@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.

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.

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±sd change -0.12±0.22 versus -0.11±0.22). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a cohort of 109 318 patients admitted to hospital with COVID-19, EQ-5D-5L UI at 1 year remained similar between the two groups.

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.

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.

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.

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.},
}

Humans
Surveys and Questionnaires
Female
Male
Adult
*Internet
Consumer Health Information
Latent Class Analysis
Information Seeking Behavior
Fuzzy Logic
Young Adult
Middle Aged

@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 & 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.},
}

*Rosa/genetics/metabolism
*Volatile Organic Compounds/metabolism
*Odorants/analysis
*Genome, Plant
*Gene Expression Regulation, Plant
Gene Regulatory Networks
Genomics/methods
Eugenol/analogs & derivatives/metabolism
Plant Proteins/genetics/metabolism
Pollination
Multiomics

@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 & purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation & 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.},
}

*Nanopore Sequencing/methods
Metagenomics/methods
Plant Diseases/microbiology
Bacteria/genetics/isolation & purification/classification
Sequence Analysis, DNA/methods
Fungi/genetics/isolation & purification/classification
Plants/microbiology
Computational Biology/methods

@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).},
}

Canada
*Soil/chemistry
Databases, Factual
Ecosystem

@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.},
}

Humans
Adolescent
*Bariatric Surgery/methods
*Pediatric Obesity/surgery
Obesity, Morbid/surgery/psychology
Gastrectomy/methods

@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 = {},
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 {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.},
}

*Machine Learning
Humans
*Viruses/genetics
*Computational Biology/methods
*Host-Pathogen Interactions/genetics/physiology
Host Microbial Interactions/genetics/physiology

@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 & health},
volume = {50},
number = {7},
pages = {567-576},
doi = {10.5271/sjweh.4177},
pmid = {39292164},
issn = {1795-990X},
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.

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.

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.

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.},
}

*Bibliometrics
*Data Mining
Humans
*Occupational Medicine
Occupational Health

@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.},
}

*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

@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 = {},
doi = {10.3390/ijms25189813},
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.},
}

*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

@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 {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.},
}

*Solanum tuberosum/microbiology
*Fertilizers
*Nitrogen/analysis
*Soil Microbiology
Transcriptome
Metabolome/drug effects
Agriculture/methods
Metagenomics
Soil/chemistry
Multiomics

@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.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10021-022-00802-4.},
}

@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 = {},
number = {},
pages = {176490},
doi = {10.1016/j.scitotenv.2024.176490},
pmid = {39326744},
issn = {1879-1026},
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 repercussions of MPs as emerging pollutants on crops within the context of integrated pollution, providing novel insights into improving sustainability in agro-ecosystems.},
}

@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 {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.},
}

*Climate Change
*Artificial Intelligence
Animals
Big Data
Microclimate
Data Collection/methods

@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 {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.},
}

*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

@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.

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.

RESULTS: The database included a total of 107,340 children who were screened clinically, of whom 10,600 (9·9%) underwent transthoracic two-dimensional echocardiography. The overall prevalence of RHD was 2.22 cases per 1000 school-attending children (95% CI:1·94 - 2·50). The highest prevalence was observed among children living in the southern Terai ecological zone (2·89 per 1000, 95% CI (2·32-3·46)) of Nepal. Among the provinces, Karnali had the highest prevalence of RHD (3·45 per 1000, 95% CI (2·42-4·48)). Among the districts screened, Kalikot had the highest RHD prevalence (5.47 per 1000, 95% CI (3.02-7.92)).

CONCLUSION: Primordial, primary and secondary prevention programmes should pay special attention to southern Terai zone, particularly the under-privileged children from remote districts.},
}

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

@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 = {},
number = {},
pages = {},
pmid = {39313745},
issn = {2662-8465},
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 {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},
doi = {10.1371/journal.pcbi.1011609},
pmid = {39269993},
issn = {1553-7358},
mesh = {Animals ; Humans ; *Malaria/transmission/prevention & 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.},
}

Animals
Humans
*Malaria/transmission/prevention & control
*Anopheles/physiology
*Mosquito Vectors/physiology
*Mosquito Control/methods
*Software
Computational Biology
Models, Biological

@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},
doi = {10.1371/journal.pcbi.1012458},
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.},
}

*Computational Biology/methods
Models, Genetic
Biological Evolution
Evolution, Molecular
Animals
Models, Statistical
Humans

@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.},
}

*United States Environmental Protection Agency
*Databases, Factual
*Software
United States
Ecotoxicology/methods
Risk Assessment/methods
Reproducibility of Results

@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.

