@article {pmid37741542, year = {2023}, author = {Chen, H and Zhang, X and Ji, C and Deng, W and Yang, G and Hao, Z and Chen, B}, title = {Physicochemical properties of environmental media can affect the adsorption of arsenic (As) by microplastics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122592}, doi = {10.1016/j.envpol.2023.122592}, pmid = {37741542}, issn = {1873-6424}, abstract = {Microplastics are emerging pollutants that can adsorb heavy metals and threaten human health through food chain. Recently, there has been increasing interest in understanding the adsorption behavior of heavy metals by microplastics in farmland soil. In particular, arsenic (As), as a carcinogen, has the potential to be adsorbed by soil microplastics. However, the mechanisms and controlling factors of As adsorption by microplastics in farmland soil under natural conditions are still unknown. Here, microplastics and As were respectively added to farmland soils with different physicochemical properties from twelve provinces of China for adsorption experiment. We performed surface analysis of microplastics, quantified As accumulation through quasi-first-order kinetic equation and developed regression models to screen the factors controlling As adsorption. The results showed that the adsorption of As by soil microplastics was a chemical process accompanied by the loss of electrons from oxygen-containing functional groups. Soil cation exchange capacity (CEC) was the main factor controlling the adsorption rate, while soil organic matter (SOM), total nitrogen (TN) and CEC mainly influenced the equilibrium adsorption capacity. This is the first report on microplastic-As adsorption in natural soil, which allows deeper insights into risk assessment, prediction and control of microplastic-As pollution in agricultural soil.}, }
@article {pmid37737917, year = {2023}, author = {Miletić, S and Beloica, J and Perović, V and Miljković, P and Lukić, S and Obradović, S and Čakmak, D and Belanović-Simić, S}, title = {Environmental sensitivity assessment and land degradation in southeastern Serbia: application of modified MEDALUS model.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {10}, pages = {1241}, pmid = {37737917}, issn = {1573-2959}, mesh = {*Environmental Monitoring ; Serbia ; *Benchmarking ; Databases, Factual ; Droughts ; }, abstract = {This paper aims to improve the methodology and results accuracy of MEDALUS model for assessing land degradation sensitivity through the application of different data detail levels and by introducing the application of Ellenberg indices in metrics related to vegetation drought sensitivity assessment. For that purpose, the MEDALUS model was applied at 2 levels of detail. Level I (municipality level) implied the use of available large-scale databases and level II (watershed) contains more detailed information about vegetation used in the calculation of the VQI and MQI factors (Fig. S6). The comparison was made using data based on CORINE Land Cover (2012) and forest inventory data, complemented with object-based classification. Results showed that data based on forest inventory data with the application of Ellenberg's indices and object-based classification have one class more, critical (C1 and C2) and that the percentage distribution of classes is different in both quantitative (area size of class sensitivity) and qualitative (aggregation and dispersion of sensitivity classes). The use of data from Forest Management Plans and the application of Ellenberg's indices affect the quality of the results and find its application in the model, especially if these results are used for monitoring and land area management on fine scales. Remote sensed data images (Sentinel-2B) were introduced into the methodology as a very important environmental monitoring tool and model results validation.}, }
@article {pmid37736012, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Rustic Shoulder-knot, Apamea sordens (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {51}, pmid = {37736012}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Apamea sordens (the Rustic Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 614 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length.}, }
@article {pmid37733803, year = {2023}, author = {Engloner, AI and Vargha, M and Kós, P and Borsodi, AK}, title = {Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0292057}, pmid = {37733803}, issn = {1932-6203}, mesh = {*Plankton/genetics ; Climate Change ; Seasons ; Rivers ; Global Warming ; *Gammaproteobacteria ; }, abstract = {In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.}, }
@article {pmid37660507, year = {2023}, author = {Isoyama, K and Matsuura, M and Hayasaka, M and Nagao, S and Nishimura, Y and Yoshioka, T and Imai, Y and Miyagi, E and Suzuki, Y and Saito, T}, title = {Nationwide trends in and regional factors associated with minimally invasive hysterectomy for benign indications in Japan.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {289}, number = {}, pages = {129-135}, doi = {10.1016/j.ejogrb.2023.08.388}, pmid = {37660507}, issn = {1872-7654}, mesh = {Female ; Humans ; Japan/epidemiology ; Retrospective Studies ; *Laparoscopy ; Databases, Factual ; Hysterectomy ; }, abstract = {OBJECTIVE: To examine the prevalence trends of minimally invasive hysterectomy for benign indications in Japan and investigate regional disparities.<br><br>STUDY DESIGN: A retrospective cohort and ecological study using "The National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) Open Data".<br><br>SETTING: Nationwide Japan.<br><br>PATIENTS: Individuals who underwent hysterectomy for benign indications from 2014 to 2020.<br><br>INTERVENTIONS: Trend analysis of minimally invasive surgery (MIS) rates through laparoscopic hysterectomies (LH) and robotic-assisted laparoscopic hysterectomies (RA-LH) at the national and prefecture levels. Examination of regional factors contributing to the disparity in MIS implementation rates by second medical service area (SMSA).<br><br>RESULTS: The number of LH has increased from 16,016 in 2014 to 27,755 in 2020. The nationwide MIS hysterectomy rate increased from 29% in 2014 to 55% in 2020 (p&#xa0;less than&#xa0;0.001). More than 50% of hysterectomies have been performed as MIS since 2019. There was an increasing trend in MIS rates in all age groups. All prefectures except one showed a significant upward trend (p&#xa0;less than&#xa0;0.05) in the MIS rates, but MIS rates varied widely (23-84%). In a multivariable model, the MIS was more likely to be performed in the SMSAs in western Japan (p&#xa0;=&#xa0;0.011), in the SMSAs where the number of laparoscopy-qualified gynecologists is 5-10 (p&#xa0;=&#xa0;0.013), and 11 or higher (p&#xa0;less than&#xa0;0.001).<br><br>CONCLUSIONS: This study reveals a shift towards minimally invasive surgery (MIS) in total hysterectomy procedures in Japan. However, significant disparities in the prevalence of MIS hysterectomy exist, potentially influenced by the number of laparoscopy-qualified gynecologists.}, }
@article {pmid37744128, year = {2021}, author = {Otto, EC and Held, BW and Gould, TJ and Blanchette, RA}, title = {Fungal Diversity in Multiple Post-harvest Aged Red Pine Stumps and Their Potential Influence on Heterobasidion Root Rot in Managed Stands Across Minnesota.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {782181}, pmid = {37744128}, issn = {2673-6128}, abstract = {Thinning operations that occur in managed red pine (Pinus resinosa) stands, create tree stumps that can serve as a habitat for fungi, especially Heterobasidion irregulare, the cause of a serious root disease. Different fungi can colonize stumps early and the community of fungi can change over time as initial fungal species become replaced. Samples were collected from both the native and non-native range of red pine from stumps that were cut at different time periods. Stumps that were harvested at 0-1, 2-3, 5-6, and 10-12 years before sampling were used to provide data on the diversity of fungi that colonize tree stumps and how these communities can change over time as well as how they influence colonization of H. irregulare. Traditional culturing methods and Illumina MiSeq sequencing were used to identify the fungi in the samples. Of particular interest was Phlebiopsis gigantea, which can colonize cut stumps and prevent H. irregulare from becoming established. Overall, P. gigantea was the most abundant fungus isolated and sequenced via Illumina MiSeq. Results show that Phlebiopsis gigantea was isolated from 90% of all stumps sampled for sites harvested within 3 years of sampling in the native range of red pine compared to 33% in the non-native range. For Illumina MiSeq, 5,940 total amplicon sequence variants (ASVs) were detected. P. gigantea represented 14% of the total reads and composed 19% of the reads in the native range and 8% in non-native range of red pine. Furthermore, P. gigantea represented 38% of the reads for stumps that were harvested within 3 years of sampling in the native range of red pine compared to 14% in the non-native range. These results help demonstrate that a higher amount of P. gigantea is present in the native range of red pine and could be acting as a native biological control agent. Additional fungi, including Resinicium bicolor, Hypochnicium cremicolor, Leptographium spp., and others identified at different cutting times are also discussed. Finally, different diversity indices revealed similar, but slightly higher diversity for southern sites via Shannon and Simpson Diversity indices. Beta diversity demonstrated a similar species composition in stumps harvested at different times with these stumps being grouped together based on harvesting years.}, }
@article {pmid37731848, year = {2023}, author = {Ohashi, K and Osanai, T and Fujiwara, K and Tanikawa, T and Tani, Y and Takamiya, S and Sato, H and Morii, Y and Ogasawara, K}, title = {Access to mechanical thrombectomy and ischemic stroke mortality in Japan: a spatial ecological study.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1209446}, pmid = {37731848}, issn = {1664-2295}, abstract = {BACKGROUND: Advances in stroke treatment have greatly improved outcomes; however, disparities in access to treatment might increase. Achieving equitable access to stroke treatment is a health policy challenge, as rapid treatment is essential for positive outcomes. This ecological cross-sectional study aimed to determine the relationship between the disparities in spatial accessibility to mechanical thrombectomy (SAMT) and stroke mortality rates in Japan, hypothesizing that disparities in SAMT may increase the differences in stroke mortality between regions.<br><br>METHODS: We used the average number of ischemic stroke (IS) deaths between 2020 and 2021 as the response variable; and SAMT, medical resources, and socioeconomic characteristics of each municipality as explanatory variables. A conditional autoregressive model was used to examine the association between the risk of stroke mortality and SAMT. The standardized mortality ratio (SMR) was mapped to understand the nationwide disparities in stroke mortality risk.<br><br>RESULTS: The median number of IS deaths was 17.5 persons per year in the municipalities (2020 to 2021). The study also found that municipalities with low SAMT were located in the northern part of Japan. The non-spatial regression model results indicated that poor accessibility, a small proportion of bachelor's degrees or higher, and a high proportion of workers in secondary industries were related to high IS mortality. Three models were evaluated using spatial analysis; Model 1 with accessibility indicators alone, Model 2 with medical resources added to Model 1, and Model 3 with socioeconomic characteristics added to Model 2. In Models 1 and 2, the population-weighted spatial accessibility index (PWSAI) showed a significant negative relationship with stroke mortality. However, this was not evident in Model 3. Mapping using Model 3 showed that the high-risk areas were predominantly located in northern Japan, excluding Hokkaido.<br><br>CONCLUSION: Access to mechanical thrombectomy was estimated, and regional differences were observed. The relationship between accessibility and IS mortality is unknown; however, regardless of accessibility, municipalities with a high proportion of workers in secondary industries and a small proportion with bachelor's degrees or above are at risk of death from stroke.}, }
@article {pmid37731597, year = {2023}, author = {Molina, MA and Melchers, WJG and Andralojc, KM and Leenders, WPJ and Huynen, MA}, title = {Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4424-4431}, pmid = {37731597}, issn = {2001-0370}, abstract = {The cervicovaginal microbiome (CVM) is a dynamic continuous microenvironment that can be clustered in microbial community state types (CSTs) and is associated with women's cervical health. Lactobacillus-depleted communities particularly associate with an increased susceptibility for persistence of high-risk human papillomavirus (hrHPV) infections and progression of disease, but the long-term ecological dynamics of CSTs after hrHPV infection diagnosis remain poorly understood. To determine such dynamics, we examined the CVM of our longitudinal cohort of 141 women diagnosed with hrHPV infection at baseline with collected cervical smears at two timepoints six-months apart. Here we describe that the long-term microbiome dissimilarity has a positive correlation with microbial diversity at both visits and that women with high abundance and dominance for Lactobacillus iners at baseline exhibit more similar microbiome composition at second visit than women with Lactobacillus-depleted communities at baseline. We further show that the species Lactobacillus acidophilus and Megasphaera genomosp type 1 associate with CST changes between both visits. Lastly, we also observe that Gardnerella vaginalis is associated with the stability of Lactobacillus-depleted communities while L. iners is associated with the instability of Megasphaera genomosp type 1-dominated communities. Our data suggest dynamic patterns of cervicovaginal CSTs during hrHPV infection, which could be potentially used to develop microbiome-based therapies against infection progression towards disease.}, }
@article {pmid37731274, year = {2023}, author = {Kazemi, A and Racil, G and Ahmadi Hekmatikar, AH and Behnam Moghadam, M and Karami, P and Henselmans, M}, title = {Improved physical performance of elite soccer players based on GPS results after 4 days of carbohydrate loading followed by 3 days of low carbohydrate diet.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {20}, number = {1}, pages = {2258837}, doi = {10.1080/15502783.2023.2258837}, pmid = {37731274}, issn = {1550-2783}, mesh = {Adult ; Humans ; *Diet, Carbohydrate Loading ; Geographic Information Systems ; *Soccer ; Diet, Carbohydrate-Restricted ; Physical Functional Performance ; Carbohydrates ; }, abstract = {BACKGROUND: Carbohydrate loading is an established sports nutrition strategy for endur- 16 ance exercise performance. We tested if carbohydrate loading could improve the performance of 17 elite soccer players under ecologically valid circumstances using Global Positioning System (GPS) data.<br><br>METHODS: Twenty-two adult Iran Premier league soccer players were divided into a carbohydrate-loading group (CLG) and Control group (CG). The carbohydrate loading group restricted carbohydrate intake for three days to 1.5&#x2009;g/kg/d while increasing exercise intensity. From days four to seven, exercise intensity was decreased and carbohydrate intake was considerably increased up to 7.5&#x2009;g/kg/d on the day of the match, during which performance was analyzed using GPS data. The control group performed the same exercise training but maintained their habitual carbohydrate intake of 5-6&#x2009;g/kg/d. The data were analyzed using a univariate ANCOVA with baseline data from a pre-intervention match as the control variable.<br><br>RESULTS: The carbohydrate loading team scored significantly higher on running distance, maximum speed and the number of top and repeated sprints; the carbohydrate loading group scored significantly lower on player load, metabolic power and running imbalance compared to the control team during their match.<br><br>CONCLUSIONS: Our findings suggest carbohydrate loading enabled elite soccer players to achieve greater running outputs with greater metabolic efficiency and lower fatigue compared to their habitual diets.}, }
@article {pmid37650794, year = {2023}, author = {Roma, P and Giromini, L and Sellbom, M and Cardinale, A and Ferracuti, S and Mazza, C}, title = {The ecological validity of the IOP-29: A follow-up study using the MMPI-2-RF and the SIMS as criterion variables.}, journal = {Psychological assessment}, volume = {35}, number = {10}, pages = {868-879}, doi = {10.1037/pas0001273}, pmid = {37650794}, issn = {1939-134X}, mesh = {Humans ; Follow-Up Studies ; *MMPI ; Databases, Factual ; Malingering ; *Psychological Trauma ; }, abstract = {Current guidelines for conducting symptom validity assessments require that professionals administer multiple symptom validity tests (SVTs) and that the SVTs selected for their evaluations provide nonredundant information. However, not many SVTs are currently available, and most of them rely on the same, (in)frequency-based, feigning detection strategy. In this context, the Inventory of Problems (IOP-29) could be a valuable addition to the assessor's toolbox because of its brevity (29 items) and its different approach to assessing the credibility of presented symptoms. As its ecological validity has been poorly investigated, the present study used a criterion groups design to examine the classification accuracy of the IOP-29 in a data set of 174 court-ordered psychological evaluations focused on psychological injury. The validity scales of the Minnesota Multiphasic Personality Inventory-2 Restructured Form and the total score of the Structured Inventory of Malingered Symptoms were used as criterion variables. Overall, the results of this study confirm that the IOP-29 is an effective measure (1.70 ≤ d ≤ 2.67) that provides valuable information when added to the multimethod assessment of symptom validity in civil forensic contexts. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, }
@article {pmid37725327, year = {2023}, author = {Liao, PJ and Lee, CH and Wang, SL and Chiou, HY and Chen, CJ and Seak, CJ and Wu, IW and Hsu, KH}, title = {Low-to-Moderate Arsenic Exposure and Urothelial Tract Cancers with a Long Latent Period of Follow-Up in an Arseniasis Area.}, journal = {Journal of epidemiology and global health}, volume = {}, number = {}, pages = {}, pmid = {37725327}, issn = {2210-6014}, support = {110-2410-H-182-013-MY3//Ministry of Science and Technology, Taiwan/ ; EMRPD1L0401//Health Aging Research Center of Chang Gung University/ ; EMRPD1L0451//Health Aging Research Center of Chang Gung University/ ; CMRPD3L0021//Chang Gung Medical Foundation/ ; CMRPD3L0022//Chang Gung Medical Foundation/ ; CMRPD1M0281//Chang Gung Medical Foundation/ ; CMRPD1M0281, CMRPD1M0282//Chang Gung Medical Foundation/ ; WJY 2020-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; WJY 2021-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; WJY 2022-HR-01//Wang Jhan-Yang Charitable Trust Fund/ ; }, abstract = {BACKGROUND: Arsenic exposure can cause adverse health effects. The effects of long-term low-to-moderate exposure and methylations remain unclear.<br><br>OBJECTIVE: This study aims to examine the association between low-to-moderate arsenic exposure and urothelial tract cancers while considering the effects of methylation capacity.<br><br>METHODS: In this study, 5,811 participants were recruited from an arseniasis area in Taiwan for inorganic arsenic metabolite analysis. This follow-up study was conducted between August 1995 and&#xa0;December 2017. We identified 85 urothelial tract cancers in these participants, including 49 bladder and 36 upper urothelial tract cancer cases. A Cox proportional hazards model was employed.<br><br>RESULTS: The analyses revealed a significant association between concentrations of inorganic arsenic in water&#x2009;>&#x2009;100 ug/L and bladder cancer occurrence, with a hazard ratio (HR) of 4.88 (95% CI 1.35-17.61). A monotonic trend was observed between concentrations of inorganic arsenic in water (from 0 to&#x2009;>&#x2009;100 ug/L) and the incidence of urothelial tract cancer, including bladder cancer (p&#x2009;<&#x2009;0.05) and upper urothelial tract cancers (p&#x2009;<&#x2009;0.05). Participants with a lower primary methylation index or higher secondary methylation index had a prominent effect.<br><br>CONCLUSIONS: Rigorous regulations and active interventions should be considered for populations with susceptible characteristics.}, }
@article {pmid37721104, year = {2023}, author = {Lu, YR and Fang, CC and He, SP}, title = {cnfishbase: A cyber Chinese fish database.}, journal = {Zoological research}, volume = {44}, number = {5}, pages = {950-953}, doi = {10.24272/j.issn.2095-8137.2023.087}, pmid = {37721104}, issn = {2095-8137}, mesh = {Animals ; *Fishes ; *Databases, Factual ; }, }
@article {pmid37718603, year = {2023}, author = {Hoyer, D and Bennett, JS and Reddish, J and Holder, S and Howard, R and Benam, M and Levine, J and Ludlow, F and Feinman, G and Turchin, P}, title = {Navigating polycrisis: long-run socio-cultural factors shape response to changing climate.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {378}, number = {1889}, pages = {20220402}, pmid = {37718603}, issn = {1471-2970}, mesh = {Humans ; *Climate Change ; Databases, Factual ; *Floods ; Head ; Social Interaction ; }, abstract = {Climate variability and natural hazards like floods and earthquakes can act as environmental shocks or socioecological stressors leading to instability and suffering throughout human history. Yet, societies experience a wide range of outcomes when facing such challenges: some suffer from social unrest, civil violence or complete collapse; others prove more resilient and maintain key social functions. We currently lack a clear, generally agreed-upon conceptual framework and evidentiary base to explore what causes these divergent outcomes. Here, we discuss efforts to develop such a framework through the Crisis Database (CrisisDB) programme. We illustrate that the impact of environmental stressors is mediated through extant cultural, political and economic structures that evolve over extended timescales (decades to centuries). These structures can generate high resilience to major shocks, facilitate positive adaptation, or, alternatively, undermine collective action and lead to unrest, violence and even societal collapse. By exposing the ways that different societies have reacted to crises over their lifetime, this framework can help identify the factors and complex social-ecological interactions that either bolster or undermine resilience to contemporary climate shocks. This article is part of the theme issue 'Climate change adaptation needs a science of culture'.}, }
@article {pmid37657322, year = {2023}, author = {Jia, H and Zhao, Y and Deng, H and Yu, H and Ge, C and Li, J}, title = {Integrated microbiome and multi-omics analysis reveal the molecular mechanisms of Eisenia fetida in response to biochar-derived dissolved and particulate matters.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132422}, doi = {10.1016/j.jhazmat.2023.132422}, pmid = {37657322}, issn = {1873-3336}, mesh = {Animals ; *Oligochaeta ; Multiomics ; *Microbiota ; Particulate Matter/toxicity ; Soil ; }, abstract = {At present, most ecotoxicological studies are still confined to focusing on the harmful effects of biochar itself on soil fauna. However, the potential ecotoxicity of different components separated from biochar to terrestrial invertebrates remains poorly understood. In this study, the dissolved matter (DM) and particulate matter (PM) were separated from biochar (BC) and then introduced into the soil-earthworm system to investigate the response mechanism of earthworms at the molecular level. The results showed that BC and DM exposure caused an increase in the abundance of Proteobacteria in the cast bacterial community, suggesting the dysbiosis of intestinal microbiota. It was also observed that the cast bacterial communities were more sensitive to DM exposure than PM exposure. Transcriptomic analysis showed that BC and DM exposure induced significant enrichment of functional pathways related to infectious and neuropathic diseases. Metabolomic profiling manifested that DM exposure caused metabolic dysfunction, antioxidant and detoxification abilities recession. Furthermore, significant differences in the responses of earthworms at transcriptomic and metabolic levels confirmed that DM exhibited greater ecotoxicity than PM. This study highlighted the significant contributions of dissolved matter to the ecotoxicity of biochar from the perspective of transcriptomic and metabolomic profiles.}, }
@article {pmid37306048, year = {2023}, author = {Mumme, S and Middleton, AD and Ciucci, P and De Groeve, J and Corradini, A and Aikens, EO and Ossi, F and Atwood, P and Balkenhol, N and Cole, EK and Debeffe, L and Dewey, SR and Fischer, C and Gude, J and Heurich, M and Hurley, MA and Jarnemo, A and Kauffman, MJ and Licoppe, A and van Loon, E and McWhirter, D and Mong, TW and Pedrotti, L and Morellet, N and Mysterud, A and Peters, W and Proffitt, K and Saïd, S and Signer, J and Sunde, P and Starý, M and Cagnacci, F}, title = {Wherever I may roam-Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents.}, journal = {Global change biology}, volume = {29}, number = {20}, pages = {5788-5801}, doi = {10.1111/gcb.16769}, pmid = {37306048}, issn = {1365-2486}, support = {//&#xc5;gerups &amp; Elsag&#xe5;rdens S&#xe4;teri AB/ ; //Assm&#xe5;sa Gods AB/ ; //Carl Piper/ ; Wildlife &amp; Landscape Research Package-project 2B//Danish Forest and Nature Agency/ ; //Ersaf Lombardia and Trento/ ; //Fondazione Edmund Mach/ ; //Grand Teton Association/ ; //Halmstad University/ ; //H&#xf6;gestad &amp; Christinehofs F&#xf6;rvaltnings AB/ ; //Holmen Skog AB/ ; //International Research School of Applied Ecology/ ; //Ittur AB/ ; //Karl-Erik &#xd6;nnesj&#xf6;s Stiftelse f&#xf6;r Vetenskaplig forskning och Utveckling/ ; //Kolm&#xe5;rdens insamlingsstiftelse/T&#xe5;by Allm&#xe4;nning/ ; //Marie-Claire Cronstedts Stiftelse/ ; //Office Fran&#xe7;ais de la Biodiversit&#xe9;/ ; //Public Service of Wallonia/ ; //Region Sk&#xe5;ne / Stiftelsen Sk&#xe5;nska Landskap/ ; //Stelvio National Park/ ; //Stiftelsen Oscar och Lili Lamms Minne/ ; //Sveaskog/ ; 5871/2005//Swedish Association for Hunting and Wildlife Management/ ; 802-0092-11//Swedish Environmental Protection Agency/ ; //Swedish University of Agricultural Sciences/ ; //Universit&#xe0; degli Studi di Trento/ ; //University of California Berkeley/ ; //Vectronic Aerospace GmbH/ ; //Vir&#xe5; Bruk AB/ ; }, mesh = {Humans ; Animals ; *Ecosystem ; *Deer/physiology ; Human Activities ; North America ; Geographic Information Systems ; }, abstract = {Human activity and associated landscape modifications alter the movements of animals with consequences for populations and ecosystems worldwide. Species performing long-distance movements are thought to be particularly sensitive to human impact. Despite the increasing anthropogenic pressure, it remains challenging to understand and predict animals' responses to human activity. Here we address this knowledge gap using 1206 Global Positioning System movement trajectories of 815 individuals from 14 red deer (Cervus elaphus) and 14 elk (Cervus canadensis) populations spanning wide environmental gradients, namely the latitudinal range from the Alps to Scandinavia in Europe, and the Greater Yellowstone Ecosystem in North America. We measured individual-level movements relative to the environmental context, or movement expression, using the standardized metric Intensity of Use, reflecting both the directionality and extent of movements. We expected movement expression to be affected by resource (Normalized Difference Vegetation Index, NDVI) predictability and topography, but those factors to be superseded by human impact. Red deer and elk movement expression varied along a continuum, from highly segmented trajectories over relatively small areas (high intensity of use), to directed transitions through restricted corridors (low intensity of use). Human activity (Human Footprint Index, HFI) was the strongest driver of movement expression, with a steep increase in Intensity of Use as HFI increased, but only until a threshold was reached. After exceeding this level of impact, the Intensity of Use remained unchanged. These results indicate the overall sensitivity of Cervus movement expression to human activity and suggest a limitation of plastic responses under high human pressure, despite the species also occurring in human-dominated landscapes. Our work represents the first comparison of metric-based movement expression across widely distributed populations of a deer genus, contributing to the understanding and prediction of animals' responses to human activity.}, }
@article {pmid37714749, year = {2023}, author = {Reid, MC and Mittler, JE and Murphy, JT and Stansfield, SE and Goodreau, SM and Abernethy, N and Herbeck, JT}, title = {Evolution of HIV virulence in response to disease-modifying vaccines: A modeling study.}, journal = {Vaccine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.vaccine.2023.08.071}, pmid = {37714749}, issn = {1873-2518}, abstract = {Pathogens face a tradeoff with respect to virulence; while more virulent strains often have higher per-contact transmission rates, they are also more likely to kill their hosts earlier. Because virulence is a heritable trait, there is concern that a disease-modifying vaccine, which reduces the disease severity of an infected vaccinee without changing the underlying pathogen genotype, may result in the evolution of higher pathogen virulence. We explored the potential for such virulence evolution with a disease-modifying HIV-1 vaccine in an agent-based stochastic epidemic model of HIV in United States men who have sex with men (MSM). In the model, vaccinated agents received no protection against infection, but experienced lower viral loads and slower disease progression. We compared the genotypic set point viral load (SPVL), a measure of HIV virulence, in populations given vaccines that varied in the degree of SPVL reduction they induce. Sensitivity analyses were conducted under varying vaccine coverage scenarios. With continual vaccination rollout under ideal circumstances of 90 % coverage over thirty years, the genotypic SPVL of vaccinated individuals evolved to become greater than the genotypic SPVL of unvaccinated individuals. This virulence evolution in turn diminished the public health benefit of the vaccine, and in some scenarios resulted in an accelerated epidemic. These findings demonstrate the complexity of viral evolution and have important implications for the design and development of HIV vaccines.}, }
@article {pmid37711328, year = {2023}, author = {Faria, AL and Latorre, J and Silva Cameirão, M and Bermúdez I Badia, S and Llorens, R}, title = {Ecologically valid virtual reality-based technologies for assessment and rehabilitation of acquired brain injury: a systematic review.}, journal = {Frontiers in psychology}, volume = {14}, number = {}, pages = {1233346}, pmid = {37711328}, issn = {1664-1078}, abstract = {PURPOSE: A systematic review was conducted to examine the state of the literature regarding using ecologically valid virtual environments and related technologies to assess and rehabilitate people with Acquired Brain Injury (ABI).<br><br>MATERIALS AND METHODS: A literature search was performed following the PRISMA guidelines using PubMed, Web of Science, ACM and IEEE databases. The focus was on assessment and intervention studies using ecologically valid virtual environments (VE). All studies were included if they involved individuals with ABI and simulated environments of the real world or Activities of Daily Living (ADL).<br><br>RESULTS: Seventy out of 363 studies were included in this review and grouped and analyzed according to the nature of its simulation, prefacing a total of 12 kitchens, 11 supermarkets, 10 shopping malls, 16 streets, 11 cities, and 10 other everyday life scenarios. These VE were mostly presented on computer screens, HMD's and laptops and patients interacted with them primarily via mouse, keyboard, and joystick. Twenty-five out of 70 studies had a non-experimental design.<br><br>CONCLUSION: Evidence about the clinical impact of ecologically valid VE is still modest, and further research with more extensive samples is needed. It is important to standardize neuropsychological and motor outcome measures to strengthen conclusions between studies.<br><br>identifier CRD42022301560, https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=301560.}, }
@article {pmid37709808, year = {2023}, author = {Cosentino, F and Castiello, G and Maiorano, L}, title = {A dataset on African bats' functional traits.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {623}, pmid = {37709808}, issn = {2052-4463}, support = {AR12117A5D86252A//Sapienza Universit&#xe0; di Roma (Sapienza University of Rome)/ ; }, mesh = {Animals ; *Chiroptera ; Databases, Factual ; Machine Learning ; Nutritional Status ; }, abstract = {Trait-based approaches are becoming extremely common in ecological modeling and the availability of traits databases is increasing. However, data availability is often biased towards particular regions and taxa, with many taxa (e.g., bats) often under-represented. Here, we present the AfroBaT dataset, a compilation of trait data on 320 African bat species containing 76,914 values for 86 traits focusing on morphology, reproduction, life-history, trophic ecology, and species distributions. All data were gathered from published literature following the ecological trait-data standard procedure. Missing data for both numerical and categorical traits were imputed with a machine learning approach including species phylogeny. Trophic ecology traits showed the highest coverage in the literature (72% of the species averaged over all traits), while reproductive traits the lowest. Our data imputation improved the coverage of AfroBaT especially for reproductive traits, going from 27% to 58% of the species covered. AfroBaT has a range of potential applications in macroecology and community ecology, and the availability of open-access data on African bats will enable collaboration and data-sharing among researchers.}, }
@article {pmid37705614, year = {2023}, author = {Mora-Rubio, A and Bravo-Ortíz, MA and Quiñones Arredondo, S and Saborit Torres, JM and Ruz, GA and Tabares-Soto, R}, title = {Classification of Alzheimer's disease stages from magnetic resonance images using deep learning.}, journal = {PeerJ. Computer science}, volume = {9}, number = {}, pages = {e1490}, pmid = {37705614}, issn = {2376-5992}, abstract = {Alzheimer's disease (AD) is a progressive type of dementia characterized by loss of memory and other cognitive abilities, including speech. Since AD is a progressive disease, detection in the early stages is essential for the appropriate care of the patient throughout its development, going from asymptomatic to a stage known as mild cognitive impairment (MCI), and then progressing to dementia and severe dementia; is worth mentioning that everyone suffers from cognitive impairment to some degree as we age, but the relevant task here is to identify which people are most likely to develop AD. Along with cognitive tests, evaluation of the brain morphology is the primary tool for AD diagnosis, where atrophy and loss of volume of the frontotemporal lobe are common features in patients who suffer from the disease. Regarding medical imaging techniques, magnetic resonance imaging (MRI) scans are one of the methods used by specialists to assess brain morphology. Recently, with the rise of deep learning (DL) and its successful implementation in medical imaging applications, it is of growing interest in the research community to develop computer-aided diagnosis systems that can help physicians to detect this disease, especially in the early stages where macroscopic changes are not so easily identified. This article presents a DL-based approach to classifying MRI scans in the different stages of AD, using a curated set of images from Alzheimer's Disease Neuroimaging Initiative and Open Access Series of Imaging Studies databases. Our methodology involves image pre-processing using FreeSurfer, spatial data-augmentation operations, such as rotation, flip, and random zoom during training, and state-of-the-art 3D convolutional neural networks such as EfficientNet, DenseNet, and a custom siamese network, as well as the relatively new approach of vision transformer architecture. With this approach, the best detection percentage among all four architectures was around 89% for AD vs. Control, 80% for Late MCI vs. Control, 66% for MCI vs. Control, and 67% for Early MCI vs. Control.}, }
@article {pmid37454795, year = {2023}, author = {Đokić, M and Manić, M and Đorđević, M and Gocić, M and Čupić, A and Jović, M and Dragović, R and Gajić, B and Smičiklas, I and Dragović, S}, title = {Remote sensing and nuclear techniques for high-resolution mapping and quantification of gully erosion in the highly erodible area of the Malčanska River Basin, Eastern Serbia.}, journal = {Environmental research}, volume = {235}, number = {}, pages = {116679}, doi = {10.1016/j.envres.2023.116679}, pmid = {37454795}, issn = {1096-0953}, mesh = {*Remote Sensing Technology ; *Ecosystem ; Geographic Information Systems ; Conservation of Natural Resources/methods ; Rivers ; Serbia ; Soil ; }, abstract = {Gully erosion leads to the formation of deep and wide channels that increase the risk of soil loss, flooding, and water pollution. In addition, this process reduces the productivity and viability of agricultural land and natural ecosystems. Preventing gully erosion is critical for maintaining ecological balance and preserving natural resources in certain areas. This paper presents a methodology integrating remote sensing and nuclear techniques to study gully erosion. The morphometric characterization of gullies using 360-degree camera photogrammetry was introduced as a new method in erosion research. This approach aims to investigate the suitability of unmanned aerial vehicle and terrestrial photogrammetry for modeling gullies, to study the variability of erosion processes in gullies at a small scale, and to compare the differences in erosion intensity between nearby gullies. The study's objectives include identifying the effective and economical method for gullies monitoring and providing a starting point for controlling and safeguarding gullies. Mainly erosion process was detected in the studied gullies, while deposition was identified at only 2 out of 39 sampling locations. The results showed an average soil redistribution rate of 16.2 t ha[-1] yr[-1] and coefficients of variation of 32%, 59%, and 91% for three investigated gullies. It was determined that aerial photogrammetry methods were not practical under the conditions prevailing in the study area. Highly detailed 3D models of the gullies were created using 360-degree photogrammetry. It was confirmed that the micro-relief obtained by photogrammetric modeling is an essential contribution to erosion research. The 360-degree camera photogrammetry serves as a reliable tool for analyzing the morphology of gullies and, in perspective, tracking changes in gully systems over time or monitoring the effectiveness of the applied protection measures.}, }
@article {pmid37413727, year = {2023}, author = {Xing, Z and Chen, S and Xu, F and Su, X and Gou, F and Shi, Y and Chen, H and Xiang, J and Li, J and Zhao, T}, title = {Quantitative analysis of TCE biodegradation pathway in landfill cover utilizing continuous monitoring, droplet digital PCR and multi-omics sequencing technology.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118509}, doi = {10.1016/j.jenvman.2023.118509}, pmid = {37413727}, issn = {1095-8630}, mesh = {*Trichloroethylene/chemistry ; Multiomics ; Biodegradation, Environmental ; Waste Disposal Facilities ; Bacteria/genetics/metabolism ; Soil ; Polymerase Chain Reaction ; Technology ; }, abstract = {The remediation of volatile chlorinated hydrocarbons in the quasi-vadose zone has become a significant challenge. We applied an integrated approach to assess the biodegradability of trichloroethylene to identify the biotransformation mechanism. The formation of the functional zone biochemical layer was assessed by analyzing the distribution of landfill gas, physical and chemical properties of cover soil, spatial-temporal variations of micro-ecology, biodegradability of landfill cover soil and distributional difference metabolic pathway. Real-time online monitoring showed that trichloroethylene continuously undergoes anaerobic dichlorination and simultaneous aerobic/anaerobic conversion-aerobic co-metabolic degradation on the vertical gradient of the landfill cover system and reduction in trans-1,2-dichloroethylene in the anoxic zone but not 1,1-dichloroethylene. PCR and diversity sequencing revealed the abundance and spatial distribution of known dichlorination-related genes within the landfill cover, with 6.61 ± 0.25 × 10[4]-6.78 ± 0.09 × 10[6] and 1.17 ± 0.78 × 10[3]-7.82 ± 0.07 × 10[5] copies per g/soil of pmoA and tceA, respectively. In addition, dominant bacteria and diversity were significantly linked with physicochemical factors, and Mesorhizobium, Pseudoxanthomonas and Gemmatimonas were responsible for biodegradation in the aerobic, anoxic and anaerobic zones. Metagenome sequencing identified 6 degradation pathways of trichloroethylene that may occur in the landfill cover; the main pathway was incomplete dechlorination accompanied by cometabolic degradation. These results indicate that the anoxic zone is important for trichloroethylene degradation.}, }
@article {pmid37331314, year = {2023}, author = {Liu, J and Xu, X and Zou, C and Lin, N and Zhang, K and Shan, N and Zhang, H and Liu, R}, title = {A Bayesian network-GIS probabilistic model for addressing human disturbance risk to ecological conservation redline areas.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118400}, doi = {10.1016/j.jenvman.2023.118400}, pmid = {37331314}, issn = {1095-8630}, mesh = {Humans ; *Geographic Information Systems ; *Conservation of Natural Resources/methods ; Bayes Theorem ; Forests ; Models, Statistical ; China ; Ecosystem ; }, abstract = {Population growth and associated ecological space occupation are posing great risks to regional ecological security and social stability. In China, "Ecological Conservation Redline" (ECR) that prohibited urbanization and industrial construction has been proposed as a national policy to resolve spatial mismatches and management contradictions. However, unfriendly human disturbance activities (e.g., cultivation, mining, and infrastructure construction) still exist within the ECR, posing a great threat to ecological stability and safety. In this article, a Bayesian network (BN)-GIS probabilistic model is proposed to spatially and quantitatively address the human disturbance risk to the ECR at the regional scale. The Bayesian models integrate multiple human activities, ecological receptors of the ECR, and their exposure relationships for calculating the human disturbance risk. The case learning method geographic information systems (GIS) is then introduced to train BN models based on the spatial attribute of variables to evaluate the spatial distribution and correlation of risks. This approach was applied to the human disturbance risk assessment for the ECR that was delineated in 2018 in Jiangsu Province, China. The results indicated that most of the ECRs were at a low or medium human disturbance risk level, while some drinking water sources and forest parks in Lianyungang City possessed the highest risk. The sensitivity analysis result showed the ECR vulnerability, especially for cropland, that contributed most to the human disturbance risk. This spatially probabilistic method can not only enhance model's prediction precision, but also help decision-makers to determine how to establish priorities for policy design and conservation interventions. Overall, it presents a foundation for later ECR adjustments as well as for human disturbance risk supervision and management at the regional scale.}, }
@article {pmid37701708, year = {2023}, author = {Paudel, S and Mueller, K and Ovando-Montejo, G and Tango, L and Rushforth, R and Lant, C}, title = {A dataset cataloging product-specific human appropriation of net primary production (HANPP) in US counties.}, journal = {Data in brief}, volume = {50}, number = {}, pages = {109530}, pmid = {37701708}, issn = {2352-3409}, abstract = {This paper describes the dataset associated with the paper "Product-Specific Human Appropriation of Net Primary Production (HANPP) in US Counties" (Paudel et al., 2023). This dataset comprises human appropriation of net primary production (HANPP) values for 3101 counties in the conterminous US for the years 1997, 2002, 2007, and 2012. For this dataset, HANPP is the carbon content of specific crop, timber, and livestock grazing products appropriated by humans in a county in a year. To calculate HANPP, raw agricultural data were downloaded from public databases such as USDA-National Agricultural Statistics Service Quick Stats and Cropland Data Layer, US Forest Service Timber Product Output, and NPP data from MODIS. These data were processed in Microsoft Excel using stoichiometry derived from established scientific literature. HANPP was partitioned by year, county, product, used and unused and above- and below-ground. This complete dataset is published in Mendeley Data and the methods used to compile them are included to make our research well documented, reproducible, and useful for future studies.}, }
@article {pmid37699986, year = {2023}, author = {Sharaf, A and Ndiribe, CC and Omotoriogun, TC and Abueg, L and Badaoui, B and Badiane Markey, FJ and Beedessee, G and Diouf, D and Duru, VC and Ebuzome, C and Eziuzor, SC and Jaufeerally Fakim, Y and Formenti, G and Ghanmi, N and Guerfali, FZ and Houaga, I and Ideozu, JE and Katee, SM and Khayi, S and Kuja, JO and Kwon-Ndung, EH and Marks, RA and Moila, AM and Mungloo-Dilmohamud, Z and Muzemil, S and Nigussie, H and Osuji, JO and Ras, V and Tchiechoua, YH and Zoclanclounon, YAB and Tolley, KA and Ziyomo, C and Mapholi, N and Muigai, AWT and Djikeng, A and Ebenezer, TE}, title = {Bridging the gap in African biodiversity genomics and bioinformatics.}, journal = {Nature biotechnology}, volume = {41}, number = {9}, pages = {1348-1354}, pmid = {37699986}, issn = {1546-1696}, mesh = {*Computational Biology ; *Genomics ; }, }
@article {pmid37230884, year = {2023}, author = {Williams, JW and Spanbauer, TL and Heintzman, PD and Blois, J and Capo, E and Goring, SJ and Monchamp, ME and Parducci, L and Von Eggers, JM and , }, title = {Strengthening global-change science by integrating aeDNA with paleoecoinformatics.}, journal = {Trends in ecology &amp; evolution}, volume = {38}, number = {10}, pages = {946-960}, doi = {10.1016/j.tree.2023.04.016}, pmid = {37230884}, issn = {1872-8383}, mesh = {*Biodiversity ; *DNA, Ancient ; Computational Biology ; DNA Barcoding, Taxonomic ; }, abstract = {Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.}, }
@article {pmid37208222, year = {2023}, author = {de Koning, K and Broekhuijsen, J and Kühn, I and Ovaskainen, O and Taubert, F and Endresen, D and Schigel, D and Grimm, V}, title = {Digital twins: dynamic model-data fusion for ecology.}, journal = {Trends in ecology &amp; evolution}, volume = {38}, number = {10}, pages = {916-926}, doi = {10.1016/j.tree.2023.04.010}, pmid = {37208222}, issn = {1872-8383}, mesh = {*Ecology ; Big Data ; Machine Learning ; *Computer Simulation ; }, abstract = {Digital twins (DTs) are an emerging phenomenon in the public and private sectors as a new tool to monitor and understand systems and processes. DTs have the potential to change the status quo in ecology as part of its digital transformation. However, it is important to avoid misguided developments by managing expectations about DTs. We stress that DTs are not just big models of everything, containing big data and machine learning. Rather, the strength of DTs is in combining data, models, and domain knowledge, and their continuous alignment with the real world. We suggest that researchers and stakeholders exercise caution in DT development, keeping in mind that many of the strengths and challenges of computational modelling in ecology also apply to DTs.}, }
@article {pmid37697042, year = {2023}, author = {Mullowney, MW and Duncan, KR and Elsayed, SS and Garg, N and van der Hooft, JJJ and Martin, NI and Meijer, D and Terlouw, BR and Biermann, F and Blin, K and Durairaj, J and Gorostiola González, M and Helfrich, EJN and Huber, F and Leopold-Messer, S and Rajan, K and de Rond, T and van Santen, JA and Sorokina, M and Balunas, MJ and Beniddir, MA and van Bergeijk, DA and Carroll, LM and Clark, CM and Clevert, DA and Dejong, CA and Du, C and Ferrinho, S and Grisoni, F and Hofstetter, A and Jespers, W and Kalinina, OV and Kautsar, SA and Kim, H and Leao, TF and Masschelein, J and Rees, ER and Reher, R and Reker, D and Schwaller, P and Segler, M and Skinnider, MA and Walker, AS and Willighagen, EL and Zdrazil, B and Ziemert, N and Goss, RJM and Guyomard, P and Volkamer, A and Gerwick, WH and Kim, HU and Müller, R and van Wezel, GP and van Westen, GJP and Hirsch, AKH and Linington, RG and Robinson, SL and Medema, MH}, title = {Artificial intelligence for natural product drug discovery.}, journal = {Nature reviews. Drug discovery}, volume = {}, number = {}, pages = {}, pmid = {37697042}, issn = {1474-1784}, abstract = {Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.}, }
@article {pmid37697020, year = {2023}, author = {Chen, L and Qin, L and Zhang, Y and Xu, H and Bu, Y and Wu, R and Liu, H and Hao, Q and Hu, H and Zhou, Y and Feng, J and Jing, Y and Han, J and Wang, X}, title = {Insights from multi-omics integration into seed germination of Taxus chinensis var mairei.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {931}, pmid = {37697020}, issn = {2399-3642}, support = {31770384//National Natural Science Foundation of China (National Science Foundation of China)/ ; 21605164//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Taxus/genetics ; Germination ; Multiomics ; Seeds ; Cycadopsida ; }, abstract = {The transition from deep dormancy to seed germination is essential for the life cycle of plants, but how this process occurs in the gymnosperm Chinese yew (Taxus chinensis var mairei), the natural source of the anticancer drug paclitaxel, remains unclear. Herein, we analyse the transcriptome, proteome, spatial metabolome, and spatial lipidome of the Chinese yew and present the multi-omics profiles of dormant and germinating seeds. Our results show that abscisic acid and gibberellic acid 12 homoeostasis is closely associated with gene transcription and protein translation, and the balance between these phytohormones thereby determines if seeds remain dormant or germinate. We find that an energy supply of carbohydrates from glycolysis and the TCA cycle feed into the pentose phosphate pathway during seed germination, and energy supplied from lipids are mainly derived from the lipolysis of triacylglycerols. Using mass spectrometry imaging, we demonstrate that the spatial distribution of plant hormones and phospholipids has a remarkable influence on embryo development. We also provide an atlas of the spatial distribution of paclitaxel C in Chinese yew seeds for the first time. The data from this study enable exploration of the germination mechanism of Chinese yew seeds across several omics levels.}, }
@article {pmid37694423, year = {2023}, author = {Jiang, BY and Zhang, YL and Li, S and Li, JJ and Zheng, ZH and Wang, HG}, title = {Spatio-temporal dynamics and sensitive distance of nighttime light environment in Pearl River Delta Protected Areas, China.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {6}, pages = {1601-1609}, doi = {10.13287/j.1001-9332.202306.020}, pmid = {37694423}, issn = {1001-9332}, mesh = {Humans ; *Rivers ; China ; *Big Data ; Light ; }, abstract = {Protected areas (PAs) are important barriers to ensure the ecological security of territory. Light pollution is a threat to PAs, which is particularly obvious in the urban agglomeration environment. We used multi-source big data (satellite remote sensing light data, land cover types and points of interest) to quantitatively analyze the temporal and spatial dynamics of nighttime light in the PAs of the Pearl River Delta (PRD) urban agglomeration from 2000 to 2018, the correlation between the night light environment within the PAs and human activity intensity outside, as well as the sensitive distance of the PAs to artificial light interference. The results showed that the total value of nighttime light data of PAs in the PRD increased from 71107 nanoW·cm[-2]·sr[-1] to 127682 nanoW·cm[-2]·sr[-1] from 2000 to 2018, the mean value per pixel increased from 15.3 nanoW·cm[-2]·sr[-1] to 23.7 nanoW·cm[-2]·sr[-1], and the lighted ratio increased from 73.3% to 86.4%, indicating that the nighttime light environment of PAs in the region were facing cumulative deterioration risks and serious challenges. The nighttime light intensity of the PAs in the core area of the PRD was much higher than that in the peripheral areas such as Zhaoqing and Huizhou, whereas the expansion degree of the PAs in the peripheral areas was higher than that in the core area. The nighttime light environment inside the PAs was positively correlated with the intensity of human activities around it. The most sensitive distance of the PAs to the artificial light interference around it was 10 km, and the interference degree tended to be stable after 30 km. We proposed that 0-10 km area outside the boundary of the PAs should be the light control core zone and 10-20 km area as the control buffer zone.}, }
@article {pmid37692385, year = {2023}, author = {Fan, R and Liu, Y and Bin, Y and Huang, J and Yi, B and Tang, X and Li, Y and Cai, Y and Yang, Z and Yang, M and Song, J and Pan, Q and Liu, Z and Ghani, MI and Hu, X and Chen, X}, title = {Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1222844}, pmid = {37692385}, issn = {1664-302X}, abstract = {Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.}, }
@article {pmid37685932, year = {2023}, author = {Milicevic, O and Loncar, A and Abazovic, D and Vukcevic, M and Despot, D and Djukic, T and Djukic, V and Milovanovic, A and Panic, N and Plecic, N and Banko, A}, title = {Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, pmid = {37685932}, issn = {1422-0067}, mesh = {Humans ; *SARS-CoV-2/genetics ; Transcriptome ; *COVID-19/genetics ; Gene Expression Profiling ; Computational Biology ; }, abstract = {Previous transcriptome profiling studies showed significantly upregulated genes and altered biological pathways in acute COVID-19. However, changes in the transcriptional signatures during a defined time frame are not yet examined and described. The aims of this study included viral metagenomics and evaluation of the total expression in time-matched and tissue-matched paired COVID-19 samples with the analysis of the host splicing profile to reveal potential therapeutic targets. Prospective analysis of paired nasopharyngeal swabs (NPS) and blood (BL) samples from 18 COVID-19 patients with acute and resolved infection performed using Kallisto, Suppa2, Centrifuge, EdgeR, PantherDB, and L1000CDS2 tools. In NPS, we discovered 6 genes with changed splicing and 40 differentially expressed genes (DEG) that yielded 88 altered pathways. Blood samples yielded 15 alternatively spliced genes. Although the unpaired DEG analysis failed, pairing identified 78 genes and 242 altered pathways with meaningful clinical interpretation and new candidate drug combinations with up to 65% overlap. Metagenomics analyses showed SARS-CoV-2 dominance during and after the acute infection, with a significant reduction in NPS (0.008 vs. 0.002, p = 0.019). Even though both NPS and BL give meaningful insights into expression changes, this is the first demonstration of how the power of blood analysis is vastly maximized by pairing. The obtained results essentially showed that pairing is a determinant between a failed and a comprehensive study. Finally, the bioinformatics results prove to be a comprehensive tool for full-action insights, drug development, and infectious disease research when designed properly.}, }
@article {pmid37598535, year = {2023}, author = {Tokatlı, C and Uğurluoğlu, A and Muhammad, S}, title = {Ecotoxicological evaluation of organic contamination in the world's two significant gateways to the Black Sea using GIS techniques: Turkish Straits.}, journal = {Marine pollution bulletin}, volume = {194}, number = {Pt A}, pages = {115405}, doi = {10.1016/j.marpolbul.2023.115405}, pmid = {37598535}, issn = {1879-3363}, mesh = {Child ; Humans ; Black Sea ; *Ecosystem ; *Geographic Information Systems ; Ecotoxicology ; Lakes ; }, abstract = {This study was carried out to determine the spatial-temporal distributions of limnological parameters of Çanakkale Strait (ÇS) and İstanbul Strait (İS), Turkiye. Fluvial (n = 11) and lacustrine (n = 4) habitats water samples were collected in the dry and rainy seasons of 2022-2023. Among limnological parameters, the highest mean electrical conductivity values of 6063 μS/cm were noted in the İS basin during the rainy season and the lowest was 0.04 mg/L for nitrite in the ÇS basin. Generally, the levels of organic contaminants and ecological risk indices were as follows: rivers of İS > rivers of ÇS > Alibey Dam Lake (İS) > Atikhisar Dam Lake (ÇS). The highest non-carcinogenic health risks of 0.88 were noted for children in the ÇS basin during the dry season and the lowest of <0.01 in Atikhisar Dam Lake during the rainy season. Multivariate statistical techniques were applied to data to categorize investigated ecosystems and sources apportionment of contaminants and geospatial distribution.}, }
@article {pmid37683992, year = {2023}, author = {Sukur, N and Milošević, N and Pogrmic-Majkic, K and Stanic, B and Andric, N}, title = {Predicting chemicals' toxicity pathway of female reproductive disorders using AOP7 and deep neural networks.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {114013}, doi = {10.1016/j.fct.2023.114013}, pmid = {37683992}, issn = {1873-6351}, abstract = {Experimental evidence shows that certain chemicals, particularly endocrine disrupting chemicals, may negatively affect the female reproductive system, thereby lowering women's fertility. However, humans are constantly exposed to a number of different chemicals with limited or no experimental data regarding their effect and the mechanism of action in the female reproductive system. To predict chemical hazards to the female reproductive system, we used a previously defined adverse outcome pathway (AOP) that links activation of the peroxisome proliferator-activated receptor γ to the reproductive toxicity in adult females (AOP7) and the Convolutional Deep Neural Network models that produce meaningful predictions when trained on a significant amount of data. The models trained using CompTox assays with intended molecular and biological targets corresponding to AOP7 achieved high performance (over 90% validation accuracy). The integration of AOP7 and Deep Neural Network identified chemicals that could negatively affect female reproduction through the mechanism described in AOP7. We provide a solution to quickly analyze the data and produce machine learning models to identify potentially active chemicals in the female reproductive system. Although we focused on the female reproductive system, this approach could be valid for a number of other chemicals and AOPs if the right data exist.}, }
@article {pmid37681394, year = {2023}, author = {Xie, X and Wu, TC and Cao, BL and Li, JZ and Xue, B}, title = {Virtual ecological technology: Concepts, systems, and application perspectives.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {8}, pages = {2297-2304}, doi = {10.13287/j.1001-9332.202308.022}, pmid = {37681394}, issn = {1001-9332}, mesh = {Humans ; *Ecosystem ; *Air Pollution ; Environment ; Geography ; Sustainable Development ; }, abstract = {Virtual ecological technology is a new technology that builds the foundation of a digital ecological system, simulates the process of ecological evolution, and establishes a global knowledge analysis system based on a unified spatio-temporal benchmark. It is a new direction for the interdisciplinary integration and development of eco-logy, geographic information science, computer science and other subjects towards modernization, informatization, and intelligence. Research, development, and application of virtual ecological technology is of great significance for the development of ecology as a discipline, ecosystem management, and regional sustainable development. Curren-tly, research on virtual ecological technology is still in its infancy and lacks a complete and clearly defined framework, making it difficult to support systematic iterative development and scientific analysis. In this paper, starting from the main theories and objectives of modern ecology, we summarized the main contents and technical requirements of virtual ecological construction, and proposed a key technical system of virtual ecology that integrated vir-tual geography and digital twin technology. From the perspective of application scenarios, we analyzed the application capabilities of virtual ecological technology in air pollution and energy analysis. Finally, we summarized the deve-lopment potential of virtual ecological technology in the digital construction of the ecological environment, intelligent computing, and realistic expression of different levels of ecological space resources transformation under the background of new generation of information technology, both at the local computing point breakthrough and the global technology point fusion aspects. This would enrich and advance the technical capabilities that support China's ecological space resource transformation.}, }
@article {pmid37454715, year = {2023}, author = {Wu, X and Zhang, X and Chen, X and Ye, A and Cao, J and Hu, X and Zhou, W}, title = {The effects of polylactic acid bioplastic exposure on midgut microbiota and metabolite profiles in silkworm (Bombyx mori): An integrated multi-omics analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122210}, doi = {10.1016/j.envpol.2023.122210}, pmid = {37454715}, issn = {1873-6424}, mesh = {Animals ; *Bombyx ; Multiomics ; Prospective Studies ; Polyesters/toxicity/metabolism ; Biopolymers/metabolism ; *Microbiota ; Larva ; }, abstract = {Polylactic acid (PLA) is a highly common biodegradable plastic and a potential threat to health and the environment. However, limited data are available on the effects of PLA exposure in the silkworm (Bombyx mori), a model organism used in toxicity studies. In this study, silkworms with or without PLA exposure (P1: 1 mg/L, P5: 5 mg/L, P25: 25 mg/L, and P0: 0 mg/L) for the entire 5th instar period were used to investigate the impact of PLA exposure on midgut morphology, larvae growth, and survival. Mitochondrial damage was observed in the P5 and P25 groups. The weights of the P25 posterior silk gland (5th day in the 5th instar), mature larvae and pupae were all significantly lower than those of the controls (P < 0.05). Dead worm cocoon rates and larva-pupa to 5th instar larvae ratios showed a positive and negative dose-dependent manner with respect to PLA concentrations, respectively. Additionally, reactive oxygen species levels and superoxide dismutase activity of the P25 midgut were significantly higher and lower when compared with controls, respectively (P < 0.05). The molecular mechanisms underlying the effects of PLA and associated physiological responses were also investigated. In the midgut metabolome, 127 significantly different metabolites (variable importance projection >1 and P < 0.05) were identified between the P0 and P25 groups and were mainly enriched for amino acid metabolism and energy supply pathways. The 16 S rDNA data showed that PLA altered microbial richness and structural composition. Microbiota, classified into 34 genera and 63 species, were significantly altered after 25 mg/L PLA exposure (P < 0.05). Spearman's correlation results showed that Bifidobacterium catenulatum and Schaalia odontolytica played potentially vital roles during exposure, as they demonstrated stronger correlations with the significantly different metabolites than other bacterial species. In sum, PLA induced toxic effects on silkworms, especially on energy- and protein-relevant metabolism, but at high concentrations (25 mg/L). This prospective mechanistic investigation on the effects of PLA on larval toxicity provides novel insight regarding the ecological risks of biodegradable plastics in the environment.}, }
@article {pmid37680963, year = {2023}, author = {Tóth, F and Zsuga, K and Kerepeczki, &#xc9; and Kovács, B and Magura, T and Körmöczi, L and Lövei, GL}, title = {Discordant spatiotemporal dynamics of functional and phylogenetic diversity of rotiferan communities exposed to aquaculture effluent.}, journal = {Ecology and evolution}, volume = {13}, number = {9}, pages = {e10503}, pmid = {37680963}, issn = {2045-7758}, abstract = {The growth of the human population brought about the global intensification of aquacultural production, and aquaculture became the fastest growing animal husbandry sector. Effluent from aquaculture is an anthropogenic environmental burden, containing organic matter, nutrients and suspended solids that affect water quality especially in the water bodies of high biodiversity and conservation value. Water quality assessment often relies on bioindicators, analysing changes in taxonomic diversity of various freshwater organismal groups. Stepping beyond taxon diversity, we used functional and phylogenetic diversities of rotifers to identify factors affecting their community organization in response to an aquaculture effluent gradient in the largest oxbow lake in the Carpathian Basin, Hungary. Sampling was carried out three times per season at five points along a 3.5 km section of the oxbow lake, including the point of effluent inflow. We used eight traits to evaluate functional diversity: body size, trophi type, feeding mode, protection type, body wall type, corona type, habitat preference and tolerance level. Functional and phylogenetic distances among the 24 species identified indicated trait conservatism. Rotiferan diversity increased with increasing distance from the point of influx in spring and summer. Among the factors affecting community organization in spring and summer, we find examples of environmental filtering, while in autumn the role of biotic interaction is more frequent. Under nutrient-rich conditions in spring and summer, organisms belonging to the same functional group were dominant, whereas under oligotrophic conditions, more diverse but less abundant groups were present. Considering functional and phylogenetic traits allowed us to identify organising forces of rotifer communities in the largest oxbow lake of the Hungarian Lowland.}, }
@article {pmid37680030, year = {2023}, author = {Moran, ME and Aparecido, LMT and Koepke, DF and Cooper, HF and Doughty, CE and Gehring, CA and Throop, HL and Whitham, TG and Allan, GJ and Hultine, KR}, title = {Limits of thermal and hydrological tolerance in a foundation tree species (Populus fremontii) in the desert southwestern United States.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19247}, pmid = {37680030}, issn = {1469-8137}, support = {DEB-1340852//National Science Foundation/ ; DEB-1340856//National Science Foundation/ ; DEB-2017895//National Science Foundation/ ; }, abstract = {Populus fremontii is among the most dominant, and ecologically important riparian tree species in the western United States and can thrive in hyper-arid riparian corridors. Yet, P. fremontii forests have rapidly declined over the last decade, particularly in places where temperatures sometimes exceed 50°C. We evaluated high temperature tolerance of leaf metabolism, leaf thermoregulation, and leaf hydraulic function in eight P. fremontii populations spanning a 5.3°C mean annual temperature gradient in a well-watered common garden, and at source locations throughout the lower Colorado River Basin. Two major results emerged. First, despite having an exceptionally high Tcrit (the temperature at which Photosystem II is disrupted) relative to other tree taxa, recent heat waves exceeded Tcrit , requiring evaporative leaf cooling to maintain leaf-to-air thermal safety margins. Second, in midsummer, genotypes from the warmest locations maintained lower midday leaf temperatures, a higher midday stomatal conductance, and maintained turgor pressure at lower water potentials than genotypes from more temperate locations. Taken together, results suggest that under well-watered conditions, P. fremontii can regulate leaf temperature below Tcrit along the warm edge of its distribution. Nevertheless, reduced Colorado River flows threaten to lower water tables below levels needed for evaporative cooling during episodic heat waves.}, }
@article {pmid37678709, year = {2023}, author = {Green Ii, DA}, title = {Tracking technologies: advances driving new insights into monarch migration.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {101111}, doi = {10.1016/j.cois.2023.101111}, pmid = {37678709}, issn = {2214-5753}, abstract = {Understanding the rules of how monarch butterflies complete their annual North American migration will be clarified by studying them within a movement ecology framework. Insect movement ecology is growing at a rapid pace due to the development of novel monitoring systems that allow ever smaller animals to be tracked at higher spatiotemporal resolution for longer periods of time. New innovations in tracking hardware and associated software, including miniaturization, energy autonomy, data management, and wireless communication, are reducing the size and increasing the capability of next generation tracking technologies, bringing the goal of tracking monarchs over their entire migration closer within reach. These tools are beginning to be leveraged to provide insight into different aspects of monarch biology and ecology, and to contribute to a growing capacity to understand insect movement ecology more broadly and its impact on human life.}, }
@article {pmid37674876, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Feathered Gothic, Tholera decimalis (Poda, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {200}, pmid = {37674876}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Tholera decimalis (the Feathered Gothic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,334.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,771 protein coding genes.}, }
@article {pmid37674686, year = {2023}, author = {Asaaga, FA and Sriram, A and Chanda, MM and Hoti, SL and Young, JC and Purse, BV}, title = {'It doesn't happen how you think, it is very complex!' Reconciling stakeholder priorities, evidence, and processes for zoonoses prioritisation in India.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1228950}, pmid = {37674686}, issn = {2296-2565}, mesh = {Animals ; Humans ; *Administrative Personnel ; *Cost of Illness ; Health Policy ; India ; Zoonoses/prevention &amp; control ; }, abstract = {BACKGROUND: Why do some zoonotic diseases receive priority from health policy decision-makers and planners whereas others receive little attention? By leveraging Shiffman and Smith's political prioritisation framework, our paper advances a political economy of disease prioritisation focusing on four key components: the strength of the actors involved in the prioritisation, the power of the ideas they use to portray the issue, the political contexts in which they operate, and the characteristics of the issue itself (e.g., overall burdens, severity, cost-effective interventions). These components afford a nuanced characterisation of how zoonotic diseases are prioritised for intervention and highlight the associated knowledge gaps affecting prioritisation outcomes. We apply this framework to the case of zoonoses management in India, specifically to identify the factors that shape disease prioritisation decision-making and outcomes.<br><br>METHODS: We conducted 26 semi-structured interviews with national, state and district level health policymakers, disease managers and technical experts involved in disease surveillance and control in India.<br><br>RESULTS: Our results show pluralistic interpretation of risks, exemplified by a disconnect between state and district level actors on priority diseases. The main factors identified as shaping prioritisation outcomes were related to the nature of the zoonoses problem (the complexity of the zoonotic disease, insufficient awareness and lack of evidence on disease burdens and impacts) as well as political, social, cultural and institutional environments (isolated departmental priorities, limited institutional authority, opaque funding mechanisms), and challenges in organisation leadership for cross-sectoral engagement.<br><br>CONCLUSION: The findings highlight a compartmentalised regulatory system for zoonoses where political, social, cultural, and media factors can influence disease management and prioritisation. A major policy window is the institutionalisation of One Health to increase the political priority for strengthening cross-sectoral engagement to address several challenges, including the creation of effective institutions to reconcile stakeholder priorities and prioritisation processes.}, }
@article {pmid37674040, year = {2023}, author = {Lu, AT and Fei, Z and Haghani, A and Robeck, TR and Zoller, JA and Li, CZ and Lowe, R and Yan, Q and Zhang, J and Vu, H and Ablaeva, J and Acosta-Rodriguez, VA and Adams, DM and Almunia, J and Aloysius, A and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, GG and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, SM and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and DiRocco, S and Dold, C and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Gorbunova, V and Goya, RG and Grant, MJ and Green, CB and Hales, EN and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaitre, JF and Levine, AJ and Li, C and Li, X and Lim, AR and Lin, DTS and Lindemann, DM and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and O'Brien, JK and O'Tierney Ginn, P and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pellegrini, M and Peters, KJ and Pedersen, AB and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Seluanov, A and Shafer, ABA and Shanmuganayagam, D and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmaohammadi, E and Spangler, ML and Spriggs, MC and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Wallingford, MC and Wang, N and Wayne, RK and Wilkinson, GS and Williams, CK and Williams, RW and Yang, XW and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, P and Zhao, Y and Zhou, W and Zimmermann, J and Ernst, J and Raj, K and Horvath, S}, title = {Author Correction: Universal DNA methylation age across mammalian tissues.}, journal = {Nature aging}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43587-023-00499-7}, pmid = {37674040}, issn = {2662-8465}, }
@article {pmid37673539, year = {2023}, author = {Pinho-Gomes, AC and Roaf, E and Fuller, G and Fowler, D and Lewis, A and ApSimon, H and Noakes, C and Johnstone, P and Holgate, S}, title = {Air pollution and climate change.}, journal = {The Lancet. Planetary health}, volume = {7}, number = {9}, pages = {e727-e728}, doi = {10.1016/S2542-5196(23)00189-4}, pmid = {37673539}, issn = {2542-5196}, }
@article {pmid37670833, year = {2023}, author = {Zhylkybekova, A and Turlayev, A and Grjibovski, AM and Koshmaganbetova, GK}, title = {Measures to support informal care for the older adults in Kazakhstan: a review of the current status.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1247684}, pmid = {37670833}, issn = {2296-2565}, mesh = {Child ; Humans ; Aged ; Kazakhstan ; *Quality of Life ; *Patient Care ; Long-Term Care ; Databases, Factual ; }, abstract = {The demand for informal caregivers to support the older adults has grown worldwide in recent decades. However, informal caregivers themselves require support. This article aims to examine existing support measures for caregivers of the older adults in the Republic of Kazakhstan. Relevant articles and grey literature were identified through manual searches on Google and Google Scholar, as well as electronic searches using indexed databases like PubMed, Web of Science, and Scopus. Moreover, the reference lists of identified sources and government ministry websites were meticulously scrutinized. This review highlights the scarcity of research on caregiver support measures in Kazakhstan, supported by the lack of peer-reviewed articles on this subject. A comprehensive analysis of the literature shows that in Kazakhstan's legislative framework, "caregivers" exclusively refers to individuals providing care for a first-degree disability. The responsibility of caring for older adults parents lies with able-bodied children. However, there is a lack of registration and assessment procedures to evaluate the burden and quality of life of caregivers. As a result, the medical and social support provided to caregivers is standardized, failing to adequately address their unique needs and requirements. The analysis of current support measures for informal caregivers highlights the need to develop support mechanisms and recognize individuals providing informal care as key figures in the long-term care system.}, }
@article {pmid37667004, year = {2023}, author = {Li, Y and Niu, Z and Zhu, M and Wang, Z and Xu, R and Li, M and Zheng, Z and Lu, Z and Dong, C and Hu, H and Yang, Y and Wu, Y and Wang, D and Yang, J and Zhang, J and Wan, D and Abbott, R and Liu, J and Yang, Y}, title = {Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {906}, pmid = {37667004}, issn = {2399-3642}, mesh = {*Rheum/genetics ; Multiomics ; Acclimatization/genetics ; Comparative Genomic Hybridization ; Down-Regulation ; }, abstract = {Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.}, }
@article {pmid37665400, year = {2023}, author = {Bayer, JM and Scully, RA and Dlabola, EK and Courtwright, JL and Hirsch, CL and Hockman-Wert, D and Miller, SW and Roper, BB and Saunders, WC and Snyder, MN}, title = {Sharing FAIR monitoring program data improves discoverability and reuse.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {10}, pages = {1141}, pmid = {37665400}, issn = {1573-2959}, mesh = {*Environmental Monitoring ; *Natural Resources ; }, abstract = {Data resulting from environmental monitoring programs are valuable assets for natural resource managers, decision-makers, and researchers. These data are often collected to inform specific reporting needs or decisions with a specific timeframe. While program-oriented data and related publications are effective for meeting program goals, sharing well-documented data and metadata allows users to research aspects outside initial program intentions. As part of an effort to integrate data from four long-term large-scale US aquatic monitoring programs, we evaluated the original datasets against the FAIR (Findable, Accessible, Interoperable, Reusable) data principles and offer recommendations and lessons learned. Differences in data governance across these programs resulted in considerable effort to access and reuse the original datasets. Requirements, guidance, and resources available to support data publishing and documentation are inconsistent across agencies and monitoring programs, resulting in various data formats and storage locations that are not easily found, accessed, or reused. Making monitoring data FAIR will reduce barriers to data discovery and reuse. Programs are continuously striving to improve data management, data products, and metadata; however, provision of related tools, consistent guidelines and standards, and more resources to do this work is needed. Given the value of these data and the significant effort required to access and reuse them, actions and steps intended on improving data documentation and accessibility are described.}, }
@article {pmid37663792, year = {2023}, author = {Boyes, D and Sims, I and Holland, PWH and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Round-winged Muslin, Thumatha senex (Hübner, 1804).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {298}, pmid = {37663792}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Thumatha senex (the Round-winged Muslin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 810.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.}, }
@article {pmid37663789, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Light Brocade, Lacanobia w-latinum (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {299}, pmid = {37663789}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Lacanobia w-latinum (the Light Brocade; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 903.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,592 protein coding genes.}, }
@article {pmid37663407, year = {2023}, author = {Günther, F and Wong, D and Elison-Davies, S and Yau, C}, title = {Identifying factors associated with user retention and outcomes of a digital intervention for substance use disorder: a retrospective analysis of real-world data.}, journal = {JAMIA open}, volume = {6}, number = {3}, pages = {ooad072}, pmid = {37663407}, issn = {2574-2531}, abstract = {OBJECTIVES: Successful delivery of digital health interventions is affected by multiple real-world factors. These factors may be identified in routinely collected, ecologically valid data from these interventions. We propose ideas for exploring these data, focusing on interventions targeting complex, comorbid conditions.<br><br>MATERIALS AND METHODS: This study retrospectively explores pre-post data collected between 2016 and 2019 from users of digital cognitive behavioral therapy (CBT)-containing psychoeducation and practical exercises-for substance use disorder (SUD) at UK addiction services. To identify factors associated with heterogenous user responses to the technology, we employed multivariable and multivariate regressions and random forest models of user-reported questionnaire data.<br><br>RESULTS: The dataset contained information from 14&#x200a;078 individuals of which 12&#x200a;529 reported complete data at baseline and 2925 did so again after engagement with the CBT. Ninety-three percent screened positive for dependence on 1 of 43 substances at baseline, and 73% screened positive for anxiety or depression. Despite pre-post improvements independent of user sociodemographics, women reported more frequent and persistent symptoms of SUD, anxiety, and depression. Retention-minimum 2 use events recorded-was associated more with deployment environment than user characteristics. Prediction accuracy of post-engagement outcomes was acceptable (Area Under Curve [AUC]: 0.74-0.79), depending non-trivially on user characteristics.<br><br>DISCUSSION: Traditionally, performance of digital health interventions is determined in controlled trials. Our analysis showcases multivariate models with which real-world data from these interventions can be explored and sources of user heterogeneity in retention and symptom reduction uncovered.<br><br>CONCLUSION: Real-world data from digital health interventions contain information on natural user-technology interactions which could enrich results from controlled trials.}, }
@article {pmid37659520, year = {2023}, author = {Schulz, G and van Beusekom, JEE and Jacob, J and Bold, S and Schöl, A and Ankele, M and Sanders, T and Dähnke, K}, title = {Low discharge intensifies nitrogen retention in rivers - A case study in the Elbe River.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166740}, doi = {10.1016/j.scitotenv.2023.166740}, pmid = {37659520}, issn = {1879-1026}, abstract = {Eutrophication due to excessive nutrient inputs is a major threat to coastal ecosystems worldwide, causing harmful algae blooms, seagrass loss and hypoxia. Decisions to combat eutrophication in the North Sea were made in the 1980s. Despite significant improvements during recent decades, high nitrogen loads and resulting eutrophication problems remain. In this study, long-term changes in nitrogen inputs to the Elbe Estuary (Germany) were characterized based on nitrogen data provided by the Elbe River Basin Community from 1985 to 2019. Additionally, surface water samples were taken at the weir separating the river from the estuary from 2011 to 2021 to characterize dissolved inorganic nitrogen concentrations and nitrate stable isotope composition. The findings suggest a close coupling of river discharge with the riverine nitrogen cycle. Nitrogen loads decreased disproportionately with decreasing discharge. This decrease is due to intensified nitrogen retention in the Elbe catchment, which can double nitrogen retention compared to average discharge conditions. Phytoplankton growth was enhanced by long residence times and high light availability at low water levels. This suggests that the recent decreases in nitrogen loads in the Elbe River were not only a result of management measures in the catchment but were also amplified by a recent long-lasting drought in the catchment. Based on projections from the Intergovernmental Panel on Climate Change, more frequent and extensive droughts are anticipated, which may lead to future seasonal shifts to nitrate limitation in the lower Elbe River.}, }
@article {pmid37658362, year = {2023}, author = {Bezerra, ALL and de Almeida, PRB and Reis, RK and Ferreira, GRON and Sousa, FJD and Gir, E and Botelho, EP}, title = {Human immunodeficiency virus epidemic scenery among brazilian women: a spatial analysis study.}, journal = {BMC women's health}, volume = {23}, number = {1}, pages = {463}, pmid = {37658362}, issn = {1472-6874}, mesh = {Humans ; Female ; Adolescent ; *HIV ; Brazil/epidemiology ; Spatial Analysis ; Databases, Factual ; *HIV Infections/epidemiology ; }, abstract = {BACKGROUND: Approximately 37.7 million people worldwide are infected with human immunodeficiency virus (HIV). Although HIV detection among women, they still representing 53% of population living with the virus. Spatial analysis techniques are powerful tools for combating HIV allowing the association of the phenomenon with socioeconomic and political factors. Therefore, the main goal of this study was to spatially analyze HIV prevalence among Brazilian women from 2007 to 2020.<br><br>METHODS: ecological study was conducted using secondary databases of the Notifiable Diseases Information System (SINAN) for HIV and Acquired Immunodeficiency Syndrom (AIDS) in Brazilian women 15 years old and over. Age-adjusted HIV/AIDS incidence rates were analyzed using spatial distribution, autocorrelation, and spatiotemporal risk analysis techniques.<br><br>RESULTS: During the study period, 119,890 cases of HIV/AIDS were reported among Brazilian women. The southeastern region had a higher age-adjusted HIV/AIDS incidence than other Brazilian regions. Hotspot HIV/AIDS incidence rates decreased in all Brazil. Piau&#xed;, Paran&#xe1;, and Minas Gerais were the only states with an increased number of cold spots. Previous spatiotemporal risk zones were observed in the states of S&#xe3;o Paulo, Rio Grande do Sul, and Rio de Janeiro. Bel&#xe9;m was a risk zone with a later spatiotemporal risk.<br><br>CONCLUSIONS: The efficiency of public policies fighting HIV has not been uniform among municipalities, although HIV/AIDS cases have decreased among Brazilian women. The social determinants of health in each municipality should be considered when local health authorities implement policies. Women empowerment should be promoted, and access to preventive, diagnostic, and treatment healthcare places should be expanded and guaranteed.}, }
@article {pmid37654707, year = {2023}, author = {LeBaron, V and Homdee, N and Ogunjirin, E and Patel, N and Blackhall, L and Lach, J}, title = {Describing and visualizing the patient and caregiver experience of cancer pain in the home context using ecological momentary assessments.}, journal = {Digital health}, volume = {9}, number = {}, pages = {20552076231194936}, pmid = {37654707}, issn = {2055-2076}, abstract = {BACKGROUND: Pain continues to be a difficult and pervasive problem for patients with cancer, and those who care for them. Remote health monitoring systems (RHMS), such as the Behavioral and Environmental Sensing and Intervention for Cancer (BESI-C), can utilize Ecological Momentary Assessments (EMAs) to provide a more holistic understanding of the patient and family experience of cancer pain within the home context.<br><br>METHODS: Participants used the BESI-C system for 2-weeks which collected data via EMAs deployed on wearable devices (smartwatches) worn by both patients with cancer and their primary family caregiver. We developed three unique EMA schemas that allowed patients and caregivers to describe patient pain events and perceived impact on quality of life from their own perspective. EMA data were analyzed to provide a descriptive summary of pain events and explore different types of data visualizations.<br><br>RESULTS: Data were collected from five (n&#x2009;=&#x2009;5) patient-caregiver dyads (total 10 individual participants, 5 patients, 5 caregivers). A total of 283 user-initiated pain event EMAs were recorded (198 by patients; 85 by caregivers) over all 5 deployments with an average severity score of 5.4/10 for patients and 4.6/10 for caregivers' assessments of patient pain. Average self-reported overall distress and pain interference levels (1&#x2009;=&#x2009;least distress; 4&#x2009;=&#x2009;most distress) were higher for caregivers (x&#xaf; 3.02, x&#xaf;2.60,respectively) compared to patients (x&#xaf; 2.82, x&#xaf; 2.25, respectively) while perceived burden of partner distress was higher for patients (i.e., patients perceived caregivers to be more distressed, x&#xaf; 3.21, than caregivers perceived patients to be distressed, x&#xaf;2.55). Data visualizations were created using time wheels, bubble charts, box plots and line graphs to graphically represent EMA findings.<br><br>CONCLUSION: Collecting data via EMAs is a viable RHMS strategy to capture longitudinal cancer pain event data from patients and caregivers that can inform personalized pain management and distress-alleviating interventions.}, }
@article {pmid37654007, year = {2023}, author = {Papadopoulos, NG and Akdis, C and Akdis, M and Damialis, A and Esposito, G and Fergadiotou, I and Goroncy, C and Guitton, P and Gotua, M and Erotokritou, K and Jartti, T and Murray, C and Nenes, A and Nikoletseas, S and Finotto, S and Pandis, SN and Ramiconi, V and Simpson, A and Soudunsaari, A and Stårbröst, A and Staiano, M and Varriale, A and Xepapadaki, P and Zuberbier, T and Annesi-Maesano, I and , }, title = {Addressing adverse synergies between chemical and biological pollutants at schools-The 'SynAir-G' hypothesis.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.15857}, pmid = {37654007}, issn = {1398-9995}, support = {101057271//HORIZON EUROPE Health/ ; }, abstract = {While the number and types of indoor air pollutants is rising, much is suspected but little is known about the impact of their potentially synergistic interactions, upon human health. Gases, particulate matter, organic compounds but also allergens and viruses, fall within the 'pollutant' definition. Distinct populations, such as children and allergy and asthma sufferers are highly susceptible, while a low socioeconomic background is a further susceptibility factor; however, no specific guidance is available. We spend most of our time indoors; for children, the school environment is of paramount importance and potentially amenable to intervention. The interactions between some pollutant classes have been studied. However, a lot is missing with respect to understanding interactions between specific pollutants of different classes in terms of concentrations, timing and sequence, to improve targeting and upgrade standards. SynAir-G is a European Commission-funded project aiming to reveal and quantify synergistic interactions between different pollutants affecting health, from mechanisms to real life, focusing on the school setting. It will develop a comprehensive and responsive multipollutant monitoring system, advance environmentally friendly interventions, and disseminate the generated knowledge to relevant stakeholders in accessible and actionable formats. The aim of this article it to put forward the SynAir-G hypothesis, and describe its background and objectives.}, }
@article {pmid37651934, year = {2023}, author = {Fang, R and Chen, T and Han, Z and Ji, W and Bai, Y and Zheng, Z and Su, Y and Jin, L and Xie, B and Wu, D}, title = {From air to airway: Dynamics and risk of inhalable bacteria in municipal solid waste treatment systems.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132407}, doi = {10.1016/j.jhazmat.2023.132407}, pmid = {37651934}, issn = {1873-3336}, abstract = {Municipal solid waste treatment (MSWT) system emits a cocktail of microorganisms that jeopardize environmental and public health. However, the dynamics and risks of airborne microbiota associated with MSWT are poorly understood. Here, we analyzed the bacterial community of inhalable air particulates (PM10, n = 71) and the potentially exposed on-site workers' throat swabs (n = 30) along with waste treatment chain in Shanghai, the largest city of China. Overall, the airborne bacteria varied largely in composition and abundance during the treatment (P < 0.05), especially in winter. Compared to the air conditions, MSWT-sources that contributed to 15 ∼ 70% of airborne bacteria more heavily influenced the PM10-laden bacterial communities (PLS-SEM, β = 0.40, P < 0.05). Moreover, our year-span analysis found PM10 as an important media spreading pathogens (10[4] ∼ 10[8] copies/day) into on-site workers. The machine-learning identified Lactobacillus and Streptococcus as pharynx-niched featured biomarker in summer and Rhodococcus and Capnocytophaga in winter (RandomForest, ntree = 500, mtry = 10, cross = 10, OOB = 0%), which closely related to their airborne counterparts (Procrustes test, P < 0.05), suggesting that MSWT a dynamic hotspot of airborne bacteria with the pronounced inhalable risks to the neighboring communities.}, }
@article {pmid37648185, year = {2023}, author = {Tan, M and Bian, Z and Dong, J and Hao, M and Qu, J}, title = {Comparing the variation and influencing factors of CO2 emission from subsidence waterbodies under different restoration modes in coal mining area.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116936}, doi = {10.1016/j.envres.2023.116936}, pmid = {37648185}, issn = {1096-0953}, abstract = {Subsidence waterbodies play an important role in carbon cycle in coal mining area. However, little effort has been made to explore the carbon dioxide (CO2) release characteristics and influencing factors in subsidence waterbodies, especially under different restoration modes. Here, we measured CO2 release fluxes (F(CO2)) across Anguo wetland (AW), louts pond (LP), fishpond (FP), fishery-floating photovoltaic wetland (FFPV), floating photovoltaic wetland (FPV) in coal mining subsidence area, with unrestored subsidence waterbodies (SW) and unaffected normal Dasha river (DR) as the control area. We sampled each waterbody and tested which physical, chemical, and biological characteristics of water and sediment related to variability in CO2. The results indicated that F(CO2) exhibited the following patterns: FFPV > FPV > FP > SW > DR > LP > AW. Trophic lake index (TLI) and microbial biomass carbon content (MBC) in sediment had a positive impact on F(CO2). The dominant archaea Euryarchaeota and Thaumarchaeota, and dominant bacteria Proteobacteria promoted F(CO2). This study can help more accurately quantify CO2 emissions and guide CO2 future emission reduction and subsidence waterbodies estoration.}, }
@article {pmid37646945, year = {2023}, author = {Bosch, M and López-Pujol, J and Blanché, C and Simon, J}, title = {DCDB: Chromosome Database of Tribe Delphinieae (Ranunculaceae): Structure, Exploitation, and Recent Development.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2703}, number = {}, pages = {173-192}, pmid = {37646945}, issn = {1940-6029}, mesh = {*Ranunculaceae ; Phylogeny ; Cytogenetic Analysis ; Databases, Factual ; Internet ; }, abstract = {An updated (and now online) version of the former chromosome database of tribe Delphinieae (Ranunculaceae) is presented (http://www.delphinieae.online). This new version is the result of an accurate, exhaustive literature and Internet research, by adding chromosome counts and all related karyological information for the genera Aconitum L., Gymnaconitum (Stapf) Wei Wang &amp; Z. D. Chen, Delphinium L. (including Staphisagria Spach), Consolida (DC.) S. F. Gray and Aconitella Spach, accumulated during the approximately last 25 years and that comprise worldwide published data from 1889 to 2021. The Delphinieae Chromosome Database (DCDB) (last updated 31.12.2021) contains a total number of 3435 reports belonging to 425 species (503 taxa), which represents 48.6% of the total species of the tribe (an increase of c. 213% and 32% compared with the 1097 and 2598 reports gathered in the 1999 and 2016 versions, respectively). This increase is due both to chromosome research progress and to improved information capture system. Moreover, recent taxonomic advances, synonymization, and new phylogenetic criteria have also been considered.The DCDB database provides the most complete currently available information on published chromosome numbers, ploidy-level estimates, and other karyological data of Delphinieae, and it is aimed to be useful for the building of cytotaxonomical databases and for specific research ongoing projects of systematics and evolution of Ranunculaceae. DCDB includes two levels of taxonomic resolution, published name (original and standardized form) and database accepted name (based on either Plants of the World - POWO or expert specialist criteria), as well as the geographic origin of each count (country, locality, geographic coordinates, elevation, or ecological information when reported in the original publication), associated karyological data if originally provided (studied material type, graphic information, chromosome measures and formulas, satellites, B chromosomes, other cytogenetic techniques used, etc.), voucher information and reference (with DOI and other links to access the original document). An effort to check the original sources and to search in grey literature allowed to indicate the counts that appear to be registered twice.}, }
@article {pmid37646941, year = {2023}, author = {Henniges, MC and Johnston, E and Pellicer, J and Hidalgo, O and Bennett, MD and Leitch, IJ}, title = {The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2703}, number = {}, pages = {111-122}, pmid = {37646941}, issn = {1940-6029}, mesh = {Genome Size ; *Genome, Plant ; Cytogenetics ; DNA, Plant/genetics ; *Databases, Nucleic Acid ; }, abstract = {Genome size is a plant character with far-reaching implications, ranging from impacts on the financial and computing feasibility of sequencing and assembling genomes all the way to influencing the very ecology and evolution of species. The increasing recognition of the role of genome size in plant science has led to a rising demand for comprehensive and easily accessible sources of genome size data. The Plant DNA C-values database has established itself as a trusted and widely used central hub for users needing to access available plant genome size data, complemented with related cytogenetic (ploidy level) and karyological (chromosome number) information where available. Since its inception in 2001, the database has undergone six major updates to incorporate newly available genome size information, leading to the most recent release (Release 7.1), which comprises data for 12,273 species across all the major land plant and some algal lineages. Here we describe how to use the database efficiently, making use of its different query and filtering settings.}, }
@article {pmid37645296, year = {2022}, author = {Anegg, M and Prakofjewa, J and Kalle, R and Sõukand, R}, title = {Local ecological knowledge and folk medicine in historical Estonia, Livonia, Courland and Galicia in Northeastern Europe, 1805-1905.}, journal = {Open research Europe}, volume = {2}, number = {}, pages = {30}, pmid = {37645296}, issn = {2732-5121}, abstract = {Background: Historical ethnobotanical data can provide valuable information about past human-nature relationships as well as serve as a basis for diachronic analysis. This data note aims to present a dataset which documented medicinal plant uses, mentioned in a selection of German-language sources from the 19 [th] century covering the historical regions of Estonia, Livonia, Courland, and Galicia. Methods: Data was mainly entered by systematic manual search in various ethnobotanical historical German-language works focused on the medicinal use of plants. Data about plant and non-plant constituents, their usage, the mode of administration, used plant parts, and their German and local names was extracted and collected into a database in the form of Use Reports.}, }
@article {pmid37644145, year = {2023}, author = {Zhao, W and Zhang, P and Chen, D and Wang, H and Gu, B and Zhang, J}, title = {Data mining from process monitoring of typical polluting enterprise.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {9}, pages = {1109}, pmid = {37644145}, issn = {1573-2959}, support = {2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 2022HT0009//Ecological Environment Research and Achievement Extension Project of Zhejiang Province/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 22gyb37//Science and Technology Plan Project of Taizhou/ ; 2021C03178//Science and Technology Program of Zhejiang Province/ ; 2021C03178//Science and Technology Program of Zhejiang Province/ ; }, mesh = {*Environmental Monitoring ; *Wastewater ; Data Mining ; China ; Electric Conductivity ; Vehicle Emissions ; }, abstract = {With the increasing volume of environmental monitoring data, extracting valuable insights from multivariate time series sensor data can facilitate comprehensive information utilization and support informed decision-making in environmental management. However, there is a dearth of comprehensive research on multivariate data analysis for process monitoring in typical polluting enterprises. In this study, an artificial neural network model based on back-propagation algorithm (BP-ANN) was developed to predict the wastewater and exhaust gas emissions using IoT data obtained from process monitoring of a typical polluting enterprise located in Taizhou, Zhejiang Province, China. The results indicate that the model constructed has a high predictive coefficient of determination (R[2]) with values of 0.8510, 0.9565, 0.9561, 0.9677, and 0.9061 for chemical oxygen demand (COD), potential of hydrogen (pH), electrical conductivity (EC), flue gas emission (FGE), and non-methane hydrocarbon concentration (NMHC) respectively. For the first time, the variable importance measure (VIM)-assisted BP-ANN was employed to investigate the internal and external correlations between wastewater and exhaust gas treatment, thereby enhancing the interpretability of mapping features in the BP-ANN model. The predicted errors for pH and FGE have been demonstrated to fall within the range of - 0.62 ~ 0.30 and - 0.21 ~ 0.15 m[3]/s, respectively, with average relative errors of 1.05% and 9.60%, which is advantageous in detecting anomalous data and forecasting pollution indicator values. Our approach successfully addresses the challenge of segregating data analysis for wastewater disposal and exhaust gas disposal in the process monitoring of polluting enterprises, while also unearthing potential variables that significantly contribute to the BP-ANN model, thereby facilitating the selection and extraction of characteristic variables.}, }
@article {pmid37642912, year = {2023}, author = {Goparaju, L and Pillutla, RCP and Venkata, SBK}, title = {Assessment of forest fire emissions in Uttarakhand State, India, using Open Geospatial data and Google Earth Engine.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37642912}, issn = {1614-7499}, abstract = {In the recent past, forest fires have increased due to the changing climate pattern. It is necessary to analyse and quantify various gaseous emissions so as to mitigate their harmful effects on air pollution. Satellite remote sensing data provides an opportunity to study the greenhouse gases in the atmosphere. The multispectral sensor of the Tropospheric Monitoring Instrument (Sentinel-5) is capable of recording the reflectance of wavelengths vital for measuring the atmospheric concentrations of methane, formaldehyde, aerosol, carbon monoxide, etc., at a spatial resolution of 0.01°. The present study utilized the Google Earth Engine (GEE) platform to study the emissions caused by forest fires in four districts of Uttarakhand State of India, which witnessed unprecedented fires in April-May 2021. All the datasets were ingested in GEE, which has the capability to analyse large datasets without the need to download them. The pre-fire period chosen was September 2020; the fire period was February-May 2021, and the post-fire period was June 2021. The variables chosen were aerosol absorbing index (AAI), carbon monoxide (CO) and nitrogen dioxide (NO2). The climate parameter temperature (Moderate Resolution Imaging Spectroradiometer Land Surface Temperature) and precipitation (from Climate Hazards Group InfraRed Precipitation (CHIRPS) Pentad) were also studied for the period mentioned. The results indicate a different trend for emissions in each district. For AAI, maximum emissions were noted in district Nainital followed by Almora, Tehri Garhwal and Garhwal. For CO emissions, the most affected district was Almora followed by Nainital, Garhwal and Tehri Garhwal. For NO2 emissions, the most affected district was Garhwal, followed by Nainital, Tehri Garhwal and Almora. Delta Normalized Burn Ratio was computed from Sentinel data (difference of pre-fire and post-fire images) to assess the burnt area severity. The Delta Normalized Burn Ratio values observed that the district with the most burnt area is Garhwal, followed by Nainital, Almora and Tehri Garhwal. The elevated temperatures and scanty rainfall patterns regulated the intensity and duration of forest fire. Monitoring the gaseous emissions as a consequence of forest fire in the GEE platform is much easier and more convenient at a regional level. Such data is much needed for mitigation measures to be implemented in time.}, }
@article {pmid37640770, year = {2023}, author = {Mudge, L and Bruno, JF}, title = {Disturbance intensification is altering the trait composition of Caribbean reefs, locking them into a low functioning state.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14022}, pmid = {37640770}, issn = {2045-2322}, support = {OCE-1737071//National Science Foundation/ ; }, mesh = {Animals ; Caribbean Region ; *Anthozoa ; Climate Change ; *Cyclonic Storms ; Databases, Factual ; *Marijuana Abuse ; Plant Weeds ; }, abstract = {Anthropogenic climate change is intensifying natural disturbance regimes, which negatively affects some species, while benefiting others. This could alter the trait composition of ecological communities and influence resilience to disturbance. We investigated how the frequency and intensification of the regional storm regime (and likely other disturbances) is altering coral species composition and in turn resistance and recovery. We developed regional databases of coral cover and composition (3144 reef locations from 1970 to 2017) and of the path and strength of cyclonic storms in the region (including 10,058 unique storm-reef intersections). We found that total living coral cover declined steadily through 2017 (the median annual loss rate was ~ 0.25% per year). Our results also indicate that despite the observed increase in the intensity of Atlantic cyclonic storms, their effect on coral cover has decreased markedly. This could be due in part to selection for disturbance-resistant taxa in response to the intensifying disturbance regime. We found that storms accelerated the loss of threatened acroporid corals but had no measurable effect on the cover of more resilient "weedy" corals, thereby increasing their relative cover. Although resistance to disturbance has increased, recovery rates have slowed due to the dominance of small, slow-growing species. This feedback loop is locking coral communities into a low-functioning state dominated by weedy species with limited ecological or societal value.}, }
@article {pmid37636281, year = {2023}, author = {Wang, F and Liu, J and Qin, G and Zhang, J and Zhou, J and Wu, J and Zhang, L and Thapa, P and Sanders, CJ and Santos, IR and Li, X and Lin, G and Weng, Q and Tang, J and Jiao, N and Ren, H}, title = {Coastal blue carbon in China as a nature-based solution toward carbon neutrality.}, journal = {Innovation (Cambridge (Mass.))}, volume = {4}, number = {5}, pages = {100481}, pmid = {37636281}, issn = {2666-6758}, abstract = {To achieve the Paris Agreement, China pledged to become "Carbon Neutral" by the 2060s. In addition to massive decarbonization, this would require significant changes in ecosystems toward negative CO2 emissions. The ability of coastal blue carbon ecosystems (BCEs), including mangrove, salt marsh, and seagrass meadows, to sequester large amounts of CO2 makes their conservation and restoration an important "nature-based solution (NbS)" for climate adaptation and mitigation. In this review, we examine how BCEs in China can contribute to climate mitigation. On the national scale, the BCEs in China store up to 118 Tg C across a total area of 1,440,377 ha, including over 75% as unvegetated tidal flats. The annual sedimental C burial of these BCEs reaches up to 2.06 Tg C year[-1], of which most occurs in salt marshes and tidal flats. The lateral C flux of mangroves and salt marshes contributes to 1.17 Tg C year[-1] along the Chinese coastline. Conservation and restoration of BCEs benefit climate change mitigation and provide other ecological services with a value of $32,000 ha[-1] year[-1]. The potential practices and technologies that can be implemented in China to improve BCE C sequestration, including their constraints and feasibility, are also outlined. Future directions are suggested to improve blue carbon estimates on aerial extent, carbon stocks, sequestration, and mitigation potential. Restoring and preserving BCEs would be a cost-effective step to achieve Carbon Neutral by 2060 in China despite various barriers that should be removed.}, }
@article {pmid37635752, year = {2023}, author = {Boyes, D and Boyes, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Powdered Quaker, Orthosia gracilis (Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {290}, pmid = {37635752}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Orthosia gracilis (the powdered quaker; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 715.5 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.43 kilobases in length.}, }
