cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5900155.v1
title: iMHEA Original Data

description: This file contains the original rainfall and water level time series compiled from the sensors of the iMHEA catchments. Data are organised by site.
DOI: 10.6084/m9.figshare.5900152
title: iMHEA Geographic Data

description: This file contains geographic data of the catchments including catchment delineation, sensor positions, drainage network, contour lines, lithology, land cover, and digital elevation. Data are organised by site and catchment.
DOI: 10.6084/m9.figshare.5900149
title: iMHEA Processing Scripts

description: This file contains customised scripts developed in MATLAB for processing the iMHEA data. Files are documented and commented to ease their use by external users.
DOI: 10.6084/m9.figshare.5900146
title: iMHEA Derived Indices

description: This file contains sensor information and geoposition, catchment physical characteristics, and climatic and hydrological indices derived from the monitored hydrometeorological data.
DOI: 10.6084/m9.figshare.5900146.v1
title: iMHEA Derived Indices

description: This file contains sensor information and geoposition, catchment physical characteristics, and climatic and hydrological indices derived from the monitored hydrometeorological data.
DOI: 10.6084/m9.figshare.5900143
title: iMHEA Maps

description: This file contains maps of each catchment or pair of catchments in the iMHEA monitoring network.
DOI: 10.6084/m9.figshare.5900143.v1
title: iMHEA Maps

description: This file contains maps of each catchment or pair of catchments in the iMHEA monitoring network.
DOI: 10.6084/m9.figshare.5900125
title: Files in the National Archives of Australia withheld from public access in 2017

description: This CSV file contains details of records held by the National Archives of Australia that were examined for release but withheld from public access in 2017. These files have an access status of 'Closed' in the NAA's online database.<br>The data of all files with an access status of 'Closed' was harvested from the NAA database on 1 January 2018. This was then filtered down to those with an access decision recorded sometime in 2017.<br>Similar datasets will be made available on an annual basis.<br>The fields in the CSV file are: barcode, control symbol, title, series, series title, contents dates, contents start year, contents end year, access status, access decision reasons (multiple values), access decision date (iso formatted).<br>The contents start year and end year have been parsed out of the original date string.<br>The access decision reasons are a list of the grounds on which access was withheld. These have been normalised to some extent to separate out references to multiple clauses of the Archives Act.
DOI: 10.6084/m9.figshare.5900125.v1
title: Files in the National Archives of Australia withheld from public access in 2017

description: This CSV file contains details of records held by the National Archives of Australia that were examined for release but withheld from public access in 2017. These files have an access status of 'Closed' in the NAA's online database.<br>The data of all files with an access status of 'Closed' was harvested from the NAA database on 1 January 2018. This was then filtered down to those with an access decision recorded sometime in 2017.<br>Similar datasets will be made available on an annual basis.<br>The fields in the CSV file are: barcode, control symbol, title, series, series title, contents dates, contents start year, contents end year, access status, access decision reasons (multiple values), access decision date (iso formatted).<br>The contents start year and end year have been parsed out of the original date string.<br>The access decision reasons are a list of the grounds on which access was withheld. These have been normalised to some extent to separate out references to multiple clauses of the Archives Act.
DOI: 10.6084/m9.figshare.5900122
title: S2 Supporting Information dataset: Water-to-air CO2 flux calculations from 6 authors for 8 seasonal underway surveys in Palasari Reservoir and Lake Batur, Bali, Indonesia.

description: Six wind-speed based parameterizations from 6 authors ( Wanninkhof (1992), MacIntyre et al. (1995), Cole & Carico (1998), McGillis et al. (2001), Crusius and Wanninkhof (2003) and Cole et al. (2010). GPS (WGS84) wit date/time stamps are included for integration with GIS software.<br><br><br>
DOI: 10.6084/m9.figshare.5900122.v1
title: S1 Supporting Information Palasar Reservoir GIS water chemistry for Survey 1.xlsx

description: Underway GPS coordinates for underways measurements of pCO2, conductivity, dissolved oxygenand chlorophyll a measured in 10 minute intervals.<br>
DOI: 10.6084/m9.figshare.5900122.v3
title: S2 Supporting Information dataset: Water-to-air CO2 flux calculations from 6 authors

