cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3338c
title: Data from: Neurofunctional abnormalities during sustained attention in severe childhood abuse

description: Childhood maltreatment is associated with adverse affective and cognitive
 consequences including impaired emotion processing, inhibition and
 attention. However, the majority of functional magnetic resonance imaging
 (fMRI) studies in childhood maltreatment have examined emotion processing,
 while very few studies have tested the neurofunctional substrates of
 cognitive functions and none of attention. This study investigated the
 association between severe childhood abuse and fMRI brain activation
 during a parametric sustained attention task with a progressively
 increasing load of sustained attention in 21 medication-naïve, drug-free
 young people with a history of childhood abuse controlling for psychiatric
 comorbidities by including 19 psychiatric controls matched for psychiatric
 diagnoses, and 27 healthy controls. Behaviorally, the participants exposed
 to childhood abuse showed increased omission errors in the task which
 correlated positively trend-wise with the duration of their abuse.
 Neurofunctionally, the participants with a history of childhood abuse, but
 not the psychiatric controls, displayed significantly reduced activation
 relative to the healthy controls during the most challenging attention
 condition only in typical attention regions including left inferior and
 dorsolateral prefrontal cortex, insula and temporal areas. We therefore
 show for the first time that severe childhood abuse is associated with
 neurofunctional abnormalities in key ventral frontal-temporal sustained
 attention regions. The findings represent a first step towards the
 delineation of abuse-related neurofunctional abnormalities in sustained
 attention, which may help in the development of effective treatments for
 victims of childhood abuse.
description: SATdata_AbuseThis file contains the fMRI data (DICOM images) for the abuse group.SATdata_HCThis file contains the fMRI data (DICOM images) for the healthy control group.SATdata_PCThis file contains the fMRI data (DICOM images) for the psychiatric control group.
DOI: 10.5061/dryad.kc596
title: Data from: Theoretical models of the influence of genomic architecture on the dynamics of speciation

description: A long-standing problem in evolutionary biology has been determining
 whether and how gradual, incremental changes at the gene level can account
 for rapid speciation and bursts of adaptive radiation. Using genome-scale
 computer simulations, we extend previous theory showing how gradual
 adaptive change can generate nonlinear population transitions, resulting
 in the rapid formation of new, reproductively isolated species. We show
 that these transitions occur via a mechanism rooted in a basic property of
 biological heredity: the organization of genes in genomes. Genomic
 organization of genes facilitates two processes: (i) the buildup of
 statistical associations among large numbers of genes, and (ii) the action
 of divergent selection on persistent combinations of alleles. When a
 population has accumulated a critical amount of standing, divergently
 selected variation, the combination of these two processes allows many
 mutations of small effect to act synergistically and precipitously split
 one population into two discontinuous, reproductively isolated groups.
 Periods of allopatry, chromosomal linkage among loci, and large-effect
 alleles can facilitate this process under some conditions, but are not
 required for it. Our results complement and extend existing theory on
 alternative stable states during population divergence, distinct phases of
 speciation, and the rapid emergence of multilocus barriers to gene flow.
 The results are thus a step toward aligning population genomic theory with
 modern empirical studies.
description: DatafileThis file is a .zip compressed archive containing subdirectories each having raw data and analysis scripts for producing the 7 figures in the paper.Flaxman_et_al_2014_MolEcol_DataPackage.zip
DOI: 10.15468/dl.bn7v7s
title: Occurrence Download

description: A dataset containing 314 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Glyptodon reticulatus"
 ]
}

 The dataset includes 314 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000448-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gj8sg9
title: Occurrence Download

description: A dataset containing 844 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "GadmGid is USA.24.74_1",
 "Geometry POLYGON((-94.36682 45.48562,-94.36308 45.46474,-94.35538 45.46751,-94.34404 45.4732,-94.33276 45.47342,-94.33168 45.48248,-94.3486 45.48036,-94.35169 45.48628,-94.36682 45.48562))",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 844 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000446-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4bupxa
title: Occurrence Download

description: A dataset containing 1260 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-80.08668 -5.46387,-81.10217 -6.45995,-82.72922 -17.1921,-66.01793 -19.09304,-64.30595 -33.81215,-66.38019 -37.7482,-52.22092 -27.16284,-54.68003 -23.17777,-44.57757 -9.63809,-41.89961 -5.14711,-41.27856 -3.55004,-40.05324 1.35594,-50.09326 2.30652,-50.46121 5.21998,-58.4935 10.39002,-80.08668 8.76725,-80.08668 -5.46387))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pygocentrus nattereri"
 ]
}

