cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35079/hbm887.rlkd.592
title: Visium (no probes) data from the fallopian tube (left) of a 19-year-old white female
DOI: 10.35079/hbm322.qbvp.523
title: Visium (no probes) data from the fallopian tube (left) of a 19-year-old white female
DOI: 10.5061/dryad.83gp7
title: Data from: A tunable refractive index matching medium for live imaging cells, tissues and model organisms

description: In light microscopy, refractive index mismatches between media and sample
 cause spherical aberrations that often limit penetration depth and
 resolution. Optical clearing techniques can alleviate these mismatches,
 but they are so far limited to fixed samples. We present Iodixanol as a
 non-toxic medium supplement that allows refractive index matching in live
 specimens and thus a substantial improvement of the live-imaging of
 primary cell cultures, planarians, zebrafish and human cerebral organoids.
description: Boothe_et_al_eLife_2017_Figure_3a_Source_DataBoothe_et_al_eLife_2017_Figure_3b_Source_DataBoothe_et_al_eLife_2017_Figure_4_Figure_Supplement_1_Source_DataBoothe_et_al_eLife_2017_Figure_4a_Source_DataBoothe_et_al_eLife_2017_Figure_4b_Source_Data
DOI: 10.35079/hbm873.wxnp.464
title: Visium (no probes) data from the fallopian tube (left) of a 19-year-old white female
DOI: 10.5061/dryad.td223
title: Data from: Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms

description: From 1980 to 1992, a series of influential papers reported on the
 discovery, genetics, and evolution of a periodic cycling of the interval
 between Drosophila male courtship song pulses. The molecular mechanisms
 underlying this periodicity were never described. To reinitiate
 investigation of this phenomenon, we previously performed automated
 segmentation of songs but failed to detect the proposed rhythm [Arthur BJ,
 et al. (2013) BMC Biol 11:11; Stern DL (2014) BMC Biol 12:38]. Kyriacou et
 al. [Kyriacou CP, et al. (2017) Proc Natl Acad Sci USA 114:1970–1975]
 report that we failed to detect song rhythms because (i) our flies did not
 sing enough and (ii) our segmenter did not identify many of the song
 pulses. Kyriacou et al. manually annotated a subset of our recordings and
 reported that two strains displayed rhythms with genotype-specific
 periodicity, in agreement with their original reports. We cannot replicate
 this finding and show that the manually annotated data, the original
 automatically segmented data, and a new dataset provide no evidence for
 either the existence of song rhythms or song periodicity differences
 between genotypes. Furthermore, we have reexamined our methods and
 analysis and find that our automated segmentation method was not biased to
 prevent detection of putative song periodicity. We conclude that there is
 no evidence for the existence of Drosophila courtship song rhythms.
description: Stern2017recordings.tarStern2017segmentationsSongs segmented using FlySongSegmenter from Stern 2017.
DOI: 10.35079/hbm973.rvwn.748
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.0859ks3
title: Data from: Flight in ground effect dramatically reduces aerodynamic costs in bats

description: Most flying animals, from insects to seabirds, perform flights close to
 ground or water when taking off or landing, drinking, and feeding or when
 traveling near water surfaces. When flying close to a surface within
 approximately one wingspan, the surface acts as an aerodynamic mirror,
 interrupting the downwash, resulting in increased pressure underneath the
 wing and suppression of wingtip vortex development. This aerodynamic
 interaction lowers the energy added to the air by the animal, reducing the
 cost of flying. Modeling suggests that flapping wings in ground effect can
 affect the expected power savings compared to gliding flight, either
 positively or negatively, depending on the wing motion. Although
 aerodynamic theory predicts substantial power reductions when animals fly
 in ground effect, quantitative measurements of savings are lacking. Here,
 we show, through wake-based power measurements, that Daubenton’s bats
 utilize 29% less aerodynamic power when flying in compared to out of
 ground effect, which is twice the predicted savings. Contrary to
 theoretical predictions we find no variation in savings with distance
 above ground when in ground effect. Given alterations in kinematics with
 ground proximity, we hypothesize that modulation of wing kinematics raises
 the achievable benefit from ground effect relative to current model
 predictions. The savings from ground effect are comparable to formation
 flight but are not limited to large bird species. Instead, ground effect
 is experienced by most flying animals and may have facilitated the
 evolution of powered animal flight.
description: Vector fields of the
 wake of Daubenton's bat flying in and out of ground
 effectContains .dat files with
 six columns containing the x,y,z location of the velocity vectors V-X, V-Y
 and V-Z. Accompanying .xlsx file contains the coding for each of the
 sequences regarding experimental condition and individual as well as
 flight characteristics such as flight speed, height above ground and wing
 beat frequency. The file Data.zip was created in Windows 7 Professional
 using the built-in "Compress folder" option and can be unzipped
 similarly on a Windows PC. You may unzip the file on a Linux or Mac OSX
 machine by accessing a command prompt, going to the directory containing
 the file Data.zip and typing ONE of the following commands: jar xvf
 Data.zip OR 7za x Data.zipData.zip
DOI: 10.15468/dl.ayjsxr
title: Occurrence Download

