cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t6d23
title: Data from: Evolutionary responses to crude oil from the Deepwater Horizon oil spill by the copepod Eurytemora affinis

description: The BP Deepwater Horizon Oil Disaster was the most catastrophic offshore
 oil spill in U.S. history, yet we still have a poor understanding of how
 organisms could evolve in response to the toxic effects of crude oil. This
 study offers a rare analysis of how fitness-related traits could evolve
 rapidly in response to crude oil toxicity. We examined evolutionary
 responses of populations of the common copepod Eurytemora affinis residing
 in the Gulf of Mexico, by comparing crude oil tolerance of populations
 collected before versus after the Deepwater Horizon oil spill of 2010. In
 addition, we imposed laboratory selection for crude oil tolerance for ~8
 generations, using an E. affinis population collected from before the oil
 spill. We found evolutionary increases in crude oil tolerance in the wild
 population following the oil spill, relative to the population collected
 before the oil spill. The post-oil spill population showed increased
 survival and rapid development time in the presence of crude oil. In
 contrast, evolutionary responses following laboratory selection were less
 clear; though, development time from metamorphosis to adult in the
 presence of crude oil did become more rapid after selection. We did find
 that the wild population, used in both experiments, harbored significant
 genetic variation in crude oil tolerance, upon which selection could act.
 Thus, our study indicated that crude oil tolerance could evolve, but
 perhaps not on the relatively short time scale of the laboratory selection
 experiment. This study contributes novel insights into evolutionary
 responses to crude oil, in directly examining fitness-related traits
 before and after an oil spill, and in observing evolutionary responses
 following laboratory selection.
description: Evolutionary Responses
 to crude oil from the Deepwater Horizon oil spill by the copepod
 Eurytemora affinisSheet 1: Before vs.
 After the Deepwater Horizon oil spill; Sheet 2: Before vs. After
 Laboratory SelectionLee_GulfOil2017
 Dryad.xlsx
DOI: 10.17632/646kw5pg6f.4
title: Supplementary Material for Phenotypic Clustering in adult SAPHO Syndrome

description: Supplementary Figure Legends 
Supplementary Figure 1
Supplementary Figure 2 A-D
Supplementary Figure 3
Supplementary Figure 4
Supplementary Table I
Supplementary Table II
DOI: 10.5061/dryad.h52f8
title: Data from: Correlates of decisional dynamics in the dorsal anterior cingulate cortex

description: We hypothesized that during binary economic choice, decision makers use
 the first option they attend as a default to which they compare the
 second. To test this idea, we recorded activity of neurons in the dorsal
 anterior cingulate cortex (dACC) of macaques choosing between gambles
 presented asynchronously. We find that ensemble encoding of the value of
 the first offer includes both choice-dependent and choice-independent
 aspects, as if reflecting a partial decision. That is, its responses are
 neither entirely pre- nor post-decisional. In contrast, coding of the
 value of the second offer is entirely decision dependent (i.e.,
 post-decisional). This result holds even when offer-value encodings are
 compared within the same time period. Additionally, we see no evidence for
 2 pools of neurons linked to the 2 offers; instead, all comparison appears
 to occur within a single functionally homogenous pool of task-selective
 neurons. These observations suggest that economic choices reflect a
 context-dependent evaluation of attended options. Moreover, they raise the
 possibility that value representations reflect, to some extent, a
 tentative commitment to a choice.
description: dACC single-unit data -
 2 subjectsMATLAB cell array, where
 each cell contains data from one recorded neurondaccdata3.mat
DOI: 10.5061/dryad.1sd59
title: Data from: Biodiversity change is uncoupled from species richness trends: consequences for conservation and monitoring

description: 1. Global concern about human impact on biological diversity has triggered
 an intense research agenda on drivers and consequences of biodiversity
 change in parallel with international policy seeking to conserve
 biodiversity and associated ecosystem functions. Quantifying the trends in
 biodiversity is far from trivial, however, as recently documented by
 meta-analyses which report little if any net change of local species
 richness through time. 2. Here, we summarize several limitations of
 species richness as a metric of biodiversity change and show that the
 expectation of directional species richness trends under changing
 conditions is invalid. Instead, we illustrate how a set of species
 turnover indices provide more information content regarding temporal
 trends in biodiversity, as they reflect how dominance and identity shift
 in communities over time. 3. We apply these metrics to three monitoring
 data sets representing different ecosystem types. In all data sets, nearly
 complete species turnover occurred, but this was disconnected from any
 species richness trends. Instead, turnover was strongly influenced by
 changes in species presence (identities) and dominance (abundances). We
 further show that these metrics can detect phases of strong compositional
 shifts in monitoring data and thus identify a different aspect of
 biodiversity change decoupled from species richness. 4. Synthesis and
 application: Temporal trends in species richness are insufficient to
 capture key changes in biodiversity in changing environments. In fact,
 reductions in environmental quality can lead to transient increases in
 species richness if immigration or extinction have different temporal
 dynamics. Thus, biodiversity monitoring programs need to go beyond
 analyses of trends in richness in favour of more meaningful assessments of
 biodiversity change.01-Jun-2017
description: Data for turnover
 analysisThe file contains three
 data sets used for calculating species turnover. This includes data on
 marine phytoplankton (DUTCH), freshwater phytoplankton (IOWA) and
 terrestrial grassland vegetation (NUTNET). Each data set contains an
 identifier for the monitored ecosystem (StationID) and the the relative
 proportion of species of average annual biomass for each year (column
 year). Species are numbered from S1 to SX. Please note that for the
 grassland data, % cover is given instead of
 proportions.data.xlsx
DOI: 10.5061/dryad.sm379
title: Data from: The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation

description: The kind and duration of phylogenetic topological “signatures” left in the
 wake of macroevolutionary events remain poorly understood. To this end, we
 examined a broad range of simulated phylogenies generated using
 trait-biased, heritable speciation probabilities and mass extinction that
 could be either random or selective on trait value, but also using
 background extinction and diversity-dependence to constrain clade sizes.
 In keeping with prior results, random mass extinction increased imbalance
 of clades that recovered to pre-extinction size, but was a relatively weak
 effect. Mass extinction that was selective on trait values tended to
 produce clades of similar or greater balance compared to random extinction
 or controls. Allowing evolution to continue past the point of clade-size
 recovery resulted in erosion and eventual erasure of this signal, with all
 treatments converging on similar values of imbalance, except for very
 intense extinction regimes targeted at taxa with high speciation rates.
 Return to a more balanced state with extended post-extinction evolution
 was also associated with loss of the previous phylogenetic root in most
 treatments. These results further demonstrate that while a mass extinction
 event can produce a recognizable phylogenetic signal, its effects become
 increasingly obscured the further an evolving clade gets from that event,
 with any sharp imbalance due to unrelated evolutionary factors.
description: CONTROL_OUTPUTFILESR-Processed output files for Control simulationsRAND0.5_OUTPUTFILESR-processed output files for random extinction, intensity = 0.5RAND0.75_OUTPUTFILESR-processed output files for random extinction, intensity = 0.75RAND0.9_OUTPUTFILESR-processed output files for random extinction, intensity = 0.9SOD0.5_OUTPUTFILESR-processed output files for SOD extinction, intensity = 0.5SOD0.75_OUTPUTFILESR-processed output files for SOD extinction, intensity = 0.75SOD0.9_OUTPUTFILESR-processed output files for SOD extinction, intensity = 0.9SOR0.5_OUTPUTFILESR-processed output files for SOR extinction, intensity = 0.5SOR0.75_OUTPUTFILESR-processed output files for SOR extinction, intensity=0.75SOR0.9_OUTPUTFILESR-processed data files for SOR extinction, intensity=0.9R_Scripts_for_Dryad_1Collection of R Scripts for processing MeSA output filesR_files_for_Dryad_2More R scripts for processing MeSA output filesExcel_files_for_DryadExcel files containing data used for main text figuresMESA_X5.tarSource code for version of MeSAMESASCRIPTSInput scripts for MeSA simulation runs
DOI: 10.15468/dl.f9cbjv
title: Occurrence Download

description: A dataset containing 2393 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Norway",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nigritella nigra",
 "Year 2014-2026"
 ]
}

 The dataset includes 2393 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001500-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hc321
title: Data from: Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin

description: Host-associated bacterial communities on the skin act as the first line of
 defence against invading pathogens. Yet, for most natural systems, we lack
 a clear understanding of how temperature variability affects structure and
 composition of skin bacterial communities and, in turn, promotes or limits
 the colonization of opportunistic pathogens. Here, we examine how natural
 temperature fluctuations might be related to changes in skin bacterial
 diversity over time in three amphibian populations infected by the
 pathogenic fungus Batrachochytrium dendrobatidis (Bd). Our focal host
 species (Eleutherodactylus coqui) is a direct-developing frog that has
 suffered declines at some populations in the last 20 years, while others
 have not experienced any changes. We quantified skin bacterial alpha- and
 beta-diversity at four sampling time points, a period encompassing two
 seasons and ample variation in natural infections and environmental
 conditions. Despite the different patterns of infection across
 populations, we detected an overall increase in bacterial diversity
 through time, characterized by the replacement of bacterial operational
 taxonomic units (OTUs). Increased frog body temperatures possibly allowed
 the colonization of bacteria as well as the recruitment of a subset of
 indicator OTUs, which could have promoted the observed changes in
 diversity patterns. Our results suggest that natural environmental
 fluctuations might be involved in creating opportunities for bacterial
 replacement, potentially attenuating pathogen transmission and thus
 contributing to host persistence in E. coqui populations.
description: Mapping_file_LongomolecoMapping file for 16S V4 rRNA amplicon analysisLongo_otu_tableRaw OTU table produced by Qiime 1.9.Longorep_setTree file produced by Qiime
DOI: 10.5061/dryad.800tj
title: Data from: Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients

description: Rationale: Current microbiologic diagnostics often fail to identify the
 etiology of lower respiratory tract infections (LRTI) in hematopoietic
 cellular transplant recipients (HCT), which precludes the implementation
 of targeted therapies. Objectives: To address the need for improved LRTI
 diagnostics, we evaluated the utility of metagenomic next generation
 sequencing (mNGS) of bronchoalveolar lavage (BAL) to detect microbial
 pathogens in HCT patients with acute respiratory illnesses. Methods: We
 enrolled 22 post-HCT adults ages 19-69 years with acute respiratory
 illnesses who underwent BAL at the University of Michigan between January
 2012 and May 2013. mNGS was performed on BAL fluid to detect microbes and
 simultaneously assess the host transcriptional response. Results were
 compared against conventional microbiologic assays. Measurements and Main
 Results: Standard of care clinical diagnostics identified microbes in
 seven patients (32%), six of which were considered pathogens by treating
 physicians, and all of which were detected by mNGS. Previously
 unrecognized LRTI pathogens were also identified in six patients for whom
 standard testing was negative (human coronavirus 229E, human rhinovirus A,
 Corynebacterium propinquum and Streptococcus mitis); findings were
 confirmed by independent PCR and 16S rRNA sequencing. Relative to patients
 without infection, patients with infection had increased expression of
 immunity related genes (p=0.022) and significantly lower diversity of
 their respiratory microbiome (p=0.017).
description: Supplemental Methods,
 Tables and FiguresDetailed methods as well
 as supplemental tables and figures.Supplement-Dryad-Data-Repository.pdfTable S6. Human Gene Count DataGene counts obtained by alignment against the ENSEMBL GRCh38 human genome build are listed. Genes and associated ENSEMBL ID are listed in rows and subjects are grouped by columns.TableS6.csv
DOI: 10.5061/dryad.1555n
title: Data from: Rapid diversification and time explain amphibian richness at different scales in the Tropical Andes, Earth's most biodiverse hotspot

description: The Tropical Andes are Earth's most species-rich biodiversity hotspot
 for both animals and plants. Nevertheless, the ecological and evolutionary
 processes underlying this extraordinary richness remain uncertain. Here,
 we examine the processes that generate high richness in the Andes relative
 to other regions in South America, and across different elevations within
 the Andes, using frogs as a model system. We combine distributional data,
 a newly generated time-calibrated phylogeny for 2318 frog species, and
 phylogenetic comparative methods to test the relative importance of
 diversification rates and colonization times for explaining Andean
 diversity at different scales. At larger scales (among regions and
 families), we find that faster diversification rates in Andean clades most
 likely explain high Andean richness. In contrast, at smaller temporal and
 spatial scales (within family-level clades, within the Andes),
 diversification rates rarely explain richness patterns. Instead, we show
 that colonization times are important for shaping elevational richness
 patterns within the Andes, with more species found in habitats colonized
 earlier. We suggest that these scale-dependent patterns might apply to
 many other richness gradients. Recognition of this scale-dependence may
 help to reconcile conflicting results among studies of richness patterns
 across habitats, regions, and organisms.
description: BEAST XML
 filesA zipped folder of the
 BEAST XML files used in this study. XMLs contain the alignments and all
 chosen settings and parameters.BEAST_XMLs.zipTime-calibrated phylogenetic tree filesTime calibrated phylogenetic tree files generated from the BEAST XMLS used in this study. The file includes all family-level trees, the backbone genus tree, and the final combined Hyloidea tree. Additionally, the alternative backbone and combined Hyloidea trees are included.Tree_Files.zipTable S1: GenBank Accession NumbersGenBank Accession numbers used for the phylogenetic analyses from this study.table_S1.xlsTable S2: Contaminated/incorrect GenBank sequencesSequences for which the species name on GenBank is different from the actual species nametable_S2.xlsTable S3: Raw distributional and rate dataDistributional dataset and raw rates for South American hyloids, including distributional data for all South American species (including those not in the tree)table_S3.xlsSupplemental AppendixSupplemental appendix that describes the methods and results for testing the main text hypotheses using an alternative topology. Generally the results were found to be consistent with those in the main text of the manuscript.Supplemental_Appendix_CRH.pdf
DOI: 10.15468/dl.xnbdze
title: Occurrence Download

description: A dataset containing 1782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Laurus novocanariensis"
 ]
}