@article {pmid37634178, year = {2023}, author = {Zhou, L and Ye, T and Zheng, S and Zhu, X and Chen, Z and Wu, Y}, title = {Experimental and modeling investigation of dual-source iron release in water-solid-gas interaction of abandoned coal mine drainage.}, journal = {Environmental geochemistry and health}, volume = {}, number = {}, pages = {}, pmid = {37634178}, issn = {1573-2983}, support = {2022YFC3702203//the National Key R&amp;D Program of China/ ; 2020ZDPYMS07//the Fundamental Research Funds for the Central Universities, China/ ; }, abstract = {After mine closure and flooding, abandoned iron-prone devices and equipment (e.g., steel bolts and ground support meshes) and iron-bearing minerals (e.g., pyrite) form a dual-source iron pollution system in mine groundwater. Dual-source iron contributes to the water-solid-gas interaction in abandoned coal mines and the release of iron at different periods after mine closure, posing environmental risks in groundwater and discharging acid mine drainage, which contains large amounts of iron. In this study, a series of hydrochemical experiments were conducted to simulate the iron release process of the dual-source system, and electrochemical experiments were carried out to reveal the reaction mechanism, characterize the dual-source iron pollution release mode and quantify the release rate ratio. PHREEQC package was used to simulate the long-term hydrogeochemistry reactions of the water-solid-gas interaction to determine the key factors and suitable conditions that inhibit dual-source iron release. The results show that the dual-source system of iron-bearing minerals (pyrite) and steel bolts promote iron release from each other. The resulting calculated annual iron release indicated that the overall iron release rate ratio is: dual-source > bolt > pyrite, indicating that mine water would remain acidic for a long time due to the continuous release of iron from the system. Numerical modeling results show that maintaining the environment temperature below 25 °C and the pH above 3.5 is an effective way to reduce the iron release rate.}, }
@article {pmid37634023, year = {2023}, author = {Medo, A and Ohte, N and Kajitani, H and Nose, T and Manabe, Y and Sugawara, T and Onishi, Y and Goto, AS and Koba, K and Arai, N and Mitsunaga, Y and Kume, M and Nishizawa, H and Kojima, D and Yokoyama, A and Yamanaka, T and Viputhanumas, T and Mitamura, H}, title = {Striped catfish (Pangasianodon hypophthalmus) exploit food sources across anaerobic decomposition- and primary photosynthetic production-based food chains.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13992}, pmid = {37634023}, issn = {2045-2322}, support = {22J13642//Japan Society for the Promotion of Science/ ; 16H05792//Japan Society for the Promotion of Science/ ; }, mesh = {*Catfishes/growth &amp; development/physiology ; Animals ; Food Chain ; Ecosystem ; Thailand ; Geologic Sediments ; }, abstract = {Dietary information from aquatic organisms is instrumental in predicting biological interactions and understanding ecosystem functionality. In freshwater habitats, generalist fish species can access a diverse array of food sources from multiple food chains. These may include primary photosynthetic production and detritus derived from both oxic and anoxic decomposition. However, the exploitation of anoxic decomposition products by fish remains insufficiently explored. This study examines feeding habits of striped catfish (Pangasianodon hypophthalmus) at both adult and juvenile stages within a tropical reservoir, using stable carbon, nitrogen, and sulfur isotope ratios (δ[13]C, δ[15]N, and δ[34]S, respectively) and fatty acid (FA) analyses. The adult catfish exhibited higher δ[15]N values compared to primary consumers that feed on primary photosynthetic producers, which suggests ingestion of food sources originating from primary photosynthetic production-based food chains. On the other hand, juvenile catfish demonstrated lower δ[15]N values than primary consumers, correlating with low δ[34]S value and large proportions of bacterial FA but contained small proportions of polyunsaturated FA. This implies that juveniles utilize food sources from both anoxic decomposition and primary photosynthetic production-based food chains. Our results indicate that food chains based on anoxic decomposition can indeed contribute to the dietary sources of tropical fish species.}, }
@article {pmid37633161, year = {2023}, author = {Shan, Y and Zhao, W and Hao, W and Kimura, T and Ukawa, S and Ohira, H and Kawamura, T and Wakai, K and Ando, M and Tamakoshi, A and Wang, C}, title = {Five-year changes of social activity and incident long-term care needs among depressed older adults: A 15-year follow up.}, journal = {Archives of gerontology and geriatrics}, volume = {116}, number = {}, pages = {105163}, doi = {10.1016/j.archger.2023.105163}, pmid = {37633161}, issn = {1872-6976}, abstract = {OBJECTIVES: To examine the effects of changes in individual/multiple social activities between 65 and 70 years of age on incident long-term care (LTC) needs between 70 and 80 in older adults with depressive symptoms.<br><br>METHODS: Participants were recruited from the New Integrated Suburban Seniority Investigation Project, an ongoing prospective cohort study. A total of 525 older adults with depressive symptoms were included. The validated 15-item Geriatric Depression Scale was used to assess depressive symptoms. A self-report questionnaire was used to measure social activities (social-related, learning, and personal). LTC needs was defined according to Japan's Long-term Care Insurance System. A competing risk model and a Laplace regression model were used to estimate the hazard ratios of LTC needs incidence and the 25th percentile difference in LTC-needs-free survival time and their 95% confidence intervals.<br><br>RESULTS: Out of 4314 person-years of mild LTC needs, 108 individuals developed it. Participants who increased their frequency of learning activities have a lower risk of developing mild LTC needs. Increasing the frequency could also prolong LTC-needs-free survival time by approximately 2.61 years. Out of 4535 person-years for severe LTC needs, 54 individuals developed it. Participants with a continuous regular frequency of learning activities had a lower risk of developing severe LTC needs. However, the association between this frequency and LTC-needs-free survival time for severe LTC needs was insignificant in the multivariable models.<br><br>CONCLUSIONS: Increased frequency of learning activities reduced the risk of LTC needs among older adults with depressive symptoms and prolonged their LTC-needs-free survival time.}, }
@article {pmid37626434, year = {2023}, author = {Kelliher, JM and Robinson, AJ and Longley, R and Johnson, LYD and Hanson, BT and Morales, DP and Cailleau, G and Junier, P and Bonito, G and Chain, PSG}, title = {The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {192}, pmid = {37626434}, issn = {2049-2618}, support = {This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; }, mesh = {*Multiomics ; Data Analysis ; Eukaryota ; *Microbiota/genetics ; Prokaryotic Cells ; }, abstract = {As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.}, }
@article {pmid37624884, year = {2023}, author = {Elser, D and Pflieger, D and Villette, C and Moegle, B and Miesch, L and Gaquerel, E}, title = {Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N-acylnornicotine innovations.}, journal = {Science advances}, volume = {9}, number = {34}, pages = {eade8984}, pmid = {37624884}, issn = {2375-2548}, mesh = {*Tobacco/genetics ; *Metabolomics ; Acclimatization ; Consensus ; Databases, Factual ; }, abstract = {Specialized metabolite (SM) diversification is a core process to plants' adaptation to diverse ecological niches. Here, we implemented a computational mass spectrometry-based metabolomics approach to exploring SM diversification in tissues of 20 species covering Nicotiana phylogenetics sections. To markedly increase metabolite annotation, we created a large in silico fragmentation database, comprising >1 million structures, and scripts for connecting class prediction to consensus substructures. Together, the approach provides an unprecedented cartography of SM diversity and section-specific innovations in this genus. As a case study and in combination with nuclear magnetic resonance and mass spectrometry imaging, we explored the distribution of N-acylnornicotines, alkaloids predicted to be specific to Repandae allopolyploids, and revealed their prevalence in the genus, albeit at much lower magnitude, as well as a greater structural diversity than previously thought. Together, the data integration approaches provided here should act as a resource for future research in plant SM evolution.}, }
@article {pmid37619239, year = {2023}, author = {Qiu, S and Yang, A and Zeng, H}, title = {Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.}, journal = {PLoS computational biology}, volume = {19}, number = {8}, pages = {e1011391}, pmid = {37619239}, issn = {1553-7358}, mesh = {Secondary Metabolism ; Cell Cycle ; Cell Proliferation ; *Computational Biology ; *Engineering ; }, abstract = {In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.}, }
@article {pmid37632753, year = {2022}, author = {Meyer, R and Davies, N and Pitz, KJ and Meyer, C and Samuel, R and Anderson, J and Appeltans, W and Barker, K and Chavez, FP and Duffy, JE and Goodwin, KD and Hudson, M and Hunter, ME and Karstensen, J and Laney, CM and Leinen, M and Mabee, P and Macklin, JA and Muller-Karger, F and Pade, N and Pearlman, J and Phillips, L and Provoost, P and Santi, I and Schigel, D and Schriml, LM and Soccodato, A and Suominen, S and Thibault, KM and Ung, V and van de Kamp, J and Wallis, E and Walls, R and Buttigieg, PL}, title = {The founding charter of the Omic Biodiversity Observation Network (Omic BON).}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, doi = {10.1093/gigascience/giad068}, pmid = {37632753}, issn = {2047-217X}, support = {N&#xb0; 862923//Horizon 2020 Framework Programme/ ; N&#xb0; 2129268//National Science Foundation/ ; }, abstract = {Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.}, }
@article {pmid37630465, year = {2023}, author = {Koga, S and Takazono, T and Kido, T and Muramatsu, K and Tokutsu, K and Tokito, T and Okuno, D and Ito, Y and Yura, H and Takeda, K and Iwanaga, N and Ishimoto, H and Sakamoto, N and Yatera, K and Izumikawa, K and Yanagihara, K and Fujino, Y and Fushimi, K and Matsuda, S and Mukae, H}, title = {Evaluation of the Effectiveness and Use of Anti-Methicillin-Resistant Staphylococcus aureus Agents for Aspiration Pneumonia in Older Patients Using a Nationwide Japanese Administrative Database.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630465}, issn = {2076-2607}, abstract = {Studies indicated potential harm from empirical broad-spectrum therapy. A recent study of hospitalizations for community-acquired pneumonia suggested that empirical anti-methicillin-resistant Staphylococcus aureus (MRSA) therapy was associated with an increased risk of death and other complications. However, limited evidence supports empirical anti-MRSA therapy for older patients with aspiration pneumonia. In a nationwide Japanese database, patients aged ≥65 years on admission with aspiration pneumonia were analyzed. Patients were divided based on presence of respiratory failure and further sub-categorized based on their condition within 3 days of hospital admission, either receiving a combination of anti-MRSA agents and other antibiotics, or not using MRSA agents. An inverse probability weighting method with estimated propensity scores was used. Out of 81,306 eligible patients, 55,098 had respiratory failure, and 26,208 did not. In the group with and without respiratory failure, 0.93% and 0.42% of the patients, respectively, received anti-MRSA agents. In patients with respiratory failure, in-hospital mortality (31.38% vs. 19.03%, p < 0.001), 30-day mortality, and 90-day mortality were significantly higher, and oxygen administration length was significantly longer in the anti-MRSA agent combination group. Anti-MRSA agent combination use did not improve the outcomes in older patients with aspiration pneumonia and respiratory failure, and should be carefully and comprehensively considered.}, }
@article {pmid37626975, year = {2023}, author = {Irwin, G and Rogatzki, MJ and Wiltshire, HD and Williams, GKR and Gu, Y and Ash, GI and Tao, D and Baker, JS}, title = {Sports-Related Concussion Assessment: A New Physiological, Biomechanical, and Cognitive Methodology Incorporating a Randomized Controlled Trial Study Protocol.}, journal = {Biology}, volume = {12}, number = {8}, pages = {}, pmid = {37626975}, issn = {2079-7737}, abstract = {BACKGROUND: Taking part in moderate-to-vigorous exercise in contact sports on a regular basis may be linked to an increase in cerebrovascular injury and head trauma. Validated objective measures are lacking in the initial post-event diagnosis of head injury. The exercise style, duration, and intensity may also confound diagnostic indicators. As a result, we propose that the new Interdisciplinary Group in Movement &amp; Performance from Acute &amp; Chronic Head Trauma (IMPACT) analyze a variety of functional (biomechanical and motor control) tests as well as related biochemistry to see how they are affected by contact in sports and head injury. The study's goal will be to look into the performance and physiological changes in rugby players after a game for head trauma and injury.<br><br>METHODS: This one-of-a-kind study will use a randomized controlled trial (RCT) utilizing a sport participation group and a non-participation control group. Forty male rugby 7 s players will be recruited for the study and allocated randomly to the experimental groups. The intervention group will participate in three straight rugby matches during a local 7 s rugby event. At the pre-match baseline, demographic and anthropometric data will be collected. This will be followed by the pre-match baseline collection of biochemical, biomechanical, and cognitive-motor task data. After three consecutive matches, the same measures will be taken. During each match, a notational analysis will be undertaken to obtain contact information. All measurements will be taken again 24, 48, and 72 h after the third match.<br><br>DISCUSSION: When the number of games increases owing to weariness and/or stressful circumstances, we expect a decline in body movement, coordination, and cognitive-motor tasks. Changes in blood biochemistry are expected to correspond to changes in biomechanics and cognitive-motor processes. This research proposal will generate considerable, ecologically valid data on the occurrence of head trauma events under game conditions, as well as the influence of these events on the biological systems of the performers. This will lead to a greater understanding of how sports participants react to exercise-induced injuries. This study's scope will have far-reaching ramifications for doctors, coaches, managers, scientists, and sports regulatory bodies concerned with the health and well-being of athletic populations at all levels of competition, including all genders and ages.}, }
@article {pmid37621575, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Buff Ermine, Spilarctia lutea (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {92}, pmid = {37621575}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Spilarctia lutea (the Buff Ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 584.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the assembled Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,304 protein coding genes.}, }
@article {pmid37620553, year = {2023}, author = {Gonzalez, A and Vihervaara, P and Balvanera, P and Bates, AE and Bayraktarov, E and Bellingham, PJ and Bruder, A and Campbell, J and Catchen, MD and Cavender-Bares, J and Chase, J and Coops, N and Costello, MJ and Dornelas, M and Dubois, G and Duffy, EJ and Eggermont, H and Fernandez, N and Ferrier, S and Geller, GN and Gill, M and Gravel, D and Guerra, CA and Guralnick, R and Harfoot, M and Hirsch, T and Hoban, S and Hughes, AC and Hunter, ME and Isbell, F and Jetz, W and Juergens, N and Kissling, WD and Krug, CB and Le Bras, Y and Leung, B and Londoño-Murcia, MC and Lord, JM and Loreau, M and Luers, A and Ma, K and MacDonald, AJ and McGeoch, M and Millette, KL and Molnar, Z and Mori, AS and Muller-Karger, FE and Muraoka, H and Navarro, L and Newbold, T and Niamir, A and Obura, D and O'Connor, M and Paganini, M and Pereira, H and Poisot, T and Pollock, LJ and Purvis, A and Radulovici, A and Rocchini, D and Schaepman, M and Schaepman-Strub, G and Schmeller, DS and Schmiedel, U and Schneider, FD and Shakya, MM and Skidmore, A and Skowno, AL and Takeuchi, Y and Tuanmu, MN and Turak, E and Turner, W and Urban, MC and Urbina-Cardona, N and Valbuena, R and van Havre, B and Wright, E}, title = {A global biodiversity observing system to unite monitoring and guide action.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {37620553}, issn = {2397-334X}, }
@article {pmid37614677, year = {2023}, author = {Boyes, D and Hammond, J and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the White-shouldered Marble, Apotomis turbidana (Hübner, 1825).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {127}, pmid = {37614677}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Apotomis turbidana (the White-shouldered Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 720.5 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,646 protein coding genes.}, }
@article {pmid37614458, year = {2023}, author = {Gavurova, B and Kelemen, M and Polishchuk, V and Mudarri, T and Smolanka, V}, title = {A fuzzy decision support model for the evaluation and selection of healthcare projects in the framework of competition.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1222125}, pmid = {37614458}, issn = {2296-2565}, mesh = {European Union ; *Policy ; *Delivery of Health Care ; Decision Support Techniques ; }, abstract = {Our research aims to support decision-making regarding the financing of healthcare projects by structural funds with policies targeting reduction of the development gap among different regions and countries of the European Union as well as the achievement of economic and social cohesion. A fuzzy decision support model for the evaluation and selection of healthcare projects should rank the project applications for the selected region, accounting for the investor's wishes in the form of a regional coefficient in order to reduce the development gap between regions. On the one hand, our proposed model evaluates project applications based on selected criteria, which may be structured, weakly structured, or unstructured. On the other hand, it also incorporates information on the level of healthcare development in the region. The obtained ranking increases the degree of validity of the decision regarding the selection of projects for financing by investors, considering the level of development of the region where the project will be implemented. At the expense of European Union (EU) structural funds, a village, city, region, or state can receive funds for modernization and development of the healthcare sector and all related processes. To minimize risks, it is necessary to implement adequate support systems for decision-making in the assessment of project applications, as well as regional policy in the region where the project will be implemented. The primary goal of this study was to develop a complex fuzzy decision support model for the evaluation and selection of projects in the field of healthcare with the aim of reducing the development gap between regions. Based on the above description, we formed the following scientific hypothesis for this research: if the project selected for financing can successfully achieve its stated goals and increase the level of development of its region, it should be evaluated positively. This evaluation can be obtained using a complex fuzzy model constructed to account for the region's level of development in terms of the availability and quality of healthcare services in the region where the project will be implemented.}, }
@article {pmid37612675, year = {2023}, author = {Sentamu, DN and Kungu, J and Dione, M and Thomas, LF}, title = {Prevention of human exposure to livestock faecal waste in the household: a scoping study of interventions conducted in sub-Saharan Africa.}, journal = {BMC public health}, volume = {23}, number = {1}, pages = {1613}, pmid = {37612675}, issn = {1471-2458}, support = {204822/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; *Livestock ; Databases, Factual ; Europe ; Feces ; *Hygiene ; }, abstract = {BACKGROUND: Poorly managed animal faecal waste can result in detrimental environmental and public health implications. Limiting human exposure to animal waste through Animal inclusive Water Sanitation and Hygiene (A-WASH) strategies is imperative to improve public health in livestock keeping households but has received little attention to date. A small number of A-WASH interventions have previously been identified through a systematic review by another research team, and published in 2017. To inform intervention design with the most up-to-date information, a scoping study was conducted to map the existing evidence for A-WASH in sub-Saharan Africa (SSA) emerging since the previous review.<br><br>METHODS: This review followed PRISMA guidelines to identify interventions in SSA published between January 2016 to October 2022. Databases searched included PubMed, PMC Europe, CabDirect and Web of Science. Studies were eligible for inclusion if they were written in English and documented interventions limiting human contact with animal faecal material in the SSA context. Key data extracted included: the intervention itself,&#xa0;its target population, cost, measure of effectiveness, quantification of effect, assessment of success, acceptability and limitations. These data were synthesized into a narrative, structured around the intervention type.<br><br>FINDINGS: Eight eligible articles were identified. Interventions to reduce human exposure to animal faecal matter were conducted in combination with 'standard' human-centric WASH practices. Identified interventions included the management of human-animal co-habitation, educational programs and the creation of child-safe spaces. No novel A-WASH interventions were identified in this review, beyond those identified by the review in 2017. Randomised Controlled Trials (RCTs) were used to evaluate six of the eight identified interventions, but as effect was evaluated through various measures, the ability to formally compare efficacy of interventions is lacking.<br><br>CONCLUSION: This study indicates that the number of A-WASH studies in SSA is increasing and the use of RCTs suggests a strong desire to create high-quality evidence within this field. There is a need for standardisation of effect measures to enable meta-analyses to be conducted to better understand intervention effectiveness. Evaluation of scalability and sustainability of interventions is still lacking in A - WASH research.}, }
@article {pmid37612396, year = {2023}, author = {Dethier, EN and Silman, M and Leiva, JD and Alqahtani, S and Fernandez, LE and Pauca, P and Çamalan, S and Tomhave, P and Magilligan, FJ and Renshaw, CE and Lutz, DA}, title = {A global rise in alluvial mining increases sediment load in tropical rivers.}, journal = {Nature}, volume = {620}, number = {7975}, pages = {787-793}, pmid = {37612396}, issn = {1476-4687}, mesh = {Animals ; Humans ; *Ecosystem ; Databases, Factual ; *Gold ; Hydrology ; Rivers ; }, abstract = {Increasing gold and mineral mining activity in rivers across the global tropics has degraded ecosystems and threatened human health[1,2]. Such river mineral mining involves intensive excavation and sediment processing in river corridors, altering river form and releasing excess sediment downstream[2]. Increased suspended sediment loads can reduce water clarity and cause siltation to levels that may result in disease and mortality in fish[3,4], poor water quality[5] and damage to human infrastructure[6]. Although river mining has been investigated at local scales, no global synthesis of its physical footprint and impacts on hydrologic systems exists, leaving its full environmental consequences unknown. We assemble and analyse a 37-year satellite database showing pervasive, increasing river mineral mining worldwide. We identify 396 mining districts in 49 countries, concentrated in tropical waterways that are almost universally altered by mining-derived sediment. Of 173 mining-affected rivers, 80% have suspended sediment concentrations (SSCs) more than double pre-mining levels. In 30 countries in which mining affects large (>50 m wide) rivers, 23 ± 19% of large river length is altered by mining-derived sediment, a globe-spanning effect representing 35,000 river kilometres, 6% (±1% s.e.) of all large tropical river reaches. Our findings highlight the ubiquity and intensity of mining-associated degradation in tropical river systems.}, }
@article {pmid37612395, year = {2023}, author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS}, title = {Landscape-scale benefits of protected areas for tropical biodiversity.}, journal = {Nature}, volume = {620}, number = {7975}, pages = {807-812}, pmid = {37612395}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; *Trees ; Mammals ; }, abstract = {The United Nations recently agreed to major expansions of global protected areas (PAs) to slow biodiversity declines[1]. However, although reserves often reduce habitat loss, their efficacy at preserving animal diversity and their influence on biodiversity in surrounding unprotected areas remain unclear[2-5]. Unregulated hunting can empty PAs of large animals[6], illegal tree felling can degrade habitat quality[7], and parks can simply displace disturbances such as logging and hunting to unprotected areas of the landscape[8] (a phenomenon called leakage). Alternatively, well-functioning PAs could enhance animal diversity within reserves as well as in nearby unprotected sites[9] (an effect called spillover). Here we test whether PAs across mega-diverse Southeast Asia contribute to vertebrate conservation inside and outside their boundaries. Reserves increased all facets of bird diversity. Large reserves were also associated with substantially enhanced mammal diversity in the adjacent unprotected landscape. Rather than PAs generating leakage that deteriorated ecological conditions elsewhere, our results are consistent with PAs inducing spillover that benefits biodiversity in surrounding areas. These findings support the United Nations goal of achieving 30% PA coverage by 2030 by demonstrating that PAs are associated with higher vertebrate diversity both inside their boundaries and in the broader landscape.}, }
@article {pmid37060443, year = {2023}, author = {Weinstein, ES and Cuthbertson, JL and Herbert, TL and Voicescu, GT and Bortolin, M and Magalini, S and Gui, D and Helou, M and Lennquist Montan, K and Montan, C and Rafalowsky, C and Ratto, G and Damele, S and Bazurro, S and Laist, I and Marzi, F and Borrello, A and Fransvea, P and Fidanzio, A and Benitez, CY and Faccincani, R and Ragazzoni, L and Caviglia, M}, title = {Advancing the scientific study of prehospital mass casualty response through a Translational Science process: the T1 scoping literature review stage.}, journal = {European journal of trauma and emergency surgery : official publication of the European Trauma Society}, volume = {49}, number = {4}, pages = {1647-1660}, pmid = {37060443}, issn = {1863-9941}, support = {101021957//European Union Horizon 2020 research and innovation program/ ; }, mesh = {Humans ; *Mass Casualty Incidents ; Translational Science, Biomedical ; Triage ; *Emergency Responders ; Databases, Factual ; }, abstract = {PURPOSE: The European Union Horizon 2020 research and innovation funding program awarded the NIGHTINGALE grant to develop a toolkit to support first responders engaged in prehospital (PH) mass casualty incident (MCI) response. To reach the projects' objectives, the NIGHTINGALE consortium used a Translational Science (TS) process. The present work is the first TS stage (T1) aimed to extract data relevant for the subsequent modified Delphi study (T2) statements.<br><br>METHODS: The authors were divided into three work groups (WGs) MCI Triage, PH Life Support and Damage Control (PHLSDC), and PH Processes (PHP). Each WG conducted simultaneous literature searches following the PRISMA extension for scoping reviews. Relevant data were extracted from the included articles and indexed using pre-identified PH MCI response themes and subthemes.<br><br>RESULTS: The initial search yielded 925 total references to be considered for title and abstract review (MCI Triage 311, PHLSDC 329, PHP 285), then 483 articles for full reference review (MCI Triage 111, PHLSDC 216, PHP 156), and finally 152 articles for the database extraction process (MCI Triage 27, PHLSDC 37, PHP 88). Most frequent subthemes and novel concepts have been identified as a basis for the elaboration of draft statements for the T2 modified Delphi study.<br><br>CONCLUSION: The three simultaneous scoping reviews allowed the extraction of relevant PH MCI subthemes and novel concepts that will enable the NIGHTINGALE consortium to create scientifically anchored statements in the T2 modified Delphi study.}, }
@article {pmid37611791, year = {2023}, author = {Sarkar, DJ and Das Sarkar, S and Santhana Kumar, V and Chanu, TN and Banerjee, T and Chakraborty, L and Bhor, M and Nag, SK and Samanta, S and Das, BK}, title = {Ameliorative effect of natural floating island as fish aggregating devices on heavy metals distribution in a freshwater wetland.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122428}, doi = {10.1016/j.envpol.2023.122428}, pmid = {37611791}, issn = {1873-6424}, abstract = {Growing human population and climate change are leading reasons for water quality deterioration globally; and ecologically important waterbodies including freshwater wetlands are in a vulnerable state due to increasing concentrations of pollutants like heavy metals. Given the declining health of these valuable resources, the present study was conducted to evaluate the effect of natural floating island in the form of fish aggregating devices (FADs) made of native weed mass on the distribution of heavy metals in the abiotic and bio compartments of a freshwater wetland. Lower concentrations of surface water heavy metals were observed inside the FADs with a reduction of 73.91%, 65.22% and 40.57-49.16% for Cd, Pb and other metals (viz. Co, Cr, Cu, Ni and Zn), respectively as compared to outside FAD. These led to 14.72-55.39% reduction in the heavy metal pollution indices inside the FAD surface water. The fish species inside the FADs were also found less contaminated (24.07-25.07% reduction) with lower health risk indices. The study signifies the valuable contribution of natural floating island as FADs in ameliorating the effect of heavy metals pollution emphasizing the tremendous role of the natural floating islands in sustainable maintenance of freshwater wetlands for better human health and livelihood.}, }
@article {pmid37601214, year = {2023}, author = {Rocha, AFBM and Freitas-Junior, R and Soares, LR and Ferreira, GLR}, title = {Breast cancer screening and diagnosis in older adults women in Brazil: why it is time to reconsider the recommendations.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1232668}, pmid = {37601214}, issn = {2296-2565}, mesh = {Humans ; Female ; Aged ; *Early Detection of Cancer ; *Breast Neoplasms/diagnosis ; Brazil/epidemiology ; State Medicine ; Databases, Factual ; }, abstract = {INTRODUCTION: Breast cancer screening in women of 70 years of age or older remains controversial due to a lack of studies that include women of this age.<br><br>METHODS: This ecological study evaluated data from the Brazilian National Health Service (SUS) on breast cancer screening and staging in this age group compared to 50-69-year olds, for Brazil as a whole and for its geographical regions, between 2013 and 2019. A secondary database was obtained from the outpatient data system of the SUS's Informatics Department, the Brazil Oncology Panel, the Brazilian Institute of Geography and Statistics, the Supplementary Health Agency and the Online Mortality Atlas.<br><br>RESULTS: There was a marked reduction in screening in women &#x2265;70&#x2009;years of age (annual percent change [APC] -3.5; p&#x2009;<&#x2009;0.001) compared to those of 50-69&#x2009;years of age (APC-2.2; p&#x2009;=&#x2009;0.010). There was a trend towards an increase in clinical staging, with a greater occurrence of stages III and IV in the &#x2265;70 group (44.3%) compared to the women of 50-69&#x2009;years of age (40.8%; p&#x2009;<&#x2009;0.001).<br><br>CONCLUSION: Considering the increasing age of the Brazilian population and the heterogeneity among older adults women, screening for the over-70s within the SUS merits greater debate insofar as the implementation of public policies is concerned.}, }
@article {pmid37600587, year = {2023}, author = {Saccheri, IJ and ,  and ,  and ,  and , }, title = {The genome sequence of the Squinting Bush Brown, Bicyclus anynana (Butler, 1879).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {280}, pmid = {37600587}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Bicyclus anynana (the Squinting Bush Brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 457.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length.}, }
@article {pmid37600586, year = {2023}, author = {Lohse, K and Hayward, A and Vila, R and ,  and ,  and ,  and Carvalho, APS and Kawahara, AY and , }, title = {The genome sequence of the Large Skipper, Ochlodes sylvanus, (Esper, 1777).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {75}, pmid = {37600586}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Ochlodes sylvanus, the Large Skipper (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 380 megabases in span. Most of the assembly (99.97%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,451 protein coding genes.}, }
@article {pmid37600582, year = {2023}, author = {Lees, D and Boyes, D and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Dotted Border, Agriopis marginaria (Fabricius, 1776).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {152}, pmid = {37600582}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Agriopis marginaria (the Dotted Border, Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 500.9 megabases in span. Most of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,443 protein coding genes.}, }
@article {pmid37598281, year = {2023}, author = {Nazari Ashani, M and Alesheikh, AA and Neisani Samani, Z and Lotfata, A and Bayat, S and Alipour, S and Hoseini, B}, title = {Socioeconomic and environmental determinants of foot and mouth disease incidence: an ecological, cross-sectional study across Iran using spatial modeling.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13526}, pmid = {37598281}, issn = {2045-2322}, mesh = {Animals ; Sheep ; Iran/epidemiology ; *Foot-and-Mouth Disease/epidemiology ; Cross-Sectional Studies ; Asia ; Goats ; Socioeconomic Factors ; }, abstract = {Foot-and-mouth disease (FMD) is a highly contagious animal disease caused by a ribonucleic acid (RNA) virus, with significant economic costs and uneven distribution across Asia, Africa, and South America. While spatial analysis and modeling of FMD are still in their early stages, this research aimed to identify socio-environmental determinants of FMD incidence in Iran at the provincial level by studying 135 outbreaks reported between March 21, 2017, and March 21, 2018. We obtained 46 potential socio-environmental determinants and selected four variables, including percentage of population, precipitation in January, percentage of sheep, and percentage of goats, to be used in spatial regression models to estimate variation in spatial heterogeneity. In our analysis, we employed global models, namely ordinary least squares (OLS), spatial error model (SEM), and spatial lag model (SLM), as well as local models, including geographically weighted regression (GWR) and multiscale geographically weighted regression (MGWR). The MGWR model yielded the highest adjusted [Formula: see text] of 90%, outperforming the other local and global models. Using local models to map the effects of environmental determinants (such as the percentage of sheep and precipitation) on the spatial variability of FMD incidence provides decision-makers with helpful information for targeted interventions. Our findings advocate for multiscale and multidisciplinary policies to reduce FMD incidence.}, }
@article {pmid37598114, year = {2023}, author = {Tom, M and Lubinevsky, H and Kanari, M}, title = {Integrative data system for monitoring biota and natural habitats in the Israeli Eastern Mediterranean marine environment.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {9}, pages = {1068}, pmid = {37598114}, issn = {1573-2959}, mesh = {Humans ; Israel ; *Environmental Monitoring ; *Biota ; Databases, Factual ; Environmental Policy ; }, abstract = {An integrative data system for monitoring the biota of the Mediterranean waters of Israel as well as selected records from adjacent Levantine basin regions is presented here, aimed at providing data and research tools for long-term bio-geographic and ecological studies and more important, providing background data for assisting governmental regulators to establish educated habitat-oriented environmental policy. The system relies on the geographic information system (GIS) online map-based platform and contains at present the following components: biotic database of ~ 170,000 recorded sampling events; uniform habitat maps of 63 benthic habitats and 2 pelagic ones, constructed using relevant bathymetric features and biotic community compositions; bathymetric hill-shade map; depth contours; raster depth grid and human interference map. Other informative auxiliary maps are planned to be added (e.g., map of potential pockmark sites, detailed maps of tiny carbonate crust nolls and more). A number of 883 cited documents were listed by us for potential extraction of sampling efforts, most of them are available to us as PDFs and are available also to the users, excluding copyright-protected ones. Forty-three major projects were depicted in addition to a variety of small studies (e.g., university theses). Thirty-five sampling devices were documented and described, and 3187 species-level identifications were already recorded. In addition, the system provides access to description of sampling devices and pictures of species and seascapes. New data is continuously deposited to the system and the system is flexible, allowing future addition of new types of information. The system site is accessible through the link: https://experience.arcgis.com/experience/40e86605ff4d4e5096ed2c901fec2a2f .}, }
@article {pmid37596254, year = {2023}, author = {Szymura, TH and Kassa, H and Swacha, G and Szymura, M and Zając, A and Kącki, Z}, title = {Spatial patterns of vascular plant species richness in Poland - a data set.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {542}, pmid = {37596254}, issn = {2052-4463}, mesh = {Checklist ; Computer Systems ; Databases, Factual ; Poland ; *Tracheophyta ; }, abstract = {Recognition of species richness spatial patterns is important for nature conservation and theoretical studies. Inventorying species richness, especially at a larger spatial extent is challenging, thus different data sources are joined and harmonized to obtain a comprehensive data set. Here we present a new data set showing vascular plant species richness in Poland based on a grid of 10 × 10 km squares. The data set was created using data from two sources: the Atlas of Distribution of Vascular Plants in Poland and the Polish Vegetation Database. Using this data set, we analysed 2,160 species with taxonomical nomenclature according to the Euro + Med PlantBase checklist in 3,283 squares covering the entire territory of Poland (ca. 312,000 km[2]). The species were divided into groups according to their status and frequency of distribution, and the statistics for each square were obtained. For purposes of analysis, sampling bias was assessed. The data set promotes theoretical analysis on species richness and reinforces the planning of nature conservations.}, }
@article {pmid37593568, year = {2023}, author = {Jaron, KS and Berg, MP and Ellers, J and Hodson, CN and Ross, L and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the springtail Allacma fusca (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {319}, pmid = {37593568}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Allacma fusca (the springtail; Arthropoda; Collembola; Symphypleona; Sminthuridae). The genome sequence is 392.8 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 14.94 kilobases in length.}, }
@article {pmid37593439, year = {2023}, author = {Santarius, T and Bieser, JCT and Frick, V and Höjer, M and Gossen, M and Hilty, LM and Kern, E and Pohl, J and Rohde, F and Lange, S}, title = {Digital sufficiency: conceptual considerations for ICTs on a finite planet.}, journal = {Annales des telecommunications}, volume = {78}, number = {5-6}, pages = {277-295}, pmid = {37593439}, issn = {1958-9395}, abstract = {ICT hold significant potential to increase resource and energy efficiencies and contribute to a circular economy. Yet unresolved is whether the aggregated net effect of ICT overall mitigates or aggravates environmental burdens. While the savings potentials have been explored, drivers that prevent these and possible counter measures have not been researched thoroughly. The concept digital sufficiency constitutes a basis to understand how ICT can become part of the essential environmental transformation. Digital sufficiency consists of four dimensions, each suggesting a set of strategies and policy proposals: (a) hardware sufficiency, which aims for fewer devices needing to be produced and their absolute energy demand being kept to the lowest level possible to perform the desired tasks; (b) software sufficiency, which covers ensuring that data traffic and hardware utilization during application are kept as low as possible; (c) user sufficiency, which strives for users applying digital devices frugally and using ICT in a way that promotes sustainable lifestyles; and (d) economic sufficiency, which aspires to digitalization supporting a transition to an economy characterized not by economic growth as the primary goal but by sufficient production and consumption within planetary boundaries. The policies for hardware and software sufficiency are relatively easily conceivable and executable. Policies for user and economic sufficiency are politically more difficult to implement and relate strongly to policies for environmental transformation in general. This article argues for comprehensive policies for digital sufficiency, which are indispensible if ICT are to play a beneficial role in overall environmental transformation.}, }
@article {pmid37590347, year = {2023}, author = {O'Keefe, FR and Dunn, RE and Weitzel, EM and Waters, MR and Martinez, LN and Binder, WJ and Southon, JR and Cohen, JE and Meachen, JA and DeSantis, LRG and Kirby, ME and Ghezzo, E and Coltrain, JB and Fuller, BT and Farrell, AB and Takeuchi, GT and MacDonald, G and Davis, EB and Lindsey, EL}, title = {Pre-Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6659}, pages = {eabo3594}, doi = {10.1126/science.abo3594}, pmid = {37590347}, issn = {1095-9203}, abstract = {The cause, or causes, of the Pleistocene megafaunal extinctions have been difficult to establish, in part because poor spatiotemporal resolution in the fossil record hinders alignment of species disappearances with archeological and environmental data. We obtained 172 new radiocarbon dates on megafauna from Rancho La Brea in California spanning 15.6 to 10.0 thousand calendar years before present (ka). Seven species of extinct megafauna disappeared by 12.9 ka, before the onset of the Younger Dryas. Comparison with high-resolution regional datasets revealed that these disappearances coincided with an ecological state shift that followed aridification and vegetation changes during the Bølling-Allerød (14.69 to 12.89 ka). Time-series modeling implicates large-scale fires as the primary cause of the extirpations, and the catalyst of this state shift may have been mounting human impacts in a drying, warming, and increasingly fire-prone ecosystem.}, }
@article {pmid37589308, year = {2022}, author = {Mendes de Farias, T and Wollbrett, J and Robinson-Rechavi, M and Bastian, F}, title = {Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37589308}, issn = {2047-217X}, support = {U01 CA215010/CA/NCI NIH HHS/United States ; }, mesh = {*Biomedical Research ; Computational Biology ; Knowledge Bases ; }, abstract = {BACKGROUND: Enhancing interoperability of bioinformatics knowledge bases is a high-priority requirement to maximize data reusability and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange value once the knowledge base is (re)used, and without interoperability, the utility lies dormant.<br><br>RESULTS: In this article, we discuss several approaches to boost interoperability depending on the interoperable parts. The findings are driven by several real-world scenario examples that were mostly implemented by Bgee, a well-established gene expression knowledge base. To better justify the findings are transferable, for each Bgee interoperability experience, we also highlight similar implementations by major bioinformatics knowledge bases. Moreover, we discuss ten general main lessons learned. These lessons can be applied in the context of any bioinformatics knowledge base to foster data reusability.<br><br>CONCLUSIONS: This work provides pragmatic methods and transferable skills to promote reusability of bioinformatics knowledge bases by focusing on interoperability.}, }
@article {pmid37587525, year = {2023}, author = {Ma, R and Li, C and Tian, H and Zhang, Y and Feng, X and Li, J and Hu, W}, title = {The current distribution of tick species in Inner Mongolia and inferring potential suitability areas for dominant tick species based on the MaxEnt model.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {286}, pmid = {37587525}, issn = {1756-3305}, support = {U22A20526//Study on pathogen spectrum, temporal and spatial distribution and transmission features of the important emerging and re-emerging zoonosis in Inner Mongolia Autonomous Region/ ; }, mesh = {Humans ; Animals ; *Ixodes ; China/epidemiology ; *Ixodidae ; Databases, Factual ; Global Warming ; }, abstract = {BACKGROUND: Ticks are known to transmit a wide range of diseases, including those caused by bacteria, viruses, and protozoa. The expansion of tick habitats has been intensified in recent years due to various factors such as global warming, alterations in microclimate, and human activities. Consequently, the probability of human exposure to diseases transmitted by ticks has increased, leading to a higher degree of risk associated with such diseases.<br><br>METHODS: In this study, we conducted a comprehensive review of domestic and international literature databases to determine the current distribution of tick species in Inner Mongolia. Next, we employed the MaxEnt model to analyze vital climatic and environmental factors influencing dominant tick distribution. Subsequently, we predicted the potential suitability areas of these dominant tick species under the near current conditions and the BCC-CSM2.MR model SSP245 scenario for the future periods of 2021-2040, 2041-2060, 2061-2080, and 2081-2100.<br><br>RESULTS: Our study revealed the presence of 23 tick species from six genera in Inner Mongolia, including four dominant tick species (Dermacentor nuttalli, Ixodes persulcatus, Dermacentor silvarum, and Hyalomma asiaticum). Dermacentor nuttalli, D. silvarum, and I. persulcatus are predominantly found in regions such as Xilin Gol and Hulunbuir. Temperature seasonality (Bio4), elevation (elev), and precipitation seasonality (Bio15) were the primary variables impacting the distribution of three tick species. In contrast, H. asiaticum is mainly distributed in Alxa and Bayannur and demonstrates heightened sensitivity to precipitation and other climatic factors. Our modeling results suggested that the potential suitability areas of these tick species would experience fluctuations over the four future periods (2021-2040, 2041-2060, 2061-2080, and 2081-2100). Specifically, by 2081-2100, the centroid of suitable habitat for D. nuttalli, H. asiaticum, and I. persulcatus was predicted to shift westward, with new suitability areas emerging in regions such as Chifeng and Xilin Gol. The centroid of suitable habitat for H. asiaticum will move northeastward, and new suitability areas are likely to appear in areas such as Ordos and Bayannur.<br><br>CONCLUSIONS: This study provided a comprehensive overview of the tick species distribution patterns in Inner Mongolia. Our research has revealed a significant diversity of tick species in the region, exhibiting a wide distribution but with notable regional disparities. Our modeling results suggested that the dominant tick species' suitable habitats will significantly expand in the future compared to their existing distribution under the near current conditions. Temperature and precipitation are the primary variables influencing these shifts in distribution. These findings can provide a valuable reference for future research on tick distribution and the surveillance of tick-borne diseases in the region.}, }
@article {pmid37586008, year = {2023}, author = {Garces, TS and Damasceno, LLV and Sousa, GJB and Cestari, VRF and Pereira, MLD and Moreira, TMM}, title = {Relationship between social development indicators and mortality due to Diabetes Mellitus in Brazil: a space-time analysis.}, journal = {Revista latino-americana de enfermagem}, volume = {31}, number = {}, pages = {e3971}, pmid = {37586008}, issn = {1518-8345}, mesh = {Humans ; *Social Change ; Brazil/epidemiology ; Spatio-Temporal Analysis ; Income ; *Diabetes Mellitus ; }, abstract = {OBJECTIVE: to identify the space-time pattern of mortality due to Diabetes Mellitus in Brazil, as well as its relationship with social development indicators.<br><br>METHOD: an ecological and time series nationwide study based on secondary data from the Unified Health System Informatics Department, with space-time analysis and inclusion of indicators in non-spatial and spatial regression models. The following was performed: overall mortality rate calculation; characterization of the sociodemographic and regional profiles of the death cases by means of descriptive and time analysis; and elaboration of thematic maps.<br><br>RESULTS: a total of 601,521&#xa0;deaths related to Diabetes Mellitus were recorded in Brazil, representing a mean mortality rate of 29.5/100,000&#xa0;inhabitants. The states of Rio Grande do Norte, Para&#xed;ba, Pernambuco, Alagoas and Sergipe, Rio de Janeiro, Paran&#xe1; and Rio Grande do Sul presented high-high clusters. By using regression models, it was verified that the Gini index (&#x3b2;=11.7) and the Family Health Strategy coverage (&#x3b2;=3.9) were the indicators that most influenced mortality due to Diabetes Mellitus in Brazil.<br><br>CONCLUSION: in Brazil, mortality due to Diabetes presents an overall increasing trend, revealing itself as strongly associated with places that have worse social indicators.<br><br>HIGHLIGHTS: (1) The time-space pattern of mortality due to Diabetes presents an increasing trend. (2) The Northeast and South regions present high rates of mortality due to Diabetes. (3) Mortality due to Diabetes is associated with worse sociodemographic indicators. (4) A relationship is observed between income, access to health and mortality due to&#xa0;Diabetes.}, }
@article {pmid37574463, year = {2023}, author = {Stapp, EK and Zipunnikov, V and Leroux, A and Cui, L and Husky, MM and Dey, D and Merikangas, KR}, title = {Specificity of affective dynamics of bipolar and major depressive disorder.}, journal = {Brain and behavior}, volume = {}, number = {}, pages = {e3134}, doi = {10.1002/brb3.3134}, pmid = {37574463}, issn = {2162-3279}, support = {ZIA MH002804/MH/NIMH NIH HHS/United States ; }, abstract = {OBJECTIVE: Here, we examine whether the dynamics of the four dimensions of the circumplex model of affect assessed by ecological momentary assessment (EMA) differ among those with bipolar disorder (BD) and major depressive disorder (MDD).<br><br>METHODS: Participants aged 11-85&#xa0;years (n&#xa0;=&#xa0;362) reported momentary sad, anxious, active, and energetic dimensional states four times per day for 2&#xa0;weeks. Individuals with lifetime mood disorder subtypes of bipolar-I, bipolar-II, and MDD derived from a semistructured clinical interview were compared to each other and to controls without a lifetime history of psychiatric disorders. Random effects from individual means, inertias, innovation (residual) variances, and cross-lags across the four affective dimensions simultaneously were derived from multivariate dynamic structural equation models.<br><br>RESULTS: All mood disorder subtypes were associated with higher levels of sad and anxious mood and lower energy than controls. Those with bipolar-I had lower average activation, and lower energy that was independent of activation, compared to MDD or controls. However, increases in activation were more likely to perpetuate in those with bipolar-I. Bipolar-II was characterized by higher lability of sad and anxious mood compared to bipolar-I and controls but not MDD. Compared to BD and controls, those with MDD exhibited cross-augmentation of sadness and anxiety, and sadness blunted energy.<br><br>CONCLUSION: Bipolar-I is more strongly characterized by activation and energy than sad and anxious mood. This distinction has potential implications for both specificity of intervention targets and differential pathways underlying these dynamic affective systems. Confirmation of the longer term stability and generalizability of these findings in future studies is necessary.}, }
@article {pmid37572835, year = {2023}, author = {Chaemsaithong, P and Jenjaroenpun, P and Pongchaikul, P and Singsaneh, A and Thaipisuttikul, I and Romero, R and Wongsurawat, T}, title = {Rapid detection of bacteria and antimicrobial resistant genes in intraamniotic infection using nanopore adaptive sampling.}, journal = {American journal of obstetrics and gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajog.2023.08.004}, pmid = {37572835}, issn = {1097-6868}, }
@article {pmid37568226, year = {2023}, author = {Leo, P and de Melo Texeira, M and Chander, AM and Singh, NK and Simpson, AC and Yurkov, A and Karouia, F and Stajich, JE and Mason, CE and Venkateswaran, K}, title = {Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities.}, journal = {IMA fungus}, volume = {14}, number = {1}, pages = {15}, pmid = {37568226}, issn = {2210-6340}, support = {18-PPR18-0011//NNH18ZDA001N-PPR/ ; }, abstract = {During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3[T], isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1[T], isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3[T] = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1[T] = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.}, }
@article {pmid36302597, year = {2023}, author = {Verbitsky, M and Krishnamurthy, S and Krithivasan, P and Hughes, D and Khan, A and Marasà, M and Vena, N and Khosla, P and Zhang, J and Lim, TY and Glessner, JT and Weng, C and Shang, N and Shen, Y and Hripcsak, G and Hakonarson, H and Ionita-Laza, I and Levy, B and Kenny, EE and Loos, RJF and Kiryluk, K and Sanna-Cherchi, S and Crosslin, DR and Furth, S and Warady, BA and Igo, RP and Iyengar, SK and Wong, CS and Parsa, A and Feldman, HI and Gharavi, AG}, title = {Genomic Disorders in CKD across the Lifespan.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {34}, number = {4}, pages = {607-618}, pmid = {36302597}, issn = {1533-3450}, support = {K25 DK128563/DK/NIDDK NIH HHS/United States ; R01 DK080099/DK/NIDDK NIH HHS/United States ; R21 DK119802/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Cohort Studies ; *Longevity ; Copper ; Prospective Studies ; *Renal Insufficiency, Chronic/epidemiology/genetics/complications ; Genomics ; Disease Progression ; Risk Factors ; }, abstract = {SIGNIFICANCE STATEMENT: Pathogenic structural genetic variants, also known as genomic disorders, have been associated with pediatric CKD. This study extends those results across the lifespan, with genomic disorders enriched in both pediatric and adult patients compared with controls. In the Chronic Renal Insufficiency Cohort study, genomic disorders were also associated with lower serum Mg, lower educational performance, and a higher risk of death. A phenome-wide association study confirmed the link between kidney disease and genomic disorders in an unbiased way. Systematic detection of genomic disorders can provide a molecular diagnosis and refine prediction of risk and prognosis.<br><br>BACKGROUND: Genomic disorders (GDs) are associated with many comorbid outcomes, including CKD. Identification of GDs has diagnostic utility.<br><br>METHODS: We examined the prevalence of GDs among participants in the Chronic Kidney Disease in Children (CKiD) cohort II (n =248), Chronic Renal Insufficiency Cohort (CRIC) study (n =3375), Columbia University CKD Biobank (CU-CKD; n =1986), and the Family Investigation of Nephropathy and Diabetes (FIND; n =1318) compared with 30,746 controls. We also performed a phenome-wide association analysis (PheWAS) of GDs in the electronic MEdical Records and GEnomics (eMERGE; n =11,146) cohort.<br><br>RESULTS: We found nine out of 248 (3.6%) CKiD II participants carried a GD, replicating prior findings in pediatric CKD. We also identified GDs in 72 out of 6679 (1.1%) adult patients with CKD in the CRIC, CU-CKD, and FIND cohorts, compared with 199 out of 30,746 (0.65%) GDs in controls (OR, 1.7; 95% CI, 1.3 to 2.2). Among adults with CKD, we found recurrent GDs at the 1q21.1, 16p11.2, 17q12, and 22q11.2 loci. The 17q12 GD (diagnostic of renal cyst and diabetes syndrome) was most frequent, present in 1:252 patients with CKD and diabetes. In the PheWAS, dialysis and neuropsychiatric phenotypes were the top associations with GDs. In CRIC participants, GDs were associated with lower serum magnesium, lower educational achievement, and higher mortality risk.<br><br>CONCLUSION: Undiagnosed GDs are detected both in children and adults with CKD. Identification of GDs in these patients can enable a precise genetic diagnosis, inform prognosis, and help stratify risk in clinical studies. GDs could also provide a molecular explanation for nephropathy and comorbidities, such as poorer neurocognition for a subset of patients.}, }
@article {pmid37549500, year = {2023}, author = {Keat-Chuan Ng, C and Linus-Lojikip, S and Mohamed, K and Hss, AS}, title = {Application of medical information system to identify dengue outbreak factors: Insights from a hyperendemic city in Malaysia.}, journal = {International journal of medical informatics}, volume = {177}, number = {}, pages = {105162}, doi = {10.1016/j.ijmedinf.2023.105162}, pmid = {37549500}, issn = {1872-8243}, mesh = {Animals ; Humans ; Cities/epidemiology ; *Dengue/epidemiology ; Malaysia/epidemiology ; Disease Outbreaks ; Information Systems ; *Zika Virus ; *Zika Virus Infection/epidemiology ; }, abstract = {BACKGROUND: Dengue is widespread globally, but it is more severe in hyperendemic regions where the virus, its vectors, and its human hosts naturally occur. The problem is particularly acute in cities, where outbreaks affect a large human population living in a wide array of socio-environmental conditions. Controlling outbreaks will rely largely on systematic data collection and analysis approaches to uncover nuances on a city-by-city basis due to the diversity of factors.<br><br>OBJECTIVE: The main objective of this study is to consolidate and analyse the dengue case dataset amassed by the e-Dengue web-based information system, developed by the Ministry of Health Malaysia, to improve our epidemiological understanding.<br><br>METHODS: We retrieved data from the e-Dengue system and integrated a total of 18,812 cases from 2012 to 2019 (8&#xa0;years) with meteorological data, geoinformatics techniques, and socio-environmental observations to identify plausible factors that could have caused dengue outbreaks in Ipoh, a hyperendemic city in Malaysia.<br><br>RESULTS: The rainfall trend characterised by a linearity of R[2]&#xa0;>&#xa0;0.99, termed the "wet-dry steps", may be the unifying factor for triggering dengue outbreaks, though it is still a hypothesis that needs further validation. Successful mapping of the dengue "reservoir" contact zones and spill-over diffusion revealed socio-environmental factors that may be controlled through preventive measures. Age is another factor to consider, as the platelet and white blood cell counts in the "below 5" age group are much greater than in other age groups.<br><br>CONCLUSIONS: Our work demonstrates the novelty of the e-Dengue system, which can identify outbreak factors at high resolution when integrated with non-medical fields. Besides dengue, the techniques and insights laid out in this paper are valuable, at large, for advancing control strategies for other mosquito-borne diseases such as malaria, chikungunya, and zika in other hyperendemic cities elsewhere globally.}, }
@article {pmid37301186, year = {2023}, author = {Yin, Q and Wu, T and Gao, R and Wu, L and Shi, Y and Wang, X and Wang, M and Xu, Z and Zhao, Y and Su, X and Su, Y and Han, X and Yuan, L and Xiang, L and Chen, S}, title = {Multi-omics reveal key enzymes involved in the formation of phenylpropanoid glucosides in Artemisia annua.}, journal = {Plant physiology and biochemistry : PPB}, volume = {201}, number = {}, pages = {107795}, doi = {10.1016/j.plaphy.2023.107795}, pmid = {37301186}, issn = {1873-2690}, mesh = {*Artemisia annua/metabolism ; Scopoletin/chemistry/metabolism/pharmacology ; Esculin/metabolism ; Multiomics ; Molecular Docking Simulation ; *Artemisinins/metabolism ; Glucosides/metabolism ; Glucose/metabolism ; Uridine Diphosphate/metabolism ; }, abstract = {Although mainly known for producing artemisinin, Artemisia annua is enriched in phenylpropanoid glucosides (PGs) with significant bioactivities. However, the biosynthesis of A. annua PGs is insufficiently investigated. Different A. annua ecotypes from distinct growing environments accumulate varying amounts of metabolites, including artemisinin and PGs such as scopolin. UDP-glucose:phenylpropanoid glucosyltransferases (UGTs) transfers glucose from UDP-glucose in PG biosynthesis. Here, we found that the low-artemisinin ecotype GS produces a higher amount of scopolin, compared to the high-artemisinin ecotype HN. By combining transcriptome and proteome analyses, we selected 28 candidate AaUGTs from 177 annotated AaUGTs. Using AlphaFold structural prediction and molecular docking, we determined the binding affinities of 16 AaUGTs. Seven of the AaUGTs enzymatically glycosylated phenylpropanoids. AaUGT25 converted scopoletin to scopolin and esculetin to esculin. The lack of accumulation of esculin in the leaf and the high catalytic efficiency of AaUGT25 on esculetin suggest that esculetin is methylated to scopoletin, the precursor of scopolin. We also discovered that AaOMT1, a previously uncharacterized O-methyltransferase, converts esculetin to scopoletin, suggesting an alternative route for producing scopoletin, which contributes to the high-level accumulation of scopolin in A. annua leaves. AaUGT1 and AaUGT25 responded to induction of stress-related phytohormones, implying the involvement of PGs in stress responses.}, }
@article {pmid37567881, year = {2023}, author = {Koludarov, I and Senoner, T and Jackson, TNW and Dashevsky, D and Heinzinger, M and Aird, SD and Rost, B}, title = {Domain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4861}, pmid = {37567881}, issn = {2041-1723}, abstract = {Three-finger toxins (3FTXs) are a functionally diverse family of toxins, apparently unique to venoms of caenophidian snakes. Although the ancestral function of 3FTXs is antagonism of nicotinic acetylcholine receptors, redundancy conferred by the accumulation of duplicate genes has facilitated extensive neofunctionalization, such that derived members of the family interact with a range of targets. 3FTXs are members of the LY6/UPAR family, but their non-toxin ancestor remains unknown. Combining traditional phylogenetic approaches, manual synteny analysis, and machine learning techniques (including AlphaFold2 and ProtT5), we have reconstructed a detailed evolutionary history of 3FTXs. We identify their immediate ancestor as a non-secretory LY6, unique to squamate reptiles, and propose that changes in molecular ecology resulting from loss of a membrane-anchoring domain and changes in gene expression, paved the way for the evolution of one of the most important families of snake toxins.}, }
@article {pmid37567871, year = {2023}, author = {Tonin, R and Wilhelmi, S and Gültas, M and Gerdol, R and Paun, O and Trucchi, E and Schmitt, AO and Wellstein, C}, title = {Ice holes microrefugia harbor genetically and functionally distinct populations of Vaccinium vitis-idaea (Ericaceae).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13055}, pmid = {37567871}, issn = {2045-2322}, support = {I52F16000110005//Free University of Bozen-Bolzano/ ; I52F16000110005//Free University of Bozen-Bolzano/ ; }, abstract = {In the mountain terrain, ice holes are little depressions between rock boulders that are characterized by the exit of cold air able to cool down the rock surface even in summer. This cold air creates cold microrefugia in warmer surroundings that preserve plant species probably over thousands of years under extra-zonal climatic conditions. We hypothesized that ice hole populations of the model species Vaccinium vitis-idaea (Ericaceae) show genetic differentiation from nearby zonal subalpine populations, and high functional trait distinctiveness, in agreement with genetic patterns. We genotyped almost 30,000 single nucleotide polymorphisms using restriction site-associated DNA sequencing and measured eight functional traits indicative of individual performance and ecological strategies. Genetic results showed high differentiation among the six populations suggesting isolation. On siliceous bedrock, ice hole individuals exhibited higher levels of admixture than those from subalpine populations which could have experienced more bottlenecks during demographic fluctuations related to glacial cycles. Ice hole and subalpine calcareous populations clearly separated from siliceous populations, indicating a possible effect of bedrock in shaping genetic patterns. Trait analysis reflected the bedrock effect on populations' differentiation. The significant correlation between trait and genetic distances suggests the genetic contribution in shaping intraspecific functional differentiation. In conclusion, extra-zonal populations reveal a prominent genetic and phenotypic differentiation determined by history and ecological contingency. Therefore, microrefugia populations can contribute to the overall variability of the species and lead to intraspecific-driven responses to upcoming environmental changes.}, }
@article {pmid37563691, year = {2023}, author = {Lotfata, A and Moosazadeh, M and Helbich, M and Hoseini, B}, title = {Socioeconomic and environmental determinants of asthma prevalence: a cross-sectional study at the U.S. County level using geographically weighted random forests.}, journal = {International journal of health geographics}, volume = {22}, number = {1}, pages = {18}, pmid = {37563691}, issn = {1476-072X}, abstract = {BACKGROUND: Some studies have established associations between the prevalence of new-onset asthma and asthma exacerbation and socioeconomic and environmental determinants. However, research remains limited concerning the shape of these associations, the importance of the risk factors, and how these factors vary geographically.<br><br>OBJECTIVE: We aimed (1) to examine ecological associations between asthma prevalence and multiple socio-physical determinants in the United States; and (2) to assess geographic variations in their relative importance.<br><br>METHODS: Our study design is cross sectional based on county-level data for 2020 across the United States. We obtained self-reported asthma prevalence data of adults aged 18&#xa0;years or older for each county. We applied conventional and geographically weighted random forest (GWRF) to investigate the associations between asthma prevalence and socioeconomic (e.g., poverty) and environmental determinants (e.g., air pollution and green space). To enhance the interpretability of the GWRF, we (1) assessed the shape of the associations through partial dependence plots, (2) ranked the determinants according to their global importance scores, and (3) mapped the local variable importance spatially.<br><br>RESULTS: Of the 3059 counties, the average asthma prevalence was 9.9 (standard deviation&#x2009;&#xb1;&#x2009;0.99). The GWRF outperformed the conventional random forest. We found an indication, for example, that temperature was inversely associated with asthma prevalence, while poverty showed positive associations. The partial dependence plots showed that these associations had a non-linear shape. Ranking the socio-physical environmental factors concerning their global importance showed that smoking prevalence and depression prevalence were most relevant, while green space and limited language were of minor relevance. The local variable importance measures showed striking geographical differences.<br><br>CONCLUSION: Our findings strengthen the evidence that socio-physical environments play a role in explaining asthma prevalence, but their relevance seems to vary geographically. The results are vital for implementing future asthma prevention programs that should be tailor-made for specific areas.}, }
@article {pmid37563227, year = {2023}, author = {Lu, AT and Fei, Z and Haghani, A and Robeck, TR and Zoller, JA and Li, CZ and Lowe, R and Yan, Q and Zhang, J and Vu, H and Ablaeva, J and Acosta-Rodriguez, VA and Adams, DM and Almunia, J and Aloysius, A and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, GG and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, SM and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and DiRocco, S and Dold, C and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Gorbunova, V and Goya, RG and Grant, MJ and Green, CB and Hales, EN and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaitre, JF and Levine, AJ and Li, C and Li, X and Lim, AR and Lin, DTS and Lindemann, DM and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and O'Brien, JK and O'Tierney Ginn, P and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pellegrini, M and Peters, KJ and Pedersen, AB and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Seluanov, A and Shafer, ABA and Shanmuganayagam, D and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmaohammadi, E and Spangler, ML and Spriggs, MC and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Wallingford, MC and Wang, N and Wayne, RK and Wilkinson, GS and Williams, CK and Williams, RW and Yang, XW and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, P and Zhao, Y and Zhou, W and Zimmermann, J and Ernst, J and Raj, K and Horvath, S}, title = {Universal DNA methylation age across mammalian tissues.}, journal = {Nature aging}, volume = {}, number = {}, pages = {}, pmid = {37563227}, issn = {2662-8465}, support = {1U01AG060908 - 01//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, abstract = {Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.}, }
@article {pmid37561875, year = {2023}, author = {Haghani, A and Li, CZ and Robeck, TR and Zhang, J and Lu, AT and Ablaeva, J and Acosta-Rodríguez, VA and Adams, DM and Alagaili, AN and Almunia, J and Aloysius, A and Amor, NMS and Ardehali, R and Arneson, A and Baker, CS and Banks, G and Belov, K and Bennett, NC and Black, P and Blumstein, DT and Bors, EK and Breeze, CE and Brooke, RT and Brown, JL and Carter, G and Caulton, A and Cavin, JM and Chakrabarti, L and Chatzistamou, I and Chavez, AS and Chen, H and Cheng, K and Chiavellini, P and Choi, OW and Clarke, S and Cook, JA and Cooper, LN and Cossette, ML and Day, J and DeYoung, J and Dirocco, S and Dold, C and Dunnum, JL and Ehmke, EE and Emmons, CK and Emmrich, S and Erbay, E and Erlacher-Reid, C and Faulkes, CG and Fei, Z and Ferguson, SH and Finno, CJ and Flower, JE and Gaillard, JM and Garde, E and Gerber, L and Gladyshev, VN and Goya, RG and Grant, MJ and Green, CB and Hanson, MB and Hart, DW and Haulena, M and Herrick, K and Hogan, AN and Hogg, CJ and Hore, TA and Huang, T and Izpisua Belmonte, JC and Jasinska, AJ and Jones, G and Jourdain, E and Kashpur, O and Katcher, H and Katsumata, E and Kaza, V and Kiaris, H and Kobor, MS and Kordowitzki, P and Koski, WR and Krützen, M and Kwon, SB and Larison, B and Lee, SG and Lehmann, M and Lemaître, JF and Levine, AJ and Li, X and Li, C and Lim, AR and Lin, DTS and Lindemann, DM and Liphardt, SW and Little, TJ and Macoretta, N and Maddox, D and Matkin, CO and Mattison, JA and McClure, M and Mergl, J and Meudt, JJ and Montano, GA and Mozhui, K and Munshi-South, J and Murphy, WJ and Naderi, A and Nagy, M and Narayan, P and Nathanielsz, PW and Nguyen, NB and Niehrs, C and Nyamsuren, B and O'Brien, JK and Ginn, PO and Odom, DT and Ophir, AG and Osborn, S and Ostrander, EA and Parsons, KM and Paul, KC and Pedersen, AB and Pellegrini, M and Peters, KJ and Petersen, JL and Pietersen, DW and Pinho, GM and Plassais, J and Poganik, JR and Prado, NA and Reddy, P and Rey, B and Ritz, BR and Robbins, J and Rodriguez, M and Russell, J and Rydkina, E and Sailer, LL and Salmon, AB and Sanghavi, A and Schachtschneider, KM and Schmitt, D and Schmitt, T and Schomacher, L and Schook, LB and Sears, KE and Seifert, AW and Shafer, ABA and Shindyapina, AV and Simmons, M and Singh, K and Sinha, I and Slone, J and Snell, RG and Soltanmohammadi, E and Spangler, ML and Spriggs, M and Staggs, L and Stedman, N and Steinman, KJ and Stewart, DT and Sugrue, VJ and Szladovits, B and Takahashi, JS and Takasugi, M and Teeling, EC and Thompson, MJ and Van Bonn, B and Vernes, SC and Villar, D and Vinters, HV and Vu, H and Wallingford, MC and Wang, N and Wilkinson, GS and Williams, RW and Yan, Q and Yao, M and Young, BG and Zhang, B and Zhang, Z and Zhao, Y and Zhao, P and Zhou, W and Zoller, JA and Ernst, J and Seluanov, A and Gorbunova, V and Yang, XW and Raj, K and Horvath, S}, title = {DNA methylation networks underlying mammalian traits.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6658}, pages = {eabq5693}, doi = {10.1126/science.abq5693}, pmid = {37561875}, issn = {1095-9203}, abstract = {Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.}, }
@article {pmid37495700, year = {2023}, author = {Hughes, LJ and Massam, MR and Morton, O and Edwards, FA and Scheffers, BR and Edwards, DP}, title = {Global hotspots of traded phylogenetic and functional diversity.}, journal = {Nature}, volume = {620}, number = {7973}, pages = {351-357}, pmid = {37495700}, issn = {1476-4687}, mesh = {Animals ; *Biodiversity ; *Birds ; *Conservation of Natural Resources/methods/trends ; Datasets as Topic ; Endangered Species ; Europe ; Extinction, Biological ; Geographic Mapping ; *Mammals ; *Phylogeny ; Tropical Climate ; United States ; *Commerce/statistics &amp; numerical data ; }, abstract = {Wildlife trade is a multibillion-dollar industry[1] targeting a hyperdiversity of species[2] and can contribute to major declines in abundance[3]. A key question is understanding the global hotspots of wildlife trade for phylogenetic (PD) and functional (FD) diversity, which underpin the conservation of evolutionary history[4], ecological functions[5] and ecosystem services benefiting humankind[6]. Using a global dataset of traded bird and mammal species, we identify that the highest levels of traded PD and FD are from tropical regions, where high numbers of evolutionary distinct and globally endangered species in trade occur. The standardized effect size (ses) of traded PD and FD also shows strong tropical epicentres, with additional hotspots of mammalian ses.PD in the eastern United States and ses.FD in Europe. Large-bodied, frugivorous and canopy-dwelling birds and large-bodied mammals are more likely to be traded whereas insectivorous birds and diurnally foraging mammals are less likely. Where trade drives localized extinctions[3], our results suggest substantial losses of unique evolutionary lineages and functional traits, with possible cascading effects for communities and ecosystems[5,7]. Avoiding unsustainable exploitation and lost community integrity requires targeted conservation efforts, especially in hotspots of traded phylogenetic and functional diversity.}, }
@article {pmid37556709, year = {2023}, author = {Pavinati, G and Lima, LV and Palmieri, IGS and Magnabosco, GT}, title = {Distribution and spatial autocorrelation of viral hepatitis B and C in Paraná, Brazil: an ecological study, 2011-2019.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {2}, pages = {e2022888}, pmid = {37556709}, issn = {2237-9622}, mesh = {Humans ; Brazil/epidemiology ; *Hepatitis B/epidemiology ; Spatial Analysis ; *Hepatitis C/epidemiology ; Information Systems ; }, abstract = {OBJECTIVE: to analyze the distribution and spatial autocorrelation of hepatitis B and C detection rates in the state of Paraná, Brazil.<br><br>METHODS: this was an ecological study of hepatitis B and C notifications held on the Notifiable Health Conditions Information System, between 2011 and 2019. Percentage change in detection rates between the first and last three-year periods was estimated. Spatial autocorrelation was analyzed using Moran's index.<br><br>RESULTS: there were 16,699 notifications of hepatitis B, with a greater reduction in detection in the North (-30.0%) and Northwest (-25.9%) macro-regions. There were clusters of high occurrence in the Foz do Igua&#xe7;u, Francisco Beltr&#xe3;o and Cascavel regions between 2011 and 2019. There were 10,920 notifications of hepatitis C, with a greater reduction in detection in the Northwest macro-region (-18.9%) and an increase in the West (51.1%). The Paranagu&#xe1; region recorded a high detection cluster between 2011 and 2016.<br><br>CONCLUSION: hepatitis B and C showed heterogeneous distribution between health regions.}, }
@article {pmid37558860, year = {2023}, author = {Béchade, B and Cabuslay, CS and Hu, Y and Mendonca, CM and Hassanpour, B and Lin, JY and Su, Y and Fiers, VJ and Anandarajan, D and Lu, R and Olson, CJ and Duplais, C and Rosen, GL and Moreau, CS and Aristilde, L and Wertz, JT and Russell, JA}, title = {Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37558860}, issn = {1751-7370}, support = {GRF-2041772//National Science Foundation (NSF)/ ; TUES-1245632//National Science Foundation (NSF)/ ; DEB-1900357//National Science Foundation (NSF)/ ; CBET-1653092//National Science Foundation (NSF)/ ; DEB-1442156//National Science Foundation (NSF)/ ; DOB-1442144//National Science Foundation (NSF)/ ; TUES-1245632//National Science Foundation (NSF)/ ; }, abstract = {While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.}, }
@article {pmid37556975, year = {2023}, author = {Song, L and Chen, Y and Liu, S and Xu, M and Cui, J}, title = {SLWE-Net: An improved lightweight U-Net for Sargassum extraction from GOCI images.}, journal = {Marine pollution bulletin}, volume = {194}, number = {Pt B}, pages = {115349}, doi = {10.1016/j.marpolbul.2023.115349}, pmid = {37556975}, issn = {1879-3363}, abstract = {The Sargassum bloom has severely impacted the ecological environment of the East China Sea and the Yellow Sea, causing significant economic losses. In recent years, deep learning has seen extensive development due to its outstanding feature extraction capabilities. However, the deep learning process typically involves a large number of parameters and computations. To address this issue, this paper proposes a lightweight deep learning network based on the U-Net framework, called SLWE-NET, which uses lightweight modules to replace the feature extraction modules in U-Net. In this experiment, SLWE-Net performed the best in both extraction accuracy and model lightweight. Compared to the formal U-Net, the number of parameters decreased by 65.83 %, the model size reduced from 94.97 MB to 32.51 MB, and the mIoU increased to 93.81 %. Therefore, the method proposed in this paper is beneficial for Sargassum extraction and provides a basis for operational monitoring.}, }
@article {pmid37554800, year = {2023}, author = {Motuziuk, O and Nozdrenko, D and Prylutska, S and Vareniuk, I and Bogutska, K and Braniuk, S and Korotkyi, O and Prylutskyy, Y and Ritter, U and Piosik, J}, title = {The effect of C60 fullerene on the mechanokinetics of muscle gastrocnemius contraction in chronically alcoholized rats.}, journal = {Heliyon}, volume = {9}, number = {8}, pages = {e18745}, pmid = {37554800}, issn = {2405-8440}, abstract = {The C60 fullerene effect (oral administration at a dose of 1 mg kg[-1]) on the selected biomechanical parameters of muscle gastrocnemius contraction, biochemical indicators of blood and muscle tissue as well as histological changes in rat muscle tissue after chronic alcoholization for 3, 6 and 9 months was studied in detail. Water-soluble C60 fullerenes were shown to reduce the pathological processes development in the muscle apparatus by an average of (35-40)%. In particular, they reduced the time occurrence of fatigue processes in muscle during the long-term development of alcoholic myopathy and inhibited oxidative processes in muscle, thereby preventing its degradation. These findings open up the possibility of using C60 fullerenes as potent antioxidants for the correction of the pathological conditions of the muscle system arising from alcohol intoxication.}, }
@article {pmid37554074, year = {2023}, author = {Mpinga, K and Rukundo, T and Mwale, O and Kamwiyo, M and Thengo, L and Ruderman, T and Matanje, B and Munyaneza, F and Connolly, E and Kulisewa, K and Udedi, M and Kachimanga, C and Dullie, L and McBain, R}, title = {Depressive disorder at the household level: prevalence and correlates of depressive symptoms among household members.}, journal = {Global health action}, volume = {16}, number = {1}, pages = {2241808}, doi = {10.1080/16549716.2023.2241808}, pmid = {37554074}, issn = {1654-9880}, abstract = {BACKGROUND: Globally, an estimated five percent of adults have major depressive disorder. However, little is known about the relationship between these individuals' depressive symptoms and their household members' mental health and well-being.<br><br>OBJECTIVES: We aimed to investigate the prevalence and predictors of depressive symptoms among adult household members of patients living with major depressive disorder in Neno District, Malawi.<br><br>METHODS: As part of a cluster randomized controlled trial providing depression care to adults with major depressive disorder, we conducted surveys with patients' household members (n&#x2009;=&#x2009;236) and inquired about their overall health, depressive symptoms, disability, and social support. We calculated prevalence rates of depressive disorder and conducted multivariable linear regression and multivariable logistic regression analyses to assess correlates of depressive symptom severity and predictors of having depressive disorder (PHQ-9), respectively, among household members.<br><br>RESULTS: We observed that roughly one in five household members (19%) screened positive for a depressive disorder (PHQ-9&#x2009;>&#x2009;9). More than half of household members endorsed six or more of the nine symptoms, with 68% reporting feeling 'down, depressed, or hopeless' in the prior two weeks. Elevated depression symptom severity was associated with greater disability (&#x3b2;&#x2009;=&#x2009;0.17, p&#x2009;<&#x2009;0.001), less social support (&#x3b2;&#x2009;= -0.04, p&#x2009;=&#x2009;0.016), and lower self-reported overall health (&#x3b2;&#x2009;=&#x2009;0.54, p&#x2009;=&#x2009;0.001). Having depressive disorder was also associated with greater disability (adjusted Odds Ratio [aOR]&#x2009;=&#x2009;1.12, p&#x2009;=&#x2009;0.001) and less social support (aOR&#x2009;=&#x2009;0.97, p&#x2009;=&#x2009;0.024).<br><br>CONCLUSIONS: In the Malawian context, we find that depressive disorder and depression symptoms are shared attributes among household members. This has implications for both screening and treatment, and it suggests that mental health should be approached from the vantage point of the broader social ecology of the household and family unit.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT04777006) - March 2, 2021.}, }
@article {pmid37552473, year = {2023}, author = {Jiang, Z and Liu, S and Zhang, D and Sha, Z}, title = {The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37552473}, issn = {1432-184X}, abstract = {To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.}, }
@article {pmid37550506, year = {2023}, author = {Sahu, N and Indic, B and Wong-Bajracharya, J and Merényi, Z and Ke, HM and Ahrendt, S and Monk, TL and Kocsubé, S and Drula, E and Lipzen, A and Bálint, B and Henrissat, B and Andreopoulos, B and Martin, FM and Bugge Harder, C and Rigling, D and Ford, KL and Foster, GD and Pangilinan, J and Papanicolaou, A and Barry, K and LaButti, K and Virágh, M and Koriabine, M and Yan, M and Riley, R and Champramary, S and Plett, KL and Grigoriev, IV and Tsai, IJ and Slot, J and Sipos, G and Plett, J and Nagy, LG}, title = {Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37550506}, issn = {2058-5276}, support = {758161//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LP2019-13/2019//Magyar Tudom&#xe1;nyos Akad&#xe9;mia (Hungarian Academy of Sciences)/ ; }, abstract = {The fungal genus Armillaria contains necrotrophic pathogens and some of the largest terrestrial organisms that cause tremendous losses in diverse ecosystems, yet how they evolved pathogenicity in a clade of dominantly non-pathogenic wood degraders remains elusive. Here we show that Armillaria species, in addition to gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer events, primarily from Ascomycota. Horizontal gene transfer might have affected plant biomass degrading and virulence abilities of Armillaria, and provides an explanation for their unusual, soft rot-like wood decay strategy. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors and two novel conserved pathogenicity-induced small secreted proteins, which induced necrosis in planta. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits of plant biomass degradation and pathogenicity in important fungal pathogens.}, }
@article {pmid37548802, year = {2023}, author = {Dong, H and Liu, Y and Cui, J and Zhu, M and Ji, W}, title = {Spatial and temporal variations of vegetation cover and its influencing factors in Shandong Province based on GEE.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {9}, pages = {1023}, pmid = {37548802}, issn = {1573-2959}, support = {42201077 and 42177453//National Natural Science Foundation of China/ ; ZR2021QD074//Natural Science Foundation of Shandong Province/ ; 17YJAZH013//the MOE Layout Foundation of Humanities and Social Sciences/ ; }, mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Soil ; Sustainable Development ; }, abstract = {Economic development has rapidly progressed since the implementation of reform and opening up policies, posing significant challenges to sustainable development, especially to vegetation, which plays a crucial role in maintaining ecosystem service functions and promoting green low-carbon transformations. In this study, we estimated the fractional vegetation cover (FVC) in Shandong Province from 2000 to 2020 using the Google Earth Engine (GEE) platform. The spatial and temporal changes in FVC were analyzed using gravity center migration analysis, trend analysis, and geographic detector, and the vegetation changes of different land use types were analyzed to reveal the internal driving mechanism of FVC changes. Our results indicate that vegetation cover in Shandong Province was in good condition during the period 2000 to 2020. The high vegetation cover classes dominated, and overall changes were relatively small, with the center of gravity of vegetation cover generally shifting towards the southwest. Land use type, soil type, population density, and GDP factors had the most significant impact on vegetation cover change in Shandong Province. The interaction of these factors enhanced the effect on vegetation cover change, with land use type and soil type having the highest degree of influence. The observational results of this study can provide data support for the policy makers to formulate new ecological restoration strategies, and the findings would help facilitate the sustainability management of regional ecosystem and natural resource planning.}, }
@article {pmid37548100, year = {2023}, author = {Anderson, LM and Lim, KO and Kummerfeld, E and Crosby, RD and Crow, SJ and Engel, SG and Forrest, L and Wonderlich, SA and Peterson, CB}, title = {Causal discovery analysis: A promising tool in advancing precision medicine for eating disorders.}, journal = {The International journal of eating disorders}, volume = {}, number = {}, pages = {}, doi = {10.1002/eat.24040}, pmid = {37548100}, issn = {1098-108X}, support = {1P20GM134969/GM/NIGMS NIH HHS/United States ; K23MH123910/MH/NIMH NIH HHS/United States ; R34MH077571/MH/NIMH NIH HHS/United States ; }, abstract = {OBJECTIVE: Precision medicine (i.e., individually tailored treatments) represents an optimal goal for treating complex psychiatric disorders, including eating disorders. Within the eating disorders field, most treatment development efforts have been limited in their ability to identify individual-level models of eating disorder psychopathology and to develop and apply an individually tailored treatment for a given individual's personalized model of psychopathology. In addition, research is still needed to identify causal relationships within a given individual's model of eating disorder psychopathology. Addressing this limitation of the current state of precision medicine-related research in the field will allow us to progress toward advancing research and practice for eating disorders treatment.<br><br>METHOD: We present a novel set of analytic tools, causal discovery analysis (CDA) methods, which can facilitate increasingly fine-grained, person-specific models of causal relations among cognitive, behavioral, and affective symptoms.<br><br>RESULTS: CDA can advance the identification of an individual's causal model that maintains that individuals' eating disorder psychopathology.<br><br>DISCUSSION: In the current article, we (1) introduce CDA methods as a set of promising analytic tools for developing precision medicine methods for eating disorders including the potential strengths and weaknesses of CDA, (2) provide recommendations for future studies utilizing this approach, and (3) outline the potential clinical implications of using CDA to generate personalized models of eating disorder psychopathology.<br><br>PUBLIC SIGNIFICANCE STATEMENT: CDA provides a novel statistical approach for identifying causal relationships among variables of interest for a given individual. Person-specific causal models may offer a promising approach to individualized treatment planning and inform future personalized treatment development efforts for eating disorders.}, }
@article {pmid37468639, year = {2023}, author = {Caglayan, E and Ayhan, F and Liu, Y and Vollmer, RM and Oh, E and Sherwood, CC and Preuss, TM and Yi, SV and Konopka, G}, title = {Molecular features driving cellular complexity of human brain evolution.}, journal = {Nature}, volume = {620}, number = {7972}, pages = {145-153}, pmid = {37468639}, issn = {1476-4687}, mesh = {Animals ; Humans ; Cell Nucleus/metabolism ; Chromatin/genetics/metabolism ; Datasets as Topic ; *Evolution, Molecular ; Genome, Human/genetics ; Genomics ; *Gyrus Cinguli/cytology/metabolism ; Macaca mulatta/genetics ; Neurons/classification/cytology ; Oligodendroglia/cytology/metabolism ; Pan troglodytes/genetics ; Single-Cell Gene Expression Analysis ; Stem Cells/cytology ; Transposases/metabolism ; Chromatin Assembly and Disassembly ; }, abstract = {Human-specific genomic changes contribute to the unique functionalities of the human brain[1-5]. The cellular heterogeneity of the human brain[6,7] and the complex regulation of gene expression highlight the need to characterize human-specific molecular features at cellular resolution. Here we analysed single-nucleus RNA-sequencing and single-nucleus assay for transposase-accessible chromatin with sequencing datasets for human, chimpanzee and rhesus macaque brain tissue from posterior cingulate cortex. We show a human-specific increase of oligodendrocyte progenitor cells and a decrease of mature oligodendrocytes across cortical tissues. Human-specific regulatory changes were accelerated in oligodendrocyte progenitor cells, and we highlight key biological pathways that may be associated with the proportional changes. We also identify human-specific regulatory changes in neuronal subtypes, which reveal human-specific upregulation of FOXP2 in only two of the neuronal subtypes. We additionally identify hundreds of new human accelerated genomic regions associated with human-specific chromatin accessibility changes. Our data also reveal that FOS::JUN and FOX motifs are enriched in the human-specifically accessible chromatin regions of excitatory neuronal subtypes. Together, our results reveal several new mechanisms underlying the evolutionary innovation of human brain at cell-type resolution.}, }
@article {pmid37543705, year = {2023}, author = {Pakulnicka, J and Kruk, M}, title = {Regional differences in water beetle communities networks settling in dystrophic lakes in northern Poland.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12699}, pmid = {37543705}, issn = {2045-2322}, mesh = {Humans ; *Ecosystem ; *Lakes ; Water ; Poland ; Community Networks ; }, abstract = {The relationships between the species that form the networks in small dystrophic lakes remain poorly recognised. To investigate and better understand the functioning of beetle communities in different ecosystems, we created three network models that we subjected to graph network analysis. This approach displays correlation-based networks of connections (edges) between objects (nodes) by evaluating the features of the whole network and the attributes of nodes and edges in the context of their roles, expressed by centrality metrics. We used this method to determine the importance of specific species in the networks and the interspecific relationships. Our analyses are based on faunal material collected from 25 dystrophic lakes in three regions of northern Poland. We found a total of 104 species representing different ecological elements and functional trophic groups. We have shown that the network of relationships between the biomass of species differs considerably in the three study regions. The Kashubian Lakeland had the highest cohesion and density, while the network in the Suwalki Lakeland was the thinnest and most heterogeneous, which might be related to the fractal structure and the degree of development of the studied lakes. Small-bodied predators that congregated in different clusters with species with similar ecological preferences dominated all networks. We found the highest correlations in the Masurian Lakeland, where we obtained the highest centralisation of the network. Small tyrphophiles typically occupied the central places in the network, while the periphery of the network consisted of clusters with different habitat preferences, including large predators. The species that were most important for network cohesion and density were mainly tyrphophilous species, such as Anacaena lutescens, Hygrotus decoratus, Enochrus melanocephalus and Hydroporus neglectus. The values of attributes determining the role of species in community networks were influenced by both biotic and environmental factors.}, }
@article {pmid37543634, year = {2023}, author = {Fu, Y and Mason, AS and Song, M and Ni, X and Liu, L and Shi, J and Wang, T and Xiao, M and Zhang, Y and Fu, D and Yu, H}, title = {Multi-omics strategies uncover the molecular mechanisms of nitrogen, phosphorus and potassium deficiency responses in Brassica napus.}, journal = {Cellular &amp; molecular biology letters}, volume = {28}, number = {1}, pages = {63}, pmid = {37543634}, issn = {1689-1392}, support = {LY23C130007//Zhejiang Provincial Natural Science Foundation of China/ ; 2021C02064-2//Medical Technology and Education of Zhejiang Province of China/ ; No. 2022E10012//Key Laboratory of Digital Upland Crops of Zhejiang Province/ ; }, mesh = {*Brassica napus/genetics/metabolism ; Phosphorus ; *Potassium Deficiency/genetics ; Nitrogen/metabolism ; Multiomics ; Transcriptome ; Potassium/metabolism ; *MicroRNAs/genetics/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {BACKGROUND: Nitrogen (N), phosphorus (P) and potassium (K) are critical macronutrients in crops, such that deficiency in any of N, P or K has substantial effects on crop growth. However, the specific commonalities of plant responses to different macronutrient deficiencies remain largely unknown.<br><br>METHODS: Here, we assessed the phenotypic and physiological performances along with whole transcriptome and metabolomic profiles of rapeseed seedlings exposed to N, P and K deficiency stresses.<br><br>RESULTS: Quantities of reactive oxygen species were significantly increased by all macronutrient deficiencies. N and K deficiencies resulted in more severe root development responses than P deficiency, as well as greater chlorophyll content reduction in leaves (associated with disrupted chloroplast structure). Transcriptome and metabolome analyses validated the macronutrient-specific responses, with more pronounced effects of N and P deficiencies on mRNAs, microRNAs (miRNAs), circular RNAs (circRNAs) and metabolites relative to K deficiency. Tissue-specific responses also occurred, with greater effects of macronutrient deficiencies on roots compared with shoots. We further uncovered a set of common responders with simultaneous roles in all three macronutrient deficiencies, including 112 mRNAs and 10 miRNAs involved in hormonal signaling, ion transport and oxidative stress in the root, and 33 mRNAs and 6 miRNAs with roles in abiotic stress response and photosynthesis in the shoot. 27 and seven common miRNA-mRNA pairs with role in miRNA-mediated regulation of oxidoreduction processes and ion transmembrane transport were identified in all three macronutrient deficiencies. No circRNA was responsive to three macronutrient deficiency stresses, but two common circRNAs were identified for two macronutrient deficiencies. Combined analysis of circRNAs, miRNAs and mRNAs suggested that two circRNAs act as decoys for miR156 and participate in oxidoreduction processes and transmembrane transport in both N- and P-deprived roots. Simultaneously, dramatic alterations of metabolites also occurred. Associations of RNAs with metabolites were observed, and suggested potential positive regulatory roles for tricarboxylic acids, azoles, carbohydrates, sterols and auxins, and negative regulatory roles for aromatic and aspartate amino acids, glucosamine-containing compounds, cinnamic acid, and nicotianamine in plant adaptation to macronutrient deficiency.<br><br>CONCLUSIONS: Our findings revealed strategies to rescue rapeseed from macronutrient deficiency stress, including reducing the expression of non-essential genes and activating or enhancing the expression of anti-stress genes, aided by plant hormones, ion transporters and stress responders. The common responders to different macronutrient deficiencies identified could be targeted to enhance nutrient use efficiency in rapeseed.}, }
@article {pmid37541986, year = {2023}, author = {Drozdovitch, V and Kukhta, T and Minenko, V and Trofimik, S and Veyalkin, I and Yauseyenka, V and Mabuchi, K and Rozhko, A}, title = {Recall of residential history and dietary habits during pregnancy and lactation in the distant past: reliability of questionnaire-based radiation doses for persons exposed in utero and early life.}, journal = {Radiation and environmental biophysics}, volume = {}, number = {}, pages = {}, pmid = {37541986}, issn = {1432-2099}, support = {HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; HHSN261201800015C/CA/NCI NIH HHS/United States ; }, abstract = {This study evaluates the reliability of information obtained by standardized questionnaires used in by personal interviews for estimation of radiation thyroid doses of 1065 individuals in the Belarusian cohort of individuals who were exposed in utero and early life following the Chernobyl accident in April 1986. Data from two interviews conducted in 2012-2017 and in 2018-2022 with mothers, who were pregnant or gave birth shortly after the Chernobyl accident, were analysed. The most reliable answers dealt with various attributes related to residential history. In contrast, the reliability of answers regarding consumption rates of milk from privately owned cows or trade network was moderate, while the agreement in responses for consumption of milk products and leafy vegetables was fair. Information from the two interviews was used to calculate thyroid doses received by the cohort members. Specifically, 'model-based' thyroid doses due to [131]I were estimated using input data on individual residential history and food consumption reported during the personal interviews and ecological data ([131]I ground deposition in the corresponding settlements). In addition, for a subset of cohort subjects (n = 205) whose mothers were measured for [131]I thyroid activity, 'measurement-based' thyroid doses were calculated by adjusting the model-based dose using a scaling factor that is defined as the ratio of measured [131]I thyroid activity to model-based [131]I thyroid activity calculated for the date of measurement. A moderate agreement was observed for total (prenatal and postnatal) model-based thyroid doses due to [131]I intake, the arithmetic mean ± standard deviation for the Jaccard similarity coefficient ([Formula: see text]) was 0.45 ± 0.34 (median = 0.39), while measurement-based doses showed a much better agreement with a [Formula: see text] of 0.78 ± 0.29 (median = 0.93). For model-based thyroid doses from external irradiation and from ingestion of [134]Cs and [137]Cs, [Formula: see text] was 0.82 ± 0.23 (median = 0.90) and 0.84 ± 0.24 (median = 0.96), respectively. Measurement-based doses due to ingestion of radiocaesium isotopes resulted in an almost perfect agreement, [Formula: see text] was 0.91 ± 0.19 (median = 1.0). The present findings suggest that long-term memory recall can be reliable, if a person is asked about unique or important life events, such as pregnancy and childbirth occurring around the time of a nuclear reactor accident. However, the substantial difference (more than 10 times) observed for model-bases doses calculated using the two questionnaires represents an important source of human factor uncertainties that needs to be considered in any dose response analyses. Other lessons learned from this study are that (i) individual measurements of radionuclides in the human body are the most valuable source of information for estimating radiation doses, and (ii) whenever a radiation accident occurs, a sample of affected people should be asked to keep a diary, if at all possible.}, }
@article {pmid37536963, year = {2023}, author = {Tobin, K and Heidari, O and Volpi, C and Sodder, S and Duncan, D}, title = {Use of geofencing interventions in population health research: a scoping review.}, journal = {BMJ open}, volume = {13}, number = {8}, pages = {e069374}, pmid = {37536963}, issn = {2044-6055}, support = {KL2 TR002317/TR/NCATS NIH HHS/United States ; R34 MH118178/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Population Health ; *Geographic Information Systems ; }, abstract = {OBJECTIVES: Technological advancements that use global positioning system (GPS), such as geofencing, provide the opportunity to examine place-based context in population health research. This review aimed to systematically identify, assess and synthesise the existing evidence on geofencing intervention design, acceptability, feasibility and/or impact.<br><br>DESIGN: Scoping review, using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guidance for reporting.<br><br>DATA SOURCES: PubMed, CINAHL, EMBASE, Web of Science, Cochrane and PsycINFO for articles in English published up to 31 December 2021.<br><br>ELIGIBILITY CRITERIA: Articles were included if geofencing was used as a mechanism for intervention delivery.<br><br>EXCLUSION CRITERIA: (1) a component or combination of GPS, geographical information system or ecological momentary assessment was used without delivery of an intervention; (2) did not include a health or health-related outcome from the geofencing intervention; or (3) was not a peer-reviewed study.<br><br>DATA EXTRACTION AND SYNTHESIS: Several researchers independently reviewed all abstracts and full-text articles for final inclusion.<br><br>RESULTS: A total of 2171 articles were found; after exclusions, nine studies were included in the review. The majority were published in 5 years preceding the search (89%). Geofences in most studies (n=5) were fixed and programmed in the mobile application carried by participants without their input. Mechanisms of geofencing interventions were classified as direct or indirect, with five studies (56%) using direct interventions. There were several different health outcomes (from smoking to problematic alcohol use) across the five studies that used a direct geofencing intervention.<br><br>CONCLUSIONS: This scoping review found geofencing to be an emerging technology that is an acceptable and feasible intervention applied to several different populations and health outcomes. Future studies should specify the rationale for the locations that are geofenced and user input. Moreover, attention to mechanisms of actions will enable scientists to understand not only whether geofencing is an appropriate and effective intervention but why it works to achieve the outcomes observed.}, }
@article {pmid37533557, year = {2023}, author = {Wang, TY and Goh, KS and Wang, LJ and Wu, LL and Wang, FY and Wu, YW}, title = {Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the Endemic Firefly of Taiwan.}, journal = {Zoological studies}, volume = {62}, number = {}, pages = {e25}, pmid = {37533557}, issn = {1810-522X}, abstract = {Abscondita cerata is the most abundant and widely distributed endemic firefly species in Taiwan and is considered a key environmental and ecological indicator organism. In this study, we report the first long-read genome sequencing of Abs. cerata sequenced by Nanopore technology. The draft genome size, 967 Mb, was measured through a hybrid approach that consisted of assembling using 11.25-Gb Nanopore long reads and polishing using 9.47-Gb BGI PE100 short reads. The drafted genome was assembled into 4,855 contigs, with the N50 reaching 325.269 kb length. The assembled genome was predicted to possess 55,206 protein-coding genes, of which 20,862 (37.78%) were functionally annotated with public databases. 47.11% of the genome sequences consisted of repeat elements; among them DNA transposons accounted for the largest proportion (26.79%). A BUSCO (Benchmarking Universal Single Copy Orthologs) evaluation demonstrated that the genome and gene completeness were 84.8% and 79%, respectively. The phylogeny constructed using 1,792 single copy genes was consistent with previous studies. The comparative transcriptome between adult male head and lantern tissues revealed (1) the vision of Abs. cerata is primarily UV-sensitive to environmental twilight, which determines when it begins its nocturnal activity, (2) the major expressed OR56d receptor may be correlated to suitable humidity sensing, and (3) Luc1-type luciferase is responsible for Abs. cerata's luminescent spectrum.}, }
@article {pmid37546168, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Lewin, T and , }, title = {The genome sequence of the double-striped pug, Gymnoscelis rufifasciata (Haworth, 1809).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {135}, pmid = {37546168}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Gymnoscelis rufifasciata (the double-striped pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 352 megabases in span. The majority of the assembly (99.82%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The mitochondrial genome was also assembled, and is 15.4 kilobases in length.}, }
@article {pmid37531569, year = {2023}, author = {Beer, RD}, title = {On the Proper Treatment of Dynamics in Cognitive Science.}, journal = {Topics in cognitive science}, volume = {}, number = {}, pages = {}, doi = {10.1111/tops.12686}, pmid = {37531569}, issn = {1756-8765}, abstract = {This essay examines the relevance of dynamical ideas for cognitive science. On its own, the mere mathematical idea of a dynamical system is too weak to serve as a scientific theory of anything, and dynamical approaches within cognitive science are too rich and varied to be subsumed under a single "dynamical hypothesis." Instead, after first attempting to dissect the different notions of "dynamics" and "cognition" at play, a more specific theoretical framework for cognitive science broadly construed is sketched. This framework draws upon not only dynamical ideas, but also such contemporaneous perspectives as situatedness, embodiment, ecological psychology, enaction, neuroethology/neuroscience, artificial life, and biogenic approaches. The paper ends with some methodological suggestions for pursuing this theoretical framework.}, }