description: A dataset containing 10006 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gunnera tinctoria",
 "HasCoordinate is true",
 "Country is one of (Netherlands, Belgium, France, Ireland, United Kingdom of Great Britain and Northern Ireland, Chile)",
 "Year is 2020,2026",
 "CoordinateUncertaintyInMeters is less than 1000"
 ]
}

 The dataset includes 10006 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000435-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.35079/hbm333.zptd.584
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.97s68c2
title: Data from: Reciprocal changes of H3K27ac and H3K27me3 at the promoter regions of the critical genes for endometrial decidualization

description: Aim: Decidualization is essential for embryo implantation and placental
 development. We aimed to obtain transcriptome and epigenome profiles for
 primary endometrial stromal cells (ESCs) and in vitro decidualized cells.
 Materials & methods: ESCs isolated from human endometrial tissues
 remained untreated (D0), or decidualized for 4 days (D4) and 8 days (D8)
 in the presence of 8-bromo-cAMP and progesterone. Results: Among the
 epigenetic modifications examined (DNA methylation, H3K27ac, H3K9me3 and
 H3K27me3), the H3K27ac patterns changed most dramatically, with a moderate
 correlation with gene expression changes, upon decidualization. Subsets of
 up- and down-regulated genes upon decidualization were associated with
 reciprocal changes of H3K27ac and H3K27me3 modifications at their promoter
 region, and were enriched with genes essential for decidualization such as
 WNT4, ZBTB16, PROK1 and GREB1. Conclusion: Our dataset is useful to
 further elucidate the molecular mechanisms underlying decidualization.
description: Tables for fpkm
 valuesTables for fpkm values
 for RNA-seq data calculated using Cufflinks:genes.fpkm_tracking,
 isoforms.fpkm_tracking, and tss_groups.fpkm_trackingfpkm_tracking.zipPeak call files for ChIP-seq dataPeak call files for CHIP-seq data produced by MACS2:EM0409D0_K27ac_macs2_peaks.narrowPeak EM0409D0_K27me3_macs2_peaks.broadPeak EM0409D0_K9me3_macs2_peaks.broadPeak EM0409D4_K27ac_macs2_peaks.narrowPeak EM0409D4_K27me3_macs2_peaks.broadPeak EM0409D4_K9me3_macs2_peaks.broadPeak EM0409D8_K27ac_macs2_peaks.narrowPeak EM0409D8_K27me3_macs2_peaks.broadPeak EM0409D8_K9me3_macs2_peaks.broadPeak EM0519D0_K27ac_macs2_peaks.narrowPeak EM0519D0_K27me3_macs2_peaks.broadPeak EM0519D0_K9me3_macs2_peaks.broadPeak EM0519D4_K27ac_macs2_peaks.narrowPeak EM0519D4_K27me3_macs2_peaks.broadPeak EM0519D4_K9me3_macs2_peaks.broadPeak EM0519D8_K27ac_macs2_peaks.narrowPeak EM0519D8_K27me3_macs2_peaks.broadPeak EM0519D8_K9me3_macs2_peaks.broadPeakmacs2.peakcalls.zipbigwig_files"bigwig_files.zip" (md5 checksum: a7cee3f55c6c3d53dd562475aa7fc1f3). The "bigwig_files.zip" file contains the following 25 bigwig files (19 files for ChIP-seq data and 6 files for RNA-sea data). EM0409_D0_H3K27ac.hg19.bw EM0409_D0_H3K27me3.hg19.bw EM0409_D0_H3K9me3.hg19.bw EM0409_D4_H3K27ac.hg19.bw EM0409_D4_H3K27me3.hg19.bw EM0409_D4_H3K9me3.hg19.bw EM0409_D4_input.hg19.bw EM0409_D8_H3K27ac.hg19.bw EM0409_D8_H3K27me3.hg19.bw EM0409_D8_H3K9me3.hg19.bw EM0519_D0_H3K27ac.hg19.bw EM0519_D0_H3K27me3.hg19.bw EM0519_D0_H3K9me3.hg19.bw EM0519_D4_H3K27ac.hg19.bw EM0519_D4_H3K27me3.hg19.bw EM0519_D4_H3K9me3.hg19.bw EM0519_D4_input.hg19.bw EM0519_D8_H3K27me3.hg19.bw EM0519_D8_H3K9me3.hg19.bw RNAseq_EM0409_D0.hg19.bw RNAseq_EM0409_D4.hg19.bw RNAseq_EM0409_D8.hg19.bw RNAseq_EM0519_D0.hg19.bw RNAseq_EM0519_D4.hg19.bw RNAseq_EM0519_D8.hg19.bw
DOI: 10.35079/hbm767.crwb.452
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.g4q6pv3
title: Data from: Of puzzles and pavements: a quantitative exploration of leaf epidermal cell shape

