our understanding of ecological interactions and microbial pathogenesis.<br><br>The software and datasets are available at https://github.com/chonghua-1983/HONMF.},
}
@article {pmid37211183,
year = {2023},
author = {Yokoyama, D and Kikuchi, J},
title = {Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.},
journal = {Environmental research},
volume = {231},
number = {Pt 3},
pages = {116202},
doi = {10.1016/j.envres.2023.116202},
pmid = {37211183},
issn = {1096-0953},
mesh = {Humans ; *Rivers ; Phylogeny ; Multiomics ; *Microbiota ; Stochastic Processes ; },
abstract = {Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.},
}
@article {pmid37209314,
year = {2023},
author = {Jiang, WJ and Wang, MT and Du, ZY and Li, JH and Shi, Y and Wang, X and Wu, LY and Chen, J and Zhong, M and Yang, J and Hu, BH and Huang, J},
title = {Bioinformatic and functional analysis of OsDHN2 under cadmium stress.},
journal = {Functional &amp; integrative genomics},
volume = {23},
number = {2},
pages = {170},
pmid = {37209314},
issn = {1438-7948},
mesh = {*Cadmium/toxicity/metabolism ; Saccharomyces cerevisiae/metabolism ; Plant Proteins/genetics/metabolism ; *Oryza/genetics/metabolism ; Computational Biology ; Gene Expression Regulation, Plant ; },
abstract = {As a toxic heavy metal, cadmium (Cd) is one of the principal pollutants influencing rice productivity and food security. Despite several studies, the underlying mechanism of Cd response in plants remains largely unclear. Dehydrins are part of the late embryogenesis abundant (LEA) family which protect plants against abiotic stresses. In this study, a Cd-responsive LEA gene, OsDHN2, was functionally characterized. The chromosome localization results indicated that OsDHN2 was located on chromosome 2 of rice. Meanwhile, cis-acting elements, such as MBS (MYB binding site involved in drought-inducibility), ARE (anaerobic induction), and ABRE (abscisic acid), were present in the OsDHN2 promoter region. Expression pattern analysis also showed that OsDHN2 expression was induced in both roots and shoots under Cd stress. Overexpression of OsDHN2 improved Cd tolerance and reduced Cd concentration in yeast. Moreover, increased expression levels of SOD1, CTA1, GSH1, or CTT1 were found in transgenic yeast under Cd stress, suggesting the increased antioxidant enzymatic activities. These results suggested that OsDHN2 is a Cd-responsive gene that has the potential to improve resistance to Cd in rice.},
}
@article {pmid37208222,
year = {2023},
author = {de Koning, K and Broekhuijsen, J and Kühn, I and Ovaskainen, O and Taubert, F and Endresen, D and Schigel, D and Grimm, V},
title = {Digital twins: dynamic model-data fusion for ecology.},
journal = {Trends in ecology &amp; evolution},
volume = {38},
number = {10},
pages = {916-926},
doi = {10.1016/j.tree.2023.04.010},
pmid = {37208222},
issn = {1872-8383},
mesh = {*Ecology ; Big Data ; Machine Learning ; *Computer Simulation ; },
abstract = {Digital twins (DTs) are an emerging phenomenon in the public and private sectors as a new tool to monitor and understand systems and processes. DTs have the potential to change the status quo in ecology as part of its digital transformation. However, it is important to avoid misguided developments by managing expectations about DTs. We stress that DTs are not just big models of everything, containing big data and machine learning. Rather, the strength of DTs is in combining data, models, and domain knowledge, and their continuous alignment with the real world. We suggest that researchers and stakeholders exercise caution in DT development, keeping in mind that many of the strengths and challenges of computational modelling in ecology also apply to DTs.},
}
@article {pmid37207732,
year = {2023},
author = {Girardi, P and Lupo, A and Mastromatteo, LY and Scrimin, S},
title = {Behavioral outcomes and exposure to perfluoroalkyl substances among children aged 6-13 years: The TEDDY child study.},
journal = {Environmental research},
volume = {231},
number = {Pt 2},
pages = {116049},
doi = {10.1016/j.envres.2023.116049},
pmid = {37207732},
issn = {1096-0953},
mesh = {Pregnancy ; Female ; Humans ; Child ; Cross-Sectional Studies ; Environmental Exposure/analysis ; *Alkanesulfonic Acids/analysis ; Alkanesulfonates/analysis ; *Fluorocarbons/analysis ; Water ; *Environmental Pollutants ; },
abstract = {BACKGROUND: Although some studies report that exposure to per- and polyfluoroalkyl substances (PFAS) during pregnancy and early life stages of a child could adversely impact neurodevelopment, literature shows mixed evidence.<br><br>OBJECTIVES: Using an ecological framework for human development, we assessed the association of risk factors for environmental PFAS exposure and childhood PFAS concentrations with behavioral difficulties among school-age children exposed to PFAS from birth, while also controlling for the important influence of the parenting and familial environment.<br><br>METHODS: The study participants included 331 school-age children (6-13 years) born in a PFAS-contaminated area in the Veneto Region (Italy). We study the associations between environmental risk factors of maternal PFAS exposure (residential time, consumption of tap water, residence in Red zone A or B), and breastfeeding duration with parent assessments of children's behavioral problems (using the Strengths and Difficulties Questionnaire [SDQ]), adjusting for socio-demographic, parenting and familial variables. The direct relationships between serum blood PFAS concentrations and SDQ scores was evaluated in a subset of children (n&#xa0;=&#xa0;79), both with single PFAS and weighted quantile sum (WQS) regressions.<br><br>RESULTS: Poisson regression models reported positive associations between high consumption of tap water and externalizing SDQ scores (Incidence Rate Ratio [IRR]: 1.18; 95% confidence interval [CI]: 1.04-1.32) and total difficulty scores (IRR: 1.14; 95% CI: 1.02-1.26). Childhood perfluorooctane sulfonate (PFOS) and perfluorohexane sulfonate (PFHxS) were associated with higher internalizing SDQ scores (4th vs. 1st quartile, PFOS IRR: 1.54, 95% CI: 1.06-2.25), externalizing scores (4th vs. 1st quartile, PFHxS IRR: 1.59, 95% CI: 1.09-2.32), and total difficulty scores (4th vs. 1st quartile, PFOS IRR: 1.37, 95% CI: 1.05-1.71; PFHxS IRR: 1.54, 95% CI: 1.09-1.90). The WQS regressions confirmed the associations reported by single-PFAS analyses.<br><br>CONCLUSIONS: We observed cross-sectional associations of tap water consumption and childhood PFOS, and PFHxS concentrations with greater behavioral difficulties.},
}
@article {pmid37207684,
year = {2023},
author = {Cocker, D and Chidziwisano, K and Mphasa, M and Mwapasa, T and Lewis, JM and Rowlingson, B and Sammarro, M and Bakali, W and Salifu, C and Zuza, A and Charles, M and Mandula, T and Maiden, V and Amos, S and Jacob, ST and Kajumbula, H and Mugisha, L and Musoke, D and Byrne, R and Edwards, T and Lester, R and Elviss, N and Roberts, AP and Singer, AC and Jewell, C and Morse, T and Feasey, NA},
title = {Investigating One Health risks for human colonisation with extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Malawian households: a longitudinal cohort study.},
journal = {The Lancet. Microbe},
volume = {4},
number = {7},
pages = {e534-e543},
pmid = {37207684},
issn = {2666-5247},
support = {MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Humans ; Escherichia coli ; Klebsiella pneumoniae ; *Escherichia coli Infections/epidemiology/microbiology ; Longitudinal Studies ; *One Health ; beta-Lactamases ; *Klebsiella Infections/epidemiology/microbiology ; *Anti-Infective Agents ; Cohort Studies ; },
abstract = {BACKGROUND: Low-income countries have high morbidity and mortality from drug-resistant infections, especially from enteric bacteria such as Escherichia coli. In these settings, sanitation infrastructure is of variable and often inadequate quality, creating risks of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales transmission. We aimed to describe the prevalence, distribution, and risks of ESBL-producing Enterobacterales colonisation in sub-Saharan Africa using a One Health approach.<br><br>METHODS: Between April 29, 2019, and Dec 3, 2020, we recruited 300 households in Malawi for this longitudinal cohort study: 100 each in urban, peri-urban, and rural settings. All households underwent a baseline visit and 195 were selected for longitudinal follow-up, comprising up to three additional visits over a 6 month period. Data on human health, antibiotic usage, health-seeking behaviours, structural and behavioural environmental health practices, and animal husbandry were captured alongside human, animal, and environmental samples. Microbiological processing determined the presence of ESBL-producing E coli and Klebsiella pneumoniae, and hierarchical logistic regression was performed to evaluate the risks of human ESBL-producing Enterobacterales colonisation.<br><br>FINDINGS: A paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites. A total of 11&#x2009;975 samples were cultured, and ESBL-producing Enterobacterales were isolated from 1190 (41&#xb7;8%) of 2845 samples of human stool, 290 (29&#xb7;8%) of 973 samples of animal stool, 339 (66&#xb7;2%) of 512 samples of river water, and 138 (46&#xb7;0%) of 300 samples of drain water. Multivariable models illustrated that human ESBL-producing E coli colonisation was associated with the wet season (adjusted odds ratio 1&#xb7;66, 95% credible interval 1&#xb7;38-2&#xb7;00), living in urban areas (2&#xb7;01, 1&#xb7;26-3&#xb7;24), advanced age (1&#xb7;14, 1&#xb7;05-1&#xb7;25), and living in households where animals were observed interacting with food (1&#xb7;62, 1&#xb7;17-2&#xb7;28) or kept inside (1&#xb7;58, 1&#xb7;00-2&#xb7;43). Human ESBL-producing K pneumoniae colonisation was associated with the wet season (2&#xb7;12, 1&#xb7;63-2&#xb7;76).<br><br>INTERPRETATION: There are extremely high levels of ESBL-producing Enterobacterales colonisation in humans and animals and extensive contamination of the wider environment in southern Malawi. Urbanisation and seasonality are key risks for ESBL-producing Enterobacterales colonisation, probably reflecting environmental drivers. Without adequate efforts to improve environmental health, ESBL-producing Enterobacterales transmission is likely to persist in this setting.<br><br>FUNDING: Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust.<br><br>TRANSLATION: For the Chichewa translation of the abstract see Supplementary Materials section.},
}
@article {pmid37205491,
year = {2023},
author = {Gao, H and Hamp, T and Ede, J and Schraiber, JG and McRae, J and Singer-Berk, M and Yang, Y and Dietrich, A and Fiziev, P and Kuderna, L and Sundaram, L and Wu, Y and Adhikari, A and Field, Y and Chen, C and Batzoglou, S and Aguet, F and Lemire, G and Reimers, R and Balick, D and Janiak, MC and Kuhlwilm, M and Orkin, JD and Manu, S and Valenzuela, A and Bergman, J and Rouselle, M and Silva, FE and Agueda, L and Blanc, J and Gut, M and de Vries, D and Goodhead, I and Harris, RA and Raveendran, M and Jensen, A and Chuma, IS and Horvath, J and Hvilsom, C and Juan, D and Frandsen, P and de Melo, FR and Bertuol, F and Byrne, H and Sampaio, I and Farias, I and do Amaral, JV and Messias, M and da Silva, MNF and Trivedi, M and Rossi, R and Hrbek, T and Andriaholinirina, N and Rabarivola, CJ and Zaramody, A and Jolly, CJ and Phillips-Conroy, J and Wilkerson, G and Abee, C and Simmons, JH and Fernandez-Duque, E and Kanthaswamy, S and Shiferaw, F and Wu, D and Zhou, L and Shao, Y and Zhang, G and Keyyu, JD and Knauf, S and Le, MD and Lizano, E and Merker, S and Navarro, A and Batallion, T and Nadler, T and Khor, CC and Lee, J and Tan, P and Lim, WK and Kitchener, AC and Zinner, D and Gut, I and Melin, A and Guschanski, K and Schierup, MH and Beck, RMD and Umapathy, G and Roos, C and Boubli, JP and Lek, M and Sunyaev, S and O'Donnell, A and Rehm, H and Xu, J and Rogers, J and Marques-Bonet, T and Kai-How Farh, K},
title = {The landscape of tolerated genetic variation in humans and primates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {37205491},
issn = {2692-8205},
support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; P30 AG012836/AG/NIA NIH HHS/United States ; R24 HD044964/HD/NICHD NIH HHS/United States ; T32 GM007748/GM/NIGMS NIH HHS/United States ; P40 OD024628/OD/NIH HHS/United States ; },
abstract = {UNLABELLED: Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.<br><br>ONE SENTENCE SUMMARY: Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.},
}
@article {pmid37198478,
year = {2023},
author = {Pairo-Castineira, E and Rawlik, K and Bretherick, AD and Qi, T and Wu, Y and Nassiri, I and McConkey, GA and Zechner, M and Klaric, L and Griffiths, F and Oosthuyzen, W and Kousathanas, A and Richmond, A and Millar, J and Russell, CD and Malinauskas, T and Thwaites, R and Morrice, K and Keating, S and Maslove, D and Nichol, A and Semple, MG and Knight, J and Shankar-Hari, M and Summers, C and Hinds, C and Horby, P and Ling, L and McAuley, D and Montgomery, H and Openshaw, PJM and Begg, C and Walsh, T and Tenesa, A and Flores, C and Riancho, JA and Rojas-Martinez, A and Lapunzina, P and , and , and , and , and Yang, J and Ponting, CP and Wilson, JF and Vitart, V and Abedalthagafi, M and Luchessi, AD and Parra, EJ and Cruz, R and Carracedo, A and Fawkes, A and Murphy, L and Rowan, K and Pereira, AC and Law, A and Fairfax, B and Hendry, SC and Baillie, JK},
title = {GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.},
journal = {Nature},
volume = {617},
number = {7962},
pages = {764-768},
pmid = {37198478},
issn = {1476-4687},
support = {MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; MC_UU_00007/15/MRC_/Medical Research Council/United Kingdom ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; MC_PC_20004/MRC_/Medical Research Council/United Kingdom ; MR/V001329/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *COVID-19/genetics ; *Critical Illness ; *Genetic Predisposition to Disease/genetics ; *Genetic Variation/genetics ; *Genome-Wide Association Study ; Genotype ; Genotyping Techniques ; Monocytes/metabolism ; Phenotype ; rab GTP-Binding Proteins/genetics ; Transcriptome ; Whole Genome Sequencing ; },
abstract = {Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown[1] to be highly efficient for discovery of genetic associations[2]. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group[3]. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).},
}
@article {pmid37196545,
year = {2023},
author = {Yang, P and Yang, W and Wei, Z and Li, Y and Yang, Y and Wang, J},
title = {Novel targets for gastric cancer: The tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis and cuproptosis.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {163},
number = {},
pages = {114883},
doi = {10.1016/j.biopha.2023.114883},
pmid = {37196545},
issn = {1950-6007},
mesh = {Humans ; *Stomach Neoplasms/drug therapy ; *Ferroptosis ; Pyroptosis ; Tumor Microenvironment ; Adenosine ; Autophagy ; },
abstract = {Gastric cancer (GC) is a fatal illness, and its mortality rate is very high all over the world. At present, it is a serious health problem for any country. It is a multifactorial disease due to the rising drug resistance and the increasing global cancer burden, the treatment of GC still faces many obstacles and problems. In recent years, research on GC is being carried out continuously, and we hope to address the new targets of GC treatment through this review. At the same time, we also hope to discover new ways to fight GC and create more gospel for clinical patients. First, we discuss the descriptive tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis, and cuproptosis. Finally, we expounded on the new or potential targets of GC treatment.},
}
@article {pmid37193271,
year = {2023},
author = {Mollicone, DJ and Kan, K and Coats, S and Mott, C and van Wollen, M and Hatch, A and Gallagher, J and Williams, S and Motzkin, D},
title = {Use of the psychomotor vigilance test to aid in the selection of risk controls in an air medical transport operation.},
journal = {Sleep advances : a journal of the Sleep Research Society},
volume = {4},
number = {1},
pages = {zpad003},
pmid = {37193271},
issn = {2632-5012},
abstract = {STUDY OBJECTIVES: This study evaluated the utility and ecological validity of the 3-minute psychomotor vigilance test (PVT) completed by safety-critical personnel in an air medical transport operation as part of a fatigue risk management program.<br><br>METHODS: Crewmembers in an air medical transport operation self-administered an alertness assessment incorporating a 3-minute PVT at different time points during their duty schedule. The prevalence of alertness deficits was evaluated based on a failure threshold of 12 errors considering both lapses and false starts. To evaluate the ecological validity of the PVT, the relative frequency of failed assessments was evaluated relative to crewmember position, timing of the assessment within the duty schedule, time of day, and sleep quantity in the last 24 h.<br><br>RESULTS: 2.1% of assessments were associated with a failing PVT score. Crewmember position, timing of assessment within the duty shift, time of day, and sleep quantity in the last 24 h were found to affect the relative frequency of failed assessments. Obtaining less than 7-9 h of sleep was associated with systematic increases in the failure rate (F[1, 54 612] = 168.1, p < .001). Obtaining less than 4 h of sleep was associated with a frequency of a failed assessment 2.99 times higher than the frequency of a failed assessment when obtaining 7-9 h of sleep.<br><br>CONCLUSIONS: Results provide evidence for the utility and ecological validity of the PVT as well as the suitability of the PVT failure threshold to support fatigue risk management in safety-critical operations.},
}
@article {pmid37188960,
year = {2023},
author = {Li, C and Wood, JC and Vu, AH and Hamilton, JP and Rodriguez Lopez, CE and Payne, RME and Serna Guerrero, DA and Gase, K and Yamamoto, K and Vaillancourt, B and Caputi, L and O'Connor, SE and Robin Buell, C},
title = {Single-cell multi-omics in the medicinal plant Catharanthus roseus.},
journal = {Nature chemical biology},
volume = {19},
number = {8},
pages = {1031-1041},
pmid = {37188960},
issn = {1552-4469},
support = {788301/ERC_/European Research Council/International ; },
mesh = {*Catharanthus/genetics ; *Plants, Medicinal/metabolism ; Multiomics ; Indole Alkaloids/metabolism ; *Antineoplastic Agents/metabolism ; Monoterpenes/metabolism ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/metabolism ; },
abstract = {Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells and high-resolution determination of gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus, a source of leading anticancer drugs. We identified clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes and extensive gene duplication of MIA pathway genes. Clustering was not limited to the linear genome, and through chromatin interaction data, MIA pathway genes were present within the same topologically associated domain, permitting the identification of a secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a single-cell metabolomics approach, permitted the identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. We also revealed cell-type-specific expression in the root MIA pathway.},
}
@article {pmid37172588,
year = {2023},
author = {Gao, X and Sun, R and Jiao, N and Liang, X and Li, G and Gao, H and Wu, X and Yang, M and Chen, C and Sun, X and Chen, L and Wu, W and Cong, Y and Zhu, R and Guo, T and Liu, Z},
title = {Integrative multi-omics deciphers the spatial characteristics of host-gut microbiota interactions in Crohn's disease.},
journal = {Cell reports. Medicine},
volume = {4},
number = {6},
pages = {101050},
pmid = {37172588},
issn = {2666-3791},
mesh = {Humans ; *Crohn Disease/complications/diagnosis/pathology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Multiomics ; Inflammation/complications ; Bacteria/genetics/metabolism ; Membrane Proteins/metabolism ; },
abstract = {Dysregulated host-microbial interactions play critical roles in initiation and perpetuation of gut inflammation in Crohn's disease (CD). However, the spatial distribution and interaction network across the intestine and its accessory tissues are still elusive. Here, we profile the host proteins and tissue microbes in 540 samples from the intestinal mucosa, submucosa-muscularis-serosa, mesenteric adipose tissues, mesentery, and mesenteric lymph nodes of 30 CD patients and spatially decipher the host-microbial interactions. We observe aberrant antimicrobial immunity and metabolic processes across multi-tissues during CD and determine bacterial transmission along with altered microbial communities and ecological patterns. Moreover, we identify several candidate interaction pairs between host proteins and microbes associated with perpetuation of gut inflammation and bacterial transmigration across multi-tissues in CD. Signature alterations in host proteins (e.g., SAA2 and GOLM1) and microbes (e.g., Alistipes and Streptococcus) are further imprinted in serum and fecal samples as potential diagnostic biomarkers, thus providing a rationale for precision diagnosis.},
}
@article {pmid37172351,
year = {2023},
author = {Zerouali, B and Santos, CAG and do Nascimento, TVM and Silva, RMD},
title = {A cloud-integrated GIS for forest cover loss and land use change monitoring using statistical methods and geospatial technology over northern Algeria.},
journal = {Journal of environmental management},
volume = {341},
number = {},
pages = {118029},
doi = {10.1016/j.jenvman.2023.118029},
pmid = {37172351},
issn = {1095-8630},
mesh = {Humans ; *Geographic Information Systems ; *Conservation of Natural Resources/methods ; Algeria ; Agriculture ; Environmental Monitoring/methods ; Technology ; },
abstract = {Over the last two decades, forest cover has experienced significant impacts from fires and deforestation worldwide due to direct human activities and climate change. This paper assesses trends in forest cover loss and land use and land cover changes in northern Algeria between 2000 and 2020 using datasets extracted from Google Earth Engine (GEE), such as the Hanssen Global Forest Change and MODIS Land Cover Type products (MCD12Q1). Classification was performed using the pixel-based supervised machine-learning algorithm called Random Forest (RF). Trends were analyzed using methods such as Mann-Kendall and Sen. The study area comprises 17 basins with high rainfall variability. The results indicated that the forest area decreased by 64.96%, from 3718 to 1266 km[2], during the 2000-2020 period, while the barren area increased by 40%, from 134,777 to 188,748 km[2]. The findings revealed that the Constantinois-Seybousse-Mellegue hydrographic basin was the most affected by deforestation and cover loss, exceeding 50% (with an area of 1018 km[2]), while the Seybouse River basin experienced the highest percentage of cover loss at 40%. Nonparametric tests showed that seven river basins (41%) had significantly increasing trends of forest cover loss. According to the obtained results, the forest loss situation in Algeria, especially in the northeastern part, is very alarming and requires an exceptional and urgent plan to protect forests and the ecological system against wildfires and climate change. The study provides a diagnosis that should encourage better protection and management of forest cover in Algeria.},
}
@article {pmid37169855,
year = {2023},
author = {Huang, L and Jin, C and Pan, Y and Zhou, L and Hu, S and Guo, Y and Meng, Y and Song, K and Pang, M and Li, H and Lin, D and Xu, X and Minor, J and Coggins, C and Jim, CY and Yan, E and Yang, Y and Tang, Z and Lindenmayer, DB},
title = {Human activities and species biological traits drive the long-term persistence of old trees in human-dominated landscapes.},
journal = {Nature plants},
volume = {9},
number = {6},
pages = {898-907},
pmid = {37169855},
issn = {2055-0278},
support = {32071652//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32025025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31988102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2022M720254//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; Humans ; *Ecosystem ; Databases, Factual ; China ; *Moths ; Plant Leaves ; },
abstract = {Old trees have many ecological and socio-cultural values. However, knowledge of the factors influencing their long-term persistence in human-dominated landscapes is limited. Here, using an extensive database (nearly 1.8 million individual old trees belonging to 1,580 species) from China, we identified which species were most likely to persist as old trees in human-dominated landscapes and where they were most likely to occur. We found that species with greater potential height, smaller leaf size and diverse human utilization attributes had the highest probability of long-term persistence. The persistence probabilities of human-associated species (taxa with diverse human utilization attributes) were relatively high in intensively cultivated areas. Conversely, the persistence probabilities of spontaneous species (taxa with no human utilization attributes and which are not cultivated) were relatively high in mountainous areas or regions inhabited by ethnic minorities. The distinctly different geographic patterns of persistence probabilities of the two groups of species were related to their dissimilar responses to heterogeneous human activities and site conditions. A small number of human-associated species dominated the current cohort of old trees, while most spontaneous species were rare and endemic. Our study revealed the potential impacts of human activities on the long-term persistence of trees and the associated shifts in species composition in human-dominated landscapes.},
}
@article {pmid37166827,
year = {2023},
author = {Haslbeck, J and Ryan, O and Dablander, F},
title = {Multimodality and skewness in emotion time series.},
journal = {Emotion (Washington, D.C.)},
volume = {23},
number = {8},
pages = {2117-2141},
doi = {10.1037/emo0001218},
pmid = {37166827},
issn = {1931-1516},
support = {/NWO_/Dutch Research Council/Netherlands ; },
mesh = {Humans ; Time Factors ; *Emotions ; *Ecological Momentary Assessment ; Data Management ; },
abstract = {The ability to measure emotional states in daily life using mobile devices has led to a surge of exciting new research on the temporal evolution of emotions. However, much of the potential of these data still remains untapped. In this paper, we reanalyze emotion measurements from seven openly available experience sampling methodology studies with a total of 835 individuals to systematically investigate the modality (unimodal, bimodal, and more than two modes) and skewness of within-person emotion measurements. We show that both multimodality and skewness are highly prevalent. In addition, we quantify the heterogeneity across items, individuals, and measurement designs. Our analysis reveals that multimodality is more likely in studies using an analog slider scale than in studies using a Likert scale; negatively valenced items are consistently more skewed than positive valenced items; and longer time series show a higher degree of modality in positive and a higher skew in negative items. We end by discussing the implications of our results for theorizing, measurement, and time series modeling. (PsycInfo Database Record (c) 2023 APA, all rights reserved).},
}
@article {pmid37165696,
year = {2024},
author = {Kudapa, H and Ghatak, A and Barmukh, R and Chaturvedi, P and Khan, A and Kale, S and Fragner, L and Chitikineni, A and Weckwerth, W and Varshney, RK},
title = {Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.).},
journal = {The plant genome},
volume = {17},
number = {1},
pages = {e20337},
doi = {10.1002/tpg2.20337},
pmid = {37165696},
issn = {1940-3372},
support = {OPP1114827//Bill and Melinda Gates Foundation/ ; SB/S9/Z-13/2019//Department of Science and Technology, Ministry of Science and Technology, India/ ; SB/WEA-01/2017//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
mesh = {*Cicer/genetics ; Multiomics ; Plant Roots/genetics ; Droughts ; Galactose/metabolism ; Uridine Diphosphate/metabolism ; },
abstract = {Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought-responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought-tolerant), and ICC 1882 (drought-sensitive) under control and drought stress conditions. Integration of transcriptomics and proteomics data identified enriched hub proteins encoding isoflavone 4'-O-methyltransferase, UDP-d-glucose/UDP-d-galactose 4-epimerase, and delta-1-pyrroline-5-carboxylate synthetase. These proteins highlighted the involvement of pathways such as antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis in activating drought stress response mechanisms. Subsequently, the integration of metabolomics data identified six metabolites (fructose, galactose, glucose, myoinositol, galactinol, and raffinose) that showed a significant correlation with galactose metabolism. Integration of root-omics data also revealed some key candidate genes underlying the drought-responsive "QTL-hotspot" region. These results provided key insights into complex molecular mechanisms underlying drought stress response in chickpea.},
}
@article {pmid37165242,
year = {2023},
author = {Liao, WW and Asri, M and Ebler, J and Doerr, D and Haukness, M and Hickey, G and Lu, S and Lucas, JK and Monlong, J and Abel, HJ and Buonaiuto, S and Chang, XH and Cheng, H and Chu, J and Colonna, V and Eizenga, JM and Feng, X and Fischer, C and Fulton, RS and Garg, S and Groza, C and Guarracino, A and Harvey, WT and Heumos, S and Howe, K and Jain, M and Lu, TY and Markello, C and Martin, FJ and Mitchell, MW and Munson, KM and Mwaniki, MN and Novak, AM and Olsen, HE and Pesout, T and Porubsky, D and Prins, P and Sibbesen, JA and Sirén, J and Tomlinson, C and Villani, F and Vollger, MR and Antonacci-Fulton, LL and Baid, G and Baker, CA and Belyaeva, A and Billis, K and Carroll, A and Chang, PC and Cody, S and Cook, DE and Cook-Deegan, RM and Cornejo, OE and Diekhans, M and Ebert, P and Fairley, S and Fedrigo, O and Felsenfeld, AL and Formenti, G and Frankish, A and Gao, Y and Garrison, NA and Giron, CG and Green, RE and Haggerty, L and Hoekzema, K and Hourlier, T and Ji, HP and Kenny, EE and Koenig, BA and Kolesnikov, A and Korbel, JO and Kordosky, J and Koren, S and Lee, H and Lewis, AP and Magalhães, H and Marco-Sola, S and Marijon, P and McCartney, A and McDaniel, J and Mountcastle, J and Nattestad, M and Nurk, S and Olson, ND and Popejoy, AB and Puiu, D and Rautiainen, M and Regier, AA and Rhie, A and Sacco, S and Sanders, AD and Schneider, VA and Schultz, BI and Shafin, K and Smith, MW and Sofia, HJ and Abou Tayoun, AN and Thibaud-Nissen, F and Tricomi, FF and Wagner, J and Walenz, B and Wood, JMD and Zimin, AV and Bourque, G and Chaisson, MJP and Flicek, P and Phillippy, AM and Zook, JM and Eichler, EE and Haussler, D and Wang, T and Jarvis, ED and Miga, KH and Garrison, E and Marschall, T and Hall, IM and Li, H and Paten, B},
title = {A draft human pangenome reference.},
journal = {Nature},
volume = {617},
number = {7960},
pages = {312-324},
pmid = {37165242},
issn = {1476-4687},
support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; U01 HG010961/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; U01 HG010973/HG/NHGRI NIH HHS/United States ; R01 HG011649/HG/NHGRI NIH HHS/United States ; U01 HG010963/HG/NHGRI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24 HG009081/HG/NHGRI NIH HHS/United States ; U24 HG010262/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R01 HG010485/HG/NHGRI NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; ZIA HG200398/ImNIH/Intramural NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; OT2 OD033761/OD/NIH HHS/United States ; R01 GM123489/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Diploidy ; *Genome, Human/genetics ; Haplotypes/genetics ; Sequence Analysis, DNA ; *Genomics/standards ; Reference Standards ; Cohort Studies ; Alleles ; Genetic Variation ; },
abstract = {Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals[1]. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.},
}
@article {pmid37162091,
year = {2023},
author = {Kawano, B and Agarwal, S and Krishnamoorthy, V and Raghunathan, K and Fernandez-Moure, JS and Haines, KL},
title = {State Firearm Laws and Rate of Assault-Related Firearm Death.},
journal = {Journal of the American College of Surgeons},
volume = {237},
number = {3},
pages = {409-418},
doi = {10.1097/XCS.0000000000000753},
pmid = {37162091},
issn = {1879-1190},
mesh = {Humans ; United States/epidemiology ; Adolescent ; *Firearms ; *Wounds, Gunshot/epidemiology ; Databases, Factual ; Forecasting ; Homicide ; },
abstract = {BACKGROUND: Studying firearm-related mortality is important to reduce preventable firearm death in the US. This study aims to determine the relationship between firearm laws and assault death with firearms.<br><br>STUDY DESIGN: This ecologic study used public data from the CDC Wide-Ranging Online Data for Epidemiologic Research on decedents age 18 years or older who died from assault with firearms between 2009 and 2018 in all 50 states and Washington, DC. The outcomes were the rate of mortality per 100,000 persons from assault death by firearm used. Exposures of interest included the presence of 7 state firearm laws extracted from the RAND State Firearm Law Database. Welch's t tests were performed to compare mean mortality rate in states with each firearm law to states without each law.<br><br>RESULTS: There were 114,945 deaths from assault with firearms from 2009 to 2018. States with "stand your ground" laws had a higher assault mortality rate from all firearms and from other/unspecified firearms than states without stand your ground laws (p = 0.026; p = 0.023). States with background checks for private sales of handguns and long guns had a lower assault mortality rate from handguns and rifles, shotguns, and large firearms, respectively, than states without either law (p = 0.019; p = 0.030).<br><br>CONCLUSIONS: Stand your ground laws are correlated with a higher rate of gun-related assault death, but background checks on private sales are correlated with a lower rate. Future studies should elucidate the specific pathways by which state laws reduce, or fail to reduce, firearm-related assault death.},
}
@article {pmid37162089,
year = {2023},
author = {Santana, BEF and Andrade, ACS and Muraro, AP},
title = {Trend of incompleteness of maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System, 2012-2020.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {32},
number = {1},
pages = {e2022725},
pmid = {37162089},
issn = {2237-9622},
mesh = {Female ; Humans ; Pregnancy ; Brazil ; *Educational Status ; *Live Birth ; Pregnancy, Multiple ; Skin Pigmentation ; Databases, Factual/standards/statistics &amp; numerical data ; Health Information Systems ; Racial Groups ; },
abstract = {OBJECTIVE: to analyze the trend of incompleteness of the maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System (SINASC) between 2012 and 2020.<br><br>METHODS: this was an ecological time series study of the incompleteness of maternal schooling and race/skin color data for Brazil, its regions and Federative Units, by means of joinpoint regression and calculation of annual percentage change (APC) and average annual percentage change.<br><br>RESULTS: a total of 26,112,301 births were registered in Brazil in the period; incompleteness of maternal schooling data decreased for Brazil (APC = -8.1%) and the Southeast (APC = -19.5%) and Midwest (APC = -17.6%) regions; as for race/skin color, there was a downward trend for Brazil (APC = -8.2%) and all regions, except the Northeast region, while nine Federative Units and the Federal District showed a stationary trend.<br><br>CONCLUSION: there was an improvement in filling out these variables on the SINASC, but with regional disparities, mainly for race/skin color.},
}
@article {pmid37161334,
year = {2023},
author = {Kortz, AR and Moyes, F and Pivello, VR and Pyšek, P and Dornelas, M and Visconti, P and Magurran, AE},
title = {Elevated compositional change in plant assemblages linked to invasion.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1998},
pages = {20222450},
pmid = {37161334},
issn = {1471-2954},
mesh = {*Tracheophyta ; Biodiversity ; Databases, Factual ; Introduced Species ; },
abstract = {Alien species are widely linked to biodiversity change, but the extent to which they are associated with the reshaping of ecological communities is not well understood. One possible mechanism is that assemblages where alien species are found exhibit elevated temporal turnover. To test this, we identified assemblages of vascular plants in the BioTIME database for those assemblages in which alien species are either present or absent and used the Jaccard measure to compute compositional dissimilarity between consecutive censuses. We found that, although alien species are typically rare in invaded assemblages, their presence is associated with an increase in the average rate of compositional change. These differences in compositional change between invaded and uninvaded assemblages are not linked to differences in species richness but rather to species replacement (turnover). Rapid compositional restructuring of assemblages is a major contributor to biodiversity change, and as such, our results suggest a role for alien species in bringing this about.},
}
@article {pmid37155680,
year = {2023},
author = {Rokhsar, JL and Raynor, B and Sheen, J and Goldstein, ND and Levy, MZ and Castillo-Neyra, R},
title = {Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.},
journal = {PLoS computational biology},
volume = {19},
number = {5},
pages = {e1011115},
pmid = {37155680},
issn = {1553-7358},
support = {K01 AI139284/AI/NIAID NIH HHS/United States ; T32 AI070077/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Dogs ; *Trypanosoma cruzi ; Insect Vectors ; *Chagas Disease/epidemiology/prevention &amp; control/veterinary ; *Triatoma/parasitology ; *Insecticides/pharmacology ; Mammals ; },
abstract = {BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi, affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.<br><br>OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.<br><br>DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.<br><br>RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.<br><br>CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.},
}
@article {pmid37155231,
year = {2023},
author = {Ondrikova, N and Harris, JP and Douglas, A and Hughes, HE and Iturriza-Gomara, M and Vivancos, R and Elliot, AJ and Cunliffe, NA and Clough, HE},
title = {Predicting Norovirus in England Using Existing and Emerging Syndromic Data: Infodemiology Study.},
journal = {Journal of medical Internet research},
volume = {25},
number = {},
pages = {e37540},
pmid = {37155231},
issn = {1438-8871},
mesh = {Humans ; Infodemiology ; *Norovirus ; England/epidemiology ; *Gastroenteritis/epidemiology ; *Caliciviridae Infections/epidemiology ; },
abstract = {BACKGROUND: Norovirus is associated with approximately 18% of the global burden of gastroenteritis and affects all age groups. There is currently no licensed vaccine or available antiviral treatment. However, well-designed early warning systems and forecasting can guide nonpharmaceutical approaches to norovirus infection prevention and control.<br><br>OBJECTIVE: This study evaluates the predictive power of existing syndromic surveillance data and emerging data sources, such as internet searches and Wikipedia page views, to predict norovirus activity across a range of age groups across England.<br><br>METHODS: We used existing syndromic surveillance and emerging syndromic data to predict laboratory data indicating norovirus activity. Two methods are used to evaluate the predictive potential of syndromic variables. First, the Granger causality framework was used to assess whether individual variables precede changes in norovirus laboratory reports in a given region or an age group. Then, we used random forest modeling to estimate the importance of each variable in the context of others with two methods: (1) change in the mean square error and (2) node purity. Finally, these results were combined into a visualization indicating the most influential predictors for norovirus laboratory reports in a specific age group and region.<br><br>RESULTS: Our results suggest that syndromic surveillance data include valuable predictors for norovirus laboratory reports in England. However, Wikipedia page views are less likely to provide prediction improvements on top of Google Trends and Existing Syndromic Data. Predictors displayed varying relevance across age groups and regions. For example, the random forest modeling based on selected existing and emerging syndromic variables explained 60% variance in the &#x2265;65 years age group, 42% in the East of England, but only 13% in the South West region. Emerging data sets highlighted relative search volumes, including "flu symptoms," "norovirus in pregnancy," and norovirus activity in specific years, such as "norovirus 2016." Symptoms of vomiting and gastroenteritis in multiple age groups were identified as important predictors within existing data sources.<br><br>CONCLUSIONS: Existing and emerging data sources can help predict norovirus activity in England in some age groups and geographic regions, particularly, predictors concerning vomiting, gastroenteritis, and norovirus in the vulnerable populations and historical terms such as stomach flu. However, syndromic predictors were less relevant in some age groups and regions likely due to contrasting public health practices between regions and health information-seeking behavior between age groups. Additionally, predictors relevant to one norovirus season may not contribute to other seasons. Data biases, such as low spatial granularity in Google Trends and especially in Wikipedia data, also play a role in the results. Moreover, internet searches can provide insight into mental models, that is, an individual's conceptual understanding of norovirus infection and transmission, which could be used in public health communication strategies.},
}
@article {pmid37155109,
year = {2023},
author = {Chen, D and Zhang, Y and Feng, Q},
title = {Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {27},
pages = {70671-70687},
pmid = {37155109},
issn = {1614-7499},
mesh = {Mining ; *Microbiota ; Rivers/chemistry ; Bacteria/genetics ; Water/chemistry ; Coal/analysis ; China ; *Water Pollutants, Chemical/analysis ; },
abstract = {Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.},
}
@article {pmid37154236,
year = {2023},
author = {Lin, F and Kennelly, EJ and Linington, RG and Long, C},
title = {Comprehensive Metabolite Profiling of Two Edible Garcinia Species Based on UPLC-ESI-QTOF-MS[E] Coupled with Bioactivity Assays.},
journal = {Journal of agricultural and food chemistry},
volume = {71},
number = {19},
pages = {7604-7617},
doi = {10.1021/acs.jafc.2c08372},
pmid = {37154236},
issn = {1520-5118},
mesh = {Chromatography, High Pressure Liquid ; *Garcinia ; Multivariate Analysis ; Metabolomics ; *Plants, Medicinal ; },
abstract = {In China, the endemic species Garcinia yunnanensis and native Garcinia xanthochymus are known as edible and medicinal plants. However, a systematic metabolomic and bioactivity evaluation of different plant parts from both species is lacking. In this study, comprehensive investigations of 11 plant parts of G. yunnanensis and 10 of G. xanthochymus employing UPLC-ESI-QTOF-MS[E]-based metabolomic analysis in conjunction with three bioactivity assays were undertaken. A customized chemotaxonomic-based in-house library containing 6456 compounds was constructed and coupled to the Progenesis QI informatic platform for metabolite annotations. From these two species, a total of 235 constituents were characterized using multiple criteria. Differences in metabolite profiles between the plant parts within each species were uncovered using multivariate analysis. Based on orthogonal partial least-squares discriminant analysis (OPLS-DA), 23 markers were identified as highly differential metabolites from G. xanthochymus and 20 from G. yunnanensis. Comparative assessment of the biological assays revealed the activity variations among different plant parts. The seeds of both species and G. yunnanensis latex exhibited excellent cytotoxic and antibacterial activities, while G. xanthochymus roots and G. yunnanensis arils showed strong anti-inflammatory effects. S-plot analysis identified 26 potential biomarkers for the observed activities, including the known cytotoxic agent cycloxanthochymol and the anti-inflammatory compound garcimultiflorone B, which likely explains some of the potent observed bioactivity.},
}
@article {pmid37152782,
year = {2023},
author = {Mori, Y and Okawara, M and Shibao, K and Kohi, S and Tamura, T and Sato, N and Fujino, Y and Fushimi, K and Matsuda, S and Hirata, K},
title = {Changes in operative trends and short-term outcomes of surgery for congenital biliary dilatation in adults using real-world data: A multilevel analysis based on a nationwide administrative database in Japan.},
journal = {Annals of gastroenterological surgery},
volume = {7},
number = {3},
pages = {471-478},
pmid = {37152782},
issn = {2475-0328},
abstract = {AIM: We aimed to evaluate the operative trends and compare the short-term outcomes between open and laparoscopic surgery for congenital biliary dilatation (CBD) in adults using real-world data from Japan.<br><br>METHODS: Data from the Japanese Diagnosis Procedure Combination database on 941 patients undergoing surgery for CBD at 357 hospitals from April 1, 2016, to March 31, 2021, were analyzed. The patients were divided into two groups: open surgery (n&#xa0;=&#xa0;764) and laparoscopic surgery (n&#xa0;=&#xa0;177). We performed a retrospective analysis via a multilevel analysis of the short-term surgical outcomes and costs between open and laparoscopic surgery.<br><br>RESULTS: The rate of laparoscopic surgery has been increasing annually and had almost doubled to 25% by 2021. There were no significant differences in the in-hospital mortality rate or postoperative morbidity between the two groups. The length of anesthesia was significantly longer in the laparoscopic than open surgery group (8.80 vs 6.16&#x2009;hours, p&#x2009;<&#x2009;.001). The time to removal of the abdominal drain and length of hospital stay were significantly shorter in the laparoscopic than open surgery group (6.12 vs 8.35&#x2009;days, p&#xa0;=&#xa0;.001 and 13.57 vs 15.79&#x2009;days, p&#x2009;<&#x2009;.001, respectively). The coefficient for cost was 463&#x2009;235 yen (95% confidence interval, 289&#x2009;679-636&#x2009;792) higher in laparoscopic than open surgery (p&#x2009;<&#x2009;.001).<br><br>CONCLUSION: The short-term results were comparable between laparoscopic and open surgery for CBD. Further investigation is needed to validate our findings and long-term outcomes.},
}
@article {pmid37150648,
year = {2023},
author = {Wieczorek, P and Pruc, M and Krajsman, M and Wieczorek, W and Cander, B and Szarpak, L and Navolokina, A and Matuszewski, M and Bragazzi, NL and Chirico, F and Smereka, J},
title = {Comparison of the bébé VieScope™ and direct laryngoscope for pediatric tongue oedema scenario: A simulation study.},
journal = {The American journal of emergency medicine},
volume = {69},
number = {},
pages = {207-208},
doi = {10.1016/j.ajem.2023.04.039},
pmid = {37150648},
issn = {1532-8171},
mesh = {Humans ; Child ; *Laryngoscopes ; Laryngoscopy ; Intubation, Intratracheal ; *Tongue Diseases ; Tongue ; Edema ; Manikins ; Equipment Design ; },
}
@article {pmid37148803,
year = {2023},
author = {Tang, Y and Hardy, TJ and Yoon, JY},
title = {Receptor-based detection of microplastics and nanoplastics: Current and future.},
journal = {Biosensors &amp; bioelectronics},
volume = {234},
number = {},
pages = {115361},
doi = {10.1016/j.bios.2023.115361},
pmid = {37148803},
issn = {1873-4235},
mesh = {Microplastics ; Plastics ; *Biosensing Techniques ; Biological Assay ; Databases, Factual ; *Water Pollutants, Chemical ; },
abstract = {Plastic pollution is an emerging environmental concern, gaining significant attention worldwide. They are classified into microplastics (MP; defined from 1 μm to 5 mm) and smaller nanoplastics (NP; <1 μm). NPs may pose higher ecological risks than MPs. Various microscopic and spectroscopic techniques have been used to detect MPs, and the same methods have occasionally been used for NPs. However, they are not based on receptors, which provide high specificity in most biosensing applications. Receptor-based micro/nanoplastics (MNP) detection can provide high specificity, distinguishing MNPs from the environmental samples and, more importantly, identifying the plastic types. It can also offer a low limit of detection (LOD) required for environmental screening. Such receptors are expected to detect NPs specifically at the molecular level. This review categorizes the receptors into cells, proteins, peptides, fluorescent dyes, polymers, and micro/nanostructures. Detection techniques used with these receptors are also summarized and categorized. There is plenty of room for future research to test for broader classes of environmental samples and many plastic types, to lower the LOD, and to apply the current techniques for NPs. Portable and handheld MNP detection should also be demonstrated for field use since the current demonstrations primarily utilized laboratory instruments. Detection on microfluidic platforms will also be crucial in miniaturizing and automating the assay and, eventually, collecting an extensive database to support machine learning-based classification of MNP types.},
}
@article {pmid37148512,
year = {2023},
author = {Wang, Y},
title = {Ecological risk identification and assessment of land remediation project based on GIS technology.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {27},
pages = {70493-70505},
pmid = {37148512},
issn = {1614-7499},
mesh = {Animals ; Geographic Information Systems ; *Volatile Organic Compounds ; *Environmental Restoration and Remediation ; *Environmental Pollutants ; Risk Assessment ; Technology ; Environmental Monitoring ; },
abstract = {A land remediation project involves the removal of potentially toxic chemicals from a polluted site. Lands abandoned by industry are often contaminated with heavy metals like mercury, lead, chemicals, arsenic, and other toxins like dichlorodiphenyltrichloroethane biphenyls from electronic devices, and volatile organic chemicals (VOCs) from lubricants and chemicals. Risk assessment in environmental settings requires modernized systematic methodologies due to the complexity of today's environmental problems. When people eat, drink, or work in polluted environments, they put their health at risk and may even get cancer. Integrating geospatial information systems (GIS) with pollutant dispersion models makes environmental risk assessment and early warning possible. This research thus presents a GIS-based ecological risk identification and assessment model (GIS-ERIAM) for assessing risk for efficient land rehabilitation. Environmental cleanup sites' catalog information is the source of these details. With satellite imagery, GIS makes it simple to keep an eye on the environment and track the abundance of different types of plants and animals The ecological risk assessment (ERA) model can support recognition and prioritize risk management. By integrating direct and indirect environment interactions, the risk conditions of the whole ecology and its elements have been quantified and demonstrated in the study. The numerical outcomes illustrate that the recommended GIS-ERIAM model improves the performance by 98.9%, risk level prediction by 97.3%, risk classification by 96.4%, and detection of soil degradation ratio of 95.6% compared to other existing methods.},
}
@article {pmid37138127,
year = {2023},
author = {Mohamadi, S and Honarmand, M and Ghazanfari, S and Hassanzadeh, R},
title = {Hotspot and accumulated hotspot analysis for assessment of groundwater quality and pollution indices using GIS in the arid region of Iran.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {27},
pages = {69955-69976},
pmid = {37138127},
issn = {1614-7499},
mesh = {Water Quality ; Environmental Monitoring/methods ; Geographic Information Systems ; Iran ; *Groundwater/analysis ; Nitrates/analysis ; *Water Pollutants, Chemical/analysis ; },
abstract = {Because groundwater quality representatives for drinking usage (i.e., Schuler method, Nitrate and Groundwater Quality Index) have been abruptly changing due to extreme events induced by global climate change and over-abstracting, applying an efficient tool for their assessments is vitally important. While hotspot analysis is introduced as an efficient tool concentrating on sharp changes in groundwater quality, it has not been closely examined. Accordingly, this study is an attempt to determine the groundwater quality proxies and assess them through hotspot and accumulated hotspot analyses. To this end, a GIS-based hotspot analysis (HA) applying Getis-Ord Gi* statistics was used. The accumulated hotspot analysis was launched to identify the Groundwater Quality Index (AHA-GQI). Moreover, Schuler method (AHA-SM) was utilized to determine the maximum levels (ML) for the hottest hotspot and the lowest levels (LL) for the coldest cold-spot, and compound levels (CL). The results revealed that a significant correlation (r = 0.8) between GQI and SM was observed. However, the correlation between GQI and nitrate was not significant and the correlation between SM and nitrate was so low (r = 0.298, sig > 0.05). The results also demonstrated that using hotspot analysis on only GQI, the correlation between GQI and SM increased from 0.8 to 0.856, while using hotspot analysis on both GQI and SM increased the correlation to 0.945. Likewise, when GQI was subjected to hotspot analysis and SM underwent accumulated hotspot analysis (i.e., AHA-SM (ML)), the correlation degree increased to the highest extent (i.e., 0.958), indicating the usefulness of including the hotspot analysis and accumulated hotspot analysis in the evaluation of groundwater quality.},
}
@article {pmid37134212,
year = {2023},
author = {Schuler, T and King, C and Matsveru, T and Back, M and Clark, K and Chin, D and Lilian, R and Gallego, B and Coiera, E and Currow, DC},
title = {Wearable-Triggered Ecological Momentary Assessments Are Feasible in People With Advanced Cancer and Their Family Caregivers: Feasibility Study from an Outpatient Palliative Care Clinic at a Cancer Center.},
journal = {Journal of palliative medicine},
volume = {26},
number = {7},
pages = {980-985},
doi = {10.1089/jpm.2022.0535},
pmid = {37134212},
issn = {1557-7740},
mesh = {Humans ; Palliative Care ; Caregivers ; Feasibility Studies ; Ecological Momentary Assessment ; Outpatients ; *Neoplasms ; *Wearable Electronic Devices ; },
abstract = {Background: Emerging digital health approaches could play a role in better personalized palliative care. Aim: We conducted a feasibility study testing wearable sensor (WS)-triggered ecological momentary assessments (EMAs) and electronic patient-reported outcomes in community palliative care with patient-caregiver dyads. Design: All wore consumer-grade WS for five weeks. Sensor-detected "stress" (heart rate variability algorithm) that passed individualized thresholds triggered a short smartphone survey. Daily sleep surveys, weekly symptom surveys (Integrated Palliative care Outcome Scale), and a poststudy experience survey were conducted. Setting/Participants: Fifteen dyads (n = 30) were recruited from an outpatient palliative care clinic for people with cancer. Results: Daytime sensor wear-time had 73% adherence. Participants perceived value in this support. Quantity and severity of "stress" events were higher in patients. Sleep disturbance was similar but for different reasons: patients (physical symptoms) and caregivers (worrying about the patient). Conclusions: EMAs are feasible and valued in community palliative care.},
}
@article {pmid37117267,
year = {2023},
author = {Minhas, BF and Beck, EA and Cheng, CC and Catchen, J},
title = {Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {6939},
pmid = {37117267},
issn = {2045-2322},
mesh = {Animals ; *Genome, Mitochondrial/genetics ; Temperature ; Heteroplasmy ; Fishes/genetics ; *Perciformes/physiology ; Antarctic Regions ; },
abstract = {Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.},
}
@article {pmid37116451,
year = {2023},
author = {Barnea, O and Cohen, N and Hindi, I and Katz, C},
title = {Noticing the unutilized resource of siblinghood: Key conclusions from a scoping review about siblings in out-of-home placements.},
journal = {Child abuse &amp; neglect},
volume = {141},
number = {},
pages = {106192},
doi = {10.1016/j.chiabu.2023.106192},
pmid = {37116451},
issn = {1873-7757},
mesh = {Child ; Humans ; *Siblings ; *Child Welfare ; Foster Home Care/methods ; Databases, Factual ; },
abstract = {BACKGROUND: Sibling bonds are often the most enduring relationship in an individual's life span. The out-of-home placement of siblings is widespread and may significantly influence children's journeys and wellbeing.<br><br>OBJECTIVE: The current scoping literature review was designed to characterize and analyze the existing knowledge regarding siblings in out-of-home placements.<br><br>METHOD: Key databases were explored using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, which identified 33 studies relevant to the current study's focus. The studies used quantitative, qualitative, and mixed methods and included a variety of out-of-home placement settings and sample characteristics.<br><br>RESULTS: Utilizing thematic analysis, the findings addressed three main themes: the sibling bond as a contributor to the wellbeing of children in out-of-home placements, trends in sibling placement, and difficulties in maintaining the sibling bond in out-of-home placements regarding micro, meso and exo factors.<br><br>CONCLUSION: A key conclusion from the review is that the welfare system struggles to address a child as a part of a sibling group and an extensive and multilayered relational network; hence, siblinghood is an unutilized resource in out-of-home placements. Future directions for practice, policy and research are included and discussed.},
}
@article {pmid37110442,
year = {2023},
author = {Maimone, G and Azzaro, M and Placenti, F and Paranhos, R and Cabral, AS and Decembrini, F and Zaccone, R and Cosenza, A and Rappazzo, AC and Patti, B and Basilone, G and Cuttitta, A and Ferreri, R and Aronica, S and Ferla, R},
title = {A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).},
journal = {Microorganisms},
volume = {11},
number = {4},
pages = {},
pmid = {37110442},
issn = {2076-2607},
abstract = {A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.},
}
@article {pmid37107825,
year = {2023},
author = {Schütt, EM and Hundsdörfer, MAJ and von Hoyningen-Huene, AJE and Lange, X and Koschmider, A and Oppelt, N},
title = {First Steps towards a near Real-Time Modelling System of Vibrio vulnificus in the Baltic Sea.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {8},
pages = {},
pmid = {37107825},
issn = {1660-4601},
mesh = {Humans ; *Vibrio vulnificus ; *Vibrio Infections ; Water ; Baltic States ; Oxygen ; },
abstract = {Over the last two decades, Vibrio vulnificus infections have emerged as an increasingly serious public health threat along the German Baltic coast. To manage related risks, near real-time (NRT) modelling of V. vulnificus quantities has often been proposed. Such models require spatially explicit input data, for example, from remote sensing or numerical model products. We tested if data from a hydrodynamic, a meteorological, and a biogeochemical model are suitable as input for an NRT model system by coupling it with field samples and assessing the models' ability to capture known ecological parameters of V. vulnificus. We also identify the most important predictors for V. vulnificus in the Baltic Sea by leveraging the St. Nicolas House Analysis. Using a 27-year time series of sea surface temperature, we have investigated trends of V. vulnificus season length, which pinpoint hotspots mainly in the east of our study region. Our results underline the importance of water temperature and salinity on V. vulnificus abundance but also highlight the potential of air temperature, oxygen, and precipitation to serve as predictors in a statistical model, albeit their relationship with V. vulnificus may not be causal. The evaluated models cannot be used in an NRT model system due to data availability constraints, but promising alternatives are presented. The results provide a valuable basis for a future NRT model for V. vulnificus in the Baltic Sea.},
}
@article {pmid37107056,
year = {2023},
author = {Olivieri, R and Vannini, P and Corzani, A and Bianco, MT and Franchi, F and Cusi, MG and Scolletta, S and Arena, F and Basagni, C and Gusinu, R and Tumbarello, M},
title = {Rapid Decrease in Fluoroquinolones Consumption following Implementation of a Simple Antimicrobial Stewardship Bundled Intervention in a University Hospital during the COVID-19 Pandemic.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
pmid = {37107056},
issn = {2079-6382},
abstract = {Fluoroquinolones (FQs) represent an class of antibiotics of medical importance, but their use has been restricted due to their ecologic impact and associated side effects. The reduction of FQs use is an important goal of antimicrobial stewardship programs (ASP). This work describes an ASP focused on overall antibiotics and FQs consumption reduction. From January 2021, an ASP was implemented in a 700-bed teaching hospital. The ASP was based on: (i) antibiotics consumption monitoring system (DDD/100 bed days); (ii) mandatory antibiotic prescription-motivation (using a dedicated informatic format) with the goal of >75% of motivated prescriptions; and (iii) data feedback and training on FQs use indications. We evaluated the impact of the intervention on overall systemic antibiotics and FQs consumption according to the objectives posed by Italian PNCAR (National Action Plan on Antimicrobial Resistance). A decrease of 6.6% in antibiotic use was observed (2019 vs. 2021). Notably, the FQs consumption fell by 48.3% from 7.1 DDD/100 bd in 2019 to 3.7 DDD/100 bd in 2021 (p < 0.001). After six months of mandatory antibiotic prescription-indication, all units achieved the target set. The study suggests that a simple, bundled ASP intervention can be rapidly effective obtaining the objectives of PNCAR on the reduction of overall antibiotics and FQs consumption.},
}
@article {pmid37106771,
year = {2023},
author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R},
title = {Boundaries Are Blurred: Wild Food Plant Knowledge Circulation across the Polish-Lithuanian-Belarusian Borderland.},
journal = {Biology},
volume = {12},
number = {4},
pages = {},
pmid = {37106771},
issn = {2079-7737},
support = {714874/ERC_/European Research Council/International ; },
abstract = {The circulation of local ecological knowledge (LEK) is a promising avenue of research for wild plant studies. To encourage the acceptance, celebration, and appreciation of biocultural diversity, which is rapidly disappearing nowadays, we need to estimate and assess multifaceted local ecological knowledge. It has direct application for local communities in informing effective policies for improving food security and building community-specific responses to environmental and social transitions. The present study draws on data collected among two ethnic groups-Lithuanians and Poles-via 200 semi-structured in-depth interviews and participant observation conducted in 2018 and 2019 in Podlasie Voivodeship (Poland), the Vilnius Region (Lithuania), and the Hrodna Region (Belarus). We aimed to observe LEK circulation in the border area through cross-ethnic and cross-country comparisons. A total of 2812 detailed use reports of wild plants were recorded. In total, 72 wild plant taxa belonging to 33 plant families were used across the food domain. Our findings show that cross-country differences were minimal, while there was some variation between the ethnic groups selected as case studies. We emphasize the need, in future studies, to combine quantitative research with qualitative approaches in order to more thoroughly identify peculiarities of cross-border circulation as a reservoir for community food resilience and biocultural diversity.},
}
@article {pmid37104570,
year = {2023},
author = {Osmanski, AB and Paulat, NS and Korstian, J and Grimshaw, JR and Halsey, M and Sullivan, KAM and Moreno-Santillán, DD and Crookshanks, C and Roberts, J and Garcia, C and Johnson, MG and Densmore, LD and Stevens, RD and , and Rosen, J and Storer, JM and Hubley, R and Smit, AFA and Dávalos, LM and Karlsson, EK and Lindblad-Toh, K and Ray, DA},
title = {Insights into mammalian TE diversity through the curation of 248 genome assemblies.},
journal = {Science (New York, N.Y.)},
volume = {380},
number = {6643},
pages = {eabn1430},
pmid = {37104570},
issn = {1095-9203},
support = {R01 HG002939/HG/NHGRI NIH HHS/United States ; R01 HG008742/HG/NHGRI NIH HHS/United States ; U24 HG010136/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Female ; Pregnancy ; *DNA Transposable Elements ; *Evolution, Molecular ; Long Interspersed Nucleotide Elements ; *Eutheria/genetics ; Datasets as Topic ; Feeding Behavior ; *Genetic Variation ; },
abstract = {We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.},
}
@article {pmid37102710,
year = {2023},
author = {Green, SJ and Torok, T and Allen, JE and Eloe-Fadrosh, E and Jackson, SA and Jiang, SC and Levine, SS and Levy, S and Schriml, LM and Thomas, WK and Wood, JM and Tighe, SW},
title = {Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report.},
journal = {Astrobiology},
volume = {23},
number = {8},
pages = {897-907},
pmid = {37102710},
issn = {1557-8070},
mesh = {United States ; Humans ; *Planets ; *Space Flight ; Extraterrestrial Environment ; Metagenomics ; United States National Aeronautics and Space Administration ; Spacecraft ; Policy ; },
abstract = {Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.},
}
@article {pmid37101136,
year = {2023},
author = {Mosquera, KD and Martínez Villegas, LE and Rocha Fernandes, G and Rocha David, M and Maciel-de-Freitas, R and A Moreira, L and Lorenzo, MG},
title = {Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {97},
pmid = {37101136},
issn = {1741-7007},
mesh = {Animals ; Humans ; Female ; *Aedes ; Mosquito Vectors ; Water ; Bacteria/genetics ; Oviposition ; Larva ; },
abstract = {BACKGROUND: Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.<br><br>RESULTS: To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.<br><br>CONCLUSIONS: Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.},
}
@article {pmid37100861,
year = {2023},
author = {Stocco, A and Pranovi, F},
title = {The paradoxical need for human intervention in the conservation of natural environments in Venice lagoon.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {6798},
pmid = {37100861},
issn = {2045-2322},
mesh = {Humans ; *Ecosystem ; *Environment ; Aquaculture ; Climate ; Geography ; Conservation of Natural Resources/methods ; },
abstract = {The Venice lagoon-the largest Mediterranean coastal lagoon-is characterized by the presence at its edges of 31 "valli da pesca", types of artificial ecosystems that mime the ecological processes of a transitional aquatic ecosystem. Constituted by a series of regulated lakes bounded by artificial embankments, the valli da pesca were established centuries ago to maximize provisioning Ecosystem Services (ESs), such as fishing and hunting. As time passed, the valli da pesca underwent an intentional isolation process leading to private management. Nonetheless, the valli da pesca are still exchanging energy and matter with the "open' lagoon and today represent an essential element within the context of lagoon conservation. This study aimed to analyze the possible effects of artificial management on both ESs supply and landscape arrangements by assessing 9 ESs (climate regulation, water purification, lifecycle support, aquaculture, waterfowl hunting, wild food, tourism, information for cognitive development, and birdwatching), along with eight landscape indicators. Obtained results suggested that the valli da pesca are today ruled under five different management strategies, according to the maximized ES. Management conditions influence the landscape pattern and achieve a series of "side effects" on the other ESs. The comparison between the managed and abandoned valli da pesca highlights the importance of anthropogenic interventions for conserving these ecosystems, as the abandoned valli da pesca show a loss of ecological gradients, landscape heterogeneity, and provisioning ESs. Nevertheless, the persistence of intrinsic geographical and morphological characteristics still prevails regardless of intentional landscape molding. The result is that the provisioning ESs capacity per unit area is higher in the abandoned valli da pesca than in the open lagoon, emphasizing the importance of these confined areas of the lagoon ecosystem. Considering the spatial distribution of multiple ESs, the provisioning ESs flow that does not occur in the abandoned valli da pesca seems to be replaced by the flow of cultural ESs. Thus, the ESs spatial pattern highlights a balancing effect between different ESs categories. The results are discussed considering the trade-offs generated by private land conservation, anthropogenic interventions, and their relevance for the ecosystem-based management of Venice lagoon.},
}
@article {pmid37099856,
year = {2023},
author = {Sutton, C and Prowse, J and McVey, L and Elshehaly, M and Neagu, D and Montague, J and Alvarado, N and Tissiman, C and O'Connell, K and Eyers, E and Faisal, M and Randell, R},
title = {Strategic workforce planning in health and social care - an international perspective: A scoping review.},
journal = {Health policy (Amsterdam, Netherlands)},
volume = {132},
number = {},
pages = {104827},
doi = {10.1016/j.healthpol.2023.104827},
pmid = {37099856},
issn = {1872-6054},
mesh = {Humans ; *Health Services Needs and Demand ; Workforce ; *Health Personnel ; Forecasting ; },
abstract = {Effective strategic workforce planning for integrated and co-ordinated health and social care is essential if future services are to be resourced such that skill mix, clinical practice and productivity meet population health and social care needs in timely, safe and accessible ways globally. This review presents international literature to illustrate how strategic workforce planning in health and social care has been undertaken around the world with examples of planning frameworks, models and modelling approaches. The databases Business Source Premier, CINAHL, Embase, Health Management Information Consortium, Medline and Scopus were searched for full texts, from 2005 to 2022, detailing empirical research, models or methodologies to explain how strategic workforce planning (with at least a one-year horizon) in health and/or social care has been undertaken, yielding ultimately 101 included references. The supply/demand of a differentiated medical workforce was discussed in 25 references. Nursing and midwifery were characterised as undifferentiated labour, requiring urgent growth to meet demand. Unregistered workers were poorly represented as was the social care workforce. One reference considered planning for health and social care workers. Workforce modelling was illustrated in 66 references with predilection for quantifiable projections. Increasingly needs-based approaches were called for to better consider demography and epidemiological impacts. This review's findings advocate for whole-system needs-based approaches that consider the ecology of a co-produced health and social care workforce.},
}
@article {pmid37098064,
year = {2023},
author = {Shea, K and Borchering, RK and Probert, WJM and Howerton, E and Bogich, TL and Li, SL and van Panhuis, WG and Viboud, C and Aguás, R and Belov, AA and Bhargava, SH and Cavany, SM and Chang, JC and Chen, C and Chen, J and Chen, S and Chen, Y and Childs, LM and Chow, CC and Crooker, I and Del Valle, SY and España, G and Fairchild, G and Gerkin, RC and Germann, TC and Gu, Q and Guan, X and Guo, L and Hart, GR and Hladish, TJ and Hupert, N and Janies, D and Kerr, CC and Klein, DJ and Klein, EY and Lin, G and Manore, C and Meyers, LA and Mittler, JE and Mu, K and Núñez, RC and Oidtman, RJ and Pasco, R and Pastore Y Piontti, A and Paul, R and Pearson, CAB and Perdomo, DR and Perkins, TA and Pierce, K and Pillai, AN and Rael, RC and Rosenfeld, K and Ross, CW and Spencer, JA and Stoltzfus, AB and Toh, KB and Vattikuti, S and Vespignani, A and Wang, L and White, LJ and Xu, P and Yang, Y and Yogurtcu, ON and Zhang, W and Zhao, Y and Zou, D and Ferrari, MJ and Pannell, D and Tildesley, MJ and Seifarth, J and Johnson, E and Biggerstaff, M and Johansson, MA and Slayton, RB and Levander, JD and Stazer, J and Kerr, J and Runge, MC},
title = {Multiple models for outbreak decision support in the face of uncertainty.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {18},
pages = {e2207537120},
pmid = {37098064},
issn = {1091-6490},
support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control ; Uncertainty ; Disease Outbreaks/prevention &amp; control ; Public Health ; Pandemics/prevention &amp; control ; },
abstract = {Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we convened multiple modeling teams to evaluate COVID-19 reopening strategies for a mid-sized United States county early in the pandemic. Projections from seventeen distinct models were inconsistent in magnitude but highly consistent in ranking interventions. The 6-mo-ahead aggregate projections were well in line with observed outbreaks in mid-sized US counties. The aggregate results showed that up to half the population could be infected with full workplace reopening, while workplace restrictions reduced median cumulative infections by 82%. Rankings of interventions were consistent across public health objectives, but there was a strong trade-off between public health outcomes and duration of workplace closures, and no win-win intermediate reopening strategies were identified. Between-model variation was high; the aggregate results thus provide valuable risk quantification for decision making. This approach can be applied to the evaluation of management interventions in any setting where models are used to inform decision making. This case study demonstrated the utility of our approach and was one of several multimodel efforts that laid the groundwork for the COVID-19 Scenario Modeling Hub, which has provided multiple rounds of real-time scenario projections for situational awareness and decision making to the Centers for Disease Control and Prevention since December 2020.},
}
@article {pmid37097029,
year = {2023},
author = {Carrol, ED and Ranjit, S and Menon, K and Bennett, TD and Sanchez-Pinto, LN and Zimmerman, JJ and Souza, DC and Sorce, LR and Randolph, AG and Ishimine, P and Flauzino de Oliveira, C and Lodha, R and Harmon, L and Watson, RS and Schlapbach, LJ and Kissoon, N and Argent, AC and , },
title = {Operationalizing Appropriate Sepsis Definitions in Children Worldwide: Considerations for the Pediatric Sepsis Definition Taskforce.},
journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies},
volume = {24},
number = {6},
pages = {e263-e271},
pmid = {37097029},
issn = {1529-7535},
support = {R01 HD105939/HD/NICHD NIH HHS/United States ; },
mesh = {Child ; Humans ; *Sepsis/diagnosis/therapy ; Hospital Mortality ; Databases, Factual ; Outcome Assessment, Health Care ; },
abstract = {Sepsis is a leading cause of global mortality in children, yet definitions for pediatric sepsis are outdated and lack global applicability and validity. In adults, the Sepsis-3 Definition Taskforce queried databases from high-income countries to develop and validate the criteria. The merit of this definition has been widely acknowledged; however, important considerations about less-resourced and more diverse settings pose challenges to its use globally. To improve applicability and relevance globally, the Pediatric Sepsis Definition Taskforce sought to develop a conceptual framework and rationale of the critical aspects and context-specific factors that must be considered for the optimal operationalization of future pediatric sepsis definitions. It is important to address challenges in developing a set of pediatric sepsis criteria which capture manifestations of illnesses with vastly different etiologies and underlying mechanisms. Ideal criteria need to be unambiguous, and capable of adapting to the different contexts in which children with suspected infections are present around the globe. Additionally, criteria need to facilitate early recognition and timely escalation of treatment to prevent progression and limit life-threatening organ dysfunction. To address these challenges, locally adaptable solutions are required, which permit individualized care based on available resources and the pretest probability of sepsis. This should facilitate affordable diagnostics which support risk stratification and prediction of likely treatment responses, and solutions for locally relevant outcome measures. For this purpose, global collaborative databases need to be established, using minimum variable datasets from routinely collected data. In summary, a "Think globally, act locally" approach is required.},
}
@article {pmid37095444,
year = {2023},
author = {Demidova, EV and Serebriiskii, IG and Vlasenkova, R and Kelow, S and Andrake, MD and Hartman, TR and Kent, T and Virtucio, J and Rosen, GL and Pomerantz, RT and Dunbrack, RL and Golemis, EA and Hall, MJ and Chen, DYT and Daly, MB and Arora, S},
title = {Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {212},
pmid = {37095444},
issn = {1471-2164},
support = {R01 DK108195/GF/NIH HHS/United States ; 1UH2CA271230-01/GF/NIH HHS/United States ; R35 GM122517/GF/NIH HHS/United States ; R35 GM122517/GM/NIGMS NIH HHS/United States ; 1R01GM130889/GF/NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; UH2 CA271230/CA/NCI NIH HHS/United States ; U01 CA164920/GF/NIH HHS/United States ; },
mesh = {Humans ; *Carcinoma, Renal Cell ; Genetic Predisposition to Disease ; DNA Replication ; Germ-Line Mutation ; *Kidney Neoplasms ; Germ Cells ; },
abstract = {BACKGROUND: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.<br><br>METHODS: Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes.<br><br>RESULTS: Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of [Formula: see text]H2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate variant genes&#xa0;in Caki RCC cells increased [Formula: see text]H2AX foci. Immortalized patient-derived B cell lines bearing the candidate variants in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol &#x3b4; and Pol &#x3b7; polymerases revealed defective enzymatic activities.<br><br>CONCLUSIONS: Together, these results suggest that constitutional defects in DNA repair underlie a subset of eoRCC cases. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.},
}
@article {pmid37094905,
year = {2023},
author = {Girón, JC and Tarasov, S and González Montaña, LA and Matentzoglu, N and Smith, AD and Koch, M and Boudinot, BE and Bouchard, P and Burks, R and Vogt, L and Yoder, M and Osumi-Sutherland, D and Friedrich, F and Beutel, RG and Mikó, I},
title = {Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.},
journal = {Systematic biology},
volume = {72},
number = {5},
pages = {1084-1100},
doi = {10.1093/sysbio/syad025},
pmid = {37094905},
issn = {1076-836X},
support = {339576//Academy of Finland/ ; //University of Helsinki/ ; MO 412/54-1//German Research Foundation/ ; },
mesh = {Animals ; Phylogeny ; *Arthropods ; Insecta ; Informatics ; Biodiversity ; },
abstract = {The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multispecies anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to: 1) use controlled vocabularies and create semiautomated computer-parsable insect morphological descriptions; 2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and 3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.},
}
@article {pmid37093376,
year = {2023},
author = {Alam, N and Saha, S and Gupta, S and Chatterjee, A},
title = {Settlement suitability analysis of a riverine floodplain in the perspective of GIS-based multicriteria decision analysis.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {24},
pages = {66002-66020},
pmid = {37093376},
issn = {1614-7499},
mesh = {Humans ; *Geographic Information Systems ; *Decision Support Techniques ; Spatial Analysis ; Sustainable Development ; Climate ; },
abstract = {Riverine floodplains are highly dynamic and the most vulnerable space on Earth particularly in flat alluvial plains of major river systems. Suitable site selection for sustainable human settlements in active floodplain areas is a critical task for decision-makers in terms of quality of lithology, ecologically fragile landmass, climate-induced hazards, immense population pressure, and environmental conservation issues. This research introduces a methodology for settlement suitability zone (SSZ) that employs GIS-based multi-criteria decision-making (MCDM) techniques. As a case study, an altered hydrological regime of the lower Ganga riparian zone was chosen to identify the SSZ as these areas are the most susceptible to riverine hazards. Twelve significant variables reflecting on topography, climate, landscape, and environment have been selected in the multi-criteria evaluation platform. The CRiteria Importance Through Intercriteria Correlation (CRITIC) method is adopted to specify the weights of the criteria and utilize an inverse distance-weighted (IDW) spatial interpolation technique to generate an SSZ map in a GIS environment. The study zone is spatially quantified into five categories, from unsuitable to high-suitable with a natural breaks (Jenks) classification method. Subsequently, the final results are validated through a receiver operating characteristics (ROC) curve using randomly selected 56 hazard-exposed location points. The outcome revealed that 8.45% of the riparian area falls under unsuitable, 21.87% under low-suitable, and 33.27% under moderate-suitable for locating human settlements. The generally suitable and high-suitable categories account for 36.40% of the total study zone. A spatial sensitivity analysis is also applied to gauge the influence of each parameter on the MCDM outcomes. The SSZ mapping results from this study can help local authorities to plan for sustainable settlement development in environmentally fragile areas.},
}
@article {pmid37082718,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Mulley, JF and , },
title = {The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {66},
pmid = {37082718},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Apotomis betuletana (the Birch Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 684 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,717 protein coding genes.},
}
@article {pmid37078321,
year = {2023},
author = {Shu, CB and Shen, YL and Liu, G and Zhang, Q and Xu, JH and Guo, Z},
title = {Impacts of Eucalyptus plantation on soil and water losses in a typical small watershed in mountainous area of southern China.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {34},
number = {4},
pages = {1015-1023},
doi = {10.13287/j.1001-9332.202304.021},
pmid = {37078321},
issn = {1001-9332},
mesh = {*Soil ; *Eucalyptus ; Geographic Information Systems ; Forests ; China ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; },
abstract = {Unreasonable exploitation of artificial forest causes severe soil erosion in the mountainous areas of sou-thern China. The spatial-temporal variations of soil erosion in typical small watershed with artificial forest has signifi-cant implications for artificial forest exploitation and sustainable development of mountainous ecological environment. In this study, we used revised universal soil loss equation (RUSLE) and geographic information system (GIS) to evaluate the spatial and temporal variations of soil erosion and its key drivers of Dadingshan watershed in mountainous area of western Guangdong. The results showed that the erosion modulus was 1948.1 t·km[-2]·a[-1] (belonging to light erosion) in the Dadingshan watershed. However, the spatial variation of soil erosion was substantial, with variation coefficient of 5.12. The maximal soil erosion modulus was 191127 t·km[-2]·a[-1]. Slight erosion (<500 t·km[-2]·a[-1]) accounted for 80.6% of the total watershed area. The moderate erosion and above (>2500 t·km[-2]·a[-1]) were mainly distributed in young Eucalyptus forest area with less than 30% of the vegetation coverage, which contributed nearly 75.7% of total soil erosion. During 2014-2019, the interannual variations of mean erosion of Dadingshan catchment was modest, but the spatial variation of soil erosion was large. Vegetation cover, slope, and rainfall were key drivers of such variation. The destruction of natural vegetation resulted by plantation exploitation was the primary cause of soil erosion in afforestation areas. Soil erosion significantly increased with the increases of slope gradient in the young forest area, which was aggravated by extreme rainfall. However, soil erosion gradually decreased with the increases of the age of Eucalypt plantation. Therefore, the hot spot of soil erosion was young forest areas of Eucalypt plantation with slope >25°, and the key period for soil erosion control was the first 2-3 years after Eucalyptus planting. We suggested that reasonable afforestation measures should be used in area with >25° slopes, and that the destruction of natural vegetation should be avoided on hillslope with >35° slope gradient. The road construction standards and forest management should be further improved to address the challenge of extreme rainfalls.},
}
@article {pmid37076812,
year = {2023},
author = {De Wolfe, TJ and Wright, ES},
title = {Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {107},
pmid = {37076812},
issn = {1471-2180},
support = {T15 LM007059/LM/NLM NIH HHS/United States ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.<br><br>RESULTS: Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an&#xa0;increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).<br><br>CONCLUSIONS: Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.},
}
@article {pmid37076624,
year = {2023},
author = {Klein, B and Ogbunugafor, CB and Schafer, BJ and Bhadricha, Z and Kori, P and Sheldon, J and Kaza, N and Sharma, A and Wang, EA and Eliassi-Rad, T and Scarpino, SV and Hinton, E},
title = {COVID-19 amplified racial disparities in the US criminal legal system.},
journal = {Nature},
volume = {617},
number = {7960},
pages = {344-350},
pmid = {37076624},
issn = {1476-4687},
support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Black or African American/legislation &amp; jurisprudence/statistics &amp; numerical data ; *COVID-19/epidemiology ; *Criminals/legislation &amp; jurisprudence/statistics &amp; numerical data ; *Prisoners/legislation &amp; jurisprudence/statistics &amp; numerical data ; United States/epidemiology ; White/legislation &amp; jurisprudence/statistics &amp; numerical data ; Datasets as Topic ; Hispanic or Latino/legislation &amp; jurisprudence/statistics &amp; numerical data ; *Racial Groups/legislation &amp; jurisprudence/statistics &amp; numerical data ; },
abstract = {The criminal legal system in the USA drives an incarceration rate that is the highest on the planet, with disparities by class and race among its signature features[1-3]. During the first year of the coronavirus disease 2019 (COVID-19) pandemic, the number of incarcerated people in the USA decreased by at least 17%-the largest, fastest reduction in prison population in American history[4]. Here we ask how this reduction influenced the racial composition of US prisons and consider possible mechanisms for these dynamics. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from the decrease in the US prison population and that the fraction of incarcerated Black and Latino people sharply increased. This pattern of increased racial disparity exists across prison systems in nearly every state and reverses a decade-long trend before 2020 and the onset of COVID-19, when the proportion of incarcerated white people was increasing amid declining numbers of incarcerated Black people[5]. Although a variety of factors underlie these trends, we find that racial inequities in average sentence length are a major contributor. Ultimately, this study reveals how disruptions caused by COVID-19 exacerbated racial inequalities in the criminal legal system, and highlights key forces that sustain mass incarceration. To advance opportunities for data-driven social science, we publicly released the data associated with this study at Zenodo[6].},
}
@article {pmid37075104,
year = {2023},
author = {Skirgård, H and Haynie, HJ and Blasi, DE and Hammarström, H and Collins, J and Latarche, JJ and Lesage, J and Weber, T and Witzlack-Makarevich, A and Passmore, S and Chira, A and Maurits, L and Dinnage, R and Dunn, M and Reesink, G and Singer, R and Bowern, C and Epps, P and Hill, J and Vesakoski, O and Robbeets, M and Abbas, NK and Auer, D and Bakker, NA and Barbos, G and Borges, RD and Danielsen, S and Dorenbusch, L and Dorn, E and Elliott, J and Falcone, G and Fischer, J and Ghanggo Ate, Y and Gibson, H and Göbel, HP and Goodall, JA and Gruner, V and Harvey, A and Hayes, R and Heer, L and Herrera Miranda, RE and Hübler, N and Huntington-Rainey, B and Ivani, JK and Johns, M and Just, E and Kashima, E and Kipf, C and Klingenberg, JV and König, N and Koti, A and Kowalik, RGA and Krasnoukhova, O and Lindvall, NLM and Lorenzen, M and Lutzenberger, H and Martins, TRA and Mata German, C and van der Meer, S and Montoya Samamé, J and Müller, M and Muradoglu, S and Neely, K and Nickel, J and Norvik, M and Oluoch, CA and Peacock, J and Pearey, IOC and Peck, N and Petit, S and Pieper, S and Poblete, M and Prestipino, D and Raabe, L and Raja, A and Reimringer, J and Rey, SC and Rizaew, J and Ruppert, E and Salmon, KK and Sammet, J and Schembri, R and Schlabbach, L and Schmidt, FWP and Skilton, A and Smith, WD and de Sousa, H and Sverredal, K and Valle, D and Vera, J and Voß, J and Witte, T and Wu, H and Yam, S and Ye, J and Yong, M and Yuditha, T and Zariquiey, R and Forkel, R and Evans, N and Levinson, SC and Haspelmath, M and Greenhill, SJ and Atkinson, QD and Gray, RD},
title = {Grambank reveals the importance of genealogical constraints on linguistic diversity and highlights the impact of language loss.},
journal = {Science advances},
volume = {9},
number = {16},
pages = {eadg6175},
pmid = {37075104},
issn = {2375-2548},
mesh = {Humans ; *Language ; *Linguistics ; Cognition ; Databases, Factual ; },
abstract = {While global patterns of human genetic diversity are increasingly well characterized, the diversity of human languages remains less systematically described. Here, we outline the Grambank database. With over 400,000 data points and 2400 languages, Grambank is the largest comparative grammatical database available. The comprehensiveness of Grambank allows us to quantify the relative effects of genealogical inheritance and geographic proximity on the structural diversity of the world's languages, evaluate constraints on linguistic diversity, and identify the world's most unusual languages. An analysis of the consequences of language loss reveals that the reduction in diversity will be strikingly uneven across the major linguistic regions of the world. Without sustained efforts to document and revitalize endangered languages, our linguistic window into human history, cognition, and culture will be seriously fragmented.},
}
@article {pmid37072018,
year = {2023},
author = {Jackson, C and Stewart, ID and Plekhanova, T and Cunningham, PS and Hazel, AL and Al-Sheklly, B and Aul, R and Bolton, CE and Chalder, T and Chalmers, JD and Chaudhuri, N and Docherty, AB and Donaldson, G and Edwardson, CL and Elneima, O and Greening, NJ and Hanley, NA and Harris, VC and Harrison, EM and Ho, LP and Houchen-Wolloff, L and Howard, LS and Jolley, CJ and Jones, MG and Leavy, OC and Lewis, KE and Lone, NI and Marks, M and McAuley, HJC and McNarry, MA and Patel, BV and Piper-Hanley, K and Poinasamy, K and Raman, B and Richardson, M and Rivera-Ortega, P and Rowland-Jones, SL and Rowlands, AV and Saunders, RM and Scott, JT and Sereno, M and Shah, AM and Shikotra, A and Singapuri, A and Stanel, SC and Thorpe, M and Wootton, DG and Yates, T and Gisli Jenkins, R and Singh, SJ and Man, WD and Brightling, CE and Wain, LV and Porter, JC and Thompson, AAR and Horsley, A and Molyneaux, PL and Evans, RA and Jones, SE and Rutter, MK and Blaikley, JF and , },
title = {Effects of sleep disturbance on dyspnoea and impaired lung function following hospital admission due to COVID-19 in the UK: a prospective multicentre cohort study.},
journal = {The Lancet. Respiratory medicine},
volume = {11},
number = {8},
pages = {673-684},
pmid = {37072018},
issn = {2213-2619},
support = {209553/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MR/M008894/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20060/MRC_/Medical Research Council/United Kingdom ; 206330/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MR/T032529/1/MRC_/Medical Research Council/United Kingdom ; SP/17/16/33519/BHF_/British Heart Foundation/United Kingdom ; RE/18/3/34214/BHF_/British Heart Foundation/United Kingdom ; FS/18/13/33281/BHF_/British Heart Foundation/United Kingdom ; MC_UU_00034/6/MRC_/Medical Research Council/United Kingdom ; COV0319/DH_/Department of Health/United Kingdom ; NIHR300669/DH_/Department of Health/United Kingdom ; MC_PC_20031/MRC_/Medical Research Council/United Kingdom ; MR/S004041/1/MRC_/Medical Research Council/United Kingdom ; RP-2017-08-ST2-014/DH_/Department of Health/United Kingdom ; MR/V027859/1/MRC_/Medical Research Council/United Kingdom ; CH/16/1/32013/BHF_/British Heart Foundation/United Kingdom ; 216606/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MR/W006111/1/MRC_/Medical Research Council/United Kingdom ; NIHR203308/DH_/Department of Health/United Kingdom ; MR/V040162/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *COVID-19/complications/epidemiology ; Prospective Studies ; Hospitalization ; *Sleep Wake Disorders/epidemiology/etiology ; Sleep/physiology ; Hospitals ; United Kingdom/epidemiology ; Lung ; },
abstract = {BACKGROUND: Sleep disturbance is common following hospital admission both for COVID-19 and other causes. The clinical associations of this for recovery after hospital admission are poorly understood despite sleep disturbance contributing to morbidity in other scenarios. We aimed to investigate the prevalence and nature of sleep disturbance after discharge following hospital admission for COVID-19 and to assess whether this was associated with dyspnoea.<br><br>METHODS: CircCOVID was a prospective multicentre cohort substudy designed to investigate the effects of circadian disruption and sleep disturbance on recovery after COVID-19 in a cohort of participants aged 18 years or older, admitted to hospital for COVID-19 in the UK, and discharged between March, 2020, and October, 2021. Participants were recruited from the Post-hospitalisation COVID-19 study (PHOSP-COVID). Follow-up data were collected at two timepoints: an early time point 2-7 months after hospital discharge and a later time point 10-14 months after hospital discharge. Sleep quality was assessed subjectively using the Pittsburgh Sleep Quality Index questionnaire and a numerical rating scale. Sleep quality was also assessed with an accelerometer worn on the wrist (actigraphy) for 14 days. Participants were also clinically phenotyped, including assessment of symptoms (ie, anxiety [Generalised Anxiety Disorder 7-item scale questionnaire], muscle function [SARC-F questionnaire], dyspnoea [Dyspnoea-12 questionnaire] and measurement of lung function), at the early timepoint after discharge. Actigraphy results were also compared to a matched UK Biobank cohort (non-hospitalised individuals and recently hospitalised individuals). Multivariable linear regression was used to define associations of sleep disturbance with the primary outcome of breathlessness and the other clinical symptoms. PHOSP-COVID is registered on the ISRCTN Registry (ISRCTN10980107).<br><br>FINDINGS: 2320 of 2468 participants in the PHOSP-COVID study attended an early timepoint research visit a median of 5 months (IQR 4-6) following discharge from 83 hospitals in the UK. Data for sleep quality were assessed by subjective measures (the Pittsburgh Sleep Quality Index questionnaire and the numerical rating scale) for 638 participants at the early time point. Sleep quality was also assessed using device-based measures (actigraphy) a median of 7 months (IQR 5-8 months) after discharge from hospital for 729 participants. After discharge from hospital, the majority (396 [62%] of 638) of participants who had been admitted to hospital for COVID-19 reported poor sleep quality in response to the Pittsburgh Sleep Quality Index questionnaire. A comparable proportion (338 [53%] of 638) of participants felt their sleep quality had deteriorated following discharge after COVID-19 admission, as assessed by the numerical rating scale. Device-based measurements were compared to an age-matched, sex-matched, BMI-matched, and time from discharge-matched UK Biobank cohort who had recently been admitted to hospital. Compared to the recently hospitalised matched UK Biobank cohort, participants in our study slept on average 65 min (95% CI 59 to 71) longer, had a lower sleep regularity index (-19%; 95% CI -20 to -16), and a lower sleep efficiency (3&#xb7;83 percentage points; 95% CI 3&#xb7;40 to 4&#xb7;26). Similar results were obtained when comparisons were made with the non-hospitalised UK Biobank cohort. Overall sleep quality (unadjusted effect estimate 3&#xb7;94; 95% CI 2&#xb7;78 to 5&#xb7;10), deterioration in sleep quality following hospital admission (3&#xb7;00; 1&#xb7;82 to 4&#xb7;28), and sleep regularity (4&#xb7;38; 2&#xb7;10 to 6&#xb7;65) were associated with higher dyspnoea scores. Poor sleep quality, deterioration in sleep quality, and sleep regularity were also associated with impaired lung function, as assessed by forced vital capacity. Depending on the sleep metric, anxiety mediated 18-39% of the effect of sleep disturbance on dyspnoea, while muscle weakness mediated 27-41% of this effect.<br><br>INTERPRETATION: Sleep disturbance following hospital admission for COVID-19 is associated with dyspnoea, anxiety, and muscle weakness. Due to the association with multiple symptoms, targeting sleep disturbance might be beneficial in treating the post-COVID-19 condition.<br><br>FUNDING: UK Research and Innovation, National Institute for Health Research, and Engineering and Physical Sciences Research Council.},
}
@article {pmid37069545,
year = {2023},
author = {Cai, P and Liu, S and Zhang, D and Xing, H and Han, M and Liu, D and Gong, L and Hu, QN},
title = {SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.},
journal = {BMC bioinformatics},
volume = {24},
number = {1},
pages = {152},
pmid = {37069545},
issn = {1471-2105},
support = {2021YFC2103001, 2019YFA0904300//National Key Research and Development Program of China/ ; 2021YFC2103001, 2019YFA0904300//National Key Research and Development Program of China/ ; 153D31KYSB20170121//International Partnership Program of the Chinese Academy of Sciences of China/ ; },
mesh = {*Synthetic Biology ; *Computational Biology/methods ; Registries ; Databases, Factual ; Software ; },
abstract = {BACKGROUND: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology.<br><br>RESULTS: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system.<br><br>CONCLUSIONS: SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.},
}
@article {pmid37069271,
year = {2023},
author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H},
title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.},
journal = {Nature methods},
volume = {20},
number = {6},
pages = {824-835},
pmid = {37069271},
issn = {1548-7105},
support = {R01 EY031597/EY/NEI NIH HHS/United States ; MC_U105188491/MRC_/Medical Research Council/United Kingdom ; RF1 MH128693/MH/NIMH NIH HHS/United States ; R01 EY011261/EY/NEI NIH HHS/United States ; R01 EY027437/EY/NEI NIH HHS/United States ; },
mesh = {*Benchmarking ; *Microscopy/methods ; Imaging, Three-Dimensional/methods ; Neurons/physiology ; Algorithms ; },
abstract = {BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.},
}
@article {pmid37060443,
year = {2023},
author = {Weinstein, ES and Cuthbertson, JL and Herbert, TL and Voicescu, GT and Bortolin, M and Magalini, S and Gui, D and Helou, M and Lennquist Montan, K and Montan, C and Rafalowsky, C and Ratto, G and Damele, S and Bazurro, S and Laist, I and Marzi, F and Borrello, A and Fransvea, P and Fidanzio, A and Benitez, CY and Faccincani, R and Ragazzoni, L and Caviglia, M},
title = {Advancing the scientific study of prehospital mass casualty response through a Translational Science process: the T1 scoping literature review stage.},
journal = {European journal of trauma and emergency surgery : official publication of the European Trauma Society},
volume = {49},
number = {4},
pages = {1647-1660},
pmid = {37060443},
issn = {1863-9941},
support = {101021957//European Union Horizon 2020 research and innovation program/ ; },
mesh = {Humans ; *Mass Casualty Incidents ; Translational Science, Biomedical ; Triage ; *Emergency Responders ; Databases, Factual ; },
abstract = {PURPOSE: The European Union Horizon 2020 research and innovation funding program awarded the NIGHTINGALE grant to develop a toolkit to support first responders engaged in prehospital (PH) mass casualty incident (MCI) response. To reach the projects' objectives, the NIGHTINGALE consortium used a Translational Science (TS) process. The present work is the first TS stage (T1) aimed to extract data relevant for the subsequent modified Delphi study (T2) statements.<br><br>METHODS: The authors were divided into three work groups (WGs) MCI Triage, PH Life Support and Damage Control (PHLSDC), and PH Processes (PHP). Each WG conducted simultaneous literature searches following the PRISMA extension for scoping reviews. Relevant data were extracted from the included articles and indexed using pre-identified PH MCI response themes and subthemes.<br><br>RESULTS: The initial search yielded 925 total references to be considered for title and abstract review (MCI Triage 311, PHLSDC 329, PHP 285), then 483 articles for full reference review (MCI Triage 111, PHLSDC 216, PHP 156), and finally 152 articles for the database extraction process (MCI Triage 27, PHLSDC 37, PHP 88). Most frequent subthemes and novel concepts have been identified as a basis for the elaboration of draft statements for the T2 modified Delphi study.<br><br>CONCLUSION: The three simultaneous scoping reviews allowed the extraction of relevant PH MCI subthemes and novel concepts that will enable the NIGHTINGALE consortium to create scientifically anchored statements in the T2 modified Delphi study.},
}
@article {pmid37049742,
year = {2023},
author = {Biswas, P and Bibi, S and Yousafi, Q and Mehmood, A and Saleem, S and Ihsan, A and Dey, D and Hasan Zilani, MN and Hasan, MN and Saleem, R and Awaji, AA and Fahmy, UA and Abdel-Daim, MM},
title = {Study of MDM2 as Prognostic Biomarker in Brain-LGG Cancer and Bioactive Phytochemicals Inhibit the p53-MDM2 Pathway: A Computational Drug Development Approach.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {7},
pages = {},
pmid = {37049742},
issn = {1420-3049},
support = {RG-10-166-43//The Deanship of Scientific Research (DSR) at King Abdulaziz University (KAU), Jeddah, Saudi Arabia/ ; },
mesh = {Humans ; Tumor Suppressor Protein p53/metabolism ; Molecular Docking Simulation ; Proto-Oncogene Proteins c-mdm2/metabolism ; DNA Copy Number Variations ; Prognosis ; *Brain Neoplasms/drug therapy/genetics/metabolism ; *Glioma/drug therapy/genetics/metabolism ; Biomarkers ; Drug Development ; Brain/metabolism ; },
abstract = {An evaluation of the expression and predictive significance of the MDM2 gene in brain lower-grade glioma (LGG) cancer was carried out using onco-informatics pipelines. Several transcriptome servers were used to measure the differential expression of the targeted MDM2 gene and search mutations and copy number variations. GENT2, Gene Expression Profiling Interactive Analysis, Onco-Lnc, and PrognoScan were used to figure out the survival rate of LGG cancer patients. The protein-protein interaction networks between MDM2 gene and its co-expressed genes were constructed by Gene-MANIA tool. Identified bioactive phytochemicals were evaluated through molecular docking using Schrödinger Suite Software, with the MDM2 (PDB ID: 1RV1) target. Protein-ligand interactions were observed with key residues of the macromolecular target. A molecular dynamics simulation of the novel bioactive compounds with the targeted protein was performed. Phytochemicals targeting MDM2 protein, such as Taxifolin and (-)-Epicatechin, have been shown with more highly stable results as compared to the control drug, and hence, concluded that phytochemicals with bioactive potential might be alternative therapeutic options for the management of LGG patients. Our once informatics-based designed pipeline has indicated that the MDM2 gene may have been a predictive biomarker for LGG cancer and selected phytochemicals possessed outstanding interaction results within the macromolecular target's active site after utilizing in silico approaches. In vitro and in vivo experiments are recommended to confirm these outcomes.},
}
@article {pmid37047894,
year = {2023},
author = {Roberts, M and Colley, K and Currie, M and Eastwood, A and Li, KH and Avery, LM and Beevers, LC and Braithwaite, I and Dallimer, M and Davies, ZG and Fisher, HL and Gidlow, CJ and Memon, A and Mudway, IS and Naylor, LA and Reis, S and Smith, P and Stansfeld, SA and Wilkie, S and Irvine, KN},
title = {The Contribution of Environmental Science to Mental Health Research: A Scoping Review.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {7},
pages = {},
pmid = {37047894},
issn = {1660-4601},
support = {/DH_/Department of Health/United Kingdom ; },
mesh = {Humans ; Mental Health ; *COVID-19 ; Pandemics ; *Environmental Science ; Environmental Exposure ; },
abstract = {Mental health is influenced by multiple complex and interacting genetic, psychological, social, and environmental factors. As such, developing state-of-the-art mental health knowledge requires collaboration across academic disciplines, including environmental science. To assess the current contribution of environmental science to this field, a scoping review of the literature on environmental influences on mental health (including conditions of cognitive development and decline) was conducted. The review protocol was developed in consultation with experts working across mental health and environmental science. The scoping review included 202 English-language papers, published between 2010 and 2020 (prior to the COVID-19 pandemic), on environmental themes that had not already been the subject of recent systematic reviews; 26 reviews on climate change, flooding, air pollution, and urban green space were additionally considered. Studies largely focused on populations in the USA, China, or Europe and involved limited environmental science input. Environmental science research methods are primarily focused on quantitative approaches utilising secondary datasets or field data. Mental health measurement was dominated by the use of self-report psychometric scales. Measures of environmental states or exposures were often lacking in specificity (e.g., limited to the presence or absence of an environmental state). Based on the scoping review findings and our synthesis of the recent reviews, a research agenda for environmental science's future contribution to mental health scholarship is set out. This includes recommendations to expand the geographical scope and broaden the representation of different environmental science areas, improve measurement of environmental exposure, prioritise experimental and longitudinal research designs, and giving greater consideration to variation between and within communities and the mediating pathways by which environment influences mental health. There is also considerable opportunity to increase interdisciplinarity within the field via the integration of conceptual models, the inclusion of mixed methods and qualitative approaches, as well as further consideration of the socio-political context and the environmental states that can help support good mental health. The findings were used to propose a conceptual model to parse contributions and connections between environmental science and mental health to inform future studies.},
}
@article {pmid37046168,
year = {2023},
author = {Chen, D and Feng, Q and Zhang, Y},
title = {Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {23},
pages = {63603-63619},
pmid = {37046168},
issn = {1614-7499},
support = {2020YFC1806501//Key Technologies Research and Development Program/ ; 41977159//National Natural Science Foundation of China/ ; },
mesh = {*Iron/analysis ; *Coal/analysis ; Environmental Pollution/analysis ; Soil/chemistry ; Sulfur/analysis ; China ; },
abstract = {In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.},
}
@article {pmid37043542,
year = {2023},
author = {Labbé, F and Abdeladhim, M and Abrudan, J and Araki, AS and Araujo, RN and Arensburger, P and Benoit, JB and Brazil, RP and Bruno, RV and Bueno da Silva Rivas, G and Carvalho de Abreu, V and Charamis, J and Coutinho-Abreu, IV and da Costa-Latgé, SG and Darby, A and Dillon, VM and Emrich, SJ and Fernandez-Medina, D and Figueiredo Gontijo, N and Flanley, CM and Gatherer, D and Genta, FA and Gesing, S and Giraldo-Calderón, GI and Gomes, B and Aguiar, ERGR and Hamilton, JGC and Hamarsheh, O and Hawksworth, M and Hendershot, JM and Hickner, PV and Imler, JL and Ioannidis, P and Jennings, EC and Kamhawi, S and Karageorgiou, C and Kennedy, RC and Krueger, A and Latorre-Estivalis, JM and Ligoxygakis, P and Meireles-Filho, ACA and Minx, P and Miranda, JC and Montague, MJ and Nowling, RJ and Oliveira, F and Ortigão-Farias, J and Pavan, MG and Horacio Pereira, M and Nobrega Pitaluga, A and Proveti Olmo, R and Ramalho-Ortigao, M and Ribeiro, JMC and Rosendale, AJ and Sant'Anna, MRV and Scherer, SE and Secundino, NFC and Shoue, DA and da Silva Moraes, C and Gesto, JSM and Souza, NA and Syed, Z and Tadros, S and Teles-de-Freitas, R and Telleria, EL and Tomlinson, C and Traub-Csekö, YM and Marques, JT and Tu, Z and Unger, MF and Valenzuela, J and Ferreira, FV and de Oliveira, KPV and Vigoder, FM and Vontas, J and Wang, L and Weedall, GD and Zhioua, E and Richards, S and Warren, WC and Waterhouse, RM and Dillon, RJ and McDowell, MA},
title = {Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World.},
journal = {PLoS neglected tropical diseases},
volume = {17},
number = {4},
pages = {e0010862},
pmid = {37043542},
issn = {1935-2735},
support = {U54 HG003079/HG/NHGRI NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Phlebotomus/parasitology ; *Psychodidae/parasitology ; *Leishmania/genetics ; *Leishmaniasis, Cutaneous ; Genomics ; },
abstract = {Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.},
}
@article {pmid37040629,
year = {2023},
author = {Beauchamp, AM and Lehmann, CU and Medford, RJ and Hughes, AE},
