cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5068/d1k39s
title: On collaborative reinforcement learning to optimize the redistribution of critical medical supplies throughout the COVID-19 pandemic

description: Objective: This work investigates how reinforcement learning and deep
 learning models can facilitate the near-optimal redistribution of medical
 equipment in order to bolster public health responses to future crises
 similar to the COVID-19 pandemic. Materials and Methods: The system
 presented is simulated with disease impact statistics from the Institute
 of Health Metrics (IHME), Center for Disease Control, and Census Bureau[1,
 2, 3]. We present a robust pipeline for data preprocessing, future demand
 inference, and a redistribution algorithm that can be adopted across broad
 scales and applications. Results: The reinforcement learning
 redistribution algorithm demonstrates performance optimality ranging from
 93-95%. Performance improves consistently with the number of random states
 participating in exchange, demonstrating average shortage reductions of
 78.74% (± 30.8) in simulations with 5 states to 93.50% (± 0.003) with 50
 states. Conclusion: These findings bolster confidence that reinforcement
 learning techniques can reliably guide resource allocation for future
 public health emergencies.
description: Summary statistics for our study are attached here for
 reference.
DOI: 10.5061/dryad.w0vt4b8pt
title: Nestedness theory suggests wetland fragments with large areas and macrophyte diversity benefit waterbirds

description: Many artificial wetland constructions are currently underway worldwide to
 compensate for the degradation of natural wetland systems. Researchers
 face the responsibility of proposing wetland management and species
 protection strategies to ensure that constructed wetlands positively
 impact waterbird diversity. Nestedness is a commonly occurring pattern for
 biotas in fragmented habitats with important implications for
 conservation; however, only a few studies have focused on seasonal
 waterbird communities in current artificial wetlands. In this study, we
 used the nestedness theory for analyzing the annual and seasonal community
 structures of waterbirds in artificial wetlands at Lake Dianchi (China) to
 suggest artificial wetland management and waterbird conservation
 strategies. We carried out three waterbird surveys per month for one year
 to observe the annual, spring, summer, autumn, and winter waterbird
 assemblages in 27 lakeside artificial wetland fragments. We used the NeD
 program to quantify nestedness patterns of waterbirds at the annual and
 seasonal levels. We also determined Spearman partial correlations to
 examine the associations of nestedness rank and habitat variables to
 explore the factors underlying nestedness patterns. We found that annual
 and all four seasonal waterbird compositions were nested, and selective
 extinction and habitat nestedness were the main factors governing
 nestedness. Further, selective colonization was the key driver of
 nestedness in autumn and winter waterbirds. We suggest that the area of
 wetland fragments should be as large as possible and that habitat
 heterogeneity should be maximized to fulfill the conservation needs of
 different seasonal waterbirds. Furthermore, we suggest that future studies
 should focus on the least area criterion, and that vegetation management
 of artificial wetland construction should be based on the notion of
 sustainable development for humans and wildlife. 
description: We carried out three waterbird surveys per month for one year to
 observe the annual, spring, summer, autumn, and winter waterbird
 assemblages in 27 lakeside artificial wetland fragments. We used the NeD
 program to quantify nestedness patterns of waterbirds at the annual and
 seasonal levels. We also determined Spearman partial correlations to
 examine the associations of nestedness rank and habitat variables to
 explore the factors underlying nestedness patterns.
DOI: 10.5061/dryad.vhhmgqnrq
title: Neurexin Photometry

