cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vd094
title: Data from: Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

description: Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred
 to as meiofauna) are ubiquitous in marine sediments and likely play
 pivotal roles in maintaining ecosystem function. Although the deep-sea
 benthos represents one of the world’s largest habitats, we lack a firm
 understanding of the biodiversity and community interactions amongst
 meiobenthic organisms in this ecosystem. Within this vast environment key
 questions concerning the historical genetic structure of species remain a
 mystery, yet have profound implications for our understanding of global
 biodiversity and how we perceive and mitigate the impact of environmental
 change and anthropogenic disturbance. Using a metagenetic approach, we
 present an intensive assessment of microbial eukaryote communities across
 depth gradients (shallow water to abyssal) and ocean basins (deep-sea
 Pacific and Atlantic). Our results show that while some taxa can maintain
 eurybathic ranges and cosmopolitan deep-sea distributions, the majority of
 species appear to be regionally restricted in marine habitats. For OCTUs
 reporting wide distributions, there appears to be a taxonomic bias towards
 a small subset of taxa in most phyla; such bias may be driven by specific
 life history traits amongst these organisms. In addition, low genetic
 divergence between geographically disparate deep-sea sites suggests either
 a shorter coalescence time between deep-sea regions or slower rates of
 evolution across this vast oceanic ecosystem. While high-throughput
 studies allow for broad assessment of genetic patterns across microbial
 eukaryote communities, intragenomic variation in rRNA gene copies and the
 patchy coverage of reference databases currently present substantial
 challenges for robust taxonomic interpretations of eukaryotic datasets.
description: Clustered_OTUdataProcessed raw data clustered into Operational Taxonomic units in the QIIME, OCTUPUS, and AmpliconNoise pipelines. Contains OTU representative sequences (FASTA files), BLAST-derived taxonomy (tab-delimited text files), and OTU mapping file displaying the site distribution within OTUs (tab-delimited text files).Raw 454 DataRaw sequence reads and associated quality file (~1.2 million sequences averaging 350-450 bp in length) generated on a GS FLX Titanium platform in August 2009.
DOI: 10.5061/dryad.vq1dc
title: Data from: Diflunisal inhibits prestin by chloride-dependent mechanism

description: The motor protein prestin is a member of the SLC26 family of anion
 antiporters and is essential to the electromotility of cochlear outer hair
 cells and for hearing. The only direct inhibitor of electromotility and
 the associated charge transfer is salicylate, possibly through direct
 interaction with an anion-binding site on prestin. In a screen to identify
 other inhibitors of prestin activity, we explored the effect of the
 non-steroid anti-inflammatory drug diflunisal, which is a derivative of
 salicylate. We recorded prestin activity by whole-cell patch clamping HEK
 cells transiently expressing prestin and mouse outer hair cells. We
 monitored the impact of diflunisal on the prestin-dependent non-linear
 capacitance and electromotility. We found that diflunisal triggers two
 prestin-associated effects: a chloride independent increase in the surface
 area and the specific capacitance of the membrane, and a chloride
 dependent inhibition of the charge transfer and the electromotility in
 outer hair cells. We conclude that diflunisal affects the cell membrane
 organization and inhibits prestin-associated charge transfer and
 electromotility at physiological chloride concentrations. The inhibitory
 effects on hair cell function are noteworthy given the proposed use of
 diflunisal to treat neurodegenerative diseases.
description: ListOfExperiments+FitParamThis Excel file lists all the experiments with the conditions for each recording, and the resulting parameters that were obtained after fitting the NLC and the electromotility curve (when applicable).HEK_NLC recordingsElectrophysiology data for HEKs expressing prestin, in the absence and presence of diflunisal (refer to the list of experiments). The original file is .dat for HEKA analysis software. Files are also provided in a text format.OHC_NLC&eMThese are the data for the outer hair cell. Files are grouped by date and experiment number (refer to the list of experiments) The electrophysiology data are provided in HEKA format as well as text format. The videos of the electromotility are provided in as Tif files. The analysis of the electromotility is also included as individual Excel files for each recording.OHC_Dimension onlyThis file contains the pictures of OHCs that were not subjected to diflunisal treatment, and used only to obtain dimension data.
DOI: 10.5061/dryad.7h0g0
title: Data from: Phylogenomic analysis of yellowjackets and hornets (Hymenoptera: Vespidae, Vespinae)