title = {Correction: The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.},
journal = {Journal of medical Internet research},
volume = {25},
number = {},
pages = {e47896},
doi = {10.2196/47896},
pmid = {37040629},
issn = {1438-8871},
abstract = {[This corrects the article DOI: 10.2196/43623.].},
}
@article {pmid37025368,
year = {2022},
author = {Lohse, K and Höök, L and Näsvall, K and Backström, N and , and , and , and , },
title = {The genome sequence of the wood white butterfly, Leptidea sinapis (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {254},
pmid = {37025368},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Leptidea sinapis (the wood white; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 686 megabases in span. The majority (99.99%) of the assembly is scaffolded into 48 chromosomal pseudomolecules, with three Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 14,800 protein coding genes.},
}
@article {pmid37022698,
year = {2023},
author = {Nartker, M and Zhou, Z and Firestone, C},
title = {When will AI misclassify? Intuiting failures on natural images.},
journal = {Journal of vision},
volume = {23},
number = {4},
pages = {4},
pmid = {37022698},
issn = {1534-7362},
mesh = {Humans ; *Artificial Intelligence ; *Image Interpretation, Computer-Assisted ; },
abstract = {Machine recognition systems now rival humans in their ability to classify natural images. However, their success is accompanied by a striking failure: a tendency to commit bizarre misclassifications on inputs specifically selected to fool them. What do ordinary people know about the nature and prevalence of such classification errors? Here, five experiments exploit the recent discovery of "natural adversarial examples" to ask whether naive observers can predict when and how machines will misclassify natural images. Whereas classical adversarial examples are inputs that have been minimally perturbed to induce misclassifications, natural adversarial examples are simply unmodified natural photographs that consistently fool a wide variety of machine recognition systems. For example, a bird casting a shadow might be misclassified as a sundial, or a beach umbrella made of straw might be misclassified as a broom. In Experiment 1, subjects accurately predicted which natural images machines would misclassify and which they would not. Experiments 2 through 4 extended this ability to how the images would be misclassified, showing that anticipating machine misclassifications goes beyond merely identifying an image as nonprototypical. Finally, Experiment 5 replicated these findings under more ecologically valid conditions, demonstrating that subjects can anticipate misclassifications not only under two-alternative forced-choice conditions (as in Experiments 1-4), but also when the images appear one at a time in a continuous stream-a skill that may be of value to human-machine teams. We suggest that ordinary people can intuit how easy or hard a natural image is to classify, and we discuss the implications of these results for practical and theoretical issues at the interface of biological and artificial vision.},
}
@article {pmid37022232,
year = {2023},
author = {Zimmerman, S and Tierney, BT and Patel, CJ and Kostic, AD},
title = {Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.},
journal = {mSystems},
volume = {8},
number = {2},
pages = {e0011823},
pmid = {37022232},
issn = {2379-5077},
support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; R01 ES032470/ES/NIEHS NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; },
abstract = {Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.},
}
@article {pmid37021385,
year = {2023},
author = {Riva, F and Fahrig, L},
title = {Obstruction of biodiversity conservation by minimum patch size criteria.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {37},
number = {5},
pages = {e14092},
doi = {10.1111/cobi.14092},
pmid = {37021385},
issn = {1523-1739},
mesh = {*Conservation of Natural Resources ; *Biodiversity ; Ecosystem ; Databases, Factual ; },
abstract = {Minimum patch size criteria for habitat protection reflect the conservation principle that a single large (SL) patch of habitat has higher biodiversity than several small (SS) patches of the same total area (SL > SS). Nonetheless, this principle is often incorrect, and biodiversity conservation requires placing more emphasis on protection of large numbers of small patches (SS > SL). We used a global database reporting the abundances of species across hundreds of patches to assess the SL > SS principle in systems where small patches are much smaller than the typical minimum patch size criteria applied for biodiversity conservation (i.e., ∼85% of patches <100 ha). The 76 metacommunities we examined included 4401 species in 1190 patches. From each metacommunity, we resampled species-area accumulation curves to evaluate how biodiversity responded to habitat existing as a few large patches or as many small patches. Counter to the SL > SS principle and consistent with previous syntheses, species richness accumulated more rapidly when adding several small patches (45.2% SS > SL vs. 19.9% SL > SS) to reach the same cumulative area, even for the very small patches in our data set. Responses of taxa to habitat fragmentation differed, which suggests that when a given total area of habitat is to be protected, overall biodiversity conservation will be most effective if that habitat is composed of as many small patches as possible, plus a few large ones. Because minimum patch size criteria often require larger patches than the small patches we examined, our results suggest that such criteria hinder efforts to protect biodiversity.},
}
@article {pmid37021064,
year = {2023},
author = {Keller, R and Spanu, A and Puhan, MA and Flahault, A and Lovis, C and Mütsch, M and Beau-Lejdstrom, R},
title = {Social media and internet search data to inform drug utilization: A systematic scoping review.},
journal = {Frontiers in digital health},
volume = {5},
number = {},
pages = {1074961},
pmid = {37021064},
issn = {2673-253X},
abstract = {INTRODUCTION: Drug utilization is currently assessed through traditional data sources such as big electronic medical records (EMRs) databases, surveys, and medication sales. Social media and internet data have been reported to provide more accessible and more timely access to medications' utilization.<br><br>OBJECTIVE: This review aims at providing evidence comparing web data on drug utilization to other sources before the COVID-19 pandemic.<br><br>METHODS: We searched Medline, EMBASE, Web of Science, and Scopus until November 25th, 2019, using a predefined search strategy. Two independent reviewers conducted screening and data extraction.<br><br>RESULTS: Of 6,563 (64%) deduplicated publications retrieved, 14 (0.2%) were included. All studies showed positive associations between drug utilization information from web and comparison data using very different methods. A total of nine (64%) studies found positive linear correlations in drug utilization between web and comparison data. Five studies reported association using other methods: One study reported similar drug popularity rankings using both data sources. Two studies developed prediction models for future drug consumption, including both web and comparison data, and two studies conducted ecological analyses but did not quantitatively compare data sources. According to the STROBE, RECORD, and RECORD-PE checklists, overall reporting quality was mediocre. Many items were left blank as they were out of scope for the type of study investigated.<br><br>CONCLUSION: Our results demonstrate the potential of web data for assessing drug utilization, although the field is still in a nascent period of investigation. Ultimately, social media and internet search data could be used to get a quick preliminary quantification of drug use in real time. Additional studies on the topic should use more standardized methodologies on different sets of drugs in order to confirm these findings. In addition, currently available checklists for study quality of reporting would need to be adapted to these new sources of scientific information.},
}
@article {pmid37018807,
year = {2023},
author = {Xavier, JMA and Firmino, RT and Pereira, IF and Xavier, MA and Costa, MCFD and Soares, RSC and Ribeiro, AIAM},
title = {The impact of the COVID-19 pandemic in Brazil: a study in tertiary dental care.},
journal = {Brazilian oral research},
volume = {37},
number = {},
pages = {025},
doi = {10.1590/1807-3107bor-2023.vol37.0025},
pmid = {37018807},
issn = {1807-3107},
mesh = {Humans ; *COVID-19 ; Pandemics ; Tertiary Healthcare ; Brazil ; Dental Care ; },
abstract = {The pandemic caused by coronavirus has resonated throughout different levels of health care in Brazil and, in this context, the present research aimed to evaluate this impact on tertiary dental care provided by the Unified Health System (SUS). Therefore, an ecological study was conducted with data obtained from the Hospital Information System processed by the Portal of the Department of Informatics of SUS. The sample consisted of patients of all sexes and age groups, whose Hospital Admission Authorizations (AIHs) were approved for dental tertiary care procedures from January 2015 to December 2020. Descriptive analyses and the ANOVA test with a significance level set at p < 0.05 were used. When the annual mean numbers of AIHs approved were evaluated, findings showed that on an average, the Southeast region authorized a higher number of procedures (p-value < 0.001), however, in the pandemic year (2020), a reduction of approximately 24.5% of these hospitalizations occurred throughout Brazil, with the Midwest being the region most affected (32.12%). A percentage increase occurred in the Surgical Treatment of Oral sinus/Oral nasal Fistula (16.1%), in addition to a significant decrease in performing procedures for Resection of Mouth Lesion (33.4%). In the pandemic year, there was a reduction of 14% in expenditures related to hospital services and 23.26% related to professional services. It was concluded that the data presented demonstrated a significant reduction in AIHs for tertiary dental care in the pandemic year.},
}
@article {pmid37016902,
year = {2025},
author = {Pandit, AA and Mahashabde, RV and Brown, CC and Acharya, M and Shoults, CC and Eswaran, H and Hayes, CJ},
title = {Association between broadband capacity and telehealth utilization among Medicare Fee-for-service beneficiaries during the COVID-19 pandemic.},
journal = {Journal of telemedicine and telecare},
volume = {31},
number = {1},
pages = {41-48},
pmid = {37016902},
issn = {1758-1109},
mesh = {Humans ; *COVID-19/epidemiology ; United States ; *Telemedicine/statistics &amp; numerical data ; *Medicare/statistics &amp; numerical data ; *Fee-for-Service Plans/statistics &amp; numerical data ; Cross-Sectional Studies ; Health Services Accessibility/statistics &amp; numerical data ; SARS-CoV-2 ; Aged ; Female ; Male ; Pandemics ; Patient Acceptance of Health Care/statistics &amp; numerical data ; },
abstract = {BACKGROUND: Telehealth is a rapidly growing modality for expanding healthcare access, especially in the post-COVID-19 era. However, telehealth requires high-quality broadband, thus making broadband a social determinant of health. The objective of this study was to evaluate the association between broadband access and telehealth utilization across the United States during the COVID-19 pandemic.<br><br>METHODS: Using a cross-sectional, ecological study design, we merged county-level data on broadband capacity (Microsoft's Rural Broadband Initiative), telehealth utilization among Medicare Fee-for-Service beneficiaries from January through September 2020 (CareJourney), and county-level socioeconomic characteristics (Area Health Resources Files). Multivariable linear regression was used to estimate the association between broadband capacity, county-level characteristics, and telehealth utilization.<br><br>RESULTS: Among the 3107 counties, those with the greatest broadband availability (quintile 5) had 47% higher telehealth utilization compared to counties with the least broadband availability (quintile 1). In the adjusted model, a 1 standard deviation (SD) increase in broadband access was associated with a 1.54 percentage point (pp) increase in telehealth utilization (P&#x2009;<&#x2009;0.001). Rural county designation (-1.96 pp; P&#x2009;<&#x2009;0.001) and 1 SD increases in average Medicare beneficiary age (-1.34 pp; P&#x2009;=&#x2009;0.001), number of nursing home beds per 1000 individuals (-0.38 pp; P&#x2009;=&#x2009;0.002), and proportion of Native Americans/Pacific Islanders (-0.59 pp; P&#x2009;<&#x2009;0.001) were associated with decreased telehealth utilization.<br><br>CONCLUSION: The association between broadband access and telehealth utilization and the decreased telehealth utilization in rural areas highlight the importance of broadband access for healthcare access and the need to continue investing in broadband infrastructure to promote equitable healthcare access across populations.},
}
@article {pmid37011221,
year = {2023},
author = {Still, CJ and Page, GFM and Rastogi, B and Griffith, DM and Aubrecht, DM and Kim, Y and Burns, SP and Hanson, CV and Kwon, H and Hawkins, L and Meinzer, FC and Sevanto, S and Roberts, DA and Goulden, M and Pau, S and Detto, M and Helliker, BR and Richardson, AD},
title = {Reply to Garen et al.: Within-canopy temperature data also do not support limited homeothermy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {15},
pages = {e2302515120},
pmid = {37011221},
issn = {1091-6490},
mesh = {Temperature ; *Body Temperature Regulation ; },
}
@article {pmid37010606,
year = {2023},
author = {Chaves, T and Azevedo, &#xc1; and Caldas, IM},
title = {Are lip prints hereditary? A systematic review.},
journal = {International journal of legal medicine},
volume = {137},
number = {4},
pages = {1203-1214},
pmid = {37010606},
issn = {1437-1596},
support = {UIDB/04004/2020//FCT/MCTES/ ; },
mesh = {Child ; Humans ; *Lip ; *Parents ; Bibliometrics ; Databases, Factual ; },
abstract = {Hereditary lip prints have been studied by several researchers. However, the literature shows no consensus among the scientific community regarding this topic. Therefore, the aim of this study was to conduct a systematic review to gather evidence to clarify whether the surface structure of lip prints is hereditary and, consequently, if a familial relationship between individuals can be established through the analysis of lip prints. The systematic review was performed following the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines. A bibliographic survey was conducted in PubMed, Scopus, and Web of Science databases, restricted to articles published between 2010 and 2020. Studies were selected according to eligibility criteria, and then the study data were collected. The risk of bias of each study was assessed and applied as additional inclusion or exclusion criteria. The results of the articles eligible for analysis were synthesized by a descriptive approach. In the seven included studies, methodological variations, including the definition of similarity, that contribute to the heterogeneity of results were identified. The data gathered allowed to conclude that there is no strong scientific evidence to support the hypothesis of the existence of heredity in the surface structure of lip prints, since it was not proven that similarities between parents and children occur systematically in all families.},
}
@article {pmid37008251,
year = {2022},
author = {Boyes, D and Wright, C and , and , and , and , and , and , },
title = {The genome sequence of the peppered moth, Biston betularia Linnaeus, 1758.},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {97},
pmid = {37008251},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Biston betularia (the peppered moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 405 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.Gene annotation of this assembly on Ensembl has identified 12,251 protein coding genes.},
}
@article {pmid37006240,
year = {2023},
author = {Yang, W and Wei, C and Cheng, J and Ding, R and Li, Y and Wang, Y and Yang, Y and Wang, J},
title = {BTG2 and SerpinB5, a novel gene pair to evaluate the prognosis of lung adenocarcinoma.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1098700},
pmid = {37006240},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; Molecular Docking Simulation ; *Lung Neoplasms/genetics ; *Adenocarcinoma of Lung/genetics ; Prognosis ; Tumor Microenvironment ; *Immediate-Early Proteins/genetics ; Tumor Suppressor Proteins/genetics ; },
abstract = {INTRODUCTION: Lung adenocarcinoma (LUAD), as the most frequent pathological subtype of non-small cell lung cancer, is often characterized by poor prognosis and low 5-year survival rate. Exploriton of new biomarkers and accurate molecular mechanisms for effectively predicting the prognosis of LUAD patients is still necessary. Presently, BTG2 and SerpinB5, which play important roles in tumors, are studied as a gene pair for the first time with the aim of exploring whether they can be used as potential prognostic markers.<br><br>METHODS: Using the bioinformatics method to explore whether BTG2 and SerpinB5 can become independent prognostic factors, and explore their clinical application value and whether they can be used as immunotherapeutic markers. In addition, we also verify the conclusions obtained from external datasets, molecular docking, and SqRT-PCR.<br><br>RESULTS: The results show that compared with normal lung tissue, BTG2 expression level was down-regulated and SerpinB5 was up-regulated in LUAD. Additionally, Kaplan-Meier survival analysis demonstrate that the prognosis of low expression level of BTG2 was poor, and that of high expression level of SerpinB5 was poor, suggesting that both of them can be used as independent prognostic factors. Moreover, the prognosis models of the two genes were constructed respectively in this study, and their prediction effect was verified by external data. Besides, ESTIMATE algorithm reveals the relationship between this gene pair and the immune microenvironment. Furthermore, patients with a high expression level of BTG2 and a low expression level of SerpinB5 have higher immunophenoscore for CTLA-4 and PD-1 inhibitors than patients with a low expression level of BTG2 and a high expression level of SerpinB5, indicating that such patients have a more obvious effect of immunotherapy.<br><br>DISCUSSION: Collectively, all the results demonstrate that BTG2 and SerpinB5 might serve as potential prognostic biomarkers and novel therapeutic targets for LUAD.},
}
@article {pmid37004043,
year = {2023},
author = {Khan, AH and Adil, M and Aziz, MA and Sõukand, R and Pieroni, A},
title = {Traditional foraging for ecological transition? Wild food ethnobotany among three ethnic groups in the highlands of the eastern Hindukush, North Pakistan.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {19},
number = {1},
pages = {9},
pmid = {37004043},
issn = {1746-4269},
mesh = {Humans ; *Ethnobotany ; Pakistan ; Ethnicity ; Plants, Edible ; *Plants, Medicinal ; },
abstract = {BACKGROUND: The Patrak Valley is home to communities, which have been inextricably linked with nature for generations, and local plant knowledge (LPK) represents an important part of their local cultural diversity. In general, globalization has come at the expense of local plant knowledge among several mountain societies, and therefore the current investigation has been undertaken to record the (possibly) last remaining wild food plant/mushroom foraging practices among Pathans, Kohistanis, and Gujjars living in the highlands of the Hindukush, North Pakistan.<br><br>METHODS: Data on the uses of wild food plants and mushrooms (WFPs) were collected through 120 semi-structured interviews. The data were cross-culturally compared among the three linguistic groups. Venn diagrams were used to visualize the comparative analysis. To determine the patterns of similarities in plant use among the different ethnic groups, we used the Jaccard similarity index (JI). The recorded data were also compared with the existing Pakistani food ethnobotanical literature.<br><br>RESULTS: A total of 68 WFPs were recorded, the majority of which were used as raw snacks and as cooked vegetables. Fruit was the most frequently reported plant part among the three researched groups. Cross-cultural comparison revealed that 37% of the used plants were commonly shared by the three studied groups. Pathans have retained rich knowledge on WFPs, and they show a comparatively closer affinity with Kohistanis is the use of WFPs compared to Gujjars. While we observed some idiosyncrasies for each of the researched groups, the distinctive plant uses among Gujjars provide insight into their food ecology, their particular human-ecological system centered on mobile pastoralism and their limited exchanges of local food/ecological knowledge due to endogamic patterns. A literature survey revealed some novel or little-known ingredients within Pakistani food ethnobotany/ethnomycology, such as Aesculus indica, Agaricus campestris, Apteranthes tuberculata, Duchesnea indica, Equisetum arvense, Eremurus himalaicus, Isodon rugosus, Morella esculenta, Sophora mollis, and Drimia indica.<br><br>CONCLUSION: The researched communities have retained important plant knowledge which could be implemented through future development programs considering that most of these traditional foraging practices fulfill environmental and social sustainability standards. Further field studies are required to thoroughly investigate the patterns of foraging among highland pastoral societies in other parts of the Hindukush region and especially their potential for the ongoing ecological transition.},
}
@article {pmid37003550,
year = {2023},
author = {Romero Starke, K and Schubert, M and Kaboth, P and Gerlach, J and Hegewald, J and Reusche, M and Friedemann, D and Zülke, A and Riedel-Heller, SG and Zeeb, H and Seidler, A},
title = {Traffic noise annoyance in the LIFE-adult study in Germany: Exposure-response relationships and a comparison to the WHO curves.},
journal = {Environmental research},
volume = {228},
number = {},
pages = {115815},
doi = {10.1016/j.envres.2023.115815},
pmid = {37003550},
issn = {1096-0953},
mesh = {Adult ; Humans ; *Noise, Transportation/adverse effects ; Environmental Exposure ; Germany ; Motor Vehicles ; Aircraft ; World Health Organization ; },
abstract = {BACKGROUND: Noise annoyance is the second-highest cause of lost disability-adjusted life-years due to environmental noise in Europe. Evidence on exposure-response relationships (ERRs) for traffic noise annoyance with more accurate exposure values is still needed.<br><br>OBJECTIVES: In an analysis of the population-based LIFE-Adult study in Leipzig, Germany, we aimed to investigate the effect of road, railway (train and tram), and aircraft noise on high annoyance (HA).<br><br>METHODS: Traffic exposure data was taken for 2012 and data on noise annoyance was evaluated between 2018 and 2021. HA was defined according to international standardized norms. We calculated risk estimates using logistic regression, controlling for age, sex, and socioeconomic status, and compared our ERRs with those from the last WHO review on this topic.<br><br>RESULTS: Aircraft noise had the highest relative risk for noise-related HA (OR&#xa0;=&#xa0;12.7, 95% CI: 9.37-17.10 per 10&#xa0;dB Lden increase). The road and railway traffic risk estimates were similar to each other (road: OR&#xa0;=&#xa0;3.55, 95% CI: 2.78-4.54; railway: OR&#xa0;=&#xa0;3.31, 95% CI: 2.77-3.97 per 10&#xa0;dB Lden increase). Compared to the WHO curves, the proportion of highly annoyed individuals was somewhat lower for road and rail traffic noise, but higher for aircraft noise.<br><br>DISCUSSION: Aircraft noise is particularly annoying. There were differences between our study's ERRs and those in the WHO review, especially for aircraft noise. These differences may be partly explained by the improved accuracy of the exposure values, as we considered secondary road networks and tram noise, and by a lack of a nighttime flight ban at the Leipzig airport. Geographical, regional and climatic variations, inconsistency in HA cut-offs, as well as temporal developments in the annoyance experience may also explain the differences. Since ERRs serve as a basis for decision making in public policies, regular updates of the curves based on new evidence is recommended.},
}
@article {pmid36999249,
year = {2023},
author = {D'Alò, F and Zucconi, L and Onofri, S and Canini, F and Cannone, N and Malfasi, F and Morais, DK and Starke, R},
title = {Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.},
journal = {Environmental microbiology reports},
volume = {15},
number = {4},
pages = {291-297},
pmid = {36999249},
issn = {1758-2229},
mesh = {*Archaea/genetics ; *Soil/chemistry ; Multiomics ; Climate Change ; Italy ; Soil Microbiology ; },
abstract = {We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.},
}
@article {pmid36998243,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Boyes, C and , },
title = {The genome sequence of the pale mottled willow, Caradrina clavipalpis (Scopoli, 1763).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {225},
pmid = {36998243},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.},
}
@article {pmid36998167,
year = {2023},
author = {Sakai, K and Nagata, T and Odagami, K and Nagata, M and Mori, T and Mori, K},
title = {Supervisors' Work Engagement Is Associated With Interactivity and Carefulness in Supporting Subordinates: A Cross-sectional Study Using Text Mining in Japan.},
journal = {Journal of occupational and environmental medicine},
volume = {65},
number = {7},
pages = {e465-e471},
pmid = {36998167},
issn = {1536-5948},
mesh = {Humans ; *Work Engagement ; Cross-Sectional Studies ; Japan ; *Attitude ; Data Mining ; },
abstract = {OBJECTIVE: This study aimed to structure supervisory support and clarify the relationship between supervisors' work engagement and support for their subordinates.<br><br>METHODS: We conducted a cross-sectional study in a manufacturing company using a questionnaire survey. Supervisors provided open-ended responses regarding the provision of support for their subordinates. Using text mining, we structured these descriptions into multiple categories, assigned words to them, and analyzed frequently mentioned categories by the level of work engagement.<br><br>RESULTS: We obtained responses from 729 participants that included 13,968 words. We structured supervisory support by three categories (contents, direction, and attitude toward support) and 11 subcategories. As supervisors' work engagement increased, the rates of mentioning information retrieval, information transmission, and carefulness increased.<br><br>CONCLUSIONS: Supervisors with work engagement could communicate with each other and be careful in providing support to their subordinates.},
}
@article {pmid36992446,
year = {2023},
author = {Howison, M and Gillani, FS and Novitsky, V and Steingrimsson, JA and Fulton, J and Bertrand, T and Howe, K and Civitarese, A and Bhattarai, L and MacAskill, M and Ronquillo, G and Hague, J and Dunn, CW and Bandy, U and Hogan, JW and Kantor, R},
title = {An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.},
journal = {Viruses},
volume = {15},
number = {3},
pages = {},
pmid = {36992446},
issn = {1999-4915},
support = {R01 AI136058/AI/NIAID NIH HHS/United States ; K24 AI134359/AI/NIAID NIH HHS/United States ; P30 AI042853/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *HIV Infections/diagnosis/epidemiology ; Public Health ; Phylogeny ; Prospective Studies ; *HIV-1/genetics ; *HIV Seropositivity ; },
abstract = {Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.},
}
@article {pmid36989356,
year = {2023},
author = {Bird, N and Ormond, L and Awah, P and Caldwell, EF and Connell, B and Elamin, M and Fadlelmola, FM and Matthew Fomine, FL and López, S and MacEachern, S and Moñino, Y and Morris, S and Näsänen-Gilmore, P and Nketsia V, NK and Veeramah, K and Weale, ME and Zeitlyn, D and Thomas, MG and Bradman, N and Hellenthal, G},
title = {Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture.},
journal = {Science advances},
volume = {9},
number = {13},
pages = {eabq2616},
pmid = {36989356},
issn = {2375-2548},
support = {/WT_/Wellcome Trust/United Kingdom ; BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; *Ethnicity/genetics ; Nigeria ; *Chromosomes ; Ghana ; Language ; Genetic Variation ; Genetics, Population ; },
abstract = {Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data have only been obtained from a small proportion of present-day ethnolinguistic groups. By analyzing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republic of the Congo, Ghana, Nigeria, and Sudan, we demonstrate a previously underappreciated fine-scale level of genetic structure within these countries, for example, correlating with historical polities in western Cameroon. By comparing genetic variation patterns among populations, we infer that many northern Cameroonian and Sudanese groups share genetic links with multiple geographically disparate populations, likely resulting from long-distance migrations. In Ghana and Nigeria, we infer signatures of intermixing dated to over 2000 years ago, corresponding to reports of environmental transformations possibly related to climate change. We also infer recent intermixing signals in multiple African populations, including Congolese, that likely relate to the expansions of Bantu language-speaking peoples.},
}
@article {pmid36981964,
year = {2023},
author = {Sui, J and Zhang, G and Lin, T and Hamm, NAS and Li, C and Wu, X and Hu, K},
title = {Quantitative Evaluation of Spatial Accessibility of Various Urban Medical Services Based on Big Data of Outpatient Appointments.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {6},
pages = {},
pmid = {36981964},
issn = {1660-4601},
mesh = {Child ; Humans ; *Big Data ; *Outpatients ; Health Services Accessibility ; Cities ; Catchment Area, Health ; },
abstract = {Equity of urban medical services affects human health and well-being in cities and is important in building 'just' cities. We carried out a quantitative analysis of the spatial accessibility of medical services considering the diverse demands of people of different ages, using outpatient appointment big data and refining the two-step floating catchment area (2SFCA) method. We used the traditional 2SFCA method to evaluate the overall spatial accessibility of medical services of 504 communities in Xiamen city, considering the total population and the supply of medical resources. Approximately half the communities had good access to medical services. The communities with high accessibility were mainly on Xiamen Island, and those with low accessibility were further from the central city. The refined 2SFCA method showed a more diverse and complex spatial distribution of accessibility to medical services. Overall, 209 communities had high accessibility to internal medicine services, 133 to surgery services, 50 to gynecology and obstetrics services, and 18 to pediatric services. The traditional method may over-evaluate or under-evaluate the accessibility of different types of medical services for most communities compared with the refined evaluation method. Our study can provide more precise information on urban medical service spatial accessibility to support just city development and design.},
}
@article {pmid36979124,
year = {2023},
author = {Schalli, M and Platzer, S and Schmutz, R and Ofner-Kopeinig, P and Reinthaler, FF and Haas, D},
title = {Dissolved Carbon Dioxide: The Lifespan of Staphylococcus aureus and Enterococcus faecalis in Bottled Carbonated Mineral Water.},
journal = {Biology},
volume = {12},
number = {3},
pages = {},
pmid = {36979124},
issn = {2079-7737},
abstract = {During the process of mineral water production, many possible contamination settings can influence the quality of bottled water. Microbial contamination can originate from different sources, for example, the ambient air, the bottles, the caps, and from the bottling machine itself. The aim of this study was to investigate the influence of three different carbon dioxide (CO2) concentrations (3.0 g/L, 5.5 g/L, and 7.0 g/L; 20 bottles each) in bottled mineral water on the bacterial growth of Staphylococcus aureus (S. aureus) and Enterococcus faecalis (Ent. faecalis). The examined mineral water was artificially contaminated before capping the bottles inside the factory. After a specific number of days, water samples were taken from freshly opened bottles and after filtration (100 mL), filters were placed on Columbia Agar with 5% Sheep blood to cultivate S. aureus and Slanetz and Bartley Agar to cultivate Ent. faecalis. The respective colony-forming units (CFU) were counted after incubation times ranging from 24 to 120 h. Colony-forming units of S. aureus were not detectable after the 16th and 27th day, whereas Ent. faecalis was not cultivable after the 5th and 13th day when stored inside the bottles. The investigation of the bottles that were stored open for a certain amount of time with CO2 bubbling out showed only single colonies for S. aureus after the 5th day and no CFUs for Ent. faecalis after the 17th day. A reduction in the two investigated bacterial strains during storage in carbonated mineral water bottles means that a proper standardized disinfection and cleaning procedure, according to valid hygiene standards of industrial bottling machines, cannot be replaced by carbonation.},
}
@article {pmid36978281,
year = {2023},
author = {Stanic, B and Milošević, N and Sukur, N and Samardzija Nenadov, D and Fa Nedeljkovic, S and Škrbić, S and Andric, N},
title = {An in silico toxicogenomic approach in constructing the aflatoxin B1-mediated regulatory network of hub genes in hepatocellular carcinoma.},
journal = {Toxicology mechanisms and methods},
volume = {33},
number = {7},
pages = {552-562},
doi = {10.1080/15376516.2023.2196686},
pmid = {36978281},
issn = {1537-6524},
mesh = {Humans ; *Carcinoma, Hepatocellular/chemically induced/genetics/metabolism ; *Liver Neoplasms/chemically induced/genetics/metabolism ; Aflatoxin B1/toxicity ; Toxicogenetics ; },
abstract = {Aflatoxin B1 (AFB1) can cause hepatocellular carcinoma (HCC) through a mutagenic mode of action but can also lead to global changes in gene expression; however, the AFB1 network of molecular pathways involved in HCC is not known. Here, we used toxicogenomic data from human liver cells exposed to AFB1 to infer the network of AFB1-responsive molecular pathways involved in HCC. The following computational tools: STRING, MCODE, cytoHubba, iRegulon, kinase enrichment tool KEA3, and DAVID were used to identify protein-protein interaction network, hub genes, transcription factors (TFs), upstream kinases, and biological processes (BPs). Predicted molecular events were validated with an external dataset, whereas the hub genes in HCC were validated using the UALCAN database. The results revealed an association between AFB1 and the hub genes involved in the cell cycle. We identified TFs that regulate the hub genes and linked them with upstream kinases including cyclin-dependent kinases, mitogen-activated protein kinase 1, and AKT. This approach enabled the construction of the AFB1-mediated regulatory network consisting of upstream kinases, TFs, hub genes, and BPs, thus revealing the signaling hierarchy and information flow that may contribute to AFB1-induced HCC. This could be a useful tool in predicting the molecular mechanisms involved in chemical-induced diseases when available toxicogenomic data exist.},
}
@article {pmid36976982,
year = {2023},
author = {Yang, D and Zhu, H and Liu, J and Zhang, Y and Wu, S and Xiong, J and Wang, F},
title = {Risk Assessment of Heavy Metals in Soils from Four Different Industrial Plants in a Medium-Sized City in North China.},
journal = {Toxics},
volume = {11},
number = {3},
pages = {},
pmid = {36976982},
issn = {2305-6304},
support = {U2003103//the Key Project of Joint Funds of the National Natural Science Foundation of China/ ; KC22075//special fund for promoting scientific and technological innovation in Xuzhou in 2022 (key research and development plan (modern agriculture) - general project/ ; No. 2020ZDPYMS10//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {Laboratory experiments were carried out to analyze 39 soil samples collected from four industrial areas in Xuzhou City using inductively coupled plasma mass spectrometry and atomic fluorescence spectrometry. The descriptive statistics of heavy metals (HMs) in the soil profiles showed that the HM content at three depths was highly variable, and most coefficients of variation (CVs) showed moderate variability. The enrichment of Cd at all depths exceeded the risk screening value, and Cd pollution occurred in four plants. The enrichment of the other HMs at three depths was mainly concentrated in the pharmaceutical plant A and chemical plant C. It was found that the different HMs had different vertical distribution characteristics. For the different industrial plants, the raw materials and products not only made the spatial distribution characteristics of the HMs different, but also caused the HM types and contents to differ. The average single pollution indices of Cd in plant A, iron-steel plant B, and plant C indicated a slight pollution level. The other seven HMs in A, B, and C and all HMs in chemical plant D belonged to the safe category. The mean values of the Nemerow pollution index in the four industrial plants belonged to the warning category. The analysis showed that none of the HMs posed potential noncarcinogenic health risks, and only the carcinogenic health risks of Cr in plants A and C were unacceptable. The carcinogenic effect of Cr through the inhalation intake of resuspended soil particulates and that of Cd, Ni, and As via direct oral ingestion were the main exposure pathways.},
}
@article {pmid36976384,
year = {2023},
author = {Huang, F and Chen, C},
title = {GIS-based approach and multivariate statistical analysis for identifying sources of heavy metals in marine sediments from the coast of Hong Kong.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {4},
pages = {518},
pmid = {36976384},
issn = {1573-2959},
mesh = {Hong Kong ; Geographic Information Systems ; Cadmium ; Lead ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury ; Geologic Sediments/chemistry ; Risk Assessment ; China ; *Water Pollutants, Chemical/analysis ; },
abstract = {Hong Kong is an urbanized coastal city which experiences substantially different metal loads from anthropogenic activities. This study was aimed at analyzing the spatial distribution and pollution evaluation of ten selected heavy metals (As, Cd, Cr, Cu, Pb, Hg, Ni, Zn, Fe, V) in the coastal sediments of Hong Kong. The distribution of heavy metal pollution in sediments has been analyzed using the geographic information system (GIS) technique, and their pollution degrees, corresponding potential ecological risks and source identifications, have been studied by applying the enrichment factor (EF) analysis, contamination factor (CF) analysis, potential ecological risk index (PEI), and integrated multivariate statistical methods, respectively. Firstly, the GIS technique was used to access the spatial distribution of the heavy metals; the result revealed that pollution trend of these metals was decreased from the inner to the outer coast sites of the studied area. Secondly, combining the EF analysis and CF analysis, we found that the pollution degree of heavy metals followed the order of Cu > Cr > Cd > Zn > Pb > Hg > Ni > Fe > As > V. Thirdly, the PERI calculations showed that Cd, Hg, and Cu were the most potential ecological risk factors compared to other metals. Finally, cluster analysis combined with principal component analysis showed that Cr, Cu, Hg, and Ni might originate from the industrial discharges and shipping activities. V, As, and Fe were mainly derived from the natural origin, whereas Cd, Pb, and Zn were identified from the municipal discharges and industrial wastewater. In conclusion, this work should be helpful in the establishment of strategies for contamination control and optimization of industrial structures in Hong Kong.},
}
@article {pmid36972774,
year = {2023},
author = {Cecchetto, M and Peruzza, L and Giubilato, E and Bernardini, I and Rovere, GD and Marcomini, A and Regoli, F and Bargelloni, L and Patarnello, T and Semenzin, E and Milan, M},
title = {An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment.},
journal = {Environmental research},
volume = {227},
number = {},
pages = {115745},
doi = {10.1016/j.envres.2023.115745},
pmid = {36972774},
issn = {1096-0953},
mesh = {Animals ; *Transcriptome ; Gene Expression Profiling/methods ; *Mytilus/genetics ; Risk Assessment/methods ; },
abstract = {The sharp decrease in the cost of RNA-sequencing and the rapid improvement in computational analysis of eco-toxicogenomic data have brought new insights into the adverse effects of chemicals on aquatic organisms. Yet, transcriptomics is generally applied qualitatively in environmental risk assessments, hampering more effective exploitation of this evidence through multidisciplinary studies. In view of this limitation, a methodology is here presented to quantitatively elaborate transcriptional data in support to environmental risk assessment. The proposed methodology makes use of results from the application of Gene Set Enrichment Analysis to recent studies investigating the response of Mytilus galloprovincialis and Ruditapes philippinarum exposed to contaminants of emerging concern. The degree of changes in gene sets and the relevance of physiological reactions are integrated in the calculation of a hazard index. The outcome is then classified according to five hazard classes (from absent to severe), providing an evaluation of whole-transcriptome effects of chemical exposure. The application to experimental and simulated datasets proved that the method can effectively discriminate different levels of altered transcriptomic responses when compared to expert judgement (Spearman correlation coefficient of 0.96). A further application to data collected in two independent studies of Salmo trutta and Xenopus tropicalis exposed to contaminants confirmed the potential extension of the methodology to other aquatic species. This methodology can serve as a proof of concept for the integration of "genomic tools" in environmental risk assessment based on multidisciplinary investigations. To this end, the proposed transcriptomic hazard index can now be incorporated into quantitative Weight of Evidence approaches and weighed, with results from other types of analysis, to elucidate the role of chemicals in adverse ecological effects.},
}
@article {pmid36972109,
year = {2023},
author = {Beauchamp, AM and Lehmann, CU and Medford, RJ and Hughes, AE},
title = {The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.},
journal = {Journal of medical Internet research},
volume = {25},
number = {},
pages = {e43623},
pmid = {36972109},
issn = {1438-8871},
support = {UL1 TR003163/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Humans ; United States/epidemiology ; *Social Media ; Cross-Sectional Studies ; Depression/epidemiology ; Income ; Mental Health ; },
abstract = {BACKGROUND: Social connectedness decreases human mortality, improves cancer survival, cardiovascular health, and body mass, results in better-controlled glucose levels, and strengthens mental health. However, few public health studies have leveraged large social media data sets to classify user network structure and geographic reach rather than the sole use of social media platforms.<br><br>OBJECTIVE: The objective of this study was to determine the association between population-level digital social connectedness and reach and depression in the population across geographies of the United States.<br><br>METHODS: Our study used an ecological assessment of aggregated, cross-sectional population measures of social connectedness, and self-reported depression across all counties in the United States. This study included all 3142 counties in the contiguous United States. We used measures obtained between 2018 and 2020 for adult residents in the study area. The study's main exposure of interest is the Social Connectedness Index (SCI), a pair-wise composite index describing the "strength of connectedness between 2 geographic areas as represented by Facebook friendship ties." This measure describes the density and geographical reach of average county residents' social network using Facebook friendships and can differentiate between local and long-distance Facebook connections. The study's outcome of interest is self-reported depressive disorder as published by the Centers for Disease Control and Prevention.<br><br>RESULTS: On average, 21% (21/100) of all adult residents in the United States reported a depressive disorder. Depression frequency was the lowest for counties in the Northeast (18.6%) and was highest for southern counties (22.4%). Social networks in northeastern counties involved moderately local connections (SCI 5-10 the 20th percentile for n=70, 36% of counties), whereas social networks in Midwest, southern, and western counties contained mostly local connections (SCI 1-2 the 20th percentile for n=598, 56.7%, n=401, 28.2%, and n=159, 38.4%, respectively). As the quantity and distance that social connections span (ie, SCI) increased, the prevalence of depressive disorders decreased by 0.3% (SE 0.1%) per rank.<br><br>CONCLUSIONS: Social connectedness and depression showed, after adjusting for confounding factors such as income, education, cohabitation, natural resources, employment categories, accessibility, and urbanicity, that a greater social connectedness score is associated with a decreased prevalence of depression.},
}
@article {pmid36966822,
year = {2023},
author = {Song, W and Song, W},
title = {Cropland fallow reduces agricultural water consumption by 303 million tons annually in Gansu Province, China.},
journal = {The Science of the total environment},
volume = {879},
number = {},
pages = {163013},
doi = {10.1016/j.scitotenv.2023.163013},
pmid = {36966822},
issn = {1879-1026},
abstract = {The high-intensity utilization of global cropland causes water shortage and food crisis, which seriously affects the realization of SDG 2 (zero hunger), SDG 6 (clean water and sanitation) and SDG 15 (life on land), and threatens the sustainable social, economic and ecological development. Cropland fallow can not only improve the quality of cropland and maintain ecosystem balance, but also have a significant water-saving effect. However, in most developing countries, such as China, cropland fallow has not yet been widely promoted, and there are few reliable fallow cropland fallow identification methods, making it even more challenging to assess the water-saving effect. To remedy this deficit, we propose a framework for mapping cropland fallow and evaluating its water savings. First, we used the Landsat series of data to interpret the annual land use/cover changes in Gansu Province, China from 1991 to 2020. Subsequently, the spatial-temporal variation of cropland fallow in Gansu province (giving up farming for one to two years) was mapped. Finally, we evaluated the water-saving effect of cropland fallow using evapotranspiration, precipitation, irrigation maps, and crop-related data, instead of actual water consumption. The results showed that the mapping accuracy of fallow land in Gansu Province was 79.50 %, which was higher than that of most known fallow mapping studies. From 1993 to 2018, the average annual fallow rate in Gansu Province, China, was 10.86 %, which was at a low level in arid/semi-arid regions worldwide. More importantly, from 2003 to 2018, cropland fallow reduces annual water consumption of 303.26 million tons in Gansu Province, accounting for 3.44 % of agricultural water use in Gansu Province and equivalent to the annual water demand of 655,000 people in Gansu Province. Based on our research, we speculate that the increasing pilot projects of cropland fallow in China can bring significant water-saving effects and help achieve China's Sustainable Development Goals.},
}
@article {pmid36964402,
year = {2023},
author = {Dec, E and Clement, J and Cheng, K and Church, GM and Fossel, MB and Rehkopf, DH and Rosero-Bixby, L and Kobor, MS and Lin, DT and Lu, AT and Fei, Z and Guo, W and Chew, YC and Yang, X and Putra, SED and Reiner, AP and Correa, A and Vilalta, A and Pirazzini, C and Passarino, G and Monti, D and Arosio, B and Garagnani, P and Franceschi, C and Horvath, S},
title = {Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity.},
journal = {GeroScience},
volume = {45},
number = {3},
pages = {1817-1835},
pmid = {36964402},
issn = {2509-2723},
support = {HHSN268201600001C/HL/NHLBI NIH HHS/United States ; HHSN268201600003C/HL/NHLBI NIH HHS/United States ; U01 AG060908/AG/NIA NIH HHS/United States ; HHSN268201800015I/HB/NHLBI NIH HHS/United States ; P30 AG012839/AG/NIA NIH HHS/United States ; HHSN268201800010I/HB/NHLBI NIH HHS/United States ; HHSN268201600002C/HL/NHLBI NIH HHS/United States ; HHSN268201600004C/HL/NHLBI NIH HHS/United States ; HHSN268201800014I/HB/NHLBI NIH HHS/United States ; R01 AG029451/AG/NIA NIH HHS/United States ; HHSN268201800013I/MD/NIMHD NIH HHS/United States ; HHSN268201800012I/HB/NHLBI NIH HHS/United States ; HHSN268201500001I/HL/NHLBI NIH HHS/United States ; HHSN268201800011I/HB/NHLBI NIH HHS/United States ; HHSN268201600018C/HL/NHLBI NIH HHS/United States ; },
mesh = {Aged, 80 and over ; Humans ; *Longevity/genetics ; *Centenarians ; DNA Methylation ; Epigenesis, Genetic/genetics ; },
abstract = {Claims surrounding exceptional longevity are sometimes disputed or dismissed for lack of credible evidence. Here, we present three DNA methylation-based age estimators (epigenetic clocks) for verifying age claims of centenarians. The three centenarian clocks were developed based on n = 7039 blood and saliva samples from individuals older than 40, including n = 184 samples from centenarians, 122 samples from semi-supercentenarians (aged 105 +), and 25 samples from supercentenarians (aged 110 +). The oldest individual was 115 years old. Our most accurate centenarian clock resulted from applying a neural network model to a training set composed of individuals older than 40. An epigenome-wide association study of age in different age groups revealed that age effects in young individuals (age < 40) are correlated (r = 0.55) with age effects in old individuals (age > 90). We present a chromatin state analysis of age effects in centenarians. The centenarian clocks are expected to be useful for validating claims surrounding exceptional old age.},
}
@article {pmid36962744,
year = {2023},
author = {Asaaga, FA and Purse, BV and Rahman, M and Srinivas, PN and Kalegowda, SD and Seshadri, T and Young, JC and Oommen, MA},
title = {The role of social vulnerability in improving interventions for neglected zoonotic diseases: The example of Kyasanur Forest Disease in India.},
journal = {PLOS global public health},
volume = {3},
number = {2},
pages = {e0000758},
pmid = {36962744},
issn = {2767-3375},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/P024335/2/MRC_/Medical Research Council/United Kingdom ; MR/T029846/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Forest-based communities manage many risks to health and socio-economic welfare including the increasing threat of emerging zoonoses that are expected to disproportionately affect poor and marginalised groups, and further impair their precarious livelihoods, particularly in Low-and-Middle Income (LMIC) settings. Yet, there is a relative dearth of empirical research on the vulnerability and adaptation pathways of poor and marginalised groups facing emerging zoonoses. Drawing on a survey of 229 households and a series of key-informant interviews in the Western Ghats, we examine the factors affecting vulnerability of smallholder and tribal households to Kyasanur Forest Disease (KFD), an often-fatal tick-borne viral haemorrhagic fever endemic in south India. Specifically, we investigate how different socio-demographic and institutional factors interact to shape KFD vulnerability and the strategies employed by households to adapt to disease consequences. Although surveyed households generally perceived KFD as an important health issue in the study region, there was variability in concern about contracting the disease. Overall results showed that poor access to land (AOR = 0.373, 95% CI: 0.152-0.916), being at or below the poverty line (AOR = 0.253, 95% CI: 0.094-0.685) and being headed by an older person (AOR = 1.038, 95% CI: 1.006-1.071) were all significant determinants of perceived KFD vulnerability. Furthermore, KFD vulnerability is also modulated by important extra-household factors including proximity to private hospitals (AOR = 3.281, 95% CI: 1.220-8.820), main roads (AOR = 2.144, 95% CI: 1.215-3.783) and study location (AOR = 0.226, 95% CI: 0.690-0.743). Our findings highlight how homogenous characterisation of smallholder and tribal communities and the 'techno-oriented' approach of existing interventions may further marginalise the most vulnerable and exacerbate existing inequalities. These findings are important for designing context-specific and appropriate health interventions (including the prioritisation of awareness raising, knowledge networks, livelihood diversification) that enhances the resilience of at-risk social groups within the KFD context. More broadly, our findings highlight how a focus on social vulnerability can help national and international health planners improve health interventions and prioritise among diseases with respect to neglected endemic zoonoses.},
}
@article {pmid36962522,
year = {2022},
author = {Sawires, R and Pearce, C and Fahey, M and Clothier, H and Gardner, K and Buttery, J},
title = {Snotwatch COVID-toes: An ecological study of chilblains and COVID-19 diagnoses in Victoria, Australia.},
journal = {PLOS global public health},
volume = {2},
number = {10},
pages = {e0000488},
pmid = {36962522},
issn = {2767-3375},
abstract = {The COVID-19 pandemic has caused widespread illness with varying clinical manifestations. One less-commonly-reported presentation of COVID-19 infection is chilblain-like lesions. We conducted an ecological analysis of chilblain presentations in comparison with confirmed and suspected COVID-19 infections in a primary care setting to establish that a relationship exists between the two. Our study collated data from three Primary Health Networks across Victoria, Australia, from 2017-2021, to understand patterns of chilblain presentations prior to and throughout the pandemic. Using a zero-inflated negative binomial regression analysis, we estimated the relationship between local minimum temperature, COVID-19 infections and the frequency of chilblain presentations. We found a 5.72 risk ratio of chilblain incidence in relation to COVID-19 infections and a 3.23 risk ratio associated with suspected COVID-19 infections. COVID-19 infections were also more strongly associated with chilblain presentations in 0-16-year-olds throughout the pandemic in Victoria. Our study statistically suggests that chilblains are significantly associated with COVID-19 infections in a primary care setting. This has major implications for clinicians aiming to diagnose COVID-19 infections or determine the cause of a presentation of chilblains. Additionally, we demonstrate the utility of large-scale primary care data in identifying an uncommon manifestation of COVID-19 infections, which will be significantly beneficial to treating physicians.},
}
@article {pmid36962247,
year = {2022},
author = {Asaaga, FA and Young, JC and Srinivas, PN and Seshadri, T and Oommen, MA and Rahman, M and Kiran, SK and Kasabi, GS and Narayanaswamy, D and Schäfer, SM and Burthe, SJ and August, T and Logie, M and Chanda, MM and Hoti, SL and Vanak, AT and Purse, BV},
title = {Co-production of knowledge as part of a OneHealth approach to better control zoonotic diseases.},
journal = {PLOS global public health},
volume = {2},
number = {3},
pages = {e0000075},
pmid = {36962247},
issn = {2767-3375},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/P024335/2/MRC_/Medical Research Council/United Kingdom ; MR/T029846/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {There is increased global and national attention on the need for effective strategies to control zoonotic diseases. Quick, effective action is, however, hampered by poor evidence-bases and limited coordination between stakeholders from relevant sectors such as public and animal health, wildlife and forestry sectors at different scales, who may not usually work together. The OneHealth approach recognises the value of cross-sectoral evaluation of human, animal and environmental health questions in an integrated, holistic and transdisciplinary manner to reduce disease impacts and/or mitigate risks. Co-production of knowledge is also widely advocated to improve the quality and acceptability of decision-making across sectors and may be particularly important when it comes to zoonoses. This paper brings together OneHealth and knowledge co-production and reflects on lessons learned for future OneHealth co-production processes by describing a process implemented to understand spill-over and identify disease control and mitigation strategies for a zoonotic disease in Southern India (Kyasanur Forest Disease). The co-production process aimed to develop a joint decision-support tool with stakeholders, and we complemented our approach with a simple retrospective theory of change on researcher expectations of the system-level outcomes of the co-production process. Our results highlight that while co-production in OneHealth is a difficult and resource intensive process, requiring regular iterative adjustments and flexibility, the beneficial outcomes justify its adoption. A key future aim should be to improve and evaluate the degree of inter-sectoral collaboration required to achieve the aims of OneHealth. We conclude by providing guidelines based on our experience to help funders and decision-makers support future co-production processes.},
}
@article {pmid36958663,
year = {2023},
author = {Lima, GDS and Menegario, AA and Suarez, CA and Kamazuka, SH and Gemeiner, H and Sánchez-Sarmiento, AM and Ferioli, RB and Barreto, AS},
title = {Pelagic and estuarine birds as sentinels of metal(loid)s in the South Atlantic Ocean: Ecological niches as main factors acting on bioaccumulation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {326},
number = {},
pages = {121452},
doi = {10.1016/j.envpol.2023.121452},
pmid = {36958663},
issn = {1873-6424},
mesh = {Humans ; Animals ; *Metals, Heavy/analysis ; Bioaccumulation ; Cadmium/analysis ; Lead/analysis ; Environmental Monitoring/methods ; Ecosystem ; *Mercury/analysis ; Birds ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; },
abstract = {Activities related to the offshore exploration and production of oil and natural gas provide economic development and an essential energy source. However, besides the risk of petroleum hydrocarbon contamination, these activities can also be sources of metals and metalloids for marine organism contamination. In this research, we evaluated the potential use of two pelagic (black-browed albatross Thalassarche melanophris and yellow-nosed albatross T. chlororhynchos) and one estuarine bird species (neotropical cormorant Nannopterum brasilianus) as sentinels of contamination of As, Cd, Cr, Cu, Pb, Mn, Mo, Zn, Ni, Ba, V, and Hg in an area under influence of oil and gas activities. The analyses were carried out in samples collected from 2015 to 2022 from 97 individuals. A factor alert; an adaptation from the contamination factor is proposed to identify individuals with high concentrations that possibly suffered contamination by anthropogenic origin. Grouping all species, the metal(loid)s with the highest concentrations were in decreasing order: Zn > Cu > Mn > Hg > As > Cd > Mo > V > Cr > Ba > Ni > Pb. Similar concentrations were observed for V, Mn, Cr and Pb among the three species. Pelagic birds showed higher levels of concentrations for Hg, As and Cd. Based on the correlations and multivariate analysis performed, the results indicate that the ecological niche factor has greater relevance in the bioaccumulation of these elements compared to the habitat. Although some individuals showed high concentrations in part of the trace elements, suggesting exposure to anthropic sources, the direct influence of oil production and exploration activities was not observed, suggesting that activities on the continent are the primary contamination source. The results of this work highlight the role of seabirds as sentinels for metal(loid)s, contributing to the knowledge of the occurrence of contaminants in the South Atlantic Ocean.},
}
@article {pmid36948010,
year = {2023},
author = {Hao, N and Sun, P and Zhao, W and Li, X},
title = {Application of a developed triple-classification machine learning model for carcinogenic prediction of hazardous organic chemicals to the US, EU, and WHO based on Chinese database.},
journal = {Ecotoxicology and environmental safety},
volume = {255},
number = {},
pages = {114806},
doi = {10.1016/j.ecoenv.2023.114806},
pmid = {36948010},
issn = {1090-2414},
mesh = {Bayes Theorem ; Carcinogenesis ; *Carcinogens/toxicity/chemistry ; *Hazardous Substances/chemistry/toxicity ; *Machine Learning ; *Organic Chemicals/toxicity/chemistry ; Support Vector Machine ; World Health Organization ; Algorithms ; United States ; European Union ; China ; Databases, Factual ; },
abstract = {Cancer, the second largest human disease, has become a major public health problem. The prediction of chemicals' carcinogenicity before their synthesis is crucial. In this paper, seven machine learning algorithms (i.e., Random Forest (RF), Logistic Regression (LR), Support Vector Machines (SVM), Complement Naive Bayes (CNB), K-Nearest Neighbor (KNN), XGBoost, and Multilayer Perceptron (MLP)) were used to construct the carcinogenicity triple classification prediction (TCP) model (i.e., 1A, 1B, Category 2). A total of 1444 descriptors of 118 hazardous organic chemicals were calculated by Discovery Studio 2020, Sybyl X-2.0 and PaDEL-Descriptor software. The constructed carcinogenicity TCP model was evaluated through five model evaluation indicators (i.e., Accuracy, Precision, Recall, F1 Score and AUC). The model evaluation results show that Accuracy, Precision, Recall, F1 Score and AUC evaluation indicators meet requirements (greater than 0.6). The accuracy of RF, LR, XGBoost, and MLP models for predicting carcinogenicity of Category 2 is 91.67%, 79.17%, 100%, and 100%, respectively. In addition, the constructed machine learning model in this study has potential for error correction. Taking XGBoost model as an example, the predicted carcinogenicity level of 1,2,3-Trichloropropane (96-18-4) is Category 2, but the actual carcinogenicity level is 1B. But the difference between Category 2 and 1B is only 0.004, indicating that the XGBoost is one optimum model of the seven constructed machine learning models. Besides, results showed that functional groups like chlorine and benzene ring might influence the prediction of carcinogenic classification. Therefore, considering functional group characteristics of chemicals before constructing the carcinogenicity prediction model of organic chemicals is recommended. The predicted carcinogenicity of the organic chemicals using the optimum machine leaning model (i.e., XGBoost) was also evaluated and verified by the toxicokinetics. The RF and XGBoost TCP models constructed in this paper can be used for carcinogenicity detection before synthesizing new organic substances. It also provides technical support for the subsequent management of organic chemicals.},
}
@article {pmid36947137,
year = {2023},
author = {James, JE and Nelson, PG and Masel, J},
title = {Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.},
journal = {Molecular biology and evolution},
volume = {40},
number = {4},
pages = {},
pmid = {36947137},
issn = {1537-1719},
mesh = {Animals ; *Proteome ; Protein Domains ; Probability ; Hydrophobic and Hydrophilic Interactions ; Databases, Protein ; },
abstract = {Protein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition.},
}
@article {pmid36947115,
year = {2023},
author = {Bautista, J and Schueller, SM},
title = {Understanding the Adoption and Use of Digital Mental Health Apps Among College Students: Secondary Analysis of a National Survey.},
journal = {JMIR mental health},
volume = {10},
number = {},
pages = {e43942},
pmid = {36947115},
issn = {2368-7959},
abstract = {BACKGROUND: Increasing rates of mental health diagnoses in college students signal the need for new opportunities to support the mental health of this population. With many mental health apps being efficacious, they may be a promising resource for college campuses to provide support to their students. However, it is important to understand why (or why not) students might want to use apps and their desired features.<br><br>OBJECTIVE: Information on students' interest in mental health apps may inform which apps are to be provided and how campuses can support their use. This study aimed to understand the interest and hesitation in app use and the relationship between mental health needs, as defined by depression, anxiety, and positive mental health, and app use.<br><br>METHODS: The web-based Healthy Minds Study collected information on mental health needs, perceptions, and service use across colleges and universities. We used a sample of 989 participants who completed the survey between 2018 and 2020 and an elective module on digital mental health. We analyzed the elective module responses using a mixed methods approach, including both descriptive and inferential statistics, along with thematic coding for open text responses.<br><br>RESULTS: The Results from this study revealed that anxiety (b=-0.07; P<.001), but not depression (b=0.03; P=.12) and positive mental health (b=-0.02; P=.17), was a significant predictor of app adoption. Prominent qualitative findings indicated that the most desired app features included tips and advice, access to resources and information, and on-demand support that involves interaction throughout the day. The participants also suggested an overall desire for human interaction to be integrated into an app. As predicted, hesitancy was encountered, and the qualitative results suggested that there was a lack of interest in the adoption of mental health app and preference.<br><br>CONCLUSIONS: The findings from this study underscore that simply providing digital mental health apps as tools may be insufficient to support their use in college campuses. Although many students were open to using a mental health app, hesitation and uncertainty were common in the participant responses. Working with colleges and universities to increase digital literacy and provide resources that allow students to gauge when app use is appropriate may be helpful when implementing mental health apps as resources in college campuses.},
}
@article {pmid36946676,
year = {2023},
author = {Oliveira, HC and Seabra, AB and Kondak, S and Adedokun, OP and Kolbert, Z},
title = {Multilevel approach to plant-nanomaterial relationships: from cells to living ecosystems.},
journal = {Journal of experimental botany},
volume = {74},
number = {12},
pages = {3406-3424},
pmid = {36946676},
issn = {1460-2431},
mesh = {Ecosystem ; *Mycorrhizae/physiology ; Plants ; Plant Roots/physiology ; Symbiosis/physiology ; *Nanostructures ; },
abstract = {Due to their unique properties, nanomaterials behave peculiarly in biosystems. Regarding plants, the interactions of nanomaterials can be interpreted on a spatial scale: from local interactions in cells to systemic effects on whole plants and on ecosystems. Interpreted on a time scale, the effects of nanomaterials on plants may be immediate or subsequent. At the cellular level, the composition and structure of the cell wall and membranes are modified by nanomaterials, promoting internalization. The effects of nanomaterials on germination and seedling physiology and on the primary and secondary metabolism in the shoot are realized at organ and organism levels. Nanomaterials interact with the beneficial ecological partners of plants. The effects of nanomaterials on plant growth-promoting rhizobacteria and legume-rhizobia symbiosis can be stimulating or inhibitory, depending on the concentration and type of nanomaterial. Nanomaterials exert a negative effect on arbuscular mycorrhiza, and vice versa. Pollinators are exposed to nanomaterials, which may affect plant reproduction. The substances released by the roots influence the availability of nanomaterials in the rhizosphere, and components of plant cells trigger internalization, translocation, and transformation of nanomaterials. Understanding of the multilevel and bidirectional relationship between plants and nanomaterials is of great relevance.},
}
@article {pmid36939939,
year = {2023},
author = {Forootan, E},
title = {GIS-based slope-adjusted curve number methods for runoff estimation.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {4},
pages = {489},
pmid = {36939939},
issn = {1573-2959},
mesh = {*Water Movements ; *Geographic Information Systems ; Environmental Monitoring/methods ; Soil ; Hydrology ; Rain ; },
abstract = {Accurate estimation of surface runoff and determination of susceptible lands to runoff generation in ungauged watersheds were the problems for hydrologic engineering which could be predicted through a simple model such as Soil Conservation Service Curve Number (SCS-CN). Due to the slope effects on this method, slope adjustment for curve number was developed to improve its precision. So, the main objectives of this study were to apply GIS-based slope SCS-CN approaches for surface runoff estimation and compare the accuracy of three slope-adjusted models including: (a) model with three empirical parameters, (b) model with two parameters slope function, and (c) model with one parameter in the region located in the central part of Iran. For this purpose, soil texture, hydrologic soil group, land use, slope, and daily rainfall volume maps were utilized. In order to provide the curve number map of the study area, land use and hydrologic soil group layers built in Arc-GIS were intersected and the curve number was determined. Then, three slope adjustment equations were used to modify curve numbers of AMC-II by employing slope map. Finally, recorded runoff data of the hydrometric station were applied to assess the performance of the models through four statistical indicators of the root mean square error (RMSE), the Nash-Sutcliffe efficiency (E), the coefficient of determination [Formula: see text], and percent bias (PB). Land use map analysis showed that rangeland was the dominant land use, whereas the soil texture map specified the greatest and smallest area belonging to loam and sandy loam textures, respectively. Although the runoff results showed the overestimation of large rainfall values and underestimation for rainfall with less than 40 mm volume in both models, the values of E (0.78), RMSE (2), PB (16), and [Formula: see text] (0.88) revealed that eq. (a) with three empirical parameters was the most accurate equation. The maximum percent of runoff generated by rainfall for eqs. (a), (b), and (c) were 68.43, 67.28, and 51.57% which showed that bareland located in south part with the slope of more than 5% was susceptible to runoff generation and should be paid attention to watershed management.},
}
@article {pmid36937826,
year = {2022},
author = {Wabnitz, K and Schwienhorst-Stich, EM and Asbeck, F and Fellmann, CS and Gepp, S and Leberl, J and Mezger, NCS and Eichinger, M},
title = {National Planetary Health learning objectives for Germany: A steppingstone for medical education to promote transformative change.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {1093720},
pmid = {36937826},
issn = {2296-2565},
mesh = {Humans ; *Education, Medical ; Curriculum ; Health Education ; Delivery of Health Care ; Germany ; },
abstract = {Physicians play an important role in adapting to and mitigating the adverse health effects of the unfolding climate and ecological crises. To fully harness this potential, future physicians need to acquire knowledge, values, skills, and leadership attributes to care for patients presenting with environmental change-related conditions and to initiate and propel transformative change in healthcare and other sectors of society including, but not limited to, the decarbonization of healthcare systems, the transition to renewable energies and the transformation of transport and food systems. Despite the potential of Planetary Health Education (PHE) to support medical students in becoming agents of change, best-practice examples of mainstreaming PHE in medical curricula remain scarce both in Germany and internationally. The process of revising and updating the Medical Licensing Regulations and the National Competency-based Catalog of Learning Objectives for Medical Education in Germany provided a window of opportunity to address this implementation challenge. In this article, we describe the development and content of national Planetary Health learning objectives for Germany. We anticipate that the learning objectives will stimulate the development and implementation of innovative Planetary Health teaching, learning and exam formats in medical schools and inform similar initiatives in other health professions. The availability of Planetary Health learning objectives in other countries will provide opportunities for cross-country and interdisciplinary exchange of experiences and validation of content, thus supporting the consolidation of Planetary Health learning objectives and the improvement of PHE for all health professionals globally.},
}
@article {pmid36934309,
year = {2023},
author = {Newbury, JB and Arseneault, L and Moffitt, TE and Odgers, CL and Howe, LD and Bakolis, I and Reuben, A and Danese, A and Sugden, K and Williams, B and Rasmussen, LJH and Trotta, A and Ambler, AP and Fisher, HL},
title = {Socioenvironmental Adversity and Adolescent Psychotic Experiences: Exploring Potential Mechanisms in a UK Longitudinal Cohort.},
journal = {Schizophrenia bulletin},
volume = {49},
number = {4},
pages = {1042-1054},
pmid = {36934309},
issn = {1745-1701},
support = {R01 HD077482/HD/NICHD NIH HHS/United States ; F32 ES034238/ES/NIEHS NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; G1002190/MRC_/Medical Research Council/United Kingdom ; F31 ES029358/ES/NIEHS NIH HHS/United States ; 218632/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/X010791/1/MRC_/Medical Research Council/United Kingdom ; F31ES029358/ES/NIEHS NIH HHS/United States ; 204823/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/M020894/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Child ; Humans ; Adolescent ; Adult ; *Psychotic Disorders/epidemiology/etiology/psychology ; Cross-Sectional Studies ; Social Environment ; Longitudinal Studies ; England/epidemiology ; },
abstract = {BACKGROUND AND HYPOTHESIS: Children exposed to socioenvironmental adversities (eg, urbanicity, pollution, neighborhood deprivation, crime, and family disadvantage) are more likely to subsequently develop subclinical psychotic experiences during adolescence (eg, hearing voices, paranoia). However, the pathways through which this occurs have not been previously investigated. We hypothesized that cognitive ability and inflammation would partly explain this association.<br><br>STUDY DESIGN: Data were utilized from the Environmental-Risk Longitudinal Twin Study, a cohort of 2232 children born in 1994-1995 in England and Wales and followed to age 18. Socioenvironmental adversities were measured from birth to age 10 and classified into physical risk (defined by high urbanicity and air pollution) and socioeconomic risk (defined by high neighborhood deprivation, neighborhood disorder, and family disadvantage). Cognitive abilities (overall, crystallized, fluid, and working memory) were assessed at age 12; and inflammatory markers (C-reactive protein, interleukin-6, soluble urokinase plasminogen activator receptor) were measured at age 18 from blood samples. Participants were interviewed at age 18 regarding psychotic experiences.<br><br>STUDY RESULTS: Higher physical risk and socioeconomic risk were associated with increased odds of psychotic experiences in adolescence. The largest mediation pathways were from socioeconomic risk via overall cognitive ability and crystallized ability, which accounted for ~11% and ~19% of the association with psychotic experiences, respectively. No statistically significant pathways were found via inflammatory markers in exploratory (partially cross-sectional) analyses.<br><br>CONCLUSIONS: Cognitive ability, especially crystallized ability, may partly explain the association between childhood socioenvironmental adversity and adolescent psychotic experiences. Interventions to support cognitive development among children living in disadvantaged settings could buffer them against developing subclinical psychotic phenomena.},
}
@article {pmid36932341,
year = {2023},
author = {Kasmi, Y and Eschbach, E and Hanel, R},
title = {Mare-MAGE curated reference database of fish mitochondrial genes.},
journal = {BMC genomic data},
volume = {24},
number = {1},
pages = {18},
pmid = {36932341},
issn = {2730-6844},
mesh = {Animals ; Databases, Nucleic Acid ; DNA Barcoding, Taxonomic ; *Fishes/genetics ; *Genes, Mitochondrial ; },
abstract = {Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.},
}
@article {pmid36931511,
year = {2023},
author = {Zhang, B and Zheng, T and Zheng, X and Jiang, S and Cao, M and Walther, M and Lu, C},
title = {Dynamics of upstream saltwater intrusion driven by tidal river in coastal aquifers.},
journal = {The Science of the total environment},
volume = {877},
number = {},
pages = {162857},
doi = {10.1016/j.scitotenv.2023.162857},
pmid = {36931511},
issn = {1879-1026},
abstract = {For the coastal aquifers, recent research have shown that the tidal has a significant effect on saltwater intrusion in the near-shore aquifer. However, it is currently unclear how the tidal river contributes to the groundwater flow and salinity distribution in the upstream aquifer of the estuary. This study examined the effects of a tidal river on the dynamic characteristics of groundwater flow and salt transport in a tidal river-coastal aquifer system using field monitoring data and numerical simulations. It was found that changes in tidal-river level led to the reversal of groundwater flow. For a tidal cycle, the maximum area of seawater intrusion is about 41.16 km[2] at the end of the high tide stage. Then the area gradually decreased to 39.02 km[2] at the end of the low tide stage. More than 2 km[2] area variation can be observed in a tidal cycle. Compared to the low tide stage, the area of SWI increased by 5 % at high tide stage. The SWI region was also spreading landward from the tidal river. In addition, we quantified the water exchange and salt flux between the tidal river and aquifer. When the tidal fell below the level of the riverbed, the water exchange rate was stabilized at about -1.6 m/h. The negative value indicated that the river was recharged by the groundwater. With the increasing of tidal water level, the water exchange rate gradually changes from negative to positive and reached the maximum value of 3.2 m/h at the beginning of the falling tide stage. The presence of a physical river dam can amplify the difference in water level between high and low tides, thereby enhancing the influence of a tidal river on water exchange and salt flux. The findings lay the foundation for gaining a comprehensive understanding of the tidal river on groundwater flow and salt transport in upstream aquifers.},
}
@article {pmid36926380,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Parkerson, L and , },
title = {The genome sequence of the garden grass-veneer, Chrysoteuchia culmella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {248},
pmid = {36926380},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Chrysoteuchia culmella (the garden grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 645 megabases in span. The majority of the assembly (99.81%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 21,251 protein coding genes.},
}
@article {pmid36925815,
year = {2022},
author = {Viner, AC and Malata, MP and Mtende, M and Membe-Gadama, G and Masamba, M and Makwakwa, E and Bamuya, C and Lissauer, D and Stock, SJ and Norman, JE and Reynolds, RM and Magowan, B and Freyne, B and Gadama, L and Cunningham-Burley, S and Nyondo-Mipando, L and Chipeta, E},
title = {Implementation of a novel ultrasound training programme for midwives in Malawi: A mixed methods evaluation using the RE-AIM framework.},
journal = {Frontiers in health services},
volume = {2},
number = {},
pages = {953677},
pmid = {36925815},
issn = {2813-0146},
support = {/WT_/Wellcome Trust/United Kingdom ; MR/N022556/1/MRC_/Medical Research Council/United Kingdom ; MR/T038683/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {INTRODUCTION: Despite recommendation that all women receive an ultrasound in pregnancy prior to 24 weeks', this remains unavailable to many women in low-income countries where trained practitioners are scarce. Although many programmes have demonstrated efficacy, few have achieved longterm sustainability, with a lack of information about how best to implement such programmes. This mixed-methods study aimed to evaluate the implementation of a novel education package to teach ultrasound-naive midwives in Malawi basic obstetric ultrasound, assessing its impact in the context of the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework.<br><br>METHODS: The study ran across six sites in Malawi between October 2020 and June 2021, encompassing three phases; pre-implementation, implementation and post-implementation. Twenty nine midwives underwent a bespoke education package with matched pre and post course surveys assessed their knowledge, attitudes and confidence and "hands on" assessments evaluating practical skills. Training evaluation forms and in-depth interviews explored their satisfaction with the package, with repeat assessment and remote image review evaluating maintenance of skills.<br><br>RESULTS: 28/29 midwives completed the training, with significant increases in knowledge, confidence and practical skills. Adherence to the education package varied, however many changes to the proposed methodology were adaptive and appeared to facilitate the efficacy of the programme. Unfortunately, despite reporting approval regarding the training itself, satisfaction regarding supervision and follow up was mixed, reflecting the difficulties encountered with providing ongoing in-person and remote support.<br><br>CONCLUSION: This programme was successful in improving trainees' knowledge, confidence and skill in performing basic obstetric ultrasound, largely on account of an adaptive approach to implementation. The maintenance of ongoing support was challenging, reflected by trainee dissatisfaction. By evaluating the success of this education package based on its implementation and not just its efficacy, we have generated new insights into the barriers to sustainable upscale, specifically those surrounding maintenance.},
}
@article {pmid36921339,
year = {2023},
author = {Zhang, H and Wang, X and Song, R and Ding, W and Li, F and Ji, L},
title = {Emerging Metabolic Profiles of Sulfonamide Antibiotics by Cytochromes P450: A Computational-Experimental Synergy Study on Emerging Pollutants.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {13},
pages = {5368-5379},
doi = {10.1021/acs.est.3c00071},
pmid = {36921339},
issn = {1520-5851},
mesh = {Humans ; *Anti-Bacterial Agents ; *Environmental Pollutants ; Sulfamethoxazole/metabolism ; Sulfanilamide ; Sulfonamides ; Cytochrome P-450 Enzyme System/metabolism ; Metabolome ; },
abstract = {Metabolism, especially by CYP450 enzymes, is the main reason for mediating the toxification and detoxification of xenobiotics in humans, while some uncommon metabolic pathways, especially for emerging pollutants, probably causing idiosyncratic toxicity are easily overlooked. The pollution of sulfonamide antibiotics in aqueous system has attracted increasing public attention. Hydroxylation of the central amine group can trigger a series of metabolic processes of sulfonamide antibiotics in humans; however, this work parallelly reported the coupling and fragmenting initiated by amino H-abstraction of sulfamethoxazole (SMX) catalyzed by human CYP450 enzymes. Elucidation of the emerging metabolic profiles was mapped via a multistep synergy between computations and experiments, involving preliminary DFT computations and in vitro and in vivo assays, profiling adverse effects, and rationalizing the fundamental factors via targeted computations. Especially, the confirmed SMX dimer was shown to potentially act as a metabolism disruptor in humans, while spin aromatic delocalization resulting in the low electron donor ability of amino radicals was revealed as the fundamental factor to enable coupling of sulfonamide antibiotics by CYP450 through the nonconventional nonrebound pathway. This work may further strengthen the synergistic use of computations prior to experiments to avoid wasteful experimental screening efforts in environmental chemistry and toxicology.},
}
@article {pmid36921166,
year = {2023},
author = {Morais, LS and Pimentel, SVT and Kawa, H and Fonseca, SC},
title = {Temporal trend of congenital syphilis in the most populous municipality of metropolitan region II of Rio de Janeiro state.},
journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo},
volume = {41},
number = {},
pages = {e2021337},
pmid = {36921166},
issn = {1984-0462},
mesh = {Pregnancy ; Adolescent ; Humans ; Female ; *Syphilis, Congenital/epidemiology ; Brazil/epidemiology ; Prenatal Care ; Incidence ; Databases, Factual ; },
abstract = {OBJECTIVE: This study aimed to explore the temporal trend in congenital syphilis, according to sociodemographic and prenatal care in the city of São Gonçalo - Rio de Janeiro, from 2007 to 2018.<br><br>METHODS: Ecological time series study, with data from SINAN (Information System for Notifiable Diseases) and SINASC (Information System on Live Births databases). We calculated annual incidence (per 1,000 live births) according to sociodemographic and prenatal variables. For the same variables, we calculated trends by logarithmic regression (Joinpoint Regression), estimating the annual percentage change.<br><br>RESULTS: A total of 2,420 cases were reported from 2007 to 2018, with an increasing trend: 64.9% per year (2010-2013) and 24.9% (2013-2018). In 2018, the highest rates were in adolescents (90.6/1,000 live births), black women (87.6/1,000 live births), low-educated women (122.8/1,000 live births), and those without prenatal care (677.4/1,000 live births). The annual percentage change of these categories was, respectively, 37.3% (2010-2018), 33.5% (2012-2018), 39.9% (2014-2018), and 85.0% (2011-2015), but all categories showed a crescent trend.<br><br>CONCLUSIONS: We identified high congenital syphilis incidences and crescent trends, especially in more vulnerable groups, pointing to social and healthcare inequalities. Prenatal care needs to be more comprehensive and qualified, primarily for young, low-educated, and black women.},
}
@article {pmid36920898,
year = {2023},
author = {Helmer, EH and Kay, S and Marcano-Vega, H and Powers, JS and Wood, TE and Zhu, X and Gwenzi, D and Ruzycki, TS},
title = {Multiscale predictors of small tree survival across a heterogeneous tropical landscape.},
journal = {PloS one},
volume = {18},
number = {3},
pages = {e0280322},
pmid = {36920898},
issn = {1932-6203},
mesh = {*Ecosystem ; Biomass ; Wood ; Introduced Species ; *Cyclonic Storms ; Tropical Climate ; },
abstract = {Uncertainties about controls on tree mortality make forest responses to land-use and climate change difficult to predict. We tracked biomass of tree functional groups in tropical forest inventories across Puerto Rico and the U.S. Virgin Islands, and with random forests we ranked 86 potential predictors of small tree survival (young or mature stems 2.5-12.6 cm diameter at breast height). Forests span dry to cloud forests, range in age, geology and past land use and experienced severe drought and storms. When excluding species as a predictor, top predictors are tree crown ratio and height, two to three species traits and stand to regional factors reflecting local disturbance and the system state (widespread recovery, drought, hurricanes). Native species, and species with denser wood, taller maximum height, or medium typical height survive longer, but short trees and species survive hurricanes better. Trees survive longer in older stands and with less disturbed canopies, harsher geoclimates (dry, edaphically dry, e.g., serpentine substrates, and highest-elevation cloud forest), or in intervals removed from hurricanes. Satellite image phenology and bands, even from past decades, are top predictors, being sensitive to vegetation type and disturbance. Covariation between stand-level species traits and geoclimate, disturbance and neighboring species types may explain why most neighbor variables, including introduced vs. native species, had low or no importance, despite univariate correlations with survival. As forests recovered from a hurricane in 1998 and earlier deforestation, small trees of introduced species, which on average have lighter wood, died at twice the rate of natives. After hurricanes in 2017, the total biomass of trees ≥12.7 cm dbh of the introduced species Spathodea campanulata spiked, suggesting that more frequent hurricanes might perpetuate this light-wooded species commonness. If hurricane recovery favors light-wooded species while drought favors others, climate change influences on forest composition and ecosystem services may depend on the frequency and severity of extreme climate events.},
}
@article {pmid36918541,
year = {2023},
author = {Young, WJ and Haessler, J and Benjamins, JW and Repetto, L and Yao, J and Isaacs, A and Harper, AR and Ramirez, J and Garnier, S and van Duijvenboden, S and Baldassari, AR and Concas, MP and Duong, T and Foco, L and Isaksen, JL and Mei, H and Noordam, R and Nursyifa, C and Richmond, A and Santolalla, ML and Sitlani, CM and Soroush, N and Thériault, S and Trompet, S and Aeschbacher, S and Ahmadizar, F and Alonso, A and Brody, JA and Campbell, A and Correa, A and Darbar, D and De Luca, A and Deleuze, JF and Ellervik, C and Fuchsberger, C and Goel, A and Grace, C and Guo, X and Hansen, T and Heckbert, SR and Jackson, RD and Kors, JA and Lima-Costa, MF and Linneberg, A and Macfarlane, PW and Morrison, AC and Navarro, P and Porteous, DJ and Pramstaller, PP and Reiner, AP and Risch, L and Schotten, U and Shen, X and Sinagra, G and Soliman, EZ and Stoll, M and Tarazona-Santos, E and Tinker, A and Trajanoska, K and Villard, E and Warren, HR and Whitsel, EA and Wiggins, KL and Arking, DE and Avery, CL and Conen, D and Girotto, G and Grarup, N and Hayward, C and Jukema, JW and Mook-Kanamori, DO and Olesen, MS and Padmanabhan, S and Psaty, BM and Pattaro, C and Ribeiro, ALP and Rotter, JI and Stricker, BH and van der Harst, P and van Duijn, CM and Verweij, N and Wilson, JG and Orini, M and Charron, P and Watkins, H and Kooperberg, C and Lin, HJ and Wilson, JF and Kanters, JK and Sotoodehnia, N and Mifsud, B and Lambiase, PD and Tereshchenko, LG and Munroe, PB},
title = {Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1411},
pmid = {36918541},
issn = {2041-1723},
support = {CH/1992001/6764/BHF_/British Heart Foundation/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; R56 HL118277/HL/NHLBI NIH HHS/United States ; MC_PC_20029/MRC_/Medical Research Council/United Kingdom ; R01 HL105756/HL/NHLBI NIH HHS/United States ; R01 HL118277/HL/NHLBI NIH HHS/United States ; K24 HL148521/HL/NHLBI NIH HHS/United States ; MR/N025083/1/MRC_/Medical Research Council/United Kingdom ; MR/R017468/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Cardiovascular Diseases/genetics ; *Atrioventricular Block ; Genome-Wide Association Study ; Risk Factors ; Arrhythmias, Cardiac/genetics ; Electrocardiography/methods ; Biomarkers ; },
abstract = {The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.},
}
@article {pmid36914632,
year = {2023},
author = {Kohyama, TI and Sheil, D and Sun, IF and Niiyama, K and Suzuki, E and Hiura, T and Nishimura, N and Hoshizaki, K and Wu, SH and Chao, WC and Nur Hajar, ZS and Rahajoe, JS and Kohyama, TS},
title = {Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1113},
pmid = {36914632},
issn = {2041-1723},
mesh = {Humans ; *Trees ; *Forests ; Biomass ; Wood ; Asia, Eastern ; Tropical Climate ; },
abstract = {Despite their fundamental importance the links between forest productivity, diversity and climate remain contentious. We consider whether variation in productivity across climates reflects adjustment among tree species and individuals, or changes in tree community structure. We analysed data from 60 plots of humid old-growth forests spanning mean annual temperatures (MAT) from 2.0 to 26.6 °C. Comparing forests at equivalent aboveground biomass (160 Mg C ha[-1]), tropical forests ≥24 °C MAT averaged more than double the aboveground woody productivity of forests <12 °C (3.7 ± 0.3 versus 1.6 ± 0.1 Mg C ha[-1] yr[-1]). Nonetheless, species with similar standing biomass and maximum stature had similar productivity across plots regardless of temperature. We find that differences in the relative contribution of smaller- and larger-biomass species explained 86% of the observed productivity differences. Species-rich tropical forests are more productive than other forests due to the high relative productivity of many short-stature, small-biomass species.},
}
@article {pmid36911337,
year = {2023},
author = {Lim, T and Lee, K and Kim, RH and Ryu, J and Cha, KH and Park, SY and Koo, SY and Hwang, KT},
title = {Effects of black raspberry extract on gut microbiota, microbial metabolites, and expressions of the genes involved in cholesterol and bile acid metabolisms in rats fed excessive choline with a high-fat diet.},
journal = {Food science and biotechnology},
volume = {32},
number = {4},
pages = {577-587},
pmid = {36911337},
issn = {2092-6456},
abstract = {UNLABELLED: In our previous study, black raspberry (BR) reduced the serum levels of trimethylamine-N-oxide and cholesterol in rats fed excessive choline with a high-fat diet (HFC). We hypothesized that gut microbiota could play a crucial role in the production of trimethylamine and microbial metabolites, and BR could influence gut microbial composition. This study aimed to elucidate the role of BR on changes in gut microbiota and microbial metabolites in the rats. The phylogenetic diversity of gut microbiota was reduced in the rats fed HFC, while that in the BR-fed group was restored. The BR supplementation enriched Bifidobacterium and reduced Clostridium cluster XIVa. In the BR-fed group, most cecal bile acids and hippuric acid increased, while serum lithocholic acid was reduced. The BR supplementation upregulated Cyp7a1 and downregulated Srebf2. These results suggest that BR extract may change gut bacterial community, modulate bile acids, and regulate gene expression toward reducing cholesterol.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01267-4.},
}
@article {pmid36911308,
year = {2023},
author = {Martinez, ND},
title = {Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology.},
journal = {Ecology and evolution},
volume = {13},
number = {3},
pages = {e9872},
pmid = {36911308},
issn = {2045-7758},
abstract = {Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.},
}
@article {pmid36901248,
year = {2023},
author = {Zeng, L and Liu, C},
title = {Exploring Factors Affecting Urban Park Use from a Geospatial Perspective: A Big Data Study in Fuzhou, China.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {5},
pages = {},
pmid = {36901248},
issn = {1660-4601},
support = {FJ2022C070//Social Science Foundation of Fujian, China/ ; },
mesh = {Humans ; Urban Population ; *Parks, Recreational ; *Big Data ; Cities ; China ; },
abstract = {Promoting research on urban park use is important for developing the ecological and environmental health benefits of parks. This study proposes uniquely integrated methods combined with big data to measure urban park use. It combines comprehensive geographic detectors and multiscale geographically weighted regression from a geospatial perspective to quantify the individual and interactive effects of the parks' characteristics, accessibility, and surrounding environment features on weekday and weekend park use. The study also explores the degree of influence of spatial changes. The results indicate that the park-surrounding facilities and services factor contributed most to use, while its interaction effect with park service capacity had the greatest impact on park use. The interaction effects showed binary or nonlinear enhancement. This suggests that park use should be promoted within multiple dimensions. Many influencing factors had significant changes in the geographic space, suggesting that city-level park zoning construction should be adopted. Finally, park use was found to be affected by users' subjective preference on weekends and convenience factors on weekdays. These findings provide a theoretical basis for the influencing mechanisms of urban park use, which can help urban planners and policymakers formulate more specific policies to successfully manage and plan urban parks.},
}
@article {pmid36900138,
year = {2023},
author = {Würstle, S and Hapfelmeier, A and Karapetyan, S and Studen, F and Isaakidou, A and Schneider, T and Schmid, RM and von Delius, S and Gundling, F and Burgkart, R and Obermeier, A and Mayr, U and Ringelhan, M and Rasch, S and Lahmer, T and Geisler, F and Turner, PE and Chan, BK and Spinner, CD and Schneider, J},
title = {Differentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {13},
number = {5},
pages = {},
pmid = {36900138},
issn = {2075-4418},
support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; },
abstract = {Ascitic fluid infection is a serious complication of liver cirrhosis. The distinction between the more common spontaneous bacterial peritonitis (SBP) and the less common secondary peritonitis in patients with liver cirrhosis is crucial due to the varying treatment approaches. This retrospective multicentre study was conducted in three German hospitals and analysed 532 SBP episodes and 37 secondary peritonitis episodes. Overall, >30 clinical, microbiological, and laboratory parameters were evaluated to identify key differentiation criteria. Microbiological characteristics in ascites followed by severity of illness and clinicopathological parameters in ascites were the most important predictors identified by a random forest model to distinguish between SBP and secondary peritonitis. To establish a point-score model, a least absolute shrinkage and selection operator (LASSO) regression model selected the ten most promising discriminatory features. By aiming at a sensitivity of 95% either to rule out or rule in SBP episodes, two cut-off scores were defined, dividing patients with infected ascites into a low-risk (score ≥ 45) and high-risk group (score < 25) for secondary peritonitis. Overall, the discrimination of secondary peritonitis from SBP remains challenging. Our univariable analyses, random forest model, and LASSO point score may help clinicians with the crucial differentiation between SBP and secondary peritonitis.},
}
@article {pmid36899307,
year = {2023},
author = {Chan, YO and Dietz, N and Zeng, S and Wang, J and Flint-Garcia, S and Salazar-Vidal, MN and Škrabišová, M and Bilyeu, K and Joshi, T},
title = {The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {107},
pmid = {36899307},
issn = {1471-2164},
support = {1920-152-0131-C//United Soybean Board/ ; 2220-152-0202//United Soybean Board/ ; },
mesh = {*Alleles ; *Internet ; *Software ; Mutation ; *Datasets as Topic ; *Glycine max/genetics ; *Zea mays/genetics ; *Arabidopsis/genetics ; Data Visualization ; Genes, Plant/genetics ; Pigmentation/genetics ; Plant Dormancy/genetics ; Gene Frequency ; Amino Acid Substitution ; Genotype ; Metadata ; *Data Mining/methods ; },
abstract = {BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize.<br><br>RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes.<br><br>CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website (https://soykb.org/SoybeanAlleleCatalogTool/), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website (https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana). Researchers can use this tool to connect variant alleles of genes with meta-information of species.},
}
@article {pmid36899120,
year = {2023},
author = {Yilanci, V and Candan, G and Shah, MI},
title = {Identifying the roles of energy and economic factors on environmental degradation in MINT economies: a hesitant fuzzy analytic hierarchy process.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {19},
pages = {55768-55781},
pmid = {36899120},
issn = {1614-7499},
mesh = {*Analytic Hierarchy Process ; Carbon Dioxide ; Cross-Sectional Studies ; Economic Development ; Economic Factors ; Investments ; Renewable Energy ; },
abstract = {Globally, research communities have been studying the different determinants of environmental degradation or pollution using different contexts and methods. In this study, we identify several energy and economic factors, such as energy consumption (EC), gross domestic product (GDP), energy production (EP), urbanization (URB), and foreign direct investment (FDI) as the most effective factors of environmental degradation by obtaining several environmental researchers' opinions and using the hesitant fuzzy analytic hierarchy process. In the later stage of the analysis, we use these variables as regressors of the ecological footprint (EF) as a proxy for environmental degradation. Since we find evidence of cross-sectional dependence among the members of the variables, we use second-generational panel tests. First, we test the stationarity of the variables using the cross-sectionally augmented IPS (CIPS) panel unit test. The results show that the regressors have different orders of integration. So, we employ the Durbin-Hausman panel cointegration test to test the existence of a long-run relationship between the variables. Having found a long-run relationship, we estimate the long-run coefficients using the common correlated effects mean group estimator, which reveals that energy consumption has an increasing effect on the EF in Indonesia and Turkey, while energy production has a negative impact in Mexico and Turkey. While GDP has an increasing effect in all countries, FDI has a similar effect in only Indonesia. Moreover, URB decreases the ecological footprint in Nigeria, while it increases in Turkey. Our approach to the evaluation of environmental degradation can be generalized to other regions as well as where there is a significant need to understand the roles of different drivers on environmental degradation or pollution.},
}
@article {pmid36895518,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Lees, D and , },
title = {The genome sequence of the yellow-legged clearwing, Synanthedon vespiformis (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {233},
pmid = {36895518},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length.},
}
@article {pmid36894986,
year = {2023},
author = {de Nies, L and Galata, V and Martin-Gallausiaux, C and Despotovic, M and Busi, SB and Snoeck, CJ and Delacour, L and Budagavi, DP and Laczny, CC and Habier, J and Lupu, PC and Halder, R and Fritz, JV and Marques, T and Sandt, E and O'Sullivan, MP and Ghosh, S and Satagopam, V and , and Krüger, R and Fagherazzi, G and Ollert, M and Hefeng, FQ and May, P and Wilmes, P},
title = {Altered infective competence of the human gut microbiome in COVID-19.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {46},
pmid = {36894986},
issn = {2049-2618},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; SARS-CoV-2/genetics ; *Microbiota ; Multiomics ; },
abstract = {BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.<br><br>RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.<br><br>CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.},
}
@article {pmid36893405,
year = {2023},
author = {Mallinson, DC and Elwert, F and Ehrenthal, DB},
title = {Spillover Effects of Prenatal Care Coordination on Older Siblings Beyond the Mother-Infant Dyad.},
journal = {Medical care},
volume = {61},
number = {4},
pages = {206-215},
pmid = {36893405},
issn = {1537-1948},
support = {P2C HD042849/HD/NICHD NIH HHS/United States ; T32 HD007014/HD/NICHD NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; UL1 TR002373/TR/NCATS NIH HHS/United States ; },
mesh = {Pregnancy ; Child ; Female ; Infant ; Humans ; Adolescent ; *Prenatal Care ; Siblings ; Mothers ; Wisconsin ; *Maternal Health Services ; },
abstract = {BACKGROUND: Pregnancy care coordination increases preventive care receipt for mothers and infants. Whether such services affect other family members' health care is unknown.<br><br>OBJECTIVE: To estimate the spillover effect of maternal exposure to Wisconsin Medicaid's Prenatal Care Coordination (PNCC) program during pregnancy with a younger sibling on the preventive care receipt for an older child.<br><br>RESEARCH DESIGN: Gain-score regressions-a sibling fixed effects strategy-estimated spillover effects while controlling for unobserved family-level confounders.<br><br>SUBJECTS: Data came from a longitudinal cohort of linked Wisconsin birth records and Medicaid claims. We sampled 21,332 sibling pairs (one older; one younger) who were born during 2008-2015, who were <4 years apart in age, and whose births were Medicaid-covered. In all, 4773 (22.4%) mothers received PNCC during pregnancy with the younger sibling.<br><br>MEASURES: The exposure was maternal PNCC receipt during pregnancy with the younger sibling (none; any). The outcome was the older sibling's number of preventive care visits or preventive care services in the younger sibling's first year of life.<br><br>RESULTS: Overall, maternal exposure to PNCC during pregnancy with the younger sibling did not affect older siblings' preventive care. However, among siblings who were 3 to <4 years apart in age, there was a positive spillover on the older sibling's receipt of care by 0.26 visits (95% CI: 0.11, 0.40 visits) and by 0.34 services (95% CI: 0.12, 0.55 services).<br><br>CONCLUSION: PNCC may only have spillover effects on siblings' preventive care in selected subpopulations but not in the broader population of Wisconsin families.},
}
@article {pmid36893162,
year = {2023},
author = {Rubenstein, DR and Solomon, J},
title = {Target-enriched enzymatic methyl sequencing: Flexible, scalable and inexpensive hybridization capture for quantifying DNA methylation.},
journal = {PloS one},
volume = {18},
number = {3},
pages = {e0282672},
pmid = {36893162},
issn = {1932-6203},
mesh = {*DNA Methylation ; Sequence Analysis, DNA/methods ; Reproducibility of Results ; Nucleic Acid Hybridization ; *Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; CpG Islands/genetics ; },
abstract = {The increasing interest in studying DNA methylation to understand how traits or diseases develop requires new and flexible approaches for quantifying DNA methylation in a diversity of organisms. In particular, we need efficient yet cost-effective ways to measure CpG methylation states over large and complete regions of the genome. Here, we develop TEEM-Seq (target-enriched enzymatic methyl sequencing), a method that combines enzymatic methyl sequencing with a custom-designed hybridization capture bait set that can be scaled to reactions including large numbers of samples in any species for which a reference genome is available. Using DNA from a passerine bird, the superb starling (Lamprotornis superbus), we show that TEEM-Seq is able to quantify DNA methylation states similarly well to the more traditional approaches of whole-genome and reduced-representation sequencing. Moreover, we demonstrate its reliability and repeatability, as duplicate libraries from the same samples were highly correlated. Importantly, the downstream bioinformatic analysis for TEEM-Seq is the same as for any sequence-based approach to studying DNA methylation, making it simple to incorporate into a variety of workflows. We believe that TEEM-Seq could replace traditional approaches for studying DNA methylation in candidate genes and pathways, and be effectively paired with other whole-genome or reduced-representation sequencing approaches to increase project sample sizes. In addition, TEEM-Seq can be combined with mRNA sequencing to examine how DNA methylation in promoters or other regulatory regions is related to the expression of individual genes or gene networks. By maximizing the number of samples in the hybridization reaction, TEEM-Seq is an inexpensive and flexible sequence-based approach for quantifying DNA methylation in species where other capture-based methods are unavailable or too expensive, particularly for non-model organisms.},
}
@article {pmid36882531,
year = {2023},
author = {Wei, Z and Jian, Z and Sun, Y and Pan, F and Han, H and Liu, Q and Mei, Y},
title = {Ecological sustainability and high-quality development of the Yellow River Delta in China based on the improved ecological footprint model.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {3821},
pmid = {36882531},
issn = {2045-2322},
abstract = {Aiming at the traditional ecological footprint model, the improved ecological footprint of the carbon footprint effectively makes up for the singularity of the ecological footprint's consideration of carbon emissions, and plays an important role in promoting high-quality development and ecological sustainability. This paper selects 2015, 2018 and 2020 as important time points for the study, corrects the ecological footprint parameter factors based on net primary productivity (NPP), measures the ecological footprint after the improvement of the carbon footprint, studies the spatial and temporal variation in the ecological footprint at the 100-m grid scale with the support of IPCC greenhouse gas inventory analysis, and analyzes the current ecological conservation status of the Yellow River Delta. Additionally, in the context of a low carbon economy, the decoupling index of carbon emissions and GDP is extended to the evaluation and analysis of high-quality development. The study showed that (1) the ecological footprint of the Yellow River Delta has increased year by year, from 0.721 hm[2]·person[- 1] to 0.758 hm[2]·person[- 1], an average annual increase of 2.9%; the ecological carrying capacity has decreased from 0.40 hm[2]·person[- 1] to 0.31 hm[2]·person[- 1], an overall decrease of 28.59%. (2) The overall ecological deficit of the Yellow River Delta grid is lightly overloaded, with most of the ecological surplus occurring in the northern and eastern parts of the study area and a few moderate and heavy overloads in the center of the core area where there is a lot of built-up land and the area is small and easy to gather. (3) Based on the low-carbon economy analysis, 2015, 2017 and 2020 reach absolute decoupling and are in the ideal scenario. However, in the rest of the years, carbon emissions and economic development are still in a large contradiction, and decoupling has fluctuated and varied greatly in the last six years. The effective combination of ecological footprint and low carbon economy analysis provides an important theoretical basis for improving ecological conservation and achieving high-quality development.},