description: Six wind-speed based parameterizations from 6 authors ( Wanninkhof (1992), MacIntyre et al. (1995), Cole & Carico (1998), McGillis et al. (2001), Crusius and Wanninkhof (2003) and Cole et al. (2010). GPS (WGS84) and date/time stamps are included for integration with GIS software.<br><br><br>
DOI: 10.6084/m9.figshare.5900122.v2
title: S2 Supporting Information Water-air CO2 flux calculations from 6 authors Dataset

description: Six wind-speed based parameterizations from 6 authors ( Wanninkhof (1992), MacIntyre et al. (1995), Cole & Carico (1998), McGillis et al. (2001), Crusius and Wanninkhof (2003) and Cole et al. (2010). GPS (WGS84) and date/time stamps are included for integration with GIS software.<br><br><br>
DOI: 10.6084/m9.figshare.5900092
title: Additional file 5: of Oxidative damage and response to Bacillus Calmette-GuĂŠrin in bladder cancer cells expressing sialyltransferase ST3GAL1

description: GENES MODULATED BY BCG IN HT1376sT (XLS 49 kb)
DOI: 10.6084/m9.figshare.5900092.v1
title: Additional file 5: of Oxidative damage and response to Bacillus Calmette-GuĂŠrin in bladder cancer cells expressing sialyltransferase ST3GAL1

description: GENES MODULATED BY BCG IN HT1376sT (XLS 49 kb)
DOI: 10.6084/m9.figshare.5900083
title: Additional file 4: of Oxidative damage and response to Bacillus Calmette-GuĂŠrin in bladder cancer cells expressing sialyltransferase ST3GAL1

description: CANCER-ASSOCIATED GENES MODULATED IN HT1376sT CELLS AS COMPARED TO HT1376T CELLS. (XLS 43 kb)
DOI: 10.6084/m9.figshare.5900083.v1
title: Additional file 4: of Oxidative damage and response to Bacillus Calmette-GuĂŠrin in bladder cancer cells expressing sialyltransferase ST3GAL1

description: CANCER-ASSOCIATED GENES MODULATED IN HT1376sT CELLS AS COMPARED TO HT1376T CELLS. (XLS 43 kb)
DOI: 10.6084/m9.figshare.5900071
title: Additional file 3: of Oxidative damage and response to Bacillus Calmette-GuĂŠrin in bladder cancer cells expressing sialyltransferase ST3GAL1

description: GENES MODULATED IN HT1376sT CELLS AS COMPARED TO HT1376T CELLS. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.5900071.v1
title: Additional file 3: of Oxidative damage and response to Bacillus Calmette-GuĂŠrin in bladder cancer cells expressing sialyltransferase ST3GAL1

description: GENES MODULATED IN HT1376sT CELLS AS COMPARED TO HT1376T CELLS. (XLSX 47 kb)
DOI: 10.6084/m9.figshare.5900056
title: Additional file 4: of StructRNAfinder: an automated pipeline and web server for RNA families prediction

description: Table in XLS format comparing the features of StructRNAfinder, webStructRNAfinder and Rfam batch search. (XLS 21 kb)
DOI: 10.6084/m9.figshare.5900056.v1
title: Additional file 4: of StructRNAfinder: an automated pipeline and web server for RNA families prediction

description: Table in XLS format comparing the features of StructRNAfinder, webStructRNAfinder and Rfam batch search. (XLS 21 kb)
DOI: 10.6084/m9.figshare.5900008
title: Additional file 2: Table S2. of The increasing importance of a continence nurse specialist to improve outcomes and save costs of urinary incontinence care: an analysis of future policy scenarios

description: Breakdown of the budgetary impact over a period of 3Â years. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5900008.v1
title: Additional file 2: Table S2. of The increasing importance of a continence nurse specialist to improve outcomes and save costs of urinary incontinence care: an analysis of future policy scenarios

description: Breakdown of the budgetary impact over a period of 3Â years. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5899999
title: Additional file 1: of StructRNAfinder: an automated pipeline and web server for RNA families prediction

description: Table in XLS format summarizing each developed Perl script part of StructRNAfinder tool. (XLS 18 kb)
DOI: 10.6084/m9.figshare.5899999.v1
title: Additional file 1: of StructRNAfinder: an automated pipeline and web server for RNA families prediction

