cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tb2rbp03g
title: Data reported in development and cross-validation of a veterans mental health risk factor screen

description: Background. VA primary care patients are routinely screened for current
 symptoms of PTSD, depression, and alcohol disorders, but many who screen
 positive do not engage in care. In addition to stigma about mental
 disorders and a high value on autonomy, some veterans may not seek care
 because of uncertainty about whether they need treatment to recover. A
 screen for mental health risk could provide an alternative motivation for
 patients to engage in care. Results. Twelve items assessing dissociation,
 emotional lability, life stress, and moral injury correctly classified 86%
 of those who later had elevated PTSD and/or depression symptoms
 (sensitivity) and 75% of those whose later symptoms were not elevated
 (specificity). Performance was also very good for 110 veterans who
 identified as members of ethnic/racial minorities. Conclusions. Mental
 health status was prospectively predicted in VA primary care patients with
 high accuracy using a screen that is brief, easy to administer, score, and
 interpret, and fits well into VA’s integrated primary care. When care is
 readily accessible, appealing to veterans, and not perceived as
 stigmatizing, information about mental health risk may result in higher
 rates of engagement than information about current mental disorder status.
description: Data from samples of veterans and traumatic injury survivors were
 analyzed to identify  mental health risk factors that are characteristics
 of individuals or stressors or of post-trauma, post-deployment, or
 post-military service resources, experiences, or responses. Twelve risk
 factors were strongly related to PTSD (r &gt; .50): current PTSD,
 depression, dissociation, negative thinking, and emotional lability
 symptoms, life stress, relationship stress, social constraints, and
 deployment experiences of a difficult environment, concerns about life and
 family, perceived threat, and moral injury. Items assessing each of these
 risk factors were selected and their validity to prospectively predict
 PTSD and/or depression 6 months later was assessed in a new sample of 232
 VA primary care patients. Twelve items assessing dissociation, emotional
 lability, life stress, and moral injury correctly classified 86% of those
 who later had elevated PTSD and/or depression symptoms (sensitivity) and
 75% of those whose later symptoms were not elevated (specificity).
 Performance was also very good for 110 veterans who identified as members
 of ethnic/racial minorities.
description: MS Excel MS Word
DOI: 10.15468/dl.qf4tp7
title: Occurrence Download

description: A dataset containing 2212 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ecdyonurus dispar"
 ]
}

 The dataset includes 2212 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003198-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7280/d1d124
title: Net loss of biomass predicted for tropical biomes in a changing climate

description: Tropical ecosystems store over half of the world’s aboveground live carbon
 as biomass, and water availability plays a key role in its distribution.
 Although precipitation and temperature are shifting across the tropics,
 their effect on biomass and carbon storage remains uncertain. Here we use
 empirical relationships between climate and aboveground biomass content to
 show that the contraction of humid regions, and expansion of those with
 intense dry periods, results in substantial carbon loss from the
 neotropics. Under a low emission scenario (RCP4.5) this could cause a
 ~14.4–23.9 Pg C (6.8–12%) net reduction of aboveground live carbon from
 1950–2100. Under a high emissions scenario (RCP8.5), net carbon losses
 could double across the tropics ~28.2–39.7 Pg C (13.3–20.1%). The
 contraction of humid regions in South America accounts for ~40% of this
 change. Climate mitigation strategies could prevent half of the carbon
 losses and help maintain the natural tropical net carbon sink.
description: This dataset contains the input data, and partial and final
 results from Uribe et al. (2023).
DOI: 10.5061/dryad.8gtht76s4
title: Non-lethal fungal infection could reduce aggression towards strangers in ants

