cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh2697092.08fu
title: SH2697092.08FU

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/sh2697093.08fu
title: SH2697093.08FU

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/sh2697094.08fu
title: SH2697094.08FU

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/sh2697095.08fu
title: SH2697095.08FU

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: 10.6084/m9.figshare.14168212
title: Additional file 3 of Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis

description: Additional file 3: Table S2. Correlation between HPSE2 expression and CpG island methylation of CRC in TCGA database.
DOI: 10.6084/m9.figshare.14168215
title: Additional file 4 of Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis

description: Additional file 4: Table S3. GSEA enrichment analysis.
DOI: 10.6084/m9.figshare.21506768.v1
title: Additional file 1 of Metagenomic and proteomic analysis of bacterial retting community and proteome profile in the degumming process of kenaf bast

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.21506771
title: Additional file 2 of Metagenomic and proteomic analysis of bacterial retting community and proteome profile in the degumming process of kenaf bast

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.14168203
title: Additional file 1 of Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis

description: Additional file 1: Table S1. Screening of methylation-regulated genes from the GEO and TCGA databases.
DOI: 10.6084/m9.figshare.14168203.v1
title: Additional file 1 of Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis

description: Additional file 1: Table S1. Screening of methylation-regulated genes from the GEO and TCGA databases.
DOI: 10.6084/m9.figshare.19411103
title: Long non-coding RNA MEG3 promotes tumor necrosis factor-alpha induced oxidative stress and apoptosis in interstitial cells of cajal via targeting the microRNA-21 /I-kappa-B-kinase beta axis

description: Interstitial Cells of Cajal (ICC) plays a critical role in the peristaltic contractions of the gastrointestinal and urinary tract. The dysfunction and loss of ICC contributes to hypokinetic disease, such as gallstoneand ureteropelvic junction obstruction . In the present study, we identified the underlying driving molecular signals of oxidative stress and apoptosis in ICC. ICC was isolated from small intestine of Balb/c mice, and stimulated with tumor necrosis factor-alpha (TNF-α). MTT and flow cytometry were performed to assess cell viability, apoptosis, and the level of reactive oxygen species in ICC, respectively. The level of malondialdehyde, superoxide dismutase, and glutathione peroxidase in cells were measured to assess oxidative stress. The expression of inflammatory factors (interleukin, IL-1 and IL-6) and apoptosis-related proteins were detected by western blot. We observed that TNF-αinduced inflammation, oxidative stress and cell apoptosis in ICC. By using quantitative real-time PCR , we verified that the expression of long non-coding RNAMEG3 was elevated by TNF-α in ICC. Silencing MEG3 reversed inflammation, oxidative stress, and cell apoptosisin TNF-α-treated ICC. Subsequently, we confirmed that MEG3 sponged cytoprotective miR-21 to upregulate the expression of I-kappa-B-kinase beta (IKKB) and activate the nuclear factor kappa-B (NF-κB) pathway. Both miR-21 overexpression and IKKB knockdown reduced TNF-α-induced above symptoms in ICC. Taken together, we can conclude that MEG3 mediates inflammation, oxidative stress and apoptosis in TNF-α-treated ICC via the miR-21/IKKB-NF-κB axis. The study improves our understanding of the molecular mechanism of ICC reduction related diseases.
DOI: 10.6084/m9.figshare.14168167.v1
title: Additional file 2 of Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity

description: Additional file 2: Table S1. Sequencing metrics for single cell and population RNA-seq libraries.
DOI: 10.6084/m9.figshare.13642451.v1
title: Additional file 2 of Molecular mapping of a novel lesion mimic gene (lm4) associated with enhanced resistance to stripe rust in bread wheat

description: Additional file 2.
DOI: 10.6084/m9.figshare.14168215.v1
title: Additional file 4 of Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosis

description: Additional file 4: Table S3. GSEA enrichment analysis.
DOI: 10.6084/m9.figshare.13642262
title: Additional file 1 of Hsa_circ_0010235 functions as an oncogenic drive in non-small cell lung cancer by modulating miR-433-3p/TIPRL axis

description: Additional file 1. Raw images of Western blot results
DOI: 10.6084/m9.figshare.13642387
title: Additional file 1 of CD9, a potential leukemia stem cell marker, regulates drug resistance and leukemia development in acute myeloid leukemia

description: Additional file 1: Table S1. Patient characteristics in this study. Table S2. Primes for Chromatin Immunoprecipitation in this study. Table S3. The 23 genes were significantly upregulated in the MRD microarray.
DOI: 10.6084/m9.figshare.13642387.v1
title: Additional file 1 of CD9, a potential leukemia stem cell marker, regulates drug resistance and leukemia development in acute myeloid leukemia

description: Additional file 1: Table S1. Patient characteristics in this study. Table S2. Primes for Chromatin Immunoprecipitation in this study. Table S3. The 23 genes were significantly upregulated in the MRD microarray.
DOI: 10.6084/m9.figshare.21506768
title: Additional file 1 of Metagenomic and proteomic analysis of bacterial retting community and proteome profile in the degumming process of kenaf bast

