cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n068q74
title: Data from: Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana

description: Stomata control gas exchanges between the plant and the atmosphere. How
 natural variation in stomata size and density contributes to resolve
 trade‐offs between carbon uptake and water‐loss in response to local
 climatic variation is not yet understood. We developed an automated
 confocal microscopy approach to characterize natural genetic variation in
 stomatal patterning in 330 fully‐sequenced Arabidopsis thaliana accessions
 collected throughout the European range of the species. We compared this
 to variation in water‐use efficiency, measured as carbon isotope
 discrimination (δ13C). We detect substantial genetic variation for stomata
 size and density segregating within Arabidopsis thaliana. A positive
 correlation between stomata size and δ13C further suggests that this
 variation has consequences on water‐use efficiency. Genome‐wide
 association analyses indicate a complex genetic architecture underlying
 not only variation in stomata patterning but also to its co‐variation with
 carbon uptake parameters. Yet, we report two novel QTL affecting δ13C
 independently of stomata patterning. This suggests that, in A. thaliana,
 both morphological and physiological variants contribute to genetic
 variance in water‐use efficiency. Patterns of regional differentiation and
 co‐variation with climatic parameters indicate that natural selection has
 contributed to shape some of this variation, especially in Southern
 Sweden, where water availability is more limited in spring relative to
 summer. These conditions are expected to favor the evolution of drought
 avoidance mechanisms over drought escape strategies.
description: Scanned leaf
 sheetsThis archive contains
 the scanned leaf sheets, used for leaf size
 measurements.Leaf_sheets.7zStomata Images Archive part 1Collection of all microscopic imagesStomata_Images.7z.001Stomata Images part 2Stomata_Images.7z.002Stomata Images part 3Stomata_Images.7z.003Stomata Images part 4Stomata_Images.7z.004Stomata Images part 5Stomata_Images.7z.005Stomata Images part 6Stomata_Images.7z.006Stomata Images part 7Stomata_Images.7z.007Stomata Images part 8Stomata_Images.7z.008Stomata Images part 9Stomata_Images.7z.009Stomata Images part 10Stomata_Images.7z.010Supplemental Table 1Table containing geographic and climatic information for each accession.Suppl_Table1.csvSupplemental Table 2Table containing phenotype data for each accessionSuppl_Table2.csvSupplemental Document 2R Markdown output documenting the statistical analysisSuppl_Document2.htmlSupplemental Document 1Supplemental MethodsSuppl_Document1.pdfImage analysis scriptsMATLAB scripts used for automatic image analysis. See README file included in the archive for further details.matlab_scripts.7z
DOI: 10.35079/hbm297.hdxp.342
title: Visium (no probes) data from the fallopian tube (right) of a 30-year-old white female
DOI: 10.35079/hbm679.ljlc.858
title: Visium (no probes) data from the fallopian tube (right) of a 30-year-old white female
DOI: 10.5061/dryad.sp025
title: Data from: Common internal allosteric network links anesthetic binding sites in a pentameric ligand-gated ion channel

description: General anesthetics bind reversibly to ion channels, modifying their
 global conformational distributions, but the underlying atomic mechanisms
 are not completely known. We examine this issue by way of the model
 protein Gloeobacter violaceous ligand-gated ion channel (GLIC) using
 computational molecular dynamics, with a coarse-grained model to enhance
 sampling. We find that in flooding simulations, both propofol and a
 generic particle localize to the crystallographic transmembrane anesthetic
 binding region, and that propofol also localizes to an extracellular
 region shared with the crystallographic ketamine binding site. Subsequent
 simulations to probe these binding modes in greater detail demonstrate
 that ligand binding induces structural asymmetry in GLIC. Consequently, we
 employ residue interaction correlation analysis to describe the internal
 allosteric network underlying the coupling of ligand and distant effector
 sites necessary for conformational change. Overall, the results suggest
 that the same allosteric network may underlie the actions of various
 anesthetics, regardless of binding site.
description: Data for "Common
 internal allosteric network links anesthetic binding sites in a pentameric
 ligand-gated ion channel"This includes the
 GROMACS files and resulting trajectories for coarse-grained molecular
 dynamics simulations of Gloeobacter violaceous ion channel (GLIC), with
 and without the ligands propofol and a generic coarse-grained particle.
 "Flooded" simulations include many copies of the respective
 ligand. Single-ligand simulations include the ligand in either
 transmembrane intrasubunit site in GLIC, or in an extracellular site in
 GLIC. Production trajectories are named like md{n}_pw.*.xtc. The nopbc.fit
 versions are postprocessed versions made where necessary, where removal of
 periodic boundary conditions and fitting on the protein were
 done.GLIC_manuscript_data.zip
DOI: 10.35079/hbm822.bcmf.267
title: Visium (no probes) data from the fallopian tube (right) of a 30-year-old white female
DOI: 10.5061/dryad.332b5
title: Data from: Directional reflectance and milli-scale feather morphology of the African Emerald Cuckoo, Chrysococcyx cupreus

