cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3596762_d2
title: Additional file 1: Figures S1-S3. of B cell depletion therapy upregulates Dkk-1 skin expression in patients with systemic sclerosis: association with enhanced resolution of skin fibrosis

description: In the baseline biopsy (A and B) Dkk-1 is not expressed in epidermis (black arrow), appendices (green arrow) and spindle-like cells (red arrows). In the follow up biopsy (C and D) there is clear expression of Dkk-1 in epidermis (black arrow), appendices (green arrow) and spindle-like cells (red arrows). All three patients responded to RTX treatment. Streptavidin biotin peroxidase (A and D × 20, B and E × 400) (ZIP 5323 kb)
DOI: 10.15468/dl.r47m2s
title: Occurrence Download

description: A dataset containing 410 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saurida macrolepis Tanaka, 1917",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 410 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032349-241126133413365/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.c.3596756_d4
title: MOESM5 of Improving total saccharification yield of Arabidopsis plants by vessel-specific complementation of caffeoyl shikimate esterase (cse) mutants

description: Additional file 5. Statistical analysis of data on height and weight of cse-2 proVND6::CSE lines using nested ANOVA. A Bartlett’s test was first performed to test homoscedasticity; nested ANOVA was performed to test the differences between the groups, followed by Tukey HSD as post hoc test. Numbers represent the genotypes 1 = wild type, 2 = cse-2, and 3 = cse-2 proVND6::CSE line 1 to line 3, respectively.
DOI: 10.6084/m9.figshare.c.3596762_d3
title: Additional file 4: Figures S8-S10. of B cell depletion therapy upregulates Dkk-1 skin expression in patients with systemic sclerosis: association with enhanced resolution of skin fibrosis

description: Dkk-1 is not expressed in epidermis (black arrow), appendices (green arrow) and spindle-like cells (red arrows) in the control patient group at baseline (A and B) and follow up biopsies (D and E). Streptavidin biotin peroxidase (A and D × 20, B and E × 400) (ZIP 5018 kb)
DOI: 10.6084/m9.figshare.c.3596774_d1
title: Additional file 1:  of Analysis of cerebrospinal fluid from cattle with central nervous system disorders after storage for 24Â hours with autologous serum

description: Classification of neurological diagnosis on the basis of the VITAMIN D algorithm [ 16 ]. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3596756_d5
title: MOESM3 of Improving total saccharification yield of Arabidopsis plants by vessel-specific complementation of caffeoyl shikimate esterase (cse) mutants

description: Additional file 3. List of primer sequences used for cloning and quantitative RT-PCR. Both forward and reverse primer sequences are shown in the 5′ to 3′ direction. Lower case letters indicate the sites for GATEWAY™ cloning (Invitrogen), while letters in bold indicate restriction sites for classical cloning.
DOI: 10.6084/m9.figshare.c.3596762_d4
title: Additional file 2: Figures S4-S6. of B cell depletion therapy upregulates Dkk-1 skin expression in patients with systemic sclerosis: association with enhanced resolution of skin fibrosis

description: Dkk-1 is not expressed in epidermis (black arrow), appendices (green arrow) and spindle-like cells (red arrows) prior to (A and B) and following RTX treatment (D and E). These patients did not respond to RTX treatment. Streptavidin biotin peroxidase (A and D × 20, B and E × 400) (ZIP 5591 kb)
DOI: 10.6084/m9.figshare.c.3596783_d1
title: Additional file 1 of Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii)

description: Gene ontology (GO) terms enrichment in Southern bluefin tuna ovary vs. testis cells transcriptome. Enriched GO terms in ovary vs. testis cells, along with the corresponding ontology, term description, number of genes associated (total count and differentially expressed) and the p-value and p-value (false discovery rate adjusted p-value) statistics as determined by goseq. (XLSX 50.5 kb)
DOI: 10.6084/m9.figshare.c.3596783_d2
title: Additional file 3 of Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii)

description: Gene ontology (GO) terms enrichment in Southern bluefin tuna crude testis vs. Percoll-enriched testis cells transcriptome. Enriched GO terms in crude testis vs. Percoll-enriched testis cells, along with the corresponding ontology, term description, number of genes associated (total count and differentially expressed) and the p-value and p-value (false discovery rate adjusted p-value) statistics as determined by goseq. (XLSX 71.6 kb)
DOI: 10.6084/m9.figshare.c.3596816_d3
title: Additional file 5: Table S5 of Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night

description: Spreadsheet listing all overrepresented gene ontology terms associated with male-biased genes. GOBIP, gene ontology biological process identifier. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.c.3596816_d4
title: Additional file 2: Table S2. of Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night