description: Many parasites interfere with the behaviour of their hosts. In social
 animals, such as ants, parasitic interference can cause changes on the
 level of the individual and also on the level of the society. The
 ant-parasitic fungus Rickia wasmannii influences the behaviour of Myrmica
 ants by expanding the host’s nestmate recognition template, thereby
 increasing the chance of the colony accepting infected non-nestmates.
 Infected ants consistently show an increase of the alkane tricosane
 (n-C23) in their cuticular hydrocarbon profiles. Although experimental
 application of single compounds often elicits aggression towards
 manipulated ants, we hypothesized that the increase of n-C23 might
 underlie the facilitated acceptance of infected non-nestmates. To test
 this, we mimicked fungal infection in M. scabrinodis by applying synthetic
 n-C23 to fresh ant corpses and observed the reaction of infected and
 uninfected workers to control and manipulated corpses. Infected ants
 appeared to be more peaceful towards infected but not uninfected
 non-nestmates. Adding n-C23 to uninfected corpses resulted in reduced
 aggression in uninfected ants. This supports the hypothesis that n-C23
 acts as a ‘pacifying’ signal. Our study indicates that parasitic
 interference with the nestmate discrimination of host ants might
 eventually change colony structure by increasing genetic heterogeneity in
 infected colonies.
description: The uploaded dataset contains four parts: three data sheet files
 (.csv) with (a) dyadic interaction assays between live individuals and
 corpses/dummies with different treatments originating from foreign
 colonies, infected or uninfected; (b) dyadic interaction assays between
 live individuals and corpses/dummies originating from the same colony as
 the live individuals - control tests; (c) chemical data referring to the
 relative abundance of n-C23 in the cuticular hydrocarbon profile
 (CHC-profile) of different samples, uninfected and infected; and (d) 10
 chromatograms (.qgd files). In all cases, data originated from the ant
 species <em>Myrmica scabrinodis</em>. The details of the tests
 and the analyses are given in the provided preprint https://doi.org/10.21203/rs.3.rs-1305759/v1. The dyadic tests were performed in a blind manner.
description: The datasheet file can be opened with any software handling .csv
 files, e.g. Microsoft Excel, Open Office, Libra Office, etc. The
 chromatograms can be handled with the software LabSolution by Shimadzu
 Corporation, but they can also be opened with OpenChrom a free software
 (https://openchrom.net/download). At the moment the latest version is 1.5.0.
DOI: 10.5061/dryad.cfxpnvx8b
title: Feeding foliar nano-selenium biofortified Panax notoginseng could reduce the occurrence of glycolipid metabolism disorder in mice caused by high-fat diets

description: Nano-selenium (nano-Se) has been extensively explored as a biostimulant
 for improving the quality of grain crops. However, there are few reports
 about the effect on the medicinal components of Chinese herbal medicine
 cultured with nano-Se. Here, we sprayed nano-Se during the cultivation of
 Panax notoginseng (SePN), and measured the changes of medicinal components
 compared with conventional Panax notoginseng (PN). Furthermore, we
 identified a more pronounced effect of SePN on reducing obesity in animals
 compared with PN. By measuring antioxidant capacity, histopathology, gene
 expression related to glycolipid metabolism, and gut microbiota
 composition, we propose a potential mechanism for SePN to improve animal
 health. Compared with the control groups, foliar spraying of nano-Se
 increased saponins content (Rb2, Rb3, Rc, F2, Rb2, and Rf) in the roots of
 Panax notoginseng, and the content of Rb2 increased by 3.9 times in
 particular. Interestingly, animal studies indicated that taking
 selenium-rich Panax notoginseng (SePN) can further ameliorate liver
 antioxidation (SOD, MDA, and GSH) and enzyme activities involved in
 glycolipid metabolism (ATGL and PFK). It also relieved inflammation and
 regulated the expression of genes (MCAD, PPAR-α, and PCSK9) related to
 fatty acid oxidation. The abundance ratio of Firmicutes/Bacteroides and
 beneficial bacteria abundance (Bifidobacterium, Butyricimonas, and
 Parasutterella) in gut microbiota were improved relative to the control.
 In summary, the application of nano-Se on PN may effectively raise the
 content of Panax notoginseng saponins (PNS) and immensely lower the risk
 of metabolic disorders of glycolipids.
description: Total genomic DNA samples were extracted using the OMEGA Soil DNA
 Kit (M5635-02) (Omega Bio-Tek, Norcross,GA, USA), and stored at −20◦C
 before further analysis. PCR amplification of the bacterial 16S rRNA genes
 V3–V4 region was performed using the forward primer 338F (5′ -
 ACTCCTACGGGAGGCAGCA-3′ ) and the reverse primer 806R (5′
 -GGACTACHVGGGTWTCTAAT-3′ ). Amplification system including 5×reaction
 buffer 5 µL, 5×GC buffer 5 µL, dNTP (2.5 mM) 2 µL, Forward primer (10 uM)
 1 µL, Reverse primer (10 uM) 1 µL, DNA Template 2 µL, ddH2O 8.75 µL, Q5
 DNA Polymerase 0.25 µL. Amplification parameters include initial
 denaturation 98◦C 2 min, denaturation 98◦C 15 s, annealing 55◦C 30 s,
 extension 72◦C 30 s, final extension 72◦C 5 min, 10◦C hold. 25-30 cycles
 dsDNA Assay Kit (Invitrogen, Carlsbad, CA, USA). PCR amplicons were
 purified and quantified with Vazyme VAHTSTM DNA Clean Beads (Vazyme,
 Nanjing, China) and quantified using the QuantiT PicoGreen dsDNA Assay Kit
 (Invitrogen, Carlsbad, CA, USA), respectively. Amplicons were pooled in
 equal amounts, and pair-end 2×250 bp sequencing was performed using the
 Illlumina NovaSeq platform with NovaSeq 6000 SP Reagent Kit (500 cycles)
 at Shanghai Personal Biotechnology Co., Ltd (Shanghai, China)
DOI: 10.5061/dryad.76hdr7t0n
title: Data for: Connecting voice profiling to genomics