description: Goal-directed behaviors are essential for normal function and
 significantly impaired in neuropsychiatric disorders. Despite extensive
 associations between genetic mutations and these disorders, the molecular
 contributions to goal-directed dysfunction remain unclear. We examined
 mice with constitutive and brain region-specific mutations in Neurexin1α,
 a neuropsychiatric disease-associated synaptic molecule, in value-based
 choice paradigms. We found Neurexin1α knockouts exhibited reduced
 selection of beneficial outcomes and impaired avoidance of costlier
 options. Reinforcement modeling suggested this was driven by deficits in
 updating and representation of value. Disruption of Neurexin1α within
 telencephalic excitatory projection neurons, but not thalamic neurons,
 recapitulated choice abnormalities of global Neurexin1α knockouts.
 Furthermore, this selective forebrain excitatory knockout of Neurexin1α
 perturbed value-modulated neural signals within striatum, a central node
 in feedback-based reinforcement learning. By relating deficits in
 value-based decision-making to region-specific Nrxn1α disruption and
 changes in value-modulated neural activity, we reveal potential neural
 substrates for the pathophysiology of neuropsychiatric disease-associated
 cognitive dysfunction.
DOI: 10.5061/dryad.jwstqjq7t
title: Contrasting association of Leptin receptor polymorphisms and haplotypes with polycystic ovary syndrome in Bahraini and Tunisian women: a case–control study

description: Background. This study examined the contribution of ethnicity to the
 association of leptin receptor gene (LEPR) genetic variants with
 polycystic ovary syndrome (PCOS) in Tunisian and Bahraini Arabic-speaking
 women. Methods. Subjects consisted of 320 women with PCOS, and 446
 eumenorrhic women from Tunisia, and 242 women with PCOS and 238 controls
 from Bahrain. Genotyping of (exonic) rs1137100 and rs1137101 and
 (intronic) rs2025804 LEPR variants was done by allelic exclusion. Results.
 The minor allele frequencies of rs1137100 and rs1137101 were significantly
 different between PCOS cases and control women from Bahrain but not
 Tunisia, and LEPR rs1137101 was associated with increased PCOS
 susceptibility only in Bahraini subjects. Furthermore, rs1137100 was
 associated with decreased PCOS risk among Bahrainis under codominant and
 recessive models; rs1137100 was negatively associated with PCOS in
 Tunisians after controlling for testosterone. In addition, rs2025804 was
 associated with increased PCOS risk among Tunisian but not Bahraini women,
 after adjusting for key covariates. Negative correlation was seen between
 rs1137101 and triglycerides in Tunisians, while HOMA-IR and insulin
 correlated with rs2025804 and rs1137101 among Bahraini subjects, and
 rs1137101 correlated with estradiol and prolactin. Taking TAG haplotype as
 common, positive association of TAA and negative association of TGG
 haplotype with PCOS was seen among Bahraini women; no three-locus
 PCOS-associated haplotypes were found in Tunisians. Conclusions. This
 study is the first to demonstrate the contribution of ethnicity to the
 association of LEPR gene variants with PCOS, thereby highlighting the
 significance of controlling for ethnicity in gene association
 investigations.
description: We selected 3 SNPs in <i>LEPR</i> gene with minor
 allele frequencies (MAF) of 5% or higher, and with reported clinical
 relevance, as noted NCBI Geneview. The selected variants were (intron 2)
 rs2025804), and the missense variants rs1137100 (Lys109Arg; exon 4) and
 rs1137101 (Gln223Arg; exon 6).
 Genotyping of the studied<i> LEPR</i> gene variants was done
 by allelic discrimination (real-time PCR), using VIC- and FAM-labelled
 probes.
description: The missing values were left as blank.
DOI: 10.5061/dryad.t4b8gtj0r
title: Color scores, COI haplotypes and SNP data for Phelotrupes auratus individuals

