cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4qk81
title: Data from: "RAD Sequencing for SNP Discovery in Two Populations of Bighorn Sheep (Ovis canadensis)" in Genomic Resources Notes accepted 1 April 2013 - 31 May 2013

description: In this work we present the development of a large set of single
 nucleotide polymorphisms (SNPs) discovered in two populations of bighorn
 sheep (Ovis canadensis). To do so we used restriction-site associated DNA
 (RAD) sequencing of four individuals from each population. Through
 alignment of reads to the domestic sheep (Ovis aries) genome we discovered
 &gt;83,000 SNPs, of which &gt;38,000 are suitable for assays such
 as an Illumina SNP chip. These loci will allow for fine-mapping of loci
 associated with horn size, and examination of the consequences of the
 genetic rescue including mapping genes underling differences in
 life-history characteristics.
description: Miller et al VCF SNP
 genotypesMiller et al VCF
 SNPs.xlsxMiller et al BAM
 FileSequence alignments (one
 .bam file per individual) of Illumnia reads to the domestic sheep
 genome.MillerBighornBAMfiles.zipMiller et al Raw ReadSequence files (one per individual) in .fastq format.MillerBighornIllumniaReads.zipMiller et al VCF SNPsRAD Loci and genotypes for 8 bighorn sheep
DOI: 10.25612/837.k6qd9r93b5vx
title: Social Vulnerability Index - CTA-Level Data

description: CDC's Social Vulnerability Index for CTAs in Harris County, TX. for 2000, 2010, 2014, 2016, 2018, and 2020.
DOI: 10.5061/dryad.h1157
title: Data from: The telomeric DNA damage response occurs in the absence of chromatin decompaction

description: Telomeres are specialized nucleoprotein structures that protect chromosome
 ends from DNA damage response (DDR) and DNA rearrangements. The telomeric
 shelterin protein TRF2 suppresses the DDR, and this function has been
 attributed to its abilities to trigger t-loop formation or prevent massive
 decompaction and loss of density of telomeric chromatin. Here, we applied
 stochastic optical reconstruction microscopy (STORM) to measure the sizes
 and shapes of functional human telomeres of different lengths and
 dysfunctional telomeres that elicit a DDR. Telomeres have an ovoid
 appearance with considerable plasticity in shape. Examination of many
 telomeres demonstrated that depletion of TRF2, TRF1, or both affected the
 sizes of only a small subset of telomeres. Costaining of telomeres with
 DDR markers further revealed that the majority of DDR signaling telomeres
 retained a normal size. Thus, DDR signaling at telomeres does not require
 decompaction. We propose that telomeres are monitored by the DDR machinery
 in the absence of telomere expansion and that the DDR is triggered by
 changes at the molecular level in structure and protein composition.
description: FiguresScripts for generating figures and the final figuresfigure_environmentPython software environment for figure creationFigure 1 and S2 and S6Data for figures 1, S2, and S6Figure 2Data for figure 2Figure 3 and 4Data for figures 3 and 4Figure 3Data for figure 3Figure 5Data for figure 5Figure S1Data for figures S1Figure S3Data for figure S3Figure S4 and S6Data for figures S4 and S6Figure S4Data for figure S4Figure S5Data for figures S5
DOI: 10.5061/dryad.40494
title: Data from: The selective myosin II inhibitor blebbistatin reversibly eliminates gastrovascular flow and stolon tip pulsations in the colonial hydroid Podocoryna carnea