description: Epidermal cells of leaves are diverse: tabular pavement cells, trichomes,
 and stomatal complexes. Pavement cells from the monocot Zea mays (maize)
 and the eudicot Arabidopsis thaliana (Arabidopsis) have highly undulate
 anticlinal walls. The molecular basis for generating these undulating
 margins has been extensively investigated in these species. This has led
 to two assumptions: first, that particular plant lineages are
 characterized by particular pavement cell shapes; and second, that
 undulatory cell shapes are common enough to be model shapes. To test these
 assumptions, we quantified pavement cell shape in epidermides from the
 leaves of 278 vascular plant taxa. We found that monocot pavement cells
 tended to have weakly undulating margins, fern cells had strongly
 undulating margins, and eudicot cells showed no particular undulation
 degree. Cells with highly undulating margins, like those of Arabidopsis
 and maize, were in the minority. We also found a trend towards more
 undulating cell margins on abaxial leaf surfaces; and that highly
 elongated leaves in ferns, monocots and gymnosperms tended to have highly
 elongated cells. Our results reveal the diversity of pavement cell shapes,
 and lays the quantitative groundwork for testing hypotheses about pavement
 cell form and function within a phylogenetic context.
description: SampleTableTable with sampled species name, order, major clade, sample number (for cell images and outlines), sample ID (for cell images and outlines), and leaf sideTable S1: Species identifiers and morphometric meansThis table provides the morphometric means (and standard deviations) by species reported in the manuscript. It is provided here as an accompaniment to the data files.Table S1.xlsxLeaf ImagesLeaf image files as sampled in the manuscript.LeafImages.zipCellCoordinatesThis file contains cell coordinate files (.txt) per cell, derived from manual tracing of cell outlines from epidermal images in the accompanying 'CellImages' file. These outlines are designed for import into R or MatLab for analyses.PhylogeneticResourcesdatamatrix and treefiles used for phyllogenetic analyses in the manuscript.Cell ImagesThis file contains all epidermal cell images used in this study. Epidermal peels were stained with Toludine Blue O. Images are saved as .tiff files.CellImages.zip
DOI: 10.35079/hbm562.rfmt.234
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.578j2
title: Data from: The comparative hydrodynamics of rapid rotation by predatory appendages

