cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r6dv6
title: Data from: Progression of neuronal damage in an in vitro model of the ischemic penumbra

description: Improvement of neuronal recovery in the ischemic penumbra around a brain
 infarct has a large potential to advance clinical recovery of patients
 with acute ischemic stroke. However, pathophysiological mechanisms leading
 to either recovery or secondary damage in the penumbra are not completely
 understood. We studied neuronal dynamics in a model system of the penumbra
 consisting of networks of cultured cortical neurons exposed to controlled
 levels and durations of hypoxia. Short periods of hypoxia (pO2≈20mmHg)
 reduced spontaneous activity, due to impeded synaptic function. After ≈6
 hours, activity and connectivity partially recovered, even during
 continuing hypoxia. If the oxygen supply was restored within 12 hours,
 changes in network connectivity were completely reversible. For longer
 periods of hypoxia (12–30 h), activity levels initially increased, but
 eventually decreased and connectivity changes became partially
 irreversible. After ≈30 hours, all functional connections disappeared and
 no activity remained. Since this complete silence seemed unrelated to
 hypoxic depths, but always followed an extended period of low activity, we
 speculate that irreversible damage (at least partly) results from
 insufficient neuronal activation. This opens avenues for therapies to
 improve recovery by neuronal activation.
description: Overview
 experimentsList of experiments that
 were used per analysisReadXDatScript to read .xdat files in MATLABCTRL experiments (1)Neural activity recordings during normoxia.CTRL(1).zipCTRL (2)control recordings during normoxia.CTRL(2).zip6 hours hypoxiaNeural activity before, during, and after 6 hours of hypoxia at pO2=20mmHg.6hours.zip12 hours hypoxiaRaw datafiles of 12 hours hypoxia at 10% of normoxia12hours.zip24 hours hypoxia (1)Neural activity recorded before, during and after 24 hours of hypoxia at pO2=20mmHg.24hours(1).zip24 hours hypoxia(2)Activity recording before, during and after 24 hours of hypoxia at pO2=20mmHg.24hours(2).zip48 hours hypoxia pO2=20mmHgActivity recording before, during and after 48 hours of hypoxia at pO2=20mmHg48hours-10%O2.zip48 hours hypoxia at pO2=80mmHg(1)Activity recording before, during and after 24 hours of hypoxia at pO2=80mmHg.48hours-50%O2(1).zip48 hours hypoxia at pO2=80mmHg(2)Activity recording before, during and after 24 hours of hypoxia at pO2=80mmHg.48hours-50%O2(2).zipLifeDeath Stainingfluorescent images of combined PI (red) and DAPI (blue)staining
DOI: 10.35079/hbm953.llpl.923
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.5061/dryad.b5908
title: Data from: The first multi-gene phylogeny of the Macrostomorpha sheds light on the evolution of sexual and asexual reproduction in basal Platyhelminthes

description: The Macrostomorpha—an early branching and species-rich clade of
 free-living flatworms—is attracting interest because it contains
 Macrostomum lignano, a versatile model organism increasingly used in
 evolutionary, developmental, and molecular biology. We elucidate the
 macrostomorphan molecular phylogeny inferred from both nuclear (18S and
 28S rDNA) and mitochondrial (16S rDNA and COI) marker genes from 40
 representatives. Although our phylogeny does not recover the
 Macrostomorpha as a statistically supported monophyletic grouping, it (i)
 confirms many taxa previously proposed based on morphological evidence,
 (ii) permits the first placement of many families and genera, and (iii)
 reveals a number of unexpected placements. Specifically, Myozona and
 Bradynectes are outside the three classic families (Macrostomidae,
 Microstomidae and Dolichomacrostomidae) and the asexually fissioning
 Myomacrostomum belongs to a new subfamily, the Myozonariinae nov. subfam.
 (Dolichomacrostomidae), rather than diverging early. While this represents
 the first evidence for asexuality among the Dolichomacrostomidae, we show
 that fissioning also occurs in another Myozonariinae, Myozonaria fissipara
 nov. sp. Together with the placement of the (also fissioning)
 Microstomidae, namely as the sister taxon of Dolichomacrostomidae, this
 suggests that fissioning is not basal within the Macrostomorpha, but
 rather restricted to the new taxon Dolichomicrostomida
 (Dolichomacrostomidae + Microstomidae). Furthermore, our phylogeny allows
 new insights into the evolution of the reproductive system, as ancestral
 state reconstructions reveal convergent evolution of gonads, and male and
 female genitalia. Finally, the convergent evolution of sperm storage
 organs in the female genitalia appears to be linked to the widespread
 occurrence of hypodermic insemination among the Macrostomorpha.
description: Janssen et al. 2015 MPE
 dataset dryadThis data file contains
 digital morphological vouchers of all sequenced specimen and additional
 information about the molecular analysis.Janssen_et_al_2015_MPE_dataset_dryad.zip
DOI: 10.35079/hbm266.znrq.299
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.5061/dryad.36sv8
title: Data from: Recent lineage diversification in a venomous snake through dispersal across the Amazon River