}
@article {pmid36880704,
year = {2023},
author = {Amato, S and Benson, JS and Stewart, B and Sarathy, A and Osler, T and Hosmer, D and An, G and Cook, A and Winchell, RJ and Malhotra, AK},
title = {Current patterns of trauma center proliferation have not led to proportionate improvements in access to care or mortality after injury: An ecologic study.},
journal = {The journal of trauma and acute care surgery},
volume = {94},
number = {6},
pages = {755-764},
pmid = {36880704},
issn = {2163-0763},
mesh = {Humans ; United States/epidemiology ; *Trauma Centers ; Income ; Geographic Information Systems ; Health Services Accessibility ; Cell Proliferation ; *Wounds and Injuries/therapy ; },
abstract = {BACKGROUND: Timely access to high-level (I/II) trauma centers (HLTCs) is essential to minimize mortality after injury. Over the last 15 years, there has been a proliferation of HLTC nationally. The current study evaluates the impact of additional HLTC on population access and injury mortality.<br><br>METHODS: A geocoded list of HLTC, with year designated, was obtained from the American Trauma Society, and 60-minute travel time polygons were created using OpenStreetMap data. Census block group population centroids, county population centroids, and American Communities Survey data from 2005 and 2020 were integrated. Age-adjusted nonoverdose injury mortality was obtained from CDC Wide-ranging Online Data for Epidemiologic Research and the Robert Wood Johnson Foundation. Geographically weighted regression models were used to identify independent predictors of HLTC access and injury mortality.<br><br>RESULTS: Over the 15-year (2005-2020) study period, the number of HLTC increased by 31.0% (445 to 583), while population access to HLTC increased by 6.9% (77.5-84.4%). Despite this increase, access was unchanged in 83.1% of counties, with a median change in access of 0.0% (interquartile range, 0.0-1.1%). Population-level age-adjusted injury mortality rates increased by 5.39 per 100,000 population during this time (60.72 to 66.11 per 100,000). Geographically weighted regression controlling for population demography and health indicators found higher median income and higher population density to be positively associated with majority (&#x2265;50%) HLTC population coverage and negatively associated with county-level nonoverdose mortality.<br><br>CONCLUSION: Over the past 15 years, the number of HLTC increased 31%, while population access to HLTC increased only 6.9%. High-level (I/II) trauma center designation is likely driven by factors other than population need. To optimize efficiency and decrease potential oversupply, the designation process should include population level metrics. Geographic information system methodology can be an effective tool to assess optimal placement.<br><br>LEVEL OF EVIDENCE: Prognostic and Epidemiological; Level IV.},
}
@article {pmid36879919,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Parker, B and Plotkin, D and Kawahara, AY and , },
title = {The genome sequence of the sallow kitten, Furcula furcula (Clerck, 1759).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {229},
pmid = {36879919},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.},
}
@article {pmid36875992,
year = {2022},
author = {Tadrent, N and Dedeine, F and Hervé, V},
title = {SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.},
journal = {F1000Research},
volume = {11},
number = {},
pages = {1522},
pmid = {36875992},
issn = {2046-1402},
mesh = {*Metagenome ; Workflow ; *Software ; Metagenomics/methods ; Computational Biology ; },
abstract = {Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.},
}
@article {pmid36877490,
year = {2024},
author = {Redhead, D and McElreath, R and Ross, CT},
title = {Reliable network inference from unreliable data: A tutorial on latent network modeling using STRAND.},
journal = {Psychological methods},
volume = {29},
number = {6},
pages = {1100-1122},
doi = {10.1037/met0000519},
pmid = {36877490},
issn = {1939-1463},
support = {//Economic and Social Research Council/ ; //Max Planck Institute for Evolutionary Anthropology; Department of Human Behavior, Ecology and Culture/ ; },
mesh = {Humans ; *Models, Statistical ; *Social Networking ; Social Network Analysis ; Data Interpretation, Statistical ; Psychology/methods ; },
abstract = {Social network analysis provides an important framework for studying the causes, consequences, and structure of social ties. However, standard self-report measures-for example, as collected through the popular "name-generator" method-do not provide an impartial representation of such ties, be they transfers, interactions, or social relationships. At best, they represent perceptions filtered through the cognitive biases of respondents. Individuals may, for example, report transfers that did not really occur, or forget to mention transfers that really did. The propensity to make such reporting inaccuracies is both an individual-level and item-level characteristic-variable across members of any given group. Past research has highlighted that many network-level properties are highly sensitive to such reporting inaccuracies. However, there remains a dearth of easily deployed statistical tools that account for such biases. To address this issue, we provide a latent network model that allows researchers to jointly estimate parameters measuring both reporting biases and a latent, underlying social network. Building upon past research, we conduct several simulation experiments in which network data are subject to various reporting biases, and find that these reporting biases strongly impact fundamental network properties. These impacts are not adequately remedied using the most frequently deployed approaches for network reconstruction in the social sciences (i.e., treating either the union or the intersection of double-sampled data as the true network), but are appropriately resolved through the use of our latent network models. To make implementation of our models easier for end-users, we provide a fully documented R package, STRAND, and include a tutorial illustrating its functionality when applied to empirical food/money sharing data from a rural Colombian population. (PsycInfo Database Record (c) 2024 APA, all rights reserved).},
}
@article {pmid36876314,
year = {2023},
author = {Zhang, J and Qian, H},
title = {U.Taxonstand: An R package for standardizing scientific names of plants and animals.},
journal = {Plant diversity},
volume = {45},
number = {1},
pages = {1-5},
pmid = {36876314},
issn = {2468-2659},
abstract = {The scientific names of organisms are key identifiers of plants and animals. Correctly treating scientific names is a prerequisite for biodiversity research and documentation. Here, we present an R package, 'U.Taxonstand', which can standardize and harmonize scientific names in plant and animal species lists at a fast speed and at a high rate of matching success. Unlike most of other similar R packages each of which works with only one taxonomic database, U.Taxonstand can work with all taxonomic databases, as long as they are properly formatted. Multiple databases for plants and animals that can be directly used by U.Taxonstand, which include bryophytes, vascular plants, amphibians, birds, fishes, mammals, and reptiles, are available online. U.Taxonstand can be a very useful tool for botanists, zoologists, ecologists and biogeographers to standardize and harmonize scientific names of organisms.},
}
@article {pmid36874580,
year = {2022},
author = {Hayward, A and Lohse, K and Laetsch, DR and Vila, R and , and , and , and Taluy, E and , },
title = {The genome sequence of the silver-studded blue, Plebejus argus (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {315},
pmid = {36874580},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Plebejus argus (silver-studded blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 382 megabases in span. The entire assembly (100%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 27.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,693 protein coding genes.},
}
@article {pmid36874578,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Seraphim, Lobophora halterata (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {313},
pmid = {36874578},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Lobophora halterata (the Seraphim; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 315 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules with the Z and W sex chromosomes assembled. The mitochondrial genome has also been assembled and is 15.7 kilobases in length.},
}
@article {pmid36874577,
year = {2022},
author = {Hawkes, W and Wotton, K and , and , and , and , and , and , },
title = {The genome sequence of the dumpy grass hoverfly, Melanostoma mellinum (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {59},
pmid = {36874577},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Melanostoma mellinum (the dumpy grass hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 731 megabases in span. The majority of the assembly (99.67%) is scaffolded into five chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 16.1 kilobases in length.},
}
@article {pmid36874564,
year = {2022},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the large yellow underwing, Noctua pronuba (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {119},
pmid = {36874564},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Noctua pronuba (the large yellow underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 529 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.},
}
@article {pmid36872222,
year = {2023},
author = {Zhang, GZ and Chen, SL and Dong, LL},
title = {[Traditional Chinese medicine microbiomics and its research strategies].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {3},
pages = {596-607},
doi = {10.19540/j.cnki.cjcmm.20221101.101},
pmid = {36872222},
issn = {1001-5302},
mesh = {Ecology ; Fermentation ; High-Throughput Nucleotide Sequencing ; *Medicine, Chinese Traditional ; *Research Design ; },
abstract = {The tight relationships between microbiome and traditional Chinese medicine(TCM)have been widely recognized. New technologies, results, and theories are emerging in the field of microbiomics in recent years with the advances in high-throughput sequencing and multi-omics technologies. Based on the previous research, the present study has proposed the concept of TCM microbiomics(TCMM), which is an interdisciplinary subject aiming at elucidating the functions and applications of microbiome in the areas of herb resources, herb processing, herb storage, and clinical effects by using modern technology of biology, ecology, and informatics. This subject essentially contains the structures, functions, interactions, molecular mechanisms, and application strategies of the microbiome associated with the quality, safety, and efficacy of TCM. Firstly, the development of the TCMM concept was summarized, with the profound understanding of TCMM on the complexity and entirety of microbiome being emphasized. Then, the research contents and applications of TCMM in promoting the sustainable development of herb resources, improving the standardization and diversification of herb fermentation, strengthening the safety of herb storage, and resolving the scientific connotation of theories and clinical efficacy of TCM are reviewed. Finally, the research strategies and methods of TCM microbiomics were elaborated from basic research, application research, and system research. TCMM is expected to promote the integrative development of TCM with frontier science and technology, thereby expanding the depth and scope of TCM study and facilitating TCM modernization.},
}
@article {pmid36868417,
year = {2023},
author = {Zhang, X and Shao, W and Huo, Y and Kong, Y and Zhang, W and Li, S and Zhou, W and Wu, X and Qin, F and Hu, X},
title = {The effects of short-term dietary exposure to SiO2 nanoparticle on the domesticated lepidopteran insect model silkworm (Bombyx mori): Evidence from the perspective of multi-omics.},
journal = {Chemosphere},
volume = {323},
number = {},
pages = {138257},
doi = {10.1016/j.chemosphere.2023.138257},
pmid = {36868417},
issn = {1879-1298},
mesh = {Animals ; *Bombyx/metabolism ; Silicon Dioxide/metabolism ; Multiomics ; Dietary Exposure ; *Nanoparticles/toxicity ; },
abstract = {Silicon dioxide nanoparticles (nSiO2) are one of the widely utilized nanoparticle (NPSs) materials, and exposure to nSiO2 is ubiquitous. With the increasing commercialization of nSiO2, the potential risk of nSiO2 release to the health and the ecological environment have been attracted more attention. In this study, the domesticated lepidopteran insect model silkworm (Bombyx mori) was utilized to evaluate the biological effects of dietary exposure to nSiO2. Histological investigations showed that nSiO2 exposure resulted in midgut tissue injury in a dose-dependent manner. Larval body mass and cocoon production were reduced by nSiO2 exposure. ROS burst was not triggered, and the activities of antioxidant enzymes were induced in the midgut of silkworm exposure to nSiO2. RNA-sequencing revealed that the differentially expressed genes induced by nSiO2 exposure were predominantly enriched into xenobiotics biodegradation and metabolism, lipid, and amino acid metabolism pathways. 16 S rDNA sequencing revealed that nSiO2 exposure altered the microbial diversity in the gut of the silkworm. Metabolomics analysis showed that the combined uni- and multivariate analysis identified 28 significant differential metabolites from the OPLS-DA model. These significant differential metabolites were predominantly enriched into the metabolic pathways, including purine metabolism and tyrosine metabolism and so. Spearman correlation analysis and the Sankey diagram established the relationship between microbe and metabolites, and some genera may play crucial and pleiotropic functions in the interaction between microbiome and host. These findings indicated that nSiO2 exposure could impact the dysregulation of genes related to xenobiotics metabolism, gut dysbiosis, and metabolic pathways and provided a valuable reference for assessing nSiO2 toxicity from a multi-dimensional perspective.},
}
@article {pmid36868153,
year = {2023},
author = {Jin, H and Zhihong, P and Jiaqing, Z and Chuxuan, L and Lu, T and Jun, J and Xinghua, L and Wenyan, G and Junkang, G and Binbin, S and Shengguo, X},
title = {Source apportionment and quantitative risk assessment of heavy metals at an abandoned zinc smelting site based on GIS and PMF models.},
journal = {Journal of environmental management},
volume = {336},
number = {},
pages = {117565},
doi = {10.1016/j.jenvman.2023.117565},
pmid = {36868153},
issn = {1095-8630},
mesh = {Humans ; Zinc/analysis ; Geographic Information Systems ; Lead ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil ; China ; Risk Assessment ; Cadmium ; },
abstract = {The abandoned smelters have caused serious hazards to the surrounding environment and residents. Taking an abandoned zinc smelter in southern China as an example, a total of 245 soil samples were collected to study spatial heterogeneity, source apportionment, and source-derived risk assessment of heavy metal(loid)s (HMs) in the region. The results showed that the mean values of all HMs concentrations were higher than the local background values, with Zn, Cd, Pb, and As contamination being the most serious and their plume penetrating to the bottom layer. Four sources were identified by principal component analysis and positive matrix factorization, with their contributions to the HMs contents ranked as: surface runoff (F2, 63.2%) > surface solid waste (F1, 22.2%) > atmospheric deposition (F3, 8.5%) > parent material (F4, 6.1%). Among these, F1 was a determinant source of human health risk with a contribution rate of 60%. Therefore, F1 was considered to be the priority control factor, but it only accounted for 22.2% of HMs contents contribution. Hg dominated the ecological risk with a contribution of 91.1%. Pb (25.7%) and As (32.9%) accounted for the non-carcinogenic risk, while As (95%) dominated the carcinogenic effect. The spatial characteristics of human health risk values derived from F1 indicated that high-risk areas were mainly distributed in the casting finished products area, electrolysis area, leaching-concentration area, and fluidization roasting area. The findings highlight the significance of priority control factors (including HMs, pollution sources and functional areas) for consideration in the integrated management of this region, thus saving costs for effective soil remediation.},
}
@article {pmid36866381,
year = {2023},
author = {Lin, J and Yu, D and Pan, R and Cai, J and Liu, J and Zhang, L and Wen, X and Peng, X and Cernava, T and Oufensou, S and Migheli, Q and Chen, X and Zhang, X},
title = {Improved YOLOX-Tiny network for detection of tobacco brown spot disease.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1135105},
pmid = {36866381},
issn = {1664-462X},
abstract = {INTRODUCTION: Tobacco brown spot disease caused by Alternaria fungal species is a major threat to tobacco growth and yield. Thus, accurate and rapid detection of tobacco brown spot disease is vital for disease prevention and chemical pesticide inputs.<br><br>METHODS: Here, we propose an improved YOLOX-Tiny network, named YOLO-Tobacco, for the detection of tobacco brown spot disease under open-field scenarios. Aiming to excavate valuable disease features and enhance the integration of different levels of features, thereby improving the ability to detect dense disease spots at different scales, we introduced hierarchical mixed-scale units (HMUs) in the neck network for information interaction and feature refinement between channels. Furthermore, in order to enhance the detection of small disease spots and the robustness of the network, we also introduced convolutional block attention modules (CBAMs) into the neck network.<br><br>RESULTS: As a result, the YOLO-Tobacco network achieved an average precision (AP) of 80.56% on the test set. The AP was 3.22%, 8.99%, and 12.03% higher than that obtained by the classic lightweight detection networks YOLOX-Tiny network, YOLOv5-S network, and YOLOv4-Tiny network, respectively. In addition, the YOLO-Tobacco network also had a fast detection speed of 69 frames per second (FPS).<br><br>DISCUSSION: Therefore, the YOLO-Tobacco network satisfies both the advantages of high detection accuracy and fast detection speed. It will likely have a positive impact on early monitoring, disease control, and quality assessment in diseased tobacco plants.},
}
@article {pmid36865376,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Lees, D and , },
title = {The genome sequence of the merveille du jour, Griposia aprilina (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {247},
pmid = {36865376},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual Griposia aprilina (the merveille du jour; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 720 megabases in span. The majority of the assembly (99.89%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.},
}
@article {pmid36865367,
year = {2022},
author = {Broad, GR and Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the setaceous Hebrew character, Xestia c-nigrum, (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {295},
pmid = {36865367},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Xestia c-nigrum (the setaceous Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 760 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.},
}
@article {pmid36864462,
year = {2023},
author = {Keuschnig, C and Vogel, TM and Barbaro, E and Spolaor, A and Koziol, K and Björkman, MP and Zdanowicz, C and Gallet, JC and Luks, B and Layton, R and Larose, C},
title = {Selection processes of Arctic seasonal glacier snowpack bacterial communities.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {35},
pmid = {36864462},
issn = {2049-2618},
mesh = {Bayes Theorem ; *Ice Cover ; Seasons ; *Bacteria/genetics ; Biodiversity ; },
abstract = {BACKGROUND: Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.<br><br>METHODS: We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.<br><br>RESULTS: While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.<br><br>CONCLUSIONS: These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.},
}
@article {pmid36863150,
year = {2023},
author = {Liu, X and Wang, Y and Meng, X and Zhang, C and Chen, Z},
title = {Improved method for benthic ecosystem health assessment by integrating chemical indexes into multiple biological indicator species-A case study of the Baiyangdian Lake, China.},
journal = {Journal of environmental management},
volume = {335},
number = {},
pages = {117530},
doi = {10.1016/j.jenvman.2023.117530},
pmid = {36863150},
issn = {1095-8630},
mesh = {Humans ; *Ecosystem ; Lakes ; Environmental Biomarkers ; Environmental Monitoring/methods ; China ; *Metals, Heavy ; },
abstract = {A comprehensive and scientific assessment of benthic ecosystem health is key to the rational selection of endogenous pollution reduction technologies for lakes. However, current assessments are mainly limited to biological indicators and ignore the actual benthic ecosystem situations, such as the impact of eutrophication and heavy metal pollution, which may lead to the one-sidedness of the evaluation results. In this study, taking Baiyangdian Lake, the largest shallow mesotrophic-eutrophic lake in the North China Plain, as an example, the chemical assessment index and biological integrity index were first combined to estimate the biological conditions, nutritional status and heavy metal pollution of lakes. The indicator system incorporated three biological assessments (benthic index of biotic integrity (B-IBI), submerged aquatic vegetation index of biological integrity (SAV-IBI) and microbial index of biological integrity (M-IBI)) and three chemical assessments (dissolved oxygen (DO), comprehensive trophic level index (TLI) and index of geoaccumulation (Igeo)). Twenty-three attributes of B-IBI, fourteen attributes of SAV-IBI and twelve attributes of M-IBI were screened by range, responsiveness, and redundancy tests to keep the core metrics that were significantly correlated with disturbance gradients or showed strong discriminatory power between reference and impaired sites. The assessment results of B-IBI, SAV-IBI, and M-IBI showed significant differences in the response to anthropogenic activities and seasonal change, among which the submerged plants showed more significant seasonal differences. It is difficult to reach a comprehensive conclusion regarding the benthic ecosystem health status based on a single biological community. In comparison with biological indicators, the score of chemical indicators is relatively low. DO, TLI and Igeo provide an essential supplement for the benthic ecosystem health assessment of lakes with eutrophication and heavy metal pollution problems. Using the new integrated assessment method, the benthic ecosystem health of Baiyangdian Lake was rated as fair, especially the northern parts of the lake adjacent to the inflow mouth of the Fu River, which were in poor condition, indicating that the lake has experienced anthropogenic disturbance, resulting in eutrophication, heavy metal pollution and biological community degradation. Whether it's spring or summer, the integrated assessment method provides a more plausible and comprehensive view of benthic ecosystem health under the pressure of increasing human activities and changing habitat and hydrological conditions, overcoming the narrow perspective and uncertainties of the single-index method. Thus, it can assist lake managers in providing technical support for ecological indication and restoration.},
}
@article {pmid36862660,
year = {2023},
author = {Nanjala, R and Nyasimi, F and Masiga, D and Kibet, CK},
title = {A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya.},
journal = {PLoS computational biology},
volume = {19},
number = {3},
pages = {e1010904},
pmid = {36862660},
issn = {1553-7358},
support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; U2R TW010677/TW/FIC NIH HHS/United States ; },
mesh = {Humans ; Kenya ; *Mentors ; *Computational Biology ; Genomics ; Students ; },
abstract = {The demand for well-trained bioinformaticians to support genomics research continues to rise. Unfortunately, undergraduate training in Kenya does not prepare students for specialization in bioinformatics. Graduates are often unaware of the career opportunities in bioinformatics, and those who are may lack mentors to help them choose a specialization. The Bioinformatics Mentorship and Incubation Program seeks to bridge the gap by laying the foundation for a bioinformatics training pipeline using project-based learning. The program selects six participants through an intensive open recruitment exercise for highly competitive students to join the program for four months. The six interns undergo intensive training within the first one and a half months before being assigned to mini-projects. We track the progress of the interns weekly through code review sessions and a final presentation at the end of the four months. We have trained five cohorts, most of whom have secured master's scholarships within and outside the country and job opportunities. We demonstrate the benefit of structured mentorship using project-based learning in filling the training gap after undergraduate programs to generate well-trained bioinformaticians who are competitive in graduate programs and bioinformatics jobs.},
}
@article {pmid36859647,
year = {2023},
author = {Nocci, M and Villa, G and Ragazzoni, L and Tofani, L and Romagnoli, S and Baldini, G and Bertini, P and Hubloue, I and Scolletta, S and Mechi, MT and Della Corte, F},
title = {Relationship between intensive care surge capacity and hospital factors: an extensive experience.},
journal = {Internal and emergency medicine},
volume = {18},
number = {5},
pages = {1521-1532},
pmid = {36859647},
issn = {1970-9366},
mesh = {Humans ; *Surge Capacity ; *COVID-19/epidemiology ; Pandemics ; Critical Care ; Intensive Care Units ; Hospitals ; Emergency Service, Hospital ; Retrospective Studies ; },
abstract = {As a prolonged surge scenario, the COVID-19 pandemic has offered an unparalleled opportunity to improve hospital surge capacity (SC) understanding and the ability to manage it. In this study, the authors report the experience of a large hospital network and evaluate potential relationships between Intensive Care Units SC (ICU-SC) and some hospital-related variables: bed occupancy, emergency department admissions, ward admission from ED, and elective surgery procedures. Pearson's partial correlation coefficient (r) has been used to define the relationship between SC and the daily values of the above variables, collected through a dedicated digital platform that also ensured a regular quality check of the data. The observation has concerned several levels of analysis, namely two different types of SC calculation (SC base-SCb and SC actual-SCa), hospital category level and multi-hospital level, and two consecutive pandemic waves. Among the 16 hospitals observed, the correlation was shown to be moderate-positive with non-ICU bed occupancy (r/ = 0.62, r/ = 0.54), strong/moderate with ICU bed occupancy (r/ = 0.72, r/ = 0.54), and moderate with ward admissions from ED (r/ = 0.50, r/ = 0.51) On the contrary, the correlation proved to be moderate-negative with ED admissions (r/ = - 0.69, r/ = - 0.62) and low with the number of elective surgery procedures (r/ = - 0.10, r/ = - 0.16). This study identified a positive correlation between SC and three variables monitored: ICU bed occupancy, non-ICU bed occupancy, and ward admissions from ED. On the contrary, the correlation was negative for ED admission and the number of elective surgery procedures. The results have been confirmed across all levels of analysis adopted.},
}
@article {pmid36859581,
year = {2023},
author = {Tucker, C and Brandt, M and Hiernaux, P and Kariryaa, A and Rasmussen, K and Small, J and Igel, C and Reiner, F and Melocik, K and Meyer, J and Sinno, S and Romero, E and Glennie, E and Fitts, Y and Morin, A and Pinzon, J and McClain, D and Morin, P and Porter, C and Loeffler, S and Kergoat, L and Issoufou, BA and Savadogo, P and Wigneron, JP and Poulter, B and Ciais, P and Kaufmann, R and Myneni, R and Saatchi, S and Fensholt, R},
title = {Sub-continental-scale carbon stocks of individual trees in African drylands.},
journal = {Nature},
volume = {615},
number = {7950},
pages = {80-86},
pmid = {36859581},
issn = {1476-4687},
mesh = {*Carbon/analysis/metabolism ; *Ecosystem ; *Trees/anatomy &amp; histology/chemistry/metabolism ; *Desert Climate ; Desiccation ; Satellite Imagery ; Africa South of the Sahara ; Machine Learning ; Wood/analysis ; Plant Roots ; Agriculture ; Environmental Restoration and Remediation ; Databases, Factual ; Biomass ; Computers ; },
abstract = {The distribution of dryland trees and their density, cover, size, mass and carbon content are not well known at sub-continental to continental scales[1-14]. This information is important for ecological protection, carbon accounting, climate mitigation and restoration efforts of dryland ecosystems[15-18]. We assessed more than 9.9 billion trees derived from more than 300,000 satellite images, covering semi-arid sub-Saharan Africa north of the Equator. We attributed wood, foliage and root carbon to every tree in the 0-1,000 mm year[-1] rainfall zone by coupling field data[19], machine learning[20-22], satellite data and high-performance computing. Average carbon stocks of individual trees ranged from 0.54 Mg C ha[-1] and 63 kg C tree[-1] in the arid zone to 3.7 Mg C ha[-1] and 98 kg tree[-1] in the sub-humid zone. Overall, we estimated the total carbon for our study area to be 0.84 (±19.8%) Pg C. Comparisons with 14 previous TRENDY numerical simulation studies[23] for our area found that the density and carbon stocks of scattered trees have been underestimated by three models and overestimated by 11 models, respectively. This benchmarking can help understand the carbon cycle and address concerns about land degradation[24-29]. We make available a linked database of wood mass, foliage mass, root mass and carbon stock of each tree for scientists, policymakers, dryland-restoration practitioners and farmers, who can use it to estimate farmland tree carbon stocks from tablets or laptops.},
}
@article {pmid36859503,
year = {2023},
author = {Jones, DL and Rhymes, JM and Green, E and Rimmer, C and Kevill, JL and Malham, SK and Weightman, AJ and Farkas, K},
title = {Poor air passenger knowledge of COVID-19 symptoms and behaviour undermines strategies aimed at preventing the import of SARS-CoV-2 into the UK.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {3494},
pmid = {36859503},
issn = {2045-2322},
mesh = {Adult ; Male ; Female ; Humans ; Aged ; SARS-CoV-2 ; *COVID-19 ; Pandemics ; *Air Travel ; United Kingdom ; },
abstract = {Air travel mediates transboundary movement of SARS-CoV-2. To prepare for future pandemics, we sought to understand air passenger behaviour and perceived risk during the COVID-19 pandemic. This study of UK adults (n = 2103) quantified knowledge of COVID-19 symptoms, perceived health risk of contracting COVID-19, likelihood of returning to the UK with COVID-19 symptoms, likelihood to obey self-quarantining guidelines, how safe air travellers felt when flying during the pandemic (n = 305), and perceptions towards face covering effectiveness.Overall knowledge of COVID-19 symptoms was poor. Men and younger age groups (18-44) were less informed than women and older age groups (44 +). A significant proportion (21%) of the population would likely travel back to the UK whilst displaying COVID-19 symptoms with many expressing that they would not fully comply with self-isolation guidelines. Overall, males and younger age groups had a reduced perceived personal risk from contracting COVID-19, posing a higher risk of transporting SARS-CoV-2 back to the UK. Poor passenger knowledge and behaviour undermines government guidelines and policies aimed at preventing SARS-CoV-2 entry into the UK. This supports the need for stricter, clearer and more targeted guidelines with point-of-departure viral testing and stricter quarantining upon arrival.},
}
@article {pmid36858189,
year = {2023},
author = {Kushwaha, B and Nagpure, NS and Srivastava, S and Pandey, M and Kumar, R and Raizada, S and Agarwal, S and Singh, M and Basheer, VS and Kumar, RG and Das, P and Das, SP and Patnaik, S and Bit, A and Srivastava, SK and Vishwakarma, AL and Joshi, CG and Kumar, D and Jena, JK},
title = {Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes.},
journal = {Gene},
volume = {864},
number = {},
pages = {147294},
doi = {10.1016/j.gene.2023.147294},
pmid = {36858189},
issn = {1879-0038},
mesh = {Animals ; Genome Size ; Evolution, Molecular ; Fishes/genetics ; Chromosomes/genetics ; Genomics ; *Perciformes/genetics ; *Catfishes/genetics ; *Cypriniformes/genetics ; Phylogeny ; },
abstract = {Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.},
}
@article {pmid36852195,
year = {2023},
author = {Streng, K and de Best, PA and Timen, A and Koopmans, MPG and van der Poel, WHM and Sikkema, RS},
title = {Rapid response screening for emerging zoonotic pathogens, barriers and opportunities: A study for enhanced preparedness of the Netherlands.},
journal = {One health (Amsterdam, Netherlands)},
volume = {16},
number = {},
pages = {100507},
pmid = {36852195},
issn = {2352-7714},
abstract = {BACKGROUND: Outbreaks of zoonotic emerging infectious diseases (EIDs) require rapid identification of potential reservoir hosts and mapping disease spread in these hosts to inform risk assessment and adequate control measures. Animals are often understudied when a novel EID is detected in humans and acquisition of animal samples is hampered by practical, ethical, and legal barriers, of which there is currently no clear overview. Therefore, the three aims of this study are (1) to map potentially available collections of animal samples, (2) to assess possibilities and barriers for reuse of these samples and (3) to assess possibilities and barriers for active animal and environmental sampling in the Netherlands.<br><br>METHODS: A literature search was performed to identify ongoing sampling activities and opportunities for reuse or active sampling. Semi-structured interviews with stakeholder organizations were conducted to gain further insight into the three research questions.<br><br>RESULTS: Various sample collections of surveillance, diagnostic and research activities exist in the Netherlands. Sample size, coverage, storage methods and type of samples collected differs per animal species which influences reuse suitability. Organizations are more likely to share samples, for reuse in outbreak investigations, when they have a pre-existing relationship with the requesting institute. Identified barriers for sharing were, among others, unfamiliarity with legislation and unsuitable data management systems. Active sampling of animals or the environment is possible through several routes. Related barriers are acquiring approval from animal- or property owners, conflicts with anonymization, and time needed to acquire ethical approval.<br><br>CONCLUSION: The animal sample collections identified would be very valuable for use in outbreak investigations. Barriers for sharing may be overcome by increasing familiarity with legislation, building (international) sharing networks and agreements before crises occur and developing systems for sample registration and biobanking. Proactive setting up of ethical approvals will allow for rapid animal sample collection to identify EID hosts and potential spillovers.},
}
@article {pmid36850776,
year = {2023},
author = {Di Paolo, S and Nijmeijer, EM and Bragonzoni, L and Gokeler, A and Benjaminse, A},
title = {Definition of High-Risk Motion Patterns for Female ACL Injury Based on Football-Specific Field Data: A Wearable Sensors Plus Data Mining Approach.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {4},
pages = {},
pmid = {36850776},
issn = {1424-8220},
mesh = {Female ; Humans ; *Anterior Cruciate Ligament Injuries ; *Football ; Rotation ; Data Mining ; *Wearable Electronic Devices ; },
abstract = {The aim of the present study was to investigate if the presence of anterior cruciate ligament (ACL) injury risk factors depicted in the laboratory would reflect at-risk patterns in football-specific field data. Twenty-four female footballers (14.9 ± 0.9 year) performed unanticipated cutting maneuvers in a laboratory setting and on the football pitch during football-specific exercises (F-EX) and games (F-GAME). Knee joint moments were collected in the laboratory and grouped using hierarchical agglomerative clustering. The clusters were used to investigate the kinematics collected on field through wearable sensors. Three clusters emerged: Cluster 1 presented the lowest knee moments; Cluster 2 presented high knee extension but low knee abduction and rotation moments; Cluster 3 presented the highest knee abduction, extension, and external rotation moments. In F-EX, greater knee abduction angles were found in Cluster 2 and 3 compared to Cluster 1 (p = 0.007). Cluster 2 showed the lowest knee and hip flexion angles (p < 0.013). Cluster 3 showed the greatest hip external rotation angles (p = 0.006). In F-GAME, Cluster 3 presented the greatest knee external rotation and lowest knee flexion angles (p = 0.003). Clinically relevant differences towards ACL injury identified in the laboratory reflected at-risk patterns only in part when cutting on the field: in the field, low-risk players exhibited similar kinematic patterns as the high-risk players. Therefore, in-lab injury risk screening may lack ecological validity.},
}
@article {pmid36848570,
year = {2023},
author = {Stenseth, NC and Schlatte, R and Liu, X and Pielke, R and Li, R and Chen, B and Bjørnstad, ON and Kusnezov, D and Gao, GF and Fraser, C and Whittington, JD and Bai, Y and Deng, K and Gong, P and Guan, D and Xiao, Y and Xu, B and Johnsen, EB},
title = {How to avoid a local epidemic becoming a global pandemic.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {10},
pages = {e2220080120},
pmid = {36848570},
issn = {1091-6490},
mesh = {Humans ; Pandemics/prevention &amp; control ; *COVID-19/epidemiology/prevention &amp; control ; SARS-CoV-2 ; Disease Outbreaks ; *Air Travel ; },
abstract = {Here, we combine international air travel passenger data with a standard epidemiological model of the initial 3 mo of the COVID-19 pandemic (January through March 2020; toward the end of which the entire world locked down). Using the information available during this initial phase of the pandemic, our model accurately describes the main features of the actual global development of the pandemic demonstrated by the high degree of coherence between the model and global data. The validated model allows for an exploration of alternative policy efficacies (reducing air travel and/or introducing different degrees of compulsory immigration quarantine upon arrival to a country) in delaying the global spread of SARS-CoV-2 and thus is suggestive of similar efficacy in anticipating the spread of future global disease outbreaks. We show that a lesson from the recent pandemic is that reducing air travel globally is more effective in reducing the global spread than adopting immigration quarantine. Reducing air travel out of a source country has the most important effect regarding the spreading of the disease to the rest of the world. Based upon our results, we propose a digital twin as a further developed tool to inform future pandemic decision-making to inform measures intended to control the spread of disease agents of potential future pandemics. We discuss the design criteria for such a digital twin model as well as the feasibility of obtaining access to the necessary online data on international air travel.},
}
@article {pmid36846939,
year = {2023},
author = {Barrile, GM and Augustine, DJ and Porensky, LM and Duchardt, CJ and Shoemaker, KT and Hartway, CR and Derner, JD and Hunter, EA and Davidson, AD},
title = {A big data-model integration approach for predicting epizootics and population recovery in a keystone species.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {33},
number = {4},
pages = {e2827},
doi = {10.1002/eap.2827},
pmid = {36846939},
issn = {1051-0761},
mesh = {Animals ; *Ecosystem ; Big Data ; *Yersinia pestis ; Sciuridae ; Climate ; Animals, Wild ; },
abstract = {Infectious diseases pose a significant threat to global health and biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife epizootics remains challenging. Disease outbreaks result from complex nonlinear interactions among a large collection of variables that rarely adhere to the assumptions of parametric regression modeling. We adopted a nonparametric machine learning approach to model wildlife epizootics and population recovery, using the disease system of colonial black-tailed prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an example. We synthesized colony data between 2001 and 2020 from eight USDA Forest Service National Grasslands across the range of BTPDs in central North America. We then modeled extinctions due to plague and colony recovery of BTPDs in relation to complex interactions among climate, topoedaphic variables, colony characteristics, and disease history. Extinctions due to plague occurred more frequently when BTPD colonies were spatially clustered, in closer proximity to colonies decimated by plague during the previous year, following cooler than average temperatures the previous summer, and when wetter winter/springs were preceded by drier summers/falls. Rigorous cross-validations and spatial predictions indicated that our final models predicted plague outbreaks and colony recovery in BTPD with high accuracy (e.g., AUC generally >0.80). Thus, these spatially explicit models can reliably predict the spatial and temporal dynamics of wildlife epizootics and subsequent population recovery in a highly complex host-pathogen system. Our models can be used to support strategic management planning (e.g., plague mitigation) to optimize benefits of this keystone species to associated wildlife communities and ecosystem functioning. This optimization can reduce conflicts among different landowners and resource managers, as well as economic losses to the ranching industry. More broadly, our big data-model integration approach provides a general framework for spatially explicit forecasting of disease-induced population fluctuations for use in natural resource management decision-making.},
}
@article {pmid36840322,
year = {2023},
author = {Hou, H and Liu, H and Xiong, J and Wang, C and Zhang, S and Ding, Z},
title = {Comparison of Soil Bacterial Communities under Canopies of Pinus tabulaeformis and Populus euramericana in a Reclaimed Waste Dump.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
pmid = {36840322},
issn = {2223-7747},
support = {No. 22BJY064//National Social Science Fund/ ; },
abstract = {To compare the effects of different remediation tree species on soil bacterial communities and provide a theoretical basis for the selection of ecosystem function promotion strategies after vegetation restoration, the characteristic changes in soil bacterial communities after Pinus tabulaeformis and Populus euramericana reclamation were explored using high-throughput sequencing and molecular ecological network methods. The results showed that: (1) With the increase in reclamation years, the reclaimed soil properties were close to the control group, and the soil properties of Pinus tabulaeformis were closer to the control group than those of P. euramericana. (2) The dominant bacteria under the canopies of P. tabulaeformis and P. euramericana was the same. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Planctomycetes, Bacteroidetes, and Cyanobacteria were the dominant bacteria in the restored soil, accounting for more than 95% of the total abundance. The average values of the Shannon diversity index, Simpson diversity index, Chao 1 richness estimator, and abundance-based coverage estimator of the bacterial community in the P. euramericana reclaimed soil were higher than those in the P. tabulaeformis reclaimed soil. The influence of reclamation years on the bacterial community of samples is greater than that of species types. (3) The results of ecological network construction showed that the total number of nodes, total number of connections, and average connectivity of the soil bacterial network under P. euramericana reclamation were greater than those under P. tabulaeformis reclamation. The bacterial molecular ecological network under P. euramericana was more abundant. (4) Among the dominant bacteria, the relative abundance of Actinobacteria was negatively correlated with soil pH, soil total nitrogen content, and the activities of urease, invertase, and alkaline phosphatase, while the relative abundance of Proteobacteria and Bacteroidetes was positively correlated with these environmental factors. The relationship between the soil bacterial community of P. tabulaeformis and P. euramericana and the environmental factors is not completely the same, and even the interaction between some environmental factors and bacteria is opposite.},
}
@article {pmid36840309,
year = {2023},
author = {Jocienė, L and Krokaitė, E and Rekašius, T and Vilčinskas, R and Judžentienė, A and Marozas, V and Kupčinskienė, E},
title = {Ionomic Parameters of Populations of Common Juniper (Juniperus communis L.) Depending on the Habitat Type.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
pmid = {36840309},
issn = {2223-7747},
abstract = {For the study of the ionomic parameters of Juniperus communis needles, fourteen sites covering most of the territory of Lithuania and belonging to distinct habitats (coastal brown dunes covered with natural Scots pine forests (G), Juniperus communis scrubs (F), transition mires and quaking bogs (D), subcontinental moss Scots pine forests (G), and xero-thermophile fringes) were selected. Concentrations of macro-, micro-, and non-essential elements were analyzed in current-year needles, sampled in September. According to the concentrations of elements in J. communis needles, the differences between the most contrasting populations were as follows: up to 2-fold for Mg, N, K, Ca, and Zn; 2- to 7-fold for P, Na, Fe, Cu, Al, Cr, Ni, and Pb; and 26- to 31-fold for Mn and Cd. The concentrations of Cd, Cr, and Ni in needles of J. communis did not reach levels harmful for conifers. When compared to all other habitats (B, F, G, and E), the populations from transition mires and quaking bogs (D) had significantly lower concentrations of main nutritional elements N (12176 µg/g d. m.), P (1054 µg/g d. m.), and K (2916 µg/g d. m.). In Juniperus communis scrubs (F), a habitat protected by EUNIS, the concentration of K in the needles was highest, while Zn and Cu concentrations were the lowest. Principal component (PC) analyses using concentrations of 15 elements as variables for the discrimination of populations or habitats allowed authors to distinguish F and B habitats from the E habitat (PC1) and F and D habitats from the G habitat (PC2). Discriminating between populations, the most important variables were concentrations of P, N, Mg, Ca, Cu, and K. Discriminating between habitats, the important variables were concentrations of N and P.},
}
@article {pmid36840203,
year = {2023},
author = {Visztra, GV and Frei, K and Hábenczyus, AA and Soóky, A and Bátori, Z and Laborczi, A and Csikós, N and Szatmári, G and Szilassi, P},
title = {Applicability of Point- and Polygon-Based Vegetation Monitoring Data to Identify Soil, Hydrological and Climatic Driving Forces of Biological Invasions-A Case Study of Ailanthus altissima, Elaeagnus angustifolia and Robinia pseudoacacia.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
pmid = {36840203},
issn = {2223-7747},
abstract = {Invasive tree species are a significant threat to native flora. They modify the environment with their allelopathic substances and inhibit the growth of native species by shading, thus reducing diversity. The most effective way to control invasive plants is to prevent their spread which requires identifying the environmental parameters promoting it. Since there are several types of invasive plant databases available, determining which database type is the most relevant for investigating the occurrence of alien plants is of great importance. In this study, we compared the efficiency and reliability of point-based (EUROSTAT Land Use and Coverage Area Frame Survey (LUCAS)) and polygon-based (National Forestry Database (NFD)) databases using geostatistical methods in ArcGIS software. We also investigated the occurrence of three invasive tree species (Ailanthus altissima, Elaeagnus angustifolia, and Robinia pseudoacacia) and their relationships with soil, hydrological, and climatic parameters such as soil organic matter content, pH, calcium carbonate content, rooting depth, water-holding capacity, distance from the nearest surface water, groundwater depth, mean annual temperature, and mean annual precipitation with generalized linear models in R-studio software. Our results show that the invasion levels of the tree species under study are generally over-represented in the LUCAS point-based vegetation maps, and the point-based database requires a dataset with a larger number of samples to be reliable. Regarding the polygon-based database, we found that the occurrence of the invasive species is generally related to the investigated soil and hydrological and climatic factors.},
}
@article {pmid36836247,
year = {2023},
author = {Wang, J and Qin, S and Fan, R and Peng, Q and Hu, X and Yang, L and Liu, Z and Baccelli, I and Migheli, Q and Berg, G and Chen, X and Cernava, T},
title = {Plant Growth Promotion and Biocontrol of Leaf Blight Caused by Nigrospora sphaerica on Passion Fruit by Endophytic Bacillus subtilis Strain GUCC4.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {2},
pages = {},
pmid = {36836247},
issn = {2309-608X},
support = {2021YFE0107700//National Key research and Development of China/ ; Guike AA21196003//Science and Technology Base &amp; Talent Project of Guangxi Province/ ; 2019-1410;2021-229;HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; KY2021-026//Outstanding Young Scientist Program of Guizhou Province/ ; 2022-36-Z01-KF12//Guangxi Key Laboratory of Rice Genetics and Breeding Opening Research Project/ ; 111 Program; D20023//Guizhou University Cultivation Project 2019-04 and Program for Introducing Talents to Chinese Universities/ ; },
abstract = {Passion fruit (Passiflora edulis Sims) is widely cultivated in tropic and sub-tropic regions for the production of fruit, flowers, cosmetics, and for pharmacological applications. Its high economic, nutritional, and medical values elicit the market demand, and the growing areas are rapidly increasing. Leaf blight caused by Nigrospora sphaerica is a new and emerging disease of passion fruit in Guizhou, in southwest China, where the unique karst mountainous landscape and climate conditions are considered potential areas of expansion for passion fruit production. Bacillus species are the most common biocontrol and plant-growth-promotion bacteria (PGPB) resources in agricultural systems. However, little is known about the endophytic existence of Bacillus spp. in the passion fruit phyllosphere as well as their potential as biocontrol agents and PGPB. In this study, 44 endophytic strains were isolated from 15 healthy passion fruit leaves, obtained from Guangxi province, China. Through purification and molecular identification, 42 of the isolates were ascribed to Bacillus species. Their inhibitory activity against N. sphaerica was tested in vitro. Eleven endophytic Bacillus spp. strains inhibited the pathogen by >65%. All of them produced biocontrol- and plant-growth-promotion-related metabolites, including indole-3-acetic acid (IAA), protease, cellulase, phosphatase, and solubilized phosphate. Furthermore, the plant growth promotion traits of the above 11 endophytic Bacillus strains were tested on passion fruit seedlings. One isolate, coded B. subtilis GUCC4, significantly increased passion fruit stem diameter, plant height, leaf length, leaf surface, fresh weight, and dry weight. In addition, B. subtilis GUCC4 reduced the proline content, which indicated its potential to positively regulate passion fruit biochemical properties and resulted in plant growth promotion effects. Finally, the biocontrol efficiencies of B. subtilis GUCC4 against N. sphaerica were determined in vivo under greenhouse conditions. Similarly to the fungicide mancozeb and to a commercial B. subtilis-based biofungicide, B. subtilis GUCC4 significantly reduced disease severity. These results suggest that B. subtilis GUCC4 has great potential as a biological control agent and as PGPB on passion fruit.},
}
@article {pmid36835681,
year = {2023},
author = {Srygley, RB and Dudley, R and Hernandez, EJ and Kainz, F and Riveros, AJ and Ellington, CP},
title = {Quantifying the Aerodynamic Power Required for Flight and Testing for Adaptive Wind Drift in Passion-Vine Butterflies Heliconius sara (Lepidoptera: Nymphalidae).},
journal = {Insects},
volume = {14},
number = {2},
pages = {},
pmid = {36835681},
issn = {2075-4450},
support = {7457-03//National Geographic Society/ ; },
abstract = {Although theoretical work on optimal migration has been largely restricted to birds, relevant free-flight data are now becoming available for migratory insects. Here we report, for the first time in passion-vine butterflies, that Heliconius sara migrates directionally. To test optimal migration models for insects, we quantified the aerodynamic power curve for free-flying H. sara as they migrated across the Panama Canal. Using synchronized stereo-images from high-speed video cameras, we reconstructed three-dimensional flight kinematics of H. sara migrating naturally across the Panama Canal. We also reconstructed flight kinematics from a single-camera view of butterflies flying through a flight tunnel. We calculated the power requirements for flight for H. sara over a range of flight velocities. The relationship between aerodynamic power and velocity was "J"-shaped across the measured velocities with a minimum power velocity of 0.9 m/s and a maximum range velocity of 2.25 m/s. Migrating H. sara did not compensate for crosswind drift. Changes in airspeed with tailwind drift were consistent with the null hypothesis that H. sara did not compensate for tailwind drift, but they were also not significantly different from those predicted to maximize the migratory range of the insects.},
}
@article {pmid36834418,
year = {2023},
author = {Liu, J and Chen, J and Yang, Y and You, H and Han, X},
title = {Construction and Optimization of an Ecological Network in the Yellow River Source Region Based on MSPA and MCR Modelling.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {4},
pages = {},
pmid = {36834418},
issn = {1660-4601},
mesh = {*Ecosystem ; Ecology ; Conservation of Natural Resources ; Rivers ; *Conservation of Water Resources ; China ; },
abstract = {The source region of the Yellow River (SRYR) is an important water conservation and farming area in China. Under the dual influence of the natural environment and external pressure, ecological patches in the region are becoming increasingly fragmented, and landscape connectivity is continuously declining, which directly affect the landscape patch pattern and SRYR sustainable development. In the SRYR, morphological spatial pattern analysis (MSPA) and landscape index methods were used to extract ecologically important sources. Based on the minimum cumulative resistance model (MCR), Linkage Mapper was used to generate a potential corridor, and then potential stepped stone patches were identified and extracted by the gravity model and betweenness centrality to build an optimal SRYR ecological network. The distribution of patches in the core area of the SRYR was fragmented, accounting for 80.53% of the total grassland area. The 10 ecological sources based on the landscape connectivity index and 15 important corridors identified based on the MCR model were mainly distributed in the central and eastern regions of the SRYR. Through betweenness centrality, 10 stepped stone patches were added, and 45 planned ecological corridors were obtained to optimize the SRYR ecological network and enhance east and west connectivity. Our research results can provide an important reference for the protection of the SRYR ecosystem, and have important guiding significance and practical value for ecological network construction in ecologically fragmented areas.},
}
@article {pmid36834206,
year = {2023},
author = {Li, Y and Liu, H and Su, L and Chen, S and Zhu, X and Zhang, P},
title = {Developmental Features, Influencing Factors, and Formation Mechanism of Underground Mining-Induced Ground Fissure Disasters in China: A Review.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {4},
pages = {},
pmid = {36834206},
issn = {1660-4601},
mesh = {*Coal Mining ; China ; Soil ; Geology ; Pressure ; Coal ; },
abstract = {Mining-induced ground fissures are one of the major geological disasters affecting coal mines. In recent years, many effective monitoring methods have been developed to explore the developmental characteristics and nature of mining-induced ground fissures for being treated scientifically. This paper is mainly on the development law and mechanism of mining ground fissure research results which have been comprehensively combed, highlighting the development trend, including the formation condition, development features, influencing factors, and mechanical mechanism of mining-induced ground fissures. Outstanding issues are discussed and future research hot spots and trends are pointed out. The major conclusions include: (1) under the shallow coal mining condition, because the rock layer fault zone directly reaches the surface, the ground fissure usually develops seriously; (2) mining-induced ground fissures are generally divided into four types: tensile fissures, compression fissures, collapsed fissures, and sliding fissures; (3) mining-induced ground fissures are affected by the coupling effect of underground mining and surface topography. The main factors are geological mining conditions, surface deformation, and surface topography, including rock and soil structure, rock and soil mechanical properties, surface horizontal deformation, surface slope, and so on; and (4) to ensure the safety of underground mining, temporary ground fissures formed during the process of coal mining must be treated when ground fissures and rock ground fissures are connected. The results of this article make up for the deficiencies of the relevant research, provide the basis and direction for future research, and have universal applicability and scientific guiding significance.},
}
@article {pmid36827177,
year = {2023},
author = {Martínez-Pernía, D and Olavarría, L and Fernández-Manjón, B and Cabello, V and Henríquez, F and Robert, P and Alvarado, L and Barría, S and Antivilo, A and Velasquez, J and Cerda, M and Farías, G and Torralva, T and Ibáñez, A and Parra, MA and Gilbert, S and Slachevsky, A},
title = {The limitations and challenges in the assessment of executive dysfunction associated with real-world functioning: The opportunity of serious games.},
journal = {Applied neuropsychology. Adult},
volume = {},
number = {},
pages = {1-17},
pmid = {36827177},
issn = {2327-9109},
support = {R01 AG057234/AG/NIA NIH HHS/United States ; },
abstract = {Nowadays, there is a broad range of methods for detecting and evaluating executive dysfunction ranging from clinical interview to neuropsychological evaluation. Nevertheless, a critical issue of these assessments is the lack of correspondence of the neuropsychological test's results with real-world functioning. This paper proposes serious games as a new framework to improve the neuropsychological assessment of real-world functioning. We briefly discuss the contribution and limitations of current methods of evaluation of executive dysfunction (paper-and-pencil tests, naturalistic observation methods, and Information and Communications Technologies) to inform on daily life functioning. Then, we analyze what are the limitations of these methods to predict real-world performance: (1) A lack of appropriate instruments to investigate the complexity of real-world functioning, (2) the vast majority of neuropsychological tests assess well-structured tasks, and (3) measurement of behaviors are based on simplistic data collection and statistical analysis. This work shows how serious games offer an opportunity to develop more efficient tools to detect executive dysfunction in everyday life contexts. Serious games provide meaningful narrative stories and virtual or real environments that immerse the user in natural and social environments with social interactions. In those highly interactive game environments, the player needs to adapt his/her behavioral performance to novel and ill-structured tasks which are suited for collecting user interaction evidence. Serious games offer a novel opportunity to develop better tools to improve diagnosis of the executive dysfunction in everyday life contexts. However, more research is still needed to implement serious games in everyday clinical practice.},
}
@article {pmid36826765,
year = {2023},
author = {Wei, T and Guo, G and Li, H and Wang, L and Jiang, Q and Jiang, C},
title = {A novel probability integral method segmental modified model for subsidence prediction applicable to thick loose layer mining areas.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {18},
pages = {52049-52061},
pmid = {36826765},
issn = {1614-7499},
support = {U21A20109//National Natural Science Foundation of China/ ; KYCX21_2294//Graduate Research and Innovation Projects of Jiangsu Province/ ; },
mesh = {*Coal Mining/methods ; *Disasters ; China ; },
abstract = {In response to the problem that the actual extent of coal mining impacts on the surface in thick loose layer mines significantly exceeds the theoretical predictions, based on the literature study, the form of influence of thick loose layer on the predicted parameters of the probability integral method is summarized and analyzed; taking into account the influence of the subsidence coefficient, the sine modification formula of the major influence radius and the logistic modification formula of the subsidence coefficient are established, respectively, and based on the characteristics of the major influence radius, a new subsidence basin demarcation point is proposed and a novel probability integral method segmental parameter modified prediction model is constructed. The simulated experiment and real data experiment results prove that the constructed probability integral method segmented parameter modified model can both reduce the convergence of surface subsidence basin edge better and take into account the predicted accuracy inside the subsidence basin. The research achievements provide scientific data support for disaster warning, pollution management, ecological restoration, and coordination between coal mining and surface city construction in thick loose layer mining areas.},
}
@article {pmid36824773,
year = {2023},
author = {Kapsetaki, SE and Compton, Z and Dolan, J and Harris, VK and Rupp, SM and Duke, EG and Harrison, TM and Aksoy, S and Giraudeau, M and Vincze, O and McGraw, KJ and Aktipis, A and Tollis, M and Boddy, AM and Maley, CC},
title = {Life history and cancer in birds: clutch size predicts cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36824773},
issn = {2692-8205},
support = {P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; U2C CA233254/CA/NCI NIH HHS/United States ; U54 CA217376/CA/NCI NIH HHS/United States ; },
abstract = {Cancer is a disease that affects nearly all multicellular life, including birds. However, little is known about what factors explain the variance in cancer prevalence among species. Litter size is positively correlated with cancer prevalence in managed species of mammals, and larger body size, but not incubation or nestling period, is linked to tumor prevalence in wild birds. Also, birds that produce more elaborate sexual traits are expected to have fewer resources for cancer defenses and thus higher cancer prevalence. In this study, we examined whether cancer prevalence is associated with a wide variety of life history traits (clutch size, incubation length, body mass, lifespan, and the extent of sexual dimorphism) across 108 species of managed birds in 25 different zoological facilities, sanctuaries, and veterinary clinics. We found that clutch size was positively correlated with cancer and neoplasia (both benign and malignant) prevalence, even after controlling for body mass. Cancer prevalence was not associated with incubation length, body mass, lifespan, or sexual dimorphism. The positive correlations of clutch size with cancer prevalence and neoplasia prevalence suggest that there may be life-history trade-offs between reproductive investment and somatic maintenance (in the form of cancer prevention mechanisms) in managed birds.},
}
@article {pmid36816807,
year = {2022},
author = {Ben Aribi, H and Ding, M and Kiran, A},
title = {Gene expression data visualization tool on the o[2]S[2]PARC platform.},
journal = {F1000Research},
volume = {11},
number = {},
pages = {1267},
pmid = {36816807},
issn = {2046-1402},
mesh = {*Gene Expression Profiling ; *Computational Biology ; Data Visualization ; Gene Ontology ; Gene Expression ; },
abstract = {Background: The identification of differentially expressed genes and their associated biological processes, molecular function, and cellular components are essential for genetic disease studies because they present potential biomarkers and therapeutic targets. Methods: In this study, we developed an o[2]S[2]PARC template to instantiate an interactive pipeline for gene expression data visualization, ontological mapping, and statistical evaluation. To demonstrate the tool's usefulness, we performed a case study on a publicly available dataset. Results: The tool enables users to identify the differentially expressed genes (DEGs) and visualize them in a volcano plot format. Ontologies associated with the DEGs are assigned and visualized in barplots. Conclusions: The "Expression data visualization" template is publicly available on the o[2]S[2]PARC platform.},
}
@article {pmid36821658,
year = {2023},
author = {D'Emic, MD and O'Connor, PM and Sombathy, RS and Cerda, I and Pascucci, TR and Varricchio, D and Pol, D and Dave, A and Coria, RA and Curry Rogers, KA},
title = {Developmental strategies underlying gigantism and miniaturization in non-avialan theropod dinosaurs.},
journal = {Science (New York, N.Y.)},
volume = {379},
number = {6634},
pages = {811-814},
doi = {10.1126/science.adc8714},
pmid = {36821658},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; *Dinosaurs/anatomy &amp; histology/classification/growth &amp; development ; Fossils ; Phylogeny ; *Body Size ; Datasets as Topic ; },
abstract = {In amniotes, the predominant developmental strategy underlying body size evolution is thought to be adjustments to the rate of growth rather than its duration. However, most theoretical and experimental studies supporting this axiom focus on pairwise comparisons and/or lack an explicit phylogenetic framework. We present the first large-scale phylogenetic comparative analysis examining developmental strategies underlying the evolution of body size, focusing on non-avialan theropod dinosaurs. We reconstruct ancestral states of growth rate and body mass in a taxonomically rich dataset, finding that contrary to expectations, changes in the rate and duration of growth played nearly equal roles in the evolution of the vast body size disparity present in non-avialan theropods-and perhaps that of amniotes in general.},
}
@article {pmid36820086,
year = {2023},
author = {Huo, J and Hu, X and Bai, J and Lv, A},
title = {Multiomics analysis revealed miRNAs as potential regulators of the immune response in Carassius auratus gills to Aeromonas hydrophila infection.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1098455},
pmid = {36820086},
issn = {1664-3224},
mesh = {Animals ; *Goldfish ; Aeromonas hydrophila ; Gills ; Zebrafish/genetics ; Multiomics ; NF-kappa B/genetics ; Phylogeny ; Immunity, Innate/genetics ; *MicroRNAs/genetics ; },
abstract = {The gill of fish is an important immune organ for pathogen defense, but its microRNA (miRNA) expression and regulatory mechanism remain unclear. In this study, we report on the histopathological and immunohistochemical features of the gills of the crucian carp Carassius auratus challenged with Aeromonas hydrophila. Small RNA libraries of the gills were constructed and sequenced on the Illumina HiSeq 2000 platform. A total of 1,165 differentially expressed miRNAs (DEMs) were identified in gills, of which 539 known and 7 unknown DEMs were significantly screened (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes/proteins were primarily involved in 33 immune-related pathways, in which the inflammatory responses were focused on the Toll-like receptor (TLR), mitogen-activated protein kinase (MAPK), and nuclear factor kappa B (NF-κB) signaling pathways. Moreover, the expression levels of 14 key miRNAs (e.g., miR-10, miR-17, miR-26a, miR-144, miR-145, and miR-146a) and their target genes (e.g., TNFα, TLR4, NF-κB, TAB1, PI3K, and IRAK1) were verified. In addition, the protein levels based on isobaric tags for relative and absolute quantification (iTRAQ) were significantly associated with the results of the quantitative real-time PCR (qRT-PCR) analysis (p < 0.01). miR-17/pre-miR-17 were identified in the regulation expression of the NF-κB target gene, and the phylogenetic tree analysis showed that the pre-miR-17 of C. auratus with the closest similarity to the zebrafish Danio rerio is highly conserved in teleosts. This is the first report of the multi-omics analysis of the miRNAs and proteins in the gills of C. auratus infected with A. hydrophila, thus enriching knowledge on the regulation mechanism of the local immune response in Cyprinidae fish.},
}
@article {pmid36815186,
year = {2023},
author = {Zhou, T and Li, W},
title = {Analysis on Logistics Efficiency Measurement of New Western Land-Sea Corridor under the Background of "Double Carbon" and Ecological Environment Protection.},
journal = {Journal of environmental and public health},
volume = {2023},
number = {},
pages = {8642841},
pmid = {36815186},
issn = {1687-9813},
mesh = {*Carbon ; *Environment ; Efficiency ; Industry ; China ; Economic Development ; },
abstract = {Under the research background of ecological environment protection and "double carbon" goal, this paper applies panel data on the logistics industry from 2010 to 2019 in 12 provinces of China's new western land-sea corridor to statically measure the logistics industry's technical efficiency after taking into account the impact of different environmental elements and to analyze the dynamics trends of total factor productivity in the logistics sector. It is measured by using the three-stage SBM model and the Malmquist-Luenberger productivity index, which considers undesirable output. The findings indicate the following: (1) In the context of "double carbon," the overall technical efficiency of the logistics sector in the new western land-sea corridor seems to be relatively low; however, the average technical efficiency of the logistics sector in the southern portion of the new western land-sea corridor does seem to be higher than that of the northern part. (2) The logistics industry's technical efficiency varies greatly by region, with locations near central China having much higher technical efficiency than remote inland areas. (3) The fundamental reason for the improvement of technical efficiency in the logistics industry is pure technical efficiency, and the driving force behind the increase in total factor productivity is technological advancement. (4) Economic development, informatization development, industrial market scale, and import and export all have a substantial influence on the logistics industry's technical efficiency. Finally, depending on the findings, policy recommendations are offered.},
}
@article {pmid36813959,
year = {2023},
author = {Cai, S and Zhao, X and Pittelkow, CM and Fan, M and Zhang, X and Yan, X},
title = {Optimal nitrogen rate strategy for sustainable rice production in China.},
journal = {Nature},
volume = {615},
number = {7950},
pages = {73-79},
pmid = {36813959},
issn = {1476-4687},
support = {CBET-2047165//National Science Foundation/ ; CBET-2025826//National Science Foundation/ ; },
mesh = {*Agriculture/economics/methods ; China ; Fertilizers/analysis/economics ; *Nitrogen/analysis/economics/metabolism ; *Oryza/metabolism ; Soil/chemistry ; *Sustainable Development ; *Crops, Agricultural/economics/metabolism/supply &amp; distribution ; Ecology ; Farmers ; Datasets as Topic ; Food Supply ; *Environmentalism ; },
abstract = {Avoiding excessive agricultural nitrogen (N) use without compromising yields has long been a priority for both research and government policy in China[1,2]. Although numerous rice-related strategies have been proposed[3-5], few studies have assessed their impacts on national food self-sufficiency and environmental sustainability and fewer still have considered economic risks faced by millions of smallholders. Here we established an optimal N rate strategy based on maximizing either economic (ON) or ecological (EON) performance using new subregion-specific models. Using an extensive on-farm dataset, we then assessed the risk of yield losses among smallholder farmers and the challenges of implementing the optimal N rate strategy. We find that meeting national rice production targets in 2030 is possible while concurrently reducing nationwide N consumption by 10% (6-16%) and 27% (22-32%), mitigating reactive N (Nr) losses by 7% (3-13%) and 24% (19-28%) and increasing N-use efficiency by 30% (3-57%) and 36% (8-64%) for ON and EON, respectively. This study identifies and targets subregions with disproportionate environmental impacts and proposes N rate strategies to limit national Nr pollution below proposed environmental thresholds, without compromising soil N stocks or economic benefits for smallholders. Thereafter, the preferable N strategy is allocated to each region based on the trade-off between economic risk and environmental benefit. To facilitate the adoption of the annually revised subregional N rate strategy, several recommendations were provided, including a monitoring network, fertilization quotas and smallholder subsidies.},
}
@article {pmid36806940,
year = {2023},
author = {Rivera-Colón, AG and Rayamajhi, N and Minhas, BF and Madrigal, G and Bilyk, KT and Yoon, V and Hüne, M and Gregory, S and Cheng, CHC and Catchen, JM},
title = {Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish.},
journal = {Molecular biology and evolution},
volume = {40},
number = {3},
pages = {},
pmid = {36806940},
issn = {1537-1719},
support = {//National Science Foundation/ ; },
mesh = {Animals ; Antarctic Regions ; *Adaptation, Physiological ; Fishes/genetics ; *Perciformes/genetics ; Genomics ; Antifreeze Proteins ; },
abstract = {White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.},
}
@article {pmid36803728,
year = {2023},
author = {Niu, L and Zhagn, L and Xi, F and Wang, J},
title = {[Influencing factors and scenario forecasting of carbon emissions in Liaoning Province, China].},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {34},
number = {2},
pages = {499-509},
doi = {10.13287/j.1001-9332.202302.001},
pmid = {36803728},
issn = {1001-9332},
mesh = {*Carbon/analysis ; *Carbon Dioxide/analysis ; Economic Development ; China ; Forecasting ; },
abstract = {Liaoning is a province with large energy consumption and carbon emissions. Management of carbon emissions in Liaoning Province is crucial to realizing China's carbon peaking and carbon neutrality goals. To clarify the driving factors and trends of carbon emissions in Liaoning Province, we analyzed the impacts of six factors on carbon emissions in Liaoning Province through STIRPAT model based on carbon emission data from 1999 to 2019. The impact factors included population, urbanization rate, per-capita GDP, secondary industry ratio, energy consumption per unit GDP, and coal consumption ratio. Nine forecasting scenarios with three economic and population growth models and three emission reduction models were set up, and their carbon emission trends under the above nine forecasting scenarios were predicted. The results showed that the main driving factor of carbon emissions in Liaoning Province was per-capita GDP, and that the main inhibitor was energy consumption per unit GDP. The carbon peak year in Liaoning Province would fluctuate between 2020 and 2055 under the nine forecasting scenarios, with peak values ranging from 544 to 1088 million tons CO2. The medium economic development growth and high carbon emission reduction scenario would be the optimal carbon emission scenario in Liaoning Province. Under this forecasting scenario, Liaoning Province could achieve carbon peak (611 million tons CO2) by 2030 without affec-ting economic development through optimizing energy structure and controlling the intensity of energy consumption. Our results would be helpful for seeking the best path for carbon emission reduction in Liaoning Province and providing a reference for its realization of carbon peaking and carbon neutrality goals.},
}
@article {pmid36795572,
year = {2023},
author = {Wang, J and Ding, R and Ouyang, T and Gao, H and Kan, H and Li, Y and Hu, Q and Yang, Y},
title = {Systematic investigation of the mechanism of herbal medicines for the treatment of prostate cancer.},
journal = {Aging},
volume = {15},
number = {4},
pages = {1004-1024},
pmid = {36795572},
issn = {1945-4589},
mesh = {Male ; Humans ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Phosphatidylinositol 3-Kinases ; Reproducibility of Results ; *Prostatic Neoplasms/drug therapy/genetics ; },
abstract = {Due to various unpleasant side effects and general ineffectiveness of current treatments for prostate cancer (PCa), more and more people with PCa try to look for complementary and alternative medicine such as herbal medicine. However, since herbal medicine has multi-components, multi-targets and multi-pathways features, its underlying molecular mechanism of action is not yet known and still needs to be systematically explored. Presently, a comprehensive approach consisting of bibliometric analysis, pharmacokinetic assessment, target prediction and network construction is firstly performed to obtain PCa-related herbal medicines and their corresponding candidate compounds and potential targets. Subsequently, a total of 20 overlapping genes between DEGs in PCa patients and the target genes of the PCa-related herbs, as well as five hub genes, i.e., CCNA2, CDK2, CTH, DPP4 and SRC were determined employing bioinformatics analysis. Further, the roles of these hub genes in PCa were also investigated through survival analysis and tumour immunity analysis. Moreover, to validate the reliability of the C-T interactions and to further explore the binding modes between ingredients and their targets, the molecular dynamics (MD) simulations were carried out. Finally, based on the modularization of the biological network, four signaling pathways, i.e., PI3K-Akt, MAPK, p53 and cell cycle were integrated to further analyze the therapeutic mechanism of PCa-related herbal medicine. All the results show the mechanism of action of herbal medicines on treating PCa from the molecular to systematic levels, providing a reference for the treatment of complex diseases using TCM.},
}
@article {pmid36792824,
year = {2023},
author = {Woodhouse, A and Swain, A and Fagan, WF and Fraass, AJ and Lowery, CM},
title = {Late Cenozoic cooling restructured global marine plankton communities.},
journal = {Nature},
volume = {614},
number = {7949},
pages = {713-718},
pmid = {36792824},
issn = {1476-4687},
mesh = {Animals ; *Aquatic Organisms/classification/isolation &amp; purification ; *Biodiversity ; *Cold Temperature ; Datasets as Topic ; *Foraminifera/classification/isolation &amp; purification ; Fossils ; *Geographic Mapping ; History, Ancient ; Phylogeny ; *Phylogeography ; *Plankton/classification/isolation &amp; purification ; *Spatio-Temporal Analysis ; Time Factors ; Hydrobiology ; },
abstract = {The geographic ranges of marine organisms, including planktonic foraminifera[1], diatoms, dinoflagellates[2], copepods[3] and fish[4], are shifting polewards owing to anthropogenic climate change[5]. However, the extent to which species will move and whether these poleward range shifts represent precursor signals that lead to extinction is unclear[6]. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here we apply a bipartite network approach to quantify group diversity, latitudinal specialization and latitudinal equitability for planktonic foraminifera over the past eight million years using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences[7]. The results depict a global, clade-wide shift towards the Equator in ecological and morphological community equitability over the past eight million years in response to temperature changes during the late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a latitudinal equitability gradient among planktonic foraminiferal functional groups which is coupled to the latitudinal biodiversity gradient only through the geologically recent past (the past two million years). Before this time, latitudinal equitability gradients indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts among marine planktonic microorganisms[1,2,8] in the recent and geological past suggest substantial poleward expansion of marine communities even under the most conservative future global warming scenarios.},
}
@article {pmid36792330,
year = {2023},
author = {Suzuki, S and Nishikawa, Y and Okada, H and Nakayama, T},
title = {Information-seeking behaviour of community pharmacists during the COVID-19 pandemic: an ecological study.},
journal = {BMJ open},
volume = {13},
number = {2},
pages = {e062465},
pmid = {36792330},
issn = {2044-6055},
mesh = {Humans ; *COVID-19/epidemiology ; Pharmacists ; Pandemics ; Information Seeking Behavior ; *Community Pharmacy Services ; },
abstract = {OBJECTIVE: To evaluate the information-seeking behaviour of pharmacists during the COVID-19 pandemic and its relation to COVID-19 and related infections and deaths within the local prefecture.<br><br>DESIGN: Ecological study.<br><br>SETTING: Japan-47 prefectures.<br><br>METHODS: The number of accesses to a Japanese web page established by the Pharmacy Informatics Group to disseminate information about infection control and the number of infections and deaths in 47 prefectures were investigated from 6 April to 30 September 2020 using the access information on the web page and publicly available information.<br><br>RESULTS: During the first 6 months of the COVID-19 pandemic, the total number of accesses was 226 130 (range: 10 984-138 898 per month), the total number of infections was 78 761 (1738-31 857) and the total number of deaths was 1470 (39-436). The correlation between the total number of accesses and that of infections per 100 000 individuals in 47 prefectures was r=0.72 (95% CI 0.55 to 0.83, p<0.001), and between the total number of accesses and deaths per 100 000 individuals in 47 prefectures was r=0.44 (95% CI 0.17 to 0.65, p=0.002).<br><br>CONCLUSIONS: The information-seeking behaviour of community pharmacists correlated positively with infection status within the community.},
}
@article {pmid36788337,
year = {2023},
author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G},
title = {Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.},
journal = {Leukemia},
volume = {37},
number = {3},
pages = {724},
doi = {10.1038/s41375-023-01839-7},
pmid = {36788337},
issn = {1476-5551},
}
@article {pmid36787802,
year = {2023},
author = {Dennis, A and Cuthbertson, DJ and Wootton, D and Crooks, M and Gabbay, M and Eichert, N and Mouchti, S and Pansini, M and Roca-Fernandez, A and Thomaides-Brears, H and Kelly, M and Robson, M and Hishmeh, L and Attree, E and Heightman, M and Banerjee, R and Banerjee, A},
title = {Multi-organ impairment and long COVID: a 1-year prospective, longitudinal cohort study.},
journal = {Journal of the Royal Society of Medicine},
volume = {116},
number = {3},
pages = {97-112},
pmid = {36787802},
issn = {1758-1095},
mesh = {Humans ; Female ; Middle Aged ; Male ; *COVID-19/epidemiology ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; Prospective Studies ; Quality of Life ; Longitudinal Studies ; },
abstract = {OBJECTIVES: To determine the prevalence of organ impairment in long COVID patients at 6 and 12 months after initial symptoms and to explore links to clinical presentation.<br><br>DESIGN: Prospective cohort study.<br><br>PARTICIPANTS: Individuals.<br><br>METHODS: In individuals recovered from acute COVID-19, we assessed symptoms, health status, and multi-organ tissue characterisation and function.<br><br>SETTING: Two non-acute healthcare settings (Oxford and London). Physiological and biochemical investigations were performed at baseline on all individuals, and those with organ impairment were reassessed.<br><br>MAIN OUTCOME MEASURES: Primary outcome was prevalence of single- and multi-organ impairment at 6 and 12 months post COVID-19.<br><br>RESULTS: A total of 536 individuals (mean age 45 years, 73% female, 89% white, 32% healthcare workers, 13% acute COVID-19 hospitalisation) completed baseline assessment (median: 6 months post COVID-19); 331 (62%) with organ impairment or incidental findings had follow-up, with reduced symptom burden from baseline (median number of symptoms 10 and 3, at 6 and 12 months, respectively). Extreme breathlessness (38% and 30%), cognitive dysfunction (48% and 38%) and poor health-related quality of life (EQ-5D-5L&#x2009;<&#x2009;0.7; 57% and 45%) were common at 6 and 12 months, and associated with female gender, younger age and single-organ impairment. Single- and multi-organ impairment were present in 69% and 23% at baseline, persisting in 59% and 27% at follow-up, respectively.<br><br>CONCLUSIONS: Organ impairment persisted in 59% of 331 individuals followed up at 1 year post COVID-19, with implications for symptoms, quality of life and longer-term health, signalling the need for prevention and integrated care of long COVID.Trial Registration: ClinicalTrials.gov Identifier: NCT04369807.},
}
@article {pmid36782205,
year = {2023},
author = {Amin, M and Aziz, MA and Pieroni, A and Nazir, A and Al-Ghamdi, AA and Kangal, A and Ahmad, K and Abbasi, AM},
title = {Edible wild plant species used by different linguistic groups of Kohistan Upper Khyber Pakhtunkhwa (KP), Pakistan.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {19},
number = {1},
pages = {6},
pmid = {36782205},
issn = {1746-4269},
support = {RSP202R483//Abdullah Ahmed Al-Ghamdi, King Saud University/ ; RSP202R483//Abdullah Ahmed Al-Ghamdi, King Saud University/ ; },
mesh = {Humans ; Pakistan ; *Plants, Edible ; *Ethnobotany/methods ; Vegetables ; Fruit ; },
abstract = {BACKGROUND: The mountainous territory of Kohistan shelters diverse food plant species and is considered one of the important hotspots of local plant knowledge. In the era of globalization and food commodification, wild food plants (WFPs) play an important role in supporting local food systems and related local knowledge is one of the important pillars of food sustainability across the region. Since the area is populated by different cultural groups and each culture has retained particular knowledge on the local plant species, therefore, to make a cross-culturally comparison, the study was planned to record and compare the local plants knowledge among three linguistic groups viz Gujjar, Kohistani and Shina in order to not only protect the local knowledge but to determine the food cultural adaptations among these groups looking through the lens of their food ethnobotanies.<br><br>METHODS: Field ethnobotanical survey was carried out in 2020-2021 to gather the data on wild food plants. We used semi-structured interviews. Use reports were counted, and the results were visualized through Venn diagrams.<br><br>RESULTS: In total, 64 plant species belonging to 45 botanical families were documented. Among these Ajuga integrifolia, Barbarea verna, Clematis grata, Impatiens edgeworthii, Ranunculus laetus (vegetables), Parrotiopsis jacquemontiana (fruit), Indigofera tinctoria (flower), Juniperus excelsa, Primula elliptica, P. macrophylla (flavoring agent), Leontopodium himalayanum (Chewing gum), and Juniperus excelsa (snuff) were reported for the first time. The highest use reports (&#x2265;&#x2009;90) were recorded for Mentha longifolia, Amaranthus hybridus, Quercus semecarpifolia, Solanum miniatum, Oxalis corniculata, Ficus palmata, and Urtica dioica. Maximum number of wild food plant species (WFPs) were reported by Kohistani, followed by Shinaki and Gujjari linguistic groups. The percentage overlap of traditional knowledge on WFPs was highest among Kohistani and Shinaki (56.0%), followed by Shinaki and Gujjars (17.0%), and Kohistani and Gujjars (15.0%). Kohistani and Shinaki groups exhibited maximum homogeneity in traditional knowledge. However, Gujjars had more knowledge on WFPs compared to Kohistani and Shinaki. In addition, some dairy products viz. Bhorus, Bagora, Bak, Cholam, Kacha, Gurloo and Poyeen were reported also reported that are consumed orally and used in traditional cuisines.<br><br>CONCLUSIONS: The study indicates that Kohistan is one of the important spots of biocultural diversity and could be recognized as biocultural refugia. WFPs have been an integral part of the traditional food systems among the studied groups, particularly the Gujjars have reported more distinct plant uses which could be referred to their distinctive ecological experiences among others. However, social change is one of the challenges that might lead to the erosion of local plant knowledge. Moreover, intercultural negotiations among the studied groups are also a matter of concern which could homogenize the local knowledge among them. Therefore, we suggest solid policy measures to protect the local knowledge and celebrate diversity across this mountain territory.},
}
@article {pmid36781356,
year = {2023},
author = {Mayne, SL and DiFiore, G and Hannan, C and Nwokeji, U and Tam, V and Filograna, C and Martin, T and South, E and Mitchell, JA and Glanz, K and Fiks, AG},
title = {Feasibility and acceptability of mobile methods to assess home and neighborhood environments related to adolescent sleep.},
journal = {Sleep health},
volume = {9},
number = {3},
pages = {331-338},
pmid = {36781356},
issn = {2352-7226},
support = {K01 HL155860/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Male ; Adolescent ; Female ; Feasibility Studies ; *Geographic Information Systems ; *Smartphone ; Noise ; Neighborhood Characteristics ; },
abstract = {OBJECTIVE: A growing evidence base suggests home and neighborhood environmental exposures may influence adolescent sleep, but few studies have assessed these relationships using methods that account for time-varying, location-specific exposures, or multiple neighborhood contexts. This study aimed to assess the feasibility and acceptability of using smartphone global positioning system (GPS) tracking and ecological momentary assessment (EMA) to assess time-varying home and neighborhood environmental exposures hypothesized to be associated with adolescent sleep.<br><br>METHODS: Adolescents aged 15-17 years in Philadelphia completed 7 days of continuous smartphone GPS tracking, which was used to identify daily levels of exposure to geocoded neighborhood factors (eg, crime, green space). Four daily EMA surveys assessed home sleep environment (eg, noise, light), stress, health behaviors, and neighborhood perceptions. Feasibility and acceptability of GPS tracking and EMA were assessed, and distributions of daily environmental exposures were examined.<br><br>RESULTS: Among 25 teens (mean age 16, 56% male), there was a high level of GPS location data captured (median daily follow-up: 24 hours). Seventy-eight percent of EMA surveys were completed overall. Most participants (96%) reported no privacy concerns related to GPS tracking and minimal burden from EMA surveys. Exposures differed between participants' home neighborhoods and locations visited outside the home neighborhood (eg, higher crime away from home). Sleep environment disruptions were present on 29% of nights (most common: uncomfortable temperature) and were reported by 52% of adolescents.<br><br>CONCLUSIONS: Results demonstrate the feasibility and acceptability of mobile methods for assessing time-varying home and neighborhood exposures relevant to adolescent sleep for up to 1 week.},
}
@article {pmid36777319,
year = {2022},
author = {Glasgow, L and Lewis, R and Charles, S},
title = {The cancer epidemic in the Caribbean region: Further opportunities to reverse the disease trend.},
journal = {Lancet regional health. Americas},
volume = {13},
number = {},
pages = {100295},
pmid = {36777319},
issn = {2667-193X},
abstract = {Cancer incidence has been rising in the Caribbean and is expected to have significant adverse implications for the health of people in the region and health systems in this decade. While developed countries, for the most part, enjoy the benefits of advanced technologies and adaptive systems in cancer control and management, a different experience confronts a large segment of the Caribbean population. The region has experienced some success in enhancing cancer services, however, there is a need to address gaps in several areas through nationally and regionally tailored initiatives. This Review complements previous publications on the challenges, actions, and progress towards cancer prevention and care in Caribbean countries but also further outlines potential positive impacts that can be derived from addressing gaps pertaining to cancer education, data management, screening and risk assessment, navigation services, gender factors, and resource development. The proposed approaches encapsulate concepts of health theories that are applicable across the ecological domains. When implemented in combination, the proposals may effectively contribute to reducing the cancer burden in the region.},
}
@article {pmid36775641,
year = {2023},
author = {Liu, L and Zhang, WQ and Hu, FC and Pang, K and Guo, YL and Zhang, T and Li, M},
title = {[Evaluation and Optimization of Rural Sewage Treatment Technologies in the Middle Reaches of the Yangtze River Based on Group Decision Making and Analytic Hierarchy Process].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {44},
number = {2},
pages = {1191-1200},
doi = {10.13227/j.hjkx.202203043},
pmid = {36775641},
issn = {0250-3301},
mesh = {*Sewage ; *Rivers ; Analytic Hierarchy Process ; Nitrogen ; Decision Making ; China ; },
abstract = {Rural sewage treatment in the Yangtze River basin is an important link to achieve the great protection of the Yangtze River, but the existing treatment technologies are difficult to choose and have various techniques and a lack of evaluation. Therefore, this study researched and collected the case information of rural sewage treatment projects in the middle reaches of the Yangtze River, analyzed the application of each treatment technology under different collection modes and discharge standards, constructed the evaluation index system of rural sewage treatment technologies, and then conducted a classification evaluation of processing technologies for each application scenario based on group decision making and the Analytic Hierarchy Process. The results showed that:the collection modes of rural sewage in the middle reaches of the Yangtze River were mainly single village or small-scale joint village, the treatment scale was mainly concentrated below 200 m[3]·d[-1], the treatment technology was most applied by the anaerobic+ecological process (28.05%), and the application of integrated equipment was also more widely used (22.47%). The technical performance in the criterion layer had the largest weight (0.5039) in the evaluation index system, followed by those of economic benefits (0.2474), operation and management (0.1559), and environmental impact (0.0928), respectively; the four indicators of TP removal rate, ton water operation cost, ammonia nitrogen removal rate, and maintenance difficulty had higher weights. The evaluation and optimization results showed that the enhanced ecological and anaerobic+ecological treatment technologies were suitable for promotion and application in the rural areas of the middle reaches of the Yangtze River. The results of this study can provide scientific basis and reference for the selection of rural sewage treatment technologies in the middle reaches of the Yangtze River.},
}
@article {pmid36771658,
year = {2023},
author = {Shah, AA and Badshah, L and Khalid, N and Shah, MA and Manduzai, AK and Faiz, A and De Chiara, M and Mattalia, G and Sõukand, R and Pieroni, A},
title = {Disadvantaged Economic Conditions and Stricter Border Rules Shape Afghan Refugees' Ethnobotany: Insights from Kohat District, NW Pakistan.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
pmid = {36771658},
issn = {2223-7747},
abstract = {The study of migrants' ethnobotany can help to address the diverse socio-ecological factors affecting temporal and spatial changes in local ecological knowledge (LEK). Through semi-structured and in-depth conversations with ninety interviewees among local Pathans and Afghan refugees in Kohat District, NW Pakistan, one hundred and forty-five wild plant and mushroom folk taxa were recorded. The plants quoted by Afghan refugees living inside and outside the camps tend to converge, while the Afghan data showed significant differences with those collected by local Pakistani Pathans. Interviewees mentioned two main driving factors potentially eroding folk plant knowledge: (a) recent stricter border policies have made it more difficult for refugees to visit their home regions in Afghanistan and therefore to also procure plants in their native country; (b) their disadvantaged economic conditions have forced them to engage more and more in urban activities in the host country, leaving little time for farming and foraging practices. Stakeholders should foster the exposure that refugee communities have to their plant resources, try to increase their socio-economic status, and facilitate both their settling outside the camps and their transnational movement for enhancing their use of wild plants, ultimately leading to improvements in their food security and health status.},
}
@article {pmid36768056,
year = {2023},
author = {Vukašinović, D and Maksimović, M and Tanasković, S and Marinković, JM and Radak, &#x110; and Maksimović, J and Vujčić, I and Prijović, N and Vlajinac, H},
title = {Body Mass Index and Late Adverse Outcomes after a Carotid Endarterectomy.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {3},
pages = {},
pmid = {36768056},
issn = {1660-4601},
mesh = {Humans ; *Endarterectomy, Carotid/adverse effects ; *Carotid Stenosis ; Body Mass Index ; Cohort Studies ; Overweight/complications/epidemiology ; Treatment Outcome ; *Stroke/epidemiology/etiology ; Obesity/complications/epidemiology ; Retrospective Studies ; *Myocardial Infarction/epidemiology/etiology ; Risk Factors ; },
abstract = {A cohort study was conducted to examine the association of an increased body mass index (BMI) with late adverse outcomes after a carotid endarterectomy (CEA). It comprised 1597 CEAs, performed in 1533 patients at the Vascular Surgery Clinic in Belgrade, from 1 January 2012 to 31 December 2017. The follow-up lasted four years after CEA. Data for late myocardial infarction and stroke were available for 1223 CEAs, data for death for 1305 CEAs, and data for restenosis for 1162 CEAs. Logistic and Cox regressions were used in the analysis. The CEAs in patients who were overweight and obese were separately compared with the CEAs in patients with a normal weight. Out of 1223 CEAs, 413 (33.8%) were performed in patients with a normal weight, 583 (47.7%) in patients who were overweight, and 220 (18.0%) in patients who were obese. According to the logistic regression analysis, the compared groups did not significantly differ in the frequency of myocardial infarction, stroke, and death, as late major adverse outcomes (MAOs), or in the frequency of restenosis. According to the Cox and logistic regression analyses, BMI was neither a predictor for late MAOs, analyzed separately or all together, nor for restenosis. In conclusion, being overweight and being obese were not related to the occurrence of late adverse outcomes after a carotid endarterectomy.},
}
@article {pmid36767964,
year = {2023},
author = {Cao, H and Ou, H and Ju, W and Pan, M and Xue, H and Zhu, F},
title = {Visual Analysis of International Environmental Security Management Research (1997-2021) Based on VOSviewer and CiteSpace.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {3},
pages = {},
pmid = {36767964},
issn = {1660-4601},
mesh = {Bayes Theorem ; *Agriculture ; Australia ; *Big Data ; China ; },
abstract = {To investigate the international development status and hot trends in the field of environmental security management in recent years, the published the environmental security management literature from 1997 to 2021, which was retrieved from Web of Science, with VOSviewer as the main and CiteSpace as the auxiliary, through the cooperation network of authors, scientific research institutions, and countries. The keywords were visualized by clustering, time zone analysis, and burst analysis. A total of 7596 articles were retrieved, forming six main clustering labels, including 28,144 authors. The research hotspots are from the fields of personal health, society, agriculture, ecological environment, energy, and sustainable development, as well as the development of internet environmental safety management, such as big data, Bayesian networks, and conceptual frameworks. Through cluster analysis, the cooperation of major research teams and scientific research institutions and the cooperation and development between countries were analyzed. The cooperation between scientific research institutions in various countries is relatively close. The United States currently occupies a dominant and authoritative position in this field. China has cooperated more closely with the United States, Britain, Australia, and India.},
}
@article {pmid36767252,
year = {2023},
author = {Liu, Q and Guo, R and Huang, Z and He, B and Li, X},
title = {The Nonlinear Impact of Mobile Human Activities on Vegetation Change in the Guangdong-Hong Kong-Macao Greater Bay Area.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {3},
pages = {},
pmid = {36767252},
issn = {1660-4601},
mesh = {Humans ; Hong Kong ; Macau ; *Ecosystem ; *Urbanization ; Human Activities ; China ; },
abstract = {Vegetation is essential for ecosystem function and sustainable urban development. In the context of urbanization, the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), as the typical urban-dominated region, has experienced a remarkable increase in social and economic activities. Their impact on vegetation is of great significance but unclear, as interannual flow data and linear methods have limitations. Therefore, in this study, we used human and vehicle flow data to build and simulate the indices of mobile human activity. In addition, we used partial least squares regression (PLSR), random forest (RF), and geographical detector (GD) models to analyze the impact of mobile human activities on vegetation change. The results showed that indices of mobile human and vehicle flow increased by 1.43 and 7.68 times from 2000 to 2019 in the GBA, respectively. Simultaneously, vegetation increased by approximately 64%, whereas vegetation decreased mainly in the urban areas of the GBA. Vegetation change had no significant linear correlation with mobile human activities, exhibiting a regression coefficient below 0.1 and a weight of coefficients of PLSR less than 40 between vegetation change and all the factors of human activities. However, a more significant nonlinear relationship between vegetation change and driving factors were obtained. In the RF regression model, vegetation decrease was significantly affected by mobile human activity of vehicle flow, with an importance score of 108.11. From the GD method, vegetation decrease was found to mainly interact with indices of mobile human and vehicle inflow, and the highest interaction force was 0.82. These results may support the attainment of sustainable social-ecological systems and global environmental change.},
}
@article {pmid36758962,
year = {2023},
author = {Lee, HE and Kim, YG and Jeong, JY and Kim, DH},
title = {Data resource profile: the Korean Community Health Status Indicators (K-CHSI) database.},
journal = {Epidemiology and health},
volume = {45},
number = {},
pages = {e2023016},
pmid = {36758962},
issn = {2092-7193},
mesh = {Humans ; Databases, Factual ; *Environment ; *Health Status Indicators ; Health Surveys ; Republic of Korea/epidemiology ; Public Health ; },
abstract = {Korean Community Health Status Indicators (K-CHSI) is a model-based database containing annual data on health outcomes and determinants at the municipal level (si/gun/gu-level regions, including mid-sized cities, counties, and districts). K-CHSI's health outcomes include overall mortality, disease incidence, prevalence rates, and self-reported health. Health determinants were measured in 5 domains: socio-demographic factors, health behaviors, social environment, physical environment, and the healthcare system. The data sources are 71 public databases, including Causes of Death Statistics, Cancer Registration Statistics, Community Health Survey, Population Census, and Census on Establishments and Statistics of Urban Plans. This dataset covers Korea's 17 metropolitan cities and provinces, with data from approximately 250 municipal regions (si/gun/gu). The current version of the database (DB version 1.3) was built using 12 years of data from 2008 to 2019. All data included in K-CHSI may be downloaded via the Korea Community Health Survey site, with no login requirement (https://chs.kdca.go.kr/chs/recsRoom/dataBaseMain.do). K-CHSI covers extensive health outcomes and health determinants at the municipal level over a period of more than 10 years, which enables ecological and time-series analyses of the relationships among various health outcomes and related factors.},
}
@article {pmid36752771,
year = {2023},
author = {Lippi, CA and Rund, SSC and Ryan, SJ},
title = {Characterizing the Vector Data Ecosystem.},
journal = {Journal of medical entomology},
volume = {60},
number = {2},
pages = {247-254},
pmid = {36752771},
issn = {1938-2928},
mesh = {Animals ; *Ecosystem ; *Vector Borne Diseases ; Databases, Factual ; },
abstract = {A growing body of information on vector-borne diseases has arisen as increasing research focus has been directed towards the need for anticipating risk, optimizing surveillance, and understanding the fundamental biology of vector-borne diseases to direct control and mitigation efforts. The scope and scale of this information, in the form of data, comprising database efforts, data storage, and serving approaches, means that it is distributed across many formats and data types. Data ranges from collections records to molecular characterization, geospatial data to interactions of vectors and traits, infection experiments to field trials. New initiatives arise, often spanning the effort traditionally siloed in specific research disciplines, and other efforts wane, perhaps in response to funding declines, different research directions, or lack of sustained interest. Thusly, the world of vector data - the Vector Data Ecosystem - can become unclear in scope, and the flows of data through these various efforts can become stymied by obsolescence, or simply by gaps in access and interoperability. As increasing attention is paid to creating FAIR (Findable Accessible Interoperable, and Reusable) data, simply characterizing what is 'out there', and how these existing data aggregation and collection efforts interact, or interoperate with each other, is a useful exercise. This study presents a snapshot of current vector data efforts, reporting on level of accessibility, and commenting on interoperability using an illustration to track a specimen through the data ecosystem to understand where it occurs for the database efforts anticipated to describe it (or parts of its extended specimen data).},
}
@article {pmid36750720,
year = {2023},
author = {Mechenich, MF and Žliobaitė, I},
title = {Eco-ISEA3H, a machine learning ready spatial database for ecometric and species distribution modeling.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {77},
pmid = {36750720},
issn = {2052-4463},
support = {314803//Academy of Finland (Suomen Akatemia)/ ; 1314803//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {Animals ; Humans ; Climate Change ; *Databases, Factual ; *Ecosystem ; Geography ; Machine Learning ; Mammals ; },
abstract = {We present the Eco-ISEA3H database, a compilation of global spatial data characterizing climate, geology, land cover, physical and human geography, and the geographic ranges of nearly 900 large mammalian species. The data are tailored for machine learning (ML)-based ecological modeling, and are intended primarily for continental- to global-scale ecometric and species distribution modeling. Such models are trained on present-day data and applied to the geologic past, or to future scenarios of climatic and environmental change. Model training requires integrated global datasets, describing species' occurrence and environment via consistent observational units. The Eco-ISEA3H database incorporates data from 17 sources, and includes 3,033 variables. The database is built on the Icosahedral Snyder Equal Area (ISEA) aperture 3 hexagonal (3H) discrete global grid system (DGGS), which partitions the Earth's surface into equal-area hexagonal cells. Source data were incorporated at six nested ISEA3H resolutions, using scripts developed and made available here. We demonstrate the utility of the database in a case study analyzing the bioclimatic envelopes of ten large, widely distributed mammalian species.},
}
@article {pmid36748522,
year = {2022},
author = {Cunningham-Oakes, E and Pointon, T and Murphy, B and Campbell-Lee, S and Connor, TR and Mahenthiralingam, E},
title = {Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis.},
journal = {Microbial genomics},
volume = {8},
number = {11},
pages = {},
pmid = {36748522},
issn = {2057-5858},
support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Retrospective Studies ; *Bacteria/genetics ; *Metagenome ; Metagenomics/methods ; Workflow ; },