description: The phylogenetic relationships among genera of the subfamily Vespinae
 (yellowjackets and hornets) remain unclear. Yellowjackets and hornets
 constitute one of the only two lineages of highly eusocial wasps, and the
 distribution of key behavioral traits correlates closely with the current
 classification of the group. The potential of the Vespinae to elucidate
 the evolution of social life, however, remains limited due to ambiguous
 genus-level relationships. Here, we address the relationships among genera
 within the Vespinae using transcriptomic (RNA-seq) data. We sequenced the
 transcriptomes of six vespid wasps, including three of the four genera
 recognized in the Vespinae, combined our data with publicly available
 transcriptomes, and assembled two matrices comprising 1,507 and 3,356
 putative single-copy genes. The results of our phylogenomic analyses
 recover Dolichovespula as more closely related to Vespa than to Vespula,
 therefore challenging the prevailing hypothesis of yellowjacket (Vespula +
 Dolichovespula) monophyly. This suggests that traits such as large colony
 size and high paternity arose in the genus Vespula following its early
 divergence from the remaining vespine genera.
description: Transcriptome assemblies
 (nucleotide)Transcriptomes assembled
 using paired-end Illumina reads and 454 GS-FLX Titanium reads. Assemblies
 were conducted using Trinity and MIRA.transcriptome_assemblies_nucleotide.zipCandidate coding regions (ORFs) identified within transcript sequences (nucleotide and peptide sequences)Candidate coding regions identified with TransDecoder.transcriptome_assemblies_orfs.zipNon-redundant candidate coding regions (peptide sequences)Protein sequences used for orthology inference.transcriptome_assemblies_orfs_nr_cdhit.zipSets of inferred orthologsWe inferred orthologs using the pipeline of Yang and Smith (2014, http://mbe.oxfordjournals.org/content/31/11/3081), aligned sequences using MAFFT, and trimmed alignments using Gblocks.orthologs.zipConcatenated orthologs used for phylogenetic analysisMatrices of concatenated orthologs in PHYLIP format and partition files used for phylogenetic analysis with RAxML.concatenated_data_matrices.zip
DOI: 10.5061/dryad.591gf
title: Data from: Identification, visualization and clonal analysis of intestinal stem cells in fish

description: Recently, a stochastic model of symmetrical stem cell division followed by
 neutral drift has been proposed for intestinal stem cells (ISCs). This
 division mode has been suggested to represent the predominant mode of stem
 cell progression in mammals. In contrast, stem cells in the retina of
 teleost fish show a preferential asymmetric division mode. To address
 whether the mode of stem cell division is following phylogenetic or
 ontogenetic routes we characterized and analysed the entire
 gastrointestinal system with a particular focus on ISCs in the teleost
 medaka (Oryzias latipes). We analysed the entire intestine in adult medaka
 by X-ray micro-computed tomography within the intact body and combined
 that analysis with the cellular and molecular composition of the
 intestinal system. This allowed correlating the 3D topography with
 functional domains of the intestinal system. Morphology and gene
 expression data consistently argue for a subdivision of the medaka
 intestine into a small and large intestine. Analysis of ISCs in
 proliferation assays and via genetically encoded lineage-tracing
 highlights a stem cell niche in the furrow between the long intestinal
 folds. This niche is functionally equivalent to the mammalian intestinal
 crypts and stem cells in this compartment are characterized by the
 expression of sox9, axin2 as well as lgr5, homologs of mammalian ISC
 markers, emphasizing the evolutionary conservation of the Wnt-pathway
 components in the stem cell niche of the intestine. Consistent with a
 preferential symmetric division mode of medaka ISCs, the stochastic,
 sparse initial labelling of ISCs ultimately resulted in extended labelled
 or unlabelled domains originating from single stem cells in the furrow
 niche contributing to both, homeostasis and growth. Thus different modes
 of stem cell division co-evolved within one organism, and in the absence
 of physical isolation in crypts, ISCs contribute to homeostatic growth.
description: Movie1-medaka anterior
 gutAghaallaei-Gruhl et
 al-development-DEVELOP:2015:134098-moviesmovie1.mp4movie2-medaka-posterior gutAghaallaei-Gruhl et al-development-DEVELOP:2015:134098-movie-2movie2.mp4movie3-medaka-GaudiRSG-10dpi10daiAghaallaei-Gruhl et al-development-DEVELOP:2015:134098-movie-3movie4-medaka-GaudiRSG-30dpi.Aghaallaei-Gruhl et al-development-DEVELOP:2015:134098-movie-4movie5-medaka-GaudiRSG-150dpiAghaallaei-Gruhl et al-development-DEVELOP:2015:134098-movie-5movie6-medaka-GaudiBBW-90dpiAghaallaei-Gruhl et al-development-DEVELOP:2015:134098-movie-6movie6-medaka-GaudiBB-90dpi.avimovie6b-Medaka-GaudiBBW-rowAghaallaei-Gruhl et al-development-DEVELOP:2015:134098-movie6b90daiBBWrawMIPwobb_1080p.avi
DOI: 10.5061/dryad.5jq5t36
title: Data from: A broadly applicable COI primer pair and an efficient single‐tube amplicon library preparation protocol for metabarcoding