description: This dataset contains a graph-based path-finding algorithm to detect
 chainlink genes for voice chains that connect the genes in chromosomal
 microdeletion regions to the FOXP2 gene. Instructions are within multiple
 README files included with the package. The code is set up to be used on
 Linux platforms.
description: This code package accompanies the manuscript titled: Connecting
 human voice profiling to genomics: A predictive algorithm for linking
 speech phenotypes to genetic microdeletion syndromes
 <strong>Data and code summary</strong>
 Two publicly available datasets were used in this paper to obtain
 the results reported in Table 1 in this manuscript. These are enumerated
 below.  1.      The ConsensusPathDB (CPDB) biological
 pathways database 2.      The HGNC human genome
 database These databases are not provided in this
 package due to licensing restrictions (on redistribution of data).
 However, there is a comprehensive README file that is included in this
 package, with instructions on how to download these databases and how to
 subsequently use the code provide to process them. Some sample
 intermediate derivatives from the databases above are provided for
 guidance and reference, for the user's convenience.
 Following the instructions in the README file will produce the
 results reported in this paper, in full. The code
 provided was written by the author of the corresponding manuscript, and is
 meant for public use, free of any restrictions whatsoever from the
 authors’ side.  In addition, the code files provided in
 this package are commented in detail (in-line with the code) for the
 user's convenience.
description: The programs in this package are written in awk. The scripts that
 call them are expected to be run on a Linux/Unix platform within a
 tc-shell environment. A comprehensive README file is included within the
 code package. It containes instructions to run the code to reproduce the
 results in the paper referenced. It also contains screenshots of commands
 and sample outputs for the user's reference.
DOI: 10.5061/dryad.h70rxwdn3
title: Data for meta-analysis of the soil greenhouse gas emissions

description: Exploring the responses of greenhouse gases (GHGs) emissions to land use
 conversion or reversion is significant for taking effective land use
 measures to alleviate global warming. A global meta-analysis was conducted
 to analyze the responses of carbon dioxide (CO2), methane (CH4) and
 nitrous oxide (N2O) emissions to land use conversion or reversion, and
 determine their temporal evolution, driving factors and potential
 mechanisms. Our results showed that CH4 and N2O responded positively to
 land use conversion while CO2 responded negatively to the changes from
 natural herb and secondary forest to plantation. By comparison, CH4
 responded negatively to land use reversion and N2O also showed negative
 response to the reversion from agricultural land to forest. The conversion
 of land use weakened the function of natural forest and grassland as CH4
 sink and the artificial nitrogen (N) addition for plantation increased N
 source for N2O release from soil, while the reversion of land use could
 alleviate them to some degree. Besides, soil carbon would impact CO2
 emission for a long time after land use conversion, and secondary forest
 reached the methane uptake level similar to that of primary forest after
 over 40 years. N2O responses had negative relationships with time interval
 under the conversions from forest to plantation, secondary forest and
 pasture. In addition, meta-regression indicated that CH4 had correlations
 with several environmental variables, and carbon-nitrogen ratio had
 contrary relationships with N2O emission responses to land use conversion
 and reversion. And the importance of driving factors displayed that CO2,
 CH4 and N2O response to land use conversion and reversion were easily
 affected by NH4+ and soil moisture, mean annual temperature and NO3-,
 total nitrogen and mean annual temperature, respectively. This study would
 provide enlightenment for scientific land management and reducing of GHG
 emissions.
DOI: 10.5061/dryad.np5hqbzwx
title: Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression

description: The koala, one of the most iconic Australian wildlife species, is facing
 several concomitant threats that are driving population declines. Some
 threats are well known and have clear methods of prevention (e.g., habitat
 loss can be reduced with stronger land-clearing control), whereas others
 are less easily addressed. One of the major current threats to koalas is
 chlamydial disease, which can have major impacts on individual survival
 and reproduction rates and can translate into population declines.
 Effective management strategies for the disease in the wild are currently
 lacking, and to date we know little about the determinants of individual
 susceptibility to disease. Here we investigated the genetic basis of
 variation in susceptibility to chlamydia using one of the most intensively
 studied wild koala populations. We combined data from veterinary
 examinations, chlamydia testing, genetic sampling and movement monitoring.
 Out of our sample of 342 wild koalas, 60 were found to have
 chlamydia. Using genotype information on 5007 SNPs to investigate
 the role of genetic variation in determining disease status, we found no
 evidence of inbreeding depression, but a heritability of 0.11 (95%CI =
 0.05 – 0.23) for the probability that koalas had chlamydia. Heritability
 of susceptibility to chlamydia could be relevant for future disease
 management, as it suggests adaptive potential for the population.
DOI: 10.5061/dryad.000000063
title: Socioeconomic impacts on Andean adolescents’ growth: variation between households, between communities, and over time

description: Background/Objectives We evaluated potential socioeconomic contributors to
 variation in Andean adolescents’ growth between households within a
 peri-urban community undergoing rapid demographic and economic change,
 between different community types (rural, peri-urban, urban), and over
 time. Because growth monitoring is widely used for assessing community
 needs and progress, we compared the prevalences of stunting, underweight,
 and overweight estimated by three different growth references. Results
 Alteños’ height averaged ∼0.8SD/∼0.6SD/∼2SDs greater than adolescents’
 height in urban and rural communities measured in 1983/1998/1977,
 respectively. Overweight prevalence was comparable to the WHO, and lower
 than MESA and Puno, references. Stunting was 8.5/2.5/0.5 times
 WHO/MESA/Puno samples, respectively. Female Alteños’ growth was positively
 associated with household and maternal income indices.
 Conclusions/Implications Both peri-urban conditions and temporal trends
 contributed to gains in Alteños’ growth. Rural out-migration can alleviate
 migrants’ poverty, partly because of more diverse economic options in
 urbanized communities, especially for women. Nonetheless, Alteños averaged
 below WHO and MESA height and weight medians. Evolved biological
 adaptations to environmental challenges, and the consequent variability in
 growth trajectories, favors using multiple growth references. Growth
 monitoring should be informed by community- and household-level studies to
 detect and understand local factors causing or alleviating health
 disparities. Lay Summary Andean adolescents exhibited elevated rates of
 stunting; their height varied with socioeconomic status within and between
 high-altitude communities. Unlike some lowland populations, the prevalence
 of overweight/obesity was not elevated. Population-specific growth
 assessments and targeted interventions (e.g., maternal education and
 employment) are likely to help alleviate disparities in Andean children’s
 growth.
description: Collection and processing protocols are given in: ME Burris, E
 Caceres, EM Chester, KA Hicks, TW McDade, L Sikkink, H Spielvogel, J
 Thornburg, VJ Vitzthum. 2022. Socioeconomic impacts on Andean adolescents’
 growth: variation between households, between communities, and over time.
 Evolutionary Medicine & Public Health, volume 10(1),
 eoac033).
DOI: 10.5281/zenodo.18401412
title: technical reports of the CEC2005, CEC2014 and SOCO2010 test suites
DOI: 10.5281/zenodo.18401411
title: technical reports of the CEC2005, CEC2014 and SOCO2010 test suites
DOI: 10.5061/dryad.3r2280gk3
title: Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species

