cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.zauteq
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Meryta schizolaena Baill."
 ]
}

 The dataset includes 46 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052148-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3fca6c
title: Occurrence Download

description: A dataset containing 2026 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mallotus peltatus (Geiseler) Müll.Arg."
 ]
}

 The dataset includes 2026 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052149-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9fj8h2
title: Occurrence Download

description: A dataset containing 649 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melastomastrum segregatum (Benth.) A.Fern. & R.Fern."
 ]
}

 The dataset includes 649 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052150-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h77tqk
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maesa argyrophylla K.Larsen & C.M.Hu"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052151-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehvbag
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Meryta senfftiana Volkens"
 ]
}

 The dataset includes 48 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052152-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cg8eab
title: Occurrence Download

description: A dataset containing 11396 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mallotus philippensis (Lam.) Müll.Arg."
 ]
}

 The dataset includes 11396 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0052153-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18112/openneuro.ds004951.v1.0.0
title: Braille letters - EEG
DOI: 10.6084/m9.figshare.16821554
title: Additional file 2 of Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

description: Additional file 2: Table S2. Synteny analysis of Gγ subunit gene regions in Rosaceae
DOI: 10.6084/m9.figshare.16821557.v1
title: Additional file 3 of Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

description: Additional file 3: Table S3. Ka, Ks, Ka/Ks, and divergence-time of paralogous genes among Gγ subunit gene family in Rosaceae
DOI: 10.6084/m9.figshare.16821560.v1
title: Additional file 4 of Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

description: Additional file 4: Table S4. Prediction of subcellular localization of Gγ subunit protein in Chinese white pear
DOI: 10.6084/m9.figshare.16821563.v1
title: Additional file 5 of Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

description: Additional file 5. Table S5. List of primers used in this work
DOI: 10.6084/m9.figshare.16821557
title: Additional file 3 of Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

description: Additional file 3: Table S3. Ka, Ks, Ka/Ks, and divergence-time of paralogous genes among Gγ subunit gene family in Rosaceae
DOI: 10.6084/m9.figshare.16821560
title: Additional file 4 of Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

description: Additional file 4: Table S4. Prediction of subcellular localization of Gγ subunit protein in Chinese white pear
DOI: 10.6084/m9.figshare.16821563
title: Additional file 5 of Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

description: Additional file 5. Table S5. List of primers used in this work
DOI: 10.6084/m9.figshare.12630113
title: Quantification of glucose metabolism in the brain of mice under chronic jet lag

description: Quantification of PET images of different brain regions. Each spreadsheet is data from a mouse under control or chronic jet lag condition. Ctrl, control; CJL, chronic jet lag.
DOI: 10.6084/m9.figshare.17870154.v1
title: Additional file 1 of Does tai chi improve psychological well-being and quality of life in patients with cardiovascular disease and/or cardiovascular risk factors? A systematic review

description: Additional file 1: Table S1. Search strategies. Table S2. Tai Chi interventions applied in the included studies. Table S3. Effect estimates of Tai Chi for psychological well-being and quality of life in people with or at risk of CVD. Table S4. Post-hoc subgroup analyses of Tai Chi for psychological well-being and quality of life in people with or at risk of CVD . Table S5. GRADE certainty assessment of the body of evidence. Figure S1. Risk of bias summary of included studies. Figure S2. Risk of bias graph of included studies. Figure S3. Forest plot of Tai Chi in combination with usual care on safety. Figure S4. Funnel plot of Tai Chi plus usual care versus usual care for mental health measured by SF-36.
DOI: 10.6084/m9.figshare.12630113.v1
title: Quantification of glucose metabolism in the brain of mice under chronic jet lag

description: Quantification of PET images of different brain regions. Each spreadsheet is data from a mouse under control or chronic jet lag condition. Ctrl, control; CJL, chronic jet lag.
DOI: 10.6084/m9.figshare.10008740
title: Metadata record for: Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data

description: This dataset contains key characteristics about the data described in the Data Descriptor Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.10008740.v1
title: Metadata record for: Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data

description: This dataset contains key characteristics about the data described in the Data Descriptor Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.20494848
title: source_data

description: Raw data for " Transition metal dichalcogenide metaphotonic and self-coupled polaritonic platform grown by chemical vapor deposition"
DOI: 10.6084/m9.figshare.12627387
title: raw data from Polyethylene glycol grafted with carboxylated graphene oxide as a novel interface modifier for polylactic acid/graphene nanocomposites

description: The raw data for Polyethylene glycol grafted with carboxylated graphene oxide as novel interface modifier for polylactic acid-graphene nanocomposites
DOI: 10.6084/m9.figshare.17870202.v1
title: Additional file 7 of An 8-ferroptosis-related genes signature from Bronchoalveolar Lavage Fluid for prognosis in patients with idiopathic pulmonary fibrosis

description: Additional file 7: Table S1. The 293 ferroptosis-related genes used in the study.
DOI: 10.6084/m9.figshare.12623235.v1
title: Additional file 1 of Airway-invasion-associated pulmonary computed tomography presentations characteristic of invasive pulmonary Aspergillosis in non-immunocompromised adults: a National Multicenter Retrospective Survey in China