abstract = {The home and personal care (HPC) industry generally relies on initial cultivation and subsequent biochemical testing for the identification of microorganisms in contaminated products. This process is slow (several days for growth), labour intensive, and misses organisms which fail to revive from the harsh environment of preserved consumer products. Since manufacturing within the HPC industry is high-throughput, the process of identification of microbial contamination could benefit from the multiple cultivation-independent methodologies that have developed for the detection and analysis of microbes. We describe a novel workflow starting with automated DNA extraction directly from a HPC product, and subsequently applying metagenomic methodologies for species and strain-level identification of bacteria. The workflow was validated by application to a historic microbial contamination of a general-purpose cleaner (GPC). A single strain of Pseudomonas oleovorans was detected metagenomically within the product. The metagenome mirrored that of a contaminant isolated in parallel by a traditional cultivation-based approach. Using a dilution series of the incident sample, we also provide evidence to show that the workflow enables detection of contaminant organisms down to 100 CFU/ml of product. To our knowledge, this is the first validated example of metagenomics analysis providing confirmatory evidence of a traditionally isolated contaminant organism, in a HPC product.},
}
@article {pmid36747723,
year = {2023},
author = {Rokhsar, JL and Raynor, B and Sheen, J and Goldstein, ND and Levy, MZ and Castillo-Neyra, R},
title = {Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {36747723},
support = {K01 AI139284/AI/NIAID NIH HHS/United States ; T32 AI070077/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi , affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.<br><br>OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.<br><br>DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.<br><br>RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.<br><br>CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.<br><br>AUTHOR SUMMARY: Chagas disease, caused by the parasite Trypanosoma cruzi , is transmitted via triatomine insect vectors. In Latin America, dogs are a common feeding source for triatomine vectors and subsequently an important reservoir of T. cruzi . One proposed intervention to reduce T. cruzi transmission is xenointoxication: treating dogs with oral insecticide to kill triatomine vectors in order to decrease overall T. cruzi transmission. Fluralaner, commonly administered to prevent ectoparasites such as fleas and ticks, is effective under laboratory conditions against the triatomine vectors. One concern with fluralaner treatment is that rapid death of the insect vectors may make the insects more available to oral ingestion by dogs; a more effective transmission pathway than stercorarian, the usual route for T. cruzi transmission. Using a mathematical model, we explored 3 different epidemiologic scenarios: high prevalence endemic disease within a domestic T. cruzi cycle, low prevalence endemic disease within a domestic T. cruzi cycle, and low prevalence endemic disease within a semi-sylvatic T. cruzi cycle. We found a range of beneficial to detrimental effects of fluralaner xenointoxication depending on the epidemiologic scenario. Our results suggest that careful field trials should be designed and carried out before wide scale implementation of fluralaner xenointoxication to reduce T. cruzi transmission.},
}
@article {pmid36746772,
year = {2023},
author = {Wu, Z and Jiang, Z and Li, Z and Jiao, P and Zhai, J and Liu, S and Han, X and Zhang, S and Sun, J and Gai, Z and Qiu, C and Xu, J and Liu, H and Qin, R and Lu, R},
title = {Multi-omics analysis reveals spatiotemporal regulation and function of heteromorphic leaves in Populus.},
journal = {Plant physiology},
volume = {192},
number = {1},
pages = {188-204},
pmid = {36746772},
issn = {1532-2548},
mesh = {*Populus/physiology ; Multiomics ; Plant Leaves/metabolism ; Transcriptome/genetics ; Chromatin/metabolism ; Gene Expression Regulation, Plant ; },
abstract = {Despite the high economic and ecological importance of forests, our knowledge of the adaptive evolution of leaf traits remains very limited. Euphrates poplar (Populus euphratica), which has high tolerance to arid environment, has evolved four heteromorphic leaf forms, including narrow (linear and lanceolate) and broad (ovate and broad-ovate) leaves on different crowns. Here, we revealed the significant functional divergence of four P. euphratica heteromorphic leaves at physiological and cytological levels. Through global analysis of transcriptome and DNA methylation across tree and leaf developmental stages, we revealed that gene expression and DNA epigenetics differentially regulated key processes involving development and functional adaptation of heteromorphic leaves, such as hormone signaling pathways, cell division, and photosynthesis. Combined analysis of gene expression, methylation, ATAC-seq, and Hi-C-seq revealed longer interaction of 3D genome, hypomethylation, and open chromatin state upregulates IAA-related genes (such as PIN-FORMED1 and ANGUSTIFOLIA3) and promotes the occurrence of broad leaves while narrow leaves were associated with highly concentrated heterochromatin, hypermethylation, and upregulated abscisic acid pathway genes (such as Pyrabactin Resistance1-like10). Therefore, development of P. euphratica heteromorphic leaves along with functional divergence was regulated by differentially expressed genes, DNA methylation, chromatin accessibility, and 3D genome remodeling to adapt to the arid desert. This study advances our understanding of differential regulation on development and functional divergence of heteromorphic leaves in P. euphratica at the multi-omics level and provides a valuable resource for investigating the adaptive evolution of heteromorphic leaves in Populus.},
}
@article {pmid36744611,
year = {2023},
author = {Smail, EJ and Alpert, JM and Mardini, MT and Kaufmann, CN and Bai, C and Gill, TM and Fillingim, RB and Cenko, E and Zapata, R and Karnati, Y and Marsiske, M and Ranka, S and Manini, TM},
title = {Feasibility of a Smartwatch Platform to Assess Ecological Mobility: Real-Time Online Assessment and Mobility Monitor.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {78},
number = {5},
pages = {821-830},
pmid = {36744611},
issn = {1758-535X},
support = {K01 AG061239/AG/NIA NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R33 AG059207/AG/NIA NIH HHS/United States ; UL1 TR001427/TR/NCATS NIH HHS/United States ; R21 AG059207/AG/NIA NIH HHS/United States ; U24 AG059624/AG/NIA NIH HHS/United States ; K01AG061239/AG/NIA NIH HHS/United States ; T32 AG062728/AG/NIA NIH HHS/United States ; P30 AG028740/AG/NIA NIH HHS/United States ; P30 AG021342/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; Pilot Projects ; Feasibility Studies ; *Quality of Life ; Surveys and Questionnaires ; *Pain ; },
abstract = {BACKGROUND: Early detection of mobility decline is critical to prevent subsequent reductions in quality of life, disability, and mortality. However, traditional approaches to mobility assessment are limited in their ability to capture daily fluctuations that align with sporadic health events. We aim to describe findings from a pilot study of our Real-time Online Assessment and Mobility Monitor (ROAMM) smartwatch application, which uniquely captures multiple streams of data in real time in ecological settings.<br><br>METHODS: Data come from a sample of 31 participants (Mage&#xa0;=&#xa0;74.7, 51.6% female) who used ROAMM for approximately 2 weeks. We describe the usability and feasibility of ROAMM, summarize prompt data using descriptive metrics, and compare prompt data with traditional survey-based questionnaires or other established measures.<br><br>RESULTS: Participants were satisfied with ROAMM's function (87.1%) and ranked the usability as "above average." Most were highly engaged (average adjusted compliance&#xa0;=&#xa0;70.7%) and the majority reported being "likely" to enroll in a 2-year study (77.4%). Some smartwatch features were correlated with their respective traditional measurements (eg, certain GPS-derived life-space mobility features (r&#xa0;=&#xa0;0.50-0.51, p < .05) and ecologically measured pain (r&#xa0;=&#xa0;0.72, p&#xa0;=&#xa0;.01), but others were not (eg, ecologically measured fatigue).<br><br>CONCLUSIONS: ROAMM was usable, acceptable, and effective at measuring mobility and risk factors for mobility decline in our pilot sample. Additional work with a larger and more diverse sample is necessary to confirm associations between smartwatch-measured features and traditional measures. By monitoring multiple data streams simultaneously in ecological settings, this technology could uniquely contribute to the evolution of mobility measurement and risk factors for mobility loss.},
}
@article {pmid36736631,
year = {2023},
author = {LaVigne, AW and DeWeese, TL and Wright, JL and Deville, C and Yegnasubramanian, S and Alcorn, SR},
title = {Radiotherapy Deserts: The Impact of Race, Poverty, and the Rural-Urban Continuum on Density of Providers and the Use of Radiation Therapy in the US.},
journal = {International journal of radiation oncology, biology, physics},
volume = {116},
number = {1},
pages = {17-27},
doi = {10.1016/j.ijrobp.2023.01.046},
pmid = {36736631},
issn = {1879-355X},
mesh = {Aged ; Humans ; Male ; Medicare/statistics &amp; numerical data ; *Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Poverty/statistics &amp; numerical data ; Rural Population/statistics &amp; numerical data ; Social Class ; United States/epidemiology ; Urban Population/statistics &amp; numerical data ; *Radiotherapy/economics/standards/statistics &amp; numerical data ; Resource-Limited Settings/statistics &amp; numerical data ; Race Factors/statistics &amp; numerical data ; Health Personnel/statistics &amp; numerical data ; Health Services Accessibility/statistics &amp; numerical data ; Health Services Needs and Demand/statistics &amp; numerical data ; Prostatic Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Breast Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Female ; Databases, Factual/statistics &amp; numerical data ; Patient-Centered Care/statistics &amp; numerical data ; *Healthcare Disparities/economics/ethnology/statistics &amp; numerical data ; },
abstract = {PURPOSE: Prior efforts to characterize disparities in radiation therapy access and receipt have not comprehensively investigated interplay between race, socioeconomic status, and geography relative to oncologic outcomes. This study sought to define these complex relationships at the US county level for prostate cancer (PC) and invasive breast (BC) cancer to build a tool that facilitates identification of "radiotherapy deserts"-regions with mismatch between radiation therapy resources and oncologic need.<br><br>METHODS AND MATERIALS: An ecologic study model was constructed using national databases to evaluate 3,141 US counties. Radiation therapy resources and use densities were operationalized as physicians to persons at risk (PPR) and use to persons at risk (UPR): the number of attending radiation oncologists and Medicare beneficiaries per 100,000 persons at risk, respectively. Oncologic need was defined by "hot zone" counties with &#x2265;2 standard deviations (SDs) above mean incidence and death rates. Univariable and multivariable logistic regressions examined links between PPR and UPR densities, epidemiologic variables, and hot zones for oncologic outcomes. Statistics are reported at a significance level of P < .05.<br><br>RESULTS: The mean (SD) PPR and UPR densities were 2.1 (5.9) and 192.6 (557.6) for PC and 1.9 (5.3) and 174.4 (501.0) for BC, respectively. Counties with high PPR and UPR densities were predominately metropolitan (odds ratio [OR], 2.9-4.4), generally with a higher percentage of Black non-Hispanic constituents (OR, 1.5-2.3). Incidence and death rate hot zones were largely nonmetropolitan (OR, 0.3-0.6), generally with a higher percentage of Black non-Hispanic constituents (OR, 3.2-6.3). Lower PPR density was associated with death rate hot zones for both types of cancer (OR, 0.8-0.9); UPR density was generally not linked to oncologic outcomes on multivariable analysis.<br><br>CONCLUSIONS: The study found that mismatch between oncologic need with PPR and UPR disproportionately affects nonmetropolitan communities with a higher percentage of Black non-Hispanic constituents. An interactive web platform (bit.ly/densitymaps) was developed to visualize "radiotherapy deserts" and drive targeted investigation of underlying barriers to care in areas of highest need, with the goal of reducing health inequities in this context.},
}
@article {pmid36735127,
year = {2023},
author = {Jiang, X and Sun, Y and Qu, Y and Zeng, H and Yang, J and Zhang, K and Liu, L},
title = {The development and future frontiers of global ecological restoration projects in the twenty-first century: a systematic review based on scientometrics.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {12},
pages = {32230-32245},
pmid = {36735127},
issn = {1614-7499},
support = {2021YFN0113//Sichuan Provincial Science and Technology Department Project/ ; QD2022A02//Scientific Research Project of Mianyang Normal University/ ; },
mesh = {Humans ; *Publications ; *Bibliometrics ; Databases, Factual ; China ; },
abstract = {Ecological restoration projects are becoming a mainstream of research, and their studies are widely followed by scholars worldwide, yet there is no comprehensive review of this research. Nowadays, bibliometrics has attracted much attention from the scientific community, and its methodological approach allows quantitative and qualitative analysis of research performance in journals or subject areas. This paper provides a systematic and comprehensive description of the progress and hotspots of ecological restoration projects from a bibliometric perspective, based on 1173 articles in the Web of Science Core Collection (WOSCC) database. Research on ecological restoration projects has shown a positive growth trend since the twenty-first century. China and the USA are the most active countries in terms of the number of relevant articles published, and more than half of the top 10 active institutions are from China, but there is less collaboration between different countries/institutions. Research in ecological restoration projects is summarized into three main research areas: the main ecological damage problems, the impact of human beings on ecological damage, and the main methods of ecological restoration. Finally, some challenges and outlooks conducive to the rapid and balanced development of ecological restoration projects are presented, which provide valuable references and help for future researchers.},
}
@article {pmid36727564,
year = {2023},
author = {Kinkar, L and Korhonen, PK and Saarma, U and Wang, T and Zhu, XQ and Harliwong, I and Yang, B and Fink, JL and Wang, D and Chang, BCH and Chelomina, GN and Koehler, AV and Young, ND and Gasser, RB},
title = {Genome-wide exploration reveals distinctive northern and southern variants of Clonorchis sinensis in the Far East.},
journal = {Molecular ecology resources},
volume = {23},
number = {4},
pages = {833-843},
doi = {10.1111/1755-0998.13760},
pmid = {36727564},
issn = {1755-0998},
support = {LP180101085,LP180101334,LP190101209//Australian Research Council/ ; PRG1209//The Estonian Ministry of Education and Research/ ; 20211331-13//The Fund for Shanxi "1331 Project"/ ; 2021XG001//The Special Research Fund of Shanxi Agricultural University for High-level Talents/ ; },
mesh = {Animals ; *Clonorchis sinensis/genetics ; *Clonorchiasis/diagnosis/epidemiology/parasitology ; Genetic Variation ; Asia, Eastern ; China/epidemiology ; },
abstract = {Clonorchis sinensis is a carcinogenic liver fluke that causes clonorchiasis-a neglected tropical disease (NTD) affecting ~35 million people worldwide. No vaccine is available, and chemotherapy relies on one anthelmintic, praziquantel. This parasite has a complex life history and is known to infect a range of species of intermediate (freshwater snails and fish) and definitive (piscivorous) hosts. Despite this biological complexity and the impact of this biocarcinogenic pathogen, there has been no previous study of molecular variation in this parasite on a genome-wide scale. Here, we conducted the first extensive nuclear genomic exploration of C. sinensis individuals (n = 152) representing five distinct populations from mainland China, and one from Far East Russia, and revealed marked genetic variation within this species between "northern" and "southern" geographical regions. The discovery of this variation indicates the existence of biologically distinct variants within C. sinensis, which may have distinct epidemiology, pathogenicity and/or chemotherapic responsiveness. The detection of high heterozygosity within C. sinensis specimens suggests that this parasite has developed mechanisms to readily adapt to changing environments and/or host species during its life history/evolution. From an applied perspective, the identification of invariable genes could assist in finding new intervention targets in this parasite, given the major clinical relevance of clonorchiasis. From a technical perspective, the genomic-informatic workflow established herein will be readily applicable to a wide range of other parasites that cause NTDs.},
}
@article {pmid36726097,
year = {2023},
author = {Alwafi, H and Naser, AY and Ashoor, DS and Aldhahir, AM and Alqahtani, JS and Minshawi, F and Salawati, E and Samannodi, M and Dairi, MS and Alansari, AK and Ekram, R},
title = {Trends in hospital admissions and prescribing due to chronic obstructive pulmonary disease and asthma in England and Wales between 1999 and 2020: an ecological study.},
journal = {BMC pulmonary medicine},
volume = {23},
number = {1},
pages = {49},
pmid = {36726097},
issn = {1471-2466},
mesh = {Humans ; Female ; Wales/epidemiology ; *Pulmonary Disease, Chronic Obstructive/drug therapy/epidemiology ; Hospitalization ; *Asthma/drug therapy/epidemiology ; England/epidemiology ; Hospitals ; Drug Prescriptions ; *Respiratory Tract Infections/drug therapy ; },
abstract = {OBJECTIVE: To investigate the trends in hospital admissions and medication prescriptions related to asthma and chronic obstructive pulmonary disease (COPD) in England and Wales.<br><br>METHODS: An ecological study was conducted between April 1999 and April 2020 using data extracted from the hospital episode statistics database in England and the patient episode database for Wales. The Office of National Statistics mid-year population estimates for 1999 through 2020 were collected, and medication prescription data for 2004-2020 were extracted from the prescription cost analysis database.<br><br>RESULTS: The total annual number of COPD and asthma hospital admissions for various causes increased by 82.2%, from 210,525 in 1999 to 383,652 in 2020, representing a 59.1% increase in hospital admission rate (from 403.77 in 1999 to 642.42 per 100,000 persons in 2020, p&#x2009;<&#x2009;0.05). Chronic obstructive pulmonary disease with acute lower respiratory infection accounted for 38.7% of hospital admissions. Around 34.7% of all hospital admissions involved patients aged 75 and older. Around 53.8% of all COPD and asthma hospital admissions were attributable to females. The annual number of prescriptions dispensed for COPD and asthma medications increased by 42.2%.<br><br>CONCLUSIONS: Throughout the study period, hospital admissions due to chronic obstructive pulmonary disease and asthma, as well as medication prescriptions, increased dramatically among all age groups. Hospitalization rates were higher for women. Further observational and epidemiological research is required to identify the factors contributing to increased hospitalization rates.},
}
@article {pmid36725822,
year = {2023},
author = {Pernet, C and Svarer, C and Blair, R and Van Horn, JD and Poldrack, RA},
title = {On the Long-term Archiving of Research Data.},
journal = {Neuroinformatics},
volume = {21},
number = {2},
pages = {243-246},
pmid = {36725822},
issn = {1559-0089},
mesh = {*Information Dissemination ; *Information Storage and Retrieval ; },
abstract = {Accessing research data at any time is what FAIR (Findable Accessible Interoperable Reusable) data sharing aims to achieve at scale. Yet, we argue that it is not sustainable to keep accumulating and maintaining all datasets for rapid access, considering the monetary and ecological cost of maintaining repositories. Here, we address the issue of cold data storage: when to dispose of data for offline storage, how can this be done while maintaining FAIR principles and who should be responsible for cold archiving and long-term preservation.},
}
@article {pmid36722081,
year = {2023},
author = {Ehlman, SM and Scherer, U and Bierbach, D and Francisco, F and Laskowski, KL and Krause, J and Wolf, M},
title = {Leveraging big data to uncover the eco-evolutionary factors shaping behavioural development.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1992},
pages = {20222115},
pmid = {36722081},
issn = {1471-2954},
mesh = {Animals ; *Big Data ; *Biological Evolution ; },
abstract = {Mapping the eco-evolutionary factors shaping the development of animals' behavioural phenotypes remains a great challenge. Recent advances in 'big behavioural data' research-the high-resolution tracking of individuals and the harnessing of that data with powerful analytical tools-have vastly improved our ability to measure and model developing behavioural phenotypes. Applied to the study of behavioural ontogeny, the unfolding of whole behavioural repertoires can be mapped in unprecedented detail with relative ease. This overcomes long-standing experimental bottlenecks and heralds a surge of studies that more finely define and explore behavioural-experiential trajectories across development. In this review, we first provide a brief guide to state-of-the-art approaches that allow the collection and analysis of high-resolution behavioural data across development. We then outline how such approaches can be used to address key issues regarding the ecological and evolutionary factors shaping behavioural development: developmental feedbacks between behaviour and underlying states, early life effects and behavioural transitions, and information integration across development.},
}
@article {pmid36719907,
year = {2023},
author = {Turtle, L and Thorpe, M and Drake, TM and Swets, M and Palmieri, C and Russell, CD and Ho, A and Aston, S and Wootton, DG and Richter, A and de Silva, TI and Hardwick, HE and Leeming, G and Law, A and Openshaw, PJM and Harrison, EM and , and Baillie, JK and Semple, MG and Docherty, AB},
title = {Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study.},
journal = {PLoS medicine},
volume = {20},
number = {1},
pages = {e1004086},
pmid = {36719907},
issn = {1549-1676},
support = {205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; MR/V028979/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; 200927/DH_/Department of Health/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Male ; Humans ; Female ; Middle Aged ; Aged ; *COVID-19 ; SARS-CoV-2 ; Prospective Studies ; Hospital Mortality ; Bayes Theorem ; Immunocompromised Host ; United Kingdom/epidemiology ; World Health Organization ; },
abstract = {BACKGROUND: Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic.<br><br>METHODS AND FINDINGS: We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. In total, 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent.<br><br>CONCLUSIONS: Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group.<br><br>TRIAL REGISTRATION: ISRCTN 66726260.},
}
@article {pmid36718952,
year = {2023},
author = {Freedman, AH and Harrigan, RJ and Zhen, Y and Hamilton, AM and Smith, TB},
title = {Evidence for ecotone speciation across an African rainforest-savanna gradient.},
journal = {Molecular ecology},
volume = {32},
number = {9},
pages = {2287-2300},
doi = {10.1111/mec.16867},
pmid = {36718952},
issn = {1365-294X},
support = {/EPA/EPA/United States ; },
mesh = {Animals ; *Rainforest ; Grassland ; Ecosystem ; Gene Frequency ; Biodiversity ; *Lizards/genetics ; Genetic Speciation ; },
abstract = {Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly probably driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.},
}
@article {pmid36716736,
year = {2022},
author = {Smith, J and Alfieri, JM and Anthony, N and Arensburger, P and Athrey, GN and Balacco, J and Balic, A and Bardou, P and Barela, P and Bigot, Y and Blackmon, H and Borodin, PM and Carroll, R and Casono, MC and Charles, M and Cheng, H and Chiodi, M and Cigan, L and Coghill, LM and Crooijmans, R and Das, N and Davey, S and Davidian, A and Degalez, F and Dekkers, JM and Derks, M and Diack, AB and Djikeng, A and Drechsler, Y and Dyomin, A and Fedrigo, O and Fiddaman, SR and Formenti, G and Frantz, LAF and Fulton, JE and Gaginskaya, E and Galkina, S and Gallardo, RA and Geibel, J and Gheyas, AA and Godinez, CJP and Goodell, A and Graves, JAM and Griffin, DK and Haase, B and Han, JL and Hanotte, O and Henderson, LJ and Hou, ZC and Howe, K and Huynh, L and Ilatsia, E and Jarvis, ED and Johnson, SM and Kaufman, J and Kelly, T and Kemp, S and Kern, C and Keroack, JH and Klopp, C and Lagarrigue, S and Lamont, SJ and Lange, M and Lanke, A and Larkin, DM and Larson, G and Layos, JKN and Lebrasseur, O and Malinovskaya, LP and Martin, RJ and Martin Cerezo, ML and Mason, AS and McCarthy, FM and McGrew, MJ and Mountcastle, J and Muhonja, CK and Muir, W and Muret, K and Murphy, TD and Ng'ang'a, I and Nishibori, M and O'Connor, RE and Ogugo, M and Okimoto, R and Ouko, O and Patel, HR and Perini, F and Pigozzi, MI and Potter, KC and Price, PD and Reimer, C and Rice, ES and Rocos, N and Rogers, TF and Saelao, P and Schauer, J and Schnabel, RD and Schneider, VA and Simianer, H and Smith, A and Stevens, MP and Stiers, K and Tiambo, CK and Tixier-Boichard, M and Torgasheva, AA and Tracey, A and Tregaskes, CA and Vervelde, L and Wang, Y and Warren, WC and Waters, PD and Webb, D and Weigend, S and Wolc, A and Wright, AE and Wright, D and Wu, Z and Yamagata, M and Yang, C and Yin, ZT and Young, MC and Zhang, G and Zhao, B and Zhou, H},
title = {Fourth Report on Chicken Genes and Chromosomes 2022.},
journal = {Cytogenetic and genome research},
volume = {162},
number = {8-9},
pages = {405-528},
doi = {10.1159/000529376},
pmid = {36716736},
issn = {1424-859X},
}
@article {pmid36714536,
year = {2023},
author = {Astorga, F and Groom, Q and Shimabukuro, PHF and Manguin, S and Noesgaard, D and Orrell, T and Sinka, M and Hirsch, T and Schigel, D},
title = {Biodiversity data supports research on human infectious diseases: Global trends, challenges, and opportunities.},
journal = {One health (Amsterdam, Netherlands)},
volume = {16},
number = {},
pages = {100484},
pmid = {36714536},
issn = {2352-7714},
abstract = {The unprecedented generation of large volumes of biodiversity data is consistently contributing to a wide range of disciplines, including disease ecology. Emerging infectious diseases are usually zoonoses caused by multi-host pathogens. Therefore, their understanding may require the access to biodiversity data related to the ecology and the occurrence of the species involved. Nevertheless, despite several data-mobilization initiatives, the usage of biodiversity data for research into disease dynamics has not yet been fully leveraged. To explore current contribution, trends, and to identify limitations, we characterized biodiversity data usage in scientific publications related to human health, contrasting patterns of studies citing the Global Biodiversity Information Facility (GBIF) with those obtaining data from other sources. We found that the studies mainly obtained data from scientific literature and other not aggregated or standardized sources. Most of the studies explored pathogen species and, particularly those with GBIF-mediated data, tended to explore and reuse data of multiple species (>2). Data sources varied according to the taxa and epidemiological roles of the species involved. Biodiversity data repositories were mainly used for species related to hosts, reservoirs, and vectors, and barely used as a source of pathogens data, which was usually obtained from human and animal-health related institutions. While both GBIF- and not GBIF-mediated data studies explored similar diseases and topics, they presented discipline biases and different analytical approaches. Research on emerging infectious diseases may require the access to geographical and ecological data of multiple species. The One Health challenge requires interdisciplinary collaboration and data sharing, which is facilitated by aggregated repositories and platforms. The contribution of biodiversity data to understand infectious disease dynamics should be acknowledged, strengthened, and promoted.},
}
@article {pmid36706978,
year = {2023},
author = {Nosenko, T and Zimmer, I and Ghirardo, A and Köllner, TG and Weber, B and Polle, A and Rosenkranz, M and Schnitzler, JP},
title = {Predicting functions of putative fungal sesquiterpene synthase genes based on multiomics data analysis.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {165},
number = {},
pages = {103779},
doi = {10.1016/j.fgb.2023.103779},
pmid = {36706978},
issn = {1096-0937},
mesh = {Multiomics ; *Sesquiterpenes/metabolism ; Genes, Fungal ; *Mycorrhizae/genetics ; Gene Expression Profiling ; },
abstract = {Sesquiterpenes (STs) are secondary metabolites, which mediate biotic interactions between different organisms. Predicting the species-specific ST repertoires can contribute to deciphering the language of communication between organisms of the same or different species. High biochemical plasticity and catalytic promiscuity of sesquiterpene synthases (STSs), however, challenge the homology-based prediction of the STS functions. Using integrated analyses of genomic, transcriptomic, volatilomic, and metabolomic data, we predict product profiles for 116 out of 146 putative STS genes identified in the genomes of 30 fungal species from different trophic groups. Our prediction method is based on the observation that STSs encoded by genes closely related phylogenetically are likely to share the initial enzymatic reactions of the ST biosynthesis pathways and, therefore, produce STs via the same reaction route. The classification by reaction routes allows to assign STs known to be emitted by a particular species to the putative STS genes from this species. Gene expression information helps to further specify these ST-to-STS assignments. Validation of the computational predictions of the STS functions using both in silico and experimental approaches shows that integrated multiomic analyses are able to correctly link cyclic STs of non-cadalane type to genes. In the process of the experimental validation, we characterized catalytic properties of several putative STS genes from the mycorrhizal fungus Laccaria bicolor. We show that the STSs encoded by the L.bicolor mycorrhiza-induced genes emit either nerolidol or α-cuprenene and α-cuparene, and discuss the possible roles of these STs in the mycorrhiza formation.},
}
@article {pmid36705582,
year = {2023},
author = {Bettisworth, B and Smith, SA and Stamatakis, A},
title = {Lagrange-NG: The next generation of Lagrange.},
journal = {Systematic biology},
volume = {72},
number = {1},
pages = {242-248},
pmid = {36705582},
issn = {1076-836X},
mesh = {Phylogeny ; *Software ; },
abstract = {Computing ancestral ranges via the Dispersion Extinction and Cladogensis (DEC) model of biogeography is characterized by an exponential number of states relative to the number of regions considered. This is because the DEC model requires computing a large matrix exponential, which typically accounts for up to 80% of overall runtime. Therefore, the kinds of biogeographical analyses that can be conducted under the DEC model are limited by the number of regions under consideration. In this work, we present a completely redesigned efficient version of the popular tool Lagrange which is up to 49 times faster with multithreading enabled, and is also 26 times faster when using only one thread. We call this new version Lagrange-NG (Lagrange-Next Generation). The increased computational efficiency allows Lagrange-NG to analyze datasets with a large number of regions in a reasonable amount of time, up to 12 regions in approximately 18 min. We achieve these speedups using a relatively new method of computing the matrix exponential based on Krylov subspaces. In order to validate the correctness of Lagrange-NG, we also introduce a novel metric on range distributions for trees so that researchers can assess the difference between any two range inferences. Finally, Lagrange-NG exhibits substantially higher adherence to coding quality standards. It improves a respective software quality indicator as implemented in the SoftWipe tool from average (5.5; Lagrange) to high (7.8; Lagrange-NG). Lagrange-NG is freely available under GPL2. [Biogeography; Phylogenetics; DEC Model.].},
}
@article {pmid36704891,
year = {2023},
author = {Crandall, ED and Toczydlowski, RH and Liggins, L and Holmes, AE and Ghoojaei, M and Gaither, MR and Wham, BE and Pritt, AL and Noble, C and Anderson, TJ and Barton, RL and Berg, JT and Beskid, SG and Delgado, A and Farrell, E and Himmelsbach, N and Queeno, SR and Trinh, T and Weyand, C and Bentley, A and Deck, J and Riginos, C and Bradburd, GS and Toonen, RJ},
title = {Importance of timely metadata curation to the global surveillance of genetic diversity.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {37},
number = {4},
pages = {e14061},
pmid = {36704891},
issn = {1523-1739},
support = {R35 GM137919/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Conservation of Natural Resources ; *Metadata ; Biodiversity ; Probability ; Genetic Variation ; },
abstract = {Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.},
}
@article {pmid36699674,
year = {2022},
author = {Siddiqui, JA and Fan, R and Naz, H and Bamisile, BS and Hafeez, M and Ghani, MI and Wei, Y and Xu, Y and Chen, X},
title = {Insights into insecticide-resistance mechanisms in invasive species: Challenges and control strategies.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1112278},
pmid = {36699674},
issn = {1664-042X},
abstract = {Threatening the global community is a wide variety of potential threats, most notably invasive pest species. Invasive pest species are non-native organisms that humans have either accidentally or intentionally spread to new regions. One of the most effective and first lines of control strategies for controlling pests is the application of insecticides. These toxic chemicals are employed to get rid of pests, but they pose great risks to people, animals, and plants. Pesticides are heavily used in managing invasive pests in the current era. Due to the overuse of synthetic chemicals, numerous invasive species have already developed resistance. The resistance development is the main reason for the failure to manage the invasive species. Developing pesticide resistance management techniques necessitates a thorough understanding of the mechanisms through which insects acquire insecticide resistance. Insects use a variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes. An overabundance of enzymes causes metabolic resistance, detoxifying pesticides and rendering them ineffective against pests. A key factor in the development of metabolic resistance is the amplification of certain metabolic enzymes, specifically esterases, Glutathione S-transferase, Cytochromes p450 monooxygenase, and hydrolyses. Additionally, insect guts offer unique habitats for microbial colonization, and gut bacteria may serve their hosts a variety of useful services. Most importantly, the detoxification of insecticides leads to resistance development. The complete knowledge of invasive pest species and their mechanisms of resistance development could be very helpful in coping with the challenges and effectively developing effective strategies for the control of invasive species. Integrated Pest Management is particularly effective at lowering the risk of chemical and environmental contaminants and the resulting health issues, and it may also offer the most effective ways to control insect pests.},
}
@article {pmid36699126,
year = {2023},
author = {Wortel, MT and Agashe, D and Bailey, SF and Bank, C and Bisschop, K and Blankers, T and Cairns, J and Colizzi, ES and Cusseddu, D and Desai, MM and van Dijk, B and Egas, M and Ellers, J and Groot, AT and Heckel, DG and Johnson, ML and Kraaijeveld, K and Krug, J and Laan, L and Lässig, M and Lind, PA and Meijer, J and Noble, LM and Okasha, S and Rainey, PB and Rozen, DE and Shitut, S and Tans, SJ and Tenaillon, O and Teotónio, H and de Visser, JAGM and Visser, ME and Vroomans, RMA and Werner, GDA and Wertheim, B and Pennings, PS},
title = {Towards evolutionary predictions: Current promises and challenges.},
journal = {Evolutionary applications},
volume = {16},
number = {1},
pages = {3-21},
pmid = {36699126},
issn = {1752-4571},
support = {R01 AI134195/AI/NIAID NIH HHS/United States ; R01 GM104239/GM/NIGMS NIH HHS/United States ; },
abstract = {Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.},
}
@article {pmid36696549,
year = {2023},
author = {Menon, K and Sorce, LR and Argent, A and Bennett, TD and Carrol, ED and Kissoon, N and Sanchez-Pinto, LN and Schlapbach, LJ and de Souza, DC and Watson, RS and Wynn, JL and Zimmerman, JJ and Ranjit, S and , },
title = {Reporting of Social Determinants of Health in Pediatric Sepsis Studies.},
journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies},
volume = {24},
number = {4},
pages = {301-310},
pmid = {36696549},
issn = {1529-7535},
support = {R01 GM128452/GM/NIGMS NIH HHS/United States ; R01 HD097081/HD/NICHD NIH HHS/United States ; R01 HD105939/HD/NICHD NIH HHS/United States ; R43 EB029863/EB/NIBIB NIH HHS/United States ; },
mesh = {Humans ; Child ; *Social Determinants of Health ; Socioeconomic Factors ; *Sepsis/epidemiology ; },
abstract = {OBJECTIVE: Standardized, consistent reporting of social determinants of health (SDOH) in studies on children with sepsis would allow for: 1) understanding the association of SDOH with illness severity and outcomes, 2) comparing populations and extrapolating study results, and 3) identification of potentially modifiable socioeconomic factors for policy makers. We, therefore, sought to determine how frequently data on SDOH were reported, which factors were collected and how these factors were defined in studies of sepsis in children.<br><br>DATA SOURCES AND SELECTION: We reviewed 106 articles (published between 2005 and 2020) utilized in a recent systematic review on physiologic criteria for pediatric sepsis.<br><br>DATA EXTRACTION: Data were extracted by two reviewers on variables that fell within the World Health Organization's SDOH categories.<br><br>DATA SYNTHESIS: SDOH were not the primary outcome in any of the included studies. Seventeen percent of articles (18/106) did not report on any SDOH, and a further 36.8% (39/106) only reported on gender/sex. Of the remaining 46.2% of articles, the most reported SDOH categories were preadmission nutritional status (35.8%, 38/106) and race/ethnicity (18.9%, 20/106). However, no two studies used the same definition of the variables reported within each of these categories. Six studies reported on socioeconomic status (3.8%, 6/106), including two from upper-middle-income and four from lower middle-income countries. Only three studies reported on parental education levels (2.8%, 3/106). No study reported on parental job security or structural conflict.<br><br>CONCLUSIONS: We found overall low reporting of SDOH and marked variability in categorizations and definitions of SDOH variables. Consistent and standardized reporting of SDOH in pediatric sepsis studies is needed to understand the role these factors play in the development and severity of sepsis, to compare and extrapolate study results between settings and to implement policies aimed at improving socioeconomic conditions related to sepsis.},
}
@article {pmid36692937,
year = {2023},
author = {de Angel, V and Adeleye, F and Zhang, Y and Cummins, N and Munir, S and Lewis, S and Laporta Puyal, E and Matcham, F and Sun, S and Folarin, AA and Ranjan, Y and Conde, P and Rashid, Z and Dobson, R and Hotopf, M},
title = {The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.},
journal = {JMIR mental health},
volume = {10},
number = {},
pages = {e42866},
pmid = {36692937},
issn = {2368-7959},
support = {/WT_/Wellcome Trust/United Kingdom ; MC_PC_17214/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.<br><br>OBJECTIVE: A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.<br><br>METHODS: A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.<br><br>RESULTS: The overall retention rate was 60%. Higher-intensity treatment (&#x3c7;[2]1=4.6; P=.03) and higher baseline anxiety (t56.28=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t50.4=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.<br><br>CONCLUSIONS: Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.},
}
@article {pmid36690591,
year = {2023},
author = {Sambo, B and Bonato, M and Sperotto, A and Torresan, S and Furlan, E and Lambert, JH and Linkov, I and Critto, A},
title = {Framework for multirisk climate scenarios across system receptors with application to the Metropolitan City of Venice.},
journal = {Risk analysis : an official publication of the Society for Risk Analysis},
volume = {43},
number = {11},
pages = {2241-2261},
doi = {10.1111/risa.14097},
pmid = {36690591},
issn = {1539-6924},
support = {//Ministero degli Affari Esteri e della Cooperazione Internazionale/ ; },
abstract = {Climate change influences the frequency of extreme events that affect both human and natural systems. It requires systemic climate change adaptation to address the complexity of risks across multiple domains and tackle the uncertainties of future scenarios. This paper introduces a multirisk analysis of climate hazard, exposure, vulnerability, and risk severity, specifically designed to hotspot geographic locations and prioritize system receptors that are affected by climate-related extremes. The analysis is demonstrated for the Metropolitan City of Venice. Representative scenarios (RCP4.5 and RCP8.5) of climate threats (i.e., storm surges, pluvial flood, heat waves, and drought) are selected and represented by projections of Regional Climate Models for a 30-year period (2021-2050). A sample of results is as follows. First, an increase in the risk is largely due to drought, pluvial flood, and storm surge, depending on the areas of interest, with the overall situation worsening under the RCP8.5 scenario. Second, particular locations have colocated vulnerable receptors at higher risk, concentrated in the urban centers (e.g., housing, railways, roads) and along the coast (e.g., beaches, wetlands, primary sector). Third, risk communication of potential environmental and socio-economic losses via the multirisk maps is useful to stakeholders and public administration. Fourth, the multirisk maps recommend priorities for future investigation and risk management, such as collection of sensor data, elaboration of mitigations, and adaptation plans at hotspot locations.},
}
@article {pmid36689893,
year = {2023},
author = {Werneck, RA and Meinberg, MF and Passos, MZ and Brandão, WC and de Moraes, EN and da Silva-Filho, AL},
title = {Quality of information regarding abnormal uterine bleeding available online.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {282},
number = {},
pages = {83-88},
doi = {10.1016/j.ejogrb.2023.01.020},
pmid = {36689893},
issn = {1872-7654},
mesh = {Humans ; Female ; Reproducibility of Results ; *Quality of Life ; *Search Engine ; Communication ; Uterine Hemorrhage ; Internet ; },
abstract = {INTRODUCTION: The Internet and electronic devices with Internet access allow for a greater fluidity of information and speed of communication, especially in the field of health. Abnormal uterine bleeding (AUB) affects approximately 3-30% of women and can negatively impact their health and quality of life. Information regarding AUB that is available on the Internet may not be clear or accurate, rendering it difficult to understand and likely to result in delayed medical evaluation, which subsequently leads to worsening of the AUB.<br><br>OBJECTIVE: To evaluate the quality of the information regarding AUB currently available on the Internet, including information regarding treatments.<br><br>METHODS: The Google Trends website was searched for the most widely used English terms related to AUB. The identified descriptors were searched individually on the Google, Yahoo!, and Bing search engines. The first 10 results of each search were pre-selected and evaluated for inclusion in this study. Selected websites were categorically divided into two groups (news/magazine and academic) and individually analyzed by three experts using the DISCERN quality criteria (reliability, general quality, and quality of information) and the presence or absence of the Health on the Net Foundation Code of Conduct (HONcode&#xae;) seal.<br><br>RESULTS: Of the 168 websites included in this study, 60.1% were allocated to the news/magazine group and 39.9% were allocated to the academic group. Over half of the websites (54.2%) did not have the HONcode&#xae; quality seal. Websites in the academic group were more likely to include accurate information regarding AUB with greater reliability than websites in the news/magazine group. There were no statistical differences regarding the general quality of the websites. Most websites were rated as either moderate quality (70.8%) or low quality (28.6%). The HONcode&#xae; criterion was found to be a confounding factor of the analyses, as the grouping and quality results of websites without this seal were significantly associated. In addition, websites in the news/magazines group were 6.7 times more likely to provide low quality information than websites in the academic group (odds ratio: 6.7; 95% confidence interval: 2.1-21.4).<br><br>CONCLUSION: The information regarding AUB that is available on the Internet is of low to moderate quality. Academic websites present more reliable information of greater quality. The presence of the HONcode&#xae; seal is considered important to determine the quality of the content of a website, especially for news/magazine websites, and may help Internet users identify websites that contain more reliable information. Algorithms and applications that categorize the quality of information and the reliability of health content may be useful tools that can help patients clarify their symptoms for several conditions including AUB.},
}
@article {pmid36685700,
year = {2022},
author = {Jazayeri, SM and Pooralinaghi, M and Torres-Navarrete, Y and Oviedo-Bayas, B and Guerra, &#xcd;E and Jácome, DH and Morán, CQ and Macias, CS and Escobar, KM and Ghafoor, SMHAS and Veiskarami, G and Jandaghi, P and Torres, ROV},
title = {Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses.},
journal = {Biotechnologia},
volume = {103},
number = {4},
pages = {355-384},
pmid = {36685700},
issn = {2353-9461},
abstract = {Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.},
}
@article {pmid36684825,
year = {2023},
author = {Liew, CY and Labadin, J and Kok, WC and Eze, MO},
title = {A methodology framework for bipartite network modeling.},
journal = {Applied network science},
volume = {8},
number = {1},
pages = {6},
pmid = {36684825},
issn = {2364-8228},
abstract = {The graph-theoretic based studies employing bipartite network approach mostly focus on surveying the statistical properties of the structure and behavior of the network systems under the domain of complex network analysis. They aim to provide the big-picture-view insights of a networked system by looking into the dynamic interaction and relationship among the vertices. Nonetheless, incorporating the features of individual vertex and capturing the dynamic interaction of the heterogeneous local rules governing each of them in the studies is lacking. The methodology in achieving this could hardly be found. Consequently, this study intends to propose a methodology framework that considers the influence of heterogeneous features of each node to the overall network behavior in modeling real-world bipartite network system. The proposed framework consists of three main stages with principal processes detailed in each stage, and three libraries of techniques to guide the modeling activities. It is iterative and process-oriented in nature and allows future network expansion. Two case studies from the domain of communicable disease in epidemiology and habitat suitability in ecology employing this framework are also presented. The results obtained suggest that the methodology could serve as a generic framework in advancing the current state of the art of bipartite network approach.},
}
@article {pmid36682374,
year = {2023},
author = {Traore, T and Shanks, S and Haider, N and Ahmed, K and Jain, V and Rüegg, SR and Razavi, A and Kock, R and Erondu, N and Rahman-Shepherd, A and Yavlinsky, A and Mboera, L and Asogun, D and McHugh, TD and Elton, L and Oyebanji, O and Okunromade, O and Ansumana, R and Djingarey, MH and Ali Ahmed, Y and Diallo, AB and Balde, T and Talisuna, A and Ntoumi, F and Zumla, A and Heymann, D and Fall, IS and Dar, O},
title = {How prepared is the world? Identifying weaknesses in existing assessment frameworks for global health security through a One Health approach.},
journal = {Lancet (London, England)},
volume = {401},
number = {10377},
pages = {673-687},
doi = {10.1016/S0140-6736(22)01589-6},
pmid = {36682374},
issn = {1474-547X},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Animals ; Humans ; Global Health ; Ecosystem ; Emergencies ; *COVID-19 ; *One Health ; Pandemics ; },
abstract = {The COVID-19 pandemic has exposed faults in the way we assess preparedness and response capacities for public health emergencies. Existing frameworks are limited in scope, and do not sufficiently consider complex social, economic, political, regulatory, and ecological factors. One Health, through its focus on the links among humans, animals, and ecosystems, is a valuable approach through which existing assessment frameworks can be analysed and new ways forward proposed. Although in the past few years advances have been made in assessment tools such as the International Health Regulations Joint External Evaluation, a rapid and radical increase in ambition is required. To sufficiently account for the range of complex systems in which health emergencies occur, assessments should consider how problems are defined across stakeholders and the wider sociopolitical environments in which structures and institutions operate. Current frameworks do little to consider anthropogenic factors in disease emergence or address the full array of health security hazards across the social-ecological system. A complex and interdependent set of challenges threaten human, animal, and ecosystem health, and we cannot afford to overlook important contextual factors, or the determinants of these shared threats. Health security assessment frameworks should therefore ensure that the process undertaken to prioritise and build capacity adheres to core One Health principles and that interventions and outcomes are assessed in terms of added value, trade-offs, and cobenefits across human, animal, and environmental health systems.},
}
@article {pmid36669842,
year = {2023},
author = {Guan, Y and Qi, Y and Zheng, L and Yang, J and Zhang, M and Zhang, Q and Ji, L},
title = {Data mining techniques for detecting signals of adverse drug reaction of cardiac therapy drugs based on Jinan adverse event reporting system database: a retrospective study.},
journal = {BMJ open},
volume = {13},
number = {1},
pages = {e068127},
pmid = {36669842},
issn = {2044-6055},
mesh = {Humans ; United States ; Retrospective Studies ; Bayes Theorem ; *Adverse Drug Reaction Reporting Systems ; *Drug-Related Side Effects and Adverse Reactions/diagnosis/epidemiology ; Data Mining ; Databases, Factual ; United States Food and Drug Administration ; },
abstract = {OBJECTIVE: Cardiac therapy drugs are widely used in the treatment of heart disease. However, the concern regarding adverse events (AEs) of cardiac therapy drugs have been rising. This study aimed to analyse cardiac therapy drug-related AEs using the Jinan adverse event reporting system (JAERS) database mining and conduct a comprehensive evaluation to provide safe medication information for patients.<br><br>DESIGN: Retrospective observational study.<br><br>SETTING: In this study, cardiac therapy drug-related AEs were detected using the JAERS database from January 2000 to March 2022.<br><br>METHODS: Reports of cardiac therapy drug-related AEs were extracted from JAERS database, and the basic information of patients, reports and common AEs were analysed. Four disproportionality analysis methods, proportional reporting ratio (PRR), reporting odds ratio (ROR), Bayesian Confidence Propagation Neural Network (BCPNN), Medicines and Healthcare products Regulatory Agency (MHRA), were used to detect cardiac therapy drug-related signals. We further checked whether the detected signals exist on drug labels in China and two developed countries, the USA and Japan.<br><br>RESULTS: In total, 168&#x2009;314 AEs were reported, of which 4788 were associated with cardiac therapy drugs. Using the PRR, ROR, MHRA and BCPNN method, we detected 52 signals, 52 signals, 33 signals and 43 signals, respectively. Among the 52 signals, 14 were not included on the drug labels of China. One (isosorbide mononitrate-head bilges) was not included on the drug labels of the three countries.<br><br>CONCLUSION: We identified 14 new cardiac therapy drug signals that did not appear on drug labels in China and 1 new signal that did not appear on drug labels in 3 counties. A causal link between cardiac therapy drugs and AEs should be evaluated in further studies.},
}
@article {pmid36661052,
year = {2023},
author = {Acerbi, A and Burns, J and Cabuk, U and Kryczka, J and Trapp, B and Valletta, JJ and Mesoudi, A},
title = {Sentiment analysis of the Twitter response to Netflix's Our Planet documentary.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {37},
number = {4},
pages = {e14060},
doi = {10.1111/cobi.14060},
pmid = {36661052},
issn = {1523-1739},
mesh = {Humans ; *Social Media ; Planets ; Sentiment Analysis ; Conservation of Natural Resources ; Attitude ; },
abstract = {The role of nature documentaries in shaping public attitudes and behavior toward conservation and wildlife issues is unclear. We analyzed the emotional content of over 2 million tweets related to Our Planet, a major nature documentary released on Netflix, with dictionary and rule-based automatic sentiment analysis. We also compared the sentiment associated with species mentioned in Our Planet and a set of control species with similar features but not mentioned in the documentary. Tweets were largely negative in sentiment at the time of release of the series. This effect was primarily linked to the highly skewed distributions of retweets and, in particular, to a single negatively valenced and massively retweeted tweet (>150,000 retweets). Species mentioned in Our Planet were associated with more negative sentiment than the control species, and this effect coincided with a short period following the airing of the series. Our results are consistent with a general negativity bias in cultural transmission and document the difficulty of evoking positive sentiment, on social media and elsewhere, in response to environmental problems.},
}
@article {pmid36656265,
year = {2023},
author = {Yu, Y and Yu, X and Zhang, D and Jin, L and Huang, J and Zhu, X and Sun, J and Yu, M and Zhu, L},
title = {Biotransformation of Organophosphate Esters by Rice and Rhizosphere Microbiome: Multiple Metabolic Pathways, Mechanism, and Toxicity Assessment.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {4},
pages = {1776-1787},
doi = {10.1021/acs.est.2c07796},
pmid = {36656265},
issn = {1520-5851},
mesh = {*Oryza ; Rhizosphere ; Esters/metabolism ; *Flame Retardants/analysis ; Organophosphates ; Biotransformation ; Phosphates ; *Microbiota ; Metabolic Networks and Pathways ; Environmental Monitoring ; China ; },
abstract = {The biotransformation behavior and toxicity of organophosphate esters (OPEs) in rice and rhizosphere microbiomes were comprehensively studied by hydroponic experiments. OPEs with lower hydrophobicity were liable to be translocated acropetally, and rhizosphere microbiome could reduce the uptake and translocation of OPEs in rice tissues. New metabolites were successfully identified in rice and rhizosphere microbiome, including hydrolysis, hydroxylated, methylated, and glutathione-, glucuronide-, and sulfate-conjugated products. Rhizobacteria and plants could cooperate to form a complex ecological interaction web for OPE elimination. Furthermore, active members of the rhizosphere microbiome during OPE degradation were revealed and the metagenomic analysis indicated that most of these active populations contained OPE-degrading genes. The results of metabolomics analyses for phytotoxicity assessment implied that several key function metabolic pathways of the rice plant were found perturbed by metabolites, such as diphenyl phosphate and monophenyl phosphate. In addition, the involved metabolism mechanisms, such as the carbohydrate metabolism, amino acid metabolism and synthesis, and nucleotide metabolism in Escherichia coli, were significantly altered after exposure to the products mixture of OPEs generated by rhizosphere microbiome. This work for the first time gives a comprehensive understanding of the entire metabolism of OPEs in plants and associated microbiome, and provides support for the ongoing risk assessment of emerging contaminants and, most critically, their transformation products.},
}
@article {pmid36654087,
year = {2022},
author = {Yang, L and Zou, K and Gao, K and Jiang, Z},
title = {A fuzzy DRBFNN-based information security risk assessment method in improving the efficiency of urban development.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {19},
number = {12},
pages = {14232-14250},
doi = {10.3934/mbe.2022662},
pmid = {36654087},
issn = {1551-0018},
mesh = {*Urban Renewal ; *Ecology/methods ; Cities ; Neural Networks, Computer ; Risk Assessment ; China ; },
abstract = {The rapid development of urban informatization is an important way for cities to achieve a higher pattern, but the accompanying information security problem become a major challenge restricting the efficiency of urban development. Therefore, effective identification and assessment of information security risks has become a key factor to improve the efficiency of urban development. In this paper, an information security risk assessment method based on fuzzy theory and neural network technology is proposed to help identify and solve the information security problem in the development of urban informatization. Combined with the theory of information ecology, this method establishes an improved fuzzy neural network model from four aspects by using fuzzy theory, neural network model and DEMATEL method, and then constructs the information security risk assessment system of smart city. According to this method, this paper analyzed 25 smart cities in China, and provided suggestions and guidance for information security control in the process of urban informatization construction.},
}
@article {pmid36653564,
year = {2023},
author = {Battin, TJ and Lauerwald, R and Bernhardt, ES and Bertuzzo, E and Gener, LG and Hall, RO and Hotchkiss, ER and Maavara, T and Pavelsky, TM and Ran, L and Raymond, P and Rosentreter, JA and Regnier, P},
title = {River ecosystem metabolism and carbon biogeochemistry in a changing world.},
journal = {Nature},
volume = {613},
number = {7944},
pages = {449-459},
pmid = {36653564},
issn = {1476-4687},
support = {1442439//National Science Foundation/ ; 1926426//National Science Foundation/ ; 1840243//National Science Foundation/ ; },
mesh = {*Carbon Cycle ; *Carbon Dioxide/analysis ; Carbon Sequestration ; *Ecosystem ; Greenhouse Gases/analysis ; *Rivers ; },
abstract = {River networks represent the largest biogeochemical nexus between the continents, ocean and atmosphere. Our current understanding of the role of rivers in the global carbon cycle remains limited, which makes it difficult to predict how global change may alter the timing and spatial distribution of riverine carbon sequestration and greenhouse gas emissions. Here we review the state of river ecosystem metabolism research and synthesize the current best available estimates of river ecosystem metabolism. We quantify the organic and inorganic carbon flux from land to global rivers and show that their net ecosystem production and carbon dioxide emissions shift the organic to inorganic carbon balance en route from land to the coastal ocean. Furthermore, we discuss how global change may affect river ecosystem metabolism and related carbon fluxes and identify research directions that can help to develop better predictions of the effects of global change on riverine ecosystem processes. We argue that a global river observing system will play a key role in understanding river networks and their future evolution in the context of the global carbon budget.},
}
@article {pmid36651964,
year = {2023},
author = {Johnson, MS and Venkataram, S and Kryazhimskiy, S},
title = {Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.},
journal = {Journal of molecular evolution},
volume = {91},
number = {3},
pages = {263-280},
pmid = {36651964},
issn = {1432-1432},
support = {R01 GM137112/GM/NIGMS NIH HHS/United States ; 1R01GM137112/GM/NIGMS NIH HHS/United States ; 1R01GM137112/GM/NIGMS NIH HHS/United States ; },
mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Sequence Analysis, DNA/methods ; Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.},
}
@article {pmid36648719,
year = {2023},
author = {Zhu, F and Su, T and Lei, B and Liang, Q and Zhou, Y and Liu, X and Wang, X and Zhang, D},
title = {Considerations on the impact of "source-sink" landscape pattern changes on urban thermal environment and cooling efficiency: a case study of Nanjing, China.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {14},
pages = {42296-42310},
pmid = {36648719},
issn = {1614-7499},
mesh = {Humans ; Cities ; *Hot Temperature ; *Environmental Monitoring/methods ; China ; Urbanization ; },
abstract = {The urban heat island effect caused by rapid urbanization has had a great impact on human health and ecological environment. The evolution of landscape patterns often affects regional thermal characteristics at the local scale. How to rationally allocate land cover types from the perspective of urban planning is a huge challenge. This paper takes Nanjing, a typical "stove city" in China, as an example to study the impact of landscape pattern changes on the urban thermal environment. Firstly, based on the "source" landscape "/sink" landscape identified by the "source-sink" landscape index, on this basis, the contributions of the "source-sink" landscape and its effects are calculated, and the temporal and spatial evolution laws are analyzed. Second, we study the cooling effect of different characteristic landscapes. The results show that the change of landscape pattern is closely related to the urban thermal environment, and the expansion of built-up areas is the main reason for the urban thermal environment. With the development of urbanization, the "source-sink" landscape structure in most districts and counties has aggravated the heat island effect, and the ratios of "sink" and "source" landscape contribution ratios with strong levels are concentrated in the suburban areas. The results of cooling efficiency research show that the cooling range of forest land is larger than that of water bodies. At the same time, we found that the cooling efficiency of the sink landscape is the highest when the area of the sink landscape is 0.18-0.9 hm[2] and the shape index is between 1 and 4. The research results can provide feasible and practical scientific suggestions for the planning and ecological construction of Nanjing.},
}
@article {pmid36648611,
year = {2023},
author = {Hu, Y and Wang, X and Xu, Y and Yang, H and Tong, Z and Tian, R and Xu, S and Yu, L and Guo, Y and Shi, P and Huang, S and Yang, G and Shi, S and Wei, F},
title = {Molecular mechanisms of adaptive evolution in wild animals and plants.},
journal = {Science China. Life sciences},
volume = {66},
number = {3},
pages = {453-495},
pmid = {36648611},
issn = {1869-1889},
mesh = {*Biological Evolution ; *Adaptation, Physiological/genetics ; *Genome, Plant/genetics ; *Animals, Wild/genetics ; Biological Coevolution/genetics ; Phenotype ; Aquatic Organisms/genetics ; Ecology/methods/trends ; Computational Biology/methods ; },
abstract = {Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.},
}
@article {pmid36647630,
year = {2023},
author = {Watts, JD and Farina, M and Kimball, JS and Schiferl, LD and Liu, Z and Arndt, KA and Zona, D and Ballantyne, A and Euskirchen, ES and Parmentier, FW and Helbig, M and Sonnentag, O and Tagesson, T and Rinne, J and Ikawa, H and Ueyama, M and Kobayashi, H and Sachs, T and Nadeau, DF and Kochendorfer, J and Jackowicz-Korczynski, M and Virkkala, A and Aurela, M and Commane, R and Byrne, B and Birch, L and Johnson, MS and Madani, N and Rogers, B and Du, J and Endsley, A and Savage, K and Poulter, B and Zhang, Z and Bruhwiler, LM and Miller, CE and Goetz, S and Oechel, WC},
title = {Carbon uptake in Eurasian boreal forests dominates the high-latitude net ecosystem carbon budget.},
journal = {Global change biology},
volume = {29},
number = {7},
pages = {1870-1889},
doi = {10.1111/gcb.16553},
pmid = {36647630},
issn = {1365-2486},
support = {1203583//NSF/ ; 8414//Gordon and Betty Moore Foundation/ ; 80NM0018D004/NASA/NASA/United States ; 80NSSC18K0770/NASA/NASA/United States ; 19-EARTH20-0105/NASA/NASA/United States ; NNX15AT74A/NASA/NASA/United States ; 80NSSC19M0113/NASA/NASA/United States ; },
mesh = {*Ecosystem ; *Taiga ; Carbon ; Carbon Dioxide ; Tundra ; Methane ; Carbon Cycle ; },
abstract = {Arctic-boreal landscapes are experiencing profound warming, along with changes in ecosystem moisture status and disturbance from fire. This region is of global importance in terms of carbon feedbacks to climate, yet the sign (sink or source) and magnitude of the Arctic-boreal carbon budget within recent years remains highly uncertain. Here, we provide new estimates of recent (2003-2015) vegetation gross primary productivity (GPP), ecosystem respiration (Reco), net ecosystem CO2 exchange (NEE; Reco - GPP), and terrestrial methane (CH4) emissions for the Arctic-boreal zone using a satellite data-driven process-model for northern ecosystems (TCFM-Arctic), calibrated and evaluated using measurements from >60 tower eddy covariance (EC) sites. We used TCFM-Arctic to obtain daily 1-km[2] flux estimates and annual carbon budgets for the pan-Arctic-boreal region. Across the domain, the model indicated an overall average NEE sink of -850 Tg CO2 -C year[-1] . Eurasian boreal zones, especially those in Siberia, contributed to a majority of the net sink. In contrast, the tundra biome was relatively carbon neutral (ranging from small sink to source). Regional CH4 emissions from tundra and boreal wetlands (not accounting for aquatic CH4) were estimated at 35 Tg CH4 -C year[-1] . Accounting for additional emissions from open water aquatic bodies and from fire, using available estimates from the literature, reduced the total regional NEE sink by 21% and shifted many far northern tundra landscapes, and some boreal forests, to a net carbon source. This assessment, based on in situ observations and models, improves our understanding of the high-latitude carbon status and also indicates a continued need for integrated site-to-regional assessments to monitor the vulnerability of these ecosystems to climate change.},
}
@article {pmid36645791,
year = {2022},
author = {Marwali, EM and Kekalih, A and Yuliarto, S and Wati, DK and Rayhan, M and Valerie, IC and Cho, HJ and Jassat, W and Blumberg, L and Masha, M and Semple, C and Swann, OV and Kohns Vasconcelos, M and Popielska, J and Murthy, S and Fowler, RA and Guerguerian, AM and Streinu-Cercel, A and Pathmanathan, MD and Rojek, A and Kartsonaki, C and Gonçalves, BP and Citarella, BW and Merson, L and Olliaro, PL and Dalton, HJ and , },
title = {Paediatric COVID-19 mortality: a database analysis of the impact of health resource disparity.},
journal = {BMJ paediatrics open},
volume = {6},
number = {1},
pages = {},
pmid = {36645791},
issn = {2399-9772},
support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; 222410/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 225288/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; 220757/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Adolescent ; Humans ; Child ; COVID-19 Testing ; Pandemics ; *COVID-19/epidemiology/therapy ; *Tuberculosis ; Health Resources ; },
abstract = {BACKGROUND: The impact of the COVID-19 pandemic on paediatric populations varied between high-income countries (HICs) versus low-income to middle-income countries (LMICs). We sought to investigate differences in paediatric clinical outcomes and identify factors contributing to disparity between countries.<br><br>METHODS: The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) COVID-19 database was queried to include children under 19 years of age admitted to hospital from January 2020 to April 2021 with suspected or confirmed COVID-19 diagnosis. Univariate and multivariable analysis of contributing factors for mortality were assessed by country group (HICs vs LMICs) as defined by the World Bank criteria.<br><br>RESULTS: A total of 12&#x2009;860 children (3819 from 21 HICs and 9041 from 15 LMICs) participated in this study. Of these, 8961 were laboratory-confirmed and 3899 suspected COVID-19 cases. About 52% of LMICs children were black, and more than 40% were infants and adolescent. Overall in-hospital mortality rate (95% CI) was 3.3% [=(3.0% to 3.6%), higher in LMICs than HICs (4.0% (3.6% to 4.4%) and 1.7% (1.3% to 2.1%), respectively). There were significant differences between country income groups in intervention profile, with higher use of antibiotics, antivirals, corticosteroids, prone positioning, high flow nasal cannula, non-invasive and invasive mechanical ventilation in HICs. Out of the 439 mechanically ventilated children, mortality occurred in 106 (24.1%) subjects, which was higher in LMICs than HICs (89 (43.6%) vs 17 (7.2%) respectively). Pre-existing infectious comorbidities (tuberculosis and HIV) and some complications (bacterial pneumonia, acute respiratory distress syndrome and myocarditis) were significantly higher in LMICs compared with HICs. On multivariable analysis, LMIC as country income group was associated with increased risk of mortality (adjusted HR 4.73 (3.16 to 7.10)).<br><br>CONCLUSION: Mortality and morbidities were higher in LMICs than HICs, and it may be attributable to differences in patient demographics, complications and access to supportive and treatment modalities.},
}
@article {pmid36643652,
year = {2023},
author = {Mugnai, F and Costantini, F and Chenuil, A and Leduc, M and Gutiérrez Ortega, JM and Meglécz, E},
title = {Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14616},
pmid = {36643652},
issn = {2167-8359},
mesh = {Databases, Factual ; *DNA Barcoding, Taxonomic ; Mediterranean Sea ; *Aquatic Organisms/genetics ; },
abstract = {BACKGROUND: In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments.<br><br>METHODS: We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency.<br><br>RESULTS: The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).},
}
@article {pmid36642073,
year = {2023},
author = {Paixão, TM and Siqueira, CEG and Tristan-Cheever, E and Fischer, FM and Martinez, MC and Christoffolete, MA and Meisinger, K and Teixeira, LR},
title = {Overweight and Obesity in Brazilian Immigrants in Massachusetts, USA: A Time Series Analysis (2009-2020).},
journal = {Obesity facts},
volume = {16},
number = {2},
pages = {109-118},
pmid = {36642073},
issn = {1662-4033},
mesh = {Adult ; Humans ; Female ; Adolescent ; Young Adult ; Middle Aged ; Male ; *Overweight/epidemiology ; Brazil/epidemiology ; Time Factors ; Obesity/epidemiology ; *Emigrants and Immigrants ; Massachusetts/epidemiology ; Prevalence ; },
abstract = {INTRODUCTION: Obesity is considered a growing public health problem by the Brazilian Ministry of Health and a global epidemic by the World Health Organization (WHO). In 2020, the Centers for Disease Control and Prevention (CDC) estimated the prevalence of adult obesity at 31.9% in the USA. The USA is one of the main destinations for Brazilian immigrants in search of better living conditions, and Massachusetts is one of the states with the highest presence of Brazilians. Changes in lifestyle and eating habits are often associated with increases in overweight and obesity in immigrants in the USA, especially Hispanics, an official classification that does not, however, include Brazilians. The aim of this study was to describe the temporal trend of overweight and obesity in Brazilian immigrants assisted by the Cambridge Health Alliance (CHA) healthcare network in Massachusetts.<br><br>METHODS: This was an ecological time series study of 128,206 records of Brazilians aged between 18 and 60 years based on hospital data from 2009 to 2020.<br><br>RESULTS: Mean age was 38.9 (SD = 10.6), and 61% of the sample were women. The prevalence of overweight and obesity was 38.4% and 25.4%, respectively. Obesity exhibited an increasing trend, while eutrophy and overweight decreased during the study period.<br><br>CONCLUSION: As little is known about the health of Brazilian immigrants in the USA, this study contributes to the literature on the subject. The observed increasing trends agree with the worldwide increase in obesity and indicate the need for future research exploring individual factors associated with immigrant acculturation.},
}
@article {pmid36641462,
year = {2023},
author = {Tulis, F and Ševčík, M and Jánošíková, R and Baláž, I and Ambros, M and Zvaríková, L and Horváth, G},
title = {The impact of the striped field mouse's range expansion on communities of native small mammals.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {753},
pmid = {36641462},
issn = {2045-2322},
mesh = {Animals ; *Mammals ; *Murinae ; Slovakia ; },
abstract = {Understanding species expansion as an element of the dispersal process is crucial to gaining a better comprehension of the functioning of the populations and the communities. Populations of the same species that are native in one area could be considered nonindigenous, naturalised or invasive somewhere else. The striped field mouse has been expanding its range in south-western Slovakia since 2010, although the origin of the spread has still not been clarified. In light of the striped field mouse's life history, the recent range expansion is considered to be the expansion of a native species. This study analyses the impact of the striped field mouse's expansion on the native population and small mammal communities and confronts the documented stages of striped field mouse expansion with the stages of invasion biology. Our research replicates the design and compares results from past research of small mammals prior to this expansion at the same three study areas with the same 20 study sites and control sites. Several years after expansion, the striped field mouse has a 100% frequency of occurrence in all study sites and has become the dominant species in two of the study areas. The native community is significantly affected by the striped field mouse's increasing dominance, specifically: (i) we found a re-ordering of the species rank, mainly in areas with higher dominance, and (ii) an initial positive impact on diversity and evenness during low dominance of the striped field mouse turned markedly negative after crossing the 25% dominance threshold. Results suggested that the variation in the striped field mouse's dominance is affected by the northern direction of its spread. Our findings show that establishment in a new area, spread and impact on the native community are stages possibly shared by both invasive and native species during their range expansion.},
}
@article {pmid36640933,
year = {2023},
author = {Gautam, P and Pandey, AK and Dubey, SK},
title = {Multi-omics approach reveals elevated potential of bacteria for biodegradation of imidacloprid.},
journal = {Environmental research},
volume = {221},
number = {},
pages = {115271},
doi = {10.1016/j.envres.2023.115271},
pmid = {36640933},
issn = {1096-0953},
mesh = {Biodegradation, Environmental ; Molecular Docking Simulation ; Multiomics ; Neonicotinoids/analysis ; *Insecticides/analysis ; Nitro Compounds/analysis/chemistry/metabolism ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Soil ; },
abstract = {The residual imidacloprid, a widely used insecticide is causing serious environmental concerns. Knowledge of its biodegradation will help in assessing its residual mass in soil. In view of this, a soil microcosm-based study was performed to test the biodegradation potential of Agrobacterium sp. InxBP2. It achieved ∼88% degradation in 20 days and followed the pseudo-first-order kinetics (k = 0.0511 day[-1] and t1/2=7 days). Whole genome sequencing of Agrobacterium sp. InxBP2 revealed a genome size of 5.44 Mbp with 5179 genes. Imidacloprid degrading genes at loci K7A42_07110 (ABC transporter substrate-binding protein), K7A42_07270 (amidohydrolase family protein), K7A42_07385 (ABC transporter ATP-binding protein), K7A42_16,845 (nitronate monooxygenase family protein), and K7A42_20,660 (FAD-dependent monooxygenase) having sequence and functional similarity with known counterparts were identified. Molecular docking of proteins encoded by identified genes with their respective degradation pathway intermediates exhibited significant binding energies (-6.56 to -4.14 kcal/mol). Molecular dynamic simulation discovered consistent interactions and binding depicting high stability of docked complexes. Proteome analysis revealed differential protein expression in imidacloprid treated versus untreated samples which corroborated with the in-silico findings. Further, the detection of metabolites proved the bacterial degradation of imidacloprid. Thus, results provided a mechanistic link between imidacloprid and associated degradative genes/enzymes of Agrobacterium sp. InxBP2. These findings will be of immense significance in carrying out the lifecycle analysis and formulating strategies for the bioremediation of soils contaminated with insecticides like imidacloprid.},
}
@article {pmid36639402,
year = {2023},
author = {Mack, M and Stojan, R and Bock, O and Voelcker-Rehage, C},
title = {The association of executive functions and physical fitness with cognitive-motor multitasking in a street crossing scenario.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {697},
pmid = {36639402},
issn = {2045-2322},
mesh = {Female ; Humans ; Aged ; *Executive Function ; *Physical Fitness ; Exercise ; Task Performance and Analysis ; Cognition ; },
abstract = {Age-related decline in cognitive-motor multitasking performance has been attributed to declines in executive functions and physical fitness (motor coordinative fitness and cardiovascular fitness). It has been suggested that those cognitive and physical resources strongly depend on lifestyle factors such as long-term regular physical activity and cognitive engagement. Although research suggests that there is covariation between components of executive functions and physical fitness, the interdependence between these components for cognitive-motor multitasking performance is not yet clear. The aim of the study was to examine the contribution and interrelationship between executive functions, motor coordinative fitness, and cardiovascular fitness on street crossing while multitasking. We used the more ecologically valid scenario to obtain results that might be directly transferable to daily life situation. Data from 50 healthy older adults (65-75 years, 17 females, recruited in two different cities in Germany) were analyzed. Participants' executive functions (composite score including six tests), motor coordinative fitness (composite score including five tests), and cardiovascular fitness (spiroergometry), as well as their street crossing performance while multitasking were assessed. Street crossing was tested under single-task (crossing a two-line road), and multitask conditions (crossing a two-line road while typing numbers on a keypad as simulation of mobile phone use). Street crossing performance was assessed by use of cognitive outcomes (typing, crossing failures) and motor outcomes (stay time, crossing speed). Linear mixed-effects models showed beneficial main effects of executive functions for typing (p = 0.004) and crossing failures (p = 0.023), and a beneficial main effect of motor coordinative fitness for stay time (p = 0.043). Commonality analysis revealed that the proportion of variance commonly explained by executive functions, motor coordinative fitness, and cardiovascular fitness was small for all street crossing outcomes. For typing and crossing failures (cognitive outcomes), the results further showed a higher relative contribution of executive functions compared to motor coordinative fitness and cardiovascular fitness. For stay time (motor outcome), the results correspondingly revealed a higher relative contribution of motor coordinative fitness compared to executive functions and cardiovascular fitness. The findings suggest that during cognitive-motor multitasking in everyday life, task performance is determined by the components of executive functions and physical fitness related to the specific task demands. Since multitasking in everyday life includes cognitive and motor tasks, it seems to be important to maintain both executive functions and physical fitness for independent living up to old age.},
}
@article {pmid36637211,
year = {2023},
author = {Feldner-Busztin, D and Firbas Nisantzis, P and Edmunds, SJ and Boza, G and Racimo, F and Gopalakrishnan, S and Limborg, MT and Lahti, L and de Polavieja, GG},
title = {Dealing with dimensionality: the application of machine learning to multi-omics data.},
journal = {Bioinformatics (Oxford, England)},
volume = {39},
number = {2},
pages = {},
pmid = {36637211},
issn = {1367-4811},
support = {//European Union's Horizon 2020 research and innovation programme/ ; CEH-DNRF143//Danish National Research Foundation/ ; },
mesh = {Humans ; *Multiomics ; *Neoplasms/genetics ; Machine Learning ; Genome ; },
abstract = {MOTIVATION: Machine learning (ML) methods are motivated by the need to automate information extraction from large datasets in order to support human users in data-driven tasks. This is an attractive approach for integrative joint analysis of vast amounts of omics data produced in next generation sequencing and other -omics assays. A systematic assessment of the current literature can help to identify key trends and potential gaps in methodology and applications. We surveyed the literature on ML multi-omic data integration and quantitatively explored the goals, techniques and data involved in this field. We were particularly interested in examining how researchers use ML to deal with the volume and complexity of these datasets.<br><br>RESULTS: Our main finding is that the methods used are those that address the challenges of datasets with few samples and many features. Dimensionality reduction methods are used to reduce the feature count alongside models that can also appropriately handle relatively few samples. Popular techniques include autoencoders, random forests and support vector machines. We also found that the field is heavily influenced by the use of The Cancer Genome Atlas dataset, which is accessible and contains many diverse experiments.<br><br>All data and processing scripts are available at this GitLab repository: https://gitlab.com/polavieja_lab/ml_multi-omics_review/ or in Zenodo: https://doi.org/10.5281/zenodo.7361807.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid36629615,
year = {2023},
author = {Brito, MIBDS and Oliveira, ECA and Barbosa, CS and Gomes, ECS},
title = {Factors associated with severe forms and deaths from schistosomiasis and application of probabilistic linkage in databases, state of Pernambuco, Brazil, 2007-2017.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {26},
number = {},
pages = {e230003},
pmid = {36629615},
issn = {1980-5497},
mesh = {Humans ; Brazil/epidemiology ; *Schistosomiasis/epidemiology ; Databases, Factual ; },
abstract = {OBJECTIVE: To verify the agreement of data on severe forms and deaths from schistosomiasis recorded in the Brazilian Notifiable Diseases Information System and the Mortality Information System, sociodemographic variables with the occurrence of severe forms and deaths, and the temporal trend of the disease in the state of Pernambuco, Brazil.<br><br>METHODS: This is an ecological, descriptive, time series study with data on severe forms and deaths from schistosomiasis in Pernambuco, from 2007 to 2017. For the linkage between databases, a function was developed in python programming language, using the Soundex method. To identify sociodemographic and health factors that correlated with the dependent variables, Pearson's correlation test was applied. For trend analysis, linear regression was applied.<br><br>RESULTS: We identified 9,085 severe cases, 1,956 deaths, and 186 cases in the linkage. The correlation between the average positivity rate with the general water supply and waste collection was 0.22 and 0.26 respectively. We verified a correlation of the average cumulative mortality rate with water supply by well or spring (r=0.27), water supply by the general network (r=0.3), waste collection (r=0.42), and road urbanization (r=0.29). We found 3,153 severe forms in 2007 with a decrease trend and 205 deaths in 2010, without a trend pattern.<br><br>CONCLUSION: There is a need for greater investments in disease control and in the quality of information, especially in the record of severe forms, considering that, due to the pathophysiology of the disease, death only occurs when the individual develops the chronic form, and its notification on the Notifiable Diseases Information System is imperative.},
}
@article {pmid36629614,
year = {2023},
author = {Batista, JFC and Oliveira, MR and Pereira, DLM and Matos, MLSDS and Souza, IT and Menezes, MO},
title = {Spatial distribution and temporal trends of AIDS in Brazil and regions between 2005 and 2020.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {26},
number = {},
pages = {e230002},
pmid = {36629614},
issn = {1980-5497},
mesh = {Humans ; Adolescent ; Young Adult ; Adult ; Brazil/epidemiology ; *Acquired Immunodeficiency Syndrome/epidemiology ; Bayes Theorem ; Information Systems ; Incidence ; },
abstract = {OBJECTIVE: To analyze the spatial distribution and the temporal trend of the AIDS incidence rate in Brazil from 2005 to 2020.<br><br>METHODS: This is an ecological, temporal, and spatial study on AIDS cases in Brazil. Data from the Notifiable Diseases Information System were stratified by year of diagnosis, region of the country/municipalities of residence, and age group (over 13 years). Incidence rates were calculated for temporal estimation using the Joinpoint model, as well as Spatial Empirical Bayes (SEB) for spatial distribution, using the Kernel density estimator.<br><br>RESULTS: The incidence rate in Brazil, in 2020, was 17.69 cases per 100 thousand inhabitants. The general trend (2005-2020) was decrease in Brazil (Annual Percent Change - APC=-2.0%), in the Southeast (APC=-4.4%) and South (APC=-3.0%) regions. The North (APC=2.3%) showed an increase trend, whereas the Southeast and Midwest regions were stationary (p>0.05). Brazil, Southeast, South, and Midwest regions showed a decrease trend in most age groups. The Northeast and North regions showed an increase in the age groups of 13-29 years and 13-24 years, respectively. The Kernel estimator showed clusters with SEB above 30/10 thousand inhabitants in the states of Para&#xed;ba, Sergipe, Alagoas, Pernambuco, S&#xe3;o Paulo, Minas Gerais, Par&#xe1;, Rio Grande do Sul, and Santa Catarina.<br><br>CONCLUSION: Brazil, the Southeast, and South regions showed a decrease in the incidence rate, whereas the North region increased and the Northeast and Midwest regions were stationary. The Southeast, South, and Northeast regions presented the largest clusters of SEB.},
}
@article {pmid36621304,
year = {2023},
author = {Liu, X and Han, Y and Luo, L and Pan, H and Cheng, T and Zhang, Q},
title = {Multiomics analysis reveals the mechanisms underlying the different floral colors and fragrances of Rosa hybrida cultivars.},
journal = {Plant physiology and biochemistry : PPB},
volume = {195},
number = {},
pages = {101-113},
doi = {10.1016/j.plaphy.2022.12.028},
pmid = {36621304},
issn = {1873-2690},
mesh = {*Rosa/genetics/metabolism ; Odorants ; Multiomics ; Color ; Plant Breeding ; Flowers/genetics/metabolism ; Gene Expression Regulation, Plant ; },
abstract = {The color and fragrance of rose flowers affect their commercial value. However, several rose varieties with new floral colors developed by the bud mutation method lost their fragrance during the breeding process, raising the question: Is there a relationship between floral color and aroma traits? Rose cultivar 'Yellow Island' (YI) with intensely aroma and yellow petals, while its bud mutant 'Past Feeling' (PF) with light aroma and pink petals mixing some yellow, two cultivars were used to explore this question using multiomics approaches. We investigated the genomic polymorphisms between PF and YI by whole-genome resequencing. 71 differentially abundant metabolites and 155 related differentially expressed genes identified in petals between PF and YI. From this, we constructed a model of metabolic changes affecting floral color and fragrance integrating shikimate, terpenoid, carotenoid, and green leaf volatile metabolites and predicted the associated key genes and transcription factors. This study provides a reference for understanding the molecular mechanism of variation in rose floral color and aroma traits.},
}
@article {pmid36620398,
year = {2023},
author = {Gries, C and Hanson, PC and O'Brien, M and Servilla, M and Vanderbilt, K and Waide, R},
title = {The Environmental Data Initiative: Connecting the past to the future through data reuse.},
journal = {Ecology and evolution},
volume = {13},
number = {1},
pages = {e9592},
pmid = {36620398},
issn = {2045-7758},
abstract = {The Environmental Data Initiative (EDI) is a trustworthy, stable data repository, and data management support organization for the environmental scientist. In a bottom-up community process, EDI was built with the premise that freely and easily available data are necessary to advance the understanding of complex environmental processes and change, to improve transparency of research results, and to democratize ecological research. EDI provides tools and support that allow the environmental researcher to easily integrate data publishing into the research workflow. Almost ten years since going into production, we analyze metadata to provide a general description of EDI's collection of data and its data management philosophy and placement in the repository landscape. We discuss how comprehensive metadata and the repository infrastructure lead to highly findable, accessible, interoperable, and reusable (FAIR) data by evaluating compliance with specific community proposed FAIR criteria. Finally, we review measures and patterns of data (re)use, assuring that EDI is fulfilling its stated premise.},
}
@article {pmid36618211,
year = {2022},
author = {Krishnan, RA and Ravindran, RM and Vincy, VS and Arun, P and Shinu, KS and Jithesh, V and Varma, RP},
title = {Analysis of daily COVID-19 death bulletin data during the first two waves of the COVID-19 pandemic in Thiruvananthapuram district, Kerala, India.},
journal = {Journal of family medicine and primary care},
volume = {11},
number = {10},
pages = {6190-6196},
pmid = {36618211},
issn = {2249-4863},
abstract = {CONTEXT: Coronavirus disease 2019 (COVID-19) mortality trends can help discern the pattern of outbreak evolution and systemic responses.<br><br>AIM: This study aimed to explore patterns of COVID-19 deaths in Thiruvananthapuram district from 31 March 2020 to 31 December 2021.<br><br>SETTING AND DESIGN: Secondary data analysis of COVID-19 deaths in Thiruvananthapuram district was performed.<br><br>MATERIALS AND METHODS: Mortality data were obtained from the district COVID-19 control room, and deaths in the first and second waves of COVID-19 were compared.<br><br>STATISTICAL ANALYSIS: We summarised data as proportions and medians with the inter-quartile range (IQR) and performed Chi-square tests to make comparisons wherever applicable.<br><br>RESULTS: As on 31 December 2021, 4587 COVID-19 deaths were reported in Thiruvananthapuram district, with a case fatality rate of 0.91%. We observed high mortality among older persons (66.7%) and men (56.6%). The leading cause of death was bronchopneumonia (60.6%). The majority (88.5%) had co-morbidities, commonly diabetes mellitus (54.9%). The median interval from diagnosis to hospitalisation was 4 days (IQR 2-7), and that from hospitalisation to death was 2 days (IQR 0-6). The deaths reported during the second wave were four times higher than those of the first wave with a higher proportion of deaths in the absence of co-morbidities (p < 0.001). The majority of the deceased were unvaccinated. Ecological analysis with vaccine coverage data indicated 5.4 times higher mortality among unvaccinated than those who received two vaccine doses.<br><br>CONCLUSIONS: The presence of co-morbidities, an unvaccinated status, and delay in hospitalisation were important reasons for COVID-19 deaths. Primary level health providers can potentially help sustaining vaccination, expeditious referral, and monitoring of COVID-19 patients.},
}
@article {pmid36617091,
year = {2023},
author = {Abdallah, M and Joung, BG and Lee, WJ and Mousoulis, C and Raghunathan, N and Shakouri, A and Sutherland, JW and Bagchi, S},
title = {Anomaly Detection and Inter-Sensor Transfer Learning on Smart Manufacturing Datasets.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {1},
pages = {},
pmid = {36617091},
issn = {1424-8220},
mesh = {*Commerce ; Databases, Factual ; Time Factors ; *Machine Learning ; },
abstract = {Smart manufacturing systems are considered the next generation of manufacturing applications. One important goal of the smart manufacturing system is to rapidly detect and anticipate failures to reduce maintenance cost and minimize machine downtime. This often boils down to detecting anomalies within the sensor data acquired from the system which has different characteristics with respect to the operating point of the environment or machines, such as, the RPM of the motor. In this paper, we analyze four datasets from sensors deployed in manufacturing testbeds. We detect the level of defect for each sensor data leveraging deep learning techniques. We also evaluate the performance of several traditional and ML-based forecasting models for predicting the time series of sensor data. We show that careful selection of training data by aggregating multiple predictive RPM values is beneficial. Then, considering the sparse data from one kind of sensor, we perform transfer learning from a high data rate sensor to perform defect type classification. We release our manufacturing database corpus (4 datasets) and codes for anomaly detection and defect type classification for the community to build on it. Taken together, we show that predictive failure classification can be achieved, paving the way for predictive maintenance.},
}
@article {pmid36613120,
year = {2023},
author = {Qin, J and Ma, M and Shi, J and Ma, S and Wu, B and Su, X},
title = {The Time-Lag Effect of Climate Factors on the Forest Enhanced Vegetation Index for Subtropical Humid Areas in China.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
pmid = {36613120},
issn = {1660-4601},
mesh = {*Ecosystem ; *Forests ; China ; Climate Change ; Temperature ; },
abstract = {Forests represent the greatest carbon reservoir in terrestrial ecosystems. Climate change drives the changes in forest vegetation growth, which in turn influences carbon sequestration capability. Exploring the dynamic response of forest vegetation to climate change is thus one of the most important scientific questions to be addressed in the precise monitoring of forest resources. This paper explores the relationship between climate factors and vegetation growth in typical forest ecosystems in China from 2007 to 2019 based on long-term meteorological monitoring data from six forest field stations in different subtropical ecological zones in China. The time-varying parameter vector autoregressive model (TVP-VAR) was used to analyze the temporal and spatial differences of the time-lag effects of climate factors, and the impact of climate change on vegetation was predicted. The enhanced vegetation index (EVI) was used to measure vegetation growth. Monthly meteorological observations and solar radiation data, including precipitation, air temperature, relative humidity, and photosynthetic effective radiation, were provided by the resource sharing service platform of the national ecological research data center. It was revealed that the time-lag effect of climate factors on the EVI vanished after a half year, and the lag accumulation tended to be steady over time. The TVP-VAR model was found to be more suitable than the vector autoregressive model (VAR). The predicted EVI values using the TVP-VAR model were close to the true values with the root mean squares error (RMSE) < 0.05. On average, each site improved its prediction accuracy by 14.81%. Therefore, the TVP-VAR model can be used to analyze the relationship of climate factors and forest EVI as well as the time-lag effect of climate factors on vegetation growth in subtropical China. The results can be used to improve the predictability of the EVI for forests and to encourage the development of intensive forest management.},
}
@article {pmid36612902,
year = {2022},
author = {Vlăduțu, DE and Ionescu, M and Mercuț, R and Noveri, L and Lăzărescu, G and Popescu, SM and Scrieciu, M and Manolea, HO and Iacov Crăițoiu, MM and Ionescu, AG and Mercuț, V},
title = {Ecological Momentary Assessment of Masseter Muscle Activity in Patients with Bruxism.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
pmid = {36612902},
issn = {1660-4601},
mesh = {Humans ; *Bruxism ; Masseter Muscle/physiology ; Ecological Momentary Assessment ; Electromyography ; Masticatory Muscles/physiology ; },
abstract = {According to the International Bruxism Consensus, bruxism refers to the activity of the masticatory muscles reflecting contraction disorders, regardless of whether it is during sleep (SB) or an awake (AB) state. The objective of the present study was to evaluate the activity of the masseter muscle by surface electromyographic (sEMG) recordings. This study was performed on 20 participants with self-reported “possible bruxism” (study group) and 20 participants with no self-reported bruxism (control group); all participants underwent an evaluation of the masseter muscle activity using the dia-BRUXO device, which provides numerical parameters regarding sEMG (the total duration and the type of bruxism specific events, the effort made by the masticatory muscles during the recording period, and the personal bruxism index of each participant). Participants from the study group presented more clenching events during AB, three times more frequent than the control group (p = 0.002, Mann−Whitney U test); for SB, the frequency of clenching and grinding events was comparable within the study group, being more frequent than for the control group; the mean value of the effort index was higher for AB (1.177%) than SB (0.470%) and the same for the duration index, with a mean value of 2.788% for AB and 1.054% for SB. All participants from the control group presented reduced values for all acquired parameters. Overall, the personal bruxism index in AB was approximately four times higher for the study group (2.251%) compared to the control group (0.585%) (p < 0.005, Mann−Whitney U test). Similar values were obtained for SB. All participants with “possible bruxism” from the study group presented a higher activity of the masseter muscle, which is specific for bruxism, thus being defined as “definite bruxism”.},
}
@article {pmid36612815,
year = {2022},
author = {Yang, X and Lei, S and Shi, Y and Wang, W},
title = {Effects of Ground Subsidence on Vegetation Chlorophyll Content in Semi-Arid Mining Area: From Leaf Scale to Canopy Scale.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
pmid = {36612815},
issn = {1660-4601},
mesh = {*Chlorophyll/analysis ; *Plants ; Plant Leaves/chemistry ; Telemetry ; Poaceae ; },
abstract = {Ground subsidence is the main cause of vegetation degradation in mining areas. It is of great significance to study the effects of ground subsidence on vegetation. At present, few studies have analyzed the effects of ground subsidence on vegetation from different scales. However, the conclusions on different scales may differ. In this experiment, chlorophyll content was used as an indicator of vegetation degradation. We conducted a long-term field survey in the Lijiahao coalfield in China. Based on field survey data and remote sensing images, we analyzed the effects of ground subsidence on chlorophyll content from two scales (leaf scale and canopy scale) and summarized the similarities and differences. We found that, regardless of leaf scale or canopy scale, the effects of subsidence on chlorophyll content have the following three characteristics: (1) mining had the least effect on chlorophyll content in the neutral area, followed by the compression area, and the greatest effect on chlorophyll content in the extension area; (2) subsidence had a slight effect on chlorophyll content of Caragana korshins, but a serious effect on chlorophyll content of Stipa baicalensis; (3) chlorophyll content was not immediately affected when the ground sank. It was the cumulative subsidence that affects chlorophyll content. The difference between leaf scale and canopy scale was that the chlorophyll content at canopy scale is more affected by mining. This means that when assessing vegetation degradation, the results obtained by remote sensing were more severe than those measured in the field. We believe that this is because the canopy chlorophyll content obtained by remote sensing is also affected by the plant canopy structure. We recommend that mining and ecological restoration should be carried out concurrently, and that ground fissures should be taken as the focus of ecological restoration. In addition, Caragana korshins ought to be widely planted. Most importantly, managers should assess the effects of ground subsidence on vegetation on different scales. However, managers need to be aware of differences at different scales.},
}
@article {pmid36612520,
year = {2022},
author = {Zhou, Z and Zhang, Z and Zhang, W and Luo, J and Zhang, K and Cao, Z and Wang, Z},
title = {The Impact of Residences and Roads on Wind Erosion in a Temperate Grassland Ecosystem: A Spatially Oriented Perspective.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
pmid = {36612520},
issn = {1660-4601},
mesh = {Humans ; *Ecosystem ; *Grassland ; Wind ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; Soil ; },
abstract = {The existence of residences and roads is an important way in which human activity affects wind erosion in arid and semiarid environments. Studies assessing the impact of these elements on wind erosion have only focused on limited plots, and their threat of erosion to the surrounding environment has been ignored by many studies. This study was based on spatially overlayed analysis of independent wind erosion distribution simulated by the revised wind erosion equation (RWEQ) and remote-sensing-image-derived residence and road distribution data. Wind erosion at different distances from residences and roads was quantified at the landscape scale of a typical temperate grassland ecosystem, explicitly demonstrating the crucial impacts of both elements on wind erosion. The results showed that wind erosion weakened as the distance from residences and roads increased due to the priority pathways of human activities, and the wind erosion around the residence was more severe than around the road. Human activities in the buffer zones 0-200 m from the residences most frequently caused severe wind erosion, with a wind soil loss of 25 t ha[-1] yr[-1] and a wind soil loss of approximately 5.25 t ha[-1] yr[-1] for 0-60 m from the roads. The characteristics of wind erosion variation in the buffer zones were also affected by residence size and the environments in which the residences were located. The variation in wind erosion was closely related to the road levels. Human activities intensified wind erosion mainly by affecting the soil and vegetation around residences and roads. Ecological management should not be limited to residences and roads but should also protect the surrounding environments. The findings of this study are aimed towards a spatial perspective that can help implement rational and effective environmental management measures for the sustainability of wind-eroded ecosystems.},
}
@article {pmid36607898,
year = {2023},
author = {Zhang, X and Chen, X and Yue, Y and Wang, S and Zhao, B and Huang, X and Li, T and Sun, Q and Wang, J},
title = {Ecological Study on Global Health Effects due to Source-Specific Ambient Fine Particulate Matter Exposure.},
journal = {Environmental science &amp; technology},
volume = {57},
number = {3},
pages = {1278-1291},
pmid = {36607898},
issn = {1520-5851},
mesh = {Particulate Matter/analysis ; *Air Pollutants/analysis ; Global Health ; *Air Pollution/analysis ; Databases, Factual ; Environmental Exposure ; },
abstract = {Ambient air pollution of fine particulate matter with diameters less than 2.5 μm (PM2.5) is associated with millions of premature deaths per year, recognized as a leading global health concern. The dose-response relation between ambient PM2.5 exposure and mortality risk is the most fundamental information for assessments of the health effects of PM2.5. The existing dose-response relations were generally developed based on the assumption of equal contribution to toxicity from various sources. However, the sources of PM2.5 may significantly influence health effects. In this study, we conducted an ecological study to investigate the global long-term correlation between source-specific PM2.5 exposure and cause-specific mortality risk (SPECM) based on the regional aggregate data of the publically available official health databases from 528 regions worldwide with a total registered population of 3.2 billion. The results provided preliminary epidemiological evidence for differing chronic health effects across various sources. The relative mortality risks of lung cancer and circulatory diseases were closely correlated with the primary emissions from industrial and residential combustion sources. Chronic lower respiratory diseases were mostly associated with the mass concentration of particulate matter.},
}
@article {pmid36607160,
year = {2023},
author = {Van Sundert, K and Leuzinger, S and Bader, MK and Chang, SX and De Kauwe, MG and Dukes, JS and Langley, JA and Ma, Z and Mariën, B and Reynaert, S and Ru, J and Song, J and Stocker, B and Terrer, C and Thoresen, J and Vanuytrecht, E and Wan, S and Yue, K and Vicca, S},
title = {When things get MESI: The Manipulation Experiments Synthesis Initiative-A coordinated effort to synthesize terrestrial global change experiments.},
journal = {Global change biology},
volume = {29},
number = {7},
pages = {1922-1938},
doi = {10.1111/gcb.16585},
pmid = {36607160},
issn = {1365-2486},
support = {PCEFP2_181115/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Ecosystem ; *Carbon Dioxide ; Biomass ; Climate Change ; Climate ; Soil ; },
abstract = {Responses of the terrestrial biosphere to rapidly changing environmental conditions are a major source of uncertainty in climate projections. In an effort to reduce this uncertainty, a wide range of global change experiments have been conducted that mimic future conditions in terrestrial ecosystems, manipulating CO2 , temperature, and nutrient and water availability. Syntheses of results across experiments provide a more general sense of ecosystem responses to global change, and help to discern the influence of background conditions such as climate and vegetation type in determining global change responses. Several independent syntheses of published data have yielded distinct databases for specific objectives. Such parallel, uncoordinated initiatives carry the risk of producing redundant data collection efforts and have led to contrasting outcomes without clarifying the underlying reason for divergence. These problems could be avoided by creating a publicly available, updatable, curated database. Here, we report on a global effort to collect and curate 57,089 treatment responses across 3644 manipulation experiments at 1145 sites, simulating elevated CO2 , warming, nutrient addition, and precipitation changes. In the resulting Manipulation Experiments Synthesis Initiative (MESI) database, effects of experimental global change drivers on carbon and nutrient cycles are included, as well as ancillary data such as background climate, vegetation type, treatment magnitude, duration, and, unique to our database, measured soil properties. Our analysis of the database indicates that most experiments are short term (one or few growing seasons), conducted in the USA, Europe, or China, and that the most abundantly reported variable is aboveground biomass. We provide the most comprehensive multifactor global change database to date, enabling the research community to tackle open research questions, vital to global policymaking. The MESI database, freely accessible at doi.org/10.5281/zenodo.7153253, opens new avenues for model evaluation and synthesis-based understanding of how global change affects terrestrial biomes. We welcome contributions to the database on GitHub.},
}
@article {pmid36604610,
year = {2023},
author = {Prager, M and Lundin, D and Ronquist, F and Andersson, AF},
title = {ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.},
journal = {BMC bioinformatics},
volume = {24},
number = {1},
pages = {6},
pmid = {36604610},
issn = {1471-2105},
support = {2019-00242//Vetenskapsr&#xe5;det/ ; },
mesh = {*DNA/genetics ; *Biodiversity ; Software ; DNA Barcoding, Taxonomic ; },
abstract = {BACKGROUND: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.<br><br>RESULTS: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure.<br><br>CONCLUSION: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.},
}
@article {pmid36602254,
year = {2023},
author = {Koenig, CJ and Vasquez, TS and Peterson, EB and Wollney, EN and Bylund, CL and Ho, EY},
title = {Mapping Uncharted Terrain: A Systematic Review of Complementary and Integrative Health Communication Using Observational Data in Biomedical Settings.},
journal = {Health communication},
volume = {38},
number = {14},
pages = {3147-3162},
doi = {10.1080/10410236.2022.2140080},
pmid = {36602254},
issn = {1532-7027},
mesh = {Humans ; *Health Communication ; Palliative Care ; },