description: Countless aquatic animals rotate appendages through the water, yet fluid
 forces are typically modeled with translational motion. To elucidate the
 hydrodynamics of rotation, we analyzed the raptorial appendages of mantis
 shrimp (Stomatopoda) using a combination of flume experiments,
 mathematical modeling and phylogenetic comparative analyses. We found that
 computationally efficient blade-element models offered an accurate
 first-order approximation of drag, when compared with a more elaborate
 computational fluid-dynamic model. Taking advantage of this efficiency, we
 compared the hydrodynamics of the raptorial appendage in different
 species, including a newly measured spearing species, Coronis scolopendra.
 The ultrafast appendages of a smasher species (Odontodactylus scyllarus)
 were an order of magnitude smaller, yet experienced values of drag-induced
 torque similar to those of a spearing species (Lysiosquillina maculata).
 The dactyl, a stabbing segment that can be opened at the distal end of the
 appendage, generated substantial additional drag in the smasher, but not
 in the spearer, which uses the segment to capture evasive prey.
 Phylogenetic comparative analyses revealed that larger mantis shrimp
 species strike more slowly, regardless of whether they smash or spear
 their prey. In summary, drag was minimally affected by shape, whereas
 size, speed and dactyl orientation dominated and differentiated the
 hydrodynamic forces across species and sizes. This study demonstrates the
 utility of simple mathematical modeling for comparative analyses and
 illustrates the multi-faceted consequences of drag during the evolutionary
 diversification of rotating appendages.
description: Coronis and reanalysis
 of old stomatopod kinematic dataKinematic data from
 Coronis scolopendra (newly reported in this study) and compiled data from
 previous kinematic studies of mantis shrimpPGLS
 analysesPhylogenetic comparative
 analysis and dataset of kinematics and size across mantis
 shrimp.Matlab files to perform
 blade element analyses and simulationsThese Matlab files were
 used for performing the blade element analyses and associated
 simulations.bladelementandsimulations.zipExplanation of computational fluid dynamics filesfile legends CFD mantis shrimp for Dryad.txtflntgz3: See Explanation of Files for CFD analysisflntgz3flntgz5: See Explanation of Files for CFD analysisflntgz5flntgz42: See Explanation of Files for CFD analysisflntgz42flntgz62:See Explanation of Files for CFD analysisflntgz62flntgz43:See Explanation of Files for CFD analysisflntgz43flntgz63: See Explanation of Files for CFD analysisflntgz63flntgz82: See Explanation of Files for CFD analysisflntgz82flntgz83: See Explanation of Files for CFD analysisflntgz83mant_new_ACIS_May: See Explanation of Files for CFD analysismant_new_ACIS_May.sat
DOI: 10.35079/hbm927.hjkw.862
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.kk73p
title: Data from: Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

description: Genetic diversity is a fundamental characteristic of species and is
 affected by many factors, including mutation rate, population size, life
 history and demography. To better understand the processes that influence
 levels of genetic diversity across taxa, we collected genome-wide
 restriction-associated DNA data from more than 500 individuals spanning 76
 nominal species of Australian scincid lizards in the genus Ctenotus. To
 avoid potential biases associated with variation in taxonomic practice
 across the group, we used coalescent-based species delimitation to
 delineate 83 species-level lineages within the genus for downstream
 analyses. We then used these genetic data to infer levels of
 within-population genetic diversity. Using a phylogenetically informed
 approach, we tested whether variation in genetic diversity could be
 explained by population size, environmental heterogeneity or historical
 demography. We find that the strongest predictor of genetic diversity is a
 novel proxy for census population size: the number of vouchered
 occurrences in museum databases. However, museum occurrences only explain
 a limited proportion of the variance in genetic diversity, suggesting that
 genetic diversity might be difficult to predict at shallower phylogenetic
 scales.
description: Variant calls, pseudo
 reference genomes, and phylogenyDataDryad.zip
DOI: 10.35079/hbm542.rndd.438
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.25740/fv059sn8146
title: Impulse responses from Sant'Aniceto in Palazzo Altemps, Rome

description: Impulser réponses measured at Chiesa di Sant'Aniceto in Rome
DOI: 10.5061/dryad.g18b090
title: Data from: Early changes in transient adenosine during cerebral ischemia and reperfusion injury