description: Identifying the evolutionary and ecological mechanisms that drive lineage
 diversification in the species-rich tropics is of broad interest to
 evolutionary biologists. Here, we use phylogeographic and demographic
 analyses of genomic scale RADseq data to assess the impact of a large
 geographic feature, the Amazon River, on lineage formation in a venomous
 pitviper, Bothrops atrox. We compared genetic differentiation in samples
 from four sites near Santarem, Brazil that spanned the Amazon and
 represented major habitat types. A species delimitation analysis
 identified each population as a distinct evolutionary lineage while a
 species tree analysis with populations as taxa revealed a phylogenetic
 tree consistent with dispersal across the Amazon from north to south.
 Phylogenetic analyses of mtDNA variation confirmed this pattern and
 suggest that all lineages originated during the mid- to late-Pleistocene.
 Historical demographic analyses support a population model of lineage
 formation through isolation between lineages with low ongoing migration
 between large populations and reject a model of differentiation through
 isolation by distance alone. Our results provide a rare example of a
 phylogeographic pattern demonstrating dispersal over evolutionary time
 scales across a large tropical river and suggest a role for the Amazon
 River as a driver of in-situ divergence by both impeding (but not
 preventing) gene flow and through parapatric differentiation along an
 ecological gradient.
description: Batrox6_Part1.txtPartial raw fastq data file (Part 1 of 3). Concatenate with Parts 2 and 3 prior to analysis.Batrox6_Part2.txtPartial raw fastq data file (Part 2 of 3). Concatenate with Parts 1 and 3 prior to analysis.Batrox6_Part3.txtPartial raw fastq data file (Part 3 of 3). Concatenate with Parts 1 and 2 prior to analysis.Batrox13.txt.tarRaw fastq data file.Batrox26.txt.tarRaw fastq data file.Batrox28.txt.tarRaw fastq data file.Batrox50B.txtRaw fastq data file.Batrox51.txtRaw fastq data file.Batrox55.txtRaw fastq data file.Batrox66.txtRaw fastq data file.Batrox69_Part1.txtPartial raw fastq data file (Part 1 of 2). Concatenate with Parts 2 prior to analysis.Batrox69_Part2.txtPartial raw fastq data file (Part 2 of 2). Concatenate with Part 1 prior to analysis.Batrox105.txtRaw fastq data file.Batrox_BarcodeFilesBarcode files (Individual sample names and associated barcode/molecular identifier) associated with AftrRAD runs.
DOI: 10.5061/dryad.2th78
title: Data from: A quantitative electrophysiological biomarker of duplication 15q11.2-q13.1 syndrome

description: Background: Duplications of 15q11.2-q13.1 (Dup15q syndrome) are highly
 penetrant for autism spectrum disorder (ASD). A distinct
 electrophysiological (EEG) pattern characterized by excessive activity in
 the beta band has been noted in clinical reports. We asked whether EEG
 power in the beta band, as well as in other frequency bands, distinguished
 children with Dup15q syndrome from those with non-syndromic ASD and then
 examined the clinical correlates of this electrophysiological biomarker in
 Dup15q syndrome. Methods: In the first study, we recorded spontaneous EEG
 from children with Dup15q syndrome (n = 11), age-and-IQ-matched children
 with ASD (n = 10) and age-matched typically developing (TD) children (n =
 9) and computed relative power in 6 frequency bands for 9 regions of
 interest (ROIs). Group comparisons were made using a repeated measures
 analysis of variance. In the second study, we recorded spontaneous EEG
 from a larger cohort of individuals with Dup15q syndrome (n = 27) across
 two sites and examined age, epilepsy, and duplication type as predictors
 of beta power using simple linear regressions. Results: Spontaneous beta1
 (12 – 20 Hz) and beta2 (20 – 30 Hz) power were significantly higher in
 Dup15q syndrome compared with both comparison groups, while delta (1 – 4
 Hz) was significantly lower than both comparison groups. Effect sizes in
 all three frequency bands were large (|d| &gt; 1). In the second
 study, we found that beta2 power was significantly related to epilepsy
 diagnosis in Dup15q syndrome. Conclusions: Here, we have identified an
 electrophysiological biomarker of Dup15q syndrome that may facilitate
 clinical stratification, treatment monitoring, and measurement of target
 engagement for future clinical trials. Future work will investigate the
 genetic and neural underpinnings of this electrophysiological signature as
 well as the functional consequences of excessive beta oscillations in
 Dup15q syndrome.
description: Study1_1Study1_2Study1_3Study1_4Study1_5Study1_6Study2_1Study2_2Study2_3Study2_4Matlab ScriptsPROTOCOL FOR PROCESSING RESTING EEGASD ControlsTD Controls
DOI: 10.35079/hbm755.hxkj.225
title: Visium (no probes) data from the ovary (left) of a 19-year-old white female
DOI: 10.35079/hbm383.hrgg.224
title: Visium (no probes) data from the fallopian tube (left) of a 19-year-old white female
DOI: 10.5061/dryad.5q0m8
title: Data from: Genomic evidence for role of inversion 3RP of Drosophila melanogaster in facilitating climate change adaptation