abstract = {Complementary and integrative health (CIH) use is diverse and highly prevalent worldwide. Prior research of CIH communication in biomedical encounters address safety, efficacy, symptom management, and overall wellness. Observational methods are rarely used to study CIH communication and avoid recall bias, preserve ecological validity, and contextualize situated clinical communication. Following PRISMA guidelines, we systematically reviewed studies at the intersection of social scientific observational research and findings about CIH communication between clinicians, patients, and caregivers in biomedical settings. We identified international, peer-reviewed publications from seven databases between January 2010 and December 2020. Titles and abstracts were first screened for inclusion, then full studies were coded using explicit criteria. We used a standard checklist was modified to assess article quality. Ten of 11,793 studies examined CIH communication using observational methods for CIH communication in biomedical settings. Studies used a range of observational techniques, including participant and non-participant observation, which includes digital audio or video recordings. Results generated two broad sets of findings, one focused on methodological insights and another on CIH communication. Despite methodological and topic similarities, included studies addressed CIH communication as a process and as proximal and intermediate health outcomes. We recommend how observational studies of CIH communication can better highlight relationships between communication processes and health outcomes. Current research using observational methods offers an incomplete picture of CIH communication in biomedical settings. Future studies should standardize how observational techniques are reported to enhance consistency and comparability within and across biomedical settings to improve comparability.},
}
@article {pmid36601075,
year = {2022},
author = {Leal, JSV and Fogal, AS and Meireles, AL and Cardoso, LO and Machado, &#xcd;E and de Menezes, MC},
title = {Health economic impacts associated with the consumption of sugar-sweetened beverages in Brazil.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1088051},
pmid = {36601075},
issn = {2296-861X},
abstract = {INTRODUCTION: The consumption of sugar-sweetened beverages (SSBs) is among the main risk factors for non-communicable diseases (NCDs). This study aimed to estimate the financial costs of hospitalizations and procedures of high and medium complexity for NCDs attributable to the consumption of SSBs in the Brazilian Unified Health System (SUS) in 2019.<br><br>METHODS: This ecological study used data from the Global Burden of Disease (GBD) 2019 and the Department of Informatics of the Unified Health System (DATASUS). The attributable costs were estimated from the population-attributable fraction (PAF) and the costs in the treatment of chronic diseases [type 2 diabetes mellitus and ischemic heart disease (IHD)], stratified by sex, age group, level of complexity of treatment, and federative units.<br><br>RESULTS: In 2019, in Brazil, US$ 14,116,240.55 were the costs of hospitalizations and procedures of high and medium complexity in the treatment of NCDs attributable to the consumption of SSBs. These values were higher in males (US$ 8,469,265.14) and the southeast and southern regions, mainly in the state of S&#xe3;o Paulo. However, when evaluating these results at a rate per 10,000 inhabitants, it was observed that the states of Paran&#xe1;, Tocantins, and Roraima had higher costs per 10,000 inhabitants. Regarding the age groups, higher costs were observed in the older age groups.<br><br>CONCLUSION: This study revealed the high financial impact of the NCDs treatment attributed to the consumption of SSBs in Brazil and the variability among Brazilian macro-regions. The results demonstrate the urgency and need for the expansion of policies to reduce the consumption of SSBs in Brazil with strategies that consider regional particularities.},
}
@article {pmid36599936,
year = {2023},
author = {Juan, D and Santpere, G and Kelley, JL and Cornejo, OE and Marques-Bonet, T},
title = {Current advances in primate genomics: novel approaches for understanding evolution and disease.},
journal = {Nature reviews. Genetics},
volume = {24},
number = {5},
pages = {314-331},
pmid = {36599936},
issn = {1471-0064},
support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Evolution, Molecular ; *Genomics/methods ; Primates/genetics ; Genome ; Phylogeny ; Genetic Variation ; },
abstract = {Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.},
}
@article {pmid36590525,
year = {2022},
author = {Prylutskyy, Y and Nozdrenko, D and Gonchar, O and Prylutska, S and Bogutska, K and Franskevych, D and Hromovyk, B and Scharff, P and Ritter, U},
title = {C60 fullerene attenuates muscle force reduction in a rat during fatigue development.},
journal = {Heliyon},
volume = {8},
number = {12},
pages = {e12449},
pmid = {36590525},
issn = {2405-8440},
abstract = {C60 fullerene (C60) as a nanocarbon particle, compatible with biological structures, capable of penetrating through cell membranes and effectively scavenging free radicals, is widely used in biomedicine. A protective effect of C60 on the biomechanics of fast (m. gastrocnemius) and slow (m. soleus) muscle contraction in rats and the pro- and antioxidant balance of muscle tissue during the development of muscle fatigue was studied compared to the same effect of the known antioxidant N-acetylcysteine (NAC). C60 and NAC were administered intraperitoneally at doses of 1 and 150 mg kg[-1], respectively, daily for 5 days and 1 h before the start of the experiment. The following quantitative markers of muscle fatigue were used: the force of muscle contraction, the level of accumulation of secondary products of lipid peroxidation (TBARS) and the oxygen metabolite H2O2, the activity of first-line antioxidant defense enzymes (superoxide dismutase (SOD) and catalase (CAT)), and the condition of the glutathione system (reduced glutathione (GSH) content and the activity of the glutathione peroxidase (GPx) enzyme). The analysis of the muscle contraction force dynamics in rats against the background of induced muscle fatigue showed, that the effect of C60, 1 h after drug administration, was (15-17)% more effective on fast muscles than on slow muscles. A further slight increase in the effect of C60 was revealed after 2 h of drug injection, (7-9)% in the case of m. gastrocnemius and (5-6)% in the case of m. soleus. An increase in the effect of using C60 occurred within 4 days (the difference between 4 and 5 days did not exceed (3-5)%) and exceeded the effect of NAC by (32-34)%. The analysis of biochemical parameters in rat muscle tissues showed that long-term application of C60 contributed to their decrease by (10-30)% and (5-20)% in fast and slow muscles, respectively, on the 5th day of the experiment. At the same time, the protective effect of C60 was higher compared to NAC by (28-44)%. The obtained results indicate the prospect of using C60 as a potential protective nano agent to improve the efficiency of skeletal muscle function by modifying the reactive oxygen species-dependent mechanisms that play an important role in the processes of muscle fatigue development.},
}
@article {pmid36581858,
year = {2022},
author = {Huang, Y and Lu, W and Zeng, M and Hu, X and Su, Z and Liu, Y and Liu, Z and Yuan, J and Li, L and Zhang, X and Huang, L and Hu, W and Wang, X and Li, S and Zhang, H},
title = {Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {245},
pmid = {36581858},
issn = {2049-2618},
mesh = {Infant, Newborn ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Inflammation ; Bacteria ; *Heart Defects, Congenital ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD.<br><br>METHODS: Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis.<br><br>RESULTS: Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD.<br><br>CONCLUSIONS: We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.},
}
@article {pmid36576353,
year = {2023},
author = {Liu, C and Economo, EP and Guénard, B},
title = {GABI-I: The global ant biodiversity informatics-island database.},
journal = {Ecology},
volume = {104},
number = {4},
pages = {e3969},
doi = {10.1002/ecy.3969},
pmid = {36576353},
issn = {1939-9170},
mesh = {Animals ; *Biodiversity ; Ecology ; *Ants ; },
abstract = {Island systems are known to harbor disproportionate amounts of geographically restricted biodiversity and to experience high rates of species loss, and they ultimately represent critical systems with significant conservation values. However, knowledge of the biodiversity value of insular systems remains highly fragmented and incomplete for many groups of organisms, especially insects. This gap limits our understanding of their global significance for biodiversity and inhibits prioritization for future exploration and conservation efforts. Here, we developed a new database to present current knowledge on ants on 2678 islands globally, based on nominal species, and provide information on their native or exotic status. In total, this database contains 7010 ant species (44.6% of the known global ant fauna) that have been recorded on islands globally from 449,232 records. In addition, this database identifies 108 large islands (area > 200 km[2]) that have received no ant sampling efforts globally. This new data set provides the most comprehensive understanding of ant diversity and composition on islands globally, opening up new opportunities to address questions on a multitude of research questions and fields related to biogeography, ecology, and evolution. This data set also provides a roadmap for future exploration and conservation actions in connection with ants on islands as well as overall ant diversity, with updates available as new records and taxonomic updates are published. There are no copyright restrictions on this database and users should cite this data paper in publications when using the data.},
}
@article {pmid36575453,
year = {2022},
author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S},
title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.},
journal = {BMC medicine},
volume = {20},
number = {1},
pages = {500},
pmid = {36575453},
issn = {1741-7015},
support = {613979//Seventh Framework Programme/ ; 245009//Seventh Framework Programme/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Obesity/genetics ; Diet ; Feeding Behavior/physiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.<br><br>METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.<br><br>RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.<br><br>CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.},
}
@article {pmid36572855,
year = {2022},
author = {Schwarz, J and Hemmerling, J and Kabisch, N and Galbusera, L and Heinze, M and von Peter, S and Wolff, J},
title = {Equal access to outreach mental health care? Exploring how the place of residence influences the use of intensive home treatment in a rural catchment area in Germany.},
journal = {BMC psychiatry},
volume = {22},
number = {1},
pages = {826},
pmid = {36572855},
issn = {1471-244X},
mesh = {Humans ; *Mental Health ; Ambulatory Care ; *Community Mental Health Services ; Catchment Area, Health ; Germany ; Health Services Accessibility ; },
abstract = {BACKGROUND: Internationally, intensive psychiatric home treatment has been increasingly implemented as a community-based alternative to inpatient admission. Since 2018, the so-called Inpatient Equivalent Home Treatment (IEHT; German: "Stationsäquivalente Behandlung", short: "StäB") has been introduced as a particularly intensive form of home treatment that provides at least one daily treatment contact in the service users' (SU) home environment. Prior research shows that this can be challenging in rural catchment areas. Our paper investigates to which extent the location of the SU home location within the catchment area as well as the distance between the home and the clinic influence the utilisation of inpatient treatment compared to IEHT.<br><br>METHOD: Routine data of one psychiatric hospital in the federal state of Brandenburg in Germany were analysed for the observational period 07/2018-06/2021. Two comparison groups were formed: SU receiving inpatient treatment and SU receiving IEHT. The SU places of residence were respectively anonymised and converted into geo-coordinates. A geographic information system (GIS) was used to visualise the places of residence, and car travel distances as well as travel times to the clinic were determined. Spatial analyses were performed to show the differences between comparison groups. In a more in-depth analysis, the proximity of SU residences to each other was examined as an indicator of possible clustering.<br><br>RESULTS: During the observational period, the location of 687 inpatient and 140 IEHT unique SU were mapped using the GIS. SU receiving treatment resided predominantly within the catchment area, and this proportion was slightly higher for SU receiving IEHT than for those treated in inpatient setting (95.3% vs. 84.7%). In the catchment area, the geographical distribution of SU place of residence was similar in the two groups. There was a general higher service provision in the more densely populated communities close to Berlin. SU with residence in peripheral communities were mainly treated within the inpatient setting. The mean travel times and distances to the place of residence only differed minimally between the two groups of SU (p&#x2009;>&#x2009;0.05). The places of residence of SU treated with IEHT were located in greater proximity to each other than those of SU treated in inpatient setting (p&#x2009;<&#x2009;0.1).<br><br>CONCLUSION: In especially peripheral parts of the examined catchment area, it may be more difficult to have access to IEHT rather than to inpatient services. The results raise questions regarding health equity and the planning of health care services and have important implications for the further development of intensive home treatment. Telehealth interventions such as blended-care approaches and an increase of flexibility in treatment intensity, e.g. eliminating the daily visit requirement, could ease the implementation of intensive home treatment especially in rural areas.},
}
@article {pmid36572749,
year = {2022},
author = {Kon, T and Fukuta, K and Chen, Z and Kon-Nanjo, K and Suzuki, K and Ishikawa, M and Tanaka, H and Burgess, SM and Noguchi, H and Toyoda, A and Omori, Y},
title = {Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1404},
pmid = {36572749},
issn = {2399-3642},
mesh = {Animals ; *Goldfish/genetics ; *Transcriptome ; Genome ; Evolution, Molecular ; Gene Expression Profiling ; },
abstract = {The recent whole-genome duplication (WGD) in goldfish (Carassius auratus) approximately 14 million years ago makes it a valuable model for studying gene evolution during the early stages after WGD. We analyzed the transcriptome of the goldfish retina at the level of single-cell (scRNA-seq) and open chromatin regions (scATAC-seq). We identified a group of genes that have undergone dosage selection, accounting for 5% of the total 11,444 ohnolog pairs. We also identified 306 putative sub/neo-functionalized ohnolog pairs that are likely to be under cell-type-specific genetic variation at single-cell resolution. Diversification in the expression patterns of several ohnolog pairs was observed in the retinal cell subpopulations. The single-cell level transcriptome analysis in this study uncovered the early stages of evolution in retinal cell of goldfish after WGD. Our results provide clues for understanding the relationship between the early stages of gene evolution after WGD and the evolution of diverse vertebrate retinal functions.},
}
@article {pmid36566315,
year = {2022},
author = {Dualib, PM and Fernandes, G and Taddei, CR and Carvalho, CRS and Sparvoli, LG and Bittencourt, C and Silva, IT and Mattar, R and Ferreira, SRG and Dib, SA and de Almeida-Pititto, B},
title = {The gut microbiome of obese postpartum women with and without previous gestational diabetes mellitus and the gut microbiota of their babies.},
journal = {Diabetology &amp; metabolic syndrome},
volume = {14},
number = {1},
pages = {194},
pmid = {36566315},
issn = {1758-5996},
support = {2018/14795-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/14795-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
abstract = {BACKGROUND: The incidence of gestational diabetes mellitus (GDM) is increasing worldwide, and has been associated with some changes in the gut microbiota. Studies have shown that the maternal gut microbiota pattern with hyperglycemia can be transmitted to the offspring. The study aimed to evaluate the gut microbiota of obese postpartum women with and without previous GDM and their offspring.<br><br>METHODS: We evaluated a total of 84 puerperal women who had (n&#x2009;=&#x2009;40) or not GDM (n&#x2009;=&#x2009;44), and their infants were also included. Stool samples were obtained 2-6&#xa0;months after delivery. The molecular profile of the fecal microbiota was obtained by sequencing V4 region of 16S rRNA gene (Illumina[&#xae;] MiSeq).<br><br>RESULTS: We found that the gut microbiota structures of the puerperal women and their infants were similar. Stratifying according to the type of delivery, the relative abundance of Victivallis genus was higher in women who had natural delivery. Exposure to exclusive breastfeeding was associated with a greater abundance of Bacteroides and Staphylococcus. The differential abundance test showed correlations to clinical and laboratory parameters. This work showed no difference in the microbiota of obese puerperal women with and without GDM and their offspring. However, breastfeeding contributed to the ecological succession of the intestinal microbiota of the offspring.<br><br>CONCLUSION: This work can contribute to understanding the potential effects of GDM and early life events on the gut microbiome of mothers and their offspring and its possible role in metabolism later in life.},
}
@article {pmid36557752,
year = {2022},
author = {Schalli, M and Inwinkl, SM and Platzer, S and Baumert, R and Reinthaler, FF and Ofner-Kopeinig, P and Haas, D},
title = {Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources.},
journal = {Microorganisms},
volume = {10},
number = {12},
pages = {},
pmid = {36557752},
issn = {2076-2607},
abstract = {Background microorganism growth on Chromogenic Coliform Agar (CCA) can be challenging. For this reason, a new alternative method with a Cefsulodin/Vancomycin (CV)-supplemented CCA should be developed in this study. CCA supplemented with CV was validated according to ÖNORM EN ISO 16140-4:2021 using water from natural sources in Styria, Austria. Results show that the alternative method using the supplemented CCA has similar values in relation to sensitivity (82.2%), specificity (98.6%) and higher selectivity (59%) compared to the reference method. Repeatability and reproducibility were acceptable for the alternative method and showed similar results with the reference method. The alternative method shows a very low false positive rate and a low false negative rate paired with good performance regarding the inclusion study. The exclusion study shows the advantage of our method by suppressing background microorganisms and facilitating the process of enumeration of Escherichia coli and other coliform bacteria on CCA plates. Aeromonas hydrophila and Pseudomonas aeruginosa growth was inhibited using the supplement. To conclude, the coliform CV selective supplement combined with CCA is an appropriate tool for coliform bacteria detection in water samples.},
}
@article {pmid36554991,
year = {2022},
author = {Xue, Y and Lin, C and Wang, Y and Liu, W and Wan, F and Zhang, Y and Ji, L},
title = {Predicting Climate Change Effects on the Potential Distribution of Two Invasive Cryptic Species of the Bemisia tabaci Species Complex in China.},
journal = {Insects},
volume = {13},
number = {12},
pages = {},
pmid = {36554991},
issn = {2075-4450},
support = {WX145-CAS-WX2021PY-0202//14th Five-year Network Security and Informatization Plan of Chinese Academy of Sciences/ ; XDA19050200//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) are two invasive cryptic species of the Bemisia tabaci species complex (Hemiptera: Aleyrodidae) that cause serious damage to agricultural and horticultural crops worldwide. To explore the possible impact of climate change on their distribution, the maximum entropy (MaxEnt) model was used to predict the potential distribution ranges of MEAM1 and MED in China under current and four future climate scenarios, using shared socioeconomic pathways (SSPs), namely SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5, over four time periods (2021-2040, 2041-2060, 2061-2080, and 2081-2100). The distribution ranges of MEAM1 and MED were extensive and similar in China under current climatic conditions, while their moderately and highly suitable habitat ranges differed. Under future climate scenarios, the areas of suitable habitat of different levels for MEAM1 and MED were predicted to increase to different degrees. However, the predicted expansion of suitable habitats varied between them, suggesting that these invasive cryptic species respond differently to climate change. Our results illustrate the difference in the effects of climate change on the geographical distribution of different cryptic species of B. tabaci and provide insightful information for further forecasting and managing the two invasive cryptic species in China.},
}
@article {pmid36554882,
year = {2022},
author = {Deng, F and Yang, Y and Zhao, E and Xu, N and Li, Z and Zheng, P and Han, Y and Gong, J},
title = {Urban Heat Island Intensity Changes in Guangdong-Hong Kong-Macao Greater Bay Area of China Revealed by Downscaling MODIS LST with Deep Learning.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {24},
pages = {},
pmid = {36554882},
issn = {1660-4601},
mesh = {Humans ; Macau ; Hong Kong ; Cities ; *Hot Temperature ; Temperature ; *Deep Learning ; China ; Environmental Monitoring/methods ; },
abstract = {The urban heat island (UHI) effect caused by urbanization negatively impacts the ecological environment and human health. It is crucial for urban planning and social development to monitor the urban heat island effect and study its mechanism. Due to spatial and temporal resolution limitations, existing land surface temperature (LST) data obtained from remote sensing data is challenging to meet the long-term fine-scale surface temperature mapping requirement. Given the above situation, this paper introduced the ResNet-based surface temperature downscaling method to make up for the data deficiency and applied it to the study of thermal environment change in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) from 2000 to 2020. The results showed (1) the ResNet-based surface temperature downscaling method achieves high accuracy (R[2] above 0.85) and is suitable for generating 30 m-resolution surface temperature data from 1 km data; (2) the area of severe heat islands in the GBA continued to increase, increasing by 7.13 times within 20 years; and (3) except for Hong Kong and Macau, the heat island intensity of most cities showed an apparent upward trend, especially the cities with rapid urban expansion such as Guangzhou, Zhongshan, and Foshan. In general, the evolution of the heat island in the GBA diverges from the central urban area to the surrounding areas, with a phenomenon of local aggregation and the area of the intense heat island in the Guangzhou-Foshan metropolitan area is the largest. This study can enrich the downscaling research methods of surface temperature products in complex areas with surface heterogeneity and provide a reference for urban spatial planning in the GBA.},
}
@article {pmid36554755,
year = {2022},
author = {Chen, D and Xiong, K and Zhang, J},
title = {Progress on the Integrity Protection in the Natural World Heritage Site and Agroforestry Development in the Buffer Zone: An Implications for the World Heritage Karst.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {24},
pages = {},
pmid = {36554755},
issn = {1660-4601},
mesh = {*Conservation of Natural Resources ; China ; Databases, Factual ; *Knowledge ; },
abstract = {In the face of increasing development pressure, how to fulfill the obligations under the World Cultural and Natural Heritage Convention and maintain the integrity of the Natural World Heritage Site (NWHS) is a major problem to be solved at present. Agroforestry (AF) development in the buffer zone maintains the integrity of NWHS and promotes sustainable ecological and economic development in the buffer zone. Still, few studies on the knowledge system of integrity protection of NWHS and AF development in the buffer zone research have been conducted. To fill this gap, this study conducts a systematic literature review based on 128 related articles retrieved from the Web of Science (WoS) database and the China National Knowledge Infrastructure (CNKI) database. Firstly, quantitative studies were conducted to analyze the annual numbers, content and study regions of the published literature. Secondly, the main research progress and achievements of integrity protection of WNHS and AF development in the buffer zone are classified and summarized. On this basis, this paper proposed key scientific issues that remain to be addressed in future, as well as exploring the implications for the World Heritage (WH) karst. This study is a scientific reference for the balanced development of NWHS integrity protection and AF in the buffer zone.},
}
@article {pmid36554342,
year = {2022},
author = {Dantas, JDC and Marinho, CDSR and Pinheiro, YT and Silva, RARD},
title = {Temporal Trend of Gestational Syphilis between 2008 and 2018 in Brazil: Association with Socioeconomic and Health Care Factors.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {24},
pages = {},
pmid = {36554342},
issn = {1660-4601},
mesh = {Pregnancy ; Female ; Humans ; *Syphilis/epidemiology ; *Pregnancy Complications, Infectious/epidemiology ; *Syphilis, Congenital/epidemiology/prevention &amp; control ; Brazil/epidemiology ; Literacy ; Delivery of Health Care ; Socioeconomic Factors ; },
abstract = {The increased number of cases in recent years has turned syphilis into a global public health problem. In 2020, 115,371 cases of acquired syphilis were reported (detection rate of 54.5 cases/100,000 inhabitants) in Brazil. In that same period, the country notified 61,441 cases of gestational syphilis (detection rate of 21.6 per 1000 live births). The number of syphilis cases points to the need to reinforce surveillance, prevention, and infection control actions, which is a worrying scenario for government organizations. This study aims to describe the temporal trend of gestational syphilis from 2008 to 2018 in Brazilian regions and to associate its detection rate with socioeconomic and health care indicators. We conducted an ecological study of temporal trends using secondary data from the Department of Informatics of the Unified Health System. The temporal trend was analyzed using the Joinpoint Regression program. The annual percent change (APC) and 95% confidence intervals (95%CI) were estimated and tested; statistical significance was assessed using the Monte Carlo permutation test. Correlations were assessed using Pearson's correlation coefficient, and statistical significance was calculated using Pearson's product-moment correlation. The gestational syphilis detection rate increased between 2008 and 2018. The South region showed the greatest trend, whereas the Midwest region presented the lowest trend. The following variables were significantly correlated with the gestational syphilis detection rate: Municipal Human Development Index, illiteracy rate, percentage of primary health care coverage, and proportion of doctors, nurses, and basic health units per inhabitant. Health policies are needed to mitigate social vulnerabilities and strengthen primary health care.},
}
@article {pmid36552295,
year = {2022},
author = {Sokhansanj, BA and Zhao, Z and Rosen, GL},
title = {Interpretable and Predictive Deep Neural Network Modeling of the SARS-CoV-2 Spike Protein Sequence to Predict COVID-19 Disease Severity.},
journal = {Biology},
volume = {11},
number = {12},
pages = {},
pmid = {36552295},
issn = {2079-7737},
support = {1919691//National Science Foundation/ ; 1936782//National Science Foundation/ ; 2107108//National Science Foundation/ ; },
abstract = {Through the COVID-19 pandemic, SARS-CoV-2 has gained and lost multiple mutations in novel or unexpected combinations. Predicting how complex mutations affect COVID-19 disease severity is critical in planning public health responses as the virus continues to evolve. This paper presents a novel computational framework to complement conventional lineage classification and applies it to predict the severe disease potential of viral genetic variation. The transformer-based neural network model architecture has additional layers that provide sample embeddings and sequence-wide attention for interpretation and visualization. First, training a model to predict SARS-CoV-2 taxonomy validates the architecture's interpretability. Second, an interpretable predictive model of disease severity is trained on spike protein sequence and patient metadata from GISAID. Confounding effects of changing patient demographics, increasing vaccination rates, and improving treatment over time are addressed by including demographics and case date as independent input to the neural network model. The resulting model can be interpreted to identify potentially significant virus mutations and proves to be a robust predctive tool. Although trained on sequence data obtained entirely before the availability of empirical data for Omicron, the model can predict the Omicron's reduced risk of severe disease, in accord with epidemiological and experimental data.},
}
@article {pmid36547621,
year = {2022},
author = {Jamal, QMS and Ahmad, V},
title = {Lysinibacilli: A Biological Factories Intended for Bio-Insecticidal, Bio-Control, and Bioremediation Activities.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {12},
pages = {},
pmid = {36547621},
issn = {2309-608X},
support = {QU-IF-03-01-27931//The Deputyship for Research &amp; Innovation, Ministry of Education, Saudi Arabia/ ; },
abstract = {Microbes are ubiquitous in the biosphere, and their therapeutic and ecological potential is not much more explored and still needs to be explored more. The bacilli are a heterogeneous group of Gram-negative and Gram-positive bacteria. Lysinibacillus are dominantly found as motile, spore-forming, Gram-positive bacilli belonging to phylum Firmicutes and the family Bacillaceae. Lysinibacillus species initially came into light due to their insecticidal and larvicidal properties. Bacillus thuringiensis, a well-known insecticidal Lysinibacillus, can control many insect vectors, including a malarial vector and another, a Plasmodium vector that transmits infectious microbes in humans. Now its potential in the environment as a piece of green machinery for remediation of heavy metal is used. Moreover, some species of Lysinibacillus have antimicrobial potential due to the bacteriocin, peptide antibiotics, and other therapeutic molecules. Thus, this review will explore the biological disease control abilities, food preservative, therapeutic, plant growth-promoting, bioremediation, and entomopathogenic potentials of the genus Lysinibacillus.},
}
@article {pmid36545372,
year = {2022},
author = {Ruttoh, RC and Obiero, JPO and Omuto, CT and Tanui, L},
title = {Assessment of Land Cover and Land Use Change Dynamics in Kibwezi Watershed, Kenya.},
journal = {TheScientificWorldJournal},
volume = {2022},
number = {},
pages = {3944810},
pmid = {36545372},
issn = {1537-744X},
mesh = {Kenya ; *Geographic Information Systems ; *Forests ; Soil ; Trees ; Environmental Monitoring/methods ; Conservation of Natural Resources ; },
abstract = {Land use and land cover (LULC) parameters influence the hydrological and ecological processes taking place in a watershed. Understanding the changes in LULC is essential in the planning and development of management strategies for water resources. The purpose of the study was to detect changes in LULC in the Kibwezi watershed in Kenya, using geospatial approaches. Supervised and unsupervised classification techniques using remote sensing (RS) and geographical information system (GIS) were used to process Landsat imagery for 1999, 2009, and 2019 while ERDAS IMAGINE™ 14 and MS Excel software were used to derive change detection, and the Soil and Water Assessment Tool (SWAT) model was used to delineate the watershed using an in-built watershed delineation tool. The watershed was classified into ten major LULC classes, namely cropland (rainfed), cropland (irrigated), cropland (perennial), crop and shrubs/trees, closed shrublands, open shrubland, shrub grasslands, wooded shrublands, riverine woodlands, and built-up land. The results showed that LULC under shrub grassland, urban areas, and crops and shrubs increased drastically by 552.5%, 366.2%, and 357.1% respectively between 1999 and 2019 with an annual increase of 35.55%, 35.38%, and 33.86% per annum. The area under open shrubland and closed shrubland declined by73.7%, and 30.4% annually. These LULC transformations pose a negative impact on the watershed resources. There is therefore a need for proper management of the watershed for sustainable socio-economic development of the Kibwezi area.},
}
@article {pmid36543718,
year = {2023},
author = {Liew, F and Talwar, S and Cross, A and Willett, BJ and Scott, S and Logan, N and Siggins, MK and Swieboda, D and Sidhu, JK and Efstathiou, C and Moore, SC and Davis, C and Mohamed, N and Nunag, J and King, C and Thompson, AAR and Rowland-Jones, SL and Docherty, AB and Chalmers, JD and Ho, LP and Horsley, A and Raman, B and Poinasamy, K and Marks, M and Kon, OM and Howard, L and Wootton, DG and Dunachie, S and Quint, JK and Evans, RA and Wain, LV and Fontanella, S and de Silva, TI and Ho, A and Harrison, E and Baillie, JK and Semple, MG and Brightling, C and Thwaites, RS and Turtle, L and Openshaw, PJM and , and , },
title = {SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination.},
journal = {EBioMedicine},
volume = {87},
number = {},
pages = {104402},
pmid = {36543718},
issn = {2352-3964},
support = {MR/V028448/1/MRC_/Medical Research Council/United Kingdom ; MR/V027859/1/MRC_/Medical Research Council/United Kingdom ; 206330/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; MR/S020039/1/MRC_/Medical Research Council/United Kingdom ; COV/GLA/20/05/CSO_/Chief Scientist Office/United Kingdom ; MR/W006111/1/MRC_/Medical Research Council/United Kingdom ; G0801952/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; G1000191/MRC_/Medical Research Council/United Kingdom ; MR/W020610/1/MRC_/Medical Research Council/United Kingdom ; G0700859/MRC_/Medical Research Council/United Kingdom ; MC_PC_20031/MRC_/Medical Research Council/United Kingdom ; MR/X009297/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20060/MRC_/Medical Research Council/United Kingdom ; G0501425/MRC_/Medical Research Council/United Kingdom ; MC_PC_20002/MRC_/Medical Research Council/United Kingdom ; MC_UU_00036/2/MRC_/Medical Research Council/United Kingdom ; CH/16/1/32013/BHF_/British Heart Foundation/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; MC_UU_00008/5/MRC_/Medical Research Council/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; CH/F/21/90010/BHF_/British Heart Foundation/United Kingdom ; MC_PC_20016/MRC_/Medical Research Council/United Kingdom ; MC_PC_20058/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adult ; Humans ; *SARS-CoV-2 ; *COVID-19/prevention &amp; control ; COVID-19 Vaccines ; Follow-Up Studies ; Vaccination ; Hospitalization ; Immunoglobulin A ; Immunoglobulin G ; Antibodies, Viral ; Antibodies, Neutralizing ; },
abstract = {BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced.<br><br>METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data.<br><br>FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p&#xa0;<&#xa0;0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p&#xa0;<&#xa0;0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p&#xa0;<&#xa0;0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p&#xa0;=&#xa0;0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R&#xa0;=&#xa0;0.05, p&#xa0;=&#xa0;0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination.<br><br>INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity.<br><br>FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript.},
}
@article {pmid36538553,
year = {2022},
author = {Vukašinović, D and Maksimović, M and Tanasković, S and Marinković, J and Gajin, P and Ilijevski, N and Vasiljević, N and Radak, &#x110; and Vlajinac, H},
title = {Body mass index and early outcomes after carotid endarterectomy.},
journal = {PloS one},
volume = {17},
number = {12},
pages = {e0278298},
pmid = {36538553},
issn = {1932-6203},
mesh = {Male ; Humans ; *Endarterectomy, Carotid/adverse effects ; Body Mass Index ; Cohort Studies ; Overweight/complications ; Treatment Outcome ; Risk Factors ; Retrospective Studies ; *Stroke/complications ; Hemorrhage/etiology ; Obesity/complications ; *Diabetes Mellitus, Type 2/complications ; *Carotid Stenosis/surgery ; Risk Assessment ; },
abstract = {As the existing data on the correlation of adiposity with adverse outcomes of carotid endarterectomy (CEA) are inconsistent, the aim of the present study is to examine the correlation of an increased body mass index with 30-day complications after carotid endarterectomy. The cohort study comprises 1586 CEAs, performed at the Clinic for Vascular Surgery in Belgrade, from 2012-2017. Out of them, 550 CEAs were performed in patients with normal body mass index (18.5-24.9), 750 in overweight (25.0-29.9), and 286 in obese (≥30) patients. The association of overweight and obesity with early outcomes of carotid endarterectomy was assessed using univariate and multivariate logistic regression analysis. Overweight patients, in whom CEAs were performed, were significantly more frequently males, compared to normal weight patients-Odds Ratio (OR) 1.51 (95% confidence interval- 1.19-1.89). Moreover, overweight patients significantly more frequently had non-insulin-dependent diabetes mellitus-OR 1.44 (1.09-1.90), and more frequently used ACEI in hospital discharge therapy-OR 1.41 (1.07-1.84) than normal weight patients. Additionally, the CEAs in them were less frequently followed by bleedings-OR 0.37 (0.16-0.83). Compared to normal weight patients, obese patients were significantly younger-OR 0.98 (0.96-0.99), and with insulin-dependent and non-insulin-dependent diabetes mellitus-OR 1.83 (1.09-3.06) and OR 2.13 (1.50-3.01) respectively. They also more frequently had increased triglyceride levels-OR 1.36 (1.01-1.83), and more frequently used oral anticoagulants in therapy before the surgery-OR 2.16 (1.11-4.19). According to the results obtained, overweight and obesity were not associated with an increased death rate, transient ischemic attack (TIA), stroke, myocardial infarction, or with minor complications, and the need for reoperation after carotid endarterectomy. The only exception was bleeding, which was significantly less frequent after CEA in overweight compared to normal weight patients.},
}
@article {pmid36529723,
year = {2022},
author = {Liu, X and Lu, X and Yang, S and Liu, Y and Wang, W and Wei, X and Ji, H and Zhang, B and Xin, W and Wen, J and Wang, J and Chen, Q},
title = {Role of exogenous abscisic acid in freezing tolerance of mangrove Kandelia obovata under natural frost condition at near 32[°]N.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {593},
pmid = {36529723},
issn = {1471-2229},
mesh = {*Rhizophoraceae ; Abscisic Acid/metabolism ; Antioxidants/metabolism ; Freezing ; Proline/metabolism ; Starch/metabolism ; Sucrose/metabolism ; },
abstract = {BACKGROUND: Mangroves possess substantial ecological, social, and economic functions in tropical and subtropical coastal wetlands. Kandelia obovata is the most cold-resistance species among mangrove plants, with a widespread distribution in China that ranges from Sanya (18° 12' N) to Wenzhou (28° 20' N). Here, we explored the temporal variations in physiological status and transcriptome profiling of K. obovata under natural frost conditions at ~ 32[o]N, as well as the positive role of exogenous abscisic acid (ABA) in cold resistance.<br><br>RESULTS: The soluble sugar (SS) and proline (Pro) functioned under freezing stress, of which SS was more important for K. obovata. Consistently, up-regulated DEGs responding to low temperature were significantly annotated to glycometabolism, such as starch and sucrose metabolism and amino sugar and nucleotide sugar metabolism. Notably, the top 2 pathways of KEGG enrichment were phenylpropanoid biosynthesis and flavonoid biosynthesis. For the antioxidant system, POD in conjunction with CAT removed hydrogen peroxide, and CAT appeared to be more important. The up-regulated DEGs responding to low temperature and ABA were also found to be enriched in arginine and proline metabolism, starch and sucrose metabolism, and peroxisome. Moreover, ABA triggered the expression of P5CS and P5CR, but inhibited the ProDH expression, which might contribute to Pro accumulation. Interestingly, there was no significant change in malondialdehyde (MDA) content during the cold event (P&#x2009;>&#x2009;0.05), suggesting foliar application of ABA effectively alleviated the adverse effects of freezing stress on K. obovata by activating the antioxidant enzyme activity and increasing osmolytes accumulation, such as Pro, and the outcome was proportional to ABA concentration.<br><br>CONCLUSIONS: This study deepened our understanding of the physiological characters and molecular mechanisms underlying the response of K. obovata to natural frost conditions and exogenous ABA at the field level, which could provide a sound theoretical foundation for expanding mangroves plantations in higher latitudes, as well as the development coastal landscape.},
}
@article {pmid36528093,
year = {2023},
author = {Milan, M and Bernardini, I and Bertolini, C and Dalla Rovere, G and Manuzzi, A and Pastres, R and Peruzza, L and Smits, M and Fabrello, J and Breggion, C and Sambo, A and Boffo, L and Gallocchio, L and Carrer, C and Sorrentino, F and Bettiol, C and Lodi, GC and Semenzin, E and Varagnolo, M and Matozzo, V and Bargelloni, L and Patarnello, T},
title = {Multidisciplinary long-term survey of Manila clam grown in farming sites subjected to different environmental conditions.},
journal = {The Science of the total environment},
volume = {863},
number = {},
pages = {160796},
doi = {10.1016/j.scitotenv.2022.160796},
pmid = {36528093},
issn = {1879-1026},
mesh = {Animals ; *Bivalvia/metabolism ; Seafood ; Agriculture ; Genomics ; },
abstract = {In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date. In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed. Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.},
}
@article {pmid36527397,
year = {2022},
author = {Viner, A and Membe-Gadama, G and Whyte, S and Kayambo, D and Masamba, M and Martin, CJH and Magowan, B and Reynolds, RM and Stock, SJ and Freyne, B and Gadama, L},
title = {Midwife-Led Ultrasound Scanning to Date Pregnancy in Malawi: Development of a Novel Training Program.},
journal = {Journal of midwifery &amp; women's health},
volume = {67},
number = {6},
pages = {728-734},
pmid = {36527397},
issn = {1542-2011},
support = {GHR Project: 17/63/08 DIPLOMATIC collaboration//National Institute for Health Research (NIHR)/ ; },
mesh = {Female ; Pregnancy ; Humans ; *Midwifery/education ; *Nurse Midwives/education ; Malawi ; },
abstract = {The use of ultrasound to determine gestational age is fundamental to the optimum management of pregnancy and is recommended for all women by the World Health Organization. However, this modality remains unavailable to many women in low-income countries where trained practitioners are scarce. Although previous initiatives have demonstrated efficacy in training midwives and technicians to perform antenatal ultrasound, these programs have often been too long and too complex to be realistic within the specific constraints of this context, highlighting the need for a novel and pragmatic approach. We describe the development and piloting of a bespoke course to teach midwives 3 fundamental components of early antenatal ultrasound scanning: (1) to identify the number of fetuses, (2) to confirm fetal viability, and (3) to determine gestational age. Having established that 5 days is insufficient, we propose that the minimum duration required to train ultrasound-naive midwives to competency is 10 days. Our completed program therefore consists of one and one-half days of didactic teaching, followed by 8 and one-half days of supervised hands-on practical training in which trainees are assessed on their skills. This package has subsequently been successfully implemented across 6 sites in Malawi, where 28 midwives have achieved competency. By describing the processes involved in our cross-continental collaboration, we explain how unexpected challenges helped shape and improve our program, demonstrating the value of preimplementation piloting and a pragmatic and adaptive approach.},
}
@article {pmid36527232,
year = {2023},
author = {Petrén, H and Köllner, TG and Junker, RR},
title = {Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv.},
journal = {The New phytologist},
volume = {237},
number = {6},
pages = {2478-2492},
doi = {10.1111/nph.18685},
pmid = {36527232},
issn = {1469-8137},
mesh = {*Phytochemicals ; *Plants ; Ecology ; Phenotype ; Databases, Factual ; },
abstract = {Plants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds. Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds' function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures. We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and - most importantly - structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets. By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.},
}
@article {pmid36526212,
year = {2023},
author = {Zhang, Z and Fan, Y and Jiao, Z},
title = {Wetland ecological index and assessment of spatial-temporal changes of wetland ecological integrity.},
journal = {The Science of the total environment},
volume = {862},
number = {},
pages = {160741},
doi = {10.1016/j.scitotenv.2022.160741},
pmid = {36526212},
issn = {1879-1026},
mesh = {*Wetlands ; *Environmental Monitoring/methods ; Ecosystem ; Soil ; Rivers ; China ; },
abstract = {Long-term, quantitative, and dynamic monitoring of regional ecological integrity using remote sensing can provide powerful decision-making support for sustainable regional development. However, existing methods are unable to accurately evaluate the quality of the surface ecological integrity because they do not consider vegetation saturation and salinization of wetlands. In addition, the ecological fragility of wetlands is characterized by a high frequency of changes in ecological conditions over time, leading to a lack of directionality in the analysis of ecological changes over long time series. To accurately assess the surface ecological integrity, this study integrates environmental salinity (Baseline-based Soil Salinity Index, BSSI) and a new vegetation element (Improved Hyperspectral Image-based Vegetation Index, IHSVI), and proposes the wetland ecological index (WEI) for the ecological integrity assessment system. Combined with the annual ecological integrity assessment using the WEI, the Mann-Kendall test was used to obtain the nodes of long-term changes. The WEI-Mann Kendall (WEI-MK) framework indicates the direction of analysis and realizes clear long-term series change monitoring. In this study, we analyzed the spatial and temporal changes in ecological integrity in the Yellow River Delta from 1991 to 2020 based on the WEI-MK framework. The results showed that: 1) Compared with Remote Sensing-based Ecological Index (RSEI), the WEI improved the accuracy of wetland integrity evaluation to 89 %. The WEI also improved accuracy of assessments in other typical regions by approximately 10 %. 2) The selection of nodes based on the WEI-MK framework clarified the direction of environmental change analysis. The results show that although the quality of the terrestrial ecological environment has improved over the past 30 years in the Yellow River Delta, that of the marine ecological environment has gradually declined. In particular, the state of the marine ecological environment after 2016 should be of concern.},
}
@article {pmid36522390,
year = {2022},
author = {Acerbi, A and Snyder, WD and Tennie, C},
title = {The method of exclusion (still) cannot identify specific mechanisms of cultural inheritance.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {21680},
pmid = {36522390},
issn = {2045-2322},
support = {714658/ERC_/European Research Council/International ; },
mesh = {Animals ; Social Behavior ; *Social Learning ; Databases, Genetic ; *Hominidae ; *Cultural Evolution ; },
abstract = {The method of exclusion identifies patterns of distributions of behaviours and/or artefact forms among different groups, where these patterns are deemed unlikely to arise from purely genetic and/or ecological factors. The presence of such patterns is often used to establish whether a species is cultural or not-i.e. whether a species uses social learning or not. Researchers using or describing this method have often pointed out that the method cannot pinpoint which specific type(s) of social learning resulted in the observed patterns. However, the literature continues to contain such inferences. In a new attempt to warn against these logically unwarranted conclusions, we illustrate this error using a novel approach. We use an individual-based model, focused on wild ape cultural patterns-as these patterns are the best-known cases of animal culture and as they also contain the most frequent usage of the unwarranted inference for specific social learning mechanisms. We built a model that contained agents unable to copy specifics of behavioural or artefact forms beyond their individual reach (which we define as "copying"). We did so, as some of the previous inference claims related to social learning mechanisms revolve around copying defined in this way. The results of our model however show that non-copying social learning can already reproduce the defining-even iconic-features of observed ape cultural patterns detected by the method of exclusion. This shows, using a novel model approach, that copying processes are not necessary to produce the cultural patterns that are sometimes still used in an attempt to identify copying processes. Additionally, our model could fully control for both environmental and genetic factors (impossible in real life) and thus offers a new validity check for the method of exclusion as related to general cultural claims-a check that the method passed. Our model also led to new and additional findings, which we likewise discuss.},
}
@article {pmid36522346,
year = {2022},
author = {Wang, H and Harrison, SP and Li, M and Prentice, IC and Qiao, S and Wang, R and Xu, H and Mengoli, G and Peng, Y and Yang, Y},
title = {The China plant trait database version 2.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {769},
pmid = {36522346},
issn = {2052-4463},
support = {694481 GC2.0//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 787203 REALM//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {China ; Ecology ; *Ecosystem ; *Plants ; Databases, Factual ; },
abstract = {Plant functional traits represent adaptive strategies to the environment, linked to biophysical and biogeochemical processes and ecosystem functioning. Compilations of trait data facilitate research in multiple fields from plant ecology through to land-surface modelling. Here we present version 2 of the China Plant Trait Database, which contains information on morphometric, physical, chemical, photosynthetic and hydraulic traits from 1529 unique species in 140 sites spanning a diversity of vegetation types. Version 2 has five improvements compared to the previous version: (1) new data from a 4-km elevation transect on the edge of Tibetan Plateau, including alpine vegetation types not sampled previously; (2) inclusion of traits related to hydraulic processes, including specific sapwood conductance, the area ratio of sapwood to leaf, wood density and turgor loss point; (3) inclusion of information on soil properties to complement the existing data on climate and vegetation (4) assessments and flagging the reliability of individual trait measurements; and (5) inclusion of standardized templates for systematical field sampling and measurements.},
}
@article {pmid36520387,
year = {2023},
author = {Melayah, D and Bontemps, Z and Bruto, M and Nguyen, A and Oger, P and Hugoni, M},
title = {Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2605},
number = {},
pages = {17-35},
pmid = {36520387},
issn = {1940-6029},
mesh = {*Ecosystem ; *Archaea/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.},
}
@article {pmid36519374,
year = {2023},
author = {Seidu, S and Gillies, C and Zaccardi, F and Reeves, K and Gallier, S and Khunti, K},
title = {Temporal trends in admissions for atrial fibrillation and severe bleeding in England: an 18-year longitudinal analysis.},
journal = {Scandinavian cardiovascular journal : SCJ},
volume = {57},
number = {1},
pages = {40-47},
doi = {10.1080/14017431.2022.2156597},
pmid = {36519374},
issn = {1651-2006},
mesh = {Humans ; *Atrial Fibrillation/diagnosis/epidemiology/therapy ; Anticoagulants/therapeutic use ; Administration, Oral ; Risk Factors ; Treatment Outcome ; Time Factors ; Hemorrhage/diagnosis/epidemiology ; *Stroke ; },
abstract = {Objective. Temporal trends in admissions for atrial fibrillation (AF) and severe bleeding associated with AF vary worldwide. We aimed to explore their temporal trends in England and their relation to the introduction of DOACs in 2014 in the UK. Design. This longitudinal ecological study utilised aggregated data that was extracted from the Hospital Episode Statistics database, which captured annual admissions for AF and severe bleeding associated with AF between 2001 and 2018. Trends in admissions over the study period and across age groups, gender and regions in England were assessed. Results. In total, there were 11,292,177 admissions for AF and 324,851 admissions for severe bleeding associated with AF. There was a steady rise in admissions for AF from 2001 to 2017 (204,808 to 1,109,295; p for trend<.001). A similar trend was observed for severe bleeding (4940 to 30,169; p for trend <.001), but the increase dropped slightly between 2013 and 2014 and continued thereafter. Conclusions. There was a rise in admissions for AF and severe bleeding in England between 2001 and 2018. There is little evidence that the slight drop in admissions for severe bleeding between 2013 and 2014 may have been caused by the introduction of DOACs in 2014. Contributors to these trends need urgent exploration.},
}
@article {pmid36517756,
year = {2022},
author = {Zhang, H and Yao, G and He, M},
title = {Transcriptome analysis of gene expression profiling from the deep sea in situ to the laboratory for the cold seep mussel Gigantidas haimaensis.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {828},
pmid = {36517756},
issn = {1471-2164},
mesh = {Animals ; *Ecosystem ; *Mytilidae/genetics ; Gene Expression Profiling ; Transcriptome ; Gene Ontology ; },
abstract = {BACKGROUND: The deep-sea mussel Gigantidas haimaensis is a representative species from the Haima cold seep ecosystem in the South China Sea that establishes endosymbiosis with chemotrophic bacteria. During long-term evolution, G. haimaensis has adapted well to the local environment of cold seeps. Until now, adaptive mechanisms responding to environmental stresses have remained poorly understood.<br><br>RESULTS: In this study, transcriptomic analysis was performed for muscle tissue of G. haimaensis in the in situ environment (MH) and laboratory environment for 0&#xa0;h (M0), 3&#xa0;h (M3) and 9&#xa0;h (M9), and 187,368 transcript sequences and 22,924 annotated differentially expressed genes (DEGs) were generated. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, these DEGs were enriched with a broad spectrum of biological processes and pathways, including those associated with antioxidants, apoptosis, chaperones, immunity and metabolism. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum and metabolism were the most affected metabolic pathways. These results may imply that G. haimaensis struggles to support the life response to environmental change by changing gene expression profiles.<br><br>CONCLUSION: The present study provides a better understanding of the biological responses and survival strategies of the mussel G. haimaensis from deep sea in situ to the laboratory environment.},
}
@article {pmid36512954,
year = {2023},
author = {Kim, B and Barrington, WE and Dobra, A and Rosenberg, D and Hurvitz, P and Belza, B},
title = {Mediating role of walking between perceived and objective walkability and cognitive function in older adults.},
journal = {Health &amp; place},
volume = {79},
number = {},
pages = {102943},
pmid = {36512954},
issn = {1873-2054},
support = {DP1 AG069874/AG/NIA NIH HHS/United States ; U01 AG006781/AG/NIA NIH HHS/United States ; U19 AG066567/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Aged ; *Exercise ; Cross-Sectional Studies ; *Environment Design ; Residence Characteristics ; Walking ; Cognition ; },
abstract = {The aim of this study was to examine the role of walking in explaining associations between perceived and objective measures of walkability and cognitive function among older adults. The study employed a cross-sectional design analyzing existing data. Data were obtained from the Adult Changes in Thought Activity Monitor study. Cognitive function and perceived walkability were measured by a survey. Objective walkability was measured using geographic information systems (GIS). Walking was measured using an accelerometer. We tested the mediating relationship based on 1,000 bootstrapped samples. Perceived walkability was associated with a 0.04 point higher cognitive function score through walking (p = 0.006). The mediating relationship accounted for 34% of the total relationship between perceived walkability and cognitive function. Walking did not have a significant indirect relationship on the association between objective walkability and cognitive function. Perceived walkability may be more relevant to walking behavior than objective walkability among older adults. Greater levels of perceived walkability may encourage older adults to undertake more walking, and more walking may in turn improve cognitive function in older adults.},
}
@article {pmid36512230,
year = {2023},
author = {Barlow, LD and Maciejowski, W and More, K and Terry, K and Vargová, R and Záhonová, K and Dacks, JB},
title = {Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2557},
number = {},
pages = {431-452},
pmid = {36512230},
issn = {1940-6029},
mesh = {*Amoeba/genetics ; Reproducibility of Results ; Genomics/methods ; Biological Evolution ; Golgi Apparatus/metabolism ; Computational Biology/methods ; },
abstract = {Taking an evolutionary approach to cell biology can yield important new information about how the cell works and how it evolved to do so. This is true of the Golgi apparatus, as it is of all systems within the cell. Comparative genomics is one of the crucial first steps to this line of research, but comes with technical challenges that must be overcome for rigor and robustness. We here introduce AMOEBAE, a workflow for mid-range scale comparative genomic analyses. It allows for customization of parameters, queries, and taxonomic sampling of genomic and transcriptomics data. This protocol article covers the rationale for an evolutionary approach to cell biological study (i.e., when would AMOEBAE be useful), how to use AMOEBAE, and discussion of limitations. It also provides an example dataset, which demonstrates that the Golgi protein AP4 Epsilon is present as the sole retained subunit of the AP4 complex in basidiomycete fungi. AMOEBAE can facilitate comparative genomic studies by balancing reproducibility and speed with user-input and interpretation. It is hoped that AMOEBAE or similar tools will encourage cell biologists to incorporate an evolutionary context into their research.},
}
@article {pmid36504957,
year = {2022},
author = {Zhang, Y and Liu, S and Wang, Y and Wang, Y},
title = {Causal relationship between particulate matter 2.5 and hypothyroidism: A two-sample Mendelian randomization study.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {1000103},
pmid = {36504957},
issn = {2296-2565},
mesh = {*Particulate Matter/adverse effects ; *Genome-Wide Association Study ; Analysis of Variance ; Databases, Factual ; Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Epidemiological surveys have found that particulate matter 2.5 (PM2.5) plays an important role in hypothyroidism. However, due to the methodological limitations of traditional observational studies, it is difficult to make causal inferences. In the present study, we assessed the causal association between PM2.5 concentrations and risk of hypothyroidism using two-sample Mendelian randomization (TSMR).<br><br>METHODS: We performed TSMR by using aggregated data from genome-wide association studies (GWAS) on the IEU Open GWAS database. We identified seven single nucleotide polymorphisms (SNPs) associated with PM2.5 concentrations as instrumental variables (IVs). We used inverse-variance weighting (IVW) as the main analytical method, and we selected MR-Egger, weighted median, simple model, and weighted model methods for quality control.<br><br>RESULTS: MR analysis showed that PM2.5 has a positive effect on the risk of hypothyroidism: An increase of 1 standard deviation (SD) in PM2.5 concentrations increases the risk of hypothyroidism by ~10.0% (odds ratio 1.10, 95% confidence interval 1.06-1.13, P = 2.93E-08, by IVW analysis); there was no heterogeneity or pleiotropy in the results.<br><br>CONCLUSION: In conclusion, increased PM2.5 concentrations are associated with an increased risk of hypothyroidism. This study provides evidence of a causal relationship between PM2.5 and the risk of hypothyroidism, so air pollution control may have important implications for the prevention of hypothyroidism.},
}
@article {pmid36503572,
year = {2022},
author = {Yan, X and Si, H and Zhu, Y and Li, S and Han, Y and Liu, H and Du, R and Pope, PB and Qiu, Q and Li, Z},
title = {Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {222},
pmid = {36503572},
issn = {2049-2618},
support = {32122083//National Natural Science Foundation of China/ ; 054575 - SuPAcow//Novo Nordisk Fonden/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Multiomics ; *Deer/microbiology ; Rumen/microbiology ; Fatty Acids, Volatile ; },
abstract = {BACKGROUND: The gastrointestinal tract (GIT) microbiome of ruminants and its metabolic repercussions vastly influence host metabolism and growth. However, a complete understanding of the bidirectional interactions that occur across the host-microbiome axis remains elusive, particularly during the critical development stages at early life. Here, we present an integrative multi-omics approach that simultaneously resolved the taxonomic and functional attributes of microbiota from five GIT regions as well as the metabolic features of the liver, muscle, urine, and serum in sika deer (Cervus nippon) across three key early life stages.<br><br>RESULTS: Within the host, analysis of metabolites over time in serum, urine, and muscle (longissimus lumborum) showed that changes in the fatty acid profile were concurrent with gains in body weight. Additional host transcriptomic and metabolomic analysis revealed that fatty acid &#x3b2;-oxidation and metabolism of tryptophan and branched chain amino acids play important roles in regulating hepatic metabolism. Across the varying regions of the GIT, we demonstrated that a complex and variable community of bacteria, viruses, and archaea colonized the GIT soon after birth, whereas microbial succession was driven by the cooperative networks of hub populations. Furthermore, GIT volatile fatty acid concentrations were marked by increased microbial metabolic pathway abundances linked to mannose (rumen) and amino acids (colon) metabolism. Significant functional shifts were also revealed across varying GIT tissues, which were dominated by host fatty acid metabolism associated with reactive oxygen species in the rumen epithelium, and the intensive immune response in both small and large intestine. Finally, we reveal a possible contributing role of necroptosis and apoptosis in enhancing ileum and colon epithelium development, respectively.<br><br>CONCLUSIONS: Our findings provide a comprehensive view for the involved mechanisms in the context of GIT microbiome and ruminant metabolic growth at early life. Video Abstract.},
}
@article {pmid36498115,
year = {2022},
author = {Li, W and Liu, R and Sun, L and Guo, Z and Gao, J},
title = {An Investigation of Employees' Intention to Comply with Information Security System-A Mixed Approach Based on Regression Analysis and fsQCA.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {23},
pages = {},
pmid = {36498115},
issn = {1660-4601},
support = {2019YFB1704103//Open Ecological Cloud ERP Platform/ ; },
mesh = {Humans ; *Intention ; *Information Systems ; Self Efficacy ; Motivation ; Regression Analysis ; },
abstract = {Employee security compliance behavior has become an important safeguard to protect the security of corporate information assets. Focusing on human factors, this paper discusses how to regulate and guide employees' compliance with information security systems through effective methods. Based on protection motivation theory (PMT), a model of employees' intention to comply with the information security system was constructed. A questionnaire survey was adopted to obtain 224 valid data points, and SPSS 26.0 was applied to verify the hypotheses underlying the research model. Then, based on the results of a regression analysis, fuzzy set qualitative comparative analysis (fsQCA) was used to explore the conditional configurations that affect employees' intention to comply with the information security system from a holistic perspective. The empirical results demonstrated that perceived severity, perceived vulnerability, response efficacy, and self-efficacy all positively influenced the employees' intention to comply with the information security system; while rewards and response costs had a negative effect. Threat appraisal had a greater effect on employees' intention to comply with the information security system compared to response appraisal. The fsQCA results showed that individual antecedent conditions are not necessary to influence employees' intention to comply with an information security system. Seven pathways exist that influence an employees' intention to comply with an information security system, with reward, self-efficacy, and response cost being the core conditions having the highest probability of occurring in each configuration of pathways, and with perceived severity and self-efficacy appearing in the core conditions of configurations with an original coverage greater than 40%. Theoretically, this study discusses the influence of the elements of PMT on employees' intention to comply with an information security system, reveals the mechanism of influence of the combination of the influencing factors on the outcome variables, and identifies the core factors and auxiliary factors in the condition configurations, providing a new broader perspective for the study of information security compliance behavior and providing some theoretical support for strengthening enterprise security management. Practically, targeted suggestions are proposed based on the research results, to increase the intention of enterprise employees to comply with information security systems, thereby improving the effectiveness of enterprise information security management and the degree of information security in enterprises.},
}
@article {pmid36497480,
year = {2022},
author = {Islam, MM and Poly, TN and Walther, BA and Yeh, CY and Seyed-Abdul, S and Li, YJ and Lin, MC},
title = {Deep Learning for the Diagnosis of Esophageal Cancer in Endoscopic Images: A Systematic Review and Meta-Analysis.},
journal = {Cancers},
volume = {14},
number = {23},
pages = {},
pmid = {36497480},
issn = {2072-6694},
abstract = {Esophageal cancer, one of the most common cancers with a poor prognosis, is the sixth leading cause of cancer-related mortality worldwide. Early and accurate diagnosis of esophageal cancer, thus, plays a vital role in choosing the appropriate treatment plan for patients and increasing their survival rate. However, an accurate diagnosis of esophageal cancer requires substantial expertise and experience. Nowadays, the deep learning (DL) model for the diagnosis of esophageal cancer has shown promising performance. Therefore, we conducted an updated meta-analysis to determine the diagnostic accuracy of the DL model for the diagnosis of esophageal cancer. A search of PubMed, EMBASE, Scopus, and Web of Science, between 1 January 2012 and 1 August 2022, was conducted to identify potential studies evaluating the diagnostic performance of the DL model for esophageal cancer using endoscopic images. The study was performed in accordance with PRISMA guidelines. Two reviewers independently assessed potential studies for inclusion and extracted data from retrieved studies. Methodological quality was assessed by using the QUADAS-2 guidelines. The pooled accuracy, sensitivity, specificity, positive and negative predictive value, and the area under the receiver operating curve (AUROC) were calculated using a random effect model. A total of 28 potential studies involving a total of 703,006 images were included. The pooled accuracy, sensitivity, specificity, and positive and negative predictive value of DL for the diagnosis of esophageal cancer were 92.90%, 93.80%, 91.73%, 93.62%, and 91.97%, respectively. The pooled AUROC of DL for the diagnosis of esophageal cancer was 0.96. Furthermore, there was no publication bias among the studies. The findings of our study show that the DL model has great potential to accurately and quickly diagnose esophageal cancer. However, most studies developed their model using endoscopic data from the Asian population. Therefore, we recommend further validation through studies of other populations as well.},
}
@article {pmid36495963,
year = {2023},
author = {Tong, H and Warren, JL and Kang, J and Li, M},
title = {Using multi-sourced big data to correlate sleep deprivation and road traffic noise: A US county-level ecological study.},
journal = {Environmental research},
volume = {220},
number = {},
pages = {115029},
doi = {10.1016/j.envres.2022.115029},
pmid = {36495963},
issn = {1096-0953},
mesh = {Humans ; *Sleep Deprivation/epidemiology ; *Noise, Transportation/adverse effects ; Bayes Theorem ; Big Data ; Sleep ; Environmental Exposure ; },
abstract = {BACKGROUND: Road traffic noise is a serious public health problem globally as it has adverse psychological and physiologic effects (i.e., sleep). Since previous studies mainly focused on individual levels, we aim to examine associations between road traffic noise and sleep deprivation on a large scale; namely, the US at county level.<br><br>METHODS: Information from a large-scale sleep survey and national traffic noise map, both obtained from government's open data, were utilized and processed with Geographic Information System (GIS) techniques. To examine the associations between traffic noise and sleep deprivation, we used a hierarchical Bayesian spatial modelling framework to simultaneously adjust for multiple socioeconomic factors while accounting for spatial correlation.<br><br>FINDINGS: With 62.90% of people not getting enough sleep, a 10 dBA increase in average sound-pressure level (SPL) or Ls10 (SPL of the relatively noisy area) in a county, was associated with a 49% (OR: 1.49; 95% CrIs:1.19-1.86) or 8% (1.08; 1.00-1.16) increase in the odds of a person in a particular county not getting enough sleep. No significant association was observed for Ls90 (SPL of the relatively quiet area). A 10% increase in noise exposure area or population ratio was associated with a 3% (1.03; 1.01-1.06) or 4% (1.04; 1.02-1.06) increase in the odds of a person within a county not getting enough sleep.<br><br>INTERPRETATION: Traffic noise can contribute to variations in sleep deprivation among counties. This study suggests that policymakers could set up different noise-management strategies for relatively quiet and noisy areas and incorporate geospatial noise indicators, such as exposure population or area ratio. Furthermore, urban planners should consider urban sprawl patterns differently in terms of noise-induced sleep problems.},
}
@article {pmid36493775,
year = {2023},
author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, &#xd6;D and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, &#xd6; and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, &#xc7; and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M},
title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.},
journal = {Current biology : CB},
volume = {33},
number = {1},
pages = {41-57.e15},
pmid = {36493775},
issn = {1879-0445},
mesh = {Humans ; Male ; History, Ancient ; *Racial Groups ; Iran ; *Genome, Human ; Gene Flow ; Human Migration ; Genetics, Population ; },
abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.},
}
@article {pmid36478393,
year = {2023},
author = {Keck, F and Couton, M and Altermatt, F},
title = {Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses.},
journal = {Molecular ecology resources},
volume = {23},
number = {4},
pages = {742-755},
doi = {10.1111/1755-0998.13746},
pmid = {36478393},
issn = {1755-0998},
support = {31003A_173074//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Swiss Federal Office for the Environment (FOEN/BAFU)/ ; //University of Zurich Research Priority Programme in Global Change and Biodiversity/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Biodiversity ; Ecology ; Databases, Nucleic Acid ; *DNA, Environmental ; },
abstract = {Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These databases vary in completeness and availability, depending on the taxonomic group studied and the genetic region targeted. The incompleteness of reference databases is an important argument to explain the nondetection by metabarcoding of species supposedly present. However, there exist further and generally overlooked problems with reference databases that can lead to false or inaccurate inferences of taxonomic assignment. Here, we synthesize all possible problems inherent to reference databases. In particular, we identify a complete, mutually nonexclusive list of seven classes of challenges when it comes to selecting, developing and using a reference database for taxonomic assignment. These are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) taxonomic conflict, (v) low taxonomic resolution, (vi) missing taxa and (vii) missing intraspecific variants. For each problem identified, we provide a description of possible consequences on the taxonomic assignment process. We illustrate the respective problem with examples taken from the literature or obtained by quantitative analyses of public databases, such as GenBank or BOLD. Finally, we discuss possible solutions to the identified problems and how to navigate them. Only by raising users' awareness of the limitations of metabarcoding data and DNA reference databases will adequate interpretations of these data be achieved.},
}
@article {pmid36478264,
year = {2023},
author = {Mairal, M and García-Verdugo, C and Le Roux, JJ and Chau, JH and van Vuuren, BJ and Hui, C and Münzbergová, Z and Chown, SL and Shaw, JD},
title = {Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos.},
journal = {Molecular ecology},
volume = {32},
number = {4},
pages = {756-771},
doi = {10.1111/mec.16809},
pmid = {36478264},
issn = {1365-294X},
mesh = {Humans ; *Genetic Variation/genetics ; *Polyploidy ; Reproduction ; Geography ; Introduced Species ; Oceans and Seas ; Microsatellite Repeats/genetics ; },
abstract = {Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyse geographical variation in genome size, genetic diversity and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity and increased self-fertilization, but we show that this is not the case for P. annua. Microsatellite data indicated low population genetic structure and lack of isolation by distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of selfing declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are probably tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy probably benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.},
}
@article {pmid36477523,
year = {2022},
author = {Takemura, LS and Barbosa, &#xc1;RG and Amaral, BS and Bosco, AAD and Lourenço, DB and Apezzato, M and Barbosa, JABA and Faria, EF and Bianco, B and Lemos, GC and Carneiro, A},
title = {Radical prostatectomies for treatment of prostate cancer: trends in a ten-year period in public health services in the city of São Paulo, Brazil.},
journal = {Einstein (Sao Paulo, Brazil)},
volume = {20},
number = {},
pages = {eAO0049},
pmid = {36477523},
issn = {2317-6385},
mesh = {United States ; Humans ; Male ; Brazil/epidemiology ; *Prostatic Neoplasms/surgery ; Health Services ; },
abstract = {OBJECTIVE: To analyze the characteristics of public health services related to radical prostatectomy, according to hospital volume of surgeries and stratified as academic and non-academic centers.<br><br>METHODS: An ecological study was conducted using a database available in TabNet platform of the Unified Health System Department of Informatics. Number of surgeries, length of hospital stay, length of stay in intensive care unit, in-hospital mortality rate, and cost of hospitalization were evaluated. The hospitals were divided into three subgroups according to surgery volume (tercile), and results were compared. The same comparisons were made among academic and non-academic centers. We considered academic centers those providing Urology residency program.<br><br>RESULTS: A total of 11,259 radical prostatectomies were performed in the city of S&#xe3;o Paulo between 2008 and 2018. We observed a significant trend of increase in radical prostatectomies for treating prostate cancer over the years (p=0.007). The length of stay in intensive care unit, and number of deaths were not statistically different among centers with diverse surgery volume, nor between academic and non-academic centers. However, length of hospital stay was significantly shorter in academic centers (p=0.043), while cost of hospitalization was significantly higher in high-volume center compared to low- (p<0.001) and intermediate-volume centers (p<0.001).<br><br>CONCLUSION: Length of hospital stay for radical prostatectomies performed in public services in the city of S&#xe3;o Paulo was shorter in academic centers, whereas hospitals with a high volume of surgeries showed greater cost of hospitalization.},
}
@article {pmid36475098,
year = {2022},
author = {Karaarslan, F and Yılmaz, H and Akkurt, HE and Kaya, FM and Şafak Yılmaz, E},
title = {Comparison of the efficacy of mud-pack and hot-pack treatments in chronic non-specific neck pain: A single-blind, randomized-controlled study.},
journal = {Turkish journal of physical medicine and rehabilitation},
volume = {68},
number = {3},
pages = {381-390},
pmid = {36475098},
issn = {2587-1250},
abstract = {OBJECTIVES: This study aims to compare the short-term efficacy of mud-pack (MP) and hot-pack (HP) treatments with the same temperature and duration on sleep, function, depression, and quality of life for chronic non-specific neck pain (CNNP) patients.<br><br>PATIENTS AND METHODS: Between December 2018 and September 2019, a total of 70 patients with CNNP diagnosis (12 males, 58 females; mean age: 50.2&#xb1;9.4 years; range, 24 to 65 years) were included. The patients were divided into two groups. The MP group (n=35) had a total of 15 sessions of MP for 20 min + transcutaneous electrical nerve stimulation (TENS) for 20 min + home exercise (HE) on five days per week for three weeks. The HP group (n=35) had 15 similar sessions of HP for 20 min + TENS for 20 min + HE. The patients were assessed with the Visual Analog Scale (VAS-pain), VAS physician's and patient's global assessments, modified Neck Disability Index (mNDI), Beck Depression Inventory (BDI), Pittsburgh Sleep Quality Index (PSQI), and Short Form-36 (SF-36) measures before treatment, at the end of post-treatment third week and one month later.<br><br>RESULTS: In the MP group, there were statistically significant improvements in all parameters at the end of treatment three-week and one-month follow-up (p<0.05), apart from SF-36 Vitality/Energy (SF-36V/E) at the end of treatment and SF-36 General Health (SF-36GH) at one month. In the HP group, there were statistically significant improvements observed for all parameters (p<0.05), apart from the SF-36 Physical Role and SF-36GH at the end of treatment third week and SF-36V/E at the first-month assessment. The VAS-pain(p<0.001), mNDI (p=0.019), BDI (p=0.002), SF-36GH (p<0.001), SF-36V/E (p<0.001) and SF-36 mental health (p<0.001) showed statistically significantly superior improvements in the MP group (p<0.05).<br><br>CONCLUSION: In CNNP patients, both MP and HP treatments are effective. However, MP therapy has more positive effects on pain, function, depression, and quality of life parameters. The MP treatment may be used in addition to TENS treatment for CNNP patients.},
}
@article {pmid36473660,
year = {2023},
author = {Simeoni, C and Furlan, E and Pham, HV and Critto, A and de Juan, S and Trégarot, E and Cornet, CC and Meesters, E and Fonseca, C and Botelho, AZ and Krause, T and N'Guetta, A and Cordova, FE and Failler, P and Marcomini, A},
title = {Evaluating the combined effect of climate and anthropogenic stressors on marine coastal ecosystems: Insights from a systematic review of cumulative impact assessment approaches.},
journal = {The Science of the total environment},
volume = {861},
number = {},
pages = {160687},
doi = {10.1016/j.scitotenv.2022.160687},
pmid = {36473660},
issn = {1879-1026},
mesh = {*Ecosystem ; *Anthropogenic Effects ; Environmental Monitoring/methods ; Risk Assessment ; Water ; },
abstract = {Cumulative impacts increasingly threaten marine and coastal ecosystems. To address this issue, the research community has invested efforts on designing and testing different methodological approaches and tools that apply cumulative impact appraisal schemes for a sound evaluation of the complex interactions and dynamics among multiple pressures affecting marine and coastal ecosystems. Through an iterative scientometric and systematic literature review, this paper provides the state of the art of cumulative impact assessment approaches and applications. It gives a specific attention to cutting-edge approaches that explore and model inter-relations among climatic and anthropogenic pressures, vulnerability and resilience of marine and coastal ecosystems to these pressures, and the resulting changes in ecosystem services flow. Despite recent advances in computer sciences and the rising availability of big data for environmental monitoring and management, this literature review evidenced that the implementation of advanced complex system methods for cumulative risk assessment remains limited. Moreover, experts have only recently started integrating ecosystem services flow into cumulative impact appraisal frameworks, but more as a general assessment endpoint within the overall evaluation process (e.g. changes in the bundle of ecosystem services against cumulative impacts). The review also highlights a lack of integrated approaches and complex tools able to frame, explain, and model spatio-temporal dynamics of marine and coastal ecosystems' response to multiple pressures, as required under relevant EU legislation (e.g., Water Framework and Marine Strategy Framework Directives). Progress in understanding cumulative impacts, exploiting the functionalities of more sophisticated machine learning-based approaches (e.g., big data integration), will support decision-makers in the achievement of environmental and sustainability objectives.},
}
@article {pmid36469956,
year = {2023},
author = {Marcusson-Clavertz, D and Persson, SD and Davidson, P and Kim, J and Cardeña, E and Kuehner, C},
title = {Mind wandering and sleep in daily life: A combined actigraphy and experience sampling study.},
journal = {Consciousness and cognition},
volume = {107},
number = {},
pages = {103447},
doi = {10.1016/j.concog.2022.103447},
pmid = {36469956},
issn = {1090-2376},
mesh = {Humans ; *Ecological Momentary Assessment ; *Attention ; Actigraphy ; Sleep ; Self Report ; },
abstract = {Individuals who sleep poorly report spending more time mind wandering during the day. However, past research has relied on self-report measures of sleep or measured mind wandering during laboratory tasks, which prevents generalization to everyday contexts. We used ambulatory assessments to examine the relations between several features of sleep (duration, fragmentation, and disturbances) and mind wandering (task-unrelated, stimulus-independent, and unguided thoughts). Participants wore a wristband device that collected actigraphy and experience-sampling data across 7 days and 8 nights. Contrary to our expectations, task-unrelated and stimulus-independent thoughts were not associated with sleep either within- or between-persons (n = 164). Instead, individual differences in unguided thoughts were associated with sleep disturbances and duration, suggesting that individuals who more often experience unguided train-of-thoughts have greater sleep disturbances and sleep longer. These results highlight the need to consider the context and features of mind wandering when relating it to sleep.},
}
@article {pmid36469554,
year = {2022},
author = {Zhao, C and Goldman, M and Smith, BJ and Pollard, KS},
title = {Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.},
journal = {Current protocols},
volume = {2},
number = {12},
pages = {e604},
pmid = {36469554},
issn = {2691-1299},
support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; },
mesh = {*Metagenome/genetics ; Genotype ; Alleles ; *Microbiota/genetics ; Nucleotides ; },
abstract = {The Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is a scalable pipeline that identifies single nucleotide variants and gene copy number variants in metagenomes using comprehensive reference databases built from public microbial genome collections (metagenotyping). MIDAS2 is the first metagenotyping tool with functionality to control metagenomic read mapping filters and to customize the reference database to the microbial community, features that improve the precision and recall of detected variants. In this article we present four basic protocols for the most common use cases of MIDAS2, along with supporting protocols for installation and use. In addition, we provide in-depth guidance on adjusting command line parameters, editing the reference database, optimizing hardware utilization, and understanding the metagenotyping results. All the steps of metagenotyping, from raw sequencing reads to population genetic analysis, are demonstrated with example data in two downloadable sequencing libraries of single-end metagenomic reads representing a mixture of multiple bacterial species. This set of protocols empowers users to accurately genotype hundreds of species in thousands of samples, providing rich genetic data for studying the evolution and strain-level ecology of microbial communities. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Species prescreening Basic Protocol 2: Download MIDAS reference database Basic Protocol 3: Population single nucleotide variant calling Basic Protocol 4: Pan-genome copy number variant calling Support Protocol 1: Installing MIDAS2 Support Protocol 2: Command line inputs Support Protocol 3: Metagenotyping with a custom collection of genomes Support Protocol 4: Metagenotyping with advanced parameters.},
}
@article {pmid36462728,
year = {2023},
author = {Sosa, CC and Clavijo-Buriticá, DC and García-Merchán, VH and López-Rozo, N and Riccio-Rengifo, C and Diaz, MV and Londoño, DA and Quimbaya, MA},
title = {GOCompare: An R package to compare functional enrichment analysis between two species.},
journal = {Genomics},
volume = {115},
number = {1},
pages = {110528},
doi = {10.1016/j.ygeno.2022.110528},
pmid = {36462728},
issn = {1089-8646},
mesh = {*Aluminum ; Genomics/methods ; Computational Biology/methods ; Algorithms ; Gene Ontology ; *Arabidopsis/genetics ; },
abstract = {Functional enrichment analysis is a cornerstone in bioinformatics as it makes possible to identify functional information by using a gene list as source. Different tools are available to compare gene ontology (GO) terms, based on a directed acyclic graph structure or content-based algorithms which are time-consuming and require a priori information of GO terms. Nevertheless, quantitative procedures to compare GO terms among gene lists and species are not available. Here we present a computational procedure, implemented in R, to infer functional information derived from comparative strategies. GOCompare provides a framework for functional comparative genomics starting from comparable lists from GO terms. The program uses functional enrichment analysis (FEA) results and implement graph theory to identify statistically relevant GO terms for both, GO categories and analyzed species. Thus, GOCompare allows finding new functional information complementing current FEA approaches and extending their use to a comparative perspective. To test our approach GO terms were obtained for a list of aluminum tolerance-associated genes in Oryza sativa subsp. japonica and their orthologues in Arabidopsis thaliana. GOCompare was able to detect functional similarities for reactive oxygen species and ion binding capabilities which are common in plants as molecular mechanisms to tolerate aluminum toxicity. Consequently, the R package exhibited a good performance when implemented in complex datasets, allowing to establish hypothesis that might explain a biological process from a functional perspective, and narrowing down the possible landscapes to design wet lab experiments.},
}
@article {pmid36458815,
year = {2022},
author = {Yang, B and García-Carreras, B and Lessler, J and Read, JM and Zhu, H and Metcalf, CJE and Hay, JA and Kwok, KO and Shen, R and Jiang, CQ and Guan, Y and Riley, S and Cummings, DA},
title = {Long term intrinsic cycling in human life course antibody responses to influenza A(H3N2): an observational and modeling study.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36458815},
issn = {2050-084X},
support = {MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; R01 AI114703/AI/NIAID NIH HHS/United States ; R01 TW008246/TW/FIC NIH HHS/United States ; MR/J008761/1/MRC_/Medical Research Council/United Kingdom ; 200187/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; R56 AG048075/AG/NIA NIH HHS/United States ; 200861/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19012/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Influenza, Human ; Influenza A Virus, H3N2 Subtype ; *Influenza Vaccines ; Antibody Formation ; Life Change Events ; Antibodies, Viral ; },
abstract = {BACKGROUND: Over a life course, human adaptive immunity to antigenically mutable pathogens exhibits competitive and facilitative interactions. We hypothesize that such interactions may lead to cyclic dynamics in immune responses over a lifetime.<br><br>METHODS: To investigate the cyclic behavior, we analyzed hemagglutination inhibition titers against 21 historical influenza A(H3N2) strains spanning 47 years from a cohort in Guangzhou, China, and applied Fourier spectrum analysis. To investigate possible biological mechanisms, we simulated individual antibody profiles encompassing known feedbacks and interactions due to generally recognized immunological mechanisms.<br><br>RESULTS: We demonstrated a long-term periodicity (about 24 years) in individual antibody responses. The reported cycles were robust to analytic and sampling approaches. Simulations suggested that individual-level cross-reaction between antigenically similar strains likely explains the reported cycle. We showed that the reported cycles are predictable at both individual and birth cohort level and that cohorts show a diversity of phases of these cycles. Phase of cycle was associated with the risk of seroconversion to circulating strains, after accounting for age and pre-existing titers of the circulating strains.<br><br>CONCLUSIONS: Our findings reveal the existence of long-term periodicities in individual antibody responses to A(H3N2). We hypothesize that these cycles are driven by preexisting antibody responses blunting responses to antigenically similar pathogens (by preventing infection and/or robust antibody responses upon infection), leading to reductions in antigen-specific responses over time until individual's increasing risk leads to an infection with an antigenically distant enough virus to generate a robust immune response. These findings could help disentangle cohort effects from individual-level exposure histories, improve our understanding of observed heterogeneous antibody responses to immunizations, and inform targeted vaccine strategy.<br><br>FUNDING: This study was supported by grants from the NIH R56AG048075 (DATC, JL), NIH R01AI114703 (DATC, BY), the Wellcome Trust 200861/Z/16/Z (SR), and 200187/Z/15/Z (SR). This work was also supported by research grants from Guangdong Government HZQB-KCZYZ-2021014 and 2019B121205009 (YG and HZ). DATC, JMR and SR acknowledge support from the National Institutes of Health Fogarty Institute (R01TW0008246). JMR acknowledges support from the Medical Research Council (MR/S004793/1) and the Engineering and Physical Sciences Research Council (EP/N014499/1). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.},
}
@article {pmid36456926,
year = {2022},
author = {Li, Y and Wei, CM and Li, XY and Meng, DC and Gu, ZJ and Qu, SP and Huang, MJ and Huang, HQ},
title = {De novo transcriptome sequencing of Impatiens uliginosa and the analysis of candidate genes related to spur development.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {553},
pmid = {36456926},
issn = {1471-2229},
mesh = {*Impatiens ; Transcriptome ; Exome Sequencing ; Cell Cycle ; Databases, Protein ; },
abstract = {BACKGROUND: Spur, a structure capable of producing and storing nectar, not only plays a vital role in the pollination process but also promotes the rapid diversification of some plant lineages, which is considered a key innovation in plants. Spur is the focus of many studies, such as evolution and ecological hypothesis, but the current understanding of spur development is limited. High-throughput sequencing of Impatiens uliginosa was carried out to study the molecular mechanism of its spur development, which is believed to provide some insights into the spur development of Impatiens.<br><br>RESULTS: Transcriptomic sequencing and analysis were performed on spurs and limbs of I. uliginosa at three developmental stages. A total of 47.83 Gb of clean data were obtained, and 49,716 unigene genes were assembled. After comparison with NR, Swiss-Prot, Pfam, COG, GO and KEGG databases, a total of 27,686 genes were annotated successfully. Through comparative analysis, 19,356 differentially expressed genes were found and enriched into 208 GO terms and 146 KEGG pathways, among which plant hormone signal transduction was the most significantly enriched pathway. One thousand thirty-two transcription factors were identified, which belonged to 33 TF families such as MYB, bHLH and TCP. Twenty candidate genes that may be involved in spur development were screened and verified by qPCR, such as SBP, IAA and ABP.<br><br>CONCLUSIONS: Transcriptome data of different developmental stages of spurs were obtained, and a series of candidate genes related to spur development were identified. The importance of genes related to cell cycle, cell division, cell elongation and hormones in spur development was clarified. This study provided valuable information and resources for understanding the molecular mechanism of spur development in Impatiens.},
}
@article {pmid36455989,
year = {2022},
author = {Van Bortel, W and Mariën, J and Jacobs, BKM and Sinzinkayo, D and Sinarinzi, P and Lampaert, E and D'hondt, R and Mafuko, JM and De Weggheleire, A and Vogt, F and Alexander, N and Wint, W and Maes, P and Vanlerberghe, V and Leclair, C},
title = {Long-lasting insecticidal nets provide protection against malaria for only a single year in Burundi, an African highland setting with marked malaria seasonality.},
journal = {BMJ global health},
volume = {7},
number = {12},
pages = {},
pmid = {36455989},
issn = {2059-7908},
mesh = {Humans ; *Insecticides ; Burundi/epidemiology ; *Malaria/epidemiology/prevention &amp; control ; *Health Information Systems ; Time Factors ; },
abstract = {BACKGROUND: Long-lasting insecticidal nets (LLINs) are one of the key interventions in the global fight against malaria. Since 2014, mass distribution campaigns of LLINs aim for universal access by all citizens of Burundi. In this context, we assess the impact of LLINs mass distribution campaigns on malaria incidence, focusing on the endemic highland health districts. We also explored the possible correlation between observed trends in malaria incidence with any variations in climate conditions.<br><br>METHODS: Malaria cases for 2011-2019 were obtained from the National Health Information System. We developed a generalised additive model based on a time series of routinely collected data with malaria incidence as the response variable and timing of LLIN distribution as an explanatory variable to investigate the duration and magnitude of the LLIN effect on malaria incidence. We added a seasonal and continuous-time component as further explanatory variables, and health district as a random effect to account for random natural variation in malaria cases between districts.<br><br>RESULTS: Malaria transmission in Burundian highlands was clearly seasonal and increased non-linearly over the study period. Further, a fast and steep decline of malaria incidence was noted during the first year after mass LLIN distribution (p<0.0001). In years 2 and 3 after distribution, malaria cases started to rise again to levels higher than before the control intervention.<br><br>CONCLUSION: This study highlights that LLINs did reduce the incidence in the first year after a mass distribution campaign, but in the context of Burundi, LLINs lost their impact after only 1&#x2009;year.},
}
@article {pmid36454025,
year = {2023},
author = {Velasco, VME and Ferreira, A and Zaman, S and Noordermeer, D and Ensminger, I and Wegrzyn, JL},
title = {A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir).},
journal = {G3 (Bethesda, Md.)},
volume = {13},
number = {2},
pages = {},
pmid = {36454025},
issn = {2160-1836},
mesh = {*Transcriptome ; *Pseudotsuga/genetics ; Gene Expression Profiling ; Molecular Sequence Annotation ; Base Sequence ; },
abstract = {Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.},
}
@article {pmid36451580,
year = {2023},
author = {Danneels, B and Blignaut, M and Marti, G and Sieber, S and Vandamme, P and Meyer, M and Carlier, A},
title = {Cyclitol metabolism is a central feature of Burkholderia leaf symbionts.},
journal = {Environmental microbiology},
volume = {25},
number = {2},
pages = {454-472},
doi = {10.1111/1462-2920.16292},
pmid = {36451580},
issn = {1462-2920},
support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Cyclitols ; *Burkholderia/genetics ; Symbiosis/genetics ; Endophytes/genetics ; Plants/microbiology ; Plant Leaves/microbiology ; Phylogeny ; },
abstract = {The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.},
}
@article {pmid36449461,
year = {2022},
author = {van der Feltz-Cornelis, CM and Sweetman, J and Allsopp, G and Attree, E and Crooks, MG and Cuthbertson, DJ and Forshaw, D and Gabbay, M and Green, A and Heightman, M and Hillman, T and Hishmeh, L and Khunti, K and Lip, GYH and Lorgelly, P and Montgomery, H and Strain, WD and Wall, E and Watkins, C and Williams, N and Wootton, DG and Banerjee, A and , },
title = {STIMULATE-ICP-Delphi (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways Delphi): Study protocol.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0277936},
pmid = {36449461},
issn = {1932-6203},
mesh = {Humans ; *COVID-19/epidemiology ; Critical Pathways ; Mental Health ; *Delivery of Health Care, Integrated ; Post-Acute COVID-19 Syndrome ; },
abstract = {INTRODUCTION: As mortality rates from COVID-19 disease fall, the high prevalence of long-term sequelae (Long COVID) is becoming increasingly widespread, challenging healthcare systems globally. Traditional pathways of care for Long Term Conditions (LTCs) have tended to be managed by disease-specific specialties, an approach that has been ineffective in delivering care for patients with multi-morbidity. The multi-system nature of Long COVID and its impact on physical and psychological health demands a more effective model of holistic, integrated care. The evolution of integrated care systems (ICSs) in the UK presents an important opportunity to explore areas of mutual benefit to LTC, multi-morbidity and Long COVID care. There may be benefits in comparing and contrasting ICPs for Long COVID with ICPs for other LTCs.<br><br>METHODS AND ANALYSIS: This study aims to evaluate health services requirements for ICPs for Long COVID and their applicability to other LTCs including multi-morbidity and the overlap with medically not yet explained symptoms (MNYES). The study will follow a Delphi design and involve an expert panel of stakeholders including people with lived experience, as well as clinicians with expertise in Long COVID and other LTCs. Study processes will include expert panel and moderator panel meetings, surveys, and interviews. The Delphi process is part of the overall STIMULATE-ICP programme, aimed at improving integrated care for people with Long COVID.<br><br>ETHICS AND DISSEMINATION: Ethical approval for this Delphi study has been obtained (Research Governance Board of the University of York) as have approvals for the other STIMULATE-ICP studies. Study outcomes are likely to inform policy for ICPs across LTCs. Results will be disseminated through scientific publication, conference presentation and communications with patients and stakeholders involved in care of other LTCs and Long COVID.<br><br>REGISTRATION: Researchregistry: https://www.researchregistry.com/browse-the-registry#home/registrationdetails/6246bfeeeaaed6001f08dadc/.},
}
@article {pmid36447758,
year = {2022},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the square-spot rustic, Xestia xanthographa (Schiffermuller, 1775).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {37},
pmid = {36447758},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Xestia xanthographa (the square-spot rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 934 megabases in span. The majority of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.},
}
@article {pmid36437091,
year = {2022},
author = {Zhang, KK and He, J and Zhong, YX and Wei, QQ and Chen, F},
title = {[Identification of Soil Heavy Metal Sources Around a Copper-silver Mining Area in Ningxia Based on GIS].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {43},
number = {11},
pages = {5192-5204},
doi = {10.13227/j.hjkx.202201113},
pmid = {36437091},
issn = {0250-3301},
mesh = {Humans ; Soil ; Copper ; Silver ; *Soil Pollutants/analysis ; Geographic Information Systems ; Cadmium/analysis ; Lead/analysis ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury/analysis ; },
abstract = {This study area was based on the catchment area of the Yaoxianzi ditch located in the arid region of western China. A total of 194 topsoil samples of 0-20 cm depth were collected using the mesh distribution method. The contents of nine heavy metals (Ni, Cu, Zn, As, Ag, Cr, Cd, Hg, and Pb) were determined using ICP-MS. The source and spatial distribution of heavy metals were analyzed using PMF and IDW. Spatial autocorrelation and clustering and outlier analysis were performed using the Spatial Statistical Analysis tool of ArcGIS. The main sources and distribution areas of heavy metals in the soil were obtained through comprehensive analysis. In the study area, the average values of Hg, Ag, Cd, and Pb were 20.48, 3.13, 2.23, and 1.12 times the background values, and the maximum values of Cd, Cu, Pb, and As were 10.92, 5.52, 2.03, and 1.39 times the filter values, respectively. The coefficients of variation of Cu, Cd, Pb, and Hg were ordered as Cu(283.23%)>Cd(224.77%)>Pb(144.40%)>Hg(67.12%) and were closely affected by human activities. The heavy metals in the soil around mining areas came from four main sources:natural parent material (32%), the mixed source of mining activities and transportation (17.1%), the mixed source of industrial activities and atmospheric sedimentation (40.3%), and the mixed source of agricultural activity and putting sandy gravel in farmland (10.6%). Cr and Ni, As and Cu, Hg, and Cd could represent these four sources of heavy metal pollution, respectively. The main sources of soil heavy metal pollution were mining activities and agricultural activities. The heavily contaminated areas were distributed in the mining areas in the south of the study area and in the planting areas in the eastern, central, and northwestern parts of the study area.},
}
@article {pmid36435969,
year = {2023},
author = {Kafkas, S and Ma, X and Zhang, X and Topçu, H and Navajas-Pérez, R and Wai, CM and Tang, H and Xu, X and Khodaeiaminjan, M and Güney, M and Paizila, A and Karcı, H and Zhang, X and Lin, J and Lin, H and Herrán, R and Rejón, CR and García-Zea, JA and Robles, F and Muñoz, CDV and Hotz-Wagenblatt, A and Min, XJ and Özkan, H and Motalebipour, EZ and Gozel, H and Çoban, N and Kafkas, NE and Kilian, A and Huang, H and Lv, X and Liu, K and Hu, Q and Jacygrad, E and Palmer, W and Michelmore, R and Ming, R},
title = {Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution.},
journal = {Plant communications},
volume = {4},
number = {3},
pages = {100497},
pmid = {36435969},
issn = {2590-3462},
mesh = {*Pistacia/genetics ; Trees/genetics ; Nuts ; Domestication ; Sex Chromosomes/genetics ; },
abstract = {Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.},
}
@article {pmid36429843,
year = {2022},
author = {Zhang, T and Wang, B and Ge, Y and Li, C},
title = {Research on Green Space Service Space Based on Crowd Aggregation and Activity Characteristics under Big Data-Take Tacheng City as an Example.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {22},
pages = {},
pmid = {36429843},
issn = {1660-4601},
mesh = {Humans ; *Parks, Recreational ; *Big Data ; Cities ; Personal Satisfaction ; },
abstract = {People-oriented planning has become the mainstream of urban space design. As an important research object of urban space, the accessibility and service level of accessibility and service level of green space as important indicators to evaluate the level of urban livability cannot be truly fed back to people's daily life. Therefore, based on big data and from the perspective of crowd activities and aggregation characteristics, this study analyzes the shortage of green space service space in Tacheng City and puts forward suggestions for improvement. The main conclusions are as follows: (1) The satisfaction of green space based on service scope covers up the imbalance of green space resources enjoyed by actual crowd activities and aggregation. (2) Although the accessibility of green space obtained by population density meets the needs in space, it cannot take care of the potential needs generated by daily crowd activities and aggregation, which leads to the overall spatial imbalance of accessibility. (3) The comprehensive analysis shows that the northeast and southwest regions are the focus of the later planning and construction. The southwest region echoes with the old urban area and attracts people's daily activities. The woodland in the northeast region, as the main green space supply, meets the potential needs of the daily population activities and aggregation of the new development urban area and the old urban area, and also serves as a place for rest and entertainment to meet the needs of the activities and aggregation of the accidental behavior of the people in the new and old urban areas after the opening up.},
}
@article {pmid36421254,
year = {2022},
author = {Würstle, S and Hapfelmeier, A and Karapetyan, S and Studen, F and Isaakidou, A and Schneider, T and Schmid, RM and von Delius, S and Gundling, F and Triebelhorn, J and Burgkart, R and Obermeier, A and Mayr, U and Heller, S and Rasch, S and Lahmer, T and Geisler, F and Chan, B and Turner, PE and Rothe, K and Spinner, CD and Schneider, J},
title = {A Novel Machine Learning-Based Point-Score Model as a Non-Invasive Decision-Making Tool for Identifying Infected Ascites in Patients with Hydropic Decompensated Liver Cirrhosis: A Retrospective Multicentre Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {36421254},
issn = {2079-6382},
support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; },
abstract = {This study is aimed at assessing the distinctive features of patients with infected ascites and liver cirrhosis and developing a scoring system to allow for the accurate identification of patients not requiring abdominocentesis to rule out infected ascites. A total of 700 episodes of patients with decompensated liver cirrhosis undergoing abdominocentesis between 2006 and 2020 were included. Overall, 34 clinical, drug, and laboratory features were evaluated using machine learning to identify key differentiation criteria and integrate them into a point-score model. In total, 11 discriminatory features were selected using a Lasso regression model to establish a point-score model. Considering pre-test probabilities for infected ascites of 10%, 15%, and 25%, the negative and positive predictive values of the point-score model for infected ascites were 98.1%, 97.0%, 94.6% and 14.9%, 21.8%, and 34.5%, respectively. Besides the main model, a simplified model was generated, containing only features that are fast to collect, which revealed similar predictive values. Our point-score model appears to be a promising non-invasive approach to rule out infected ascites in clinical routine with high negative predictive values in patients with hydropic decompensated liver cirrhosis, but further external validation in a prospective study is needed.},
}
@article {pmid36419146,
year = {2022},
author = {Atkins, S and Heimo, L and Carter, DJ and Ribas Closa, M and Vanleeuw, L and Chenciner, L and Wambi, P and Sidney-Annerstedt, K and Egere, U and Verkuijl, S and Brands, A and Masini, T and Viney, K and Wingfield, T and Lönnroth, K and Boccia, D},
title = {The socioeconomic impact of tuberculosis on children and adolescents: a scoping review and conceptual framework.},
journal = {BMC public health},
volume = {22},
number = {1},
pages = {2153},
pmid = {36419146},
issn = {1471-2458},
support = {001/WHO_/World Health Organization/International ; MR/V004832/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Child ; Humans ; Adolescent ; *Tuberculosis/epidemiology ; Social Stigma ; Databases, Factual ; Educational Status ; Knowledge ; },
