cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rm660
title: Data from: Regulation of cell protrusions by small GTPases during fusion of the neural folds

description: Epithelial fusion is a crucial process in embryonic development, and its
 failure underlies several clinically important birth defects. For example,
 failure of neural fold fusion during neurulation leads to open neural tube
 defects including spina bifida. Using mouse embryos, we show that cell
 protrusions emanating from the apposed neural fold tips, at the interface
 between the neuroepithelium and the surface ectoderm, are required for
 completion of neural tube closure. By genetically ablating the
 cytoskeletal regulators Rac1 or Cdc42 in the dorsal neuroepithelium, or in
 the surface ectoderm, we show that these protrusions originate from
 surface ectodermal cells and that Rac1 is necessary for the formation of
 membrane ruffles which typify late closure stages, whereas Cdc42 is
 required for the predominance of filopodia in early neurulation. This
 study provides evidence for the essential role and molecular regulation of
 membrane protrusions prior to fusion of a key organ primordium in
 mammalian development.
description: Protrusion
 classificationThis dataset contains
 all the SEM images used for protrusion classification in Rolo et al.,
 along with a spreadsheet containing information about the embryos used
 (cross, genotype, somite-stage (ss)). All images were acquired at 2000x
 magnification with a with a JEOL 7401 FEGSEM (see Materials and Methods
 for full details).
DOI: 10.5064/f6vanjl8/f7wd5o
title: Silan-Ciruelas_PHL_Opt1_6B_Nica_1-5_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/hjpygm
title: Silan-Ciruelas_TUR_Opt2_5A_EdaDamla_1-5_Low_Low-Median.pdf
DOI: 10.5061/dryad.59q56g6
title: Data from: A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination

description: Genetic linkage maps are essential for comparative genomics, high quality
 genome sequence assembly and fine scale quantitative trait locus (QTL)
 mapping. In the present study we identified and genotyped markers via
 restriction-site associated DNA (RAD) sequencing and constructed a genetic
 linkage map based on 1,597 SNP markers of an interspecific F2 cross of two
 closely related Lake Victoria cichlids (Pundamilia pundamilia and P. sp.
 'red head'). The SNP markers were distributed on 22 linkage
 groups and the total map size was 1,594 cM with an average marker distance
 of 1.01 cM. This high-resolution genetic linkage map was used to anchor
 the scaffolds of the Pundamilia genome and estimate recombination rates
 along the genome. Via QTL mapping we identified a major QTL for sex in a
 ∼1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus
 LG 23 (Ore-LG23) and includes a well-known vertebrate sex-determination
 gene (amh).
description: marker position
 Pundamilia linkage mapText file giving the
 position of 1,597 loci on the Pundamilia linkage map and the respective
 positions on Pundamilia and Oreochromis referencesP_cross.MarkerPositions.txtchain file converting P_nyererei_v1 to v2Chain files to convert position between original (v1.0) and new reference (v2.0) of PundamiliaP_nyererei_v1.To.P_nyererei_v2.chainchain file converting P_nyererei_v2 to v1Chain files to convert position between new reference (v2.0) and original (v1.0) of PundamiliaP_nyererei_v2.To.P_nyererei_v1.chainP_nyererei_v2 annotationAnnotation file matching reference v2.0 position based on NCBI annotation release 101P_nyererei_v2.gff.gzrecombination rates PundamiliaText file giving the extrapolated recombination rates along Pundamilia reference genomeP_nyererei_v2.RecRates.txtgenotype file Pundamiliavcf file containing 7401 genotypes of 224 Pundamilia individualsP_cross.224ids.7401pos.vcfphenotypes for Pundamilia crossphenotypes for 224 Pundamilia individuals containing id, sex, size, and family idP_cross.Pheno.txtP_nyererei reference v2Fasta file of the improved Pundamilia reference genome (v2.0)P_nyererei_v2.fasta.gz
DOI: 10.5064/f6vanjl8/kjddfb
title: Silan-Ciruelas_USA_Opt2_5B_AnaliliaReglaGutierrez_1-5_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/ehtdj9
title: Silan-Ciruelas_TUR_Opt1_8B_Zeynep_1-5_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/w1ba2r
title: Silan-Ciruelas_FRA_Opt1_3A_1_Low-Median-High.pdf
DOI: 10.5064/f6vanjl8/apasak
title: Silan-Ciruelas_TUR_Opt2_4A_EdaDamla_1_High_Median-High.pdf
DOI: 10.5061/dryad.j3528bt
title: Data from: Detecting local diversity-dependence in diversification