@article {pmid37531181, year = {2023}, author = {Murray, A and Ushakova, A and Zhu, X and Yang, Y and Xiao, Z and Brown, R and Speyer, L and Ribeaud, D and Eisner, M}, title = {Predicting Participation Willingness in Ecological Momentary Assessment of General Population Health and Behavior: Machine Learning Study.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e41412}, doi = {10.2196/41412}, pmid = {37531181}, issn = {1438-8871}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Young Adult ; Humans ; *Ecological Momentary Assessment ; *Tobacco Use ; Machine Learning ; Research Design ; Health Behavior ; }, abstract = {BACKGROUND: Ecological momentary assessment (EMA) is widely used in health research to capture individuals' experiences in the flow of daily life. The majority of EMA studies, however, rely on nonprobability sampling approaches, leaving open the possibility of nonrandom participation concerning the individual characteristics of interest in EMA research. Knowledge of the factors that predict participation in EMA research is required to evaluate this possibility and can also inform optimal recruitment strategies.<br><br>OBJECTIVE: This study aimed to examine the extent to which being willing to participate in EMA research is related to respondent characteristics and to identify the most critical predictors of participation.<br><br>METHODS: We leveraged the availability of comprehensive data on a general young adult population pool of potential EMA participants and used and compared logistic regression, classification and regression trees, and random forest approaches to evaluate respondents' characteristic predictors of willingness to participate in the Decades-to-Minutes EMA study.<br><br>RESULTS: In unadjusted logistic regression models, gender, migration background, anxiety, attention deficit hyperactivity disorder symptoms, stress, and prosociality were significant predictors of participation willingness; in logistic regression models, mutually adjusting for all predictors, migration background, tobacco use, and social exclusion were significant predictors. Tree-based approaches also identified migration status, tobacco use, and prosociality as prominent predictors. However, overall, willingness to participate in the Decades-to-Minutes EMA study was only weakly predictable from respondent characteristics. Cross-validation areas under the curve for the best models were only in the range of 0.56 to 0.57.<br><br>CONCLUSIONS: Results suggest that migration background is the single most promising target for improving EMA participation and sample representativeness; however, more research is needed to improve prediction of participation in EMA studies in health.}, }
@article {pmid37529296, year = {2023}, author = {Kumar, V and Goyal, N and Prasad, A and Babu, S and Khare, K and Yadav, G}, title = {Quantification of pollen viability in Lantana camara by digital holographic microscopy.}, journal = {Quantitative plant biology}, volume = {4}, number = {}, pages = {e7}, pmid = {37529296}, issn = {2632-8828}, abstract = {Pollen grains represent the male gametes of seed plants and their viability is critical for sexual reproduction in the plant life cycle. Palynology and viability studies have traditionally been used to address a range of botanical, ecological and geological questions, but recent work has revealed the importance of pollen viability in invasion biology as well. Here, we report an efficient visual method for assessing the viability of pollen using digital holographic microscopy (DHM). Imaging data reveal that quantitative phase information provided by the technique can be correlated with viability as indicated by the outcome of the colorimetric test. We successfully test this method on pollen grains of Lantana camara, a well-known alien invasive plant in the tropical world. Our results show that pollen viability may be assessed accurately without the usual staining procedure and suggest potential applications of the DHM methodology to a number of emerging areas in plant science.}, }
@article {pmid37527270, year = {2023}, author = {Kandel, AW and Sommer, C and Kanaeva, Z and Bolus, M and Bruch, AA and Groth, C and Haidle, MN and Hertler, C and Heß, J and Malina, M and Märker, M and Hochschild, V and Mosbrugger, V and Schrenk, F and Conard, NJ}, title = {The ROCEEH Out of Africa Database (ROAD): A large-scale research database serves as an indispensable tool for human evolutionary studies.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0289513}, pmid = {37527270}, issn = {1932-6203}, mesh = {Humans ; *Artificial Intelligence ; Databases, Factual ; *Geographic Information Systems ; Software ; Africa ; }, abstract = {Large scale databases are critical for helping scientists decipher long-term patterns in human evolution. This paper describes the conception and development of such a research database and illustrates how big data can be harnessed to formulate new ideas about the past. The Role of Culture in Early Expansions of Humans (ROCEEH) is a transdisciplinary research center whose aim is to study the origins of culture and the multifaceted aspects of human expansions across Africa and Eurasia over the last three million years. To support its research, the ROCEEH team developed an online tool named the ROCEEH Out of Africa Database (ROAD) and implemented its web-based applications. ROAD integrates geographical data as well as archaeological, paleoanthropological, paleontological and paleobotanical content within a robust chronological framework. In fact, a unique feature of ROAD is its ability to dynamically link scientific data both spatially and temporally, thereby allowing its reuse in ways that were not originally conceived. The data stem from published sources spanning the last 150 years, including those generated by the research team. Descriptions of these data rely on the development of a standardized vocabulary and profit from online explanations of each table and attribute. By synthesizing legacy data, ROAD facilitates the reuse of heritage data in novel ways. Database queries yield structured information in a variety of interoperable formats. By visualizing data on maps, users can explore this vast dataset and develop their own theories. By downloading data, users can conduct further quantitative analyses, for example with Geographic Information Systems, modeling programs and artificial intelligence. In this paper, we demonstrate the innovative nature of ROAD and show how it helps scientists studying human evolution to access datasets from different fields, thereby connecting the social and natural sciences. Because it permits the reuse of "old" data in new ways, ROAD is now an indispensable tool for researchers of human evolution and paleogeography.}, }
@article {pmid37526960, year = {2023}, author = {Parfitt, KM and Green, AE and Connor, TR and Neill, DR and Mahenthiralingam, E}, title = {Identification of two distinct phylogenomic lineages and model strains for the understudied cystic fibrosis lung pathogen Burkholderia multivorans.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {8}, pages = {}, doi = {10.1099/mic.0.001366}, pmid = {37526960}, issn = {1465-2080}, support = {204457/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Animals ; Mice ; Phylogeny ; Multilocus Sequence Typing ; *Burkholderia Infections ; *Cystic Fibrosis/complications ; *Burkholderia/genetics ; *Burkholderia cepacia complex/genetics ; Lung ; }, abstract = {Burkholderia multivorans is the dominant Burkholderia pathogen recovered from lung infection in people with cystic fibrosis. However, as an understudied pathogen there are knowledge gaps in relation to its population biology, phenotypic traits and useful model strains. A phylogenomic study of B. multivorans was undertaken using a total of 283 genomes, of which 73 were sequenced and 49 phenotypically characterized as part of this study. Average nucleotide identity analysis (ANI) and phylogenetic alignment of core genes demonstrated that the B. multivorans population separated into two distinct evolutionary clades, defined as lineage 1 (n=58 genomes) and lineage 2 (n=221 genomes). To examine the population biology of B. multivorans, a representative subgroup of 77 B. multivorans genomes (28 from the reference databases and the 49 novel short-read genome sequences) were selected based on multilocus sequence typing (MLST), isolation source and phylogenetic placement criteria. Comparative genomics was used to identify B. multivorans lineage-specific genes - ghrB_1 in lineage 1 and glnM_2 in lineage 2 - and diagnostic PCRs targeting them were successfully developed. Phenotypic analysis of 49 representative B. multivorans strains showed considerable inter-strain variance, but the majority of the isolates tested were motile and capable of biofilm formation. A striking absence of B. multivorans protease activity in vitro was observed, but no lineage-specific phenotypic differences were demonstrated. Using phylogenomic and phenotypic criteria, three model B. multivorans CF strains were identified, BCC0084 (lineage 1), BCC1272 (lineage 2a) and BCC0033 lineage 2b, and their complete genome sequences determined. B. multivorans CF strains BCC0033 and BCC0084, and the environmental reference strain, ATCC 17616, were all capable of short-term survival within a murine lung infection model. By mapping the population biology, identifying lineage-specific PCRs and model strains, we provide much needed baseline resources for future studies of B. multivorans.}, }
@article {pmid37518126, year = {2023}, author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM}, title = {Fauna and taxonomy of Diamesinae (Diptera, Chironomidae) from the Caucasus, with a morphological description and DNA barcoding of new taxa and a discussion of diagnostic problems for Diamesa Meigen and Pseudodiamesa Goetghebuer.}, journal = {Zootaxa}, volume = {5271}, number = {2}, pages = {313-328}, doi = {10.11646/zootaxa.5271.2.6}, pmid = {37518126}, issn = {1175-5334}, mesh = {Male ; Animals ; *Chironomidae/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; DNA ; Databases, Nucleic Acid ; }, abstract = {As a result of the revision of adult males as well as available literature data, 26 species of the subfamily Diamesinae are registered for the Caucasus, belonging to 5 genera. Four species are recorded for the first time for this region, one species, D. elbrusica sp. nov., and one subspecies, D. sakartvella gidanica subsp. nov., are new to science and are described. Six species are classified as endemics of the Caucasus. Distribution of other species of Caucasian Diamesinae is discussed. DNA barcodes of 102 specimens and 20 species of four genera, Boreoheptagyia Brundin, Diamesa Meigen, Pseudodiamesa Goetghebuer and Syndiamesa Kieffer were obtained in this study. Of these, 12 species were deposed in the GenBank and BOLD systems for the first time. We have established that D. cinerella group includes D. kasymovi and probably D. lavillei whereas D. zernyi group includes D. vaillanti and D. valentinae. Highly supported phylogeny and results of species delimitation suggest the description of D. elbrusica sp. nov. and D. sakartvella gidanica subsp. nov. Ps. aff. branickii and Ps. aff. nivosa are new species based on DNA barcoding. The results of species delimitation show that genus Pseudodiamesa includes 10 (ASAP, GMYC), 14 (mPTP) or 21 (BOLD) distinct molecular taxonomic units (mOTUs) among which only Ps. stackelbergi have an undoubted species status that requires a large revision using both morphological and molecular approaches.}, }
@article {pmid37517987, year = {2023}, author = {Wang, Y and Xue, K and Hu, R and Ding, B and Zeng, H and Li, R and Xu, B and Pang, Z and Song, X and Li, C and Du, J and Yang, X and Zhang, Z and Hao, Y and Cui, X and Guo, K and Gao, Q and Zhang, Y and Zhu, J and Sun, J and Li, Y and Jiang, L and Zhou, H and Luo, C and Zhang, Z and Gao, Q and Chen, S and Ji, B and Xu, X and Chen, H and Li, Q and Zhao, L and Xu, S and Liu, Y and Hu, L and Wu, J and Yang, Q and Dong, S and He, J and Zhao, X and Wang, S and Piao, S and Yu, G and Fu, B}, title = {Vegetation structural shift tells environmental changes on the Tibetan Plateau over 40 years.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2023.07.035}, pmid = {37517987}, issn = {2095-9281}, abstract = {Structural information of grassland changes on the Tibetan Plateau is essential for understanding alterations in critical ecosystem functioning and their underlying drivers that may reflect environmental changes. However, such information at the regional scale is still lacking due to methodological limitations. Beyond remote sensing indicators only recognizing vegetation productivity, we utilized multivariate data fusion and deep learning to characterize formation-based plant community structure in alpine grasslands at the regional scale of the Tibetan Plateau for the first time and compared it with the earlier version of Vegetation Map of China for historical changes. Over the past 40 years, we revealed that (1) the proportion of alpine meadows in alpine grasslands increased from 50% to 69%, well-reflecting the warming and wetting trend; (2) dominances of Kobresia pygmaea and Stipa purpurea formations in alpine meadows and steppes were strengthened to 76% and 92%, respectively; (3) the climate factor mainly drove the distribution of Stipa purpurea formation, but not the recent distribution of Kobresia pygmaea formation that was likely shaped by human activities. Therefore, the underlying mechanisms of grassland changes over the past 40 years were considered to be formation dependent. Overall, the first exploration for structural information of plant community changes in this study not only provides a new perspective to understand drivers of grassland changes and their spatial heterogeneity at the regional scale of the Tibetan Plateau, but also innovates large-scale vegetation study paradigm.}, }
@article {pmid37511196, year = {2023}, author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T}, title = {Multi-Drug Resistance in Bacterial Genomes-A Comprehensive Bioinformatic Analysis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511196}, issn = {1422-0067}, support = {UI/BD/153078/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; SFRH/BD/04631/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UIDP/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, mesh = {*Genome, Bacterial ; Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Computational Biology ; Drug Resistance, Multiple ; Drug Resistance, Multiple, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance is presently one of the greatest threats to public health. The excessive and indiscriminate use of antibiotics imposes a continuous selective pressure that triggers the emergence of multi-drug resistance. We performed a large-scale analysis of closed bacterial genomes to identify multi-drug resistance considering the ResFinder antimicrobial classes. We found that more than 95% of the genomes harbor genes associated with resistance to disinfectants, glycopeptides, macrolides, and tetracyclines. On average, each genome encodes resistance to more than nine different classes of antimicrobial drugs. We found higher-than-expected co-occurrences of resistance genes in both plasmids and chromosomes for several classes of antibiotic resistance, including classes categorized as critical according to the World Health Organization (WHO). As a result of antibiotic-resistant priority pathogens, higher-than-expected co-occurrences appear in plasmids, increasing the potential for resistance dissemination. For the first time, co-occurrences of antibiotic resistance have been investigated for priority pathogens as defined by the WHO. For critically important pathogens, co-occurrences appear in plasmids, not in chromosomes, suggesting that the resistances may be epidemic and probably recent. These results hint at the need for new approaches to treating infections caused by critically important bacteria.}, }
@article {pmid37508724, year = {2023}, author = {Pinto Pereira, SM and Nugawela, MD and McOwat, K and Dalrymple, E and Xu, L and Ladhani, SN and Simmons, R and Chalder, T and Swann, O and Ford, T and Heyman, I and Segal, T and Semple, MG and Rojas, NK and CLoCk Consortium,  and Shafran, R and Stephenson, T}, title = {Symptom Profiles of Children and Young People 12 Months after SARS-CoV-2 Testing: A National Matched Cohort Study (The CLoCk Study).}, journal = {Children (Basel, Switzerland)}, volume = {10}, number = {7}, pages = {}, pmid = {37508724}, issn = {2227-9067}, support = {COVLT0022//UK Research and Innovation/ ; COVLT0022//National Institute for Health Research/ ; MR/P020372/1//UK Medical Research Council Career Development Award/ ; }, abstract = {BACKGROUND: Although 99% of children and young people have been exposed to SARS-CoV-2, the long-term prevalence of post-COVID-19 symptoms in young people is unclear. The aim of this study is to describe symptom profiles 12 months after SARS-CoV-2 testing.<br><br>METHOD: A matched cohort study of a national sample of 20,202 children and young people who took a SARS-CoV-2 PCR test between September 2020 and March 2021.<br><br>RESULTS: 12 months post-index-test, there was a difference in the number of symptoms reported by initial negatives who never tested positive (NN) compared to the other three groups who had at least one positive test (p < 0.001). Similarly, 10.2% of the NN group described five-plus symptoms at 12 months compared to 15.9-24.0% in the other three groups who had at least one positive test. The most common symptoms were tiredness, sleeping difficulties, shortness of breath, and headaches for all four groups. For all these symptoms, the initial test positives with subsequent reports of re-infection had higher prevalences than other positive groups (p < 0.001). Symptom profiles, mental health, well-being, fatigue, and quality of life did not vary by vaccination status.<br><br>CONCLUSIONS: Following the pandemic, many young people, particularly those that have had multiple SARS-CoV-2 positive tests, experience a range of symptoms that warrant consideration and potential investigation and intervention.}, }
@article {pmid37508342, year = {2023}, author = {Oravec, P and Wittlinger, L and Máliš, F}, title = {Endangered Forest Communities in Central Europe: Mapping Current and Potential Distributions of Euro-Siberian Steppic Woods with Quercus spp. in South Slovak Basin.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, pmid = {37508342}, issn = {2079-7737}, support = {1/0706/20//Constantine the Philosopher University in Nitra/ ; APVV-19-0319//Technical University in Zvolen/ ; }, abstract = {In this article we focus on the issue of determining the presence and status of the priority habitat 91I0* Euro-Siberian steppic woods with Quercus spp. in the South Slovak basin. As part of the issue, we try to verify the correctness of the procedure of the State Nature Conservancy of the Slovak Republic in the search for potential habitats and areas of European importance by converting the typological map to a map of habitats. Habitat 91I0* occurs in Slovakia in the form of three subtypes, namely Thermophilous and supra-Mediterranean oak woods (Carpineto-Quercetum and Betuleto-Quercetum), Acidophilous oak forests (Quercetum), while the last-named subtype is divided into two subunits: Medio-European acidophilous oak forests-part A and Pannonic hairy greenweed sessile oak woods-part B. Due to the current unsatisfactory state of the mentioned habitats, the requirement of the State Nature Conservancy of the Slovak Republic is to find and add new areas with the occurrence of habitat 91I0* in the south of Central Slovakia. During the mapping in the Lučenecká and Rimavská basins, greater emphasis was placed on the occurrence of the subtype Thermophilic Pontic-Pannonian oak forests on loess and sand, but its presence has not been confirmed. Subsequently, we focused on the search and identification of habitats in the model area, which is the area of European importance SKUEV0957 Uderinky. The result is a map of habitats in this area, which we then compare with a typological map, which determines the reliability of the converter used by the State Nature Conservancy of the Slovak Republic.}, }
@article {pmid37188960, year = {2023}, author = {Li, C and Wood, JC and Vu, AH and Hamilton, JP and Rodriguez Lopez, CE and Payne, RME and Serna Guerrero, DA and Gase, K and Yamamoto, K and Vaillancourt, B and Caputi, L and O'Connor, SE and Robin Buell, C}, title = {Single-cell multi-omics in the medicinal plant Catharanthus roseus.}, journal = {Nature chemical biology}, volume = {19}, number = {8}, pages = {1031-1041}, pmid = {37188960}, issn = {1552-4469}, support = {788301//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; }, mesh = {*Catharanthus/genetics ; *Plants, Medicinal/metabolism ; Multiomics ; Indole Alkaloids/metabolism ; *Antineoplastic Agents/metabolism ; Monoterpenes/metabolism ; Gene Expression Regulation, Plant ; Plant Proteins/genetics/metabolism ; }, abstract = {Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells and high-resolution determination of gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus, a source of leading anticancer drugs. We identified clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes and extensive gene duplication of MIA pathway genes. Clustering was not limited to the linear genome, and through chromatin interaction data, MIA pathway genes were present within the same topologically associated domain, permitting the identification of a secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a single-cell metabolomics approach, permitted the identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. We also revealed cell-type-specific expression in the root MIA pathway.}, }
@article {pmid36661052, year = {2023}, author = {Acerbi, A and Burns, J and Cabuk, U and Kryczka, J and Trapp, B and Valletta, JJ and Mesoudi, A}, title = {Sentiment analysis of the Twitter response to Netflix's Our Planet documentary.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {37}, number = {4}, pages = {e14060}, doi = {10.1111/cobi.14060}, pmid = {36661052}, issn = {1523-1739}, mesh = {Humans ; *Social Media ; Planets ; Sentiment Analysis ; Conservation of Natural Resources ; Attitude ; }, abstract = {The role of nature documentaries in shaping public attitudes and behavior toward conservation and wildlife issues is unclear. We analyzed the emotional content of over 2 million tweets related to Our Planet, a major nature documentary released on Netflix, with dictionary and rule-based automatic sentiment analysis. We also compared the sentiment associated with species mentioned in Our Planet and a set of control species with similar features but not mentioned in the documentary. Tweets were largely negative in sentiment at the time of release of the series. This effect was primarily linked to the highly skewed distributions of retweets and, in particular, to a single negatively valenced and massively retweeted tweet (>150,000 retweets). Species mentioned in Our Planet were associated with more negative sentiment than the control species, and this effect coincided with a short period following the airing of the series. Our results are consistent with a general negativity bias in cultural transmission and document the difficulty of evoking positive sentiment, on social media and elsewhere, in response to environmental problems.}, }
@article {pmid37504804, year = {2023}, author = {Gaboutchian, AV and Knyaz, VA and Maschenko, EN and Dac, LX and Maksimov, AA and Emelyanov, AV and Korost, DV and Stepanov, NV}, title = {Measuring Dental Enamel Thickness: Morphological and Functional Relevance of Topographic Mapping.}, journal = {Journal of imaging}, volume = {9}, number = {7}, pages = {}, pmid = {37504804}, issn = {2313-433X}, abstract = {The interest in the development of dental enamel thickness measurement techniques is connected to the importance of metric data in taxonomic assessments and evolutionary research as well as in other directions of dental studies. At the same time, advances in non-destructive imaging techniques and the application of scanning methods, such as micro-focus-computed X-ray tomography, has enabled researchers to study the internal morpho-histological layers of teeth with a greater degree of accuracy and detail. These tendencies have contributed to changes in established views in different areas of dental research, ranging from the interpretation of morphology to metric assessments. In fact, a significant amount of data have been obtained using traditional metric techniques, which now should be critically reassessed using current technologies and methodologies. Hence, we propose new approaches for measuring dental enamel thickness using palaeontological material from the territories of northern Vietnam by means of automated and manually operated techniques. We also discuss method improvements, taking into account their relevance for dental morphology and occlusion. As we have shown, our approaches demonstrate the potential to form closer links between the metric data and dental morphology and provide the possibility for objective and replicable studies on dental enamel thickness through the application of automated techniques. These features are likely to be effective in more profound taxonomic research and for the development of metric and analytical systems. Our technique provides scope for its targeted application in clinical methods, which could help to reveal functional changes in the masticatory system. However, this will likely require improvements in clinically applicable imaging techniques.}, }
@article {pmid37499537, year = {2023}, author = {Wu, M and Liu, X and Tu, W and Xia, J and Zou, Y and Gong, X and Yu, P and Huang, WE and Wang, H}, title = {Deep insight into oriented propionate production from food waste: Microbiological interpretation and design practice.}, journal = {Water research}, volume = {243}, number = {}, pages = {120399}, doi = {10.1016/j.watres.2023.120399}, pmid = {37499537}, issn = {1879-2448}, abstract = {Using mixed microbial cultures (MMCs) for oriented volatile fatty acids (VFAs) refining in an open environment is a typical challenge due to the microbial diversiform and the process complexity. Especially for carbohydrate-rich waste (such as food waste), butyrate-type fermentation is usually dominant in a single-stage MMCs anaerobic process, while the production of odd-carbon VFAs (such as propionate) is difficult although it plays a significant role in chemicals industries. In this study, firstly, we gave a new perspective on the rationality of the oriented propionate production using MMCs with lactate as feedstock by conducting in-depth microbial informatics and reaction analysis. Secondly, we verified the feasibility of the "food waste-lactate-propionate" route to reverse the original butyrate-type fermentation situation and explore mechanisms for maintaining stability. In the first stage, a defined lactate fermentation microbiome was used to produce lactate-containing broth (80% of total chemical oxygen demand) at pH=4. In the second stage, an undomesticated undefined anaerobic microbiome was used to drive propionate production (45.26% ± 2.23% of total VFAs) under optimized conditions (C/N = 100:1-200:1 and pH=5.0). The low pH environment in the first stage enhanced the lactic acid bacteria to resist the invasion of non-functional flanking bacteria, making the community stable. In the second stage, the system maintained the propionate-type fermentation due to the absence of the ecological niche of the invasive lactic acid bacteria; The selection of propionate-producing specialists was a necessary but not sufficient condition for propionate-type fermentation. At last, this study proposed an enhanced engineering strategy framework for understanding elaborate MMCs fermentation.}, }
@article {pmid37494338, year = {2023}, author = {Kiyingi, M and Nankabirwa, JI and Wiltshire, CS and Nangendo, J and Kiweewa, JM and Katahoire, AR and Semitala, FC}, title = {Perspectives of people living with HIV on barriers to timely ART initiation following referral for antiretroviral therapy: A qualitative study at an urban HIV clinic in Kampala, Uganda.}, journal = {PLOS global public health}, volume = {3}, number = {7}, pages = {e0001483}, pmid = {37494338}, issn = {2767-3375}, abstract = {Early initiation of antiretroviral therapy (ART) after HIV diagnosis prevents HIV transmission, progression of HIV to AIDS and improves quality of life. However, little is known about the barriers to timely ART initiation among patients who test HIV positive in settings different from where they will receive HIV treatment, hence are referred in the routine setting. Therefore, we explored the perspectives of people living with HIV on barriers faced to initiate ART following HIV testing and referral for treatment. In this qualitative study, we purposively sampled and enrolled 17 patients attending the Mulago ISS clinic. We selected patients (≥18 years) who previously were received as referrals for HIV treatment and had delayed ART initiation, as ascertained from their records. We conducted in-depth interviews, which were audio recorded, transcribed and translated. We used Atlas.ti version 9 software for data management. Data analysis followed thematic and framework analysis techniques and we adopted the socio-ecological model to categorize final themes. Key themes were found at organizational level including; negative experiences at the place of HIV diagnosis attributed to inadequate counselling and support, unclear communication of HIV-positive results and ambiguous referral procedures; and, long waiting time when patients reached the HIV clinic. At individual level, the themes identified were; immediate denial with late acceptance of HIV-positive results attributed to severe emotional and psychological distress at receiving results, fear of perceived side effects and long duration on ART. At interpersonal level, we found that anticipated and enacted stigma after HIV diagnosis resulted in non-disclosure, discrimination and lack of social support. We found that challenges at entry (during HIV test) and navigation of the HIV care system in addition to individual and interpersonal factors contributed to delayed ART initiation. Interventions during HIV testing would facilitate early ART initiation among patients referred for HIV care.}, }
@article {pmid37491491, year = {2023}, author = {Ma, Y and Zheng, M and Xu, F and Qian, Y and Liu, M and Zheng, X and Liu, J}, title = {Modeling and exploring the coordination relationship between green infrastructure and land use eco-efficiency: an urban agglomeration perspective.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37491491}, issn = {1614-7499}, support = {42201471//National Natural Science Foundation of China/ ; 72033005//National Natural Science Foundation of China/ ; 42171113//National Natural Science Foundation of China/ ; KF-2020-05-063//Ministry of Natural Resources/ ; }, abstract = {In limited land space, improving the construction of infrastructure with ecological services can help to achieve the goal of promoting land use eco-efficiency (LUEE). In view of this, this study constructed interactive coordination relationship model of green infrastructure (GI) and LUEE that involves entropy method model, super-efficiency slack-based measure (SBM) model with undesirable outputs, and coupling coordination degree model. The interactive coordination relationship model can help to study and reveal the mechanisms of interaction and the coordination relationship between GI and LUEE from a land benefit and ecological perspective. We took the Beijing-Tianjin-Hebei urban agglomeration as the study area. The results showed that the assessment results of GI showed a decreasing trend from 2000 to 2020. LUEE in different cities displayed obvious variability with efficiency values ranging from 0.5666 to 2.4437. The relationship between GI and LUEE is in the stage of uncoordinated development in 53.8% of cities, mainly concentrated in the eastern and southern parts of the study area. The unnatural human activities are the critical factors affecting interactive coupling coordination degree of LUEE and GI. It is clarified that the level of coordination relationship of the two can be used as an important indicator to judge the sustainable development of urban agglomerations. Intensive use of land, optimal connection of geographic information, and localization of policies would help improve the balance and coordination between the two. This study provides interesting research ideas and novel modeling approaches for the study of green and sustainable development of urban agglomerations.}, }
@article {pmid37484483, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Mulley, JF and , }, title = {The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {45}, pmid = {37484483}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Idaea aversata (the Riband Wave; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 17.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,165 protein coding genes.}, }
@article {pmid37484482, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Burnished Brass, Diachrysia chrysitis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {82}, pmid = {37484482}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Diachrysia chrysitis (the Burnished Brass; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 386 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,320 protein coding genes.}, }
@article {pmid37476650, year = {2023}, author = {Crowley, LM and Barclay, M and Roy, HE and Brown, PMJ and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the orange ladybird, Halyzia sedecimguttata (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {186}, pmid = {37476650}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Halyzia sedecimguttata (the orange ladybird, Arthropoda; Insecta; Coleoptera, Coccinellidae). The genome sequence is 919.1 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 27,547 protein coding genes.}, }
@article {pmid37475130, year = {2023}, author = {Yang, G and Cao, JM and Cui, HL and Zhan, XM and Duan, G and Zhu, YG}, title = {Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c08673}, pmid = {37475130}, issn = {1520-5851}, abstract = {Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.}, }
@article {pmid37471432, year = {2023}, author = {Alwan, NA and Clutterbuck, D and Pantelic, M and Hayer, J and Fisher, L and Hishmeh, L and Heightman, M and Allsopp, G and Wootton, D and Khan, A and Hastie, C and Jackson, M and Rayner, C and Brown, D and Parrett, E and Jones, G and Smith, K and Clarke, R and Mcfarland, S and Gabbay, M and Banerjee, A and , }, title = {Long Covid active case finding study protocol: A co-produced community-based pilot within the STIMULATE-ICP study (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0284297}, pmid = {37471432}, issn = {1932-6203}, abstract = {BACKGROUND AND AIM: Long Covid is a significant public health concern with potentially negative implications for health inequalities. We know that those who are already socially disadvantaged in society are more exposed to COVID-19, experience the worst health outcomes and are more likely to suffer economically. We also know that these groups are more likely to experience stigma and have negative healthcare experiences even before the pandemic. However, little is known about disadvantaged groups' experiences of Long Covid, and preliminary evidence suggests they may be under-represented in those who access formal care. We will conduct a pilot study in a defined geographical area in London, United Kingdom to test the feasibility of a community-based approach of identifying Long Covid cases that have not been clinically diagnosed and have not been referred to Long Covid specialist services. We will explore the barriers to accessing recognition, care, and support, as well as experiences of stigma and perceived discrimination.<br><br>METHODS: This protocol and study materials were co-produced with a Community Advisory Board (CAB) made up primarily of people living with Long Covid. Working with voluntary organisations, a study leaflet will be distributed in the local community to highlight Long Covid symptoms and invite those experiencing them to participate in the study if they are not formally diagnosed. Potential participants will be assessed according to the study's inclusion criteria and offered the opportunity to participate if they fit them. Awareness of Long Covid and associated symptoms, experiences of trying to access care, as well as stigma and discrimination will be explored through qualitative interviews with participants. Upon completion of the interviews, participants will be offered a referral to the local social prescribing team to receive support that is personalised to them potentially including, but not restricted to, liaising with their primary care provider and the regional Long Covid clinic.}, }
@article {pmid36716736, year = {2022}, author = {Smith, J and Alfieri, JM and Anthony, N and Arensburger, P and Athrey, GN and Balacco, J and Balic, A and Bardou, P and Barela, P and Bigot, Y and Blackmon, H and Borodin, PM and Carroll, R and Casono, MC and Charles, M and Cheng, H and Chiodi, M and Cigan, L and Coghill, LM and Crooijmans, R and Das, N and Davey, S and Davidian, A and Degalez, F and Dekkers, JM and Derks, M and Diack, AB and Djikeng, A and Drechsler, Y and Dyomin, A and Fedrigo, O and Fiddaman, SR and Formenti, G and Frantz, LAF and Fulton, JE and Gaginskaya, E and Galkina, S and Gallardo, RA and Geibel, J and Gheyas, AA and Godinez, CJP and Goodell, A and Graves, JAM and Griffin, DK and Haase, B and Han, JL and Hanotte, O and Henderson, LJ and Hou, ZC and Howe, K and Huynh, L and Ilatsia, E and Jarvis, ED and Johnson, SM and Kaufman, J and Kelly, T and Kemp, S and Kern, C and Keroack, JH and Klopp, C and Lagarrigue, S and Lamont, SJ and Lange, M and Lanke, A and Larkin, DM and Larson, G and Layos, JKN and Lebrasseur, O and Malinovskaya, LP and Martin, RJ and Martin Cerezo, ML and Mason, AS and McCarthy, FM and McGrew, MJ and Mountcastle, J and Muhonja, CK and Muir, W and Muret, K and Murphy, TD and Ng'ang'a, I and Nishibori, M and O'Connor, RE and Ogugo, M and Okimoto, R and Ouko, O and Patel, HR and Perini, F and Pigozzi, MI and Potter, KC and Price, PD and Reimer, C and Rice, ES and Rocos, N and Rogers, TF and Saelao, P and Schauer, J and Schnabel, RD and Schneider, VA and Simianer, H and Smith, A and Stevens, MP and Stiers, K and Tiambo, CK and Tixier-Boichard, M and Torgasheva, AA and Tracey, A and Tregaskes, CA and Vervelde, L and Wang, Y and Warren, WC and Waters, PD and Webb, D and Weigend, S and Wolc, A and Wright, AE and Wright, D and Wu, Z and Yamagata, M and Yang, C and Yin, ZT and Young, MC and Zhang, G and Zhao, B and Zhou, H}, title = {Fourth Report on Chicken Genes and Chromosomes 2022.}, journal = {Cytogenetic and genome research}, volume = {162}, number = {8-9}, pages = {405-528}, doi = {10.1159/000529376}, pmid = {36716736}, issn = {1424-859X}, }
@article {pmid37469857, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Oak-tree Pug, Eupithecia dodoneata (Guenée, 1858).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {133}, pmid = {37469857}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eupithecia dodoneata (the Oak-tree Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 353.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, }
@article {pmid37467926, year = {2023}, author = {Otálora, P and Guzmán, JL and Acién, FG and Berenguel, M and Reul, A}, title = {An artificial intelligence approach for identification of microalgae cultures.}, journal = {New biotechnology}, volume = {77}, number = {}, pages = {58-67}, doi = {10.1016/j.nbt.2023.07.003}, pmid = {37467926}, issn = {1876-4347}, abstract = {In this work, a model for the characterization of microalgae cultures based on artificial neural networks has been developed. The characterization of microalgae cultures is essential to guarantee the quality of the biomass, and the objective of this work is to achieve a simple and fast method to address this issue. Data acquisition was performed using FlowCam, a device capable of capturing images of the cells detected in a culture sample, which are used as inputs by the model. The model can distinguish between 6 different genera of microalgae, having been trained with several species of each genus. It was further complemented with a classification threshold to discard unwanted objects while improving the overall accuracy of the model. The model achieved an accuracy of up to 97.27% when classifying a culture. The results demonstrate the effectiveness of the Deep Learning models for the characterization of microalgae cultures, it being a useful tool for the monitoring of microalgae cultures in large-scale production facilities while providing accurate characterization over a wide range of genera.}, }
@article {pmid37466563, year = {2023}, author = {Xavier, DR and Albuquerque, MP and Sousa-Carmo, SVT and Pinter, A}, title = {Evaluation of completeness and timeliness of data in the National Information System for Notifiable Diseases for spotted fever in the state of São Paulo, Brazil, 2007-2017.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {2}, pages = {e2022416}, pmid = {37466563}, issn = {2237-9622}, mesh = {Humans ; *Population Surveillance/methods ; Brazil/epidemiology ; Disease Notification ; *Spotted Fever Group Rickettsiosis ; Information Systems ; }, abstract = {OBJECTIVE: to evaluate the completeness and timeliness of notifications of cases of spotted fever (SF) held on the Notifiable Health Conditions Information System (SINAN) in São Paulo State, Brazil, from 2007 to 2017.<br><br>METHODS: this was a descriptive and ecological study of confirmed human cases of SF regarding completeness and timeliness of ten fields of the notification form (good if &#x2265; 90% for most variables); time series analysis was performed using the Prais-Winsten technique.<br><br>RESULTS: we analyzed 736 records; among essential fields, only "Discharge date" showed poor completeness (68.5%). Timeliness was good for the "Investigation" and "Closure" fields; other time lapses were not adequate.<br><br>CONCLUSION: in S&#xe3;o Paulo state, data completeness was good for most variables, whereas timeliness was not adequate (except for "Closure" and "Investigation"), pointing to the need for health education and communication actions about SF.}, }
@article {pmid37466561, year = {2023}, author = {Barbosa, JS and Tartaro, L and Vasconcelos, LDR and Nedel, M and Serafini, JF and Svirski, SGS and Souza, LS and Agranonik, M}, title = {Assessment of incompleteness of Mortality Information System records on deaths from external causes in the state of Rio Grande do Sul, Brazil, 2000-2019.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {2}, pages = {e2022301}, doi = {10.1590/S2237-96222023000200006}, pmid = {37466561}, issn = {2237-9622}, mesh = {Humans ; Brazil/epidemiology ; *Suicide ; Information Systems ; Skin Pigmentation ; }, abstract = {OBJECTIVE: to evaluate the incompleteness of Mortality Information System (Sistema de Informações sobre Mortalidade - SIM) data on deaths from external causes (ECs) in the state of Rio Grande do Sul, Brazil, 2000-2019.<br><br>METHODS: This was an ecological study, using SIM data on all deaths from external causes and, specifically, from transport accident, homicides, suicides and falls; the analysis of the trend of incompleteness was performed by means of Prais-Winsten regression, with a 5% significance level.<br><br>RESULTS: A total of 146,882 deaths were evaluated; sex (0.1%), place of death (0.1%) and age (0.4%) showed the lowest incompleteness in 2019; the proportion of incompleteness showed a decreasing trend for the place of death and schooling, an increasing trend for marital status and a stable trend for age and race/skin color, among all types of death evaluated.<br><br>CONCLUSION: the variables analyzed reached a high degree of completion; with the exception of marital status and schooling, for which unsatisfactory scores persisted for deaths from ECs, both total and by subgroups.}, }
@article {pmid37221394, year = {2023}, author = {Drott, MT and Park, SC and Wang, YW and Harrow, L and Keller, NP and Pringle, A}, title = {Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1236-1246}, pmid = {37221394}, issn = {1751-7370}, support = {T32 ES007015/ES/NIEHS NIH HHS/United States ; R01 GM112739/GM/NIGMS NIH HHS/United States ; }, mesh = {*Amanita/genetics ; *Agaricales/genetics ; Computational Biology ; }, abstract = {The poisonous European mushroom Amanita phalloides (the "death cap") is invading California. Whether the death caps' toxic secondary metabolites are evolving as it invades is unknown. We developed a bioinformatic pipeline to identify the MSDIN genes underpinning toxicity and probed 88 death cap genomes from an invasive Californian population and from the European range, discovering a previously unsuspected diversity of MSDINs made up of both core and accessory elements. Each death cap individual possesses a unique suite of MSDINs, and toxin genes are significantly differentiated between Californian and European samples. MSDIN genes are maintained by strong natural selection, and chemical profiling confirms MSDIN genes are expressed and result in distinct phenotypes; our chemical profiling also identified a new MSDIN peptide. Toxin genes are physically clustered within genomes. We contextualize our discoveries by probing for MSDINs in genomes from across the order Agaricales, revealing MSDIN diversity originated in independent gene family expansions among genera. We also report the discovery of an MSDIN in an Amanita outside the "lethal Amanitas" clade. Finally, the identification of an MSDIN gene and its associated processing gene (POPB) in Clavaria fumosa suggest the origin of MSDINs is older than previously suspected. The dynamic evolution of MSDINs underscores their potential to mediate ecological interactions, implicating MSDINs in the ongoing invasion. Our data change the understanding of the evolutionary history of poisonous mushrooms, emphasizing striking parallels to convergently evolved animal toxins. Our pipeline provides a roadmap for exploring secondary metabolites in other basidiomycetes and will enable drug prospecting.}, }
@article {pmid37467038, year = {2023}, author = {Sommerhoff, A and Ehring, T and Takano, K}, title = {Effects of Induced Mindfulness at Night on Repetitive Negative Thinking: Ecological Momentary Assessment Study.}, journal = {JMIR mental health}, volume = {10}, number = {}, pages = {e44365}, doi = {10.2196/44365}, pmid = {37467038}, issn = {2368-7959}, abstract = {BACKGROUND: Repetitive negative thinking (RNT) is a cognitive risk factor for various disorders. Although brief mindfulness-based interventions (MBIs; lasting 20-30 minutes or shorter) are effective tools to reduce RNT, the effect of a minimal (5-minute) MBI remains largely unknown.<br><br>OBJECTIVE: We investigated the acute changes in RNT induced by a 10-day minimal MBI (body scan before sleeping) using an ecological momentary assessment (EMA) administered during the MBI training phase. In addition, we examined longer-term effects on the postintervention and 2-month follow-up assessments for questionnaire-based RNT and psychological distress.<br><br>METHODS: A total of 68 participants (community sample, aged 18-55 years; n=58, 85% women) were randomly allocated to either the intervention group (n=35, 51%) or the no-training control group (n=33, 49%). Both groups completed a 10-day EMA phase of RNT, during which only the intervention group performed a daily 5-minute body scan before sleeping.<br><br>RESULTS: The intervention group showed a significantly larger reduction in questionnaire-based RNT than the control group at the follow-up assessment (for growth-curve modeling analysis [GMA], dGMA=-0.91; P<.001), but this effect was not observed during the EMA phase or at the postintervention assessment. Furthermore, the intervention group showed significantly larger decreases in stress both at the postintervention (dGMA=-0.78; P<.001) and follow-up (dGMA=-0.60; P<.001) assessments than the control group. We found no intervention effects on depressive and anxiety symptoms.<br><br>CONCLUSIONS: A 5-minute body scan before sleeping reduces RNT and stress when continued for at least 10 days; however, the results suggest that this effect only appears with some time lag because no acute changes during and immediately after the intervention emerged for RNT.}, }
@article {pmid37465614, year = {2023}, author = {Asefa, A and Reuber, V and Miehe, G and Wraase, L and Wube, T and Schabo, DG and Farwig, N}, title = {Human activities modulate reciprocal effects of a subterranean ecological engineer rodent, Tachyoryctes macrocephalus, on Afroalpine vegetation cover.}, journal = {Ecology and evolution}, volume = {13}, number = {7}, pages = {e10337}, pmid = {37465614}, issn = {2045-7758}, abstract = {Human activities, directly and indirectly, impact ecological engineering activities of subterranean rodents. As engineering activities of burrowing rodents are affected by, and reciprocally affect vegetation cover via feeding, burrowing and mound building, human influence such as settlements and livestock grazing, could have cascading effects on biodiversity and ecosystem processes such as bioturbation. However, there is limited understanding of the relationship between human activities and burrowing rodents. The aim of this study was therefore to understand how human activities influence the ecological engineering activity of the giant root-rat (Tachyoryctes macrocephalus), a subterranean rodent species endemic to the Afroalpine ecosystem of the Bale Mountains of Ethiopia. We collected data on human impact, burrowing activity and vegetation during February and March of 2021. Using path analysis, we tested (1) direct effects of human settlement on the patterns of livestock grazing intensity, (2) direct and indirect impacts of humans and livestock grazing intensity on the root-rat burrow density and (3) whether human settlement and livestock grazing influence the effects of giant root-rat burrow density on vegetation and vice versa. We found lower levels of livestock grazing intensity further from human settlement than in its proximity. We also found a significantly increased giant root-rat burrow density with increasing livestock grazing intensity. Seasonal settlement and livestock grazing intensity had an indirect negative and positive effect on giant root-rat burrow density, respectively, both via vegetation cover. Analysing the reciprocal effects of giant root-rat on vegetation, we found a significantly decreased vegetation cover with increasing density of giant root-rat burrows, and indirectly with increasing livestock grazing intensity via giant root-rat burrow density. Our results demonstrate that giant root-rats play a synanthropic engineering role that affects vegetation structure and ecosystem processes.}, }
@article {pmid37463417, year = {2023}, author = {Williams, TA and Davin, AA and Morel, B and Szánthó, LL and Spang, A and Stamatakis, A and Hugenholtz, P and Szöllősi, GJ}, title = {Parameter estimation and species tree rooting using ALE and GeneRax.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evad134}, pmid = {37463417}, issn = {1759-6653}, abstract = {ALE and GeneRax are tools for probabilistic gene tree-species tree reconciliation. Based on a common underlying statistical model of how gene trees evolve along species trees, these methods rely on gene versus species tree discordance to infer gene duplication, transfer and loss events, map gene family origins and root species trees. Published analyses have used these methods to root species trees of Archaea, Bacteria and several eukaryotic groups, as well as to infer ancestral gene repertoires. However, it was recently suggested that reconciliation-based estimates of duplication and transfer events using the ALE/GeneRax model were unreliable, with potential implications for species tree rooting. Here, we assess these criticisms and find that the methods are accurate when applied to simulated data and in generally good agreement with alternative methodological approaches on empirical data. In particular, ALE recovers variation in gene duplication and transfer frequencies across lineages that is consistent with the known biology of studied clades. In plants and opisthokonts, ALE recovers the consensus species tree root; in Bacteria - where there is less certainty about the root position - ALE agrees with alternative approaches on the most likely root region. Overall, ALE and related approaches are promising tools for studying genome evolution.}, }
@article {pmid37455607, year = {2023}, author = {Hutchins, L and Mc Cartney, A and Graham, N and Gillespie, R and Guzman, A}, title = {Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13822}, pmid = {37455607}, issn = {1755-0998}, support = {//Berkeley Food Institute Faculty Seed Grant/ ; //National Science Foundation Innovations at the Nexus of Food, Energy, and Water Systems/ ; }, abstract = {Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as farm sites near a natural habitat had higher OTU richness than those farther away. We also provide evidence that management factors such as the number of Polynesian crops cultivated may drive arthropod community composition. Through this case study, we emphasize the context-dependent opportunities and challenges for operationalizing IDS by utilizing participatory research methods, expanding novel data management tools through the Local Contexts Hub, and developing and nurturing community partnerships-all while highlighting the potential of agroecosystems for arthropod conservation. Overall, the workflow and the example presented here can help researchers take tangible steps to achieve IDS, which often seems elusive with the expanding use of genomic data.}, }
@article {pmid37454924, year = {2023}, author = {Le, DH and Nguyen, TH and Takasu, F}, title = {Spatial metapopulation dynamics with local and global colonization.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {111579}, doi = {10.1016/j.jtbi.2023.111579}, pmid = {37454924}, issn = {1095-8541}, abstract = {We revisit a spatial metapopulation model on continuous space as a stochastic point pattern dynamics. In the model, local patches as points are distributed with a certain spatial configuration and status of each patch changes stochastically between occupied and empty: an occupied patch becomes empty by local extinction and an empty patch becomes occupied both by local and global colonization. We carry out simulation analysis and derive an analytical model in terms of singlet, pair and triplet probabilities that describe the stochastic dynamics. Using a simple closure that approximates triplet probabilities by singlet and pair probabilities, we show that equilibrium singlet and pair probabilities can be analytically derived. The derived equilibrium properties successfully describe simulation results under a certain condition where the range of local colonization and the proportion of global colonization play key roles. Our model is an extension of the classical non-spatial Levins model to a spatially explicit metapopulation model. We appeal the advantage of point pattern approach to study spatial dynamics in general ecology and call for the need to deepen our understanding of mathematical tools to explore point pattern dynamics.}, }
@article {pmid37448139, year = {2023}, author = {Ewers, I and Rajter, L and Czech, L and Mahé, F and Stamatakis, A and Dunthorn, M}, title = {Interpreting phylogenetic placements for taxonomic assignment of environmental DNA.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {e12990}, doi = {10.1111/jeu.12990}, pmid = {37448139}, issn = {1550-7408}, support = {//Alexander von Humboldt-Stiftung/ ; }, abstract = {Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA-ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA-ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA-ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest.}, }
@article {pmid37447657, year = {2023}, author = {Li, J and Cai, Y and Gong, X and Jiang, J and Lu, Y and Meng, X and Zhang, L}, title = {Semantic Retrieval of Remote Sensing Images Based on the Bag-of-Words Association Mapping Method.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {13}, pages = {}, pmid = {37447657}, issn = {1424-8220}, support = {41961063//National Natural Science Foundation of China/ ; }, mesh = {*Algorithms ; *Semantics ; Remote Sensing Technology ; Information Storage and Retrieval ; Pattern Recognition, Automated/methods ; }, abstract = {With the increasing demand for remote sensing image applications, extracting the required images from a huge set of remote sensing images has become a hot topic. The previous retrieval methods cannot guarantee the efficiency, accuracy, and interpretability in the retrieval process. Therefore, we propose a bag-of-words association mapping method that can explain the semantic derivation process of remote sensing images. The method constructs associations between low-level features and high-level semantics through visual feature word packets. An improved FP-Growth method is proposed to achieve the construction of strong association rules to semantics. A feedback mechanism is established to improve the accuracy of subsequent retrievals by reducing the semantic probability of incorrect retrieval results. The public datasets AID and NWPU-RESISC45 were used to validate these experiments. The experimental results show that the average accuracies of the two datasets reach 87.5% and 90.8%, which are 22.5% and 20.3% higher than VGG16, and 17.6% and 15.6% higher than ResNet18, respectively. The experimental results were able to validate the effectiveness of our proposed method.}, }
@article {pmid37443081, year = {2023}, author = {Sharo, AG and Zou, Y and Adhikari, AN and Brenner, SE}, title = {ClinVar and HGMD genomic variant classification accuracy has improved over time, as measured by implied disease burden.}, journal = {Genome medicine}, volume = {15}, number = {1}, pages = {51}, pmid = {37443081}, issn = {1756-994X}, support = {HD077627/NH/NIH HHS/United States ; }, mesh = {*Genetic Variation ; *Databases, Genetic ; Gene Frequency ; Genotype ; Genomics ; }, abstract = {BACKGROUND: Curated databases of genetic variants assist clinicians and researchers in interpreting genetic variation. Yet, these databases contain some misclassified variants. It is unclear whether variant misclassification is abating as these databases rapidly grow and implement new guidelines.<br><br>METHODS: Using archives of ClinVar and HGMD, we investigated how variant misclassification has changed over 6&#xa0;years, across different ancestry groups. We considered inborn errors of metabolism (IEMs) screened in newborns as a model system because these disorders are often highly penetrant with neonatal phenotypes. We used samples from the 1000 Genomes Project (1KGP) to identify individuals with genotypes that were classified by the databases as pathogenic. Due to the rarity of IEMs, nearly all such classified pathogenic genotypes indicate likely variant misclassification in ClinVar or HGMD.<br><br>RESULTS: While the false-positive rates of both ClinVar and HGMD have improved over time, HGMD variants currently imply two orders of magnitude more affected individuals in 1KGP than ClinVar variants. We observed that African ancestry individuals have a significantly increased chance of being incorrectly indicated to be affected by a screened IEM when HGMD variants are used. However, this bias affecting genomes of African ancestry was no longer significant once common variants were removed in accordance with recent variant classification guidelines. We discovered that ClinVar variants classified as Pathogenic or Likely Pathogenic are reclassified sixfold more often than DM or DM? variants in HGMD, which has likely resulted in ClinVar's lower false-positive rate.<br><br>CONCLUSIONS: Considering misclassified variants that have since been reclassified reveals our increasing understanding of rare genetic variation. We found that variant classification guidelines and allele frequency databases comprising genetically diverse samples are important factors in reclassification. We also discovered that ClinVar variants common in European and South Asian individuals were more likely to be reclassified to a lower confidence category, perhaps due to an increased chance of these variants being classified by multiple submitters. We discuss features for variant classification databases that would support their continued improvement.}, }
@article {pmid37440444, year = {2023}, author = {Pokolm, M and Kirchhain, M and Müller, D and Jordet, G and Memmert, D}, title = {Head movement direction in football - a field study on visual scanning activity during the UEFA-U17 and -U21 European Championship 2019.}, journal = {Journal of sports sciences}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/02640414.2023.2235160}, pmid = {37440444}, issn = {1466-447X}, abstract = {Visual exploration (scanning) of one's environment is a key aspect in team sports. Based on Gibson's (1979) ecological approach of visual perception, this study aims to advance the understanding of scanning by focusing on the direction of head movements in football and its implications for subsequent on-ball actions. The video-based data analysis consisted of nine selected matches and 162 players of the Union of European Football Associations (UEFA) U17 and U21 European Championship 2019. The results indicate that the direction of the last scan prior to receiving the ball is related to the foot used for the first ball contact. This relationship was further analysed in view of the game context (direction of play and opponent pressure) and with information about the player's dominant foot. The findings reveal a relationship between the direction of the last scan before receiving the ball and the direction the game is proceeded in. Further, when a player performs the last scan to the side of their dominant foot, the probability increases that their dominant foot is used for the subsequent first ball contact. Depending on the direction of the last scan, opponent pressure had various effects on the foot used for the first contact.}, }
@article {pmid37438069, year = {2023}, author = {Yao, L and Yang, Y and Wang, Z and Pan, X and Xu, L}, title = {Compliance with ecological momentary assessment programmes in the elderly: a systematic review and meta-analysis.}, journal = {BMJ open}, volume = {13}, number = {7}, pages = {e069523}, pmid = {37438069}, issn = {2044-6055}, mesh = {Aged ; Humans ; *Ecological Momentary Assessment ; *Health Status ; PubMed ; Publication Bias ; Research Personnel ; }, abstract = {OBJECTIVE: Ecological momentary assessment (EMA) refers to the repeated sampling of information about an individual's symptoms and behaviours, enabling the capture of ecologically meaningful real-time information in a timely manner. Compliance with EMA is critical in determining the validity of an assessment. However, there is limited evidence related to how the elderly comply with EMA programmes or the factors that are associated with compliance.<br><br>DESIGN: Systematic review and meta-analysis.<br><br>DATA SOURCES: PubMed, Embase, the Cochrane Library and Web of Science were searched up to 17 July 2022.<br><br>ELIGIBILITY CRITERIA: We included observational studies on EMA in the elderly reported in English.<br><br>DATA EXTRACTION AND SYNTHESIS: Two investigators independently performed screening and data extraction. Discrepancies were resolved by discussion or a third investigator. A systematic review was carried out to characterise the basic characteristics of the participants and EMA programmes. Random-effects meta-analysis was conducted to assess overall compliance and to explore factors associated with differences in compliance among the elderly.<br><br>RESULTS: A total of 20 studies with 2047 participants were included in the systematic review and meta-analysis. Meta-analysis showed that the combined compliance rate was 86.41% (95% CI: 77.38% to 92.20%; I[2]=96.4%; p<0.001). Subgroup analysis revealed high levels of heterogeneity in terms of the methods used to assess population classification, assessment method and assessment frequency, although these may not be the sources of heterogeneity. Meta-regression analysis showed that population classification and assessment period might have a significant impact on heterogeneity (p<0.05). Egger's test indicated significant publication bias (p<0.001).<br><br>CONCLUSIONS: Compliance with EMA programmes is high in the elderly. It is recommended that scholars design reasonable EMA programmes according to the health status of the elderly in the future.}, }
@article {pmid37437086, year = {2023}, author = {Hua, QQH and Young, C and Pukala, TL and Martino, JC and Hoffmann, P and Gillanders, BM and Doubleday, ZA}, title = {Better late than never: Optimising the proteomic analysis of field-collected octopus.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288084}, doi = {10.1371/journal.pone.0288084}, pmid = {37437086}, issn = {1932-6203}, mesh = {Animals ; *Octopodiformes ; Proteomics ; Chromatography, Liquid ; Computational Biology ; Electrophoresis, Polyacrylamide Gel ; Fixatives ; }, abstract = {Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to inadequate protocols for the sampling and preparation of animal tissues from the field. Although RNAlater is an ideal alternative to freezing for tissue preservation in transcriptomics studies, its suitability for the field could be more broadly examined. Moreover, existing protocols require samples to be preserved immediately to maintain protein integrity, yet the effects of delays in preservation on proteomic analyses have not been thoroughly tested. Hence, we optimised a proteomic workflow for wild-caught samples. First, we conducted a preliminary in-lab test using SDS-PAGE analysis on aquaria-reared Octopus berrima confirming that RNAlater can effectively preserve proteins up to 6 h after incubation, supporting its use in the field. Subsequently, we collected arm tips from wild-caught Octopus berrima and preserved them in homemade RNAlater immediately, 3 h, and 6 h after euthanasia. Processed tissue samples were analysed by liquid chromatography tandem mass spectrometry to ascertain protein differences between time delay in tissue preservation, as well as the influence of sex, tissue type, and tissue homogenisation methods. Over 3500 proteins were identified from all tissues, with bioinformatic analysis revealing protein abundances were largely consistent regardless of sample treatment. However, nearly 10% additional proteins were detected from tissues homogenised with metal beads compared to liquid nitrogen methods, indicating the beads were more efficient at extracting proteins. Our optimised workflow demonstrates that sampling non-model organisms from remote field sites is achievable and can facilitate extensive proteomic coverage without compromising protein integrity.}, }
@article {pmid37436329, year = {2023}, author = {Barros, ZDS and Rodrigues, BGM and Frota, KMG and Penha, JCD and Nascimento, FFD and Rodrigues, MTP and Mascarenhas, MDM}, title = {Syphilis detection rate trend in aged people: Brazil, 2011-2019.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {26}, number = {}, pages = {e230033}, pmid = {37436329}, issn = {1980-5497}, mesh = {Aged ; Humans ; Male ; Female ; *Syphilis/diagnosis/epidemiology ; Brazil/epidemiology ; Regression Analysis ; Linear Models ; Information Systems ; }, abstract = {OBJECTIVE: To analyze the trend in the detection rate of syphilis in elderly people in Brazil from 2011 to 2019.<br><br>METHODS: An ecological, time-series study with data from the Notifiable Diseases Information System. The temporal trend of syphilis detection rates was analyzed according to the Prais-Winsten linear regression method.<br><br>RESULTS: 62,765 cases of syphilis in aged people were reported. There was a growing trend in the rate of syphilis detection in aged people in Brazil. The increase was of approximately six times, with a mean increase of 25% each year (annual percent change [APC]: 25.0; 95%CI 22.1-28.1). The increase in the detection rate was identified in both genders and for all age groups, with emphasis on the increase in females (APC: 49.1; 95%CI 21.9-26.8) and in the group aged 70 to 79 years old (APC: 25.8; 95%CI 23.3-28.3). All macro-regions of the country showed an increasing trend, with emphasis on the Northeast (APC: 51.2; 95%CI 43.0-59.8) and South (APC: 49.2; 95%CI 32.3-68.3).<br><br>CONCLUSION: The growing trend in the detection rate of syphilis in aged people throughout Brazil highlights the need for planning and developing effective and multidisciplinary prevention actions and assistance adapted to this public.}, }
@article {pmid37433877, year = {2023}, author = {Pairo-Castineira, E and Rawlik, K and Bretherick, AD and Qi, T and Wu, Y and Nassiri, I and McConkey, GA and Zechner, M and Klaric, L and Griffiths, F and Oosthuyzen, W and Kousathanas, A and Richmond, A and Millar, J and Russell, CD and Malinauskas, T and Thwaites, R and Morrice, K and Keating, S and Maslove, D and Nichol, A and Semple, MG and Knight, J and Shankar-Hari, M and Summers, C and Hinds, C and Horby, P and Ling, L and McAuley, D and Montgomery, H and Openshaw, PJM and Begg, C and Walsh, T and Tenesa, A and Flores, C and Riancho, JA and Rojas-Martinez, A and Lapunzina, P and ,  and ,  and ,  and ,  and Yang, J and Ponting, CP and Wilson, JF and Vitart, V and Abedalthagafi, M and Luchessi, AD and Parra, EJ and Cruz, R and Carracedo, A and Fawkes, A and Murphy, L and Rowan, K and Pereira, AC and Law, A and Fairfax, B and Hendry, SC and Baillie, JK}, title = {Author Correction: GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-023-06383-z}, pmid = {37433877}, issn = {1476-4687}, }
@article {pmid37432953, year = {2023}, author = {Medina, P and Russell, SL and Corbett-Detig, R}, title = {Deep data mining reveals variable abundance and distribution of microbial reproductive manipulators within and among diverse host species.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288261}, pmid = {37432953}, issn = {1932-6203}, support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster/genetics ; *Arthropods ; Data Mining ; Ecology ; Reproduction ; *Wolbachia/genetics ; }, abstract = {Bacterial symbionts that manipulate the reproduction of their hosts are important factors in invertebrate ecology and evolution, and are being leveraged for host biological control. Infection prevalence restricts which biological control strategies are possible and is thought to be strongly influenced by the density of symbiont infection within hosts, termed titer. Current methods to estimate infection prevalence and symbiont titers are low-throughput, biased towards sampling infected species, and rarely measure titer. Here we develop a data mining approach to estimate symbiont infection frequencies within host species and titers within host tissues. We applied this approach to screen ~32,000 publicly available sequence samples from the most common symbiont host taxa, discovering 2,083 arthropod and 119 nematode infected samples. From these data, we estimated that Wolbachia infects approximately 44% of all arthropod and 34% of all nematode species, while other reproductive manipulators only infect 1-8% of arthropod and nematode species. Although relative titers within hosts were highly variable within and between arthropod species, a combination of arthropod host species and Wolbachia strain explained approximately 36% of variation in Wolbachia titer across the dataset. To explore potential mechanisms for host control of symbiont titer, we leveraged population genomic data from the model system Drosophila melanogaster. In this host, we found a number of SNPs associated with titer in candidate genes potentially relevant to host interactions with Wolbachia. Our study demonstrates that data mining is a powerful tool to detect bacterial infections and quantify infection intensities, thus opening an array of previously inaccessible data for further analysis in host-symbiont evolution.}, }
@article {pmid37430538, year = {2023}, author = {Zhang, R and Zou, X and Deng, X and Wang, Z and Chen, Y and Lin, C and Xing, H and Dai, F}, title = {Fast and Accurate ROI Extraction for Non-Contact Dorsal Hand Vein Detection in Complex Backgrounds Based on Improved U-Net.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {10}, pages = {}, pmid = {37430538}, issn = {1424-8220}, support = {IEC\NSFC\191320//International Exchanges 2019 Cost Share (NSFC)/ ; }, mesh = {*Hand/diagnostic imaging ; *Veins/diagnostic imaging ; Image Processing, Computer-Assisted ; Information Storage and Retrieval ; Normal Distribution ; }, abstract = {In response to the difficulty of traditional image processing methods to quickly and accurately extract regions of interest from non-contact dorsal hand vein images in complex backgrounds, this study proposes a model based on an improved U-Net for dorsal hand keypoint detection. The residual module was added to the downsampling path of the U-Net network to solve the model degradation problem and improve the feature information extraction ability of the network; the Jensen-Shannon (JS) divergence loss function was used to supervise the final feature map distribution so that the output feature map tended to Gaussian distribution and improved the feature map multi-peak problem; and Soft-argmax is used to calculate the keypoint coordinates of the final feature map to realize end-to-end training. The experimental results showed that the accuracy of the improved U-Net network model reached 98.6%, which was 1% better than the original U-Net network model; the improved U-Net network model file was only 1.16 M, which achieved a higher accuracy than the original U-Net network model with significantly reduced model parameters. Therefore, the improved U-Net model in this study can realize dorsal hand keypoint detection (for region of interest extraction) for non-contact dorsal hand vein images and is suitable for practical deployment in low-resource platforms such as edge-embedded systems.}, }
@article {pmid37430467, year = {2023}, author = {Peltier, DMP and Carbone, MS and McIntire, CD and Robertson, N and Thompson, RA and Malone, S and LeMoine, J and Richardson, AD and McDowell, NG and Adams, HD and Pockman, WT and Trowbridge, AM}, title = {Carbon starvation following a decade of experimental drought consumes old reserves in Pinus edulis.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19119}, pmid = {37430467}, issn = {1469-8137}, support = {1755345//Division of Integrative Organismal Systems/ ; 1755346//Division of Integrative Organismal Systems/ ; 1936205//Division of Integrative Organismal Systems/ ; 1-842493//National Science Foundation/ ; 1019284//U.S. Department of Agriculture/ ; }, abstract = {Shifts in the age or turnover time of non-structural carbohydrates (NSC) may underlie changes in tree growth under long-term increases in drought stress associated with climate change. But NSC responses to drought are challenging to quantify, due in part to large NSC stores in trees and subsequently long response times of NSC to climate variation. We measured NSC age (Δ[14] C) along with a suite of ecophysiological metrics in Pinus edulis trees experiencing either extreme short-term drought (-90% ambient precipitation plot, 2020-2021) or a decade of severe drought (-45% plot, 2010-2021). We tested the hypothesis that carbon starvation - consumption exceeding synthesis and storage - increases the age of sapwood NSC. One year of extreme drought had no impact on NSC pool size or age, despite significant reductions in predawn water potential, photosynthetic rates/capacity, and twig and needle growth. By contrast, long-term drought halved the age of the sapwood NSC pool, coupled with reductions in sapwood starch concentrations (-75%), basal area increment (-39%), and bole respiration rates (-28%). Our results suggest carbon starvation takes time, as tree carbon reserves appear resilient to extreme disturbance in the short term. However, after a decade of drought, trees apparently consumed old stored NSC to support metabolism.}, }
@article {pmid37430226, year = {2023}, author = {Demidova, EV and Serebriiskii, IG and Vlasenkova, R and Kelow, S and Andrake, MD and Hartman, TR and Kent, T and Virtucio, J and Rosen, GL and Pomerantz, RT and Dunbrack, RL and Golemis, EA and Hall, MJ and Chen, DYT and Daly, MB and Arora, S}, title = {Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {388}, pmid = {37430226}, issn = {1471-2164}, }
@article {pmid37428511, year = {2023}, author = {Minich, M and Zhao, Q and Eickhoff, J and Moreno, MA}, title = {In the Mood for Music: Listening to Music and Other Smartphone Uses Improve Adolescent Mood.}, journal = {Cyberpsychology, behavior and social networking}, volume = {}, number = {}, pages = {}, doi = {10.1089/cyber.2022.0344}, pmid = {37428511}, issn = {2152-2723}, abstract = {Rates of adolescent mood disorders and adolescent smartphone use have risen in parallel, leading some to suggest that smartphone use might have detrimental effects on adolescents' moods. Alternatively, it is possible that adolescents turn to smartphone use when experiencing negative mood. Past experimental study suggests that certain smartphone activities can reduce adolescents' negative moods or induce more positive moods, but little is known about the effects of real-world smartphone use, which can involve many different activities. A sample of N = 253 adolescents participated in an Ecological Momentary Assessment (EMA) procedure, which assessed which smartphone activities they were engaged in at random moments throughout the day. This procedure also prompted adolescents to rate their moods before and during smartphone use. Adolescents reported mood improvements during almost all smartphone activities and did not report that moods became more negative during any smartphone activity. Mood improvements were the largest when adolescents said they were listening to music, podcasts, or audiobooks. This may suggest some adolescent smartphone use is driven by a desire to alleviate negative mood.}, }
@article {pmid37415394, year = {2023}, author = {Serra, A and Mozgunov, P and Davies, G and Jaki, T}, title = {Determining the minimum duration of treatment in tuberculosis: An order restricted non-inferiority trial design.}, journal = {Pharmaceutical statistics}, volume = {}, number = {}, pages = {}, doi = {10.1002/pst.2320}, pmid = {37415394}, issn = {1539-1612}, support = {MC_UU_00002/14/MRC_/Medical Research Council/United Kingdom ; MC_UU_00002/19/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Tuberculosis (TB) is one of the biggest killers among infectious diseases worldwide. Together with the identification of drugs that can provide benefits to patients, the challenge in TB is also the optimisation of the duration of these treatments. While conventional duration of treatment in TB is 6 months, there is evidence that shorter durations might be as effective but could be associated with fewer side effects and may be associated with better adherence. Based on a recent proposal of an adaptive order-restricted superiority design that employs the ordering assumptions within various duration of the same drug, we propose a non-inferiority (typically used in TB trials) adaptive design that effectively uses the order assumption. Together with the general construction of the hypothesis testing and expression for type I and type II errors, we focus on how the novel design was proposed for a TB trial concept. We consider a number of practical aspects such as choice of the design parameters, randomisation ratios, and timings of the interim analyses, and how these were discussed with the clinical team.}, }
@article {pmid37408609, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Spruce Carpet Moth, Thera britannica (Turner, 1925).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {114}, pmid = {37408609}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Thera britannica (the Spruce Carpet Moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 381 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,457 protein coding genes.}, }
@article {pmid37407490, year = {2023}, author = {Shinohara, N and Zhao, W and Shan, Y and Ukawa, S and Ohira, H and Kawamura, T and Okabayashi, S and Wakai, K and Ando, M and Tsushita, K and Tamakoshi, A}, title = {Temporal change in the association between life satisfaction and functional decline with gender differences: an age-specific prospective cohort study.}, journal = {Environmental health and preventive medicine}, volume = {28}, number = {}, pages = {42}, doi = {10.1265/ehpm.23-00019}, pmid = {37407490}, issn = {1347-4715}, mesh = {Male ; Adult ; Humans ; Female ; Aged ; Cohort Studies ; Prospective Studies ; Sex Factors ; *Personal Satisfaction ; Age Factors ; }, abstract = {BACKGROUND: Although life satisfaction (LS) has been shown to predict mortality, research studying the relationship between LS and functional decline is scarce. This study examined the association between LS and functional decline across four time points in young-old Japanese adults.<br><br>METHODS: We analysed 1,899 community-dwelling 65-year-olds in this age-specific cohort study conducted between 2000 and 2005. The Life Satisfaction Index K was used to evaluate LS and was classified into quartiles. Functional decline was determined using the Japanese Long-Term Care Insurance (LTCI) system: 1) mild disability; 2) severe disability; 3) all-cause mortality; 4) mild or severe disability; 5) severe disability or death; 6) mild or severe disability, or death. Adjusted hazard ratios (HR) with 95% confidence intervals (CI) were calculated using the Cox proportional hazard model. The analyses were conducted in the 8[th], 10[th], 12[th], and 14[th] years to assess the effect of LS on functional decline across time points.<br><br>RESULTS: The impact of LS gradually weakened over time. In the 8[th] year (aged 72-73), a higher LS was associated with a lower risk of mild or severe disability among the women participants (adjusted HR [95% CI] = 0.30 [0.11-0.81]). However, the effect disappeared gradually (adjusted HR [95% CI] = 0.55 [0.27-1.14]) in the 10[th] year (aged 74-75), 0.72 (0.41-1.26) in the 12[th] year (aged 76-77), and 0.68 (0.41-1.14) in the 14[th] year (aged 78-79). This trend continued in severe disability or death (adjusted HR [95% CI] = 0.24 [0.06-0.70], 0.31 [0.11-0.76], 0.57 [0.28-1.14], and 0.60 [0.32-1.12]) and mild or severe disability, or death (adjusted HR [95% CI] = 0.30 [0.14-0.68], 0.46 [0.24-0.87], 0.67 [0.41-1.10], and 0.65 [0.42-1.02]) in the 8[th], 10[th], 12[th], and 14[th] years, respectively. No statistically significant association was found among men at any time points or in any classification of outcomes.<br><br>CONCLUSIONS: Higher LS scores in 65-year-old women were associated with a lower risk for functional decline in any combination of mild disability, severe disability, or death. Additionally, the effect of LS was observed to weaken over time.<br><br>TRIAL REGISTRATION: This is not an intervention survey and does not require registration.}, }
@article {pmid36998167, year = {2023}, author = {Sakai, K and Nagata, T and Odagami, K and Nagata, M and Mori, T and Mori, K}, title = {Supervisors' Work Engagement Is Associated With Interactivity and Carefulness in Supporting Subordinates: A Cross-sectional Study Using Text Mining in Japan.}, journal = {Journal of occupational and environmental medicine}, volume = {65}, number = {7}, pages = {e465-e471}, pmid = {36998167}, issn = {1536-5948}, mesh = {Humans ; *Work Engagement ; Cross-Sectional Studies ; Japan ; *Attitude ; Data Mining ; }, abstract = {OBJECTIVE: This study aimed to structure supervisory support and clarify the relationship between supervisors' work engagement and support for their subordinates.<br><br>METHODS: We conducted a cross-sectional study in a manufacturing company using a questionnaire survey. Supervisors provided open-ended responses regarding the provision of support for their subordinates. Using text mining, we structured these descriptions into multiple categories, assigned words to them, and analyzed frequently mentioned categories by the level of work engagement.<br><br>RESULTS: We obtained responses from 729 participants that included 13,968 words. We structured supervisory support by three categories (contents, direction, and attitude toward support) and 11 subcategories. As supervisors' work engagement increased, the rates of mentioning information retrieval, information transmission, and carefulness increased.<br><br>CONCLUSIONS: Supervisors with work engagement could communicate with each other and be careful in providing support to their subordinates.}, }
@article {pmid37402922, year = {2023}, author = {Li, K and Zhou, Y and Huang, X and Xiao, H and Shan, Y}, title = {Low-carbon development pathways for resource-based cities in China under the carbon peaking and carbon neutrality goals.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37402922}, issn = {1614-7499}, abstract = {Resource-based cities are important strategic bases for securing resources in China and have made great contributions to the country's economic development. Long-term extensive resource development has made resource-based cities an important region constraining China from achieving comprehensive low-carbon development. Therefore, it is of great significance to explore the low-carbon transition path of resource-based cities for their energy greening, industrial transformation, and high-quality economic development. This study compiled the CO2 emission inventory of resource-based cities in China from 2005 to 2017, explored the contribution to CO2 emissions from three perspectives (driver, industry, and city), and predicted the peak of CO2 emissions in resource-based cities. The results show that resource-based cities contribute 18.4% of the country's GDP and emit 44.4% of the country's CO2 and that economic growth and CO2 emissions have not yet been decoupled. The per capita CO2 emissions and emission intensity of resource-based cities are 1.8 times and 2.4 times higher than the national average, respectively. Economic growth and energy intensity are the biggest drivers and main inhibitors of CO2 emissions growth. Industrial restructuring has become the biggest inhibitor of CO2 emissions growth. Based on the different resource endowments, industrial structures, and socio-economic development levels of resource-based cities, we propose differentiated low-carbon transition pathways. This study can provide references for cities to develop differentiated low-carbon development paths under the "double carbon" target.}, }
@article {pmid37396199, year = {2023}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Northern Deep-brown Dart, Aporophyla lueneburgensis (Freyer, 1848).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {149}, pmid = {37396199}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Aporophyla lueneburgensis (the Northern Deep-brown Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 978.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,580 protein coding genes.}, }
@article {pmid37394173, year = {2023}, author = {Fan, W and Song, X and Liu, M and Shan, B and Ma, M and Liu, Y}, title = {Spatio-temporal evolution of resources and environmental carrying capacity and its influencing factors -A case study of shandong peninsula urban agglomeration.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116469}, doi = {10.1016/j.envres.2023.116469}, pmid = {37394173}, issn = {1096-0953}, abstract = {Promoting ecological conservation and high-quality development in the Yellow River basin is an important objective in China's 14th Five-Year Plan. Understanding the spatio-temporal evolution of and factors affecting the resources and environmental carrying capacity (RECC) of the urban agglomerations is critical for boosting high-quality green-oriented development. We first combined the Driver-Pressure-State-Impact-Response (DPSIR) framework and the improved Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) model to evaluate the RECC of Shandong Peninsula urban agglomeration in 2000, 2010 and 2020; we then used trend analysis and spatial autocorrelation analysis to understand the spatio-temporal evolution and distribution pattern of RECC. Furthermore, we employed Geodetector to detect the influencing factors and classified the urban agglomeration into six zones based on the weighted Voronoi diagram of RECC as well as specific conditions of the study area. The results show that the RECC of Shandong Peninsula urban agglomeration increased consistently over time, from 0.3887 in 2000 to 0.4952 in 2010 and 0.6097 in 2020, respectively. Geographically, RECC decreased gradually from the northeast coast to the southwest inland. Globally，only in 2010 the RECC presented a significant spatial positive correlation, and that in the other years were not significant. The high-high cluster is mainly located in Weifang, while the low-low cluster in Jining. Furthermore, our study reveals three key factors-advancement of industrial structure, resident consumption level, and water consumption per ten thousand yuan of industrial added value-that affected the distribution of RECC. Other factors, including the interactions between residents' consumption level and environmental regulation, residents' consumption level and advancement of industrial structure, as well as between the proportion of R&amp;D expenditure in GDP and resident consumption level also played important roles resulting in the variation of RECC among different cities within the urban agglomeration. Accordingly, we proposed suggestions for achieving high-quality development for different zones.}, }
@article {pmid37391265, year = {2023}, author = {Docherty, AB and Farrell, J and Thorpe, M and Egan, C and Dunn, S and Norman, L and Shaw, CA and Law, A and Leeming, G and Norris, L and Brooks, A and Prodan, B and MacLeod, R and Baxter, R and Morris, C and Rennie, D and Oosthuyzen, W and Semple, MG and Baillie, JK and Pius, R and Seth, S and Harrison, EM and Lone, NI}, title = {Patient emergency health-care use before hospital admission for COVID-19 and long-term outcomes in Scotland: a national cohort study.}, journal = {The Lancet. Digital health}, volume = {5}, number = {7}, pages = {e446-e457}, pmid = {37391265}, issn = {2589-7500}, mesh = {Adult ; Humans ; Cohort Studies ; Retrospective Studies ; *COVID-19 Vaccines ; *COVID-19/epidemiology/therapy ; Hospitals ; }, abstract = {BACKGROUND: It is unclear what effect the pattern of health-care use before admission to hospital with COVID-19 (index admission) has on the long-term outcomes for patients. We sought to describe mortality and emergency readmission to hospital after discharge following the index admission (index discharge), and to assess associations between these outcomes and patterns of health-care use before such admissions.<br><br>METHODS: We did a national, retrospective, complete cohort study by extracting data from several national databases and linking the databases for all adult patients admitted to hospital in Scotland with COVID-19. We used latent class trajectory modelling to identify distinct clusters of patients on the basis of their emergency admissions to hospital in the 2 years before the index admission. The primary outcomes were mortality and emergency readmission up to 1 year after index admission. We used multivariable regression models to explore associations between these outcomes and patient demographics, vaccination status, level of care received in hospital, and previous emergency hospital use.<br><br>FINDINGS: Between March 1, 2020, and Oct 25, 2021, 33&#x2008;580 patients were admitted to hospital with COVID-19 in Scotland. Overall, the Kaplan-Meier estimate of mortality within 1 year of index admission was 29&#xb7;6% (95% CI 29&#xb7;1-30&#xb7;2). The cumulative incidence of emergency hospital readmission within 30 days of index discharge was 14&#xb7;4% (95% CI 14&#xb7;0-14&#xb7;8), with the number increasing to 35&#xb7;6% (34&#xb7;9-36&#xb7;3) patients at 1 year. Among the 33&#x2008;580 patients, we identified four distinct patterns of previous emergency hospital use: no admissions (n=18&#x2008;772 [55&#xb7;9%]); minimal admissions (n=12&#x2008;057 [35&#xb7;9%]); recently high admissions (n=1931 [5&#xb7;8%]), and persistently high admissions (n=820 [2&#xb7;4%]). Patients with recently or persistently high admissions were older, more multimorbid, and more likely to have hospital-acquired COVID-19 than patients with no or minimal admissions. People in the minimal, recently high, and persistently high admissions groups had an increased risk of mortality and hospital readmission compared with those in the no admissions group. Compared with the no admissions group, mortality was highest in the recently high admissions group (post-hospital mortality HR 2&#xb7;70 [95% CI 2&#xb7;35-2&#xb7;81]; p<0&#xb7;0001) and the risk of readmission was highest in the persistently high admissions group (3&#xb7;23 [2&#xb7;89-3&#xb7;61]; p<0&#xb7;0001).<br><br>INTERPRETATION: Long-term mortality and readmission rates for patients hospitalised with COVID-19 were high; within 1 year, one in three patients had died and a third had been readmitted as an emergency. Patterns of hospital use before index admission were strongly predictive of mortality and readmission risk, independent of age, pre-existing comorbidities, and COVID-19 vaccination status. This increasingly precise identification of individuals at high risk of poor outcomes from COVID-19 will enable targeted support.<br><br>FUNDING: Chief Scientist Office Scotland, UK National Institute for Health Research, and UK Research and Innovation.}, }
@article {pmid37335075, year = {2023}, author = {Burger, J and Gochfeld, M and Giffen, N and Brown, KG and Cortes, M and Ng, K and Kosson, DS}, title = {Comparing land cover and interior forests on contaminated land and the surrounding region: Oak Ridge Reservation as a case study.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {86}, number = {15}, pages = {501-517}, doi = {10.1080/15287394.2023.2223231}, pmid = {37335075}, issn = {1528-7394}, mesh = {*Conservation of Natural Resources/methods ; *Forests ; Databases, Factual ; Ecosystem ; }, abstract = {Pressure from expanding populations has resulted in a need for protection, reclamation, and restoration of damaged land to productive, beneficial health uses. The objective of this investigation was to 1) compare land cover on the Department of Energy (DOE) Oak Ridge Reservation (ORR) with the surrounding region, 2) select an indicator to evaluate ORR's protection of ecological resources, and 3) develop and implement a method to compare the amount of the indicator on ORR with the regions using National Land Cover Database (NLCD). Data demonstrated that ORR has a higher % of forests (deciduous, coniferous, mixed) than the 10 km and 30 km areas surrounding ORR, suggesting that obligations are being met to protect the ecology and environment. The findings also indicate that the interior forest at ORR is fragmented more than is the interior forest in the 30 km buffer zone, suggesting a need for DOE and managers of other lands to take into consideration the importance of intact interior forest when developing land or planning roads. The study describes the basis for specific ecological parameters such as interior forest that are important to consider when planning and executing remediation, restoration, and other management actions.}, }
@article {pmid36999249, year = {2023}, author = {D'Alò, F and Zucconi, L and Onofri, S and Canini, F and Cannone, N and Malfasi, F and Morais, DK and Starke, R}, title = {Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.}, journal = {Environmental microbiology reports}, volume = {15}, number = {4}, pages = {291-297}, pmid = {36999249}, issn = {1758-2229}, support = {2015N8F555//Italian PRIN 2015 (Projects of Relevant National Interest) RESACC/ ; }, mesh = {*Archaea/genetics ; *Soil/chemistry ; Multiomics ; Climate Change ; Italy ; Soil Microbiology ; }, abstract = {We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.}, }
@article {pmid37389324, year = {2022}, author = {Ebdon, S and Lohse, K and ,  and ,  and ,  and Jansen Van Rensburg, A and , }, title = {The genome sequence of the northern brown argus, Aricia artaxerxes (Fabricius, 1793).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {314}, pmid = {37389324}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Aricia artaxerxes (the northern brown argus; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 458 megabases in span. Most of the assembly (99.99%) is scaffolded into 23 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,688 protein coding genes.}, }
@article {pmid37387279, year = {2023}, author = {Wang, QX and Feng, QY and Zhu, XQ}, title = {[Determination of bisphenols in sediment by accelerated solvent extraction and solid-phase extraction purification coupled with ultra performance liquid chromatography-tandem mass spectrometry].}, journal = {Se pu = Chinese journal of chromatography}, volume = {41}, number = {7}, pages = {582-590}, doi = {10.3724/SP.J.1123.2022.12015}, pmid = {37387279}, issn = {1872-2059}, abstract = {Bisphenols are endocrine disruptors that are characterized with bioaccumulation, persistence, and estrogenic activity. Even low contents of bisphenols can exert adverse effects on human health and the ecological environment. Herein, a method combining accelerated solvent extraction and solid-phase extraction purification with ultra performance liquid chromatography-tandem mass spectrometry was developed for the accurate detection of bisphenol A (BPA), bisphenol B (BPB), bisphenol F (BPF), bisphenol S (BPS), bisphenol Z (BPZ), bisphenol AF (BPAF), and bisphenol AP (BPAP) in sediments. The mass spectrometric parameters of the seven bisphenols were optimized, and the response values, separation effects, and chromatographic peak shapes of the target compounds were compared under three different mobile phase conditions. The sediment samples were pretreated by accelerated solvent extraction, and orthogonal tests were used to optimize the extraction solvent, extraction temperature, and cycle number. The results showed that the use of 0.05% (v/v) ammonia and acetonitrile as the mobile phase for gradient elution could rapidly separate the seven bisphenols on an Acquity UPLC BEH C18 column (100 mm×2.1 mm, 1.7 μm). The gradient program was as follows: 0-2 min, 60%A; 2-6 min, 60%A-40%A; 6-6.5 min, 40%A; 6.5-7 min, 40%A-60%A; 7-8 min, 60%A. Orthogonal experiments indicated that the optimal extraction conditions were as follows: extraction solvent of acetonitrile, extraction temperature of 100 ℃, and cycle number of three. The seven bisphenols showed good linearity in the range of 1.0-200 μg/L, with correlation coefficients (r[2]) greater than 0.999, and the limits of detection were 0.01-0.3 ng/g. The recoveries for the seven bisphenols ranged from 74.9% to 102.8% at three spiking levels (2.0, 10, 20 ng/g), with relative standard deviations ranging from 6.2% to 10.3%. The established method was applied to detect the seven bisphenols in sediment samples collected from Luoma Lake and its inflow rivers. BPA, BPB, BPF, BPS, and BPAF were detected in the sediments of the lake, and BPA, BPF, and BPS were detected in the sediments of its inflow rivers. The detection frequency of BPA and BPF was 100%, and the contents of these bisphenols in the sediment were 11.9-38.0 ng/g and 11.0-27.3 ng/g, respectively. The developed method is simple, rapid with high accuracy and precision, and is suitable for the determination of the seven bisphenols in sediment.}, }
@article {pmid37387086, year = {2023}, author = {Sijm-Eeken, M and Marcilly, R and Jaspers, M and Peute, L}, title = {Organizational and Human Factors in Green Medical Informatics - A Case Study in Dutch Hospitals.}, journal = {Studies in health technology and informatics}, volume = {305}, number = {}, pages = {537-540}, doi = {10.3233/SHTI230552}, pmid = {37387086}, issn = {1879-8365}, abstract = {Medical Informatics brings methods and solutions that could support reducing healthcare's ecological footprint. Initial frameworks for Green Medical Informatics solutions are available, however these do not address organizational and human factors. Including these factors in evaluation or analysis of (technical) interventions aimed at making healthcare more sustainable, is essential for improving usability as well as effectiveness of these interventions. Interviews with healthcare professionals from Dutch hospitals led to preliminary insights into which organizational and human factors impact the implementation and adoption of sustainable solutions. Results indicate that forming multi-disciplinary teams is considered an important factor for realizing intended outcomes in terms of reducing carbon emissions and waste. Some other key factors mentioned are formalizing tasks, allocating budget and time, creating awareness and changing protocols to promote sustainable diagnosis and treatment procedures.}, }
@article {pmid37379842, year = {2023}, author = {Talley, J and Pusdekar, S and Feltenberger, A and Ketner, N and Evers, J and Liu, M and Gosh, A and Palmer, SE and Wardill, TJ and Gonzalez-Bellido, PT}, title = {Predictive saccades and decision making in the beetle-predating saffron robber fly.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2023.06.019}, pmid = {37379842}, issn = {1879-0445}, abstract = {Internal predictions about the sensory consequences of self-motion, encoded by corollary discharge, are ubiquitous in the animal kingdom, including for fruit flies, dragonflies, and humans. In contrast, predicting the future location of an independently moving external target requires an internal model. With the use of internal models for predictive gaze control, vertebrate predatory species compensate for their sluggish visual systems and long sensorimotor latencies. This ability is crucial for the timely and accurate decisions that underpin a successful attack. Here, we directly demonstrate that the robber fly Laphria saffrana, a specialized beetle predator, also uses predictive gaze control when head tracking potential prey. Laphria uses this predictive ability to perform the difficult categorization and perceptual decision task of differentiating a beetle from other flying insects with a low spatial resolution retina. Specifically, we show that (1) this predictive behavior is part of a saccade-and-fixate strategy, (2) the relative target angular position and velocity, acquired during fixation, inform the subsequent predictive saccade, and (3) the predictive saccade provides Laphria with additional fixation time to sample the frequency of the prey's specular wing reflections. We also demonstrate that Laphria uses such wing reflections as a proxy for the wingbeat frequency of the potential prey and that consecutively flashing LEDs to produce apparent motion elicits attacks when the LED flicker frequency matches that of the beetle's wingbeat cycle.}, }
@article {pmid37377567, year = {2023}, author = {Schwienhorst-Stich, EM and Wabnitz, K and Geck, E and Gepp, S and Jung, L and Mumm, A and Schmid, J and Simmenroth, A and Simon, J and Eichinger, M}, title = {Initiatives promoting planetary health education in Germany: An overview.}, journal = {GMS journal for medical education}, volume = {40}, number = {3}, pages = {Doc38}, pmid = {37377567}, issn = {2366-5017}, mesh = {Germany ; *Education, Medical ; Health Education ; Curriculum ; Schools, Medical ; }, abstract = {Planetary health education focuses on the climate and ecological crises and their adverse health effects. Given the acceleration of these crises, nationwide integration of planetary health education into undergraduate and graduate education, postgraduate training and continuing education for all health professionals has repeatedly been called for. Since 2019, planetary health education has been promoted by several national initiatives in Germany that are summarized in this commentary: 1. National Working Group Planetary Health Education, 2. Manual for planetary health education, 3. Catalog of National Planetary Health Learning Objectives in the National Competency-Based Catalog of Learning Objectives for Medical Education, 4. Working Group Climate, Environment and Health Impact Assessment at the Institute for Medical and Pharmaceutical Examinations, 5. Planetary Health Report Card, and 6. PlanetMedEd study: planetary health education in medical schools in Germany. We hope these initiatives promote collaboration across institutions involved in educating and training health professionals, inter-professional cooperation as well as rapid implementation of planetary health education.}, }
@article {pmid37375921, year = {2023}, author = {Qi, Y and Ma, L and Ghani, MI and Peng, Q and Fan, R and Hu, X and Chen, X}, title = {Effects of Drought Stress Induced by Hypertonic Polyethylene Glycol (PEG-6000) on Passiflora edulis Sims Physiological Properties.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {37375921}, issn = {2223-7747}, support = {2021-229, HZJD [2022]001//Guizhou Provincial Science and Technology Program/ ; Guike AA21196003//Science and Technology Base &amp; Talent Project of Guangxi Province/ ; 2021YFD1100303-3//National Key Research and Development Program of China/ ; 2019-04//Guizhou University Cultivation Project/ ; }, abstract = {Passion fruit is known to be sensitive to drought, and in order to study the physiological and biochemical changes that occur in passion fruit seedlings under drought stress, a hypertonic polyethylene glycol (PEG) solution (5%, 10%, 15%, and 20%) was used to simulate drought stress in passion fruit seedlings. We explored the physiological changes in passion fruit seedlings under drought stress induced by PEG to elucidate their response to drought stress and provide a theoretical basis for drought-resistant cultivation of passion fruit seedlings. The results show that drought stress induced by PEG had a significant effect on the growth and physiological indices of passion fruit. Drought stress significantly decreased fresh weight, chlorophyll content, and root vitality. Conversely, the contents of soluble protein (SP), proline (Pro), and malondialdehyde (MDA) increased gradually with the increasing PEG concentration and prolonged stress duration. After nine days, the SP, Pro and MDA contents were higher in passion fruit leaves and roots under 20% PEG treatments compared with the control. Additionally, with the increase in drought time, the activities of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) showed an increasing trend and then a decreasing trend, and they reached the highest value at the sixth day of drought stress. After rehydration, SP, Pro and MDA contents in the leaves and roots of passion fruit seedlings was reduced. Among all the stress treatments, 20% PEG had the most significant effect on passion fruit seedlings. Therefore, our study demonstrated sensitive concentrations of PEG to simulate drought stress on passion fruit and revealed the physiological adaptability of passion fruit to drought stress.}, }
@article {pmid37368895, year = {2023}, author = {Aceves-Bueno, E and Nenadovic, M and Dove, I and Atkins-Davis, C and Aceves-Bueno, JS and Trejo-Ramirez, A and Rivas-Ochoa, C and Rodriguez-Van Dyck, S and Weaver, AH}, title = {Sustaining small-scale fisheries through a nation-wide Territorial Use Rights in Fisheries system.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0286739}, pmid = {37368895}, issn = {1932-6203}, mesh = {*Fisheries ; *Conservation of Natural Resources ; Territoriality ; Mexico ; Data Management ; Ecosystem ; }, abstract = {Territorial Use rights in Fisheries (TURFs) are used around the world to manage small-scale fisheries and they've shown varying levels of success. Our understanding of what leads to different performance levels is limited due to several reasons. Firstly, these systems are often present in areas with low monitoring capacity where data is scarce. Secondly, past research has centered on the analysis of successful cases, with little attention paid to entire systems. Thirdly, research has been ahistorical, disconnected from the development process of TURF systems. Fourthly, TURFs are often viewed as homogenous ignoring the socio-ecological conditions under which they develop. To address these gaps, the study focuses on Mexico as a case study and context. The research first presents a historical overview of the development of TURF systems in Mexico, including the institutional and legal frameworks that have shaped their evolution. The paper then presents a TURF database that maps all TURF systems in Mexico, including their geographical locations and characteristics. In addition, the study presents case studies based on identified archetypes that showcase the diversity of TURF systems in Mexico, highlighting the different types of systems and the challenges they face. By presenting a comprehensive map of all TURF systems in Mexico, this research paper aims to make an important addition to the case studies in the global literature on TURF systems and provide a valuable resource for marine resource management policymakers, researchers, and practitioners.}, }
@article {pmid37372376, year = {2023}, author = {Cheng, CC and Rivera-Colón, AG and Minhas, BF and Wilson, L and Rayamajhi, N and Vargas-Chacoff, L and Catchen, JM}, title = {Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie Eleginops maclovinus-The Closest Ancestral Proxy of Antarctic Cryonotothenioids.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/genes14061196}, pmid = {37372376}, issn = {2073-4425}, support = {ANT114218, OPP1645087//National Science Foundation/ ; }, abstract = {The basal South American notothenioid Eleginops maclovinus (Patagonia blennie or róbalo) occupies a uniquely important phylogenetic position in Notothenioidei as the singular closest sister species to the Antarctic cryonotothenioid fishes. Its genome and the traits encoded therein would be the nearest representatives of the temperate ancestor from which the Antarctic clade arose, providing an ancestral reference for deducing polar derived changes. In this study, we generated a gene- and chromosome-complete assembly of the E. maclovinus genome using long read sequencing and HiC scaffolding. We compared its genome architecture with the more basally divergent Cottoperca gobio and the derived genomes of nine cryonotothenioids representing all five Antarctic families. We also reconstructed a notothenioid phylogeny using 2918 proteins of single-copy orthologous genes from these genomes that reaffirmed E. maclovinus' phylogenetic position. We additionally curated E. maclovinus' repertoire of circadian rhythm genes, ascertained their functionality by transcriptome sequencing, and compared its pattern of gene retention with C. gobio and the derived cryonotothenioids. Through reconstructing circadian gene trees, we also assessed the potential role of the retained genes in cryonotothenioids by referencing to the functions of the human orthologs. Our results found E. maclovinus to share greater conservation with the Antarctic clade, solidifying its evolutionary status as the direct sister and best suited ancestral proxy of cryonotothenioids. The high-quality genome of E. maclovinus will facilitate inquiries into cold derived traits in temperate to polar evolution, and conversely on the paths of readaptation to non-freezing habitats in various secondarily temperate cryonotothenioids through comparative genomic analyses.}, }