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 vitro and in 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.

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.},
}

Humans
*Precision Medicine
*MicroRNAs/genetics
*Diabetes Mellitus/therapy/genetics
*Biological Products/therapeutic use
*Global Health
Metabolomics
Computational Biology
Biomarkers/blood
Genomics

@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.},
}

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

@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.},
}

*Photosynthesis/physiology
*Synechocystis/metabolism/physiology
*Light
*Models, Biological
Computational Biology
Carbon Dioxide/metabolism
Carbon Cycle/physiology
Phycobilisomes/metabolism
Computer Simulation

@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&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.},
}

*Single-Cell Analysis/methods
*Polyploidy
Animals
Computational Biology/methods

@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 & Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {529},
pmid = {39309423},
issn = {2398-502X},
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 & 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},
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.},
}

Bangladesh
*Environmental Monitoring/methods
*Remote Sensing Technology
*Geographic Information Systems
*Conservation of Natural Resources
*Islands
*Ecosystem
Risk Assessment/methods
Humans
Bayes Theorem

@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},
doi = {10.1016/j.cell.2024.08.010},
pmid = {39303692},
issn = {1097-4172},
mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation & 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.},
}

Animals
*COVID-19/epidemiology/virology
*SARS-CoV-2/genetics/isolation & purification
*Animals, Wild/virology
*Phylogeny
Humans
Pandemics

@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.},
}

Humans
*Ecosystem
Mycobacterium ulcerans/pathogenicity
Buruli Ulcer/transmission/microbiology
Models, Biological
Computational Biology
Animals

@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.},
}

*Metagenomics/methods
*Metagenome
*Viruses/genetics/classification
*Computational Biology/methods
*Data Mining
*High-Throughput Nucleotide Sequencing
Humans
Animals

@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 & 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 & 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 = {},
number = {},
pages = {},
pmid = {39294496},
issn = {1546-1718},
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 {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 & 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 & numerical data ; Middle Aged ; Health Surveys ; Gender-Based Violence/statistics & numerical data ; Information Systems/statistics & 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.},
}

Humans
Brazil/epidemiology
Female
Adult
Young Adult
Adolescent
*Sex Offenses/statistics & numerical data
Middle Aged
Health Surveys
Gender-Based Violence/statistics & numerical data
Information Systems/statistics & numerical data
Information Sources

@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},
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 & dosage/adverse effects/therapeutic use ; *Interrupted Time Series Analysis ; Female ; Databases, Factual ; Electronic Health Records/statistics & 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.

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.

RESULTS: Regulatory interventions were associated with an immediate and significant decrease level of DID (the number of DDD dispensed per 100 000 inhabitants and day) and incidence. The DID was 70% less than expected 12 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.

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.},
}

Humans
Spain/epidemiology
*Norpregnadienes/administration & dosage/adverse effects/therapeutic use
*Interrupted Time Series Analysis
Female
Databases, Factual
Electronic Health Records/statistics & numerical data
Risk Evaluation and Mitigation
Male
Adult
Middle Aged

@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},
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},
doi = {10.1007/s11538-024-01353-6},
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.},
}

*Tumor Microenvironment/immunology
Humans
*Mathematical Concepts
*Models, Biological
*Neoplasms/pathology/immunology
Computer Simulation
Computational Biology
Macrophages/immunology/pathology

@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 & numerical data ; Treatment Outcome ; Health Care Costs/statistics & 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.

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.

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 (€2099) by 23.7% compared with dressings without TLC-NOSF (€2751) (p<0.001), as well as the resources used.

