cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t47g3
title: Data from: Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci

description: Background: The adaptive immune system generates a remarkable range of
 antigen-specific T-cell receptors (TCRs), allowing the recognition of a
 diverse set of antigens. Most of this diversity is encoded in the
 complementarity determining region 3 (CDR3) of the β chain of the αβ TCR,
 which is generated by somatic recombination of noncontiguous variable (V),
 diversity (D), and joining (J) gene segments. Deletion and non-templated
 insertion of nucleotides at the D-J and V-DJ junctions further increases
 diversity. Many of these gene segments are annotated as non-functional
 owing to defects in their primary sequence, the absence of motifs
 necessary for rearrangement, or chromosomal locations outside the TCR
 locus. Methods: We sought to utilize a novel method, based on
 high-throughput sequencing of rearranged TCR genes in a large cohort of
 individuals, to evaluate the use of functional and non-functional alleles.
 We amplified and sequenced genomic DNA from the peripheral blood of 587
 healthy volunteers using a multiplexed polymerase chain reaction assay
 that targets the variable region of the rearranged TCRβ locus, and we
 determined the presence and the proportion of productive rearrangements
 for each TCRβ V gene segment in each individual. We then used this
 information to annotate the functional status of TCRβ V gene segments in
 this cohort. Results: For most TCRβ V gene segments, our method agrees
 with previously reported functional annotations. However, we identified
 novel non-functional alleles for several gene segments, some of which were
 used exclusively in our cohort to the detriment of reported functional
 alleles. We also saw that some gene segments reported to have both
 functional and non-functional alleles consistently behaved in our cohort
 as either functional or non-functional, suggesting that some reported
 alleles were not present in the population studied. Conclusions: In this
 proof-of-principle study, we used high-throughput sequencing of the TCRβ
 locus of a large cohort of healthy volunteers to evaluate the use of
 functional and non-functional alleles of individual TCRβ V gene segments.
 With some modifications, our method has the potential to be extended to
 gene segments in the α, γ, and δ TCR loci, as well as the genes encoding
 for B-cell receptor chains.
description: hip-samplesThe zipped file contains 587 .tsv files, one each for each of the 587 subjects included in the study. Each .tsv file (named with the unique identifier for that subject, for example HIPNNNN.tsv) contains a row for each unique nucleotide sequence identified in the analysis. Column titles are defined in the attached ReadMe.
DOI: 10.5061/dryad.8tn4660
title: Data from: An automated approach to the quantitation of vocalizations and vocal learning in the songbird.

description: Studies of learning mechanisms critically depend on the ability to
 accurately assess learning outcomes. This assessment can be impeded by the
 often complex, multidimensional nature of behavior. We present a novel,
 automated approach to evaluating imitative learning. Conceptually, our
 approach estimates how much of the content present in a reference behavior
 is absent from the learned behavior. We validate our approach through
 examination of songbird vocalizations, complex learned behaviors the study
 of which has provided many insights into sensory-motor learning in general
 and vocal learning in particular. Historically, learning has been
 holistically assessed by human inspection or through comparison of
 specific song features selected by experimenters (e.g. fundamental
 frequency, spectral entropy). In contrast, our approach uses statistical
 models to broadly capture the structure of each song, and then estimates
 the divergence between the two models. We show that our measure of song
 learning (Song Divergence) is well correlated with human evaluation of
 song learning. We then expand the analysis beyond learning and show that
 Song Divergence also detects the typical song deterioration that occurs
 following deafening. Finally, we illustrate how this measure can be
 extended to quantify differences in other complex behaviors such as human
 speech and handwriting. This approach potentially provides a framework for
 assessing learning across a broad range of behaviors like song that can be
 described as a set of discrete and repeated motor actions.
description: Vocalization data for
 assessing the utility of the measure Song Divergence.This is a compressed
 archive of the vocalization data used in evaluating the utility of
 'Song Divergence'.pcb_data.tar.gz
DOI: 10.5061/dryad.b4q8k
title: Data from: White matter alterations in Parkinson's disease with normal cognition precede grey matter atrophy