description: Additional file 1: Table S1. Underlying conditions of IPA patients. Figure S1. Radiological presentations of IPA patients.
DOI: 10.6084/m9.figshare.24164987
title: Additional file 7 of Expansion of human bone marrow-derived mesenchymal stromal cells with enhanced immunomodulatory properties

description: Additional file 7: Supplemental Table 1. Differentially expressed genes (DEGs) in bone marrow-derived MSCs from six human donors, cultured at high confluency (MSC-HC) versus low confluency (MSC-LC).
DOI: 10.6084/m9.figshare.24164987.v1
title: Additional file 7 of Expansion of human bone marrow-derived mesenchymal stromal cells with enhanced immunomodulatory properties

description: Additional file 7: Supplemental Table 1. Differentially expressed genes (DEGs) in bone marrow-derived MSCs from six human donors, cultured at high confluency (MSC-HC) versus low confluency (MSC-LC).
DOI: 10.6084/m9.figshare.24164990
title: Additional file 8 of Expansion of human bone marrow-derived mesenchymal stromal cells with enhanced immunomodulatory properties

description: Additional file 8: Supplemental Table 2. Differentially expressed genes (DEGs) in bone marrow-derived MSCs unique to responders (Donor 1, Donor 2, Donor 4, Donor 5), cultured at high confluency (MSC-HC) versus low confluency (MSC-LC).
DOI: 10.6084/m9.figshare.24164990.v1
title: Additional file 8 of Expansion of human bone marrow-derived mesenchymal stromal cells with enhanced immunomodulatory properties

description: Additional file 8: Supplemental Table 2. Differentially expressed genes (DEGs) in bone marrow-derived MSCs unique to responders (Donor 1, Donor 2, Donor 4, Donor 5), cultured at high confluency (MSC-HC) versus low confluency (MSC-LC).
DOI: 10.34731/1a9s-ax66
title: Multi-year aboveground data of minirhizotron facilities in Selhausen - DATA

description: Here, we presented a comprehensive data set collected from leaf to canopy using sophisticated and comprehensive sensing techniques (leaf chlorophyll content, hourly leaf stomatal conductance and photosynthesis, canopy CO2 exchange, sap flow, soil respiration, and canopy temperature) including detailed crop growth characteristics based on destructive methods (seasonal dynamics of crop height, leaf area index, above-ground biomass, and yield). Data were acquired under field conditions with contrasting soil types, water treatments, and different cultivars of wheat and maize together with minirhizotron facilities which collected the belowground processes (root and soil characteristics). The data from 2016 up to now will be made available (together with the below-ground data).  The data in this repository correspond to the article "Multi-year aboveground data of minirhizotron facilities in Selhausen.
DOI: 10.5281/zenodo.5931365
title: Annotated image training set for the copepod Temora longicornis

description: The zip files contain annotated training data on images captured in an experiment of Temora longicornis. the images are a subset of a much larger imaging dataset, that is part of a master thesis. Annotation was done using the in Computer Vision Annotation Tool. The copepod, faecal pellets and the well  were manually labeled using rectangle. The images were captured using an automated imaging platform similar to the one by Heuschele et al 2019. The datasets were exported in the Coco1.0 dataset format. 
description: Research was funded by the Norwegian Research Council to the project MULTICOP (301153)
DOI: 10.5281/zenodo.5931366
title: Annotated image training set for the copepod Temora longicornis

description: The zip files contain annotated training data on images captured in an experiment of Temora longicornis. the images are a subset of a much larger imaging dataset, that is part of a master thesis. Annotation was done using the in Computer Vision Annotation Tool. The copepod, faecal pellets and the well  were manually labeled using rectangle. The images were captured using an automated imaging platform similar to the one by Heuschele et al 2019. The datasets were exported in the Coco1.0 dataset format. 
description: Research was funded by the Norwegian Research Council to the project MULTICOP (301153)
DOI: 10.6084/m9.figshare.17870341
title: Additional file 1 of Common variants in breast cancer risk loci predispose to distinct tumor subtypes

description: Additional file 1. Figures S1 and S2 and Table S1-S4. This file contains supplementary figures 1-2 and supplementary tables 1-4.
DOI: 10.6084/m9.figshare.23391614.v4
title: The annotation results of gene structure and functional prediction.

description:  The assembled draft genome of Yunling cattle 、annotation results of repeated sequences, gene structure and functional prediction.
DOI: 10.6084/m9.figshare.16821754
title: Additional file 5 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 5: Table S5. KEGG function classification the assembled unigenes in R. xanthina f. spontanea. (XLSX 2156 kb)
DOI: 10.6084/m9.figshare.12627387.v1
title: raw data from Polyethylene glycol grafted with carboxylated graphene oxide as a novel interface modifier for polylactic acid/graphene nanocomposites

description: The raw data for Polyethylene glycol grafted with carboxylated graphene oxide as novel interface modifier for polylactic acid-graphene nanocomposites
DOI: 10.6084/m9.figshare.12627387.v2
title: raw data from Polyethylene glycol grafted with carboxylated graphene oxide as a novel interface modifier for polylactic acid/graphene nanocomposites