description: Table in XLS format summarizing each developed Perl script part of StructRNAfinder tool. (XLS 18 kb)
DOI: 10.6084/m9.figshare.5899975
title: Additional file 5: Table S5. of In vitro and in silico validation of CA3 and FHL1 downregulation in oral cancer

description: List of accession numbers for the ORESTES data used in the study. (XLSX 20500 kb)
DOI: 10.6084/m9.figshare.5899975.v1
title: Additional file 5: Table S5. of In vitro and in silico validation of CA3 and FHL1 downregulation in oral cancer

description: List of accession numbers for the ORESTES data used in the study. (XLSX 20500 kb)
DOI: 10.6084/m9.figshare.5899900
title: Additional file 2: of Wnt-signaling enhances neural crest migration of melanoma cells and induces an invasive phenotype

description: Table S1. List of 44 differentially expressed genes in human SKMEL28 melanoma cells (FC: fold change treatments vs. control, left columns) compared to the gene expression data of MLANAhigh versus MLANAlow melanoma samples from the TCGA database (right columns). (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.5899900.v1
title: Additional file 2: of Wnt-signaling enhances neural crest migration of melanoma cells and induces an invasive phenotype

description: Table S1. List of 44 differentially expressed genes in human SKMEL28 melanoma cells (FC: fold change treatments vs. control, left columns) compared to the gene expression data of MLANAhigh versus MLANAlow melanoma samples from the TCGA database (right columns). (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.5899867
title: Additional file 4: Table S3. of Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota

description: T1D-associated SNPs used for risk score calculation. Related to Fig.Â 7. (XLSX 49Â kb)
DOI: 10.6084/m9.figshare.5899867.v1
title: Additional file 4: Table S3. of Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota

description: T1D-associated SNPs used for risk score calculation. Related to Fig.Â 7. (XLSX 49Â kb)
DOI: 10.6084/m9.figshare.5899834
title: Additional file 3: Table S2. of Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota

description: OTU associations with all T1D-associated risk alleles. Related to Fig.Â 7. (XLSX 61Â kb)
DOI: 10.6084/m9.figshare.5899834.v1
title: Additional file 3: Table S2. of Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota

description: OTU associations with all T1D-associated risk alleles. Related to Fig.Â 7. (XLSX 61Â kb)
DOI: 10.6084/m9.figshare.5899828
title: Additional file 3: of Real-time positioning of a specific object in the big data environment

description: Test samples from the SOGOU Chinese Thesaurus that contains 300 thousand phrases. (TXT 2350 kb)
DOI: 10.6084/m9.figshare.5899828.v1
title: Additional file 3: of Real-time positioning of a specific object in the big data environment

description: Test samples from the SOGOU Chinese Thesaurus that contains 300 thousand phrases. (TXT 2350 kb)
DOI: 10.6084/m9.figshare.5899813
title: Additional file 2: Table S1. of Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota

description: OTU associations with IL-2/Treg pathway risk alleles. Related to Fig.Â 7. (XLSX 67Â kb)
DOI: 10.6084/m9.figshare.5899813.v1
title: Additional file 2: Table S1. of Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota

description: OTU associations with IL-2/Treg pathway risk alleles. Related to Fig.Â 7. (XLSX 67Â kb)
DOI: 10.6084/m9.figshare.5899807
title: Additional file 2: of Real-time positioning of a specific object in the big data environment

description: Test samples from the SOGOU Chinese Thesaurus that contains 250 thousand phrases. (TXT 1956 kb)
DOI: 10.6084/m9.figshare.5899807.v1
title: Additional file 2: of Real-time positioning of a specific object in the big data environment

description: Test samples from the SOGOU Chinese Thesaurus that contains 250 thousand phrases. (TXT 1956 kb)
DOI: 10.6084/m9.figshare.5899786
title: Additional file 1: of Real-time positioning of a specific object in the big data environment

description: Test samples from the SOGOU Chinese Thesaurus that contains 200 thousand phrases. (TXT 1564 kb)
DOI: 10.6084/m9.figshare.5899786.v1
title: Additional file 1: of Real-time positioning of a specific object in the big data environment

description: Test samples from the SOGOU Chinese Thesaurus that contains 200 thousand phrases. (TXT 1564 kb)
DOI: 10.6084/m9.figshare.5899750
title: supplemental data_reviewed.docx