description: Introduction: While progressive MRI brain changes characterize advanced
 Parkinson's disease (PD), little has been discovered about structural
 alterations in the earliest phase of the disease, i.e. in patients with
 motor symptoms and with normal cognition. Our study aimed to detect grey
 matter (GM) and white matter (WM) changes in PD patients without cognitive
 impairment. Methods: Twenty PD patients and twenty-one healthy controls
 (HC) were tested for attention, executive function, working memory, and
 visuospatial and language domains. High-resolution T1-weighted and 60
 directional diffusion-weighted 3T MRI images were acquired. The cortical,
 deep GM and WM volumes and density, as well as the diffusion properties of
 WM, were calculated. Analyses were repeated on data flipped to the side of
 the disease origin. Results: PD patients did not show any significant
 differences from HC in cognitive functioning or in brain volumes.
 Decreased GM intensity was found in the left superior parietal lobe in the
 right (p&lt;0.02) and left (p&lt;0.01) flipped data. The analysis
 of original, un-flipped data demonstrated elevated axial diffusivity
 (p&lt;0.01) in the superior and anterior corona radiata, internal
 capsule, and external capsule in the left hemisphere of PD relative to HC,
 while higher mean and radial diffusivity were discovered in the right
 (p&lt;0.02 and p&lt;0.03, respectively) and left (p&lt;0.02
 and p&lt;0.02, respectively) in the fronto-temporal WM utilizing
 flipped data. Conclusions: PD patients without cognitive impairment and GM
 atrophy demonstrated widespread alterations of WM microstructure. Thus, WM
 impairment in PD might be a sensitive sign preceding the neuronal loss in
 associated GM regions.
description: MRI data from control
 and Parkinson's subjectsThe file
 Vanicek_etal_MRI_data.tar extracts to a folder called
 Vanicek_etal_MRI_data. Within this folder are two sub-directories. MRI
 data for control subjects (c_NN) are located in the sub-directory Control,
 and MRI data for subjects diagnosed with Parkinson's (p_NN) are in
 the sub-directory Parkinsons.Vanicek_etal_MRI_data.tar
DOI: 10.5061/dryad.5d5b3
title: Data from: Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

description: Ongoing speciation in most African malaria vectors gives rise to cryptic
 populations, which differ remarkably in their behaviour, ecology and
 capacity to vector malaria parasites. Understanding the population
 structure and the drivers of genetic differentiation among mosquitoes is
 crucial for effective disease control because heterogeneity within species
 contribute to variability in malaria cases and allow fractions of vector
 populations to escape control efforts. To examine the population structure
 and the potential impacts of recent large-scale control interventions, we
 have investigated the genomic patterns of differentiation in mosquitoes
 belonging to the Anopheles nili group — a large taxonomic group that
 diverged ~3Myr ago. Using 4343 single nucleotide polymorphisms (SNPs), we
 detected strong population structure characterized by high FST values
 between multiple divergent populations adapted to different habitats
 within the Central African rainforest. Delineating the cryptic species
 within the Anopheles nili group is challenging due to incongruence between
 morphology, ribosomal DNA and SNP markers consistent with incomplete
 lineage sorting and/or interspecific gene flow. A very high proportion of
 loci are fixed (FST = 1) within the genome of putative species, which
 suggests that ecological and/or reproductive barriers are maintained by
 strong selection on a substantial number of genes.
description: Information on Anopheles
 nili samples sequenced from CameroonAn_nili_datafile.xlsxIndividual fastq files for Anopheles nili from CameroonAnopheles_nili_fastq.tar.gz
DOI: 10.5061/dryad.gb291
title: Data from: Proteome-wide lysine acetylation in cortical astrocytes and alterations that occur during infection with brain parasite Toxoplasma gondii

description: Lysine acetylation is a reversible post-translational modification (PTM)
 that has been detected on thousands of proteins in nearly all cellular
 compartments. The role of this widespread PTM has yet to be fully
 elucidated, but can impact protein localization, interactions, activity,
 and stability. Here we present the first proteome-wide survey of lysine
 acetylation in cortical astrocytes, a subtype of glia that is a component
 of the blood-brain barrier and a key regulator of neuronal function and
 plasticity. We identified 529 lysine acetylation sites across 304 proteins
 found in multiple cellular compartments that largely function in RNA
 processing/transcription, metabolism, chromatin biology, and translation.
 Two hundred and seventy-seven of the acetylated lysines we identified on
 186 proteins have not been reported previously in any other cell type. We
 also mapped an acetylome of astrocytes infected with the brain parasite,
 Toxoplasma gondii. It has been shown that infection with T. gondii
 modulates host cell gene expression, including several lysine
 acetyltransferase (KAT) and deacetylase (KDAC) genes, suggesting that the
 host acetylome may also be altered during infection. In the T.
 gondii-infected astrocytes, we identified 34 proteins exhibiting a level
 of acetylation &gt;2-fold and 24 with a level of acetylation
 &lt;2-fold relative to uninfected astrocytes. Our study documents the
 first acetylome map for cortical astrocytes, uncovers novel lysine
 acetylation sites, and demonstrates that T. gondii infection produces an
 altered acetylome.
description: 031314_21886_MS_v.mzXML.zip031314_21886_MS_v031314_21887_MS_v.mzXML031314_21887_MS_v031314_21888_MS_v.mzXML031314_21888_MS_v031314_21889_MS_v.mzXML031314_21889_MS_vmzXML filesRAW filesThe RAW files in this dataset can be converted to .mzXML using Proteowizard (available at http://proteowizard.sourceforge.net) and then viewed using Skyline (available through MacCoss Lab at https://skyline.gs.washington.edu/labkey/project/home/begin.view).
DOI: 10.15468/dl.ssvb5k
title: Occurrence Download