description: Selection on quantitative traits by heterogeneous climatic conditions can
 lead to substantial trait variation across a species range. In the context
 of rapidly changing environments, however, it is equally important to
 understand selection on trait plasticity. To evaluate the role of
 selection in driving divergences in traits and their associated
 plasticities within a widespread species, we compared molecular and
 quantitative trait variation in Populus fremontii (Fremont cottonwood), a
 foundation riparian distributed throughout Arizona. Using SNP data and
 genotypes from 16 populations reciprocally planted in three common
 gardens, we first performed QST-FST analyses to detect selection on traits
 and trait plasticity. We then explored the environmental drivers of
 selection using trait-climate and plasticity-climate regressions. Three
 major findings emerged: 1) There was significant genetic variation in
 traits expressed in each of the common gardens and in the phenotypic
 plasticity of traits across gardens, both of which were heritable. 2)
 Based on QST-FST comparisons, there was evidence of selection in all
 traits measured; however, this result varied from no effect in one garden
 to highly significant in another, indicating that detection of past
 selection is environmentally dependent. We also found strong evidence of
 divergent selection on plasticity across environments for two traits. 3)
 Traits and/or their plasticity were often correlated with population
 source climate (R2 up to 0.77 and 0.66, respectively). These results
 suggest that steep climate gradients across the Southwest have played a
 major role in shaping the evolution of divergent phenotypic responses in
 populations and genotypes now experiencing climate change.
description: See associated publication.
description: See associated README file.
DOI: 10.7272/q6h993f9
title: Splice altering variant predictions in four archaic hominin genomes

description: This file contains high-quality autosomal SNVs that occur among four
 high-coverage archaic genomes aligned to the hg19/GRCh37 reference genome.
 Each entry corresponds to a single variant with a distinct GENCODE, Human
 Release 24, annotation per genomic position. Data per variant includes the
 genomic position, reference/alternate alleles, archaic genotypes, gene
 annotation, and additional data relevant to the analysis of splicing
 variants: SpliceAI annotations gene constraint measured using data from
 gnomAD variant conservation measured using phyloP allele origin allele
 frequencies in modern humans from the Thousand Genomes Project and gnomAD
 introgression metadata sQTL data from GTEx
description: All data in this file are publicly available (see below). Archaic
 variants were filtered using bcftools to retain high-quality sites and
 high-quality genotypes. Missing data and irrelevant fields per variant are
 marked as "n/a". Only variants matching a filtered archaic
 variant were included from the other datasets (see below). The dataframe
 was created using Pandas in a Python Jupyter notebook. Data used
 in this notebook: Altai Neanderthal SNVs
 (http://ftp.eva.mpg.de/neandertal/Vindija/VCF/Altai/) Browning et al. 2018 Introgressed Variants (https://data.mendeley.com/datasets/y7hyt83vxr/1) Chagyrskaya Neanderthal SNVs (http://ftp.eva.mpg.de/neandertal/Chagyrskaya/VCF/) Denisovan SNVs (http://ftp.eva.mpg.de/neandertal/Vindija/VCF/Denisova/) gnomAD allele frequencies (https://gnomad.broadinstitute.org/downloads#v3-variants) gnomAD constraint (https://storage.googleapis.com/gcp-public-data--gnomad/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz) phyloP (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP46way/primates.phyloP46way.bw) sQTLs (https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_sQTL.tar) Thousand Genomes Project (http://hgdownload.soe.ucsc.edu/gbdb/hg38/1000Genomes/) Vernot et al. 2016 Introgressed Tag SNPs (https://drive.google.com/drive/folders/0B9Pc7_zItMCVM05rUmhDc0hkWmc?resourcekey=0-zwKyJGRuooD9bWPRZ0vBzQ) Vindija Neanderthal SNVs (http://ftp.eva.mpg.de/neandertal/Vindija/VCF/Vindija33.19/)
description: Any text editor can be used to open this file. We recommend using
 software that can handle large dataframes well such as R or
 Python.