description: We studied the population genetic structure underlying the geographic
 variation in the structural color of the geotrupid dung beetle,
 Phelotrupes auratus, which exhibits metallic body colors of different
 reflectance wavelengths perceived as red, green, and indigo. These forms
 occur parapatrically in an area of Japan. The color variation was not
 related to variation in climatic factors. Using single-nucleotide
 polymorphisms (SNPs) from restriction-site associated DNA sequences, we
 discriminated five groups of populations (west/red, south/green,
 south/indigo, south/red, and east/red) by a combination of genetic
 clusters (west, south, and east) and three color forms. There were three
 transition zones for the color forms: two between the red and green forms
 were hybrid zones with steep genetic clines, which implies the existence
 of barriers to gene flow between regions with different colors. The
 remaining transition zone between the green and indigo forms lacked
 genetic differentiation, despite the evident color changes, which implies
 regionally specific selection on the different colors. In a genome-wide
 association study, we identified four SNPs that were associated with the
 red/green or indigo color and were not linked with one another, which
 implies that the coloration was controlled by multiple loci, each
 affecting the expression of a different color range. These loci may have
 controlled the transitions between different combinations of colors. Our
 study demonstrates that geographic color variation within a species can be
 maintained by nonuniform interactions among barriers to gene flow, locally
 specific selection on different colors, and the effects of different color
 loci.
DOI: 10.5061/dryad.wm37pvmm6
title: Eosinophil-derived neurotoxin (EDN): a biologically and analytically attractive asthma biomarker

description: There is a growing body of evidence for the utility of eosinophil-derived
 neurotoxin (EDN) as a biomarker in asthma, including association with
 eosinophilic airway inflammation, assessment of disease severity and
 potential for predicting pathogenic risks, including exacerbations.
 However, to interpret any biomarker data with confidence, it is first
 important to understand the preanalytical factors and biological variation
 that may affect its reliable measurement and results interpretation. In
 this study we defined the healthy serum EDN reference range for men and
 women as 1.98 to 26.10 ng/mL, with no significant gender differences.
 Smoking did not impact the mean EDN levels and no circadian rhythm was
 identified for EDN, unlike blood eosinophils (EOS) where levels peaked at
 00:00h. EDN expression in different cell types was investigated and shown
 to occur primarily in eosinophils, indicating they are likely to be the
 main cellular repository for EDN. We also confirm that the quantification
 of serum EDN is not influenced by the type of storage tube used, and it is
 stable at ambient temperature or when refrigerated for at least 7 days and
 for up to one year when frozen at -20°C or -80°C. In summary, EDN is a
 stable biomarker that may prove useful in precision medicine approaches by
 enabling the identification of a subpopulation of asthma patients with
 activated eosinophils and a more severe form of the disease.
description: Data was collected using a commercially available ELISA. Data
 here is that obtained from the ELISA assay. In the publication
 statistical evaluations (tests, confidence intervals,
 correlations) were based on log transformed EDN measurements, or log
 transformed eosinophil counts, due to the log-normal characteristic of
 this type of data. Presented group means and confidence intervals are
 back-transformed to linear scale. The reference interval was determined
 according to the Clinical Laboratory Standards Institutes guidance. The
 reference interval is set at 95% of the  upper and lower values measured
 from a population, meaning that the lower and upper reference limits are
 estimated as the 2.5<sup>th</sup> and
 97.5<sup>th</sup> percentile.
 Temporal changes in EDN and eosinophils were analysed using a mixed model
 for repeated measurements, with log of EDN and log of eosinophils as
 response variables, timepoint and cohort (asthma, healthy) as factors with
 interaction, and subject as a random effect to account for within-subject
 correlation.
description: Where an EDN ELISA value could not be obtained, due to a sample
 not being aquired, this is highlighted as ND in the dataset ie not
 determined.
DOI: 10.5061/dryad.1ns1rn8sj
title: Linkage of hospital records and death certificates by a search engine and machine learning: training and test set data

description: INTRODUCTION: Vital status is of central importance to hospital clinical
 research. However, hospital information systems record only in-hospital
 death information. Recently, the French government released a publicly
 available dataset containing death-certificate data for over 25 million
 individuals. The objective of this study was to link French death
 certificates to the Bordeaux University Hospital records to complete the
 vital status information. MATERIALS AND METHODS: Our linkage strategy was
 composed of a search engine to reduce the number of comparisons and
 machine-learning algorithms. The overall pipeline was evaluated by
 assembling a file containing 3,565 in-hospital deaths and 15,000 alive
 persons. RESULTS: The recall and precision of our linkage strategy were
 97.5% and 99.97% for the upper threshold and 99.4% and 98.9% for the lower
 threshold, respectively. CONCLUSION: In this article, we demonstrated the
 feasibility of accurately linking hospital records with death certificates
 using a search engine and machine learning.
description: README file included
DOI: 10.5061/dryad.0zpc866wh
title: Single molecule tracking and analysis framework including theory-predicted parameter settings