description: Diverse plumages have evolved among birds through complex morphological
 modifications. We investigate how the interplay of light with surface and
 subsurface feather morphology determines the direction of light
 propagation, an understudied aspect of avian visual signalling. We
 hypothesize that milli-scale modifications of feathers produce anisotropic
 reflectance, the direction of which may be predicted by the orientation of
 the milli-scale structure. The subject of this study is the African
 Emerald Cuckoo, Chrysococcyx cupreus, noted for its shimmering green
 iridescent appearance. Using a spherical gantry, we measured the change in
 the directional reflectance across the feather surface and over a
 hemisphere of incident lighting directions. Using a microCT scanner, we
 also studied the morphology of the structural branches of the barb. We
 tracked the changes in the directional reflectance to the orientation of
 the structural branches as observed in the CT data. We conclude that (i)
 the far-field signal of the feather consists of multiple specular
 components, each associated with a different structural branch and (ii)
 the direction of each specular component is correlated to the orientation
 of the corresponding structure.
description: Directional scattering
 measurements of a Chrysococcyx cupreus tertial feather (OS
 X)SimpleBrowser_cu03338.dmgDirectional scattering measurements of a Chrysococcyx cupreus tertial feather (Windows)SimpleBrowser-win32_cu03338.iso
DOI: 10.5061/dryad.6300n
title: Data from: Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

description: Although population genomic studies using next generation sequencing (NGS)
 data are becoming increasingly common, studies focusing on phylogenetic
 inference using these data are in their infancy. Here, we use NGS data
 generated from reduced representation genomic libraries of
 restriction-site-associated DNA (RAD) markers to infer phylogenetic
 relationships among 16 species of cichlid fishes from a single rocky
 island community within Lake Victoria's cichlid adaptive radiation.
 Previous attempts at sequence-based phylogenetic analyses in Victoria
 cichlids have shown extensive sharing of genetic variation among species
 and no resolution of species or higher-level relationships. These patterns
 have generally been attributed to the very recent origin (&lt;15 000
 years) of the radiation, and ongoing hybridization between species. We
 show that as we increase the amount of sequence data used in phylogenetic
 analyses, we produce phylogenetic trees with unprecedented resolution for
 this group. In trees derived from our largest data supermatrices (3 to
 &gt;5.8 million base pairs in width), species are reciprocally
 monophyletic with high bootstrap support, and the majority of internal
 branches on the tree have high support. Given the difficulty of the
 phylogenetic problem that the Lake Victoria cichlid adaptive radiation
 represents, these results are striking. The strict interpretation of the
 topologies we present here warrants caution because many questions remain
 about phylogenetic inference with very large genomic data set and because
 we can with the current analysis not distinguish between effects of shared
 ancestry and post-speciation gene flow. However, these results provide the
 first conclusive evidence for the monophyly of species in the Lake
 Victoria cichlid radiation and demonstrate the power that NGS data sets
 hold to resolve even the most difficult of phylogenetic challenges.
description: Supermatrix
 aphylip format file for
 supermatrix a, min individuals 145m125M2_mincov145noref.phySupermatrix bphylip format file for supermatrix b, min individuals 125m125M2_mincov125noref.phym125M2_mincov115norefm125M2_mincov110norefm125M2_mincov100norefm125M2_mincov075norefm125M2_mincov015norefm125M2_mincov001.vcf
DOI: 10.35079/hbm628.lmxg.267
title: Visium (no probes) data from the ovary (right) of a 30-year-old white female
DOI: 10.5061/dryad.3s795
title: Data from: Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution

description: The Heliconius butterflies are a widely studied adaptive radiation of 46
 species spread across Central and South America, several of which are
 known to hybridize in the wild. Here, we present a substantially improved
 assembly of the Heliconius melpomene genome, developed using novel methods
 that should be applicable to improving other genome assemblies produced
 using short read sequencing. First, we whole-genome-sequenced a pedigree
 to produce a linkage map incorporating 99% of the genome. Second, we
 incorporated haplotype scaffolds extensively to produce a more complete
 haploid version of the draft genome. Third, we incorporated ∼20x coverage
 of Pacific Biosciences sequencing, and scaffolded the haploid genome using
 an assembly of this long-read sequence. These improvements result in a
 genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb,
 an N50 number of 34, and with 99% of the genome placed, and 84% anchored
 on chromosomes. We use the new genome assembly to confirm that the
 Heliconius genome underwent 10 chromosome fusions since the split with its
 sister genus Eueides, over a period of about 6 million yr.
description: Eueides.Hmel2.vcf.gzVariant calls for Eueides isabella cross aligned to Hmel2.faGitHub.tar.gzA snapshot of the bespoke code written to reassemble the genome, available from https://github.com/johnomics/Heliconius_melpomene_version_2, commit f826fd1 from Dec 10, 2015Genome.tar.gzA snapshot of the Hmel2 distribution available from butterflygenome.orgHmel_cross.Hmel_haplotype_scaffolds.vcf.gzVariant calls for Heliconius melpomene mapping cross aligned to Hmel1-1 haplotype scaffolds (Hmel_haplotype_scaffolds.fas)Hmel_cross.Hmel1-1_primaryScaffolds.vcf.gzVariant calls for Heliconius melpomene mapping cross aligned to Hmel1-1 primary scaffolds (Hmel1-1_primaryScaffolds.fa)Hmel_cross.linkage_map.clean.db.gzSQLite3 database containing scaffold_map and chromosome_map tables used to reassemble genome, fixing all identified linkage errors, recalculating cM values and reversing chromosomes where necessaryHmel_cross.linkage_map.db.gzSQLite3 database containing marker information for linkage map (see README.txt for table descriptions)Hmel1-1_haploid.fa.gzHmel1-2 genome collapsed by HaploMergerHmel1-2_haploid.fa.gzHmel1-2_pacbio_merge.fa.gzHmel1-2_haploid and pacbio_haploid merged by HaploMergerHmel1-2.fa.gzHmel1-1 genome updated to correct all identified misassembliespacbio_falcon_assembly.fa.gzInitial assembly of PacBio reads with FALCONpacbio_haploid.fa.gzFALCON PacBio assembly collapsed by HaploMergerreaddepth_gc_1kb_windows.Hmel2.adjusted.tsv.gzGC content and median read depths unadjusted and adjusted for GC content in 1kb windows for F1 fatherreaddepth_gc_1kb.windows.Hmel2.adjusted.tsv.gzREADME
DOI: 10.35079/hbm525.tlbl.435
title: Visium (no probes) data from the ovary (right) of a 30-year-old white female
DOI: 10.5281/zenodo.18373533
title: Sentinel VIlnius area data for Swift-Gan

description: Collection of Seninel-1 VV and VH data and Sentinel-2 all optical band data over the period from 2024-01-01 till 2025-01-01 over Vilnius and area around it.

Data is saved as .tiff files one for each band and collection date.
DOI: 10.5281/zenodo.18373534
title: Sentinel VIlnius area data for Swift-Gan

description: Collection of Seninel-1 VV and VH data and Sentinel-2 all optical band data over the period from 2024-01-01 till 2025-01-01 over Vilnius and area around it.

Data is saved as .tiff files one for each band and collection date.
DOI: 10.5061/dryad.h38853n
title: Data from: Y chromosome sequences reveal a short Beringian Standstill, rapid expansion, and early population structure of Native American founders