@article {pmid37366114, year = {2023}, author = {Sahoo, P and Jana, P and Kundu, S and Mishra, S and Chattopadhyay, K and Mukherjee, A and Ghosh, CK}, title = {Quercetin@Gd[3+] doped Prussian blue nanocubes induce the pyroptotic death of MDA-MB-231 cells: combinational targeted multimodal therapy, dual modal MRI, intuitive modelling of r1-r2 relaxivities.}, journal = {Journal of materials chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3tb00316g}, pmid = {37366114}, issn = {2050-7518}, abstract = {Quercetin (Qu), a potential bioflavonoid has gained considerable interest as a promising chemotherapeutic drug which can inhibit the proliferation of triple-negative breast cancer (TNBC) cells due to its regulation of the expression of tumor-suppressor gene metastasis and antioxidant property. Notably, Qu exhibits a very negligible cytotoxic effect on normal cells, even with high-dose treatment, while it is shows high affinity to TNBC. However, the efficiency of Qu is limited clinically due to its poor bioavailability, caused by its low aqueous solubility (2.15 μg mL[-1] at 25 °C), rapid gastrointestinal digestion and chemical instability in alkaline and neutral media. Herein, polydopamine (PDA)-coated, NH2-PEG-NH2 and hyaluronic acid (HA)-functionalized Gd[3+]-doped Prussian blue nanocubes (GPBNC) are reported as a multifunctional platform for the codelivery of Qu as a chemotherapeutic agent and GPBNC as a photodynamic (PDT) and photothermal (PTT) agent with improved therapeutic efficiency to overcome theses barriers. PDA, NH2-PEG-NH2 and HA stabilize GPBNC@Qu and facilitate bioavailability and active-targeting, while absorption of near infrared (NIR) (808 nm; 1 W cm[-2]) induces PDT and PTT activities and dual T1-T2-weighted magnetic resonance imaging (MRI) with high relaxometric parameters (r1 10.06 mM[-1] s[-1] and r2 24.96 mM[-1] s[-1] at a magnetic field of 3 T). The designed platform shows a pH-responsive Qu release profile and NIR-induced therapeutic efficiency of ∼79% in 20 minutes of irradiation, wherein N-terminal gardermin D (N-GSDMD) and a P2X7-receptor-mediated pyroptosis pathway induces cell death, corroborating the up-regulation of NLRP3, caspase-1, caspase-5, N-GSDMD, IL-1β, cleaved Pannexin-1 and P2X7 proteins. More interestingly, the increasing relaxivity values of Prussian blue nanocubes with Gd[3+] doping have been explained on the basis of Solomon-Bloembergen-Morgan theory, considering inner- and outer-sphere relaxivity, wherein crystal defects, coordinated water molecules, tumbling rate, metal to water proton distance, correlation time, magnetisation value etc. play a significant role. In summary, our study suggests that GPBNC could be a beneficial nanocarrier for theranostic purposes against TNBC, while our conceptual study clearly demonstrates the role of various factors in increasing relaxometric parameters.}, }
@article {pmid37365013, year = {2023}, author = {Azzouz, D and Chen, Z and Izmirly, PM and Chen, LA and Li, Z and Zhang, C and Mieles, D and Trujillo, K and Heguy, A and Pironti, A and Putzel, GG and Schwudke, D and Fenyo, D and Buyon, JP and Alekseyenko, AV and Gisch, N and Silverman, GJ}, title = {Longitudinal gut microbiome analyses and blooms of pathogenic strains during lupus disease flares.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1136/ard-2023-223929}, pmid = {37365013}, issn = {1468-2060}, abstract = {OBJECTIVE: Whereas genetic susceptibility for systemic lupus erythematosus (SLE) has been well explored, the triggers for clinical disease flares remain elusive. To investigate relationships between microbiota community resilience and disease activity, we performed the first longitudinal analyses of lupus gut-microbiota communities.<br><br>METHODS: In an observational study, taxononomic analyses, including multivariate analysis of &#xdf;-diversity, assessed time-dependent alterations in faecal communities from patients and healthy controls. From gut blooms, strains were isolated, with genomes and associated glycans analysed.<br><br>RESULTS: Multivariate analyses documented that, unlike healthy controls, significant temporal community-wide ecological microbiota instability was common in SLE patients, and transient intestinal growth spikes of several pathogenic species were documented. Expansions of only the anaerobic commensal, Ruminococcus (blautia) gnavus (RG) occurred at times of high-disease activity, and were detected in almost half of patients during lupus nephritis (LN) disease flares. Whole genome sequence analysis of RG strains isolated during these flares documented 34 genes postulated to aid adaptation and expansion within a host with an inflammatory condition. Yet, the most specific feature of strains found during lupus flares was the common expression of a novel type of cell membrane-associated lipoglycan. These lipoglycans share conserved structural features documented by mass spectroscopy, and highly immunogenic repetitive antigenic-determinants, recognised by high-level serum IgG2 antibodies, that spontaneously arose, concurrent with RG blooms and lupus flares.<br><br>CONCLUSIONS: Our findings rationalise how blooms of the RG pathobiont may be common drivers of clinical flares of often remitting-relapsing lupus disease, and highlight the potential pathogenic properties of specific strains isolated from active LN patients.}, }
@article {pmid37363228, year = {2023}, author = {Sauer, FG and Lange, U and Schmidt-Chanasit, J and Kiel, E and Wiatrowska, B and Myczko, &#x141; and Lühken, R}, title = {Overwintering Culex torrentium in abandoned animal burrows as a reservoir for arboviruses in Central Europe.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100572}, pmid = {37363228}, issn = {2352-7714}, abstract = {Culex pipiens s.s./Culex torrentium belong to the most widespread mosquito taxa in Europe and are the main vectors of Sindbis, West Nile and Usutu virus. The adult overwintering females can act as reservoir for these arthropod-borne viruses (arboviruses), thus contributing to their local persistence when transmission cycles are interrupted during the winter. However, the main overwintering sites of Cx. torrentium are unknown. In a study from 2017, 3455 Cx. pipiens s.s./Cx. torrentium specimens were collected from abandoned animal burrows in Poznan, Poland. These specimens were retrospectively identified to species-level with a PCR assay, which revealed Cx. torrentium as dominant species (> 60%). Motivated by these results, we conducted a field study from February to July 2022 to systematically analyse the overwintering site patterns of Cx. pipiens s.s./Cx. torrentium. Mosquitoes were sampled using pipe traps in abandoned animal burrows (n = 20) and with aspirators in nearby anthropogenic overwintering sites (n = 23). All Cx. pipiens s.s./Cx. torrentium were screened for Flaviviridae RNA. In total, 4710 mosquitoes of five different taxa were collected from anthropogenic sites. 3977 of them were identified as Cx. p. pipiens/Cx. torrentium (Cx. p. pipiens: 85%, Cx torrentium: 1%, pools with both species: 14%). In contrast, only Cx. p. pipiens/Cx. torrentium (1688 specimens) were collected from animal burrows dominated by Cx. torrentium (52%), followed by pools with both species (40%) and Cx. p pipiens (8%). A single pool of 10 Cx. torrentium specimens collected from an animal burrow was positive for Usutu virus. The detection of Usutu virus demonstrates that Cx. torrentium can act as winter reservoir for arboviruses. Abandoned animal burrows may by the primary overwintering site for the species and should be considered in future surveillance programmes, when sampling overwintering mosquitoes.}, }
@article {pmid37363059, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Mouse Moth, Amphipyra tragopoginis (Clerck 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {54}, pmid = {37363059}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Amphipyra tragopoginis (the Mouse Moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 806 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 13,359 protein coding genes.}, }
@article {pmid37359433, year = {2023}, author = {Fu, D and Abawi, F and Carneiro, H and Kerzel, M and Chen, Z and Strahl, E and Liu, X and Wermter, S}, title = {A Trained Humanoid Robot can Perform Human-Like Crossmodal Social Attention and Conflict Resolution.}, journal = {International journal of social robotics}, volume = {}, number = {}, pages = {1-16}, doi = {10.1007/s12369-023-00993-3}, pmid = {37359433}, issn = {1875-4791}, abstract = {To enhance human-robot social interaction, it is essential for robots to process multiple social cues in a complex real-world environment. However, incongruency of input information across modalities is inevitable and could be challenging for robots to process. To tackle this challenge, our study adopted the neurorobotic paradigm of crossmodal conflict resolution to make a robot express human-like social attention. A behavioural experiment was conducted on 37 participants for the human study. We designed a round-table meeting scenario with three animated avatars to improve ecological validity. Each avatar wore a medical mask to obscure the facial cues of the nose, mouth, and jaw. The central avatar shifted its eye gaze while the peripheral avatars generated sound. Gaze direction and sound locations were either spatially congruent or incongruent. We observed that the central avatar's dynamic gaze could trigger crossmodal social attention responses. In particular, human performance was better under the congruent audio-visual condition than the incongruent condition. Our saliency prediction model was trained to detect social cues, predict audio-visual saliency, and attend selectively for the robot study. After mounting the trained model on the iCub, the robot was exposed to laboratory conditions similar to the human experiment. While the human performance was overall superior, our trained model demonstrated that it could replicate attention responses similar to humans.}, }
@article {pmid37352503, year = {2023}, author = {Park, Y and Shimada, T and Son, SW and Park, HJ}, title = {Invasion and interaction determine population composition in an open evolving ecological system.}, journal = {Chaos (Woodbury, N.Y.)}, volume = {33}, number = {6}, pages = {}, doi = {10.1063/5.0142978}, pmid = {37352503}, issn = {1089-7682}, mesh = {*Ecosystem ; Population Dynamics ; *Models, Biological ; }, abstract = {It is well-known that interactions between species determine the population composition in an ecosystem. Conventional studies have focused on fixed population structures to reveal how interactions shape population compositions. However, interaction structures are not fixed but change over time due to invasions. Thus, invasion and interaction play an important role in shaping communities. Despite its importance, however, the interplay between invasion and interaction has not been well explored. Here, we investigate how invasion affects the population composition with interactions in open evolving ecological systems considering generalized Lotka-Volterra-type dynamics. Our results show that the system has two distinct regimes. One is characterized by low diversity with abrupt changes of dominant species in time, appearing when the interaction between species is strong and invasion slowly occurs. On the other hand, frequent invasions can induce higher diversity with slow changes in abundances despite strong interactions. It is because invasion happens before the system reaches its equilibrium, which drags the system from its equilibrium all the time. All species have similar abundances in this regime, which implies that fast invasion induces regime shift. Therefore, whether invasion or interaction dominates determines the population composition.}, }
@article {pmid37352137, year = {2023}, author = {Dias Marques, V and Massago, M and da Silva, MT and Roskowski, I and de Lima, DAN and Dos Santos, L and Louro, E and Gonçalves, ST and Pedroso, RB and Obale, AM and Pelloso, SM and Vissoci, JRN and Staton, CA and Nihei, OK and Carvalho, MDB and Dutra, AC and de Andrade, L}, title = {Exploring regional disparities in lung cancer mortality in a Brazilian state: A cross-sectional ecological study.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0287371}, pmid = {37352137}, issn = {1932-6203}, mesh = {Humans ; Adult ; Brazil/epidemiology ; Cross-Sectional Studies ; Socioeconomic Factors ; Cities ; *Lung Neoplasms/epidemiology ; }, abstract = {BACKGROUND: Lung cancer (LC) is one of the main causes of mortality in Brazil; geographic, cultural, socioeconomic and health access factors can affect the development of the disease. We explored the geospatial distribution of LC mortality, and associated factors, between 2015 and 2019, in Parana state, Brazil.<br><br>METHODS AND FINDINGS: We obtained mortality (from the Brazilian Health Informatics Department) and population rates (from the Brazilian Institute of Geography and Statistics [IBGE]) in people over 40 years old, accessibility of oncology centers by municipality, disease diagnosis rate (from Brazilian Ministry of Health), the tobacco production rate (IBGE) and Parana Municipal Performance Index (IPDM) (from Parana Institute for Economic and Social Development). Global Moran's Index and Local Indicators of Spatial Association were performed to evaluate the spatial distribution of LC mortality in Parana state. Ordinary Least Squares Regression and Geographically Weighted Regression were used to verify spatial association between LC mortality and socioeconomic indicators and health service coverage. A strong spatial autocorrelation of LC mortality was observed, with the detection of a large cluster of high LC mortality in the South of Parana state. Spatial regression analysis showed that all independent variables analyzed were directly related to LC mortality by municipality in Paran&#xe1;.<br><br>CONCLUSIONS: There is a disparity in the LC mortality in Parana state, and inequality of socioeconomic and accessibility to health care services could be associated with it. Our findings may help health managers to intensify actions in regions with vulnerability in the detection and treatment of LC.}, }
@article {pmid37351546, year = {2023}, author = {Boyes, D and Goate, Z and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the Lesser Swallow Prominent, Pheosia gnoma (Fabricius, 1777).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {192}, pmid = {37351546}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Pheosia gnoma (the Lesser Swallow Prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 271.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.0 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,628 protein coding genes.}, }
@article {pmid37346819, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Mother Shipton moth , Euclidia mi (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {108}, pmid = {37346819}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Euclidia mi (the Mother Shipton moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 2,320 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,454 protein coding genes.}, }
@article {pmid37346773, year = {2022}, author = {Boyes, D and Sims, I and Lees, D and ,  and ,  and ,  and ,  and ,  and ,  and Dove, A and , }, title = {The genome sequence of the Kent black arches, Meganola albula (Denis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {310}, pmid = {37346773}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Meganola albula (the Kent black arches; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 405 megabases in span. Most of the assembly (99.95%) is scaffolded into 30 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.}, }
@article {pmid37344755, year = {2023}, author = {Adelisardou, F and Mederly, P and Minkina, T}, title = {Assessment of soil- and water-related ecosystem services with coupling the factors of climate and land-use change (Example of the Nitra region, Slovakia).}, journal = {Environmental geochemistry and health}, volume = {}, number = {}, pages = {}, pmid = {37344755}, issn = {1573-2983}, abstract = {Climate and land use change can profoundly impact the provision of ecosystem services (ES) over time, particularly in the landscape of open fields along with growing urbanization and rising demand for space, food and energy. Policymakers are keen on knowing the combined effects of climate and land use change on ESs as a critical issue in human well-being. However, deep knowledge of how to identify these relationships is still lacking. This research aims to undertake a comprehensive assessment of soil- and water-related ES, and improvement in understanding how they are affected by climate and land use change. We applied the Integrated Valuation of Ecosystem Services and Trade-offs model for four ES (soil retention, nutrient delivery ratio, carbon storage, and water yield) for the years 2000 and 2018 in the Nitra region, Slovakia. We investigated the spatial and temporal changes in ES provision and determined the hotspots and coldspots of multiple ES. We found that soil retention, water yield, and carbon storage display a rising trend while the nutrient delivery ratio showed a decreasing trend over the past 18 years. Although all the mentioned services mainly attributed to land use change, the relative contribution of climate change was not deniable. Forests in the north and east and distributed urbanization and agriculture are the hotspots and coldspots for all ESs, respectively. Our results, in terms of determining the relative importance of land use and climate change and identifying the sensitive areas of ES provision, provide a scientific basis for ecosystem conservation and management priority setting at the local and regional levels.}, }
@article {pmid37343007, year = {2023}, author = {Isaacson, JE and Ye, JJ and Silva, LL and Hernandes Rocha, TA and de Andrade, L and Scheidt, JFHC and Wen, FH and Sachett, J and Monteiro, WM and Staton, CA and Vissoci, JRN and Gerardo, CJ}, title = {Antivenom access impacts severity of Brazilian snakebite envenoming: A geographic information system analysis.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {6}, pages = {e0011305}, pmid = {37343007}, issn = {1935-2735}, mesh = {Humans ; *Snake Bites/epidemiology/therapy ; Antivenins/therapeutic use ; Brazil/epidemiology ; Geographic Information Systems ; Cross-Sectional Studies ; }, abstract = {BACKGROUND: Snakebite envenoming (SBE) is a neglected tropical disease capable of causing both significant disability and death. The burden of SBE is especially high in low- and middle-income countries. The aim of this study was to perform a geospatial analysis evaluating the association of sociodemographics and access to care indicators on moderate and severe cases of SBE in Brazil.<br><br>METHODS: We conducted an ecological, cross-sectional study of SBE in Brazil from 2014 to 2019 using the open access National System Identification of Notifiable Diseases (SINAN) database. We then collected a set of indicators from the Brazil Census of 2010 and performed a Principal Component Analysis to create variables related to health, economics, occupation, education, infrastructure, and access to care. Next, a descriptive and exploratory spatial analysis was conducted to evaluate the geospatial association of moderate and severe events. These variables related to events were evaluated using Geographically Weighted Poisson Regression. T-values were plotted in choropleth maps and considered statistically significant when values were <-1.96 or >+1.96.<br><br>RESULTS: We found that the North region had the highest number of SBE cases by population (47.83/100,000), death rates (0.18/100,000), moderate and severe rates (22.96/100,000), and proportion of cases that took more than three hours to reach healthcare assistance (44.11%). The Northeast and Midwest had the next poorest indicators. Life expectancy, young population structure, inequality, electricity, occupation, and more than three hours to reach healthcare were positively associated with greater cases of moderate and severe events, while income, illiteracy, sanitation, and access to care were negatively associated. The remaining indicators showed a positive association in some areas of the country and a negative association in other areas.<br><br>CONCLUSION: Regional disparities in SBE incidence and rates of poor outcomes exist in Brazil, with the North region disproportionately affected. Multiple indicators were associated with rates of moderate and severe events, such as sociodemographic and health care indicators. Any approach to improving snakebite care must work to ensure the timeliness of antivenom administration.}, }
@article {pmid37172588, year = {2023}, author = {Gao, X and Sun, R and Jiao, N and Liang, X and Li, G and Gao, H and Wu, X and Yang, M and Chen, C and Sun, X and Chen, L and Wu, W and Cong, Y and Zhu, R and Guo, T and Liu, Z}, title = {Integrative multi-omics deciphers the spatial characteristics of host-gut microbiota interactions in Crohn's disease.}, journal = {Cell reports. Medicine}, volume = {4}, number = {6}, pages = {101050}, doi = {10.1016/j.xcrm.2023.101050}, pmid = {37172588}, issn = {2666-3791}, mesh = {Humans ; *Crohn Disease/complications/diagnosis/pathology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Multiomics ; Inflammation/complications ; Bacteria/genetics/metabolism ; Membrane Proteins/metabolism ; }, abstract = {Dysregulated host-microbial interactions play critical roles in initiation and perpetuation of gut inflammation in Crohn's disease (CD). However, the spatial distribution and interaction network across the intestine and its accessory tissues are still elusive. Here, we profile the host proteins and tissue microbes in 540 samples from the intestinal mucosa, submucosa-muscularis-serosa, mesenteric adipose tissues, mesentery, and mesenteric lymph nodes of 30 CD patients and spatially decipher the host-microbial interactions. We observe aberrant antimicrobial immunity and metabolic processes across multi-tissues during CD and determine bacterial transmission along with altered microbial communities and ecological patterns. Moreover, we identify several candidate interaction pairs between host proteins and microbes associated with perpetuation of gut inflammation and bacterial transmigration across multi-tissues in CD. Signature alterations in host proteins (e.g., SAA2 and GOLM1) and microbes (e.g., Alistipes and Streptococcus) are further imprinted in serum and fecal samples as potential diagnostic biomarkers, thus providing a rationale for precision diagnosis.}, }
@article {pmid37340013, year = {2023}, author = {Tulis, F and Ševčík, M and Jánošíková, R and Baláž, I and Ambros, M and Zvaríková, L and Horváth, G}, title = {Author Correction: The impact of the striped field mouse's range expansion on communities of native small mammals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {10006}, doi = {10.1038/s41598-023-36731-y}, pmid = {37340013}, issn = {2045-2322}, }
@article {pmid37336403, year = {2023}, author = {Li, W and Feng, Q and Southam, G and Jin, T and Li, Z}, title = {Changes in microbial community structure during the biooxidation of iron and inorganic/organic sulfur provide prediction of acid mine drainage from coal spoil.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164945}, doi = {10.1016/j.scitotenv.2023.164945}, pmid = {37336403}, issn = {1879-1026}, abstract = {To thoroughly investigate the formation mechanism of acid mine drainage (AMD) from coal mine spoil, this study conducted microbial shake flask experiments on gangue possessing inorganic and organic sulfur to predict the future generation of AMD. The results revealed that microbial-mediated sulfur oxidation effectively lowered the pH of leachate and increased metal ion and sulfate concentrations. The oxidation of pyrite sulfur and thiophene sulfur contributed to 70 % and 30 % of the total acid production, respectively, highlighting the importance of both processes in coal mine acidification. The abundance and diversity of the microbial community increased, with "new" iron and sulfur oxidizing bacterial species during acidification, with "new" iron and sulfur oxidizing bacterial species, such as Sulfobacillus sp. and Acidibacillus sp., emerging and constituting approximately one-third of the bacterial population. These bacteria survived desiccation and proliferated faster than A. ferrooxidans YQ-N3 when conditions favored growth.}, }
@article {pmid37270983, year = {2023}, author = {Vo, HT and Vrachioli, M and Frick, F and Sauer, J and Brucet Balmana, S and Benejam Vidal, L and Mehner, T and Lemmens, P and Oertli, B and Boissezon, A and Beklioğlu, M and Dolcerocca, A and Meerhoff, M}, title = {Socio-economic or environmental benefits from pondscapes? Deriving stakeholder preferences using analytic hierarchy process and compositional data analysis.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118298}, doi = {10.1016/j.jenvman.2023.118298}, pmid = {37270983}, issn = {1095-8630}, mesh = {Humans ; *Ecosystem ; *Analytic Hierarchy Process ; Biodiversity ; Ponds ; Socioeconomic Factors ; Conservation of Natural Resources ; }, abstract = {Ponds occupy a large share of standing water worldwide and play an important role in providing various ecosystem services. There are concerted efforts of the European Union either to create new ponds, or to restore and preserve existing ponds as nature-based solutions to provide benefits to ecosystem and human well-being. As part of the EU PONDERFUL project, selected pondscapes (i.e. landscapes of ponds) in eight different countries - hereafter "demo-sites", are studied to comprehensively understand their characteristics and their efficiency to provide ecosystem services. In addition, the needs and knowledge of stakeholders who own, work, research, or benefit from the pondscapes are also important, because of their capabilities to create, manage and develop the pondscapes. Therefore, we established connection with stakeholders to study their preferences and visions on the pondscapes. Using the analytic hierarchy process, this study shows that in general stakeholders in the European and Turkish demo-sites prefer environmental benefits to economic benefits, while stakeholders in the Uruguayan demo-sites rank the economic benefits higher. More specifically, in the European and Turkish demo-sites, the biodiversity benefits, i.e. life-cycle maintenance, habitat and gene pool protection, receive the highest ranking among all groups. On the other hand, stakeholders at the Uruguayan demo-sites rank provisioning benefits as the most important, because many ponds in Uruguayan demo-sites are being used for agricultural purposes. Understanding those preferences helps policy makers to address the needs of stakeholders more correctly, when considering any action or policy for the pondscapes.}, }
@article {pmid37169855, year = {2023}, author = {Huang, L and Jin, C and Pan, Y and Zhou, L and Hu, S and Guo, Y and Meng, Y and Song, K and Pang, M and Li, H and Lin, D and Xu, X and Minor, J and Coggins, C and Jim, CY and Yan, E and Yang, Y and Tang, Z and Lindenmayer, DB}, title = {Human activities and species biological traits drive the long-term persistence of old trees in human-dominated landscapes.}, journal = {Nature plants}, volume = {9}, number = {6}, pages = {898-907}, pmid = {37169855}, issn = {2055-0278}, support = {32071652//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32025025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31988102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2022M720254//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Humans ; *Ecosystem ; Databases, Factual ; China ; *Moths ; Plant Leaves ; }, abstract = {Old trees have many ecological and socio-cultural values. However, knowledge of the factors influencing their long-term persistence in human-dominated landscapes is limited. Here, using an extensive database (nearly 1.8 million individual old trees belonging to 1,580 species) from China, we identified which species were most likely to persist as old trees in human-dominated landscapes and where they were most likely to occur. We found that species with greater potential height, smaller leaf size and diverse human utilization attributes had the highest probability of long-term persistence. The persistence probabilities of human-associated species (taxa with diverse human utilization attributes) were relatively high in intensively cultivated areas. Conversely, the persistence probabilities of spontaneous species (taxa with no human utilization attributes and which are not cultivated) were relatively high in mountainous areas or regions inhabited by ethnic minorities. The distinctly different geographic patterns of persistence probabilities of the two groups of species were related to their dissimilar responses to heterogeneous human activities and site conditions. A small number of human-associated species dominated the current cohort of old trees, while most spontaneous species were rare and endemic. Our study revealed the potential impacts of human activities on the long-term persistence of trees and the associated shifts in species composition in human-dominated landscapes.}, }
@article {pmid37335471, year = {2023}, author = {Viruel, J and Hidalgo, O and Pokorny, L and Forest, F and Gravendeel, B and Wilkin, P and Leitch, IJ}, title = {A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2672}, number = {}, pages = {115-126}, pmid = {37335471}, issn = {1940-6029}, mesh = {Humans ; *Ploidies ; *Genome ; Computational Biology ; Polyploidy ; }, abstract = {Whole genome duplications (WGD) are frequent in many plant lineages; however, ploidy level variation is unknown in most species. The most widely used methods to estimate ploidy levels in plants are chromosome counts, which require living specimens, and flow cytometry estimates, which necessitate living or relatively recently collected samples. Newly described bioinformatic methods have been developed to estimate ploidy levels using high-throughput sequencing data, and these have been optimized in plants by calculating allelic ratio values from target capture data. This method relies on the maintenance of allelic ratios from the genome to the sequence data. For example, diploid organisms will generate allelic data in a 1:1 proportion, with an increasing number of possible allelic ratio combinations occurring in individuals with higher ploidy levels. In this chapter, we explain step-by-step this bioinformatic approach for the estimation of ploidy level.}, }
@article {pmid37325324, year = {2023}, author = {Douet Vannucci, V and Marchand, T and Hennequin, A and Caci, H and Staccini, P}, title = {The EPIDIA4Kids protocol for a digital epidemiology study on brain functioning in children, based on a multimodality biometry tool running on an unmodified tablet.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1185565}, pmid = {37325324}, issn = {2296-2565}, mesh = {Humans ; Child ; *Mental Disorders ; Brain/diagnostic imaging ; Biometry ; }, abstract = {INTRODUCTION: Neurodevelopment and related mental disorders (NDDs) are one of the most frequent disabilities among young people. They have complex clinical phenotypes often associated with transnosographic dimensions, such as emotion dysregulation and executive dysfunction, that lead to adverse impacts in personal, social, academic, and occupational functioning. Strong overlap exists then across NDDs phenotypes that are challenging for diagnosis and therapeutic intervention. Recently, digital epidemiology uses the rapidly growing data streams from various devices to advance our understanding of health's and disorders' dynamics, both in individuals and the general population, once coupled with computational science. An alternative transdiagnostic approach using digital epidemiology may thus better help understanding brain functioning and hereby NDDs in the general population.<br><br>OBJECTIVE: The EPIDIA4Kids study aims to propose and evaluate in children, a new transdiagnostic approach for brain functioning examination, combining AI-based multimodality biometry and clinical e-assessments on an unmodified tablet. We will examine this digital epidemiology approach in an ecological context through data-driven methods to characterize cognition, emotion, and behavior, and ultimately the potential of transdiagnostic models of NDDs for children in real-life practice.<br><br>METHODS AND ANALYSIS: The EPIDIA4Kids is an uncontrolled open-label study. 786 participants will be recruited and enrolled if eligible: they are (1) aged 7 to 12&#x2009;years and (2) are French speaker/reader; (3) have no severe intellectual deficiencies. Legal representative and children will complete online demographic, psychosocial and health assessments. During the same visit, children will perform additionally a paper/pencil neuro-assessments followed by a 30-min gamified assessment on a touch-screen tablet. Multi-stream data including questionnaires, video, audio, digit-tracking, will be collected, and the resulting multimodality biometrics will be generated using machine- and deep-learning algorithms. The trial will start in March 2023 and is expected to end by December 2024.<br><br>DISCUSSION: We hypothesize that the biometrics and digital biomarkers will be capable of detecting early onset symptoms of neurodevelopment compared to paper-based screening while as or more accessible in real-life practice.}, }
@article {pmid37316182, year = {2023}, author = {Eliason, PH and Galarneau, JM and Kolstad, AT and Pankow, MP and West, SW and Bailey, S and Miutz, L and Black, AM and Broglio, SP and Davis, GA and Hagel, BE and Smirl, JD and Stokes, KA and Takagi, M and Tucker, R and Webborn, N and Zemek, R and Hayden, A and Schneider, KJ and Emery, CA}, title = {Prevention strategies and modifiable risk factors for sport-related concussions and head impacts: a systematic review and meta-analysis.}, journal = {British journal of sports medicine}, volume = {57}, number = {12}, pages = {749-761}, doi = {10.1136/bjsports-2022-106656}, pmid = {37316182}, issn = {1473-0480}, mesh = {Adolescent ; Child ; Humans ; *Brain Concussion/prevention &amp; control ; *Football ; Rugby ; *Hockey ; Databases, Factual ; }, abstract = {OBJECTIVES: To evaluate prevention strategies, their unintended consequences and modifiable risk factors for sport-related concussion (SRC) and/or head impact risk.<br><br>DESIGN: This systematic review and meta-analysis was registered on PROSPERO (CRD42019152982) and conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.<br><br>DATA SOURCES: Eight databases (MEDLINE, CINAHL, APA PsycINFO, Cochrane (Systematic Review and Controlled Trails Registry), SPORTDiscus, EMBASE, ERIC0 were searched in October 2019 and updated in March 2022, and references searched from any identified systematic review.<br><br>ELIGIBILITY CRITERIA: Study inclusion criteria were as follows: (1) original data human research studies, (2) investigated SRC or head impacts, (3) evaluated an SRC prevention intervention, unintended consequence or modifiable risk factor, (4) participants competing in any sport, (5) analytic study design, (6) systematic reviews and meta-analyses were included to identify original data manuscripts in reference search and (7) peer-reviewed. Exclusion criteria were as follows: (1) review articles, pre-experimental, ecological, case series or case studies and (2) not written in English.<br><br>RESULTS: In total, 220 studies were eligible for inclusion and 192 studies were included in the results based on methodological criteria as assessed through the Scottish Intercollegiate Guidelines Network high ('++') or acceptable ('+') quality. Evidence was available examining protective gear (eg, helmets, headgear, mouthguards) (n=39), policy and rule changes (n=38), training strategies (n=34), SRC management strategies (n=12), unintended consequences (n=5) and modifiable risk factors (n=64). Meta-analyses demonstrated a protective effect of mouthguards in collision sports (incidence rate ratio, IRR 0.74; 95%&#x2009;CI 0.64 to 0.89). Policy disallowing bodychecking in child and adolescent ice hockey was associated with a 58% lower concussion rate compared with bodychecking leagues (IRR 0.42; 95%&#x2009;CI 0.33 to 0.53), and evidence supports no unintended injury consequences of policy disallowing bodychecking. In American football, strategies limiting contact in practices were associated with a 64% lower practice-related concussion rate (IRR 0.36; 95%&#x2009;CI 0.16 to 0.80). Some evidence also supports up to 60% lower concussion rates with implementation of a neuromuscular training warm-up programme in rugby. More research examining potentially modifiable risk factors (eg, neck strength, optimal tackle technique) are needed to inform concussion prevention strategies.<br><br>CONCLUSIONS: Policy and rule modifications, personal protective equipment, and neuromuscular training strategies may help to prevent SRC.<br><br>PROSPERO REGISTRATION NUMBER: CRD42019152982.}, }
@article {pmid37311775, year = {2023}, author = {Nemesházi, E and Bókony, V}, title = {HerpSexDet: the herpetological database of sex determination and sex reversal.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {377}, pmid = {37311775}, issn = {2052-4463}, mesh = {Animals ; *Animals, Wild ; Databases, Factual ; *Ecology ; Phenotype ; Species Specificity ; Sex Determination Processes ; }, abstract = {Wildlife exhibits various sex-determination systems where sex chromosomes and environmental temperatures may both contribute to individual sexual development. The causes and consequences of this variability are important questions for evolutionary ecology, especially in light of ongoing environmental change. Amphibians and reptiles are emerging as a key group for studying these questions, with new data accumulating acceleratingly. We collected empirical data from earlier databases, reviews and primary literature to create the most up-to-date database on herpetological sex determination. We named our database HerpSexDet, which currently features data on genetic and temperature-dependent sex determination as well as reports on sex reversal for a total of 192 amphibian and 697 reptile species. This dataset, which we will regularly update in the future, facilitates interspecific comparative studies on the evolution of sex determination and its consequences for species-specific traits such as life history and conservation status, and may also help guiding future research by identifying species or higher taxa that are potentially most enlightening for the study of environmentally driven sex reversal.}, }
@article {pmid37263027, year = {2023}, author = {Mokarram, M and Mokarram, MJ and Najafi, A}, title = {Thermal power plants pollution assessment based on deep neural networks, remote sensing, and GIS: A real case study in Iran.}, journal = {Marine pollution bulletin}, volume = {192}, number = {}, pages = {115069}, doi = {10.1016/j.marpolbul.2023.115069}, pmid = {37263027}, issn = {1879-3363}, mesh = {Environmental Monitoring/methods ; Geographic Information Systems ; Iran ; Carbon Dioxide/analysis ; Remote Sensing Technology ; *Air Pollution/analysis ; Neural Networks, Computer ; Water/analysis ; Power Plants ; *Air Pollutants/analysis ; }, abstract = {To investigate the impact of the Bandar Abbas thermal power plant on the waters of the Persian Gulf coast, a combination of satellite images and ground data was utilized to determine the Sea Surface Temperature (SST) as a thermal index, Total Organic Carbon (TOC) and Chemical Oxygen Demand (COD) as biological indices. Additionally, measurements of SO2, O3, NO2, CO2, CO, and CH4 values in the atmosphere were taken to determine the plant's impact on air pollution. Temperature values of the water for different months were predicted using Long Short-Term Memory (LSTM), Support Vector Regression (SVR), and Cascade neural networks. The results indicate that the waters near thermal power plants exhibit the highest temperatures in July and September, with temperatures reaching approximately 50 °C. Furthermore, the SST values were found to be strongly correlated with ecological indices. The Multiple Linear Regression (MLR) analysis revealed a strong correlation between the temperature and TOC, COD, and O2 in water (RTOC[2]=0.98), [Formula: see text] , RCOD[2]=0.87 and O3, NO3, CO2, and CO in the air ([Formula: see text]). Finally, the results demonstrate that the LSTM method exhibited high accuracy in predicting the water temperature (R[2] = 0.98).}, }
@article {pmid37211183, year = {2023}, author = {Yokoyama, D and Kikuchi, J}, title = {Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.}, journal = {Environmental research}, volume = {231}, number = {Pt 3}, pages = {116202}, doi = {10.1016/j.envres.2023.116202}, pmid = {37211183}, issn = {1096-0953}, mesh = {Humans ; *Rivers ; Phylogeny ; Multiomics ; *Microbiota ; Stochastic Processes ; }, abstract = {Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.}, }
@article {pmid36651964, year = {2023}, author = {Johnson, MS and Venkataram, S and Kryazhimskiy, S}, title = {Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.}, journal = {Journal of molecular evolution}, volume = {91}, number = {3}, pages = {263-280}, pmid = {36651964}, issn = {1432-1432}, support = {R01 GM137112/GM/NIGMS NIH HHS/United States ; 1R01GM137112/GM/NIGMS NIH HHS/United States ; 1R01GM137112/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Sequence Analysis, DNA/methods ; Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.}, }
@article {pmid37307237, year = {2023}, author = {Tardelli, VS and Bianco, MCM and Patel, R and Areco, KCN and Bandiera-Paiva, P and Tardelli, AO and Segura, LE and Castaldelli-Maia, JM and Fidalgo, TM and Martins, SS}, title = {Overdose death rates in Brazil: an ecological analysis by region.}, journal = {Revista brasileira de psiquiatria (Sao Paulo, Brazil : 1999)}, volume = {}, number = {}, pages = {}, doi = {10.47626/1516-4446-2023-3146}, pmid = {37307237}, issn = {1809-452X}, }
@article {pmid37302594, year = {2023}, author = {Haas, D and Ilieva, M and Fritz, T and Galler, H and Habib, J and Kriso, A and Kropsch, M and Ofner-Kopeinig, P and Reinthaler, FF and Strasser, A and Zentner, E and Schalli, M}, title = {Background concentrations of airborne, culturable fungi and dust particles in urban, rural and mountain regions.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164700}, doi = {10.1016/j.scitotenv.2023.164700}, pmid = {37302594}, issn = {1879-1026}, abstract = {Geographic location and meteorological factors can affect the content of bioaerosol concentrations. This study was conducted to determine the natural background concentrations of culturable fungal spores and dust particles in three different geographical areas. Focus was given to the dominant airborne genera Cladosporium, Penicillium, Aspergillus and the species Aspergillus fumigatus. The influence of weather conditions on the microorganism concentrations in urban, rural and mountain regions were examined. Possible correlations between particle counts and culturable fungal spore concentrations were investigated. 125 measurements of the air were conducted using the air sampler MAS-100NT® and the particle counter Alphasense OPC-N3. The analyses of the collected samples were based on culture methods using different media. The highest median of fungal spore concentrations was detected in the urban region and was of 2.0 × 10[3] CFU/m[3] for xerophilic fungi and 1.7 × 10[3] CFU/m[3] for the genus Cladosporium. The concentrations of fine and coarse particles in rural and urban regions were the highest of 1.9 × 10[7] pa/m[3] and 1.3 × 10[7] pa/m[3], respectively. Little cloud cover and slight wind had a positive influence on the concentration of fungal spores. Furthermore, correlations were observed between air temperature and the concentrations of xerophilic fungi as well as the genera Cladosporium. In contrast, relative humidity correlated negatively with total fungi and Cladosporium and no correlation was found with the other fungi. For the region of Styria in summer and early autumn, the natural background concentration for xerophilic fungi ranged between 3.5 × 10[2] and 4.7 × 10[3] CFU/m[3] air. No significant differences were detected between the fungal spore concentrations in urban, rural and mountainous regions. The data of this study could be used as a reference to compare the natural background concentrations of airborne culturable fungi in further studies concerning air quality assessment.}, }
@article {pmid37297635, year = {2023}, author = {Ojukwu, EN and Okoye, HU and Saewyc, E}, title = {Social Correlates of HIV-Risky Behaviours among African Canadian Adolescents Living in British Columbia, Canada: A Secondary Data Analysis.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {11}, pages = {}, pmid = {37297635}, issn = {1660-4601}, mesh = {Humans ; Adolescent ; British Columbia/epidemiology ; *Secondary Data Analysis ; Black or African American ; Sexual Behavior ; *HIV Infections/epidemiology ; Risk-Taking ; }, abstract = {Studies have linked HIV-risky behaviours among young people to several socio-contextual factors. However, the social factors that might increase African Canadian adolescents' exposure to HIV-risky behaviours, including unprotected sex and forced or multiple-sexual partnerships, have received little or no attention in the literature. Using data from the British Columbia Adolescent Health Surveys (2003-2018) and guided by intersectionality and socio-ecological frameworks, we examined the social determinants of HIV-risky behaviours (HRB) among African Canadian adolescents in British Columbia. We observed a general decline in HRB from 2008 to 2018. However, more than half (54.5%) of the 1042 who were sexually experienced in 2018 reported having 2 or more sexual partners, and nearly half reported condom-less sex. Our results demonstrate an important need to evaluate the impacts of several social factors on health outcomes for a unique, marginalized population.}, }
@article {pmid37216923, year = {2023}, author = {Ma, Y and Liu, L and Ma, Y and Zhang, S}, title = {HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {6}, pages = {}, pmid = {37216923}, issn = {1367-4811}, mesh = {*Multiomics ; Software ; Algorithms ; *Microbiota ; Cluster Analysis ; }, abstract = {MOTIVATION: The accumulation of multi-omics microbiome data provides an unprecedented opportunity to understand the diversity of bacterial, fungal, and viral components from different conditions. The changes in the composition of viruses, bacteria, and fungi communities have been associated with environments and critical illness. However, identifying and dissecting the heterogeneity of microbial samples and cross-kingdom interactions remains challenging.<br><br>RESULTS: We propose HONMF for the integrative analysis of multi-modal microbiome data, including bacterial, fungal, and viral composition profiles. HONMF enables identification of microbial samples and data visualization, and also facilitates downstream analysis, including feature selection and cross-kingdom association analysis between species. HONMF is an unsupervised method based on hypergraph induced orthogonal non-negative matrix factorization, where it assumes that latent variables are specific for each composition profile and integrates the distinct sets of latent variables through graph fusion strategy, which better tackles the distinct characteristics in bacterial, fungal, and viral microbiome. We implemented HONMF on several multi-omics microbiome datasets from different environments and tissues. The experimental results demonstrate the superior performance of HONMF in data visualization and clustering. HONMF also provides rich biological insights by implementing discriminative microbial feature selection and bacterium-fungus-virus association analysis, which improves our understanding of ecological interactions and microbial pathogenesis.<br><br>The software and datasets are available at https://github.com/chonghua-1983/HONMF.}, }
@article {pmid37259063, year = {2023}, author = {Ormaasen, I and Rudi, K and Diep, DB and Snipen, L}, title = {Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {295}, pmid = {37259063}, issn = {1471-2164}, mesh = {*Metagenome ; Humans ; Child, Preschool ; Child ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Data Mining ; *Gastrointestinal Microbiome/drug effects ; Bacteriocins/pharmacology ; Genome ; }, abstract = {BACKGROUND: Our knowledge about the ecological role of bacterial antimicrobial peptides (bacteriocins) in the human gut is limited, particularly in relation to their role in the diversification of the gut microbiota during early life. The aim of this paper was therefore to address associations between bacteriocins and bacterial diversity in the human gut microbiota. To investigate this, we did an extensive screening of 2564 healthy human gut metagenomes for the presence of predicted bacteriocin-encoding genes, comparing bacteriocin gene presence to strain diversity and age.<br><br>RESULTS: We found that the abundance of bacteriocin genes was significantly higher in infant-like metagenomes (<&#x2009;2&#xa0;years) compared to adult-like metagenomes (2-107&#xa0;years). By comparing infant-like metagenomes with and without a given bacteriocin, we found that bacteriocin presence was associated with increased strain diversities.<br><br>CONCLUSIONS: Our findings indicate that bacteriocins may play a role in the strain diversification during the infant gut microbiota establishment.}, }
@article {pmid37277721, year = {2023}, author = {Zhong, H and Luo, J and Tang, L and Liao, S and Lu, Z and Lin, G and Murphy, RW and Liu, L}, title = {Association filtering and generative adversarial networks for predicting lncRNA-associated disease.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {234}, pmid = {37277721}, issn = {1471-2105}, mesh = {*RNA, Long Noncoding/genetics ; Algorithms ; Computational Biology/methods ; }, abstract = {BACKGROUND: Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and understand pathogenesis, and thus better diagnose preventable diseases.<br><br>RESULTS: Herein, we offer the LDAF_GAN method for predicting lncRNA-associated disease based on association filtering and generative adversarial networks. Experimentation used two types of data: lncRNA-disease associated data without lncRNA sequence features, and fused lncRNA sequence features. LDAF_GAN uses a generator and discriminator, and differs from the original GAN by the addition of a filtering operation and negative sampling. Filtering allows the generator output to filter out unassociated diseases before being fed into the discriminator. Thus, the results generated by the model focuses only on lncRNAs associated with disease. Negative sampling takes a portion of disease terms with 0 from the association matrix as negative samples, which are assumed to be unassociated with lncRNA. A regular term is added to the loss function to avoid producing a vector with all values of 1, which can fool the discriminator. Thus, the model requires that generated positive samples are close to 1, and negative samples are close to 0. The model achieved a superior fitting effect; LDAF_GAN had superior performance in predicting fivefold cross-validations on the two datasets with AUC values of 0.9265 and 0.9278, respectively. In the case study, LDAF_GAN predicted disease association for six lncRNAs-H19, MALAT1, XIST, ZFAS1, UCA1, and ZEB1-AS1-and with the top ten predictions of 100%, 80%, 90%, 90%, 100%, and 90%, respectively, which were reported by previous studies.<br><br>CONCLUSION: LDAF_GAN efficiently predicts the potential association of existing lncRNAs and the potential association of new lncRNAs with diseases. The results of fivefold cross-validation, tenfold cross-validation, and case studies suggest that the model has great predictive potential for lncRNA-disease association prediction.}, }
@article {pmid37273367, year = {2023}, author = {Ekram, R and Nazer, MS}, title = {Hospital Admission Profile Due to Osteoarthritis: An Ecological Study.}, journal = {Cureus}, volume = {15}, number = {5}, pages = {e38435}, pmid = {37273367}, issn = {2168-8184}, abstract = {Background Osteoarthritis (OA) is also known as degenerative joint disease and is considered the major cause of joint pain and disability. Furthermore, OA is the most common, costly, and disabling form of joint diseases. The objective of this study is to explore the hospital admission profile due to OA between the period 1999 and 2019 in England and Wales. Method This is an ecological study that used health care data in the United Kingdom. Patients who were hospitalized for OA in England and Wales between 1999 and 2019 formed the study population. The Hospital Episode Statistics in England and the Patient Episode Database for Wales databases were used in this study. The difference in the admission rate during the study period was estimated using the chi-squared test. Results The admission rate during the study period increased by 112.1% for all hospital admission related to OA. The most common type of admission was related to gonarthrosis, which accounted for 46.7% of the total number of admissions for OA. The increase in admission rate across different types of admissions related to OA was not consistent. The highest increase in the admission rate was observed for polyarthrosis (604.6%). Admission rates related to OA were observed to be directly related to age. The highest increase in the admission rate during the study period was for the age group of 15-59 years (102.1%). Admission rate due to OA was higher among females compared to males. Conclusion The increase in admission rates for the various OA-related admissions was not consistent. This study found that the age range of 15 to 59 years experienced the greatest increase in admission rates. Female gender is a high risk factor for OA, especially in women around menopause.}, }
@article {pmid37267326, year = {2023}, author = {Spencer, N and Łukasik, P and Meyer, M and Veloso, C and McCutcheon, JP}, title = {No Transcriptional Compensation for Extreme Gene Dosage Imbalance in Fragmented Bacterial Endosymbionts of Cicadas.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evad100}, pmid = {37267326}, issn = {1759-6653}, abstract = {Bacteria that form long-term intracellular associations with host cells lose many genes, a process that often results in tiny, gene-dense, and stable genomes. Paradoxically, the same evolutionary processes that drive genome reduction and simplification may sometimes cause genome expansion and complexification. A bacterial endosymbiont of cicadas, Hodgkinia cicadicola, exemplifies this paradox. In many cicada species, a single Hodgkinia lineage with a tiny, gene-dense genome has split into several interdependent cell and genome lineages. Each new Hodgkinia lineage encodes a unique subset of the ancestral unsplit genome in a complementary way, such that the collective gene contents of all lineages match the total found in the ancestral single genome. This splitting creates genetically distinct Hodgkinia cells that must function together to carry out basic cellular processes. It also creates a gene dosage problem where some genes are encoded by only a small fraction of cells while others are much more abundant. Here, by sequencing DNA and RNA of Hodgkinia from different cicada species with different amounts of splitting - along with its structurally stable, unsplit partner endosymbiont Sulcia muelleri - we show that Hodgkinia does not transcriptionally compensate to rescue the wildly unbalanced gene and genome ratios that result from lineage splitting. We also find that Hodgkinia has a reduced capacity for basic transcriptional control independent of the splitting process. Our findings reveal another layer of degeneration further pushing the limits of canonical molecular and cell biology in Hodgkinia and may partially explain its propensity to go extinct through symbiont replacement.}, }
@article {pmid37010606, year = {2023}, author = {Chaves, T and Azevedo, &#xc1; and Caldas, IM}, title = {Are lip prints hereditary? A systematic review.}, journal = {International journal of legal medicine}, volume = {137}, number = {4}, pages = {1203-1214}, pmid = {37010606}, issn = {1437-1596}, mesh = {Child ; Humans ; *Lip ; *Parents ; Bibliometrics ; Databases, Factual ; }, abstract = {Hereditary lip prints have been studied by several researchers. However, the literature shows no consensus among the scientific community regarding this topic. Therefore, the aim of this study was to conduct a systematic review to gather evidence to clarify whether the surface structure of lip prints is hereditary and, consequently, if a familial relationship between individuals can be established through the analysis of lip prints. The systematic review was performed following the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines. A bibliographic survey was conducted in PubMed, Scopus, and Web of Science databases, restricted to articles published between 2010 and 2020. Studies were selected according to eligibility criteria, and then the study data were collected. The risk of bias of each study was assessed and applied as additional inclusion or exclusion criteria. The results of the articles eligible for analysis were synthesized by a descriptive approach. In the seven included studies, methodological variations, including the definition of similarity, that contribute to the heterogeneity of results were identified. The data gathered allowed to conclude that there is no strong scientific evidence to support the hypothesis of the existence of heredity in the surface structure of lip prints, since it was not proven that similarities between parents and children occur systematically in all families.}, }
@article {pmid37205491, year = {2023}, author = {Gao, H and Hamp, T and Ede, J and Schraiber, JG and McRae, J and Singer-Berk, M and Yang, Y and Dietrich, A and Fiziev, P and Kuderna, L and Sundaram, L and Wu, Y and Adhikari, A and Field, Y and Chen, C and Batzoglou, S and Aguet, F and Lemire, G and Reimers, R and Balick, D and Janiak, MC and Kuhlwilm, M and Orkin, JD and Manu, S and Valenzuela, A and Bergman, J and Rouselle, M and Silva, FE and Agueda, L and Blanc, J and Gut, M and de Vries, D and Goodhead, I and Harris, RA and Raveendran, M and Jensen, A and Chuma, IS and Horvath, J and Hvilsom, C and Juan, D and Frandsen, P and de Melo, FR and Bertuol, F and Byrne, H and Sampaio, I and Farias, I and do Amaral, JV and Messias, M and da Silva, MNF and Trivedi, M and Rossi, R and Hrbek, T and Andriaholinirina, N and Rabarivola, CJ and Zaramody, A and Jolly, CJ and Phillips-Conroy, J and Wilkerson, G and Abee, C and Simmons, JH and Fernandez-Duque, E and Kanthaswamy, S and Shiferaw, F and Wu, D and Zhou, L and Shao, Y and Zhang, G and Keyyu, JD and Knauf, S and Le, MD and Lizano, E and Merker, S and Navarro, A and Batallion, T and Nadler, T and Khor, CC and Lee, J and Tan, P and Lim, WK and Kitchener, AC and Zinner, D and Gut, I and Melin, A and Guschanski, K and Schierup, MH and Beck, RMD and Umapathy, G and Roos, C and Boubli, JP and Lek, M and Sunyaev, S and O'Donnell, A and Rehm, H and Xu, J and Rogers, J and Marques-Bonet, T and Kai-How Farh, K}, title = {The landscape of tolerated genetic variation in humans and primates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37205491}, abstract = {UNLABELLED: Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.<br><br>ONE SENTENCE SUMMARY: Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.}, }
@article {pmid37265476, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Hammond, J and , }, title = {The genome sequence of the Elbow-stripe Grass-veneer, Agriphila geniculea (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {86}, pmid = {37265476}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Agriphila geniculea (the Elbow-stripe Grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 781.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,132 protein coding genes.}, }
@article {pmid37148512, year = {2023}, author = {Wang, Y}, title = {Ecological risk identification and assessment of land remediation project based on GIS technology.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {27}, pages = {70493-70505}, pmid = {37148512}, issn = {1614-7499}, mesh = {Animals ; Geographic Information Systems ; *Volatile Organic Compounds ; *Environmental Restoration and Remediation ; *Environmental Pollutants ; Risk Assessment ; Technology ; Environmental Monitoring ; }, abstract = {A land remediation project involves the removal of potentially toxic chemicals from a polluted site. Lands abandoned by industry are often contaminated with heavy metals like mercury, lead, chemicals, arsenic, and other toxins like dichlorodiphenyltrichloroethane biphenyls from electronic devices, and volatile organic chemicals (VOCs) from lubricants and chemicals. Risk assessment in environmental settings requires modernized systematic methodologies due to the complexity of today's environmental problems. When people eat, drink, or work in polluted environments, they put their health at risk and may even get cancer. Integrating geospatial information systems (GIS) with pollutant dispersion models makes environmental risk assessment and early warning possible. This research thus presents a GIS-based ecological risk identification and assessment model (GIS-ERIAM) for assessing risk for efficient land rehabilitation. Environmental cleanup sites' catalog information is the source of these details. With satellite imagery, GIS makes it simple to keep an eye on the environment and track the abundance of different types of plants and animals The ecological risk assessment (ERA) model can support recognition and prioritize risk management. By integrating direct and indirect environment interactions, the risk conditions of the whole ecology and its elements have been quantified and demonstrated in the study. The numerical outcomes illustrate that the recommended GIS-ERIAM model improves the performance by 98.9%, risk level prediction by 97.3%, risk classification by 96.4%, and detection of soil degradation ratio of 95.6% compared to other existing methods.}, }
@article {pmid37138127, year = {2023}, author = {Mohamadi, S and Honarmand, M and Ghazanfari, S and Hassanzadeh, R}, title = {Hotspot and accumulated hotspot analysis for assessment of groundwater quality and pollution indices using GIS in the arid region of Iran.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {27}, pages = {69955-69976}, pmid = {37138127}, issn = {1614-7499}, mesh = {Water Quality ; Environmental Monitoring/methods ; Geographic Information Systems ; Iran ; *Groundwater/analysis ; Nitrates/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Because groundwater quality representatives for drinking usage (i.e., Schuler method, Nitrate and Groundwater Quality Index) have been abruptly changing due to extreme events induced by global climate change and over-abstracting, applying an efficient tool for their assessments is vitally important. While hotspot analysis is introduced as an efficient tool concentrating on sharp changes in groundwater quality, it has not been closely examined. Accordingly, this study is an attempt to determine the groundwater quality proxies and assess them through hotspot and accumulated hotspot analyses. To this end, a GIS-based hotspot analysis (HA) applying Getis-Ord Gi* statistics was used. The accumulated hotspot analysis was launched to identify the Groundwater Quality Index (AHA-GQI). Moreover, Schuler method (AHA-SM) was utilized to determine the maximum levels (ML) for the hottest hotspot and the lowest levels (LL) for the coldest cold-spot, and compound levels (CL). The results revealed that a significant correlation (r = 0.8) between GQI and SM was observed. However, the correlation between GQI and nitrate was not significant and the correlation between SM and nitrate was so low (r = 0.298, sig > 0.05). The results also demonstrated that using hotspot analysis on only GQI, the correlation between GQI and SM increased from 0.8 to 0.856, while using hotspot analysis on both GQI and SM increased the correlation to 0.945. Likewise, when GQI was subjected to hotspot analysis and SM underwent accumulated hotspot analysis (i.e., AHA-SM (ML)), the correlation degree increased to the highest extent (i.e., 0.958), indicating the usefulness of including the hotspot analysis and accumulated hotspot analysis in the evaluation of groundwater quality.}, }
@article {pmid37263997, year = {2023}, author = {Duncanson, L and Liang, M and Leitold, V and Armston, J and Krishna Moorthy, SM and Dubayah, R and Costedoat, S and Enquist, BJ and Fatoyinbo, L and Goetz, SJ and Gonzalez-Roglich, M and Merow, C and Roehrdanz, PR and Tabor, K and Zvoleff, A}, title = {The effectiveness of global protected areas for climate change mitigation.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2908}, pmid = {37263997}, issn = {2041-1723}, abstract = {Forests play a critical role in stabilizing Earth's climate. Establishing protected areas (PAs) represents one approach to forest conservation, but PAs were rarely created to mitigate climate change. The global impact of PAs on the carbon cycle has not previously been quantified due to a lack of accurate global-scale carbon stock maps. Here we used ~412 million lidar samples from NASA's GEDI mission to estimate a total PA aboveground carbon (C) stock of 61.43 Gt (+/- 0.31), 26% of all mapped terrestrial woody C. Of this total, 9.65 + /- 0.88 Gt of additional carbon was attributed to PA status. These higher C stocks are primarily from avoided emissions from deforestation and degradation in PAs compared to unprotected forests. This total is roughly equivalent to one year of annual global fossil fuel emissions. These results underscore the importance of conservation of high biomass forests for avoiding carbon emissions and preserving future sequestration.}, }
@article {pmid37116451, year = {2023}, author = {Barnea, O and Cohen, N and Hindi, I and Katz, C}, title = {Noticing the unutilized resource of siblinghood: Key conclusions from a scoping review about siblings in out-of-home placements.}, journal = {Child abuse &amp; neglect}, volume = {141}, number = {}, pages = {106192}, doi = {10.1016/j.chiabu.2023.106192}, pmid = {37116451}, issn = {1873-7757}, mesh = {Child ; Humans ; *Siblings ; *Child Welfare ; Foster Home Care/methods ; Databases, Factual ; }, abstract = {BACKGROUND: Sibling bonds are often the most enduring relationship in an individual's life span. The out-of-home placement of siblings is widespread and may significantly influence children's journeys and wellbeing.<br><br>OBJECTIVE: The current scoping literature review was designed to characterize and analyze the existing knowledge regarding siblings in out-of-home placements.<br><br>METHOD: Key databases were explored using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, which identified 33 studies relevant to the current study's focus. The studies used quantitative, qualitative, and mixed methods and included a variety of out-of-home placement settings and sample characteristics.<br><br>RESULTS: Utilizing thematic analysis, the findings addressed three main themes: the sibling bond as a contributor to the wellbeing of children in out-of-home placements, trends in sibling placement, and difficulties in maintaining the sibling bond in out-of-home placements regarding micro, meso and exo factors.<br><br>CONCLUSION: A key conclusion from the review is that the welfare system struggles to address a child as a part of a sibling group and an extensive and multilayered relational network; hence, siblinghood is an unutilized resource in out-of-home placements. Future directions for practice, policy and research are included and discussed.}, }
@article {pmid36846939, year = {2023}, author = {Barrile, GM and Augustine, DJ and Porensky, LM and Duchardt, CJ and Shoemaker, KT and Hartway, CR and Derner, JD and Hunter, EA and Davidson, AD}, title = {A big data-model integration approach for predicting epizootics and population recovery in a keystone species.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {33}, number = {4}, pages = {e2827}, doi = {10.1002/eap.2827}, pmid = {36846939}, issn = {1051-0761}, mesh = {Animals ; *Ecosystem ; Big Data ; *Yersinia pestis ; Sciuridae ; Climate ; Animals, Wild ; }, abstract = {Infectious diseases pose a significant threat to global health and biodiversity. Yet, predicting the spatiotemporal dynamics of wildlife epizootics remains challenging. Disease outbreaks result from complex nonlinear interactions among a large collection of variables that rarely adhere to the assumptions of parametric regression modeling. We adopted a nonparametric machine learning approach to model wildlife epizootics and population recovery, using the disease system of colonial black-tailed prairie dogs (BTPD, Cynomys ludovicianus) and sylvatic plague as an example. We synthesized colony data between 2001 and 2020 from eight USDA Forest Service National Grasslands across the range of BTPDs in central North America. We then modeled extinctions due to plague and colony recovery of BTPDs in relation to complex interactions among climate, topoedaphic variables, colony characteristics, and disease history. Extinctions due to plague occurred more frequently when BTPD colonies were spatially clustered, in closer proximity to colonies decimated by plague during the previous year, following cooler than average temperatures the previous summer, and when wetter winter/springs were preceded by drier summers/falls. Rigorous cross-validations and spatial predictions indicated that our final models predicted plague outbreaks and colony recovery in BTPD with high accuracy (e.g., AUC generally >0.80). Thus, these spatially explicit models can reliably predict the spatial and temporal dynamics of wildlife epizootics and subsequent population recovery in a highly complex host-pathogen system. Our models can be used to support strategic management planning (e.g., plague mitigation) to optimize benefits of this keystone species to associated wildlife communities and ecosystem functioning. This optimization can reduce conflicts among different landowners and resource managers, as well as economic losses to the ranching industry. More broadly, our big data-model integration approach provides a general framework for spatially explicit forecasting of disease-induced population fluctuations for use in natural resource management decision-making.}, }
@article {pmid35549599, year = {2023}, author = {Truong, M and Yeganeh, L and Cartwright, A and Ward, E and Ibrahim, J and Cuschieri, D and Dawson, M and Bugeja, L}, title = {Domestic/Family Homicide: A Systematic Review of Empirical Evidence.}, journal = {Trauma, violence &amp; abuse}, volume = {24}, number = {3}, pages = {1908-1928}, doi = {10.1177/15248380221082084}, pmid = {35549599}, issn = {1552-8324}, mesh = {Humans ; United States ; *Homicide ; Risk Factors ; Sexual Partners ; Databases, Factual ; Protective Factors ; *Intimate Partner Violence ; }, abstract = {BACKGROUND: Domestic/family homicide (D/FH) is a global social, economic and public health problem. To date, the research studies into risk factors associated with D/FH has largely focused on intimate partner homicide (IPH). A more contemporary approach recognizes that D/FH extends beyond the intimate partner relationship. This systematic review sought to identify and quantify the individual, relationship, community and societal factors in the empirical evidence literature on D/FH.<br><br>METHODS: Eight electronic databases were searched from January 1999 to December 2020. Published journal articles on studies of D/FH were included if the study included victims and/or perpetrator of D/FH, reported risk and/or protective factors associated with D/FH, reported primary data and was published in English. Factors were descriptively synthesized by the categories of the social ecological model and D/FH sub-type.<br><br>RESULTS: Three hundred and forty published articles met the inclusion criteria. From 1999 to 2020 the number of articles on D/FH increased globally from 10 to 40 respectively, declining to 23 in 2020. Almost half of the articles examined populations located in the Americas (160, 47.1%), predominately the United States and the majority of articles used quantitative designs (277, 81.5%). The forms of homicide more commonly studied were intimate partner (171, 50.3%), and filicide (98, 28.8%). Approximately 90% of articles reported individual victim and perpetrator factors, 64.7% examined relationship factors, 17.9% examined community factors and 15.6% examined societal factors.<br><br>CONCLUSION: To inform universal and targeted D/FH elimination and prevention strategies, more research across different regions and a greater emphasis on community and societal-level factors is needed.}, }
@article {pmid37262156, year = {2023}, author = {Gao, H and Hamp, T and Ede, J and Schraiber, JG and McRae, J and Singer-Berk, M and Yang, Y and Dietrich, ASD and Fiziev, PP and Kuderna, LFK and Sundaram, L and Wu, Y and Adhikari, A and Field, Y and Chen, C and Batzoglou, S and Aguet, F and Lemire, G and Reimers, R and Balick, D and Janiak, MC and Kuhlwilm, M and Orkin, JD and Manu, S and Valenzuela, A and Bergman, J and Rousselle, M and Silva, FE and Agueda, L and Blanc, J and Gut, M and de Vries, D and Goodhead, I and Harris, RA and Raveendran, M and Jensen, A and Chuma, IS and Horvath, JE and Hvilsom, C and Juan, D and Frandsen, P and de Melo, FR and Bertuol, F and Byrne, H and Sampaio, I and Farias, I and do Amaral, JV and Messias, M and da Silva, MNF and Trivedi, M and Rossi, R and Hrbek, T and Andriaholinirina, N and Rabarivola, CJ and Zaramody, A and Jolly, CJ and Phillips-Conroy, J and Wilkerson, G and Abee, C and Simmons, JH and Fernandez-Duque, E and Kanthaswamy, S and Shiferaw, F and Wu, D and Zhou, L and Shao, Y and Zhang, G and Keyyu, JD and Knauf, S and Le, MD and Lizano, E and Merker, S and Navarro, A and Bataillon, T and Nadler, T and Khor, CC and Lee, J and Tan, P and Lim, WK and Kitchener, AC and Zinner, D and Gut, I and Melin, A and Guschanski, K and Schierup, MH and Beck, RMD and Umapathy, G and Roos, C and Boubli, JP and Lek, M and Sunyaev, S and O'Donnell-Luria, A and Rehm, HL and Xu, J and Rogers, J and Marques-Bonet, T and Farh, KK}, title = {The landscape of tolerated genetic variation in humans and primates.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6648}, pages = {eabn8153}, doi = {10.1126/science.abn8197}, pmid = {37262156}, issn = {1095-9203}, abstract = {Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.}, }
@article {pmid37258861, year = {2023}, author = {Abdelsalam, NA and Elshora, H and El-Hadidi, M}, title = {Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {133-174}, pmid = {37258861}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Ecology ; Computational Biology/methods ; Data Analysis ; }, abstract = {Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the potential of a myriad of ecosystems and biomes. Metagenomics studies the composition and functions of microbial communities and paves the way to multiple applications in medicine, industry, and ecology. Nonetheless, the immense amount of sequencing data of metagenomics research and the few user-friendly analysis tools and pipelines carry a new challenge to the data analysis.Web-based bioinformatics tools are now being developed to facilitate the analysis of complex metagenomic data without prior knowledge of any programming languages or special installation. Specialized web tools help answer researchers' main questions on the taxonomic classification, functional capabilities, discrepancies between two ecosystems, and the probable functional correlations between the members of a specific microbial community. With an Internet connection and a few clicks, researchers can conveniently and efficiently analyze the metagenomic datasets, summarize results, and visualize key information on the composition and the functional potential of metagenomic samples under study. This chapter provides a simple guide to a few of the fundamental web-based services used for metagenomic data analyses, such as BV-BRC, RDP, MG-RAST, MicrobiomeAnalyst, METAGENassist, and MGnify.}, }
@article {pmid37258857, year = {2023}, author = {Wang, D}, title = {Metagenomics Databases for Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {55-67}, pmid = {37258857}, issn = {1940-6029}, mesh = {Phylogeny ; *Metagenomics ; Bacteria/genetics ; Databases, Genetic ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).}, }
@article {pmid37255989, year = {2023}, author = {Pauley, E and Drake, TM and Griffith, DM and Sigfrid, L and Lone, NI and Harrison, EM and Baillie, JK and Scott, JT and Walsh, TS and Semple, MG and Docherty, AB and , }, title = {Recovery from Covid-19 critical illness: A secondary analysis of the ISARIC4C CCP-UK cohort study and the RECOVER trial.}, journal = {Journal of the Intensive Care Society}, volume = {24}, number = {2}, pages = {162-169}, pmid = {37255989}, issn = {1751-1437}, abstract = {BACKGROUND: We aimed to compare the prevalence and severity of fatigue in survivors of Covid-19 versus non-Covid-19 critical illness, and to explore potential associations between baseline characteristics and worse recovery.<br><br>METHODS: We conducted a secondary analysis of two prospectively collected datasets. The population included was 92 patients who received invasive mechanical ventilation (IMV) with Covid-19, and 240 patients who received IMV with non-Covid-19 illness before the pandemic. Follow-up data were collected post-hospital discharge using self-reported questionnaires. The main outcome measures were self-reported fatigue severity and the prevalence of severe fatigue (severity >7/10) 3 and 12-months post-hospital discharge.<br><br>RESULTS: Covid-19 IMV-patients were significantly younger with less prior comorbidity, and more males, than pre-pandemic IMV-patients. At 3-months, the prevalence (38.9% [7/18] vs. 27.1% [51/188]) and severity (median 5.5/10 vs 5.0/10) of fatigue were similar between the Covid-19 and pre-pandemic populations, respectively. At 6-months, the prevalence (10.3% [3/29] vs. 32.5% [54/166]) and severity (median 2.0/10 vs. 5.7/10) of fatigue were less in the Covid-19 cohort. In the total sample of IMV-patients included (i.e. all Covid-19 and pre-pandemic patients), having Covid-19 was significantly associated with less severe fatigue (severity <7/10) after adjusting for age, sex and prior comorbidity (adjusted OR 0.35 (95%CI 0.15-0.76, p=0.01).<br><br>CONCLUSION: Fatigue may be less severe after Covid-19 than after other critical illness.}, }
@article {pmid37253577, year = {2023}, author = {Lee, K and McMorris, BJ and Chi, CL and Looman, WS and Burns, MK and Delaney, CW}, title = {Using data-driven analytics and ecological systems theory to identify risk and protective factors for school absenteeism among secondary students.}, journal = {Journal of school psychology}, volume = {98}, number = {}, pages = {148-180}, doi = {10.1016/j.jsp.2023.03.002}, pmid = {37253577}, issn = {1873-3506}, mesh = {Adolescent ; Humans ; Protective Factors ; *Absenteeism ; *Students ; Schools ; Forecasting ; }, abstract = {Chronic absenteeism is an administrative term defining extreme failure for students to be present at school, which can have devastating long-term impacts on students. Although numerous prior studies have investigated associated variables and interventions, there are few studies that utilize both theory-driven and data-informed approaches to investigate absenteeism. The current study applied data-driven machine learning techniques, grounded in "The Kids and Teens at School" (KiTeS) theoretical framework, to student-level data (N = 121,005) to identify risk and protective variables that are highly associated with school absences. A total of 18 risk and protective variables were identified; all 18 variables were characteristics of the microsystem or mesosystem, emphasizing school absences' proximity to variables within inner ecological systems rather than the exosystem or macrosystem. Implications for future studies and health infrastructure are discussed.}, }
@article {pmid37253238, year = {2023}, author = {Borg, JM and Buskell, A and Kapitany, R and Powers, ST and Reindl, E and Tennie, C}, title = {Evolved Open-Endedness in Cultural Evolution: A New Dimension in Open-Ended Evolution Research.}, journal = {Artificial life}, volume = {}, number = {}, pages = {1-22}, doi = {10.1162/artl_a_00406}, pmid = {37253238}, issn = {1530-9185}, abstract = {The goal of Artificial Life research, as articulated by Chris Langton, is "to contribute to theoretical biology by locating life-as-we-know-it within the larger picture of life-as-it-could-be." The study and pursuit of open-ended evolution in artificial evolutionary systems exemplify this goal. However, open-ended evolution research is hampered by two fundamental issues: the struggle to replicate open-endedness in an artificial evolutionary system and our assumption that we only have one system (genetic evolution) from which to draw inspiration. We argue not only that cultural evolution should be seen as another real-world example of an open-ended evolutionary system but that the unique qualities seen in cultural evolution provide us with a new perspective from which we can assess the fundamental properties of, and ask new questions about, open-ended evolutionary systems, especially with regard to evolved open-endedness and transitions from bounded to unbounded evolution. Here we provide an overview of culture as an evolutionary system, highlight the interesting case of human cultural evolution as an open-ended evolutionary system, and contextualize cultural evolution by developing a new framework of (evolved) open-ended evolution. We go on to provide a set of new questions that can be asked once we consider cultural evolution within the framework of open-ended evolution and introduce new insights that we may be able to gain about evolved open-endedness as a result of asking these questions.}, }
@article {pmid37252922, year = {2023}, author = {Hassard, F and Vu, M and Rahimzadeh, S and Castro-Gutierrez, V and Stanton, I and Burczynska, B and Wildeboer, D and Baio, G and Brown, MR and Garelick, H and Hofman, J and Kasprzyk-Hordern, B and Majeed, A and Priest, S and Denise, H and Khalifa, M and Bassano, I and Wade, MJ and Grimsley, J and Lundy, L and Singer, AC and Di Cesare, M}, title = {Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286259}, pmid = {37252922}, issn = {1932-6203}, abstract = {BACKGROUND: Schools are high-risk settings for infectious disease transmission. Wastewater monitoring for infectious diseases has been used to identify and mitigate outbreaks in many near-source settings during the COVID-19 pandemic, including universities and hospitals but less is known about the technology when applied for school health protection. This study aimed to implement a wastewater surveillance system to detect SARS-CoV-2 and other public health markers from wastewater in schools in England.<br><br>METHODS: A total of 855 wastewater samples were collected from 16 schools (10 primary, 5 secondary and 1 post-16 and further education) over 10 months of school term time. Wastewater was analysed for SARS-CoV-2 genomic copies of N1 and E genes by RT-qPCR. A subset of wastewater samples was sent for genomic sequencing, enabling determination of the presence of SARS-CoV-2 and emergence of variant(s) contributing to COVID-19 infections within schools. In total, >280 microbial pathogens and >1200 AMR genes were screened using RT-qPCR and metagenomics to consider the utility of these additional targets to further inform on health threats within the schools.<br><br>RESULTS: We report on wastewater-based surveillance for COVID-19 within English primary, secondary and further education schools over a full academic year (October 2020 to July 2021). The highest positivity rate (80.4%) was observed in the week commencing 30th November 2020 during the emergence of the Alpha variant, indicating most schools contained people who were shedding the virus. There was high SARS-CoV-2 amplicon concentration (up to 9.2x106 GC/L) detected over the summer term (8th June - 6th July 2021) during Delta variant prevalence. The summer increase of SARS-CoV-2 in school wastewater was reflected in age-specific clinical COVID-19 cases. Alpha variant and Delta variant were identified in the wastewater by sequencing of samples collected from December to March and June to July, respectively. Lead/lag analysis between SARS-CoV-2 concentrations in school and WWTP data sets show a maximum correlation between the two-time series when school data are lagged by two weeks. Furthermore, wastewater sample enrichment coupled with metagenomic sequencing and rapid informatics enabled the detection of other clinically relevant viral and bacterial pathogens and AMR.<br><br>CONCLUSIONS: Passive wastewater monitoring surveillance in schools can identify cases of COVID-19. Samples can be sequenced to monitor for emerging and current variants of concern at the resolution of school catchments. Wastewater based monitoring for SARS-CoV-2 is a useful tool for SARS-CoV-2 passive surveillance and could be applied for case identification and containment, and mitigation in schools and other congregate settings with high risks of transmission. Wastewater monitoring enables public health authorities to develop targeted prevention and education programmes for hygiene measures within undertested communities across a broad range of use cases.}, }
@article {pmid37247155, year = {2023}, author = {Wang, Y and Lin, C and Wang, H and Wang, W and Wang, S and Zheng, R}, title = {Implementation of pollution source assessment and treatment strategy for plateau railway construction in China: an AHP-cloud model approach.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {6}, pages = {749}, pmid = {37247155}, issn = {1573-2959}, mesh = {*Analytic Hierarchy Process ; *Sewage ; Environmental Monitoring ; Environmental Pollution ; China ; }, abstract = {During the construction process of railways in the plateau region, various types of pollution sources can have serious or even irreversible impacts on the plateau ecology. To address pollution source treatment during the construction process, protect the ecological environment along the railway, and maintain the ecological balance, we collected geological and environmental data and analyzed the influencing factors of pollution sources. Taking sewage as the main research subject, we propose a new method based on the Analytic Hierarchy Process (AHP)-cloud model to classify the pollution source treatment level, establish an index system, and select the ecological environment level, sewage rate, and pollutant characteristics as the three main influencing factors. Finally, we divide the pollution source treatment level into I, II, and III, corresponding to V1 = {I-level} = {high impact}, V2 = {II-level} = {moderate impact}, and V3 = {III-level} = {low impact}. Based on the comprehensive factor weight analysis and the field engineering conditions of the studied railway in the western plateau of China, we classify the pollution source treatment level of six tunnels and propose treatment suggestions for each level. To advance the efficient implementation of environmental protection during the construction of the plateau railway, we propose three policy recommendations that can positively contribute to environmental protection and green development. This work provides theoretical and technical guidance for the treatment of pollution sources in the construction of the plateau railway, which also serves as a significant reference for other similar projects.}, }
@article {pmid37251658, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Lees, D and , }, title = {The genome sequence of the long-horned flat-body, Carcina quercana (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {16}, pmid = {37251658}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Carcina quercana (the long-horned flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 409 megabases in span. Most of the assembly (99.96%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,108 protein coding genes.}, }
@article {pmid37251651, year = {2023}, author = {Dhellemmes, F and Aspillaga, E and Monk, CT}, title = {ATfiltR: A solution for managing and filtering detections from passive acoustic telemetry data.}, journal = {MethodsX}, volume = {10}, number = {}, pages = {102222}, pmid = {37251651}, issn = {2215-0161}, abstract = {Acoustic telemetry is a popular and cost-efficient method for tracking the movements of animals in the aquatic ecosystem. But data acquired via acoustic telemetry often contains spurious detections that must be identified and excluded by researchers to ensure valid results. Such data management is difficult as the amount of data collected often surpasses the capabilities of simple spreadsheet applications. ATfiltR is an open-source package programmed in R that allows users to integrate all telemetry data collected into a single file, to conditionally attribute animal data and location data to detections and to filter spurious detections based on customizable rules. Such tool will likely be useful to new researchers in acoustic telemetry and enhance results reproducibility.•ATfiltR compiles telemetry files and identifies and stores all data that was collected outside of your study period (e.g. when your receivers were on land for servicing) elsewhere.•As spurious detections are unlikely to appear sequentially in the data, ATfiltR finds all detections that occurred only once (per receiver or in the whole array) within a user-designated time period and stores them elsewhere.•ATfiltR identifies detections that are impossible given the animals' swimming speeds and the receivers detection range and stores them elsewhere.}, }
@article {pmid37244965, year = {2023}, author = {Mattalia, G and Svanberg, I and Ståhlberg, S and Kuznetsova, N and Prūse, B and Kolosova, V and Aziz, MA and Kalle, R and Sõukand, R}, title = {Outdoor activities foster local plant knowledge in Karelia, NE Europe.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8627}, pmid = {37244965}, issn = {2045-2322}, support = {714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; 714874/ERC_/European Research Council/International ; }, mesh = {Humans ; Adult ; Child ; Europe ; Finland/epidemiology ; *Plants, Edible ; *Allergens ; Food ; }, abstract = {Wild edible plants, particularly berries, are relevant nutritional elements in the Nordic countries. In contrast to decreasing global trends, approximately 60% of the Finnish population is actively involved in (berry) foraging. We conducted 67 interviews with Finns and Karelians living in Finnish Karelia to: (a) detect the use of wild edible plants, (b) compare those results with the published data about neighbouring Russian Karelians, and (c) document the sources of local plant knowledge. The results revealed three main findings. First, we observed a similarity in wild food plant knowledge among Karelians and Finns from Karelia. Second, we detected divergences in wild food plant knowledge among Karelians living on both sides of the Finnish-Russian border. Third, the sources of local plant knowledge include vertical transmission, acquisition through literary sources, acquisition from "green" nature shops promoting healthy lifestyles, childhood foraging activities performed during the famine period following WWII, and outdoor recreational activities. We argue that the last two types of activities in particular may have influenced knowledge and connectedness with the surrounding environment and its resources at a stage of life that is crucial for shaping adult environmental behaviours. Future research should address the role of outdoor activities in maintaining (and possibly enhancing) local ecological knowledge in the Nordic countries.}, }
@article {pmid37243228, year = {2023}, author = {Tokito, T and Kido, T and Muramatsu, K and Tokutsu, K and Okuno, D and Yura, H and Takemoto, S and Ishimoto, H and Takazono, T and Sakamoto, N and Obase, Y and Ishimatsu, Y and Fujino, Y and Yatera, K and Fushimi, K and Matsuda, S and Mukae, H}, title = {Impact of Administering Intravenous Azithromycin within 7 Days of Hospitalization for Influenza Virus Pneumonia: A Propensity Score Analysis Using a Nationwide Administrative Database.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, pmid = {37243228}, issn = {1999-4915}, mesh = {Humans ; Azithromycin/therapeutic use ; *Influenza, Human/drug therapy ; Propensity Score ; Retrospective Studies ; *Pneumonia/drug therapy ; Hospitalization ; *Respiratory Insufficiency ; *Orthomyxoviridae ; }, abstract = {The potential antimicrobial and anti-inflammatory effectiveness of azithromycin against severe influenza is yet unclear. We retrospectively investigated the effect of intravenous azithromycin administration within 7 days of hospitalization in patients with influenza virus pneumonia and respiratory failure. Using Japan's national administrative database, we enrolled and classified 5066 patients with influenza virus pneumonia into severe, moderate, and mild groups based on their respiratory status within 7 days of hospitalization. The primary endpoints were total, 30-day, and 90-day mortality rates. The secondary endpoints were the duration of intensive-care unit management, invasive mechanical ventilation, and hospital stay. The inverse probability of the treatment weighting method with estimated propensity scores was used to minimize data collection bias. Use of intravenous azithromycin was proportional to the severity of respiratory failure (mild: 1.0%, moderate: 3.1%, severe: 14.8%). In the severe group, the 30-day mortality rate was significantly lower with azithromycin (26.49% vs. 36.65%, p = 0.038). In the moderate group, the mean duration of invasive mechanical ventilation after day 8 was shorter with azithromycin; there were no significant differences in other endpoints between the severe and moderate groups. These results suggest that intravenous azithromycin has favorable effects in patients with influenza virus pneumonia using mechanical ventilation or oxygen.}, }
@article {pmid37240180, year = {2023}, author = {Lafleur, S and Bodein, A and Mbuya Malaïka Mutombo, J and Mathieu, A and Joly Beauparlant, C and Minne, X and Chandad, F and Droit, A and Houde, VP}, title = {Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, pmid = {37240180}, issn = {1422-0067}, mesh = {Humans ; Multiomics ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; U937 Cells ; *Periodontitis/microbiology ; *Microbiota/genetics ; Bacteria/metabolism ; Cytokines/metabolism ; RNA-Binding Proteins ; }, abstract = {Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.}, }
@article {pmid37172351, year = {2023}, author = {Zerouali, B and Santos, CAG and do Nascimento, TVM and Silva, RMD}, title = {A cloud-integrated GIS for forest cover loss and land use change monitoring using statistical methods and geospatial technology over northern Algeria.}, journal = {Journal of environmental management}, volume = {341}, number = {}, pages = {118029}, doi = {10.1016/j.jenvman.2023.118029}, pmid = {37172351}, issn = {1095-8630}, mesh = {Humans ; *Geographic Information Systems ; *Conservation of Natural Resources/methods ; Algeria ; Agriculture ; Environmental Monitoring/methods ; Technology ; }, abstract = {Over the last two decades, forest cover has experienced significant impacts from fires and deforestation worldwide due to direct human activities and climate change. This paper assesses trends in forest cover loss and land use and land cover changes in northern Algeria between 2000 and 2020 using datasets extracted from Google Earth Engine (GEE), such as the Hanssen Global Forest Change and MODIS Land Cover Type products (MCD12Q1). Classification was performed using the pixel-based supervised machine-learning algorithm called Random Forest (RF). Trends were analyzed using methods such as Mann-Kendall and Sen. The study area comprises 17 basins with high rainfall variability. The results indicated that the forest area decreased by 64.96%, from 3718 to 1266 km[2], during the 2000-2020 period, while the barren area increased by 40%, from 134,777 to 188,748 km[2]. The findings revealed that the Constantinois-Seybousse-Mellegue hydrographic basin was the most affected by deforestation and cover loss, exceeding 50% (with an area of 1018 km[2]), while the Seybouse River basin experienced the highest percentage of cover loss at 40%. Nonparametric tests showed that seven river basins (41%) had significantly increasing trends of forest cover loss. According to the obtained results, the forest loss situation in Algeria, especially in the northeastern part, is very alarming and requires an exceptional and urgent plan to protect forests and the ecological system against wildfires and climate change. The study provides a diagnosis that should encourage better protection and management of forest cover in Algeria.}, }
@article {pmid37232406, year = {2023}, author = {Watson, SJ and Aguirre, BA and Wright, AJ}, title = {Soil versus atmospheric drought: A test case of plant functional trait responses.}, journal = {Ecology}, volume = {}, number = {}, pages = {e4109}, doi = {10.1002/ecy.4109}, pmid = {37232406}, issn = {1939-9170}, abstract = {Climate change alters mean global surface temperatures, precipitation regimes, and atmospheric moisture. Resultant drought affects the composition and diversity of terrestrial ecosystems worldwide. To date, there are no assessments of the combined impacts of reduced precipitation and atmospheric drying on functional trait distributions of any species in an outdoor experiment. Here, we examined whether soil and atmospheric drought affect the functional traits of a focal grass species (Poa secunda) growing in monoculture and 8-species grass communities in outdoor mesocosms. We focused on specific leaf area (SLA), leaf area, stomatal density, root:shoot ratio, and fine root:coarse root ratio responses. Leaf area and overall growth were reduced with soil drying. Root:shoot ratio only increased for P. secunda growing in monoculture under combined atmospheric and soil drought. Plant energy allocation strategy (measured using principal components) differed when P. secunda was grown in combined soil and atmospheric drought conditions compared with soil drought alone. Given a lack of outdoor manipulations of this kind, our results emphasize the importance of atmospheric drying on functional trait responses more broadly. We suggest that drought methods focused purely on soil water inputs may be imprecisely predicting drought effects on other terrestrial organisms as well (other plants, arthropods, and higher trophic levels). This article is protected by copyright. All rights reserved.}, }
@article {pmid37226845, year = {2023}, author = {Bizzotto, E and Bonetto, A and Marcomini, A and Vighi, M}, title = {Environmental exposure and ecotoxicological properties of a new generation fluorosurfactant (cC6O4): A comparison with selected legacy perfluoroalkyl acids (PFAA).}, journal = {Integrated environmental assessment and management}, volume = {}, number = {}, pages = {}, doi = {10.1002/ieam.4794}, pmid = {37226845}, issn = {1551-3793}, abstract = {Cyclic C6O4 (cC6O4, CAS number 1190931-27-1) is a new generation polyfluorinated alkyl substance (PFAS) used as polymerisation aid in the synthesis of fluoropolymers, produced in Italy since 2011. A review of the properties of cC6O4, focused on environmental distribution and ecotoxicology, was conducted. EQC model was applied, using default environmental scenarios, to estimate environmental distribution and fate. In a situation of static thermodynamic equilibrium in a closed system (level I) cC6O4 distributes mainly to water (97.6%) and in a minor amount to soil (2.3%). In a more realistic scenario (level III), with dynamic condition in an open system, with advection in air and water and with equal emissions in air and water, the major amount of the compound is transported through water advection. Monitoring data, mainly referred to surface and groundwater, are available for water bodies close to the production sites (maximum measured concentration 52 μg/L) as well as for a wider area in the river Po watershed with concentrations generally lower than 1 μg/L. Few values are also available for concentration in biota. Effect data indicate low toxicity on all tested organisms with NOEC values always higher than the maximum concentrations tested (100 mg/L for acute tests). Bioaccumulation potential is also very low. A comparison with selected widely used PFAS with five to eight C atoms indicate that cC6O4 is substantially less dangerous to aquatic organisms. At the time being, an ecological risk for the aquatic ecosystem may be excluded even in directly exposed ecosystems. However, for a complete assessment of the suitability of cC6O4 as substitute of other PFAS (namely PFOA), more comprehensive chronic experiments are necessary, to produce realistic NOECs, as well as higher tier experiments (e.g., mesocosms) capable to provide ecologically relevant endpoints. Moreover, a more accurate evaluation of the environmental persistence would be necessary.}, }
@article {pmid37226152, year = {2023}, author = {Bakó, C and Balázs, VL and Kerekes, E and Kocsis, B and Nagy, DU and Szabó, P and Micalizzi, G and Mondello, L and Krisch, J and Pethő, D and Horváth, G}, title = {Flowering phenophases influence the antibacterial and anti-biofilm effects of Thymus vulgaris L. essential oil.}, journal = {BMC complementary medicine and therapies}, volume = {23}, number = {1}, pages = {168}, pmid = {37226152}, issn = {2662-7671}, mesh = {*Oils, Volatile/pharmacology ; *Thymus Plant ; Gas Chromatography-Mass Spectrometry ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: Essential oils are becoming increasingly popular in medicinal applications because of their antimicrobial effect. Thymus vulgaris L. (Lamiaceae) is a well-known and widely cultivated medicinal plant, which is used as a remedy for cold, cough and gastrointestinal symptoms. Essential oil content of thyme is responsible for its antimicrobial activity, however, it has been reported that the chemical composition of essential oils influences its biological activity. In order to explore flowering phenophases influence on the chemical composition of thyme essential oil and its antibacterial and anti-biofilm activity, plant materials were collected at the beginning of flowering, in full bloom and at the end of flowering periods in 2019.<br><br>METHODS: Essential oils from fresh and dried plant materials were distilled and analyzed with gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detection (GC-FID). The antibacterial activity was performed by broth microdilution and thin layer chromatography-direct bioautography (TLC-DB) assays and the anti-biofilm effect by crystal violet assay, respectively. Scanning electron microscopy was applied to illustrate the cellular changes of bacterial cells after essential oil treatment.<br><br>RESULTS: Thymol (52.33-62.46%) was the main component in the thyme essential oils. Thyme oil distilled from fresh plant material and collected at the beginning of flowering period exerted the highest antibacterial and anti-biofilm activity against Haemophilus influenzae, H. parainfluenzae and Pseudomonas aeruginosa.<br><br>CONCLUSION: The different flowering periods of Thymus vulgaris influence the antibacterial and anti-biofilm activity of its essential oils, therefore, the collection time has to be taken into consideration and not only the full bloom, but the beginning of flowering period may provide biological active thyme essential oil.}, }
@article {pmid37225998, year = {2023}, author = {Tao, F and Huang, Y and Hungate, BA and Manzoni, S and Frey, SD and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Jiang, L and Lehmann, J and Wang, YP and Houlton, BZ and Ahrens, B and Mishra, U and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Microbial carbon use efficiency promotes global soil carbon storage.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37225998}, issn = {1476-4687}, abstract = {Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.}, }
@article {pmid37225767, year = {2023}, author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Lacombe, B and Le Roux, X and Perrier, L and Sales-Mabily, L and Laumond, M and Vinyeta, M and Moulin, P and Beurier, G and Rouan, L and Cornet, D and Vasseur, F}, title = {AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {314}, pmid = {37225767}, issn = {2052-4463}, mesh = {Adaptation, Physiological ; *Arabidopsis/genetics ; Biological Evolution ; Databases, Factual ; Plant Leaves ; }, abstract = {Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.}, }
@article {pmid37224178, year = {2023}, author = {Passmore, S and Barth, W and Greenhill, SJ and Quinn, K and Sheard, C and Argyriou, P and Birchall, J and Bowern, C and Calladine, J and Deb, A and Diederen, A and Metsäranta, NP and Araujo, LH and Schembri, R and Hickey-Hall, J and Honkola, T and Mitchell, A and Poole, L and Rácz, PM and Roberts, SG and Ross, RM and Thomas-Colquhoun, E and Evans, N and Jordan, FM}, title = {Kinbank: A global database of kinship terminology.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0283218}, pmid = {37224178}, issn = {1932-6203}, mesh = {Humans ; Female ; Male ; *Sexism ; *Anthropology ; Databases, Factual ; Family ; Interdisciplinary Studies ; }, abstract = {For a single species, human kinship organization is both remarkably diverse and strikingly organized. Kinship terminology is the structured vocabulary used to classify, refer to, and address relatives and family. Diversity in kinship terminology has been analyzed by anthropologists for over 150 years, although recurrent patterning across cultures remains incompletely explained. Despite the wealth of kinship data in the anthropological record, comparative studies of kinship terminology are hindered by data accessibility. Here we present Kinbank, a new database of 210,903 kinterms from a global sample of 1,229 spoken languages. Using open-access and transparent data provenance, Kinbank offers an extensible resource for kinship terminology, enabling researchers to explore the rich diversity of human family organization and to test longstanding hypotheses about the origins and drivers of recurrent patterns. We illustrate our contribution with two examples. We demonstrate strong gender bias in the phonological structure of parent terms across 1,022 languages, and we show that there is no evidence for a coevolutionary relationship between cross-cousin marriage and bifurcate-merging terminology in Bantu languages. Analysing kinship data is notoriously challenging; Kinbank aims to eliminate data accessibility issues from that challenge and provide a platform to build an interdisciplinary understanding of kinship.}, }
@article {pmid37224319, year = {2022}, author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and ,  and ,  and ,  and Wahlberg, N and , }, title = {The genome sequence of the high brown fritillary, Fabriciana adippe (Dennis &amp; Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {298}, pmid = {37224319}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Fabriciana adippe (the high brown fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 485 megabases in span. Most of the assembly (99.98%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.1 kilobases in length. Gene annotation of this assembly in Ensembl identified 13,536 protein coding genes.}, }
@article {pmid37221042, year = {2023}, author = {Chaudhary, S and Wu, Y and Strongman, D and Wang, Y}, title = {CIGAF-a database and interactive platform for insect-associated trichomycete fungi.}, journal = {Database : the journal of biological databases and curation}, volume = {2023}, number = {}, pages = {}, doi = {10.1093/database/baad038}, pmid = {37221042}, issn = {1758-0463}, mesh = {Animals ; *Insecta ; Databases, Factual ; *Fungi ; Metadata ; Software ; }, abstract = {Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.}, }
@article {pmid37209314, year = {2023}, author = {Jiang, WJ and Wang, MT and Du, ZY and Li, JH and Shi, Y and Wang, X and Wu, LY and Chen, J and Zhong, M and Yang, J and Hu, BH and Huang, J}, title = {Bioinformatic and functional analysis of OsDHN2 under cadmium stress.}, journal = {Functional &amp; integrative genomics}, volume = {23}, number = {2}, pages = {170}, pmid = {37209314}, issn = {1438-7948}, mesh = {*Cadmium/toxicity/metabolism ; Saccharomyces cerevisiae/metabolism ; Plant Proteins/genetics/metabolism ; *Oryza/genetics/metabolism ; Computational Biology ; Gene Expression Regulation, Plant ; }, abstract = {As a toxic heavy metal, cadmium (Cd) is one of the principal pollutants influencing rice productivity and food security. Despite several studies, the underlying mechanism of Cd response in plants remains largely unclear. Dehydrins are part of the late embryogenesis abundant (LEA) family which protect plants against abiotic stresses. In this study, a Cd-responsive LEA gene, OsDHN2, was functionally characterized. The chromosome localization results indicated that OsDHN2 was located on chromosome 2 of rice. Meanwhile, cis-acting elements, such as MBS (MYB binding site involved in drought-inducibility), ARE (anaerobic induction), and ABRE (abscisic acid), were present in the OsDHN2 promoter region. Expression pattern analysis also showed that OsDHN2 expression was induced in both roots and shoots under Cd stress. Overexpression of OsDHN2 improved Cd tolerance and reduced Cd concentration in yeast. Moreover, increased expression levels of SOD1, CTA1, GSH1, or CTT1 were found in transgenic yeast under Cd stress, suggesting the increased antioxidant enzymatic activities. These results suggested that OsDHN2 is a Cd-responsive gene that has the potential to improve resistance to Cd in rice.}, }
@article {pmid37207732, year = {2023}, author = {Girardi, P and Lupo, A and Mastromatteo, LY and Scrimin, S}, title = {Behavioral outcomes and exposure to perfluoroalkyl substances among children aged 6-13 years: The TEDDY child study.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116049}, doi = {10.1016/j.envres.2023.116049}, pmid = {37207732}, issn = {1096-0953}, abstract = {BACKGROUND: Although some studies report that exposure to per- and polyfluoroalkyl substances (PFAS) during pregnancy and early life stages of a child could adversely impact neurodevelopment, literature shows mixed evidence.<br><br>OBJECTIVES: Using an ecological framework for human development, we assessed the association of risk factors for environmental PFAS exposure and childhood PFAS concentrations with behavioral difficulties among school-age children exposed to PFAS from birth, while also controlling for the important influence of the parenting and familial environment.<br><br>METHODS: The study participants included 331 school-age children (6-13 years) born in a PFAS-contaminated area in the Veneto Region (Italy). We study the associations between environmental risk factors of maternal PFAS exposure (residential time, consumption of tap water, residence in Red zone A or B), and breastfeeding duration with parent assessments of children's behavioral problems (using the Strengths and Difficulties Questionnaire [SDQ]), adjusting for socio-demographic, parenting and familial variables. The direct relationships between serum blood PFAS concentrations and SDQ scores was evaluated in a subset of children (n&#x202f;=&#x202f;79), both with single PFAS and weighted quantile sum (WQS) regressions.<br><br>RESULTS: Poisson regression models reported positive associations between high consumption of tap water and externalizing SDQ scores (Incidence Rate Ratio [IRR]: 1.18; 95% confidence interval [CI]: 1.04-1.32) and total difficulty scores (IRR: 1.14; 95% CI: 1.02-1.26). Childhood perfluorooctane sulfonate (PFOS) and perfluorohexane sulfonate (PFHxS) were associated with higher internalizing SDQ scores (4th vs. 1st quartile, PFOS IRR: 1.54, 95% CI: 1.06-2.25), externalizing scores (4th vs. 1st quartile, PFHxS IRR: 1.59, 95% CI: 1.09-2.32), and total difficulty scores (4th vs. 1st quartile, PFOS IRR: 1.37, 95% CI: 1.05-1.71; PFHxS IRR: 1.54, 95% CI: 1.09-1.90). The WQS regressions confirmed the associations reported by single-PFAS analyses.<br><br>CONCLUSIONS: We observed cross-sectional associations of tap water consumption and childhood PFOS, and PFHxS concentrations with greater behavioral difficulties.}, }