description: Whether there are ecological limits to species diversification is a hotly
 debated topic. Molecular phylogenies show slowdowns in lineage
 accumulation, suggesting that speciation rates decline with increasing
 diversity. A maximum likelihood method to detect diversity-dependent
 diversification from phylogenetic branching times exists, but it assumes
 that diversity-dependence is a global phenomenon and therefore ignores
 that the underlying species interactions are mostly local, and not all
 species in the phylogeny co-occur locally. Here, we explore whether this
 maximum likelihood method based on the non-spatial diversity-dependence
 model can detect local diversity-dependence, by applying it to
 phylogenies, simulated with a spatial stochastic model of
 local-diversity-dependent speciation, extinction and dispersal between two
 local communities. We find that type I errors (falsely detecting
 diversity-dependence) are low, and the power to detect
 diversity-dependence is high when dispersal rates are not too low.
 Interestingly, when dispersal is high the power to detect
 diversity-dependence is even higher than in the non-spatial model.
 Moreover, estimates of intrinsic speciation rate, extinction rate and
 ecological limit strongly depend on dispersal rate. We conclude that the
 non-spatial diversity-dependent approach can be used to detect
 diversity-dependence in clades of species that live in not too
 disconnected areas, but parameter estimates must be interpreted
 cautiously.
description: Scenario3Scenario3.rar contains 100 tree data generated under Scenario 3 as mentioned in the paper.Scenario4Scenario4.rar contains 100 tree data generated under Scenario 4 as mentioned in the paper.Scenario5Scenario5.rar contains 100 tree data generated under Scenario 5 as mentioned in the paper.Scenario1Scenario1.rar contains 100 tree data generated under Scenario 1 as mentioned in the paper.Scenario2Scenario2.rar contains 100 tree data generated under Scenario 2 as mentioned in the paper.https://unishare.nl/index.php/s/LA6uO9Xf5TfKwR4The compelete file contains all simulate data and bootstrapping analysis. The external link is as following: https://unishare.nl/index.php/s/LA6uO9Xf5TfKwR4
DOI: 10.5064/f6vanjl8/ded5jq
title: Silan-Ciruelas_TUR_Opt2_4B_EdaDamla_1_High_Median-High.pdf
DOI: 10.5064/f6vanjl8/tllkf0
title: Silan-Ciruelas_PHL_Opt1-19A-Christelle_20years_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/s0p3l4
title: Silan-Ciruelas_BRA_Opt2_11A_MariaPaula_5-10_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/yqnkph
title: Silan-Ciruelas_PHL_Opt1_9B_Nica_5-10_Low_Low-Med.pdf
DOI: 10.5061/dryad.n435p
title: Data from: Platyzoan paraphyly based on phylogenomic data supports a non-coelomate ancestry of Spiralia

description: Based on molecular data three major clades have been recognized within
 Bilateria: Deuterostomia, Ecdysozoa and Spiralia. Within Spiralia,
 small-sized and simply organized animals such as flatworms, gastrotrichs
 and gnathostomulids have recently been grouped together as Platyzoa.
 However, the representation of putative platyzoans was low in the
 respective molecular phylogenetic studies, in terms of both, taxon number
 and sequence data. Furthermore, increased substitution rates in platyzoan
 taxa raised the possibility that monophyletic Platyzoa represents an
 artefact due to long-branch attraction. In order to overcome such
 problems, we employed a phylogenomic approach, thereby substantially
 increasing i) the number of sampled species within Platyzoa and ii)
 species-specific sequence coverage in datasets of up to 82,162 amino acid
 positions. Using established and new measures (long-branch score) we
 disentangled phylogenetic signal from misleading effects such as
 long-branch attraction. In doing so, our phylogenomic analyses did not
 recover a monophyletic origin of platyzoan taxa that, instead, appeared
 paraphyletic with respect to the other spiralians. Platyhelminthes and
 Gastrotricha formed a monophylum, which we name Rouphozoa. To the
 exclusion of Gnathifera, Rouphozoa and all other spiralians represent a
 monophyletic group, which we name Platytrochozoa. Platyzoan paraphyly
 suggests that the last common ancestor of Spiralia was a simple-bodied
 organism lacking coelomic cavities, segmentation and complex brain
 structures, and that more complex animals such as annelids evolved from
 such a simply organized ancestor. This conclusion contradicts alternative
 evolutionary scenarios proposing an annelid-like ancestor of Bilateria and
 Spiralia and several independent events of secondary reduction.
description: Struck_Platyzoa2014
DOI: 10.5064/f6vanjl8/hixmpo
title: Silan-Ciruelas_FRA_Opt1_6A_1_5_High_Low-Median.pdf
DOI: 10.5064/f6vanjl8/ye8kdr
title: Silan-Ciruelas_TUR_Opt2_19A_Kerem_Over20_Low_Median-High.pdf
DOI: 10.5281/zenodo.18009620
title: Reporter-gene-assisted small molecule inhibitor screening of heterochromatin boundary maintenance in Plasmodium falciparum