abstract = {BACKGROUND: Tuberculosis (TB) has been repeatedly shown to have socioeconomic impacts in both individual-level and ecological studies; however, much less is known about this effect among children and adolescents and the extent to which being affected by TB during childhood and adolescence can have life-course implications. This paper describes the results of the development of a conceptual framework and scoping review to review the evidence on the short- and long-term socioeconomic impact of tuberculosis on children and adolescents.<br><br>OBJECTIVES: To increase knowledge of the socioeconomic impact of TB on children and adolescents.<br><br>METHODS: We developed a conceptual framework of the socioeconomic impact of TB on children and adolescents, and used scoping review methods to search for evidence supporting or disproving it. We searched four academic databases from 1 January 1990 to 6 April 2021 and conducted targeted searches of grey literature. We extracted data using a standard form and analysed data thematically.<br><br>RESULTS: Thirty-six studies (29 qualitative, five quantitative and two mixed methods studies) were included in the review. Overall, the evidence supported the conceptual framework, suggesting a severe socioeconomic impact of TB on children and adolescents through all the postulated pathways. Effects ranged from impoverishment, stigma, and family separation, to effects on nutrition and missed education opportunities. TB did not seem to exert a different socioeconomic impact when directly or indirectly affecting children/adolescents, suggesting that TB can affect this group even when they are not affected by the disease. No study provided sufficient follow-up to observe the long-term socioeconomic effect of TB in this age group.<br><br>CONCLUSION: The evidence gathered in this review reinforces our understanding of the impact of TB on children and adolescents and highlights the importance of considering effects during the entire life course. Both ad-hoc and sustainable social protection measures and strategies are essential to mitigate the socioeconomic consequences of TB among children and adolescents.},
}
@article {pmid36418825,
year = {2023},
author = {Debnath, J and Sahariah, D and Lahon, D and Nath, N and Chand, K and Meraj, G and Farooq, M and Kumar, P and Kanga, S and Singh, SK},
title = {Geospatial modeling to assess the past and future land use-land cover changes in the Brahmaputra Valley, NE India, for sustainable land resource management.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {49},
pages = {106997-107020},
pmid = {36418825},
issn = {1614-7499},
mesh = {*Environmental Monitoring ; *Geographic Information Systems ; Remote Sensing Technology ; Agriculture ; India ; Water ; Conservation of Natural Resources ; },
abstract = {Satellite remote sensing and geographic information system (GIS) have revolutionalized the mapping, quantifying, and assessing the land surface processes, particularly analyzing the past and future land use-land cover (LULC) change patterns. Worldwide river basins have observed enormous changes in the land system dynamics as a result of anthropogenic factors such as population, urbanization, development, and agriculture. As is the scenario of various other river basins, the Brahmaputra basin, which falls in China, Bhutan, India, and Bangladesh, is also witnessing the same environmental issues. The present study has been conducted on the Brahmaputra Valley in Assam, India (a sub-basin of the larger Brahmaputra basin) and assessed its LULC changes using a maximum likelihood classification algorithm. The study also simulated the changing LULC pattern for the years 2030, 2040, and 2050 using the GIS-based cellular automata Markov model (CA-Markov) to understand the implications of the ongoing trends in the LULC change for future land system dynamics. The current rate of change of the LULC in the region was assessed using the 48 years of earth observation satellite data from 1973 to 2021. It was observed that from 1973 to 2021, the area under vegetation cover and water body decreased by 19.48 and 47.13%, respectively. In contrast, cultivated land, barren land, and built-up area increased by 7.60, 20.28, and 384.99%, respectively. It was found that the area covered by vegetation and water body has largely been transitioned to cultivated land and built-up classes. The research predicted that, by the end of 2050, the area covered by vegetation, cultivated land, and water would remain at 39.75, 32.31, and 4.91%, respectively, while the area covered by built-up areas will increase by up to 18.09%. Using the kappa index (ki) as an accuracy indicator of the simulated future LULCs, the predicted LULC of 2021 was validated against the observed LULC of 2021, and the very high ki observed validated the generated simulation LULC products. The research concludes that significant LULC changes are taking place in the study area with a decrease in vegetation cover and water body and an increase of area under built-up. Such trends will continue in the future and shall have disastrous environmental consequences unless necessary land resource management strategies are not implemented. The main factors responsible for the changing dynamics of LULC in the study area are urbanization, population growth, climate change, river bank erosion and sedimentation, and intensive agriculture. This study is aimed at providing the policy and decision-makers of the region with the necessary what-if scenarios for better decision-making. It shall also be useful in other countries of the Brahmaputra basin for transboundary integrated river basin management of the whole region.},
}
@article {pmid36418120,
year = {2022},
author = {Kumpik, DP and Santos-Rodriguez, R and Selwood, J and Coulthard, E and Twomey, N and Craddock, I and Ben-Shlomo, Y},
title = {A longitudinal observational study of home-based conversations for detecting early dementia: protocol for the CUBOId TV task.},
journal = {BMJ open},
volume = {12},
number = {11},
pages = {e065033},
pmid = {36418120},
issn = {2044-6055},
support = {MC_PC_16029/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; Pregnancy ; Female ; *Cognitive Dysfunction/diagnosis/psychology ; Neuropsychological Tests ; Longitudinal Studies ; Biomarkers ; *Dementia/diagnosis/psychology ; Observational Studies as Topic ; },
abstract = {INTRODUCTION: Limitations in effective dementia therapies mean that early diagnosis and monitoring are critical for disease management, but current clinical tools are impractical and/or unreliable, and disregard short-term symptom variability. Behavioural biomarkers of cognitive decline, such as speech, sleep and activity patterns, can manifest prodromal pathological changes. They can be continuously measured at home with smart sensing technologies, and permit leveraging of interpersonal interactions for optimising diagnostic and prognostic performance. Here we describe the ContinUous behavioural Biomarkers Of cognitive Impairment (CUBOId) study, which explores the feasibility of multimodal data fusion for in-home monitoring of mild cognitive impairment (MCI) and early Alzheimer's disease (AD). The report focuses on a subset of CUBOId participants who perform a novel speech task, the 'TV task', designed to track changes in ecologically valid conversations with disease progression.<br><br>METHODS AND ANALYSIS: CUBOId is a longitudinal observational study. Participants have diagnoses of MCI or AD, and controls are their live-in partners with no such diagnosis. Multimodal activity data were passively acquired from wearables and in-home fixed sensors over timespans of 8-25 months. At two time points participants completed the TV task over 5&#x2009;days by recording audio of their conversations as they watched a favourite TV programme, with further testing to be completed after removal of the sensor installations. Behavioural testing is supported by neuropsychological assessment for deriving ground truths on cognitive status. Deep learning will be used to generate fused multimodal activity-speech embeddings for optimisation of diagnostic and predictive performance from speech alone.<br><br>ETHICS AND DISSEMINATION: CUBOId was approved by an NHS Research Ethics Committee (Wales REC; ref: 18/WA/0158) and is sponsored by University of Bristol. It is supported by the National Institute for Health Research Clinical Research Network West of England. Results will be reported at conferences and in peer-reviewed scientific journals.},
}
@article {pmid36416261,
year = {2023},
author = {Guo, S and Xu, Z and Dong, X and Hu, D and Jiang, Y and Wang, Q and Zhang, J and Zhou, Q and Liu, S and Song, W},
title = {GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D964-D968},
pmid = {36416261},
issn = {1362-4962},
support = {I01 HX000551/HX/HSRD VA/United States ; },
mesh = {Humans ; RNA-Seq/methods ; Cell Line ; *Databases, Genetic ; *Software ; },
abstract = {Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.},
}
@article {pmid36414269,
year = {2022},
author = {Nguyen, PY and Kanukula, R and McKenzie, JE and Alqaidoom, Z and Brennan, SE and Haddaway, NR and Hamilton, DG and Karunananthan, S and McDonald, S and Moher, D and Nakagawa, S and Nunan, D and Tugwell, P and Welch, VA and Page, MJ},
title = {Changing patterns in reporting and sharing of review data in systematic reviews with meta-analysis of the effects of interventions: cross sectional meta-research study.},
journal = {BMJ (Clinical research ed.)},
volume = {379},
number = {},
pages = {e072428},
pmid = {36414269},
issn = {1756-1833},
mesh = {Humans ; Cross-Sectional Studies ; PubMed ; *Research Design ; Systematic Reviews as Topic ; *Information Dissemination ; },
abstract = {OBJECTIVES: To examine changes in completeness of reporting and frequency of sharing data, analytical code, and other review materials in systematic reviews over time; and factors associated with these changes.<br><br>DESIGN: Cross sectional meta-research study.<br><br>POPULATION: Random sample of 300 systematic reviews with meta-analysis of aggregate data on the effects of a health, social, behavioural, or educational intervention. Reviews were indexed in PubMed, Science Citation Index, Social Sciences Citation Index, Scopus, and Education Collection in November 2020.<br><br>MAIN OUTCOME MEASURES: The extent of complete reporting and the frequency of sharing review materials in the systematic reviews indexed in 2020 were compared with 110 systematic reviews indexed in February 2014. Associations between completeness of reporting and various factors (eg, self-reported use of reporting guidelines, journal policies on data sharing) were examined by calculating risk ratios and 95% confidence intervals.<br><br>RESULTS: Several items were reported suboptimally among 300 systematic reviews from 2020, such as a registration record for the review (n=113; 38%), a full search strategy for at least one database (n=214; 71%), methods used to assess risk of bias (n=185; 62%), methods used to prepare data for meta-analysis (n=101; 34%), and source of funding for the review (n=215; 72%). Only a few items not already reported at a high frequency in 2014 were reported more frequently in 2020. No evidence indicated that reviews using a reporting guideline were more completely reported than reviews not using a guideline. Reviews published in 2020 in journals that mandated either data sharing or inclusion of data availability statements were more likely to share their review materials (eg, data, code files) than reviews in journals without such mandates (16/87 (18%) v 4/213 (2%)).<br><br>CONCLUSION: Incomplete reporting of several recommended items for systematic reviews persists, even in reviews that claim to have followed a reporting guideline. Journal policies on data sharing might encourage sharing of review materials.},
}
@article {pmid36412269,
year = {2022},
author = {Ebenezer, TE and Low, RS and O'Neill, EC and Huang, I and DeSimone, A and Farrow, SC and Field, RA and Ginger, ML and Guerrero, SA and Hammond, M and Hampl, V and Horst, G and Ishikawa, T and Karnkowska, A and Linton, EW and Myler, P and Nakazawa, M and Cardol, P and Sánchez-Thomas, R and Saville, BJ and Shah, MR and Simpson, AGB and Sur, A and Suzuki, K and Tyler, KM and Zimba, PV and Hall, N and Field, MC},
title = {Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world.},
journal = {Biology open},
volume = {11},
number = {11},
pages = {},
pmid = {36412269},
issn = {2046-6390},
support = {BBS/E/J/000C0618/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Euglena/physiology ; Biotechnology ; Symbiosis ; },
abstract = {Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.},
}
@article {pmid36408293,
year = {2022},
author = {Ebdon, S and Bisschop, G and Lohse, K and Saccheri, I and Davies, J and , and , and , and , },
title = {The genome sequence of the orange-tip butterfly, Anthocharis cardamines (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {260},
pmid = {36408293},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.},
}
@article {pmid36407110,
year = {2022},
author = {Michel, L and Palma, K and Cerda, M and Lagadec, R and Mayeur, H and Fuentès, M and Besseau, L and Martin, P and Magnanou, E and Blader, P and Concha, ML and Mazan, S},
title = {Diversification of habenular organization and asymmetries in teleosts: Insights from the Atlantic salmon and European eel.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {1015074},
pmid = {36407110},
issn = {2296-634X},
abstract = {Habenulae asymmetries are widespread across vertebrates and analyses in zebrafish, the reference model organism for this process, have provided insight into their molecular nature, their mechanisms of formation and their important roles in the integration of environmental and internal cues with a variety of organismal adaptive responses. However, the generality of the characteristics identified in this species remains an open question, even on a relatively short evolutionary scale, in teleosts. To address this question, we have characterized the broad organization of habenulae in the Atlantic salmon and quantified the asymmetries in each of the identified subdomains. Our results show that a highly conserved partitioning into a dorsal and a ventral component is retained in the Atlantic salmon and that asymmetries are mainly observed in the former as in zebrafish. A remarkable difference is that a prominent left-restricted pax6 positive nucleus is observed in the Atlantic salmon, but undetectable in zebrafish. This nucleus is not observed outside teleosts, and harbors a complex presence/absence pattern in this group, retaining its location and cytoarchitectonic organization in an elopomorph, the European eel. These findings suggest an ancient origin and high evolvability of this trait in the taxon. Taken together, our data raise novel questions about the variability of asymmetries across teleosts and their biological significance depending on ecological contexts.},
}
@article {pmid36405737,
year = {2022},
author = {Yousaf, M and Ismail, S and Ullah, A and Bibi, S},
title = {Immuno-informatics profiling of monkeypox virus cell surface binding protein for designing a next generation multi-valent peptide-based vaccine.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1035924},
pmid = {36405737},
issn = {1664-3224},
mesh = {Humans ; *Monkeypox virus ; Molecular Docking Simulation ; Membrane Proteins ; *Mpox (monkeypox) ; Vaccines, Subunit ; Epitopes, T-Lymphocyte ; },
abstract = {Monkeypox is a viral etiological agent with hallmarks analogous to those observed in smallpox cases in the past. The ongoing outbreak of Monkeypox viral infection is becoming a global health problem. Multi-valent peptide based next generation vaccines provides us a promising solution to combat these emerging infectious diseases by eliciting cell-mediated and humoral immune response. Considering the success rate of subtractive proteomics pipeline and reverse vaccinology approach, in this study, we have developed a novel, next-generation, multi-valent, in silico peptide based vaccine construct by employing cell surface binding protein. After analyzing physiochemical and biological properties of the selected target, the protein was subjected to B cell derived T cell epitope mapping. Iterative scrutinization lead to the identification of two highly antigenic, virulent, non-allergic, non-toxic, water soluble, and Interferon-gamma inducer epitopes i.e. HYITENYRN and TTSPVRENY. We estimated that the shortlisted epitopes for vaccine construction, roughly correspond to 99.74% of the world's population. UK, Finland and Sweden had the highest overall population coverage at 100% which is followed by Austria (99.99%), Germany (99.99%), France (99.98%), Poland (99.96), Croatia (99.93), Czech Republic (99.87%), Belgium (99.87), Italy (99.86%), China (97.83%), India (97.35%) and Pakistan (97.13%). The designed vaccine construct comprises of 150 amino acids with a molecular weight of 16.97242 kDa. Molecular docking studies of the modelled MEMPV (Multi-epitope Monkeypox Vaccine) with MHC I (PDB ID: 1I1Y), MHC II (PDB ID: 1KG0), and other immune mediators i.e. toll like receptors TLR3 (PDB ID: 2A0Z), and TLR4 (PDB ID: 4G8A) revealed strong binding affinity with immune receptors. Host immune simulation results predicted that the designed vaccine has strong potency to induce immune responses against target pathogen in the form of cellular and antibody-dependent immunity. Our findings suggest that the hypothesized vaccine candidate can be utilized as a potential therapeutic against Monkeypox however experimental study is required to validate the results and safe immunogenicity.},
}
@article {pmid36400569,
year = {2023},
author = {Wu, L and Yan, B and Han, J and Li, R and Xiao, J and He, S and Bo, X},
title = {TOXRIC: a comprehensive database of toxicological data and benchmarks.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D1432-D1445},
pmid = {36400569},
issn = {1362-4962},
mesh = {Humans ; Benchmarking ; *Databases, Factual ; *Toxicology/methods ; Software ; },
abstract = {The toxic effects of compounds on environment, humans, and other organisms have been a major focus of many research areas, including drug discovery and ecological research. Identifying the potential toxicity in the early stage of compound/drug discovery is critical. The rapid development of computational methods for evaluating various toxicity categories has increased the need for comprehensive and system-level collection of toxicological data, associated attributes, and benchmarks. To contribute toward this goal, we proposed TOXRIC (https://toxric.bioinforai.tech/), a database with comprehensive toxicological data, standardized attribute data, practical benchmarks, informative visualization of molecular representations, and an intuitive function interface. The data stored in TOXRIC contains 113 372 compounds, 13 toxicity categories, 1474 toxicity endpoints covering in vivo/in vitro endpoints and 39 feature types, covering structural, target, transcriptome, metabolic data, and other descriptors. All the curated datasets of endpoints and features can be retrieved, downloaded and directly used as output or input to Machine Learning (ML)-based prediction models. In addition to serving as a data repository, TOXRIC also provides visualization of benchmarks and molecular representations for all endpoint datasets. Based on these results, researchers can better understand and select optimal feature types, molecular representations, and baseline algorithms for each endpoint prediction task. We believe that the rich information on compound toxicology, ML-ready datasets, benchmarks and molecular representation distribution can greatly facilitate toxicological investigations, interpretation of toxicological mechanisms, compound/drug discovery and the development of computational methods.},
}
@article {pmid36399502,
year = {2023},
author = {Camargo, AP and Nayfach, S and Chen, IA and Palaniappan, K and Ratner, A and Chu, K and Ritter, SJ and Reddy, TBK and Mukherjee, S and Schulz, F and Call, L and Neches, RY and Woyke, T and Ivanova, NN and Eloe-Fadrosh, EA and Kyrpides, NC and Roux, S},
title = {IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D733-D743},
pmid = {36399502},
issn = {1362-4962},
mesh = {*Databases, Genetic ; *Genome, Viral ; Metadata ; Metagenomics ; Software ; },
abstract = {Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.},
}
@article {pmid36399496,
year = {2023},
author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D603-D610},
pmid = {36399496},
issn = {1362-4962},
support = {F32 AT011475/AT/NCCIH NIH HHS/United States ; R01 AI155694/AI/NIAID NIH HHS/United States ; U24 AT010811/AT/NCCIH NIH HHS/United States ; },
mesh = {*Genomics ; *Genome ; Multigene Family ; Biosynthetic Pathways/genetics ; },
abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}
@article {pmid36394851,
year = {2023},
author = {Zhang, L and Gong, R and Shi, L and Wen, M and Sun, X and Yabroff, KR and Han, X},
title = {Association of Residential Racial and Economic Segregation With Cancer Mortality in the US.},
journal = {JAMA oncology},
volume = {9},
number = {1},
pages = {122-126},
pmid = {36394851},
issn = {2374-2445},
mesh = {Male ; Female ; Humans ; Racial Groups ; Residential Segregation ; Risk Factors ; *Racism ; Health Status Disparities ; *Neoplasms ; },
abstract = {IMPORTANCE: Residential segregation is a structural risk factor for poor cancer outcomes. Previous research examining the association of residential segregation with cancer outcomes was limited by older data, restricted geographic areas, and few cancer sites. To guide targeted interventions, a comprehensive evaluation of the association between segregation and cancer outcomes is needed.<br><br>OBJECTIVE: To examine the association of residential racial and economic segregation with cancer mortality at the US county level for all cancers combined and for the 13 cancer types that represent the top 10 causes of cancer deaths in males or females.<br><br>This ecological study used county-level sociodemographic data from the 2015-2019 American Community Survey linked with 2015-2019 county-level mortality data. Data analysis was performed from September 2021 to April 2022.<br><br>EXPOSURES: Residential racial and economic segregation measured by the Index of Concentration at the Extremes (ICE) and categorized into quintiles 1 (most deprived) through 5 (most privileged).<br><br>MAIN OUTCOMES AND MEASURES: Age-adjusted cancer mortality was the outcome. Multilevel linear mixed modeling was used to calculate the adjusted mortality rate ratio (aRR).<br><br>RESULTS: A total of 3110 counties were included. The age-adjusted mortality rates of all cancers combined were 179.8, 177.3, 167.6, 159.6, and 146.1 per 100&#x202f;000 population (P&#x2009;<&#x2009;.001 for trend) for the 5 ICE categories (most deprived to least deprived), respectively. Compared with the least deprived counties, aRRs for all cancers combined were 1.22 (95% CI, 1.20-1.24) for the most deprived counties, followed by 1.17 (95% CI, 1.15-1.19), 1.10 (95% CI, 1.09-1.12), and 1.06 (95% CI, 1.04-1.08) for the other 3 quintiles, respectively (P&#x2009;<&#x2009;.001 for trend). Segregation was associated with increased mortality from 12 of 13 selected cancer sites, in which aRRs ranged from 1.06 (95% CI, 1.02-1.09) for brain and other nervous system cancer to 1.49 (95% CI, 1.43-1.54) for lung and bronchus cancer.<br><br>CONCLUSIONS AND RELEVANCE: The findings of this ecological study suggest that residential racial and economic segregation is associated with higher cancer mortality at the county level, highlighting opportunities for geographically targeted cancer prevention and control efforts.},
}
@article {pmid36384190,
year = {2023},
author = {Liu, H and Wu, M and Gao, H and Gao, J and Wang, S},
title = {Application of [15]N tracing and bioinformatics for estimating microbial-mediated nitrogen cycle processes in oil-contaminated soils.},
journal = {Environmental research},
volume = {217},
number = {},
pages = {114799},
doi = {10.1016/j.envres.2022.114799},
pmid = {36384190},
issn = {1096-0953},
mesh = {Nitrogen Cycle ; Nitrogen/analysis ; Soil/chemistry ; *Microbiota ; Soil Microbiology ; Computational Biology ; *Soil Pollutants/analysis ; },
abstract = {Crude oil pollution can profoundly alter the nitrogen (N) cycle in the soil. Here, a 30-day incubation with [15]N tracer approach was performed to assess the impacts of crude oil concentrations (medium: 10,000 mg kg[-1]; heavy: 50,000 mg kg[-1]) on soil N cycling based on a numerical model. Results showed that crude oil pollution significantly increased the gross N-transformation rates, but the rates of oxidation of recalcitrant organic N, the immbolization of NO3[-] and the adsorption of NH4[+] changed differently as a function of hydrocarbon concentrations. There was no significant difference of the oxidation rate of recalcitrant organic N between the medium and heavy oil-contaminated soils (medium: 0.1149 mmol N kg[-1] d[-1]; heavy: 0.1299 mmol N kg[-1] d[-1]), but the rates of NO3[-] immobilization (0.1135 mmol N kg[-1] d[-1]) and NH4[+] adsorption were the highest (0.1148 mmol N kg[-1] d[-1]) in the moderately oil-contaminated soils than those in the heavy polluted soil (0.0849 mmol N kg[-1] d[-1] and 0.0034 mmol N kg[-1] d[-1], respectively). The NO3[-] immobilization rate was 2.5-fold higher than its reduction rate, indicating that NO3[-] immobilization played a more important role during the process of NO3[-] transformation. Microbial community structure analysis indicated that phyla of Actinobacteria and Ascomycota respectively promoted the immobilization of NO3[-] to recalcitrant organic N and the reduction of NO3[-] to NH4[+]. The genus of Aspergillus was related to net NH4[+] production, and the genera of Penicillium and Acremonium were responsible for oxidation of recalcitrant organic N to NO3[-].},
}
@article {pmid36383289,
year = {2022},
author = {McGuinness, KN and Klau, GW and Morrison, SM and Moore, EK and Seipp, J and Falkowski, PG and Nanda, V},
title = {Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution.},
journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
volume = {52},
number = {4},
pages = {263-275},
pmid = {36383289},
issn = {1573-0875},
support = {K12GM093854/NH/NIH HHS/United States ; 80NSSC18M0093//NASA Astrobiology Institute/ ; K12GM093854/NH/NIH HHS/United States ; },
mesh = {*Metalloproteins ; Minerals ; *Iron-Sulfur Proteins/chemistry/metabolism ; Sulfur/chemistry/metabolism ; Iron/chemistry ; },
abstract = {Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfide minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infinite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are finite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a finite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere.},
}
@article {pmid36378489,
year = {2022},
author = {Gupta, VK and Bakshi, U and Chang, D and Lee, AR and Davis, JM and Chandrasekaran, S and Jin, YS and Freeman, MF and Sung, J},
title = {TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes.},
journal = {mSystems},
volume = {7},
number = {6},
pages = {e0092522},
pmid = {36378489},
issn = {2379-5077},
support = {R35 GM133475/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Metagenome/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Multigene Family/genetics ; },
abstract = {Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.},
}
@article {pmid36378100,
year = {2022},
author = {Oh, AY and Rising, CJ and Gaysynsky, A and Tsakraklides, S and Huang, GC and Chou, WS and Blake, KD and Vanderpool, RC},
title = {Advancing multi-level health communication research: A Delphi study on barriers and opportunities.},
journal = {Translational behavioral medicine},
volume = {12},
number = {12},
pages = {1133-1145},
pmid = {36378100},
issn = {1613-9860},
support = {HHSN261201800002B/CA/NCI NIH HHS/United States ; HHSN261201800002C/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Delphi Technique ; *Interdisciplinary Communication ; Consensus ; Surveys and Questionnaires ; *Health Communication ; },
abstract = {Adopting a multi-level perspective that considers the many interrelated contexts influencing health could make health communication interventions more effective and equitable. However, despite increasing interest in the use of multi-level approaches, multi-level health communication (MLHC) interventions are infrequently utilized. We therefore sought to conduct a modified Delphi study to better understand how researchers conceptualize MLHC interventions and identify opportunities for advancing MLHC work. Communication and health behavior experts were invited to complete two rounds of surveys about the characteristics, benefits, pitfalls, best practices, barriers, and facilitators of MLHC interventions; the role of technology in facilitating MLHC interventions; and ways to advance MLHC intervention research (46 experts completed the first survey, 44 completed both surveys). Survey data were analyzed using a mixed-methods approach. Panelists reached consensus on two components of the proposed definition of MLHC interventions and also put forward a set of best practices for these interventions. Panelists felt that most health intervention research could benefit from a multi-level approach, and generally agreed that MLHC approaches offered certain advantages over single-level approaches. However, they also expressed concern related to the time, cost, and complexity of MLHC interventions. Although panelists felt that technology could potentially support MLHC interventions, they also recognized the potential for technology to exacerbate disparities. Finally, panelists prioritized a set of methodological advances and practical supports that would be needed to facilitate future MLHC intervention research. The results of this study point to several future directions for the field, including advancing how interactions between levels are assessed, increasing the empirical evidence base demonstrating the advantages of MLHC interventions, and identifying best practices for the use of technology. The findings also suggest that researchers may need additional support to overcome the perceived practical challenges of conducting MLHC interventions.},
}
@article {pmid36374834,
year = {2022},
author = {Boyle, BL and Maitner, BS and Barbosa, GGC and Sajja, RK and Feng, X and Merow, C and Newman, EA and Park, DS and Roehrdanz, PR and Enquist, BJ},
title = {Geographic name resolution service: A tool for the standardization and indexing of world political division names, with applications to species distribution modeling.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0268162},
pmid = {36374834},
issn = {1932-6203},
mesh = {Databases, Factual ; *Biodiversity ; *Names ; Reference Standards ; },
abstract = {Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This otherwise simple validation is complicated by the difficulty of matching political division names to the correct geospatial object. Spelling errors, abbreviations, alternative codes, and synonyms in multiple languages present daunting name disambiguation challenges. The inability to resolve political division names reduces usable data, and analysis of erroneous observations can lead to flawed results. Here, we present the Geographic Name Resolution Service (GNRS), an application for correcting, standardizing, and indexing world political division names. The GNRS resolves political division names against a reference database that combines names and codes from GeoNames with geospatial object identifiers from the Global Administrative Areas Database (GADM). In a trial resolution of political division names extracted from >270 million species occurrences, only 1.9%, representing just 6% of occurrences, matched exactly to GADM political divisions in their original form. The GNRS was able to resolve, completely or in part, 92% of the remaining 378,568 political division names, or 86% of the full biodiversity occurrence dataset. In assessing geocoordinate accuracy for >239 million species occurrences, resolution of political divisions by the GNRS enabled the detection of an order of magnitude more errors and an order of magnitude more error-free occurrences. By providing a novel solution to a significant data quality impediment, the GNRS liberates a tremendous amount of biodiversity data for quantitative biodiversity research. The GNRS runs as a web service and is accessible via an API, an R package, and a web-based graphical user interface. Its modular architecture is easily integrated into existing data validation workflows.},
}
@article {pmid36371952,
year = {2023},
author = {Zhao, H and Liu, X and Jiang, T and Cai, C and Gu, K and Liu, Y and He, P},
title = {Activated abscisic acid pathway and C4 pathway, inhibited cell cycle progression, responses of Ulva prolifera to short term high temperature elucidated by multi-omics.},
journal = {Marine environmental research},
volume = {183},
number = {},
pages = {105796},
doi = {10.1016/j.marenvres.2022.105796},
pmid = {36371952},
issn = {1879-0291},
mesh = {*Ulva/metabolism ; Temperature ; Abscisic Acid/metabolism ; Multiomics ; Cell Cycle ; Eutrophication ; China ; },
abstract = {The annual outbreak of green tides since 2007 has destroyed coastal waters' ecological environment and caused substantial economic losses. Ulva prolifera, known as the dominant species of green tides, is influenced by temperatures. Omics-based technology was used to analyze U. prolifera under 12 h of treatment at 30 °C in the work. High temperature has the following advantages, e.g., activating the abscisic acid signaling pathway, improving the heat tolerance of U. prolifera, up-regulating metabolites such as glycolipids, glyceroyl, and glutamic acid to maintain the stability and fluidity of cells, and reducing the stimulatory effect of external stress on cells. The key genes and proteins of the tricarboxylic acid cycle, glycolysis, and pentose phosphorylation pathways were inhibited; however, the key enzyme pyruvate phospho-dikinase of the C4 pathway was up-regulated. The C4 pathway was activated in U. prolifera in response to high-temperature stress and may play a key role in photosynthesis. Besides, U. prolifera metabolizing amino acids was active. High temperature inhibited genes and proteins related to DNA replication and cell cycle in the transcriptome and proteome as well as the growth and reproduction of U. prolifera.},
}
@article {pmid36365380,
year = {2022},
author = {Ganie, IB and Ahmad, Z and Shahzad, A and Zaushintsena, A and Neverova, O and Ivanova, S and Wasi, A and Tahseen, S},
title = {Biotechnological Intervention and Secondary Metabolite Production in Centella asiatica L.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
pmid = {36365380},
issn = {2223-7747},
support = {1144-r//Comprehensive Scientific and Technical Program/ ; },
abstract = {Centella asiatica L., commonly known as Gotu kola, Indian pennywort, and Asiatic pennyworts, is an herbaceous perennial plant that belongs to the family Apiaceae and has long been used in the traditional medicine system. The plant is known to produce a wide range of active metabolites such as triterpenoids including asiatic acid, asiaticoside, brahmoside, and madecassic acid along with other constituents including centellose, centelloside, and madecassoside, etc., which show immense pharmacological activity. Due to its beneficial role in neuroprotection activity, the plant has been considered as a brain tonic. However, limited cultivation, poor seed viability with low germination rate, and overexploitation for decades have led to severe depletion and threatened its wild stocks. The present review aimed to provide up-to-date information on biotechnological tools applied to this endangered medicinal plant for its in vitro propagation, direct or indirect regeneration, synthetic seed production, strategies for secondary metabolite productions including different elicitors. In addition, a proposed mechanism for the biosynthesis of triterpenoids is also discussed.},
}
@article {pmid36362326,
year = {2022},
author = {Decewicz, P and Kitowicz, M and Radlinska, M},
title = {Characteristics and Comparative Genomic Analysis of a Novel Virus, VarioGold, the First Bacteriophage of Variovorax.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
pmid = {36362326},
issn = {1422-0067},
support = {no. 2017/25/B/NZ8/00472//National Science Centre (Poland)/ ; },
mesh = {*Bacteriophages ; Prophages/genetics ; Sequence Analysis, DNA ; Computational Biology ; Genomics ; Genome, Viral ; },
abstract = {Variovorax represents a widespread and ecologically significant genus of soil bacteria. Despite the ecological importance of these bacteria, our knowledge about the viruses infecting Variovorax spp. is quite poor. This study describes the isolation and characterization of the mitomycin-induced phage, named VarioGold. To the best of our knowledge, VarioGold represents the first characterized virus for this genus. Comparative genomic analyses suggested that VarioGold is distinct from currently known bacteriophages at both the nucleotide and protein levels; thus, it could be considered a new virus genus. In addition, another 37 prophages were distinguished in silico within the complete genomic sequences of Variovorax spp. that are available in public databases. The similarity networking analysis highlighted their general high diversity, which, despite clustering with previously described phages, shows their unique genetic load. Therefore, the novelty of Variovorax phages warrants the great enrichment of databases, which could, in turn, improve bioinformatic strategies for finding (pro)phages.},
}
@article {pmid36357425,
year = {2022},
author = {Oliveira-Rodrigues, C and Correia, AM and Valente, R and Gil, &#xc1; and Gandra, M and Liberal, M and Rosso, M and Pierce, G and Sousa-Pinto, I},
title = {Assessing data bias in visual surveys from a cetacean monitoring programme.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {682},
pmid = {36357425},
issn = {2052-4463},
mesh = {Animals ; *Cetacea/physiology ; Data Collection ; Datasets as Topic ; Bias ; },
abstract = {Long-term monitoring datasets are fundamental to understand physical and ecological responses to environmental changes, supporting management and conservation. The data should be reliable, with the sources of bias identified and quantified. CETUS Project is a cetacean monitoring programme in the Eastern North Atlantic, based on visual methods of data collection. This study aims to assess data quality and bias in the CETUS dataset, by 1) applying validation methods, through photographic confirmation of species identification; 2) creating data quality criteria to evaluate the observer's experience; and 3) assessing bias to the number of sightings collected and to the success in species identification. Through photographic validation, the species identification of 10 sightings was corrected and a new species was added to the CETUS dataset. The number of sightings collected was biased by external factors, mostly by sampling effort but also by weather conditions. Ultimately, results highlight the importance of identifying and quantifying data bias, while also yielding guidelines for data collection and processing, relevant for species monitoring programmes based on visual methods.},
}
@article {pmid36352171,
year = {2022},
author = {Mohsen, A and Zeidan, B and Elshemy, M},
title = {Water quality assessment of Lake Burullus, Egypt, utilizing statistical and GIS modeling as environmental hydrology applications.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {1},
pages = {93},
pmid = {36352171},
issn = {1573-2959},
mesh = {*Water Quality ; *Lakes ; Hydrology ; Geographic Information Systems ; Egypt ; Environmental Monitoring/methods ; },
abstract = {GIS is a very powerful tool for analyzing huge amount of data and connecting them with the geography; moreover, recently, there is great advancement in the field. The main objective of this study is to assess the water quality (WQ) and trophic status (TS) conditions of Lake Burullus, Egypt, using statistical modeling (PCA/FA and CA), WQ index (L-WQI), and trophic status index (Carlson TSI and TRIX) approaches, in addition to using GIS tools for building models able to automatically calculate the various indices and producing color coded maps for the lake. The results indicated that PCA/FA grouped the twenty-four WQ parameters into nine principal components explaining 72.6% of the total variance, domestic, and agriculture pollution were dominant. CA divided the twelve sampling stations into most and least polluted groups. The lake WQ was classified as a "Very Poor," according to L-WQI. Moreover, the results of the Carlson TSI and TRIX indices were coincided and classified the eutrophication levels in the lake as "Hyper-Eutrophic" and "Elevated Trophic," respectively. Based on the results of this study, Lake Burullus needs urgent plans for recovering its WQ. Pre-treatment for its drains' effluents and implementing of a periodical WQ monitoring program are highly recommended.},
}
@article {pmid36350456,
year = {2022},
author = {Zhang, X and Dong, X and Liu, F and Lv, T and Wu, Z and Ranagalage, M},
title = {Spatiotemporal dynamics of ecological security in a typical conservation region of southern China based on catastrophe theory and GIS.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {1},
pages = {90},
doi = {10.1007/s10661-022-10669-6},
pmid = {36350456},
issn = {1573-2959},
support = {No. GJJ200542//the Science and Technology Project of Jiangxi Education Department/ ; },
mesh = {*Ecology/methods ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Environmental Monitoring ; Ecosystem ; China ; },
abstract = {Ecological security assessment can effectively reflect the ecological status of a region and reveal its level of sustainable development. In this paper, an ecological security-oriented evaluation system was constructed, and the ecological security level of the Dongjiangyuan region from 2000 to 2020 was evaluated based on catastrophe theory and GIS. The results were as follows: (1) As shown in the land use and cover maps, by 2020, the forestland area had decreased the most, and the artificial surface area had increased the most. (2) The ecological security index of the Dongjiangyuan region showed a low trend in the artificial surface area and its surrounding areas. The quite low values of the ecological security index in 2000 and 2010 were improved in 2020 due to the increase in ecological services capacity. The increased vegetation cover from 2000 to 2020 promoted the improved ecological service capacity. (3) The rapid urbanization process in the Dongjiangyuan region resulted in a lower ecological sensitivity index value. Notably, the ecological sensitivity index of the study area had a slightly decreasing trend. (4) The spatial autocorrelation showed that the proportion of hot and cold spots from 2000 to 2020 decreased by 2.96% and 6.91%, respectively. This study can provide a scientific basis and decision-making guidance for ecological management in the Dongjiangyuan region in the future.},
}
@article {pmid36348471,
year = {2022},
author = {Baaijens, JA and Zulli, A and Ott, IM and Nika, I and van der Lugt, MJ and Petrone, ME and Alpert, T and Fauver, JR and Kalinich, CC and Vogels, CBF and Breban, MI and Duvallet, C and McElroy, KA and Ghaeli, N and Imakaev, M and Mckenzie-Bennett, MF and Robison, K and Plocik, A and Schilling, R and Pierson, M and Littlefield, R and Spencer, ML and Simen, BB and , and Hanage, WP and Grubaugh, ND and Peccia, J and Baym, M},
title = {Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {236},
pmid = {36348471},
issn = {1474-760X},
support = {T35 HL007649/HL/NHLBI NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R35 GM133700/GM/NIGMS NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; TL1 TR001864/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *SARS-CoV-2/genetics ; Wastewater ; RNA, Viral/genetics ; Transcriptome ; *COVID-19 ; },
abstract = {Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable.},
}
@article {pmid36344967,
year = {2022},
author = {Toh, H and Yang, C and Formenti, G and Raja, K and Yan, L and Tracey, A and Chow, W and Howe, K and Bergeron, LA and Zhang, G and Haase, B and Mountcastle, J and Fedrigo, O and Fogg, J and Kirilenko, B and Munegowda, C and Hiller, M and Jain, A and Kihara, D and Rhie, A and Phillippy, AM and Swanson, SA and Jiang, P and Clegg, DO and Jarvis, ED and Thomson, JA and Stewart, R and Chaisson, MJP and Bukhman, YV},
title = {A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.},
journal = {BMC biology},
volume = {20},
number = {1},
pages = {245},
pmid = {36344967},
issn = {1741-7007},
mesh = {Humans ; Animals ; Haplotypes ; *Diabetes Mellitus, Type 2/genetics ; Murinae ; Genome ; Genomics ; },
abstract = {BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.<br><br>RESULTS: We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.<br><br>CONCLUSIONS: Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.},
}
@article {pmid36334202,
year = {2023},
author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y},
title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {9},
pages = {24284-24298},
pmid = {36334202},
issn = {1614-7499},
support = {21-1-4-sf-11-nsh//science and technology program for public wellbeing of qingdao/ ; },
mesh = {*Denitrification ; Bioreactors/microbiology ; Seasons ; Multiomics ; Proteomics ; *Microbiota ; Biofilms ; Nitrogen ; },
abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.},
}
@article {pmid36333350,
year = {2022},
author = {Zhang, X and Zhang, B and Li, J and Yao, Y and Wang, J and Liu, J and Yu, F},
title = {A database of seed plants on taxonomy, geography and ecology in the Qinling-Daba Mountains and adjacent areas.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {672},
pmid = {36333350},
issn = {2052-4463},
mesh = {Humans ; *Biodiversity ; China ; Ecology ; Ecosystem ; Geography ; Plants ; *Seeds ; Databases, Factual ; },
abstract = {The Qinling-Daba Mountains span subtropical and warm temperate zones and are one of the most remarkable biodiversity hotspots in China. Establishing a complete checklist of seed plants organized by nature reserves in the Qinling-Daba Mountains and adjacent areas is an important basis for managing and utilizing plant resources. First, we collected seed plant species data from published checklists representing 58 nature reserves in the Qinling-Daba Mountains and adjacent areas; second, we comprehensively and systematically sorted and integrated these data; third, we proofread and revised the data with the help of the R language and Flora of China dataset; and finally, we set up a seed plant database containing 96148 records, including the name, order, family, genus, life form, and endemism of each species for the entirety of the Qinling-Daba Mountains. The database contains 9491 species of seed plants belonging to 1729 genera, 211 families, and 59 orders, accounting for 39% of China's seed plants.},
}
@article {pmid36329351,
year = {2022},
author = {Pillay, R and Watson, JEM and Hansen, AJ and Jantz, PA and Aragon-Osejo, J and Armenteras, D and Atkinson, SC and Burns, P and Ervin, J and Goetz, SJ and González-Del-Pliego, P and Robinson, NP and Supples, C and Virnig, ALS and Williams, BA and Venter, O},
title = {Humid tropical vertebrates are at lower risk of extinction and population decline in forests with higher structural integrity.},
journal = {Nature ecology &amp; evolution},
volume = {6},
number = {12},
pages = {1840-1849},
pmid = {36329351},
issn = {2397-334X},
mesh = {Animals ; Humans ; *Tropical Climate ; *Conservation of Natural Resources ; Forests ; Biodiversity ; Vertebrates ; },
abstract = {Reducing deforestation underpins global biodiversity conservation efforts. However, this focus on retaining forest cover overlooks the multitude of anthropogenic pressures that can degrade forest quality and imperil biodiversity. We use remotely sensed indices of tropical rainforest structural condition and associated human pressures to quantify the relative importance of forest cover, structural condition and integrity (the cumulative effect of condition and pressures) on vertebrate species extinction risk and population trends across the global humid tropics. We found that tropical rainforests of high integrity (structurally intact and under low pressures) were associated with lower likelihood of species being threatened and having declining populations, compared with forest cover alone (without consideration of condition and pressures). Further, species were more likely to be threatened or have declining populations if their geographic ranges contained high proportions of degraded forest than if their ranges contained lower proportions of forest cover but of high quality. Our work suggests that biodiversity conservation policies to preserve forest integrity are now urgently required alongside ongoing efforts to halt deforestation in the hyperdiverse humid tropics.},
}
@article {pmid36324785,
year = {2022},
author = {Gao, Y and Gong, L and Liu, H and Kong, Y and Wu, X and Guo, Y and Hu, D},
title = {Research on the influencing factors of users' information processing in online health communities based on heuristic-systematic model.},
journal = {Frontiers in psychology},
volume = {13},
number = {},
pages = {966033},
pmid = {36324785},
issn = {1664-1078},
abstract = {With the rapid development of the Internet and the normalization of COVID-19 epidemic prevention and control, Online health communities (OHCs) have gradually become one of the important ways for people to obtain health information, and users have to go through a series of information processing when facing the massive amount of data. Understanding the factors influencing user information processing is necessary to promote users' health literacy, health knowledge popularization and health behavior shaping. Based on the Heuristic-Systematic Model (HSM), Information Ecology Theory, Privacy Trade-Off and Self-Efficacy Theory, we constructed a model of factors influencing user information processing in online health communities. We found that information quality and emotional support had indirect effects on heuristic and systematic information processing, and these effects were mediated by privacy concerns and self-efficacy. In our research model, systematic information processing was most positively influenced directly by self-efficacy. Privacy concerns had a direct negative correlation with both dual information processing pathways. Therefore, OHCs managers should develop relevant regulations to ensure the information quality in OHCs and improve privacy protection services to promote user information processing by improving users' self-efficacy and reducing their privacy concerns. Providing a user-friendly and interactive environment for users is also recommended to create more emotional support, thus facilitating more systematic information processing.},
}
@article {pmid36324701,
year = {2022},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the angle shades moth, Phlogophora meticulosa (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {89},
pmid = {36324701},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Phlogophora meticulosa (the angle shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 539 megabases in span. The majority of the assembly, 95.17%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Some unassigned scaffolds are identified as belonging to the W chromosome based on half-depth coverage and comparison to other Noctuidae W chromosomes. The mitochondrial genome was also assembled and is 15.4 kilobases in length.},
}
@article {pmid36323316,
year = {2022},
author = {Vatanen, T and Ang, QY and Siegwald, L and Sarker, SA and Le Roy, CI and Duboux, S and Delannoy-Bruno, O and Ngom-Bru, C and Boulangé, CL and Stražar, M and Avila-Pacheco, J and Deik, A and Pierce, K and Bullock, K and Dennis, C and Sultana, S and Sayed, S and Rahman, M and Ahmed, T and Modesto, M and Mattarelli, P and Clish, CB and Vlamakis, H and Plichta, DR and Sakwinska, O and Xavier, RJ},
title = {A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning.},
journal = {Cell},
volume = {185},
number = {23},
pages = {4280-4297.e12},
doi = {10.1016/j.cell.2022.10.011},
pmid = {36323316},
issn = {1097-4172},
mesh = {Infant ; Child ; Female ; Humans ; Child, Preschool ; *Bifidobacterium longum/metabolism ; Bifidobacterium/metabolism ; Weaning ; Oligosaccharides/metabolism ; Bangladesh ; Milk, Human ; Feces/microbiology ; },
abstract = {The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates. The clade was highly prevalent in Bangladesh, present globally (at lower prevalence), and correlated with many other gut taxa and metabolites, indicating an important role in gut ecology. We also found that the B. longum clades and associated metabolites were implicated in childhood diarrhea and early growth, including positive associations between growth measures and B. longum subsp. infantis, indolelactate and N-acetylglutamate. Our data demonstrate geographic, cultural, seasonal, and ecological heterogeneity that should be accounted for when identifying microbiome factors implicated in and potentially benefiting infant development.},
}
@article {pmid36322519,
year = {2022},
author = {Wood, ALC and Kirby, KR and Ember, CR and Silbert, S and Passmore, S and Daikoku, H and McBride, J and Paulay, F and Flory, MJ and Szinger, J and D'Arcangelo, G and Bradley, KK and Guarino, M and Atayeva, M and Rifkin, J and Baron, V and El Hajli, M and Szinger, M and Savage, PE},
title = {The Global Jukebox: A public database of performing arts and culture.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0275469},
pmid = {36322519},
issn = {1932-6203},
mesh = {Humans ; Reproducibility of Results ; *Music ; Cross-Cultural Comparison ; Language ; Databases, Factual ; Culture ; },
abstract = {Standardized cross-cultural databases of the arts are critical to a balanced scientific understanding of the performing arts, and their role in other domains of human society. This paper introduces the Global Jukebox as a resource for comparative and cross-cultural study of the performing arts and culture. The Global Jukebox adds an extensive and detailed global database of the performing arts that enlarges our understanding of human cultural diversity. Initially prototyped by Alan Lomax in the 1980s, its core is the Cantometrics dataset, encompassing standardized codings on 37 aspects of musical style for 5,776 traditional songs from 1,026 societies. The Cantometrics dataset has been cleaned and checked for reliability and accuracy, and includes a full coding guide with audio training examples (https://theglobaljukebox.org/?songsofearth). Also being released are seven additional datasets coding and describing instrumentation, conversation, popular music, vowel and consonant placement, breath management, social factors, and societies. For the first time, all digitized Global Jukebox data are being made available in open-access, downloadable format (https://github.com/theglobaljukebox), linked with streaming audio recordings (theglobaljukebox.org) to the maximum extent allowed while respecting copyright and the wishes of culture-bearers. The data are cross-indexed with the Database of Peoples, Languages, and Cultures (D-PLACE) to allow researchers to test hypotheses about worldwide coevolution of aesthetic patterns and traditions. As an example, we analyze the global relationship between song style and societal complexity, showing that they are robustly related, in contrast to previous critiques claiming that these proposed relationships were an artifact of autocorrelation (though causal mechanisms remain unresolved).},
}
@article {pmid36318246,
year = {2023},
author = {Lei, B and Xu, Y and Lei, Y and Li, C and Zhou, P and Wang, L and Yang, Q and Li, X and Li, F and Liu, C and Cui, C and Chen, T and Ni, W and Hu, S},
title = {CRAMdb: a comprehensive database for composition and roles of microbiome in animals.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D700-D707},
pmid = {36318246},
issn = {1362-4962},
mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Databases, Factual ; },
abstract = {CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals. It focuses on the composition and roles of the microbiome in various animal species. The main goal of the CRAMdb is to facilitate the reuse of animal metagenomic data, and enable cross-host and cross-phenotype comparisons. To this end, we consistently annotated microbiomes (including 16S, 18S, ITS and metagenomics sequencing data) of 516 animals from 475 projects spanning 43 phenotype pairs to construct the database that is equipped with 9430 bacteria, 278 archaea, 2216 fungi and 458 viruses. CRAMdb provides two main contents: microbiome composition data, illustrating the landscape of the microbiota (bacteria, archaea, fungi, and viruses) in various animal species, and microbiome association data, revealing the relationships between the microbiota and various phenotypes across different animal species. More importantly, users can quickly compare the composition of the microbiota of interest cross-host or body site and the associated taxa that differ between phenotype pairs cross-host or cross-phenotype. CRAMdb is freely available at (http://www.ehbio.com/CRAMdb).},
}
@article {pmid36316770,
year = {2022},
author = {Ohashi, K and Osanai, T and Fujiwara, K and Tanikawa, T and Tani, Y and Takamiya, S and Sato, H and Morii, Y and Bando, K and Ogasawara, K},
title = {Spatial-temporal analysis of cerebral infarction mortality in Hokkaido, Japan: an ecological study using a conditional autoregressive model.},
journal = {International journal of health geographics},
volume = {21},
number = {1},
pages = {16},
pmid = {36316770},
issn = {1476-072X},
mesh = {Humans ; Bayes Theorem ; Japan/epidemiology ; *Stroke ; Socioeconomic Factors ; Cerebral Infarction/diagnosis/epidemiology/therapy ; },
abstract = {BACKGROUND: Accessibility to stroke treatments is a challenge that depends on the place of residence. However, recent advances in medical technology have improved health outcomes. Nevertheless, the geographic heterogeneity of medical resources may increase regional disparities. Therefore, evaluating spatial and temporal influences of the medical system on regional outcomes and advanced treatment of cerebral infarction are important from a health policy perspective. This spatial and temporal study aims to identify factors associated with mortality and to clarify regional disparities in cerebral infarction mortality at municipality level.<br><br>METHODS: This ecological study used public data between 2010 and 2020 from municipalities in Hokkaido, Japan. We applied spatial and temporal condition autoregression analysis in a Bayesian setting, with inference based on the Markov chain Monte Carlo simulation. The response variable was the number of deaths due to cerebral infarction (ICD-10 code: I63). The explanatory variables were healthcare accessibility and socioeconomic status.<br><br>RESULTS: The large number of emergency hospitals per 10,000 people (relative risk (RR)&#x2009;=&#x2009;0.906, credible interval (Cr)&#x2009;=&#x2009;0.861 to 0.954) was associated with low mortality. On the other hand, the large number of general hospitals per 10,000 people (RR&#x2009;=&#x2009;1.123, Cr&#x2009;=&#x2009;1.068 to 1.178) and longer distance to primary stroke centers (RR&#x2009;=&#x2009;1.064, Cr&#x2009;=&#x2009;1.014 to 1.110) were associated with high mortality. The standardized mortality ratio decreased from 2010 to 2020 in Hokkaido by approximately 44%. Regional disparity in mortality remained at the same level from 2010 to 2015, after which it narrowed by approximately 5% to 2020. After mapping, we identified municipalities with high mortality rates that emerged in Hokkaido's central and northeastern parts.<br><br>CONCLUSION: Cerebral infarction mortality rates and the disparity in Hokkaido improved during the study period (2010-2020). This study emphasized that healthcare accessibility through places such as emergency hospitals and primary stroke centers was important in determining cerebral infarction mortality at the municipality level. In addition, this study identified municipalities with high mortality rates that require healthcare policy changes. The impact of socioeconomic factors on stroke is a global challenge, and improving access to healthcare may reduce disparities in outcomes.},
}
@article {pmid36316345,
year = {2022},
author = {Yfantidou, S and Karagianni, C and Efstathiou, S and Vakali, A and Palotti, J and Giakatos, DP and Marchioro, T and Kazlouski, A and Ferrari, E and Girdzijauskas, &#x160;},
title = {LifeSnaps, a 4-month multi-modal dataset capturing unobtrusive snapshots of our lives in the wild.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {663},
pmid = {36316345},
issn = {2052-4463},
support = {RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; RAIS No 813162//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; },
mesh = {Humans ; *Ecological Momentary Assessment ; Exercise ; *Mental Health ; Sleep ; Surveys and Questionnaires ; },
abstract = {Ubiquitous self-tracking technologies have penetrated various aspects of our lives, from physical and mental health monitoring to fitness and entertainment. Yet, limited data exist on the association between in the wild large-scale physical activity patterns, sleep, stress, and overall health, and behavioral and psychological patterns due to challenges in collecting and releasing such datasets, including waning user engagement or privacy considerations. In this paper, we present the LifeSnaps dataset, a multi-modal, longitudinal, and geographically-distributed dataset containing a plethora of anthropological data, collected unobtrusively for the total course of more than 4 months by n = 71 participants. LifeSnaps contains more than 35 different data types from second to daily granularity, totaling more than 71 M rows of data. The participants contributed their data through validated surveys, ecological momentary assessments, and a Fitbit Sense smartwatch and consented to make these data available to empower future research. We envision that releasing this large-scale dataset of multi-modal real-world data will open novel research opportunities and potential applications in multiple disciplines.},
}
@article {pmid36311410,
year = {2022},
author = {Nicotra, AB and Geange, SR and Bahar, NHA and Carle, H and Catling, A and Garcia, A and Harris, RJ and Head, ML and Jin, M and Whitehead, MR and Zurcher, H and Beckmann, EA},
title = {An innovative approach to using an intensive field course to build scientific and professional skills.},
journal = {Ecology and evolution},
volume = {12},
number = {10},
pages = {e9446},
pmid = {36311410},
issn = {2045-7758},
abstract = {This paper reports on the design and evaluation of Field Studies in Functional Ecology (FSFE), a two-week intensive residential field course that enables students to master core content in functional ecology alongside skills that facilitate their transition from "student" to "scientist." We provide an overview of the course structure, showing how the constituent elements have been designed and refined over successive iterations of the course. We detail how FSFE students: (1) Work closely with discipline specialists to develop a small group project that tests an hypothesis to answer a genuine scientific question in the field; (2) Learn critical skills of data management and communication; and (3) Analyze, interpret, and present their results in the format of a scientific symposium. This process is repeated in an iterative "cognitive apprenticeship" model, supported by a series of workshops that name and explicitly instruct the students in "hard" and "soft" skills (e.g., statistics and teamwork, respectively) critically relevant for research and other careers. FSFE students develop a coherent and nuanced understanding of how to approach and execute ecological studies. The sophisticated knowledge and ecological research skills that they develop during the course is demonstrated through high-quality presentations and peer-reviewed publications in an open-access, student-led journal. We outline our course structure and evaluate its efficacy to show how this novel combination of field course elements allows students to gain maximum value from their educational journey, and to develop cognitive, affective, and reflective tools to help apply their skills as scientists.},
}
@article {pmid36308510,
year = {2023},
author = {Sun, Y and Chang, J and Fang, J},
title = {Above- and belowground net-primary productivity: A field-based global database of grasslands.},
journal = {Ecology},
volume = {104},
number = {2},
pages = {e3904},
doi = {10.1002/ecy.3904},
pmid = {36308510},
issn = {1939-9170},
mesh = {*Ecosystem ; *Grassland ; Temperature ; Databases, Factual ; Carbon ; },
abstract = {Net primary productivity (NPP) over global grasslands is crucial for understanding the terrestrial carbon cycling and for the assessments of wild herbivores food security. During the past few decades, numerous field investigations have been conducted to estimate grassland NPP since the measuring criterion released by the International Biological Program. However, a comprehensive NPP database, particularly for belowground NPP (BNPP), in global grasslands is rare to date. Here, field NPP measurements from 438 publications (1957-2018) in global grasslands were collected, critically filtered, and incorporated in a comprehensive global database with observations for aboveground NPP (ANPP), BNPP, total NPP (TNPP), and BNPP fraction (fBNPP). Associated information on geographical locations, climatic records, grassland types, land use patterns, manipulations subjected to manipulative experiments, sampling year of study sites, as well as NPP measurement methods are also documented. This database included 2985 entries from 1785 study sites. Among them, 806 entries contained paired data of ANPP and BNPP, resulting in the 806 fBNPP data. The study sites encompassed global grasslands with latitudinal range of 54.5° S~78.9° N, longitudinal range of 157.4° W~175.8° E, and altitudes from 0 to 5168 m above sea level, covering broad climatic gradients (-17.6 to 28.8°C in mean annual temperature and 63-2052 mm in mean annual precipitation). This global database is the world's largest paired data of ANPP and BNPP field measurements in grasslands. It can be used to study the spatio-temporal patterns of NPP and its allocation, evaluate the responses of above- and below-ground carbon components to future global changes, and validate the NPP estimation by empirical or process-based models in global grasslands. The database can be freely used for noncommercial applications. We kindly request users cite this data paper when using the database, respecting all the hard work during data compilation.},
}
@article {pmid36305818,
year = {2023},
author = {Chen, Y and Zhang, X and Peng, X and Jin, Y and Ding, P and Xiao, J and Li, C and Wang, F and Chang, A and Yue, Q and Pu, M and Chen, P and Shen, J and Li, M and Jia, T and Wang, H and Huang, L and Guo, G and Zhang, W and Liu, H and Wang, X and Chen, D},
title = {SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D1150-D1159},
pmid = {36305818},
issn = {1362-4962},
mesh = {*Databases, Factual ; *Single-Cell Analysis ; Humans ; Animals ; Biological Evolution ; Plants/genetics ; Ecology ; },
abstract = {It is a challenge to efficiently integrate and present the tremendous amounts of single-cell data generated from multiple tissues of various species. Here, we create a new database named SPEED for single-cell pan-species atlas in the light of ecology and evolution for development and diseases (freely accessible at http://8.142.154.29 or http://speedatlas.net). SPEED is an online platform with 4 data modules, 7 function modules and 2 display modules. The 'Pan' module is applied for the interactive analysis of single cell sequencing datasets from 127 species, and the 'Evo', 'Devo', and 'Diz' modules provide comprehensive analysis of single-cell atlases on 18 evolution datasets, 28 development datasets, and 85 disease datasets. The 'C2C', 'G2G' and 'S2S' modules explore intercellular communications, genetic regulatory networks, and cross-species molecular evolution. The 'sSearch', 'sMarker', 'sUp', and 'sDown' modules allow users to retrieve specific data information, obtain common marker genes for cell types, freely upload, and download single-cell datasets, respectively. Two display modules ('HOME' and 'HELP') offer easier access to the SPEED database with informative statistics and detailed guidelines. All in all, SPEED is an integrated platform for single-cell RNA sequencing (scRNA-seq) and single-cell whole-genome sequencing (scWGS) datasets to assist the deep-mining and understanding of heterogeneity among cells, tissues, and species at multi-levels, angles, and orientations, as well as provide new insights into molecular mechanisms of biological development and pathogenesis.},
}
@article {pmid36302928,
year = {2022},
author = {Hammoud, R and Tognin, S and Burgess, L and Bergou, N and Smythe, M and Gibbons, J and Davidson, N and Afifi, A and Bakolis, I and Mechelli, A},
title = {Smartphone-based ecological momentary assessment reveals mental health benefits of birdlife.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {17589},
pmid = {36302928},
issn = {2045-2322},
support = {MR/S026428/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Ecological Momentary Assessment ; Smartphone ; Mental Health ; Retrospective Studies ; *Mobile Applications ; },
abstract = {The mental health benefits of everyday encounters with birdlife for mental health are poorly understood. Previous studies have typically relied on retrospective questionnaires or artificial set-ups with little ecological validity. In the present study, we used the Urban Mind smartphone application to examine the impact of seeing or hearing birds on self-reported mental wellbeing in real-life contexts. A sample of 1292 participants completed a total of 26,856 ecological momentary assessments between April 2018 and October 2021. Everyday encounters with birdlife were associated with time-lasting improvements in mental wellbeing. These improvements were evident not only in healthy people but also in those with a diagnosis of depression, the most common mental illness across the world. These findings have potential implications for both environmental and wildlife protection and mental healthcare policies. Specific measures, aimed at preserving and increasing everyday encounters with birdlife in urban areas, should be implemented.},
}
@article {pmid36302597,
year = {2023},
author = {Verbitsky, M and Krishnamurthy, S and Krithivasan, P and Hughes, D and Khan, A and Marasà, M and Vena, N and Khosla, P and Zhang, J and Lim, TY and Glessner, JT and Weng, C and Shang, N and Shen, Y and Hripcsak, G and Hakonarson, H and Ionita-Laza, I and Levy, B and Kenny, EE and Loos, RJF and Kiryluk, K and Sanna-Cherchi, S and Crosslin, DR and Furth, S and Warady, BA and Igo, RP and Iyengar, SK and Wong, CS and Parsa, A and Feldman, HI and Gharavi, AG},
title = {Genomic Disorders in CKD across the Lifespan.},
journal = {Journal of the American Society of Nephrology : JASN},
volume = {34},
number = {4},
pages = {607-618},
pmid = {36302597},
issn = {1533-3450},
support = {U01 DK066143/DK/NIDDK NIH HHS/United States ; U01 DK066174/DK/NIDDK NIH HHS/United States ; K25 DK128563/DK/NIDDK NIH HHS/United States ; UL1 TR004419/TR/NCATS NIH HHS/United States ; R21 DK119802/DK/NIDDK NIH HHS/United States ; R01 DK080099/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Cohort Studies ; *Longevity ; Prospective Studies ; *Renal Insufficiency, Chronic/epidemiology/genetics/complications ; Genomics ; Disease Progression ; Risk Factors ; },
abstract = {SIGNIFICANCE STATEMENT: Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis.<br><br>BACKGROUND: Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility.<br><br>METHODS: We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II (n =248), Chronic Renal Insufficiency Cohort (CRIC) study (n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort.<br><br>RESULTS: We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk.<br><br>CONCLUSION: Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.},
}
@article {pmid36300397,
year = {2022},
author = {Kulikowski, CA},
title = {50 Years of Achievements and Persistent Challenges for Biomedical and Health Informatics and John Mantas' Educational and Nursing Informatics Contributions.},
journal = {Studies in health technology and informatics},
volume = {300},
number = {},
pages = {1-11},
doi = {10.3233/SHTI220936},
pmid = {36300397},
issn = {1879-8365},
mesh = {*Nursing Informatics ; *Medical Informatics ; Cybernetics ; Expert Systems ; },
abstract = {Biomedical and Health Informatics (BMHI) have been essential catalysts for achievements in medical research and healthcare applications over the past 50 years. These include increasingly sophisticated information systems and data bases for documentation and processing, standardization of biomedical data, nomenclatures, and vocabularies to assist with large scale literature indexing and text analysis for information retrieval, and methods for computationally modeling and analyzing research and clinical data. Statistical and AI techniques for decision support, instrumentation integration, and workflow aids with improved data/information management tools are critical for scientific discoveries in the - omics revolutions with their related drug and vaccine breakthroughs and their translation to clinical and preventive healthcare. Early work on biomedical image and pattern recognition, knowledge-based expert systems, innovative database, software and simulation techniques, natural language processing and computational ontologies have all been invaluable for basic research and education. However, these methods are still in their infancy and many fundamental open scientific problems abound. Scientifically this is due to persistent limitations in understanding biological processes within complex living environments and ecologies. In clinical practice the modeling of fluid practitioner roles and methods as they adjust to novel cybernetic technologies present great opportunities but also the potential of unintended e-iatrogenic harms which must be constrained in order to adhere to ethical Hippocratic norms of responsible behavior. Balancing the art, science, and technologies of BMHI has been a hallmark of debates about the field's historical evolution. The present article reviews selected milestones, achievements, and challenges in BMHI education mainly, from a historical perspective, including some commentaries from leaders and pioneers in the field, a selection of which have been published online recently by the International Medical Informatics Association (IMIA) as the first volume of an IMIA History WG eBook. The focus of this chapter is primarily on the development of BMHI in terms of those of its educational activities which have been most significant during the first half century of IMIA, and it concentrates mainly on the leadership and contributions of John Mantas who is being honored on his retirement by the Symposia in Athens for which this chapter has been written.},
}
@article {pmid36297864,
year = {2022},
author = {Macchia, A and Biribicchi, C and Zaratti, C and Testa Chiari, K and D'Ambrosio, M and Toscano, D and Izzo, FC and La Russa, MF},
title = {Mattel's Barbie: Investigation of a Symbol-Analysis of Polymeric Matrices and Degradation Phenomena for Sixteen Dolls from 1959 to 1976.},
journal = {Polymers},
volume = {14},
number = {20},
pages = {},
pmid = {36297864},
issn = {2073-4360},
abstract = {Mattel's Barbie dolls are the most famous and iconic dolls since 1959. Today, they are being collected by individuals and often conserved in museum environments due to their cultural and historical significance reflecting everyday life and historical events. However, just like most museum objects made of plastics, both historical and more recent Barbies show evident degradation phenomena. Firstly, Barbies were made of plasticized polyvinyl chloride (PVC), affected by the migration of additives-mostly the plasticizers-from the bulk phase to the outermost layer, appearing as a tacky and glossy exudate. Over the years, Barbies' polymeric constituents were replaced with more stable ones, whose additives migration is limited compared to PVC, even though still occurring. Multispectral photography in visible (VIS) and ultraviolet (UV) light, microscopical observations in VIS and UV light, and Fourier Transform Infrared spectroscopy in the Attenuated Total Reflectance mode (FT-IR ATR) were performed to characterize the constituent materials of 15 Barbies produced between 1959 and 1976, bridging the information gap on their processing over the years. The micro-invasive multi-analytical approach also allowed for the characterization of the degradation products, permitting the reference of the exudated compound to the specific bulk polymer.},
}
@article {pmid36297101,
year = {2022},
author = {Maugeri, A and Magnano San Lio, R and Favara, G and La Rosa, MC and La Mastra, C and Riela, PM and Guarnera, L and Battiato, S and Barchitta, M and Agodi, A},
title = {Impact of Eating Context on Dietary Choices of College Students: Evidence from the HEALTHY-UNICT Project.},
journal = {Nutrients},
volume = {14},
number = {20},
pages = {},
pmid = {36297101},
issn = {2072-6643},
support = {Programma ricerca di ateneo UNICT 2020-22 linea 4, PIAno di inCEntivi per la RIcerca di Ateneo 2020/2022//University of Catania, Italy, Department of Medical and Surgical Science and Advanced Tech-nologies 'GF Ingrassia'/ ; },
mesh = {Humans ; *Diet ; *Vegetables ; Feeding Behavior ; Meals ; Students ; },
abstract = {While personal characteristics have been evaluated as determinants of dietary choices over the years, only recently studies have looked at the impact of eating context. Examining eating context, however, can be challenging. Here, we propose the use of a web-app for the Ecological Momentary Assessment of dietary habits among 138 college students from Catania (Italy) and therefore for examining the impact of eating context on dietary choices. Eating away from home was associated with lower odds of consuming vegetables, fruits, and legumes and higher odds of consuming processed meat, salty snacks, and alcoholic drinks compared with eating at home. Eating in the company of other people was associated with higher odds of consuming vegetables, red meat, fish, legumes, milk, and sugar-sweetened beverages and lower odds of consuming nuts than eating alone. This study proposed a new way to capture and assess how eating environment might affect dietary habits. Based on our results, meal location and social context have significant effects on the dietary choices of college students, pointing to the need to incorporate these aspects into further epidemiological studies.},
}
@article {pmid36296237,
year = {2022},
author = {Trego, A and Keating, C and Nzeteu, C and Graham, A and O'Flaherty, V and Ijaz, UZ},
title = {Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data.},
journal = {Microorganisms},
volume = {10},
number = {10},
pages = {},
pmid = {36296237},
issn = {2076-2607},
support = {NE/L011956/1//Natural Environment Research Council/ ; EP/P029329/1//Engineering and Physical Sciences Research Council/ ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; TC/2014/0016//Enterprise Ireland/ ; 14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 16/RC/3889/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.},
}
@article {pmid36295335,
year = {2022},
author = {Cherevko, AG and Krygin, AS and Ivanov, AI and Soots, RA and Antonova, IV},
title = {Benefits of Printed Graphene with Variable Resistance for Flexible and Ecological 5G Band Antennas.},
journal = {Materials (Basel, Switzerland)},
volume = {15},
number = {20},
pages = {},
pmid = {36295335},
issn = {1996-1944},
support = {FZSR-2022-0009//Ministry of Science and Higher Education of the Russian Federation/ ; 071-03-2022-001//Ministry of Digital Development, Telecommunications and Mass Media of the RF/ ; },
abstract = {The possibility of creating antennas of the 5G standard (5.2-5.9 GHz) with specified electrodynamic characteristics by printing layers of variable thickness using a graphene suspension has been substantiated experimentally and by computer simulation. A graphene suspension for screen printing on photographic paper and other flexible substrates was prepared by means of exfoliation from graphite. The relation between the graphene layer thickness and its sheet resistance was studied with the aim of determining the required thickness of the antenna conductive layer. To create a two-sided dipole, a technology has been developed for the double-sided deposition of graphene layers on photographic paper. The electrodynamic characteristics of graphene and copper antennas of identical design are compared. The antenna design corresponds to the operating frequency of 2.4 GHz. It was found that the use of graphene as a conductive layer made it possible to suppress the fundamental (first) harmonic (2.45 GHz) and to observe radiation at the second harmonic (5.75 GHz). This effect is assumed to observe in the case when the thickness of graphene is lower than that of the skin depth. The result indicates the possibility of changing the antenna electrodynamic characteristics by adjusting the graphene layer thickness.},
}
@article {pmid36293641,
year = {2022},
author = {Zou, H and Liu, Y and Li, B and Luo, W},
title = {Sustainable Development Efficiency of Cultural Landscape Heritage in Urban Fringe Based on GIS-DEA-MI, a Case Study of Wuhan, China.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {20},
pages = {},
pmid = {36293641},
issn = {1660-4601},
support = {20YJC760145//Ministry of Education, Humanities and Social Sciences Youth Fund/ ; 20Y044//Humanities and Social Sciences Fund of Hubei Education Department/ ; XJ2021005501//Hubei University of Technology Green Industry Science and Technology Leading Program/ ; 2020EJB004//Innovation Demonstration Base of Ecological Environment Geotechnical and Ecological Restoration of Rivers and Lakes/ ; },
mesh = {Humans ; Cities ; *Conservation of Natural Resources/methods ; *Sustainable Development ; Geographic Information Systems ; Urbanization ; China ; },
abstract = {Cultural landscape heritage refers to the rare and irreplaceable cultural landscapes recognized by UNESCO and the World Heritage Committee. It is recognized as a "common works of nature and human beings" of outstanding significance and universal value, and is a type of world heritage. Dueto construction, land isincreasingly limited in urban and rural areasin the process of urbanization, and cultural landscape heritage faces a huge threat, especially larger culturallandscapeheritagelocated at the edgesof cities. However, most of the existing studies have mainly focused on the material protection of heritage but have not paid enough attention to the non-material aspects of heritage sites, failing to reveal the inseparable nature of heritage and land. Therefore, this study takes sustainable development efficiency as its analysis tool, examines two pieces of cultural landscape heritage (the Panlongcheng site and the Tomb of the King of the Ming Dynasty) in the urban edge area of Wuhan, China as examples, innovates and establishes a multidimensional evaluation method based on the GIS-DEA-Ml model, and compares the dynamic changes of the spatial development efficiency and non-spatial development efficiency of the above two cultural landscape heritage cases. The results show that: both the spatial development efficiency and non-spatial development efficiency of Panlongcheng from 2010 to 2019 are significantly higher than that of the Tomb. This method makes up for the deficiency of traditional subjective qualitative analysis. It can be used to study the development efficiency of cultural landscape heritage more objectively and comprehensively, and promote the overall sustainable development of material and intangible cultural heritage. It can provide the basis for early decision-making and post-implementation evaluation for the preservation and utilization of cultural landscape heritage under the background of urban renewal.},
}
@article {pmid36293613,
year = {2022},
author = {Aleni, C and Rinaldi, C and Bettio, V and Mazzucco, E and Antona, A and Meini, C and Loria, E and Bonvicini, P and Cracas, SV and Caristia, S and Rimedio, A and Faggiano, F and Ferrante, D and Capello, D},
title = {Public Attitude towards Biobanking: An Italian University Survey.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {20},
pages = {},
pmid = {36293613},
issn = {1660-4601},
mesh = {Humans ; *Biological Specimen Banks ; Universities ; Attitude ; Public Opinion ; Surveys and Questionnaires ; *Biomedical Research ; },
abstract = {Biobanks have established a critical role in biomedical research by collecting, preserving, organizing, and disseminating biospecimens and related health data, contributing to precision medicine development. Participation in biobanks is influenced by several factors, such as trust in institutions and scientists, knowledge about biobanking, and the consideration of benefit sharing. Understanding public attitudes, fears, and concerns toward biobanking is fundamental to designing targeted interventions to increase trust towards biobanks. The aim of our study was to investigate the level of knowledge and perception of biobanks in students and personnel of the University of Piemonte Orientale. An online questionnaire was designed and administered via e-mail. A total of 17,758 UPO personnel and students were invited to participate in the survey, and 1521 (9.3%) subjects completed the survey. The results showed that 65.0% of the participants were aware of the term "biobank" and knew what the activity of a biobank was, and 76.3% of subjects were willing to provide biospecimens to a research biobank, whereas 67.3% of the respondents were willing to contribute, in addition to biospecimens, their health and lifestyle data. Concerns were raised about the confidentiality of the information (25.6%) and the commercial use of the samples (25.0%). In conclusion, participants were aware of the role that biobanks play in research and were eager to participate for the sake of furthering scientific research. Still, several concerns need to be addressed regarding the confidentiality of the data along with the commercial use of the samples and associated data.},
}
@article {pmid36289166,
year = {2022},
author = {Navidi, MN and Chatrenour, M and Seyedmohammadi, J and Khaki, BD and Moradi-Majd, N and Mirzaei, S},
title = {Ecological potential assessment and land use area estimation of agricultural lands based on multi-time images of Sentinel-2 using ANP-WLC and GIS in Bastam, Iran.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {1},
pages = {36},
pmid = {36289166},
issn = {1573-2959},
mesh = {Agriculture ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; *Geographic Information Systems ; Iran ; Soil ; },
abstract = {The use of land-based ecological potential is a key management factor in achieving sustainable development and conserving soil and water resources. The purpose of this study is to use multi-time images of Sentinel-2 to determine the area of agricultural lands and evaluate their ecological potential in Bastam, Semnan Province, Iran. Therefore, in the first step, the most common agricultural lands (including apricot and grape orchards), field crops (including wheat and forage maize), and their phenological period were determined. Then, the information was classified using, namely support vector machine, maximum likelihood, and minimum distance. In the next step, soil, topography, and climate data were extracted according to expert opinions and the analysis of the basin's natural potential. The ecological evaluation models of the region were applied to homogeneous units, and after calculating the ecological potential index by the integrated ANP-WLC model, the ecological potential map was generated. The results of the land use classification showed that the support vector machine model and the minimum distance, respectively, had the best and worst performance with kappa coefficient of 0.82 and 0.61. The highest area of cultivated lands (3423 hectares) was estimated for wheat and the lowest (738 hectares) for forage maize. Moreover, the results of the ecological potential evaluation showed that 60% of apricot orchards, and 40.19% of the wheat fields, were in the class of good ecological potential. Overall, 2290 hectares were in the poor class, and 4030 hectares in the excellent class in terms of ecological potential.},
}
@article {pmid36287517,
year = {2022},
author = {Gonçalves, ICM and Freitas, RF and Aquino, EC and Carneiro, JA and Lessa, ADC},
title = {Mortality trend from falls in Brazilian older adults from 2000 to 2019.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {25},
number = {},
pages = {e220031},
doi = {10.1590/1980-549720220031.2},
pmid = {36287517},
issn = {1980-5497},
mesh = {Male ; Humans ; Female ; Aged ; *Accidental Falls ; Brazil/epidemiology ; *Quality of Life ; Retrospective Studies ; Information Systems ; Mortality ; },
abstract = {OBJECTIVE: To analyze the trend of mortality from falls among older adults in Brazil from 2000 to 2019.<br><br>METHODS: This is an epidemiological, analytical study with an ecological time-series design. A retrospective analysis was performed using secondary health data extracted from the Brazilian Mortality Information System in the specific period. Standardized rates of general and sex- and age-specific mortality were calculated. To observe the mortality trend, the Prais-Winsten model and the Annual Increase Rate (AIR) were used.<br><br>RESULTS: We identified 135,209 deaths resulting from falls in older adults in the period from 2000 to 2019. Mortality from falls in general, during the study period, had an upward trend (&#x3b2;=0.023; p<0.001; AIR=5.45%). We observed that both men (&#x3b2;=0.022; p<0.001; AIR=5.19%) and women (&#x3b2;=0.024; p<0.001; AIR=5.72%) had an upward trend. Regarding age group, the results also pointed to an upward mortality trend in all age strata, although higher in older people aged &#x2265;80 years (&#x3b2;=0.027; p<0.001; AIR=6.38%).<br><br>CONCLUSION: There was an upward trend in mortality rates in Brazil during the time series studied. These findings suggest the importance of defining a line of care for this age group, focusing on promoting health in older adults and preventing the risk of falls, aiming at a reduction in the number of deaths from this cause and favoring the quality of life of this population.},
}
@article {pmid36287142,
year = {2022},
author = {Miller-Ter Kuile, A and Apigo, A and Bui, A and Butner, K and Childress, JN and Copeland, S and DiFiore, BP and Forbes, ES and Klope, M and Motta, CI and Orr, D and Plummer, KA and Preston, DL and Young, HS},
title = {Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts.},
journal = {Biology letters},
volume = {18},
number = {10},
pages = {20220364},
pmid = {36287142},
issn = {1744-957X},
mesh = {Animals ; *Food Chain ; *Ecosystem ; Predatory Behavior/physiology ; Invertebrates ; Diet ; },
abstract = {Predator-prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods: diet DNA and stable isotopes, for two trophic groups (top predators and intermediate predators) in both low- and high-productivity habitats to elucidate where in the food chain trophic structure shifts in response to changes in underlying ecosystem productivity. We demonstrate that while top predators show increases in isotopic trophic position (δ[15]N) with productivity, neither their isotopic niche size nor their DNA diet composition changes. Conversely, intermediate predators show clear turnover in DNA diet composition towards a more predatory prey base in high-productivity habitats. Taking this multi-trophic approach highlights how predator identity shapes responses in predator-prey interactions across environments with different underlying productivity, building predictive power for understanding the outcomes of ongoing anthropogenic change.},
}
@article {pmid36284162,
year = {2022},
author = {Geneva, AJ and Park, S and Bock, DG and de Mello, PLH and Sarigol, F and Tollis, M and Donihue, CM and Reynolds, RG and Feiner, N and Rasys, AM and Lauderdale, JD and Minchey, SG and Alcala, AJ and Infante, CR and Kolbe, JJ and Schluter, D and Menke, DB and Losos, JB},
title = {Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1126},
pmid = {36284162},
issn = {2399-3642},
support = {T32 GM007103/GM/NIGMS NIH HHS/United States ; DEB-1927194//National Science Foundation (NSF)/ ; IOS-1827647//National Science Foundation (NSF)/ ; DEB-1927156//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Lizards/genetics ; Genome ; Sex Chromosomes ; Genomics ; X Chromosome ; },
abstract = {Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei - a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei.},
}
@article {pmid36270368,
year = {2023},
author = {Derx, J and Kılıç, HS and Linke, R and Cervero-Aragó, S and Frick, C and Schijven, J and Kirschner, AKT and Lindner, G and Walochnik, J and Stalder, G and Sommer, R and Saracevic, E and Zessner, M and Blaschke, AP and Farnleitner, AH},
title = {Probabilistic fecal pollution source profiling and microbial source tracking for an urban river catchment.},
journal = {The Science of the total environment},
volume = {857},
number = {Pt 2},
pages = {159533},
doi = {10.1016/j.scitotenv.2022.159533},
pmid = {36270368},
issn = {1879-1026},
mesh = {Animals ; Humans ; Rivers ; Water Pollution/analysis ; Water Microbiology ; *Cryptosporidiosis ; Escherichia coli ; Environmental Monitoring/methods ; *Cryptosporidium ; Feces/chemistry ; Giardia ; Water/analysis ; },
abstract = {We developed an innovative approach to estimate the occurrence and extent of fecal pollution sources for urban river catchments. The methodology consists of 1) catchment surveys complemented by literature data where needed for probabilistic estimates of daily produced fecal indicator (FIBs, E. coli, enterococci) and zoonotic reference pathogen numbers (Campylobacter, Cryptosporidium and Giardia) excreted by human and animal sources in a river catchment, 2) generating a hypothesis about the dominant sources of fecal pollution and selecting a source targeted monitoring design, and 3) verifying the results by comparing measured concentrations of the informed choice of parameters (i.e. chemical tracers, C. perfringensspores, and host-associated genetic microbial source tracking (MST) markers) in the river, and by multi-parametric correlation analysis. We tested the approach at a study area in Vienna, Austria. The daily produced microbial particle numbers according to the probabilistic estimates indicated that, for the dry weather scenario, the discharge of treated wastewater (WWTP) was the primary contributor to fecal pollution. For the wet weather scenario, 80-99 % of the daily produced FIBs and pathogens resulted from combined sewer overflows (CSOs) according to the probabilistic estimates. When testing our hypothesis in the river, the measured concentrations of the human genetic fecal marker were log10 4 higher than for selected animal genetic fecal markers. Our analyses showed for the first-time statistical relationships between C. perfringens spores (used as conservative microbial tracer for communal sewage) and a human genetic fecal marker (i.e. HF183/BacR287) with the reference pathogen Giardia in river water (Spearman rank correlation: 0.78-0.83, p < 0.05. The developed approach facilitates urban water safety management and provides a robust basis for microbial fate and transport models and microbial infection risk assessment.},
}
@article {pmid36264457,
year = {2023},
author = {Nasiruddin, M and Islam, ARMT and Siddique, MAB and Hasanuzaman, M and Hassan, MM and Akbor, MA and Hasan, M and Islam, MS and Khan, R and Al Amin, M and Pal, SC and Idris, AM and Kumar, S},
title = {Distribution, sources, and pollution levels of toxic metal(loid)s in an urban river (Ichamati), Bangladesh using SOM and PMF modeling with GIS tool.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {8},
pages = {20934-20958},
pmid = {36264457},
issn = {1614-7499},
support = {The authors extend their appreciation to the Deanship of Scientific Research at King Khalid University for funding this work through Research Group under grant number (RGP2/169/43)//King Khalid University/ ; },
mesh = {Humans ; *Metals, Heavy/analysis ; Environmental Monitoring ; Geographic Information Systems ; Rivers ; Bangladesh ; Cadmium/analysis ; Lead/analysis ; Geologic Sediments/analysis ; *Water Pollutants, Chemical/analysis ; Water Quality ; Risk Assessment ; China ; },
abstract = {Indexical assessment coupled with a self-organizing map (SOM) and positive matrix factorization (PMF) modeling of toxic metal(loid)s in sediment and water of the aquatic environment provides valuable information from the environmental management perspective. However, in northwest Bangladesh, indexical and modeling assessments of toxic metal(loid)s in surface water and sediment are still rare. Toxic metal(loid)s were measured in sediment and surface water from an urban polluted river (Ichamati) in northwest Bangladesh using an atomic absorption spectrophotometer to assess distribution, pollution levels, sources, and potential environmental risks to the aquatic environment. The mean concentrations (mg/kg) of metal(loid)s in water are as follows: Fe (871) > Mn (382) > Cr (72.4) > Zn (34.2) > Co (20.8) > Pb (17.6) > Ni (16.7) > Ag (14.9) > As (9.0) > Cu (5.63) > Cd (2.65), while in sediment, the concentration follows the order, Fe (18,725) > Mn (551) > Zn (213) > Cu (47.6) > Cr (30.2) > Ni (24.2) > Pb (23.8) > Co (9.61) > As (8.23) > Cd (0.80) > Ag (0.60). All metal concentrations were within standard guideline values except for Cr and Pb for water and Cd, Zn, Cu, Pb, and As for sediment. The outcomes of eco-environmental indices, including contamination and enrichment factors and geo-accumulation index, differed spatially, indicating that most of the sediment sites were moderately to highly polluted by Cd, Zn, and As. Cd and Zn content can trigger ecological risks. The positive matrix factorization (PMF) model recognized three probable sources of sediment, i.e., natural source (49.39%), industrial pollution (19.72%), and agricultural source (30.92%), and three possible sources of water, i.e., geogenic source (45.41%), industrial pollution (22.88%), and industrial point source (31.72%), respectively. SOM analysis identified four spatial patterns, e.g., Fe-Mn-Ag, Cd-Cu, Cr-Pb-As-Ni, and Zn-Co in water and three patterns, e.g., Mn-Co-Ni-Cr, Cd-Cu-Pb-Zn, and As-Fe-Ag in sediment. The spatial distribution of entropy water quality index values shows that the southwestern area possesses "poor" quality water. Overall, the levels of metal(loid) pollution in the investigated river surpassed a critical threshold, which might have serious consequences for the river's aquatic biota and human health in the long run.},
}
@article {pmid36263952,
year = {2023},
author = {Jensen, MA and Blatz, DJ and LaLone, CA},
title = {Defining the Biologically Plausible Taxonomic Domain of Applicability of an Adverse Outcome Pathway: A Case Study Linking Nicotinic Acetylcholine Receptor Activation to Colony Death.},
journal = {Environmental toxicology and chemistry},
volume = {42},
number = {1},
pages = {71-87},
pmid = {36263952},
issn = {1552-8618},
mesh = {Animals ; Bees ; *Adverse Outcome Pathways ; *Receptors, Nicotinic/genetics ; Ecotoxicology/methods ; Databases, Factual ; Amino Acid Sequence ; Risk Assessment ; },
abstract = {For the majority of developed adverse outcome pathways (AOPs), the taxonomic domain of applicability (tDOA) is typically narrowly defined with a single or a handful of species. Defining the tDOA of an AOP is critical for use in regulatory decision-making, particularly when considering protection of untested species. Structural and functional conservation are two elements that can be considered when defining the tDOA. Publicly accessible bioinformatics approaches, such as the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool, take advantage of existing and growing databases of protein sequence and structural information to provide lines of evidence toward structural conservation of key events (KEs) and KE relationships (KERs) of an AOP. It is anticipated that SeqAPASS results could readily be combined with data derived from empirical toxicity studies to provide evidence of both structural and functional conservation, to define the tDOA for KEs, KERs, and AOPs. Such data could be incorporated in the AOP-Wiki as lines of evidence toward biological plausibility for the tDOA. We present a case study describing the process of using bioinformatics to define the tDOA of an AOP using an AOP linking the activation of the nicotinic acetylcholine receptor to colony death/failure in Apis mellifera. Although the AOP was developed to gain a particular biological understanding relative to A. mellifera health, applicability to other Apis bees, as well as non-Apis bees, has yet to be defined. The present study demonstrates how bioinformatics can be utilized to rapidly take advantage of existing protein sequence and structural knowledge to enhance and inform the tDOA of KEs, KERs, and AOPs, focusing on providing evidence of structural conservation across species. Environ Toxicol Chem 2023;42:71-87. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.},
}
@article {pmid36261521,
year = {2022},
author = {Klunk, J and Vilgalys, TP and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB},
title = {Evolution of immune genes is associated with the Black Death.},
journal = {Nature},
volume = {611},
number = {7935},
pages = {312-319},
pmid = {36261521},
issn = {1476-4687},
support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; F32 GM140568/GM/NIGMS NIH HHS/United States ; R01 GM146051/GM/NIGMS NIH HHS/United States ; R56 AI146556/AI/NIAID NIH HHS/United States ; R01 GM134376/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Aminopeptidases/genetics/immunology ; *DNA, Ancient ; *Plague/genetics/immunology/microbiology/mortality ; *Yersinia pestis/immunology/pathogenicity ; *Selection, Genetic/immunology ; Europe/epidemiology/ethnology ; *Immunity/genetics ; Datasets as Topic ; *Genetic Predisposition to Disease ; London/epidemiology ; Denmark/epidemiology ; },
abstract = {Infectious diseases are among the strongest selective pressures driving human evolution[1,2]. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis[3]. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population[4]. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.},
}
@article {pmid36261519,
year = {2022},
author = {Jandt, U and Bruelheide, H and Jansen, F and Bonn, A and Grescho, V and Klenke, RA and Sabatini, FM and Bernhardt-Römermann, M and Blüml, V and Dengler, J and Diekmann, M and Doerfler, I and Döring, U and Dullinger, S and Haider, S and Heinken, T and Horchler, P and Kuhn, G and Lindner, M and Metze, K and Müller, N and Naaf, T and Peppler-Lisbach, C and Poschlod, P and Roscher, C and Rosenthal, G and Rumpf, SB and Schmidt, W and Schrautzer, J and Schwabe, A and Schwartze, P and Sperle, T and Stanik, N and Storm, C and Voigt, W and Wegener, U and Wesche, K and Wittig, B and Wulf, M},
title = {More losses than gains during one century of plant biodiversity change in Germany.},
journal = {Nature},
volume = {611},
number = {7936},
pages = {512-518},
pmid = {36261519},
issn = {1476-4687},
mesh = {*Biodiversity ; Germany ; *Plants/classification ; Species Specificity ; Time Factors ; Datasets as Topic ; },
abstract = {Long-term analyses of biodiversity data highlight a 'biodiversity conservation paradox': biological communities show substantial species turnover over the past century[1,2], but changes in species richness are marginal[1,3-5]. Most studies, however, have focused only on the incidence of species, and have not considered changes in local abundance. Here we asked whether analysing changes in the cover of plant species could reveal previously unrecognized patterns of biodiversity change and provide insights into the underlying mechanisms. We compiled and analysed a dataset of 7,738 permanent and semi-permanent vegetation plots from Germany that were surveyed between 2 and 54 times from 1927 to 2020, in total comprising 1,794 species of vascular plants. We found that decrements in cover, averaged across all species and plots, occurred more often than increments; that the number of species that decreased in cover was higher than the number of species that increased; and that decrements were more equally distributed among losers than were gains among winners. Null model simulations confirmed that these trends do not emerge by chance, but are the consequence of species-specific negative effects of environmental changes. In the long run, these trends might result in substantial losses of species at both local and regional scales. Summarizing the changes by decade shows that the inequality in the mean change in species cover of losers and winners diverged as early as the 1960s. We conclude that changes in species cover in communities represent an important but understudied dimension of biodiversity change that should more routinely be considered in time-series analyses.},
}
@article {pmid36261518,
year = {2022},
author = {Jarvis, ED and Formenti, G and Rhie, A and Guarracino, A and Yang, C and Wood, J and Tracey, A and Thibaud-Nissen, F and Vollger, MR and Porubsky, D and Cheng, H and Asri, M and Logsdon, GA and Carnevali, P and Chaisson, MJP and Chin, CS and Cody, S and Collins, J and Ebert, P and Escalona, M and Fedrigo, O and Fulton, RS and Fulton, LL and Garg, S and Gerton, JL and Ghurye, J and Granat, A and Green, RE and Harvey, W and Hasenfeld, P and Hastie, A and Haukness, M and Jaeger, EB and Jain, M and Kirsche, M and Kolmogorov, M and Korbel, JO and Koren, S and Korlach, J and Lee, J and Li, D and Lindsay, T and Lucas, J and Luo, F and Marschall, T and Mitchell, MW and McDaniel, J and Nie, F and Olsen, HE and Olson, ND and Pesout, T and Potapova, T and Puiu, D and Regier, A and Ruan, J and Salzberg, SL and Sanders, AD and Schatz, MC and Schmitt, A and Schneider, VA and Selvaraj, S and Shafin, K and Shumate, A and Stitziel, NO and Stober, C and Torrance, J and Wagner, J and Wang, J and Wenger, A and Xiao, C and Zimin, AV and Zhang, G and Wang, T and Li, H and Garrison, E and Haussler, D and Hall, I and Zook, JM and Eichler, EE and Phillippy, AM and Paten, B and Howe, K and Miga, KH and , },
title = {Semi-automated assembly of high-quality diploid human reference genomes.},
journal = {Nature},
volume = {611},
number = {7936},
pages = {519-531},
pmid = {36261518},
issn = {1476-4687},
support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; U01 HG010961/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U01 CA253481/CA/NCI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; K99 HG010906/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; R01 HG010040/HG/NHGRI NIH HHS/United States ; U41 HG010972/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Chromosome Mapping/standards ; *Diploidy ; *Genome, Human/genetics ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing/methods/standards ; Sequence Analysis, DNA/methods/standards ; Reference Standards ; *Genomics/methods/standards ; Chromosomes, Human/genetics ; Genetic Variation/genetics ; },
abstract = {The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society[1,2]. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals[3,4]. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome[5]. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity[6]. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.},
}
@article {pmid36257775,
year = {2022},
author = {Peltier, DMP and Anderegg, WRL and Guo, JS and Ogle, K},
title = {Contemporary tree growth shows altered climate memory.},
journal = {Ecology letters},
volume = {25},
number = {12},
pages = {2663-2674},
doi = {10.1111/ele.14130},
pmid = {36257775},
issn = {1461-0248},
support = {1458867//Division of Biological Infrastructure/ ; 1643245//Division of Environmental Biology/ ; //National Science Foundation/ ; },
mesh = {*Trees ; *Climate Change ; Droughts ; Temperature ; },
abstract = {Trees are long-lived organisms, exhibiting temporally complex growth arising from strong climatic "memory." But conditions are becoming increasingly arid in the western USA. Using a century-long tree-ring network, we find altered climate memory across the entire range of a widespread western US conifer: growth is supported by precipitation falling further into the past (+15 months), while increasingly impacted by more recent temperature conditions (-8 months). Tree-ring datasets can be biased, so we confirm altered climate memory in a second, ecologically-sampled tree-ring network. Predicted drought responses show trees may have also become more sensitive to repeat drought. Finally, plots near sites with relatively longer precipitation memory and shorter temperature memory had significantly lower recent mortality rates (R[2] = 0.61). We argue that increased drought frequency has altered climate memory, demonstrate how non-stationarity may arise from failure to account for memory, and suggest memory length may be predictive of future tree mortality.},
}
@article {pmid36255408,
year = {2023},
author = {Sorokina, M and Ukubayev, T and Koichubekov, B},
title = {Tuberculosis incidence and its socioeconomic determi-nants: developing a parsimonious model.},
journal = {Annali di igiene : medicina preventiva e di comunita},
volume = {35},
number = {4},
pages = {468-479},
doi = {10.7416/ai.2022.2549},
pmid = {36255408},
issn = {1120-9135},
mesh = {Humans ; Incidence ; *Tuberculosis/epidemiology ; Socioeconomic Factors ; Linear Models ; },
abstract = {BACKGROUND: Tuberculosis is a widespread communicable disease, which is one of the top 10 causes of demise globally. Several regression models have been built, and then utilized for the Tuberculosis incidence projections. However, when fitting a multiple linear regression model, an analysis must account for multicollinearity aspects. The present study aimed to develop a parsimonious model that produces unbiased results based on socioeconomic variables as predictors of Tuberculosis incidence.<br><br>STUDY DESIGN: Ecological study.<br><br>METHODS: Data were collected from the Karaganda Regional Center of Phthisio-pulmonology and Bureau of National Statistics. By multiple linear regression model, we investigated associations between Tuberculosis incidence rate and socioeconomic determinants in Karaganda region, Kazakhstan, during 2001-2019. A Principal components analysis was performed on the socioeconomic variables with oblique rotation. Furthermore, associations of Tuberculosis incidence with the principal components derived from the Principal components analysis were assessed.<br><br>RESULTS: The incidence of Tuberculosis in Karaganda region decreased over the period of 2001-2019. Economic development and healthcare capacity were negatively correlated with Tuberculosis incidence. A multiple linear regression equation on Tuberculosis incidence (y) was developed with economic development (x1) and healthcare capacity (x2) clustering two components (utilizing Principal components analysis) to eliminate collinearity: y = 1442 - 454.3x1 - 211.4x2. The incidence of Tuberculosis decreased with the increase of economic development and healthcare capacity.<br><br>CONCLUSIONS: In conclusion, the study indicated that economic development and healthcare capacity are closely associated with the incidence of Tuberculosis. The findings support the implementation of optimal preventive measures for Tuberculosis control, including improving the level of economic status, increasing social protection, health expenditure, and strengthening health sector capacity, which are key determinants of the incidence of Tuberculosis.},