description: Blebbistatin reversibly disrupted both stolon tip pulsations and
 gastrovascular flow in the colonial hydroid Podocoryna carnea. Epithelial
 longitudinal muscles of polyps were unaffected by blebbistatin, as polyps
 contracted when challenged with a pulse of KCl. Latrunculin B, which
 sequesters G actin preventing F actin assembly, caused stolons to retract,
 exposing focal adhesions where the tip epithelial cells adhere to the
 substratum. These results are consistent with earlier suggestions that
 non-muscle myosin II provides the motive force for stolon tip pulsations
 and further suggest that tip oscillations are functionally coupled to
 hydrorhizal axial muscle contraction.
description: Intact replicate 1_prior
 to reagentTiff files from
 time-lapse movie acquired during blebbistatin treatment of intact stolon
 tipIntact replicate 1_after
 reagentIntact replicate
 1_recoverytiff images from period
 of film following clearance of blebbistatinIntact replicate 2_prior
 to reagentIntact replicate 2_after
 reagentIntact replicate
 2_recoveryIntact replicate 3_prior
 to reagentIntact replicate 3_after
 reagentIntact replicate
 3_recoveryintact replicate 4 prior
 to reagentintact replicate 4 after
 reagentintact replicate 4
 recoveryIntact replicate 5 prior
 to reagentIntact replicate 5 after
 reagentIntact replicate 5
 recoveryIsolated replicate 2
 prior to reagentIsolated replicate 2
 after reagent addedIsolated replicate 2
 recoveryIsolated replicate 3
 prior to reagentIsolated replicate 3
 after reagentIsolated replicate 3
 recoveryLatrunculin replicate 1
 prior to reagentLatrunculin replicate 1
 after reagentLatrunculin replicate 1
 recoveryLatrunculin rep 2_fig
 7_pt 1Latrunculin rep 2_fig
 7_pt 2Latrunculin replicate 3
 prior to reagentLatrunculin replicate 3
 after reagentLatrunculin replicate 3
 recoveryIsolated rep 1_fig 6_pt
 1aIsolated rep 1_fig 6_pt
 1bIsolated rep 1_fig 6_pt
 2aIsolated rep 1_fig 6_pt
 2bIsolated rep 1_fig 6_pt
 2cIsolated rep 1_fig 6_pt
 2dIntact rep 6_fig 5_part
 1aIntact rep 6_fig 5_part
 1bIntact rep 6_fig 5_part
 1cIntact rep 6_fig 5_part
 1dIntact_rep 6_fig 5_pt
 2aIntact_rep 6_fig 5_pt
 2bIntact_rep 6_fig 5_pt
 2cIntact_rep 6_fig 5_pt
 2dIntact_rep 6_fig 5_pt
 2eIntact_rep 6_fig 5_pt
 2fIntact_rep 6_fig 5_pt
 2gIntact_rep 6_fig 5_pt
 2hIntact_rep 6_fig 5_pt
 2iIntact_rep 6_fig 5_pt
 2jFigure 5 time and
 lengthFigure 6 time and
 lengthFigure 7 time and
 lengthREAD
 MEKey
 to all other files
DOI: 10.5061/dryad.2f8j75d
title: Data from: Validation of diffusion tensor imaging measures of nigrostriatal neurons in macaques

description: Objective: Interpretation of diffusion MRI in the living brain requires
 validation against gold standard histological measures. We compared
 diffusion values of the nigrostriatal tract to PET and histological
 results in non-human primates (NHPs) with varying degrees of unilateral
 nigrostriatal injury induced by MPTP, a toxin selective for dopaminergic
 neurons. Methods: Sixteen NHPs had MRI and PET scans of three different
 presynaptic radioligands and blinded video-based motor ratings before and
 after unilateral carotid artery infusion of variable doses of MPTP.
 Diffusion measures of connections between midbrain and striatum were
 calculated. Then animals were euthanized to quantify striatal dopamine
 concentration, stereologic measures of striatal tyrosine hydroxylase (TH)
 immunostained fiber density and unbiased stereologic counts of TH stained
 nigral cells. Results: Diffusion measures correlated with MPTP dose,
 nigral TH-positive cell bodies and striatal TH-positive fiber density but
 did not correlate with in vitro nigrostriatal terminal field measures or
 in vivo PET measures of striatal uptake of presynaptic markers. Once
 nigral TH cell count loss exceeded 50% the stereologic terminal field
 measures reached a near zero floor effect but the diffusion measures
 continued to correlate with nigral cell counts. Conclusion: Diffusion
 measures in the nigrostriatal tract correlate with nigral dopamine neurons
 and striatal fiber density, but have the same relationship to terminal
 field measures as a previous report of striatal PET measures of
 presynaptic neurons. These diffusion measures have the potential to act as
 non-invasive index of the severity of nigrostriatal injury. Diffusion
 imaging of the nigrostriatal tract could potentially have diagnostic value
 in humans with Parkinson disease or related disorders.
description: bluto_140418monkey 1casey_100712monkey 2gate_110104monkey 3gilbert_150330monkey 4hoover_140620monkey 5koba_100614monkey 6lumpy_150306monkey 7marconi_110913monkey 8otter_140328monkey 9pecos_100219monkey 10pinto_131210monkey 11sony_110120monkey 12tosh_110413monkey 13wally_150113monkey 14whitey_150501monkey 15xero_110831monkey 16MonkeyDataSharingmonkey data
DOI: 10.5061/dryad.rs2qp
title: Data from: Inhibition decorrelates visual feature representations in the inner retina