description: Supplementary Table for Chaper 3: Reporter-gene-assisted small molecule inhibitor screening of heterochromatin boundary maintenance in Plasmodium falciparum
DOI: 10.5281/zenodo.18009621
title: Reporter-gene-assisted small molecule inhibitor screening of heterochromatin boundary maintenance in Plasmodium falciparum

description: Supplementary Table for Chaper 3: Reporter-gene-assisted small molecule inhibitor screening of heterochromatin boundary maintenance in Plasmodium falciparum
DOI: 10.5061/dryad.vv34p8h
title: Data from: Deep phenotyping in zebrafish reveals genetic and diet-induced adiposity changes that may inform disease risk

description: The regional distribution of adipose tissues is implicated in a wide range
 of diseases. For example, proportional increases in visceral adipose
 tissue increase the risk for insulin resistance, diabetes and
 cardiovascular disease. Zebrafish offer a tractable model system by which
 to obtain unbiased and quantitative phenotypic information on regional
 adiposity, and deep phenotyping can explore complex disease-related
 adiposity traits. To facilitate deep phenotyping of zebrafish adiposity
 traits, we used pairwise correlations between 67 adiposity traits to
 generate stage-specific adiposity profiles that describe changing
 adiposity patterns and relationships during growth. Linear discriminant
 analysis classified individual fish according to adiposity profile with
 87.5% accuracy. Deep phenotyping of eight previously uncharacterized
 zebrafish mutants identified neuropilin 2b as a novel gene that alters
 adipose distribution. When we applied deep phenotyping to identify changes
 in adiposity during diet manipulations, zebrafish that underwent food
 restriction and re-feeding had widespread adiposity changes when compared
 to continuously-fed, equivalently-sized control animals. In particular,
 internal adipose tissues (e.g., visceral adipose) exhibited a reduced
 capacity to replenish lipid following food restriction. Together, these
 results in zebrafish establish a new deep phenotyping technique as an
 unbiased and quantitative method to help uncover new relationships between
 genotype, diet and adiposity.
description: minchin_rawls_2018_dryad_uploadNile Red images saved as .tif files for the mutant and food restricted cohorts. Image# corresponds to Fish# in Supplemental Table 1, and DRYAD# in Supplemental Table 2.JLR_DRYAD_UPLOAD.zip
DOI: 10.5064/f6vanjl8/y5dnuj
title: Silan-Ciruelas_FRA_Opt1_21A_Hector_LGBT_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/csvpu5
title: Silan-Ciruelas_TUR_Opt2_23A_Anil_LGBT_Unknown_Median-High.pdf
DOI: 10.5064/f6vanjl8/axswav
title: Silan-Ciruelas_TUR_Opt2_13A_NejlaNaz_10-20_Low_Low-Median.pdf
DOI: 10.5061/dryad.q8150
title: Data from: High specificity in circulating tumor cell identification is required for accurate evaluation of programmed death-ligand 1