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.13642448
title: Additional file 1 of Molecular mapping of a novel lesion mimic gene (lm4) associated with enhanced resistance to stripe rust in bread wheat

description: Additional file 1.
DOI: 10.6084/m9.figshare.14168206
title: Additional file 2 of Genome-wide epistasis analysis for Alzheimer’s disease and implications for genetic risk prediction

description: Additional file 2: Table S1. Nominal significant SNP-SNP interactions (BOOST). Table S2. Nominal significant SNP-SNP interactions (Logistic regression). Table S3. Nominal significant SNP-SNP interactions (Joint effect). Table S4. Co-expression and eQTL analysis of significant genetic interactions (FDR &lt; 0.1). Table S5. Selected genetic interactions that showed non-random prediction in both ADNI and ROSMAP.
DOI: 10.6084/m9.figshare.14168278
title: Additional file 3 of OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species

description: Additional file 3: Table S3 Number of homozygous small nucleotide polymorphisms in 33 O. rufipogon.
DOI: 10.6084/m9.figshare.14168278.v1
title: Additional file 3 of OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species

description: Additional file 3: Table S3 Number of homozygous small nucleotide polymorphisms in 33 O. rufipogon.
DOI: 10.6084/m9.figshare.14168275.v1
title: Additional file 2 of OryzaGenome2.1: Database of Diverse Genotypes in Wild Oryza Species

description: Additional file 2: Table S2. Summary of K-mer analysis using genotypes of 217 wild Oryza accessions.
DOI: 10.6084/m9.figshare.22318312
title: Tripadvisor tourist review English

description: This is the data set of English reviews used to analyse the results from 'Identifying the role of intangible cultural heritage in distinguishing cities: A social media study of heritage, place, and sense in Guangzhou, China'.
DOI: 10.6084/m9.figshare.22318312.v1
title: English tourist review

description: This is the data set of English reviews used to analyse the results from 'Identifying the role of intangible cultural heritage in distinguishing cities: A social media study of heritage, place, and sense in Guangzhou, China'.
DOI: 10.6084/m9.figshare.22317484.v1
title: Tripadvisor review Chinese.xlsx

description: This is the data set of Chinese reviews used to analyse the results from 'Identifying the role of intangible cultural heritage in distinguishing cities: A social media study of heritage, place, and sense in Guangzhou, China'.
DOI: 10.6084/m9.figshare.22320859
title: Article cording for literature analysis

description: These are codes after the first step of publication analyzing the content of intangible cultural heritage tourism.
DOI: 10.6084/m9.figshare.22320859.v2
title: Article cording for literature analysis

description: These are codes after the first step of publication analyzing the content of intangible cultural heritage tourism.
DOI: 10.6084/m9.figshare.22320859.v1
title: Article cording in for literature analysis

description: These are codes after the first step of publication analysing
DOI: 10.5519/qd.9ja22j5q
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (196 records)
DOI: 10.6084/m9.figshare.22320853.v1
title: Articles analysied in literature review

description: These are publications collected for literature review
DOI: 10.6084/m9.figshare.22320853
title: Articles analysed in literature review

description: These are publications collected for literature review on the content of intangible cultural heritage tourism.
DOI: 10.5281/zenodo.7709450
title: Data for Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response

description: Data from simulations used to generate the figures in the paper <em>Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response</em>. To reproduce analyses, extract <em>colony_data.zip</em> in the <em>data</em> folder after cloning the <em>vivarium-ecoli</em> repository. The extracted folder contains the following items: <em>sim_dfs</em>: a folder containing the CSV files that represent a subset of the raw simulation data used for downstream analyses. <em>glc_10000_fluxome.csv</em>: Each row represents a reaction in central carbon metabolism (in same order as listed in <em>validation/ecoli/flat/toya_2010_central_carbon_fluxes.tsv</em>). Each column represents a single time point for a single cell in a baseline glucose simulation (seed 10000). Each value is a flux (mmol/L/hr). Provided as input to <em>ecoli/analysis/centralCarbonMetabolism.py </em>script to reproduce fluxome validation plot. <em>glc_10000_proteome_avgs.csv</em>: Each row represents a protein monomer (in same order as <em>sim_data.translation.monomer_data["id"]</em> where <em>sim_data</em> is <em>reconstruction/sim_data/kb/validationData.cPickle</em>). Each column represents a cell in a baseline glucose simulation (seed 10000). Each row represents a protein monomer. Each value represents the average count of a given protein monomer for a given cell. Provided as input to <em>ecoli/analysis/proteinCountsValidation.py</em> script to reproduce proteome validation plot. <em>glc_10000_expressome.csv</em>: Each column represents a gene (with the exception of the final two metadata columns: "Time" and "Agent ID"). Each row represents a specific cell (agent) at a specific time in a baseline glucose simulation (seed 10000). Each value represents the number of new RNA transcripts for a given gene in a given cell at a given time. Provided as input to <em>ecoli/analysis/antibiotics_colony/subgen_gene_plots/count_subgen.py</em> script to calculate number of sub-generational genes among all genes and antibiotic response genes. <em>glc_10000_total_mrna.json</em>: Mapping of agent IDs for all cells in a baseline glucose simulation (seed 10000) to their average total mRNA count. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. 2C,D. <em>jenner_2013.csv</em>: Data extracted from Fig. 2C of 10.1073/pnas.1216691110. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. S6A. <em>olson_2006.csv</em>: Data extracted from Fig. 2D of 10.1128/AAC.01499-05. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. S6A. <em>lysis_ratios.csv</em>: Data extracted from Fig. 2 of 10.1099/00221287-31-3-339. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. 4N.
DOI: 10.6084/m9.figshare.22320853.v2
title: Articles analysed in literature review