 The dataset includes 1260 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000444-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n3s7d
title: Data from: Only accessible information is useful: insights from gradient-mediated patterning

description: Information theory is gaining popularity as a tool to characterise
 performance of biological systems. However, information is commonly
 quantified without reference to whether or how a system could extract and
 use it; as a result, information-theoretic quantities are easily
 misinterpreted. Here we take the example of pattern-forming developmental
 systems which are commonly structured as cascades of sequential gene
 expression steps. Such a multi-tiered structure appears to constitute
 sub-optimal use of the positional information provided by the input
 morphogen because noise is added at each tier. However, one must
 distinguish between the total information in a morphogen and information
 that can be usefully extracted and interpreted by downstream elements. We
 demonstrate that quantifying the information that is accessible to the
 system naturally explains the prevalence of multi-tiered network
 architectures as a consequence of the noise inherent to the control of
 gene expression. We support our argument with empirical observations from
 patterning along the major body axis of the fruit fly embryo. We use this
 example to highlight the limitations of the standard information-theoretic
 characterisation of biological signaling, which are frequently
 de-emphasized, and illustrate how they can be resolved.
description: Data and scripts -
 Master fileThe raw imaging data
 (Leica SP5) and MatLab analysis scripts reproducing all data-dependent
 figures in the paper (Fig. 4 and Supplementary Figures S1, S2 and S3).
 Archive split into volumes to keep file size under 1Gb. Download all
 files, unzip, then run "RUN_ME.m" in Matlab to process the data
 and generate all the figures. Data acquired by Shawn C. Little, analysis
 scripts by Mikhail Tikhonov.data_and_scripts.zipData and scripts - Archive Volume 2Volume 2 of a split zip archivedata_and_scripts.z01Data and scripts - Archive Volume 3Volume 3 of a split zip archivedata_and_scripts.z02Data and scripts - Archive Volume 4Volume 4 of a split zip archivedata_and_scripts.z03
DOI: 10.15468/dl.hzqrj3
title: Occurrence Download

description: A dataset containing 4981 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus pseudostrobus"
 ]
}

 The dataset includes 4981 records from 159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000445-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.r36sg
title: Data from: Positive selection in coding regions and motif duplication in regulatory regions of bottlenose dolphin MHC class II genes

description: The vertebrate immune response is mediated through highly adaptive,
 quickly evolving cell surface receptors, the major histocompatibility
 complex (MHC). MHC molecules bind and present a diverse array of
 pathogenic molecules and trigger a cascade of defenses. Use of MHC
 variation as a marker for population health has also evolved quickly
 following advances in sequencing methods. We applied a combination of
 traditional and next generation sequencing methodology to characterize
 coding (peptide binding region) and regulatory (proximal promoter)
 sequence variation in MHC Class II DQA and DQB genes between estuarine and
 coastal populations of the bottlenose dolphin, Tursiops truncatus, an apex
 predator whose health status is indicative of anthropogenic impacts on the
 ecosystem. The coding regions had 10 alleles each at DQA and DQB; the
 promoters had 6 and 7 alleles at DQA and DQB, respectively with variation
 within key regulatory motifs. Positive selection was observed for the
 coding regions of both genes while both coding and promoter regions
 exhibited geographic differences in allele composition that likely
 indicates diversifying selection across habitats. Most notable was the
 discovery of a complete duplication of a 14-bp T-box motif in the DQA
 promoter. Four class II promoter regions (DQA, DQB, DRA, DRB) were
 characterized in species from four cetacean families (Delphinidae,
 Monodontidae, Lipotidae, and Physeteridae) and revealed substantial
 promoter structural diversity across this order. Peptide binding regions
 may not be the only source of adaptive potential within cetacean MHC for
 responding to pathogenic threats. These findings are the first analysis of
 cetacean MHC regulatory motifs, which may divulge unique immunogenetic
 strategies among cetaceans and reveal how MHC transcriptional control
 continues to evolve. The combined MHC regulatory and coding data provide
 new genetic context for distinct vulnerability profiles between coastal
 and estuarine populations, which are key concerns for health and risk
 management.
description: Ion Torrent fastq data
 for dolphin DQA and DQBThe MHC class II genes,
 DQA and DQB, were PCR amplified in 95 bottlenose dolphins from Florida
 Atlantic coastal and estuarine habitats. The proximal promoter and peptide
 binding regions from both genes were amplified with barcoded primers and
 products were ~350 bp. Samples were pooled and sequenced on Ion Torrent
 PGM using a 318 chip. See the README file for barcode and sample
 information.R_2013_09_26_15_29_01_user_LIL-34_OCorry-Crowe_Pagan_Auto_user_LIL-34_OCorry-Crowe_Pagan_65.fastq.fastq
DOI: 10.5061/dryad.c2124
title: Data from: Signatures of diversifying selection in European pig breeds