description: The nucleotide variation in the cytochrome c oxidase subunit I (COI) gene
 makes it ideal for assigning sequences to species. However, this
 variability also makes it difficult to design truly universal primers.
 Here, we present the forward primer “Sauron-S878”, specifically designed
 to facilitate library preparation for metabarcoding. This primer is
 modified to improve the coverage of terrestrial species compared to the
 primer mCOIintF, optimized for aquatic systems, which raised the in-silico
 coverage from 74.4% to 98.3% of available NCBI sequences (perfect match in
 3’-region, up to 3 mismatches in remaining primer). When paired with the
 reverse primer “jgHCO2198” (fragment length ~313 bp) these primers
 amplified 98.4% of 255 tested DNA extracts from various taxa, which is
 better than many other common COI barcoding primers. Furthermore, a single
 tube protocol was developed, wherein these primers amplify the target
 gene, and attach MIDs and Illumina sequencing adapters in one reaction.
 This eliminates the need for re-amplification or enzymatic ligation during
 library preparation while keeping the flexibility to modularly combine
 primers and MIDs. Using the single tube approach, three replicates of
 three mock samples were sequenced on a MiSeq platform with no adverse
 effects compared to commercial Nextera indexing kits. From this run 75% of
 all included taxa could be recovered, with no considerable bias among
 taxonomic groups. Despite the fact that 98.4% of the extracts were
 confirmed to amplify in-vitro, this number was lower than expected. A
 reason for this discrepancy was a clear link between the relative
 concentration of a specific DNA type in the template and the number of
 returned reads for this DNA. We would argue that such a bias may be
 especially problematic in metabarcoding where samples usually contain
 trace DNA in unknown amounts. However, how this affects the completeness
 of metabarcoding results has yet been poorly investigated.
description: Allignment_SauronReads of Sequenced Mock Samplesraw data of Mock Samples sequenced on the Illumina MiSeq Plattform. Split by Mock Sample Pool, Primers Used, Library Preparation Protocol, and Replicate numberNGS_Sequences.rar
DOI: 10.5061/dryad.k7455
title: Data from: Identification of novel variants in LTBP2 and PXDN using whole-exome sequencing in developmental and congenital glaucoma

description: Background Primary congenital glaucoma (PCG) is the most common form of
 glaucoma in children. PCG occurs due to the developmental defects in the
 trabecular meshwork and anterior chamber of the eye. The purpose of this
 study is to identify the causative genetic variants in three families with
 developmental and primary congenital glaucoma (PCG) with a recessive
 inheritance pattern. Methods DNA samples were obtained from consanguineous
 families of Pakistani ancestry. The CYP1B1 gene was sequenced in the
 affected probands by conventional Sanger DNA sequencing. Whole exome
 sequencing (WES) was performed in DNA samples of four individuals
 belonging to three different CYP1B1-negative families. Variants identified
 by WES were validated by Sanger sequencing. Results WES identified
 potentially causative novel mutations in the latent transforming growth
 factor beta binding protein 2 (LTBP2) gene in two PCG families. In the
 first family a novel missense mutation (c.4934G&gt;A; p.Arg1645Glu)
 co-segregates with the disease phenotype, and in the second family a novel
 frameshift mutation (c.4031_4032insA; p.Asp1345Glyfs*6) was identified. In
 a third family with developmental glaucoma a novel mutation
 (c.3496G&gt;A; p.Gly1166Arg) was identified in the PXDN gene, which
 segregates with the disease. Conclusions We identified three novel
 mutations in glaucoma families using WES; two in the LTBP2 gene and one in
 the PXDN gene. The results will not only enhance our current understanding
 of the genetic basis of glaucoma, but may also contribute to a better
 understanding of the diverse phenotypic consequences caused by mutations
 in these genes.
description: DNA12-14956.hcdiffsExome sequencing dataDNA13-07606.hcdiffsExome sequencing dataDNA13-07610.hcdiffsDNA13-07602.hcdiffs
DOI: 10.5061/dryad.kr8kk
title: Data from: Haplotype-phased synthetic long reads from short-read sequencing