description: ANOVA data for microbial biomass carbon, soil basal respiration, metabolic quotient and b-glucosidase enzyme. Variations and standard errors of A) microbial biomass carbon, B) soil basal respiration, C) metabolic quotient and D) β-glicosidase enzyme, in 6 periods of exposure after soil contamination with recommended doses of the pesticides Kraft® 36 EC, Score® 250 EC and the mixture of both. <b> </b>
DOI: 10.6084/m9.figshare.5899750.v1
title: supplemental data_reviewed.docx

description: ANOVA data for microbial biomass carbon, soil basal respiration, metabolic quotient and b-glucosidase enzyme. Variations and standard errors of A) microbial biomass carbon, B) soil basal respiration, C) metabolic quotient and D) β-glicosidase enzyme, in 6 periods of exposure after soil contamination with recommended doses of the pesticides Kraft® 36 EC, Score® 250 EC and the mixture of both. <b> </b>
DOI: 10.6084/m9.figshare.5899741
title: S1 Supporting Information Water-air CO2 flux Dataset

description: Wind-speed based parameterization formulas with respective authors for Palasari Reservoir and Lake Batur, Bali, including
DOI: 10.6084/m9.figshare.5899741.v1
title: S1 Supporting Information Water-air CO2 flux Dataset

description: Wind-speed based parameterization formulas with respective authors for Palasari Reservoir and Lake Batur, Bali, including
DOI: 10.6084/m9.figshare.5899705
title: Bacteria for emoji proposal

description: Proposal to add a virus and bacteria emoji characters submitted in 21st February, 2018.
DOI: 10.6084/m9.figshare.5899675
title: Exploring autophagy with Gene Ontology

description: Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation. The Gene Ontology (GO) is a freely available resource that describes how and where gene products function in biological systems. It consists of 3 interrelated structured vocabularies that outline what gene products do at the biochemical level, where they act in a cell and the overall biological objectives to which their actions contribute. It also consists of ‘annotations’ that associate gene products with the terms. Here we describe how we represent autophagy in GO, how we create and define terms relevant to autophagy researchers and how we interrelate those terms to generate a coherent view of the process, therefore allowing an interoperable description of its biological aspects. We also describe how annotation of gene products with GO terms improves data analysis and interpretation, hence bringing a significant benefit to this field of study.
DOI: 10.6084/m9.figshare.5899675.v1
title: Exploring autophagy with Gene Ontology

description: Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation. The Gene Ontology (GO) is a freely available resource that describes how and where gene products function in biological systems. It consists of 3 interrelated structured vocabularies that outline what gene products do at the biochemical level, where they act in a cell and the overall biological objectives to which their actions contribute. It also consists of ‘annotations’ that associate gene products with the terms. Here we describe how we represent autophagy in GO, how we create and define terms relevant to autophagy researchers and how we interrelate those terms to generate a coherent view of the process, therefore allowing an interoperable description of its biological aspects. We also describe how annotation of gene products with GO terms improves data analysis and interpretation, hence bringing a significant benefit to this field of study.
DOI: 10.6084/m9.figshare.5899672
title: HEPES activates a MiT/TFE-dependent lysosomal-autophagic gene network in cultured cells: A call for caution

description: In recent years, the lysosome has emerged as a highly dynamic, transcriptionally regulated organelle that is integral to nutrient-sensing and metabolic rewiring. This is coordinated by a lysosome-to-nucleus signaling nexus in which MTORC1 controls the subcellular distribution of the microphthalmia-transcription factor E (MiT/TFE) family of “master lysosomal regulators”. Yet, despite the importance of the lysosome in cellular metabolism, the impact of traditional in vitro culture media on lysosomal dynamics and/or MiT/TFE localization has not been fully appreciated. Here, we identify HEPES, a chemical buffering agent that is broadly applied in cell culture, as a potent inducer of lysosome biogenesis. Supplementation of HEPES to cell growth media is sufficient to decouple the MiT/TFE family members–TFEB, TFE3 and MITF–from regulatory mechanisms that control their cytosolic retention. Increased MiT/TFE nuclear import in turn drives the expression of a global network of lysosomal-autophagic and innate host-immune response genes, altering lysosomal dynamics, proteolytic capacity, autophagic flux, and inflammatory signaling. In addition, siRNA-mediated MiT/TFE knockdown effectively blunted HEPES-induced lysosome biogenesis and gene expression profiles. Mechanistically, we show that MiT/TFE activation in response to HEPES requires its macropinocytic ingestion and aberrant lysosomal storage/pH, but is independent of MTORC1 signaling. Altogether, our data underscore the cautionary use of chemical buffering agents in cell culture media due to their potentially confounding effects on experimental results.
DOI: 10.6084/m9.figshare.5899672.v1
title: HEPES activates a MiT/TFE-dependent lysosomal-autophagic gene network in cultured cells: A call for caution