description: Imaging, tracking and analyzing individual biomolecules in living systems
 is a powerful technology to obtain quantitative kinetic and spatial
 information such as reaction rates, diffusion coefficients and
 localization maps. Common tracking tools often operate on single movies
 and require additional manual steps to analyze whole data sets or to
 compare different experimental conditions. We report a fast and
 comprehensive single molecule tracking and analysis framework (TrackIt) to
 simultaneously process several multi‐movie data sets. A user‐friendly GUI
 offers convenient tracking visualization, multiple state‐of‐the‐art
 analysis procedures, display of results, and data im‐ and export at
 different levels to utilize external software tools. We applied our
 framework to quantify dissociation rates of a transcription factor in the
 nucleus and found that tracking errors, similar to fluorophore
 photobleaching, have to be considered for reliable analysis. Accordingly,
 we developed an algorithm, which accounts for both tracking losses and
 suggests optimized tracking parameters when evaluating reaction rates. Our
 versatile and extensible framework facilitates quantitative analysis of
 single molecule experiments at different experimental conditions.
DOI: 10.5061/dryad.q573n5th7
title: Intraspecific genomic variation and local adaptation in a young hybrid species

description: Hybridization increases genetic variation, hence hybrid species may have
 greater evolutionary potential once their admixed genomes have stabilized
 and incompatibilities have been purged. Yet, little is known about how
 such hybrid lineages evolve at the genomic level following their
 formation, in particular their adaptive potential. Here we investigate how
 the Italian sparrow (Passer italiae), a homoploid hybrid species, has
 evolved and locally adapted to its variable environment. Using restriction
 site-associated DNA sequencing (RAD-seq) on several populations across the
 Italian peninsula, we evaluate how genomic constraints and novel genetic
 variation have influenced population divergence and adaptation. We show
 that population divergence within this hybrid species has evolved in
 response to climatic variation, suggesting ongoing local adaptation. As
 found previously in other non-hybrid species, climatic differences appear
 to increase population differentiation. We also report strong population
 divergence in a gene known to affect beak morphology. Most of the strongly
 divergent loci among Italian sparrow populations do not seem to be
 differentiated between its parent species, the house and Spanish sparrows.
 Unlike in the hybrid, population divergence within each of the parental
 taxa has occurred mostly at loci with high allele frequency difference
 between the parental species, suggesting that novel combinations of
 parental alleles in the hybrid have not necessarily enhanced its
 evolutionary potential. Rather, our study suggests that constraints linked
 to incompatibilities may have restricted the evolution of this admixed
 genome, both during and after hybrid species formation.
description: Genomic DNA was purified from blood samples. Double digestion of
 the genomic DNA for ddRAD sequencing was performed using EcoR I and MseI
 restriction enzymes. Molecular identifier tags were added with PCR
 amplification. Library pools were size selected for fragments between
 500-600bp. The size selected library pools were then sequenced using an
 Illumina Nextseq500 machine and the 1x75bp sequencing format. A series of
 genomic tools were used to filter raw reads and call variants, vcftools,
 plink, bcftools, GATK, among others. Here we provide
 the VCF files and final data files generated from statistical analysis. As
 well as the scripts used to analyse the data. Scripts for processing the
 raw reads to obtain final VCF are included as well as the scripts used for
 the statistical analysis and final figures found in the study. All files
 used in the R scripts are also provided.
description: The README.txt file explain the different categories of files and
 those used by the scripts.
DOI: 10.25338/b81k92
title: Sex and tissue-specific evolution of developmental plasticity in Drosophila melanogaster