description: Next-generation DNA sequencing has revolutionized the study of biology.
 However, the short read lengths of the dominant instruments complicate
 assembly of complex genomes and haplotype phasing of mixtures of similar
 sequences. Here we demonstrate a method to reconstruct the sequences of
 individual nucleic acid molecules up to 11.6 kilobases in length from
 short (150-bp) reads. We show that our method can construct
 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic
 samples, full-length mRNA sequences from human cancer cell lines, and
 individual HIV env gene variants from a mixture. The preparation of
 multiple samples can be multiplexed into a single tube, further reducing
 effort and cost relative to competing approaches. Our approach generates
 sequencing libraries in three days from less than one microgram of DNA in
 a single-tube format without custom equipment or specialized expertise.
description: gelsemium_velvet_assemblygelsemium_velvet_assembly.fastagelsemium_sspace_assemblygelsemium_sspace_assembly.fasta
DOI: 10.5281/zenodo.18377369
title: Datasets for "Imposing Boundary Conditions on Neural Operators via Learned Function Extensions"

description: This is a collection of 18 datasets created by the work "Imposing Boundary Conditions on Neural Operatorsvia Learned Function Extensions."  More details about the datasets are available in the paper.
description: This collection contains multiple datasets, available for download in the pages referenced below. Please see the readme.md file for instructions on how use these files.




Problem
Geometry
Configuration
Folder name
DOI


Poisson
Circle
Dirichlet
poisson-circle-bc1
10.5281/zenodo.18376965


Poisson
Square
Dirichlet
poisson-square-bc1
10.5281/zenodo.18377306


Poisson
Boomerang
Dirichlet
poisson-boomerang-bc1
10.5281/zenodo.18377477


Poisson
Circle
Mixed
poisson-circle-bc4
10.5281/zenodo.18377489


Poisson
Square
Mixed
poisson-square-bc4
10.5281/zenodo.18377501


Poisson
Boomerang
Mixed
poisson-boomerang-bc4
10.5281/zenodo.18377507


Poisson
Circle
Mixed+
poisson-circle-bc5
10.5281/zenodo.18377511


Poisson
Square
Mixed+
poisson-square-bc5
10.5281/zenodo.18377514


Poisson
Boomerang
Mixed+
poisson-boomerang-bc5
10.5281/zenodo.18377531


Elasticity
Circle$^H$
Steel
elasticity-circlehollow-m1


10.5281/zenodo.18377539



Elasticity
Square$^H$
Steel
elasticity-squarehollow-m1
10.5281/zenodo.18377676


Elasticity
Boomerang$^H$
Steel
elasticity-boomcircletri-m1
10.5281/zenodo.18377692


Elasticity
Circle$^H$
Bone
elasticity-circlehollow-m2
10.5281/zenodo.18377699


Elasticity
Square$^H$
Bone
elasticity-squarehollow-m2
10.5281/zenodo.18377706


Elasticity
Boomerang$^H$
Bone
elasticity-boomcircletri-m2
10.5281/zenodo.18377714


Hyperelasticity
Circle$^H$
Rubber
elasticity-circlehollow-m3
10.5281/zenodo.18377723


Hyperelasticity
Square$^H$
Rubber
elasticity-squarehollow-m3
10.5281/zenodo.18377727


Hyperelasticity
Boomerang$^H$
Rubber
elasticity-boomcircletri-m3
10.5281/zenodo.18377757
DOI: 10.5281/zenodo.18377370
title: Datasets for "Imposing Boundary Conditions on Neural Operators via Learned Function Extensions"

description: This is a collection of 18 datasets created by the work "Imposing Boundary Conditions on Neural Operatorsvia Learned Function Extensions."  More details about the datasets are available in the paper.
description: This collection contains multiple datasets, available for download in the pages referenced below. Please see the readme.md file for instructions on how use these files.