@article {pmid37207684, year = {2023}, author = {Cocker, D and Chidziwisano, K and Mphasa, M and Mwapasa, T and Lewis, JM and Rowlingson, B and Sammarro, M and Bakali, W and Salifu, C and Zuza, A and Charles, M and Mandula, T and Maiden, V and Amos, S and Jacob, ST and Kajumbula, H and Mugisha, L and Musoke, D and Byrne, R and Edwards, T and Lester, R and Elviss, N and Roberts, AP and Singer, AC and Jewell, C and Morse, T and Feasey, NA}, title = {Investigating One Health risks for human colonisation with extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Malawian households: a longitudinal cohort study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(23)00062-9}, pmid = {37207684}, issn = {2666-5247}, abstract = {BACKGROUND: Low-income countries have high morbidity and mortality from drug-resistant infections, especially from enteric bacteria such as Escherichia coli. In these settings, sanitation infrastructure is of variable and often inadequate quality, creating risks of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales transmission. We aimed to describe the prevalence, distribution, and risks of ESBL-producing Enterobacterales colonisation in sub-Saharan Africa using a One Health approach.<br><br>METHODS: Between April 29, 2019, and Dec 3, 2020, we recruited 300 households in Malawi for this longitudinal cohort study: 100 each in urban, peri-urban, and rural settings. All households underwent a baseline visit and 195 were selected for longitudinal follow-up, comprising up to three additional visits over a 6 month period. Data on human health, antibiotic usage, health-seeking behaviours, structural and behavioural environmental health practices, and animal husbandry were captured alongside human, animal, and environmental samples. Microbiological processing determined the presence of ESBL-producing E coli and Klebsiella pneumoniae, and hierarchical logistic regression was performed to evaluate the risks of human ESBL-producing Enterobacterales colonisation.<br><br>FINDINGS: A paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites. A total of 11&#x2009;975 samples were cultured, and ESBL-producing Enterobacterales were isolated from 1190 (41&#xb7;8%) of 2845 samples of human stool, 290 (29&#xb7;8%) of 973 samples of animal stool, 339 (66&#xb7;2%) of 512 samples of river water, and 138 (46&#xb7;0%) of 300 samples of drain water. Multivariable models illustrated that human ESBL-producing E coli colonisation was associated with the wet season (adjusted odds ratio 1&#xb7;66, 95% credible interval 1&#xb7;38-2&#xb7;00), living in urban areas (2&#xb7;01, 1&#xb7;26-3&#xb7;24), advanced age (1&#xb7;14, 1&#xb7;05-1&#xb7;25), and living in households where animals were observed interacting with food (1&#xb7;62, 1&#xb7;17-2&#xb7;28) or kept inside (1&#xb7;58, 1&#xb7;00-2&#xb7;43). Human ESBL-producing K pneumoniae colonisation was associated with the wet season (2&#xb7;12, 1&#xb7;63-2&#xb7;76).<br><br>INTERPRETATION: There are extremely high levels of ESBL-producing Enterobacterales colonisation in humans and animals and extensive contamination of the wider environment in southern Malawi. Urbanisation and seasonality are key risks for ESBL-producing Enterobacterales colonisation, probably reflecting environmental drivers. Without adequate efforts to improve environmental health, ESBL-producing Enterobacterales transmission is likely to persist in this setting.<br><br>FUNDING: Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust.<br><br>TRANSLATION: For the Chichewa translation of the abstract see Supplementary Materials section.}, }
@article {pmid36880704, year = {2023}, author = {Amato, S and Benson, JS and Stewart, B and Sarathy, A and Osler, T and Hosmer, D and An, G and Cook, A and Winchell, RJ and Malhotra, AK}, title = {Current patterns of trauma center proliferation have not led to proportionate improvements in access to care or mortality after injury: An ecologic study.}, journal = {The journal of trauma and acute care surgery}, volume = {94}, number = {6}, pages = {755-764}, pmid = {36880704}, issn = {2163-0763}, mesh = {Humans ; United States/epidemiology ; *Trauma Centers ; Income ; Geographic Information Systems ; Health Services Accessibility ; Cell Proliferation ; *Wounds and Injuries/therapy ; }, abstract = {BACKGROUND: Timely access to high-level (I/II) trauma centers (HLTCs) is essential to minimize mortality after injury. Over the last 15 years, there has been a proliferation of HLTC nationally. The current study evaluates the impact of additional HLTC on population access and injury mortality.<br><br>METHODS: A geocoded list of HLTC, with year designated, was obtained from the American Trauma Society, and 60-minute travel time polygons were created using OpenStreetMap data. Census block group population centroids, county population centroids, and American Communities Survey data from 2005 and 2020 were integrated. Age-adjusted nonoverdose injury mortality was obtained from CDC Wide-ranging Online Data for Epidemiologic Research and the Robert Wood Johnson Foundation. Geographically weighted regression models were used to identify independent predictors of HLTC access and injury mortality.<br><br>RESULTS: Over the 15-year (2005-2020) study period, the number of HLTC increased by 31.0% (445 to 583), while population access to HLTC increased by 6.9% (77.5-84.4%). Despite this increase, access was unchanged in 83.1% of counties, with a median change in access of 0.0% (interquartile range, 0.0-1.1%). Population-level age-adjusted injury mortality rates increased by 5.39 per 100,000 population during this time (60.72 to 66.11 per 100,000). Geographically weighted regression controlling for population demography and health indicators found higher median income and higher population density to be positively associated with majority (&#x2265;50%) HLTC population coverage and negatively associated with county-level nonoverdose mortality.<br><br>CONCLUSION: Over the past 15 years, the number of HLTC increased 31%, while population access to HLTC increased only 6.9%. High-level (I/II) trauma center designation is likely driven by factors other than population need. To optimize efficiency and decrease potential oversupply, the designation process should include population level metrics. Geographic information system methodology can be an effective tool to assess optimal placement.<br><br>LEVEL OF EVIDENCE: Prognostic and Epidemiological; Level IV.}, }
@article {pmid36747723, year = {2023}, author = {Rokhsar, JL and Raynor, B and Sheen, J and Goldstein, ND and Levy, MZ and Castillo-Neyra, R}, title = {Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {36747723}, abstract = {BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi , affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.<br><br>OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.<br><br>DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.<br><br>RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.<br><br>CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.<br><br>AUTHOR SUMMARY: Chagas disease, caused by the parasite Trypanosoma cruzi , is transmitted via triatomine insect vectors. In Latin America, dogs are a common feeding source for triatomine vectors and subsequently an important reservoir of T. cruzi . One proposed intervention to reduce T. cruzi transmission is xenointoxication: treating dogs with oral insecticide to kill triatomine vectors in order to decrease overall T. cruzi transmission. Fluralaner, commonly administered to prevent ectoparasites such as fleas and ticks, is effective under laboratory conditions against the triatomine vectors. One concern with fluralaner treatment is that rapid death of the insect vectors may make the insects more available to oral ingestion by dogs; a more effective transmission pathway than stercorarian, the usual route for T. cruzi transmission. Using a mathematical model, we explored 3 different epidemiologic scenarios: high prevalence endemic disease within a domestic T. cruzi cycle, low prevalence endemic disease within a domestic T. cruzi cycle, and low prevalence endemic disease within a semi-sylvatic T. cruzi cycle. We found a range of beneficial to detrimental effects of fluralaner xenointoxication depending on the epidemiologic scenario. Our results suggest that careful field trials should be designed and carried out before wide scale implementation of fluralaner xenointoxication to reduce T. cruzi transmission.}, }
@article {pmid37198478, year = {2023}, author = {Pairo-Castineira, E and Rawlik, K and Bretherick, AD and Qi, T and Wu, Y and Nassiri, I and McConkey, GA and Zechner, M and Klaric, L and Griffiths, F and Oosthuyzen, W and Kousathanas, A and Richmond, A and Millar, J and Russell, CD and Malinauskas, T and Thwaites, R and Morrice, K and Keating, S and Maslove, D and Nichol, A and Semple, MG and Knight, J and Shankar-Hari, M and Summers, C and Hinds, C and Horby, P and Ling, L and McAuley, D and Montgomery, H and Openshaw, PJM and Begg, C and Walsh, T and Tenesa, A and Flores, C and Riancho, JA and Rojas-Martinez, A and Lapunzina, P and ,  and ,  and ,  and ,  and Yang, J and Ponting, CP and Wilson, JF and Vitart, V and Abedalthagafi, M and Luchessi, AD and Parra, EJ and Cruz, R and Carracedo, A and Fawkes, A and Murphy, L and Rowan, K and Pereira, AC and Law, A and Fairfax, B and Hendry, SC and Baillie, JK}, title = {GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37198478}, issn = {1476-4687}, abstract = {Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown[1] to be highly efficient for discovery of genetic associations[2]. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group[3]. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).}, }
@article {pmid37104570, year = {2023}, author = {Osmanski, AB and Paulat, NS and Korstian, J and Grimshaw, JR and Halsey, M and Sullivan, KAM and Moreno-Santillán, DD and Crookshanks, C and Roberts, J and Garcia, C and Johnson, MG and Densmore, LD and Stevens, RD and ,  and Rosen, J and Storer, JM and Hubley, R and Smit, AFA and Dávalos, LM and Karlsson, EK and Lindblad-Toh, K and Ray, DA}, title = {Insights into mammalian TE diversity through the curation of 248 genome assemblies.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6643}, pages = {eabn1430}, doi = {10.1126/science.abn1430}, pmid = {37104570}, issn = {1095-9203}, support = {R01 HG002939/HG/NHGRI NIH HHS/United States ; U24 HG010136/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Female ; Pregnancy ; *DNA Transposable Elements ; *Evolution, Molecular ; Long Interspersed Nucleotide Elements ; *Eutheria/genetics ; Datasets as Topic ; Feeding Behavior ; *Genetic Variation ; }, abstract = {We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.}, }
@article {pmid37196545, year = {2023}, author = {Yang, P and Yang, W and Wei, Z and Li, Y and Yang, Y and Wang, J}, title = {Novel targets for gastric cancer: The tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis and cuproptosis.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {163}, number = {}, pages = {114883}, doi = {10.1016/j.biopha.2023.114883}, pmid = {37196545}, issn = {1950-6007}, abstract = {Gastric cancer (GC) is a fatal illness, and its mortality rate is very high all over the world. At present, it is a serious health problem for any country. It is a multifactorial disease due to the rising drug resistance and the increasing global cancer burden, the treatment of GC still faces many obstacles and problems. In recent years, research on GC is being carried out continuously, and we hope to address the new targets of GC treatment through this review. At the same time, we also hope to discover new ways to fight GC and create more gospel for clinical patients. First, we discuss the descriptive tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis, and cuproptosis. Finally, we expounded on the new or potential targets of GC treatment.}, }
@article {pmid37193271, year = {2023}, author = {Mollicone, DJ and Kan, K and Coats, S and Mott, C and van Wollen, M and Hatch, A and Gallagher, J and Williams, S and Motzkin, D}, title = {Use of the psychomotor vigilance test to aid in the selection of risk controls in an air medical transport operation.}, journal = {Sleep advances : a journal of the Sleep Research Society}, volume = {4}, number = {1}, pages = {zpad003}, pmid = {37193271}, issn = {2632-5012}, abstract = {STUDY OBJECTIVES: This study evaluated the utility and ecological validity of the 3-minute psychomotor vigilance test (PVT) completed by safety-critical personnel in an air medical transport operation as part of a fatigue risk management program.<br><br>METHODS: Crewmembers in an air medical transport operation self-administered an alertness assessment incorporating a 3-minute PVT at different time points during their duty schedule. The prevalence of alertness deficits was evaluated based on a failure threshold of 12 errors considering both lapses and false starts. To evaluate the ecological validity of the PVT, the relative frequency of failed assessments was evaluated relative to crewmember position, timing of the assessment within the duty schedule, time of day, and sleep quantity in the last 24 h.<br><br>RESULTS: 2.1% of assessments were associated with a failing PVT score. Crewmember position, timing of assessment within the duty shift, time of day, and sleep quantity in the last 24 h were found to affect the relative frequency of failed assessments. Obtaining less than 7-9 h of sleep was associated with systematic increases in the failure rate (F[1, 54 612] = 168.1, p < .001). Obtaining less than 4 h of sleep was associated with a frequency of a failed assessment 2.99 times higher than the frequency of a failed assessment when obtaining 7-9 h of sleep.<br><br>CONCLUSIONS: Results provide evidence for the utility and ecological validity of the PVT as well as the suitability of the PVT failure threshold to support fatigue risk management in safety-critical operations.}, }
@article {pmid37148803, year = {2023}, author = {Tang, Y and Hardy, TJ and Yoon, JY}, title = {Receptor-based detection of microplastics and nanoplastics: Current and future.}, journal = {Biosensors &amp; bioelectronics}, volume = {234}, number = {}, pages = {115361}, doi = {10.1016/j.bios.2023.115361}, pmid = {37148803}, issn = {1873-4235}, mesh = {Microplastics ; Plastics ; *Biosensing Techniques ; Biological Assay ; Databases, Factual ; *Water Pollutants, Chemical ; }, abstract = {Plastic pollution is an emerging environmental concern, gaining significant attention worldwide. They are classified into microplastics (MP; defined from 1 μm to 5 mm) and smaller nanoplastics (NP; <1 μm). NPs may pose higher ecological risks than MPs. Various microscopic and spectroscopic techniques have been used to detect MPs, and the same methods have occasionally been used for NPs. However, they are not based on receptors, which provide high specificity in most biosensing applications. Receptor-based micro/nanoplastics (MNP) detection can provide high specificity, distinguishing MNPs from the environmental samples and, more importantly, identifying the plastic types. It can also offer a low limit of detection (LOD) required for environmental screening. Such receptors are expected to detect NPs specifically at the molecular level. This review categorizes the receptors into cells, proteins, peptides, fluorescent dyes, polymers, and micro/nanostructures. Detection techniques used with these receptors are also summarized and categorized. There is plenty of room for future research to test for broader classes of environmental samples and many plastic types, to lower the LOD, and to apply the current techniques for NPs. Portable and handheld MNP detection should also be demonstrated for field use since the current demonstrations primarily utilized laboratory instruments. Detection on microfluidic platforms will also be crucial in miniaturizing and automating the assay and, eventually, collecting an extensive database to support machine learning-based classification of MNP types.}, }
@article {pmid37165242, year = {2023}, author = {Liao, WW and Asri, M and Ebler, J and Doerr, D and Haukness, M and Hickey, G and Lu, S and Lucas, JK and Monlong, J and Abel, HJ and Buonaiuto, S and Chang, XH and Cheng, H and Chu, J and Colonna, V and Eizenga, JM and Feng, X and Fischer, C and Fulton, RS and Garg, S and Groza, C and Guarracino, A and Harvey, WT and Heumos, S and Howe, K and Jain, M and Lu, TY and Markello, C and Martin, FJ and Mitchell, MW and Munson, KM and Mwaniki, MN and Novak, AM and Olsen, HE and Pesout, T and Porubsky, D and Prins, P and Sibbesen, JA and Sirén, J and Tomlinson, C and Villani, F and Vollger, MR and Antonacci-Fulton, LL and Baid, G and Baker, CA and Belyaeva, A and Billis, K and Carroll, A and Chang, PC and Cody, S and Cook, DE and Cook-Deegan, RM and Cornejo, OE and Diekhans, M and Ebert, P and Fairley, S and Fedrigo, O and Felsenfeld, AL and Formenti, G and Frankish, A and Gao, Y and Garrison, NA and Giron, CG and Green, RE and Haggerty, L and Hoekzema, K and Hourlier, T and Ji, HP and Kenny, EE and Koenig, BA and Kolesnikov, A and Korbel, JO and Kordosky, J and Koren, S and Lee, H and Lewis, AP and Magalhães, H and Marco-Sola, S and Marijon, P and McCartney, A and McDaniel, J and Mountcastle, J and Nattestad, M and Nurk, S and Olson, ND and Popejoy, AB and Puiu, D and Rautiainen, M and Regier, AA and Rhie, A and Sacco, S and Sanders, AD and Schneider, VA and Schultz, BI and Shafin, K and Smith, MW and Sofia, HJ and Abou Tayoun, AN and Thibaud-Nissen, F and Tricomi, FF and Wagner, J and Walenz, B and Wood, JMD and Zimin, AV and Bourque, G and Chaisson, MJP and Flicek, P and Phillippy, AM and Zook, JM and Eichler, EE and Haussler, D and Wang, T and Jarvis, ED and Miga, KH and Garrison, E and Marschall, T and Hall, IM and Li, H and Paten, B}, title = {A draft human pangenome reference.}, journal = {Nature}, volume = {617}, number = {7960}, pages = {312-324}, pmid = {37165242}, issn = {1476-4687}, support = {R01 HG002385/HG/NHGRI NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Diploidy ; *Genome, Human/genetics ; Haplotypes/genetics ; Sequence Analysis, DNA ; *Genomics/standards ; Reference Standards ; Cohort Studies ; Alleles ; Genetic Variation ; }, abstract = {Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals[1]. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.}, }
@article {pmid37162089, year = {2023}, author = {Santana, BEF and Andrade, ACS and Muraro, AP}, title = {Trend of incompleteness of maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System, 2012-2020.}, journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil}, volume = {32}, number = {1}, pages = {e2022725}, pmid = {37162089}, issn = {2237-9622}, mesh = {Female ; Humans ; Pregnancy ; Brazil ; *Educational Status ; *Live Birth ; Pregnancy, Multiple ; Skin Pigmentation ; Databases, Factual/standards/statistics &amp; numerical data ; Health Information Systems ; Racial Groups ; }, abstract = {OBJECTIVE: to analyze the trend of incompleteness of the maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System (SINASC) between 2012 and 2020.<br><br>METHODS: this was an ecological time series study of the incompleteness of maternal schooling and race/skin color data for Brazil, its regions and Federative Units, by means of joinpoint regression and calculation of annual percentage change (APC) and average annual percentage change.<br><br>RESULTS: a total of 26,112,301 births were registered in Brazil in the period; incompleteness of maternal schooling data decreased for Brazil (APC = -8.1%) and the Southeast (APC = -19.5%) and Midwest (APC = -17.6%) regions; as for race/skin color, there was a downward trend for Brazil (APC = -8.2%) and all regions, except the Northeast region, while nine Federative Units and the Federal District showed a stationary trend.<br><br>CONCLUSION: there was an improvement in filling out these variables on the SINASC, but with regional disparities, mainly for race/skin color.}, }
@article {pmid37093376, year = {2023}, author = {Alam, N and Saha, S and Gupta, S and Chatterjee, A}, title = {Settlement suitability analysis of a riverine floodplain in the perspective of GIS-based multicriteria decision analysis.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {24}, pages = {66002-66020}, pmid = {37093376}, issn = {1614-7499}, mesh = {Humans ; *Geographic Information Systems ; *Decision Support Techniques ; Spatial Analysis ; Sustainable Development ; Climate ; }, abstract = {Riverine floodplains are highly dynamic and the most vulnerable space on Earth particularly in flat alluvial plains of major river systems. Suitable site selection for sustainable human settlements in active floodplain areas is a critical task for decision-makers in terms of quality of lithology, ecologically fragile landmass, climate-induced hazards, immense population pressure, and environmental conservation issues. This research introduces a methodology for settlement suitability zone (SSZ) that employs GIS-based multi-criteria decision-making (MCDM) techniques. As a case study, an altered hydrological regime of the lower Ganga riparian zone was chosen to identify the SSZ as these areas are the most susceptible to riverine hazards. Twelve significant variables reflecting on topography, climate, landscape, and environment have been selected in the multi-criteria evaluation platform. The CRiteria Importance Through Intercriteria Correlation (CRITIC) method is adopted to specify the weights of the criteria and utilize an inverse distance-weighted (IDW) spatial interpolation technique to generate an SSZ map in a GIS environment. The study zone is spatially quantified into five categories, from unsuitable to high-suitable with a natural breaks (Jenks) classification method. Subsequently, the final results are validated through a receiver operating characteristics (ROC) curve using randomly selected 56 hazard-exposed location points. The outcome revealed that 8.45% of the riparian area falls under unsuitable, 21.87% under low-suitable, and 33.27% under moderate-suitable for locating human settlements. The generally suitable and high-suitable categories account for 36.40% of the total study zone. A spatial sensitivity analysis is also applied to gauge the influence of each parameter on the MCDM outcomes. The SSZ mapping results from this study can help local authorities to plan for sustainable settlement development in environmentally fragile areas.}, }
@article {pmid37161334, year = {2023}, author = {Kortz, AR and Moyes, F and Pivello, VR and Pyšek, P and Dornelas, M and Visconti, P and Magurran, AE}, title = {Elevated compositional change in plant assemblages linked to invasion.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1998}, pages = {20222450}, pmid = {37161334}, issn = {1471-2954}, mesh = {*Tracheophyta ; Biodiversity ; Databases, Factual ; Introduced Species ; }, abstract = {Alien species are widely linked to biodiversity change, but the extent to which they are associated with the reshaping of ecological communities is not well understood. One possible mechanism is that assemblages where alien species are found exhibit elevated temporal turnover. To test this, we identified assemblages of vascular plants in the BioTIME database for those assemblages in which alien species are either present or absent and used the Jaccard measure to compute compositional dissimilarity between consecutive censuses. We found that, although alien species are typically rare in invaded assemblages, their presence is associated with an increase in the average rate of compositional change. These differences in compositional change between invaded and uninvaded assemblages are not linked to differences in species richness but rather to species replacement (turnover). Rapid compositional restructuring of assemblages is a major contributor to biodiversity change, and as such, our results suggest a role for alien species in bringing this about.}, }
@article {pmid37076624, year = {2023}, author = {Klein, B and Ogbunugafor, CB and Schafer, BJ and Bhadricha, Z and Kori, P and Sheldon, J and Kaza, N and Sharma, A and Wang, EA and Eliassi-Rad, T and Scarpino, SV and Hinton, E}, title = {COVID-19 amplified racial disparities in the US criminal legal system.}, journal = {Nature}, volume = {617}, number = {7960}, pages = {344-350}, pmid = {37076624}, issn = {1476-4687}, mesh = {Humans ; Black or African American/legislation &amp; jurisprudence/statistics &amp; numerical data ; *COVID-19/epidemiology ; *Criminals/legislation &amp; jurisprudence/statistics &amp; numerical data ; *Prisoners/legislation &amp; jurisprudence/statistics &amp; numerical data ; United States/epidemiology ; White/legislation &amp; jurisprudence/statistics &amp; numerical data ; Datasets as Topic ; Hispanic or Latino/legislation &amp; jurisprudence/statistics &amp; numerical data ; *Racial Groups/legislation &amp; jurisprudence/statistics &amp; numerical data ; }, abstract = {The criminal legal system in the USA drives an incarceration rate that is the highest on the planet, with disparities by class and race among its signature features[1-3]. During the first year of the coronavirus disease 2019 (COVID-19) pandemic, the number of incarcerated people in the USA decreased by at least 17%-the largest, fastest reduction in prison population in American history[4]. Here we ask how this reduction influenced the racial composition of US prisons and consider possible mechanisms for these dynamics. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from the decrease in the US prison population and that the fraction of incarcerated Black and Latino people sharply increased. This pattern of increased racial disparity exists across prison systems in nearly every state and reverses a decade-long trend before 2020 and the onset of COVID-19, when the proportion of incarcerated white people was increasing amid declining numbers of incarcerated Black people[5]. Although a variety of factors underlie these trends, we find that racial inequities in average sentence length are a major contributor. Ultimately, this study reveals how disruptions caused by COVID-19 exacerbated racial inequalities in the criminal legal system, and highlights key forces that sustain mass incarceration. To advance opportunities for data-driven social science, we publicly released the data associated with this study at Zenodo[6].}, }
@article {pmid37155680, year = {2023}, author = {Rokhsar, JL and Raynor, B and Sheen, J and Goldstein, ND and Levy, MZ and Castillo-Neyra, R}, title = {Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.}, journal = {PLoS computational biology}, volume = {19}, number = {5}, pages = {e1011115}, doi = {10.1371/journal.pcbi.1011115}, pmid = {37155680}, issn = {1553-7358}, abstract = {BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi, affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.<br><br>OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.<br><br>DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.<br><br>RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.<br><br>CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.}, }
@article {pmid37155231, year = {2023}, author = {Ondrikova, N and Harris, JP and Douglas, A and Hughes, HE and Iturriza-Gomara, M and Vivancos, R and Elliot, AJ and Cunliffe, NA and Clough, HE}, title = {Predicting Norovirus in England Using Existing and Emerging Syndromic Data: Infodemiology Study.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e37540}, doi = {10.2196/37540}, pmid = {37155231}, issn = {1438-8871}, mesh = {Humans ; Infodemiology ; *Norovirus ; England/epidemiology ; *Gastroenteritis/epidemiology ; *Caliciviridae Infections/epidemiology ; }, abstract = {BACKGROUND: Norovirus is associated with approximately 18% of the global burden of gastroenteritis and affects all age groups. There is currently no licensed vaccine or available antiviral treatment. However, well-designed early warning systems and forecasting can guide nonpharmaceutical approaches to norovirus infection prevention and control.<br><br>OBJECTIVE: This study evaluates the predictive power of existing syndromic surveillance data and emerging data sources, such as internet searches and Wikipedia page views, to predict norovirus activity across a range of age groups across England.<br><br>METHODS: We used existing syndromic surveillance and emerging syndromic data to predict laboratory data indicating norovirus activity. Two methods are used to evaluate the predictive potential of syndromic variables. First, the Granger causality framework was used to assess whether individual variables precede changes in norovirus laboratory reports in a given region or an age group. Then, we used random forest modeling to estimate the importance of each variable in the context of others with two methods: (1) change in the mean square error and (2) node purity. Finally, these results were combined into a visualization indicating the most influential predictors for norovirus laboratory reports in a specific age group and region.<br><br>RESULTS: Our results suggest that syndromic surveillance data include valuable predictors for norovirus laboratory reports in England. However, Wikipedia page views are less likely to provide prediction improvements on top of Google Trends and Existing Syndromic Data. Predictors displayed varying relevance across age groups and regions. For example, the random forest modeling based on selected existing and emerging syndromic variables explained 60% variance in the &#x2265;65 years age group, 42% in the East of England, but only 13% in the South West region. Emerging data sets highlighted relative search volumes, including "flu symptoms," "norovirus in pregnancy," and norovirus activity in specific years, such as "norovirus 2016." Symptoms of vomiting and gastroenteritis in multiple age groups were identified as important predictors within existing data sources.<br><br>CONCLUSIONS: Existing and emerging data sources can help predict norovirus activity in England in some age groups and geographic regions, particularly, predictors concerning vomiting, gastroenteritis, and norovirus in the vulnerable populations and historical terms such as stomach flu. However, syndromic predictors were less relevant in some age groups and regions likely due to contrasting public health practices between regions and health information-seeking behavior between age groups. Additionally, predictors relevant to one norovirus season may not contribute to other seasons. Data biases, such as low spatial granularity in Google Trends and especially in Wikipedia data, also play a role in the results. Moreover, internet searches can provide insight into mental models, that is, an individual's conceptual understanding of norovirus infection and transmission, which could be used in public health communication strategies.}, }
@article {pmid36758962, year = {2023}, author = {Lee, HE and Kim, YG and Jeong, JY and Kim, DH}, title = {Data resource profile: the Korean Community Health Status Indicators (K-CHSI) database.}, journal = {Epidemiology and health}, volume = {45}, number = {}, pages = {e2023016}, doi = {10.4178/epih.e2023016}, pmid = {36758962}, issn = {2092-7193}, mesh = {Humans ; *Health Status Indicators ; Health Surveys ; Databases, Factual ; *Environment ; Republic of Korea/epidemiology ; }, abstract = {Korean Community Health Status Indicators (K-CHSI) is a model-based database containing annual data on health outcomes and determinants at the municipal level (si/gun/gu-level regions, including mid-sized cities, counties, and districts). K-CHSI's health outcomes include overall mortality, disease incidence, prevalence rates, and self-reported health. Health determinants were measured in 5 domains: socio-demographic factors, health behaviors, social environment, physical environment, and the healthcare system. The data sources are 71 public databases, including Causes of Death Statistics, Cancer Registration Statistics, Community Health Survey, Population Census, and Census on Establishments and Statistics of Urban Plans. This dataset covers Korea's 17 metropolitan cities and provinces, with data from approximately 250 municipal regions (si/gun/gu). The current version of the database (DB version 1.3) was built using 12 years of data from 2008 to 2019. All data included in K-CHSI may be downloaded via the Korea Community Health Survey site, with no login requirement (https://chs.kdca.go.kr/chs/recsRoom/dataBaseMain.do). K-CHSI covers extensive health outcomes and health determinants at the municipal level over a period of more than 10 years, which enables ecological and time-series analyses of the relationships among various health outcomes and related factors.}, }
@article {pmid37155109, year = {2023}, author = {Chen, D and Zhang, Y and Feng, Q}, title = {Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37155109}, issn = {1614-7499}, abstract = {Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.}, }
@article {pmid37154236, year = {2023}, author = {Lin, F and Kennelly, EJ and Linington, RG and Long, C}, title = {Comprehensive Metabolite Profiling of Two Edible Garcinia Species Based on UPLC-ESI-QTOF-MS[E] Coupled with Bioactivity Assays.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.2c08372}, pmid = {37154236}, issn = {1520-5118}, abstract = {In China, the endemic species Garcinia yunnanensis and native Garcinia xanthochymus are known as edible and medicinal plants. However, a systematic metabolomic and bioactivity evaluation of different plant parts from both species is lacking. In this study, comprehensive investigations of 11 plant parts of G. yunnanensis and 10 of G. xanthochymus employing UPLC-ESI-QTOF-MS[E]-based metabolomic analysis in conjunction with three bioactivity assays were undertaken. A customized chemotaxonomic-based in-house library containing 6456 compounds was constructed and coupled to the Progenesis QI informatic platform for metabolite annotations. From these two species, a total of 235 constituents were characterized using multiple criteria. Differences in metabolite profiles between the plant parts within each species were uncovered using multivariate analysis. Based on orthogonal partial least-squares discriminant analysis (OPLS-DA), 23 markers were identified as highly differential metabolites from G. xanthochymus and 20 from G. yunnanensis. Comparative assessment of the biological assays revealed the activity variations among different plant parts. The seeds of both species and G. yunnanensis latex exhibited excellent cytotoxic and antibacterial activities, while G. xanthochymus roots and G. yunnanensis arils showed strong anti-inflammatory effects. S-plot analysis identified 26 potential biomarkers for the observed activities, including the known cytotoxic agent cycloxanthochymol and the anti-inflammatory compound garcimultiflorone B, which likely explains some of the potent observed bioactivity.}, }
@article {pmid37152782, year = {2023}, author = {Mori, Y and Okawara, M and Shibao, K and Kohi, S and Tamura, T and Sato, N and Fujino, Y and Fushimi, K and Matsuda, S and Hirata, K}, title = {Changes in operative trends and short-term outcomes of surgery for congenital biliary dilatation in adults using real-world data: A multilevel analysis based on a nationwide administrative database in Japan.}, journal = {Annals of gastroenterological surgery}, volume = {7}, number = {3}, pages = {471-478}, pmid = {37152782}, issn = {2475-0328}, abstract = {AIM: We aimed to evaluate the operative trends and compare the short-term outcomes between open and laparoscopic surgery for congenital biliary dilatation (CBD) in adults using real-world data from Japan.<br><br>METHODS: Data from the Japanese Diagnosis Procedure Combination database on 941 patients undergoing surgery for CBD at 357 hospitals from April 1, 2016, to March 31, 2021, were analyzed. The patients were divided into two groups: open surgery (n&#xa0;=&#xa0;764) and laparoscopic surgery (n&#xa0;=&#xa0;177). We performed a retrospective analysis via a multilevel analysis of the short-term surgical outcomes and costs between open and laparoscopic surgery.<br><br>RESULTS: The rate of laparoscopic surgery has been increasing annually and had almost doubled to 25% by 2021. There were no significant differences in the in-hospital mortality rate or postoperative morbidity between the two groups. The length of anesthesia was significantly longer in the laparoscopic than open surgery group (8.80 vs 6.16&#x2009;hours, p&#x2009;<&#x2009;.001). The time to removal of the abdominal drain and length of hospital stay were significantly shorter in the laparoscopic than open surgery group (6.12 vs 8.35&#x2009;days, p&#xa0;=&#xa0;.001 and 13.57 vs 15.79&#x2009;days, p&#x2009;<&#x2009;.001, respectively). The coefficient for cost was 463&#x2009;235 yen (95% confidence interval, 289&#x2009;679-636&#x2009;792) higher in laparoscopic than open surgery (p&#x2009;<&#x2009;.001).<br><br>CONCLUSION: The short-term results were comparable between laparoscopic and open surgery for CBD. Further investigation is needed to validate our findings and long-term outcomes.}, }
@article {pmid37150648, year = {2023}, author = {Wieczorek, P and Pruc, M and Krajsman, M and Wieczorek, W and Cander, B and Szarpak, L and Navolokina, A and Matuszewski, M and Bragazzi, NL and Chirico, F and Smereka, J}, title = {Comparison of the bébé VieScope™ and direct laryngoscope for pediatric tongue oedema scenario: A simulation study.}, journal = {The American journal of emergency medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajem.2023.04.039}, pmid = {37150648}, issn = {1532-8171}, }
@article {pmid37134212, year = {2023}, author = {Schuler, T and King, C and Matsveru, T and Back, M and Clark, K and Chin, D and Lilian, R and Gallego, B and Coiera, E and Currow, DC}, title = {Wearable-Triggered Ecological Momentary Assessments Are Feasible in People With Advanced Cancer and Their Family Caregivers: Feasibility Study from an Outpatient Palliative Care Clinic at a Cancer Center.}, journal = {Journal of palliative medicine}, volume = {}, number = {}, pages = {}, doi = {10.1089/jpm.2022.0535}, pmid = {37134212}, issn = {1557-7740}, abstract = {Background: Emerging digital health approaches could play a role in better personalized palliative care. Aim: We conducted a feasibility study testing wearable sensor (WS)-triggered ecological momentary assessments (EMAs) and electronic patient-reported outcomes in community palliative care with patient-caregiver dyads. Design: All wore consumer-grade WS for five weeks. Sensor-detected "stress" (heart rate variability algorithm) that passed individualized thresholds triggered a short smartphone survey. Daily sleep surveys, weekly symptom surveys (Integrated Palliative care Outcome Scale), and a poststudy experience survey were conducted. Setting/Participants: Fifteen dyads (n = 30) were recruited from an outpatient palliative care clinic for people with cancer. Results: Daytime sensor wear-time had 73% adherence. Participants perceived value in this support. Quantity and severity of "stress" events were higher in patients. Sleep disturbance was similar but for different reasons: patients (physical symptoms) and caregivers (worrying about the patient). Conclusions: EMAs are feasible and valued in community palliative care.}, }
@article {pmid37117267, year = {2023}, author = {Minhas, BF and Beck, EA and Cheng, CC and Catchen, J}, title = {Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6939}, pmid = {37117267}, issn = {2045-2322}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Temperature ; Heteroplasmy ; Fishes/genetics ; *Perciformes/physiology ; Antarctic Regions ; }, abstract = {Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.}, }
@article {pmid37110442, year = {2023}, author = {Maimone, G and Azzaro, M and Placenti, F and Paranhos, R and Cabral, AS and Decembrini, F and Zaccone, R and Cosenza, A and Rappazzo, AC and Patti, B and Basilone, G and Cuttitta, A and Ferreri, R and Aronica, S and Ferla, R}, title = {A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110442}, issn = {2076-2607}, abstract = {A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.}, }
@article {pmid36746772, year = {2023}, author = {Wu, Z and Jiang, Z and Li, Z and Jiao, P and Zhai, J and Liu, S and Han, X and Zhang, S and Sun, J and Gai, Z and Qiu, C and Xu, J and Liu, H and Qin, R and Lu, R}, title = {Multi-omics analysis reveals spatiotemporal regulation and function of heteromorphic leaves in Populus.}, journal = {Plant physiology}, volume = {192}, number = {1}, pages = {188-204}, pmid = {36746772}, issn = {1532-2548}, mesh = {*Populus/physiology ; Multiomics ; Plant Leaves/metabolism ; Transcriptome/genetics ; Chromatin/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {Despite the high economic and ecological importance of forests, our knowledge of the adaptive evolution of leaf traits remains very limited. Euphrates poplar (Populus euphratica), which has high tolerance to arid environment, has evolved four heteromorphic leaf forms, including narrow (linear and lanceolate) and broad (ovate and broad-ovate) leaves on different crowns. Here, we revealed the significant functional divergence of four P. euphratica heteromorphic leaves at physiological and cytological levels. Through global analysis of transcriptome and DNA methylation across tree and leaf developmental stages, we revealed that gene expression and DNA epigenetics differentially regulated key processes involving development and functional adaptation of heteromorphic leaves, such as hormone signaling pathways, cell division, and photosynthesis. Combined analysis of gene expression, methylation, ATAC-seq, and Hi-C-seq revealed longer interaction of 3D genome, hypomethylation, and open chromatin state upregulates IAA-related genes (such as PIN-FORMED1 and ANGUSTIFOLIA3) and promotes the occurrence of broad leaves while narrow leaves were associated with highly concentrated heterochromatin, hypermethylation, and upregulated abscisic acid pathway genes (such as Pyrabactin Resistance1-like10). Therefore, development of P. euphratica heteromorphic leaves along with functional divergence was regulated by differentially expressed genes, DNA methylation, chromatin accessibility, and 3D genome remodeling to adapt to the arid desert. This study advances our understanding of differential regulation on development and functional divergence of heteromorphic leaves in P. euphratica at the multi-omics level and provides a valuable resource for investigating the adaptive evolution of heteromorphic leaves in Populus.}, }
@article {pmid37107825, year = {2023}, author = {Schütt, EM and Hundsdörfer, MAJ and von Hoyningen-Huene, AJE and Lange, X and Koschmider, A and Oppelt, N}, title = {First Steps towards a near Real-Time Modelling System of Vibrio vulnificus in the Baltic Sea.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {8}, pages = {}, pmid = {37107825}, issn = {1660-4601}, mesh = {Humans ; *Vibrio vulnificus ; *Vibrio Infections ; Water ; Baltic States ; Oxygen ; }, abstract = {Over the last two decades, Vibrio vulnificus infections have emerged as an increasingly serious public health threat along the German Baltic coast. To manage related risks, near real-time (NRT) modelling of V. vulnificus quantities has often been proposed. Such models require spatially explicit input data, for example, from remote sensing or numerical model products. We tested if data from a hydrodynamic, a meteorological, and a biogeochemical model are suitable as input for an NRT model system by coupling it with field samples and assessing the models' ability to capture known ecological parameters of V. vulnificus. We also identify the most important predictors for V. vulnificus in the Baltic Sea by leveraging the St. Nicolas House Analysis. Using a 27-year time series of sea surface temperature, we have investigated trends of V. vulnificus season length, which pinpoint hotspots mainly in the east of our study region. Our results underline the importance of water temperature and salinity on V. vulnificus abundance but also highlight the potential of air temperature, oxygen, and precipitation to serve as predictors in a statistical model, albeit their relationship with V. vulnificus may not be causal. The evaluated models cannot be used in an NRT model system due to data availability constraints, but promising alternatives are presented. The results provide a valuable basis for a future NRT model for V. vulnificus in the Baltic Sea.}, }
@article {pmid37107056, year = {2023}, author = {Olivieri, R and Vannini, P and Corzani, A and Bianco, MT and Franchi, F and Cusi, MG and Scolletta, S and Arena, F and Basagni, C and Gusinu, R and Tumbarello, M}, title = {Rapid Decrease in Fluoroquinolones Consumption following Implementation of a Simple Antimicrobial Stewardship Bundled Intervention in a University Hospital during the COVID-19 Pandemic.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {37107056}, issn = {2079-6382}, abstract = {Fluoroquinolones (FQs) represent an class of antibiotics of medical importance, but their use has been restricted due to their ecologic impact and associated side effects. The reduction of FQs use is an important goal of antimicrobial stewardship programs (ASP). This work describes an ASP focused on overall antibiotics and FQs consumption reduction. From January 2021, an ASP was implemented in a 700-bed teaching hospital. The ASP was based on: (i) antibiotics consumption monitoring system (DDD/100 bed days); (ii) mandatory antibiotic prescription-motivation (using a dedicated informatic format) with the goal of >75% of motivated prescriptions; and (iii) data feedback and training on FQs use indications. We evaluated the impact of the intervention on overall systemic antibiotics and FQs consumption according to the objectives posed by Italian PNCAR (National Action Plan on Antimicrobial Resistance). A decrease of 6.6% in antibiotic use was observed (2019 vs. 2021). Notably, the FQs consumption fell by 48.3% from 7.1 DDD/100 bd in 2019 to 3.7 DDD/100 bd in 2021 (p < 0.001). After six months of mandatory antibiotic prescription-indication, all units achieved the target set. The study suggests that a simple, bundled ASP intervention can be rapidly effective obtaining the objectives of PNCAR on the reduction of overall antibiotics and FQs consumption.}, }
@article {pmid37106771, year = {2023}, author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R}, title = {Boundaries Are Blurred: Wild Food Plant Knowledge Circulation across the Polish-Lithuanian-Belarusian Borderland.}, journal = {Biology}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/biology12040571}, pmid = {37106771}, issn = {2079-7737}, support = {714874/ERC_/European Research Council/International ; }, abstract = {The circulation of local ecological knowledge (LEK) is a promising avenue of research for wild plant studies. To encourage the acceptance, celebration, and appreciation of biocultural diversity, which is rapidly disappearing nowadays, we need to estimate and assess multifaceted local ecological knowledge. It has direct application for local communities in informing effective policies for improving food security and building community-specific responses to environmental and social transitions. The present study draws on data collected among two ethnic groups-Lithuanians and Poles-via 200 semi-structured in-depth interviews and participant observation conducted in 2018 and 2019 in Podlasie Voivodeship (Poland), the Vilnius Region (Lithuania), and the Hrodna Region (Belarus). We aimed to observe LEK circulation in the border area through cross-ethnic and cross-country comparisons. A total of 2812 detailed use reports of wild plants were recorded. In total, 72 wild plant taxa belonging to 33 plant families were used across the food domain. Our findings show that cross-country differences were minimal, while there was some variation between the ethnic groups selected as case studies. We emphasize the need, in future studies, to combine quantitative research with qualitative approaches in order to more thoroughly identify peculiarities of cross-border circulation as a reservoir for community food resilience and biocultural diversity.}, }
@article {pmid37102710, year = {2023}, author = {Green, SJ and Torok, T and Allen, JE and Eloe-Fadrosh, E and Jackson, SA and Jiang, SC and Levine, SS and Levy, S and Schriml, LM and Thomas, WK and Wood, JM and Tighe, SW}, title = {Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {}, doi = {10.1089/ast.2022.0044}, pmid = {37102710}, issn = {1557-8070}, abstract = {Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.}, }
@article {pmid37101136, year = {2023}, author = {Mosquera, KD and Martínez Villegas, LE and Rocha Fernandes, G and Rocha David, M and Maciel-de-Freitas, R and A Moreira, L and Lorenzo, MG}, title = {Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {97}, pmid = {37101136}, issn = {1741-7007}, mesh = {Animals ; Humans ; Female ; *Aedes ; Mosquito Vectors ; Water ; Bacteria/genetics ; Oviposition ; Larva ; }, abstract = {BACKGROUND: Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.<br><br>RESULTS: To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.<br><br>CONCLUSIONS: Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.}, }
@article {pmid37100861, year = {2023}, author = {Stocco, A and Pranovi, F}, title = {The paradoxical need for human intervention in the conservation of natural environments in Venice lagoon.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6798}, pmid = {37100861}, issn = {2045-2322}, mesh = {Humans ; *Ecosystem ; *Environment ; Aquaculture ; Climate ; Geography ; Conservation of Natural Resources/methods ; }, abstract = {The Venice lagoon-the largest Mediterranean coastal lagoon-is characterized by the presence at its edges of 31 "valli da pesca", types of artificial ecosystems that mime the ecological processes of a transitional aquatic ecosystem. Constituted by a series of regulated lakes bounded by artificial embankments, the valli da pesca were established centuries ago to maximize provisioning Ecosystem Services (ESs), such as fishing and hunting. As time passed, the valli da pesca underwent an intentional isolation process leading to private management. Nonetheless, the valli da pesca are still exchanging energy and matter with the "open' lagoon and today represent an essential element within the context of lagoon conservation. This study aimed to analyze the possible effects of artificial management on both ESs supply and landscape arrangements by assessing 9 ESs (climate regulation, water purification, lifecycle support, aquaculture, waterfowl hunting, wild food, tourism, information for cognitive development, and birdwatching), along with eight landscape indicators. Obtained results suggested that the valli da pesca are today ruled under five different management strategies, according to the maximized ES. Management conditions influence the landscape pattern and achieve a series of "side effects" on the other ESs. The comparison between the managed and abandoned valli da pesca highlights the importance of anthropogenic interventions for conserving these ecosystems, as the abandoned valli da pesca show a loss of ecological gradients, landscape heterogeneity, and provisioning ESs. Nevertheless, the persistence of intrinsic geographical and morphological characteristics still prevails regardless of intentional landscape molding. The result is that the provisioning ESs capacity per unit area is higher in the abandoned valli da pesca than in the open lagoon, emphasizing the importance of these confined areas of the lagoon ecosystem. Considering the spatial distribution of multiple ESs, the provisioning ESs flow that does not occur in the abandoned valli da pesca seems to be replaced by the flow of cultural ESs. Thus, the ESs spatial pattern highlights a balancing effect between different ESs categories. The results are discussed considering the trade-offs generated by private land conservation, anthropogenic interventions, and their relevance for the ecosystem-based management of Venice lagoon.}, }
@article {pmid37099856, year = {2023}, author = {Sutton, C and Prowse, J and McVey, L and Elshehaly, M and Neagu, D and Montague, J and Alvarado, N and Tissiman, C and O'Connell, K and Eyers, E and Faisal, M and Randell, R}, title = {Strategic workforce planning in health and social care - an international perspective: A scoping review.}, journal = {Health policy (Amsterdam, Netherlands)}, volume = {132}, number = {}, pages = {104827}, doi = {10.1016/j.healthpol.2023.104827}, pmid = {37099856}, issn = {1872-6054}, abstract = {Effective strategic workforce planning for integrated and co-ordinated health and social care is essential if future services are to be resourced such that skill mix, clinical practice and productivity meet population health and social care needs in timely, safe and accessible ways globally. This review presents international literature to illustrate how strategic workforce planning in health and social care has been undertaken around the world with examples of planning frameworks, models and modelling approaches. The databases Business Source Premier, CINAHL, Embase, Health Management Information Consortium, Medline and Scopus were searched for full texts, from 2005 to 2022, detailing empirical research, models or methodologies to explain how strategic workforce planning (with at least a one-year horizon) in health and/or social care has been undertaken, yielding ultimately 101 included references. The supply/demand of a differentiated medical workforce was discussed in 25 references. Nursing and midwifery were characterised as undifferentiated labour, requiring urgent growth to meet demand. Unregistered workers were poorly represented as was the social care workforce. One reference considered planning for health and social care workers. Workforce modelling was illustrated in 66 references with predilection for quantifiable projections. Increasingly needs-based approaches were called for to better consider demography and epidemiological impacts. This review's findings advocate for whole-system needs-based approaches that consider the ecology of a co-produced health and social care workforce.}, }
@article {pmid37098064, year = {2023}, author = {Shea, K and Borchering, RK and Probert, WJM and Howerton, E and Bogich, TL and Li, SL and van Panhuis, WG and Viboud, C and Aguás, R and Belov, AA and Bhargava, SH and Cavany, SM and Chang, JC and Chen, C and Chen, J and Chen, S and Chen, Y and Childs, LM and Chow, CC and Crooker, I and Del Valle, SY and España, G and Fairchild, G and Gerkin, RC and Germann, TC and Gu, Q and Guan, X and Guo, L and Hart, GR and Hladish, TJ and Hupert, N and Janies, D and Kerr, CC and Klein, DJ and Klein, EY and Lin, G and Manore, C and Meyers, LA and Mittler, JE and Mu, K and Núñez, RC and Oidtman, RJ and Pasco, R and Pastore Y Piontti, A and Paul, R and Pearson, CAB and Perdomo, DR and Perkins, TA and Pierce, K and Pillai, AN and Rael, RC and Rosenfeld, K and Ross, CW and Spencer, JA and Stoltzfus, AB and Toh, KB and Vattikuti, S and Vespignani, A and Wang, L and White, LJ and Xu, P and Yang, Y and Yogurtcu, ON and Zhang, W and Zhao, Y and Zou, D and Ferrari, MJ and Pannell, D and Tildesley, MJ and Seifarth, J and Johnson, E and Biggerstaff, M and Johansson, MA and Slayton, RB and Levander, JD and Stazer, J and Kerr, J and Runge, MC}, title = {Multiple models for outbreak decision support in the face of uncertainty.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {18}, pages = {e2207537120}, doi = {10.1073/pnas.2207537120}, pmid = {37098064}, issn = {1091-6490}, abstract = {Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we convened multiple modeling teams to evaluate COVID-19 reopening strategies for a mid-sized United States county early in the pandemic. Projections from seventeen distinct models were inconsistent in magnitude but highly consistent in ranking interventions. The 6-mo-ahead aggregate projections were well in line with observed outbreaks in mid-sized US counties. The aggregate results showed that up to half the population could be infected with full workplace reopening, while workplace restrictions reduced median cumulative infections by 82%. Rankings of interventions were consistent across public health objectives, but there was a strong trade-off between public health outcomes and duration of workplace closures, and no win-win intermediate reopening strategies were identified. Between-model variation was high; the aggregate results thus provide valuable risk quantification for decision making. This approach can be applied to the evaluation of management interventions in any setting where models are used to inform decision making. This case study demonstrated the utility of our approach and was one of several multimodel efforts that laid the groundwork for the COVID-19 Scenario Modeling Hub, which has provided multiple rounds of real-time scenario projections for situational awareness and decision making to the Centers for Disease Control and Prevention since December 2020.}, }
@article {pmid37097029, year = {2023}, author = {Carrol, ED and Ranjit, S and Menon, K and Bennett, TD and Sanchez-Pinto, LN and Zimmerman, JJ and Souza, DC and Sorce, LR and Randolph, AG and Ishimine, P and Flauzino de Oliveira, C and Lodha, R and Harmon, L and Watson, RS and Schlapbach, LJ and Kissoon, N and Argent, AC and , }, title = {Operationalizing Appropriate Sepsis Definitions in Children Worldwide: Considerations for the Pediatric Sepsis Definition Taskforce.}, journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies}, volume = {}, number = {}, pages = {}, doi = {10.1097/PCC.0000000000003263}, pmid = {37097029}, issn = {1529-7535}, abstract = {Sepsis is a leading cause of global mortality in children, yet definitions for pediatric sepsis are outdated and lack global applicability and validity. In adults, the Sepsis-3 Definition Taskforce queried databases from high-income countries to develop and validate the criteria. The merit of this definition has been widely acknowledged; however, important considerations about less-resourced and more diverse settings pose challenges to its use globally. To improve applicability and relevance globally, the Pediatric Sepsis Definition Taskforce sought to develop a conceptual framework and rationale of the critical aspects and context-specific factors that must be considered for the optimal operationalization of future pediatric sepsis definitions. It is important to address challenges in developing a set of pediatric sepsis criteria which capture manifestations of illnesses with vastly different etiologies and underlying mechanisms. Ideal criteria need to be unambiguous, and capable of adapting to the different contexts in which children with suspected infections are present around the globe. Additionally, criteria need to facilitate early recognition and timely escalation of treatment to prevent progression and limit life-threatening organ dysfunction. To address these challenges, locally adaptable solutions are required, which permit individualized care based on available resources and the pretest probability of sepsis. This should facilitate affordable diagnostics which support risk stratification and prediction of likely treatment responses, and solutions for locally relevant outcome measures. For this purpose, global collaborative databases need to be established, using minimum variable datasets from routinely collected data. In summary, a "Think globally, act locally" approach is required.}, }
@article {pmid37095444, year = {2023}, author = {Demidova, EV and Serebriiskii, IG and Vlasenkova, R and Kelow, S and Andrake, MD and Hartman, TR and Kent, T and Virtucio, J and Rosen, GL and Pomerantz, RT and Dunbrack, RL and Golemis, EA and Hall, MJ and Chen, DYT and Daly, MB and Arora, S}, title = {Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {212}, pmid = {37095444}, issn = {1471-2164}, support = {P30 CA006927/CA/NCI NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; P30 CA006927/CA/NCI NIH HHS/United States ; 1R01GM130889/GF/NIH HHS/United States ; R35 GM122517/GF/NIH HHS/United States ; R01 DK108195/GF/NIH HHS/United States ; U01 CA164920/GF/NIH HHS/United States ; 1UH2CA271230-01/GF/NIH HHS/United States ; }, mesh = {Humans ; *Carcinoma, Renal Cell ; Genetic Predisposition to Disease ; DNA Replication ; Germ-Line Mutation ; *Kidney Neoplasms ; Germ Cells ; }, abstract = {BACKGROUND: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.<br><br>METHODS: Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes.<br><br>RESULTS: Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of [Formula: see text]H2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate variant genes&#xa0;in Caki RCC cells increased [Formula: see text]H2AX foci. Immortalized patient-derived B cell lines bearing the candidate variants in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol &#x3b4; and Pol &#x3b7; polymerases revealed defective enzymatic activities.<br><br>CONCLUSIONS: Together, these results suggest that constitutional defects in DNA repair underlie a subset of eoRCC cases. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.}, }
@article {pmid37094905, year = {2023}, author = {Girón, JC and Tarasov, S and González Montaña, LA and Matentzoglu, N and Smith, AD and Koch, M and Boudinot, BE and Bouchard, P and Burks, R and Vogt, L and Yoder, M and Osumi-Sutherland, D and Friedrich, F and Beutel, R and Mikó, I}, title = {Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syad025}, pmid = {37094905}, issn = {1076-836X}, abstract = {The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multi-species anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to (1) use controlled vocabularies and create semi-automated computer-parsable insect morphological descriptions; (2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and (3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.}, }
@article {pmid37082718, year = {2023}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Mulley, JF and , }, title = {The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {66}, pmid = {37082718}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Apotomis betuletana (the Birch Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 684 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,717 protein coding genes.}, }
@article {pmid36899120, year = {2023}, author = {Yilanci, V and Candan, G and Shah, MI}, title = {Identifying the roles of energy and economic factors on environmental degradation in MINT economies: a hesitant fuzzy analytic hierarchy process.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {19}, pages = {55768-55781}, pmid = {36899120}, issn = {1614-7499}, mesh = {Cross-Sectional Studies ; *Analytic Hierarchy Process ; Economic Development ; Carbon Dioxide ; Investments ; Economic Factors ; *Mentha ; Renewable Energy ; }, abstract = {Globally, research communities have been studying the different determinants of environmental degradation or pollution using different contexts and methods. In this study, we identify several energy and economic factors, such as energy consumption (EC), gross domestic product (GDP), energy production (EP), urbanization (URB), and foreign direct investment (FDI) as the most effective factors of environmental degradation by obtaining several environmental researchers' opinions and using the hesitant fuzzy analytic hierarchy process. In the later stage of the analysis, we use these variables as regressors of the ecological footprint (EF) as a proxy for environmental degradation. Since we find evidence of cross-sectional dependence among the members of the variables, we use second-generational panel tests. First, we test the stationarity of the variables using the cross-sectionally augmented IPS (CIPS) panel unit test. The results show that the regressors have different orders of integration. So, we employ the Durbin-Hausman panel cointegration test to test the existence of a long-run relationship between the variables. Having found a long-run relationship, we estimate the long-run coefficients using the common correlated effects mean group estimator, which reveals that energy consumption has an increasing effect on the EF in Indonesia and Turkey, while energy production has a negative impact in Mexico and Turkey. While GDP has an increasing effect in all countries, FDI has a similar effect in only Indonesia. Moreover, URB decreases the ecological footprint in Nigeria, while it increases in Turkey. Our approach to the evaluation of environmental degradation can be generalized to other regions as well as where there is a significant need to understand the roles of different drivers on environmental degradation or pollution.}, }
@article {pmid37078321, year = {2023}, author = {Shu, CB and Shen, YL and Liu, G and Zhang, Q and Xu, JH and Guo, Z}, title = {Impacts of Eucalyptus plantation on soil and water losses in a typical small watershed in mountainous area of southern China.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {4}, pages = {1015-1023}, doi = {10.13287/j.1001-9332.202304.021}, pmid = {37078321}, issn = {1001-9332}, mesh = {*Soil ; *Eucalyptus ; Geographic Information Systems ; Forests ; China ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; }, abstract = {Unreasonable exploitation of artificial forest causes severe soil erosion in the mountainous areas of sou-thern China. The spatial-temporal variations of soil erosion in typical small watershed with artificial forest has signifi-cant implications for artificial forest exploitation and sustainable development of mountainous ecological environment. In this study, we used revised universal soil loss equation (RUSLE) and geographic information system (GIS) to evaluate the spatial and temporal variations of soil erosion and its key drivers of Dadingshan watershed in mountainous area of western Guangdong. The results showed that the erosion modulus was 1948.1 t·km[-2]·a[-1] (belonging to light erosion) in the Dadingshan watershed. However, the spatial variation of soil erosion was substantial, with variation coefficient of 5.12. The maximal soil erosion modulus was 191127 t·km[-2]·a[-1]. Slight erosion (<500 t·km[-2]·a[-1]) accounted for 80.6% of the total watershed area. The moderate erosion and above (>2500 t·km[-2]·a[-1]) were mainly distributed in young Eucalyptus forest area with less than 30% of the vegetation coverage, which contributed nearly 75.7% of total soil erosion. During 2014-2019, the interannual variations of mean erosion of Dadingshan catchment was modest, but the spatial variation of soil erosion was large. Vegetation cover, slope, and rainfall were key drivers of such variation. The destruction of natural vegetation resulted by plantation exploitation was the primary cause of soil erosion in afforestation areas. Soil erosion significantly increased with the increases of slope gradient in the young forest area, which was aggravated by extreme rainfall. However, soil erosion gradually decreased with the increases of the age of Eucalypt plantation. Therefore, the hot spot of soil erosion was young forest areas of Eucalypt plantation with slope >25°, and the key period for soil erosion control was the first 2-3 years after Eucalyptus planting. We suggested that reasonable afforestation measures should be used in area with >25° slopes, and that the destruction of natural vegetation should be avoided on hillslope with >35° slope gradient. The road construction standards and forest management should be further improved to address the challenge of extreme rainfalls.}, }
@article {pmid37076812, year = {2023}, author = {De Wolfe, TJ and Wright, ES}, title = {Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {107}, pmid = {37076812}, issn = {1471-2180}, support = {T15 LM007059/LM/NLM NIH HHS/United States ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Workflow ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.<br><br>RESULTS: Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an&#xa0;increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).<br><br>CONCLUSIONS: Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.}, }
@article {pmid35737561, year = {2023}, author = {Swerdlow, BA and Sandel, DB and Johnson, SL}, title = {Shame on me for needing you: A multistudy examination of links between receiving interpersonal emotion regulation and experiencing shame.}, journal = {Emotion (Washington, D.C.)}, volume = {23}, number = {3}, pages = {737-752}, doi = {10.1037/emo0001109}, pmid = {35737561}, issn = {1931-1516}, support = {/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Emotions/physiology ; *Emotional Regulation ; Shame ; Hostility ; Data Management ; }, abstract = {Recent theory and research have drawn attention to interpersonal dimensions of emotion regulation. Yet, few empirical investigations of the outcomes of interpersonal emotion regulation have been conducted. We propose that one negative affective outcome of received interpersonal emotion regulation of conceptual and practical interest is shame. In the present series of studies, participants from six disparate samples reported on experiences of receiving interpersonal emotion regulation using autobiographical recall and ecological sampling paradigms (total analyzed n = 1,868; total analyzed k = 2,515 instances of receiving interpersonal emotion regulation). We sought to quantify the frequency and distinctiveness of shame as an outcome of receiving interpersonal emotion regulation. We used an exploratory-confirmatory approach to identify robust and generalizable correlates of shame. We considered individual (e.g., trait external shame-proneness), situational (e.g., desire for regulation), relational (e.g., perceived closeness with the provider), and interaction-specific (e.g., perceptions of provider hostility) variables. Our results indicate that it is not uncommon for people to experience receiving interpersonal emotion regulation as shame-inducing, and these perceptions are distinct from their evaluations of the overall helpfulness of the interaction. An internal mini meta-analysis showed that the strongest correlates of shame across studies and samples were individual differences in nonacceptance of negative emotions and expressive suppression and interaction-specific ratings of provider responsiveness and hostility. We discuss the conceptual, methodological, and practical implications of these findings for studying interpersonal emotion regulation and shame. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, }
@article {pmid37075104, year = {2023}, author = {Skirgård, H and Haynie, HJ and Blasi, DE and Hammarström, H and Collins, J and Latarche, JJ and Lesage, J and Weber, T and Witzlack-Makarevich, A and Passmore, S and Chira, A and Maurits, L and Dinnage, R and Dunn, M and Reesink, G and Singer, R and Bowern, C and Epps, P and Hill, J and Vesakoski, O and Robbeets, M and Abbas, NK and Auer, D and Bakker, NA and Barbos, G and Borges, RD and Danielsen, S and Dorenbusch, L and Dorn, E and Elliott, J and Falcone, G and Fischer, J and Ghanggo Ate, Y and Gibson, H and Göbel, HP and Goodall, JA and Gruner, V and Harvey, A and Hayes, R and Heer, L and Herrera Miranda, RE and Hübler, N and Huntington-Rainey, B and Ivani, JK and Johns, M and Just, E and Kashima, E and Kipf, C and Klingenberg, JV and König, N and Koti, A and Kowalik, RGA and Krasnoukhova, O and Lindvall, NLM and Lorenzen, M and Lutzenberger, H and Martins, TRA and Mata German, C and van der Meer, S and Montoya Samamé, J and Müller, M and Muradoglu, S and Neely, K and Nickel, J and Norvik, M and Oluoch, CA and Peacock, J and Pearey, IOC and Peck, N and Petit, S and Pieper, S and Poblete, M and Prestipino, D and Raabe, L and Raja, A and Reimringer, J and Rey, SC and Rizaew, J and Ruppert, E and Salmon, KK and Sammet, J and Schembri, R and Schlabbach, L and Schmidt, FWP and Skilton, A and Smith, WD and de Sousa, H and Sverredal, K and Valle, D and Vera, J and Voß, J and Witte, T and Wu, H and Yam, S and Ye, J and Yong, M and Yuditha, T and Zariquiey, R and Forkel, R and Evans, N and Levinson, SC and Haspelmath, M and Greenhill, SJ and Atkinson, QD and Gray, RD}, title = {Grambank reveals the importance of genealogical constraints on linguistic diversity and highlights the impact of language loss.}, journal = {Science advances}, volume = {9}, number = {16}, pages = {eadg6175}, pmid = {37075104}, issn = {2375-2548}, mesh = {Humans ; *Language ; *Linguistics ; Cognition ; Databases, Factual ; }, abstract = {While global patterns of human genetic diversity are increasingly well characterized, the diversity of human languages remains less systematically described. Here, we outline the Grambank database. With over 400,000 data points and 2400 languages, Grambank is the largest comparative grammatical database available. The comprehensiveness of Grambank allows us to quantify the relative effects of genealogical inheritance and geographic proximity on the structural diversity of the world's languages, evaluate constraints on linguistic diversity, and identify the world's most unusual languages. An analysis of the consequences of language loss reveals that the reduction in diversity will be strikingly uneven across the major linguistic regions of the world. Without sustained efforts to document and revitalize endangered languages, our linguistic window into human history, cognition, and culture will be seriously fragmented.}, }
@article {pmid37072018, year = {2023}, author = {Jackson, C and Stewart, ID and Plekhanova, T and Cunningham, PS and Hazel, AL and Al-Sheklly, B and Aul, R and Bolton, CE and Chalder, T and Chalmers, JD and Chaudhuri, N and Docherty, AB and Donaldson, G and Edwardson, CL and Elneima, O and Greening, NJ and Hanley, NA and Harris, VC and Harrison, EM and Ho, LP and Houchen-Wolloff, L and Howard, LS and Jolley, CJ and Jones, MG and Leavy, OC and Lewis, KE and Lone, NI and Marks, M and McAuley, HJC and McNarry, MA and Patel, BV and Piper-Hanley, K and Poinasamy, K and Raman, B and Richardson, M and Rivera-Ortega, P and Rowland-Jones, SL and Rowlands, AV and Saunders, RM and Scott, JT and Sereno, M and Shah, AM and Shikotra, A and Singapuri, A and Stanel, SC and Thorpe, M and Wootton, DG and Yates, T and Gisli Jenkins, R and Singh, SJ and Man, WD and Brightling, CE and Wain, LV and Porter, JC and Thompson, AAR and Horsley, A and Molyneaux, PL and Evans, RA and Jones, SE and Rutter, MK and Blaikley, JF and , }, title = {Effects of sleep disturbance on dyspnoea and impaired lung function following hospital admission due to COVID-19 in the UK: a prospective multicentre cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(23)00124-8}, pmid = {37072018}, issn = {2213-2619}, abstract = {BACKGROUND: Sleep disturbance is common following hospital admission both for COVID-19 and other causes. The clinical associations of this for recovery after hospital admission are poorly understood despite sleep disturbance contributing to morbidity in other scenarios. We aimed to investigate the prevalence and nature of sleep disturbance after discharge following hospital admission for COVID-19 and to assess whether this was associated with dyspnoea.<br><br>METHODS: CircCOVID was a prospective multicentre cohort substudy designed to investigate the effects of circadian disruption and sleep disturbance on recovery after COVID-19 in a cohort of participants aged 18 years or older, admitted to hospital for COVID-19 in the UK, and discharged between March, 2020, and October, 2021. Participants were recruited from the Post-hospitalisation COVID-19 study (PHOSP-COVID). Follow-up data were collected at two timepoints: an early time point 2-7 months after hospital discharge and a later time point 10-14 months after hospital discharge. Sleep quality was assessed subjectively using the Pittsburgh Sleep Quality Index questionnaire and a numerical rating scale. Sleep quality was also assessed with an accelerometer worn on the wrist (actigraphy) for 14 days. Participants were also clinically phenotyped, including assessment of symptoms (ie, anxiety [Generalised Anxiety Disorder 7-item scale questionnaire], muscle function [SARC-F questionnaire], dyspnoea [Dyspnoea-12 questionnaire] and measurement of lung function), at the early timepoint after discharge. Actigraphy results were also compared to a matched UK Biobank cohort (non-hospitalised individuals and recently hospitalised individuals). Multivariable linear regression was used to define associations of sleep disturbance with the primary outcome of breathlessness and the other clinical symptoms. PHOSP-COVID is registered on the ISRCTN Registry (ISRCTN10980107).<br><br>FINDINGS: 2320 of 2468 participants in the PHOSP-COVID study attended an early timepoint research visit a median of 5 months (IQR 4-6) following discharge from 83 hospitals in the UK. Data for sleep quality were assessed by subjective measures (the Pittsburgh Sleep Quality Index questionnaire and the numerical rating scale) for 638 participants at the early time point. Sleep quality was also assessed using device-based measures (actigraphy) a median of 7 months (IQR 5-8 months) after discharge from hospital for 729 participants. After discharge from hospital, the majority (396 [62%] of 638) of participants who had been admitted to hospital for COVID-19 reported poor sleep quality in response to the Pittsburgh Sleep Quality Index questionnaire. A comparable proportion (338 [53%] of 638) of participants felt their sleep quality had deteriorated following discharge after COVID-19 admission, as assessed by the numerical rating scale. Device-based measurements were compared to an age-matched, sex-matched, BMI-matched, and time from discharge-matched UK Biobank cohort who had recently been admitted to hospital. Compared to the recently hospitalised matched UK Biobank cohort, participants in our study slept on average 65 min (95% CI 59 to 71) longer, had a lower sleep regularity index (-19%; 95% CI -20 to -16), and a lower sleep efficiency (3&#xb7;83 percentage points; 95% CI 3&#xb7;40 to 4&#xb7;26). Similar results were obtained when comparisons were made with the non-hospitalised UK Biobank cohort. Overall sleep quality (unadjusted effect estimate 3&#xb7;94; 95% CI 2&#xb7;78 to 5&#xb7;10), deterioration in sleep quality following hospital admission (3&#xb7;00; 1&#xb7;82 to 4&#xb7;28), and sleep regularity (4&#xb7;38; 2&#xb7;10 to 6&#xb7;65) were associated with higher dyspnoea scores. Poor sleep quality, deterioration in sleep quality, and sleep regularity were also associated with impaired lung function, as assessed by forced vital capacity. Depending on the sleep metric, anxiety mediated 18-39% of the effect of sleep disturbance on dyspnoea, while muscle weakness mediated 27-41% of this effect.<br><br>INTERPRETATION: Sleep disturbance following hospital admission for COVID-19 is associated with dyspnoea, anxiety, and muscle weakness. Due to the association with multiple symptoms, targeting sleep disturbance might be beneficial in treating the post-COVID-19 condition.<br><br>FUNDING: UK Research and Innovation, National Institute for Health Research, and Engineering and Physical Sciences Research Council.}, }
@article {pmid37069545, year = {2023}, author = {Cai, P and Liu, S and Zhang, D and Xing, H and Han, M and Liu, D and Gong, L and Hu, QN}, title = {SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {152}, pmid = {37069545}, issn = {1471-2105}, mesh = {*Synthetic Biology ; *Computational Biology/methods ; Registries ; Databases, Factual ; Software ; }, abstract = {BACKGROUND: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology.<br><br>RESULTS: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system.<br><br>CONCLUSIONS: SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.}, }
@article {pmid37069271, year = {2023}, author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H}, title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {37069271}, issn = {1548-7105}, support = {R01 EB028159/EB/NIBIB NIH HHS/United States ; RF1 MH128693/MH/NIMH NIH HHS/United States ; }, abstract = {BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.}, }
@article {pmid37049742, year = {2023}, author = {Biswas, P and Bibi, S and Yousafi, Q and Mehmood, A and Saleem, S and Ihsan, A and Dey, D and Hasan Zilani, MN and Hasan, MN and Saleem, R and Awaji, AA and Fahmy, UA and Abdel-Daim, MM}, title = {Study of MDM2 as Prognostic Biomarker in Brain-LGG Cancer and Bioactive Phytochemicals Inhibit the p53-MDM2 Pathway: A Computational Drug Development Approach.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {7}, pages = {}, pmid = {37049742}, issn = {1420-3049}, mesh = {Humans ; Tumor Suppressor Protein p53/metabolism ; Molecular Docking Simulation ; Proto-Oncogene Proteins c-mdm2/metabolism ; DNA Copy Number Variations ; Prognosis ; *Brain Neoplasms/drug therapy/genetics/metabolism ; *Glioma/drug therapy/genetics/metabolism ; Biomarkers ; Drug Development ; Brain/metabolism ; }, abstract = {An evaluation of the expression and predictive significance of the MDM2 gene in brain lower-grade glioma (LGG) cancer was carried out using onco-informatics pipelines. Several transcriptome servers were used to measure the differential expression of the targeted MDM2 gene and search mutations and copy number variations. GENT2, Gene Expression Profiling Interactive Analysis, Onco-Lnc, and PrognoScan were used to figure out the survival rate of LGG cancer patients. The protein-protein interaction networks between MDM2 gene and its co-expressed genes were constructed by Gene-MANIA tool. Identified bioactive phytochemicals were evaluated through molecular docking using Schrödinger Suite Software, with the MDM2 (PDB ID: 1RV1) target. Protein-ligand interactions were observed with key residues of the macromolecular target. A molecular dynamics simulation of the novel bioactive compounds with the targeted protein was performed. Phytochemicals targeting MDM2 protein, such as Taxifolin and (-)-Epicatechin, have been shown with more highly stable results as compared to the control drug, and hence, concluded that phytochemicals with bioactive potential might be alternative therapeutic options for the management of LGG patients. Our once informatics-based designed pipeline has indicated that the MDM2 gene may have been a predictive biomarker for LGG cancer and selected phytochemicals possessed outstanding interaction results within the macromolecular target's active site after utilizing in silico approaches. In vitro and in vivo experiments are recommended to confirm these outcomes.}, }
@article {pmid36736631, year = {2023}, author = {LaVigne, AW and DeWeese, TL and Wright, JL and Deville, C and Yegnasubramanian, S and Alcorn, SR}, title = {Radiotherapy Deserts: The Impact of Race, Poverty, and the Rural-Urban Continuum on Density of Providers and the Use of Radiation Therapy in the US.}, journal = {International journal of radiation oncology, biology, physics}, volume = {116}, number = {1}, pages = {17-27}, doi = {10.1016/j.ijrobp.2023.01.046}, pmid = {36736631}, issn = {1879-355X}, mesh = {Aged ; Humans ; Male ; Medicare/statistics &amp; numerical data ; *Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Poverty/statistics &amp; numerical data ; Rural Population/statistics &amp; numerical data ; Social Class ; United States/epidemiology ; Urban Population/statistics &amp; numerical data ; *Radiotherapy/economics/standards/statistics &amp; numerical data ; Resource-Limited Settings/statistics &amp; numerical data ; Race Factors/statistics &amp; numerical data ; Health Personnel/statistics &amp; numerical data ; Health Services Accessibility/statistics &amp; numerical data ; Health Services Needs and Demand/statistics &amp; numerical data ; Prostatic Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Breast Neoplasms/economics/epidemiology/ethnology/radiotherapy ; Female ; Databases, Factual/statistics &amp; numerical data ; Patient-Centered Care/statistics &amp; numerical data ; *Healthcare Disparities/economics/ethnology/statistics &amp; numerical data ; }, abstract = {PURPOSE: Prior efforts to characterize disparities in radiation therapy access and receipt have not comprehensively investigated interplay between race, socioeconomic status, and geography relative to oncologic outcomes. This study sought to define these complex relationships at the US county level for prostate cancer (PC) and invasive breast (BC) cancer to build a tool that facilitates identification of "radiotherapy deserts"-regions with mismatch between radiation therapy resources and oncologic need.<br><br>METHODS AND MATERIALS: An ecologic study model was constructed using national databases to evaluate 3,141 US counties. Radiation therapy resources and use densities were operationalized as physicians to persons at risk (PPR) and use to persons at risk (UPR): the number of attending radiation oncologists and Medicare beneficiaries per 100,000 persons at risk, respectively. Oncologic need was defined by "hot zone" counties with &#x2265;2 standard deviations (SDs) above mean incidence and death rates. Univariable and multivariable logistic regressions examined links between PPR and UPR densities, epidemiologic variables, and hot zones for oncologic outcomes. Statistics are reported at a significance level of P < .05.<br><br>RESULTS: The mean (SD) PPR and UPR densities were 2.1 (5.9) and 192.6 (557.6) for PC and 1.9 (5.3) and 174.4 (501.0) for BC, respectively. Counties with high PPR and UPR densities were predominately metropolitan (odds ratio [OR], 2.9-4.4), generally with a higher percentage of Black non-Hispanic constituents (OR, 1.5-2.3). Incidence and death rate hot zones were largely nonmetropolitan (OR, 0.3-0.6), generally with a higher percentage of Black non-Hispanic constituents (OR, 3.2-6.3). Lower PPR density was associated with death rate hot zones for both types of cancer (OR, 0.8-0.9); UPR density was generally not linked to oncologic outcomes on multivariable analysis.<br><br>CONCLUSIONS: The study found that mismatch between oncologic need with PPR and UPR disproportionately affects nonmetropolitan communities with a higher percentage of Black non-Hispanic constituents. An interactive web platform (bit.ly/densitymaps) was developed to visualize "radiotherapy deserts" and drive targeted investigation of underlying barriers to care in areas of highest need, with the goal of reducing health inequities in this context.}, }
@article {pmid37047894, year = {2023}, author = {Roberts, M and Colley, K and Currie, M and Eastwood, A and Li, KH and Avery, LM and Beevers, LC and Braithwaite, I and Dallimer, M and Davies, ZG and Fisher, HL and Gidlow, CJ and Memon, A and Mudway, IS and Naylor, LA and Reis, S and Smith, P and Stansfeld, SA and Wilkie, S and Irvine, KN}, title = {The Contribution of Environmental Science to Mental Health Research: A Scoping Review.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {7}, pages = {}, pmid = {37047894}, issn = {1660-4601}, mesh = {Humans ; Mental Health ; *COVID-19 ; Pandemics ; *Environmental Science ; Environmental Exposure ; }, abstract = {Mental health is influenced by multiple complex and interacting genetic, psychological, social, and environmental factors. As such, developing state-of-the-art mental health knowledge requires collaboration across academic disciplines, including environmental science. To assess the current contribution of environmental science to this field, a scoping review of the literature on environmental influences on mental health (including conditions of cognitive development and decline) was conducted. The review protocol was developed in consultation with experts working across mental health and environmental science. The scoping review included 202 English-language papers, published between 2010 and 2020 (prior to the COVID-19 pandemic), on environmental themes that had not already been the subject of recent systematic reviews; 26 reviews on climate change, flooding, air pollution, and urban green space were additionally considered. Studies largely focused on populations in the USA, China, or Europe and involved limited environmental science input. Environmental science research methods are primarily focused on quantitative approaches utilising secondary datasets or field data. Mental health measurement was dominated by the use of self-report psychometric scales. Measures of environmental states or exposures were often lacking in specificity (e.g., limited to the presence or absence of an environmental state). Based on the scoping review findings and our synthesis of the recent reviews, a research agenda for environmental science's future contribution to mental health scholarship is set out. This includes recommendations to expand the geographical scope and broaden the representation of different environmental science areas, improve measurement of environmental exposure, prioritise experimental and longitudinal research designs, and giving greater consideration to variation between and within communities and the mediating pathways by which environment influences mental health. There is also considerable opportunity to increase interdisciplinarity within the field via the integration of conceptual models, the inclusion of mixed methods and qualitative approaches, as well as further consideration of the socio-political context and the environmental states that can help support good mental health. The findings were used to propose a conceptual model to parse contributions and connections between environmental science and mental health to inform future studies.}, }
@article {pmid37046168, year = {2023}, author = {Chen, D and Feng, Q and Zhang, Y}, title = {Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-023-26775-y}, pmid = {37046168}, issn = {1614-7499}, abstract = {In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.}, }
@article {pmid36947137, year = {2023}, author = {James, JE and Nelson, PG and Masel, J}, title = {Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.}, journal = {Molecular biology and evolution}, volume = {40}, number = {4}, pages = {}, pmid = {36947137}, issn = {1537-1719}, mesh = {Animals ; *Proteome ; Protein Domains ; Probability ; Hydrophobic and Hydrophilic Interactions ; Databases, Protein ; }, abstract = {Protein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition.}, }
@article {pmid34021761, year = {2021}, author = {Halder, S and Ghosh, S and Chattopadhyay, J and Chatterjee, S}, title = {Bistability in cell signalling and its significance in identifying potential drug-targets.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {22}, pages = {4156-4163}, doi = {10.1093/bioinformatics/btab395}, pmid = {34021761}, issn = {1367-4811}, mesh = {*Signal Transduction ; *Protein Interaction Domains and Motifs ; Computational Biology ; }, abstract = {MOTIVATION: Bistability is one of the salient dynamical features in various all-or-none kinds of decision-making processes. The presence of bistability in a cell signalling network plays a key role in input-output (I/O) relation. Our study is aiming to capture and emphasize the role of motif structure influencing the I/O relation between two nodes in the context of bistability. Here, a model-based analysis is made to investigate the critical conditions responsible for the emergence of different bistable protein-protein interaction (PPI) motifs and their possible applications to find the potential drug-targets.<br><br>RESULTS: The global sensitivity analysis is used to identify sensitive parameters and their role in maintaining the bistability. Additionally, the bistable switching through hysteresis is explored to develop an understanding of the underlying mechanisms involved in the cell signalling processes, when significant motifs exhibiting bistability have emerged. Further, we elaborate the application of the results by the implication of the emerged PPI motifs to identify potential drug-targets in three cancer networks, which is validated with existing databases. The influence of stochastic perturbations that could hinder desired functionality of any signalling networks is also described here.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid37043542, year = {2023}, author = {Labbé, F and Abdeladhim, M and Abrudan, J and Araki, AS and Araujo, RN and Arensburger, P and Benoit, JB and Brazil, RP and Bruno, RV and Bueno da Silva Rivas, G and Carvalho de Abreu, V and Charamis, J and Coutinho-Abreu, IV and da Costa-Latgé, SG and Darby, A and Dillon, VM and Emrich, SJ and Fernandez-Medina, D and Figueiredo Gontijo, N and Flanley, CM and Gatherer, D and Genta, FA and Gesing, S and Giraldo-Calderón, GI and Gomes, B and Aguiar, ERGR and Hamilton, JGC and Hamarsheh, O and Hawksworth, M and Hendershot, JM and Hickner, PV and Imler, JL and Ioannidis, P and Jennings, EC and Kamhawi, S and Karageorgiou, C and Kennedy, RC and Krueger, A and Latorre-Estivalis, JM and Ligoxygakis, P and Meireles-Filho, ACA and Minx, P and Miranda, JC and Montague, MJ and Nowling, RJ and Oliveira, F and Ortigão-Farias, J and Pavan, MG and Horacio Pereira, M and Nobrega Pitaluga, A and Proveti Olmo, R and Ramalho-Ortigao, M and Ribeiro, JMC and Rosendale, AJ and Sant'Anna, MRV and Scherer, SE and Secundino, NFC and Shoue, DA and da Silva Moraes, C and Gesto, JSM and Souza, NA and Syed, Z and Tadros, S and Teles-de-Freitas, R and Telleria, EL and Tomlinson, C and Traub-Csekö, YM and Marques, JT and Tu, Z and Unger, MF and Valenzuela, J and Ferreira, FV and de Oliveira, KPV and Vigoder, FM and Vontas, J and Wang, L and Weedall, GD and Zhioua, E and Richards, S and Warren, WC and Waterhouse, RM and Dillon, RJ and McDowell, MA}, title = {Genomic analysis of two phlebotomine sand fly vectors of leishmania from the new and old World.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {4}, pages = {e0010862}, doi = {10.1371/journal.pntd.0010862}, pmid = {37043542}, issn = {1935-2735}, abstract = {Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.}, }
@article {pmid37040629, year = {2023}, author = {Beauchamp, AM and Lehmann, CU and Medford, RJ and Hughes, AE}, title = {Correction: The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e47896}, doi = {10.2196/47896}, pmid = {37040629}, issn = {1438-8871}, abstract = {[This corrects the article DOI: 10.2196/43623.].}, }
@article {pmid34469515, year = {2021}, author = {Sundell, D and Öhrman, C and Svensson, D and Karlsson, E and Brindefalk, B and Myrtennäs, K and Ahlinder, J and Antwerpen, MH and Walter, MC and Forsman, M and Stenberg, P and Sjödin, A}, title = {FlexTaxD: flexible modification of taxonomy databases for improved sequence classification.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {21}, pages = {3932-3933}, doi = {10.1093/bioinformatics/btab621}, pmid = {34469515}, issn = {1367-4811}, mesh = {*Software ; Databases, Factual ; }, abstract = {SUMMARY: The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.<br><br>Source code is freely available at https://github.com/FOI-Bioinformatics/flextaxd and installable through Bioconda.}, }
@article {pmid37025368, year = {2022}, author = {Lohse, K and Höök, L and Näsvall, K and Backström, N and ,  and ,  and ,  and , }, title = {The genome sequence of the wood white butterfly, Leptidea sinapis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {254}, pmid = {37025368}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Leptidea sinapis (the wood white; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 686 megabases in span. The majority (99.99%) of the assembly is scaffolded into 48 chromosomal pseudomolecules, with three Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 14,800 protein coding genes.}, }
@article {pmid37022698, year = {2023}, author = {Nartker, M and Zhou, Z and Firestone, C}, title = {When will AI misclassify? Intuiting failures on natural images.}, journal = {Journal of vision}, volume = {23}, number = {4}, pages = {4}, pmid = {37022698}, issn = {1534-7362}, mesh = {Humans ; *Artificial Intelligence ; *Image Interpretation, Computer-Assisted ; }, abstract = {Machine recognition systems now rival humans in their ability to classify natural images. However, their success is accompanied by a striking failure: a tendency to commit bizarre misclassifications on inputs specifically selected to fool them. What do ordinary people know about the nature and prevalence of such classification errors? Here, five experiments exploit the recent discovery of "natural adversarial examples" to ask whether naive observers can predict when and how machines will misclassify natural images. Whereas classical adversarial examples are inputs that have been minimally perturbed to induce misclassifications, natural adversarial examples are simply unmodified natural photographs that consistently fool a wide variety of machine recognition systems. For example, a bird casting a shadow might be misclassified as a sundial, or a beach umbrella made of straw might be misclassified as a broom. In Experiment 1, subjects accurately predicted which natural images machines would misclassify and which they would not. Experiments 2 through 4 extended this ability to how the images would be misclassified, showing that anticipating machine misclassifications goes beyond merely identifying an image as nonprototypical. Finally, Experiment 5 replicated these findings under more ecologically valid conditions, demonstrating that subjects can anticipate misclassifications not only under two-alternative forced-choice conditions (as in Experiments 1-4), but also when the images appear one at a time in a continuous stream-a skill that may be of value to human-machine teams. We suggest that ordinary people can intuit how easy or hard a natural image is to classify, and we discuss the implications of these results for practical and theoretical issues at the interface of biological and artificial vision.}, }
@article {pmid36725822, year = {2023}, author = {Pernet, C and Svarer, C and Blair, R and Van Horn, JD and Poldrack, RA}, title = {On the Long-term Archiving of Research Data.}, journal = {Neuroinformatics}, volume = {21}, number = {2}, pages = {243-246}, pmid = {36725822}, issn = {1559-0089}, mesh = {*Information Dissemination ; *Information Storage and Retrieval ; }, abstract = {Accessing research data at any time is what FAIR (Findable Accessible Interoperable Reusable) data sharing aims to achieve at scale. Yet, we argue that it is not sustainable to keep accumulating and maintaining all datasets for rapid access, considering the monetary and ecological cost of maintaining repositories. Here, we address the issue of cold data storage: when to dispose of data for offline storage, how can this be done while maintaining FAIR principles and who should be responsible for cold archiving and long-term preservation.}, }
@article {pmid37022232, year = {2023}, author = {Zimmerman, S and Tierney, BT and Patel, CJ and Kostic, AD}, title = {Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0011823}, doi = {10.1128/msystems.00118-23}, pmid = {37022232}, issn = {2379-5077}, abstract = {Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.}, }
@article {pmid36948010, year = {2023}, author = {Hao, N and Sun, P and Zhao, W and Li, X}, title = {Application of a developed triple-classification machine learning model for carcinogenic prediction of hazardous organic chemicals to the US, EU, and WHO based on Chinese database.}, journal = {Ecotoxicology and environmental safety}, volume = {255}, number = {}, pages = {114806}, doi = {10.1016/j.ecoenv.2023.114806}, pmid = {36948010}, issn = {1090-2414}, mesh = {Bayes Theorem ; Carcinogenesis ; *Carcinogens/toxicity/chemistry ; *Hazardous Substances/chemistry/toxicity ; *Machine Learning ; *Organic Chemicals/toxicity/chemistry ; Support Vector Machine ; World Health Organization ; Algorithms ; United States ; European Union ; China ; Databases, Factual ; }, abstract = {Cancer, the second largest human disease, has become a major public health problem. The prediction of chemicals' carcinogenicity before their synthesis is crucial. In this paper, seven machine learning algorithms (i.e., Random Forest (RF), Logistic Regression (LR), Support Vector Machines (SVM), Complement Naive Bayes (CNB), K-Nearest Neighbor (KNN), XGBoost, and Multilayer Perceptron (MLP)) were used to construct the carcinogenicity triple classification prediction (TCP) model (i.e., 1A, 1B, Category 2). A total of 1444 descriptors of 118 hazardous organic chemicals were calculated by Discovery Studio 2020, Sybyl X-2.0 and PaDEL-Descriptor software. The constructed carcinogenicity TCP model was evaluated through five model evaluation indicators (i.e., Accuracy, Precision, Recall, F1 Score and AUC). The model evaluation results show that Accuracy, Precision, Recall, F1 Score and AUC evaluation indicators meet requirements (greater than 0.6). The accuracy of RF, LR, XGBoost, and MLP models for predicting carcinogenicity of Category 2 is 91.67%, 79.17%, 100%, and 100%, respectively. In addition, the constructed machine learning model in this study has potential for error correction. Taking XGBoost model as an example, the predicted carcinogenicity level of 1,2,3-Trichloropropane (96-18-4) is Category 2, but the actual carcinogenicity level is 1B. But the difference between Category 2 and 1B is only 0.004, indicating that the XGBoost is one optimum model of the seven constructed machine learning models. Besides, results showed that functional groups like chlorine and benzene ring might influence the prediction of carcinogenic classification. Therefore, considering functional group characteristics of chemicals before constructing the carcinogenicity prediction model of organic chemicals is recommended. The predicted carcinogenicity of the organic chemicals using the optimum machine leaning model (i.e., XGBoost) was also evaluated and verified by the toxicokinetics. The RF and XGBoost TCP models constructed in this paper can be used for carcinogenicity detection before synthesizing new organic substances. It also provides technical support for the subsequent management of organic chemicals.}, }
@article {pmid37021064, year = {2023}, author = {Keller, R and Spanu, A and Puhan, MA and Flahault, A and Lovis, C and Mütsch, M and Beau-Lejdstrom, R}, title = {Social media and internet search data to inform drug utilization: A systematic scoping review.}, journal = {Frontiers in digital health}, volume = {5}, number = {}, pages = {1074961}, pmid = {37021064}, issn = {2673-253X}, abstract = {INTRODUCTION: Drug utilization is currently assessed through traditional data sources such as big electronic medical records (EMRs) databases, surveys, and medication sales. Social media and internet data have been reported to provide more accessible and more timely access to medications' utilization.<br><br>OBJECTIVE: This review aims at providing evidence comparing web data on drug utilization to other sources before the COVID-19 pandemic.<br><br>METHODS: We searched Medline, EMBASE, Web of Science, and Scopus until November 25th, 2019, using a predefined search strategy. Two independent reviewers conducted screening and data extraction.<br><br>RESULTS: Of 6,563 (64%) deduplicated publications retrieved, 14 (0.2%) were included. All studies showed positive associations between drug utilization information from web and comparison data using very different methods. A total of nine (64%) studies found positive linear correlations in drug utilization between web and comparison data. Five studies reported association using other methods: One study reported similar drug popularity rankings using both data sources. Two studies developed prediction models for future drug consumption, including both web and comparison data, and two studies conducted ecological analyses but did not quantitatively compare data sources. According to the STROBE, RECORD, and RECORD-PE checklists, overall reporting quality was mediocre. Many items were left blank as they were out of scope for the type of study investigated.<br><br>CONCLUSION: Our results demonstrate the potential of web data for assessing drug utilization, although the field is still in a nascent period of investigation. Ultimately, social media and internet search data could be used to get a quick preliminary quantification of drug use in real time. Additional studies on the topic should use more standardized methodologies on different sets of drugs in order to confirm these findings. In addition, currently available checklists for study quality of reporting would need to be adapted to these new sources of scientific information.}, }
@article {pmid37018807, year = {2023}, author = {Xavier, JMA and Firmino, RT and Pereira, IF and Xavier, MA and Costa, MCFD and Soares, RSC and Ribeiro, AIAM}, title = {The impact of the COVID-19 pandemic in Brazil: a study in tertiary dental care.}, journal = {Brazilian oral research}, volume = {37}, number = {}, pages = {025}, doi = {10.1590/1807-3107bor-2023.vol37.0025}, pmid = {37018807}, issn = {1807-3107}, mesh = {Humans ; *COVID-19 ; Pandemics ; Tertiary Healthcare ; Brazil ; Dental Care ; }, abstract = {The pandemic caused by coronavirus has resonated throughout different levels of health care in Brazil and, in this context, the present research aimed to evaluate this impact on tertiary dental care provided by the Unified Health System (SUS). Therefore, an ecological study was conducted with data obtained from the Hospital Information System processed by the Portal of the Department of Informatics of SUS. The sample consisted of patients of all sexes and age groups, whose Hospital Admission Authorizations (AIHs) were approved for dental tertiary care procedures from January 2015 to December 2020. Descriptive analyses and the ANOVA test with a significance level set at p < 0.05 were used. When the annual mean numbers of AIHs approved were evaluated, findings showed that on an average, the Southeast region authorized a higher number of procedures (p-value < 0.001), however, in the pandemic year (2020), a reduction of approximately 24.5% of these hospitalizations occurred throughout Brazil, with the Midwest being the region most affected (32.12%). A percentage increase occurred in the Surgical Treatment of Oral sinus/Oral nasal Fistula (16.1%), in addition to a significant decrease in performing procedures for Resection of Mouth Lesion (33.4%). In the pandemic year, there was a reduction of 14% in expenditures related to hospital services and 23.26% related to professional services. It was concluded that the data presented demonstrated a significant reduction in AIHs for tertiary dental care in the pandemic year.}, }
@article {pmid37016902, year = {2023}, author = {Pandit, AA and Mahashabde, RV and Brown, CC and Acharya, M and Shoults, CC and Eswaran, H and Hayes, CJ}, title = {Association between broadband capacity and telehealth utilization among Medicare Fee-for-service beneficiaries during the COVID-19 pandemic.}, journal = {Journal of telemedicine and telecare}, volume = {}, number = {}, pages = {1357633X231166026}, doi = {10.1177/1357633X231166026}, pmid = {37016902}, issn = {1758-1109}, abstract = {BACKGROUND: Telehealth is a rapidly growing modality for expanding healthcare access, especially in the post-COVID-19 era. However, telehealth requires high-quality broadband, thus making broadband a social determinant of health. The objective of this study was to evaluate the association between broadband access and telehealth utilization across the United States during the COVID-19 pandemic.<br><br>METHODS: Using a cross-sectional, ecological study design, we merged county-level data on broadband capacity (Microsoft's Rural Broadband Initiative), telehealth utilization among Medicare Fee-for-Service beneficiaries from January through September 2020 (CareJourney), and county-level socioeconomic characteristics (Area Health Resources Files). Multivariable linear regression was used to estimate the association between broadband capacity, county-level characteristics, and telehealth utilization.<br><br>RESULTS: Among the 3107 counties, those with the greatest broadband availability (quintile 5) had 47% higher telehealth utilization compared to counties with the least broadband availability (quintile 1). In the adjusted model, a 1 standard deviation (SD) increase in broadband access was associated with a 1.54 percentage point (pp) increase in telehealth utilization (P&#x2009;<&#x2009;0.001). Rural county designation (-1.96 pp; P&#x2009;<&#x2009;0.001) and 1 SD increases in average Medicare beneficiary age (-1.34 pp; P&#x2009;=&#x2009;0.001), number of nursing home beds per 1000 individuals (-0.38 pp; P&#x2009;=&#x2009;0.002), and proportion of Native Americans/Pacific Islanders (-0.59 pp; P&#x2009;<&#x2009;0.001) were associated with decreased telehealth utilization.<br><br>CONCLUSION: The association between broadband access and telehealth utilization and the decreased telehealth utilization in rural areas highlight the importance of broadband access for healthcare access and the need to continue investing in broadband infrastructure to promote equitable healthcare access across populations.}, }
@article {pmid37011221, year = {2023}, author = {Still, CJ and Page, GFM and Rastogi, B and Griffith, DM and Aubrecht, DM and Kim, Y and Burns, SP and Hanson, CV and Kwon, H and Hawkins, L and Meinzer, FC and Sevanto, S and Roberts, DA and Goulden, M and Pau, S and Detto, M and Helliker, BR and Richardson, AD}, title = {Reply to Garen et al.: Within-canopy temperature data also do not support limited homeothermy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {15}, pages = {e2302515120}, doi = {10.1073/pnas.2302515120}, pmid = {37011221}, issn = {1091-6490}, mesh = {Temperature ; *Body Temperature Regulation ; }, }
@article {pmid36478393, year = {2023}, author = {Keck, F and Couton, M and Altermatt, F}, title = {Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses.}, journal = {Molecular ecology resources}, volume = {23}, number = {4}, pages = {742-755}, doi = {10.1111/1755-0998.13746}, pmid = {36478393}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic ; Biodiversity ; Ecology ; Databases, Nucleic Acid ; *DNA, Environmental ; }, abstract = {Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These databases vary in completeness and availability, depending on the taxonomic group studied and the genetic region targeted. The incompleteness of reference databases is an important argument to explain the nondetection by metabarcoding of species supposedly present. However, there exist further and generally overlooked problems with reference databases that can lead to false or inaccurate inferences of taxonomic assignment. Here, we synthesize all possible problems inherent to reference databases. In particular, we identify a complete, mutually nonexclusive list of seven classes of challenges when it comes to selecting, developing and using a reference database for taxonomic assignment. These are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) taxonomic conflict, (v) low taxonomic resolution, (vi) missing taxa and (vii) missing intraspecific variants. For each problem identified, we provide a description of possible consequences on the taxonomic assignment process. We illustrate the respective problem with examples taken from the literature or obtained by quantitative analyses of public databases, such as GenBank or BOLD. Finally, we discuss possible solutions to the identified problems and how to navigate them. Only by raising users' awareness of the limitations of metabarcoding data and DNA reference databases will adequate interpretations of these data be achieved.}, }