description: [No abstract entered]
description: Porcine_60K_Data_Wilkinsonetal2013.tarMapping and variant calling data on SSC5:98000000-99000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_98000000-99000000.tarMapping and variant calling data on SSC5:3100000-34000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_3100000-34000000.tarMapping and variant calling data on SSC11:53500000-55500000SSC11_53500000-55500000.tar
DOI: 10.5061/dryad.2t8n4sd
title: Data from: Ninety years of change on a Low Wooded Island, Great Barrier Reef

description: We assess ninety years of change on a Low Wooded Island (Low Isles, Great
 Barrier Reef), employing drones and topographic profiling to accurately
 survey ramparts, mangroves, the reef flat and the sand cay. A comparison
 with maps from the 1928-29 Great Barrier Reef Expedition revealed the
 redistribution of an outer rampart and inward movement of shingle ridges.
 Remarkable lateral expansion of the mangrove woodland some 400 m has
 occurred as carbonate sand deposition has increased reef flat elevation,
 obscuring coral microatolls. The sand cay has stayed relatively constant
 in size, moving 44 m in a north-easterly direction and rotating slightly.
 We conclude that the existing configuration of landforms likely represents
 an equilibrium with local biophysical conditions, including sea level,
 wave dynamics, vegetation growth and storms and cyclones. The variable
 nature of ramparts and the presence of a trough that prevents the
 continuous spread of mangroves across a uniformly flat colonisation
 surface precludes the interpretation of landform changes with respect to a
 geomorphic evolutionary sequence. Moreover, longer-term implications of
 environmental change for these landforms can only be evaluated once the
 specific nature of the local carbonate budget, including the relative
 contribution of corals, foraminifera and Halimeda has been elucidated.
description: Drone image mosaic and
 topographic profilesAn orthomosaic of drone
 images and a series of five topographic profilesLow_isles_change_data.zip
DOI: 10.5061/dryad.6nv2t4p
title: Data from: Modern spandrels: the roles of genetic drift, gene flow and natural selection in the formation of parallel clines

description: Urban environments offer the opportunity to study the role of adaptive and
 non-adaptive evolutionary processes on an unprecedented scale. While the
 presence of parallel clines in heritable phenotypic traits is often
 considered strong evidence for the role of natural selection, non-adaptive
 evolutionary processes can also generate clines, and this may be more
 likely when traits have a non-additive genetic basis due to epistasis. In
 this paper, we use spatially-explicit simulations modelled according to
 the cyanogenesis (HCN) polymorphism in white clover (Trifolium repens) to
 examine the formation of phenotypic clines along urbanization gradients
 under varying levels of drift, gene flow and selection. HCN results from
 an epistatic interaction between two Mendelian-inherited loci. Our results
 demonstrate that the genetic architecture of this trait makes natural
 populations susceptible to decreases in HCN frequencies via drift.
 Gradients in the strength of drift across a landscape resulted in
 phenotypic clines with lower frequencies of HCN in strongly drifting
 populations, giving the misleading appearance of deterministic adaptive
 changes in the phenotype. Studies of heritable phenotypic change in urban
 populations should generate null models of phenotypic evolution based on
 the genetic architecture underlying focal traits prior to invoking
 selection’s role in generating adaptive differentiation.
description: Santangelo-et-al_Proc-B_2018_Raw-data-example This zipped folder contains example raw data files. There are multiple subdirectories, each of which contains multiple data files in .csv format. The README.md file within the zipped folder describes the subdirectories and data files in detail.   Santangelo-et-al_Proc-B_2018_Summary-datasets This zipped folder contains the summary datasets used in generating the results for the manuscript. There are multiple subdirectories, each of which contains multiple data files in .csv format. The README.md file within the zipped folder describes the subdirectories and data files in detail.   All code used in generating the projects data is available on this GitHub repository
DOI: 10.5061/dryad.mb463
title: Data from: Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420