Problem
Geometry
Configuration
Folder name
DOI


Poisson
Circle
Dirichlet
poisson-circle-bc1
10.5281/zenodo.18376965


Poisson
Square
Dirichlet
poisson-square-bc1
10.5281/zenodo.18377306


Poisson
Boomerang
Dirichlet
poisson-boomerang-bc1
10.5281/zenodo.18377477


Poisson
Circle
Mixed
poisson-circle-bc4
10.5281/zenodo.18377489


Poisson
Square
Mixed
poisson-square-bc4
10.5281/zenodo.18377501


Poisson
Boomerang
Mixed
poisson-boomerang-bc4
10.5281/zenodo.18377507


Poisson
Circle
Mixed+
poisson-circle-bc5
10.5281/zenodo.18377511


Poisson
Square
Mixed+
poisson-square-bc5
10.5281/zenodo.18377514


Poisson
Boomerang
Mixed+
poisson-boomerang-bc5
10.5281/zenodo.18377531


Elasticity
Circle$^H$
Steel
elasticity-circlehollow-m1


10.5281/zenodo.18377539



Elasticity
Square$^H$
Steel
elasticity-squarehollow-m1
10.5281/zenodo.18377676


Elasticity
Boomerang$^H$
Steel
elasticity-boomcircletri-m1
10.5281/zenodo.18377692


Elasticity
Circle$^H$
Bone
elasticity-circlehollow-m2
10.5281/zenodo.18377699


Elasticity
Square$^H$
Bone
elasticity-squarehollow-m2
10.5281/zenodo.18377706


Elasticity
Boomerang$^H$
Bone
elasticity-boomcircletri-m2
10.5281/zenodo.18377714


Hyperelasticity
Circle$^H$
Rubber
elasticity-circlehollow-m3
10.5281/zenodo.18377723


Hyperelasticity
Square$^H$
Rubber
elasticity-squarehollow-m3
10.5281/zenodo.18377727


Hyperelasticity
Boomerang$^H$
Rubber
elasticity-boomcircletri-m3
10.5281/zenodo.18377757
DOI: 10.5061/dryad.tp736
title: Data from: Influence of in-situ oil sands development on caribou (Rangifer tarandus) movement

description: In-situ oil sands development (ISD) involves a network of facilities,
 wells, roads and pipelines to extract and transport subsurface bitumen.
 This technology is rapidly expanding and there is uncertainty whether ISDs
 restrict animal movement, leading to increased extinction probabilities
 for some wide-ranging species. Here we test for effects of simulated
 future (i.e., 50 years from now) and current ISDs on simulated movements
 of woodland caribou (Rangifer tarandus), a threatened species across North
 America. In simulations of future scenarios, we varied the spacing and
 permeability of ISDs and the presence/absence of protected areas.
 Permeability was measured as the number of times simulated caribou crossed
 ISDs with different levels of modelled permeability. We estimated the
 effects of these factors on caribou step length and annual home range
 size, key metrics of small and large spatiotemporal scales of movement,
 respectively. Current caribou crossings of above-ground pipeline features
 of ISDs were measured using camera traps and compared to expected caribou
 crossing rates based on present-day caribou movement simulations. Current
 crossing rates were evaluated within the context of predicted future
 crossing success rates necessary to maintain caribou step lengths and home
 ranges. With few exceptions, permeability across ISDs was the main factor
 affecting caribou movement, more so than spacing between developments or
 the presence of protected areas. However, minimal permeability (crossing
 rates of c. 15% to 60%, relative to an undisturbed site was needed to
 maintain existing home range size and step lengths. The effect of
 permeability on home range size and step length was non-linear, suggesting
 that small increases in permeability would provide a disproportionately
 greater benefit to caribou movement. Our predictions demonstrate that
 maintaining permeability across ISDs is more important than spacing
 between leases or including protected areas, and thus provides clear
 direction for mitigation efforts for features that will exist on the
 landscape for decades to come.
description: caribou_movement_simulation_20140810Simulated caribou movement location output for each scenario.
DOI: 10.5281/zenodo.18326067
title: Source Data - Hybrid antiferroelectric–ferroelectric domain walls in noncollinear antipolar oxides