@article {pmid37008251, year = {2022}, author = {Boyes, D and Wright, C and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the peppered moth, Biston betularia Linnaeus, 1758.}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {97}, pmid = {37008251}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Biston betularia (the peppered moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 405 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.Gene annotation of this assembly on Ensembl has identified 12,251 protein coding genes.}, }
@article {pmid37006240, year = {2023}, author = {Yang, W and Wei, C and Cheng, J and Ding, R and Li, Y and Wang, Y and Yang, Y and Wang, J}, title = {BTG2 and SerpinB5, a novel gene pair to evaluate the prognosis of lung adenocarcinoma.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1098700}, pmid = {37006240}, issn = {1664-3224}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; Molecular Docking Simulation ; *Lung Neoplasms/genetics ; *Adenocarcinoma of Lung/genetics ; Prognosis ; Tumor Microenvironment ; *Immediate-Early Proteins/genetics ; Tumor Suppressor Proteins/genetics ; }, abstract = {INTRODUCTION: Lung adenocarcinoma (LUAD), as the most frequent pathological subtype of non-small cell lung cancer, is often characterized by poor prognosis and low 5-year survival rate. Exploriton of new biomarkers and accurate molecular mechanisms for effectively predicting the prognosis of LUAD patients is still necessary. Presently, BTG2 and SerpinB5, which play important roles in tumors, are studied as a gene pair for the first time with the aim of exploring whether they can be used as potential prognostic markers.<br><br>METHODS: Using the bioinformatics method to explore whether BTG2 and SerpinB5 can become independent prognostic factors, and explore their clinical application value and whether they can be used as immunotherapeutic markers. In addition, we also verify the conclusions obtained from external datasets, molecular docking, and SqRT-PCR.<br><br>RESULTS: The results show that compared with normal lung tissue, BTG2 expression level was down-regulated and SerpinB5 was up-regulated in LUAD. Additionally, Kaplan-Meier survival analysis demonstrate that the prognosis of low expression level of BTG2 was poor, and that of high expression level of SerpinB5 was poor, suggesting that both of them can be used as independent prognostic factors. Moreover, the prognosis models of the two genes were constructed respectively in this study, and their prediction effect was verified by external data. Besides, ESTIMATE algorithm reveals the relationship between this gene pair and the immune microenvironment. Furthermore, patients with a high expression level of BTG2 and a low expression level of SerpinB5 have higher immunophenoscore for CTLA-4 and PD-1 inhibitors than patients with a low expression level of BTG2 and a high expression level of SerpinB5, indicating that such patients have a more obvious effect of immunotherapy.<br><br>DISCUSSION: Collectively, all the results demonstrate that BTG2 and SerpinB5 might serve as potential prognostic biomarkers and novel therapeutic targets for LUAD.}, }
@article {pmid37004043, year = {2023}, author = {Khan, AH and Adil, M and Aziz, MA and Sõukand, R and Pieroni, A}, title = {Traditional foraging for ecological transition? Wild food ethnobotany among three ethnic groups in the highlands of the eastern Hindukush, North Pakistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {19}, number = {1}, pages = {9}, pmid = {37004043}, issn = {1746-4269}, abstract = {BACKGROUND: The Patrak Valley is home to communities, which have been inextricably linked with nature for generations, and local plant knowledge (LPK) represents an important part of their local cultural diversity. In general, globalization has come at the expense of local plant knowledge among several mountain societies, and therefore the current investigation has been undertaken to record the (possibly) last remaining wild food plant/mushroom foraging practices among Pathans, Kohistanis, and Gujjars living in the highlands of the Hindukush, North Pakistan.<br><br>METHODS: Data on the uses of wild food plants and mushrooms (WFPs) were collected through 120 semi-structured interviews. The data were cross-culturally compared among the three linguistic groups. Venn diagrams were used to visualize the comparative analysis. To determine the patterns of similarities in plant use among the different ethnic groups, we used the Jaccard similarity index (JI). The recorded data were also compared with the existing Pakistani food ethnobotanical literature.<br><br>RESULTS: A total of 68 WFPs were recorded, the majority of which were used as raw snacks and as cooked vegetables. Fruit was the most frequently reported plant part among the three researched groups. Cross-cultural comparison revealed that 37% of the used plants were commonly shared by the three studied groups. Pathans have retained rich knowledge on WFPs, and they show a comparatively closer affinity with Kohistanis is the use of WFPs compared to Gujjars. While we observed some idiosyncrasies for each of the researched groups, the distinctive plant uses among Gujjars provide insight into their food ecology, their particular human-ecological system centered on mobile pastoralism and their limited exchanges of local food/ecological knowledge due to endogamic patterns. A literature survey revealed some novel or little-known ingredients within Pakistani food ethnobotany/ethnomycology, such as Aesculus indica, Agaricus campestris, Apteranthes tuberculata, Duchesnea indica, Equisetum arvense, Eremurus himalaicus, Isodon rugosus, Morella esculenta, Sophora mollis, and Drimia indica.<br><br>CONCLUSION: The researched communities have retained important plant knowledge which could be implemented through future development programs considering that most of these traditional foraging practices fulfill environmental and social sustainability standards. Further field studies are required to thoroughly investigate the patterns of foraging among highland pastoral societies in other parts of the Hindukush region and especially their potential for the ongoing ecological transition.}, }
@article {pmid37003550, year = {2023}, author = {Romero Starke, K and Schubert, M and Kaboth, P and Gerlach, J and Hegewald, J and Reusche, M and Friedemann, D and Zülke, A and Riedel-Heller, SG and Zeeb, H and Seidler, A}, title = {Traffic noise annoyance in the LIFE-adult study in Germany: Exposure-response relationships and a comparison to the WHO curves.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115815}, doi = {10.1016/j.envres.2023.115815}, pmid = {37003550}, issn = {1096-0953}, abstract = {BACKGROUND: Noise annoyance is the second-highest cause of lost disability-adjusted life-years due to environmental noise in Europe. Evidence on exposure-response relationships (ERRs) for traffic noise annoyance with more accurate exposure values is still needed.<br><br>OBJECTIVES: In an analysis of the population-based LIFE-Adult study in Leipzig, Germany, we aimed to investigate the effect of road, railway (train and tram), and aircraft noise on high annoyance (HA).<br><br>METHODS: Traffic exposure data was taken for 2012 and data on noise annoyance was evaluated between 2018 and 2021. HA was defined according to international standardized norms. We calculated risk estimates using logistic regression, controlling for age, sex, and socioeconomic status, and compared our ERRs with those from the last WHO review on this topic.<br><br>RESULTS: Aircraft noise had the highest relative risk for noise-related HA (OR&#x202f;=&#x202f;12.7, 95% CI: 9.37-17.10 per 10&#x202f;dB Lden increase). The road and railway traffic risk estimates were similar to each other (road: OR&#x202f;=&#x202f;3.55, 95% CI: 2.78-4.54; railway: OR&#x202f;=&#x202f;3.31, 95% CI: 2.77-3.97 per 10&#x202f;dB Lden increase). Compared to the WHO curves, the proportion of highly annoyed individuals was somewhat lower for road and rail traffic noise, but higher for aircraft noise.<br><br>DISCUSSION: Aircraft noise is particularly annoying. There were differences between our study's ERRs and those in the WHO review, especially for aircraft noise. These differences may be partly explained by the improved accuracy of the exposure values, as we considered secondary road networks and tram noise, and by a lack of a nighttime flight ban at the Leipzig airport. Geographical, regional and climatic variations, inconsistency in HA cut-offs, as well as temporal developments in the annoyance experience may also explain the differences. Since ERRs serve as a basis for decision making in public policies, regular updates of the curves based on new evidence is recommended.}, }
@article {pmid36998243, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Boyes, C and , }, title = {The genome sequence of the pale mottled willow, Caradrina clavipalpis (Scopoli, 1763).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {225}, pmid = {36998243}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.}, }
@article {pmid36992446, year = {2023}, author = {Howison, M and Gillani, FS and Novitsky, V and Steingrimsson, JA and Fulton, J and Bertrand, T and Howe, K and Civitarese, A and Bhattarai, L and MacAskill, M and Ronquillo, G and Hague, J and Dunn, CW and Bandy, U and Hogan, JW and Kantor, R}, title = {An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992446}, issn = {1999-4915}, support = {R01 AI136058, K24 AI134359, P30 AI042853/NH/NIH HHS/United States ; }, mesh = {Humans ; *HIV Infections/diagnosis/epidemiology ; Public Health ; Phylogeny ; Prospective Studies ; *HIV-1/genetics ; *HIV Seropositivity ; }, abstract = {Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.}, }
@article {pmid36989356, year = {2023}, author = {Bird, N and Ormond, L and Awah, P and Caldwell, EF and Connell, B and Elamin, M and Fadlelmola, FM and Matthew Fomine, FL and López, S and MacEachern, S and Moñino, Y and Morris, S and Näsänen-Gilmore, P and Nketsia V, NK and Veeramah, K and Weale, ME and Zeitlyn, D and Thomas, MG and Bradman, N and Hellenthal, G}, title = {Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture.}, journal = {Science advances}, volume = {9}, number = {13}, pages = {eabq2616}, pmid = {36989356}, issn = {2375-2548}, mesh = {Humans ; *Ethnicity/genetics ; Nigeria ; *Chromosomes ; Ghana ; Language ; Genetic Variation ; Genetics, Population ; }, abstract = {Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data have only been obtained from a small proportion of present-day ethnolinguistic groups. By analyzing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republic of the Congo, Ghana, Nigeria, and Sudan, we demonstrate a previously underappreciated fine-scale level of genetic structure within these countries, for example, correlating with historical polities in western Cameroon. By comparing genetic variation patterns among populations, we infer that many northern Cameroonian and Sudanese groups share genetic links with multiple geographically disparate populations, likely resulting from long-distance migrations. In Ghana and Nigeria, we infer signatures of intermixing dated to over 2000 years ago, corresponding to reports of environmental transformations possibly related to climate change. We also infer recent intermixing signals in multiple African populations, including Congolese, that likely relate to the expansions of Bantu language-speaking peoples.}, }
@article {pmid36981964, year = {2023}, author = {Sui, J and Zhang, G and Lin, T and Hamm, NAS and Li, C and Wu, X and Hu, K}, title = {Quantitative Evaluation of Spatial Accessibility of Various Urban Medical Services Based on Big Data of Outpatient Appointments.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {6}, pages = {}, pmid = {36981964}, issn = {1660-4601}, mesh = {Child ; Humans ; *Big Data ; *Outpatients ; Health Services Accessibility ; Cities ; Catchment Area, Health ; }, abstract = {Equity of urban medical services affects human health and well-being in cities and is important in building 'just' cities. We carried out a quantitative analysis of the spatial accessibility of medical services considering the diverse demands of people of different ages, using outpatient appointment big data and refining the two-step floating catchment area (2SFCA) method. We used the traditional 2SFCA method to evaluate the overall spatial accessibility of medical services of 504 communities in Xiamen city, considering the total population and the supply of medical resources. Approximately half the communities had good access to medical services. The communities with high accessibility were mainly on Xiamen Island, and those with low accessibility were further from the central city. The refined 2SFCA method showed a more diverse and complex spatial distribution of accessibility to medical services. Overall, 209 communities had high accessibility to internal medicine services, 133 to surgery services, 50 to gynecology and obstetrics services, and 18 to pediatric services. The traditional method may over-evaluate or under-evaluate the accessibility of different types of medical services for most communities compared with the refined evaluation method. Our study can provide more precise information on urban medical service spatial accessibility to support just city development and design.}, }
@article {pmid36979124, year = {2023}, author = {Schalli, M and Platzer, S and Schmutz, R and Ofner-Kopeinig, P and Reinthaler, FF and Haas, D}, title = {Dissolved Carbon Dioxide: The Lifespan of Staphylococcus aureus and Enterococcus faecalis in Bottled Carbonated Mineral Water.}, journal = {Biology}, volume = {12}, number = {3}, pages = {}, pmid = {36979124}, issn = {2079-7737}, abstract = {During the process of mineral water production, many possible contamination settings can influence the quality of bottled water. Microbial contamination can originate from different sources, for example, the ambient air, the bottles, the caps, and from the bottling machine itself. The aim of this study was to investigate the influence of three different carbon dioxide (CO2) concentrations (3.0 g/L, 5.5 g/L, and 7.0 g/L; 20 bottles each) in bottled mineral water on the bacterial growth of Staphylococcus aureus (S. aureus) and Enterococcus faecalis (Ent. faecalis). The examined mineral water was artificially contaminated before capping the bottles inside the factory. After a specific number of days, water samples were taken from freshly opened bottles and after filtration (100 mL), filters were placed on Columbia Agar with 5% Sheep blood to cultivate S. aureus and Slanetz and Bartley Agar to cultivate Ent. faecalis. The respective colony-forming units (CFU) were counted after incubation times ranging from 24 to 120 h. Colony-forming units of S. aureus were not detectable after the 16th and 27th day, whereas Ent. faecalis was not cultivable after the 5th and 13th day when stored inside the bottles. The investigation of the bottles that were stored open for a certain amount of time with CO2 bubbling out showed only single colonies for S. aureus after the 5th day and no CFUs for Ent. faecalis after the 17th day. A reduction in the two investigated bacterial strains during storage in carbonated mineral water bottles means that a proper standardized disinfection and cleaning procedure, according to valid hygiene standards of industrial bottling machines, cannot be replaced by carbonation.}, }
@article {pmid36978281, year = {2023}, author = {Stanic, B and Milošević, N and Sukur, N and Samardzija Nenadov, D and Fa Nedeljkovic, S and Škrbić, S and Andric, N}, title = {An in silico toxicogenomic approach in constructing the aflatoxin B1-mediated regulatory network of hub genes in hepatocellular carcinoma.}, journal = {Toxicology mechanisms and methods}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/15376516.2023.2196686}, pmid = {36978281}, issn = {1537-6524}, abstract = {Aflatoxin B1 (AFB1) can cause hepatocellular carcinoma (HCC) through a mutagenic mode of action but can also lead to global changes in gene expression; however, the AFB1 network of molecular pathways involved in HCC is not known. Here, we used toxicogenomic data from human liver cells exposed to AFB1 to infer the network of AFB1-responsive molecular pathways involved in HCC. The following computational tools: STRING, MCODE, cytoHubba, iRegulon, kinase enrichment tool KEA3, and DAVID were used to identify protein-protein interaction network, hub genes, transcription factors (TFs), upstream kinases, and biological processes (BPs). Predicted molecular events were validated with an external dataset, whereas the hub genes in HCC were validated using the UALCAN database. The results revealed an association between AFB1 and the hub genes involved in cell cycle. We identified TFs that regulate the hub genes and linked them with upstream kinases including cyclin-dependent kinases, mitogen-activated protein kinase 1, and AKT. This approach enabled the construction of the AFB1-mediated regulatory network consisting of upstream kinases, TFs, hub genes, and BPs, thus revealing the signaling hierarchy and information flow that may contribute to AFB1-induced HCC. This could be a useful tool in predicting the molecular mechanisms involved in chemical-induced diseases when available toxicogenomic data exist.}, }
@article {pmid36976384, year = {2023}, author = {Huang, F and Chen, C}, title = {GIS-based approach and multivariate statistical analysis for identifying sources of heavy metals in marine sediments from the coast of Hong Kong.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {4}, pages = {518}, pmid = {36976384}, issn = {1573-2959}, mesh = {Hong Kong ; Geographic Information Systems ; Cadmium ; Lead ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury ; Geologic Sediments/chemistry ; Risk Assessment ; China ; *Water Pollutants, Chemical/analysis ; }, abstract = {Hong Kong is an urbanized coastal city which experiences substantially different metal loads from anthropogenic activities. This study was aimed at analyzing the spatial distribution and pollution evaluation of ten selected heavy metals (As, Cd, Cr, Cu, Pb, Hg, Ni, Zn, Fe, V) in the coastal sediments of Hong Kong. The distribution of heavy metal pollution in sediments has been analyzed using the geographic information system (GIS) technique, and their pollution degrees, corresponding potential ecological risks and source identifications, have been studied by applying the enrichment factor (EF) analysis, contamination factor (CF) analysis, potential ecological risk index (PEI), and integrated multivariate statistical methods, respectively. Firstly, the GIS technique was used to access the spatial distribution of the heavy metals; the result revealed that pollution trend of these metals was decreased from the inner to the outer coast sites of the studied area. Secondly, combining the EF analysis and CF analysis, we found that the pollution degree of heavy metals followed the order of Cu > Cr > Cd > Zn > Pb > Hg > Ni > Fe > As > V. Thirdly, the PERI calculations showed that Cd, Hg, and Cu were the most potential ecological risk factors compared to other metals. Finally, cluster analysis combined with principal component analysis showed that Cr, Cu, Hg, and Ni might originate from the industrial discharges and shipping activities. V, As, and Fe were mainly derived from the natural origin, whereas Cd, Pb, and Zn were identified from the municipal discharges and industrial wastewater. In conclusion, this work should be helpful in the establishment of strategies for contamination control and optimization of industrial structures in Hong Kong.}, }
@article {pmid36976982, year = {2023}, author = {Yang, D and Zhu, H and Liu, J and Zhang, Y and Wu, S and Xiong, J and Wang, F}, title = {Risk Assessment of Heavy Metals in Soils from Four Different Industrial Plants in a Medium-Sized City in North China.}, journal = {Toxics}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/toxics11030217}, pmid = {36976982}, issn = {2305-6304}, abstract = {Laboratory experiments were carried out to analyze 39 soil samples collected from four industrial areas in Xuzhou City using inductively coupled plasma mass spectrometry and atomic fluorescence spectrometry. The descriptive statistics of heavy metals (HMs) in the soil profiles showed that the HM content at three depths was highly variable, and most coefficients of variation (CVs) showed moderate variability. The enrichment of Cd at all depths exceeded the risk screening value, and Cd pollution occurred in four plants. The enrichment of the other HMs at three depths was mainly concentrated in the pharmaceutical plant A and chemical plant C. It was found that the different HMs had different vertical distribution characteristics. For the different industrial plants, the raw materials and products not only made the spatial distribution characteristics of the HMs different, but also caused the HM types and contents to differ. The average single pollution indices of Cd in plant A, iron-steel plant B, and plant C indicated a slight pollution level. The other seven HMs in A, B, and C and all HMs in chemical plant D belonged to the safe category. The mean values of the Nemerow pollution index in the four industrial plants belonged to the warning category. The analysis showed that none of the HMs posed potential noncarcinogenic health risks, and only the carcinogenic health risks of Cr in plants A and C were unacceptable. The carcinogenic effect of Cr through the inhalation intake of resuspended soil particulates and that of Cd, Ni, and As via direct oral ingestion were the main exposure pathways.}, }
@article {pmid36972774, year = {2023}, author = {Cecchetto, M and Peruzza, L and Giubilato, E and Bernardini, I and Rovere, GD and Marcomini, A and Regoli, F and Bargelloni, L and Patarnello, T and Semenzin, E and Milan, M}, title = {An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115745}, doi = {10.1016/j.envres.2023.115745}, pmid = {36972774}, issn = {1096-0953}, abstract = {The sharp decrease in the cost of RNA-sequencing and the rapid improvement in computational analysis of eco-toxicogenomic data have brought new insights into the adverse effects of chemicals on aquatic organisms. Yet, transcriptomics is generally applied qualitatively in environmental risk assessments, hampering more effective exploitation of this evidence through multidisciplinary studies. In view of this limitation, a methodology is here presented to quantitatively elaborate transcriptional data in support to environmental risk assessment. The proposed methodology makes use of results from the application of Gene Set Enrichment Analysis to recent studies investigating the response of Mytilus galloprovincialis and Ruditapes philippinarum exposed to contaminants of emerging concern. The degree of changes in gene sets and the relevance of physiological reactions are integrated in the calculation of a hazard index. The outcome is then classified according to five hazard classes (from absent to severe), providing an evaluation of whole-transcriptome effects of chemical exposure. The application to experimental and simulated datasets proved that the method can effectively discriminate different levels of altered transcriptomic responses when compared to expert judgement (Spearman correlation coefficient of 0.96). A further application to data collected in two independent studies of Salmo trutta and Xenopus tropicalis exposed to contaminants confirmed the potential extension of the methodology to other aquatic species. This methodology can serve as a proof of concept for the integration of "genomic tools" in environmental risk assessment based on multidisciplinary investigations. To this end, the proposed transcriptomic hazard index can now be incorporated into quantitative Weight of Evidence approaches and weighed, with results from other types of analysis, to elucidate the role of chemicals in adverse ecological effects.}, }
@article {pmid36972109, year = {2023}, author = {Beauchamp, AM and Lehmann, CU and Medford, RJ and Hughes, AE}, title = {The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.}, journal = {Journal of medical Internet research}, volume = {25}, number = {}, pages = {e43623}, doi = {10.2196/43623}, pmid = {36972109}, issn = {1438-8871}, mesh = {Adult ; Humans ; United States/epidemiology ; *Social Media ; Cross-Sectional Studies ; Depression/epidemiology ; Income ; Mental Health ; }, abstract = {BACKGROUND: Social connectedness decreases human mortality, improves cancer survival, cardiovascular health, and body mass, results in better-controlled glucose levels, and strengthens mental health. However, few public health studies have leveraged large social media data sets to classify user network structure and geographic reach rather than the sole use of social media platforms.<br><br>OBJECTIVE: The objective of this study was to determine the association between population-level digital social connectedness and reach and depression in the population across geographies of the United States.<br><br>METHODS: Our study used an ecological assessment of aggregated, cross-sectional population measures of social connectedness, and self-reported depression across all counties in the United States. This study included all 3142 counties in the contiguous United States. We used measures obtained between 2018 and 2020 for adult residents in the study area. The study's main exposure of interest is the Social Connectedness Index (SCI), a pair-wise composite index describing the "strength of connectedness between 2 geographic areas as represented by Facebook friendship ties." This measure describes the density and geographical reach of average county residents' social network using Facebook friendships and can differentiate between local and long-distance Facebook connections. The study's outcome of interest is self-reported depressive disorder as published by the Centers for Disease Control and Prevention.<br><br>RESULTS: On average, 21% (21/100) of all adult residents in the United States reported a depressive disorder. Depression frequency was the lowest for counties in the Northeast (18.6%) and was highest for southern counties (22.4%). Social networks in northeastern counties involved moderately local connections (SCI 5-10 the 20th percentile for n=70, 36% of counties), whereas social networks in Midwest, southern, and western counties contained mostly local connections (SCI 1-2 the 20th percentile for n=598, 56.7%, n=401, 28.2%, and n=159, 38.4%, respectively). As the quantity and distance that social connections span (ie, SCI) increased, the prevalence of depressive disorders decreased by 0.3% (SE 0.1%) per rank.<br><br>CONCLUSIONS: Social connectedness and depression showed, after adjusting for confounding factors such as income, education, cohabitation, natural resources, employment categories, accessibility, and urbanicity, that a greater social connectedness score is associated with a decreased prevalence of depression.}, }
@article {pmid36966822, year = {2023}, author = {Song, W and Song, W}, title = {Cropland fallow reduces agricultural water consumption by 303 million tons annually in Gansu Province, China.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163013}, doi = {10.1016/j.scitotenv.2023.163013}, pmid = {36966822}, issn = {1879-1026}, abstract = {The high-intensity utilization of global cropland causes water shortage and food crisis, which seriously affects the realization of SDG 2 (zero hunger), SDG 6 (clean water and sanitation) and SDG 15 (life on land), and threatens the sustainable social, economic and ecological development. Cropland fallow can not only improve the quality of cropland and maintain ecosystem balance, but also have a significant water-saving effect. However, in most developing countries, such as China, cropland fallow has not yet been widely promoted, and there are few reliable fallow cropland fallow identification methods, making it even more challenging to assess the water-saving effect. To remedy this deficit, we propose a framework for mapping cropland fallow and evaluating its water savings. First, we used the Landsat series of data to interpret the annual land use/cover changes in Gansu Province, China from 1991 to 2020. Subsequently, the spatial-temporal variation of cropland fallow in Gansu province (giving up farming for one to two years) was mapped. Finally, we evaluated the water-saving effect of cropland fallow using evapotranspiration, precipitation, irrigation maps, and crop-related data, instead of actual water consumption. The results showed that the mapping accuracy of fallow land in Gansu Province was 79.50 %, which was higher than that of most known fallow mapping studies. From 1993 to 2018, the average annual fallow rate in Gansu Province, China, was 10.86 %, which was at a low level in arid/semi-arid regions worldwide. More importantly, from 2003 to 2018, cropland fallow reduces annual water consumption of 303.26 million tons in Gansu Province, accounting for 3.44 % of agricultural water use in Gansu Province and equivalent to the annual water demand of 655,000 people in Gansu Province. Based on our research, we speculate that the increasing pilot projects of cropland fallow in China can bring significant water-saving effects and help achieve China's Sustainable Development Goals.}, }
@article {pmid36868153, year = {2023}, author = {Jin, H and Zhihong, P and Jiaqing, Z and Chuxuan, L and Lu, T and Jun, J and Xinghua, L and Wenyan, G and Junkang, G and Binbin, S and Shengguo, X}, title = {Source apportionment and quantitative risk assessment of heavy metals at an abandoned zinc smelting site based on GIS and PMF models.}, journal = {Journal of environmental management}, volume = {336}, number = {}, pages = {117565}, doi = {10.1016/j.jenvman.2023.117565}, pmid = {36868153}, issn = {1095-8630}, mesh = {Humans ; Zinc/analysis ; Geographic Information Systems ; Lead ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Soil ; China ; Risk Assessment ; Cadmium ; }, abstract = {The abandoned smelters have caused serious hazards to the surrounding environment and residents. Taking an abandoned zinc smelter in southern China as an example, a total of 245 soil samples were collected to study spatial heterogeneity, source apportionment, and source-derived risk assessment of heavy metal(loid)s (HMs) in the region. The results showed that the mean values of all HMs concentrations were higher than the local background values, with Zn, Cd, Pb, and As contamination being the most serious and their plume penetrating to the bottom layer. Four sources were identified by principal component analysis and positive matrix factorization, with their contributions to the HMs contents ranked as: surface runoff (F2, 63.2%) > surface solid waste (F1, 22.2%) > atmospheric deposition (F3, 8.5%) > parent material (F4, 6.1%). Among these, F1 was a determinant source of human health risk with a contribution rate of 60%. Therefore, F1 was considered to be the priority control factor, but it only accounted for 22.2% of HMs contents contribution. Hg dominated the ecological risk with a contribution of 91.1%. Pb (25.7%) and As (32.9%) accounted for the non-carcinogenic risk, while As (95%) dominated the carcinogenic effect. The spatial characteristics of human health risk values derived from F1 indicated that high-risk areas were mainly distributed in the casting finished products area, electrolysis area, leaching-concentration area, and fluidization roasting area. The findings highlight the significance of priority control factors (including HMs, pollution sources and functional areas) for consideration in the integrated management of this region, thus saving costs for effective soil remediation.}, }
@article {pmid36648611, year = {2023}, author = {Hu, Y and Wang, X and Xu, Y and Yang, H and Tong, Z and Tian, R and Xu, S and Yu, L and Guo, Y and Shi, P and Huang, S and Yang, G and Shi, S and Wei, F}, title = {Molecular mechanisms of adaptive evolution in wild animals and plants.}, journal = {Science China. Life sciences}, volume = {66}, number = {3}, pages = {453-495}, pmid = {36648611}, issn = {1869-1889}, mesh = {*Biological Evolution ; *Adaptation, Physiological/genetics ; *Genome, Plant/genetics ; *Animals, Wild/genetics ; Biological Coevolution/genetics ; Phenotype ; Aquatic Organisms/genetics ; Ecology/methods/trends ; Computational Biology/methods ; }, abstract = {Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.}, }
@article {pmid36964402, year = {2023}, author = {Dec, E and Clement, J and Cheng, K and Church, GM and Fossel, MB and Rehkopf, DH and Rosero-Bixby, L and Kobor, MS and Lin, DT and Lu, AT and Fei, Z and Guo, W and Chew, YC and Yang, X and Putra, SED and Reiner, AP and Correa, A and Vilalta, A and Pirazzini, C and Passarino, G and Monti, D and Arosio, B and Garagnani, P and Franceschi, C and Horvath, S}, title = {Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {36964402}, issn = {2509-2723}, support = {U01AG060908/AG/NIA NIH HHS/United States ; }, abstract = {Claims surrounding exceptional longevity are sometimes disputed or dismissed for lack of credible evidence. Here, we present three DNA methylation-based age estimators (epigenetic clocks) for verifying age claims of centenarians. The three centenarian clocks were developed based on n = 7039 blood and saliva samples from individuals older than 40, including n = 184 samples from centenarians, 122 samples from semi-supercentenarians (aged 105 +), and 25 samples from supercentenarians (aged 110 +). The oldest individual was 115 years old. Our most accurate centenarian clock resulted from applying a neural network model to a training set composed of individuals older than 40. An epigenome-wide association study of age in different age groups revealed that age effects in young individuals (age < 40) are correlated (r = 0.55) with age effects in old individuals (age > 90). We present a chromatin state analysis of age effects in centenarians. The centenarian clocks are expected to be useful for validating claims surrounding exceptional old age.}, }
@article {pmid36962744, year = {2023}, author = {Asaaga, FA and Purse, BV and Rahman, M and Srinivas, PN and Kalegowda, SD and Seshadri, T and Young, JC and Oommen, MA}, title = {The role of social vulnerability in improving interventions for neglected zoonotic diseases: The example of Kyasanur Forest Disease in India.}, journal = {PLOS global public health}, volume = {3}, number = {2}, pages = {e0000758}, pmid = {36962744}, issn = {2767-3375}, abstract = {Forest-based communities manage many risks to health and socio-economic welfare including the increasing threat of emerging zoonoses that are expected to disproportionately affect poor and marginalised groups, and further impair their precarious livelihoods, particularly in Low-and-Middle Income (LMIC) settings. Yet, there is a relative dearth of empirical research on the vulnerability and adaptation pathways of poor and marginalised groups facing emerging zoonoses. Drawing on a survey of 229 households and a series of key-informant interviews in the Western Ghats, we examine the factors affecting vulnerability of smallholder and tribal households to Kyasanur Forest Disease (KFD), an often-fatal tick-borne viral haemorrhagic fever endemic in south India. Specifically, we investigate how different socio-demographic and institutional factors interact to shape KFD vulnerability and the strategies employed by households to adapt to disease consequences. Although surveyed households generally perceived KFD as an important health issue in the study region, there was variability in concern about contracting the disease. Overall results showed that poor access to land (AOR = 0.373, 95% CI: 0.152-0.916), being at or below the poverty line (AOR = 0.253, 95% CI: 0.094-0.685) and being headed by an older person (AOR = 1.038, 95% CI: 1.006-1.071) were all significant determinants of perceived KFD vulnerability. Furthermore, KFD vulnerability is also modulated by important extra-household factors including proximity to private hospitals (AOR = 3.281, 95% CI: 1.220-8.820), main roads (AOR = 2.144, 95% CI: 1.215-3.783) and study location (AOR = 0.226, 95% CI: 0.690-0.743). Our findings highlight how homogenous characterisation of smallholder and tribal communities and the 'techno-oriented' approach of existing interventions may further marginalise the most vulnerable and exacerbate existing inequalities. These findings are important for designing context-specific and appropriate health interventions (including the prioritisation of awareness raising, knowledge networks, livelihood diversification) that enhances the resilience of at-risk social groups within the KFD context. More broadly, our findings highlight how a focus on social vulnerability can help national and international health planners improve health interventions and prioritise among diseases with respect to neglected endemic zoonoses.}, }
@article {pmid36962522, year = {2022}, author = {Sawires, R and Pearce, C and Fahey, M and Clothier, H and Gardner, K and Buttery, J}, title = {Snotwatch COVID-toes: An ecological study of chilblains and COVID-19 diagnoses in Victoria, Australia.}, journal = {PLOS global public health}, volume = {2}, number = {10}, pages = {e0000488}, pmid = {36962522}, issn = {2767-3375}, abstract = {The COVID-19 pandemic has caused widespread illness with varying clinical manifestations. One less-commonly-reported presentation of COVID-19 infection is chilblain-like lesions. We conducted an ecological analysis of chilblain presentations in comparison with confirmed and suspected COVID-19 infections in a primary care setting to establish that a relationship exists between the two. Our study collated data from three Primary Health Networks across Victoria, Australia, from 2017-2021, to understand patterns of chilblain presentations prior to and throughout the pandemic. Using a zero-inflated negative binomial regression analysis, we estimated the relationship between local minimum temperature, COVID-19 infections and the frequency of chilblain presentations. We found a 5.72 risk ratio of chilblain incidence in relation to COVID-19 infections and a 3.23 risk ratio associated with suspected COVID-19 infections. COVID-19 infections were also more strongly associated with chilblain presentations in 0-16-year-olds throughout the pandemic in Victoria. Our study statistically suggests that chilblains are significantly associated with COVID-19 infections in a primary care setting. This has major implications for clinicians aiming to diagnose COVID-19 infections or determine the cause of a presentation of chilblains. Additionally, we demonstrate the utility of large-scale primary care data in identifying an uncommon manifestation of COVID-19 infections, which will be significantly beneficial to treating physicians.}, }
@article {pmid36962247, year = {2022}, author = {Asaaga, FA and Young, JC and Srinivas, PN and Seshadri, T and Oommen, MA and Rahman, M and Kiran, SK and Kasabi, GS and Narayanaswamy, D and Schäfer, SM and Burthe, SJ and August, T and Logie, M and Chanda, MM and Hoti, SL and Vanak, AT and Purse, BV}, title = {Co-production of knowledge as part of a OneHealth approach to better control zoonotic diseases.}, journal = {PLOS global public health}, volume = {2}, number = {3}, pages = {e0000075}, pmid = {36962247}, issn = {2767-3375}, abstract = {There is increased global and national attention on the need for effective strategies to control zoonotic diseases. Quick, effective action is, however, hampered by poor evidence-bases and limited coordination between stakeholders from relevant sectors such as public and animal health, wildlife and forestry sectors at different scales, who may not usually work together. The OneHealth approach recognises the value of cross-sectoral evaluation of human, animal and environmental health questions in an integrated, holistic and transdisciplinary manner to reduce disease impacts and/or mitigate risks. Co-production of knowledge is also widely advocated to improve the quality and acceptability of decision-making across sectors and may be particularly important when it comes to zoonoses. This paper brings together OneHealth and knowledge co-production and reflects on lessons learned for future OneHealth co-production processes by describing a process implemented to understand spill-over and identify disease control and mitigation strategies for a zoonotic disease in Southern India (Kyasanur Forest Disease). The co-production process aimed to develop a joint decision-support tool with stakeholders, and we complemented our approach with a simple retrospective theory of change on researcher expectations of the system-level outcomes of the co-production process. Our results highlight that while co-production in OneHealth is a difficult and resource intensive process, requiring regular iterative adjustments and flexibility, the beneficial outcomes justify its adoption. A key future aim should be to improve and evaluate the degree of inter-sectoral collaboration required to achieve the aims of OneHealth. We conclude by providing guidelines based on our experience to help funders and decision-makers support future co-production processes.}, }
@article {pmid36958663, year = {2023}, author = {Lima, GDS and Menegario, AA and Suarez, CA and Kamazuka, SH and Gemeiner, H and Sánchez-Sarmiento, AM and Ferioli, RB and Barreto, AS}, title = {Pelagic and estuarine birds as sentinels of metal(loid)s in the South Atlantic Ocean: Ecological niches as main factors acting on bioaccumulation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121452}, doi = {10.1016/j.envpol.2023.121452}, pmid = {36958663}, issn = {1873-6424}, abstract = {Activities related to the offshore exploration and production of oil and natural gas provide economic development and an essential energy source. However, besides the risk of petroleum hydrocarbon contamination, these activities can also be sources of metals and metalloids for marine organism contamination. In this research, we evaluated the potential use of two pelagic (black-browed albatross Thalassarche melanophris and yellow-nosed albatross T. chlororhynchos) and one estuarine bird species (neotropical cormorant Nannopterum brasilianus) as sentinels of contamination of As, Cd, Cr, Cu, Pb, Mn, Mo, Zn, Ni, Ba, V, and Hg in an area under influence of oil and gas activities. The analyses were carried out in samples collected from 2015 to 2022 from 97 individuals. A factor alert; an adaptation from the contamination factor is proposed to identify individuals with high concentrations that possibly suffered contamination by anthropogenic origin. Grouping all species, the metal(loid)s with the highest concentrations were in decreasing order: Zn > Cu > Mn > Hg > As > Cd > Mo > V > Cr > Ba > Ni > Pb. Similar concentrations were observed for V, Mn, Cr and Pb among the three species. Pelagic birds showed higher levels of concentrations for Hg, As and Cd. Based on the correlations and multivariate analysis performed, the results indicate that the ecological niche factor has greater relevance in the bioaccumulation of these elements compared to the habitat. Although some individuals showed high concentrations in part of the trace elements, suggesting exposure to anthropic sources, the direct influence of oil production and exploration activities was not observed, suggesting that activities on the continent are the primary contamination source. The results of this work highlight the role of seabirds as sentinels for metal(loid)s, contributing to the knowledge of the occurrence of contaminants in the South Atlantic Ocean.}, }
@article {pmid36947115, year = {2023}, author = {Bautista, J and Schueller, SM}, title = {Understanding the Adoption and Use of Digital Mental Health Apps Among College Students: Secondary Analysis of a National Survey.}, journal = {JMIR mental health}, volume = {10}, number = {}, pages = {e43942}, doi = {10.2196/43942}, pmid = {36947115}, issn = {2368-7959}, abstract = {BACKGROUND: Increasing rates of mental health diagnoses in college students signal the need for new opportunities to support the mental health of this population. With many mental health apps being efficacious, they may be a promising resource for college campuses to provide support to their students. However, it is important to understand why (or why not) students might want to use apps and their desired features.<br><br>OBJECTIVE: Information on students' interest in mental health apps may inform which apps are to be provided and how campuses can support their use. This study aimed to understand the interest and hesitation in app use and the relationship between mental health needs, as defined by depression, anxiety, and positive mental health, and app use.<br><br>METHODS: The web-based Healthy Minds Study collected information on mental health needs, perceptions, and service use across colleges and universities. We used a sample of 989 participants who completed the survey between 2018 and 2020 and an elective module on digital mental health. We analyzed the elective module responses using a mixed methods approach, including both descriptive and inferential statistics, along with thematic coding for open text responses.<br><br>RESULTS: The Results from this study revealed that anxiety (b=-0.07; P<.001), but not depression (b=0.03; P=.12) and positive mental health (b=-0.02; P=.17), was a significant predictor of app adoption. Prominent qualitative findings indicated that the most desired app features included tips and advice, access to resources and information, and on-demand support that involves interaction throughout the day. The participants also suggested an overall desire for human interaction to be integrated into an app. As predicted, hesitancy was encountered, and the qualitative results suggested that there was a lack of interest in the adoption of mental health app and preference.<br><br>CONCLUSIONS: The findings from this study underscore that simply providing digital mental health apps as tools may be insufficient to support their use in college campuses. Although many students were open to using a mental health app, hesitation and uncertainty were common in the participant responses. Working with colleges and universities to increase digital literacy and provide resources that allow students to gauge when app use is appropriate may be helpful when implementing mental health apps as resources in college campuses.}, }
@article {pmid36946676, year = {2023}, author = {Oliveira, HC and Seabra, AB and Kondak, S and Adedokun, OP and Kolbert, Z}, title = {Multilevel approach of plant-nanomaterial relationship: from cells to living ecosystems.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erad107}, pmid = {36946676}, issn = {1460-2431}, abstract = {Due to their unique properties, nanomaterials (NMs) behave peculiarly in biosystems. Regarding plants, the interactions of NMs can be interpreted on a spatial scale: from local interactions in cells to systemic effects on whole plants and on ecosystems. Interpreted on a time scale, the effects of NMs on plants may be immediate or subsequent. At the cellular level, the composition and structure of the cell wall and membranes are modified by NMs, promoting internalization. The effects of NMs on germination and seedling physiology and on the primary and secondary metabolisms in the shoot are realized at organ and organism levels. Nanomaterials interact with the beneficial ecological partners of plants. The effects of NMs on plant growth-promoting rhizobacteria and legume-rhizobia symbiosis can be stimulating or inhibitory, depending on the concentration and type of NM. Nanomaterials exert a negative effect on arbuscular mycorrhiza, and vice versa. Pollinators are exposed to NMs, which may affect plant reproduction. The substances released by the roots influence the availability of NMs in the rhizosphere and components of plant cells trigger internalization, translocation, and transformation of NMs. Understanding of the multilevel and bidirectional relationship between plants and NMs is of great relevance in practice.}, }
@article {pmid36939939, year = {2023}, author = {Forootan, E}, title = {GIS-based slope-adjusted curve number methods for runoff estimation.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {4}, pages = {489}, pmid = {36939939}, issn = {1573-2959}, mesh = {*Water Movements ; *Geographic Information Systems ; Environmental Monitoring/methods ; Soil ; Hydrology ; Rain ; }, abstract = {Accurate estimation of surface runoff and determination of susceptible lands to runoff generation in ungauged watersheds were the problems for hydrologic engineering which could be predicted through a simple model such as Soil Conservation Service Curve Number (SCS-CN). Due to the slope effects on this method, slope adjustment for curve number was developed to improve its precision. So, the main objectives of this study were to apply GIS-based slope SCS-CN approaches for surface runoff estimation and compare the accuracy of three slope-adjusted models including: (a) model with three empirical parameters, (b) model with two parameters slope function, and (c) model with one parameter in the region located in the central part of Iran. For this purpose, soil texture, hydrologic soil group, land use, slope, and daily rainfall volume maps were utilized. In order to provide the curve number map of the study area, land use and hydrologic soil group layers built in Arc-GIS were intersected and the curve number was determined. Then, three slope adjustment equations were used to modify curve numbers of AMC-II by employing slope map. Finally, recorded runoff data of the hydrometric station were applied to assess the performance of the models through four statistical indicators of the root mean square error (RMSE), the Nash-Sutcliffe efficiency (E), the coefficient of determination [Formula: see text], and percent bias (PB). Land use map analysis showed that rangeland was the dominant land use, whereas the soil texture map specified the greatest and smallest area belonging to loam and sandy loam textures, respectively. Although the runoff results showed the overestimation of large rainfall values and underestimation for rainfall with less than 40 mm volume in both models, the values of E (0.78), RMSE (2), PB (16), and [Formula: see text] (0.88) revealed that eq. (a) with three empirical parameters was the most accurate equation. The maximum percent of runoff generated by rainfall for eqs. (a), (b), and (c) were 68.43, 67.28, and 51.57% which showed that bareland located in south part with the slope of more than 5% was susceptible to runoff generation and should be paid attention to watershed management.}, }
@article {pmid36821658, year = {2023}, author = {D'Emic, MD and O'Connor, PM and Sombathy, RS and Cerda, I and Pascucci, TR and Varricchio, D and Pol, D and Dave, A and Coria, RA and Curry Rogers, KA}, title = {Developmental strategies underlying gigantism and miniaturization in non-avialan theropod dinosaurs.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6634}, pages = {811-814}, doi = {10.1126/science.adc8714}, pmid = {36821658}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; *Dinosaurs/anatomy &amp; histology/classification/growth &amp; development ; Fossils ; Phylogeny ; *Body Size ; Datasets as Topic ; }, abstract = {In amniotes, the predominant developmental strategy underlying body size evolution is thought to be adjustments to the rate of growth rather than its duration. However, most theoretical and experimental studies supporting this axiom focus on pairwise comparisons and/or lack an explicit phylogenetic framework. We present the first large-scale phylogenetic comparative analysis examining developmental strategies underlying the evolution of body size, focusing on non-avialan theropod dinosaurs. We reconstruct ancestral states of growth rate and body mass in a taxonomically rich dataset, finding that contrary to expectations, changes in the rate and duration of growth played nearly equal roles in the evolution of the vast body size disparity present in non-avialan theropods-and perhaps that of amniotes in general.}, }
@article {pmid36937826, year = {2022}, author = {Wabnitz, K and Schwienhorst-Stich, EM and Asbeck, F and Fellmann, CS and Gepp, S and Leberl, J and Mezger, NCS and Eichinger, M}, title = {National Planetary Health learning objectives for Germany: A steppingstone for medical education to promote transformative change.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {1093720}, pmid = {36937826}, issn = {2296-2565}, mesh = {Humans ; *Education, Medical ; Curriculum ; Health Education ; Delivery of Health Care ; Germany ; }, abstract = {Physicians play an important role in adapting to and mitigating the adverse health effects of the unfolding climate and ecological crises. To fully harness this potential, future physicians need to acquire knowledge, values, skills, and leadership attributes to care for patients presenting with environmental change-related conditions and to initiate and propel transformative change in healthcare and other sectors of society including, but not limited to, the decarbonization of healthcare systems, the transition to renewable energies and the transformation of transport and food systems. Despite the potential of Planetary Health Education (PHE) to support medical students in becoming agents of change, best-practice examples of mainstreaming PHE in medical curricula remain scarce both in Germany and internationally. The process of revising and updating the Medical Licensing Regulations and the National Competency-based Catalog of Learning Objectives for Medical Education in Germany provided a window of opportunity to address this implementation challenge. In this article, we describe the development and content of national Planetary Health learning objectives for Germany. We anticipate that the learning objectives will stimulate the development and implementation of innovative Planetary Health teaching, learning and exam formats in medical schools and inform similar initiatives in other health professions. The availability of Planetary Health learning objectives in other countries will provide opportunities for cross-country and interdisciplinary exchange of experiences and validation of content, thus supporting the consolidation of Planetary Health learning objectives and the improvement of PHE for all health professionals globally.}, }
@article {pmid36934309, year = {2023}, author = {Newbury, JB and Arseneault, L and Moffitt, TE and Odgers, CL and Howe, LD and Bakolis, I and Reuben, A and Danese, A and Sugden, K and Williams, B and Rasmussen, LJH and Trotta, A and Ambler, AP and Fisher, HL}, title = {Socioenvironmental Adversity and Adolescent Psychotic Experiences: Exploring Potential Mechanisms in a UK Longitudinal Cohort.}, journal = {Schizophrenia bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1093/schbul/sbad017}, pmid = {36934309}, issn = {1745-1701}, support = {G1002190/MRC_/Medical Research Council/United Kingdom ; 218632/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; F31ES029358/ES/NIEHS NIH HHS/United States ; MR/M020894/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND AND HYPOTHESIS: Children exposed to socioenvironmental adversities (eg, urbanicity, pollution, neighborhood deprivation, crime, and family disadvantage) are more likely to subsequently develop subclinical psychotic experiences during adolescence (eg, hearing voices, paranoia). However, the pathways through which this occurs have not been previously investigated. We hypothesized that cognitive ability and inflammation would partly explain this association.<br><br>STUDY DESIGN: Data were utilized from the Environmental-Risk Longitudinal Twin Study, a cohort of 2232 children born in 1994-1995 in England and Wales and followed to age 18. Socioenvironmental adversities were measured from birth to age 10 and classified into physical risk (defined by high urbanicity and air pollution) and socioeconomic risk (defined by high neighborhood deprivation, neighborhood disorder, and family disadvantage). Cognitive abilities (overall, crystallized, fluid, and working memory) were assessed at age 12; and inflammatory markers (C-reactive protein, interleukin-6, soluble urokinase plasminogen activator receptor) were measured at age 18 from blood samples. Participants were interviewed at age 18 regarding psychotic experiences.<br><br>STUDY RESULTS: Higher physical risk and socioeconomic risk were associated with increased odds of psychotic experiences in adolescence. The largest mediation pathways were from socioeconomic risk via overall cognitive ability and crystallized ability, which accounted for ~11% and ~19% of the association with psychotic experiences, respectively. No statistically significant pathways were found via inflammatory markers in exploratory (partially cross-sectional) analyses.<br><br>CONCLUSIONS: Cognitive ability, especially crystallized ability, may partly explain the association between childhood socioenvironmental adversity and adolescent psychotic experiences. Interventions to support cognitive development among children living in disadvantaged settings could buffer them against developing subclinical psychotic phenomena.}, }
@article {pmid36932341, year = {2023}, author = {Kasmi, Y and Eschbach, E and Hanel, R}, title = {Mare-MAGE curated reference database of fish mitochondrial genes.}, journal = {BMC genomic data}, volume = {24}, number = {1}, pages = {18}, pmid = {36932341}, issn = {2730-6844}, mesh = {Animals ; Horses/genetics ; Female ; *Ecosystem ; *Genes, Mitochondrial ; Angiotensin Receptor Antagonists ; DNA Barcoding, Taxonomic ; Angiotensin-Converting Enzyme Inhibitors ; Fishes/genetics ; Databases, Nucleic Acid ; }, abstract = {Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fish meta-barcoding based on mitochondrial genes. The Mare-MAGE database contains quality-checked sequences of the mitochondrial 12S ribosomal RNA and Cytochrome c Oxidase I gene. All sequences were obtained from the National Center for Biotechnology Information- GenBank (NBCI-GenBank), the European Nucleotide Archive (ENA), AquaGene Database and BOLD database, and have undergone intensive processing. They were checked for false annotations and non-target anomalies, according to the Integrated Taxonomic Information System (ITIS) and FishBase. The dataset is compiled in ARB-Home, FASTA and Qiime2 formats, and is publicly available from the Mare-MAGE database website (http://mare-mage.weebly.com/). It includes altogether 231,333 COI and 12S rRNA gene sequences of fish, covering 19,506 species of 4,058 genera and 586 families.}, }
@article {pmid36931511, year = {2023}, author = {Zhang, B and Zheng, T and Zheng, X and Jiang, S and Cao, M and Walther, M and Lu, C}, title = {Dynamics of upstream saltwater intrusion driven by tidal river in coastal aquifers.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {162857}, doi = {10.1016/j.scitotenv.2023.162857}, pmid = {36931511}, issn = {1879-1026}, abstract = {For the coastal aquifers, recent research have shown that the tidal has a significant effect on saltwater intrusion in the near-shore aquifer. However, it is currently unclear how the tidal river contributes to the groundwater flow and salinity distribution in the upstream aquifer of the estuary. This study examined the effects of a tidal river on the dynamic characteristics of groundwater flow and salt transport in a tidal river-coastal aquifer system using field monitoring data and numerical simulations. It was found that changes in tidal-river level led to the reversal of groundwater flow. For a tidal cycle, the maximum area of seawater intrusion is about 41.16 km[2] at the end of the high tide stage. Then the area gradually decreased to 39.02 km[2] at the end of the low tide stage. More than 2 km[2] area variation can be observed in a tidal cycle. Compared to the low tide stage, the area of SWI increased by 5 % at high tide stage. The SWI region was also spreading landward from the tidal river. In addition, we quantified the water exchange and salt flux between the tidal river and aquifer. When the tidal fell below the level of the riverbed, the water exchange rate was stabilized at about -1.6 m/h. The negative value indicated that the river was recharged by the groundwater. With the increasing of tidal water level, the water exchange rate gradually changes from negative to positive and reached the maximum value of 3.2 m/h at the beginning of the falling tide stage. The presence of a physical river dam can amplify the difference in water level between high and low tides, thereby enhancing the influence of a tidal river on water exchange and salt flux. The findings lay the foundation for gaining a comprehensive understanding of the tidal river on groundwater flow and salt transport in upstream aquifers.}, }
@article {pmid36926380, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Parkerson, L and , }, title = {The genome sequence of the garden grass-veneer, Chrysoteuchia culmella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {248}, pmid = {36926380}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Chrysoteuchia culmella (the garden grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 645 megabases in span. The majority of the assembly (99.81%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl has identified 21,251 protein coding genes.}, }
@article {pmid36921166, year = {2023}, author = {Morais, LS and Pimentel, SVT and Kawa, H and Fonseca, SC}, title = {Temporal trend of congenital syphilis in the most populous municipality of metropolitan region II of Rio de Janeiro state.}, journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo}, volume = {41}, number = {}, pages = {e2021337}, pmid = {36921166}, issn = {1984-0462}, mesh = {Pregnancy ; Adolescent ; Humans ; Female ; *Syphilis, Congenital/epidemiology ; Brazil/epidemiology ; Prenatal Care ; Incidence ; Databases, Factual ; }, abstract = {OBJECTIVE: This study aimed to explore the temporal trend in congenital syphilis, according to sociodemographic and prenatal care in the city of São Gonçalo - Rio de Janeiro, from 2007 to 2018.<br><br>METHODS: Ecological time series study, with data from SINAN (Information System for Notifiable Diseases) and SINASC (Information System on Live Births databases). We calculated annual incidence (per 1,000 live births) according to sociodemographic and prenatal variables. For the same variables, we calculated trends by logarithmic regression (Joinpoint Regression), estimating the annual percentage change.<br><br>RESULTS: A total of 2,420 cases were reported from 2007 to 2018, with an increasing trend: 64.9% per year (2010-2013) and 24.9% (2013-2018). In 2018, the highest rates were in adolescents (90.6/1,000 live births), black women (87.6/1,000 live births), low-educated women (122.8/1,000 live births), and those without prenatal care (677.4/1,000 live births). The annual percentage change of these categories was, respectively, 37.3% (2010-2018), 33.5% (2012-2018), 39.9% (2014-2018), and 85.0% (2011-2015), but all categories showed a crescent trend.<br><br>CONCLUSIONS: We identified high congenital syphilis incidences and crescent trends, especially in more vulnerable groups, pointing to social and healthcare inequalities. Prenatal care needs to be more comprehensive and qualified, primarily for young, low-educated, and black women.}, }
@article {pmid36868417, year = {2023}, author = {Zhang, X and Shao, W and Huo, Y and Kong, Y and Zhang, W and Li, S and Zhou, W and Wu, X and Qin, F and Hu, X}, title = {The effects of short-term dietary exposure to SiO2 nanoparticle on the domesticated lepidopteran insect model silkworm (Bombyx mori): Evidence from the perspective of multi-omics.}, journal = {Chemosphere}, volume = {323}, number = {}, pages = {138257}, doi = {10.1016/j.chemosphere.2023.138257}, pmid = {36868417}, issn = {1879-1298}, mesh = {Animals ; *Bombyx/metabolism ; Silicon Dioxide/metabolism ; Multiomics ; Dietary Exposure ; *Nanoparticles/toxicity ; }, abstract = {Silicon dioxide nanoparticles (nSiO2) are one of the widely utilized nanoparticle (NPSs) materials, and exposure to nSiO2 is ubiquitous. With the increasing commercialization of nSiO2, the potential risk of nSiO2 release to the health and the ecological environment have been attracted more attention. In this study, the domesticated lepidopteran insect model silkworm (Bombyx mori) was utilized to evaluate the biological effects of dietary exposure to nSiO2. Histological investigations showed that nSiO2 exposure resulted in midgut tissue injury in a dose-dependent manner. Larval body mass and cocoon production were reduced by nSiO2 exposure. ROS burst was not triggered, and the activities of antioxidant enzymes were induced in the midgut of silkworm exposure to nSiO2. RNA-sequencing revealed that the differentially expressed genes induced by nSiO2 exposure were predominantly enriched into xenobiotics biodegradation and metabolism, lipid, and amino acid metabolism pathways. 16 S rDNA sequencing revealed that nSiO2 exposure altered the microbial diversity in the gut of the silkworm. Metabolomics analysis showed that the combined uni- and multivariate analysis identified 28 significant differential metabolites from the OPLS-DA model. These significant differential metabolites were predominantly enriched into the metabolic pathways, including purine metabolism and tyrosine metabolism and so. Spearman correlation analysis and the Sankey diagram established the relationship between microbe and metabolites, and some genera may play crucial and pleiotropic functions in the interaction between microbiome and host. These findings indicated that nSiO2 exposure could impact the dysregulation of genes related to xenobiotics metabolism, gut dysbiosis, and metabolic pathways and provided a valuable reference for assessing nSiO2 toxicity from a multi-dimensional perspective.}, }
@article {pmid36735127, year = {2023}, author = {Jiang, X and Sun, Y and Qu, Y and Zeng, H and Yang, J and Zhang, K and Liu, L}, title = {The development and future frontiers of global ecological restoration projects in the twenty-first century: a systematic review based on scientometrics.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {12}, pages = {32230-32245}, pmid = {36735127}, issn = {1614-7499}, mesh = {Humans ; *Publications ; *Bibliometrics ; Databases, Factual ; China ; }, abstract = {Ecological restoration projects are becoming a mainstream of research, and their studies are widely followed by scholars worldwide, yet there is no comprehensive review of this research. Nowadays, bibliometrics has attracted much attention from the scientific community, and its methodological approach allows quantitative and qualitative analysis of research performance in journals or subject areas. This paper provides a systematic and comprehensive description of the progress and hotspots of ecological restoration projects from a bibliometric perspective, based on 1173 articles in the Web of Science Core Collection (WOSCC) database. Research on ecological restoration projects has shown a positive growth trend since the twenty-first century. China and the USA are the most active countries in terms of the number of relevant articles published, and more than half of the top 10 active institutions are from China, but there is less collaboration between different countries/institutions. Research in ecological restoration projects is summarized into three main research areas: the main ecological damage problems, the impact of human beings on ecological damage, and the main methods of ecological restoration. Finally, some challenges and outlooks conducive to the rapid and balanced development of ecological restoration projects are presented, which provide valuable references and help for future researchers.}, }
@article {pmid36925815, year = {2022}, author = {Viner, AC and Malata, MP and Mtende, M and Membe-Gadama, G and Masamba, M and Makwakwa, E and Bamuya, C and Lissauer, D and Stock, SJ and Norman, JE and Reynolds, RM and Magowan, B and Freyne, B and Gadama, L and Cunningham-Burley, S and Nyondo-Mipando, L and Chipeta, E}, title = {Implementation of a novel ultrasound training programme for midwives in Malawi: A mixed methods evaluation using the RE-AIM framework.}, journal = {Frontiers in health services}, volume = {2}, number = {}, pages = {953677}, pmid = {36925815}, issn = {2813-0146}, abstract = {INTRODUCTION: Despite recommendation that all women receive an ultrasound in pregnancy prior to 24 weeks', this remains unavailable to many women in low-income countries where trained practitioners are scarce. Although many programmes have demonstrated efficacy, few have achieved longterm sustainability, with a lack of information about how best to implement such programmes. This mixed-methods study aimed to evaluate the implementation of a novel education package to teach ultrasound-naive midwives in Malawi basic obstetric ultrasound, assessing its impact in the context of the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework.<br><br>METHODS: The study ran across six sites in Malawi between October 2020 and June 2021, encompassing three phases; pre-implementation, implementation and post-implementation. Twenty nine midwives underwent a bespoke education package with matched pre and post course surveys assessed their knowledge, attitudes and confidence and "hands on" assessments evaluating practical skills. Training evaluation forms and in-depth interviews explored their satisfaction with the package, with repeat assessment and remote image review evaluating maintenance of skills.<br><br>RESULTS: 28/29 midwives completed the training, with significant increases in knowledge, confidence and practical skills. Adherence to the education package varied, however many changes to the proposed methodology were adaptive and appeared to facilitate the efficacy of the programme. Unfortunately, despite reporting approval regarding the training itself, satisfaction regarding supervision and follow up was mixed, reflecting the difficulties encountered with providing ongoing in-person and remote support.<br><br>CONCLUSION: This programme was successful in improving trainees' knowledge, confidence and skill in performing basic obstetric ultrasound, largely on account of an adaptive approach to implementation. The maintenance of ongoing support was challenging, reflected by trainee dissatisfaction. By evaluating the success of this education package based on its implementation and not just its efficacy, we have generated new insights into the barriers to sustainable upscale, specifically those surrounding maintenance.}, }
@article {pmid36921339, year = {2023}, author = {Zhang, H and Wang, X and Song, R and Ding, W and Li, F and Ji, L}, title = {Emerging Metabolic Profiles of Sulfonamide Antibiotics by Cytochromes P450: A Computational-Experimental Synergy Study on Emerging Pollutants.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c00071}, pmid = {36921339}, issn = {1520-5851}, abstract = {Metabolism, especially by CYP450 enzymes, is the main reason for mediating the toxification and detoxification of xenobiotics in humans, while some uncommon metabolic pathways, especially for emerging pollutants, probably causing idiosyncratic toxicity are easily overlooked. The pollution of sulfonamide antibiotics in aqueous system has attracted increasing public attention. Hydroxylation of the central amine group can trigger a series of metabolic processes of sulfonamide antibiotics in humans; however, this work parallelly reported the coupling and fragmenting initiated by amino H-abstraction of sulfamethoxazole (SMX) catalyzed by human CYP450 enzymes. Elucidation of the emerging metabolic profiles was mapped via a multistep synergy between computations and experiments, involving preliminary DFT computations and in vitro and in vivo assays, profiling adverse effects, and rationalizing the fundamental factors via targeted computations. Especially, the confirmed SMX dimer was shown to potentially act as a metabolism disruptor in humans, while spin aromatic delocalization resulting in the low electron donor ability of amino radicals was revealed as the fundamental factor to enable coupling of sulfonamide antibiotics by CYP450 through the nonconventional nonrebound pathway. This work may further strengthen the synergistic use of computations prior to experiments to avoid wasteful experimental screening efforts in environmental chemistry and toxicology.}, }
@article {pmid36920898, year = {2023}, author = {Helmer, EH and Kay, S and Marcano-Vega, H and Powers, JS and Wood, TE and Zhu, X and Gwenzi, D and Ruzycki, TS}, title = {Multiscale predictors of small tree survival across a heterogeneous tropical landscape.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0280322}, doi = {10.1371/journal.pone.0280322}, pmid = {36920898}, issn = {1932-6203}, abstract = {Uncertainties about controls on tree mortality make forest responses to land-use and climate change difficult to predict. We tracked biomass of tree functional groups in tropical forest inventories across Puerto Rico and the U.S. Virgin Islands, and with random forests we ranked 86 potential predictors of small tree survival (young or mature stems 2.5-12.6 cm diameter at breast height). Forests span dry to cloud forests, range in age, geology and past land use and experienced severe drought and storms. When excluding species as a predictor, top predictors are tree crown ratio and height, two to three species traits and stand to regional factors reflecting local disturbance and the system state (widespread recovery, drought, hurricanes). Native species, and species with denser wood, taller maximum height, or medium typical height survive longer, but short trees and species survive hurricanes better. Trees survive longer in older stands and with less disturbed canopies, harsher geoclimates (dry, edaphically dry, e.g., serpentine substrates, and highest-elevation cloud forest), or in intervals removed from hurricanes. Satellite image phenology and bands, even from past decades, are top predictors, being sensitive to vegetation type and disturbance. Covariation between stand-level species traits and geoclimate, disturbance and neighboring species types may explain why most neighbor variables, including introduced vs. native species, had low or no importance, despite univariate correlations with survival. As forests recovered from a hurricane in 1998 and earlier deforestation, small trees of introduced species, which on average have lighter wood, died at twice the rate of natives. After hurricanes in 2017, the total biomass of trees ≥12.7 cm dbh of the introduced species Spathodea campanulata spiked, suggesting that more frequent hurricanes might perpetuate this light-wooded species commonness. If hurricane recovery favors light-wooded species while drought favors others, climate change influences on forest composition and ecosystem services may depend on the frequency and severity of extreme climate events.}, }
@article {pmid36918541, year = {2023}, author = {Young, WJ and Haessler, J and Benjamins, JW and Repetto, L and Yao, J and Isaacs, A and Harper, AR and Ramirez, J and Garnier, S and van Duijvenboden, S and Baldassari, AR and Concas, MP and Duong, T and Foco, L and Isaksen, JL and Mei, H and Noordam, R and Nursyifa, C and Richmond, A and Santolalla, ML and Sitlani, CM and Soroush, N and Thériault, S and Trompet, S and Aeschbacher, S and Ahmadizar, F and Alonso, A and Brody, JA and Campbell, A and Correa, A and Darbar, D and De Luca, A and Deleuze, JF and Ellervik, C and Fuchsberger, C and Goel, A and Grace, C and Guo, X and Hansen, T and Heckbert, SR and Jackson, RD and Kors, JA and Lima-Costa, MF and Linneberg, A and Macfarlane, PW and Morrison, AC and Navarro, P and Porteous, DJ and Pramstaller, PP and Reiner, AP and Risch, L and Schotten, U and Shen, X and Sinagra, G and Soliman, EZ and Stoll, M and Tarazona-Santos, E and Tinker, A and Trajanoska, K and Villard, E and Warren, HR and Whitsel, EA and Wiggins, KL and Arking, DE and Avery, CL and Conen, D and Girotto, G and Grarup, N and Hayward, C and Jukema, JW and Mook-Kanamori, DO and Olesen, MS and Padmanabhan, S and Psaty, BM and Pattaro, C and Ribeiro, ALP and Rotter, JI and Stricker, BH and van der Harst, P and van Duijn, CM and Verweij, N and Wilson, JG and Orini, M and Charron, P and Watkins, H and Kooperberg, C and Lin, HJ and Wilson, JF and Kanters, JK and Sotoodehnia, N and Mifsud, B and Lambiase, PD and Tereshchenko, LG and Munroe, PB}, title = {Genetic architecture of spatial electrical biomarkers for cardiac arrhythmia and relationship with cardiovascular disease.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1411}, pmid = {36918541}, issn = {2041-1723}, support = {R01 HL118277/HL/NHLBI NIH HHS/United States ; R56 HL118277/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Cardiovascular Diseases/genetics ; *Atrioventricular Block ; Genome-Wide Association Study ; Risk Factors ; Arrhythmias, Cardiac/genetics ; Electrocardiography/methods ; Biomarkers ; }, abstract = {The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic influences with PR interval and QRS duration. Phenome-wide scanning indicate associations with atrial fibrillation, atrioventricular block and arterial embolism and genetically determined QRS-T angle measures are associated with fascicular and bundle branch block (and also atrioventricular block for the frontal QRS-T angle). We identify potential biology involved in the QRS-T angle and their genetic relationships with cardiovascular traits and diseases, may inform future research and risk prediction.}, }
@article {pmid36859581, year = {2023}, author = {Tucker, C and Brandt, M and Hiernaux, P and Kariryaa, A and Rasmussen, K and Small, J and Igel, C and Reiner, F and Melocik, K and Meyer, J and Sinno, S and Romero, E and Glennie, E and Fitts, Y and Morin, A and Pinzon, J and McClain, D and Morin, P and Porter, C and Loeffler, S and Kergoat, L and Issoufou, BA and Savadogo, P and Wigneron, JP and Poulter, B and Ciais, P and Kaufmann, R and Myneni, R and Saatchi, S and Fensholt, R}, title = {Sub-continental-scale carbon stocks of individual trees in African drylands.}, journal = {Nature}, volume = {615}, number = {7950}, pages = {80-86}, pmid = {36859581}, issn = {1476-4687}, mesh = {*Carbon/analysis/metabolism ; *Ecosystem ; *Trees/anatomy &amp; histology/chemistry/metabolism ; *Desert Climate ; Desiccation ; Satellite Imagery ; Africa South of the Sahara ; Machine Learning ; Wood/analysis ; Plant Roots ; Agriculture ; Environmental Restoration and Remediation ; Databases, Factual ; Biomass ; Computers ; }, abstract = {The distribution of dryland trees and their density, cover, size, mass and carbon content are not well known at sub-continental to continental scales[1-14]. This information is important for ecological protection, carbon accounting, climate mitigation and restoration efforts of dryland ecosystems[15-18]. We assessed more than 9.9 billion trees derived from more than 300,000 satellite images, covering semi-arid sub-Saharan Africa north of the Equator. We attributed wood, foliage and root carbon to every tree in the 0-1,000 mm year[-1] rainfall zone by coupling field data[19], machine learning[20-22], satellite data and high-performance computing. Average carbon stocks of individual trees ranged from 0.54 Mg C ha[-1] and 63 kg C tree[-1] in the arid zone to 3.7 Mg C ha[-1] and 98 kg tree[-1] in the sub-humid zone. Overall, we estimated the total carbon for our study area to be 0.84 (±19.8%) Pg C. Comparisons with 14 previous TRENDY numerical simulation studies[23] for our area found that the density and carbon stocks of scattered trees have been underestimated by three models and overestimated by 11 models, respectively. This benchmarking can help understand the carbon cycle and address concerns about land degradation[24-29]. We make available a linked database of wood mass, foliage mass, root mass and carbon stock of each tree for scientists, policymakers, dryland-restoration practitioners and farmers, who can use it to estimate farmland tree carbon stocks from tablets or laptops.}, }
@article {pmid36813959, year = {2023}, author = {Cai, S and Zhao, X and Pittelkow, CM and Fan, M and Zhang, X and Yan, X}, title = {Optimal nitrogen rate strategy for sustainable rice production in China.}, journal = {Nature}, volume = {615}, number = {7950}, pages = {73-79}, pmid = {36813959}, issn = {1476-4687}, mesh = {*Agriculture/economics/methods ; China ; Fertilizers/analysis/economics ; *Nitrogen/analysis/economics/metabolism ; *Oryza/metabolism ; Soil/chemistry ; *Sustainable Development ; *Crops, Agricultural/economics/metabolism/supply &amp; distribution ; Ecology ; Farmers ; Datasets as Topic ; Food Supply ; *Environmentalism ; }, abstract = {Avoiding excessive agricultural nitrogen (N) use without compromising yields has long been a priority for both research and government policy in China[1,2]. Although numerous rice-related strategies have been proposed[3-5], few studies have assessed their impacts on national food self-sufficiency and environmental sustainability and fewer still have considered economic risks faced by millions of smallholders. Here we established an optimal N rate strategy based on maximizing either economic (ON) or ecological (EON) performance using new subregion-specific models. Using an extensive on-farm dataset, we then assessed the risk of yield losses among smallholder farmers and the challenges of implementing the optimal N rate strategy. We find that meeting national rice production targets in 2030 is possible while concurrently reducing nationwide N consumption by 10% (6-16%) and 27% (22-32%), mitigating reactive N (Nr) losses by 7% (3-13%) and 24% (19-28%) and increasing N-use efficiency by 30% (3-57%) and 36% (8-64%) for ON and EON, respectively. This study identifies and targets subregions with disproportionate environmental impacts and proposes N rate strategies to limit national Nr pollution below proposed environmental thresholds, without compromising soil N stocks or economic benefits for smallholders. Thereafter, the preferable N strategy is allocated to each region based on the trade-off between economic risk and environmental benefit. To facilitate the adoption of the annually revised subregional N rate strategy, several recommendations were provided, including a monitoring network, fertilization quotas and smallholder subsidies.}, }
@article {pmid36914632, year = {2023}, author = {Kohyama, TI and Sheil, D and Sun, IF and Niiyama, K and Suzuki, E and Hiura, T and Nishimura, N and Hoshizaki, K and Wu, SH and Chao, WC and Nur Hajar, ZS and Rahajoe, JS and Kohyama, TS}, title = {Contribution of tree community structure to forest productivity across a thermal gradient in eastern Asia.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1113}, pmid = {36914632}, issn = {2041-1723}, mesh = {Humans ; *Trees ; *Forests ; Biomass ; Wood ; Asia, Eastern ; Tropical Climate ; }, abstract = {Despite their fundamental importance the links between forest productivity, diversity and climate remain contentious. We consider whether variation in productivity across climates reflects adjustment among tree species and individuals, or changes in tree community structure. We analysed data from 60 plots of humid old-growth forests spanning mean annual temperatures (MAT) from 2.0 to 26.6 °C. Comparing forests at equivalent aboveground biomass (160 Mg C ha[-1]), tropical forests ≥24 °C MAT averaged more than double the aboveground woody productivity of forests <12 °C (3.7 ± 0.3 versus 1.6 ± 0.1 Mg C ha[-1] yr[-1]). Nonetheless, species with similar standing biomass and maximum stature had similar productivity across plots regardless of temperature. We find that differences in the relative contribution of smaller- and larger-biomass species explained 86% of the observed productivity differences. Species-rich tropical forests are more productive than other forests due to the high relative productivity of many short-stature, small-biomass species.}, }
@article {pmid36911337, year = {2023}, author = {Lim, T and Lee, K and Kim, RH and Ryu, J and Cha, KH and Park, SY and Koo, SY and Hwang, KT}, title = {Effects of black raspberry extract on gut microbiota, microbial metabolites, and expressions of the genes involved in cholesterol and bile acid metabolisms in rats fed excessive choline with a high-fat diet.}, journal = {Food science and biotechnology}, volume = {32}, number = {4}, pages = {577-587}, pmid = {36911337}, issn = {2092-6456}, abstract = {UNLABELLED: In our previous study, black raspberry (BR) reduced the serum levels of trimethylamine-N-oxide and cholesterol in rats fed excessive choline with a high-fat diet (HFC). We hypothesized that gut microbiota could play a crucial role in the production of trimethylamine and microbial metabolites, and BR could influence gut microbial composition. This study aimed to elucidate the role of BR on changes in gut microbiota and microbial metabolites in the rats. The phylogenetic diversity of gut microbiota was reduced in the rats fed HFC, while that in the BR-fed group was restored. The BR supplementation enriched Bifidobacterium and reduced Clostridium cluster XIVa. In the BR-fed group, most cecal bile acids and hippuric acid increased, while serum lithocholic acid was reduced. The BR supplementation upregulated Cyp7a1 and downregulated Srebf2. These results suggest that BR extract may change gut bacterial community, modulate bile acids, and regulate gene expression toward reducing cholesterol.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-023-01267-4.}, }
@article {pmid36911308, year = {2023}, author = {Martinez, ND}, title = {Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology.}, journal = {Ecology and evolution}, volume = {13}, number = {3}, pages = {e9872}, pmid = {36911308}, issn = {2045-7758}, abstract = {Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.}, }
@article {pmid36901248, year = {2023}, author = {Zeng, L and Liu, C}, title = {Exploring Factors Affecting Urban Park Use from a Geospatial Perspective: A Big Data Study in Fuzhou, China.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {5}, pages = {}, pmid = {36901248}, issn = {1660-4601}, mesh = {Humans ; Urban Population ; *Parks, Recreational ; *Big Data ; Cities ; China ; }, abstract = {Promoting research on urban park use is important for developing the ecological and environmental health benefits of parks. This study proposes uniquely integrated methods combined with big data to measure urban park use. It combines comprehensive geographic detectors and multiscale geographically weighted regression from a geospatial perspective to quantify the individual and interactive effects of the parks' characteristics, accessibility, and surrounding environment features on weekday and weekend park use. The study also explores the degree of influence of spatial changes. The results indicate that the park-surrounding facilities and services factor contributed most to use, while its interaction effect with park service capacity had the greatest impact on park use. The interaction effects showed binary or nonlinear enhancement. This suggests that park use should be promoted within multiple dimensions. Many influencing factors had significant changes in the geographic space, suggesting that city-level park zoning construction should be adopted. Finally, park use was found to be affected by users' subjective preference on weekends and convenience factors on weekdays. These findings provide a theoretical basis for the influencing mechanisms of urban park use, which can help urban planners and policymakers formulate more specific policies to successfully manage and plan urban parks.}, }
@article {pmid36900138, year = {2023}, author = {Würstle, S and Hapfelmeier, A and Karapetyan, S and Studen, F and Isaakidou, A and Schneider, T and Schmid, RM and von Delius, S and Gundling, F and Burgkart, R and Obermeier, A and Mayr, U and Ringelhan, M and Rasch, S and Lahmer, T and Geisler, F and Turner, PE and Chan, BK and Spinner, CD and Schneider, J}, title = {Differentiation of Spontaneous Bacterial Peritonitis from Secondary Peritonitis in Patients with Liver Cirrhosis: Retrospective Multicentre Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, pmid = {36900138}, issn = {2075-4418}, abstract = {Ascitic fluid infection is a serious complication of liver cirrhosis. The distinction between the more common spontaneous bacterial peritonitis (SBP) and the less common secondary peritonitis in patients with liver cirrhosis is crucial due to the varying treatment approaches. This retrospective multicentre study was conducted in three German hospitals and analysed 532 SBP episodes and 37 secondary peritonitis episodes. Overall, >30 clinical, microbiological, and laboratory parameters were evaluated to identify key differentiation criteria. Microbiological characteristics in ascites followed by severity of illness and clinicopathological parameters in ascites were the most important predictors identified by a random forest model to distinguish between SBP and secondary peritonitis. To establish a point-score model, a least absolute shrinkage and selection operator (LASSO) regression model selected the ten most promising discriminatory features. By aiming at a sensitivity of 95% either to rule out or rule in SBP episodes, two cut-off scores were defined, dividing patients with infected ascites into a low-risk (score ≥ 45) and high-risk group (score < 25) for secondary peritonitis. Overall, the discrimination of secondary peritonitis from SBP remains challenging. Our univariable analyses, random forest model, and LASSO point score may help clinicians with the crucial differentiation between SBP and secondary peritonitis.}, }
@article {pmid36642073, year = {2023}, author = {Paixão, TM and Siqueira, CEG and Tristan-Cheever, E and Fischer, FM and Martinez, MC and Christoffolete, MA and Meisinger, K and Teixeira, LR}, title = {Overweight and Obesity in Brazilian Immigrants in Massachusetts, USA: A Time Series Analysis (2009-2020).}, journal = {Obesity facts}, volume = {16}, number = {2}, pages = {109-118}, doi = {10.1159/000527286}, pmid = {36642073}, issn = {1662-4033}, abstract = {INTRODUCTION: Obesity is considered a growing public health problem by the Brazilian Ministry of Health and a global epidemic by the World Health Organization (WHO). In 2020, the Centers for Disease Control and Prevention (CDC) estimated the prevalence of adult obesity at 31.9% in the USA. The USA is one of the main destinations for Brazilian immigrants in search of better living conditions, and Massachusetts is one of the states with the highest presence of Brazilians. Changes in lifestyle and eating habits are often associated with increases in overweight and obesity in immigrants in the USA, especially Hispanics, an official classification that does not, however, include Brazilians. The aim of this study was to describe the temporal trend of overweight and obesity in Brazilian immigrants assisted by the Cambridge Health Alliance (CHA) healthcare network in Massachusetts.<br><br>METHODS: This was an ecological time series study of 128,206 records of Brazilians aged between 18 and 60 years based on hospital data from 2009 to 2020.<br><br>RESULTS: Mean age was 38.9 (SD = 10.6), and 61% of the sample were women. The prevalence of overweight and obesity was 38.4% and 25.4%, respectively. Obesity exhibited an increasing trend, while eutrophy and overweight decreased during the study period.<br><br>CONCLUSION: As little is known about the health of Brazilian immigrants in the USA, this study contributes to the literature on the subject. The observed increasing trends agree with the worldwide increase in obesity and indicate the need for future research exploring individual factors associated with immigrant acculturation.}, }
@article {pmid36899307, year = {2023}, author = {Chan, YO and Dietz, N and Zeng, S and Wang, J and Flint-Garcia, S and Salazar-Vidal, MN and Škrabišová, M and Bilyeu, K and Joshi, T}, title = {The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {107}, pmid = {36899307}, issn = {1471-2164}, abstract = {BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize.<br><br>RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes.<br><br>CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website (https://soykb.org/SoybeanAlleleCatalogTool/), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website (https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana). Researchers can use this tool to connect variant alleles of genes with meta-information of species.}, }
@article {pmid36894986, year = {2023}, author = {de Nies, L and Galata, V and Martin-Gallausiaux, C and Despotovic, M and Busi, SB and Snoeck, CJ and Delacour, L and Budagavi, DP and Laczny, CC and Habier, J and Lupu, PC and Halder, R and Fritz, JV and Marques, T and Sandt, E and O'Sullivan, MP and Ghosh, S and Satagopam, V and ,  and Krüger, R and Fagherazzi, G and Ollert, M and Hefeng, FQ and May, P and Wilmes, P}, title = {Altered infective competence of the human gut microbiome in COVID-19.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {46}, pmid = {36894986}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; SARS-CoV-2/genetics ; *Microbiota ; Multiomics ; }, abstract = {BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.<br><br>RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.<br><br>CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.}, }
@article {pmid36893162, year = {2023}, author = {Rubenstein, DR and Solomon, J}, title = {Target-enriched enzymatic methyl sequencing: Flexible, scalable and inexpensive hybridization capture for quantifying DNA methylation.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282672}, pmid = {36893162}, issn = {1932-6203}, mesh = {*DNA Methylation ; Sequence Analysis, DNA/methods ; Reproducibility of Results ; Nucleic Acid Hybridization ; *Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; CpG Islands/genetics ; }, abstract = {The increasing interest in studying DNA methylation to understand how traits or diseases develop requires new and flexible approaches for quantifying DNA methylation in a diversity of organisms. In particular, we need efficient yet cost-effective ways to measure CpG methylation states over large and complete regions of the genome. Here, we develop TEEM-Seq (target-enriched enzymatic methyl sequencing), a method that combines enzymatic methyl sequencing with a custom-designed hybridization capture bait set that can be scaled to reactions including large numbers of samples in any species for which a reference genome is available. Using DNA from a passerine bird, the superb starling (Lamprotornis superbus), we show that TEEM-Seq is able to quantify DNA methylation states similarly well to the more traditional approaches of whole-genome and reduced-representation sequencing. Moreover, we demonstrate its reliability and repeatability, as duplicate libraries from the same samples were highly correlated. Importantly, the downstream bioinformatic analysis for TEEM-Seq is the same as for any sequence-based approach to studying DNA methylation, making it simple to incorporate into a variety of workflows. We believe that TEEM-Seq could replace traditional approaches for studying DNA methylation in candidate genes and pathways, and be effectively paired with other whole-genome or reduced-representation sequencing approaches to increase project sample sizes. In addition, TEEM-Seq can be combined with mRNA sequencing to examine how DNA methylation in promoters or other regulatory regions is related to the expression of individual genes or gene networks. By maximizing the number of samples in the hybridization reaction, TEEM-Seq is an inexpensive and flexible sequence-based approach for quantifying DNA methylation in species where other capture-based methods are unavailable or too expensive, particularly for non-model organisms.}, }
@article {pmid36895518, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Lees, D and , }, title = {The genome sequence of the yellow-legged clearwing, Synanthedon vespiformis (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {233}, pmid = {36895518}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length.}, }
@article {pmid36893405, year = {2023}, author = {Mallinson, DC and Elwert, F and Ehrenthal, DB}, title = {Spillover Effects of Prenatal Care Coordination on Older Siblings Beyond the Mother-Infant Dyad.}, journal = {Medical care}, volume = {61}, number = {4}, pages = {206-215}, doi = {10.1097/MLR.0000000000001822}, pmid = {36893405}, issn = {1537-1948}, abstract = {BACKGROUND: Pregnancy care coordination increases preventive care receipt for mothers and infants. Whether such services affect other family members' health care is unknown.<br><br>OBJECTIVE: To estimate the spillover effect of maternal exposure to Wisconsin Medicaid's Prenatal Care Coordination (PNCC) program during pregnancy with a younger sibling on the preventive care receipt for an older child.<br><br>RESEARCH DESIGN: Gain-score regressions-a sibling fixed effects strategy-estimated spillover effects while controlling for unobserved family-level confounders.<br><br>SUBJECTS: Data came from a longitudinal cohort of linked Wisconsin birth records and Medicaid claims. We sampled 21,332 sibling pairs (one older; one younger) who were born during 2008-2015, who were <4 years apart in age, and whose births were Medicaid-covered. In all, 4773 (22.4%) mothers received PNCC during pregnancy with the younger sibling.<br><br>MEASURES: The exposure was maternal PNCC receipt during pregnancy with the younger sibling (none; any). The outcome was the older sibling's number of preventive care visits or preventive care services in the younger sibling's first year of life.<br><br>RESULTS: Overall, maternal exposure to PNCC during pregnancy with the younger sibling did not affect older siblings' preventive care. However, among siblings who were 3 to <4 years apart in age, there was a positive spillover on the older sibling's receipt of care by 0.26 visits (95% CI: 0.11, 0.40 visits) and by 0.34 services (95% CI: 0.12, 0.55 services).<br><br>CONCLUSION: PNCC may only have spillover effects on siblings' preventive care in selected subpopulations but not in the broader population of Wisconsin families.}, }
@article {pmid36882531, year = {2023}, author = {Wei, Z and Jian, Z and Sun, Y and Pan, F and Han, H and Liu, Q and Mei, Y}, title = {Ecological sustainability and high-quality development of the Yellow River Delta in China based on the improved ecological footprint model.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3821}, pmid = {36882531}, issn = {2045-2322}, abstract = {Aiming at the traditional ecological footprint model, the improved ecological footprint of the carbon footprint effectively makes up for the singularity of the ecological footprint's consideration of carbon emissions, and plays an important role in promoting high-quality development and ecological sustainability. This paper selects 2015, 2018 and 2020 as important time points for the study, corrects the ecological footprint parameter factors based on net primary productivity (NPP), measures the ecological footprint after the improvement of the carbon footprint, studies the spatial and temporal variation in the ecological footprint at the 100-m grid scale with the support of IPCC greenhouse gas inventory analysis, and analyzes the current ecological conservation status of the Yellow River Delta. Additionally, in the context of a low carbon economy, the decoupling index of carbon emissions and GDP is extended to the evaluation and analysis of high-quality development. The study showed that (1) the ecological footprint of the Yellow River Delta has increased year by year, from 0.721 hm[2]·person[- 1] to 0.758 hm[2]·person[- 1], an average annual increase of 2.9%; the ecological carrying capacity has decreased from 0.40 hm[2]·person[- 1] to 0.31 hm[2]·person[- 1], an overall decrease of 28.59%. (2) The overall ecological deficit of the Yellow River Delta grid is lightly overloaded, with most of the ecological surplus occurring in the northern and eastern parts of the study area and a few moderate and heavy overloads in the center of the core area where there is a lot of built-up land and the area is small and easy to gather. (3) Based on the low-carbon economy analysis, 2015, 2017 and 2020 reach absolute decoupling and are in the ideal scenario. However, in the rest of the years, carbon emissions and economic development are still in a large contradiction, and decoupling has fluctuated and varied greatly in the last six years. The effective combination of ecological footprint and low carbon economy analysis provides an important theoretical basis for improving ecological conservation and achieving high-quality development.}, }
@article {pmid36522346, year = {2022}, author = {Wang, H and Harrison, SP and Li, M and Prentice, IC and Qiao, S and Wang, R and Xu, H and Mengoli, G and Peng, Y and Yang, Y}, title = {The China plant trait database version 2.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {769}, pmid = {36522346}, issn = {2052-4463}, mesh = {China ; Ecology ; *Ecosystem ; *Plants ; Databases, Factual ; }, abstract = {Plant functional traits represent adaptive strategies to the environment, linked to biophysical and biogeochemical processes and ecosystem functioning. Compilations of trait data facilitate research in multiple fields from plant ecology through to land-surface modelling. Here we present version 2 of the China Plant Trait Database, which contains information on morphometric, physical, chemical, photosynthetic and hydraulic traits from 1529 unique species in 140 sites spanning a diversity of vegetation types. Version 2 has five improvements compared to the previous version: (1) new data from a 4-km elevation transect on the edge of Tibetan Plateau, including alpine vegetation types not sampled previously; (2) inclusion of traits related to hydraulic processes, including specific sapwood conductance, the area ratio of sapwood to leaf, wood density and turgor loss point; (3) inclusion of information on soil properties to complement the existing data on climate and vegetation (4) assessments and flagging the reliability of individual trait measurements; and (5) inclusion of standardized templates for systematical field sampling and measurements.}, }
@article {pmid36879919, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Parker, B and Plotkin, D and Kawahara, AY and , }, title = {The genome sequence of the sallow kitten, Furcula furcula (Clerck, 1759).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {229}, pmid = {36879919}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.}, }
@article {pmid35363913, year = {2023}, author = {Zhu, M and Wang, Z and Yang, Y and Wang, Z and Mu, W and Liu, J}, title = {Multi-omics reveal differentiation and maintenance of dimorphic flowers in an alpine plant on the Qinghai-Tibet Plateau.}, journal = {Molecular ecology}, volume = {32}, number = {6}, pages = {1411-1424}, doi = {10.1111/mec.16449}, pmid = {35363913}, issn = {1365-294X}, mesh = {Tibet ; *Multiomics ; *Plants/genetics ; Transcriptome/genetics ; Flowers/genetics ; }, abstract = {Dimorphic flowers growing on a single individual plant play a critical role in extreme adaption and reproductive assurance in plants and have high ecological and evolutionary significance. However, the omics bases underlying such a differentiation and maintenance remain largely unknown. We aimed to investigate this through genomic, transcriptome and metabolomic analyses of dimorphic flowers in an alpine biennial, Sinoswertia tetraptera (Gentianaceae). A high-quality chromosome-level genome sequence (903 Mb) was first assembled for S. tetraptera with 31,359 protein-coding genes annotated. Two rounds of recent independent whole-genome duplication (WGD) were revealed. Numerous genes from the recent species-specific WGD were found to be differentially expressed in the two types of flowers, and this may have helped contribute to the origin of this innovative trait. The genes with contrasting expressions between flowers were related to biosynthesis of hormones, floral pigments (carotenoids and flavonoids) and iridoid compounds, which are involved in both flower development and colour. Metabolomic analyses similarly suggested differential concentrations of these chemicals in the two types of flowers. The expression interactions between multiple genes may together lead to contrasting morphology and chemical concentration and open versus closed pollination of the dimorphic flowers in this species for reproductive assurance.}, }
@article {pmid36752771, year = {2023}, author = {Lippi, CA and Rund, SSC and Ryan, SJ}, title = {Characterizing the Vector Data Ecosystem.}, journal = {Journal of medical entomology}, volume = {60}, number = {2}, pages = {247-254}, pmid = {36752771}, issn = {1938-2928}, mesh = {Animals ; *Ecosystem ; *Vector Borne Diseases ; Databases, Factual ; }, abstract = {A growing body of information on vector-borne diseases has arisen as increasing research focus has been directed towards the need for anticipating risk, optimizing surveillance, and understanding the fundamental biology of vector-borne diseases to direct control and mitigation efforts. The scope and scale of this information, in the form of data, comprising database efforts, data storage, and serving approaches, means that it is distributed across many formats and data types. Data ranges from collections records to molecular characterization, geospatial data to interactions of vectors and traits, infection experiments to field trials. New initiatives arise, often spanning the effort traditionally siloed in specific research disciplines, and other efforts wane, perhaps in response to funding declines, different research directions, or lack of sustained interest. Thusly, the world of vector data - the Vector Data Ecosystem - can become unclear in scope, and the flows of data through these various efforts can become stymied by obsolescence, or simply by gaps in access and interoperability. As increasing attention is paid to creating FAIR (Findable Accessible Interoperable, and Reusable) data, simply characterizing what is 'out there', and how these existing data aggregation and collection efforts interact, or interoperate with each other, is a useful exercise. This study presents a snapshot of current vector data efforts, reporting on level of accessibility, and commenting on interoperability using an illustration to track a specimen through the data ecosystem to understand where it occurs for the database efforts anticipated to describe it (or parts of its extended specimen data).}, }
@article {pmid36876314, year = {2023}, author = {Zhang, J and Qian, H}, title = {U.Taxonstand: An R package for standardizing scientific names of plants and animals.}, journal = {Plant diversity}, volume = {45}, number = {1}, pages = {1-5}, pmid = {36876314}, issn = {2468-2659}, abstract = {The scientific names of organisms are key identifiers of plants and animals. Correctly treating scientific names is a prerequisite for biodiversity research and documentation. Here, we present an R package, 'U.Taxonstand', which can standardize and harmonize scientific names in plant and animal species lists at a fast speed and at a high rate of matching success. Unlike most of other similar R packages each of which works with only one taxonomic database, U.Taxonstand can work with all taxonomic databases, as long as they are properly formatted. Multiple databases for plants and animals that can be directly used by U.Taxonstand, which include bryophytes, vascular plants, amphibians, birds, fishes, mammals, and reptiles, are available online. U.Taxonstand can be a very useful tool for botanists, zoologists, ecologists and biogeographers to standardize and harmonize scientific names of organisms.}, }
@article {pmid36874580, year = {2022}, author = {Hayward, A and Lohse, K and Laetsch, DR and Vila, R and ,  and ,  and ,  and Taluy, E and , }, title = {The genome sequence of the silver-studded blue, Plebejus argus (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {315}, pmid = {36874580}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Plebejus argus (silver-studded blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 382 megabases in span. The entire assembly (100%) is scaffolded into 23 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 27.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,693 protein coding genes.}, }
@article {pmid36706978, year = {2023}, author = {Nosenko, T and Zimmer, I and Ghirardo, A and Köllner, TG and Weber, B and Polle, A and Rosenkranz, M and Schnitzler, JP}, title = {Predicting functions of putative fungal sesquiterpene synthase genes based on multiomics data analysis.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {165}, number = {}, pages = {103779}, doi = {10.1016/j.fgb.2023.103779}, pmid = {36706978}, issn = {1096-0937}, mesh = {Multiomics ; *Sesquiterpenes/metabolism ; Genes, Fungal ; *Mycorrhizae/genetics ; Gene Expression Profiling ; }, abstract = {Sesquiterpenes (STs) are secondary metabolites, which mediate biotic interactions between different organisms. Predicting the species-specific ST repertoires can contribute to deciphering the language of communication between organisms of the same or different species. High biochemical plasticity and catalytic promiscuity of sesquiterpene synthases (STSs), however, challenge the homology-based prediction of the STS functions. Using integrated analyses of genomic, transcriptomic, volatilomic, and metabolomic data, we predict product profiles for 116 out of 146 putative STS genes identified in the genomes of 30 fungal species from different trophic groups. Our prediction method is based on the observation that STSs encoded by genes closely related phylogenetically are likely to share the initial enzymatic reactions of the ST biosynthesis pathways and, therefore, produce STs via the same reaction route. The classification by reaction routes allows to assign STs known to be emitted by a particular species to the putative STS genes from this species. Gene expression information helps to further specify these ST-to-STS assignments. Validation of the computational predictions of the STS functions using both in silico and experimental approaches shows that integrated multiomic analyses are able to correctly link cyclic STs of non-cadalane type to genes. In the process of the experimental validation, we characterized catalytic properties of several putative STS genes from the mycorrhizal fungus Laccaria bicolor. We show that the STSs encoded by the L.bicolor mycorrhiza-induced genes emit either nerolidol or α-cuprenene and α-cuparene, and discuss the possible roles of these STs in the mycorrhiza formation.}, }