description: A dataset containing 64488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2026-01-01",
 "EventDate is less than or equal to 2026-01-31",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 },
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 64488 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000409-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.10f4p
title: Data from: The role of plasma and urine metabolomics in identifying new biomarkers in severe newborn asphyxia: a study of asphyxiated newborn pigs following cardiopulmonary resuscitation

description: Background: Optimizing resuscitation is important to prevent morbidity and
 mortality from perinatal asphyxia. The metabolism of cells and tissues is
 severely disturbed during asphyxia and resuscitation, and metabolomic
 analyses provide a snapshot of many small molecular weight metabolites in
 body fluids or tissues. In this study metabolomics profiles were studied
 in newborn pigs that were asphyxiated and resuscitated using different
 protocols to identify biomarkers for subject characterization,
 intervention effects and possibly prognosis. Methods: A total of 125
 newborn Noroc pigs were anesthetized, mechanically ventilated and
 inflicted progressive asphyxia until asystole. Pigs were randomized to
 resuscitation with a FiO2 0.21 or 1.0, different duration of ventilation
 before initiation of chest compressions (CC), and different CC to
 ventilation ratios. Plasma and urine samples were obtained at baseline,
 and 2 h and 4 h after return of spontaneous circulation (ROSC, heart rate
 &gt; = 100 bpm). Metabolomics profiles of the samples were analyzed by
 nuclear magnetic resonance spectroscopy. Results: Plasma and urine showed
 severe metabolic alterations consistent with hypoxia and acidosis 2 h and
 4 h after ROSC. Baseline plasma hypoxanthine and lipoprotein
 concentrations were inversely correlated to the duration of hypoxia
 sustained before asystole occurred, but there was no evidence for a
 differential metabolic response to the different resuscitation protocols
 or in terms of survival. Conclusions: Metabolic profiles of asphyxiated
 newborn pigs showed severe metabolic alterations. Consistent with
 previously published reports, we found no evidence of differences between
 established and alternative resuscitation protocols. Lactate and pyruvate
 may have a prognostic value, but have to be independently confirmed.
description: MetadataTabular data. Animal ID, intervention group, time under hypoxia, time to ROSC.NMR-Spectra-002-0351H NMR spectra in raw Bruker format. Part 1 / 5.NMR-Spectra-036-0591H NMR spectra in raw Bruker format. Part 2 / 5.NMR-Spectra-060-0801H NMR spectra in raw Bruker format. Part 3 / 5.NMR-Spectra-081-1041H NMR spectra in raw Bruker format. Part 4 / 5.NMR-Spectra-105-1251H NMR spectra in raw Bruker format. Part 5 / 5.
DOI: 10.5061/dryad.40c7c
title: Data from: Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites

description: Single nucleotide polymorphisms (SNPs) are replacing microsatellites for
 population genetic analyses, but it is not apparent how many SNPs are
 needed or how well SNPs correlate with microsatellites. We used data from
 the gopher tortoise, Gopherus polyphemus—a species with small populations,
 to compare SNPs and microsatellites to estimate population genetic
 parameters. Specifically, we compared one SNP data set (16 tortoises from
 four populations sequenced at 17 901 SNPs) to two microsatellite data
 sets, a full data set of 101 tortoises and a partial data set of 16
 tortoises previously genotyped at 10 microsatellites. For the full
 microsatellite data set, observed heterozygosity, expected heterozygosity
 and FST were correlated between SNPs and microsatellites; however, allelic
 richness was not. The same was true for the partial microsatellite data
 set, except that allelic richness, but not observed heterozygosity, was
 correlated. The number of clusters estimated by structure differed for
 each data set (SNPs = 2; partial microsatellite = 3; full microsatellite =
 4). Principle component analyses (PCA) showed four clusters for all data
 sets. More than 800 SNPs were needed to correlate with allelic richness,
 observed heterozygosity and expected heterozygosity, but only 100 were
 needed for FST. The number of SNPs typically obtained from next-generation
 sequencing (NGS) far exceeds the number needed to correlate with
 microsatellite parameter estimates. Our study illustrates that diversity,
 FST and PCA results from microsatellites can mirror those obtained with
 SNPs. These results may be generally applicable to small populations, a
 defining feature of endangered and threatened species, because theory
 predicts that genetic drift will tend to outweigh selection in small
 populations.
description: ALL-samples-Q30-snps-recal-beagle-polymorphic.vcfVariant call format (VCF) file for 16 Gopherus polyphemus samples for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2016) Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites. Molecular Ecology Resources. For detailed steps on how this file was created see: https://github.com/jelber2/immunome_2014/blob/master/README.mdALL-samples-recal03.bamBinary alignment map (BAM) file for 16 Gopherus polyphemus samples for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2016) Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites. Molecular Ecology Resources. For detailed steps on how this file was created see: https://github.com/jelber2/immunome_2014/blob/master/README.md
DOI: 10.5061/dryad.5ng71
title: Data from: Niche evolution and thermal adaptation in the temperate species Drosophila americana