description: The Americas were the last inhabitable continents to be occupied by
 humans, with a growing multidisciplinary consensus for entry 15-25
 thousand years ago (kya) from northeast Asia via the former Beringia land
 bridge. Autosomal DNA analyses have dated the separation of Native
 American ancestors from the Asian gene pool to 23 kya or later, and mtDNA
 analyses to ~25 kya, followed by isolation (‘Beringian Standstill’) for
 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we
 present a calibrated sequence-based analysis of 222 Native American and
 relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C, with
 four major conclusions. First, we identify three to four independent
 lineages as autochthonous and likely founders: the major Q-M3 and rarer
 Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in
 South America, and possibly C3-P39/Z30536 in North America. Second, from
 the divergence times and Eurasian/American distribution of lineages, we
 estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky according to
 alternative models, and entry south of the ice sheet after 19.5 kya.
 Third, we describe the star-like expansion of Q-M848 (within Q-M3)
 starting at 15 kya in the Americas, followed by establishment of
 substantial spatial structure in South America by 12 kya. Fourth, the deep
 branches of the Q-CTS1780 lineage present at low frequencies throughout
 the Americas today may reflect a separate out-of-Beringia dispersal after
 the melting of the glaciers at the end of the Pleistocene.
description: Y chromosome sequences
 of 20 Native AmericansTarball with 20 Native
 American cram files.Ychrom_Pinotti2018.tar
DOI: 10.5061/dryad.8m2g3
title: Data from: Eye coding mechanisms in early human face event-related potentials

description: In humans, the N170 event-related potential (ERP) is an integrated measure
 of cortical activity that varies in amplitude and latency across trials.
 Researchers often conjecture that N170 variations reflect cortical
 mechanisms of stimulus coding for recognition. Here, to settle the
 conjecture and understand cortical information processing mechanisms, we
 unraveled the coding function of N170 latency and amplitude variations in
 possibly the simplest socially important natural visual task: face
 detection. On each experimental trial, 16 observers saw face and noise
 pictures sparsely sampled with small Gaussian apertures.
 Reverse-correlation methods coupled with information theory revealed that
 the presence of the eye specifically covaries with behavioral and neural
 measurements: the left eye strongly modulates reaction times and lateral
 electrodes represent mainly the presence of the contralateral eye during
 the rising part of the N170, with maximum sensitivity before the N170
 peak. Furthermore, single-trial N170 latencies code more about the
 presence of the contralateral eye than N170 amplitudes and early latencies
 are associated with faster reaction times. The absence of these effects in
 control images that did not contain a face refutes alternative accounts
 based on retinal biases or allocation of attention to the eye location on
 the face. We conclude that the rising part of the N170, roughly 120–170 ms
 post-stimulus, is a critical time-window in human face processing
 mechanisms, reflecting predominantly, in a face detection task, the
 encoding of a single feature: the contralateral eye.
description: EEG responses to bubbled
 face and noise imagesThis data package
 provides EEG data recorded from 15 subjects during a face detection task.
 Stimuli were face images or noise textures, presented sampled with a
 bubble mask (gaussian apertures). Data include current source density
 sensor EEG data (trials x time x sensors), full bubble masks, reaction
 times and categorical responses for each trial. The 7zip archive contains
 a Matlab .mat file (v7.3, HDF5) for each subject, metadata Matlab file,
 readme.txt and example script showing calculation of
 ERPs.data.7z
DOI: 10.35079/hbm585.dcxg.975
title: Visium (no probes) data from the ovary (right) of a 30-year-old white female
DOI: 10.6084/m9.figshare.25537690
title: Biological subphenotypes in patients hospitalized with suspected infection in Thailand: a secondary analysis of a prospective observational study

description: Using an existing cohort of prospectively enrolled patients hospitalized with suspected infection in northeastern Thailand, we measured 15 circulating biomarkers from a random selection of 585 subjects and developed latent profile models to identify biological subphenotypes. Characteristics and outcomes of patients were compared by subphenotype assignment. A parsimonious model was developed to predict subphenotype classification, and underlying biological processes were assessed by factor analysis.
DOI: 10.6084/m9.figshare.25537690.v1
title: Biological subphenotypes in patients hospitalized with suspected infection in Thailand: a secondary analysis of a prospective observational study

description: Using an existing cohort of prospectively enrolled patients hospitalized with suspected infection in northeastern Thailand, we measured 15 circulating biomarkers from a random selection of 585 subjects and developed latent profile models to identify biological subphenotypes. Characteristics and outcomes of patients were compared by subphenotype assignment. A parsimonious model was developed to predict subphenotype classification, and underlying biological processes were assessed by factor analysis.
DOI: 10.35079/hbm842.dvqd.422
title: Visium (no probes) data from the ovary (right) of a 30-year-old white female
DOI: 10.35079/hbm965.bhnk.963
title: Visium (no probes) data from the ovary (right) of a 30-year-old white female
DOI: 10.5061/dryad.g27mq71
title: Data from: Elementary sensory-motor transformations underlying olfactory navigation in walking fruit flies