@article {pmid36874578, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Holland, PWH and , }, title = {The genome sequence of the Seraphim, Lobophora halterata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {313}, pmid = {36874578}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Lobophora halterata (the Seraphim; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 315 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules with the Z and W sex chromosomes assembled. The mitochondrial genome has also been assembled and is 15.7 kilobases in length.}, }
@article {pmid36874577, year = {2022}, author = {Hawkes, W and Wotton, K and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the dumpy grass hoverfly, Melanostoma mellinum (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {59}, pmid = {36874577}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Melanostoma mellinum (the dumpy grass hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 731 megabases in span. The majority of the assembly (99.67%) is scaffolded into five chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 16.1 kilobases in length.}, }
@article {pmid36874564, year = {2022}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the large yellow underwing, Noctua pronuba (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {119}, pmid = {36874564}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Noctua pronuba (the large yellow underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 529 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. The mitochondrial genome was also assembled and is 15.3 kilobases in length.}, }
@article {pmid36872222, year = {2023}, author = {Zhang, GZ and Chen, SL and Dong, LL}, title = {[Traditional Chinese medicine microbiomics and its research strategies].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {48}, number = {3}, pages = {596-607}, doi = {10.19540/j.cnki.cjcmm.20221101.101}, pmid = {36872222}, issn = {1001-5302}, abstract = {The tight relationships between microbiome and traditional Chinese medicine(TCM)have been widely recognized. New technologies, results, and theories are emerging in the field of microbiomics in recent years with the advances in high-throughput sequencing and multi-omics technologies. Based on the previous research, the present study has proposed the concept of TCM microbiomics(TCMM), which is an interdisciplinary subject aiming at elucidating the functions and applications of microbiome in the areas of herb resources, herb processing, herb storage, and clinical effects by using modern technology of biology, ecology, and informatics. This subject essentially contains the structures, functions, interactions, molecular mechanisms, and application strategies of the microbiome associated with the quality, safety, and efficacy of TCM. Firstly, the development of the TCMM concept was summarized, with the profound understanding of TCMM on the complexity and entirety of microbiome being emphasized. Then, the research contents and applications of TCMM in promoting the sustainable development of herb resources, improving the standardization and diversification of herb fermentation, strengthening the safety of herb storage, and resolving the scientific connotation of theories and clinical efficacy of TCM are reviewed. Finally, the research strategies and methods of TCM microbiomics were elaborated from basic research, application research, and system research. TCMM is expected to promote the integrative development of TCM with frontier science and technology, thereby expanding the depth and scope of TCM study and facilitating TCM modernization.}, }
@article {pmid36866381, year = {2023}, author = {Lin, J and Yu, D and Pan, R and Cai, J and Liu, J and Zhang, L and Wen, X and Peng, X and Cernava, T and Oufensou, S and Migheli, Q and Chen, X and Zhang, X}, title = {Improved YOLOX-Tiny network for detection of tobacco brown spot disease.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1135105}, pmid = {36866381}, issn = {1664-462X}, abstract = {INTRODUCTION: Tobacco brown spot disease caused by Alternaria fungal species is a major threat to tobacco growth and yield. Thus, accurate and rapid detection of tobacco brown spot disease is vital for disease prevention and chemical pesticide inputs.<br><br>METHODS: Here, we propose an improved YOLOX-Tiny network, named YOLO-Tobacco, for the detection of tobacco brown spot disease under open-field scenarios. Aiming to excavate valuable disease features and enhance the integration of different levels of features, thereby improving the ability to detect dense disease spots at different scales, we introduced hierarchical mixed-scale units (HMUs) in the neck network for information interaction and feature refinement between channels. Furthermore, in order to enhance the detection of small disease spots and the robustness of the network, we also introduced convolutional block attention modules (CBAMs) into the neck network.<br><br>RESULTS: As a result, the YOLO-Tobacco network achieved an average precision (AP) of 80.56% on the test set. The AP was 3.22%, 8.99%, and 12.03% higher than that obtained by the classic lightweight detection networks YOLOX-Tiny network, YOLOv5-S network, and YOLOv4-Tiny network, respectively. In addition, the YOLO-Tobacco network also had a fast detection speed of 69 frames per second (FPS).<br><br>DISCUSSION: Therefore, the YOLO-Tobacco network satisfies both the advantages of high detection accuracy and fast detection speed. It will likely have a positive impact on early monitoring, disease control, and quality assessment in diseased tobacco plants.}, }
@article {pmid36862660, year = {2023}, author = {Nanjala, R and Nyasimi, F and Masiga, D and Kibet, CK}, title = {A mentorship and incubation program using project-based learning to build a professional bioinformatics pipeline in Kenya.}, journal = {PLoS computational biology}, volume = {19}, number = {3}, pages = {e1010904}, pmid = {36862660}, issn = {1553-7358}, support = {U24 HG006941/HG/NHGRI NIH HHS/United States ; U2R TW010677/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; Kenya ; *Mentors ; *Computational Biology ; Genomics ; Students ; }, abstract = {The demand for well-trained bioinformaticians to support genomics research continues to rise. Unfortunately, undergraduate training in Kenya does not prepare students for specialization in bioinformatics. Graduates are often unaware of the career opportunities in bioinformatics, and those who are may lack mentors to help them choose a specialization. The Bioinformatics Mentorship and Incubation Program seeks to bridge the gap by laying the foundation for a bioinformatics training pipeline using project-based learning. The program selects six participants through an intensive open recruitment exercise for highly competitive students to join the program for four months. The six interns undergo intensive training within the first one and a half months before being assigned to mini-projects. We track the progress of the interns weekly through code review sessions and a final presentation at the end of the four months. We have trained five cohorts, most of whom have secured master's scholarships within and outside the country and job opportunities. We demonstrate the benefit of structured mentorship using project-based learning in filling the training gap after undergraduate programs to generate well-trained bioinformaticians who are competitive in graduate programs and bioinformatics jobs.}, }
@article {pmid36873713, year = {2021}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the swallow prominent, Pheosia tremula (Clerck, 1759).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {335}, pmid = {36873713}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Pheosia tremula (the swallow prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 290 megabases in span. The majority of the assembly, 99.94%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, }
@article {pmid36873714, year = {2021}, author = {Hawkes, W and Wotton, K and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the tapered dronefly, Eristalis pertinax (Scopoli, 1763).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {292}, pmid = {36873714}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eristalis tenax (the tapered dronefly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 487 megabases in span. The majority of the assembly (95.23%) is scaffolded into seven chromosomal pseudomolecules, with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.}, }
@article {pmid36866282, year = {2021}, author = {Hawkes, W and Wotton, K and Smith, M and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the two-banded wasp hoverfly, Chrysotoxum bicinctum (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {321}, pmid = {36866282}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Chrysotoxum bicinctum (the two-banded wasp hoverfly; Arthropoda; Insecta; Diptera; Syriphidae). The genome sequence is 913 megabases in span. The majority of the assembly (98.81%) is scaffolded into five chromosomal pseudomolecules, with the X sex chromosome assembled.}, }
@article {pmid36865376, year = {2022}, author = {Boyes, D and ,  and ,  and ,  and ,  and ,  and Lees, D and , }, title = {The genome sequence of the merveille du jour, Griposia aprilina (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {247}, pmid = {36865376}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Griposia aprilina (the merveille du jour; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 720 megabases in span. The majority of the assembly (99.89%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.}, }
@article {pmid36865367, year = {2022}, author = {Broad, GR and Boyes, D and ,  and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the setaceous Hebrew character, Xestia c-nigrum, (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {295}, pmid = {36865367}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Xestia c-nigrum (the setaceous Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 760 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.}, }
@article {pmid36864462, year = {2023}, author = {Keuschnig, C and Vogel, TM and Barbaro, E and Spolaor, A and Koziol, K and Björkman, MP and Zdanowicz, C and Gallet, JC and Luks, B and Layton, R and Larose, C}, title = {Selection processes of Arctic seasonal glacier snowpack bacterial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {35}, pmid = {36864462}, issn = {2049-2618}, abstract = {BACKGROUND: Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories.<br><br>METHODS: We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis.<br><br>RESULTS: While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers.<br><br>CONCLUSIONS: These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.}, }
@article {pmid36863150, year = {2023}, author = {Liu, X and Wang, Y and Meng, X and Zhang, C and Chen, Z}, title = {Improved method for benthic ecosystem health assessment by integrating chemical indexes into multiple biological indicator species-A case study of the Baiyangdian Lake, China.}, journal = {Journal of environmental management}, volume = {335}, number = {}, pages = {117530}, doi = {10.1016/j.jenvman.2023.117530}, pmid = {36863150}, issn = {1095-8630}, abstract = {A comprehensive and scientific assessment of benthic ecosystem health is key to the rational selection of endogenous pollution reduction technologies for lakes. However, current assessments are mainly limited to biological indicators and ignore the actual benthic ecosystem situations, such as the impact of eutrophication and heavy metal pollution, which may lead to the one-sidedness of the evaluation results. In this study, taking Baiyangdian Lake, the largest shallow mesotrophic-eutrophic lake in the North China Plain, as an example, the chemical assessment index and biological integrity index were first combined to estimate the biological conditions, nutritional status and heavy metal pollution of lakes. The indicator system incorporated three biological assessments (benthic index of biotic integrity (B-IBI), submerged aquatic vegetation index of biological integrity (SAV-IBI) and microbial index of biological integrity (M-IBI)) and three chemical assessments (dissolved oxygen (DO), comprehensive trophic level index (TLI) and index of geoaccumulation (Igeo)). Twenty-three attributes of B-IBI, fourteen attributes of SAV-IBI and twelve attributes of M-IBI were screened by range, responsiveness, and redundancy tests to keep the core metrics that were significantly correlated with disturbance gradients or showed strong discriminatory power between reference and impaired sites. The assessment results of B-IBI, SAV-IBI, and M-IBI showed significant differences in the response to anthropogenic activities and seasonal change, among which the submerged plants showed more significant seasonal differences. It is difficult to reach a comprehensive conclusion regarding the benthic ecosystem health status based on a single biological community. In comparison with biological indicators, the score of chemical indicators is relatively low. DO, TLI and Igeo provide an essential supplement for the benthic ecosystem health assessment of lakes with eutrophication and heavy metal pollution problems. Using the new integrated assessment method, the benthic ecosystem health of Baiyangdian Lake was rated as fair, especially the northern parts of the lake adjacent to the inflow mouth of the Fu River, which were in poor condition, indicating that the lake has experienced anthropogenic disturbance, resulting in eutrophication, heavy metal pollution and biological community degradation. Whether it's spring or summer, the integrated assessment method provides a more plausible and comprehensive view of benthic ecosystem health under the pressure of increasing human activities and changing habitat and hydrological conditions, overcoming the narrow perspective and uncertainties of the single-index method. Thus, it can assist lake managers in providing technical support for ecological indication and restoration.}, }
@article {pmid36866281, year = {2021}, author = {Boyes, D and Holland, PWH and ,  and ,  and ,  and ,  and ,  and , }, title = {The genome sequence of the snout, Hypena proboscidalis (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {236}, pmid = {36866281}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Hypena proboscidalis (the snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 637 megabases in span. The majority of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.}, }
@article {pmid36859647, year = {2023}, author = {Nocci, M and Villa, G and Ragazzoni, L and Tofani, L and Romagnoli, S and Baldini, G and Bertini, P and Hubloue, I and Scolletta, S and Mechi, MT and Della Corte, F}, title = {Relationship between intensive care surge capacity and hospital factors: an extensive experience.}, journal = {Internal and emergency medicine}, volume = {}, number = {}, pages = {1-12}, pmid = {36859647}, issn = {1970-9366}, abstract = {As a prolonged surge scenario, the COVID-19 pandemic has offered an unparalleled opportunity to improve hospital surge capacity (SC) understanding and the ability to manage it. In this study, the authors report the experience of a large hospital network and evaluate potential relationships between Intensive Care Units SC (ICU-SC) and some hospital-related variables: bed occupancy, emergency department admissions, ward admission from ED, and elective surgery procedures. Pearson's partial correlation coefficient (r) has been used to define the relationship between SC and the daily values of the above variables, collected through a dedicated digital platform that also ensured a regular quality check of the data. The observation has concerned several levels of analysis, namely two different types of SC calculation (SC base-SCb and SC actual-SCa), hospital category level and multi-hospital level, and two consecutive pandemic waves. Among the 16 hospitals observed, the correlation was shown to be moderate-positive with non-ICU bed occupancy (r/ = 0.62, r/ = 0.54), strong/moderate with ICU bed occupancy (r/ = 0.72, r/ = 0.54), and moderate with ward admissions from ED (r/ = 0.50, r/ = 0.51) On the contrary, the correlation proved to be moderate-negative with ED admissions (r/ = - 0.69, r/ = - 0.62) and low with the number of elective surgery procedures (r/ = - 0.10, r/ = - 0.16). This study identified a positive correlation between SC and three variables monitored: ICU bed occupancy, non-ICU bed occupancy, and ward admissions from ED. On the contrary, the correlation was negative for ED admission and the number of elective surgery procedures. The results have been confirmed across all levels of analysis adopted.}, }
@article {pmid36859503, year = {2023}, author = {Jones, DL and Rhymes, JM and Green, E and Rimmer, C and Kevill, JL and Malham, SK and Weightman, AJ and Farkas, K}, title = {Poor air passenger knowledge of COVID-19 symptoms and behaviour undermines strategies aimed at preventing the import of SARS-CoV-2 into the UK.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3494}, pmid = {36859503}, issn = {2045-2322}, abstract = {Air travel mediates transboundary movement of SARS-CoV-2. To prepare for future pandemics, we sought to understand air passenger behaviour and perceived risk during the COVID-19 pandemic. This study of UK adults (n = 2103) quantified knowledge of COVID-19 symptoms, perceived health risk of contracting COVID-19, likelihood of returning to the UK with COVID-19 symptoms, likelihood to obey self-quarantining guidelines, how safe air travellers felt when flying during the pandemic (n = 305), and perceptions towards face covering effectiveness.Overall knowledge of COVID-19 symptoms was poor. Men and younger age groups (18-44) were less informed than women and older age groups (44 +). A significant proportion (21%) of the population would likely travel back to the UK whilst displaying COVID-19 symptoms with many expressing that they would not fully comply with self-isolation guidelines. Overall, males and younger age groups had a reduced perceived personal risk from contracting COVID-19, posing a higher risk of transporting SARS-CoV-2 back to the UK. Poor passenger knowledge and behaviour undermines government guidelines and policies aimed at preventing SARS-CoV-2 entry into the UK. This supports the need for stricter, clearer and more targeted guidelines with point-of-departure viral testing and stricter quarantining upon arrival.}, }
@article {pmid36858189, year = {2023}, author = {Kushwaha, B and Nagpure, NS and Srivastava, S and Pandey, M and Kumar, R and Raizada, S and Agarwal, S and Singh, M and Basheer, VS and Kumar, RG and Das, P and Das, SP and Patnaik, S and Bit, A and Kumar Srivastava, S and Vishwakarma, AL and Joshi, CG and Kumar, D and Jena, JK}, title = {Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes.}, journal = {Gene}, volume = {}, number = {}, pages = {147294}, doi = {10.1016/j.gene.2023.147294}, pmid = {36858189}, issn = {1879-0038}, abstract = {Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (28 commercially important, 10 vulnerable and 14 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.}, }
@article {pmid36852195, year = {2023}, author = {Streng, K and de Best, PA and Timen, A and Koopmans, MPG and van der Poel, WHM and Sikkema, RS}, title = {Rapid response screening for emerging zoonotic pathogens, barriers and opportunities: A study for enhanced preparedness of the Netherlands.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100507}, pmid = {36852195}, issn = {2352-7714}, abstract = {BACKGROUND: Outbreaks of zoonotic emerging infectious diseases (EIDs) require rapid identification of potential reservoir hosts and mapping disease spread in these hosts to inform risk assessment and adequate control measures. Animals are often understudied when a novel EID is detected in humans and acquisition of animal samples is hampered by practical, ethical, and legal barriers, of which there is currently no clear overview. Therefore, the three aims of this study are (1) to map potentially available collections of animal samples, (2) to assess possibilities and barriers for reuse of these samples and (3) to assess possibilities and barriers for active animal and environmental sampling in the Netherlands.<br><br>METHODS: A literature search was performed to identify ongoing sampling activities and opportunities for reuse or active sampling. Semi-structured interviews with stakeholder organizations were conducted to gain further insight into the three research questions.<br><br>RESULTS: Various sample collections of surveillance, diagnostic and research activities exist in the Netherlands. Sample size, coverage, storage methods and type of samples collected differs per animal species which influences reuse suitability. Organizations are more likely to share samples, for reuse in outbreak investigations, when they have a pre-existing relationship with the requesting institute. Identified barriers for sharing were, among others, unfamiliarity with legislation and unsuitable data management systems. Active sampling of animals or the environment is possible through several routes. Related barriers are acquiring approval from animal- or property owners, conflicts with anonymization, and time needed to acquire ethical approval.<br><br>CONCLUSION: The animal sample collections identified would be very valuable for use in outbreak investigations. Barriers for sharing may be overcome by increasing familiarity with legislation, building (international) sharing networks and agreements before crises occur and developing systems for sample registration and biobanking. Proactive setting up of ethical approvals will allow for rapid animal sample collection to identify EID hosts and potential spillovers.}, }
@article {pmid36850776, year = {2023}, author = {Di Paolo, S and Nijmeijer, EM and Bragonzoni, L and Gokeler, A and Benjaminse, A}, title = {Definition of High-Risk Motion Patterns for Female ACL Injury Based on Football-Specific Field Data: A Wearable Sensors Plus Data Mining Approach.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {4}, pages = {}, pmid = {36850776}, issn = {1424-8220}, mesh = {Female ; Humans ; *Anterior Cruciate Ligament Injuries ; *Football ; Rotation ; Data Mining ; *Wearable Electronic Devices ; }, abstract = {The aim of the present study was to investigate if the presence of anterior cruciate ligament (ACL) injury risk factors depicted in the laboratory would reflect at-risk patterns in football-specific field data. Twenty-four female footballers (14.9 ± 0.9 year) performed unanticipated cutting maneuvers in a laboratory setting and on the football pitch during football-specific exercises (F-EX) and games (F-GAME). Knee joint moments were collected in the laboratory and grouped using hierarchical agglomerative clustering. The clusters were used to investigate the kinematics collected on field through wearable sensors. Three clusters emerged: Cluster 1 presented the lowest knee moments; Cluster 2 presented high knee extension but low knee abduction and rotation moments; Cluster 3 presented the highest knee abduction, extension, and external rotation moments. In F-EX, greater knee abduction angles were found in Cluster 2 and 3 compared to Cluster 1 (p = 0.007). Cluster 2 showed the lowest knee and hip flexion angles (p < 0.013). Cluster 3 showed the greatest hip external rotation angles (p = 0.006). In F-GAME, Cluster 3 presented the greatest knee external rotation and lowest knee flexion angles (p = 0.003). Clinically relevant differences towards ACL injury identified in the laboratory reflected at-risk patterns only in part when cutting on the field: in the field, low-risk players exhibited similar kinematic patterns as the high-risk players. Therefore, in-lab injury risk screening may lack ecological validity.}, }
@article {pmid36848570, year = {2023}, author = {Stenseth, NC and Schlatte, R and Liu, X and Pielke, R and Li, R and Chen, B and Bjørnstad, ON and Kusnezov, D and Gao, GF and Fraser, C and Whittington, JD and Bai, Y and Deng, K and Gong, P and Guan, D and Xiao, Y and Xu, B and Johnsen, EB}, title = {How to avoid a local epidemic becoming a global pandemic.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {10}, pages = {e2220080120}, doi = {10.1073/pnas.2220080120}, pmid = {36848570}, issn = {1091-6490}, mesh = {Humans ; Pandemics/prevention &amp; control ; *COVID-19/epidemiology/prevention &amp; control ; SARS-CoV-2 ; Disease Outbreaks ; *Air Travel ; }, abstract = {Here, we combine international air travel passenger data with a standard epidemiological model of the initial 3 mo of the COVID-19 pandemic (January through March 2020; toward the end of which the entire world locked down). Using the information available during this initial phase of the pandemic, our model accurately describes the main features of the actual global development of the pandemic demonstrated by the high degree of coherence between the model and global data. The validated model allows for an exploration of alternative policy efficacies (reducing air travel and/or introducing different degrees of compulsory immigration quarantine upon arrival to a country) in delaying the global spread of SARS-CoV-2 and thus is suggestive of similar efficacy in anticipating the spread of future global disease outbreaks. We show that a lesson from the recent pandemic is that reducing air travel globally is more effective in reducing the global spread than adopting immigration quarantine. Reducing air travel out of a source country has the most important effect regarding the spreading of the disease to the rest of the world. Based upon our results, we propose a digital twin as a further developed tool to inform future pandemic decision-making to inform measures intended to control the spread of disease agents of potential future pandemics. We discuss the design criteria for such a digital twin model as well as the feasibility of obtaining access to the necessary online data on international air travel.}, }
@article {pmid36840322, year = {2023}, author = {Hou, H and Liu, H and Xiong, J and Wang, C and Zhang, S and Ding, Z}, title = {Comparison of Soil Bacterial Communities under Canopies of Pinus tabulaeformis and Populus euramericana in a Reclaimed Waste Dump.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840322}, issn = {2223-7747}, abstract = {To compare the effects of different remediation tree species on soil bacterial communities and provide a theoretical basis for the selection of ecosystem function promotion strategies after vegetation restoration, the characteristic changes in soil bacterial communities after Pinus tabulaeformis and Populus euramericana reclamation were explored using high-throughput sequencing and molecular ecological network methods. The results showed that: (1) With the increase in reclamation years, the reclaimed soil properties were close to the control group, and the soil properties of Pinus tabulaeformis were closer to the control group than those of P. euramericana. (2) The dominant bacteria under the canopies of P. tabulaeformis and P. euramericana was the same. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Planctomycetes, Bacteroidetes, and Cyanobacteria were the dominant bacteria in the restored soil, accounting for more than 95% of the total abundance. The average values of the Shannon diversity index, Simpson diversity index, Chao 1 richness estimator, and abundance-based coverage estimator of the bacterial community in the P. euramericana reclaimed soil were higher than those in the P. tabulaeformis reclaimed soil. The influence of reclamation years on the bacterial community of samples is greater than that of species types. (3) The results of ecological network construction showed that the total number of nodes, total number of connections, and average connectivity of the soil bacterial network under P. euramericana reclamation were greater than those under P. tabulaeformis reclamation. The bacterial molecular ecological network under P. euramericana was more abundant. (4) Among the dominant bacteria, the relative abundance of Actinobacteria was negatively correlated with soil pH, soil total nitrogen content, and the activities of urease, invertase, and alkaline phosphatase, while the relative abundance of Proteobacteria and Bacteroidetes was positively correlated with these environmental factors. The relationship between the soil bacterial community of P. tabulaeformis and P. euramericana and the environmental factors is not completely the same, and even the interaction between some environmental factors and bacteria is opposite.}, }
@article {pmid36840309, year = {2023}, author = {Jocienė, L and Krokaitė, E and Rekašius, T and Vilčinskas, R and Judžentienė, A and Marozas, V and Kupčinskienė, E}, title = {Ionomic Parameters of Populations of Common Juniper (Juniperus communis L.) Depending on the Habitat Type.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840309}, issn = {2223-7747}, abstract = {For the study of the ionomic parameters of Juniperus communis needles, fourteen sites covering most of the territory of Lithuania and belonging to distinct habitats (coastal brown dunes covered with natural Scots pine forests (G), Juniperus communis scrubs (F), transition mires and quaking bogs (D), subcontinental moss Scots pine forests (G), and xero-thermophile fringes) were selected. Concentrations of macro-, micro-, and non-essential elements were analyzed in current-year needles, sampled in September. According to the concentrations of elements in J. communis needles, the differences between the most contrasting populations were as follows: up to 2-fold for Mg, N, K, Ca, and Zn; 2- to 7-fold for P, Na, Fe, Cu, Al, Cr, Ni, and Pb; and 26- to 31-fold for Mn and Cd. The concentrations of Cd, Cr, and Ni in needles of J. communis did not reach levels harmful for conifers. When compared to all other habitats (B, F, G, and E), the populations from transition mires and quaking bogs (D) had significantly lower concentrations of main nutritional elements N (12176 µg/g d. m.), P (1054 µg/g d. m.), and K (2916 µg/g d. m.). In Juniperus communis scrubs (F), a habitat protected by EUNIS, the concentration of K in the needles was highest, while Zn and Cu concentrations were the lowest. Principal component (PC) analyses using concentrations of 15 elements as variables for the discrimination of populations or habitats allowed authors to distinguish F and B habitats from the E habitat (PC1) and F and D habitats from the G habitat (PC2). Discriminating between populations, the most important variables were concentrations of P, N, Mg, Ca, Cu, and K. Discriminating between habitats, the important variables were concentrations of N and P.}, }
@article {pmid36816807, year = {2022}, author = {Ben Aribi, H and Ding, M and Kiran, A}, title = {Gene expression data visualization tool on the o[2]S[2]PARC platform.}, journal = {F1000Research}, volume = {11}, number = {}, pages = {1267}, pmid = {36816807}, issn = {2046-1402}, mesh = {*Gene Expression Profiling ; *Computational Biology ; Data Visualization ; Gene Ontology ; Gene Expression ; }, abstract = {Background: The identification of differentially expressed genes and their associated biological processes, molecular function, and cellular components are essential for genetic disease studies because they present potential biomarkers and therapeutic targets. Methods: In this study, we developed an o[2]S[2]PARC template to instantiate an interactive pipeline for gene expression data visualization, ontological mapping, and statistical evaluation. To demonstrate the tool's usefulness, we performed a case study on a publicly available dataset. Results: The tool enables users to identify the differentially expressed genes (DEGs) and visualize them in a volcano plot format. Ontologies associated with the DEGs are assigned and visualized in barplots. Conclusions: The "Expression data visualization" template is publicly available on the o[2]S[2]PARC platform.}, }
@article {pmid36820086, year = {2023}, author = {Huo, J and Hu, X and Bai, J and Lv, A}, title = {Multiomics analysis revealed miRNAs as potential regulators of the immune response in Carassius auratus gills to Aeromonas hydrophila infection.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1098455}, pmid = {36820086}, issn = {1664-3224}, mesh = {Animals ; *Goldfish ; Aeromonas hydrophila ; Gills ; Zebrafish/genetics ; Multiomics ; NF-kappa B/genetics ; Phylogeny ; Immunity, Innate/genetics ; *MicroRNAs/genetics ; }, abstract = {The gill of fish is an important immune organ for pathogen defense, but its microRNA (miRNA) expression and regulatory mechanism remain unclear. In this study, we report on the histopathological and immunohistochemical features of the gills of the crucian carp Carassius auratus challenged with Aeromonas hydrophila. Small RNA libraries of the gills were constructed and sequenced on the Illumina HiSeq 2000 platform. A total of 1,165 differentially expressed miRNAs (DEMs) were identified in gills, of which 539 known and 7 unknown DEMs were significantly screened (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes/proteins were primarily involved in 33 immune-related pathways, in which the inflammatory responses were focused on the Toll-like receptor (TLR), mitogen-activated protein kinase (MAPK), and nuclear factor kappa B (NF-κB) signaling pathways. Moreover, the expression levels of 14 key miRNAs (e.g., miR-10, miR-17, miR-26a, miR-144, miR-145, and miR-146a) and their target genes (e.g., TNFα, TLR4, NF-κB, TAB1, PI3K, and IRAK1) were verified. In addition, the protein levels based on isobaric tags for relative and absolute quantification (iTRAQ) were significantly associated with the results of the quantitative real-time PCR (qRT-PCR) analysis (p < 0.01). miR-17/pre-miR-17 were identified in the regulation expression of the NF-κB target gene, and the phylogenetic tree analysis showed that the pre-miR-17 of C. auratus with the closest similarity to the zebrafish Danio rerio is highly conserved in teleosts. This is the first report of the multi-omics analysis of the miRNAs and proteins in the gills of C. auratus infected with A. hydrophila, thus enriching knowledge on the regulation mechanism of the local immune response in Cyprinidae fish.}, }
@article {pmid35549363, year = {2023}, author = {Wylie, MS and Colasante, T and De France, K and Lin, L and Hollenstein, T}, title = {Momentary emotion regulation strategy use and success: Testing the influences of emotion intensity and habitual strategy use.}, journal = {Emotion (Washington, D.C.)}, volume = {23}, number = {2}, pages = {375-386}, doi = {10.1037/emo0001074}, pmid = {35549363}, issn = {1931-1516}, mesh = {Humans ; Female ; Young Adult ; Adult ; Male ; *Emotional Regulation/physiology ; Emotions/physiology ; Ecological Momentary Assessment ; Data Management ; }, abstract = {Successful emotion regulation (ER) is important for a wide range of psychosocial outcomes. Specific ER strategies have been identified as being more or less likely to be successful. However, recent evidence suggests significant individual differences in the association between strategy implementation and ER success. Indeed, 2 key factors may play an important role in moderating the link between ER strategy use and ER success in the moment: (a) the intensity of the specific emotional experience, and (b) the relative frequency in using a given ER strategy. Experience-sampling across 14-days (N = 304, Mage = 19.14, % female = 87.5) was used to assess whether emotion intensity and trait ER strategy use were differentially associated with perceived regulatory success depending on which ER strategy was used. Multilevel modeling revealed that more intense emotions were associated with lower perceived success for all strategies. Additionally, habitual reappraisal predicted greater success and habitual rumination predicted lower success. We discuss the possibility that results reflected intensity-based ER strategy choices and add to the growing call to abandon the reductive labeling of ER strategies as either "adaptive" or "maladaptive." (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, }
@article {pmid36840203, year = {2023}, author = {Visztra, GV and Frei, K and Hábenczyus, AA and Soóky, A and Bátori, Z and Laborczi, A and Csikós, N and Szatmári, G and Szilassi, P}, title = {Applicability of Point- and Polygon-Based Vegetation Monitoring Data to Identify Soil, Hydrological and Climatic Driving Forces of Biological Invasions-A Case Study of Ailanthus altissima, Elaeagnus angustifolia and Robinia pseudoacacia.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/plants12040855}, pmid = {36840203}, issn = {2223-7747}, abstract = {Invasive tree species are a significant threat to native flora. They modify the environment with their allelopathic substances and inhibit the growth of native species by shading, thus reducing diversity. The most effective way to control invasive plants is to prevent their spread which requires identifying the environmental parameters promoting it. Since there are several types of invasive plant databases available, determining which database type is the most relevant for investigating the occurrence of alien plants is of great importance. In this study, we compared the efficiency and reliability of point-based (EUROSTAT Land Use and Coverage Area Frame Survey (LUCAS)) and polygon-based (National Forestry Database (NFD)) databases using geostatistical methods in ArcGIS software. We also investigated the occurrence of three invasive tree species (Ailanthus altissima, Elaeagnus angustifolia, and Robinia pseudoacacia) and their relationships with soil, hydrological, and climatic parameters such as soil organic matter content, pH, calcium carbonate content, rooting depth, water-holding capacity, distance from the nearest surface water, groundwater depth, mean annual temperature, and mean annual precipitation with generalized linear models in R-studio software. Our results show that the invasion levels of the tree species under study are generally over-represented in the LUCAS point-based vegetation maps, and the point-based database requires a dataset with a larger number of samples to be reliable. Regarding the polygon-based database, we found that the occurrence of the invasive species is generally related to the investigated soil and hydrological and climatic factors.}, }
@article {pmid36836247, year = {2023}, author = {Wang, J and Qin, S and Fan, R and Peng, Q and Hu, X and Yang, L and Liu, Z and Baccelli, I and Migheli, Q and Berg, G and Chen, X and Cernava, T}, title = {Plant Growth Promotion and Biocontrol of Leaf Blight Caused by Nigrospora sphaerica on Passion Fruit by Endophytic Bacillus subtilis Strain GUCC4.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/jof9020132}, pmid = {36836247}, issn = {2309-608X}, abstract = {Passion fruit (Passiflora edulis Sims) is widely cultivated in tropic and sub-tropic regions for the production of fruit, flowers, cosmetics, and for pharmacological applications. Its high economic, nutritional, and medical values elicit the market demand, and the growing areas are rapidly increasing. Leaf blight caused by Nigrospora sphaerica is a new and emerging disease of passion fruit in Guizhou, in southwest China, where the unique karst mountainous landscape and climate conditions are considered potential areas of expansion for passion fruit production. Bacillus species are the most common biocontrol and plant-growth-promotion bacteria (PGPB) resources in agricultural systems. However, little is known about the endophytic existence of Bacillus spp. in the passion fruit phyllosphere as well as their potential as biocontrol agents and PGPB. In this study, 44 endophytic strains were isolated from 15 healthy passion fruit leaves, obtained from Guangxi province, China. Through purification and molecular identification, 42 of the isolates were ascribed to Bacillus species. Their inhibitory activity against N. sphaerica was tested in vitro. Eleven endophytic Bacillus spp. strains inhibited the pathogen by >65%. All of them produced biocontrol- and plant-growth-promotion-related metabolites, including indole-3-acetic acid (IAA), protease, cellulase, phosphatase, and solubilized phosphate. Furthermore, the plant growth promotion traits of the above 11 endophytic Bacillus strains were tested on passion fruit seedlings. One isolate, coded B. subtilis GUCC4, significantly increased passion fruit stem diameter, plant height, leaf length, leaf surface, fresh weight, and dry weight. In addition, B. subtilis GUCC4 reduced the proline content, which indicated its potential to positively regulate passion fruit biochemical properties and resulted in plant growth promotion effects. Finally, the biocontrol efficiencies of B. subtilis GUCC4 against N. sphaerica were determined in vivo under greenhouse conditions. Similarly to the fungicide mancozeb and to a commercial B. subtilis-based biofungicide, B. subtilis GUCC4 significantly reduced disease severity. These results suggest that B. subtilis GUCC4 has great potential as a biological control agent and as PGPB on passion fruit.}, }
@article {pmid36835681, year = {2023}, author = {Srygley, RB and Dudley, R and Hernandez, EJ and Kainz, F and Riveros, AJ and Ellington, CP}, title = {Quantifying the Aerodynamic Power Required for Flight and Testing for Adaptive Wind Drift in Passion-Vine Butterflies Heliconius sara (Lepidoptera: Nymphalidae).}, journal = {Insects}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/insects14020112}, pmid = {36835681}, issn = {2075-4450}, abstract = {Although theoretical work on optimal migration has been largely restricted to birds, relevant free-flight data are now becoming available for migratory insects. Here we report, for the first time in passion-vine butterflies, that Heliconius sara migrates directionally. To test optimal migration models for insects, we quantified the aerodynamic power curve for free-flying H. sara as they migrated across the Panama Canal. Using synchronized stereo-images from high-speed video cameras, we reconstructed three-dimensional flight kinematics of H. sara migrating naturally across the Panama Canal. We also reconstructed flight kinematics from a single-camera view of butterflies flying through a flight tunnel. We calculated the power requirements for flight for H. sara over a range of flight velocities. The relationship between aerodynamic power and velocity was "J"-shaped across the measured velocities with a minimum power velocity of 0.9 m/s and a maximum range velocity of 2.25 m/s. Migrating H. sara did not compensate for crosswind drift. Changes in airspeed with tailwind drift were consistent with the null hypothesis that H. sara did not compensate for tailwind drift, but they were also not significantly different from those predicted to maximize the migratory range of the insects.}, }
@article {pmid36834418, year = {2023}, author = {Liu, J and Chen, J and Yang, Y and You, H and Han, X}, title = {Construction and Optimization of an Ecological Network in the Yellow River Source Region Based on MSPA and MCR Modelling.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, doi = {10.3390/ijerph20043724}, pmid = {36834418}, issn = {1660-4601}, abstract = {The source region of the Yellow River (SRYR) is an important water conservation and farming area in China. Under the dual influence of the natural environment and external pressure, ecological patches in the region are becoming increasingly fragmented, and landscape connectivity is continuously declining, which directly affect the landscape patch pattern and SRYR sustainable development. In the SRYR, morphological spatial pattern analysis (MSPA) and landscape index methods were used to extract ecologically important sources. Based on the minimum cumulative resistance model (MCR), Linkage Mapper was used to generate a potential corridor, and then potential stepped stone patches were identified and extracted by the gravity model and betweenness centrality to build an optimal SRYR ecological network. The distribution of patches in the core area of the SRYR was fragmented, accounting for 80.53% of the total grassland area. The 10 ecological sources based on the landscape connectivity index and 15 important corridors identified based on the MCR model were mainly distributed in the central and eastern regions of the SRYR. Through betweenness centrality, 10 stepped stone patches were added, and 45 planned ecological corridors were obtained to optimize the SRYR ecological network and enhance east and west connectivity. Our research results can provide an important reference for the protection of the SRYR ecosystem, and have important guiding significance and practical value for ecological network construction in ecologically fragmented areas.}, }
@article {pmid36834206, year = {2023}, author = {Li, Y and Liu, H and Su, L and Chen, S and Zhu, X and Zhang, P}, title = {Developmental Features, Influencing Factors, and Formation Mechanism of Underground Mining-Induced Ground Fissure Disasters in China: A Review.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, doi = {10.3390/ijerph20043511}, pmid = {36834206}, issn = {1660-4601}, abstract = {Mining-induced ground fissures are one of the major geological disasters affecting coal mines. In recent years, many effective monitoring methods have been developed to explore the developmental characteristics and nature of mining-induced ground fissures for being treated scientifically. This paper is mainly on the development law and mechanism of mining ground fissure research results which have been comprehensively combed, highlighting the development trend, including the formation condition, development features, influencing factors, and mechanical mechanism of mining-induced ground fissures. Outstanding issues are discussed and future research hot spots and trends are pointed out. The major conclusions include: (1) under the shallow coal mining condition, because the rock layer fault zone directly reaches the surface, the ground fissure usually develops seriously; (2) mining-induced ground fissures are generally divided into four types: tensile fissures, compression fissures, collapsed fissures, and sliding fissures; (3) mining-induced ground fissures are affected by the coupling effect of underground mining and surface topography. The main factors are geological mining conditions, surface deformation, and surface topography, including rock and soil structure, rock and soil mechanical properties, surface horizontal deformation, surface slope, and so on; and (4) to ensure the safety of underground mining, temporary ground fissures formed during the process of coal mining must be treated when ground fissures and rock ground fissures are connected. The results of this article make up for the deficiencies of the relevant research, provide the basis and direction for future research, and have universal applicability and scientific guiding significance.}, }
@article {pmid36827177, year = {2023}, author = {Martínez-Pernía, D and Olavarría, L and Fernández-Manjón, B and Cabello, V and Henríquez, F and Robert, P and Alvarado, L and Barría, S and Antivilo, A and Velasquez, J and Cerda, M and Farías, G and Torralva, T and Ibáñez, A and Parra, MA and Gilbert, S and Slachevsky, A}, title = {The limitations and challenges in the assessment of executive dysfunction associated with real-world functioning: The opportunity of serious games.}, journal = {Applied neuropsychology. Adult}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/23279095.2023.2174438}, pmid = {36827177}, issn = {2327-9109}, abstract = {Nowadays, there is a broad range of methods for detecting and evaluating executive dysfunction ranging from clinical interview to neuropsychological evaluation. Nevertheless, a critical issue of these assessments is the lack of correspondence of the neuropsychological test's results with real-world functioning. This paper proposes serious games as a new framework to improve the neuropsychological assessment of real-world functioning. We briefly discuss the contribution and limitations of current methods of evaluation of executive dysfunction (paper-and-pencil tests, naturalistic observation methods, and Information and Communications Technologies) to inform on daily life functioning. Then, we analyze what are the limitations of these methods to predict real-world performance: (1) A lack of appropriate instruments to investigate the complexity of real-world functioning, (2) the vast majority of neuropsychological tests assess well-structured tasks, and (3) measurement of behaviors are based on simplistic data collection and statistical analysis. This work shows how serious games offer an opportunity to develop more efficient tools to detect executive dysfunction in everyday life contexts. Serious games provide meaningful narrative stories and virtual or real environments that immerse the user in natural and social environments with social interactions. In those highly interactive game environments, the player needs to adapt his/her behavioral performance to novel and ill-structured tasks which are suited for collecting user interaction evidence. Serious games offer a novel opportunity to develop better tools to improve diagnosis of the executive dysfunction in everyday life contexts. However, more research is still needed to implement serious games in everyday clinical practice.}, }
@article {pmid36826765, year = {2023}, author = {Wei, T and Guo, G and Li, H and Wang, L and Jiang, Q and Jiang, C}, title = {A novel probability integral method segmental modified model for subsidence prediction applicable to thick loose layer mining areas.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36826765}, issn = {1614-7499}, abstract = {In response to the problem that the actual extent of coal mining impacts on the surface in thick loose layer mines significantly exceeds the theoretical predictions, based on the literature study, the form of influence of thick loose layer on the predicted parameters of the probability integral method is summarized and analyzed; taking into account the influence of the subsidence coefficient, the sine modification formula of the major influence radius and the logistic modification formula of the subsidence coefficient are established, respectively, and based on the characteristics of the major influence radius, a new subsidence basin demarcation point is proposed and a novel probability integral method segmental parameter modified prediction model is constructed. The simulated experiment and real data experiment results prove that the constructed probability integral method segmented parameter modified model can both reduce the convergence of surface subsidence basin edge better and take into account the predicted accuracy inside the subsidence basin. The research achievements provide scientific data support for disaster warning, pollution management, ecological restoration, and coordination between coal mining and surface city construction in thick loose layer mining areas.}, }
@article {pmid36792824, year = {2023}, author = {Woodhouse, A and Swain, A and Fagan, WF and Fraass, AJ and Lowery, CM}, title = {Late Cenozoic cooling restructured global marine plankton communities.}, journal = {Nature}, volume = {614}, number = {7949}, pages = {713-718}, pmid = {36792824}, issn = {1476-4687}, mesh = {Animals ; *Aquatic Organisms/classification/isolation &amp; purification ; *Biodiversity ; *Cold Temperature ; Datasets as Topic ; *Foraminifera/classification/isolation &amp; purification ; Fossils ; *Geographic Mapping ; History, Ancient ; Phylogeny ; *Phylogeography ; *Plankton/classification/isolation &amp; purification ; *Spatio-Temporal Analysis ; Time Factors ; Hydrobiology ; }, abstract = {The geographic ranges of marine organisms, including planktonic foraminifera[1], diatoms, dinoflagellates[2], copepods[3] and fish[4], are shifting polewards owing to anthropogenic climate change[5]. However, the extent to which species will move and whether these poleward range shifts represent precursor signals that lead to extinction is unclear[6]. Understanding the development of marine biodiversity patterns over geological time and the factors that influence them are key to contextualizing these current trends. The fossil record of the macroperforate planktonic foraminifera provides a rich and phylogenetically resolved dataset that provides unique opportunities for understanding marine biogeography dynamics and how species distributions have responded to ancient climate changes. Here we apply a bipartite network approach to quantify group diversity, latitudinal specialization and latitudinal equitability for planktonic foraminifera over the past eight million years using Triton, a recently developed high-resolution global dataset of planktonic foraminiferal occurrences[7]. The results depict a global, clade-wide shift towards the Equator in ecological and morphological community equitability over the past eight million years in response to temperature changes during the late Cenozoic bipolar ice sheet formation. Collectively, the Triton data indicate the presence of a latitudinal equitability gradient among planktonic foraminiferal functional groups which is coupled to the latitudinal biodiversity gradient only through the geologically recent past (the past two million years). Before this time, latitudinal equitability gradients indicate that higher latitudes promoted community equitability across ecological and morphological groups. Observed range shifts among marine planktonic microorganisms[1,2,8] in the recent and geological past suggest substantial poleward expansion of marine communities even under the most conservative future global warming scenarios.}, }
@article {pmid36815186, year = {2023}, author = {Zhou, T and Li, W}, title = {Analysis on Logistics Efficiency Measurement of New Western Land-Sea Corridor under the Background of "Double Carbon" and Ecological Environment Protection.}, journal = {Journal of environmental and public health}, volume = {2023}, number = {}, pages = {8642841}, pmid = {36815186}, issn = {1687-9813}, mesh = {*Carbon ; *Environment ; Efficiency ; Industry ; China ; Economic Development ; }, abstract = {Under the research background of ecological environment protection and "double carbon" goal, this paper applies panel data on the logistics industry from 2010 to 2019 in 12 provinces of China's new western land-sea corridor to statically measure the logistics industry's technical efficiency after taking into account the impact of different environmental elements and to analyze the dynamics trends of total factor productivity in the logistics sector. It is measured by using the three-stage SBM model and the Malmquist-Luenberger productivity index, which considers undesirable output. The findings indicate the following: (1) In the context of "double carbon," the overall technical efficiency of the logistics sector in the new western land-sea corridor seems to be relatively low; however, the average technical efficiency of the logistics sector in the southern portion of the new western land-sea corridor does seem to be higher than that of the northern part. (2) The logistics industry's technical efficiency varies greatly by region, with locations near central China having much higher technical efficiency than remote inland areas. (3) The fundamental reason for the improvement of technical efficiency in the logistics industry is pure technical efficiency, and the driving force behind the increase in total factor productivity is technological advancement. (4) Economic development, informatization development, industrial market scale, and import and export all have a substantial influence on the logistics industry's technical efficiency. Finally, depending on the findings, policy recommendations are offered.}, }
@article {pmid36806940, year = {2023}, author = {Rivera-Colón, AG and Rayamajhi, N and Fazal Minhas, B and Madrigal, G and Bilyk, KT and Yoon, V and Hüne, M and Gregory, S and Cheng, CC and Catchen, JM}, title = {Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad029}, pmid = {36806940}, issn = {1537-1719}, abstract = {White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.}, }
@article {pmid36334202, year = {2023}, author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y}, title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {9}, pages = {24284-24298}, pmid = {36334202}, issn = {1614-7499}, mesh = {*Denitrification ; Bioreactors/microbiology ; Seasons ; Multiomics ; Proteomics ; *Microbiota ; Biofilms ; Nitrogen ; }, abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.}, }
@article {pmid36803728, year = {2023}, author = {Niu, L and Zhagn, L and Xi, F and Wang, J}, title = {[Influencing factors and scenario forecasting of carbon emissions in Liaoning Province, China].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {34}, number = {2}, pages = {499-509}, doi = {10.13287/j.1001-9332.202302.001}, pmid = {36803728}, issn = {1001-9332}, mesh = {*Carbon/analysis ; *Carbon Dioxide/analysis ; Economic Development ; China ; Forecasting ; }, abstract = {Liaoning is a province with large energy consumption and carbon emissions. Management of carbon emissions in Liaoning Province is crucial to realizing China's carbon peaking and carbon neutrality goals. To clarify the driving factors and trends of carbon emissions in Liaoning Province, we analyzed the impacts of six factors on carbon emissions in Liaoning Province through STIRPAT model based on carbon emission data from 1999 to 2019. The impact factors included population, urbanization rate, per-capita GDP, secondary industry ratio, energy consumption per unit GDP, and coal consumption ratio. Nine forecasting scenarios with three economic and population growth models and three emission reduction models were set up, and their carbon emission trends under the above nine forecasting scenarios were predicted. The results showed that the main driving factor of carbon emissions in Liaoning Province was per-capita GDP, and that the main inhibitor was energy consumption per unit GDP. The carbon peak year in Liaoning Province would fluctuate between 2020 and 2055 under the nine forecasting scenarios, with peak values ranging from 544 to 1088 million tons CO2. The medium economic development growth and high carbon emission reduction scenario would be the optimal carbon emission scenario in Liaoning Province. Under this forecasting scenario, Liaoning Province could achieve carbon peak (611 million tons CO2) by 2030 without affec-ting economic development through optimizing energy structure and controlling the intensity of energy consumption. Our results would be helpful for seeking the best path for carbon emission reduction in Liaoning Province and providing a reference for its realization of carbon peaking and carbon neutrality goals.}, }
@article {pmid36795572, year = {2023}, author = {Wang, J and Ding, R and Ouyang, T and Gao, H and Kan, H and Li, Y and Hu, Q and Yang, Y}, title = {Systematic investigation of the mechanism of herbal medicines for the treatment of prostate cancer.}, journal = {Aging}, volume = {15}, number = {}, pages = {}, doi = {10.18632/aging.204516}, pmid = {36795572}, issn = {1945-4589}, abstract = {Due to various unpleasant side effects and general ineffectiveness of current treatments for prostate cancer (PCa), more and more people with PCa try to look for complementary and alternative medicine such as herbal medicine. However, since herbal medicine has multi-components, multi-targets and multi-pathways features, its underlying molecular mechanism of action is not yet known and still needs to be systematically explored. Presently, a comprehensive approach consisting of bibliometric analysis, pharmacokinetic assessment, target prediction and network construction is firstly performed to obtain PCa-related herbal medicines and their corresponding candidate compounds and potential targets. Subsequently, a total of 20 overlapping genes between DEGs in PCa patients and the target genes of the PCa-related herbs, as well as five hub genes, i.e., CCNA2, CDK2, CTH, DPP4 and SRC were determined employing bioinformatics analysis. Further, the roles of these hub genes in PCa were also investigated through survival analysis and tumour immunity analysis. Moreover, to validate the reliability of the C-T interactions and to further explore the binding modes between ingredients and their targets, the molecular dynamics (MD) simulations were carried out. Finally, based on the modularization of the biological network, four signaling pathways, i.e., PI3K-Akt, MAPK, p53 and cell cycle were integrated to further analyze the therapeutic mechanism of PCa-related herbal medicine. All the results show the mechanism of action of herbal medicines on treating PCa from the molecular to systematic levels, providing a reference for the treatment of complex diseases using TCM.}, }
@article {pmid36792330, year = {2023}, author = {Suzuki, S and Nishikawa, Y and Okada, H and Nakayama, T}, title = {Information-seeking behaviour of community pharmacists during the COVID-19 pandemic: an ecological study.}, journal = {BMJ open}, volume = {13}, number = {2}, pages = {e062465}, pmid = {36792330}, issn = {2044-6055}, mesh = {Humans ; *COVID-19/epidemiology ; Pharmacists ; Pandemics ; Information Seeking Behavior ; *Community Pharmacy Services ; }, abstract = {OBJECTIVE: To evaluate the information-seeking behaviour of pharmacists during the COVID-19 pandemic and its relation to COVID-19 and related infections and deaths within the local prefecture.<br><br>DESIGN: Ecological study.<br><br>SETTING: Japan-47 prefectures.<br><br>METHODS: The number of accesses to a Japanese web page established by the Pharmacy Informatics Group to disseminate information about infection control and the number of infections and deaths in 47 prefectures were investigated from 6 April to 30 September 2020 using the access information on the web page and publicly available information.<br><br>RESULTS: During the first 6 months of the COVID-19 pandemic, the total number of accesses was 226 130 (range: 10 984-138 898 per month), the total number of infections was 78 761 (1738-31 857) and the total number of deaths was 1470 (39-436). The correlation between the total number of accesses and that of infections per 100 000 individuals in 47 prefectures was r=0.72 (95% CI 0.55 to 0.83, p<0.001), and between the total number of accesses and deaths per 100 000 individuals in 47 prefectures was r=0.44 (95% CI 0.17 to 0.65, p=0.002).<br><br>CONCLUSIONS: The information-seeking behaviour of community pharmacists correlated positively with infection status within the community.}, }
@article {pmid36640933, year = {2023}, author = {Gautam, P and Pandey, AK and Dubey, SK}, title = {Multi-omics approach reveals elevated potential of bacteria for biodegradation of imidacloprid.}, journal = {Environmental research}, volume = {221}, number = {}, pages = {115271}, doi = {10.1016/j.envres.2023.115271}, pmid = {36640933}, issn = {1096-0953}, mesh = {Biodegradation, Environmental ; Molecular Docking Simulation ; Multiomics ; Neonicotinoids/analysis ; *Insecticides/analysis ; Nitro Compounds/analysis/chemistry/metabolism ; Bacteria/metabolism ; *Soil Pollutants/analysis ; Soil ; }, abstract = {The residual imidacloprid, a widely used insecticide is causing serious environmental concerns. Knowledge of its biodegradation will help in assessing its residual mass in soil. In view of this, a soil microcosm-based study was performed to test the biodegradation potential of Agrobacterium sp. InxBP2. It achieved ∼88% degradation in 20 days and followed the pseudo-first-order kinetics (k = 0.0511 day[-1] and t1/2=7 days). Whole genome sequencing of Agrobacterium sp. InxBP2 revealed a genome size of 5.44 Mbp with 5179 genes. Imidacloprid degrading genes at loci K7A42_07110 (ABC transporter substrate-binding protein), K7A42_07270 (amidohydrolase family protein), K7A42_07385 (ABC transporter ATP-binding protein), K7A42_16,845 (nitronate monooxygenase family protein), and K7A42_20,660 (FAD-dependent monooxygenase) having sequence and functional similarity with known counterparts were identified. Molecular docking of proteins encoded by identified genes with their respective degradation pathway intermediates exhibited significant binding energies (-6.56 to -4.14 kcal/mol). Molecular dynamic simulation discovered consistent interactions and binding depicting high stability of docked complexes. Proteome analysis revealed differential protein expression in imidacloprid treated versus untreated samples which corroborated with the in-silico findings. Further, the detection of metabolites proved the bacterial degradation of imidacloprid. Thus, results provided a mechanistic link between imidacloprid and associated degradative genes/enzymes of Agrobacterium sp. InxBP2. These findings will be of immense significance in carrying out the lifecycle analysis and formulating strategies for the bioremediation of soils contaminated with insecticides like imidacloprid.}, }
@article {pmid36527232, year = {2023}, author = {Petrén, H and Köllner, TG and Junker, RR}, title = {Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv.}, journal = {The New phytologist}, volume = {237}, number = {6}, pages = {2478-2492}, doi = {10.1111/nph.18685}, pmid = {36527232}, issn = {1469-8137}, mesh = {*Phytochemicals ; *Plants ; Ecology ; Phenotype ; Databases, Factual ; }, abstract = {Plants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds. Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds' function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures. We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and - most importantly - structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets. By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.}, }
@article {pmid36264457, year = {2023}, author = {Nasiruddin, M and Islam, ARMT and Siddique, MAB and Hasanuzaman, M and Hassan, MM and Akbor, MA and Hasan, M and Islam, MS and Khan, R and Al Amin, M and Pal, SC and Idris, AM and Kumar, S}, title = {Distribution, sources, and pollution levels of toxic metal(loid)s in an urban river (Ichamati), Bangladesh using SOM and PMF modeling with GIS tool.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {8}, pages = {20934-20958}, pmid = {36264457}, issn = {1614-7499}, mesh = {Humans ; *Metals, Heavy/analysis ; Environmental Monitoring ; Geographic Information Systems ; Rivers ; Bangladesh ; Cadmium/analysis ; Lead/analysis ; Geologic Sediments/analysis ; *Water Pollutants, Chemical/analysis ; Water Quality ; Risk Assessment ; China ; }, abstract = {Indexical assessment coupled with a self-organizing map (SOM) and positive matrix factorization (PMF) modeling of toxic metal(loid)s in sediment and water of the aquatic environment provides valuable information from the environmental management perspective. However, in northwest Bangladesh, indexical and modeling assessments of toxic metal(loid)s in surface water and sediment are still rare. Toxic metal(loid)s were measured in sediment and surface water from an urban polluted river (Ichamati) in northwest Bangladesh using an atomic absorption spectrophotometer to assess distribution, pollution levels, sources, and potential environmental risks to the aquatic environment. The mean concentrations (mg/kg) of metal(loid)s in water are as follows: Fe (871) > Mn (382) > Cr (72.4) > Zn (34.2) > Co (20.8) > Pb (17.6) > Ni (16.7) > Ag (14.9) > As (9.0) > Cu (5.63) > Cd (2.65), while in sediment, the concentration follows the order, Fe (18,725) > Mn (551) > Zn (213) > Cu (47.6) > Cr (30.2) > Ni (24.2) > Pb (23.8) > Co (9.61) > As (8.23) > Cd (0.80) > Ag (0.60). All metal concentrations were within standard guideline values except for Cr and Pb for water and Cd, Zn, Cu, Pb, and As for sediment. The outcomes of eco-environmental indices, including contamination and enrichment factors and geo-accumulation index, differed spatially, indicating that most of the sediment sites were moderately to highly polluted by Cd, Zn, and As. Cd and Zn content can trigger ecological risks. The positive matrix factorization (PMF) model recognized three probable sources of sediment, i.e., natural source (49.39%), industrial pollution (19.72%), and agricultural source (30.92%), and three possible sources of water, i.e., geogenic source (45.41%), industrial pollution (22.88%), and industrial point source (31.72%), respectively. SOM analysis identified four spatial patterns, e.g., Fe-Mn-Ag, Cd-Cu, Cr-Pb-As-Ni, and Zn-Co in water and three patterns, e.g., Mn-Co-Ni-Cr, Cd-Cu-Pb-Zn, and As-Fe-Ag in sediment. The spatial distribution of entropy water quality index values shows that the southwestern area possesses "poor" quality water. Overall, the levels of metal(loid) pollution in the investigated river surpassed a critical threshold, which might have serious consequences for the river's aquatic biota and human health in the long run.}, }
@article {pmid36788337, year = {2023}, author = {Bayer, N and Hausmann, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G}, title = {Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.}, journal = {Leukemia}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41375-023-01839-7}, pmid = {36788337}, issn = {1476-5551}, }
@article {pmid36194325, year = {2023}, author = {Zhou, Y and Hu, Z and Geng, Q and Ma, J and Liu, J and Wang, M and Wang, Y}, title = {Monitoring and analysis of desertification surrounding Qinghai Lake (China) using remote sensing big data.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {7}, pages = {17420-17436}, pmid = {36194325}, issn = {1614-7499}, mesh = {Humans ; *Remote Sensing Technology ; *Conservation of Natural Resources/methods ; Lakes ; Big Data ; Environmental Monitoring/methods ; China ; }, abstract = {Desertification is one of the most serious ecological environmental problems in the world. Monitoring the spatiotemporal dynamics of desertification is crucial for its control. The region around Qinghai Lake, in the northeastern part of the Qinghai-Tibet Plateau in China, is a special ecological function area and a climate change sensitive area, making its environmental conditions a great concern. Using cloud computing via Google Earth Engine (GEE), we collected Landsat 5 TM, Landsat 8 OLI/TIRS, and MODIS Albedo images from 2000 to 2020 in the region around Qinghai Lake, acquired land surface albedo (Albedo), and normalized vegetation index (NDVI) to build a remote sensing monitoring model of desertification. Our results showed that the desertification difference index based on the Albedo-NDVI feature space could reflect the degree of desertification in the region around Qinghai Lake. GEE offers significant advantages, such as massive data processing and long-term dynamic monitoring. The desertification land area fluctuated downward in the study area from 2000 to 2020, and the overall desertification status improved. Natural factors, such as climate change from warm-dry to warm-wet and decreased wind speed, and human factors improved the desertification situation. The findings indicate that desertification in the region around Qinghai Lake has been effectively controlled, and the overall desertification trend is improving.}, }
@article {pmid36787802, year = {2023}, author = {Dennis, A and Cuthbertson, DJ and Wootton, D and Crooks, M and Gabbay, M and Eichert, N and Mouchti, S and Pansini, M and Roca-Fernandez, A and Thomaides-Brears, H and Kelly, M and Robson, M and Hishmeh, L and Attree, E and Heightman, M and Banerjee, R and Banerjee, A}, title = {Multi-organ impairment and long COVID: a 1-year prospective, longitudinal cohort study.}, journal = {Journal of the Royal Society of Medicine}, volume = {}, number = {}, pages = {1410768231154703}, doi = {10.1177/01410768231154703}, pmid = {36787802}, issn = {1758-1095}, abstract = {OBJECTIVES: To determine the prevalence of organ impairment in long COVID patients at 6 and 12 months after initial symptoms and to explore links to clinical presentation.<br><br>DESIGN: Prospective cohort study.<br><br>PARTICIPANTS: Individuals.<br><br>METHODS: In individuals recovered from acute COVID-19, we assessed symptoms, health status, and multi-organ tissue characterisation and function.<br><br>SETTING: Two non-acute healthcare settings (Oxford and London). Physiological and biochemical investigations were performed at baseline on all individuals, and those with organ impairment were reassessed.<br><br>MAIN OUTCOME MEASURES: Primary outcome was prevalence of single- and multi-organ impairment at 6 and 12 months post COVID-19.<br><br>RESULTS: A total of 536 individuals (mean age 45 years, 73% female, 89% white, 32% healthcare workers, 13% acute COVID-19 hospitalisation) completed baseline assessment (median: 6 months post COVID-19); 331 (62%) with organ impairment or incidental findings had follow-up, with reduced symptom burden from baseline (median number of symptoms 10 and 3, at 6 and 12 months, respectively). Extreme breathlessness (38% and 30%), cognitive dysfunction (48% and 38%) and poor health-related quality of life (EQ-5D-5L&#x2009;<&#x2009;0.7; 57% and 45%) were common at 6 and 12 months, and associated with female gender, younger age and single-organ impairment. Single- and multi-organ impairment were present in 69% and 23% at baseline, persisting in 59% and 27% at follow-up, respectively.<br><br>CONCLUSIONS: Organ impairment persisted in 59% of 331 individuals followed up at 1 year post COVID-19, with implications for symptoms, quality of life and longer-term health, signalling the need for prevention and integrated care of long COVID.Trial Registration: ClinicalTrials.gov Identifier: NCT04369807.}, }
@article {pmid36782205, year = {2023}, author = {Amin, M and Aziz, MA and Pieroni, A and Nazir, A and Al-Ghamdi, AA and Kangal, A and Ahmad, K and Abbasi, AM}, title = {Edible wild plant species used by different linguistic groups of Kohistan Upper Khyber Pakhtunkhwa (KP), Pakistan.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {19}, number = {1}, pages = {6}, pmid = {36782205}, issn = {1746-4269}, abstract = {BACKGROUND: The mountainous territory of Kohistan shelters diverse food plant species and is considered one of the important hotspots of local plant knowledge. In the era of globalization and food commodification, wild food plants (WFPs) play an important role in supporting local food systems and related local knowledge is one of the important pillars of food sustainability across the region. Since the area is populated by different cultural groups and each culture has retained particular knowledge on the local plant species, therefore, to make a cross-culturally comparison, the study was planned to record and compare the local plants knowledge among three linguistic groups viz Gujjar, Kohistani and Shina in order to not only protect the local knowledge but to determine the food cultural adaptations among these groups looking through the lens of their food ethnobotanies.<br><br>METHODS: Field ethnobotanical survey was carried out in 2020-2021 to gather the data on wild food plants. We used semi-structured interviews. Use reports were counted, and the results were visualized through Venn diagrams.<br><br>RESULTS: In total, 64 plant species belonging to 45 botanical families were documented. Among these Ajuga integrifolia, Barbarea verna, Clematis grata, Impatiens edgeworthii, Ranunculus laetus (vegetables), Parrotiopsis jacquemontiana (fruit), Indigofera tinctoria (flower), Juniperus excelsa, Primula elliptica, P. macrophylla (flavoring agent), Leontopodium himalayanum (Chewing gum), and Juniperus excelsa (snuff) were reported for the first time. The highest use reports (&#x2265;&#x2009;90) were recorded for Mentha longifolia, Amaranthus hybridus, Quercus semecarpifolia, Solanum miniatum, Oxalis corniculata, Ficus palmata, and Urtica dioica. Maximum number of wild food plant species (WFPs) were reported by Kohistani, followed by Shinaki and Gujjari linguistic groups. The percentage overlap of traditional knowledge on WFPs was highest among Kohistani and Shinaki (56.0%), followed by Shinaki and Gujjars (17.0%), and Kohistani and Gujjars (15.0%). Kohistani and Shinaki groups exhibited maximum homogeneity in traditional knowledge. However, Gujjars had more knowledge on WFPs compared to Kohistani and Shinaki. In addition, some dairy products viz. Bhorus, Bagora, Bak, Cholam, Kacha, Gurloo and Poyeen were reported also reported that are consumed orally and used in traditional cuisines.<br><br>CONCLUSIONS: The study indicates that Kohistan is one of the important spots of biocultural diversity and could be recognized as biocultural refugia. WFPs have been an integral part of the traditional food systems among the studied groups, particularly the Gujjars have reported more distinct plant uses which could be referred to their distinctive ecological experiences among others. However, social change is one of the challenges that might lead to the erosion of local plant knowledge. Moreover, intercultural negotiations among the studied groups are also a matter of concern which could homogenize the local knowledge among them. Therefore, we suggest solid policy measures to protect the local knowledge and celebrate diversity across this mountain territory.}, }
@article {pmid36781356, year = {2023}, author = {Mayne, SL and DiFiore, G and Hannan, C and Nwokeji, U and Tam, V and Filograna, C and Martin, T and South, E and Mitchell, JA and Glanz, K and Fiks, AG}, title = {Feasibility and acceptability of mobile methods to assess home and neighborhood environments related to adolescent sleep.}, journal = {Sleep health}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.sleh.2023.01.014}, pmid = {36781356}, issn = {2352-7226}, abstract = {OBJECTIVE: A growing evidence base suggests home and neighborhood environmental exposures may influence adolescent sleep, but few studies have assessed these relationships using methods that account for time-varying, location-specific exposures, or multiple neighborhood contexts. This study aimed to assess the feasibility and acceptability of using smartphone global positioning system (GPS) tracking and ecological momentary assessment (EMA) to assess time-varying home and neighborhood environmental exposures hypothesized to be associated with adolescent sleep.<br><br>METHODS: Adolescents aged 15-17 years in Philadelphia completed 7 days of continuous smartphone GPS tracking, which was used to identify daily levels of exposure to geocoded neighborhood factors (eg, crime, green space). Four daily EMA surveys assessed home sleep environment (eg, noise, light), stress, health behaviors, and neighborhood perceptions. Feasibility and acceptability of GPS tracking and EMA were assessed, and distributions of daily environmental exposures were examined.<br><br>RESULTS: Among 25 teens (mean age 16, 56% male), there was a high level of GPS location data captured (median daily follow-up: 24 hours). Seventy-eight percent of EMA surveys were completed overall. Most participants (96%) reported no privacy concerns related to GPS tracking and minimal burden from EMA surveys. Exposures differed between participants' home neighborhoods and locations visited outside the home neighborhood (eg, higher crime away from home). Sleep environment disruptions were present on 29% of nights (most common: uncomfortable temperature) and were reported by 52% of adolescents.<br><br>CONCLUSIONS: Results demonstrate the feasibility and acceptability of mobile methods for assessing time-varying home and neighborhood exposures relevant to adolescent sleep for up to 1 week.}, }
@article {pmid36775641, year = {2023}, author = {Liu, L and Zhang, WQ and Hu, FC and Pang, K and Guo, YL and Zhang, T and Li, M}, title = {[Evaluation and Optimization of Rural Sewage Treatment Technologies in the Middle Reaches of the Yangtze River Based on Group Decision Making and Analytic Hierarchy Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {2}, pages = {1191-1200}, doi = {10.13227/j.hjkx.202203043}, pmid = {36775641}, issn = {0250-3301}, mesh = {*Sewage ; *Rivers ; Analytic Hierarchy Process ; Nitrogen ; Decision Making ; China ; }, abstract = {Rural sewage treatment in the Yangtze River basin is an important link to achieve the great protection of the Yangtze River, but the existing treatment technologies are difficult to choose and have various techniques and a lack of evaluation. Therefore, this study researched and collected the case information of rural sewage treatment projects in the middle reaches of the Yangtze River, analyzed the application of each treatment technology under different collection modes and discharge standards, constructed the evaluation index system of rural sewage treatment technologies, and then conducted a classification evaluation of processing technologies for each application scenario based on group decision making and the Analytic Hierarchy Process. The results showed that:the collection modes of rural sewage in the middle reaches of the Yangtze River were mainly single village or small-scale joint village, the treatment scale was mainly concentrated below 200 m[3]·d[-1], the treatment technology was most applied by the anaerobic+ecological process (28.05%), and the application of integrated equipment was also more widely used (22.47%). The technical performance in the criterion layer had the largest weight (0.5039) in the evaluation index system, followed by those of economic benefits (0.2474), operation and management (0.1559), and environmental impact (0.0928), respectively; the four indicators of TP removal rate, ton water operation cost, ammonia nitrogen removal rate, and maintenance difficulty had higher weights. The evaluation and optimization results showed that the enhanced ecological and anaerobic+ecological treatment technologies were suitable for promotion and application in the rural areas of the middle reaches of the Yangtze River. The results of this study can provide scientific basis and reference for the selection of rural sewage treatment technologies in the middle reaches of the Yangtze River.}, }
@article {pmid36767964, year = {2023}, author = {Cao, H and Ou, H and Ju, W and Pan, M and Xue, H and Zhu, F}, title = {Visual Analysis of International Environmental Security Management Research (1997-2021) Based on VOSviewer and CiteSpace.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, pmid = {36767964}, issn = {1660-4601}, mesh = {Bayes Theorem ; *Agriculture ; Australia ; *Big Data ; China ; }, abstract = {To investigate the international development status and hot trends in the field of environmental security management in recent years, the published the environmental security management literature from 1997 to 2021, which was retrieved from Web of Science, with VOSviewer as the main and CiteSpace as the auxiliary, through the cooperation network of authors, scientific research institutions, and countries. The keywords were visualized by clustering, time zone analysis, and burst analysis. A total of 7596 articles were retrieved, forming six main clustering labels, including 28,144 authors. The research hotspots are from the fields of personal health, society, agriculture, ecological environment, energy, and sustainable development, as well as the development of internet environmental safety management, such as big data, Bayesian networks, and conceptual frameworks. Through cluster analysis, the cooperation of major research teams and scientific research institutions and the cooperation and development between countries were analyzed. The cooperation between scientific research institutions in various countries is relatively close. The United States currently occupies a dominant and authoritative position in this field. China has cooperated more closely with the United States, Britain, Australia, and India.}, }
@article {pmid36777713, year = {2021}, author = {Dussex, N and van der Valk, T and Morales, HE and Wheat, CW and Díez-Del-Molino, D and von Seth, J and Foster, Y and Kutschera, VE and Guschanski, K and Rhie, A and Phillippy, AM and Korlach, J and Howe, K and Chow, W and Pelan, S and Mendes Damas, JD and Lewin, HA and Hastie, AR and Formenti, G and Fedrigo, O and Guhlin, J and Harrop, TWR and Le Lec, MF and Dearden, PK and Haggerty, L and Martin, FJ and Kodali, V and Thibaud-Nissen, F and Iorns, D and Knapp, M and Gemmell, NJ and Robertson, F and Moorhouse, R and Digby, A and Eason, D and Vercoe, D and Howard, J and Jarvis, ED and Robertson, BC and Dalén, L}, title = {Population genomics of the critically endangered kākāpō.}, journal = {Cell genomics}, volume = {1}, number = {1}, pages = {100002}, pmid = {36777713}, issn = {2666-979X}, abstract = {The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.}, }
@article {pmid36777319, year = {2022}, author = {Glasgow, L and Lewis, R and Charles, S}, title = {The cancer epidemic in the Caribbean region: Further opportunities to reverse the disease trend.}, journal = {Lancet regional health. Americas}, volume = {13}, number = {}, pages = {100295}, pmid = {36777319}, issn = {2667-193X}, abstract = {Cancer incidence has been rising in the Caribbean and is expected to have significant adverse implications for the health of people in the region and health systems in this decade. While developed countries, for the most part, enjoy the benefits of advanced technologies and adaptive systems in cancer control and management, a different experience confronts a large segment of the Caribbean population. The region has experienced some success in enhancing cancer services, however, there is a need to address gaps in several areas through nationally and regionally tailored initiatives. This Review complements previous publications on the challenges, actions, and progress towards cancer prevention and care in Caribbean countries but also further outlines potential positive impacts that can be derived from addressing gaps pertaining to cancer education, data management, screening and risk assessment, navigation services, gender factors, and resource development. The proposed approaches encapsulate concepts of health theories that are applicable across the ecological domains. When implemented in combination, the proposals may effectively contribute to reducing the cancer burden in the region.}, }
@article {pmid36771658, year = {2023}, author = {Shah, AA and Badshah, L and Khalid, N and Shah, MA and Manduzai, AK and Faiz, A and De Chiara, M and Mattalia, G and Sõukand, R and Pieroni, A}, title = {Disadvantaged Economic Conditions and Stricter Border Rules Shape Afghan Refugees' Ethnobotany: Insights from Kohat District, NW Pakistan.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36771658}, issn = {2223-7747}, abstract = {The study of migrants' ethnobotany can help to address the diverse socio-ecological factors affecting temporal and spatial changes in local ecological knowledge (LEK). Through semi-structured and in-depth conversations with ninety interviewees among local Pathans and Afghan refugees in Kohat District, NW Pakistan, one hundred and forty-five wild plant and mushroom folk taxa were recorded. The plants quoted by Afghan refugees living inside and outside the camps tend to converge, while the Afghan data showed significant differences with those collected by local Pakistani Pathans. Interviewees mentioned two main driving factors potentially eroding folk plant knowledge: (a) recent stricter border policies have made it more difficult for refugees to visit their home regions in Afghanistan and therefore to also procure plants in their native country; (b) their disadvantaged economic conditions have forced them to engage more and more in urban activities in the host country, leaving little time for farming and foraging practices. Stakeholders should foster the exposure that refugee communities have to their plant resources, try to increase their socio-economic status, and facilitate both their settling outside the camps and their transnational movement for enhancing their use of wild plants, ultimately leading to improvements in their food security and health status.}, }
@article {pmid36768056, year = {2023}, author = {Vukašinović, D and Maksimović, M and Tanasković, S and Marinković, JM and Radak, &#x110; and Maksimović, J and Vujčić, I and Prijović, N and Vlajinac, H}, title = {Body Mass Index and Late Adverse Outcomes after a Carotid Endarterectomy.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, pmid = {36768056}, issn = {1660-4601}, abstract = {A cohort study was conducted to examine the association of an increased body mass index (BMI) with late adverse outcomes after a carotid endarterectomy (CEA). It comprised 1597 CEAs, performed in 1533 patients at the Vascular Surgery Clinic in Belgrade, from 1 January 2012 to 31 December 2017. The follow-up lasted four years after CEA. Data for late myocardial infarction and stroke were available for 1223 CEAs, data for death for 1305 CEAs, and data for restenosis for 1162 CEAs. Logistic and Cox regressions were used in the analysis. The CEAs in patients who were overweight and obese were separately compared with the CEAs in patients with a normal weight. Out of 1223 CEAs, 413 (33.8%) were performed in patients with a normal weight, 583 (47.7%) in patients who were overweight, and 220 (18.0%) in patients who were obese. According to the logistic regression analysis, the compared groups did not significantly differ in the frequency of myocardial infarction, stroke, and death, as late major adverse outcomes (MAOs), or in the frequency of restenosis. According to the Cox and logistic regression analyses, BMI was neither a predictor for late MAOs, analyzed separately or all together, nor for restenosis. In conclusion, being overweight and being obese were not related to the occurrence of late adverse outcomes after a carotid endarterectomy.}, }
@article {pmid36767252, year = {2023}, author = {Liu, Q and Guo, R and Huang, Z and He, B and Li, X}, title = {The Nonlinear Impact of Mobile Human Activities on Vegetation Change in the Guangdong-Hong Kong-Macao Greater Bay Area.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {3}, pages = {}, doi = {10.3390/ijerph20031874}, pmid = {36767252}, issn = {1660-4601}, abstract = {Vegetation is essential for ecosystem function and sustainable urban development. In the context of urbanization, the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), as the typical urban-dominated region, has experienced a remarkable increase in social and economic activities. Their impact on vegetation is of great significance but unclear, as interannual flow data and linear methods have limitations. Therefore, in this study, we used human and vehicle flow data to build and simulate the indices of mobile human activity. In addition, we used partial least squares regression (PLSR), random forest (RF), and geographical detector (GD) models to analyze the impact of mobile human activities on vegetation change. The results showed that indices of mobile human and vehicle flow increased by 1.43 and 7.68 times from 2000 to 2019 in the GBA, respectively. Simultaneously, vegetation increased by approximately 64%, whereas vegetation decreased mainly in the urban areas of the GBA. Vegetation change had no significant linear correlation with mobile human activities, exhibiting a regression coefficient below 0.1 and a weight of coefficients of PLSR less than 40 between vegetation change and all the factors of human activities. However, a more significant nonlinear relationship between vegetation change and driving factors were obtained. In the RF regression model, vegetation decrease was significantly affected by mobile human activity of vehicle flow, with an importance score of 108.11. From the GD method, vegetation decrease was found to mainly interact with indices of mobile human and vehicle inflow, and the highest interaction force was 0.82. These results may support the attainment of sustainable social-ecological systems and global environmental change.}, }
@article {pmid36750720, year = {2023}, author = {Mechenich, MF and Žliobaitė, I}, title = {Eco-ISEA3H, a machine learning ready spatial database for ecometric and species distribution modeling.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {77}, pmid = {36750720}, issn = {2052-4463}, mesh = {Animals ; Humans ; Climate Change ; *Databases, Factual ; *Ecosystem ; Geography ; Machine Learning ; Mammals ; }, abstract = {We present the Eco-ISEA3H database, a compilation of global spatial data characterizing climate, geology, land cover, physical and human geography, and the geographic ranges of nearly 900 large mammalian species. The data are tailored for machine learning (ML)-based ecological modeling, and are intended primarily for continental- to global-scale ecometric and species distribution modeling. Such models are trained on present-day data and applied to the geologic past, or to future scenarios of climatic and environmental change. Model training requires integrated global datasets, describing species' occurrence and environment via consistent observational units. The Eco-ISEA3H database incorporates data from 17 sources, and includes 3,033 variables. The database is built on the Icosahedral Snyder Equal Area (ISEA) aperture 3 hexagonal (3H) discrete global grid system (DGGS), which partitions the Earth's surface into equal-area hexagonal cells. Source data were incorporated at six nested ISEA3H resolutions, using scripts developed and made available here. We demonstrate the utility of the database in a case study analyzing the bioclimatic envelopes of ten large, widely distributed mammalian species.}, }
@article {pmid36748522, year = {2022}, author = {Cunningham-Oakes, E and Pointon, T and Murphy, B and Campbell-Lee, S and Connor, TR and Mahenthiralingam, E}, title = {Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36748522}, issn = {2057-5858}, mesh = {Retrospective Studies ; *Bacteria/genetics ; *Metagenome ; Metagenomics/methods ; Workflow ; }, abstract = {The home and personal care (HPC) industry generally relies on initial cultivation and subsequent biochemical testing for the identification of microorganisms in contaminated products. This process is slow (several days for growth), labour intensive, and misses organisms which fail to revive from the harsh environment of preserved consumer products. Since manufacturing within the HPC industry is high-throughput, the process of identification of microbial contamination could benefit from the multiple cultivation-independent methodologies that have developed for the detection and analysis of microbes. We describe a novel workflow starting with automated DNA extraction directly from a HPC product, and subsequently applying metagenomic methodologies for species and strain-level identification of bacteria. The workflow was validated by application to a historic microbial contamination of a general-purpose cleaner (GPC). A single strain of Pseudomonas oleovorans was detected metagenomically within the product. The metagenome mirrored that of a contaminant isolated in parallel by a traditional cultivation-based approach. Using a dilution series of the incident sample, we also provide evidence to show that the workflow enables detection of contaminant organisms down to 100 CFU/ml of product. To our knowledge, this is the first validated example of metagenomics analysis providing confirmatory evidence of a traditionally isolated contaminant organism, in a HPC product.}, }
@article {pmid36637211, year = {2023}, author = {Feldner-Busztin, D and Firbas Nisantzis, P and Edmunds, SJ and Boza, G and Racimo, F and Gopalakrishnan, S and Limborg, MT and Lahti, L and de Polavieja, GG}, title = {Dealing with dimensionality: the application of machine learning to multi-omics data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {2}, pages = {}, pmid = {36637211}, issn = {1367-4811}, mesh = {Humans ; *Multiomics ; *Neoplasms/genetics ; Machine Learning ; Genome ; }, abstract = {MOTIVATION: Machine learning (ML) methods are motivated by the need to automate information extraction from large datasets in order to support human users in data-driven tasks. This is an attractive approach for integrative joint analysis of vast amounts of omics data produced in next generation sequencing and other -omics assays. A systematic assessment of the current literature can help to identify key trends and potential gaps in methodology and applications. We surveyed the literature on ML multi-omic data integration and quantitatively explored the goals, techniques and data involved in this field. We were particularly interested in examining how researchers use ML to deal with the volume and complexity of these datasets.<br><br>RESULTS: Our main finding is that the methods used are those that address the challenges of datasets with few samples and many features. Dimensionality reduction methods are used to reduce the feature count alongside models that can also appropriately handle relatively few samples. Popular techniques include autoencoders, random forests and support vector machines. We also found that the field is heavily influenced by the use of The Cancer Genome Atlas dataset, which is accessible and contains many diverse experiments.<br><br>All data and processing scripts are available at this GitLab repository: https://gitlab.com/polavieja_lab/ml_multi-omics_review/ or in Zenodo: https://doi.org/10.5281/zenodo.7361807.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36171318, year = {2023}, author = {Wen, C and Zhen, Z and Zhang, L and Yan, C}, title = {A bibliometric analysis of river health based on publications in the last three decades.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {6}, pages = {15400-15413}, pmid = {36171318}, issn = {1614-7499}, mesh = {Humans ; *Rivers ; *Bibliometrics ; Australia ; China ; Databases, Factual ; Publications ; }, abstract = {Rivers are a vital part of the earth's environment and the basis for human survival. River health has been widely concerned by scholars and practitioners, and the number of studies in this area is increasing. In order to examine the evolution of river health research and identify the research frontiers, a total of 675 articles were retrieved from the Web of Science Core Collection database, and CiteSpace was used for bibliometrics. The results revealed that the research on river health is multidisciplinary. Freshwater Biology and Ecological Indicators were two of the most influential journals. Researchers and institutions from America, Australia, and China were the core research forces, and a certain gap was observed between developed and developing countries in river health. The most productive institution was Michigan State University, followed by Griffith University and Hohai University. There are three development trends in river health: (1) Research scale is expanding; (2) Research methods are diversified and interdisciplinary; and (3) Evaluation index is more comprehensive and systematic. The frontier of river health had been expanded from the connotation of river health to the evaluation methods, evaluation indexes, and comprehensive river ecological research. Overall, research on river health is a well-developed and promising research field. This study provides a framework in the river health field for new researchers and helps scholars to identify further potential perspectives on collaborators, research frontiers, hotspots, and research trends.}, }
@article {pmid36744611, year = {2023}, author = {Smail, EJ and Alpert, JM and Mardini, MT and Kaufmann, CN and Bai, C and Gill, TM and Fillingim, RB and Cenko, E and Zapata, R and Karnati, Y and Marsiske, M and Ranka, S and Manini, TM}, title = {Feasibility of A Smartwatch Platform to Assess Ecological Mobility: Real-time Online Assessment and Mobility Monitor (ROAMM).}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/gerona/glad046}, pmid = {36744611}, issn = {1758-535X}, abstract = {BACKGROUND: Early detection of mobility decline is critical to prevent subsequent reductions in quality of life, disability, and mortality. However, traditional approaches to mobility assessment are limited in their ability to capture daily fluctuations that align with sporadic health events. We aim to describe findings from a pilot study of our Real-time Online Assessment and Mobility Monitor (ROAMM) smartwatch application, which uniquely captures multiple streams of data in real-time in ecological settings.<br><br>METHODS: Data come from a sample of 31 participants (Mage=74.7, 51.6% female) who used ROAMM for approximately two weeks. We describe the usability and feasibility of ROAMM, summarize prompt data using descriptive metrics, and compare prompt data with traditional survey-based questionnaires or other established measures.<br><br>RESULTS: Participants were satisfied with ROAMM's function (87.1%) and ranked the usability as "above average." Most were highly engaged (average adjusted compliance = 70.7%) and the majority reported being "likely" to enroll in a two-year study (77.4%). Some smartwatch features were correlated with their respective traditional measurements (e.g., certain GPS-derived life-space mobility features (r=0.50-0.51, p<0.05) and ecologically-measured pain (r=0.72, p=0.01)), but others were not (e.g., ecologically-measured fatigue).<br><br>CONCLUSION: ROAMM was usable, acceptable, and effective at measuring mobility and risk factors for mobility decline in our pilot sample. Additional work with a larger and more diverse sample is necessary to confirm associations between smartwatch-measured features and traditional measures. By monitoring multiple data streams simultaneously in ecological settings, this technology could uniquely contribute to the evolution of mobility measurement and risk factors for mobility loss.}, }
@article {pmid36727564, year = {2023}, author = {Kinkar, L and Korhonen, PK and Saarma, U and Wang, T and Zhu, XQ and Harliwong, I and Yang, B and Fink, JL and Wang, D and Chang, BCH and Chelomina, GN and Koehler, AV and Young, ND and Gasser, RB}, title = {Genome-wide exploration reveals distinctive northern and southern variants of Clonorchis sinensis in the Far East.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13760}, pmid = {36727564}, issn = {1755-0998}, abstract = {Clonorchis sinensis is a carcinogenic liver fluke that causes clonorchiasis - a neglected tropical disease (NTD) affecting ~ 35 million people worldwide. No vaccine is available, and chemotherapy relies on one anthelmintic, praziquantel. This parasite has a complex life history and is known to infect a range of species of intermediate (freshwater snails and fish) and definitive (piscivorous) hosts. Despite this biological complexity and the impact of this biocarcinogenic pathogen, there has been no previous study of molecular variation in this parasite on a genome-wide scale. Here, we conducted the first extensive nuclear genomic exploration of C. sinensis individuals (n = 152) representing five distinct populations from mainland China, and one from Far East Russia, and revealed marked genetic variation within this species between 'northern' and 'southern' geographic regions. The discovery of this variation indicates the existence of biologically distinct variants within C. sinensis, which may have distinct epidemiology, pathogenicity and/or chemotherapic responsiveness. The detection of high heterozygosity within C. sinensis specimens suggests that this parasite has developed mechanisms to readily adapt to changing environments and/or host species during its life history/evolution. From an applied perspective, the identification of invariable genes could assist in finding new intervention targets in this parasite, given the major clinical relevance of clonorchiasis. From a technical perspective, the genomic-informatic workflow established herein will be readily applicable to a wide range of other parasites that cause NTDs.}, }
@article {pmid36495963, year = {2023}, author = {Tong, H and Warren, JL and Kang, J and Li, M}, title = {Using multi-sourced big data to correlate sleep deprivation and road traffic noise: A US county-level ecological study.}, journal = {Environmental research}, volume = {220}, number = {}, pages = {115029}, doi = {10.1016/j.envres.2022.115029}, pmid = {36495963}, issn = {1096-0953}, mesh = {Humans ; *Sleep Deprivation/epidemiology ; *Noise, Transportation/adverse effects ; Bayes Theorem ; Big Data ; Sleep ; Environmental Exposure ; }, abstract = {BACKGROUND: Road traffic noise is a serious public health problem globally as it has adverse psychological and physiologic effects (i.e., sleep). Since previous studies mainly focused on individual levels, we aim to examine associations between road traffic noise and sleep deprivation on a large scale; namely, the US at county level.<br><br>METHODS: Information from a large-scale sleep survey and national traffic noise map, both obtained from government's open data, were utilized and processed with Geographic Information System (GIS) techniques. To examine the associations between traffic noise and sleep deprivation, we used a hierarchical Bayesian spatial modelling framework to simultaneously adjust for multiple socioeconomic factors while accounting for spatial correlation.<br><br>FINDINGS: With 62.90% of people not getting enough sleep, a 10 dBA increase in average sound-pressure level (SPL) or Ls10 (SPL of the relatively noisy area) in a county, was associated with a 49% (OR: 1.49; 95% CrIs:1.19-1.86) or 8% (1.08; 1.00-1.16) increase in the odds of a person in a particular county not getting enough sleep. No significant association was observed for Ls90 (SPL of the relatively quiet area). A 10% increase in noise exposure area or population ratio was associated with a 3% (1.03; 1.01-1.06) or 4% (1.04; 1.02-1.06) increase in the odds of a person within a county not getting enough sleep.<br><br>INTERPRETATION: Traffic noise can contribute to variations in sleep deprivation among counties. This study suggests that policymakers could set up different noise-management strategies for relatively quiet and noisy areas and incorporate geospatial noise indicators, such as exposure population or area ratio. Furthermore, urban planners should consider urban sprawl patterns differently in terms of noise-induced sleep problems.}, }
@article {pmid36085224, year = {2023}, author = {Gul, S and Bibi, T and Rahim, S and Gul, Y and Niaz, A and Mumtaz, S and Shedayi, AA}, title = {Spatio-temporal change detection of land use and land cover in Malakand Division Khyber Pakhtunkhwa, Pakistan, using remote sensing and geographic information system.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {4}, pages = {10982-10994}, pmid = {36085224}, issn = {1614-7499}, mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; Pakistan ; Conservation of Natural Resources ; Environmental Monitoring/methods ; Agriculture ; }, abstract = {The land use land cover (LULC) change due to the rapidly growing population is a common feature of the urban area. The rapidly growing population in Malakand Division is a greater threat to the LULC of the area due to its negative impact on environment and ecology. This research aims to detect the variations in LULC from 1991 to 2017 in the Malakand Division, Khyber Pakhtunkhwa (KP) province of Pakistan. The study relies on secondary dataset downloaded from the US Geological Survey (1991, 2001, 2011, and 2017 imageries) and the United Nations Office for the Coordination of Humanitarian Affairs (UN OCHA) website. Maximum likelihood technique under supervised image classification was opted to analyze the LULC changes in between 1991 and 2017. The results were based on six major land use classes including agriculture built-up area, vegetation cover, water bodies, snow cover, and barren land. The results from 1991 to 2017 show a substantial reduction in snow cover and barren land which is consequence of climate change. A known change has been recorded in built-up area which shows an increase from 1.02 to 6.2% with a change of 5.18% of the total land. The vegetation cover water bodies were also showing increase in area. The vegetation cover increased from 28.89 to 44.67% while barren land decreased from 45.68 to 40.29% of the total area. Furthermore, the built-up area increased from 1.02 to 6.2%, whereas water covers increased from 0.63% (1991) to 0.86% (2017) of the total area. The study concludes that there is an immense need for planning to preserve the natural habitat for sustainable development in the area.}, }
@article {pmid35462586, year = {2023}, author = {Zhan, Y and Chang, Y and Tao, Y and Zhang, H and Lin, Y and Deng, J and Ma, T and Ding, G and Wei, Y and Li, J}, title = {Insight into the dynamic microbial community and core bacteria in composting from different sources by advanced bioinformatics methods.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {4}, pages = {8956-8966}, pmid = {35462586}, issn = {1614-7499}, mesh = {Animals ; Sheep ; Soil ; *Composting ; Manure/analysis ; *Refuse Disposal ; Bacteria/genetics ; Computational Biology ; *Microbiota ; Vegetables ; Chickens ; }, abstract = {Microbial communities are important for high composting efficiency and good quality composts. This study was conducted to compare the changes of physicochemical and bacterial characteristics in composting from different raw materials, including chicken manure (CM), duck manure (DM), sheep manure (SM), food waste (FW), and vegetable waste (VW). The role and interactions of core bacteria and their contribution to maturity in diverse composts were analyzed by advanced bioinformatics methods combined sequencing with co-occurrence network and structural equation modeling (SEM). Results indicated that there were obviously different bacterial composition and diversity in composting from diverse sources. FW had a low pH and different physiochemical characteristics compared to other composts but they all achieved similar maturity products. Redundancy analysis suggested total organic carbon, phosphorus, and temperature governed the composition of microbial species but key factors were different in diverse composts. Network analysis showed completely different interactions of core bacterial community from diverse composts but Thermobifida was the ubiquitous core bacteria in composting bacterial network. Sphaerobacter and Lactobacillus as core genus were presented in the starting mesophilic and thermophilic phases of composting from manure (CM, DM, SM) and municipal solid waste (FW, VW), respectively. SEM indicated core bacteria had the positive, direct, and the biggest (> 80%) effects on composting maturity. Therefore, this study presents theoretical basis to identify and enhance the core bacteria for improving full-scale composting efficiency facing more and more organic wastes.}, }