description: These are publications collected for literature review on the content of intangible cultural heritage tourism.
DOI: 10.5281/zenodo.7686398
title: Data for Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response

description: Data from simulations used to generate the figures in the paper <em>Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in the antibiotic response</em>. To reproduce analyses, extract <em>colony_data.zip</em> in the <em>data</em> folder after cloning the <em>vivarium-ecoli</em> repository. The extracted folder contains the following items: <em>sim_dfs</em>: a folder containing the CSV files that represent a subset of the raw simulation data used for downstream analyses. <em>glc_10000_fluxome.csv</em>: Each row represents a reaction in central carbon metabolism (in same order as listed in <em>validation/ecoli/flat/toya_2010_central_carbon_fluxes.tsv</em>). Each column represents a single time point for a single cell in a baseline glucose simulation (seed 10000). Each value is a flux (mmol/L/hr). Provided as input to <em>ecoli/analysis/centralCarbonMetabolism.py </em>script to reproduce fluxome validation plot. <em>glc_10000_proteome_avgs.csv</em>: Each row represents a protein monomer (in same order as <em>sim_data.translation.monomer_data["id"]</em> where <em>sim_data</em> is <em>reconstruction/sim_data/kb/validationData.cPickle</em>). Each column represents a cell in a baseline glucose simulation (seed 10000). Each row represents a protein monomer. Each value represents the average count of a given protein monomer for a given cell. Provided as input to <em>ecoli/analysis/proteinCountsValidation.py</em> script to reproduce proteome validation plot. <em>glc_10000_expressome.csv</em>: Each column represents a gene (with the exception of the final two metadata columns: "Time" and "Agent ID"). Each row represents a specific cell (agent) at a specific time in a baseline glucose simulation (seed 10000). Each value represents the number of new RNA transcripts for a given gene in a given cell at a given time. Provided as input to <em>ecoli/analysis/antibiotics_colony/subgen_gene_plots/count_subgen.py</em> script to calculate number of sub-generational genes among all genes and antibiotic response genes. <em>glc_10000_total_mrna.json</em>: Mapping of agent IDs for all cells in a baseline glucose simulation (seed 10000) to their average total mRNA count. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. 2C,D. <em>jenner_2013.csv</em>: Data extracted from Fig. 2C of 10.1073/pnas.1216691110. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. S6A. <em>olson_2006.csv</em>: Data extracted from Fig. 2D of 10.1128/AAC.01499-05. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. S6A. <em>lysis_ratios.csv</em>: Data extracted from Fig. 2 of 10.1099/00221287-31-3-339. Used by <em>ecoli/analysis/antibiotics_colony/plot.py </em>to generate Fig. 4N.
DOI: 10.7284/152736
title: Multibeam Echosounder data collected during research cruise NBP9407 using a SeaBeam 2112 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152735
title: Multibeam Echosounder data collected during research cruise NBP9501 using a SeaBeam 2112 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152740
title: Multibeam Echosounder data collected during research cruise NBP9602 using a SeaBeam 2112 instrument system onboard the platform RV Nathaniel B. Palmer

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152479
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC2108A using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152477
title: Anemometer data collected during research cruise OC2108A using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152482
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC2108A using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152484
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC2108A using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152489
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC2108A using a Trimble ABX-Two instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152486
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC2108A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152490
title: Radiometer data collected during research cruise OC2108A using a RMRCo PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152483
title: Water Temperature data collected during research cruise OC2108A using a SeaBird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152485
title: Water Temperature data collected during research cruise OC2108A using a SeaBird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152478
title: Timeserver data collected during research cruise OC2108A using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152491
title: Transmissometer data collected during research cruise OC2108A using a WETLabs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152480
title: TSG (Thermosalinograph) data collected during research cruise OC2108A using a SeaBird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/152488
title: Winch data collected during research cruise OC2108A using a Markey Markey DESH-5/COM-15 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/150323
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise TN388 using a Hawaii UHDAS instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/150327
title: Anemometer data collected during research cruise TN388 using a RMYoung 06206 instrument system onboard the platform RV Thomas G. Thompson

description: Original (unprocessed) data collected during a Field_expedition