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.},
}

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 & numerical data
Treatment Outcome
Health Care Costs/statistics & numerical data

@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 {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.},
}

Animals
Chromosomes, Insect
Genome Size
*Genome, Insect
*Hymenoptera/genetics
Wasps/parasitology
Datasets as Topic

@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 = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.13881},
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/ ; },
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 = {},
doi = {10.3390/ma17174339},
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 = {},
doi = {10.3390/plants13172353},
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 = {},
doi = {10.3390/ijms25179297},
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.},
}

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

@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 & evolution},
volume = {},
number = {},
pages = {},
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.},
}

Animals
*Phylogeny
*Orthoptera/genetics/classification
Transcriptome/genetics
Computational Biology/methods
DNA Probes/genetics
Evolution, Molecular

@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.},
}

*Environmental Pollutants/toxicity
*Ecotoxicology/methods
*Proteomics
Genomics
Metabolomics
Animals
Humans
Multiomics

@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 {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},
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 {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},
doi = {10.1371/journal.pcbi.1011914},
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.},
}

*Algorithms
*Computational Biology/methods
*Software
Models, Biological
Machine Learning
Computer Graphics
Models, Statistical
Humans

@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 {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},
doi = {10.1371/journal.pone.0308013},
pmid = {39264914},
issn = {1932-6203},
mesh = {*Flowers/genetics/metabolism/growth & 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.},
}

*Flowers/genetics/metabolism/growth & development
*Gene Expression Regulation, Plant
*Gene Expression Profiling
*Fraxinus/genetics
*Transcriptome
Signal Transduction/genetics
Plant Proteins/genetics/metabolism
Gene Ontology
Genes, Plant

@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},
doi = {10.1002/bdr2.2395},
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).

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.

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.

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.},
}

Humans
*Environmental Pollutants
*Databases, Factual
Risk Assessment/methods
Environmental Exposure/adverse effects
United States
United States Environmental Protection Agency
Pesticides/adverse effects/toxicity

@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},
doi = {10.3897/BDJ.12.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.

NEW INFORMATION: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb & Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam & 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 Prószyński & 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 PhintellaBösenberg & Strand, 1906, SilerSimon, 1889, Phintelloides Kanesharatnam & Benjamin, 2019 andProszynskiaKanesharatnam & Benjamin, 2019. The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam & 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(Bösenberg & 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, ÅJ 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},
doi = {10.12688/f1000research.134798.2},
pmid = {39262445},
issn = {2046-1402},
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.

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.

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.

CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.},
}

*Metagenomics/methods
Humans
*Metadata
High-Throughput Nucleotide Sequencing/methods
Software
Metagenome
Computational Biology/methods
DNA, Ancient/analysis

@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 & Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {214},
doi = {10.12688/wellcomeopenres.19252.1},
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 {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},
doi = {10.12688/wellcomeopenres.21627.1},
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},
doi = {10.12688/wellcomeopenres.20841.1},
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},
doi = {10.1098/rsif.2024.0301},
pmid = {39257281},
issn = {1742-5662},
support = {//Helmholtz-Gemeinschaft/ ; //Bundesministerium für Bildung und Forschung/ ; //Sächsisches Staatsministerium für Wissenschaft und Kunst/ ; },
mesh = {*COVID-19/epidemiology/prevention & control ; Humans ; New Zealand/epidemiology ; Switzerland/epidemiology ; Germany/epidemiology ; *SARS-CoV-2 ; Pandemics/prevention & 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.},
}

*COVID-19/epidemiology/prevention & control
Humans
New Zealand/epidemiology
Switzerland/epidemiology
Germany/epidemiology
*SARS-CoV-2
Pandemics/prevention & control

@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 = {},
doi = {10.1093/gigascience/giae054},
pmid = {39250076},
issn = {2047-217X},
support = {//European Cooperation in Science and Technology/ ; //Fundação para a Ciência 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.},
}

Animals
*Venoms
*Internet
*Computational Biology/methods
*Big Data
Databases, Factual

@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 & 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.},
}

Animals
*Zebrafish
*Ethinyl Estradiol/toxicity
*Water Pollutants, Chemical/toxicity
Endocrine Disruptors/toxicity
Transcriptome/drug effects
Multiomics

@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.},
}

*Alzheimer Disease/classification/physiopathology/diagnosis
Humans
*Electroencephalography/methods
*Signal Processing, Computer-Assisted
Male
Female
Databases, Factual
Aged

@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 {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.},
}

Animals
*Copepoda/drug effects
*Mercury/toxicity
*Water Pollutants, Chemical/toxicity
*Microplastics/toxicity
Reproduction/drug effects
Apoptosis/drug effects
Proteomics
Multiomics

@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 {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},
doi = {10.1371/journal.pone.0295662},
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.},
}