description: Chromosomal inversion polymorphisms are common in animals and plants, and
 recent models suggest that alternative arrangements spread by capturing
 different combinations of alleles acting additively or epistatically to
 favour local adaptation. It is also thought that inversions typically
 maintain favoured combinations for a long time by suppressing
 recombination between alternative chromosomal arrangements. Here, we
 consider patterns of linkage disequilibrium and genetic divergence in an
 old inversion polymorphism in Drosophila melanogaster (In(3R)Payne) known
 to be associated with climate change adaptation and a recent invasion
 event into Australia. We extracted, karyotyped and sequenced whole
 chromosomes from two Australian populations, so that changes in the
 arrangement of the alleles between geographically separated tropical and
 temperate areas could be compared. Chromosome-wide linkage disequilibrium
 (LD) analysis revealed strong LD within the region spanned by In(3R)Payne.
 This genomic region also showed strong differentiation between the
 tropical and the temperate populations, but no differentiation between
 different karyotypes from the same population, after controlling for
 chromosomal arrangement. Patterns of differentiation across the chromosome
 arm and in gene ontologies were enhanced by the presence of the inversion.
 These data support the notion that inversions are strongly selected by
 bringing together combinations of genes, but it is still not clear if such
 combinations act additively or epistatically. Our data suggest that
 climatic adaptation through inversions can be dynamic, reflecting changes
 in the relative abundance of different forms of an inversion and ongoing
 evolution of allelic content within an inversion.
description: Scripts and manual for
 bioinformatic analysesRVR_pipeline.shChr 3L -&gt; Population - Is [Alignment Files]3LIs_crams.tar.bz2Chr 3L -&gt; Population - Ys [Alignment Files]3LYs_crams.tar.bz2Chr 3L -&gt; Population - Ii [Alignment Files]3LIi_crams.tar.bz2Chr 3R -&gt; Population - Is [Alignment Files]3RIs_crams.tar.bz2Chr 3R -&gt; Population - Ys [Alignment Files]3RYs_crams.tar.bz2Chr 3R -&gt; Population - Ii [Alignment Files]3RIi_crams.tar.bz2Imputed and combined variant call filesVCF files for 3 populations after data imputation3L-3R_Imputed_Merged_Variant_calls.tar.gzRaw variant calls from alignment filesVCF files created using GATK UnifiedGenotyper from alignment files3L-3R_Raw_variant_calls.tar.gzFst calculationsFST calculations for all comparisons per SNP and in 200kb windows sliding every 20kb, using VCFTOOLSFst_calculations_VCFTOOLS.tar.gz
DOI: 10.35079/hbm684.qknr.622
title: Visium (no probes) data from the fallopian tube (left) of a 19-year-old white female
DOI: 10.35079/hbm859.vpnb.462
title: Visium (no probes) data from the fallopian tube (left) of a 19-year-old white female
DOI: 10.5061/dryad.qs43p
title: Data from: Mosquitoes host communities of bacteria that are essential for development but vary greatly between local habitats