description: Spreadsheet listing all differentially expressed genes in females exposed to the ALAN treatment based on adjusted p-values. Gene = gene ID; base Mean = the mean of the normalized counts for all samples; log2FoldChange = Log 2 fold change in expression low-light relative to control; lfcMLE = unshrunken maximum likelihood estimates of Log2 fold change in expression; lfcSE = Standard Error of log2FoldChange; Stat = Wald statisic; pvalue; padj = p value adjusted after Benjamini-Hochberg; Annotation = functional annotation of the gene; Domain(s) = Interpro domain annotations. (XLS 19 kb)
DOI: 10.6084/m9.figshare.c.3596816_d5
title: Additional file 1: Table S1. of Sex-specific gene expression in the mosquito Culex pipiens f. molestus in response to artificial light at night

description: Spreadsheet listing all differentially expressed genes in males exposed to the ALAN treatment. Gene = gene ID; base Mean = the mean of the normalized counts for all samples;log2FoldChange = Log 2 fold change in expression low-light relative to control; lfcMLE = unshrunken maximum likelihood estimates of Log2 fold change in expression; lfcSE = Standard Error of log2FoldChange; Stat = Wald statisic; pvalue; padj = p value adjusted after Benjamini-Hochberg; Annotation = functional annotation of the gene; Domain(s) = Interpro domain annotations. Genes that are differentially expressed with an absolute fold change greater than 2 (FC &gt; 2) are shown in bold. (XLS 65 kb)
DOI: 10.25378/janelia.24164004.v1
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse kidney glomerulus (jrc_mus-kidney-glomerulus-2)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample:</b> Kidney glomerulus from a wild-type, 3 months old mouse, strain: C57BL/6 from Jackson Lab<b>Sample Description:</b> A dataset featuring isotropic 3D electron microscopy date of the mouse kidney glomerulus obtained from a 3-month-old C57BL/6 mouse, sourced from Jackson Laboratory. The mouse underwent anesthesia in accordance with IACUC guidelines. The kidney tissue was prepared through perfusion fixation and reducing osmium. The sample was then subjected to dehydration, infiltration with graded ethanol and Epon resin, and polymerized in a 60°C oven. The sample was provided by Kayvon Pedram and Guoqiang Yu (HHMI/Janelia), prepared for imaging by Wei-Ping Li and Guoqiang Yu (HHMI/Janelia), x-ray imaged and trimmed by Nirmala Iyer (HHMI/Janelia) and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Protocol:</b> Mouse anesthesia was performed as IACUC guidelines. Following perfusion fixation and reducing osmium, the sample was subjected to dehydration, infiltration with graded ethanol and Epon resin, and polymerized in a 60°C oven.<b>Contributions:</b> Sample provided by Kayvon Pedram and Guoqiang Yu (HHMI/Janelia), prepared for imaging by Wei-Ping Li and Guoqiang Yu (HHMI/Janelia), x-ray imaged and trimmed by Nirmala Iyer (HHMI/Janelia) and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Acquisition ID:</b> jrc_mus-kidney-glomerulus-2<b>Voxel size (nm):</b> 4 x 4 x 4 (x, y, z)<b>Data dimensions (µm): </b>18.98 x 24.61 x 26.54 (x, y, z)<b>Imaging start date:</b> 2023-04-12<b>Imaging duration (days):</b> 7<b>Primary energy (eV): </b>1<b>Imaging current (nA)</b>: .75<b>Scanning speed (MHz): </b>.2<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_mus-kidney-glomerulus-2/jrc_mus-kidney-glomerulus-2.zarr/recon-1/em/<b>EM DOI</b>: https://doi.org/10.25378/janelia.24164004<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-kidney-glomerulus-2<b>Publication: </b>Xu et al., 2021<br>
DOI: 10.25378/janelia.24164004
title: Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse kidney glomerulus (jrc_mus-kidney-glomerulus-2)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<b>Sample:</b> Kidney glomerulus from a wild-type, 3 months old mouse, strain: C57BL/6 from Jackson Lab<b>Sample Description:</b> A dataset featuring isotropic 3D electron microscopy date of the mouse kidney glomerulus obtained from a 3-month-old C57BL/6 mouse, sourced from Jackson Laboratory. The mouse underwent anesthesia in accordance with IACUC guidelines. The kidney tissue was prepared through perfusion fixation and reducing osmium. The sample was then subjected to dehydration, infiltration with graded ethanol and Epon resin, and polymerized in a 60°C oven. The sample was provided by Kayvon Pedram and Guoqiang Yu (HHMI/Janelia), prepared for imaging by Wei-Ping Li and Guoqiang Yu (HHMI/Janelia), x-ray imaged and trimmed by Nirmala Iyer (HHMI/Janelia) and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Protocol:</b> Mouse anesthesia was performed as IACUC guidelines. Following perfusion fixation and reducing osmium, the sample was subjected to dehydration, infiltration with graded ethanol and Epon resin, and polymerized in a 60°C oven.<b>Contributions:</b> Sample provided by Kayvon Pedram and Guoqiang Yu (HHMI/Janelia), prepared for imaging by Wei-Ping Li and Guoqiang Yu (HHMI/Janelia), x-ray imaged and trimmed by Nirmala Iyer (HHMI/Janelia) and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).<b>Acquisition ID:</b> jrc_mus-kidney-glomerulus-2<b>Voxel size (nm):</b> 4 x 4 x 4 (x, y, z)<b>Data dimensions (µm): </b>18.98 x 24.61 x 26.54 (x, y, z)<b>Imaging start date:</b> 2023-04-12<b>Imaging duration (days):</b> 7<b>Primary energy (eV): </b>1<b>Imaging current (nA)</b>: .75<b>Scanning speed (MHz): </b>.2<b>Dataset URL: </b>s3://janelia-cosem-datasets/jrc_mus-kidney-glomerulus-2/jrc_mus-kidney-glomerulus-2.zarr/recon-1/em/<b>EM DOI</b>: https://doi.org/10.25378/janelia.24164004<b>Visualization Website</b>: https://openorganelle.janelia.org/datasets/jrc_mus-kidney-glomerulus-2<b>Publication: </b>Xu et al., 2021<br>
DOI: 10.6084/m9.figshare.c.3596864_d1
title: Additional file 9: Table 9. of Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek)