description: Background: Expression of programmed-death ligand 1 (PD-L1) in non-small
 cell lung cancer (NSCLC) is typically evaluated through invasive biopsies;
 however, recent advances in the identification of circulating tumor cells
 (CTCs) may be a less invasive method to assay tumor cells for these
 purposes. These liquid biopsies rely on accurate identification of CTCs
 from the diverse populations in the blood, where some tumor cells share
 characteristics with normal blood cells. While many blood cells can be
 excluded by their high expression of CD45, neutrophils and other immature
 myeloid subsets have low to absent expression of CD45 and also express
 PD-L1. Furthermore, cytokeratin is typically used to identify CTCs, but
 neutrophils may stain non-specifically for intracellular antibodies,
 including cytokeratin, thus preventing accurate evaluation of PD-L1
 expression on tumor cells. This holds even greater significance when
 evaluating PD-L1 in epithelial cell adhesion molecule (EpCAM) positive and
 EpCAM negative CTCs (as in epithelial-mesenchymal transition (EMT)).
 Methods: To evaluate the impact of CTC misidentification on PD-L1
 evaluation, we utilized CD11b to identify myeloid cells. CTCs were
 isolated from patients with metastatic NSCLC using EpCAM, MUC1 or Vimentin
 capture antibodies and exclusion-based sample preparation (ESP)
 technology. Results: Large populations of CD11b+CD45lo cells were
 identified in buffy coats and stained non-specifically for intracellular
 antibodies including cytokeratin. The amount of CD11b+ cells misidentified
 as CTCs varied among patients; accounting for 33–100% of traditionally
 identified CTCs. Cells captured with vimentin had a higher frequency of
 CD11b+ cells at 41%, compared to 20% and 18% with MUC1 or EpCAM,
 respectively. Cells misidentified as CTCs ultimately skewed PD-L1
 expression to varying degrees across patient samples. Conclusions:
 Interfering myeloid populations can be differentiated from true CTCs with
 additional staining criteria, thus improving the specificity of CTC
 identification and the accuracy of biomarker evaluation.
description: Raw
 DataThis file contains the
 raw data supporting all figures in the manuscript. Flow cytometry data is
 in FCS file format, and can be read with programs such as flowjo. JEX data
 is in arff format and can be read with the R application as described in
 the manuscript.
DOI: 10.5064/f6vanjl8/t76prd
title: Silan-Ciruelas_BRA_Opt2_13B_10_20_Low_Low-Median.pdf
DOI: 10.5064/f6vanjl8/uoel4h
title: Silan-Ciruelas_USA_Opt2_24A_Marina_LGBTQ+AnyLength_High_Median-High.pdf
DOI: 10.5061/dryad.th865
title: Data from: Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland

description: Genetic diversity in experimental, domesticated and wild populations of
 the related yeasts, Saccharomyces cerevisiae and S. paradoxus has been
 well described at the global scale. We investigated the population
 genomics of a local population on a small spatial scale to address two
 main questions. First, is there genomic variation in a S. paradoxus
 population at a spatial scale spanning centimeters (microsites) to tens of
 meters? Second, does the distribution of genomic variants persist over
 time? Our sample consisted of 42 S. paradoxus strains from 2014 and 43
 strains from 2015 collected from the same 72 microsites around four host
 trees (Quercus rubra and Q. alba) within 1km2 in a mixed hardwood forest
 in southern Ontario. Six additional S. paradoxus strains recovered from
 adjacent maple and beech trees in 2015 are also included in the sample.
 Whole-genome sequencing and genomic SNP analysis revealed five
 differentiated groups (clades) within the sampled area. The signal of
 persistence of genotypes in their microsites from 2014 to 2015 was highly
 significant. Isolates from the same tree tended to be more related than
 strains from different trees, with limited evidence of dispersal between
 trees. In growth assays, one genotype had a significantly longer lag phase
 than the other strains. Our results indicate that different clades
 co-exist at fine spatial scale, and that population structure persists
 over at least a one year interval in these wild yeasts, suggesting the
 efficacy of yearly sampling to follow longer term genetic dynamics in
 future studies.
description: cohort SNP
 filevariant file of all
 strains, contains all single nucleotide polymorphic sites that are
 bi-allelic only.all_bi-allelic-non-missing.vcf.gz
DOI: 10.5064/f6vanjl8/qdrs7k
title: Silan-Ciruelas_PHL_Opt2_25A_Rozel_NonMonogamous_Any.pdf
DOI: 10.5064/f6vanjl8/9fwcsp
title: Silan-Ciruelas_TUR_Opt1_15A_NejlaNaz_10-20_Low_Median-High.pdf
DOI: 10.5064/f6vanjl8/vm1nk7
title: Silan-Ciruelas_TUR_Opt2_25A_Anil_Non-Monogamous.pdf
DOI: 10.5061/dryad.2343k
title: Data from: Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the above-ground vegetation