}
@article {pmid36254310,
year = {2022},
author = {Cui, J and Khomkrich, K},
title = {Ethnic Music Inheritance and Environmental Monitoring Using Big Data Analysis from the Cultural Perspective.},
journal = {Journal of environmental and public health},
volume = {2022},
number = {},
pages = {2485596},
pmid = {36254310},
issn = {1687-9813},
mesh = {Big Data ; China ; Data Analysis ; Environmental Monitoring ; Ethnicity/genetics ; Humans ; *Music ; },
abstract = {Ethnic music has too many expectations due to its significance to the national culture. It serves as a mirror, reflecting all the true characteristics of many geographical areas and ethnic groupings. Instilling national self-confidence and fostering national unity are essential outcomes of this. The optimal design plan for Xinjiang folk music inheritance and environmental monitoring based on big data technology is presented in this study from the standpoint of cultural ecology. Big data technology can categorize users who are interested in Xinjiang ethnic music, and after that, through customized recommendation filtering, consumers may be presented with Xinjiang ethnic music that meets their interests. Last but not least, a simulation test and analysis are performed. The algorithm's accuracy is 7.86% higher than that of the conventional algorithm, according to the simulation data. By studying and calculating the user's behavioral traits and interests, this result demonstrates in detail how the recommender system can display the user's content efficiently. However, there are numerous possibilities and varied contexts for the use of clustering techniques in recommender systems. It is crucially vital for directing the protection of ethnic music and fostering the inheritance and development of ethnic culture to conduct design study on the Xinjiang region's ethnic music heritage and development with cultural ecology as the central guiding principle. This article is from "A comprehensive study of Uygur Muqam music art with Chinese characteristics," which aims to improve the data reserve of the world and Southeast Asia on the research of Chinese Uighur Muqam art. Improve the inheritance and development of music in Xinjiang, China, and provide more detailed data to more scholars. This study adopts qualitative research methods and field survey data. The author proposes to focus on the perspective of cultural ecology, based on the use of big data technology, to improve the inheritance and development of Xinjiang national music.},
}
@article {pmid36249208,
year = {2022},
author = {Qamar, AI and Gronwald, L and Timmesfeld, N and Diebner, HH},
title = {Local socio-structural predictors of COVID-19 incidence in Germany.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {970092},
pmid = {36249208},
issn = {2296-2565},
mesh = {*COVID-19/epidemiology ; Germany/epidemiology ; Humans ; Incidence ; Risk Factors ; Socioeconomic Factors ; },
abstract = {Socio-economic conditions and social attitudes are known to represent epidemiological determinants. Credible knowledge on socio-economic driving factors of the COVID-19 epidemic is still incomplete. Based on linear random effects regression, an ecological model is derived to estimate COVID-19 incidence in German rural/urban districts from local socio-economic factors and popularity of political parties in terms of their share of vote. Thereby, records provided by Germany's public health institute (Robert Koch Institute) of weekly notified 7-day incidences per 100,000 inhabitants per district from the outset of the epidemic in 2020 up to December 1, 2021, are used to construct the dependent variable. Local socio-economic conditions including share of votes, retrieved from the Federal Statistical Office of Germany, have been used as potential risk factors. Socio-economic parameters like per capita income, proportions of protection seekers and social benefit claimants, and educational level have negligible impact on incidence. To the contrary, incidence significantly increases with population density and we observe a strong association with vote shares. Popularity of the right-wing party Alternative for Germany (AfD) bears a considerable risk of increasing COVID-19 incidence both in terms of predicting the maximum incidences during three epidemic periods (alternatively, cumulative incidences over the periods are used to quantify the dependent variable) and in a time-continuous sense. Thus, districts with high AfD popularity rank on top in the time-average regarding COVID-19 incidence. The impact of the popularity of the Free Democrats (FDP) is markedly intermittent in the course of time showing two pronounced peaks in incidence but also occasional drops. A moderate risk emanates from popularities of the Green Party (GRÜNE) and the Christian Democratic Union (CDU/CSU) compared to the other parties with lowest risk level. In order to effectively combat the COVID-19 epidemic, public health policymakers are well-advised to account for social attitudes and behavioral patterns reflected in local popularities of political parties, which are conceived as proper surrogates for these attitudes. Whilst causal relations between social attitudes and the presence of parties remain obscure, the political landscape in terms of share of votes constitutes at least viable predictive "markers" relevant for public health policy making.},
}
@article {pmid36248684,
year = {2022},
author = {Laroche, J and Tomassini, A and Volpe, G and Camurri, A and Fadiga, L and D'Ausilio, A},
title = {Interpersonal sensorimotor communication shapes intrapersonal coordination in a musical ensemble.},
journal = {Frontiers in human neuroscience},
volume = {16},
number = {},
pages = {899676},
pmid = {36248684},
issn = {1662-5161},
abstract = {Social behaviors rely on the coordination of multiple effectors within one's own body as well as between the interacting bodies. However, little is known about how coupling at the interpersonal level impacts coordination among body parts at the intrapersonal level, especially in ecological, complex, situations. Here, we perturbed interpersonal sensorimotor communication in violin players of an orchestra and investigated how this impacted musicians' intrapersonal movements coordination. More precisely, first section violinists were asked to turn their back to the conductor and to face the second section of violinists, who still faced the conductor. Motion capture of head and bow kinematics showed that altering the usual interpersonal coupling scheme increased intrapersonal coordination. Our perturbation also induced smaller yet more complex head movements, which spanned multiple, faster timescales that closely matched the metrical levels of the musical score. Importantly, perturbation differentially increased intrapersonal coordination across these timescales. We interpret this behavioral shift as a sensorimotor strategy that exploits periodical movements to effectively tune sensory processing in time and allows coping with the disruption in the interpersonal coupling scheme. As such, head movements, which are usually deemed to fulfill communicative functions, may possibly be adapted to help regulate own performance in time.},
}
@article {pmid36247175,
year = {2022},
author = {Sukma, P and Srinok, K and Papong, S and Supakata, N},
title = {Chula model for sustainable municipal solid waste management in university canteens.},
journal = {Heliyon},
volume = {8},
number = {10},
pages = {e10975},
pmid = {36247175},
issn = {2405-8440},
abstract = {Managing the large amount and variety of waste produced by university canteens is challenging. This study used life cycle assessment (LCA) to investigate sustainable municipal solid waste (MSW) management solutions for Chulalongkorn University (CU) canteens. This study assessed three scenarios for MSW management in CU canteens: the past scenario (prior to the Chula Zero Waste Project in 2016; S1); the current scenario (2017-2021, when the Chula Zero Waste Project's MSW management system was used; S2); and the future scenario (after 2021 with the new MSW management option for CU canteens under Chula Zero Waste; S3). The obtained results were characterized by eight impact categories: climate change, ozone depletion, terrestrial acidification, freshwater eutrophication, human toxicity, photochemical oxidant formation, particulate matter formation, and fossil depletion. The LCA results show that the future scenario (S3) under the Chula Zero Waste Project is sustainable for MSW management. The most environmentally sustainable MSW plan for CU canteens is to reduce, separate it at the source, and reuse materials instead of landfilling mixed waste.},
}
@article {pmid36239541,
year = {2023},
author = {Keck, F and Altermatt, F},
title = {Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb.},
journal = {Molecular ecology resources},
volume = {23},
number = {2},
pages = {511-518},
doi = {10.1111/1755-0998.13723},
pmid = {36239541},
issn = {1755-0998},
support = {//Bundesamt f&#xfc;r Umwelt/ ; 31003A_173074//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //University of Zurich Research Priority Program Global Change and Biodiversity/ ; },
mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Biodiversity ; Gene Library ; Databases, Nucleic Acid ; },
abstract = {DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.},
}
@article {pmid36228685,
year = {2023},
author = {Seyed Hashtroudi, M and Aghadadashi, V and Mehdinia, A and Sheijooni Fumani, N},
title = {Combining theoretical concepts and Geographic Information System (GIS) to highlight source, risk, and hotspots of sedimentary PAHs: A case study of Chabahar Bay.},
journal = {Environmental research},
volume = {216},
number = {Pt 1},
pages = {114540},
doi = {10.1016/j.envres.2022.114540},
pmid = {36228685},
issn = {1096-0953},
mesh = {Geographic Information Systems ; Geologic Sediments/analysis ; Bays ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Vehicle Emissions/analysis ; China ; },
abstract = {Sedimentary PAHs are regionalized variables and their levels, source, and ecological hazards must be discussed in relation to their spatial locations. Our research targeted GIS and Chabahar Bay-Iran to trace spatial variability of PAHs, improve the diagnostic ratios and receptor models in source identification, and determine hotspot of PAH-originated hazards. The entropy Voronoi map distinguished an "entropy strip" in which ∑22PAHs levels increased sharply. Different molecular signatures were individually interpolated and the indicative ratios of distinctive sources were extracted and summed by GIS. The resulting code map reduced potential disagreement among molecular signatures and highlighted the areas where petroleum inputs are prevalent. PCA-MLR analysis extracted three potential sources including fossil fuel combustion (54.36%), petrogenic inputs (29.03%), and vehicle exhaust emissions (16.61%). Interpolated risk layers were re-arranged and overlaid via Fuzzy Membership Functions. The obtained ''Fuzzy AND" map showed the hotspot of the study area in the vicinity of a seasonal estuary.},
}
@article {pmid36226159,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Phillips, D and , },
title = {The genome sequence of the brimstone moth, Opisthograptis luteolata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {227},
pmid = {36226159},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Opisthograptis luteolata (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.},
}
@article {pmid36225383,
year = {2022},
author = {Richardson, AD and Kong, GV and Taylor, KM and Le Moine, JM and Bowker, MA and Barber, JJ and Basler, D and Carbone, MS and Hayer, M and Koch, GW and Salvatore, MR and Sonnemaker, AW and Trilling, DE},
title = {Soil-atmosphere fluxes of CO2, CH4, and N2O across an experimentally-grown, successional gradient of biocrust community types.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {979825},
pmid = {36225383},
issn = {1664-302X},
abstract = {Biological soil crusts (biocrusts) are critical components of dryland and other ecosystems worldwide, and are increasingly recognized as novel model ecosystems from which more general principles of ecology can be elucidated. Biocrusts are often diverse communities, comprised of both eukaryotic and prokaryotic organisms with a range of metabolic lifestyles that enable the fixation of atmospheric carbon and nitrogen. However, how the function of these biocrust communities varies with succession is incompletely characterized, especially in comparison to more familiar terrestrial ecosystem types such as forests. We conducted a greenhouse experiment to investigate how community composition and soil-atmosphere trace gas fluxes of CO2, CH4, and N2O varied from early-successional light cyanobacterial biocrusts to mid-successional dark cyanobacteria biocrusts and late-successional moss-lichen biocrusts and as biocrusts of each successional stage matured. Cover type richness increased as biocrusts developed, and richness was generally highest in the late-successional moss-lichen biocrusts. Microbial community composition varied in relation to successional stage, but microbial diversity did not differ significantly among stages. Net photosynthetic uptake of CO2 by each biocrust type also increased as biocrusts developed but tended to be moderately greater (by up to ≈25%) for the mid-successional dark cyanobacteria biocrusts than the light cyanobacterial biocrusts or the moss-lichen biocrusts. Rates of soil C accumulation were highest for the dark cyanobacteria biocrusts and light cyanobacteria biocrusts, and lowest for the moss-lichen biocrusts and bare soil controls. Biocrust CH4 and N2O fluxes were not consistently distinguishable from the same fluxes measured from bare soil controls; the measured rates were also substantially lower than have been reported in previous biocrust studies. Our experiment, which uniquely used greenhouse-grown biocrusts to manipulate community composition and accelerate biocrust development, shows how biocrust function varies along a dynamic gradient of biocrust successional stages.},
}
@article {pmid36224329,
year = {2022},
author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G},
title = {Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.},
journal = {Leukemia},
volume = {36},
number = {11},
pages = {2705-2714},
pmid = {36224329},
issn = {1476-5551},
support = {P 31494/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology ; *Gastrointestinal Microbiome ; Immunity ; },
abstract = {The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45[+] leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.},
}
@article {pmid36224130,
year = {2022},
author = {Zhao, CH and Shen, HY and Wang, ZH and Liang, YP and Zhao, Y and Xie, H and Tang, CL},
title = {[Hydrochemical and Isotopic Characteristics in the Surface Water of the Fenhe River Basin and Influence Factors].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {43},
number = {10},
pages = {4440-4448},
doi = {10.13227/j.hjkx.202201103},
pmid = {36224130},
issn = {0250-3301},
mesh = {Calcium Sulfate ; Carbonates ; Environmental Monitoring/methods ; *Groundwater/chemistry ; Hydrogen ; Minerals ; Oxygen Isotopes ; Sulfides ; *Water Pollutants, Chemical/analysis ; Water Quality ; },
abstract = {The Fenhe River Basin is the mother river of Shanxi Province. Due to the over-exploitation of water resources and the impact of social and economic development, the ecological environment has deteriorated. After a series of treatment and protection measures, the water quality has since been improved. Mathematical statistics, Piper diagrams, Gibbs model, hydrogen and oxygen isotopes, and other methods were used to analyze the characteristics and sources of hydrochemistry in the surface water of the Fenhe River basin, which revealed the evolution process of surface water quality of the Fenhe River basin. The results showed that the content of the main hydrochemical components in the main stream surface water of Fenhe River basin increased gradually along the runoff path. The hydrochemical types of surface water of Fenhe River basin were mainly HCO3·SO4·Cl-Ca·Na·Mg and SO4·HCO3·Cl-Ca·Na·Mg. There were great differences in hydrochemical components of tributaries and karst water in the basin. There were also great differences in hydrochemical components of tributaries in the basin. The hydrochemical types of surface water of karst water were mainly SO4·HCO3-Ca·Mg. The hydrochemical composition of surface water in Fenhe River basin was mainly affected by rock weathering and evaporation crystallization, whereas rainfall had little effect. Na[+] and K[+] mainly came from the dissolution of evaporated salt rocks with Na in the surrounding loess. Ca[2+], Mg[2+], and HCO3[-] mainly came from the dissolution of carbonate rocks. SO4[2-] may have also come from the dissolution of sulfide minerals in the loess layer around Fenhe River in addition to the dissolution of gypsum. The values of δD and δ[18]O of Fenhe River surface water were gradually enriched from upstream to downstream. The characteristics of hydrogen and oxygen isotopes further showed that the surface water was mainly affected by evaporation. The results of this study can provide evidence for ecological restoration and protection and ecological civilization construction in the Fenhe River basin.},
}
@article {pmid36215495,
year = {2022},
author = {Zhao, J and Jin, L and Wu, D and Xie, JW and Li, J and Fu, XW and Cong, ZY and Fu, PQ and Zhang, Y and Luo, XS and Feng, XB and Zhang, G and Tiedje, JM and Li, XD},
title = {Global airborne bacterial community-interactions with Earth's microbiomes and anthropogenic activities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {42},
pages = {e2204465119},
pmid = {36215495},
issn = {1091-6490},
mesh = {*Air Microbiology ; Anthropogenic Effects ; Bacteria/genetics ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Airborne bacteria are an influential component of the Earth's microbiomes, but their community structure and biogeographic distribution patterns have yet to be understood. We analyzed the bacterial communities of 370 air particulate samples collected from 63 sites around the world and constructed an airborne bacterial reference catalog with more than 27 million nonredundant 16S ribosomal RNA (rRNA) gene sequences. We present their biogeographic pattern and decipher the interlacing of the microbiome co-occurrence network with surface environments of the Earth. While the total abundance of global airborne bacteria in the troposphere (1.72 × 10[24] cells) is 1 to 3 orders of magnitude lower than that of other habitats, the number of bacterial taxa (i.e., richness) in the atmosphere (4.71 × 10[8] to 3.08 × 10[9]) is comparable to that in the hydrosphere, and its maximum occurs in midlatitude regions, as is also observed in other ecosystems. The airborne bacterial community harbors a unique set of dominant taxa (24 species); however, its structure appears to be more easily perturbed, due to the more prominent role of stochastic processes in shaping community assembly. This is corroborated by the major contribution of surface microbiomes to airborne bacteria (averaging 46.3%), while atmospheric conditions such as meteorological factors and air quality also play a role. Particularly in urban areas, human impacts weaken the relative importance of plant sources of airborne bacteria and elevate the occurrence of potential pathogens from anthropogenic sources. These findings serve as a key reference for predicting planetary microbiome responses and the health impacts of inhalable microbiomes with future changes in the environment.},
}
@article {pmid36215030,
year = {2023},
author = {Yang, Z and Wang, J and Huang, Y and Wang, S and Wei, L and Liu, D and Weng, Y and Xiang, J and Zhu, Q and Yang, Z and Nie, X and Yu, Y and Yang, Z and Yang, QY},
title = {CottonMD: a multi-omics database for cotton biological study.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D1446-D1456},
pmid = {36215030},
issn = {1362-4962},
mesh = {*Databases, Factual ; Genome ; Genomics/methods ; *Multiomics ; Phenotype ; *Gossypium/chemistry/genetics ; },
abstract = {Cotton is an important economic crop, and many loci for important traits have been identified, but it remains challenging and time-consuming to identify candidate or causal genes/variants and clarify their roles in phenotype formation and regulation. Here, we first collected and integrated the multi-omics datasets including 25 genomes, transcriptomes in 76 tissue samples, epigenome data of five species and metabolome data of 768 metabolites from four tissues, and genetic variation, trait and transcriptome datasets from 4180 cotton accessions. Then, a cotton multi-omics database (CottonMD, http://yanglab.hzau.edu.cn/CottonMD/) was constructed. In CottonMD, multiple statistical methods were applied to identify the associations between variations and phenotypes, and many easy-to-use analysis tools were provided to help researchers quickly acquire the related omics information and perform multi-omics data analysis. Two case studies demonstrated the power of CottonMD for identifying and analyzing the candidate genes, as well as the great potential of integrating multi-omics data for cotton genetic breeding and functional genomics research.},
}
@article {pmid36213026,
year = {2022},
author = {Wen, Y},
title = {Analysis of Regional Economy Development on Local Environmental Protection and Natural Resources Utilization from the Perspective of Big Data.},
journal = {Journal of environmental and public health},
volume = {2022},
number = {},
pages = {9461377},
pmid = {36213026},
issn = {1687-9813},
mesh = {Big Data ; China ; Cities ; *Conservation of Natural Resources ; *Economic Development ; Natural Resources ; Rivers ; },
abstract = {The ecological restoration and civilization construction is one of the key tasks in China. The economic development of different regions has different effects on the resource protection and utilization. In the face of complex natural conditions and resource-rich areas, how to carry out the ecological environment promotion work is put forward. The urbanization level of the Yangtze River region increases from 17.9% to 60.6%, showing the characteristics of rapid expansion. In the face of urban diseases such as unreasonable industrial layout, it is urgent to improve regional economy and promote green urban development from the perspective of big data. Adhering to the concept of ecological priority, the development of digital technology drove the development of local economy in 2019, accounting for 43% of the national population. While promoting the economic development, it is of great significance to ensure the efficiency of resource utilization and promote the high-quality development of common economy.},
}
@article {pmid36212380,
year = {2022},
author = {Shao, P and Peng, Y and Wu, Y and Wang, J and Pan, Z and Yang, Y and Aini, N and Guo, C and Shui, G and Chao, L and Tian, X and An, Q and Yang, Q and You, C and Lu, L and Zhang, X and Wang, M and Nie, X},
title = {Genome-wide association study and transcriptome analysis reveal key genes controlling fruit branch angle in cotton.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {988647},
pmid = {36212380},
issn = {1664-462X},
abstract = {Fruit branch angle (FBA), a pivotal component of cotton plant architecture, is vital for field and mechanical harvesting. However, the molecular mechanism of FBA formation is poorly understood in cotton. To uncover the genetic basis for FBA formation in cotton, we performed a genome-wide association study (GWAS) of 163 cotton accessions with re-sequencing data. A total of 55 SNPs and 18 candidate genes were significantly associated with FBA trait. By combining GWAS and transcriptome analysis, four genes underlying FBA were identified. An FBA-associated candidate gene Ghi_A09G08736, which is homologous to SAUR46 in Arabidopsis thaliana, was detected in our study. In addition, transcriptomic evidence was provided to show that gravity and light were implicated in the FBA formation. This study provides new insights into the genetic architecture of FBA that informs architecture breeding in cotton.},
}
@article {pmid36210994,
year = {2022},
author = {Ju, X},
title = {Application of Big Data Technology to Promote Agricultural Structure Adjustment and High-Quality Development of Modern Agriculture.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {5222760},
pmid = {36210994},
issn = {1687-5273},
mesh = {*Agriculture ; *Big Data ; China ; Conservation of Natural Resources ; Remote Sensing Technology ; Technology ; },
abstract = {The implementation of the strategy of rural revitalization is a major ministerial work made by the Nineteenth National Congress of the Communist Party of China and is the general grasp of contemporary agriculture, peasants, and rural work. In recent years, with the rapid development of remote sensing technology and deep learning technology, the demand for the technology for the classification of crops on satellite remote sensing images based on deep learning technology has increased in agricultural insurance and land survey. Therefore, this paper trains one, which is 85.9%-92.8%, the accuracy of corn classification is 77%-93%, and the accuracy of forest classification is 77%-87.6%. Subsequently, the overall accuracy of classifying all directories through the multi-temporal validation data set between May 2017 and October 2017 reached 92.6%. Such a multi-time combination method can be used for monthly, timely, and efficient iteration of agricultural insurance and crop yield estimation, which will be more accurate each time. These methods can also be further applied to the growth and change monitoring of large agricultural planting areas, adding bricks and tiles to China's agricultural remote sensing. If the countryside is to be revitalized, agriculture must develop rapidly at the same time, industries must flourish, ecology must be livable, rural customs must be civilized, and life must be prosperous. Modern agriculture is a comprehensive circulation system with high yield, high quality, low consumption, ecology, environmental protection, and high efficiency. The development of modern agriculture is inseparable from the industrialization of agriculture, the globalization of agriculture, the digitization of agriculture, the integration of agriculture, the adjustment of agricultural structure, and agricultural innovation. Only the continuous development of modern agriculture can make rural revitalization enter a new journey.},
}
@article {pmid36209915,
year = {2022},
author = {Chetty, M and Hallinan, J and Ruz, GA and Wipat, A},
title = {Computational intelligence and machine learning in bioinformatics and computational biology.},
journal = {Bio Systems},
volume = {222},
number = {},
pages = {104792},
doi = {10.1016/j.biosystems.2022.104792},
pmid = {36209915},
issn = {1872-8324},
mesh = {*Computational Biology ; *Artificial Intelligence ; Machine Learning ; },
}
@article {pmid36207680,
year = {2022},
author = {Asghari-Jafarabadi, M and Gholipour, K and Khodayari-Zarnaq, R and Azmin, M and Alizadeh, G},
title = {Estimation of myocardial infarction death in Iran: artificial neural network.},
journal = {BMC cardiovascular disorders},
volume = {22},
number = {1},
pages = {438},
pmid = {36207680},
issn = {1471-2261},
mesh = {Humans ; *Hypercholesterolemia/diagnosis/epidemiology ; Iran/epidemiology ; Male ; *Myocardial Infarction/diagnosis/epidemiology ; Neural Networks, Computer ; Obesity/diagnosis/epidemiology ; Overweight ; Risk Factors ; },
abstract = {BACKGROUND: Examining past trends and predicting the future helps policymakers to design effective interventions to deal with myocardial infarction (MI) with a clear understanding of the current and future situation. The aim of this study was to estimate the death rate due to MI in Iran by artificial neural network (ANN).<br><br>METHODS: In this ecological study, the prevalence of diabetes, hypercholesterolemia over 200, hypertension, overweight and obesity were estimated for the years 2017-2025. ANN and Linear regression model were used. Also, Specialists were also asked to predict the death rate due to MI by considering the conditions of 3 conditions (optimistic, pessimistic, and probable), and the predicted process was compared with the modeling process.<br><br>RESULTS: Death rate due to MI in Iran is expected to decrease on average, while there will be a significant decrease in the prevalence of hypercholesterolemia 1.031 (-&#x2009;24.81, 26.88). Also, the trend of diabetes 10.48 (111.45, -&#x2009;132.42), blood pressure -&#x2009;110.48 (-&#x2009;174.04, -&#x2009;46.91) and obesity and overweight -&#x2009;35.84 (-&#x2009;18.66, -&#x2009;5.02) are slowly increasing. MI death rate in Iran is higher in men but is decreasing on average. Experts' forecasts are different and have predicted a completely upward trend.<br><br>CONCLUSION: The trend predicted by the modeling shows that the death rate due to MI will decrease in the future with a low slope. Improving the infrastructure for providing preventive services to reduce the risk factors for cardiovascular disease in the community is one of the priority measures in the current situation.},
}
@article {pmid36202356,
year = {2023},
author = {Jones, DL and Rhymes, JM and Wade, MJ and Kevill, JL and Malham, SK and Grimsley, JMS and Rimmer, C and Weightman, AJ and Farkas, K},
title = {Suitability of aircraft wastewater for pathogen detection and public health surveillance.},
journal = {The Science of the total environment},
volume = {856},
number = {Pt 2},
pages = {159162},
pmid = {36202356},
issn = {1879-1026},
mesh = {Adult ; Male ; Humans ; *Wastewater ; Public Health Surveillance ; SARS-CoV-2 ; *COVID-19/epidemiology ; Aircraft ; },
abstract = {International air travel is now widely recognised as one of the primary mechanisms responsible for the transnational movement and global spread of SARS-CoV-2. Monitoring the viral load and novel lineages within human-derived wastewater collected from aircraft and at air transport hubs has been proposed as an effective way to monitor the importation frequency of viral pathogens. The success of this approach, however, is highly dependent on the bathroom and defecation habits of air passengers during their journey. In this study of UK adults (n = 2103), we quantified the likelihood of defecation prior to departure, on the aircraft and upon arrival on both short- and long-haul flights. The results were then used to assess the likelihood of capturing the signal from infected individuals at UK travel hubs. To obtain a representative cross-section of the population, the survey was stratified by geographical region, gender, age, parenting status, and social class. We found that an individual's likelihood to defecate on short-haul flights (< 6 h in duration) was low (< 13 % of the total), but was higher on long-haul flights (< 36 %; > 6 h in duration). This behaviour pattern was higher among males and younger age groups. The maximum likelihood of defecation was prior to departure (< 39 %). Based on known SARS-CoV-2 faecal shedding rates (30-60 %) and an equal probability of infected individuals being on short- (71 % of inbound flights) and long-haul flights (29 %), we estimate that aircraft wastewater is likely to capture ca. 8-14 % of SARS-CoV-2 cases entering the UK. Monte Carlo simulations predicted that SARS-CoV-2 would be present in wastewater on 14 % of short-haul flights and 62 % of long-haul flights under current pandemic conditions. We conclude that aircraft wastewater alone is insufficient to effectively monitor all the transboundary entries of faecal-borne pathogens but can form part of a wider strategy for public heath surveillance at national borders.},
}
@article {pmid36198068,
year = {2022},
author = {Wanchai, V and Jenjaroenpun, P and Leangapichart, T and Arrey, G and Burnham, CM and Tümmler, MC and Delgado-Calle, J and Regenberg, B and Nookaew, I},
title = {CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.},
journal = {Briefings in bioinformatics},
volume = {23},
number = {6},
pages = {},
pmid = {36198068},
issn = {1477-4054},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R37 CA251763/CA/NCI NIH HHS/United States ; T32 GM106999/GM/NIGMS NIH HHS/United States ; },
mesh = {*DNA, Circular/genetics ; *Genome ; DNA/genetics ; Eukaryotic Cells ; },
abstract = {Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL's performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL's capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.},
}
@article {pmid36197407,
year = {2022},
author = {Cunha, APD and Cruz, MMD},
title = {Analysis of trend in mortality due to HIV/AIDS-defining and non-HIV/AIDS defining illnesses according to sociodemographic characteristics, by Federative Unit and Brazil, 2000-2018.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {31},
number = {2},
pages = {e2022093},
pmid = {36197407},
issn = {2237-9622},
mesh = {*Acquired Immunodeficiency Syndrome/epidemiology ; Brazil/epidemiology ; Humans ; Information Systems ; Time Factors ; },
abstract = {OBJECTIVE: To analyze the temporal trend of mortality rate due to HIV/AIDS defining and non-HIV/AIDS defining illnesses in Brazil between 2000 and 2018.<br><br>METHODS: This was an ecological time series study, using data from the Mortality Information System, in Brazil and the Federative Units. Trend analysis was performed by means of Prais-Winsten regression model, according to overall mortality rate, sex, age group, marital status and race/skin color.<br><br>RESULTS: A total of 237,435 deaths were recorded in the period. In the country, defining illnesses showed higher rates (7.4 to 4.4 deaths/100,000 inhabitants in the period) than those observed among non-defining diseases (0.4 to 0.8 death/100,000 inhabitants in the period). It could be seen a decrease in overall mortality due to defining diseases (-6.3%; 95%CI -8.8;-3.8); while it increased due to non-defining diseases (11.0%; 95%CI 6.5;15.7).<br><br>CONCLUSION: There was a change in HIV/AIDS mortality profile over the years, with a decrease in deaths due to HIV/AIDS-defining diseases.},
}
@article {pmid36197074,
year = {2022},
author = {Gonçalves, BP and Hall, M and Jassat, W and Balan, V and Murthy, S and Kartsonaki, C and Semple, MG and Rojek, A and Baruch, J and Reyes, LF and Dasgupta, A and Dunning, J and Citarella, BW and Pritchard, M and Martín-Quiros, A and Sili, U and Baillie, JK and Aryal, D and Arabi, Y and Rashan, A and Angheben, A and Caoili, J and Carrier, FM and Harrison, EM and Gómez-Junyent, J and Figueiredo-Mello, C and Douglas, JJ and Mat Nor, MB and Chow, YP and Wong, XC and Bertagnolio, S and Thwin, SS and Streinu-Cercel, A and Salazar, L and Rishu, A and Rangappa, R and Ong, DSY and Hashmi, M and Carson, G and Diaz, J and Fowler, R and Kraemer, MUG and Wils, EJ and Horby, P and Merson, L and Olliaro, PL and , },
title = {An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36197074},
issn = {2050-084X},
support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; 200927/WT_/Wellcome Trust/United Kingdom ; 205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 222410/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; MR/S032304/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_19025/MRC_/Medical Research Council/United Kingdom ; 001/WHO_/World Health Organization/International ; 225288/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; 222048/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*COVID-19/epidemiology/virology ; Humans ; *SARS-CoV-2/genetics ; },
abstract = {BACKGROUND: Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings.<br><br>METHODS: Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries.<br><br>RESULTS: Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61-0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population.<br><br>CONCLUSIONS: Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.<br><br>FUNDING: Bronner P. Gon&#xe7;alves, Peter Horby, Gail Carson, Piero L. Olliaro, Valeria Balan, Barbara Wanjiru Citarella, and research costs were supported by the UK Foreign, Commonwealth and Development Office (FCDO) and Wellcome [215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z]; and Janice Caoili and Madiha Hashmi were supported by the UK FCDO and Wellcome [222048/Z/20/Z]. Peter Horby, Gail Carson, Piero L. Olliaro, Kalynn Kennon and Joaquin Baruch were supported by the Bill &amp; Melinda Gates Foundation [OPP1209135]; Laura Merson was supported by University of Oxford's COVID-19 Research Response Fund - with thanks to its donors for their philanthropic support. Matthew Hall was supported by a Li Ka Shing Foundation award to Christophe Fraser. Moritz U.G. Kraemer was supported by the Branco Weiss Fellowship, Google.org, the Oxford Martin School, the Rockefeller Foundation, and the European Union Horizon 2020 project MOOD (#874850). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Contributions from Srinivas Murthy, Asgar Rishu, Rob Fowler, James Joshua Douglas, Fran&#xe7;ois Martin Carrier were supported by CIHR Coronavirus Rapid Research Funding Opportunity OV2170359 and coordinated out of Sunnybrook Research Institute. Contributions from Evert-Jan Wils and David S.Y. Ong were supported by a grant from foundation Bevordering Onderzoek Franciscus; and Andrea Angheben by the Italian Ministry of Health "Fondi Ricerca corrente-L1P6" to IRCCS Ospedale Sacro Cuore-Don Calabria. The data contributions of J.Kenneth Baillie, Malcolm G. Semple, and Ewen M. Harrison were supported by grants from the National Institute for Health Research (NIHR; award CO-CIN-01), the Medical Research Council (MRC; grant MC_PC_19059), and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE) (award 200907), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award 200927), Liverpool Experimental Cancer Medicine Centre (grant C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award IS-BRC-1215-20013), and NIHR Clinical Research Network providing infrastructure support. All funders of the ISARIC Clinical Characterisation Group are listed in the appendix.},
}
@article {pmid36195605,
year = {2022},
author = {Peters, K and König-Ries, B},
title = {Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {598},
pmid = {36195605},
issn = {2052-4463},
mesh = {Biodiversity ; *Bryophyta ; Computational Biology/methods ; *Hepatophyta ; Image Processing, Computer-Assisted/methods ; },
abstract = {Macro- and microscopic images of organisms are pivotal in biodiversity research. Despite that bioimages have manifold applications such as assessing the diversity of form and function, FAIR bioimaging data in the context of biodiversity are still very scarce, especially for difficult taxonomic groups such as bryophytes. Here, we present a high-quality reference dataset containing macroscopic and bright-field microscopic images documenting various phenotypic characters of the species belonging to the liverwort family of Scapaniaceae occurring in Europe. To encourage data reuse in biodiversity and adjacent research areas, we annotated the imaging data with machine-actionable metadata using community-accepted semantics. Furthermore, raw imaging data are retained and any contextual image processing like multi-focus image fusion and stitching were documented to foster good scientific practices through source tracking and provenance. The information contained in the raw images are also of particular interest for machine learning and image segmentation used in bioinformatics and computational ecology. We expect that this richly annotated reference dataset will encourage future studies to follow our principles.},
}
@article {pmid36195601,
year = {2022},
author = {Pottier, P and Lin, HY and Oh, RRY and Pollo, P and Rivera-Villanueva, AN and Valdebenito, JO and Yang, Y and Amano, T and Burke, S and Drobniak, SM and Nakagawa, S},
title = {A comprehensive database of amphibian heat tolerance.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {600},
pmid = {36195601},
issn = {2052-4463},
support = {Scientia Doctoral Scholarship//University of New South Wales (UNSW Australia)/ ; Scientia Doctoral Scholarship//University of New South Wales (UNSW Australia)/ ; Scientia Doctoral Scholarship//University of New South Wales (UNSW Australia)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FT180100354//Department of Education and Training | Australian Research Council (ARC)/ ; DE180100202//Department of Education and Training | Australian Research Council (ARC)/ ; DP200100367//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {*Amphibians ; Animals ; Databases, Factual ; Hot Temperature ; Temperature ; *Thermotolerance ; },
abstract = {Rising temperatures represent a significant threat to the survival of ectothermic animals. As such, upper thermal limits represent an important trait to assess the vulnerability of ectotherms to changing temperatures. For instance, one may use upper thermal limits to estimate current and future thermal safety margins (i.e., the proximity of upper thermal limits to experienced temperatures), use this trait together with other physiological traits in species distribution models, or investigate the plasticity and evolvability of these limits for buffering the impacts of changing temperatures. While datasets on thermal tolerance limits have been previously compiled, they sometimes report single estimates for a given species, do not present measures of data dispersion, and are biased towards certain parts of the globe. To overcome these limitations, we systematically searched the literature in seven languages to produce the most comprehensive dataset to date on amphibian upper thermal limits, spanning 3,095 estimates across 616 species. This resource will represent a useful tool to evaluate the vulnerability of amphibians, and ectotherms more generally, to changing temperatures.},
}
@article {pmid36194325,
year = {2023},
author = {Zhou, Y and Hu, Z and Geng, Q and Ma, J and Liu, J and Wang, M and Wang, Y},
title = {Monitoring and analysis of desertification surrounding Qinghai Lake (China) using remote sensing big data.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {7},
pages = {17420-17436},
pmid = {36194325},
issn = {1614-7499},
mesh = {Humans ; *Remote Sensing Technology ; *Conservation of Natural Resources/methods ; Lakes ; Big Data ; Environmental Monitoring/methods ; China ; },
abstract = {Desertification is one of the most serious ecological environmental problems in the world. Monitoring the spatiotemporal dynamics of desertification is crucial for its control. The region around Qinghai Lake, in the northeastern part of the Qinghai-Tibet Plateau in China, is a special ecological function area and a climate change sensitive area, making its environmental conditions a great concern. Using cloud computing via Google Earth Engine (GEE), we collected Landsat 5 TM, Landsat 8 OLI/TIRS, and MODIS Albedo images from 2000 to 2020 in the region around Qinghai Lake, acquired land surface albedo (Albedo), and normalized vegetation index (NDVI) to build a remote sensing monitoring model of desertification. Our results showed that the desertification difference index based on the Albedo-NDVI feature space could reflect the degree of desertification in the region around Qinghai Lake. GEE offers significant advantages, such as massive data processing and long-term dynamic monitoring. The desertification land area fluctuated downward in the study area from 2000 to 2020, and the overall desertification status improved. Natural factors, such as climate change from warm-dry to warm-wet and decreased wind speed, and human factors improved the desertification situation. The findings indicate that desertification in the region around Qinghai Lake has been effectively controlled, and the overall desertification trend is improving.},
}
@article {pmid36191222,
year = {2022},
author = {Yang, L and Constantino, SM and Grenfell, BT and Weber, EU and Levin, SA and Vasconcelos, VV},
title = {Sociocultural determinants of global mask-wearing behavior.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {41},
pages = {e2213525119},
pmid = {36191222},
issn = {1091-6490},
mesh = {*COVID-19/epidemiology/prevention &amp; control ; Humans ; *Masks ; *Pandemics/prevention &amp; control ; Public Policy ; Risk ; SARS-CoV-2 ; Social Conditions ; },
abstract = {Behavioral responses influence the trajectories of epidemics. During the COVID-19 pandemic, nonpharmaceutical interventions (NPIs) reduced pathogen transmission and mortality worldwide. However, despite the global pandemic threat, there was substantial cross-country variation in the adoption of protective behaviors that is not explained by disease prevalence alone. In particular, many countries show a pattern of slow initial mask adoption followed by sharp transitions to high acceptance rates. These patterns are characteristic of behaviors that depend on social norms or peer influence. We develop a game-theoretic model of mask wearing where the utility of wearing a mask depends on the perceived risk of infection, social norms, and mandates from formal institutions. In this model, increasing pathogen transmission or policy stringency can trigger social tipping points in collective mask wearing. We show that complex social dynamics can emerge from simple individual interactions and that sociocultural variables and local policies are important for recovering cross-country variation in the speed and breadth of mask adoption. These results have implications for public health policy and data collection.},
}
@article {pmid36188695,
year = {2022},
author = {Zhang, W},
title = {Design of Urban Garden Landscape Visualization System Based on GIS and Remote Sensing Technology.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {9592376},
pmid = {36188695},
issn = {1687-5273},
mesh = {Cities ; Environmental Monitoring/methods ; Gardens ; *Geographic Information Systems ; Hot Temperature ; *Remote Sensing Technology ; },
abstract = {Urban green ecological space is an important manifestation of the environmental characteristics of a green city. The research results show that the urban green ecological space has obvious cooling and humidity effects, which are very important for reducing the urban heat island effect. Remote sensing technology describes the slow-release effects of urban green parks in different seasons from the two perspectives of thermal slow-release intensity and thermal slow-release distance. In this paper, UAV remote sensing is used to extract the internal and external factors of the urban green environment characteristics and to identify the main factors that affect the slow-release heat effect and seasonal changes of the urban green environment. In addition, it analyzes the factors that affect the urban environmental temperature within the environmental temperature slow-release range of urban green space, establishes a model to predict the environmental temperature within the thermal slow-release range outside the park, and realizes the largest thermal slow release in the urban greening ecological space. These are new technologies created in the context of digitization, which include image understanding and synthesis, which involve the use of computer graphics and image processing technology to convert data into graphics or images displayed on the screen to achieve an interactive process.},
}
@article {pmid36187697,
year = {2022},
author = {Ekpenyong, N and Heitz Tokpa, K and Nwankwo, O and O'Donnell, D and Rodriguez Franco, D and Berté, S and Amani Kouassi, S and Eteng, G and Undelikwo, V and Auer, C and Guessan Bi, GB and Oyo-Ita, A and Bosch-Capblanch, X},
title = {Using and improving the PHISICC paper-based tools in the health facility laboratories: Examples of Human Centered Design taking systems thinking into practice, in Côte d'Ivoire and Nigeria.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {916397},
pmid = {36187697},
issn = {2296-2565},
mesh = {Cote d'Ivoire ; Health Facilities ; Humans ; *Laboratories ; Nigeria ; Systems Analysis ; *Universal Design ; },
abstract = {BACKGROUND: Health workers in low- and middle-income countries are increasingly demanded to collect more and more data to report them to higher levels of the health information system (HIS), in detriment of useful data for clinical and public health decision-making, potentially compromising the quality of their health care provison. In order to support health workers' decision-making, we engaged with partners in Côte d'Ivoire, Mozambique and Nigeria in a research project to conceive, design, produce, implement and test paper-based health information tools: the PHISICC tools. Our aim was to understand the use of PHISICC tools by health workers and to improve them based on their feedback.<br><br>METHODS: The design Health Facility Laboratories (HF Labs) in C&#xf4;te d'Ivoire and in Nigeria were set up after months of use of PHISICC tools. Activities were structured in three phases or 'sprints' of co-creative research. We used a transdisciplinary approach, including anthropology and Human Centered Design (HCD), observations, shadowing, structured interviews and co-creation.<br><br>RESULTS: Health workers appreciated the standardization of the tools across different health care areas, with a common visual language that optimized use. Several design issues were raised, in terms of formats and contents. They strongly appreciated how the PHISICC registers guided their clinical decision-making and how it facilitated tallying and counting for monthly reporting. However, adherence to new procedures was not universal. The co-creation sessions resulted in modifications to the PHISICC tools of out-patient care and postnatal care.<br><br>DISCUSSION: Although health systems and systemic thinking allowed the teams to embrace complexity, it was the HCD approach that actually produced a shift in researchers' mind-set: from HIS as data management tools to HIS as quality of care instruments. HCD allowed navigating the complexity of health systems interventions due to its capacity to operate change: it not only allowed us to understand how the PHISICC tools were used but also how to further improve them. In the absence of (or even with) an analytical health systems framework, HCD approaches can work in real-life situations for the ideation, testing and implementation of interventions to improve health systems and health status outcomes.},
}
@article {pmid36179444,
year = {2022},
author = {Chin, JM and Growns, B and Sebastian, J and Page, MJ and Nakagawa, S},
title = {The transparency and reproducibility of systematic reviews in forensic science.},
journal = {Forensic science international},
volume = {340},
number = {},
pages = {111472},
doi = {10.1016/j.forsciint.2022.111472},
pmid = {36179444},
issn = {1872-6283},
mesh = {*Benchmarking ; Databases, Factual ; *Forensic Sciences ; Reproducibility of Results ; Systematic Reviews as Topic ; },
abstract = {Systematic reviews are indispensable tools for both reliably informing decision-makers about the state of the field and for identifying areas that need further study. Their value, however, depends on their transparency and reproducibility. Readers should be able to determine what was searched for and when, where the authors searched, and whether that search was predetermined or evolved based on what was found. In this article, we measured the transparency and reproducibility of systematic reviews in forensic science, a field where courts, policymakers, and legislators count on systematic reviews to make informed decisions. In a sample of 100 systematic reviews published between 2018 and 2021, we found that completeness of reporting varied markedly. For instance, 50 % of reviews claimed to follow a reporting guideline and such statements were only modestly related to compliance with that reporting guideline. As to specific reporting items, 82 % reported all of the databases searched, 22 % reported the review's full Boolean search logic, and just 7 % reported the review was registered. Among meta-analyses (n = 23), only one stated data was available and none stated the analytic code was available. After considering the results, we end with recommendations for improved regulation of reporting practices, especially among journals. Our results may serve as a useful benchmark as the field evolves.},
}
@article {pmid36175492,
year = {2022},
author = {Leonardi, M and Boschin, F and Boscato, P and Manica, A},
title = {Following the niche: the differential impact of the last glacial maximum on four European ungulates.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1038},
pmid = {36175492},
issn = {2399-3642},
mesh = {Animals ; Archaeology ; Databases, Factual ; *Deer ; Ecosystem ; Horses ; Species Specificity ; Sus scrofa ; Swine ; },
abstract = {Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.},
}
@article {pmid36174014,
year = {2022},
author = {Porter, TM and Hajibabaei, M},
title = {MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0274260},
pmid = {36174014},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Biomarkers ; *Computational Biology ; Ecology ; Eukaryota ; },
abstract = {Multi-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as for molecular ecology and biomonitoring applications in different sectors from academic research to regulatory agencies and industry. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are often used to process animal metabarcode markers from the same study. MetaWorks provides a harmonized processing environment, pipeline, and taxonomic assignment approach for demultiplexed Illumina reads for all biota using a wide range of metabarcoding markers such as 16S, ITS, and COI. A Conda environment is provided to quickly gather most of the programs and dependencies for the pipeline. Several workflows are provided such as: taxonomically assigning exact sequence variants, provides an option to generate operational taxonomic units, and facilitates single-read processing. Pipelines are automated using Snakemake to minimize user intervention and facilitate scalability. All pipelines use the RDP classifier to provide taxonomic assignments with confidence measures. We extend the functionality of the RDP classifier for taxonomically assigning 16S (bacteria), ITS (fungi), and 28S (fungi), to also support COI (eukaryotes), rbcL (eukaryotes, land plants, diatoms), 12S (fish, vertebrates), 18S (eukaryotes, diatoms) and ITS (fungi, plants). MetaWorks properly handles ITS by trimming flanking conserved rRNA gene regions as well as protein coding genes by providing two options for removing obvious pseudogenes. MetaWorks can be downloaded from https://github.com/terrimporter/MetaWorks and quickstart instructions, pipeline details, and a tutorial for new users can be found at https://terrimporter.github.io/MetaWorksSite.},
}
@article {pmid36172318,
year = {2022},
author = {Yin, G and Liu, J},
title = {Research on Movement Analysis and Guidance in Dance Learning Based on Data Mining.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {9327442},
pmid = {36172318},
issn = {1687-5273},
mesh = {Data Mining ; Humans ; *Learning ; *Movement ; Students ; },
abstract = {In dance, we must understand the essential meaning of dance movements from the inside and express them on the basis of dance. Therefore, in the process of developing new dance teaching methods, it is necessary to improve the basic education of dance students, so that they can express the emotions conveyed by dance through body language and movements, and improve dance expression ability. In this context, we made the research and reached the following conclusions: (1) the number of frames of different dance types is also different, and the number of frames to be learned is also increasing. The dance with the highest number of frames is Latin2, which has 3635 frames, and the dance with the highest number of frames that need to be learned is also Latin2, which requires 2519 frames to learn. (2) The data mining method is still the highest among the three methods, and the accuracy of the complete teaching method is 82%, which is the lowest among the three methods, and the accuracy of the decentralized teaching method is 87%. No matter in the test set or the mixed test set, the curve values of deep mining are very stable. First of all, human movements emphasize that in dance, the essential meaning of dance movements needs to be understood from the inside and expressed through the foundation of dance. Therefore, when developing new dance teaching methods, it is necessary to strengthen the basic dance training of students so that students can express the emotions conveyed by dance through body language and movements and improve their dance expression ability. We conduct research in this ecological environment. Different types of dance learning process using different frames, different types of dance in the algorithm transport have different recognition methods, using better and different algorithms can achieve the best performance. Both groups in the Hip Hop dance had a shorter average learning time than both groups in the Latin dance.},
}
@article {pmid36171318,
year = {2023},
author = {Wen, C and Zhen, Z and Zhang, L and Yan, C},
title = {A bibliometric analysis of river health based on publications in the last three decades.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {6},
pages = {15400-15413},
pmid = {36171318},
issn = {1614-7499},
support = {XDA23030203//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {Humans ; *Rivers ; *Bibliometrics ; Australia ; China ; Databases, Factual ; Publications ; },
abstract = {Rivers are a vital part of the earth's environment and the basis for human survival. River health has been widely concerned by scholars and practitioners, and the number of studies in this area is increasing. In order to examine the evolution of river health research and identify the research frontiers, a total of 675 articles were retrieved from the Web of Science Core Collection database, and CiteSpace was used for bibliometrics. The results revealed that the research on river health is multidisciplinary. Freshwater Biology and Ecological Indicators were two of the most influential journals. Researchers and institutions from America, Australia, and China were the core research forces, and a certain gap was observed between developed and developing countries in river health. The most productive institution was Michigan State University, followed by Griffith University and Hohai University. There are three development trends in river health: (1) Research scale is expanding; (2) Research methods are diversified and interdisciplinary; and (3) Evaluation index is more comprehensive and systematic. The frontier of river health had been expanded from the connotation of river health to the evaluation methods, evaluation indexes, and comprehensive river ecological research. Overall, research on river health is a well-developed and promising research field. This study provides a framework in the river health field for new researchers and helps scholars to identify further potential perspectives on collaborators, research frontiers, hotspots, and research trends.},
}
@article {pmid36169445,
year = {2022},
author = {Martins, ACM and Giordani, F and Gonçalves, MC and Guaraldo, L and Rozenfeld, S},
title = {[Deaths from adverse drug events in Brazil: Mortality Information System as a source of information].},
journal = {Cadernos de saude publica},
volume = {38},
number = {8},
pages = {e00291221},
doi = {10.1590/0102-311XPT291221},
pmid = {36169445},
issn = {1678-4464},
mesh = {Aged ; Brazil/epidemiology ; Child ; *Drug-Related Side Effects and Adverse Reactions ; Humans ; Information Systems ; Middle Aged ; Psychotropic Drugs/adverse effects ; Retrospective Studies ; },
abstract = {Adverse drug events (ADEs) are harmful events caused by medication, and some of which can lead to death. Death records are an important source of information when using codes from the 10th revision of the International Classification of Diseases (ICD-10) suggestive of ADE. This study aimed to identify the ADEs registered in Brazililian Mortality Information System (SIM), analyzing data distribution by year, age group, and type of event. This is an ecological study with retrospective data collection, identifying ADEs in the SIM, using the ICD-10 codes. The study included deaths that occurred in Brazil from 2008 to 2016. An increase in the number of deaths associated with ADE was observed from 2008 to 2016, with a mortality rate per 1 million inhabitants ranging from 8.70 to 14.40 in the period. Most events corresponded to mental and behavioral disorders due to the use of psychotropic drugs. Most deaths (12,311) related to ADE codes were identified in several chapters of the ICD-10. Chapter XX, about adverse events, allowed the identification of a smaller number of deaths (4,893). Higher event rates were observed among individuals aged 60 years and over (39.8/1 million) and children younger than one year (22.0/1 million). The identification of ADE-related deaths on the SIM is an important strategy for addressing undesirable drug-related events. Deaths related to the use of psychotropic drugs were the most frequent ADE-related deaths and the elderly were the age group most affected by ADEs.},
}
@article {pmid36167554,
year = {2022},
author = {Kim, J and Lee, C and Ko, BJ and Yoo, DA and Won, S and Phillippy, AM and Fedrigo, O and Zhang, G and Howe, K and Wood, J and Durbin, R and Formenti, G and Brown, S and Cantin, L and Mello, CV and Cho, S and Rhie, A and Kim, H and Jarvis, ED},
title = {False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {204},
pmid = {36167554},
issn = {1474-760X},
support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; R03 NS115145/NS/NINDS NIH HHS/United States ; ZIA HG200398/ImNIH/Intramural NIH HHS/United States ; R03 NS059755/NS/NINDS NIH HHS/United States ; WT206194/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Base Composition/genetics ; Chromosomes ; *Genome/genetics ; Sequence Analysis, DNA ; *Vertebrates/genetics ; },
abstract = {BACKGROUND: Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements.<br><br>RESULTS: Here we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna's hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5'-proximal promoters and 5' exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies.<br><br>CONCLUSIONS: Our findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.},
}
@article {pmid36167140,
year = {2023},
author = {Tölgyesi, C and Hábenczyus, AA and Kelemen, A and Török, P and Valkó, O and Deák, B and Erdős, L and Tóth, B and Csikós, N and Bátori, Z},
title = {How to not trade water for carbon with tree planting in water-limited temperate biomes?.},
journal = {The Science of the total environment},
volume = {856},
number = {Pt 1},
pages = {158960},
doi = {10.1016/j.scitotenv.2022.158960},
pmid = {36167140},
issn = {1879-1026},
mesh = {*Ecosystem ; *Carbon ; Water ; Sand ; Forests ; Soil ; },
abstract = {The most widespread nature-based solution for mitigating climate change is tree planting. When realized as forest restoration in historically forested biomes, it can efficiently contribute to the sequestration of atmospheric carbon and can also entail significant biodiversity and ecosystem service benefits. Conversely, tree planting in naturally open biomes can have adverse effects, of which water shortage due to increased evapotranspiration is among the most alarming ones. Here we assessed how soil texture affects the strength of the trade-off between tree cover and water balance in the forest-steppe biome, where the global pressure for afforestation is threatening with increasing tree cover above historical levels. Here we monitored vertical soil moisture dynamics in four stands in each of the most common forest types of lowland Hungary on well-drained, sandy (natural poplar groves, and Robinia and pine plantations) and on poorly drained, silty-clayey soils (natural oak stands and Robinia plantations), and neighboring grasslands. We found that forests on sand retain moisture in the topsoil (approx. 20 cm) throughout the year, but a thick dry layer develops below that during the vegetation period, significantly impeding groundwater recharge. Neighboring sandy grasslands showed an opposite pattern, with often dry topsoil but intact moisture reserves below, allowing deep percolation. In contrast, forests on silty-clayey soils did not desiccate lower soil layers compared neighboring grasslands, which in turn showed moisture patterns similar to sandy grasslands. We conclude that, in water-limited temperate biomes where landscape-wide water regime depends on deep percolation, soil texture should drive the spatial allocation of tree-based climate mitigation efforts. On sand, the establishment of new forests should be kept to a minimum and grassland restoration should be preferred. The trade-off between water and carbon is less pronounced on silty-clayey soils, making forest patches and wooded rangelands viable targets for both climate mitigation and ecosystem restoration.},
}
@article {pmid36166925,
year = {2023},
author = {Koo, SY and Hwang, KT and Hwang, S and Choi, KY and Park, YJ and Choi, JH and Truong, TQ and Kim, SM},
title = {Nanoencapsulation enhances the bioavailability of fucoxanthin in microalga Phaeodactylum tricornutum extract.},
journal = {Food chemistry},
volume = {403},
number = {},
pages = {134348},
doi = {10.1016/j.foodchem.2022.134348},
pmid = {36166925},
issn = {1873-7072},
mesh = {Humans ; Mice ; Animals ; Biological Availability ; *Microalgae/metabolism ; Caco-2 Cells ; Xanthophylls/metabolism ; },
abstract = {The marine carotenoid fucoxanthin (FX) has various health benefits but suffers from poor bioavailability. We hypothesize that the bioavailability of FX in microalga Phaeodactylum tricornutum extract (PE) could be improved through nanoencapsulation. Here, we developed two types of nanoparticles: one consisting of alginate and casein (A-C-PE, 246 nm diameter, 79.6% encapsulation efficiency) and the other A-C-PE coated with chitosan (CS-A-C-PE, 258 nm, 78.1%). Both types of nanoparticles incorporating PE showed controlled FX release during simulated gastrointestinal digestion, as well as 1.8-fold improvement of membrane permeability in Caco-2/TC7 cells compared to non-encapsulated PE. Pharmacokinetic behavior of two FX metabolites (fucoxanthinol and amarouciaxanthin A) in mouse plasma was monitored after oral administration. The results showed that 31.8-332.1% more FX metabolites from the nanoparticles were absorbed into plasma than those from PE. In conclusion, encapsulation of PE in both types of nanoparticles significantly promoted the bioavailability of FX.},
}
@article {pmid36157711,
year = {2022},
author = {Mihaljevic, JR and Borkovec, S and Ratnavale, S and Hocking, TD and Banister, KE and Eppinger, JE and Hepp, C and Doerry, E},
title = {SPARSEMODr: Rapidly simulate spatially explicit and stochastic models of COVID-19 and other infectious diseases.},
journal = {Biology methods &amp; protocols},
volume = {7},
number = {1},
pages = {bpac022},
pmid = {36157711},
issn = {2396-8923},
abstract = {Building realistically complex models of infectious disease transmission that are relevant for informing public health is conceptually challenging and requires knowledge of coding architecture that can implement key modeling conventions. For example, many of the models built to understand COVID-19 dynamics have included stochasticity, transmission dynamics that change throughout the epidemic due to changes in host behavior or public health interventions, and spatial structures that account for important spatio-temporal heterogeneities. Here we introduce an R package, SPARSEMODr, that allows users to simulate disease models that are stochastic and spatially explicit, including a model for COVID-19 that was useful in the early phases of the epidemic. SPARSEMOD stands for SPAtial Resolution-SEnsitive Models of Outbreak Dynamics, and our goal is to demonstrate particular conventions for rapidly simulating the dynamics of more complex, spatial models of infectious disease. In this report, we outline the features and workflows of our software package that allow for user-customized simulations. We believe the example models provided in our package will be useful in educational settings, as the coding conventions are adaptable, and will help new modelers to better understand important assumptions that were built into sophisticated COVID-19 models.},
}
@article {pmid36155927,
year = {2023},
author = {Russo, A and Blettner, M and Merzenich, H and Wollschlaeger, D and Erdmann, F and Gianicolo, E},
title = {Incidence of childhood leukemia before and after shut down of nuclear power plants in Germany in 2011: A population-based register study during 2004 to 2019.},
journal = {International journal of cancer},
volume = {152},
number = {5},
pages = {913-920},
doi = {10.1002/ijc.34303},
pmid = {36155927},
issn = {1097-0215},
mesh = {Child ; Humans ; *Nuclear Power Plants ; Incidence ; Case-Control Studies ; *Leukemia/epidemiology ; Germany/epidemiology ; },
abstract = {The association between leukemia and proximity to nuclear-power-plants (NPPs) has been assessed in several countries with inconsistent results. A case-control study from Germany had shown an increased risk for childhood leukemia (diagnoses 1980-2003) near NPPs. Germany began shutting down nuclear reactors in 2011, following the Fukushima disaster. We tested whether the previously observed association between leukemia and proximity to NPP persisted despite the shutdown. We used an ecological study design to investigate the incidence of leukemia during 2004 to 2019 in children aged 0 to 14 years living near NPPs where at least one reactor was shut down in 2011. We defined study and control areas as municipalities whose surface area was at least 75% within 10 km or between 10 and 50 km of NPPs, respectively. We calculated age-standardized rates and incidence rate ratios (IRR) using control-areas as the reference. We also computed standardized incidence ratios (SIR) separately for each NPP using incidence rates of the German population as a reference. IRR decreased from 1.20 (95% confidence interval: 0.81-1.77) in 2004 to 2011 to 1.12 (0.75-1.68) in 2012 to 2019. Analyses of single plants showed an excess of childhood leukemia during 2004 to 2019 for the Unterweser-NPP, based only on three cases, and the Krümmel-NPP (n = 14; SIR: 1.98, 1.17-3.35). We found slightly decreasing of leukemia incidence rate ratios after the shutdown of nuclear reactors in 2011. Due to the small number of cases, risk estimates have large uncertainty. Further research including a longer follow-up is warranted. The consistent excess of incidence cases around Krümmel may require analytical epidemiological analysis.},
}
@article {pmid36149894,
year = {2022},
author = {Zhang, L and Chen, L and Yu, XA and Duvallet, C and Isazadeh, S and Dai, C and Park, S and Frois-Moniz, K and Duarte, F and Ratti, C and Alm, EJ and Ling, F},
title = {MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.},
journal = {PLoS computational biology},
volume = {18},
number = {9},
pages = {e1010472},
pmid = {36149894},
issn = {1553-7358},
mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Pandemics ; Population Density ; Sewage ; Wastewater ; },
abstract = {The metagenome embedded in urban sewage is an attractive new data source to understand urban ecology and assess human health status at scales beyond a single host. Analyzing the viral fraction of wastewater in the ongoing COVID-19 pandemic has shown the potential of wastewater as aggregated samples for early detection, prevalence monitoring, and variant identification of human diseases in large populations. However, using census-based population size instead of real-time population estimates can mislead the interpretation of data acquired from sewage, hindering assessment of representativeness, inference of prevalence, or comparisons of taxa across sites. Here, we show that taxon abundance and sub-species diversisty in gut-associated microbiomes are new feature space to utilize for human population estimation. Using a population-scale human gut microbiome sample of over 1,100 people, we found that taxon-abundance distributions of gut-associated multi-person microbiomes exhibited generalizable relationships with respect to human population size. Here and throughout this paper, the human population size is essentially the sample size from the wastewater sample. We present a new algorithm, MicrobiomeCensus, for estimating human population size from sewage samples. MicrobiomeCensus harnesses the inter-individual variability in human gut microbiomes and performs maximum likelihood estimation based on simultaneous deviation of multiple taxa's relative abundances from their population means. MicrobiomeCensus outperformed generic algorithms in data-driven simulation benchmarks and detected population size differences in field data. New theorems are provided to justify our approach. This research provides a mathematical framework for inferring population sizes in real time from sewage samples, paving the way for more accurate ecological and public health studies utilizing the sewage metagenome.},
}
@article {pmid36141528,
year = {2022},
author = {Emelyanova, A and Savolainen, A and Oksanen, A and Nieminen, P and Loginova, O and Abass, K and Rautio, A},
title = {Research on Selected Wildlife Infections in the Circumpolar Arctic-A Bibliometric Review.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {18},
pages = {},
pmid = {36141528},
issn = {1660-4601},
mesh = {Alaska/epidemiology ; Animals ; *Animals, Wild ; Arctic Regions ; Bibliometrics ; *Communicable Diseases/epidemiology/veterinary ; Humans ; Mammals ; },
abstract = {One Health, a multidisciplinary approach to public health, which integrates human, animal, and environmental studies, is prudent for circumpolar Arctic health research. The objective of our bibliometric review was to identify and compare research in select infectious diseases in Arctic wildlife species with importance to human health indexed in English language databases (PubMed, Scopus) and the Russian database eLibrary.ru. Included articles (in English and Russian languages) needed to meet the following criteria: (1) data comes from the Arctic, (2) articles report original research or surveillance reports, (3) articles were published between 1990 and 2018, and (4) research relates to naturally occurring infections. Of the included articles (total n = 352), most were from Russia (n = 131, 37%), Norway (n = 58, 16%), Canada (n = 39, 11%), and Alaska (n = 39, 11%). Frequently reported infectious agents among selected mammals were Trichinella spp. (n = 39), Brucella spp. (n = 25), rabies virus (n = 11), Echinococcus spp. (n = 10), and Francisella tularensis (n = 9). There were 25 articles on anthrax in eLibrary.ru, while there were none in the other two databases. We identified future directions where opportunities for further research, collaboration, systematic reviews, or monitoring programs are possible and needed.},
}
@article {pmid36138772,
year = {2022},
author = {Botella, C and Bonnet, P and Hui, C and Joly, A and Richardson, DM},
title = {Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion.},
journal = {Biology},
volume = {11},
number = {9},
pages = {},
pmid = {36138772},
issn = {2079-7737},
support = {//DSI-NRF Centre of Excellence for Invasion Biology/ ; 89967//Millennium Trust, the National Research Foundation of South Africa/ ; CZ.02.2.69/0.0/0.0/18_053/0017850//Mobility 2020 project (Ministry of Education, Youth and Sports of the Czech Republic)/ ; RVO 67985939//long-term research development project (Czech Academy of Sciences)/ ; },
abstract = {Plant invasions generate massive ecological and economic costs worldwide. Predicting their spatial dynamics is crucial to the design of effective management strategies and the prevention of invasions. Earlier studies highlighted the crucial role of long-distance dispersal in explaining the speed of many invasions. In addition, invasion speed depends highly on the duration of its lag phase, which may depend on the scaling of fecundity with age, especially for woody plants, even though empirical proof is still rare. Bayesian dynamic species distribution models enable the fitting of process-based models to partial and heterogeneous observations using a state-space modeling approach, thus offering a tool to test such hypotheses on past invasions over large spatial scales. We use such a model to explore the roles of long-distance dispersal and age-structured fecundity in the transient invasion dynamics of Plectranthus barbatus, a woody plant invader in South Africa. Our lattice-based model accounts for both short and human-mediated long-distance dispersal, as well as age-structured fecundity. We fitted our model on opportunistic occurrences, accounting for the spatio-temporal variations of the sampling effort and the variable detection rates across datasets. The Bayesian framework enables us to integrate a priori knowledge on demographic parameters and control identifiability issues. The model revealed a massive wave of spatial spread driven by human-mediated long-distance dispersal during the first decade and a subsequent drastic population growth, leading to a global equilibrium in the mid-1990s. Without long-distance dispersal, the maximum population would have been equivalent to 30% of the current equilibrium population. We further identified the reproductive maturity at three years old, which contributed to the lag phase before the final wave of population growth. Our results highlighted the importance of the early eradication of weedy horticultural alien plants around urban areas to hamper and delay the invasive spread.},
}
@article {pmid36130600,
year = {2022},
author = {Bidel, F and Bennett, NC and Wardill, TJ},
title = {Octopus bimaculoides' arm recruitment and use during visually evoked prey capture.},
journal = {Current biology : CB},
volume = {32},
number = {21},
pages = {4727-4733.e3},
doi = {10.1016/j.cub.2022.08.080},
pmid = {36130600},
issn = {1879-0445},
mesh = {Animals ; *Octopodiformes/physiology ; Movement/physiology ; Extremities/physiology ; Adaptation, Physiological ; },
abstract = {Octopus' limb hyper-redundancy complicates traditional motor control system theory due to its extensive sensory inputs, subsequent decision-making, and arm coordination. Octopuses are thought to reduce flexibility control complexity by relying on highly stereotypical motor primitives (e.g., reaching[1][,][2][,][3][,][4] and crawling[5]) and multi-level processes to coordinate movement,[6][,][7] utilizing extensive peripheral nervous system (PNS) processing.[2][,][8][,][9] Division of labor along the anterior-posterior axis[10] and limb specialization of the four anterior arms in T-maze food retrieval[11] further simplify control. However, specific arm recruitment and coordination during visually guided reaching behavior remains poorly understood. Here, we investigated visually evoked Octopus bimaculoides' prey capture capabilities[12][,][13] by eliciting and examining prey-specific arm recruitment. When striking crabs, octopuses preferred synchronous arm recruitment, while sequential arm recruitment with a characteristic swaying movement is employed for shrimp. Such behavioral selection aligns with specific prey escape strategies and the octopus' flexible arm biomechanical constraints. Although side bias existed, we found significant bilateral symmetry, with one side being functionally a mirror of the other rather than anterior arm use being functionally equal and differing to posterior arm use. Among arms, the second limb is unequivocally dominant for goal-directed monocularly driven prey capture. Although the eight arms share gross anatomy and are considered equipotential,[10][,][14] such arm use for specific actions could reflect subtle evolutionary adaptations. Finally, we quantitatively show, corroborating earlier observations,[10][,][15] that octopuses employ a dimension reduction strategy by actively deciding to recruit adjacent arms over other available arms during either sequential or synchronous visually evoked prey attack.},
}
@article {pmid36130260,
year = {2022},
author = {Sun, D and Ding, S and Cai, P and Zhang, D and Han, M and Hu, QN},
title = {BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {22},
pages = {5137-5138},
doi = {10.1093/bioinformatics/btac640},
pmid = {36130260},
issn = {1367-4811},
support = {2020YFA0908300//National Key Research and Development Program of China/ ; 153D31KYSB20170121//CAS International Partnership Programme of the Chinese Academy of Sciences of China/ ; },
mesh = {*Metabolic Engineering/methods ; *Synthetic Biology ; Databases, Factual ; },
abstract = {SUMMARY: Advances in metabolic engineering have boosted the production of bulk chemicals, resulting in tons of production volumes of some bulk chemicals with very low prices. A decrease in the production cost and overproduction of bulk chemicals makes it necessary and desirable to explore the potential to synthesize higher-value products from them. It is also useful and important for society to explore the use of design methods involving synthetic biology to increase the economic value of these bulk chemicals. Therefore, we developed 'BioBulkFoundary', which provides an elaborate analysis of the biosynthetic potential of bulk chemicals based on the state-of-art exploration of pathways to synthesize value-added chemicals, along with associated comprehensive technology and economic database into a user-friendly framework.<br><br>Freely available on the web at http://design.rxnfinder.org/biobulkfoundary/.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid36127081,
year = {2022},
author = {Barrigon, ML and Porras-Segovia, A and Courtet, P and Lopez-Castroman, J and Berrouiguet, S and Pérez-Rodríguez, MM and Artes, A and , and Baca-Garcia, E},
title = {Smartphone-based Ecological Momentary Intervention for secondary prevention of suicidal thoughts and behaviour: protocol for the SmartCrisis V.2.0 randomised clinical trial.},
journal = {BMJ open},
volume = {12},
number = {9},
pages = {e051807},
pmid = {36127081},
issn = {2044-6055},
mesh = {Ecological Momentary Assessment ; Humans ; Randomized Controlled Trials as Topic ; Secondary Prevention ; *Smartphone ; Suicidal Ideation ; *Telemedicine ; },
abstract = {INTRODUCTION: Suicide is one of the leading public health issues worldwide. Mobile health can help us to combat suicide through monitoring and treatment. The SmartCrisis V.2.0 randomised clinical trial aims to evaluate the effectiveness of a smartphone-based Ecological Momentary Intervention to prevent suicidal thoughts and behaviour.<br><br>METHODS AND ANALYSIS: The SmartCrisis V.2.0 study is a randomised clinical trial with two parallel groups, conducted among patients with a history of suicidal behaviour treated at five sites in France and Spain. The intervention group will be monitored using Ecological Momentary Assessment (EMA) and will receive an Ecological Momentary Intervention called 'SmartSafe' in addition to their treatment as usual (TAU). TAU will consist of mental health follow-up of the patient (scheduled appointments with a psychiatrist) in an outpatient Suicide Prevention programme, with predetermined clinical appointments according to the Brief Intervention Contact recommendations (1, 2, 4, 7 and 11 weeks and 4, 6, 9 and 12 months). The control group would receive TAU and be monitored using EMA.<br><br>ETHICS AND DISSEMINATION: This study has been approved by the Ethics Committee of the University Hospital Fundaci&#xf3;n Jim&#xe9;nez D&#xed;az. It is expected that, in the near future, our mobile health intervention and monitoring system can be implemented in routine clinical practice. Results will be disseminated through peer-reviewed journals and psychiatric congresses. Reference number EC005-21_FJD. Participants gave informed consent to participate in the study before taking part.<br><br>TRIAL REGISTRATION NUMBER: NCT04775160.},
}
@article {pmid36123315,
year = {2022},
author = {Fontana, F and Alessandri, G and Tarracchini, C and Bianchi, MG and Rizzo, SM and Mancabelli, L and Lugli, GA and Argentini, C and Vergna, LM and Anzalone, R and Longhi, G and Viappiani, A and Taurino, G and Chiu, M and Turroni, F and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M},
title = {Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.},
journal = {Environmental microbiology},
volume = {24},
number = {12},
pages = {5825-5839},
pmid = {36123315},
issn = {1462-2920},
mesh = {Humans ; Infant ; *Bifidobacterium/genetics ; *Multiomics ; Reproducibility of Results ; Feces/microbiology ; Metagenomics ; Bacteria ; },
abstract = {The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.},
}
@article {pmid36120670,
year = {2022},
author = {Liu, X and Wang, J and Rui, X and Zhang, J},
title = {Application of GIS Technology-Supported Cross Media Fusion Method Based on Deep Learning in Landscape Performance Evaluation.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {8339895},
pmid = {36120670},
issn = {1687-5273},
mesh = {Algorithms ; *Deep Learning ; Geographic Information Systems ; Humans ; Neural Networks, Computer ; Technology ; },
abstract = {GIS technology can provide reasonable and sustainable data support for landscape planning and ecological development and make wetland landscape planning consider the spatial layout of landscape and the optimal allocation of resources more. The key technologies of cross media intelligence mainly focus on intelligent information retrieval, analysis and reasoning, knowledge map construction, and intelligent storage. Convolutional neural network (CNN), as one of the representative algorithms of deep learning, plays an important role in retrieving landscape data and extracting image and text features across media. Further retrieval of media data, in-depth text processing, and image feature data extraction are realized by using deep learning technology, and comprehensive in-depth analysis is carried out by combining landscape plane images, three-dimensional images, and vector information in GIS technology. Provide quantitative information for the evaluation system of human landscape, economy, history, and region, so as to formulate a scientific and reasonable performance evaluation system.},
}
@article {pmid36114727,
year = {2022},
author = {Ma, X and Zhu, X and Xie, Q and Jin, J and Zhou, Y and Luo, Y and Liu, Y and Tian, J and Zhao, Y},
title = {Monitoring nature's calendar from space: Emerging topics in land surface phenology and associated opportunities for science applications.},
journal = {Global change biology},
volume = {28},
number = {24},
pages = {7186-7204},
pmid = {36114727},
issn = {1365-2486},
mesh = {*Ecosystem ; Seasons ; *Climate Change ; Carbon ; Water ; },
abstract = {Vegetation phenology has been viewed as the nature's calendar and an integrative indicator of plant-climate interactions. The correct representation of vegetation phenology is important for models to accurately simulate the exchange of carbon, water, and energy between the vegetated land surface and the atmosphere. Remote sensing has advanced the monitoring of vegetation phenology by providing spatially and temporally continuous data that together with conventional ground observations offers a unique contribution to our knowledge about the environmental impact on ecosystems as well as the ecological adaptations and feedback to global climate change. Land surface phenology (LSP) is defined as the use of satellites to monitor seasonal dynamics in vegetated land surfaces and to estimate phenological transition dates. LSP, as an interdisciplinary subject among remote sensing, ecology, and biometeorology, has undergone rapid development over the past few decades. Recent advances in sensor technologies, as well as data fusion techniques, have enabled novel phenology retrieval algorithms that refine phenology details at even higher spatiotemporal resolutions, providing new insights into ecosystem dynamics. As such, here we summarize the recent advances in LSP and the associated opportunities for science applications. We focus on the remaining challenges, promising techniques, and emerging topics that together we believe will truly form the very frontier of the global LSP research field.},
}
@article {pmid36112603,
year = {2022},
author = {Miller, JC and Satheesh Babu, AK and Petersen, C and Wankhade, UD and Robeson, MS and Putich, MN and Mueller, JE and O'Farrell, AS and Cho, JM and Chintapalli, SV and Jalili, T and Symons, JD and Anandh Babu, PV},
title = {Gut Microbes Are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome-Induced Vascular Inflammation.},
journal = {Molecular nutrition &amp; food research},
volume = {66},
number = {22},
pages = {e2200112},
pmid = {36112603},
issn = {1613-4133},
support = {R03 AG052848/AG/NIA NIH HHS/United States ; R01 AT010247/AT/NCCIH NIH HHS/United States ; R01 HL141540/HL/NHLBI NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; R03AGO52848/HL/NHLBI NIH HHS/United States ; },
mesh = {Male ; Mice ; Animals ; *Fragaria/chemistry ; *Metabolic Syndrome/etiology/drug therapy ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Inflammation ; },
abstract = {SCOPE: Metabolic syndrome (MetS) alters the gut microbial ecology and increases the risk of cardiovascular disease. This study investigates whether strawberry consumption reduces vascular complications in an animal model of MetS and identifies whether this effect is associated with changes in the composition of gut microbes.<br><br>METHODS AND RESULTS: Seven-week-old male mice consume diets with 10% (C) or 60% kcal from fat (high-fat diet fed mice; HF) for 12 weeks and subgroups are fed a 2.35% freeze-dried strawberry supplemented diet (C+SB or HF+SB). This nutritional dose is equivalent to &#x2248;160 g of strawberry. After 12 weeks treatment, vascular inflammation is enhanced in HF versus C mice as shown by an increased monocyte binding to vasculature, elevated serum chemokines, and increased mRNA expression of inflammatory molecules. However, strawberry supplementation suppresses vascular inflammation in HF+SB versus HF mice. Metabolic variables, blood pressure, and indices of vascular function were similar among the groups. Further, the abundance of opportunistic microbe is decreased in HF+SB. Importantly, circulating chemokines are positively associated with opportunistic microbes and negatively associated with the commensal microbes (Bifidobacterium and Facalibaculum).<br><br>CONCLUSION: Dietary strawberry decreases the abundance of opportunistic microbe and this is associated with a decrease in vascular inflammation resulting from MetS.},
}
@article {pmid36112284,
year = {2023},
author = {Badapalli, PK and Kottala, RB and Madiga, R and Golla, V},
title = {An integrated approach for the assessment and monitoring of land degradation and desertification in semi-arid regions using physico-chemical and geospatial modeling techniques.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {55},
pages = {116751-116764},
pmid = {36112284},
issn = {1614-7499},
mesh = {*Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Soil ; },
abstract = {Land degradation (LD) and desertification are serious ecological, environmental, and social-economic threats in the world, and there is a demanding need to develop accountable and reproducible techniques to assess them at different scales. This study assesses LD and desertification with the help of remote sensing (RS) and geographical information system (GIS) in the study region for the period past 29 years, i.e., from 1990 to 2019. The severity of LD and desertification was assessed quantitatively by collecting twelve soil samples in the study region and analyzing the eleven soil physico-chemical parameters and these values have made correlated with digital number (DN) values with LANDSAT 8 OLI/TIRS satellite image. The land cover analysis of LANDSAT imagery revealed that the water body slightly increased from 0.29% in 1990 to 0.46% in 2019, and built-up-land increased from 2.87% in 1990 to 5.31% in 2019. Vegetation decreased from 52.03% in 1990 to 28.57%. Fallow land, degraded land, and desertified lands increased at alarming rates, respectively 13.71% to 26.35, 18.57% to 22.31%, and 12.53% to 17.00%. It is also established that the multi-temporal analysis of change detection data can provide a sophisticated measure of ecosystem health and variation, and that, over the last 29 years, considerable progress has been made in the respective research.},
}
@article {pmid36111781,
year = {2022},
author = {Eyre, MT and Souza, FN and Carvalho-Pereira, TSA and Nery, N and de Oliveira, D and Cruz, JS and Sacramento, GA and Khalil, H and Wunder, EA and Hacker, KP and Hagan, JE and Childs, JE and Reis, MG and Begon, M and Diggle, PJ and Ko, AI and Giorgi, E and Costa, F},
title = {Linking rattiness, geography and environmental degradation to spillover Leptospira infections in marginalised urban settings: An eco-epidemiological community-based cohort study in Brazil.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36111781},
issn = {2050-084X},
support = {U01 AI088752/AI/NIAID NIH HHS/United States ; F31 AI114245/NH/NIH HHS/United States ; 102330/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; F31 AI114245/AI/NIAID NIH HHS/United States ; R01 TW009504/TW/FIC NIH HHS/United States ; R01 AI052473/NH/NIH HHS/United States ; R01 TW009504/NH/NIH HHS/United States ; R25 TW009338/NH/NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 AI052473/AI/NIAID NIH HHS/United States ; R25 TW009338/TW/FIC NIH HHS/United States ; U01 AI088752/NH/NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 001/WHO_/World Health Organization/International ; 964635/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adult ; Animals ; Brazil/epidemiology ; Cohort Studies ; Epidemiologic Studies ; Geography ; Humans ; *Leptospirosis/epidemiology ; Male ; *Poverty Areas ; Rats ; Zoonoses/epidemiology ; },
abstract = {BACKGROUND: Zoonotic spillover from animal reservoirs is responsible for a significant global public health burden, but the processes that promote spillover events are poorly understood in complex urban settings. Endemic transmission of Leptospira, the agent of leptospirosis, in marginalised urban communities occurs through human exposure to an environment contaminated by bacteria shed in the urine of the rat reservoir. However, it is unclear to what extent transmission is driven by variation in the distribution of rats or by the dispersal of bacteria in rainwater runoff and overflow from open sewer systems.<br><br>METHODS: We conducted an eco-epidemiological study in a high-risk community in Salvador, Brazil, by prospectively following a cohort of 1401 residents to ascertain serological evidence for leptospiral infections. A concurrent rat ecology study was used to collect information on the fine-scale spatial distribution of 'rattiness', our proxy for rat abundance and exposure of interest. We developed and applied a novel geostatistical framework for joint spatial modelling of multiple indices of disease reservoir abundance and human infection risk.<br><br>RESULTS: The estimated infection rate was 51.4 (95%CI 40.4, 64.2) infections per 1000 follow-up events. Infection risk increased with age until 30 years of age and was associated with male gender. Rattiness was positively associated with infection risk for residents across the entire study area, but this effect was stronger in higher elevation areas (OR 3.27 95% CI 1.68, 19.07) than in lower elevation areas (OR 1.14 95% CI 1.05, 1.53).<br><br>CONCLUSIONS: These findings suggest that, while frequent flooding events may disperse bacteria in regions of low elevation, environmental risk in higher elevation areas is more localised and directly driven by the distribution of local rat populations. The modelling framework developed may have broad applications in delineating complex animal-environment-human interactions during zoonotic spillover and identifying opportunities for public health intervention.<br><br>FUNDING: This work was supported by the Oswaldo Cruz Foundation and Secretariat of Health Surveillance, Brazilian Ministry of Health, the National Institutes of Health of the United States (grant numbers F31 AI114245, R01 AI052473, U01 AI088752, R01 TW009504 and R25 TW009338); the Wellcome Trust (102330/Z/13/Z), and by the Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia (FAPESB/JCB0020/2016). MTE was supported by a Medical Research UK doctorate studentship. FBS participated in this study under a FAPESB doctorate scholarship.},
}
@article {pmid36109660,
year = {2022},
author = {Negesse, A and Woyraw, W and Temesgen, H and Teka, Y and Yismaw, L and Akalu, TY and Deml, YA and Sume, BW and Negesse, Y and Taddege, T and Kidie, WD and Teym, A and Asmare, B and Hune, Y and Damte, D and Getaneh, T and Gebre, T and Tilahun, B and Tenagne, A and Tegegne, E and Birhanu, MY and Mekonen, H and Shiferaw, M and Kassahun, W and Desalegn, BB},
title = {Spatial exploration of non-resilience to food insecurity, its association with COVID-19 and household coping strategies in East Gojjam districts, Northwest Ethiopia, 2020.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15511},
pmid = {36109660},
issn = {2045-2322},
mesh = {Adaptation, Psychological ; *COVID-19/epidemiology ; Cross-Sectional Studies ; Ethiopia/epidemiology ; Family Characteristics ; Food Insecurity ; *Food Supply ; Humans ; Male ; Pandemics ; Socioeconomic Factors ; },
abstract = {The coronavirus disease-2019 (COVID-19) pandemic has posed a significant multifaceted threat to the global community. Ethiopia, as a Sub-Saharan African country, is suffering from chronic food insecurity, and the emergence of such a pandemic will exacerbate the situation. As a result, this study investigated the spatial variation of non-resilience to food insecurity, its relationship with COVID-19, and household coping strategies to become resilient in the long run among households in the East Gojjam Zone of Northwest Ethiopia. From September 22 to December 24, 2020, an agro-ecological-based cross-sectional study of 3532 households was conducted to assess the spatial distribution and associated factors of non-resilience to household food insecurity. The enumeration areas (EAs) and households were chosen using a multistage sampling technique. Data were gathered using a semi-structured questionnaire and checklist using an Android device loaded with an Open Data Kit (ODK) template. Binary logistic regression was used to identify the specific factors associated with household non-resilience to food insecurity. A thematic analysis was conducted to investigate the opportunities and challenges of resilience for household food insecurity. Nearly two-thirds (62.5%) of the households were farmers, 67.9% lived in rural areas, and nearly three-quarters (73.8%) earned less than or equal to ETB 2100 per month. Males headed more than four-fifths of the households (81.7%). We found that nearly two-thirds of the households (60.02%), 95% CI 58.40, 61.64) were food insecure. After bivariate logistic regression, we found that households who were divorced (AOR = 2.54 (1.65, 3.87)), daily laborers (AOR = 2.37 (1.15, 4.87)), government employees (AOR = 2.06 (1.05, 4.05)), residents of highland and hot areas (AOR = 11.5 (5.37, 16.77)) and lowland areas (AOR = 1.35 (1.02, 3.15)) were frustrated by COVID-19 (AOR = 1.23 (1.02, 1.50)) and price inflation (1.89 (AOR = 1.42, 2.56))) were at higher odds of being non-resilient to household food insecurity at a 95% confidence level. Geospatial hot spot analysis revealed that Kurar kebele (the lowest government administrative unit) in Dejen District and Debre Markos town were the red-hotspot areas of household non-resilience to food insecurity. Less than a quarter of the households attempted to cope with food insecurity by adjusting their food consumption, while more than 60% of the households chose none of the coping strategies tested. According to the thematic analysis, the degree of poverty (lack of asset ownership), the COVID-19 pandemic, farm decreased variety, and low crop productivity were identified as challenges to coping with the hardship of resilience to food insecurity. During the COVID-19 pandemic and public emergency, the proportion of households that were unprepared for food insecurity reached its peak. It was recognized that a segment of the population with low economic capacity was more vulnerable to food insecurity and less resilient. Tough developmental gains will be undermined in this case. As a result, each responsible body and stakeholder should develop and implement solid corrective plans for the local context.},
}
@article {pmid36109545,
year = {2022},
author = {Domma, F and Condino, F and Franceschi, S and De Luca, DL and Biondi, D},
title = {On the extreme hydrologic events determinants by means of Beta-Singh-Maddala reparameterization.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15537},
pmid = {36109545},
issn = {2045-2322},
mesh = {*Hydrology ; },
abstract = {In previous studies, beta-k distribution and distribution functions strongly related to that, have played important roles in representing extreme events. Among these distributions, the Beta-Singh-Maddala turned out to be adequate for modelling hydrological extreme events. Starting from this distribution, the aim of the paper is to express the model as a function of indexes of hydrological interest and simultaneously investigate on their dependence with a set of explanatory variables in such a way to explore on possible determinants of extreme hydrologic events. Finally, an application to a real hydrologic dataset is considered in order to show the potentiality of the proposed model in describing data and in understanding effects of covariates on frequently adopted hydrological indicators.},
}
@article {pmid36108049,
year = {2022},
author = {Tegally, H and San, JE and Cotten, M and Moir, M and Tegomoh, B and Mboowa, G and Martin, DP and Baxter, C and Lambisia, AW and Diallo, A and Amoako, DG and Diagne, MM and Sisay, A and Zekri, AN and Gueye, AS and Sangare, AK and Ouedraogo, AS and Sow, A and Musa, AO and Sesay, AK and Abias, AG and Elzagheid, AI and Lagare, A and Kemi, AS and Abar, AE and Johnson, AA and Fowotade, A and Oluwapelumi, AO and Amuri, AA and Juru, A and Kandeil, A and Mostafa, A and Rebai, A and Sayed, A and Kazeem, A and Balde, A and Christoffels, A and Trotter, AJ and Campbell, A and Keita, AK and Kone, A and Bouzid, A and Souissi, A and Agweyu, A and Naguib, A and Gutierrez, AV and Nkeshimana, A and Page, AJ and Yadouleton, A and Vinze, A and Happi, AN and Chouikha, A and Iranzadeh, A and Maharaj, A and Batchi-Bouyou, AL and Ismail, A and Sylverken, AA and Goba, A and Femi, A and Sijuwola, AE and Marycelin, B and Salako, BL and Oderinde, BS and Bolajoko, B and Diarra, B and Herring, BL and Tsofa, B and Lekana-Douki, B and Mvula, B and Njanpop-Lafourcade, BM and Marondera, BT and Khaireh, BA and Kouriba, B and Adu, B and Pool, B and McInnis, B and Brook, C and Williamson, C and Nduwimana, C and Anscombe, C and Pratt, CB and Scheepers, C and Akoua-Koffi, CG and Agoti, CN and Mapanguy, CM and Loucoubar, C and Onwuamah, CK and Ihekweazu, C and Malaka, CN and Peyrefitte, C and Grace, C and Omoruyi, CE and Rafaï, CD and Morang'a, CM and Erameh, C and Lule, DB and Bridges, DJ and Mukadi-Bamuleka, D and Park, D and Rasmussen, DA and Baker, D and Nokes, DJ and Ssemwanga, D and Tshiabuila, D and Amuzu, DSY and Goedhals, D and Grant, DS and Omuoyo, DO and Maruapula, D and Wanjohi, DW and Foster-Nyarko, E and Lusamaki, EK and Simulundu, E and Ong'era, EM and Ngabana, EN and Abworo, EO and Otieno, E and Shumba, E and Barasa, E and Ahmed, EB and Ahmed, EA and Lokilo, E and Mukantwari, E and Philomena, E and Belarbi, E and Simon-Loriere, E and Anoh, EA and Manuel, E and Leendertz, F and Taweh, FM and Wasfi, F and Abdelmoula, F and Takawira, FT and Derrar, F and Ajogbasile, FV and Treurnicht, F and Onikepe, F and Ntoumi, F and Muyembe, FM and Ragomzingba, FEZ and Dratibi, FA and Iyanu, FA and Mbunsu, GK and Thilliez, G and Kay, GL and Akpede, GO and van Zyl, GU and Awandare, GA and Kpeli, GS and Schubert, G and Maphalala, GP and Ranaivoson, HC and Omunakwe, HE and Onywera, H and Abe, H and Karray, H and Nansumba, H and Triki, H and Kadjo, HAA and Elgahzaly, H and Gumbo, H and Mathieu, H and Kavunga-Membo, H and Smeti, I and Olawoye, IB and Adetifa, IMO and Odia, I and Ben Boubaker, IB and Muhammad, IA and Ssewanyana, I and Wurie, I and Konstantinus, IS and Halatoko, JWA and Ayei, J and Sonoo, J and Makangara, JC and Tamfum, JM and Heraud, JM and Shaffer, JG and Giandhari, J and Musyoki, J and Nkurunziza, J and Uwanibe, JN and Bhiman, JN and Yasuda, J and Morais, J and Kiconco, J and Sandi, JD and Huddleston, J and Odoom, JK and Morobe, JM and Gyapong, JO and Kayiwa, JT and Okolie, JC and Xavier, JS and Gyamfi, J and Wamala, JF and Bonney, JHK and Nyandwi, J and Everatt, J and Nakaseegu, J and Ngoi, JM and Namulondo, J and Oguzie, JU and Andeko, JC and Lutwama, JJ and Mogga, JJH and O'Grady, J and Siddle, KJ and Victoir, K and Adeyemi, KT and Tumedi, KA and Carvalho, KS and Mohammed, KS and Dellagi, K and Musonda, KG and Duedu, KO and Fki-Berrajah, L and Singh, L and Kepler, LM and Biscornet, L and de Oliveira Martins, L and Chabuka, L and Olubayo, L and Ojok, LD and Deng, LL and Ochola-Oyier, LI and Tyers, L and Mine, M and Ramuth, M and Mastouri, M and ElHefnawi, M and Mbanne, M and Matsheka, MI and Kebabonye, M and Diop, M and Momoh, M and Lima Mendonça, MDL and Venter, M and Paye, MF and Faye, M and Nyaga, MM and Mareka, M and Damaris, MM and Mburu, MW and Mpina, MG and Owusu, M and Wiley, MR and Tatfeng, MY and Ayekaba, MO and Abouelhoda, M and Beloufa, MA and Seadawy, MG and Khalifa, MK and Matobo, MM and Kane, M and Salou, M and Mbulawa, MB and Mwenda, M and Allam, M and Phan, MVT and Abid, N and Rujeni, N and Abuzaid, N and Ismael, N and Elguindy, N and Top, NM and Dia, N and Mabunda, N and Hsiao, NY and Silochi, NB and Francisco, NM and Saasa, N and Bbosa, N and Murunga, N and Gumede, N and Wolter, N and Sitharam, N and Ndodo, N and Ajayi, NA and Tordo, N and Mbhele, N and Razanajatovo, NH and Iguosadolo, N and Mba, N and Kingsley, OC and Sylvanus, O and Femi, O and Adewumi, OM and Testimony, O and Ogunsanya, OA and Fakayode, O and Ogah, OE and Oludayo, OE and Faye, O and Smith-Lawrence, P and Ondoa, P and Combe, P and Nabisubi, P and Semanda, P and Oluniyi, PE and Arnaldo, P and Quashie, PK and Okokhere, PO and Bejon, P and Dussart, P and Bester, PA and Mbala, PK and Kaleebu, P and Abechi, P and El-Shesheny, R and Joseph, R and Aziz, RK and Essomba, RG and Ayivor-Djanie, R and Njouom, R and Phillips, RO and Gorman, R and Kingsley, RA and Neto Rodrigues, RMDESA and Audu, RA and Carr, RAA and Gargouri, S and Masmoudi, S and Bootsma, S and Sankhe, S and Mohamed, SI and Femi, S and Mhalla, S and Hosch, S and Kassim, SK and Metha, S and Trabelsi, S and Agwa, SH and Mwangi, SW and Doumbia, S and Makiala-Mandanda, S and Aryeetey, S and Ahmed, SS and Ahmed, SM and Elhamoumi, S and Moyo, S and Lutucuta, S and Gaseitsiwe, S and Jalloh, S and Andriamandimby, SF and Oguntope, S and Grayo, S and Lekana-Douki, S and Prosolek, S and Ouangraoua, S and van Wyk, S and Schaffner, SF and Kanyerezi, S and Ahuka-Mundeke, S and Rudder, S and Pillay, S and Nabadda, S and Behillil, S and Budiaki, SL and van der Werf, S and Mashe, T and Mohale, T and Le-Viet, T and Velavan, TP and Schindler, T and Maponga, TG and Bedford, T and Anyaneji, UJ and Chinedu, U and Ramphal, U and George, UE and Enouf, V and Nene, V and Gorova, V and Roshdy, WH and Karim, WA and Ampofo, WK and Preiser, W and Choga, WT and Ahmed, YA and Ramphal, Y and Bediako, Y and Naidoo, Y and Butera, Y and de Laurent, ZR and , and Ouma, AEO and von Gottberg, A and Githinji, G and Moeti, M and Tomori, O and Sabeti, PC and Sall, AA and Oyola, SO and Tebeje, YK and Tessema, SK and de Oliveira, T and Happi, C and Lessells, R and Nkengasong, J and Wilkinson, E},
title = {The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6615},
pages = {eabq5358},
pmid = {36108049},
issn = {1095-9203},
support = {MR/J01477X/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/P028071/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; U54 TW012041/TW/FIC NIH HHS/United States ; MC_UU_00027/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_20045/MRC_/Medical Research Council/United Kingdom ; MC_PC_19026/MRC_/Medical Research Council/United Kingdom ; U19 AI089696/AI/NIAID NIH HHS/United States ; U01 HG007480/HG/NHGRI NIH HHS/United States ; K24 AI131924/AI/NIAID NIH HHS/United States ; MC_PC_20001/MRC_/Medical Research Council/United Kingdom ; K24 AI131928/AI/NIAID NIH HHS/United States ; U2R TW010673/TW/FIC NIH HHS/United States ; U01 AI151698/AI/NIAID NIH HHS/United States ; U19 AI129387/AI/NIAID NIH HHS/United States ; 001/WHO_/World Health Organization/International ; U01 AI151812/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; },
mesh = {Africa/epidemiology ; *COVID-19/epidemiology/virology ; *Epidemiological Monitoring ; Genomics ; Humans ; *Pandemics ; *SARS-CoV-2/genetics ; },
abstract = {Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.},
}
@article {pmid36107252,
year = {2022},
author = {Lukasová, V and Bičárová, S and Buchholcerová, A and Adamčíková, K},
title = {Low sensitivity of Pinus mugo to surface ozone pollution in the subalpine zone of continental Europe.},
journal = {International journal of biometeorology},
volume = {66},
number = {11},
pages = {2311-2324},
pmid = {36107252},
issn = {1432-1254},
support = {VEGA 2/0093/21//Agent&#xfa;ra Ministerstva &#x160;kolstva, Vedy, V&#xfd;skumu a &#x160;portu SR/ ; },
mesh = {Humans ; *Ozone/analysis ; *Air Pollutants/analysis ; *Pinus ; Environmental Monitoring ; Plant Leaves ; Polyesters/analysis/pharmacology ; },
abstract = {High altitudes have been exposed to enhanced levels of surface ozone (O3) concentrations over recent decades compared to the pre-industrial era. The responses of vegetation to this toxic pollutant are species-specific and depend on the climate conditions. In this paper, we explored the reaction of Pinus mugo (P. mugo) to O3-induced stress in the continental climate of an ozone-rich mountain area in the High Tatra Mountains (Western Carpathians). The effects of O3 doses modelled by a deposition model, O3 concentrations and other factors on P. mugo were identified from (a) satellite-based data via NDVI (normalised differenced vegetation index) over 2000-2020 and (b) visible injury on needle samples gathered from P. mugo individuals at ground-truth sites in 2019 and 2020. Analysing the NDVI trend, we observed non-significant changes (p > 0.05) in the greenness of P. mugo despite growing in an environment with the average seasonal O3 concentration around 51.6 ppbv, the maximum hourly concentrations more than 90 ppbv and increasing trend of O3 doses by 0.1 mmol m[-2] PLA (plant leaf area) year[-1]. The visible O3 injury of samples collected at study sites was low (mean injury observed on 1-10% of needles' surface), and the symptoms of injury caused by other biotic and abiotic factors prevailed over those caused by O3. In addition, the correlation analyses between NDVI and the climatic factors indicated a significant (p < 0.05) and positive relationship with photosynthetic active radiation (R = 0.45) in July, and with stomatal conductance (R = 0.52) and temperature factor (R = 0.43) in August. Therefore, we concluded that the positive effect of climate conditions, which support the growth processes of P. mugo, may suppress the negative effect of the mean O3 doses of 17.8 mmol m[-2] PLA accumulated over the growing season.},