description: The raw data for Polyethylene glycol grafted with carboxylated graphene oxide as novel interface modifier for polylactic acid-graphene nanocomposites
DOI: 10.6084/m9.figshare.16821748.v1
title: Additional file 3 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 3: Table S3. Species distribution frequency of the BLAST hits based on Nr database.
DOI: 10.6084/m9.figshare.16821760.v1
title: Additional file 7 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 7: Table S7. GO enrichment analysis of DEGs at -20°C vs. 23°C in R. xanthina f. spontanea. (XLSX 117 kb)
DOI: 10.6084/m9.figshare.16821763.v1
title: Additional file 8 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 8: Table S8. KEGG enrichment analysis of DEGs at 4°C vs. 23°C in R. xanthina f. spontanea. (XLSX 743 kb)
DOI: 10.6084/m9.figshare.21540408
title: Additional file 14 of A comprehensive pan-cancer analysis of necroptosis molecules in four gynecologic cancers

description: Additional file 14: Supplementary Table 2. The results of expression differences for pan-cancer analysis.
DOI: 10.6084/m9.figshare.14196624
title: Additional file 1 of Integrative proteomic and lipidomic analysis of Kaili Sour Soup-mediated attenuation of high-fat diet-induced nonalcoholic fatty liver disease in a rat model

description: Additional file 1: Figure S1. Proteins identified by TMT quantitative proteomics analysis.
DOI: 10.6084/m9.figshare.14196624.v1
title: Additional file 1 of Integrative proteomic and lipidomic analysis of Kaili Sour Soup-mediated attenuation of high-fat diet-induced nonalcoholic fatty liver disease in a rat model

description: Additional file 1: Figure S1. Proteins identified by TMT quantitative proteomics analysis.
DOI: 10.6084/m9.figshare.16821721.v1
title: Additional file 10 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 10: Table S10. GO enrichment analysis of 468 DEGs under low-temperature stress in R. xanthina f. spontanea. (XLSX 91 kb)
DOI: 10.5281/zenodo.10522472
title: Replication Kit - What the Fix? A Study of ASATs Rule Documentation

description: Contains all artefacts for our publication: What the Fix? A Study of ASATs Rule Documentation @ ICPC 2024Content



survey: Archive from LimeSurvey, rules annotated used and raw results

taxonomy_validation: Rules annotated by the authors to validate the taxonomy and notebook computing kappa values

website: Build of the companion webpage (currently hosted at https://icpc2024-asats.github.io)


Paper abstractAutomatic Static Analysis Tools (ASATs) are widely used by software developers to diffuse and enforce coding practices. Yet, we know little about the documentation of ASATs, despite it being critical to learn about the coding practices in the first place. We shed light on this through a two-phase study. First, we analyze the documentation of more than 100 rules of 16 ASATs for multiple programming languages, and distill a taxonomy of the goals of the documentation and its types of contents. Then, we conduct a survey to assess the effectiveness of the documentation in terms of its goals and types of contents. We highlight opportunities for improvement in ASAT documentation.
DOI: 10.5281/zenodo.10522473
title: Replication Kit - What the Fix? A Study of ASATs Rule Documentation

description: Contains all artefacts for our publication: What the Fix? A Study of ASATs Rule Documentation @ ICPC 2024Content



survey: Archive from LimeSurvey, rules annotated used and raw results

taxonomy_validation: Rules annotated by the authors to validate the taxonomy and notebook computing kappa values

website: Build of the companion webpage (currently hosted at https://icpc2024-asats.github.io)


Paper abstractAutomatic Static Analysis Tools (ASATs) are widely used by software developers to diffuse and enforce coding practices. Yet, we know little about the documentation of ASATs, despite it being critical to learn about the coding practices in the first place. We shed light on this through a two-phase study. First, we analyze the documentation of more than 100 rules of 16 ASATs for multiple programming languages, and distill a taxonomy of the goals of the documentation and its types of contents. Then, we conduct a survey to assess the effectiveness of the documentation in terms of its goals and types of contents. We highlight opportunities for improvement in ASAT documentation.
DOI: 10.6084/m9.figshare.14724643.v1
title: Supplementary Files S7 De-novo repeat libraries: Excel factsheet with description and fasta files. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.14724661.v1
title: Supplementary Files S4 Annotation for intact LINE retrotransposons and DNA transposons. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

description: It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in <i>Drosophila</i>. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.
DOI: 10.6084/m9.figshare.16821724
title: Additional file 11 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 11: Table S11. KEGG enrichment analysis of 468 DEGs under low-temperature stress in R. xanthina f. spontanea. (XLSX 66 kb)
DOI: 10.6084/m9.figshare.16821742.v1
title: Additional file 1 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 1: Table S1. Overview of the sequencing and assembly of the transcriptome.
DOI: 10.6084/m9.figshare.16821727.v1
title: Additional file 12 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 12: Table S12. qRT-PCR analysis of expression levels under low-temperature stress in R. xanthina f. spontanea. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.16821745
title: Additional file 2 of Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

description: Additional file 2: Table S2. N50 of transcripts or unigenes from nine samples.