description: Marker test of g779p, g34480p, g34458p, DMB-SSR158 and OPW02a4 on mungbean recombinant inbred lines (RILs). (XLSX 432Â kb)
DOI: 10.15468/dl.f4fh26
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Saurida tweddlei Russell, 2015",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032351-241126133413365/datasets/export for details.
DOI: 10.6084/m9.figshare.c.3596864_d5
title: Additional file 4: Table S4. of Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek)

description: Nucleotide variations (NVs) in the 2-kb promoter region of DEGs. (XLS 79Â kb)
DOI: 10.6084/m9.figshare.c.3596894_d1
title: Additional file 3: Table S1. of Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

description: List of recombination profiles for Malagasy sequences. For each of the recombination profiles, the numbers of associated recombination events are indicated, as well as species and accession numbers of the corresponding recombinant sequences. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3596906_d2
title: Additional file 3: of On Predicting lung cancer subtypes using ‘omic’ data from tumor and tumor-adjacent histologically-normal tissue

description: Formatted TCGA dataset used in this study, along with sample IDs for classification task TAHNADC vs.TumorADC in DNA methylation. (CSV 41150 kb)
DOI: 10.6084/m9.figshare.c.3596915_d1
title: Additional file 1: of Predictors of Chlamydia Trachomatis testing: perceived norms, susceptibility, changes in partner status, and underestimation of own risk

description: Database, syntax, and additional information for the study "Predictors of Chlamydia Trachomatis testing: perceived norms, susceptibility, changes in partner status, and underestimation of own risk". (ZIP 104Â kb)
DOI: 10.6084/m9.figshare.c.3596906_d3
title: Additional file 2: of On Predicting lung cancer subtypes using ‘omic’ data from tumor and tumor-adjacent histologically-normal tissue

description: Formatted TCGA dataset used in this study, along with sample IDs for classification task TAHNSCC vs.TumorSCC in gene expression. (CSV 24086 kb)
DOI: 10.6084/m9.figshare.c.3596948_d2
title: Additional file 3: of PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies

description: A list of domains that are tested for expression and purification. (XLS 41 kb)
DOI: 10.6084/m9.figshare.c.3596948_d3
title: Additional file 2: of PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies

description: A list of putative structural units. (XLS 48 kb)
DOI: 10.6084/m9.figshare.c.3596936_d7
title: Additional file 3: of Transcriptomic comparison between two Vitis vinifera L. varieties (Trincadeira and Touriga Nacional) in abiotic stress conditions

description: Gene expression responses shared between the two varieties under high light and heat. TN, Touriga Nacional; TR, Trincadeira; H, heat stress; L, high light stress. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3596948_d4
title: Additional file 4: of PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies

description: Experimental constructs that successfully produce antibodies. (XLS 37 kb)
DOI: 10.15468/dl.vh4cqr
title: Occurrence Download

description: A dataset containing 45234 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Vespula germanica (Fabricius, 1793)"
 ]
}

 The dataset includes 45234 records from 457 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032350-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1120170.10fu
title: SH1120170.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1120173.10fu
title: SH1120173.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1120175.10fu
title: SH1120175.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1120177.10fu
title: SH1120177.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1120179.10fu
title: SH1120179.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1120181.10fu
title: SH1120181.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.