}
@article {pmid36107138,
year = {2023},
author = {Bassing, SB and DeVivo, M and Ganz, TR and Kertson, BN and Prugh, LR and Roussin, T and Satterfield, L and Windell, RM and Wirsing, AJ and Gardner, B},
title = {Are we telling the same story? Comparing inferences made from camera trap and telemetry data for wildlife monitoring.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {33},
number = {1},
pages = {e2745},
doi = {10.1002/eap.2745},
pmid = {36107138},
issn = {1051-0761},
mesh = {Animals ; *Animals, Wild ; *Ecosystem ; Geographic Information Systems ; Surveys and Questionnaires ; Telemetry ; },
abstract = {Estimating habitat and spatial associations for wildlife is common across ecological studies and it is well known that individual traits can drive population dynamics and vice versa. Thus, it is commonly assumed that individual- and population-level data should represent the same underlying processes, but few studies have directly compared contemporaneous data representing these different perspectives. We evaluated the circumstances under which data collected from Lagrangian (individual-level) and Eulerian (population-level) perspectives could yield comparable inference to understand how scalable information is from the individual to the population. We used Global Positioning System (GPS) collar (Lagrangian) and camera trap (Eulerian) data for seven species collected simultaneously in eastern Washington (2018-2020) to compare inferences made from different survey perspectives. We fit the respective data streams to resource selection functions (RSFs) and occupancy models and compared estimated habitat- and space-use patterns for each species. Although previous studies have considered whether individual- and population-level data generated comparable information, ours is the first to make this comparison for multiple species simultaneously and to specifically ask whether inferences from the two perspectives differed depending on the focal species. We found general agreement between the predicted spatial distributions for most paired analyses, although specific habitat relationships differed. We hypothesize the discrepancies arose due to differences in statistical power associated with camera and GPS-collar sampling, as well as spatial mismatches in the data. Our research suggests data collected from individual-based sampling methods can capture coarse population-wide patterns for a diversity of species, but results differ when interpreting specific wildlife-habitat relationships.},
}
@article {pmid36103465,
year = {2022},
author = {Nam, S and Jeon, S and Lee, SJ and Ash, G and Nelson, LE and Granger, DA},
title = {Real-time racial discrimination, affective states, salivary cortisol and alpha-amylase in Black adults.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0273081},
pmid = {36103465},
issn = {1932-6203},
support = {R25 MH067127/MH/NIMH NIH HHS/United States ; },
mesh = {Adult ; Cross-Sectional Studies ; Humans ; *Hydrocortisone ; *Racism/psychology ; Retrospective Studies ; Saliva ; Stress, Psychological/psychology ; alpha-Amylases ; },
abstract = {Perceived racial discrimination has been associated with the autonomic nervous system (ANS) and hypothalamic-pituitary-adrenal (HPA) axis activities-two major stress response systems. To date, most studies have used cross-sectional data that captured retrospective measures of the racial discrimination associated with current physiological stress responses. The purpose of this study was to examine the relationship between racial discrimination measured in real-time and physiological stress responses. Twelve healthy Black adults completed baseline surveys and self-collected saliva samples 4x/day for 4 days to measure cortisol and alpha amylase (AA) as a proxy of HPA and ANS systems, respectively. Real-time racial discrimination was measured using ecological momentary assessments (EMA) sent to participants 5x/day for 7 days. Multilevel models were conducted to examine the relationship between racial discrimination and stress responses. In multilevel models, the previous day's racial discrimination was significantly associated with the next day's cortisol level at wakening (β = 0.81, partial r = 0.74, p<0.01) and diurnal slope (β = -0.85, partial r = -0.73, p<0.01). Also, microaggressions were significantly associated with the diurnal cortisol slope in the same day, indicating that on the day when people reported more microaggressions than usual, a flatter diurnal slope of cortisol was observed (β = -0.50, partial r = -0.64, p<0.01). The concurrent use of salivary biomarkers and EMA was feasible methods to examine the temporal relationship between racial discrimination and physiological stress responses. The within-person approach may help us understand the concurrent or lagged effects of racial discrimination on the stress responses. Further studies are needed to confirm the observed findings with a large sample size and to improve stress related health outcomes in racial/ethnic minorities.},
}
@article {pmid36102834,
year = {2022},
author = {Débarre, F and Lecoeur, E and Guimier, L and Jauffret-Roustide, M and Jannot, AS},
title = {The French Covid-19 vaccination policy did not solve vaccination inequities: a nationwide study on 64.5 million people.},
journal = {European journal of public health},
volume = {32},
number = {5},
pages = {825-830},
pmid = {36102834},
issn = {1464-360X},
mesh = {*COVID-19/epidemiology/prevention &amp; control ; *COVID-19 Vaccines ; Emigration and Immigration ; Humans ; Policy ; Vaccination ; },
abstract = {BACKGROUND: To encourage Covid-19 vaccination, France introduced during the Summer 2021 a 'Sanitary Pass', which morphed into a 'Vaccine Pass' in early 2022. While the sanitary pass led to an increase in Covid-19 vaccination rates, spatial heterogeneities in vaccination rates remained. To identify potential determinants of these heterogeneities and evaluate the French sanitary and vaccine passes' efficacies in reducing them, we used a data-driven approach on exhaustive nationwide data, gathering 141 socio-economic, political and geographic indicators.<br><br>METHODS: We considered the association between vaccination rates and each indicator at different time points: before the sanitary pass announcement (week 2021-W27), before the sanitary pass came into force (week 2021-W31) and 1 month after (week 2021-W35) and the equivalent dates for the vaccine pass (weeks 2021-W49, 2022-W03 and 2022-W07).<br><br>RESULTS: The indicators most associated with vaccination rates were the share of local income coming from unemployment benefits, overcrowded households rate, immigrants rate and vote for an 'anti-establishment' candidate at the 2017 Presidential election. These associations increase over time. Consequently, living in a district below the median of such indicator decreases the probability to be vaccinated by about 30% at the end of the studied period, and this probability gradually decreases by deciles of these indicators.<br><br>CONCLUSIONS: Our analysis reveals that factors related to poverty, immigration and trust in the government are strong determinants of vaccination rate, and that vaccination inequities tended to increase after the introduction of the French sanitary and vaccination passes.},
}
@article {pmid36100598,
year = {2022},
author = {Metz, S and Huber, P and Mateus-Barros, E and Junger, PC and de Melo, M and Bagatini, IL and Izaguirre, I and Câmara Dos Reis, M and Llames, ME and Accattatis, V and Quiroga, MV and Devercelli, M and Schiaffino, MR and Niño-García, JP and Bastidas Navarro, M and Modenutti, B and Vieira, H and Saraceno, M and Sabio Y García, CA and Pereira, E and González-Revello, A and Piccini, C and Unrein, F and Alonso, C and Sarmento, H},
title = {A georeferenced rRNA amplicon database of aquatic microbiomes from South America.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {565},
pmid = {36100598},
issn = {2052-4463},
mesh = {Bacteria/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; Water Microbiology ; },
abstract = {The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.},
}
@article {pmid36095758,
year = {2022},
author = {Golovatch, S and Vandenspiegel, D},
title = {Carinobolus gen. nov. and Costabolus gen. nov., two new, remarkably crested, monospecific genera of spirobolidan millipedes from West Africa, with the proposal of a new tribe, Amblybolini tribus nova (Diplopoda, Spirobolida, Pachybolidae).},
journal = {Zootaxa},
volume = {5150},
number = {1},
pages = {97-110},
doi = {10.11646/zootaxa.5150.1.5},
pmid = {36095758},
issn = {1175-5334},
mesh = {Africa, Western ; Animals ; *Arthropods ; },
abstract = {Two new genera, Carinobolus gen. nov. and Costabolus gen. nov., both belonging to the very large, widespread, pantropical family Pachybolidae, are described based on Carinobolus complex sp. nov. and Costabolus baculus sp. nov., respectively. Chiefly based on the posterior gonopod being distinctly articulated at midlength, both new genera seem to be especially similar to Amblybolus Keeton, 1964a (three species in western Africa) and Atlanticobolus Hoffman, 1979 (one species from an island off the Brazilian coast), all of them meriting a separate tribal category, Amblybolini tribus nova. A key is proposed to distinguish all four presently accepted genera of the new tribe. The new genera and species are clearly distinguished in showing unusually strongly crested/ribbed metazonae, a character that is only very seldom observed in Pachybolidae generally, and apparently unique among Afrotropical members. Being rather similar in many respects, both new genera and species differ from each other sufficiently well in gonopodal and leg structure, even though both come from forests in southeastern Nigeria close to the border to Cameroon.},
}
@article {pmid36095211,
year = {2022},
author = {Still, CJ and Page, G and Rastogi, B and Griffith, DM and Aubrecht, DM and Kim, Y and Burns, SP and Hanson, CV and Kwon, H and Hawkins, L and Meinzer, FC and Sevanto, S and Roberts, D and Goulden, M and Pau, S and Detto, M and Helliker, B and Richardson, AD},
title = {No evidence of canopy-scale leaf thermoregulation to cool leaves below air temperature across a range of forest ecosystems.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {38},
pages = {e2205682119},
pmid = {36095211},
issn = {1091-6490},
mesh = {*Carbon/metabolism ; *Carbon Cycle ; *Forests ; *Plant Leaves/anatomy &amp; histology/metabolism ; Temperature ; },
abstract = {Understanding and predicting the relationship between leaf temperature (Tleaf) and air temperature (Tair) is essential for projecting responses to a warming climate, as studies suggest that many forests are near thermal thresholds for carbon uptake. Based on leaf measurements, the limited leaf homeothermy hypothesis argues that daytime Tleaf is maintained near photosynthetic temperature optima and below damaging temperature thresholds. Specifically, leaves should cool below Tair at higher temperatures (i.e., > ∼25-30°C) leading to slopes <1 in Tleaf/Tair relationships and substantial carbon uptake when leaves are cooler than air. This hypothesis implies that climate warming will be mitigated by a compensatory leaf cooling response. A key uncertainty is understanding whether such thermoregulatory behavior occurs in natural forest canopies. We present an unprecedented set of growing season canopy-level leaf temperature (Tcan) data measured with thermal imaging at multiple well-instrumented forest sites in North and Central America. Our data do not support the limited homeothermy hypothesis: canopy leaves are warmer than air during most of the day and only cool below air in mid to late afternoon, leading to Tcan/Tair slopes >1 and hysteretic behavior. We find that the majority of ecosystem photosynthesis occurs when canopy leaves are warmer than air. Using energy balance and physiological modeling, we show that key leaf traits influence leaf-air coupling and ultimately the Tcan/Tair relationship. Canopy structure also plays an important role in Tcan dynamics. Future climate warming is likely to lead to even greater Tcan, with attendant impacts on forest carbon cycling and mortality risk.},
}
@article {pmid36094211,
year = {2022},
author = {Njoroge, SM and Madé, LF and von Mentzer, A and Kulohoma, BW and Kamanu, TK and Ouko, TT and Kiiru, J and Ward, MJ and Thomson, NR and Fèvre, EM and Woolhouse, M and Kariuki, S},
title = {Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.},
journal = {Microbiology resource announcements},
volume = {11},
number = {10},
pages = {e0041622},
pmid = {36094211},
issn = {2576-098X},
support = {G1100783/1//UKRI | Medical Research Council (MRC)/ ; BB/L019019/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; WT103953MA//Wellcome Trust (WT)/ ; G1100783/MRC_/Medical Research Council/United Kingdom ; R01 AI099525/AI/NIAID NIH HHS/United States ; MR/R015090/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.},
}
@article {pmid36090080,
year = {2022},
author = {Chang, Y and Chen, F and Zhu, Y and You, Y and Cheng, Y and Ma, J},
title = {Influence of revegetation on soil microbial community and its assembly process in the open-pit mining area of the Loess Plateau, China.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {992816},
pmid = {36090080},
issn = {1664-302X},
abstract = {Vegetation recovery is an important marker of ecosystem health in the mining area. Clarifying the influence of vegetation recovery on the characteristics of soil microbial community and its assembly process can improve our understanding of the ecological resilience and self-maintaining mechanism in the open-pit mining area. For this purpose, we employed MiSeq high-throughput sequencing coupled with null model analysis to determine the composition, molecular ecological network characteristics, key bacterial and fungal clusters, and the assembly mechanism of the soil microbial communities in shrubs (BL), coniferous forest (CF), broad-leaved forests (BF), mixed forest (MF), and the control plot (CK, the poplar plantation nearby that had been continuously grown for over 30 a without disturbance). The results showed that the vegetation restoration model had a significant influence on the α-diversity of the microbial community (p < 0.05). Compared with CK, Sobs and Shannon index of MF and CF have increased by 35.29, 3.50, and 25.18%, 1.05%, respectively, whereas there was no significant difference in the α-diversity of fungal community among different vegetation restoration types, Actinobacteria, Chloroflexi, Proteobacteria, and Acidobacteria were the dominant phyla. The diversity of the first two phyla was significantly higher than those of CK. However, the diversity of the last two phyla was dramatically lower than those of CK (p < 0.05). Ascomycota and Basidiomycota were dominant phyla in the fungal community. The abundance and diversity of Ascomycota were significantly higher than those of CK, while the abundance and diversity of the latter were considerably lower than those of CK (p < 0.05). The stochastic process governed the assembly of the soil microbial community, and the contribution rate to the bacterial community construction of CK, CF, BF, and MF was 100.0%. Except for MF, where the soil fungal community assembly was governed by the deterministic process, all other fungal communities were governed by the stochastic process. Proteobacteria and Acidobacteria are key taxa of the bacterial network, while Mortierellales, Thelebolales, Chaetothyriales, and Hypocreales are the key taxa of the fungal network. All these results might provide the theoretical foundation for restoring the fragile ecosystem in the global mining region.},
}
@article {pmid36089013,
year = {2023},
author = {Lyu, Y and Wu, Z and Wu, H and Pang, X and Qin, K and Wang, B and Ding, S and Chen, D and Chen, J},
title = {Tracking long-term population exposure risks to PM2.5 and ozone in urban agglomerations of China 2015-2021.},
journal = {The Science of the total environment},
volume = {854},
number = {},
pages = {158599},
doi = {10.1016/j.scitotenv.2022.158599},
pmid = {36089013},
issn = {1879-1026},
mesh = {Humans ; *Air Pollutants/analysis ; Particulate Matter/analysis ; *Ozone ; Pandemics ; *COVID-19/epidemiology ; *Air Pollution/analysis ; China/epidemiology ; },
abstract = {China has experienced severe air pollution in the past decade, especially PM2.5 and emerging ozone pollution recently. In this study, we comprehensively analyzed long-term population exposure risks to PM2.5 and ozone in urban agglomerations of China during 2015-2021 regarding two-stage clean-air actions based on the Ministry of Ecology and the Environment (MEE) air monitoring network. Overall, the ratio of the population living in the regions exceeding the Chinese National Ambient Air Quality Standard (35 μg/m[3]) decreases by 29.9 % for PM2.5 from 2015 to 2021, driven by high proportions in the Middle Plain (MP, 42.3 %) and Lan-Xi (35.0 %) regions. However, this ratio almost remains unchanged for ozone and even increases by 1.5 % in the MP region. As expected, the improved air quality leads to 234.7 × 10[3] avoided premature mortality (ΔMort), mainly ascribed to the reduction in PM2.5 concentration. COVID-19 pandemic may influence the annual variation of PM2.5-related ΔMort as it affects the shape of the population exposure curve to become much steeper. Although all eleven urban agglomerations share stroke (43.6 %) and ischaemic heart disease (IHD, 30.1 %) as the two largest contributors to total ΔMort, cause-specific ΔMort is highly regional heterogeneous, in which ozone-related ΔMort is significantly higher (21 %) in the Tibet region than other urban agglomeration. Despite ozone-related ΔMort being one order of magnitude lower than PM2.5-related ΔMort from 2015 to 2021, ozone-related ΔMort is predicted to increase in major urban agglomerations initially along with a continuous decline for PM2.5-related ΔMort from 2020 to 2060, highlighting the importance of ozone control. Coordinated controls of PM2.5 and O3 are warranted for reducing health burdens in China during achieving carbon neutrality.},
}
@article {pmid36088355,
year = {2022},
author = {Mull, CG and Pacoureau, N and Pardo, SA and Ruiz, LS and García-Rodríguez, E and Finucci, B and Haack, M and Harry, A and Judah, AB and VanderWright, W and Yin, JS and Kindsvater, HK and Dulvy, NK},
title = {Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {559},
pmid = {36088355},
issn = {2052-4463},
mesh = {Animals ; Conservation of Natural Resources ; Databases, Factual ; Internationality ; *Life History Traits ; *Sharks ; },
abstract = {A curated database of shark and ray biological data is increasingly necessary both to support fisheries management and conservation efforts, and to test the generality of hypotheses of vertebrate macroecology and macroevolution. Sharks and rays are one of the most charismatic, evolutionary distinct, and threatened lineages of vertebrates, comprising around 1,250 species. To accelerate shark and ray conservation and science, we developed Sharkipedia as a curated open-source database and research initiative to make all published biological traits and population trends accessible to everyone. Sharkipedia hosts information on 58 life history traits from 274 sources, for 170 species, from 39 families, and 12 orders related to length (n = 9 traits), age (8), growth (12), reproduction (19), demography (5), and allometric relationships (5), as well as 871 population time-series from 202 species. Sharkipedia relies on the backbone taxonomy of the IUCN Red List and the bibliography of Shark-References. Sharkipedia has profound potential to support the rapidly growing data demands of fisheries management, international trade regulation as well as anchoring vertebrate macroecology and macroevolution.},
}
@article {pmid36085224,
year = {2023},
author = {Gul, S and Bibi, T and Rahim, S and Gul, Y and Niaz, A and Mumtaz, S and Shedayi, AA},
title = {Spatio-temporal change detection of land use and land cover in Malakand Division Khyber Pakhtunkhwa, Pakistan, using remote sensing and geographic information system.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {4},
pages = {10982-10994},
pmid = {36085224},
issn = {1614-7499},
mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; Pakistan ; Conservation of Natural Resources ; Environmental Monitoring/methods ; Agriculture ; },
abstract = {The land use land cover (LULC) change due to the rapidly growing population is a common feature of the urban area. The rapidly growing population in Malakand Division is a greater threat to the LULC of the area due to its negative impact on environment and ecology. This research aims to detect the variations in LULC from 1991 to 2017 in the Malakand Division, Khyber Pakhtunkhwa (KP) province of Pakistan. The study relies on secondary dataset downloaded from the US Geological Survey (1991, 2001, 2011, and 2017 imageries) and the United Nations Office for the Coordination of Humanitarian Affairs (UN OCHA) website. Maximum likelihood technique under supervised image classification was opted to analyze the LULC changes in between 1991 and 2017. The results were based on six major land use classes including agriculture built-up area, vegetation cover, water bodies, snow cover, and barren land. The results from 1991 to 2017 show a substantial reduction in snow cover and barren land which is consequence of climate change. A known change has been recorded in built-up area which shows an increase from 1.02 to 6.2% with a change of 5.18% of the total land. The vegetation cover water bodies were also showing increase in area. The vegetation cover increased from 28.89 to 44.67% while barren land decreased from 45.68 to 40.29% of the total area. Furthermore, the built-up area increased from 1.02 to 6.2%, whereas water covers increased from 0.63% (1991) to 0.86% (2017) of the total area. The study concludes that there is an immense need for planning to preserve the natural habitat for sustainable development in the area.},
}
@article {pmid36074761,
year = {2022},
author = {Cappellato, M and Baruzzo, G and Di Camillo, B},
title = {Investigating differential abundance methods in microbiome data: A benchmark study.},
journal = {PLoS computational biology},
volume = {18},
number = {9},
pages = {e1010467},
pmid = {36074761},
issn = {1553-7358},
mesh = {*Benchmarking ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Reproducibility of Results ; },
abstract = {The development of increasingly efficient and cost-effective high throughput DNA sequencing techniques has enhanced the possibility of studying complex microbial systems. Recently, researchers have shown great interest in studying the microorganisms that characterise different ecological niches. Differential abundance analysis aims to find the differences in the abundance of each taxa between two classes of subjects or samples, assigning a significance value to each comparison. Several bioinformatic methods have been specifically developed, taking into account the challenges of microbiome data, such as sparsity, the different sequencing depth constraint between samples and compositionality. Differential abundance analysis has led to important conclusions in different fields, from health to the environment. However, the lack of a known biological truth makes it difficult to validate the results obtained. In this work we exploit metaSPARSim, a microbial sequencing count data simulator, to simulate data with differential abundance features between experimental groups. We perform a complete comparison of recently developed and established methods on a common benchmark with great effort to the reliability of both the simulated scenarios and the evaluation metrics. The performance overview includes the investigation of numerous scenarios, studying the effect on methods' results on the main covariates such as sample size, percentage of differentially abundant features, sequencing depth, feature variability, normalisation approach and ecological niches. Mainly, we find that methods show a good control of the type I error and, generally, also of the false discovery rate at high sample size, while recall seem to depend on the dataset and sample size.},
}
@article {pmid36071746,
year = {2022},
author = {Prenzel, F and Treudler, R and Lipek, T and Vom Hove, M and Kage, P and Kuhs, S and Kaiser, T and Bastl, M and Bumberger, J and Genuneit, J and Hornick, T and Klotz, S and Zarnowski, J and Boege, M and Zebralla, V and Simon, JC and Dunker, S},
title = {Invasive Growth of Ailanthus altissima Trees is Associated with a High Rate of Sensitization in Atopic Patients.},
journal = {Journal of asthma and allergy},
volume = {15},
number = {},
pages = {1217-1226},
pmid = {36071746},
issn = {1178-6965},
abstract = {PURPOSE: Ailanthus altissima is one of the world's most invasive species with a globally problematic spread. Pollen is dispersed locally and partially airborne. We aimed at investigating if (i) A. altissima pollen can be detected in relevant quantity in the air and if (ii) sensitization to A. altissima can be detected in patients with seasonal exacerbation of atopic diseases.<br><br>PATIENTS AND METHODS: We recorded distribution of A. altissima in Leipzig, Germany. In 2019 and 2020, pollen was collected with a Hirst-type pollen trap placed on the roof of the University Hospital. Specific IgE investigations were performed in children and adults with history of atopic diseases with deterioration between May and July. We analysed specific IgE for A. altissima, Alternaria sp., birch, grasses, profilins, polcalcins and crossreacting carbohydrates.<br><br>RESULTS: We found abundant growth of A. altissima and pollen was detected from early June to mid-July with a maximum pollen concentration of 31 pollen/m[3]. Out of 138 patients (63 female, 69 children/adolescents), 95 (69%) had seasonal allergic rhinitis, 84 (61%) asthma, and 43 (31%) atopic dermatitis. Sensitization to A. altissima was shown in 59 (42%). There were no significant differences between age groups. In 59% of patients sensitized (35/59), there was no sensitization to possibly cross-reacting structures.<br><br>CONCLUSION: Sensitization to A. altissima pollen could be detected in 42% of our patients with atopic diseases, suggesting allergenic potential of this neophyte. In the context of further spread with climate change, eradication strategies and population-based sensitization studies are needed.},
}
@article {pmid36071164,
year = {2022},
author = {Arostegui, MC and Gaube, P and Woodworth-Jefcoats, PA and Kobayashi, DR and Braun, CD},
title = {Anticyclonic eddies aggregate pelagic predators in a subtropical gyre.},
journal = {Nature},
volume = {609},
number = {7927},
pages = {535-540},
pmid = {36071164},
issn = {1476-4687},
mesh = {Animals ; Cyclonic Storms ; Datasets as Topic ; *Ecosystem ; Fisheries ; Food Chain ; Nutrients/analysis ; Pacific Ocean ; *Predatory Behavior ; Tropical Climate ; *Water ; *Water Movements ; },
abstract = {Ocean eddies are coherent, rotating features that can modulate pelagic ecosystems across many trophic levels. These mesoscale features, which are ubiquitous at mid-latitudes[1], may increase productivity of nutrient-poor regions[2,3], accumulate prey[4] and modulate habitat conditions in the water column[5]. However, in nutrient-poor subtropical gyres-the largest marine biome-the role of eddies in modulating behaviour throughout the pelagic predator community remains unknown despite predictions for these gyres to expand[6] and pelagic predators to become increasingly important for food security[7]. Using a large-scale fishery dataset in the North Pacific Subtropical Gyre, we show a pervasive pattern of increased pelagic predator catch inside anticyclonic eddies relative to cyclones and non-eddy areas. Our results indicate that increased mesopelagic prey abundance in anticyclone cores[4,8] may be attracting diverse predators, forming ecological hotspots where these predators aggregate and exhibit increased abundance. In this energetically quiescent gyre, we expect that isolated mesoscale features (and the habitat conditions in them) exhibit primacy over peripheral submesoscale dynamics in structuring the foraging opportunities of pelagic predators. Our finding that eddies influence coupling of epi- to mesopelagic communities corroborates the growing evidence that deep scattering layer organisms are vital prey for a suite of commercially important predator species[9] and, thus, provide valuable ecosystem services.},
}
@article {pmid36071118,
year = {2022},
author = {Brown, JM and Bossomaier, T and Barnett, L},
title = {Information flow in first-order potts model phase transition.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15145},
pmid = {36071118},
issn = {2045-2322},
mesh = {Entropy ; *Hot Temperature ; Phase Transition ; Thermodynamics ; },
abstract = {Phase transitions abound in nature and society, and, from species extinction to stock market collapse, their prediction is of widespread importance. In earlier work we showed that Global Transfer Entropy, a general measure of information flow, was found to peaks away from the transition on the disordered side for the Ising model, a canonical second order transition. Here we show that (a) global transfer entropy also peaks on the disordered side of the transition of finite first order transitions, such as ecology dynamics on coral reefs, which have latent heat and no correlation length divergence, and (b) analysis of information flow across state boundaries unifies both transition orders. We obtain the first information-theoretic result for the high-order Potts model and the first demonstration of early warning of a first order transition. The unexpected earlier finding that global transfer entropy peaks on the disordered side of a transition is also found for finite first order systems, albeit not in the thermodynamic limit. By noting that the interface length of clusters in each phase is the dominant region of information flow, we unify the information theoretic behaviour of first and second order transitions.},
}
@article {pmid36058075,
year = {2022},
author = {Maloney, KO and Buchanan, C and Jepsen, RD and Krause, KP and Cashman, MJ and Gressler, BP and Young, JA and Schmid, M},
title = {Explainable machine learning improves interpretability in the predictive modeling of biological stream conditions in the Chesapeake Bay Watershed, USA.},
journal = {Journal of environmental management},
volume = {322},
number = {},
pages = {116068},
doi = {10.1016/j.jenvman.2022.116068},
pmid = {36058075},
issn = {1095-8630},
mesh = {Agriculture ; *Bays ; Ecosystem ; Environmental Monitoring/methods ; Machine Learning ; *Rivers ; },
abstract = {Anthropogenic alterations have resulted in widespread degradation of stream conditions. To aid in stream restoration and management, baseline estimates of conditions and improved explanation of factors driving their degradation are needed. We used random forests to model biological conditions using a benthic macroinvertebrate index of biotic integrity for small, non-tidal streams (upstream area ≤200 km[2]) in the Chesapeake Bay watershed (CBW) of the mid-Atlantic coast of North America. We utilized several global and local model interpretation tools to improve average and site-specific model inferences, respectively. The model was used to predict condition for 95,867 individual catchments for eight periods (2001, 2004, 2006, 2008, 2011, 2013, 2016, 2019). Predicted conditions were classified as Poor, FairGood, or Uncertain to align with management needs and individual reach lengths and catchment areas were summed by condition class for the CBW for each period. Global permutation and local Shapley importance values indicated percent of forest, development, and agriculture in upstream catchments had strong impacts on predictions. Development and agriculture negatively influenced stream condition for model average (partial dependence [PD] and accumulated local effect [ALE] plots) and local (individual condition expectation and Shapley value plots) levels. Friedman's H-statistic indicated large overall interactions for these three land covers, and bivariate global plots (PD and ALE) supported interactions among agriculture and development. Total stream length and catchment area predicted in FairGood conditions decreased then increased over the 19-years (length/area: 66.6/65.4% in 2001, 66.3/65.2% in 2011, and 66.6/65.4% in 2019). Examination of individual catchment predictions between 2001 and 2019 showed those predicted to have the largest decreases in condition had large increases in development; whereas catchments predicted to exhibit the largest increases in condition showed moderate increases in forest cover. Use of global and local interpretative methods together with watershed-wide and individual catchment predictions support conservation practitioners that need to identify widespread and localized patterns, especially acknowledging that management actions typically take place at individual-reach scales.},
}
@article {pmid36053136,
year = {2022},
author = {Kelleher, K and McGinnity, P and Howard, BJ and Boyer, P and Vidal, M and Bildstein, OM},
title = {The use of the IAEA MARIS database in determining the variability of sediment distribution coefficients in the marine environment and potential implications for marine dispersion modelling.},
journal = {Journal of radiological protection : official journal of the Society for Radiological Protection},
volume = {42},
number = {3},
pages = {},
doi = {10.1088/1361-6498/ac8a53},
pmid = {36053136},
issn = {1361-6498},
mesh = {Geologic Sediments ; Information Systems ; *Radioactivity ; Seawater ; *Water Pollutants, Radioactive/analysis ; },
abstract = {A prototype tool has been developed for deriving sediment distribution coefficients,Kd, in the marine environment by harvesting simultaneous measurements of activity concentrations of radionuclides in seawater and sediments based on the International Atomic Energy Agency's Marine Radioactivity Information System (MARIS). As a case study, theKdvariability in the Baltic Sea was investigated as this region has been extensively monitored by HELCOM since 1984 resulting in a comprehensive dataset with good spatial and temporal coverage and required ancillary parameters. The prototype tool was used to derive a dataset ofin-situapparentKd(a)values derived from measurements of seawater and sediment in quasi-equilibrium conditions from the Baltic Sea over a period of approximately 35 years. For Cs, a comprehensive analysis of the Baltic SeaKd(a)dataset was undertaken, focusing on the temporal trend ofKd(a)and comparing the results toKdvalues derived elsewhere. For Sr and Pu, for which there were fewer data records available a more rudimentary analysis was carried out. The CsKd(a)median values derived from[137]Cs data in this study were estimated to be 2154 l kg[-1]for seabed sediment and 10 000 l kg[-1]for suspended sediment. The value derived for seabed sediment is in good agreement with the previously recommended ocean margin CsKdvalue of 4000 l kg[-1]. The analysis demonstrated the important distinction in the Baltic Sea betweenKdvalues for seabed sediment and suspended sediments, which differed by an order of magnitude. The analysis also highlighted the dependence ofKdvalues on the variation in both the salinity of seawater and the type of seabed sediment. Such variability can significantly influence outcomes when modelling the behaviour of radionuclides in marine dispersion modelling.},
}
@article {pmid36051895,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Gibbs, M and , },
title = {The genome sequence of the clay, Mythimna ferrago (Fabricius, 1787).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {177},
pmid = {36051895},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Mythimna ferrago (the clay; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 861 megabases in span. The majority of the assembly (99.98%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 14,075 protein coding genes.},
}
@article {pmid36050321,
year = {2022},
author = {Young, WJ and Lahrouchi, N and Isaacs, A and Duong, T and Foco, L and Ahmed, F and Brody, JA and Salman, R and Noordam, R and Benjamins, JW and Haessler, J and Lyytikäinen, LP and Repetto, L and Concas, MP and van den Berg, ME and Weiss, S and Baldassari, AR and Bartz, TM and Cook, JP and Evans, DS and Freudling, R and Hines, O and Isaksen, JL and Lin, H and Mei, H and Moscati, A and Müller-Nurasyid, M and Nursyifa, C and Qian, Y and Richmond, A and Roselli, C and Ryan, KA and Tarazona-Santos, E and Thériault, S and van Duijvenboden, S and Warren, HR and Yao, J and Raza, D and Aeschbacher, S and Ahlberg, G and Alonso, A and Andreasen, L and Bis, JC and Boerwinkle, E and Campbell, A and Catamo, E and Cocca, M and Cutler, MJ and Darbar, D and De Grandi, A and De Luca, A and Ding, J and Ellervik, C and Ellinor, PT and Felix, SB and Froguel, P and Fuchsberger, C and Gögele, M and Graff, C and Graff, M and Guo, X and Hansen, T and Heckbert, SR and Huang, PL and Huikuri, HV and Hutri-Kähönen, N and Ikram, MA and Jackson, RD and Junttila, J and Kavousi, M and Kors, JA and Leal, TP and Lemaitre, RN and Lin, HJ and Lind, L and Linneberg, A and Liu, S and MacFarlane, PW and Mangino, M and Meitinger, T and Mezzavilla, M and Mishra, PP and Mitchell, RN and Mononen, N and Montasser, ME and Morrison, AC and Nauck, M and Nauffal, V and Navarro, P and Nikus, K and Pare, G and Patton, KK and Pelliccione, G and Pittman, A and Porteous, DJ and Pramstaller, PP and Preuss, MH and Raitakari, OT and Reiner, AP and Ribeiro, ALP and Rice, KM and Risch, L and Schlessinger, D and Schotten, U and Schurmann, C and Shen, X and Shoemaker, MB and Sinagra, G and Sinner, MF and Soliman, EZ and Stoll, M and Strauch, K and Tarasov, K and Taylor, KD and Tinker, A and Trompet, S and Uitterlinden, A and Völker, U and Völzke, H and Waldenberger, M and Weng, LC and Whitsel, EA and Wilson, JG and Avery, CL and Conen, D and Correa, A and Cucca, F and Dörr, M and Gharib, SA and Girotto, G and Grarup, N and Hayward, C and Jamshidi, Y and Järvelin, MR and Jukema, JW and Kääb, S and Kähönen, M and Kanters, JK and Kooperberg, C and Lehtimäki, T and Lima-Costa, MF and Liu, Y and Loos, RJF and Lubitz, SA and Mook-Kanamori, DO and Morris, AP and O'Connell, JR and Olesen, MS and Orini, M and Padmanabhan, S and Pattaro, C and Peters, A and Psaty, BM and Rotter, JI and Stricker, B and van der Harst, P and van Duijn, CM and Verweij, N and Wilson, JF and Arking, DE and Ramirez, J and Lambiase, PD and Sotoodehnia, N and Mifsud, B and Newton-Cheh, C and Munroe, PB},
title = {Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5144},
pmid = {36050321},
issn = {2041-1723},
support = {MR/N025083/1/MRC_/Medical Research Council/United Kingdom ; R01 HL139731/HL/NHLBI NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; R01 HL105756/HL/NHLBI NIH HHS/United States ; T32 HL007604/HL/NHLBI NIH HHS/United States ; K24 HL148521/HL/NHLBI NIH HHS/United States ; MR/R010676/1/MRC_/Medical Research Council/United Kingdom ; R01 HL142825/HL/NHLBI NIH HHS/United States ; R01 DK107786/DK/NIDDK NIH HHS/United States ; K23 HL127704/HL/NHLBI NIH HHS/United States ; R01 DK110113/DK/NIDDK NIH HHS/United States ; U01 AG068221/AG/NIA NIH HHS/United States ; R01 HL128914/HL/NHLBI NIH HHS/United States ; R01 HL141989/HL/NHLBI NIH HHS/United States ; R01 HL143070/HL/NHLBI NIH HHS/United States ; U54 GM115428/GM/NIGMS NIH HHS/United States ; MR/R017468/1/MRC_/Medical Research Council/United Kingdom ; T32 HL139439/HL/NHLBI NIH HHS/United States ; R01 HL142302/HL/NHLBI NIH HHS/United States ; R01 HL138737/HL/NHLBI NIH HHS/United States ; K24 HL105780/HL/NHLBI NIH HHS/United States ; U01 HG007416/HG/NHGRI NIH HHS/United States ; U24 AG051129/AG/NIA NIH HHS/United States ; R01 DK124097/DK/NIDDK NIH HHS/United States ; MR/S019669/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Arrhythmias, Cardiac/genetics ; Death, Sudden, Cardiac ; *Electrocardiography/methods ; Genetic Testing ; Humans ; Male ; },
abstract = {The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry analyses (>250,000 individuals) we identify 177, 156 and 121 independent loci for QT, JT and QRS, respectively, including a male-specific X-chromosome locus. Using gene-based rare-variant methods, we identify associations with Mendelian disease genes. Enrichments are observed in established pathways for QT and JT, and previously unreported genes indicated in insulin-receptor signalling and cardiac energy metabolism. In contrast for QRS, connective tissue components and processes for cell growth and extracellular matrix interactions are significantly enriched. We demonstrate polygenic risk score associations with atrial fibrillation, conduction disease and sudden cardiac death. Prioritization of druggable genes highlight potential therapeutic targets for arrhythmia. Together, these results substantially advance our understanding of the genetic architecture of ventricular depolarization and repolarization.},
}
@article {pmid36048827,
year = {2022},
author = {Omoru, OB and Pereira, F and Janga, SC and Manzourolajdad, A},
title = {A Putative long-range RNA-RNA interaction between ORF8 and Spike of SARS-CoV-2.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0260331},
pmid = {36048827},
issn = {1932-6203},
support = {R01 GM123314/GM/NIGMS NIH HHS/United States ; },
mesh = {*COVID-19 ; Genome, Viral ; Humans ; RNA, Viral/genetics ; *SARS-CoV-2/genetics ; *Spike Glycoprotein, Coronavirus/genetics ; *Viral Proteins/genetics ; },
abstract = {SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV-1 responsible for the 2002-2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into other viral proteins. In this work, we performed a comparative analysis for novel long-range RNA-RNA interactions that may involve the Spike region. Comparing in-silico fragment-based predictions between reference sequences of SARS-CoV-1 and SARS-CoV-2 revealed several predictions amongst which a thermodynamically stable long-range RNA-RNA interaction between (23660-23703 Spike) and (28025-28060 ORF8) unique to SARS-CoV-2 was observed. The patterns of sequence variation using data gathered worldwide further supported the predicted stability of the sub-interacting region (23679-23690 Spike) and (28031-28042 ORF8). Such RNA-RNA interactions can potentially impact viral life cycle including sub-genomic RNA production rates.},
}
@article {pmid36044830,
year = {2023},
author = {Niestroj, SC and Steden, S and Boecker, M and Brodkin, ES and Konrad, K},
title = {The Development and Validation of the First German Open Scale of Social Information Processing.},
journal = {Psychopathology},
volume = {56},
number = {1-2},
pages = {52-63},
doi = {10.1159/000525950},
pmid = {36044830},
issn = {1423-033X},
mesh = {Male ; Child ; Female ; Adolescent ; Humans ; *Social Behavior ; *Cognition ; Aggression/psychology ; Social Perception ; Emotions ; },
abstract = {INTRODUCTION: This study introduces the first German Open Scale of Social Information Processing (GOSSIP) and evaluates its psychometric properties. Even though social information processing (SIP) and its important role in developmental psychopathology is a rising field of interest, model-based standardized assessment tools are still scarce.<br><br>METHODS: GOSSIP was developed to assess SI processes in boys and girls aged eight to 21 years. First, 61 vignettes (combinations of pictures and short written descriptions of the situation depicted) were evaluated by an expert group and piloted with 48 healthy participants (aged 8-21). The best-rated vignettes were then implemented in a Web-based application. 191 participants completed GOSSIP. Of those, 76 answered additional questionnaires to assess their social skills and psychopathology. Internal consistencies for the emotional and cognitive GOSSIP scales were determined. Latent profile analysis (LPA) was used to identify subgroups of children and adolescents characterized by specific SIP profiles (i.e., patterns of emotional, cognitive, and behavioral responses to the GOSSIP). Furthermore, the external validity of the participants' attribution tendencies in GOSSIP was evaluated in real life by smartphone-based Ecological Momentary Assessments (EMA).<br><br>RESULTS: The internal consistencies for the emotional and cognitive scales (angry, ashamed, physical aggression, pro-social response, revenge, and outcome expectancy) were good to excellent. The scales of hostile interpretation, relation aggression, sadness, and exclusion showed borderline/acceptable internal consistency. Correlation analysis confirmed convergent validity with self-reported social skills and external validity with ratings of aggressive and pro-social behaviors. The LPA revealed three profiles as the best fit of the data. The first group is named "aggressors," the second "social-emotional group," and a third named "ashamed-internalizing group." However, no significant association was found between the attribution tendencies derived from GOSSIP and EMA data.<br><br>DISCUSSION/CONCLUSION: GOSSIP is the first model-based German Web-based assessment for several SIP mechanisms that showed overall adequate psychometric properties. GOSSIP can be used to classify individuals into SIP profiles that differ in terms of their cognitive and emotional response tendencies and therefore could contribute to the development of targeted interventions. Integrating assessments of emotional responses into GOSSIP revealed an important role of "shame" in SIP and the development of psychopathology. Furthermore, the lack of external validity between GOSSIP and EMA calls into question how attribution tendencies are best assessed in future studies.},
}
@article {pmid36041271,
year = {2022},
author = {Sokhansanj, BA and Rosen, GL},
title = {Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning.},
journal = {Computers in biology and medicine},
volume = {149},
number = {},
pages = {105969},
pmid = {36041271},
issn = {1879-0534},
mesh = {*COVID-19/epidemiology ; Humans ; Machine Learning ; Mutation ; Phylogeny ; Retrospective Studies ; SARS-CoV-2 ; Severity of Illness Index ; *Spike Glycoprotein, Coronavirus/genetics ; },
abstract = {Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack sequence-level information for the virus. Studies which do obtain viral genome sequences are generally limited in time, location, and population scope. Retrospective meta-analyses require time-consuming data extraction from heterogeneous formats and are limited to publicly available reports. Fortuitously, a subset of GISAID, the global SARS-CoV-2 sequence repository, includes "patient status" metadata that can indicate whether a sequence record is associated with mild or severe disease. While GISAID lacks data on comorbidities relevant to severity, such as obesity and chronic disease, it does include metadata for age and sex to use as additional attributes in modeling. With these caveats, previous efforts have demonstrated that genotype-patient status models can be fit to GISAID data, particularly when country-of-origin is used as an additional feature. But are these models robust and biologically meaningful? This paper shows that, in fact, temporal and geographic biases in sequences submitted to GISAID, as well as the evolving pandemic response, particularly reduction in severe disease due to vaccination, create complex issues for model development and interpretation. This paper poses a potential solution: efficient mixed effects machine learning using GPBoost, treating country as a random effect group. Training and validation using temporally split GISAID data and emerging Omicron variants demonstrates that GPBoost models are more predictive of the impact of spike protein mutations on patient outcomes than fixed effect XGBoost, LightGBM, random forests, and elastic net logistic regression models.},
}
@article {pmid36039768,
year = {2024},
author = {De Calheiros Velozo, J and Habets, J and George, SV and Niemeijer, K and Minaeva, O and Hagemann, N and Herff, C and Kuppens, P and Rintala, A and Vaessen, T and Riese, H and Delespaul, P},
title = {Designing daily-life research combining experience sampling method with parallel data.},
journal = {Psychological medicine},
volume = {54},
number = {1},
pages = {98-107},
doi = {10.1017/S0033291722002367},
pmid = {36039768},
issn = {1469-8978},
mesh = {Humans ; *Ecological Momentary Assessment ; *Life Change Events ; Research Design ; },
abstract = {BACKGROUND: Ambulatory monitoring is gaining popularity in mental and somatic health care to capture an individual's wellbeing or treatment course in daily-life. Experience sampling method collects subjective time-series data of patients' experiences, behavior, and context. At the same time, digital devices allow for less intrusive collection of more objective time-series data with higher sampling frequencies and for prolonged sampling periods. We refer to these data as parallel data. Combining these two data types holds the promise to revolutionize health care. However, existing ambulatory monitoring guidelines are too specific to each data type, and lack overall directions on how to effectively combine them.<br><br>METHODS: Literature and expert opinions were integrated to formulate relevant guiding principles.<br><br>RESULTS: Experience sampling and parallel data must be approached as one holistic time series right from the start, at the study design stage. The fluctuation pattern and volatility of the different variables of interest must be well understood to ensure that these data are compatible. Data have to be collected and operationalized in a manner that the minimal common denominator is able to answer the research question with regard to temporal and disease severity resolution. Furthermore, recommendations are provided for device selection, data management, and analysis. Open science practices are also highlighted throughout. Finally, we provide a practical checklist with the delineated considerations and an open-source example demonstrating how to apply it.<br><br>CONCLUSIONS: The provided considerations aim to structure and support researchers as they undertake the new challenges presented by this exciting multidisciplinary research field.},
}
@article {pmid36039277,
year = {2022},
author = {Stokes, J and Bower, P and Guthrie, B and Mercer, SW and Rice, N and Ryan, AM and Sutton, M},
title = {Cuts to local government spending, multimorbidity and health-related quality of life: A longitudinal ecological study in England.},
journal = {The Lancet regional health. Europe},
volume = {19},
number = {},
pages = {100436},
pmid = {36039277},
issn = {2666-7762},
support = {MR/T027517/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: Population health has stagnated or is declining in many high-income countries. We analysed whether nationally administered austerity cuts in England were associated with prevalence of multimorbidity (individuals with two or more long-term conditions) and health-related quality of life.<br><br>METHODS: We conducted an observational, longitudinal study on 147 local authorities in England. We examined associations of changes in spending over time (2009/10-2017/18), in total and by budget line, with (i) prevalence of multimorbidity, 2+ conditions (2011/12-2017/18), and (ii) health-related quality of life (EQ-5D-5L) score (2012/13-2016/17). We estimated linear, log-log regression models, incorporating local authority fixed-effects, time-varying demographic and socio-economic confounders, and time trends.<br><br>FINDINGS: All local authorities experienced real spending cuts, varying from 42% (Barking and Dagenham) to 0&#xb7;3% (Sefton). A 1% cut in per capita total service expenditure was associated with a 0&#xb7;10% (95% CI 0&#xb7;03 to 0&#xb7;16) increase in prevalence of multimorbidity. We found no association (0&#xb7;003%; 95% CI -0&#xb7;01 to 0&#xb7;01) with health-related quality of life. By budget line, after controlling for other spending, a 1% cut in public health expenditure was associated with a 0&#xb7;15% (95% CI 0&#xb7;11 to 0&#xb7;20) increase in prevalence of multimorbidity, and a 1% cut in adult social care expenditure was associated with a 0&#xb7;01% (95% CI 0&#xb7;002 to 0&#xb7;02) decrease in average health-related quality of life.<br><br>INTERPRETATION: Fiscal austerity is associated with worse multimorbidity and health-related quality of life. Policymakers should consider the potential health consequences of local government expenditure cuts and knock-on effects for health systems.<br><br>FUNDING: Medical Research Council.},
}
@article {pmid36037884,
year = {2022},
author = {Luoma, E and Laurila-Pant, M and Altarriba, E and Nevalainen, L and Helle, I and Granhag, L and Lehtiniemi, M and Srėbalienė, G and Olenin, S and Lehikoinen, A},
title = {A multi-criteria decision analysis model for ship biofouling management in the Baltic Sea.},
journal = {The Science of the total environment},
volume = {852},
number = {},
pages = {158316},
doi = {10.1016/j.scitotenv.2022.158316},
pmid = {36037884},
issn = {1879-1026},
mesh = {*Biofouling/prevention &amp; control ; Ships ; Carbon Dioxide ; Bayes Theorem ; Water ; Decision Support Techniques ; },
abstract = {Biofouling of ship hulls form a vector for the introduction of non-indigenous organisms worldwide. Through increasing friction, the organisms attached to ships' hulls increase the fuel consumption, leading to both higher fuel costs and air emissions. At the same time, ship biofouling management causes both ecological risks and monetary costs. All these aspects should be considered case-specifically in the search of sustainable management strategies. Applying Bayesian networks, we developed a multi-criteria decision analysis model to compare biofouling management strategies in the Baltic Sea, given the characteristics of a ship, its operating profile and operational environment, considering the comprehensive environmental impact and the monetary costs. The model is demonstrated for three scenarios (SC1-3) and sub-scenarios (A-C), comparing the alternative biofouling management strategies in relation to NIS (non-indigenous species) introduction risk, eco-toxicological risk due to biocidal coating, carbon dioxide emissions and costs related to fuel consumption, in-water cleaning and hull coating. The scenarios demonstrate that by the careful consideration of the hull fouling management strategy, both money and environment can be saved. We suggest biocidal-free coating with a regular in-water cleaning using a capture system is generally the lowest-risk option. The best biocidal-free coating type and the optimal in-water cleaning interval should be evaluated case-specifically, though. In some cases, however, biocidal coating remains a justifiable option.},
}
@article {pmid36036236,
year = {2022},
author = {Strobl, MR and Vollmann, U and Eckl-Dorna, J and Radakovics, A and Ibl, V and Schnurer, M and Brenner, M and Dermendjiev, G and Weckwerth, W and Neumüller, M and Frommlet, F and Demir, H and Bublin, M and Müller, C and Bohle, B},
title = {Identification of apple cultivars hypoallergenic for birch pollen-allergic individuals by a multidisciplinary in vitro and in vivo approach.},
journal = {Clinical and translational allergy},
volume = {12},
number = {8},
pages = {e12186},
pmid = {36036236},
issn = {2045-7022},
support = {P 32953/FWF_/Austrian Science Fund FWF/Austria ; P33891 (to VI), W1212, P32953, I4437//Austrian Science Funds/ ; &#xd6;NB17947//Austrian Jubil&#xe4;umsfond/ ; //Medical University of Vienna/ ; //Danube Allergy Research Cluster/ ; },
abstract = {BACKGROUND: Birch pollen-related apple allergy is the most frequent IgE-mediated food allergy in Central-Northern Europe with Mal d 1 as major allergen. Its concentration in apples varies with the cultivar and storage time. Year-round appealing, hypoallergenic cultivars still are needed to satisfy the nutritional needs of affected individuals. We characterized three promising cultivars by multidisciplinary in vitro assays including long-term storage and by clinical challenges of allergic individuals before and after the birch pollen season.<br><br>METHODS: Proteins were extracted from fruits of 'Santana', 'Golden Delicious' (GD), and three genuine cultivars in November 2018 and April 2019. Mal d 1-levels were analysed by mass spectrometry, SDS-PAGE, immunoblotting, competitive ELISA, and basophil activation tests. Twenty-eight allergic individuals underwent single-blinded open food challenges and skin testing with the cultivars and birch pollen in November 2018 and May 2019. Allergen-specific IgE-levels were determined.<br><br>RESULTS: After storage all cultivars except 'Santana' were of appealing appearance and taste. Their Mal d 1 content had increased, also reflected by significantly amplified basophil activation and stronger reactions in clinical challenges. Besides, individuals showed boosted reactivity after pollen exposure indicated by enhanced allergen-specific IgE-levels and skin reactions to birch pollen. Still, all cultivars remained significantly less allergenic than GD and comparable to Santana in November 2018 in all assessments except for skin testing.<br><br>CONCLUSIONS: Combined expertise in pomology and allergology identified promising new cultivars for allergic consumers. The evaluation of hypoallergenic apples should incorporate long-term storage and birch pollen exposure. Basophil activation tests may be suitable in the selection of promising cultivars for oral challenges.},
}
@article {pmid36035686,
year = {2022},
author = {Del Vecchio, S and Sharma, SK and Pavan, M and Acosta, ATR and Bacchetta, G and de Bello, F and Isermann, M and Michalet, R and Buffa, G},
title = {Within-species variation of seed traits of dune engineering species across a European climatic gradient.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {978205},
pmid = {36035686},
issn = {1664-462X},
abstract = {Within-species variation is a key component of biodiversity and linking it to climatic gradients may significantly improve our understanding of ecological processes. High variability can be expected in plant traits, but it is unclear to which extent it varies across populations under different climatic conditions. Here, we investigated seed trait variability and its environmental dependency across a latitudinal gradient of two widely distributed dune-engineering species (Thinopyrum junceum and Calamagrostis arenaria). Seed germination responses against temperature and seed mass were compared within and among six populations exposed to a gradient of temperature and precipitation regimes (Spiekeroog, DE; Bordeaux, FR; Valencia, ES; Cagliari, IT, Rome, IT; Venice, IT). Seed germination showed opposite trends in response to temperature experienced during emergence in both species: with some expectation, in populations exposed to severe winters, seed germination was warm-cued, whereas in populations from warm sites with dry summer, seed germination was cold-cued. In C. arenaria, variability in seed germination responses disappeared once the seed coat was incised. Seed mass from sites with low precipitation was smaller than that from sites with higher precipitation and was better explained by rainfall continentality than by aridity in summer. Within-population variability in seed germination accounted for 5 to 54%, while for seed mass it was lower than 40%. Seed trait variability can be considerable both within- and among-populations even at broad spatial scale. The variability may be hardly predictable since it only partially correlated with the analyzed climatic variables, and with expectation based on the climatic features of the seed site of origin. Considering seed traits variability in the analysis of ecological processes at both within- and among-population levels may help elucidate unclear patterns of species dynamics, thereby contributing to plan adequate measures to counteract biodiversity loss.},
}
@article {pmid36033213,
year = {2022},
author = {Pho, AT and Mangal, S and Bakken, S},
title = {Human Papillomavirus Vaccination Among Transgender and Gender Diverse People in the United States: An Integrative Review.},
journal = {Transgender health},
volume = {7},
number = {4},
pages = {303-313},
pmid = {36033213},
issn = {2688-4887},
abstract = {OBJECTIVE: This integrative review explores the barriers to and facilitators for human papillomavirus (HPV) vaccination among adult transgender and gender diverse (TGD) people in the United States.<br><br>DATA SOURCE: A systematic search of electronic databases included PubMed/MEDLINE, CINAHL, and EMBASE from 1985 to 2020.<br><br>Inclusion criteria included studies from the United States that described HPV vaccination barriers or facilitators and included adult TGD participants, both quantitative and qualitative studies. Exclusion criteria were studies that reported only HPV vaccine prevalence, non-English/non-U.S. studies, and studies limited to pediatric populations.<br><br>DATA EXTRACTION: Two investigators used Covidence software to screen studies and manage data extraction. Quality of the quantitative studies was appraised using a checklist proposed by the Joanna Briggs Institute (JBI); qualitative studies were appraised using quality criteria informed by the literature.<br><br>DATA SYNTHESIS: The Social Ecological Model guided the review to organize barriers to and facilitators for HPV vaccination at the patient-, provider-, and system-levels.<br><br>RESULTS: Database searches and hand-searching yielded 843 citations. After screening, eight articles were retained in the review. Seven were cross-sectional studies and one was a qualitative focus-group. All retained quantitative studies met six of the eight JBI quality checklist items.<br><br>CONCLUSION: The low proportion of TGD participants in the retained studies highlights a gap in knowledge about HPV vaccination among this population. Future studies of HPV vaccination should recruit TGD people to better represent their perspectives.},
}
@article {pmid36032727,
year = {2022},
author = {Kenzie, ES and Parks, EL and Carney, N and Wakeland, W},
title = {System dynamics modeling for traumatic brain injury: Mini-review of applications.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {10},
number = {},
pages = {854358},
pmid = {36032727},
issn = {2296-4185},
abstract = {Traumatic brain injury (TBI) is a highly complex phenomenon involving a cascade of disruptions across biomechanical, neurochemical, neurological, cognitive, emotional, and social systems. Researchers and clinicians urgently need a rigorous conceptualization of brain injury that encompasses nonlinear and mutually causal relations among the factors involved, as well as sources of individual variation in recovery trajectories. System dynamics, an approach from systems science, has been used for decades in fields such as management and ecology to model nonlinear feedback dynamics in complex systems. In this mini-review, we summarize some recent uses of this approach to better understand acute injury mechanisms, recovery dynamics, and care delivery for TBI. We conclude that diagram-based approaches like causal-loop diagramming have the potential to support the development of a shared paradigm of TBI that incorporates social support aspects of recovery. When developed using adequate data from large-scale studies, simulation modeling presents opportunities for improving individualized treatment and care delivery.},
}
@article {pmid36030325,
year = {2022},
author = {Cooney, DB and Rossine, FW and Morris, DH and Levin, SA},
title = {A PDE Model for Protocell Evolution and the Origin of Chromosomes via Multilevel Selection.},
journal = {Bulletin of mathematical biology},
volume = {84},
number = {10},
pages = {109},
doi = {10.1007/s11538-022-01062-y},
pmid = {36030325},
issn = {1522-9602},
mesh = {*Artificial Cells ; Chromosomes ; Genome ; Mathematical Concepts ; Models, Biological ; },
abstract = {The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper, we formulate a minimal model of the evolution of proto-chromosomes within protocells. We model a simple protocell composed of two types of genes: a "fast gene" with an advantage for gene-level self-replication and a "slow gene" that replicates more slowly at the gene level, but which confers an advantage for protocell-level reproduction. Protocell-level replication capacity depends on cellular composition of fast and slow genes. We use a partial differential equation to describe how the composition of genes within protocells evolves over time under within-cell and between-cell competition, considering an infinite population of protocells that each contain infinitely many genes. We find that the gene-level advantage of fast replicators casts a long shadow on the multilevel dynamics of protocell evolution: no level of between-protocell competition can produce coexistence of the fast and slow replicators when the two genes are equally needed for protocell-level reproduction. By introducing a "dimer replicator" consisting of a linked pair of the slow and fast genes, we show analytically that coexistence between the two genes can be promoted in pairwise multilevel competition between fast and dimer replicators, and provide numerical evidence for coexistence in trimorphic competition between fast, slow, and dimer replicators. Our results suggest that dimerization, or the formation of a simple chromosome-like dimer replicator, can help to overcome the shadow of lower-level selection and work in concert with deterministic multilevel selection in protocells featuring high gene copy number to allow for the coexistence of two genes that are complementary at the protocell level but compete at the level of individual gene-level replication. These results for the PDE model complement existing results on the benefits of dimerization in the case of low genetic copy number, for which it has been shown that genetic linkage can help to overcome the stochastic loss of necessary genetic templates.},
}
@article {pmid36016080,
year = {2022},
author = {Yousaf, M and Ullah, A and Sarosh, N and Abbasi, SW and Ismail, S and Bibi, S and Hasan, MM and Albadrani, GM and Talaat Nouh, NA and Abdulhakim, JA and Abdel-Daim, MM and Bin Emran, T},
title = {Design of Multi-Epitope Vaccine for Staphylococcus saprophyticus: Pan-Genome and Reverse Vaccinology Approach.},
journal = {Vaccines},
volume = {10},
number = {8},
pages = {},
pmid = {36016080},
issn = {2076-393X},
support = {PNURSP2022R30//This research was supported by Princess Nourah bint Abdulrahman University Researchers Supporting Project number (PNURSP2022R30), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia./ ; },
abstract = {Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E. coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.},
}
@article {pmid36016053,
year = {2022},
author = {Tropea, M and Fedele, G and De Luca, R and Miriello, D and De Rango, F},
title = {Automatic Stones Classification through a CNN-Based Approach.},
journal = {Sensors (Basel, Switzerland)},
volume = {22},
number = {16},
pages = {},
pmid = {36016053},
issn = {1424-8220},
mesh = {Bayes Theorem ; Cluster Analysis ; Machine Learning ; *Neural Networks, Computer ; *Support Vector Machine ; },
abstract = {This paper presents an automatic recognition system for classifying stones belonging to different Calabrian quarries (Southern Italy). The tool for stone recognition has been developed in the SILPI project (acronym of "Sistema per l'Identificazione di Lapidei Per Immagini"), financed by POR Calabria FESR-FSE 2014-2020. Our study is based on the Convolutional Neural Network (CNNs) that is used in literature for many different tasks such as speech recognition, neural language processing, bioinformatics, image classification and much more. In particular, we propose a two-stage hybrid approach based on the use of a model of Deep Learning (DL), in our case the CNN, in the first stage and a model of Machine Learning (ML) in the second one. In this work, we discuss a possible solution to stones classification which uses a CNN for the feature extraction phase and the Softmax or Multinomial Logistic Regression (MLR), Support Vector Machine (SVM), k-Nearest Neighbors (kNN), Random Forest (RF) and Gaussian Naive Bayes (GNB) ML techniques in order to perform the classification phase basing our study on the approach called Transfer Learning (TL). We show the image acquisition process in order to collect adequate information for creating an opportune database of the stone typologies present in the Calabrian quarries, also performing the identification of quarries in the considered region. Finally, we show a comparison of different DL and ML combinations in our Two-Stage Hybrid Model solution.},
}
@article {pmid36007741,
year = {2022},
author = {Ali, A and Farhan, SB and Zhang, Y and Nasir, J and Farhan, H and Zamir, UB and Gao, H},
title = {Changes in temporal pattern and spatial distribution of environmental pollutants in 8 Asian countries owing to COVID-19 pandemic.},
journal = {Chemosphere},
volume = {308},
number = {Pt 1},
pages = {136075},
pmid = {36007741},
issn = {1879-1298},
mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; *COVID-19/epidemiology ; Carbon Monoxide/analysis ; Environmental Monitoring/methods ; *Environmental Pollutants ; Formaldehyde ; Humans ; Nitrogen Dioxide/analysis ; *Ozone/analysis ; Pakistan ; Pandemics ; Particulate Matter/analysis ; Sulfur Dioxide/analysis ; },
abstract = {This study investigated the changes in air pollutant's concentration, spatio-temporal distribution and sensitivity of changes in air pollutant's concentration during pre and post COVID-19 outbreak. We employed Google Earth Engine Platform to access remote sensing datasets of air pollutants across Asian continent. Air pollution and cumulative confirmed-COVID cases data of Asian countries (Afghanistan, Bangladesh, China, India, Iran, Iraq, Pakistan, and Saudi Arabia) have been collected and analyzed for 2019 and 2020. The results indicate that aerosol index (AI) and nitrogen dioxide (NO2) is significantly reduced during COVID outbreak i.e. in year 2020. In addition, we found significantly positive (P < 0.05, 95% confidence interval, two-tailed) correlation between changes in AI and NO2 concentration for net active-COVID case increment in almost each country. For other atmospheric gases i.e. carbon monoxide (CO), formaldehyde (HCHO), ozone (O3), and Sulfur dioxide (SO2), insignificant and/or significant negative correlation is also observed. These results suggest that the atmospheric concentration of AI and NO2 are good indicators of human activities. Furthermore, the changes in O3 shows significantly negative correlation for net active-COVID case increment. In conclusion, we observed significant positive environmental impact of COVID-19 restrictions in Asia. This study would help and assist environmentalist and policy makers in restraining air pollution by implementing efficient restrictions on human activities with minimal economic loss.},
}
@article {pmid36007087,
year = {2022},
author = {Wang, Y and Cai, G and Yang, L and Zhang, N and Du, M},
title = {Monitoring of urban ecological environment including air quality using satellite imagery.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0266759},
pmid = {36007087},
issn = {1932-6203},
mesh = {*Air Pollution ; China ; Environment ; Environmental Monitoring/methods ; Remote Sensing Technology ; *Satellite Imagery ; },
abstract = {Rapid urbanisation has highlighted problems in the urban ecological environment and stimulated research on the evaluation of urban environments. In previous studies, key factors such as greenness, wetness, and temperature were extracted from satellite images to assess the urban ecological environment. Although air pollution has become increasingly serious as urbanisation proceeds, information on air pollution is not included in existing models. The Sentinel-5P satellite launched by the European Space Agency in 2017 is a reliable data source for monitoring air quality. By making full use of images from Landsat 8, Sentinel-2A, and Sentinel-5P, this work attempts to construct a new remote sensing monitoring index for urban ecology by adding air quality information to the existing remote sensing ecological index. The proposed index was tested in the Beijing metropolitan area using satellite data from 2020. The results obtained using the proposed index differ greatly in the central urban region and near large bodies of water from those obtained using the existing remote sensing monitoring model, indicating that air quality plays a significant role in evaluating the urban ecological environment. Because the model constructed in this study integrates information on vegetation, soil, humidity, heat, and air quality, it can comprehensively and objectively reflect the quality of the urban ecological environment. Consequently, the proposed remote sensing index provides a new approach to effectively monitoring the urban ecological environment.},
}
@article {pmid35999898,
year = {2021},
author = {Waterhouse, RM and Adam-Blondon, AF and Agosti, D and Baldrian, P and Balech, B and Corre, E and Davey, RP and Lantz, H and Pesole, G and Quast, C and Glöckner, FO and Raes, N and Sandionigi, A and Santamaria, M and Addink, W and Vohradsky, J and Nunes-Jorge, A and Willassen, NP and Lanfear, J},
title = {Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR.},
journal = {F1000Research},
volume = {10},
number = {},
pages = {},
pmid = {35999898},
issn = {2046-1402},
support = {BB/CSP1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016855/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9783/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9814/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Biodiversity ; *Biological Science Disciplines ; Computational Biology ; Europe ; },
abstract = {Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.},
}
@article {pmid36002452,
year = {2022},
author = {Yang, C and Liu, H and Li, Q and Wang, X and Ma, W and Liu, C and Fang, X and Tang, Y and Shi, T and Wang, Q and Xu, Y and Zhang, J and Li, X and Xu, G and Chen, J and Su, M and Wang, S and Wu, J and Huang, L and Li, X and Wu, G},
title = {Human expansion into Asian highlands in the 21st Century and its effects.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {4955},
pmid = {36002452},
issn = {2041-1723},
mesh = {Asia ; Asia, Southeastern ; *Asian People ; *Ecosystem ; Humans ; },
abstract = {Most intensive human activities occur in lowlands. However, sporadic reports indicate that human activities are expanding in some Asian highlands. Here we investigate the expansions of human activities in highlands and their effects over Asia from 2000 to 2020 by combining earth observation data and socioeconomic data. We find that ∼23% of human activity expansions occur in Asian highlands and ∼76% of these expansions in highlands comes from ecological lands, reaching 95% in Southeast Asia. The expansions of human activities in highlands intensify habitat fragmentation and result in large ecological costs in low and lower-middle income countries, and they also support Asian developments. We estimate that cultivated land net growth in the Asian highlands contributed approximately 54% in preventing the net loss of the total cultivated land. Moreover, the growth of highland artificial surfaces may provide living and working spaces for ∼40 million people. Our findings suggest that highland developments hold dual effects and provide new insight for regional sustainable developments.},
}
@article {pmid36002035,
year = {2024},
author = {Polanowska, KE and Iwański, S and Leśniak, MM and Seniów, J},
title = {Computer-assisted training of executive functions in adult patients with non-progressive acquired brain damage - a pilot study on efficacy of a new therapeutic application.},
journal = {Applied neuropsychology. Adult},
volume = {31},
number = {6},
pages = {1180-1191},
doi = {10.1080/23279095.2022.2114354},
pmid = {36002035},
issn = {2327-9109},
mesh = {Humans ; *Executive Function/physiology ; Male ; Pilot Projects ; Female ; Middle Aged ; Adult ; *Brain Injuries/complications/rehabilitation ; *Therapy, Computer-Assisted ; Aged ; Problem Solving/physiology ; Activities of Daily Living ; Social Skills ; },
abstract = {Executive dysfunction is most often caused by post-traumatic or post-stroke damage to the prefrontal regions of the brain. The aim of this study was to compare the efficacy of two computer-assisted therapy programs for executive dysfunctions in patients with acquired brain injury. Patients were trained using either a newly developed application ExeSystem (designed to help improve the ability to manage and control one's own behavior by performing tasks imitating natural, everyday situations) or a combination of two commercial applications RehaCom and CogniPlus. Data collected after a three-week period of therapy conducted in two 15-person groups of participants indicated comparable efficacy of both therapy programs in improving quality of daily functioning, executive attention, as well as planning and problem-solving but not memory. The improvement in social competence (p = .028) was the only advantage of therapy with the ExeSystem. Therapeutic interactions using computer programs were shown to be positively evaluated by patients (p < .01). This study confirmed at least equal efficacy of computer-based executive function therapy using ExeSystem compared to RehaCom and CogniPlus. However, despite the implementation of a more ecological and comprehensive approach to the content of a new application, the benefits of this approach were limited.},
}
@article {pmid36001546,
year = {2022},
author = {Diodato, N and Borrelli, P and Panagos, P and Bellocchi, G},
title = {Global assessment of storm disaster-prone areas.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0272161},
pmid = {36001546},
issn = {1932-6203},
mesh = {*Disasters ; Geographic Information Systems ; Humans ; Hydrology ; *Rain ; Soil ; },
abstract = {BACKGROUND: Advances in climate change research contribute to improved forecasts of hydrological extremes with potentially severe impacts on human societies and natural landscapes. Rainfall erosivity density (RED), i.e. rainfall erosivity (MJ mm hm-2 h-1 yr-1) per rainfall unit (mm), is a measure of rainstorm aggressiveness and a proxy indicator of damaging hydrological events.<br><br>METHODS AND FINDINGS: Here, using downscaled RED data from 3,625 raingauges worldwide and log-normal ordinary kriging with probability mapping, we identify damaging hydrological hazard-prone areas that exceed warning and alert thresholds (1.5 and 3.0 MJ hm-2 h-1, respectively). Applying exceedance probabilities in a geographical information system shows that, under current climate conditions, hazard-prone areas exceeding a 50% probability cover ~31% and ~19% of the world's land at warning and alert states, respectively.<br><br>CONCLUSION: RED is identified as a key driver behind the spatial growth of environmental disruption worldwide (with tropical Latin America, South Africa, India and the Indian Archipelago most affected).},
}
@article {pmid36001047,
year = {2023},
author = {Shaffer, M and Thurimella, K and Sterrett, JD and Lozupone, CA},
title = {SCNIC: Sparse correlation network investigation for compositional data.},
journal = {Molecular ecology resources},
volume = {23},
number = {1},
pages = {312-325},
pmid = {36001047},
issn = {1755-0998},
support = {T15 LM009451/LM/NLM NIH HHS/United States ; 4 T15 LM009451-10//U.S. National Library of Medicine/ ; //National Science Foundation/ ; },
mesh = {*Software ; Algorithms ; *Microbiota ; },
abstract = {Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.},
}
@article {pmid36000659,
year = {2022},
author = {Santos, JS and Cruz, AJS and Ruas, CM and Pereira Júnior, EA and Mattos, FF and Klevens, M and Abreu, MHNG},
title = {Factors associated with the use of a public information system of dentist-prescribed antibiotics in Minas Gerais, Brazil.},
journal = {Ciencia &amp; saude coletiva},
volume = {27},
number = {9},
pages = {3741-3750},
doi = {10.1590/1413-81232022279.07422022},
pmid = {36000659},
issn = {1678-4561},
mesh = {*Anti-Bacterial Agents ; Brazil ; *Dentists ; Humans ; Information Systems ; Socioeconomic Factors ; },
abstract = {This article aims to investigate the association between socioeconomic factors, health care organizations, and the use of a management and monitoring system for the dispensing of antibiotics prescribed by dentists in public health services in Minas Gerais, Brazil. This is an ecological-epidemiological study that analyzed secondary data from the Integrated Pharmaceutical Care Management System (SIGAF) of the Department of Health of the state of MG, Brazil, in 2017. Thirteen independent variables were analyzed to assess their influence on municipal adherence to SIGAF system considering dental prescriptions of antibiotics. Descriptive statistical analyses were performed, and the Classification and Regression Tree technique was used to identify the municipal variables associated with the outcome. A total of 57,279 antibiotic courses prescribed by dentists and recorded in SIGAF were examined. Socioeconomic factors were not associated with the use of SIGAF to record these prescriptions. Oral healthcare coverage was positively associated with the use of SIGAF for the dispensing of antibiotics prescribed by dentists. Dental Specialties Center were negatively associated with the outcome. Municipalities with high oral healthcare coverage and those without a Dental Specialties Center were more likely to use SIGAF.},
}
@article {pmid35999848,
year = {2022},
author = {Kopperud, BT and Lidgard, S and Liow, LH},
title = {Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13921},
pmid = {35999848},
issn = {2167-8359},
mesh = {Animals ; *Biodiversity ; *Bryozoa ; Information Storage and Retrieval ; },
abstract = {We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.},
}
@article {pmid35990172,
year = {2022},
author = {Xiao, H and Xu, Z and Ren, J and Zhou, Y and Lin, R and Bao, S and Zhang, L and Lu, S and Lee, CKM and Liu, J},
title = {Navigating Chinese cities to achieve sustainable development goals by 2030.},
journal = {Innovation (Cambridge (Mass.))},
volume = {3},
number = {5},
pages = {100288},
pmid = {35990172},
issn = {2666-6758},
abstract = {Achieving the 17 United Nations sustainable development goals (SDGs) in China largely depends on the transition of cities toward sustainable development. However, significant knowledge gaps exist in evaluating the SDG index at the city scale and in understanding how to simulate pathways to achieve the 17 SDGs for Chinese cities by 2030. This study aimed to quantify the SDG index of 285 Chinese cities and developed a forecasting model to simulate the performance of each SDG in each city until 2030 using varied scenarios. The results indicated that although the SDG index in Chinese cities increased by 33.97% during 2005-2016, Chinese cities, which continued their past paths, achieved an average of only five SDGs by 2030. To promote the joint achievement of all SDGs, we designed different paths for all SDGs of each of the 285 cities and simulated their SDG index until 2030. Under the scenarios, 216 Chinese cities (75.79%) could achieve 9-13 more SDGs in 2030 and the overall SDG index can improve from 74.57 in 2030 to 97.49 (target score 100) by adopting more intensive path adjustment. We lastly determined a cost-effective path for each SDG of each city to promote joint achievement of all SDGs by 2030. The proposed simulation model and cost-effective path serve as a foundation for other countries to simulate SDG progress and develop pathways for achieving SDGs in the future.},
}
@article {pmid35990120,
year = {2022},
author = {Zhang, H},
title = {The Impact of Tax Reduction and Fee Reduction Based on Big Data Algorithm on the High-Quality Development of the Real Economy under the Action of Coupling Effect or Substitution Effect.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {2828687},
pmid = {35990120},
issn = {1687-5273},
mesh = {Algorithms ; *Big Data ; China ; Ecology ; *Economic Development ; },
abstract = {The basic idea of the mass of medical growth is to adhere to local market price thinking with a Chinese touch and follow the development policy of "quality first, efficiency first." It insists on properly handling a series of important relationships betwixt socialism and market economy, the first to drive the rich later, the government and the market, equality and efficiency, short-term growth and long-term development, China and the international economy, ecology and growth of the region. Under the guidance of the qualitative thinking theory, it combines the strategic goals of China's economic qualitative development and actively draws on the research results of other countries. It uses big data algorithms to focus on the impact of qualitative development on tax and income reduction in the real economy. It conducts research experiments on the impact of tax reduction and fee reduction based on big data algorithms on the top-notch growth of the real economy. Its experimental data show that: in 2018, the share of primary, tertiary, and primary sector in China's dimensional economy top-notch growth coordination index was 7.2%, 40.7%, and 52.2%, respectively. Its contribution rate to economic growth was 4.2%, 36.1%, and 59.7%, respectively. From these data, it can be concluded that the top-notch growth of the real economy is getting better and better under the influence of tax reduction and fee reduction by big data algorithms.},
}
@article {pmid35983321,
year = {2022},
author = {Zhu, Y and Ge, X and Wang, L and You, Y and Cheng, Y and Ma, J and Chen, F},
title = {Biochar rebuilds the network complexity of rare and abundant microbial taxa in reclaimed soil of mining areas to cooperatively avert cadmium stress.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {972300},
pmid = {35983321},
issn = {1664-302X},
abstract = {Understanding the interactions between the soil microbial communities and species is critical in the remediation of heavy metal-contaminated soil. Biochar has been widely applied as a stabilizer in the in situ remediation of cadmium (Cd)-contaminated soils in mining areas. However, the rebuilding of the microbial taxa of rare and abundant species by biochar and their cooperative resistance to Cd stress remains elusive. In this pursuit, the present study envisaged the effects of two types of biochars viz., poplar bark biochar (PB) and thiourea-modified poplar bark biochar (TP) on the rare and abundant bacterial and fungal taxa by using pot experiments. The results demonstrated that the PB and TP treatments significantly reduced the leached Cd content, by 35.13 and 68.05%, respectively, compared with the control group (CK), in the reclaimed soil of the mining area. The application of biochar significantly improved the physicochemical properties like pH and Soil Organic Matter (SOM) of the soil. It was observed that TP treatment was superior to the PB and CK groups in increasing the diversity of the soil abundant and rare species of microbial taxa. Compared with the CK group, the application of PB and TP enhanced and elevated the complexity of the microbial networks of rare and abundant taxa, increased the number and types of network core microorganisms, reshaped the network core microorganisms and hubs, and boosted the microbial resistance to Cd stress. Our results indicate the response of rare and abundant microbial taxa to biochar application and the mechanism of their synergistic remediation of Cd-contaminated soil, thereby providing technical feasibility for in situ remediation of Cd-contaminated soil in mining areas.},
}
@article {pmid35977400,
year = {2022},
author = {IJdema, F and De Smet, J and Crauwels, S and Lievens, B and Van Campenhout, L},
title = {Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {9},
pages = {},
pmid = {35977400},
issn = {1574-6941},
mesh = {Animals ; Bacteria/genetics ; *Diptera/microbiology ; Genes, rRNA ; Larva/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.},
}
@article {pmid35975694,
year = {2022},
author = {Orlando, CG and Possell, M and Price, C and Banks, PB and Mercorelli, L and McArthur, C},
title = {A new conceptual and quantitative approach to exploring and defining potential open-access olfactory information.},
journal = {The New phytologist},
volume = {236},
number = {4},
pages = {1605-1619},
pmid = {35975694},
issn = {1469-8137},
mesh = {*Odorants ; *Plants/chemistry ; Reproducibility of Results ; Trees/chemistry ; },
abstract = {All organisms emit odour, providing 'open-access' olfactory information for any receiver with the right sensory apparatus. Characterizing open-access information emitted by groups of organisms, such as plant species, provides the means to answer significant questions about ecological interactions and their evolution. We present a new conceptual framework defining information reliability and a practical method to characterize and recover information from amongst olfactory noise. We quantified odour emissions from two tree species, one focal group and one outgroup, to demonstrate our approach using two new R statistical functions. We explore the consequences of relaxing or tightening criteria defining information and, from thousands of odour combinations, we identify and quantify those few likely to be informative. Our method uses core general principles characterizing information while incorporating knowledge of how receivers detect and discriminate odours. We can now map information in consistency-precision reliability space, explore the concept of information, and test information-noise boundaries, and between cues and signals.},
}
@article {pmid35974327,
year = {2022},
author = {Garza, DR and von Meijenfeldt, FAB and van Dijk, B and Boleij, A and Huynen, MA and Dutilh, BE},
title = {Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {101},
pmid = {35974327},
issn = {2730-7182},
mesh = {Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; *Genome, Bacterial/genetics ; Genomics ; Humans ; Phylogeny ; Prokaryotic Cells ; },
abstract = {BACKGROUND: Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of gene products with each other and with the organism's external environment. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions.<br><br>RESULTS: We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. The frequency by which reactions are retained in functional networks when stochastic gene loss is simulated in diverse environments allowed us to disentangle the metabolic reactions whose presence depends on the metabolite composition of the external environment (constrained by "nutrition") from those that are independent of the environment (constrained by "nature"). By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets.<br><br>CONCLUSION: We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics.},
}
@article {pmid35972961,
year = {2022},
author = {Ramírez-Castañeda, V and Westeen, EP and Frederick, J and Amini, S and Wait, DR and Achmadi, AS and Andayani, N and Arida, E and Arifin, U and Bernal, MA and Bonaccorso, E and Bonachita Sanguila, M and Brown, RM and Che, J and Condori, FP and Hartiningtias, D and Hiller, AE and Iskandar, DT and Jiménez, RA and Khelifa, R and Márquez, R and Martínez-Fonseca, JG and Parra, JL and Peñalba, JV and Pinto-García, L and Razafindratsima, OH and Ron, SR and Souza, S and Supriatna, J and Bowie, RCK and Cicero, C and McGuire, JA and Tarvin, RD},
title = {A set of principles and practical suggestions for equitable fieldwork in biology.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {34},
pages = {e2122667119},
pmid = {35972961},
issn = {1091-6490},
mesh = {*Bioethical Issues ; *Biology/ethics ; Humans ; },
abstract = {Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.},
}
@article {pmid35972940,
year = {2022},
author = {Vimercati, G and Probert, AF and Volery, L and Bernardo-Madrid, R and Bertolino, S and Céspedes, V and Essl, F and Evans, T and Gallardo, B and Gallien, L and González-Moreno, P and Grange, MC and Hui, C and Jeschke, JM and Katsanevakis, S and Kühn, I and Kumschick, S and Pergl, J and Pyšek, P and Rieseberg, L and Robinson, TB and Saul, WC and Sorte, CJB and Vilà, M and Wilson, JRU and Bacher, S},
title = {The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity.},
journal = {PLoS biology},
volume = {20},
number = {8},
pages = {e3001729},
pmid = {35972940},
issn = {1545-7885},
support = {I 4011/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {*Biodiversity ; Ecosystem ; Human Activities ; Humans ; *Introduced Species ; },
abstract = {Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions.},
}
@article {pmid35969597,
year = {2022},
author = {Ramasawmy, M and Mu, Y and Clutterbuck, D and Pantelic, M and Lip, GYH and van der Feltz-Cornelis, C and Wootton, D and Williams, NH and Montgomery, H and Mallinson Cookson, R and Attree, E and Gabbay, M and Heightman, M and Alwan, NA and Banerjee, A and Lorgelly, P and , },
title = {STIMULATE-ICP-CAREINEQUAL (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways) study protocol: Defining usual care and examining inequalities in Long Covid support.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0271978},
pmid = {35969597},
issn = {1932-6203},
support = {COV-LT2-0043/DH_/Department of Health/United Kingdom ; },
mesh = {*COVID-19/complications/epidemiology/therapy ; Critical Pathways ; *Delivery of Health Care, Integrated ; Humans ; Longitudinal Studies ; Post-Acute COVID-19 Syndrome ; },
abstract = {INTRODUCTION: Individuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor. In a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients' experiences of stigma and discrimination.<br><br>METHODS AND ANALYSIS: A mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received.<br><br>ETHICS AND DISSEMINATION: Ethical approval was obtained from South Central-Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.},
}
@article {pmid35964757,
year = {2022},
author = {Loli, M and Kefalas, G and Dafis, S and Mitoulis, SA and Schmidt, F},
title = {Bridge-specific flood risk assessment of transport networks using GIS and remotely sensed data.},
journal = {The Science of the total environment},
volume = {850},
number = {},
pages = {157976},
doi = {10.1016/j.scitotenv.2022.157976},
pmid = {35964757},
issn = {1879-1026},
mesh = {*Floods ; *Geographic Information Systems ; Hydrology ; Reproducibility of Results ; Risk Assessment ; },
abstract = {A novel framework for the expedient assessment of flood risk to transportation networks focused on the response of the most critical and vulnerable infrastructure assets, the bridges, is developed, validated and applied. Building upon the recent French guidelines on scour risk (CEREMA, 2019), this paper delivers a thorough methodology, that incorporates three key, risk parameters: (i) the hydrodynamic loading, a hazard component of equal significance to scour, for the assessment of hazard; (ii) the correlation of select scour indicators with a new index relating to flow velocity, a primary measure of the adverse impacts of flow-structure interaction, enabling a more accurate and automated, assessment of bridge susceptibility to scour; (iii) the use of a new, comprehensive indicator, namely the Indicator of Flood Hazard Intensity (IFHI) which incorporates, in a simple yet efficient way, the key parameters controlling the severity of flood impact on bridges, namely flow velocity, floodwater height, flow obstruction, and sediment type. The framework is implemented for the analysis of flood risk in a case study area, considering an inventory of 117 bridges of diverse construction characteristics, which were affected by a major flood that impacted Greece in September 2020. The reliability of the method is validated against an extensive record of inspected and documented bridge damages. Regional scale analysis is facilitated by the adoption of the Multi-Criteria Decision-Making method for flood hazard indexing, considering geomorphological, meteorological, hydrological, and land use/cover data, based on the processing of remotely sensed imagery and openly available geospatial datasets in GIS.},
}
@article {pmid35964726,
year = {2022},
author = {Karimian, H and Zou, W and Chen, Y and Xia, J and Wang, Z},
title = {Landscape ecological risk assessment and driving factor analysis in Dongjiang river watershed.},
journal = {Chemosphere},
volume = {307},
number = {Pt 3},
pages = {135835},
doi = {10.1016/j.chemosphere.2022.135835},
pmid = {35964726},
issn = {1879-1298},
mesh = {China ; *Environmental Monitoring/methods ; Factor Analysis, Statistical ; Humans ; Risk Assessment ; *Rivers ; Urbanization ; },
abstract = {The ecological and environmental quality of Dongjiang river watershed has great influence on Guangdong, Hong Kong and Macao. The landscape ecological risk assessment model could effectively monitor and assess environmental quality. In this study, spatial autocorrelation and geographic detector methods were used to explore the spatial characteristics of landscape ecological risk and their driving factors in the Dongjiang river watershed for four decades. The results showed that the ecological risks of Dongjiang River Source Watershed are mainly classified as low and intermediate, which are distributed in the hilly regions and the marginal mountainous regions at the junction of the Xunwu and Dingnan counties. From 1980 to 2018, the area of regions with the low ecological risk increased by 587.01 km [2]. The size of regions with moderate, high and severe ecological risk decreased by 165.6 km [2], 258.82 km[2] and 162.58 km[2], respectively. Moreover, landscape ecological risk values exhibited an apparent spatial dependency, and high-risk areas cluster together. Among influencing factors, population density has the most significant impact on the change of landscape ecological risk in the Dongjiang river watershed, followed by elevation (DEM), human interface, vegetation index (NDVI), and urbanization level. However, the interaction of driving factors has a greater impact on the ecological risk of the Dongjiang river watershed than a single driving factor. The research provides good knowledge for environmental quality management, and the proposed methods can be used for other regions.},
}
@article {pmid35960845,
year = {2022},
author = {Amend, AS and Swift, SOI and Darcy, JL and Belcaid, M and Nelson, CE and Buchanan, J and Cetraro, N and Fraiola, KMS and Frank, K and Kajihara, K and McDermot, TG and McFall-Ngai, M and Medeiros, M and Mora, C and Nakayama, KK and Nguyen, NH and Rollins, RL and Sadowski, P and Sparagon, W and Téfit, MA and Yew, JY and Yogi, D and Hynson, NA},
title = {A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {33},
pages = {e2204146119},
pmid = {35960845},
issn = {1091-6490},
support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacteria ; *Ecosystem ; *Microbiota ; *Plants/microbiology ; },
abstract = {Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.},
}
@article {pmid35960769,
year = {2022},
author = {Ali, MA and Iqbal, MS and Ahmad, KS and Akbar, M and Mehmood, A and Hussain, SA and Arshad, N and Munir, S and Masood, H and Ahmad, T and Kaloi, GM and Islam, M},
title = {Plant species diversity assessment and monitoring in catchment areas of River Chenab, Punjab, Pakistan.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0272654},
pmid = {35960769},
issn = {1932-6203},
mesh = {Biodiversity ; *Ecosystem ; Humans ; Pakistan ; Plants ; Potassium ; *Rivers ; Soil/chemistry ; Trees ; },
abstract = {BACKGROUND: Biodiversity data is crucial for sustainable development and making decisions regarding natural resources and its conservation. The study goal was to use quantitative ecological approaches to determine the species richness and diversity of wild flora and the ultimate impact of environmental factors on vegetation dynamics.<br><br>METHODS: Quadrats having sizes of 1&#xd7;1 for herbs, 5&#xd7;5 for shrubs, and 10&#xd7;10 m2 for trees were used. Various phytosociological characteristics were investigated in association with a wide variety of environmental variables. Soil analysis based on texture, moisture, pH, electrical conductivity (EC), organic matter (OM), available potassium (K), and phosphorus (P) were examined. The existing state of vegetation along the River Chenab was assessed using SWOT analysis and a future conservation strategy was devised.<br><br>RESULTS: One hundred twenty different plant speies were divided into 51 families including 92 dicots, 17 monocots, 6 pteridophytes and 1 bryophyte species. Herbs accounted for 89 followed by shrubs (16 species) and trees (15 species). Correlation analysis revealed a highly positive correlation between relative density and relative frequency (0.956**). Shannon and Simpson's diversity indices elaborated that site 3 and 7 with clay loamy soil had non-significant alpha diversity and varies from site to site. Diversity analysis showed that site 10 was most diverse (22.25) in terms of species richness. The principal coordinate analysis expressed that different environmental variables including OM, soil pH, P, K, and EC affect vegetation significantly, therefore, loamy soil showed presence and dispersal of more vegetation as compared to loam, sandy and sandy loam soils. Further, 170 ppm of available potassium had significant affect on plant diversity and distribution.<br><br>CONCLUSION: Asteraceae family was found dominant as dicot while poaceae among monocot. Adhatoda vasica was one of the unique species and found in Head Maralla site. For evenness, site 3 had maximum value 0.971. Most of the soil represented loamy soil texture where site 2 and 4 possess high soil moisture content. SWOT analysis revealed strengths as people prefered plants for medicine, food and economic purposes. In weakness, agricultural practices, soil erosion and flooding affected the vegetation. In opportunities, Forest and Irrigation Departments were planting plants for the restoration of ecosystem. Threats include anthropogenic activities overgrazing, urbanization and road infrastructure at Head Maralla, habitat fragmentation at Head Khanki, and extensive fish farming at Head Qadirabad. Future conservation efforts should be concentrated on SWOT analysis outcome in terms of stopping illegal consumption of natural resources, restoration of plant biodiversity through reforestation, designating protected areas and multiplying rare species locally.},
}
@article {pmid35959935,
year = {2023},
author = {Stahlke, AR and Chang, J and Tembrock, LR and Sim, SB and Chudalayandi, S and Geib, SM and Scheffler, BE and Perera, OP and Gilligan, TM and Childers, AK and Hackett, KJ and Coates, BS},
title = {A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein.},
journal = {Genome biology and evolution},
volume = {15},
number = {3},
pages = {},
pmid = {35959935},
issn = {1759-6653},
mesh = {Animals ; *Insecticides/pharmacology ; *Bacillus thuringiensis/genetics ; Zea mays ; Sex Chromosomes ; *Lepidoptera ; Bacterial Proteins/genetics ; Plants, Genetically Modified ; Hemolysin Proteins/genetics ; *Moths/genetics ; Pest Control, Biological ; Larva ; },
abstract = {Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.},
}
@article {pmid35955104,
year = {2022},
author = {Zhou, X and Shen, D and Gu, X},
title = {Influences of Land Policy on Urban Ecological Corridors Governance: A Case Study from Shanghai.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {15},
pages = {},
pmid = {35955104},
issn = {1660-4601},
mesh = {Agriculture ; China ; Cities ; Conservation of Natural Resources ; Ecosystem ; *Forests ; *Policy ; },
abstract = {The analysis of land use change (LUC) characteristics and the impact of policies related to urban ecological space is required to improve spatial planning and to support decision making regarding green infrastructure (GI) investment. This study employed Geo-informatic Tupu analysis and Fluctuation Potential Tupu analysis methods to analyze the characteristics of LUC in an urban ecological corridor (EC). To help understand the influence of land use policy on GI governance and support the optimization of spatial planning, we proposed a situation-structure-implementation-outcome (SSIO) policy cascade analysis framework. SSIO takes "place" as its starting point, then couples the local policy with the governance structure to promote the sustainability of urban commons governance. The results show that the land use type within an EC in the city is mainly cultivated land. However, between 2009 and 2019, cultivated land, construction land, and facility agricultural land all showed a decreasing trend, while forest land and garden land types underwent increasing trends. The LUC Tupu unit highlights the transition from cultivated land to forest land. Forest land has the greatest increase in area and accounts for 52.34% of the area of increasing land use. Cultivated land shows the greatest decrease in area and accounts for 70.30% of the area of decreasing trends. Based on the local policy situation of the metropolis, a land policy governance mechanism can be constructed by the establishment of a governance structure with local government as the core, using land consolidation as the platform, taking ecological spatial planning and inefficient construction land reduction as typical policy tools, and experimentally integrating the concept of Nature-based Solutions (NbS). In general, these findings may be applicable to other rapidly urbanizing cities around the world that are developing complex land use policies for ecological space governance.},
}
@article {pmid35954991,
year = {2022},
author = {Wang, Q and Yang, K and Li, L and Zhu, Y},
title = {Assessing the Terrain Gradient Effect of Landscape Ecological Risk in the Dianchi Lake Basin of China Using Geo-Information Tupu Method.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {15},
pages = {},
pmid = {35954991},
issn = {1660-4601},
mesh = {China ; *Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; *Lakes ; Risk Assessment/methods ; },
abstract = {The assessment of landscape ecological risk (LER) in different terrain gradients is beneficial to ecological environmental protection and risk management in different terrain gradients. Due to the impact of urban expansion, the landscape pattern of the Dianchi Lake basin (DLB) changed obviously, resulting in significant spatial difference of LER. At present, the LER assessment of the DLB is not clear, and the evolution mechanism of LER in different terrain gradients has not been revealed. Based on the LER assessment model, the geo-information Tupu method, the terrain niche gradient, and distribution index, this paper analyzed the LER and its terrain gradient effect in the DLB of China. The conclusions are as follows: (1) Since 1995, the land use type has mainly changed from grassland and cultivated land to construction land in the DLB of China. (2) The LERs in the DLB of China were mainly low, med low, and med high due to the transformation of land use type. The dominance distribution of the low and high LER was obviously constrained by terrain gradient. While the dominance distribution of med-low LER expanded to med-high terrain gradient, the dominance distribution of the med-high LER decreased to med-low terrain gradient. (3) The Tupu LERs were mainly a stable type of "medium" risk and anaphase change type of "med-high to medium" risk. The dominant distribution regions of the stable type, the prophase change type, and the continuous change type were relatively stable; the anaphase and middle change type expanded to the higher terrain gradient, and the repeated change type decreased to the med-high terrain gradient. In the process of ecological risk management and protection in the DLB, attention should be paid to the water area structure and LER control in med-high and high terrain gradients.},
}
@article {pmid35954559,
year = {2022},
author = {Lamberti-Castronuovo, A and Valente, M and Aleni, C and Hubloue, I and Ragazzoni, L and Barone-Adesi, F},
title = {Using Ambulatory Care Sensitive Conditions to Assess Primary Health Care Performance during Disasters: A Systematic Review.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {15},
pages = {},
pmid = {35954559},
issn = {1660-4601},
mesh = {Ambulatory Care ; Ambulatory Care Sensitive Conditions ; Databases, Factual ; *Disasters ; Hospitalization ; Humans ; *Primary Health Care ; },
abstract = {Ambulatory care sensitive conditions (ACSCs) are health conditions for which appropriate primary care intervention could prevent hospital admission. ACSC hospitalization rates are a well-established parameter for assessing the performance of primary health care (PHC). Although this indicator has been extensively used to monitor the performance of PHC systems in peacetime, its consideration during disasters has been neglected. The World Health Organization (WHO) has acknowledged the importance of PHC in guaranteeing continuity of care during and after a disaster for avoiding negative health outcomes. We conducted a systematic review to evaluate the extent and nature of research activity on the use of ACSCs during disasters, with an eye toward finding innovative ways to assess the level of PHC function at times of crisis. Online databases were searched to identify papers. A final list of nine publications was retrieved. The analysis of the reviewed articles confirmed that ACSCs can serve as a useful indicator of PHC performance during disasters, with several caveats that must be considered. The reviewed articles cover several disaster scenarios and a wide variety of methodologies showing the connection between ACSCs and health system performance. The strengths and weaknesses of using different methodologies are explored and recommendations are given for using ACSCs to assess PHC performance during disasters.},
}
@article {pmid35951711,
year = {2022},
author = {Nishimura, T and Tokuda, IT and Miyachi, S and Dunn, JC and Herbst, CT and Ishimura, K and Kaneko, A and Kinoshita, Y and Koda, H and Saers, JPP and Imai, H and Matsuda, T and Larsen, ON and Jürgens, U and Hirabayashi, H and Kojima, S and Fitch, WT},
title = {Evolutionary loss of complexity in human vocal anatomy as an adaptation for speech.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6607},
pages = {760-763},
doi = {10.1126/science.abm1574},
pmid = {35951711},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Humans ; *Larynx/anatomy &amp; histology ; *Phonation ; Phonetics ; *Primates ; *Speech ; Speech Acoustics ; *Vocal Cords/anatomy &amp; histology ; },
abstract = {Human speech production obeys the same acoustic principles as vocal production in other animals but has distinctive features: A stable vocal source is filtered by rapidly changing formant frequencies. To understand speech evolution, we examined a wide range of primates, combining observations of phonation with mathematical modeling. We found that source stability relies upon simplifications in laryngeal anatomy, specifically the loss of air sacs and vocal membranes. We conclude that the evolutionary loss of vocal membranes allows human speech to mostly avoid the spontaneous nonlinear phenomena and acoustic