@article {pmid33907064, year = {2023}, author = {Ibayashi, K and Fujino, Y and Mimaki, M and Fujimoto, K and Matsuda, S and Goto, YI}, title = {Estimation of the Number of Patients With Mitochondrial Diseases: A Descriptive Study Using a Nationwide Database in Japan.}, journal = {Journal of epidemiology}, volume = {33}, number = {2}, pages = {68-75}, pmid = {33907064}, issn = {1349-9092}, mesh = {Male ; Female ; Humans ; Adult ; Middle Aged ; Japan/epidemiology ; Prevalence ; Databases, Factual ; Tokyo ; *Mitochondrial Diseases/epidemiology ; }, abstract = {BACKGROUND: To provide a better healthcare system for patients with mitochondrial diseases, it is important to understand the basic epidemiology of these conditions, including the number of patients affected. However, little information about them has appeared in Japan to date.<br><br>METHODS: To gather data of patients with mitochondrial diseases, we estimated the number of patients with mitochondrial diseases from April 2018 through March 2019 using a national Japanese health care claims database, the National Database (NDB). Further, we calculated the prevalence of patients, and sex ratio, age class, and geographical distribution.<br><br>RESULTS: From April 2018 through March 2019, the number of patients with mitochondrial diseases was 3,629, and the prevalence was 2.9 (95% confidence interval [CI], 2.8-3.0) per 100,000 general population. The ratio of females and males was 53 to 47, and the most frequent age class was 40-49 years old. Tokyo had the greatest number of patients with mitochondrial diseases, at 477, whereas Yamanashi had the fewest, at 13. Kagoshima had the highest prevalence of patients with mitochondrial diseases, 8.4 (95% CI, 7.1-10.0) per 100,000 population, whereas Yamanashi had the lowest, 1.6 (95% CI, 0.8-2.7).<br><br>CONCLUSION: The number of patients with mitochondrial diseases estimated by this study, 3,269, was more than double that indicated by the Japanese government. This result may imply that about half of all patients are overlooked for reasons such as low severity of illness, suggesting that the Japanese healthcare system needs to provide additional support for these patients.}, }
@article {pmid36726097, year = {2023}, author = {Alwafi, H and Naser, AY and Ashoor, DS and Aldhahir, AM and Alqahtani, JS and Minshawi, F and Salawati, E and Samannodi, M and Dairi, MS and Alansari, AK and Ekram, R}, title = {Trends in hospital admissions and prescribing due to chronic obstructive pulmonary disease and asthma in England and Wales between 1999 and 2020: an ecological study.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {49}, pmid = {36726097}, issn = {1471-2466}, mesh = {Humans ; Female ; Wales/epidemiology ; *Pulmonary Disease, Chronic Obstructive/drug therapy/epidemiology ; Hospitalization ; *Asthma/drug therapy/epidemiology ; England/epidemiology ; Hospitals ; Drug Prescriptions ; *Respiratory Tract Infections/drug therapy ; }, abstract = {OBJECTIVE: To investigate the trends in hospital admissions and medication prescriptions related to asthma and chronic obstructive pulmonary disease (COPD) in England and Wales.<br><br>METHODS: An ecological study was conducted between April 1999 and April 2020 using data extracted from the hospital episode statistics database in England and the patient episode database for Wales. The Office of National Statistics mid-year population estimates for 1999 through 2020 were collected, and medication prescription data for 2004-2020 were extracted from the prescription cost analysis database.<br><br>RESULTS: The total annual number of COPD and asthma hospital admissions for various causes increased by 82.2%, from 210,525 in 1999 to 383,652 in 2020, representing a 59.1% increase in hospital admission rate (from 403.77 in 1999 to 642.42 per 100,000 persons in 2020, p&#x2009;<&#x2009;0.05). Chronic obstructive pulmonary disease with acute lower respiratory infection accounted for 38.7% of hospital admissions. Around 34.7% of all hospital admissions involved patients aged 75 and older. Around 53.8% of all COPD and asthma hospital admissions were attributable to females. The annual number of prescriptions dispensed for COPD and asthma medications increased by 42.2%.<br><br>CONCLUSIONS: Throughout the study period, hospital admissions due to chronic obstructive pulmonary disease and asthma, as well as medication prescriptions, increased dramatically among all age groups. Hospitalization rates were higher for women. Further observational and epidemiological research is required to identify the factors contributing to increased hospitalization rates.}, }
@article {pmid35947263, year = {2023}, author = {Liu, S and Zhang, Y and Cai, J}, title = {Operation of high-speed rail and reduction of corporate pollution: evidence from China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {2}, pages = {3562-3575}, pmid = {35947263}, issn = {1614-7499}, mesh = {Humans ; China ; *Asian People ; Databases, Factual ; *Economic Development ; Environmental Pollution ; }, abstract = {As an environmentally friendly means of transport, the high-speed rail (HSR) is conducive to promoting corporate performance. An innovative approach extends the impact of HSR networks on pollution emissions from the regional level to the micro-enterprise level. Based on the quasi-natural experiment of the opening of HSR, a difference-in-difference model is used to investigate the impact of HSR on enterprise pollution emission levels and its action mechanism by using the matched data from the Chinese Enterprise Pollution Emission Database, the Chinese Industrial Enterprise Database, and the Chinese City Statistical Yearbook from 2000 to 2010. The results show that opening HSR significantly reduces the enterprises' pollution emission level, while reducing the number of polluting enterprises and transportation costs as well as improving the innovation capacity of enterprises are the corresponding action mechanisms. The impact of HSR on the enterprises' pollution emission varies with industry intensity, population size, and regional economic development level. The conclusions not only provide important insights to increase the ecological quality of China's environment through transportation infrastructure upgrades but also bring some guidance to more developing countries to improve their air environment.}, }
@article {pmid36722081, year = {2023}, author = {Ehlman, SM and Scherer, U and Bierbach, D and Francisco, F and Laskowski, KL and Krause, J and Wolf, M}, title = {Leveraging big data to uncover the eco-evolutionary factors shaping behavioural development.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1992}, pages = {20222115}, doi = {10.1098/rspb.2022.2115}, pmid = {36722081}, issn = {1471-2954}, mesh = {Animals ; *Big Data ; *Biological Evolution ; }, abstract = {Mapping the eco-evolutionary factors shaping the development of animals' behavioural phenotypes remains a great challenge. Recent advances in 'big behavioural data' research-the high-resolution tracking of individuals and the harnessing of that data with powerful analytical tools-have vastly improved our ability to measure and model developing behavioural phenotypes. Applied to the study of behavioural ontogeny, the unfolding of whole behavioural repertoires can be mapped in unprecedented detail with relative ease. This overcomes long-standing experimental bottlenecks and heralds a surge of studies that more finely define and explore behavioural-experiential trajectories across development. In this review, we first provide a brief guide to state-of-the-art approaches that allow the collection and analysis of high-resolution behavioural data across development. We then outline how such approaches can be used to address key issues regarding the ecological and evolutionary factors shaping behavioural development: developmental feedbacks between behaviour and underlying states, early life effects and behavioural transitions, and information integration across development.}, }
@article {pmid36719907, year = {2023}, author = {Turtle, L and Thorpe, M and Drake, TM and Swets, M and Palmieri, C and Russell, CD and Ho, A and Aston, S and Wootton, DG and Richter, A and de Silva, TI and Hardwick, HE and Leeming, G and Law, A and Openshaw, PJM and Harrison, EM and ,  and Baillie, JK and Semple, MG and Docherty, AB}, title = {Outcome of COVID-19 in hospitalised immunocompromised patients: An analysis of the WHO ISARIC CCP-UK prospective cohort study.}, journal = {PLoS medicine}, volume = {20}, number = {1}, pages = {e1004086}, doi = {10.1371/journal.pmed.1004086}, pmid = {36719907}, issn = {1549-1676}, abstract = {BACKGROUND: Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic.<br><br>METHODS AND FINDINGS: We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. Approximately 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent.<br><br>CONCLUSIONS: Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group.<br><br>TRIAL REGISTRATION: ISRCTN 66726260.}, }
@article {pmid36718952, year = {2023}, author = {Freedman, AH and Harrigan, RJ and Zhen, Y and Hamilton, AM and Smith, TB}, title = {Evidence for Ecotone Speciation Across an African Rainforest-Savanna Gradient.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16867}, pmid = {36718952}, issn = {1365-294X}, abstract = {Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly likely driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.}, }
@article {pmid36308510, year = {2023}, author = {Sun, Y and Chang, J and Fang, J}, title = {Above- and belowground net-primary productivity: A field-based global database of grasslands.}, journal = {Ecology}, volume = {104}, number = {2}, pages = {e3904}, doi = {10.1002/ecy.3904}, pmid = {36308510}, issn = {1939-9170}, mesh = {*Ecosystem ; *Grassland ; Temperature ; Databases, Factual ; Carbon ; }, abstract = {Net primary productivity (NPP) over global grasslands is crucial for understanding the terrestrial carbon cycling and for the assessments of wild herbivores food security. During the past few decades, numerous field investigations have been conducted to estimate grassland NPP since the measuring criterion released by the International Biological Program. However, a comprehensive NPP database, particularly for belowground NPP (BNPP), in global grasslands is rare to date. Here, field NPP measurements from 438 publications (1957-2018) in global grasslands were collected, critically filtered, and incorporated in a comprehensive global database with observations for aboveground NPP (ANPP), BNPP, total NPP (TNPP), and BNPP fraction (fBNPP). Associated information on geographical locations, climatic records, grassland types, land use patterns, manipulations subjected to manipulative experiments, sampling year of study sites, as well as NPP measurement methods are also documented. This database included 2985 entries from 1785 study sites. Among them, 806 entries contained paired data of ANPP and BNPP, resulting in the 806 fBNPP data. The study sites encompassed global grasslands with latitudinal range of 54.5° S~78.9° N, longitudinal range of 157.4° W~175.8° E, and altitudes from 0 to 5168 m above sea level, covering broad climatic gradients (-17.6 to 28.8°C in mean annual temperature and 63-2052 mm in mean annual precipitation). This global database is the world's largest paired data of ANPP and BNPP field measurements in grasslands. It can be used to study the spatio-temporal patterns of NPP and its allocation, evaluate the responses of above- and below-ground carbon components to future global changes, and validate the NPP estimation by empirical or process-based models in global grasslands. The database can be freely used for noncommercial applications. We kindly request users cite this data paper when using the database, respecting all the hard work during data compilation.}, }
@article {pmid36714536, year = {2023}, author = {Astorga, F and Groom, Q and Shimabukuro, PHF and Manguin, S and Noesgaard, D and Orrell, T and Sinka, M and Hirsch, T and Schigel, D}, title = {Biodiversity data supports research on human infectious diseases: Global trends, challenges, and opportunities.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100484}, pmid = {36714536}, issn = {2352-7714}, abstract = {The unprecedented generation of large volumes of biodiversity data is consistently contributing to a wide range of disciplines, including disease ecology. Emerging infectious diseases are usually zoonoses caused by multi-host pathogens. Therefore, their understanding may require the access to biodiversity data related to the ecology and the occurrence of the species involved. Nevertheless, despite several data-mobilization initiatives, the usage of biodiversity data for research into disease dynamics has not yet been fully leveraged. To explore current contribution, trends, and to identify limitations, we characterized biodiversity data usage in scientific publications related to human health, contrasting patterns of studies citing the Global Biodiversity Information Facility (GBIF) with those obtaining data from other sources. We found that the studies mainly obtained data from scientific literature and other not aggregated or standardized sources. Most of the studies explored pathogen species and, particularly those with GBIF-mediated data, tended to explore and reuse data of multiple species (>2). Data sources varied according to the taxa and epidemiological roles of the species involved. Biodiversity data repositories were mainly used for species related to hosts, reservoirs, and vectors, and barely used as a source of pathogens data, which was usually obtained from human and animal-health related institutions. While both GBIF- and not GBIF-mediated data studies explored similar diseases and topics, they presented discipline biases and different analytical approaches. Research on emerging infectious diseases may require the access to geographical and ecological data of multiple species. The One Health challenge requires interdisciplinary collaboration and data sharing, which is facilitated by aggregated repositories and platforms. The contribution of biodiversity data to understand infectious disease dynamics should be acknowledged, strengthened, and promoted.}, }
@article {pmid36705582, year = {2023}, author = {Bettisworth, B and Smith, SA and Stamatakis, A}, title = {Lagrange-NG: The next generation of Lagrange.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syad002}, pmid = {36705582}, issn = {1076-836X}, abstract = {Computing ancestral ranges via the Dispersion Extinction and Cladogensis (DEC) model of biogeography is characterized by an exponential number of states relative to the number of regions considered. This is because the DEC model requires computing a large matrix exponential, which typically accounts for up to 80% of overall runtime. Therefore, the kinds of biogeographical analyses that can be conducted under the DEC model are limited by the number of regions under consideration. In this work, we present a completely redesigned efficient version of the popular tool Lagrange which is up to 49 times faster with multi-threading enabled, and is also 26 times faster when using only one thread. We call this new version Lagrange-NG (Lagrange-Next Generation). The increased computational efficiency allows Lagrange-NG to analyze datasets with a large number of regions in a reasonable amount of time, up to 12 regions in approximately 18 minutes. We achieve these speedups using a relatively new method of computing the matrix exponential based on Krylov subspaces. In order to validate the correctness of Lagrange-NG, we also introduce a novel metric on range distributions for trees so that researchers can assess the difference between any two range inferences. Finally, Lagrange-NG exhibits substantially higher adherence to coding quality standards. It improves a respective software quality indicator as implemented in the SoftWipe tool from average (5.5; Lagrange) to high (7.8; Lagrange-NG). Lagrange-NG is freely available under GPL2.}, }
@article {pmid36621304, year = {2023}, author = {Liu, X and Han, Y and Luo, L and Pan, H and Cheng, T and Zhang, Q}, title = {Multiomics analysis reveals the mechanisms underlying the different floral colors and fragrances of Rosa hybrida cultivars.}, journal = {Plant physiology and biochemistry : PPB}, volume = {195}, number = {}, pages = {101-113}, doi = {10.1016/j.plaphy.2022.12.028}, pmid = {36621304}, issn = {1873-2690}, mesh = {*Rosa/genetics/metabolism ; Odorants ; Multiomics ; Color ; Plant Breeding ; Flowers/genetics/metabolism ; Gene Expression Regulation, Plant ; }, abstract = {The color and fragrance of rose flowers affect their commercial value. However, several rose varieties with new floral colors developed by the bud mutation method lost their fragrance during the breeding process, raising the question: Is there a relationship between floral color and aroma traits? Rose cultivar 'Yellow Island' (YI) with intensely aroma and yellow petals, while its bud mutant 'Past Feeling' (PF) with light aroma and pink petals mixing some yellow, two cultivars were used to explore this question using multiomics approaches. We investigated the genomic polymorphisms between PF and YI by whole-genome resequencing. 71 differentially abundant metabolites and 155 related differentially expressed genes identified in petals between PF and YI. From this, we constructed a model of metabolic changes affecting floral color and fragrance integrating shikimate, terpenoid, carotenoid, and green leaf volatile metabolites and predicted the associated key genes and transcription factors. This study provides a reference for understanding the molecular mechanism of variation in rose floral color and aroma traits.}, }
@article {pmid36704891, year = {2023}, author = {Crandall, ED and Toczydlowski, RH and Liggins, L and Holmes, AE and Ghoojaei, M and Gaither, MR and Wham, BE and Pritt, AL and Noble, C and Anderson, TJ and Barton, RL and Berg, JT and Beskid, SG and Delgado, A and Farrell, E and Himmelsbach, N and Queeno, SR and Trinh, T and Weyand, C and Bentley, A and Deck, J and Riginos, C and Bradburd, GS and Toonen, RJ}, title = {The importance of timely metadata curation to the global surveillance of genetic diversity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/cobi.14061}, pmid = {36704891}, issn = {1523-1739}, abstract = {Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and from direct communication with authors. Starting with 848 candidate genomic datasets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 datasets (N = 440 datasets comprising 45,105 individuals from 762 species in 17 phyla). Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declined significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever. This article is protected by copyright. All rights reserved.}, }
@article {pmid36699674, year = {2022}, author = {Siddiqui, JA and Fan, R and Naz, H and Bamisile, BS and Hafeez, M and Ghani, MI and Wei, Y and Xu, Y and Chen, X}, title = {Insights into insecticide-resistance mechanisms in invasive species: Challenges and control strategies.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {1112278}, pmid = {36699674}, issn = {1664-042X}, abstract = {Threatening the global community is a wide variety of potential threats, most notably invasive pest species. Invasive pest species are non-native organisms that humans have either accidentally or intentionally spread to new regions. One of the most effective and first lines of control strategies for controlling pests is the application of insecticides. These toxic chemicals are employed to get rid of pests, but they pose great risks to people, animals, and plants. Pesticides are heavily used in managing invasive pests in the current era. Due to the overuse of synthetic chemicals, numerous invasive species have already developed resistance. The resistance development is the main reason for the failure to manage the invasive species. Developing pesticide resistance management techniques necessitates a thorough understanding of the mechanisms through which insects acquire insecticide resistance. Insects use a variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes. An overabundance of enzymes causes metabolic resistance, detoxifying pesticides and rendering them ineffective against pests. A key factor in the development of metabolic resistance is the amplification of certain metabolic enzymes, specifically esterases, Glutathione S-transferase, Cytochromes p450 monooxygenase, and hydrolyses. Additionally, insect guts offer unique habitats for microbial colonization, and gut bacteria may serve their hosts a variety of useful services. Most importantly, the detoxification of insecticides leads to resistance development. The complete knowledge of invasive pest species and their mechanisms of resistance development could be very helpful in coping with the challenges and effectively developing effective strategies for the control of invasive species. Integrated Pest Management is particularly effective at lowering the risk of chemical and environmental contaminants and the resulting health issues, and it may also offer the most effective ways to control insect pests.}, }
@article {pmid36699126, year = {2023}, author = {Wortel, MT and Agashe, D and Bailey, SF and Bank, C and Bisschop, K and Blankers, T and Cairns, J and Colizzi, ES and Cusseddu, D and Desai, MM and van Dijk, B and Egas, M and Ellers, J and Groot, AT and Heckel, DG and Johnson, ML and Kraaijeveld, K and Krug, J and Laan, L and Lässig, M and Lind, PA and Meijer, J and Noble, LM and Okasha, S and Rainey, PB and Rozen, DE and Shitut, S and Tans, SJ and Tenaillon, O and Teotónio, H and de Visser, JAGM and Visser, ME and Vroomans, RMA and Werner, GDA and Wertheim, B and Pennings, PS}, title = {Towards evolutionary predictions: Current promises and challenges.}, journal = {Evolutionary applications}, volume = {16}, number = {1}, pages = {3-21}, pmid = {36699126}, issn = {1752-4571}, abstract = {Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.}, }
@article {pmid36696549, year = {2023}, author = {Menon, K and Sorce, LR and Argent, A and Bennett, TD and Carrol, ED and Kissoon, N and Sanchez-Pinto, LN and Schlapbach, LJ and de Souza, DC and Watson, RS and Wynn, JL and Zimmerman, JJ and Ranjit, S and ,  and , }, title = {Reporting of Social Determinants of Health in Pediatric Sepsis Studies.}, journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies}, volume = {}, number = {}, pages = {}, doi = {10.1097/PCC.0000000000003184}, pmid = {36696549}, issn = {1529-7535}, abstract = {OBJECTIVE: Standardized, consistent reporting of social determinants of health (SDOH) in studies on children with sepsis would allow for: 1) understanding the association of SDOH with illness severity and outcomes, 2) comparing populations and extrapolating study results, and 3) identification of potentially modifiable socioeconomic factors for policy makers. We, therefore, sought to determine how frequently data on SDOH were reported, which factors were collected and how these factors were defined in studies of sepsis in children.<br><br>DATA SOURCES AND SELECTION: We reviewed 106 articles (published between 2005 and 2020) utilized in a recent systematic review on physiologic criteria for pediatric sepsis.<br><br>DATA EXTRACTION: Data were extracted by two reviewers on variables that fell within the World Health Organization's SDOH categories.<br><br>DATA SYNTHESIS: SDOH were not the primary outcome in any of the included studies. Seventeen percent of articles (18/106) did not report on any SDOH, and a further 36.8% (39/106) only reported on gender/sex. Of the remaining 46.2% of articles, the most reported SDOH categories were preadmission nutritional status (35.8%, 38/106) and race/ethnicity (18.9%, 20/106). However, no two studies used the same definition of the variables reported within each of these categories. Six studies reported on socioeconomic status (3.8%, 6/106), including two from upper-middle-income and four from lower middle-income countries. Only three studies reported on parental education levels (2.8%, 3/106). No study reported on parental job security or structural conflict.<br><br>CONCLUSIONS: We found overall low reporting of SDOH and marked variability in categorizations and definitions of SDOH variables. Consistent and standardized reporting of SDOH in pediatric sepsis studies is needed to understand the role these factors play in the development and severity of sepsis, to compare and extrapolate study results between settings and to implement policies aimed at improving socioeconomic conditions related to sepsis.}, }
@article {pmid36692937, year = {2023}, author = {de Angel, V and Adeleye, F and Zhang, Y and Cummins, N and Munir, S and Lewis, S and Laporta Puyal, E and Matcham, F and Sun, S and Folarin, AA and Ranjan, Y and Conde, P and Rashid, Z and Dobson, R and Hotopf, M}, title = {The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.}, journal = {JMIR mental health}, volume = {10}, number = {}, pages = {e42866}, doi = {10.2196/42866}, pmid = {36692937}, issn = {2368-7959}, abstract = {BACKGROUND: Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.<br><br>OBJECTIVE: A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.<br><br>METHODS: A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.<br><br>RESULTS: The overall retention rate was 60%. Higher-intensity treatment (&#x3c7;[2]1=4.6; P=.03) and higher baseline anxiety (t56.28=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t50.4=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.<br><br>CONCLUSIONS: Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.}, }
@article {pmid36690591, year = {2023}, author = {Sambo, B and Bonato, M and Sperotto, A and Torresan, S and Furlan, E and Lambert, JH and Linkov, I and Critto, A}, title = {Framework for multirisk climate scenarios across system receptors with application to the Metropolitan City of Venice.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {}, number = {}, pages = {}, doi = {10.1111/risa.14097}, pmid = {36690591}, issn = {1539-6924}, abstract = {Climate change influences the frequency of extreme events that affect both human and natural systems. It requires systemic climate change adaptation to address the complexity of risks across multiple domains and tackle the uncertainties of future scenarios. This paper introduces a multirisk analysis of climate hazard, exposure, vulnerability, and risk severity, specifically designed to hotspot geographic locations and prioritize system receptors that are affected by climate-related extremes. The analysis is demonstrated for the Metropolitan City of Venice. Representative scenarios (RCP4.5 and RCP8.5) of climate threats (i.e., storm surges, pluvial flood, heat waves, and drought) are selected and represented by projections of Regional Climate Models for a 30-year period (2021-2050). A sample of results is as follows. First, an increase in the risk is largely due to drought, pluvial flood, and storm surge, depending on the areas of interest, with the overall situation worsening under the RCP8.5 scenario. Second, particular locations have colocated vulnerable receptors at higher risk, concentrated in the urban centers (e.g., housing, railways, roads) and along the coast (e.g., beaches, wetlands, primary sector). Third, risk communication of potential environmental and socio-economic losses via the multirisk maps is useful to stakeholders and public administration. Fourth, the multirisk maps recommend priorities for future investigation and risk management, such as collection of sensor data, elaboration of mitigations, and adaptation plans at hotspot locations.}, }
@article {pmid36689893, year = {2023}, author = {Werneck, RA and Meinberg, MF and Passos, MZ and Brandão, WC and de Moraes, EN and da Silva-Filho, AL}, title = {Quality of information regarding abnormal uterine bleeding available online.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {282}, number = {}, pages = {83-88}, doi = {10.1016/j.ejogrb.2023.01.020}, pmid = {36689893}, issn = {1872-7654}, abstract = {INTRODUCTION: The Internet and electronic devices with Internet access allow for a greater fluidity of information and speed of communication, especially in the field of health. Abnormal uterine bleeding (AUB) affects approximately 3-30% of women and can negatively impact their health and quality of life. Information regarding AUB that is available on the Internet may not be clear or accurate, rendering it difficult to understand and likely to result in delayed medical evaluation, which subsequently leads to worsening of the AUB.<br><br>OBJECTIVE: To evaluate the quality of the information regarding AUB currently available on the Internet, including information regarding treatments.<br><br>METHODS: The Google Trends website was searched for the most widely used English terms related to AUB. The identified descriptors were searched individually on the Google, Yahoo!, and Bing search engines. The first 10 results of each search were pre-selected and evaluated for inclusion in this study. Selected websites were categorically divided into two groups (news/magazine and academic) and individually analyzed by three experts using the DISCERN quality criteria (reliability, general quality, and quality of information) and the presence or absence of the Health on the Net Foundation Code of Conduct (HONcode&#xae;) seal.<br><br>RESULTS: Of the 168 websites included in this study, 60.1% were allocated to the news/magazine group and 39.9% were allocated to the academic group. Over half of the websites (54.2%) did not have the HONcode&#xae; quality seal. Websites in the academic group were more likely to include accurate information regarding AUB with greater reliability than websites in the news/magazine group. There were no statistical differences regarding the general quality of the websites. Most websites were rated as either moderate quality (70.8%) or low quality (28.6%). The HONcode&#xae; criterion was found to be a confounding factor of the analyses, as the grouping and quality results of websites without this seal were significantly associated. In addition, websites in the news/magazines group were 6.7 times more likely to provide low quality information than websites in the academic group (odds ratio: 6.7; 95% confidence interval: 2.1-21.4).<br><br>CONCLUSION: The information regarding AUB that is available on the Internet is of low to moderate quality. Academic websites present more reliable information of greater quality. The presence of the HONcode&#xae; seal is considered important to determine the quality of the content of a website, especially for news/magazine websites, and may help Internet users identify websites that contain more reliable information. Algorithms and applications that categorize the quality of information and the reliability of health content may be useful tools that can help patients clarify their symptoms for several conditions including AUB.}, }
@article {pmid36669842, year = {2023}, author = {Guan, Y and Qi, Y and Zheng, L and Yang, J and Zhang, M and Zhang, Q and Ji, L}, title = {Data mining techniques for detecting signals of adverse drug reaction of cardiac therapy drugs based on Jinan adverse event reporting system database: a retrospective study.}, journal = {BMJ open}, volume = {13}, number = {1}, pages = {e068127}, doi = {10.1136/bmjopen-2022-068127}, pmid = {36669842}, issn = {2044-6055}, mesh = {Humans ; United States ; Retrospective Studies ; Bayes Theorem ; *Adverse Drug Reaction Reporting Systems ; *Drug-Related Side Effects and Adverse Reactions/diagnosis/epidemiology ; Data Mining ; Databases, Factual ; United States Food and Drug Administration ; }, abstract = {OBJECTIVE: Cardiac therapy drugs are widely used in the treatment of heart disease. However, the concern regarding adverse events (AEs) of cardiac therapy drugs have been rising. This study aimed to analyse cardiac therapy drug-related AEs using the Jinan adverse event reporting system (JAERS) database mining and conduct a comprehensive evaluation to provide safe medication information for patients.<br><br>DESIGN: Retrospective observational study.<br><br>SETTING: In this study, cardiac therapy drug-related AEs were detected using the JAERS database from January 2000 to March 2022.<br><br>METHODS: Reports of cardiac therapy drug-related AEs were extracted from JAERS database, and the basic information of patients, reports and common AEs were analysed. Four disproportionality analysis methods, proportional reporting ratio (PRR), reporting odds ratio (ROR), Bayesian Confidence Propagation Neural Network (BCPNN), Medicines and Healthcare products Regulatory Agency (MHRA), were used to detect cardiac therapy drug-related signals. We further checked whether the detected signals exist on drug labels in China and two developed countries, the USA and Japan.<br><br>RESULTS: In total, 168&#x2009;314 AEs were reported, of which 4788 were associated with cardiac therapy drugs. Using the PRR, ROR, MHRA and BCPNN method, we detected 52 signals, 52 signals, 33 signals and 43 signals, respectively. Among the 52 signals, 14 were not included on the drug labels of China. One (isosorbide mononitrate-head bilges) was not included on the drug labels of the three countries.<br><br>CONCLUSION: We identified 14 new cardiac therapy drug signals that did not appear on drug labels in China and 1 new signal that did not appear on drug labels in 3 counties. A causal link between cardiac therapy drugs and AEs should be evaluated in further studies.}, }
@article {pmid36685700, year = {2022}, author = {Jazayeri, SM and Pooralinaghi, M and Torres-Navarrete, Y and Oviedo-Bayas, B and Guerra, &#xcd;E and Jácome, DH and Morán, CQ and Macias, CS and Escobar, KM and Ghafoor, SMHAS and Veiskarami, G and Jandaghi, P and Torres, ROV}, title = {Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses.}, journal = {Biotechnologia}, volume = {103}, number = {4}, pages = {355-384}, pmid = {36685700}, issn = {2353-9461}, abstract = {Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.}, }
@article {pmid36684825, year = {2023}, author = {Liew, CY and Labadin, J and Kok, WC and Eze, MO}, title = {A methodology framework for bipartite network modeling.}, journal = {Applied network science}, volume = {8}, number = {1}, pages = {6}, pmid = {36684825}, issn = {2364-8228}, abstract = {The graph-theoretic based studies employing bipartite network approach mostly focus on surveying the statistical properties of the structure and behavior of the network systems under the domain of complex network analysis. They aim to provide the big-picture-view insights of a networked system by looking into the dynamic interaction and relationship among the vertices. Nonetheless, incorporating the features of individual vertex and capturing the dynamic interaction of the heterogeneous local rules governing each of them in the studies is lacking. The methodology in achieving this could hardly be found. Consequently, this study intends to propose a methodology framework that considers the influence of heterogeneous features of each node to the overall network behavior in modeling real-world bipartite network system. The proposed framework consists of three main stages with principal processes detailed in each stage, and three libraries of techniques to guide the modeling activities. It is iterative and process-oriented in nature and allows future network expansion. Two case studies from the domain of communicable disease in epidemiology and habitat suitability in ecology employing this framework are also presented. The results obtained suggest that the methodology could serve as a generic framework in advancing the current state of the art of bipartite network approach.}, }
@article {pmid36682374, year = {2023}, author = {Traore, T and Shanks, S and Haider, N and Ahmed, K and Jain, V and Rüegg, SR and Razavi, A and Kock, R and Erondu, N and Rahman-Shepherd, A and Yavlinsky, A and Mboera, L and Asogun, D and McHugh, TD and Elton, L and Oyebanji, O and Okunromade, O and Ansumana, R and Djingarey, MH and Ali Ahmed, Y and Diallo, AB and Balde, T and Talisuna, A and Ntoumi, F and Zumla, A and Heymann, D and Socé Fall, I and Dar, O}, title = {How prepared is the world? Identifying weaknesses in existing assessment frameworks for global health security through a One Health approach.}, journal = {Lancet (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1016/S0140-6736(22)01589-6}, pmid = {36682374}, issn = {1474-547X}, abstract = {The COVID-19 pandemic has exposed faults in the way we assess preparedness and response capacities for public health emergencies. Existing frameworks are limited in scope, and do not sufficiently consider complex social, economic, political, regulatory, and ecological factors. One Health, through its focus on the links among humans, animals, and ecosystems, is a valuable approach through which existing assessment frameworks can be analysed and new ways forward proposed. Although in the past few years advances have been made in assessment tools such as the International Health Regulations Joint External Evaluation, a rapid and radical increase in ambition is required. To sufficiently account for the range of complex systems in which health emergencies occur, assessments should consider how problems are defined across stakeholders and the wider sociopolitical environments in which structures and institutions operate. Current frameworks do little to consider anthropogenic factors in disease emergence or address the full array of health security hazards across the social-ecological system. A complex and interdependent set of challenges threaten human, animal, and ecosystem health, and we cannot afford to overlook important contextual factors, or the determinants of these shared threats. Health security assessment frameworks should therefore ensure that the process undertaken to prioritise and build capacity adheres to core One Health principles and that interventions and outcomes are assessed in terms of added value, trade-offs, and cobenefits across human, animal, and environmental health systems.}, }
@article {pmid36659170, year = {2020}, author = {Gong, P and Chen, B and Li, X and Liu, H and Wang, J and Bai, Y and Chen, J and Chen, X and Fang, L and Feng, S and Feng, Y and Gong, Y and Gu, H and Huang, H and Huang, X and Jiao, H and Kang, Y and Lei, G and Li, A and Li, X and Li, X and Li, Y and Li, Z and Li, Z and Liu, C and Liu, C and Liu, M and Liu, S and Mao, W and Miao, C and Ni, H and Pan, Q and Qi, S and Ren, Z and Shan, Z and Shen, S and Shi, M and Song, Y and Su, M and Ping Suen, H and Sun, B and Sun, F and Sun, J and Sun, L and Sun, W and Tian, T and Tong, X and Tseng, Y and Tu, Y and Wang, H and Wang, L and Wang, X and Wang, Z and Wu, T and Xie, Y and Yang, J and Yang, J and Yuan, M and Yue, W and Zeng, H and Zhang, K and Zhang, N and Zhang, T and Zhang, Y and Zhao, F and Zheng, Y and Zhou, Q and Clinton, N and Zhu, Z and Xu, B}, title = {Mapping essential urban land use categories in China (EULUC-China): preliminary results for 2018.}, journal = {Science bulletin}, volume = {65}, number = {3}, pages = {182-187}, doi = {10.1016/j.scib.2019.12.007}, pmid = {36659170}, issn = {2095-9281}, }
@article {pmid36656265, year = {2023}, author = {Yu, Y and Yu, X and Zhang, D and Jin, L and Huang, J and Zhu, X and Sun, J and Yu, M and Zhu, L}, title = {Biotransformation of Organophosphate Esters by Rice and Rhizosphere Microbiome: Multiple Metabolic Pathways, Mechanism, and Toxicity Assessment.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c07796}, pmid = {36656265}, issn = {1520-5851}, abstract = {The biotransformation behavior and toxicity of organophosphate esters (OPEs) in rice and rhizosphere microbiomes were comprehensively studied by hydroponic experiments. OPEs with lower hydrophobicity were liable to be translocated acropetally, and rhizosphere microbiome could reduce the uptake and translocation of OPEs in rice tissues. New metabolites were successfully identified in rice and rhizosphere microbiome, including hydrolysis, hydroxylated, methylated, and glutathione-, glucuronide-, and sulfate-conjugated products. Rhizobacteria and plants could cooperate to form a complex ecological interaction web for OPE elimination. Furthermore, active members of the rhizosphere microbiome during OPE degradation were revealed and the metagenomic analysis indicated that most of these active populations contained OPE-degrading genes. The results of metabolomics analyses for phytotoxicity assessment implied that several key function metabolic pathways of the rice plant were found perturbed by metabolites, such as diphenyl phosphate and monophenyl phosphate. In addition, the involved metabolism mechanisms, such as the carbohydrate metabolism, amino acid metabolism and synthesis, and nucleotide metabolism in Escherichia coli, were significantly altered after exposure to the products mixture of OPEs generated by rhizosphere microbiome. This work for the first time gives a comprehensive understanding of the entire metabolism of OPEs in plants and associated microbiome, and provides support for the ongoing risk assessment of emerging contaminants and, most critically, their transformation products.}, }
@article {pmid36654087, year = {2022}, author = {Yang, L and Zou, K and Gao, K and Jiang, Z}, title = {A fuzzy DRBFNN-based information security risk assessment method in improving the efficiency of urban development.}, journal = {Mathematical biosciences and engineering : MBE}, volume = {19}, number = {12}, pages = {14232-14250}, doi = {10.3934/mbe.2022662}, pmid = {36654087}, issn = {1551-0018}, abstract = {The rapid development of urban informatization is an important way for cities to achieve a higher pattern, but the accompanying information security problem become a major challenge restricting the efficiency of urban development. Therefore, effective identification and assessment of information security risks has become a key factor to improve the efficiency of urban development. In this paper, an information security risk assessment method based on fuzzy theory and neural network technology is proposed to help identify and solve the information security problem in the development of urban informatization. Combined with the theory of information ecology, this method establishes an improved fuzzy neural network model from four aspects by using fuzzy theory, neural network model and DEMATEL method, and then constructs the information security risk assessment system of smart city. According to this method, this paper analyzed 25 smart cities in China, and provided suggestions and guidance for information security control in the process of urban informatization construction.}, }
@article {pmid36653564, year = {2023}, author = {Battin, TJ and Lauerwald, R and Bernhardt, ES and Bertuzzo, E and Gener, LG and Hall, RO and Hotchkiss, ER and Maavara, T and Pavelsky, TM and Ran, L and Raymond, P and Rosentreter, JA and Regnier, P}, title = {River ecosystem metabolism and carbon biogeochemistry in a changing world.}, journal = {Nature}, volume = {613}, number = {7944}, pages = {449-459}, pmid = {36653564}, issn = {1476-4687}, abstract = {River networks represent the largest biogeochemical nexus between the continents, ocean and atmosphere. Our current understanding of the role of rivers in the global carbon cycle remains limited, which makes it difficult to predict how global change may alter the timing and spatial distribution of riverine carbon sequestration and greenhouse gas emissions. Here we review the state of river ecosystem metabolism research and synthesize the current best available estimates of river ecosystem metabolism. We quantify the organic and inorganic carbon flux from land to global rivers and show that their net ecosystem production and carbon dioxide emissions shift the organic to inorganic carbon balance en route from land to the coastal ocean. Furthermore, we discuss how global change may affect river ecosystem metabolism and related carbon fluxes and identify research directions that can help to develop better predictions of the effects of global change on riverine ecosystem processes. We argue that a global river observing system will play a key role in understanding river networks and their future evolution in the context of the global carbon budget.}, }
@article {pmid36648719, year = {2023}, author = {Zhu, F and Su, T and Lei, B and Liang, Q and Zhou, Y and Liu, X and Wang, X and Zhang, D}, title = {Considerations on the impact of "source-sink" landscape pattern changes on urban thermal environment and cooling efficiency: a case study of Nanjing, China.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36648719}, issn = {1614-7499}, abstract = {The urban heat island effect caused by rapid urbanization has had a great impact on human health and ecological environment. The evolution of landscape patterns often affects regional thermal characteristics at the local scale. How to rationally allocate land cover types from the perspective of urban planning is a huge challenge. This paper takes Nanjing, a typical "stove city" in China, as an example to study the impact of landscape pattern changes on the urban thermal environment. Firstly, based on the "source" landscape "/sink" landscape identified by the "source-sink" landscape index, on this basis, the contributions of the "source-sink" landscape and its effects are calculated, and the temporal and spatial evolution laws are analyzed. Second, we study the cooling effect of different characteristic landscapes. The results show that the change of landscape pattern is closely related to the urban thermal environment, and the expansion of built-up areas is the main reason for the urban thermal environment. With the development of urbanization, the "source-sink" landscape structure in most districts and counties has aggravated the heat island effect, and the ratios of "sink" and "source" landscape contribution ratios with strong levels are concentrated in the suburban areas. The results of cooling efficiency research show that the cooling range of forest land is larger than that of water bodies. At the same time, we found that the cooling efficiency of the sink landscape is the highest when the area of the sink landscape is 0.18-0.9 hm[2] and the shape index is between 1 and 4. The research results can provide feasible and practical scientific suggestions for the planning and ecological construction of Nanjing.}, }
@article {pmid36400569, year = {2023}, author = {Wu, L and Yan, B and Han, J and Li, R and Xiao, J and He, S and Bo, X}, title = {TOXRIC: a comprehensive database of toxicological data and benchmarks.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1432-D1445}, pmid = {36400569}, issn = {1362-4962}, mesh = {Humans ; Benchmarking ; *Databases, Factual ; *Toxicology/methods ; Software ; }, abstract = {The toxic effects of compounds on environment, humans, and other organisms have been a major focus of many research areas, including drug discovery and ecological research. Identifying the potential toxicity in the early stage of compound/drug discovery is critical. The rapid development of computational methods for evaluating various toxicity categories has increased the need for comprehensive and system-level collection of toxicological data, associated attributes, and benchmarks. To contribute toward this goal, we proposed TOXRIC (https://toxric.bioinforai.tech/), a database with comprehensive toxicological data, standardized attribute data, practical benchmarks, informative visualization of molecular representations, and an intuitive function interface. The data stored in TOXRIC contains 113 372 compounds, 13 toxicity categories, 1474 toxicity endpoints covering in vivo/in vitro endpoints and 39 feature types, covering structural, target, transcriptome, metabolic data, and other descriptors. All the curated datasets of endpoints and features can be retrieved, downloaded and directly used as output or input to Machine Learning (ML)-based prediction models. In addition to serving as a data repository, TOXRIC also provides visualization of benchmarks and molecular representations for all endpoint datasets. Based on these results, researchers can better understand and select optimal feature types, molecular representations, and baseline algorithms for each endpoint prediction task. We believe that the rich information on compound toxicology, ML-ready datasets, benchmarks and molecular representation distribution can greatly facilitate toxicological investigations, interpretation of toxicological mechanisms, compound/drug discovery and the development of computational methods.}, }
@article {pmid35999848, year = {2022}, author = {Kopperud, BT and Lidgard, S and Liow, LH}, title = {Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13921}, pmid = {35999848}, issn = {2167-8359}, mesh = {Animals ; *Biodiversity ; *Bryozoa ; Information Storage and Retrieval ; }, abstract = {We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.}, }
@article {pmid36647630, year = {2023}, author = {Watts, JD and Farina, M and Kimball, JS and Schiferl, LD and Liu, Z and Arndt, KA and Zona, D and Ballantyne, A and Euskirchen, ES and Parmentier, FW and Helbig, M and Sonnentag, O and Tagesson, T and Rinne, J and Ikawa, H and Ueyama, M and Kobayashi, H and Sachs, T and Nadeau, DF and Kochendorfer, J and Jackowicz-Korczynski, M and Virkkala, A and Aurela, M and Commane, R and Byrne, B and Birch, L and Johnson, MS and Madani, N and Rogers, B and Du, J and Endsley, A and Savage, K and Poulter, B and Zhang, Z and Bruhwiler, LM and Miller, CE and Goetz, S and Oechel, WC}, title = {Carbon uptake in Eurasian boreal forests dominates the high-latitude net ecosystem carbon budget.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16553}, pmid = {36647630}, issn = {1365-2486}, support = {80NM0018D004/NASA/NASA/United States ; 80NSSC18K0770/NASA/NASA/United States ; 19-EARTH20-0105/NASA/NASA/United States ; NNX15AT74A/NASA/NASA/United States ; 80NSSC19M0113/NASA/NASA/United States ; }, abstract = {Arctic-boreal landscapes are experiencing profound warming, along with changes in ecosystem moisture status and disturbance from fire. This region is of global importance in terms of carbon feedbacks to climate, yet the sign (sink or source) and magnitude of the Arctic-boreal carbon budget within recent years remains highly uncertain. Here, we provide new estimates of recent (2003-2015) vegetation gross primary productivity (GPP), ecosystem respiration (Reco), net ecosystem CO2 exchange (NEE; Reco - GPP), and terrestrial methane (CH4) emissions for the Arctic-boreal zone using a satellite data-driven process-model for northern ecosystems (TCFM-Arctic), calibrated and evaluated using measurements from >60 tower eddy covariance (EC) sites. We used TCFM-Arctic to obtain daily 1-km[2] flux estimates and annual carbon budgets for the pan-Arctic-boreal region. Across the domain, the model indicated an overall average NEE sink of -850 Tg CO2 -C year[-1] . Eurasian boreal zones, especially those in Siberia, contributed to a majority of the net sink. In contrast, the tundra biome was relatively carbon neutral (ranging from small sink to source). Regional CH4 emissions from tundra and boreal wetlands (not accounting for aquatic CH4) were estimated at 35 Tg CH4 -C year[-1] . Accounting for additional emissions from open water aquatic bodies and from fire, using available estimates from the literature, reduced the total regional NEE sink by 21% and shifted many far northern tundra landscapes, and some boreal forests, to a net carbon source. This assessment, based on in situ observations and models, improves our understanding of the high-latitude carbon status and also indicates a continued need for integrated site-to-regional assessments to monitor the vulnerability of these ecosystems to climate change.}, }
@article {pmid36643652, year = {2023}, author = {Mugnai, F and Costantini, F and Chenuil, A and Leduc, M and Gutiérrez Ortega, JM and Meglécz, E}, title = {Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14616}, pmid = {36643652}, issn = {2167-8359}, mesh = {Humans ; *DNA Barcoding, Taxonomic ; Databases, Factual ; Mediterranean Sea ; }, abstract = {BACKGROUND: In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments.<br><br>METHODS: We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency.<br><br>RESULTS: The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).}, }
@article {pmid36462728, year = {2023}, author = {Sosa, CC and Clavijo-Buriticá, DC and García-Merchán, VH and López-Rozo, N and Riccio-Rengifo, C and Diaz, MV and Londoño, DA and Quimbaya, MA}, title = {GOCompare: An R package to compare functional enrichment analysis between two species.}, journal = {Genomics}, volume = {115}, number = {1}, pages = {110528}, doi = {10.1016/j.ygeno.2022.110528}, pmid = {36462728}, issn = {1089-8646}, mesh = {*Aluminum ; Genomics/methods ; Computational Biology/methods ; Algorithms ; Gene Ontology ; *Arabidopsis/genetics ; }, abstract = {Functional enrichment analysis is a cornerstone in bioinformatics as it makes possible to identify functional information by using a gene list as source. Different tools are available to compare gene ontology (GO) terms, based on a directed acyclic graph structure or content-based algorithms which are time-consuming and require a priori information of GO terms. Nevertheless, quantitative procedures to compare GO terms among gene lists and species are not available. Here we present a computational procedure, implemented in R, to infer functional information derived from comparative strategies. GOCompare provides a framework for functional comparative genomics starting from comparable lists from GO terms. The program uses functional enrichment analysis (FEA) results and implement graph theory to identify statistically relevant GO terms for both, GO categories and analyzed species. Thus, GOCompare allows finding new functional information complementing current FEA approaches and extending their use to a comparative perspective. To test our approach GO terms were obtained for a list of aluminum tolerance-associated genes in Oryza sativa subsp. japonica and their orthologues in Arabidopsis thaliana. GOCompare was able to detect functional similarities for reactive oxygen species and ion binding capabilities which are common in plants as molecular mechanisms to tolerate aluminum toxicity. Consequently, the R package exhibited a good performance when implemented in complex datasets, allowing to establish hypothesis that might explain a biological process from a functional perspective, and narrowing down the possible landscapes to design wet lab experiments.}, }
@article {pmid36318246, year = {2023}, author = {Lei, B and Xu, Y and Lei, Y and Li, C and Zhou, P and Wang, L and Yang, Q and Li, X and Li, F and Liu, C and Cui, C and Chen, T and Ni, W and Hu, S}, title = {CRAMdb: a comprehensive database for composition and roles of microbiome in animals.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D700-D707}, pmid = {36318246}, issn = {1362-4962}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Databases, Factual ; }, abstract = {CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals. It focuses on the composition and roles of the microbiome in various animal species. The main goal of the CRAMdb is to facilitate the reuse of animal metagenomic data, and enable cross-host and cross-phenotype comparisons. To this end, we consistently annotated microbiomes (including 16S, 18S, ITS and metagenomics sequencing data) of 516 animals from 475 projects spanning 43 phenotype pairs to construct the database that is equipped with 9430 bacteria, 278 archaea, 2216 fungi and 458 viruses. CRAMdb provides two main contents: microbiome composition data, illustrating the landscape of the microbiota (bacteria, archaea, fungi, and viruses) in various animal species, and microbiome association data, revealing the relationships between the microbiota and various phenotypes across different animal species. More importantly, users can quickly compare the composition of the microbiota of interest cross-host or body site and the associated taxa that differ between phenotype pairs cross-host or cross-phenotype. CRAMdb is freely available at (http://www.ehbio.com/CRAMdb).}, }
@article {pmid36645791, year = {2022}, author = {Marwali, EM and Kekalih, A and Yuliarto, S and Wati, DK and Rayhan, M and Valerie, IC and Cho, HJ and Jassat, W and Blumberg, L and Masha, M and Semple, C and Swann, OV and Kohns Vasconcelos, M and Popielska, J and Murthy, S and Fowler, RA and Guerguerian, AM and Streinu-Cercel, A and Pathmanathan, MD and Rojek, A and Kartsonaki, C and Gonçalves, BP and Citarella, BW and Merson, L and Olliaro, PL and Dalton, HJ and , }, title = {Paediatric COVID-19 mortality: a database analysis of the impact of health resource disparity.}, journal = {BMJ paediatrics open}, volume = {6}, number = {1}, pages = {}, doi = {10.1136/bmjpo-2022-001657}, pmid = {36645791}, issn = {2399-9772}, abstract = {BACKGROUND: The impact of the COVID-19 pandemic on paediatric populations varied between high-income countries (HICs) versus low-income to middle-income countries (LMICs). We sought to investigate differences in paediatric clinical outcomes and identify factors contributing to disparity between countries.<br><br>METHODS: The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) COVID-19 database was queried to include children under 19 years of age admitted to hospital from January 2020 to April 2021 with suspected or confirmed COVID-19 diagnosis. Univariate and multivariable analysis of contributing factors for mortality were assessed by country group (HICs vs LMICs) as defined by the World Bank criteria.<br><br>RESULTS: A total of 12&#x2009;860 children (3819 from 21 HICs and 9041 from 15 LMICs) participated in this study. Of these, 8961 were laboratory-confirmed and 3899 suspected COVID-19 cases. About 52% of LMICs children were black, and more than 40% were infants and adolescent. Overall in-hospital mortality rate (95% CI) was 3.3% [=(3.0% to 3.6%), higher in LMICs than HICs (4.0% (3.6% to 4.4%) and 1.7% (1.3% to 2.1%), respectively). There were significant differences between country income groups in intervention profile, with higher use of antibiotics, antivirals, corticosteroids, prone positioning, high flow nasal cannula, non-invasive and invasive mechanical ventilation in HICs. Out of the 439 mechanically ventilated children, mortality occurred in 106 (24.1%) subjects, which was higher in LMICs than HICs (89 (43.6%) vs 17 (7.2%) respectively). Pre-existing infectious comorbidities (tuberculosis and HIV) and some complications (bacterial pneumonia, acute respiratory distress syndrome and myocarditis) were significantly higher in LMICs compared with HICs. On multivariable analysis, LMIC as country income group was associated with increased risk of mortality (adjusted HR 4.73 (3.16 to 7.10)).<br><br>CONCLUSION: Mortality and morbidities were higher in LMICs than HICs, and it may be attributable to differences in patient demographics, complications and access to supportive and treatment modalities.}, }
@article {pmid36635306, year = {2023}, author = {Siddik, MAB and Dickson, KE and Rising, J and Ruddell, BL and Marston, LT}, title = {Interbasin water transfers in the United States and Canada.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {27}, pmid = {36635306}, issn = {2052-4463}, mesh = {United States ; Humans ; *Ecosystem ; *Water Supply ; Canada ; Hydrology ; Surveys and Questionnaires ; }, abstract = {Interbasin water transfers (IBTs) can have a significant impact on the environment, water availability, and economies within the basins importing and exporting water, as well as basins downstream of these water transfers. The lack of comprehensive data identifying and describing IBTs inhibits understanding of the role IBTs play in supplying water for society, as well as their collective hydrologic impact. We develop three connected datasets inventorying IBTs in the United States and Canada, including their features, geospatial details, and water transfer volumes. We surveyed the academic and gray literature, as well as local, state, and federal water agencies, to collect, process, and verify IBTs in Canada and the United States. Our comprehensive IBT datasets represent all known transfers of untreated water that cross subregion (US) or subdrainage area (CA) boundaries, characterizing a total of 641 IBT projects. The infrastructure-level data made available by these data products can be used to close water budgets, connect water supplies to water use, and better represent human impacts within hydrologic and ecosystem models.}, }
@article {pmid36641462, year = {2023}, author = {Filip, T and Michal, &#x160; and Radoslava, J and Ivan, B and Michal, A and Lucia, Z and Gyözö, H}, title = {The impact of the striped field mouse's range expansion on communities of native small mammals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {753}, pmid = {36641462}, issn = {2045-2322}, abstract = {Understanding species expansion as an element of the dispersal process is crucial to gaining a better comprehension of the functioning of the populations and the communities. Populations of the same species that are native in one area could be considered nonindigenous, naturalised or invasive somewhere else. The striped field mouse has been expanding its range in south-western Slovakia since 2010, although the origin of the spread has still not been clarified. In light of the striped field mouse's life history, the recent range expansion is considered to be the expansion of a native species. This study analyses the impact of the striped field mouse's expansion on the native population and small mammal communities and confronts the documented stages of striped field mouse expansion with the stages of invasion biology. Our research replicates the design and compares results from past research of small mammals prior to this expansion at the same three study areas with the same 20 study sites and control sites. Several years after expansion, the striped field mouse has a 100% frequency of occurrence in all study sites and has become the dominant species in two of the study areas. The native community is significantly affected by the striped field mouse's increasing dominance, specifically: (i) we found a re-ordering of the species rank, mainly in areas with higher dominance, and (ii) an initial positive impact on diversity and evenness during low dominance of the striped field mouse turned markedly negative after crossing the 25% dominance threshold. Results suggested that the variation in the striped field mouse's dominance is affected by the northern direction of its spread. Our findings show that establishment in a new area, spread and impact on the native community are stages possibly shared by both invasive and native species during their range expansion.}, }
@article {pmid36639402, year = {2023}, author = {Mack, M and Stojan, R and Bock, O and Voelcker-Rehage, C}, title = {The association of executive functions and physical fitness with cognitive-motor multitasking in a street crossing scenario.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {697}, pmid = {36639402}, issn = {2045-2322}, abstract = {Age-related decline in cognitive-motor multitasking performance has been attributed to declines in executive functions and physical fitness (motor coordinative fitness and cardiovascular fitness). It has been suggested that those cognitive and physical resources strongly depend on lifestyle factors such as long-term regular physical activity and cognitive engagement. Although research suggests that there is covariation between components of executive functions and physical fitness, the interdependence between these components for cognitive-motor multitasking performance is not yet clear. The aim of the study was to examine the contribution and interrelationship between executive functions, motor coordinative fitness, and cardiovascular fitness on street crossing while multitasking. We used the more ecologically valid scenario to obtain results that might be directly transferable to daily life situation. Data from 50 healthy older adults (65-75 years, 17 females, recruited in two different cities in Germany) were analyzed. Participants' executive functions (composite score including six tests), motor coordinative fitness (composite score including five tests), and cardiovascular fitness (spiroergometry), as well as their street crossing performance while multitasking were assessed. Street crossing was tested under single-task (crossing a two-line road), and multitask conditions (crossing a two-line road while typing numbers on a keypad as simulation of mobile phone use). Street crossing performance was assessed by use of cognitive outcomes (typing, crossing failures) and motor outcomes (stay time, crossing speed). Linear mixed-effects models showed beneficial main effects of executive functions for typing (p = 0.004) and crossing failures (p = 0.023), and a beneficial main effect of motor coordinative fitness for stay time (p = 0.043). Commonality analysis revealed that the proportion of variance commonly explained by executive functions, motor coordinative fitness, and cardiovascular fitness was small for all street crossing outcomes. For typing and crossing failures (cognitive outcomes), the results further showed a higher relative contribution of executive functions compared to motor coordinative fitness and cardiovascular fitness. For stay time (motor outcome), the results correspondingly revealed a higher relative contribution of motor coordinative fitness compared to executive functions and cardiovascular fitness. The findings suggest that during cognitive-motor multitasking in everyday life, task performance is determined by the components of executive functions and physical fitness related to the specific task demands. Since multitasking in everyday life includes cognitive and motor tasks, it seems to be important to maintain both executive functions and physical fitness for independent living up to old age.}, }
@article {pmid36629615, year = {2023}, author = {Brito, MIBDS and Oliveira, ECA and Barbosa, CS and Gomes, ECS}, title = {Factors associated with severe forms and deaths from schistosomiasis and application of probabilistic linkage in databases, state of Pernambuco, Brazil, 2007-2017.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {26}, number = {}, pages = {e230003}, doi = {10.1590/1980-549720230003.2}, pmid = {36629615}, issn = {1980-5497}, mesh = {Humans ; Brazil/epidemiology ; *Schistosomiasis/epidemiology ; Databases, Factual ; }, abstract = {OBJECTIVE: To verify the agreement of data on severe forms and deaths from schistosomiasis recorded in the Brazilian Notifiable Diseases Information System and the Mortality Information System, sociodemographic variables with the occurrence of severe forms and deaths, and the temporal trend of the disease in the state of Pernambuco, Brazil.<br><br>METHODS: This is an ecological, descriptive, time series study with data on severe forms and deaths from schistosomiasis in Pernambuco, from 2007 to 2017. For the linkage between databases, a function was developed in python programming language, using the Soundex method. To identify sociodemographic and health factors that correlated with the dependent variables, Pearson's correlation test was applied. For trend analysis, linear regression was applied.<br><br>RESULTS: We identified 9,085 severe cases, 1,956 deaths, and 186 cases in the linkage. The correlation between the average positivity rate with the general water supply and waste collection was 0.22 and 0.26 respectively. We verified a correlation of the average cumulative mortality rate with water supply by well or spring (r=0.27), water supply by the general network (r=0.3), waste collection (r=0.42), and road urbanization (r=0.29). We found 3,153 severe forms in 2007 with a decrease trend and 205 deaths in 2010, without a trend pattern.<br><br>CONCLUSION: There is a need for greater investments in disease control and in the quality of information, especially in the record of severe forms, considering that, due to the pathophysiology of the disease, death only occurs when the individual develops the chronic form, and its notification on the Notifiable Diseases Information System is imperative.}, }
@article {pmid36629614, year = {2023}, author = {Batista, JFC and Oliveira, MR and Pereira, DLM and Matos, MLSDS and Souza, IT and Menezes, MO}, title = {Spatial distribution and temporal trends of AIDS in Brazil and regions between 2005 and 2020.}, journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology}, volume = {26}, number = {}, pages = {e230002}, doi = {10.1590/1980-549720230002}, pmid = {36629614}, issn = {1980-5497}, mesh = {Humans ; Adolescent ; Young Adult ; Adult ; Brazil/epidemiology ; *Acquired Immunodeficiency Syndrome/epidemiology ; Bayes Theorem ; Information Systems ; Incidence ; }, abstract = {OBJECTIVE: To analyze the spatial distribution and the temporal trend of the AIDS incidence rate in Brazil from 2005 to 2020.<br><br>METHODS: This is an ecological, temporal, and spatial study on AIDS cases in Brazil. Data from the Notifiable Diseases Information System were stratified by year of diagnosis, region of the country/municipalities of residence, and age group (over 13 years). Incidence rates were calculated for temporal estimation using the Joinpoint model, as well as Spatial Empirical Bayes (SEB) for spatial distribution, using the Kernel density estimator.<br><br>RESULTS: The incidence rate in Brazil, in 2020, was 17.69 cases per 100 thousand inhabitants. The general trend (2005-2020) was decrease in Brazil (Annual Percent Change - APC=-2.0%), in the Southeast (APC=-4.4%) and South (APC=-3.0%) regions. The North (APC=2.3%) showed an increase trend, whereas the Southeast and Midwest regions were stationary (p>0.05). Brazil, Southeast, South, and Midwest regions showed a decrease trend in most age groups. The Northeast and North regions showed an increase in the age groups of 13-29 years and 13-24 years, respectively. The Kernel estimator showed clusters with SEB above 30/10 thousand inhabitants in the states of Para&#xed;ba, Sergipe, Alagoas, Pernambuco, S&#xe3;o Paulo, Minas Gerais, Par&#xe1;, Rio Grande do Sul, and Santa Catarina.<br><br>CONCLUSION: Brazil, the Southeast, and South regions showed a decrease in the incidence rate, whereas the North region increased and the Northeast and Midwest regions were stationary. The Southeast, South, and Northeast regions presented the largest clusters of SEB.}, }
@article {pmid35615290, year = {2022}, author = {Adhikari, JN and Bhattarai, BP and Rokaya, MB and Thapa, TB}, title = {Land use/land cover changes in the central part of the Chitwan Annapurna Landscape, Nepal.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13435}, pmid = {35615290}, issn = {2167-8359}, mesh = {*Conservation of Natural Resources ; Nepal ; *Environmental Monitoring/methods ; Geographic Information Systems ; Remote Sensing Technology ; }, abstract = {BACKGROUND: Land use/land cover assessment and monitoring of the land cover dynamics are essential to know the ecological, physical and anthropogenic processes in the landscape. Previous studies have indicated changes in the landscape of mid-hills of Nepal in the past few decades. But there is a lack of study in the Chitwan Annapurna Landscape; hence, this study was carried out to fill in study gap that existed in the area.<br><br>METHODS: This study evaluates land use/land cover dynamics between 2000 to 2020 in the central part of the Chitwan Annapurna Landscape, Nepal by using Landsat images. The Landsat images were classified into eight different classes using remote sensing and geographic information system (GIS). The accuracy assessment of classified images was evaluated by calculating actual accuracy, producer's accuracy, user's accuracy and kappa coefficient based on the ground-truthing points for 2020 and Google Earth and topographic maps for images of 2010 and 2000.<br><br>RESULTS: The results of land use/land cover analysis of Landsat image 2020 showed that the study area was composed of grassland (1.73%), barren area (1.76%), riverine forest (1.93%), water body (1.97%), developed area (4.13%), Sal dominated forest (15.4%), cropland (28.13%) and mixed forest (44.95%). The results of land cover change between 2000 to 2020 indicated an overall increase in Sal dominated forest (7.6%), developed area (31.34%), mixed forest (37.46%) and decrease in riverine forest (11.29%), barren area (20.03%), croplands (29.87%) and grasslands (49.71%). The classification of the images of 2000, 2010 and 2020 had 81%, 81.6% and 84.77% overall accuracy, respectively. This finding can be used as a baseline information for the development of a proper management plan to protect wildlife habitats and forecasting possible future changes, if needed.}, }
@article {pmid35833012, year = {2022}, author = {Ramirez-Delgado, D and Cicala, F and Gonzalez-Sanchez, RA and Avalos-Tellez, R and Solana-Arellano, E and Licea-Navarro, A}, title = {Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13235}, pmid = {35833012}, issn = {2167-8359}, mesh = {Animals ; *Sea Lions/genetics ; RNA, Ribosomal, 16S/genetics ; Mexico ; Bacteria/genetics ; Computational Biology ; }, abstract = {BACKGROUND: The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.<br><br>METHODS: We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S&#x2122; Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter&#x2122; Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.<br><br>RESULTS: As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.}, }
@article {pmid35791366, year = {2022}, author = {Zheng, C and Yang, X and Liu, Z and Liu, K and Huang, Y}, title = {Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13239}, pmid = {35791366}, issn = {2167-8359}, mesh = {*Soil/chemistry ; *Agriculture ; Geographic Information Systems ; Nutrients ; Phosphorus ; Nitrogen/analysis ; }, abstract = {It is of great significance to promote the quantitative research of soil science and the implementation of precision agriculture. On this basis, taking Xuwen County as the research object, this paper comprehensively analyzed the soil characteristics of cultivated land in Xuwen County and clarify the soil nutrient content and spatial distribution characteristics of cultivated land in Xuwen County, this paper comprehensively applied the methods of geostatistics, geographic information system (GIS) and fuzzy mathematics, and referred to the cultivated land quality grade standard (GB/T 33469-2016), to analyze the soil characteristics and evaluate the soil fertility of this region. The results show that the optimal interpolation model of soil pH and available phosphorus (AP) is a Gaussian model, and the optimal interpolation model of soil organic matter (SOM), available nitrogen (AN) and available potassium (AK) is a J-Bessel model. In addition, the spatial correlation of AK is weak, whereas pH, SOM, AN and AP show moderate spatial correlation. The proportion of excellent, good, average, medium and poor comprehensive fertility index are 26.00%, 32.67%, 19.33%, 19.00% and 3.00%, respectively. The overall level of soil fertility in Xuwen County is above the average, and the fertility quality presents an obvious trend of high in the South and low in the North. Areas that above average fertility are mainly distributed in Maichen Town, Qujie Town, Nanshan Town and Chengbei Town. The results can provide theoretical basis for improving the utilization rate of chemical fertilizer, fine management of cultivated land and ecological environment in this region, which can help in decision-making of precision fertilization.}, }
@article {pmid36416261, year = {2023}, author = {Guo, S and Xu, Z and Dong, X and Hu, D and Jiang, Y and Wang, Q and Zhang, J and Zhou, Q and Liu, S and Song, W}, title = {GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D964-D968}, pmid = {36416261}, issn = {1362-4962}, mesh = {Humans ; RNA-Seq/methods ; Cell Line ; *Databases, Genetic ; *Software ; }, abstract = {Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.}, }
@article {pmid36399502, year = {2023}, author = {Camargo, AP and Nayfach, S and Chen, IA and Palaniappan, K and Ratner, A and Chu, K and Ritter, SJ and Reddy, TBK and Mukherjee, S and Schulz, F and Call, L and Neches, RY and Woyke, T and Ivanova, NN and Eloe-Fadrosh, EA and Kyrpides, NC and Roux, S}, title = {IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D733-D743}, pmid = {36399502}, issn = {1362-4962}, mesh = {*Metadata ; Software ; Databases, Genetic ; Genome, Viral ; Metagenomics ; *Virtual Reality ; }, abstract = {Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.}, }
@article {pmid36305818, year = {2023}, author = {Chen, Y and Zhang, X and Peng, X and Jin, Y and Ding, P and Xiao, J and Li, C and Wang, F and Chang, A and Yue, Q and Pu, M and Chen, P and Shen, J and Li, M and Jia, T and Wang, H and Huang, L and Guo, G and Zhang, W and Liu, H and Wang, X and Chen, D}, title = {SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1150-D1159}, pmid = {36305818}, issn = {1362-4962}, mesh = {Databases, Factual ; *Single-Cell Analysis ; }, abstract = {It is a challenge to efficiently integrate and present the tremendous amounts of single-cell data generated from multiple tissues of various species. Here, we create a new database named SPEED for single-cell pan-species atlas in the light of ecology and evolution for development and diseases (freely accessible at http://8.142.154.29 or http://speedatlas.net). SPEED is an online platform with 4 data modules, 7 function modules and 2 display modules. The 'Pan' module is applied for the interactive analysis of single cell sequencing datasets from 127 species, and the 'Evo', 'Devo', and 'Diz' modules provide comprehensive analysis of single-cell atlases on 18 evolution datasets, 28 development datasets, and 85 disease datasets. The 'C2C', 'G2G' and 'S2S' modules explore intercellular communications, genetic regulatory networks, and cross-species molecular evolution. The 'sSearch', 'sMarker', 'sUp', and 'sDown' modules allow users to retrieve specific data information, obtain common marker genes for cell types, freely upload, and download single-cell datasets, respectively. Two display modules ('HOME' and 'HELP') offer easier access to the SPEED database with informative statistics and detailed guidelines. All in all, SPEED is an integrated platform for single-cell RNA sequencing (scRNA-seq) and single-cell whole-genome sequencing (scWGS) datasets to assist the deep-mining and understanding of heterogeneity among cells, tissues, and species at multi-levels, angles, and orientations, as well as provide new insights into molecular mechanisms of biological development and pathogenesis.}, }
@article {pmid36617091, year = {2023}, author = {Abdallah, M and Joung, BG and Lee, WJ and Mousoulis, C and Raghunathan, N and Shakouri, A and Sutherland, JW and Bagchi, S}, title = {Anomaly Detection and Inter-Sensor Transfer Learning on Smart Manufacturing Datasets.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {1}, pages = {}, pmid = {36617091}, issn = {1424-8220}, mesh = {*Commerce ; Databases, Factual ; Time Factors ; *Machine Learning ; }, abstract = {Smart manufacturing systems are considered the next generation of manufacturing applications. One important goal of the smart manufacturing system is to rapidly detect and anticipate failures to reduce maintenance cost and minimize machine downtime. This often boils down to detecting anomalies within the sensor data acquired from the system which has different characteristics with respect to the operating point of the environment or machines, such as, the RPM of the motor. In this paper, we analyze four datasets from sensors deployed in manufacturing testbeds. We detect the level of defect for each sensor data leveraging deep learning techniques. We also evaluate the performance of several traditional and ML-based forecasting models for predicting the time series of sensor data. We show that careful selection of training data by aggregating multiple predictive RPM values is beneficial. Then, considering the sparse data from one kind of sensor, we perform transfer learning from a high data rate sensor to perform defect type classification. We release our manufacturing database corpus (4 datasets) and codes for anomaly detection and defect type classification for the community to build on it. Taken together, we show that predictive failure classification can be achieved, paving the way for predictive maintenance.}, }
@article {pmid36612401, year = {2022}, author = {Liu, F and Sun, D and Zhang, Y and Hong, S and Wang, M and Dong, J and Yan, C and Yang, Q}, title = {Tourist Landscape Preferences in a Historic Block Based on Spatiotemporal Big Data-A Case Study of Fuzhou, China.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, pmid = {36612401}, issn = {1660-4601}, mesh = {*Big Data ; Surveys and Questionnaires ; China ; *Sustainable Development ; Hot Temperature ; }, abstract = {Historic blocks are valuable architectural and landscape heritage, and it is important to explore the distribution characteristics of tourists to historic blocks and their landscape preferences to realize the scientific construction and conservation of historic blocks and promote their sustainable development. At present, few studies combine the analysis of tourist distribution characteristics with landscape preferences. This study takes the historic block of Three Lanes and Seven Alleys in Fuzhou as an example, combines field research and questionnaires to construct a landscape preference evaluation indicator system for the historic block, measures the distribution characteristics of tourists in the block through the heat value of tourist flow obtained from the Tencent regional heat map, and analyses the influence of landscape preference indicators on the heat value of tourist flow in the block through stepwise multiple linear regression. The research shows that: (1) the spatial and temporal variation in the heat value of tourist flow tends to be consistent throughout the block, from 7 a.m. to 6 p.m., showing a "rising, slightly fluctuating and then stabilizing" state, both on weekdays and on weekends. (2) The factors influencing the heat value of tourist flow in the different spatial samples are various, with commercial atmosphere, plant landscape, accessibility of the road space, architecture, and the surrounding environment having a significant impact on the heat value of tourist flow. Based on the analysis of the landscape preferences of tourists in the historic block, a landscape optimization strategy is proposed to provide a reference for the management and construction of the block.}, }
@article {pmid36384190, year = {2023}, author = {Liu, H and Wu, M and Gao, H and Gao, J and Wang, S}, title = {Application of [15]N tracing and bioinformatics for estimating microbial-mediated nitrogen cycle processes in oil-contaminated soils.}, journal = {Environmental research}, volume = {217}, number = {}, pages = {114799}, doi = {10.1016/j.envres.2022.114799}, pmid = {36384190}, issn = {1096-0953}, mesh = {Nitrogen Cycle ; Nitrogen/analysis ; Soil/chemistry ; *Microbiota ; Soil Microbiology ; Computational Biology ; *Soil Pollutants/analysis ; }, abstract = {Crude oil pollution can profoundly alter the nitrogen (N) cycle in the soil. Here, a 30-day incubation with [15]N tracer approach was performed to assess the impacts of crude oil concentrations (medium: 10,000 mg kg[-1]; heavy: 50,000 mg kg[-1]) on soil N cycling based on a numerical model. Results showed that crude oil pollution significantly increased the gross N-transformation rates, but the rates of oxidation of recalcitrant organic N, the immbolization of NO3[-] and the adsorption of NH4[+] changed differently as a function of hydrocarbon concentrations. There was no significant difference of the oxidation rate of recalcitrant organic N between the medium and heavy oil-contaminated soils (medium: 0.1149 mmol N kg[-1] d[-1]; heavy: 0.1299 mmol N kg[-1] d[-1]), but the rates of NO3[-] immobilization (0.1135 mmol N kg[-1] d[-1]) and NH4[+] adsorption were the highest (0.1148 mmol N kg[-1] d[-1]) in the moderately oil-contaminated soils than those in the heavy polluted soil (0.0849 mmol N kg[-1] d[-1] and 0.0034 mmol N kg[-1] d[-1], respectively). The NO3[-] immobilization rate was 2.5-fold higher than its reduction rate, indicating that NO3[-] immobilization played a more important role during the process of NO3[-] transformation. Microbial community structure analysis indicated that phyla of Actinobacteria and Ascomycota respectively promoted the immobilization of NO3[-] to recalcitrant organic N and the reduction of NO3[-] to NH4[+]. The genus of Aspergillus was related to net NH4[+] production, and the genera of Penicillium and Acremonium were responsible for oxidation of recalcitrant organic N to NO3[-].}, }
@article {pmid35186498, year = {2022}, author = {Reijnders, MJMF}, title = {Wei2GO: weighted sequence similarity-based protein function prediction.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12931}, pmid = {35186498}, issn = {2167-8359}, mesh = {*Software ; *Algorithms ; Molecular Sequence Annotation ; Proteins/genetics ; Databases, Protein ; }, abstract = {BACKGROUND: Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases.<br><br>METHODS: This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations.<br><br>RESULTS: Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes.<br><br>AVAILABILITY: Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.}, }
@article {pmid36620398, year = {2023}, author = {Gries, C and Hanson, PC and O'Brien, M and Servilla, M and Vanderbilt, K and Waide, R}, title = {The Environmental Data Initiative: Connecting the past to the future through data reuse.}, journal = {Ecology and evolution}, volume = {13}, number = {1}, pages = {e9592}, pmid = {36620398}, issn = {2045-7758}, abstract = {The Environmental Data Initiative (EDI) is a trustworthy, stable data repository, and data management support organization for the environmental scientist. In a bottom-up community process, EDI was built with the premise that freely and easily available data are necessary to advance the understanding of complex environmental processes and change, to improve transparency of research results, and to democratize ecological research. EDI provides tools and support that allow the environmental researcher to easily integrate data publishing into the research workflow. Almost ten years since going into production, we analyze metadata to provide a general description of EDI's collection of data and its data management philosophy and placement in the repository landscape. We discuss how comprehensive metadata and the repository infrastructure lead to highly findable, accessible, interoperable, and reusable (FAIR) data by evaluating compliance with specific community proposed FAIR criteria. Finally, we review measures and patterns of data (re)use, assuring that EDI is fulfilling its stated premise.}, }
@article {pmid36618211, year = {2022}, author = {Krishnan, RA and Ravindran, RM and Vincy, VS and Arun, P and Shinu, KS and Jithesh, V and Varma, RP}, title = {Analysis of daily COVID-19 death bulletin data during the first two waves of the COVID-19 pandemic in Thiruvananthapuram district, Kerala, India.}, journal = {Journal of family medicine and primary care}, volume = {11}, number = {10}, pages = {6190-6196}, pmid = {36618211}, issn = {2249-4863}, abstract = {CONTEXT: Coronavirus disease 2019 (COVID-19) mortality trends can help discern the pattern of outbreak evolution and systemic responses.<br><br>AIM: This study aimed to explore patterns of COVID-19 deaths in Thiruvananthapuram district from 31 March 2020 to 31 December 2021.<br><br>SETTING AND DESIGN: Secondary data analysis of COVID-19 deaths in Thiruvananthapuram district was performed.<br><br>MATERIALS AND METHODS: Mortality data were obtained from the district COVID-19 control room, and deaths in the first and second waves of COVID-19 were compared.<br><br>STATISTICAL ANALYSIS: We summarised data as proportions and medians with the inter-quartile range (IQR) and performed Chi-square tests to make comparisons wherever applicable.<br><br>RESULTS: As on 31 December 2021, 4587 COVID-19 deaths were reported in Thiruvananthapuram district, with a case fatality rate of 0.91%. We observed high mortality among older persons (66.7%) and men (56.6%). The leading cause of death was bronchopneumonia (60.6%). The majority (88.5%) had co-morbidities, commonly diabetes mellitus (54.9%). The median interval from diagnosis to hospitalisation was 4 days (IQR 2-7), and that from hospitalisation to death was 2 days (IQR 0-6). The deaths reported during the second wave were four times higher than those of the first wave with a higher proportion of deaths in the absence of co-morbidities (p < 0.001). The majority of the deceased were unvaccinated. Ecological analysis with vaccine coverage data indicated 5.4 times higher mortality among unvaccinated than those who received two vaccine doses.<br><br>CONCLUSIONS: The presence of co-morbidities, an unvaccinated status, and delay in hospitalisation were important reasons for COVID-19 deaths. Primary level health providers can potentially help sustaining vaccination, expeditious referral, and monitoring of COVID-19 patients.}, }
@article {pmid36613120, year = {2023}, author = {Qin, J and Ma, M and Shi, J and Ma, S and Wu, B and Su, X}, title = {The Time-Lag Effect of Climate Factors on the Forest Enhanced Vegetation Index for Subtropical Humid Areas in China.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijerph20010799}, pmid = {36613120}, issn = {1660-4601}, abstract = {Forests represent the greatest carbon reservoir in terrestrial ecosystems. Climate change drives the changes in forest vegetation growth, which in turn influences carbon sequestration capability. Exploring the dynamic response of forest vegetation to climate change is thus one of the most important scientific questions to be addressed in the precise monitoring of forest resources. This paper explores the relationship between climate factors and vegetation growth in typical forest ecosystems in China from 2007 to 2019 based on long-term meteorological monitoring data from six forest field stations in different subtropical ecological zones in China. The time-varying parameter vector autoregressive model (TVP-VAR) was used to analyze the temporal and spatial differences of the time-lag effects of climate factors, and the impact of climate change on vegetation was predicted. The enhanced vegetation index (EVI) was used to measure vegetation growth. Monthly meteorological observations and solar radiation data, including precipitation, air temperature, relative humidity, and photosynthetic effective radiation, were provided by the resource sharing service platform of the national ecological research data center. It was revealed that the time-lag effect of climate factors on the EVI vanished after a half year, and the lag accumulation tended to be steady over time. The TVP-VAR model was found to be more suitable than the vector autoregressive model (VAR). The predicted EVI values using the TVP-VAR model were close to the true values with the root mean squares error (RMSE) < 0.05. On average, each site improved its prediction accuracy by 14.81%. Therefore, the TVP-VAR model can be used to analyze the relationship of climate factors and forest EVI as well as the time-lag effect of climate factors on vegetation growth in subtropical China. The results can be used to improve the predictability of the EVI for forests and to encourage the development of intensive forest management.}, }
@article {pmid36612902, year = {2022}, author = {Vlăduțu, DE and Ionescu, M and Mercuț, R and Noveri, L and Lăzărescu, G and Popescu, SM and Scrieciu, M and Manolea, HO and Iacov Crăițoiu, MM and Ionescu, AG and Mercuț, V}, title = {Ecological Momentary Assessment of Masseter Muscle Activity in Patients with Bruxism.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijerph20010581}, pmid = {36612902}, issn = {1660-4601}, abstract = {According to the International Bruxism Consensus, bruxism refers to the activity of the masticatory muscles reflecting contraction disorders, regardless of whether it is during sleep (SB) or an awake (AB) state. The objective of the present study was to evaluate the activity of the masseter muscle by surface electromyographic (sEMG) recordings. This study was performed on 20 participants with self-reported "possible bruxism" (study group) and 20 participants with no self-reported bruxism (control group); all participants underwent an evaluation of the masseter muscle activity using the dia-BRUXO device, which provides numerical parameters regarding sEMG (the total duration and the type of bruxism specific events, the effort made by the masticatory muscles during the recording period, and the personal bruxism index of each participant). Participants from the study group presented more clenching events during AB, three times more frequent than the control group (p = 0.002, Mann-Whitney U test); for SB, the frequency of clenching and grinding events was comparable within the study group, being more frequent than for the control group; the mean value of the effort index was higher for AB (1.177%) than SB (0.470%) and the same for the duration index, with a mean value of 2.788% for AB and 1.054% for SB. All participants from the control group presented reduced values for all acquired parameters. Overall, the personal bruxism index in AB was approximately four times higher for the study group (2.251%) compared to the control group (0.585%) (p < 0.005, Mann-Whitney U test). Similar values were obtained for SB. All participants with "possible bruxism" from the study group presented a higher activity of the masseter muscle, which is specific for bruxism, thus being defined as "definite bruxism".}, }
@article {pmid36612815, year = {2022}, author = {Yang, X and Lei, S and Shi, Y and Wang, W}, title = {Effects of Ground Subsidence on Vegetation Chlorophyll Content in Semi-Arid Mining Area: From Leaf Scale to Canopy Scale.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijerph20010493}, pmid = {36612815}, issn = {1660-4601}, abstract = {Ground subsidence is the main cause of vegetation degradation in mining areas. It is of great significance to study the effects of ground subsidence on vegetation. At present, few studies have analyzed the effects of ground subsidence on vegetation from different scales. However, the conclusions on different scales may differ. In this experiment, chlorophyll content was used as an indicator of vegetation degradation. We conducted a long-term field survey in the Lijiahao coalfield in China. Based on field survey data and remote sensing images, we analyzed the effects of ground subsidence on chlorophyll content from two scales (leaf scale and canopy scale) and summarized the similarities and differences. We found that, regardless of leaf scale or canopy scale, the effects of subsidence on chlorophyll content have the following three characteristics: (1) mining had the least effect on chlorophyll content in the neutral area, followed by the compression area, and the greatest effect on chlorophyll content in the extension area; (2) subsidence had a slight effect on chlorophyll content of Caragana korshins, but a serious effect on chlorophyll content of Stipa baicalensis; (3) chlorophyll content was not immediately affected when the ground sank. It was the cumulative subsidence that affects chlorophyll content. The difference between leaf scale and canopy scale was that the chlorophyll content at canopy scale is more affected by mining. This means that when assessing vegetation degradation, the results obtained by remote sensing were more severe than those measured in the field. We believe that this is because the canopy chlorophyll content obtained by remote sensing is also affected by the plant canopy structure. We recommend that mining and ecological restoration should be carried out concurrently, and that ground fissures should be taken as the focus of ecological restoration. In addition, Caragana korshins ought to be widely planted. Most importantly, managers should assess the effects of ground subsidence on vegetation on different scales. However, managers need to be aware of differences at different scales.}, }
@article {pmid36612520, year = {2022}, author = {Zhou, Z and Zhang, Z and Zhang, W and Luo, J and Zhang, K and Cao, Z and Wang, Z}, title = {The Impact of Residences and Roads on Wind Erosion in a Temperate Grassland Ecosystem: A Spatially Oriented Perspective.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijerph20010198}, pmid = {36612520}, issn = {1660-4601}, abstract = {The existence of residences and roads is an important way in which human activity affects wind erosion in arid and semiarid environments. Studies assessing the impact of these elements on wind erosion have only focused on limited plots, and their threat of erosion to the surrounding environment has been ignored by many studies. This study was based on spatially overlayed analysis of independent wind erosion distribution simulated by the revised wind erosion equation (RWEQ) and remote-sensing-image-derived residence and road distribution data. Wind erosion at different distances from residences and roads was quantified at the landscape scale of a typical temperate grassland ecosystem, explicitly demonstrating the crucial impacts of both elements on wind erosion. The results showed that wind erosion weakened as the distance from residences and roads increased due to the priority pathways of human activities, and the wind erosion around the residence was more severe than around the road. Human activities in the buffer zones 0-200 m from the residences most frequently caused severe wind erosion, with a wind soil loss of 25 t ha[-1] yr[-1] and a wind soil loss of approximately 5.25 t ha[-1] yr[-1] for 0-60 m from the roads. The characteristics of wind erosion variation in the buffer zones were also affected by residence size and the environments in which the residences were located. The variation in wind erosion was closely related to the road levels. Human activities intensified wind erosion mainly by affecting the soil and vegetation around residences and roads. Ecological management should not be limited to residences and roads but should also protect the surrounding environments. The findings of this study are aimed towards a spatial perspective that can help implement rational and effective environmental management measures for the sustainability of wind-eroded ecosystems.}, }
@article {pmid36607160, year = {2023}, author = {Van Sundert, K and Leuzinger, S and Bader, MK and Chang, SX and De Kauwe, MG and Dukes, JS and Langley, JA and Ma, Z and Mariën, B and Reynaert, S and Ru, J and Song, J and Stocker, B and Terrer, C and Thoresen, J and Vanuytrecht, E and Wan, S and Yue, K and Vicca, S}, title = {When things get MESI: the Manipulation Experiments Synthesis Initiative - a coordinated effort to synthesize terrestrial global change experiments.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16585}, pmid = {36607160}, issn = {1365-2486}, abstract = {Responses of the terrestrial biosphere to rapidly changing environmental conditions are a major source of uncertainty in climate projections. In an effort to reduce this uncertainty, a wide range of global change experiments have been conducted that mimic future conditions in terrestrial ecosystems, manipulating CO2 , temperature, nutrient and water availability. Syntheses of results across experiments provide a more general sense of ecosystem responses to global change, and help to discern the influence of background conditions such as climate and vegetation type in determining global change responses. Several independent syntheses of published data have yielded distinct databases for specific objectives. Such parallel, uncoordinated initiatives carry the risk of producing redundant data collection efforts and have led to contrasting outcomes without clarifying the underlying reason for divergence. These problems could be avoided by creating a publicly available, updatable, curated database. Here, we report on a global effort to collect and curate 57,089 treatment responses across 3,644 manipulation experiments at 1,145 sites, simulating elevated CO2 , warming, nutrient addition and precipitation changes. In the resulting Manipulation Experiments Synthesis Initiative (MESI) database, effects of experimental global change drivers on carbon and nutrient cycles are included, as well as ancillary data such as background climate, vegetation type, treatment magnitude, duration, and, unique to our database, measured soil properties. Our analysis of the database indicates that most experiments are short-term (one or few growing seasons), conducted in the USA, Europe or China, and that the most abundantly reported variable is aboveground biomass. We provide the most comprehensive multifactor global change database to date, enabling the research community to tackle open research questions, vital to global policymaking. The MESI database, freely accessible at doi.org/10.5281/zenodo.7153253, opens new avenues for model evaluation and synthesis-based understanding of how global change affects terrestrial biomes. We welcome contributions to the database on GitHub.}, }
@article {pmid35900623, year = {2023}, author = {Sharma, N and Kaushal, A and Yousuf, A and Sood, A and Kaur, S and Sharda, R}, title = {Geospatial technology for assessment of soil erosion and prioritization of watersheds using RUSLE model for lower Sutlej sub-basin of Punjab, India.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {1}, pages = {515-531}, pmid = {35900623}, issn = {1614-7499}, mesh = {Humans ; *Soil ; *Soil Erosion ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; Geographic Information Systems ; India ; Technology ; }, abstract = {Erosion of soil by water coupled with human activities is considered as one of the most serious agents of land degradation, posing severe threat to agricultural productivity, soil health, water quality, and ecological setup. The assessment of soil erosion and recognition of problematic watersheds are pre-requisite for management of erosion hazards. In the present study, Revised Universal Soil Loss Equation (RUSLE) integrated with remote sensing (RS) and geographic information system (GIS) has been used to assess the soil erosion in lower Sutlej River basin of Punjab, India, and prioritize the watersheds for implementation of land and water conservation measures. The total basin area was about 8577 km[2] which was divided into 14 sub-watersheds with the area ranging from 357.8 to 1354 km[2]. The data on rainfall (IMD gridded data), soil characteristics (FAO soil map), topography (ALOS PALSAR DEM) and land use (ESRI land use and land cover map) were prepared in the form of raster layers and overlaid together to determine the average annual soil loss. The results revealed that the average annual soil loss varied from 1.26 to 25 t ha[-1], whereas total soil loss was estimated to be 2,441,639 tonnes. The spatial distribution map of soil erosion showed that about 94.4% and 4.7% of the total area suffered from very slight erosion (0-5 t ha[-1] year[-1]) and slight erosion (5-10 t ha[-1] year[-1]), respectively, whereas 0.11% (9.38 km[2]) experienced very severe soil loss (> 25 t ha[-1] year[-1]). Based on estimated average annual soil loss of sub-watersheds, WS8 was assigned the highest priority for implementation of soil and water conservation measures (323.5 t ha[-1] year[-1]), followed by WS9 (303.8 t ha[-1] year[-1]), whereas WS2 was given last priority owing to its lowest value of soil loss (122.02 t ha[-1] year[-1]). The present study urges that conservation strategies should be carried out in accordance with the priority ranking of diverse watersheds. These findings can certainly be used to implement soil conservation plans and management practices in order to diminish soil loss in the river basin.}, }
@article {pmid36604610, year = {2023}, author = {Prager, M and Lundin, D and Ronquist, F and Andersson, AF}, title = {ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {6}, pmid = {36604610}, issn = {1471-2105}, abstract = {BACKGROUND: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.<br><br>RESULTS: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure.<br><br>CONCLUSION: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.}, }
@article {pmid36602254, year = {2023}, author = {Koenig, CJ and Vasquez, TS and Peterson, EB and Wollney, EN and Bylund, CL and Ho, EY}, title = {Mapping Uncharted Terrain: A Systematic Review of Complementary and Integrative Health Communication Using Observational Data in Biomedical Settings.}, journal = {Health communication}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/10410236.2022.2140080}, pmid = {36602254}, issn = {1532-7027}, abstract = {Complementary and integrative health (CIH) use is diverse and highly prevalent worldwide. Prior research of CIH communication in biomedical encounters address safety, efficacy, symptom management, and overall wellness. Observational methods are rarely used to study CIH communication and avoid recall bias, preserve ecological validity, and contextualize situated clinical communication. Following PRISMA guidelines, we systematically reviewed studies at the intersection of social scientific observational research and findings about CIH communication between clinicians, patients, and caregivers in biomedical settings. We identified international, peer-reviewed publications from seven databases between January 2010 and December 2020. Titles and abstracts were first screened for inclusion, then full studies were coded using explicit criteria. We used a standard checklist was modified to assess article quality. Ten of 11,793 studies examined CIH communication using observational methods for CIH communication in biomedical settings. Studies used a range of observational techniques, including participant and non-participant observation, which includes digital audio or video recordings. Results generated two broad sets of findings, one focused on methodological insights and another on CIH communication. Despite methodological and topic similarities, included studies addressed CIH communication as a process and as proximal and intermediate health outcomes. We recommend how observational studies of CIH communication can better highlight relationships between communication processes and health outcomes. Current research using observational methods offers an incomplete picture of CIH communication in biomedical settings. Future studies should standardize how observational techniques are reported to enhance consistency and comparability within and across biomedical settings to improve comparability.}, }
@article {pmid36601075, year = {2022}, author = {Leal, JSV and Fogal, AS and Meireles, AL and Cardoso, LO and Machado, &#xcd;E and de Menezes, MC}, title = {Health economic impacts associated with the consumption of sugar-sweetened beverages in Brazil.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1088051}, pmid = {36601075}, issn = {2296-861X}, abstract = {INTRODUCTION: The consumption of sugar-sweetened beverages (SSBs) is among the main risk factors for non-communicable diseases (NCDs). This study aimed to estimate the financial costs of hospitalizations and procedures of high and medium complexity for NCDs attributable to the consumption of SSBs in the Brazilian Unified Health System (SUS) in 2019.<br><br>METHODS: This ecological study used data from the Global Burden of Disease (GBD) 2019 and the Department of Informatics of the Unified Health System (DATASUS). The attributable costs were estimated from the population-attributable fraction (PAF) and the costs in the treatment of chronic diseases [type 2 diabetes mellitus and ischemic heart disease (IHD)], stratified by sex, age group, level of complexity of treatment, and federative units.<br><br>RESULTS: In 2019, in Brazil, US$ 14,116,240.55 were the costs of hospitalizations and procedures of high and medium complexity in the treatment of NCDs attributable to the consumption of SSBs. These values were higher in males (US$ 8,469,265.14) and the southeast and southern regions, mainly in the state of S&#xe3;o Paulo. However, when evaluating these results at a rate per 10,000 inhabitants, it was observed that the states of Paran&#xe1;, Tocantins, and Roraima had higher costs per 10,000 inhabitants. Regarding the age groups, higher costs were observed in the older age groups.<br><br>CONCLUSION: This study revealed the high financial impact of the NCDs treatment attributed to the consumption of SSBs in Brazil and the variability among Brazilian macro-regions. The results demonstrate the urgency and need for the expansion of policies to reduce the consumption of SSBs in Brazil with strategies that consider regional particularities.}, }
@article {pmid36599936, year = {2023}, author = {Juan, D and Santpere, G and Kelley, JL and Cornejo, OE and Marques-Bonet, T}, title = {Current advances in primate genomics: novel approaches for understanding evolution and disease.}, journal = {Nature reviews. Genetics}, volume = {}, number = {}, pages = {}, pmid = {36599936}, issn = {1471-0064}, abstract = {Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.}, }
@article {pmid36107138, year = {2023}, author = {Bassing, SB and DeVivo, M and Ganz, TR and Kertson, BN and Prugh, LR and Roussin, T and Satterfield, L and Windell, RM and Wirsing, AJ and Gardner, B}, title = {Are we telling the same story? Comparing inferences made from camera trap and telemetry data for wildlife monitoring.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {33}, number = {1}, pages = {e2745}, doi = {10.1002/eap.2745}, pmid = {36107138}, issn = {1051-0761}, mesh = {Animals ; *Animals, Wild ; *Ecosystem ; Geographic Information Systems ; Surveys and Questionnaires ; Telemetry ; }, abstract = {Estimating habitat and spatial associations for wildlife is common across ecological studies and it is well known that individual traits can drive population dynamics and vice versa. Thus, it is commonly assumed that individual- and population-level data should represent the same underlying processes, but few studies have directly compared contemporaneous data representing these different perspectives. We evaluated the circumstances under which data collected from Lagrangian (individual-level) and Eulerian (population-level) perspectives could yield comparable inference to understand how scalable information is from the individual to the population. We used Global Positioning System (GPS) collar (Lagrangian) and camera trap (Eulerian) data for seven species collected simultaneously in eastern Washington (2018-2020) to compare inferences made from different survey perspectives. We fit the respective data streams to resource selection functions (RSFs) and occupancy models and compared estimated habitat- and space-use patterns for each species. Although previous studies have considered whether individual- and population-level data generated comparable information, ours is the first to make this comparison for multiple species simultaneously and to specifically ask whether inferences from the two perspectives differed depending on the focal species. We found general agreement between the predicted spatial distributions for most paired analyses, although specific habitat relationships differed. We hypothesize the discrepancies arose due to differences in statistical power associated with camera and GPS-collar sampling, as well as spatial mismatches in the data. Our research suggests data collected from individual-based sampling methods can capture coarse population-wide patterns for a diversity of species, but results differ when interpreting specific wildlife-habitat relationships.}, }
@article {pmid36239541, year = {2023}, author = {Keck, F and Altermatt, F}, title = {Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb.}, journal = {Molecular ecology resources}, volume = {23}, number = {2}, pages = {511-518}, doi = {10.1111/1755-0998.13723}, pmid = {36239541}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Biodiversity ; Gene Library ; Databases, Nucleic Acid ; }, abstract = {DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and valid