description: Developmental plasticity influences the size of adult tissues in insects.
 Tissues can have unique responses to environmental perturbation during
 development, however, the prevalence of within species evolution of
 tissue-specific developmental plasticity remains unclear. To address this,
 we studied the effects of temperature and nutrition on wing and femur size
 in D. melanogaster populations from a temperate and tropical region. Wings
 were more sensitive to temperature, while wings and femurs were equally
 responsive to nutrition in both populations and sexes. The temperate
 population was larger under all conditions, except for femurs of starved
 females. In line with this, we observed greater femur size plasticity in
 response to starvation in temperate females, leading to differences in
 sexual dimorphism between populations such that the slope of the reaction
 norm of sexual dimorphism in the tropical population was double that of
 the temperate population. Lastly, we observed a significant trend for
 steeper slopes of reaction norms in temperate than in tropical females,
 but not in males. These findings highlight that plasticity divergence
 between populations can evolve heterogeneously across sexes and tissues
 and that nutritional plasticity can alter sexual dimorphism in D.
 melanogaster.
DOI: 10.5061/dryad.5x69p8d1x
title: Bedrock weathering controls on terrestrial carbon-nitrogen-climate interactions

description: Anthropogenic nitrogen deposition is widely considered to increase
 CO2 sequestration by land plant communities on a global scale.
 Here, we suggest that bedrock nitrogen weathering contributes
 significantly more to nitrogen-carbon interactions than anthropogenic
 nitrogen deposition. This working hypothesis is based on the application
 of empirical results into a global biogeochemical simulation model from
 the mid-1800s to the end of the 21st century. We demonstrate that rock
 nitrogen inputs have contributed roughly 2 to 11 times more to net primary
 productivity gains than nitrogen deposition since pre-industrial times.
 Projections based on RCP 8.5 show that rock nitrogen inputs and biological
 nitrogen fixation contribute 2 to 5 times more to terrestrial carbon
 uptake than anthropogenic nitrogen deposition through year 2101. The
 enhancement of carbon uptake via rock nitrogen weathering partially
 resolves nitrogen-carbon discrepancies in Earth system models and offers
 an alternative explanation for lack of progressive nitrogen limitation in
 the terrestrial biosphere. We conclude that natural N inputs
 impart major control over terrestrial CO2 sequestration in Earth’s
 ecosystems.
DOI: 10.15468/dl.58672u
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Palandra aequatorialis"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002678-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.w3r2280pg
title: Testing the multiple stressor hypothesis: chlorothalonil exposure alters transmission potential of a bumblebee pathogen but not individual host health

description: Numerous threats to pollinator health are putting pollinator populations
 and their essential ecosystem services in jeopardy. Although individual
 threats are widely studied, their co-occurrence may exacerbate negative
 effects, as posited by the multiple stressor hypothesis. A prominent
 branch of this hypothesis concerns pesticide-pathogen co-exposure. A
 landscape analysis in bumble bees (Bombus spp.) demonstrated a positive
 association between local use of the fungicide chlorothalonil and
 prevalence of a microsporidian pathogen Nosema bombi in
 declining species. This is suggestive of an interaction, but causation
 needs establishing. We tested the multiple stressor hypothesis with
 field-realistic chlorothalonil and N. bombi exposures in
 worker-produced B. impatiens microcolonies.
 Chlorothalonil was not avoided in preference assays, setting the stage for
 co-exposure. However, contrary to the multiple stressor hypothesis,
 pathogen and pesticide co-exposure did not affect survival. Bees in this
 study showed a surprising level of tolerance to N.
 bombi infection, which also did not differ between chlorothalonil
 and control treatments. However, transmission-ready spore loads were
 higher in infected bees previously exposed to the fungicide. Thus,
 co-exposure could have consequences for pathogen dynamics in host
 communities. This underlines the importance of considering both within-
 and between-host processes when addressing the multiple stressor
 hypothesis in relation to pathogens.
description: See the uploaded README
 file (READ_ME_Calhoun_et_al_Chlorothalonil_Nosema.txt).