description: Adenosine is an important neuromodulator in the central nervous system,
 and tissue adenosine levels increase during ischemic events, attenuating
 excitotoxic neuronal injury. Recently, our lab developed an
 electrochemical fast-scan cyclic voltammetry (FSCV) method that identified
 rapid, spontaneous changes in adenosine concentrations that last only
 about 3 seconds. Here, we investigated the effects of cerebral ischemia
 and reperfusion on the concentration and frequency of transient adenosine
 release in the caudate-putamen. In anesthetized rats, data were collected
 for four hours: two hours of normoxia, 30 min of cerebral ischemia induced
 by bilateral common carotid artery occlusion, and 90 min of reperfusion.
 Transient adenosine release was increased during the cerebral ischemia
 period and remained elevated during reperfusion. The total number of
 adenosine transients increased by 52% during cerebral ischemia and
 reperfusion compared to normoxia. The concentration of adenosine per event
 did not increase but the cumulative adenosine concentration during
 cerebral ischemia and reperfusion increased by 53% because of the higher
 frequency of events. Further, we evaluated the role of A2A antagonist,
 SCH442416, a putative neuroprotective agent to affect adenosine
 transients. SCH442416 significantly decreased the transient frequency
 during cerebral ischemia-reperfusion by 27% and the cumulative
 concentration by 31%. Our results demonstrate that this mode of rapid
 adenosine release increases during early cerebral ischemia-reperfusion
 injury. Rapid adenosine release could provide fast, local neuromodulation
 and neuroprotection during cerebral ischemia.
description: Control
 ratsControl rats - hdcv data
 filesControl.zipI-R ratsI-R rats - hdcv data filesI-R.zipA2A ratsA2A-stroke rats - hdcv data filesA2A.zip
DOI: 10.35079/hbm787.cmgm.272
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.7fg32
title: Data from: Ensembler: enabling high-throughput molecular simulations at the superfamily scale

description: The rapidly expanding body of available genomic and protein structural
 data provides a rich resource for understanding protein dynamics with
 biomolecular simulation. While computational infrastructure has grown
 rapidly, simulations on an omics scale are not yet widespread, primarily
 because software infrastructure to enable simulations at this scale has
 not kept pace. It should now be possible to study protein dynamics across
 entire (super)families, exploiting both available structural biology data
 and conformational similarities across homologous proteins. Here, we
 present a new tool for enabling high-throughput simulation in the genomics
 era. Ensembler takes any set of sequences—from a single sequence to an
 entire superfamily—and shepherds them through various stages of modeling
 and refinement to produce simulation-ready structures. This includes
 comparative modeling to all relevant PDB structures (which may span
 multiple conformational states of interest), reconstruction of missing
 loops, addition of missing atoms, culling of nearly identical structures,
 assignment of appropriate protonation states, solvation in explicit
 solvent, and refinement and filtering with molecular simulation to ensure
 stable simulation. The output of this pipeline is an ensemble of
 structures ready for subsequent molecular simulations using computer
 clusters, supercomputers, or distributed computing projects like
 Folding@home. Ensembler thus automates much of the time-consuming process
 of preparing protein models suitable for simulation, while allowing
 scalability up to entire superfamilies. A particular advantage of this
 approach can be found in the construction of kinetic models of
 conformational dynamics—such as Markov state models (MSMs)—which benefit
 from a diverse array of initial configurations that span the accessible
 conformational states to aid sampling. We demonstrate the power of this
 approach by constructing models for all catalytic domains in the human
 tyrosine kinase family, using all available kinase catalytic domain
 structures from any organism as structural templates. Ensembler is free
 and open source software licensed under the GNU General Public License
 (GPL) v2. It is compatible with Linux and OS X. The latest release can be
 installed via the conda package manager, and the latest source can be
 downloaded from https://github.com/choderalab/ensembler.
description: ensembler_dataset-datafilestar archive containing target and template data files for tyrosine kinase Ensembler project, plus README and script for generating the same data. Extract using 'tar xvf ensembler_dataset-datafiles.tar'. The ensembler_dataset-models* tar archives contain model data and should be extracted at the same location as this archive.ensembler_dataset-models-ABL1-EPHA2ensembler_dataset-models-EPHA3-ERBB4ensembler_dataset-models-FAK1-INSRRensembler_dataset-models-INSR-LMTK3ensembler_dataset-models-LTK-RONensembler_dataset-models-ROR1-TYRO3ensembler_dataset-models-UFO-ZAP70