description: Mosquitoes are insects of interest because several species vector
 disease-causing pathogens to humans and other vertebrates. We previously
 reported that mosquitoes from long-term laboratory cultures require living
 bacteria in their gut to develop, but development does not depend on
 particular species of bacteria. Here, we focused on three distinct but
 interrelated areas of study to better understand the role of bacteria in
 mosquito development by studying field and laboratory populations of Aedes
 aegypti, Aedes albopictus and Culex quinquefasciatus from the southeastern
 United States. Sequence analysis of bacterial 16S rRNA gene amplicons
 showed that bacterial community composition differed substantially in
 larvae from different collection sites, whereas larvae from the same site
 shared similarities. Although previously unknown to be infected by
 Wolbachia, results also indicated that Ae. aegypti from one field site
 hosted a dual infection. Regardless of collection site or factors like
 Wolbachia infection, however, each mosquito species required living
 bacteria in their digestive tract to develop. Results also identified
 several concerns in using antibiotics to eliminate the bacterial community
 in larvae in order to study its developmental consequences. Altogether,
 our results indicate that several mosquito species require living bacteria
 for development. We also hypothesize these species do not rely on
 particular bacteria because larvae do not reliably encounter the same
 bacteria in the aquatic habitats they develop in.
description: Raw data files and R
 scriptOligotyping input
 sequences part 1 of 3seqs_split_1.fastaOligotyping input sequences part 2 of 3seqs_split_2.fastaOligotyping input sequences part 3 of 3seqs_split_3.fastaOligotyping input taxonomic assignmentstax_assignments.txtQIIME input sequences part 1 of 3qiime_seqs_split_1.fastaQIIME input sequences part 2 of 3qiime_seqs_split_2.fastaQIIME input sequences part 3 of 3qiime_seqs_split_3.fasta
DOI: 10.5061/dryad.q2b49
title: Data from: GIbPSs: a toolkit for fast and accurate analyses of genotyping-by-sequencing data without a reference genome

description: Genotyping-by-sequencing (GBS) and related methods are increasingly used
 for studies of non-model organisms from population genetic to phylogenetic
 scales. We present GIbPSs, a new genotyping toolkit for the analysis of
 data from various protocols such as RAD, double-digest RAD, GBS, and
 two-enzyme GBS without a reference genome. GIbPSs can handle paired-end
 GBS data and is able to assign reads from both strands of a restriction
 fragment to the same locus. GIbPSs is most suitable for population genetic
 and phylogeographic analyses. It avoids genotyping errors due to indel
 variation by identifying and discarding affected loci. GIbPSs creates a
 genotype database that offers rich functionality for data filtering and
 export in numerous formats. We performed comparative analyses of simulated
 and real GBS data with GIbPSs and another program, pyRAD. This program
 accounts for indel variation by aligning homologous sequences. GIbPSs
 performed better than pyRAD in several aspects. It required much less
 computation time and displayed higher genotyping accuracy. GIbPSs retained
 smaller numbers of loci overall in analyses of real GBS data. It
 nevertheless delivered more complete genotype matrices with greater locus
 overlap between individuals and greater numbers of loci sampled in all
 individuals.
description: M_tanosi_1Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.M_tanosi_2Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.M_tanosi_3Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.M_tanosi_4Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.M_tanosi_5Three pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.M_tanosi_6Two pairs of gzip-compressed fastq files with paired-end GBS sequence data from Microcebus tanosi.
DOI: 10.35079/hbm477.hnmq.387
title: Visium (no probes) data from the fallopian tube (left) of a 19-year-old white female
DOI: 10.5061/dryad.gn250
title: Data from: Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding

description: The ESCRT machinery mediates reverse membrane scission. By quantitative
 fluorescence lattice light-sheet microscopy, we have shown that ESCRT-III
 subunits polymerize rapidly on yeast endosomes, together with the
 recruitment of at least two Vps4 hexamers. During their 3-45 second
 lifetimes, the ESCRT-III assemblies accumulated 75-200 Snf7 and 15-50
 Vps24 molecules. Productive budding events required at least two
 additional Vps4 hexamers. Membrane budding was associated with continuous,
 stochastic exchange of Vps4 and ESCRT-III components, rather than steady
 growth of fixed assemblies, and depended on Vps4 ATPase activity. An
 all-or-none step led to final release of ESCRT-III and Vps4. Tomographic
 electron microscopy demonstrated that acute disruption of Vps4 recruitment
 stalled membrane budding. We propose a model in which multiple Vps4
 hexamers (four or more) draw together several ESCRT-III filaments. This
 process induces cargo crowding and inward membrane buckling, followed by
 constriction of the nascent bud neck and ultimately ILV generation by
 vesicle fission.
description: source
 fileNotes: 1. includes all
 detected and tracked object data from deskewed volumes. 2. Analyzed data
 excluded objects at volume boundaries, cut tracks and compound tracks. 3.
 Fitted amplitudes are converted to single molecule values from the
 calibration curve generated for each power condition before each
 experiment.Source
 file.matSource File
 notes.xlsx
DOI: 10.5061/dryad.43n2j
title: Data from: Fetal genome profiling at 5 weeks of gestation after noninvasive isolation of trophoblast cells from the endocervical canal

