cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0935742.10fu
title: SH0935742.10FU

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/sh0935743.10fu
title: SH0935743.10FU

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: 10.15468/dl.kcczsh
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bimeria vestita Wright, 1859",
 "Country is Brazil",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099828-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh0935744.10fu
title: SH0935744.10FU

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/sh0935745.10fu
title: SH0935745.10FU

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: 10.15468/dl.62frj9
title: Occurrence Download

description: A dataset containing 41877 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myotis nattereri (Kuhl, 1817)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 41877 records from 1455 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099825-240626123714530/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.21077759
title: Additional file 11 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 11: Table S11. Median Availability of Orphan Drugs at Drug-Level in China From 2017 to 2020 (%).
DOI: 10.6084/m9.figshare.21077777.v1
title: Additional file 1 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 1: Table S1. The questionnaire on the availability and prices of surveyed orphan drugs in leading provincial institutions.
DOI: 10.6084/m9.figshare.21077780
title: Additional file 2 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 2: Table S2. List of 79 orphan drugs surveyed in 30 public tertiary hospitals in China (99 drug-indication matches).
DOI: 10.6084/m9.figshare.20029283
title: A Comparison of Bayesian Multivariate Versus Univariate Normal Regression Models for Prediction

description: In many moderate dimensional applications we have multiple response variables that are associated with a common set of predictors. When the main objective is prediction of the response variables, a natural question is: do multivariate regression models that accommodate dependency among the response variables improve prediction compared to their univariate counterparts? Note that in this article, by univariate versus multivariate regression models we refer to regression models with a single versus multiple response variables, respectively. We assume that under both scenarios, there are multiple covariates. Our question is motivated by an application in climate science, which involves the prediction of multiple metrics that measure the activity, intensity, severity etc. of a hurricane season. Average sea surface temperatures (SSTs) during the hurricane season have been used as predictors for each of these metrics, in separate univariate regression models, in the literature. Since the true SSTs are yet to be observed during prediction, typically their forecasts from multiple climate models are used as predictors. Some climate models have a few missing values so we develop Bayesian univariate/multivariate normal regression models, that can handle missing covariates and variable selection uncertainty. Whether Bayesian multivariate normal regression models improve prediction compared to their univariate counterparts is not clear from the existing literature, and in this work we try to fill this gap.
DOI: 10.6084/m9.figshare.21077762.v1
title: Additional file 12 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 12: Table S12. Availability classification of Orphan Drugs at Drug-Level in China From 2017 to 2020 (%).
DOI: 10.6084/m9.figshare.21077789.v1
title: Additional file 5 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 5: Table S5. List of the surveyed 30 leading provincial institutions of the National Network to Collaborate on Diagnosis and Treatment of Rare Diseases in China.
DOI: 10.6084/m9.figshare.21077780.v1
title: Additional file 2 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 2: Table S2. List of 79 orphan drugs surveyed in 30 public tertiary hospitals in China (99 drug-indication matches).
DOI: 10.6084/m9.figshare.21077792.v1
title: Additional file 6 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 6: Table S6. The median unit prices of generic orphan drugs surveyed in 30 leading provincial institutions in China from 2017-2020 (USD).
DOI: 10.6084/m9.figshare.21077795.v1
title: Additional file 7 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 7: Table S7. The daily disposable income per capita of urban or rural residents from 2017 to 2020 in China.
DOI: 10.6084/m9.figshare.21077798
title: Additional file 8 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 8: Table S8. The coverage of NBMI of surveyed orphan drugs in China from 2017-2020.
DOI: 10.6084/m9.figshare.21077795
title: Additional file 7 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 7: Table S7. The daily disposable income per capita of urban or rural residents from 2017 to 2020 in China.
DOI: 10.6084/m9.figshare.21077786
title: Additional file 4 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 4: Table S4. ICD-11 categories of surveyed drugs in China.
DOI: 10.6084/m9.figshare.21077792
title: Additional file 6 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 6: Table S6. The median unit prices of generic orphan drugs surveyed in 30 leading provincial institutions in China from 2017-2020 (USD).
DOI: 10.6084/m9.figshare.21077801.v1
title: Additional file 9 of Evaluating the national system for rare diseases in China from the point of drug access: progress and challenges

description: Additional file 9: Table S9. Median of hospital-level availability for orphan drugs in each efficacy group.
DOI: 10.6084/m9.figshare.7446452.v1
title: Additional file 4: of Basal position of two new complete mitochondrial genomes of parasitic Cymothoida (Crustacea: Isopoda) challenges the monophyly of the suborder and phylogeny of the entire order

description: Table S1. Primers used to amplify and sequence the mitochondrial genomes of the two parasitic cymothoid isopods Ichthyoxenos japonensis and Tachaea chinensis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.13212391
title: Additional file 2 of Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens

description: Additional file 2. The information of differentially expressed genes (DEGs) in uterus between young (42 wk. of age) and aged hen groups (72 wk. of age).
DOI: 10.6084/m9.figshare.13212395.v1
title: Additional file 4 of Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection

description: Additional file 4 : Supplementary Figure 3.
DOI: 10.6084/m9.figshare.7446347
title: Additional file 1: of The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism

description: All OTU in a given gut microbial community. (XLSX 180 kb)
DOI: 10.6084/m9.figshare.22649524.v1
title: Additional file 1 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 1: Fig. S1. Phenotype analysis of Ck137956-/- mice. Fig. S2. Gene ontology enrichment analysis of down-regulated genes in Ck137956-/- pachytene spermatocytes. Fig. S3. Analysis of Ck137956-interacting protein Miwi. Fig. S4. Verification of siRNA knock down efficiency.
DOI: 10.6084/m9.figshare.22649536.v1
title: Additional file 5 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 5. Proteomic profiling of Ck137956+/- and Ck137956-/- round spermatids.
DOI: 10.34740/kaggle/dsv/7594192
title: LUFlow Network Intrusion Detection Data Set
DOI: 10.6084/m9.figshare.22649530.v1
title: Additional file 3 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 3. RNA-seq profiling of Ck137956+/- and Ck137956-/- pachytene spermatocytes.
DOI: 10.6084/m9.figshare.13213690.v1
title: Experimental data from Adaptive stochastic resonance in bistable system driven by noisy NLFM signal: phenomenon and application

description: The bearing outer raceway fault signal under the speed-varying condition
DOI: 10.6084/m9.figshare.22649536
title: Additional file 5 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 5. Proteomic profiling of Ck137956+/- and Ck137956-/- round spermatids.
DOI: 10.6084/m9.figshare.7446347.v1
title: Additional file 1: of The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism

description: All OTU in a given gut microbial community. (XLSX 180 kb)
DOI: 10.6084/m9.figshare.22649539.v1
title: Additional file 6 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 6. Includes individual values depicted in Figs. 1, 2, 3 and 5.
DOI: 10.6084/m9.figshare.22649530
title: Additional file 3 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 3. RNA-seq profiling of Ck137956+/- and Ck137956-/- pachytene spermatocytes.
DOI: 10.5281/zenodo.10605957
title: MITO END-3: efficacy of Avelumab immunotherapy according to molecular profiling in first line endometrial cancer therapy

description: Immunotherapy combined to chemotherapy significantly improves progression free survival compared to first line chemotherapy alone in advanced endometrial cancer, with a much larger effect size in microsatellite-instability high (MSI-H) cases. New biomarkers might help to select patients that may have benefit among those with a microsatellite-stable (MSS) tumor.


Methods.


In a pre-planned translational analysis of the MITO END-3 trial we assessed the significance of genomic abnormalities in patients randomized to standard carboplatin/paclitaxel without or with avelumab.


Results.


Out of 125 randomized patients, 109 had samples eligible for Next Generation Sequencing (NGS) analysis and 102 had MSI tested. According to The Cancer Genome Atlas (TCGA) there were 29 cases MSI-H, 26 MSS TP53 wild type (wt), 47 MSS TP53 mutated (mut), and one case with POLE mutation. Four mutated genes were present in more than 30 % of cases: TP53, PIK3CA, ARID1A, PTEN. Eleven patients (10 %) had a BRCA 1/2 mutation (5 in MSI-H and 6 in MSS). High TMB (≥ 10Muts/Mb) was observed in all MSI-H patients, in 4 out of 47 MSS/TP53mut, and in no case in the MSS/TP53wt category. The effect of avelumab on progression-free survival (PFS) significantly varied according to TCGA categories, being favorable in MSI-H and worst in MSS/TP53mut (P interaction=0.003); a similar non-significant trend was seen in survival analysis. ARID1A and PTEN also showed a statistically significant interaction with treatment effect, that was better in presence of the mutation (ARID1A P interaction=0.01; PTEN P interaction=0.002).


Conclusion


The MITO END-3 trial results suggest that TP53 mutation is associated with poor effect of avelumab, while mutations of PTEN and ARID1A are related to a positive effect of the drug in patients with advanced endometrial cancer.
DOI: 10.5281/zenodo.7739755
title: Biskyrmion-based artificial neuron data

description: Data used in the publication
DOI: 10.5281/zenodo.7739756
title: Biskyrmion-based artificial neuron data

description: Data used in the publication
DOI: 10.5281/zenodo.8134240
title: MITO END-3: efficacy of Avelumab immunotherapy according to molecular profiling in first line endometrial cancer therapy

description: Immunotherapy combined to chemotherapy significantly improves progression free survival compared to first line chemotherapy alone in advanced endometrial cancer, with a much larger effect size in microsatellite-instability high (MSI-H) cases. New biomarkers might help to select patients that may have benefit among those with a microsatellite-stable (MSS) tumor.


Methods.


In a pre-planned translational analysis of the MITO END-3 trial we assessed the significance of genomic abnormalities in patients randomized to standard carboplatin/paclitaxel without or with avelumab.


Results.