description: In recent years, the lysosome has emerged as a highly dynamic, transcriptionally regulated organelle that is integral to nutrient-sensing and metabolic rewiring. This is coordinated by a lysosome-to-nucleus signaling nexus in which MTORC1 controls the subcellular distribution of the microphthalmia-transcription factor E (MiT/TFE) family of “master lysosomal regulators”. Yet, despite the importance of the lysosome in cellular metabolism, the impact of traditional in vitro culture media on lysosomal dynamics and/or MiT/TFE localization has not been fully appreciated. Here, we identify HEPES, a chemical buffering agent that is broadly applied in cell culture, as a potent inducer of lysosome biogenesis. Supplementation of HEPES to cell growth media is sufficient to decouple the MiT/TFE family members–TFEB, TFE3 and MITF–from regulatory mechanisms that control their cytosolic retention. Increased MiT/TFE nuclear import in turn drives the expression of a global network of lysosomal-autophagic and innate host-immune response genes, altering lysosomal dynamics, proteolytic capacity, autophagic flux, and inflammatory signaling. In addition, siRNA-mediated MiT/TFE knockdown effectively blunted HEPES-induced lysosome biogenesis and gene expression profiles. Mechanistically, we show that MiT/TFE activation in response to HEPES requires its macropinocytic ingestion and aberrant lysosomal storage/pH, but is independent of MTORC1 signaling. Altogether, our data underscore the cautionary use of chemical buffering agents in cell culture media due to their potentially confounding effects on experimental results.
DOI: 10.6084/m9.figshare.5899666
title: CleanedData.xlsx

description: Source Data for Slow and Deliberate Cooperation in the Commons
DOI: 10.6084/m9.figshare.5899666.v1
title: CleanedData.xlsx

description: Source Data for Slow and Deliberate Cooperation in the Commons
DOI: 10.6084/m9.figshare.5899654
title: Anthozoans: 31,829 baits targeting 2,590 conserved loci (Anthozoan-UCE-1.7Kv1.fasta.zip)

description: A target enrichment bait set designed from 2,590 conserved UCE loci and exons identified among Anthozoans. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
DOI: 10.6084/m9.figshare.5899654.v1
title: Anthozoans: 31,829 baits targeting 2,590 conserved loci (Anthozoan-UCE-1.7Kv1.fasta.zip)

description: A target enrichment bait set designed from 2,590 conserved UCE loci and exons identified among Anthozoans. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
DOI: 10.6084/m9.figshare.5899651
title: BSDB Meeting Programs

description: These are the programs of historical meetings organised by the British Society for Developmental Biology (BSDB), starting from the inaugural meeting in 1964.<br>
DOI: 10.6084/m9.figshare.5899651.v1
title: BSDB Meeting Programs

description: These are the programs of historical meetings organised by the British Society for Developmental Biology (BSDB), starting from the inaugural meeting in 1964.<br>
DOI: 10.6084/m9.figshare.5899651.v2
title: BSDB Meeting Programs

description: These are the programs of historical meetings organised by the British Society for Developmental Biology (BSDB), starting from the inaugural meeting in 1964.<br>
DOI: 10.6084/m9.figshare.5899651.v3
title: BSDB Meeting Programs

description: These are the programs of historical meetings organised by the British Society for Developmental Biology (BSDB), starting from the inaugural meeting in 1964.<br>
DOI: 10.6084/m9.figshare.5899651.v4
title: BSDB Meeting Programs

description: These are the programs of historical meetings organised by the British Society for Developmental Biology (BSDB), starting from the inaugural meeting in 1964.<br>
DOI: 10.6084/m9.figshare.5899651.v5
title: BSDB Meeting Programs

description: These are the programs of historical meetings organised by the British Society for Developmental Biology (BSDB), starting from the inaugural meeting in 1964.<br>