description: Antibiotic resistance is one of the biggest threats to human health
 globally. Alarmingly, multidrug-resistant and extensively drug-resistant
 Mycobacterium tuberculosis have now spread worldwide. Some key
 antituberculosis antibiotics are prodrugs, for which resistance mechanisms
 are mainly driven by mutations in the bacterial enzymatic pathway required
 for their bioactivation. We have developed drug-like molecules that
 activate a cryptic alternative bioactivation pathway of ethionamide in M.
 tuberculosis, circumventing the classic activation pathway in which
 resistance mutations have now been observed. The first-of-its-kind
 molecule, named SMARt-420 (Small Molecule Aborting Resistance), not only
 fully reverses ethionamide-acquired resistance and clears
 ethionamide-resistant infection in mice, it also increases the basal
 sensitivity of bacteria to ethionamide.
description: BCG_DMSO.fastqPart 1 of Databases S1 (transcriptomic data) BCG_DMSO.fastqBCG_BDM41906.fastqPart 2 of Databases S1 (transcriptomic data) BCG_BDM41906.fastqBCG_SMARt-420.fastqPart 3 of Databases S1 (transcriptomic data) BCG_SMARt-420.fastq
DOI: 10.5061/dryad.c0t6s
title: Data from: The breakdown of genomic ancestry blocks in hybrid lineages given a finite number of recombination sites

description: When a lineage originates from hybridization genomic blocks of contiguous
 ancestry from different ancestors are fragmented through genetic
 recombination. The resulting blocks are delineated by so called
 “junctions”, which accumulate with every generation that passes. Modeling
 the accumulation of ancestry block junctions can elucidate processes and
 timeframes of genomic admixture. Previous models have not addressed
 ancestry block dynamics for chromosomes that consist of a finite number of
 recombination sites. However, genomic data typically consist of
 informative markers that are interspersed with fragments for which no
 ancestry information is available. Hence, repeated recombination events
 may occur between markers, effectively removing existing junctions. Here,
 we present an analytical treatment of the dynamics of the mean number of
 junctions over time, taking into account the number of recombination sites
 per chromosome, population size, genetic map length and the frequency of
 the ancestral species in the founding hybrid swarm. We describe the
 expected number of junctions using equidistant molecular markers and
 estimate the number of junctions using random markers. This extended
 theory of junctions thus reflects properties of empirical data and can
 serve to study the genomic patterns following admixture.
description: README_SupplementOverall README of the contents of all files on dryad for 'The breakdown of genomic ancestry bocks in hybrid lineages given a finite number of recombination sites'Supplementary InformationThe file ‘Supplementary Information.pdf’ contains the following subjects: 1) Deriving the maximum accurate time 2) The effect of non-uniform recombination rate 3) Graphical proof analogous to figure 2, but for random markers 4) Simulations of variation in the number of junctionsFigure_2_dataFiles and R scripts used to create figure 2Figure_3R code to reproduce figure 3Figure_4_dataFiles and data used to create figure 4Figure_5_dataFiles and data used to create figure 5Figure_6_dataFiles and data used to create figure 6 and figure S3.Figure_S2_dataFiles and data used to create figure S2Figure_S4_dataFiles and data used to create figure S4Standalone CodeFor those not willing or able to install the R package ‘junctions’ from CRAN, we provide stand-alone code. The code is accompanied by a walkthrough vignette.
DOI: 10.5061/dryad.qm44087
title: Data from: Human-like Cmah inactivation in mice increases running endurance and decreases muscle fatigability: implications for human evolution

description: Compared to other primates, humans are exceptional long-distance runners,
 a feature that emerged in genus Homo ~2 million years ago (mya) and is
 classically attributed to anatomical and physiological adaptations such as
 an enlarged gluteus maximus and improved heat dissipation. However, no
 underlying genetic changes have currently been defined. Two-three mya, an
 exon deletion in the CMP-Neu5Ac Hydroxylase (CMAH) gene also became fixed
 in our ancestral lineage. Cmah loss in mice exacerbates disease severity
 in multiple mouse models for muscular dystrophy, a finding only partially
 attributed to differences in immune reactivity. We evaluated the exercise
 capacity of Cmah-/- mice and observed an increased performance during
 forced treadmill testing and after 15 days of voluntary wheel running.
 Cmah-/- hindlimb muscle exhibited more capillaries and a greater fatigue
 resistance in situ. Maximal coupled respiration was also higher in Cmah
 null mice ex vivo and relevant differences in metabolic pathways were also
 noted. Taken together, these data suggest that CMAH loss contributes to an
 improved skeletal muscle capacity for oxygen utilization. If translatable
 to humans, CMAH loss could have provided a selective advantage for
 ancestral Homo during the transition from forest dwelling to increased
 resource exploration and hunter/gatherer behavior in the open savannah.
description: Metabolomics
 dataMetabolomics of the
 soleus (~20mg) from WT vs Cmah null mice with or without 15 days of
 voluntary exercise training. This data was generated by the West Coast
 Metabolomics Center at UC Davis.Metabolomics.csvNanozoom images part 1Raw images with lead ATPase staining used to determine capillary densityNanozoom_images_1.zipNanozoom_images_2Nanozoom_images_3Nanozoom_images_4