description: The retina extracts visual features for transmission to the brain.
 Different types of bipolar cell split the photoreceptor input into
 parallel channels and provide the excitatory drive for downstream visual
 circuits. Mouse bipolar cell types have been described at great anatomical
 and genetic detail, but a similarly deep understanding of their functional
 diversity is lacking. Here, by imaging light-driven glutamate release from
 more than 13,000 bipolar cell axon terminals in the intact retina, we show
 that bipolar cell functional diversity is generated by the interplay of
 dendritic excitatory inputs and axonal inhibitory inputs. The resulting
 centre and surround components of bipolar cell receptive fields interact
 to decorrelate bipolar cell output in the spatial and temporal domains.
 Our findings highlight the importance of inhibitory circuits in generating
 functionally diverse excitatory pathways and suggest that decorrelation of
 parallel visual pathways begins as early as the second synapse of the
 mouse visual system.
description: FrankeEtAl_BCs_2017_main This data file contains the main dataset used for the clustering shown in Fig. 2 of the paper. Details about the different variables are available in the attached pdf. FrankeEtAl_BCs_2017_v1.mat   FrankeEtAl_BCs_2017_chirp_byrepeat This file contains the individual repeats in response to the chirp stimulus. For details, see pdf.     FrankeEtAl_BCs_2017_step_byrepeat This file contains the individual repeats in response to the step stimulus. For details, see pdf.     FrankeEtAl_BCs_2017_noise_raw This file contains the response traces for the dense noise stimulus used for mapping RFs. For details, see pdf.     FrankeEtAl_BCs_2017_cs_update This file contains the response traces to the center-surround noise from Fig. 5. For details, see pdf.     FrankeEtAl_BCs_2017_drugdata This file contains the responses to the same stimuli as in the main dataset under application of different drugs as for the analysis shown in Fig. 4. For details, see pdf.
DOI: 10.5061/dryad.hs07534
title: Data from: Similar hybrid composition among different age and sex classes in the Myrtle–Audubon's warbler hybrid zone

description: Hybrid zones provide a key natural context within which to study the
 barriers between incipient species. In some avian hybrid zones, there is
 indirect evidence of selection against hybrid offspring, yet the source of
 that selection is often unclear. We examined the frequency distribution of
 hybrids between Myrtle Warblers (Setophaga coronata coronata) and
 Audubon's Warblers (S. c. auduboni), using data to quantify—for the
 first time at a genomic scale—the composition of hybrids in this hybrid
 zone. We sampled birds during the breeding season and during fall
 migration and compared the frequencies of hybrids of different sex and age
 classes. Specifically, we tested for evidence of early-generation hybrids
 being significantly under- or over-represented in any of these classes, as
 would be expected if hybrids have lower or higher fitness than
 non-hybrids. We found that the genomic composition of birds in the hybrid
 zone spans the full ancestry spectrum. Across all our sampling periods, we
 found an excess of birds that had more Audubon's ancestry, with a
 stronger bias toward Audubon's ancestry in fall migrants than in
 breeding birds, consistent with asymmetric introgression. Notably, we did
 not find any differences in hybrid frequencies between juvenile and adult
 age classes or between males and females. Therefore, our results do not
 support large differences in viability between male and female hybrids or
 between different age classes of hybrids.
description: Plate_1_2-index_1_ATCACG_R1.fastqPlate_1_2-index_2_CGATGT_R1.fastqPlate_1_2-index_3_TTAGGC_R1.fastqPlate_1_2-index_4_TGACCA_R1.fastqPlate_1_2-index_5_ACAGTG_R1.fastqPlate_1_2-index_6_GCCAAT_R1.fastqPlate_1_2-index_7_CAGATC_R1.fastqPlate_1_2-index_8_ACTTGA_R1.fastqPlate_1_2-index_9_GATCAG_R1.fastqPlate_1_2-index_10_TAGCTT_R1.fastqPlate_3_4-index_1_ATCACG_R1.fastqPlate_3_4-index_2_CGATGT_R1.fastqPlate_3_4-index_3_TTAGGC_R1.fastqPlate_3_4-index_4_TGACCA_R1.fastqPlate_3_4-index_5_ACAGTG_R1.fastqPlate_3_4-index_6_GCCAAT_R1.fastqPlate_3_4-index_7_CAGATC_R1.fastqPlate_3_4-index_8_ACTTGA_R1.fastqPlate_3_4-index_9_GATCAG_R1.fastqPlate_3_4-index_10_TAGCTT_R1.fastqSample-barcode Plate InfoSample information and associated barcodes/indexes for demultiplexing RAW ddRAD data. Illumina data generated from single end chemistry on the HighSeq2500 platform. Additional sample information can be found in the Appendix of the journal publisher's website.sample_barcode_plate_info.xlsx
DOI: 10.34740/kaggle/dsv/14633025
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.wkc5ss
title: Occurrence Download

description: A dataset containing 605 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Masticophis flagellum",
 "Year 1960-2026"
 ]
}