description: Odor attraction in walking Drosophila melanogaster is commonly used to
 relate neural function to behavior, but the algorithms underlying
 attraction are unclear. Here we develop a high-throughput assay to measure
 olfactory behavior in response to well-controlled sensory stimuli. We show
 that odor evokes two behaviors: an upwind run during odor (ON response),
 and a local search at odor offset (OFF response). Wind orientation
 requires antennal mechanoreceptors, but search is driven solely by odor.
 Using dynamic odor stimuli, we measure the dependence of these two
 behaviors on odor intensity and history. Based on these data, we develop a
 navigation model that recapitulates the behavior of flies in our
 apparatus, and generates realistic trajectories when run in a turbulent
 boundary layer plume. The ability to parse olfactory navigation into
 quantifiable elementary sensori-motor transformations provides a
 foundation for dissecting neural circuits that govern olfactory behavior.
description: Behavioral
 dataAlvarezSalvadoBehaviorData.zipPlume measurements in air10302017_10cms_bounded_2.h510302017_10cms_bounded_README.txt
DOI: 10.5061/dryad.t0m6p
title: Data from: Resolving coiled shapes reveals new reorientation behaviors in C. elegans

description: We exploit the reduced space of C. elegans postures to develop a novel
 tracking algorithm which captures both simple shapes and also
 self-occluding coils, an important, yet unexplored, component of 2D worm
 behavior. We apply our algorithm to show that visually complex, coiled
 sequences are a superposition of two simpler patterns: the body wave
 dynamics and a head-curvature pulse. We demonstrate the precise ΩΩ-turn
 dynamics of an escape response and uncover a surprising new dichotomy in
 spontaneous, large-amplitude coils; deep reorientations occur not only
 through classical ΩΩ-shaped postures but also through larger postural
 excitations which we label here as δδ-turns. We find that omega and delta
 turns occur independently, suggesting a distinct triggering mechanism, and
 are the serpentine analog of a random left-right step. Finally, we show
 that omega and delta turns occur with approximately equal rates and adapt
 to food-free conditions on a similar timescale, a simple strategy to avoid
 navigational bias.
description: Foraging
 datasetForaging.tar.gzEscape response datasetEscapeResponse.tar.gz
DOI: 10.34740/kaggle/dsv/14630890
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.35079/hbm928.jbmp.267
title: Visium (no probes) data from the ovary (right) of a 30-year-old white female
DOI: 10.5061/dryad.1fm3f
title: Data from: Museum genomics: low-cost and high-accuracy genetic data from historical specimens

description: Natural history collections are unparalleled repositories of geographic
 and temporal variation in faunal conditions. Molecular studies offer an
 opportunity to uncover much of this variation; however, genetic studies of
 historical museum specimens typically rely on extracting highly degraded
 and chemically modified DNA samples from skins, skulls or other dried
 samples. Despite this limitation, obtaining short fragments of DNA
 sequences using traditional PCR amplification of DNA has been the primary
 method for genetic study of historical specimens. Few labs have succeeded
 in obtaining genome-scale sequences from historical specimens, and then
 only with considerable effort and cost. Here we describe a low cost
 approach using high-throughput next-generation sequencing (NGS) to obtain
 reliable genome-scale sequence data from a traditionally preserved mammal
 skin and skull using a simple extraction protocol. We show that single
 nucleotide polymorphisms (SNPs) from the genome sequences obtained
 independently from the skin and from the skull are highly repeatable
 compared to a reference genome.
description: dryad.tar.bz2This tarball consists of three main types of files. 1. library*.sorted.bam =&gt; These are the files that resulted from using Bowtie to map the trimmed reads in the seq/ dir to the the RGSC3.4 assembly. Also included are associated index (*.bai) files 2. assembleMito.fa =&gt; This is the assembly of the sequenced rat's mitochondrial genome resulting from de novo assembly of the reads using ABySS. 3. seq/ contains the reads trimmed for contamination, adapter, and low-quality as discussed in the publication. library5* is derived from the molar. library6* is derived from the toe. *_1_* reads are forward reads; *_2_* reads are reverse reads. Any reads that lost their mate-pair during the trimming process are not included here although they were used for mapping. These reads are available from S. Singhal upon request. Note: scripts used for analysis and other data are available from S. Singhal upon request.