description: Single-gene mutations account for more than 6000 diseases, 10% of all
 pediatric hospital admissions, and 20% of infant deaths. Down syndrome and
 other aneuploidies occur in more than 0.2% of births worldwide and are on
 the rise because of advanced reproductive age. Birth defects of genetic
 origin can be diagnosed in utero after invasive extraction of fetal
 tissues. Noninvasive testing with circulating cell-free fetal DNA is
 limited by a low fetal DNA fraction. Both modalities are unavailable until
 the end of the first trimester. We have isolated intact trophoblast cells
 from Papanicolaou smears collected noninvasively at 5 to 19 weeks of
 gestation for next-generation sequencing of fetal DNA. Consecutive matched
 maternal, placental, and fetal samples (n = 20) were profiled by multiplex
 targeted DNA sequencing of 59 short tandem repeat and 94 single-nucleotide
 variant sites across all 24 chromosomes. The data revealed fetal DNA
 fractions of 85 to 99.9%, with 100% correct fetal haplotyping. This
 noninvasive platform has the potential to provide comprehensive fetal
 genomic profiling as early as 5 weeks of gestation.
description: Data-set-1Data-set-2Data-set-3Data-set-4Data-set-5Data-set-6Data-set-7Data-set-8Data-set-9Data-set-10
DOI: 10.35079/hbm926.qqpb.289
title: Visium (no probes) data from the fallopian tube (left) of a 19-year-old white female
DOI: 10.5061/dryad.b6vh6
title: Data from: The aggregate site frequency spectrum (aSFS) for comparative population genomic inference

description: Understanding how assemblages of species responded to past climate change
 is a central goal of comparative phylogeography and comparative population
 genomics, and an endeavor that has increasing potential to integrate with
 community ecology. New sequencing technology now provides the potential to
 gain complex demographic inference at unprecedented resolution across
 assemblages of non-model species. To this end, we introduce the aggregate
 site frequency spectrum (aSFS), an expansion of the site frequency
 spectrum to use single nucleotide polymorphism (SNP) datasets collected
 from multiple, co-distributed species for assemblage-level demographic
 inference. We describe how the aSFS is constructed over an arbitrary
 number of independent population samples and then demonstrate how the aSFS
 can differentiate various multi-species demographic histories under a wide
 range of sampling configurations while allowing effective population sizes
 and expansion magnitudes to vary independently. We subsequently couple the
 aSFS with a hierarchical approximate Bayesian computation (hABC) framework
 to estimate degree of temporal synchronicity in expansion times across
 taxa, including an empirical demonstration with a dataset consisting of
 five populations of the threespine stickleback (Gasterosteus aculeatus).
 Corroborating what is generally understood about the recent post-glacial
 origins of these populations, the joint aSFS/hABC analysis strongly
 suggests that the stickleback data are most consistent with synchronous
 expansion after the Last Glacial Maximum (posterior probability = 0.99).
 The aSFS will have general application for multi-level statistical
 frameworks to test models involving assemblages and/or communities and as
 large-scale SNP data from non-model species become routine, the aSFS
 expands the potential for powerful next-generation comparative population
 genomic inference.
description: Simulation Scripts and
 ResultsSimulation parameter
 files, scripts, and results. Each directory pertains to a separate
 simulation run. The directories are numerically ordered according to their
 respective simulation run's presentation in the paper. Each directory
 is named according to its specific simulation run or section in the
 Supporting Materials. Within each directory is a "Description"
 file that lists the scripts used and the parameterizations
 utilized.simulation_scripts_results.zipStickleback DataStickleback RAD-seq data bioinformatics scripts and files. Data files include sorted raw reads, reference genome, alignment files, stacks outputs, intermediate files between stacks outputs and per-population SFSs, and SFSs.stickleback_data.zip
DOI: 10.15468/dl.xmqb2r
title: Occurrence Download

description: A dataset containing 653 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Funaria hygrometrica"
 ]
}

 The dataset includes 653 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000433-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.