 The dataset includes 605 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000819-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.h4j7hv4
title: Data from: Roads to isolation: similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes

description: Freshwater species often show high levels of endemism and risk of
 extinction owing to their limited dispersal abilities. This is exemplified
 by the stenotopic freshwater crab, Johora singaporensis which is one of
 the world's 100 most threatened species, and currently inhabits less
 than 0.01 km2 of five low order hill streams within the highly urbanized
 island city‐state of Singapore. We compared populations of J.
 singaporensis with that of the non‐threatened, widespread, abundant, and
 eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly
 high congruence between their population genomic histories. Based on 2,617
 and 2,470 genome‐wide SNPs mined via the double‐digest
 restriction‐associated DNA sequencing method for ~90 individuals of J.
 singaporensis and P. maculata, respectively, the populations are strongly
 isolated (FST = 0.146–0.371), have low genetic diversity for both species
 (also for COI), and show signatures of recent genetic bottlenecks. The
 most genetically isolated populations for both species are separated from
 other populations by one of the oldest roads in Singapore. These results
 suggest that anthropogenic developments may have impacted stream‐dependent
 species in a uniform manner, regardless of ubiquity, habitat preference,
 or dispersal modes of the species. While signs of inbreeding were not
 detected for the critically endangered species, the genetic
 distinctiveness and low diversity of the populations call for genetic
 rescue and connecting corridors between the remaining fragments of the
 natural habitat.
description: Demultiplexed fastq
 files for each sample - J. singaporensis20160308_JSIN_sub1_flt_fastq20160308_JSIN_sub1_flt_fastq.tar.gzDemultiplexed fastq files for each sample - P. maculata20160518_PMAC_flt_fastq20160518_PMAC_flt_fastq.tar.gz
DOI: 10.5061/dryad.5h8k3
title: Data from: Letting the “cat” out of the bag: pouch young development of the extinct Tasmanian tiger revealed by X-ray computed tomography

description: The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was an iconic
 Australian marsupial predator that was hunted to extinction in the early
 1900s. Despite sharing striking similarities with canids, they failed to
 evolve many of the specialized anatomical features that characterize
 carnivorous placental mammals. These evolutionary limitations are thought
 to arise from functional constraints associated with the marsupial mode of
 reproduction, in which otherwise highly altricial young use their
 well-developed forelimbs to climb to the pouch and mouth to suckle. Here
 we present the first 3D digital developmental series of the thylacine
 throughout its pouch life using X-ray computed tomography on all known
 ethanol-preserved specimens. Based on detailed skeletal measurements, we
 refine the species growth curve to improve age estimates for the
 specimens. Comparison of allometric growth trends in the appendicular
 skeleton (fore- and hindlimbs) with that of other placental and marsupial
 mammals revealed that despite their unique adult morphologies, thylacines
 retained a generalized early marsupial ontogeny. Our approach also
 revealed mislabelled specimens that possessed large epipubic bones
 (vestigial in thylacine) and differing vertebral numbers. All of our
 generated CT models are publicly available, preserving their developmental
 morphology and providing a novel digital resource for future studies of
 this unique marsupial.
description: DZCU 8021.1 (1.5
 weeks)Specimen DZCU8021 from
 Charles University, Prague. Specimen represents a single ~1.5 week old
 individual from a litter of four preserved pouch young. Zipped tiff stack
 with included reconstruction parametersNMV C5755 (4.5
 weeks)Specimen C5755 from
 Museums Victoria, Melbourne, Australia. Specimen represents a single ~4.5
 week old individual from a litter of three preserved pouch young. Zipped
 tiff stack with included reconstruction parametersTMAG A931 (5.25
 weeks)Specimen A931 from
 Tasmanian Museum and Art Gallery. Specimen represents a single ~5.25 week
 old individual from a litter of two preserved pouch young. Zipped DiCOM
 stack with included reconstruction parametersTMAG A930 (9
 weeks)Specimen A930 from
 Tasmanian Museum and Art Gallery, Tasmania, Australia. Specimen represents
 a single ~9 week old preserved pouch young. Zipped DiCOM stack with
 included reconstruction parametersAMS P762 (12
 weeks)Specimen P762 from
 Australia Museum, New South Wales, Australia. Specimen represents a single
 ~12 week old preserved pouch young. Zipped DiCOM stack with included
 reconstruction parametersTMAG A934 (non
 thylacine)Misidentified pouch
 young specimen A934 from Tasmanian Museum and Art Gallery, Tasmania,
 Australia. Specimen is a Dasyurid pouch young, though the exact species
 unknown. Zipped DiCOM stack with included reconstruction
 parameters
DOI: 10.5061/dryad.38s74
title: Data from: T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm

description: We present an ultrahigh resolution in vivo human brain magnetic resonance
 imaging (MRI) dataset. It consists of T1-weighted whole brain anatomical
 data acquired at 7 Tesla with a nominal isotropic resolution of 250 μm of
 a single young healthy Caucasian subject and was recorded using
 prospective motion correction. The raw data amounts to approximately
 1.2 TB and was acquired in eight hours total scan time. The resolution of
 this dataset is far beyond any previously published in vivo structural
 whole brain dataset. Its potential use is to build an in vivo MR brain
 atlas. Methods for image reconstruction and image restoration can be
 improved as the raw data is made available. Pre-processing and
 segmentation procedures can possibly be enhanced for high magnetic field
 strength and ultrahigh resolution data. Furthermore, potential resolution
 induced changes in quantitative data analysis can be assessed, e.g.,
 cortical thickness or volumetric measures, as high quality images with an
 isotropic resolution of 1 and 0.5 mm of the same subject are included in
 the repository as well.
description: Averaged T1-weighted
 MPRAGE with an isotropic resolution of 250 µmThis folder contains
 structural data of a single young healthy Caucasian subject in NIfTI file
 format. This dataset has been build by registering eight single
 T1-weighted MPRAGE volumes with a native isotropic resolution of 250 µm
 and the average to increase the SNR.MPRAGE_250um.tarAll averages of T1-weighted MPRAGE with an isotropic resolution of 250 µmThis folder contains all prior averages of the registration process to build the final T1-weighted MPRAGE volume with an isotropic resolution of 250 µm.averages.tarPre-Processed T1-weighted MPRAGE volumesThis folder contains all eight single pre-processed T1-weighted MPRAGE volumes used to generate the average with an isotropic resolution of 250 µm. Additionally, 1 and 0.5 mm pre-processed data of the same subject are included in the folder. Pre-processing consists of AC-PC alignment and bias field correction. Details can be found in the readme.derivatives.tarSourcedata of T1-weighted MPRAGE volumesThis folder contains all eight single unprocessed T1-weighted MPRAGE volumes used to generate the average with an isotropic resolution of 250 µm. Additionally, 1 and 0.5 mm unprocessed data of the same subject and motion tracking information of all acquisitions is included in the archive.sourcedata.tar
DOI: 10.5061/dryad.gp40h
title: Data from: A daily global mesoscale ocean eddy dataset from satellite altimetry

description: Mesoscale ocean eddies are ubiquitous coherent rotating structures of
 water with radial scales on the order of 100 kilometers. Eddies play a key
 role in the transport and mixing of momentum and tracers across the World
 Ocean. We present a global daily mesoscale ocean eddy dataset that
 contains ~45 million mesoscale features and 3.3 million eddy trajectories
 that persist at least two days as identified in the AVISO dataset over a
 period of 1993–2014. This dataset, along with the open-source eddy
 identification software, extract eddies with any parameters (minimum size,
 lifetime, etc.), to study global eddy properties and dynamics, and to
 empirically estimate the impact eddies have on mass or heat transport.
 Furthermore, our open-source software may be used to identify mesoscale
 features in model simulations and compare them to observed features.
 Finally, this dataset can be used to study the interaction between
 mesoscale ocean eddies and other components of the Earth System.
description: Global mesoscale ocean
 eddy featuresA database of ocean
 eddies identified in daily satellite altimeter data. Each file contains
 the eddy features identified on that day. Each day has two file one for
 cyclonic and another for anticyclonic eddies. Each eddy object contains
 geographical and physical information as well as the grid cells that make
 up the eddy's body.eddies.zipGlobal daily eddy trajectoriesUsing the eddies found in our eddy database, we generated trajectories for eddies that had at least 1cm amplitude and 9 grid cells in size. This is just an example eddy trajectories dataset and researchers can filter our eddy database to construct eddy trajectories that meet their needstracks.txttracks_readme.txt