description: The study of ecological niche evolution is fundamental for understanding
 how the environment influences species’ geographical distributions and
 their adaptation to divergent environments. Here we present a study of the
 ecological niche, demographic history and thermal performance (locomotor
 activity, developmental time and fertility/viability) of the temperate
 species Drosophila americana and its two chromosomal forms. Temperature is
 the environmental factor that contributes most to the species’ and
 chromosomal forms’ ecological niches, although precipitation is also
 important in the model of the southern populations. The past distribution
 model of the species predicts a drastic reduction in the suitable area for
 the distribution of the species during the Last Glacial Maximum (LGM),
 suggesting a strong bottleneck. However, DNA analyses did not detect a
 bottleneck signature during the LGM. These contrasting results could
 indicate that D. americana niche preference evolves with environmental
 change and, thus, there is no evidence to support niche conservatism in
 this species. Thermal performance experiments show no difference in the
 locomotor activity across a temperature range of 15 to 38oC between flies
 from the north and the south of its distribution. However, we found
 significant differences in developmental time and fertility/viability
 between the two chromosomal forms at the model’s optimal temperatures for
 the two forms. However, results do not indicate that they perform better
 for the traits studied here in their respective optimal niche
 temperatures. This suggests that behaviour plays an important role in
 thermoregulation, supporting the capacity of this species to adapt to
 different climatic conditions across its latitudinal distribution.
description: sequence
 alignmentsNexus alignments of the
 16 genes used in the studysequences.zipchrom2-3 final runThis folder contains the xml file used as input in BEAST analysis plus the trees and csv files from the runsLogCombined run filesThis folder contains the xml, trees, csv and log files resulting from combining the two independent BEAST runs with LogCombinerLogCombined_final_runs.zipchrom2-3 final run 2This folder contains the xml file used as input in the second BEAST run plus the trees and csv output filesD_americana average ENMThis folder contains the results from Maxent analysis for the whole species; average from 10 replicatesD_americana average cold ENMThis folder contains mxd, csv and plots resulting from te maxent analysis using cold-related variablesD_a_americana cold ENMMaxent results for the D. a. americana chromosomal form using the cold-related variablesD_a_americana ENMMaxent modelling results for the D. a. americana chromosomal form.D_a_texana cold ENMMaxent modelling results for the D. a. texana chromosomal form using cold-realted variables.D_a_texana ENMMaxent results for D. a. texana chromosomal form.
DOI: 10.5061/dryad.4gb62
title: Data from: A suite of potentially amplifiable microsatellite loci for ten reptiles of conservation concern from Africa and Asia

description: Here we document the addition of thousands of potentially amplifiable
 microsatellite loci (PALs) and associated primer sequences for public use.
 We conducted whole-genome shotgun sequencing to obtain ultra-low coverage,
 random genomic sampling from ten African and Asian squamate reptile
 species (representing ten genera). We used unique genomic processing
 methods and generated PALs for the following species: Acrochordus
 granulatus, Ahaetulla prasina, Cerberus rhynchops, Gonocephalus kuhlii,
 Ophiophagus hannah, Python bivittatus, Tribolonotus gracilis, Trimeresurus
 sabahi (Popeia sabahi), Uromastyx geryi and Varanus exanthematicus. All
 taxa included, as well as other related taxa not included in our study,
 are exploited heavily by the international skin and pet trades, yet
 researchers and conservation agencies currently lack substantial genetic
 resources for guiding conservation and management. Using stringent
 filtering methods, we generated between 467 and 8641 PALs for each of the
 ten species (52,164 PALs total), yielding a rich database of
 microsatellite loci and amplification primers for these taxa. In addition
 to the ten species targeted in our study, microsatellite markers provided
 in this database can likely be applied to a variety of closely related
 taxa that are also of conservation and commercial interest.
description: PALsPAL files are provided
 for each species described in the publication in text
 format.A_gran_readsA_pras_readsC_rhyn_readsG_kuhl_readsT_grac_readsT_saba_readsU_geyr_readsV_exan_reads