description: Soil conditions and microclimate are important determinants of the
 fine-scale distribution of plant species in the Arctic, creating locally
 heterogeneous vegetation. We hypothesize that root-associated fungal (RAF)
 communities respond to the same fine-scale environmental gradients as the
 aboveground vegetation, creating a coherent pattern between aboveground
 vegetation and RAF. We explored how RAF communities of the ectomycorrhizal
 (ECM) plant Bistorta vivipara and aboveground vegetation structure of
 arctic plants were affected by biotic and abiotic variables at 0.3–3.0-m
 scales. RAF communities were determined using pyrosequencing. Composition
 and spatial structure of RAF and aboveground vegetation in relation to
 collected biotic and abiotic variables were analysed by ordination and
 semi-variance analyses. The vegetation was spatially structured along soil
 C and N gradients, whereas RAF lacked significant spatial structure. A
 weak relationship between RAF community composition and the cover of two
 ECM plants, B. vivipara and S. polaris, was found, and RAF richness
 increased with host root length and root weight. Results suggest that the
 fine-scale spatial structure of RAF communities of B. vivipara and the
 aboveground vegetation are driven by different factors. At fine spatial
 scales, neighbouring ECM plants may affect RAF community composition,
 whereas soil nutrients gradients structure the vegetation.
description: sm1.742sm2.743sm3.744Hellinger transformed OTU table_76_samplesVegetation data from 76 subplotSample cordinates and env variablesScript for DCA analysisScript for NMDS analysisOrdisurf
DOI: 10.5064/f6vanjl8/rnic8r
title: Silan-Ciruelas_USA_Opt2_10B_Jon_5-10_High_Low-Median.pdf
DOI: 10.5281/zenodo.16908902
title: LLM output for the educational study of AI in Nephrology

description: LLM files for further study
DOI: 10.5281/zenodo.16908903
title: LLM output for the educational study of AI in Nephrology

description: LLM files for further study
DOI: 10.15468/dl.6c9cce
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thevetia peruviana",
 "Country is Niue",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025043-250811113504898/datasets/export for details.
DOI: 10.15468/dl.x983d5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thevetia peruviana",
 "Country is Papua New Guinea",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025045-250811113504898/datasets/export for details.
DOI: 10.15468/dl.59f874
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypopygus isbruckeri)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025044-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8r3k62
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thevetia peruviana",
 "Country is Rwanda",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025046-250811113504898/datasets/export for details.
DOI: 10.15468/dl.3x8arb
title: Occurrence Download

description: A dataset containing 661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is TICKS (ACARI: IXODIDAE) IN KARELIA",
 "Geometry POLYGON((15.85277 55.24421,52.14723 55.24421,52.14723 69.75579,15.85277 69.75579,15.85277 55.24421))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 661 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025047-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.29203574
title: <b>Intervention Comprising </b><b>Three-Month </b><b>School-Based Exercise </b><b>Intervention </b><b>and</b><b>and</b><b> </b><b>Exercise Logging</b><b>Data Recording</b><b> </b><b>Can </b><b>Improve</b><b>s</b><b> </b><b>Physical Health, </b><b>Affects </b><b>Self-Efficacy</b><b>,</b><b> and </b><b>e</b><b>Health Literacy</b>

description: The data of the impact of short-duration physical exercise sessions and daily exercise recordings on the physical health and psychological health of junior high school students in Japan
DOI: 10.6084/m9.figshare.29203574.v1
title: <b>Intervention Comprising </b><b>Three-Month </b><b>School-Based Exercise </b><b>Intervention </b><b>and</b><b>and</b><b> </b><b>Exercise Logging</b><b>Data Recording</b><b> </b><b>Can </b><b>Improve</b><b>s</b><b> </b><b>Physical Health, </b><b>Affects </b><b>Self-Efficacy</b><b>,</b><b> and </b><b>e</b><b>Health Literacy</b>

description: The data of the impact of short-duration physical exercise sessions and daily exercise recordings on the physical health and psychological health of junior high school students in Japan
DOI: 10.15468/dl.ka2d82
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Winteria telescopa Brauer, 1901",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((9.7509 37.8496,8.9648 37.5879,8.9648 28.8496,17.9648 28.8496,17.9648 31.4107,15.9933 31.8399,15.7087 32.5876,15.3783 32.8575,13.447 33.3951,12.448 33.3201,11.5958 33.6971,11.3566 34.2292,11.7126 34.4306,11.838 34.8337,11.4958 36.0284,11.2722 36.2509,11.6203 36.7533,11.5006 37.3226,11.1934 37.5676,10.5795 37.5806,9.7509 37.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010104-250525065834625/datasets/export for details.