 The dataset includes 1782 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001504-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2t208
title: Data from: A cell-based mechanical model of coronary artery tunica media

description: A three-dimensional cell-based mechanical model of coronary artery tunica
 media is proposed. The model is composed of spherical cells forming a
 hexagonal close-packed lattice. Tissue anisotropy is taken into account by
 varying interaction forces with the direction of intercellular connection.
 Several cell-centre interaction potentials for repulsion and attraction
 are considered, including the Hertz contact model and its neo-Hookean
 extension, the Johnson–Kendall–Roberts model of adhesive contact, and a
 wormlike chain model. The model is validated against data from in vitro
 uni-axial tension tests performed on dissected strips of tunica media. The
 wormlike chain potential in combination with the neo-Hookean Hertz contact
 model produces stress–stretch curves which represent the experimental data
 very well.
description: Axial stretch
 simulationIn-silico stretching in
 the axial direction. The colour palette represents the distribution of
 axial projections of intercellular forces SX, [N].X-stretch_X_stress.aviCircumferential stretch simulationIn-silico stretching in circumferential direction. The colour palette represents the distribution of circumferential projections of intercellular forces SZ, [N].Z-stretch.aviStent deployment simulation.Stent deployment is simulated by imposing a kinematic boundary condition on the radial displacements of the cells contacting with the struts (these cells are shown in red in Figure 10a). The radial displacements of stent struts equal to 0.1 of the vessel’s inner radius. The colour palette represents the distribution of circumferential projections of intercellular forces SFI, [N].stenting_slow.aviOpening angle modellingSimulation of an open angle formation for a ring fragment of tunica media with an axial cut. The colour palette represents the circumferential forces distribution SFI, [N]op_angle_bend_asym_force3D.avi
DOI: 10.15468/dl.8rywkc
title: Occurrence Download

description: A dataset containing 1782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Laurus novocanariensis"
 ]
}

 The dataset includes 1782 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001501-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b0cs1
title: Data from: Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury

description: Animals living in desert environments are forced to survive despite severe
 heat, intense solar radiation, and both acute and chronic dehydration.
 These animals have evolved phenotypes that effectively address these
 environmental stressors. To begin to understand the ways in which the
 desert-adapted rodent P. eremicus survives, we performed an experiment
 where we subjected reproductively mature adults to 72 hours of water
 deprivation, during which they lost on average 23% of their body weight.
 The animals reacted via a series of changes in the kidney, which included
 modulating expression of genes responsible for reducing the rate of
 transcription and maintaining water and salt balance. Extracellular matrix
 turnover appeared to be decreased, and apoptosis was limited. Serum
 creatinine and other biomarkers of kidney injury were not elevated, which
 is different than the canonical human response, suggesting that changes in
 gene expression related to acute dehydration may effectively prohibit
 widespread kidney damage in the cactus mouse.
description: kidney.fasta.dammit.fastaFasta file of transcriptskidney.fasta.dammit.gff3Annotation data for transcripts, in gff3 format.
DOI: 10.5061/dryad.mn1pp
title: Data from: Kinematics of chisel-tooth digging by African mole-rats

description: Mole-rats are known to use their protruding, chisel-like incisors to dig
 underground networks of tunnels, but it remains unknown how these incisors
 are used to break and displace the soil. Theoretically, different
 excavation strategies can be used. Mole-rats could either use their head
 depressor muscles to power scooping motions of the upper incisors (by
 nose-down head rotations) or the lower incisors (by nose-up head
 rotations), or their jaw adductors to grab and break the soil after
 penetrating both sets of incisors into the ground, or a combination of
 these mechanisms. To identify how chisel-tooth digging works, a kinematic
 analysis of this behaviour was performed based on high-speed videos of 19
 individuals from the African mole-rat species Fukomys micklemi placed
 inside transparent tubes in a laboratory setting. Our analysis showed that
 the soil is penetrated by both the upper and lower incisors at a
 relatively high gape angle, generally with the head rotated nose-up.
 Initially, the upper incisors remain approximately stationary to function
 as an anchor to allow an upward movement of the lower incisors to grab the
 soil. Next, a quick, nose-down rotation of the head further detaches the
 soil and drops the soil below the head. Consequently, both jaw adduction
 and head depression are jointly used to power tooth-digging in F.
 micklemi. The same mechanism, but with longer digging cycles, and soil
 being thrown down at smaller gape sizes, was used when digging in harder
 soil.
description: DATA_DEPOSIT_MOLERAT_KINEMATICS_VAN_WASSENBERGH_HEINDRYCKX_ADRIAENSThis Excel workbook contains the individual and raw kinematic profiles used for the analyses in the manuscript. More information on the content can be found on the worksheet INFO.