*Databases, Factual
*Metadata
Isotopes
Internet

@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 {pmid39238468,
year = {2024},
author = {Liu, L and Liu, Y and Min, L and Zhou, Z and He, X and Xie, Y and Cao, W and Deng, S and Lin, X and He, X and Chen, X},
title = {Most pleiotropic effects of gene knockouts are evolutionarily transient in yeasts.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae189},
pmid = {39238468},
issn = {1537-1719},
abstract = {Pleiotropy, the phenomenon in which a single gene influences multiple traits, is a fundamental concept in genetics. However, the evolutionary mechanisms underlying pleiotropy require further investigation. In this study, we conducted parallel gene knockouts targeting 100 transcription factors in two strains of Saccharomyces cerevisiae. We systematically examined and quantified the pleiotropic effects of these knockouts on gene expression levels for each transcription factor. Our results showed that the knockout of a single gene generally affected the expression levels of multiple genes in both strains, indicating various degrees of pleiotropic effects. Strikingly, the pleiotropic effects of the knockouts change rapidly between strains in different genetic backgrounds, and ∼85% of them were non-conserved. Further analysis revealed that the conserved effects tended to be functionally associated with the deleted transcription factors, while the non-conserved effects appeared to be more ad hoc responses. In addition, we measured 184 yeast cell morphological traits in these knockouts and found consistent patterns. In order to investigate the evolutionary processes underlying pleiotropy, we examined the pleiotropic effects of standing genetic variations in a population consisting of ∼1000 hybrid progenies of the two strains. We observed that newly evolved expression quantitative trait loci (eQTLs) impacted the expression of a greater number of genes than did old eQTLs, suggesting that natural selection is gradually eliminating maladaptive or slightly deleterious pleiotropic responses. Overall, our results show that, although being prevalent for new mutations, the majority of pleiotropic effects observed are evolutionarily transient, which explains how evolution proceeds despite complicated pleiotropic effects.},
}

@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.},
}

*Metagenomics/methods
*Computational Biology/methods
*Food Microbiology/methods
*Bacteria/genetics
*High-Throughput Nucleotide Sequencing/methods
Metagenome
Microbiota/genetics

@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},
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.},
}

China
*Rivers
*Ecosystem
*Environmental Monitoring/methods
Conservation of Natural Resources
Plant Development
Geographic Information Systems
Plants

@article {pmid39233066,
year = {2024},
author = {Wen, J and Chuai, X and Xiang, A and Liu, Y and Wang, T and Xu, 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 = {},
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 {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.},
}

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

@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 = {1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support/ ; 1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Pittsburgh Supercomputing Center/ ; },
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.},
}

*Phylogeny
*DNA Barcoding, Taxonomic/methods
Computational Biology/methods
DNA, Environmental/genetics
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods

@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.

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.

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.

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.

LEVEL OF EVIDENCE: Level 3.},
}

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

@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},
doi = {10.1098/rstb.2022.0525},
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'.},
}

Animals
Female
*Reproduction
*Reindeer/physiology
Newfoundland and Labrador
Social Behavior
Geographic Information Systems

@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},
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 {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 = {},
number = {},
pages = {e2403393},
doi = {10.1002/advs.202403393},
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/ ; },
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 & control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention & 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.

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.

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.

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.},
}

*RNA, Ribosomal, 16S/genetics
*Klebsiella pneumoniae/virology/genetics
*Intensive Care Units
*Decontamination/methods
*Bacteriophages/genetics
Humans
Polymerase Chain Reaction/methods
Cross Infection/prevention & control/microbiology
Disinfectants/pharmacology
Klebsiella Infections/prevention & control/microbiology
Sequence Analysis, DNA

@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 = {},
number = {},
pages = {124871},
doi = {10.1016/j.envpol.2024.124871},
pmid = {39222768},
issn = {1873-6424},
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 = {},
doi = {10.1093/bib/bbae424},
pmid = {39222062},
issn = {1477-4054},
support = {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.},
}

Humans
*Microbiota/genetics
*Metagenomics/methods
Computational Biology/methods
Metagenome
High-Throughput Nucleotide Sequencing/methods
Software
Algorithms
Sequence Analysis, DNA/methods

@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.},
}

China
*Floods
*Cities
Models, Theoretical
Geographic Information Systems
Socioeconomic Factors

@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.},
}

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

@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 & 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.},
}

*Ginkgo biloba/genetics/embryology
*Seeds/genetics/growth & development
Imaging, Three-Dimensional/methods
Gene Expression Regulation, Plant
Plant Proteins/metabolism/genetics
X-Ray Microtomography
Cotyledon/genetics
Multiomics