Out of 125 randomized patients, 109 had samples eligible for Next Generation Sequencing (NGS) analysis and 102 had MSI tested. According to The Cancer Genome Atlas (TCGA) there were 29 cases MSI-H, 26 MSS TP53 wild type (wt), 47 MSS TP53 mutated (mut), and one case with POLE mutation. Four mutated genes were present in more than 30 % of cases: TP53, PIK3CA, ARID1A, PTEN. Eleven patients (10 %) had a BRCA 1/2 mutation (5 in MSI-H and 6 in MSS). High TMB (≥ 10Muts/Mb) was observed in all MSI-H patients, in 4 out of 47 MSS/TP53mut, and in no case in the MSS/TP53wt category. The effect of avelumab on progression-free survival (PFS) significantly varied according to TCGA categories, being favorable in MSI-H and worst in MSS/TP53mut (P interaction=0.003); a similar non-significant trend was seen in survival analysis. ARID1A and PTEN also showed a statistically significant interaction with treatment effect, that was better in presence of the mutation (ARID1A P interaction=0.01; PTEN P interaction=0.002).


Conclusion


The MITO END-3 trial results suggest that TP53 mutation is associated with poor effect of avelumab, while mutations of PTEN and ARID1A are related to a positive effect of the drug in patients with advanced endometrial cancer.
DOI: 10.5281/zenodo.8134241
title: MITO END-3: efficacy of Avelumab immunotherapy according to molecular profiling in first line endometrial cancer therapy

description: Immunotherapy combined to chemotherapy significantly improves progression free survival compared to first line chemotherapy alone in advanced endometrial cancer, with a much larger effect size in microsatellite-instability high (MSI-H) cases. New biomarkers might help to select patients that may have benefit among those with a microsatellite-stable (MSS) tumor. Methods. In a pre-planned translational analysis of the MITO END-3 trial we assessed the significance of genomic abnormalities in patients randomized to standard carboplatin/paclitaxel without or with avelumab. Results. Out of 125 randomized patients, 109 had samples eligible for Next Generation Sequencing (NGS) analysis and 102 had MSI tested. According to The Cancer Genome Atlas (TCGA) there were 29 cases MSI-H, 26 MSS TP53 wild type (wt), 47 MSS TP53 mutated (mut), and one case with <em>POLE</em> mutation. Four mutated genes were present in more than 30 % of cases: <em>TP53</em>,<em> PIK3CA</em>,<em> ARID1A</em>,<em> PTEN</em>. Eleven patients (10 %) had a BRCA 1/2 mutation (5 in MSI-H and 6 in MSS). High TMB (≥ 10Muts/Mb) was observed in all MSI-H patients, in 4 out of 47 MSS/<em>TP53</em>mut, and in no case in the MSS/<em>TP53</em>wt category. The effect of avelumab on progression-free survival (PFS) significantly varied according to TCGA categories, being favorable in MSI-H and worst in MSS/TP53mut (P interaction=0.003); a similar non-significant trend was seen in survival analysis. <em>ARID1A</em> and <em>PTEN</em> also showed a statistically significant interaction with treatment effect, that was better in presence of the mutation (<em>ARID1A</em> P interaction=0.01; <em>PTEN</em> P interaction=0.002). Conclusion The MITO END-3 trial results suggest that <em>TP53 </em>mutation is associated with poor effect of avelumab, while mutations of <em>PTEN</em> and <em>ARID1A</em> are related to a positive effect of the drug in patients with advanced endometrial cancer.
DOI: 10.6084/m9.figshare.22649542
title: Additional file 7 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 7. Includes individual values depicted in Additional file 1: Figure S1 and S4.
DOI: 10.6084/m9.figshare.7446452
title: Additional file 4: of Basal position of two new complete mitochondrial genomes of parasitic Cymothoida (Crustacea: Isopoda) challenges the monophyly of the suborder and phylogeny of the entire order

description: Table S1. Primers used to amplify and sequence the mitochondrial genomes of the two parasitic cymothoid isopods Ichthyoxenos japonensis and Tachaea chinensis. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7446473.v1
title: Additional file 7: of Basal position of two new complete mitochondrial genomes of parasitic Cymothoida (Crustacea: Isopoda) challenges the monophyly of the suborder and phylogeny of the entire order

description: Table S2. Comparison of 17 isopod mitochondrial genomes. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.25195502
title: Processed_Data_for_ESG_paper.zip

description: The zip file contains data used to create the figures in the ESG paper. The dataset include Ic_vcf_data, carbon_flux_TRENDY.mat, hydrometeo_variables.mat, LAl_spring_GlMMS.mat, SOS_freeze_thaw.mat, mca_input, and XGBoost model input.
DOI: 10.6084/m9.figshare.21602251
title: Additional file 1 of Glycoproteomics revealed novel N-glycosylation biomarkers for early diagnosis of lung adenocarcinoma cancers

description: Additional file 1: Table S1. MS identified information in this study.
DOI: 10.6084/m9.figshare.22649539
title: Additional file 6 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 6. Includes individual values depicted in Figs. 1, 2, 3 and 5.
DOI: 10.6084/m9.figshare.22649533
title: Additional file 4 of Regulation of Miwi-mediated mRNA stabilization by Ck137956/Tssa is essential for male fertility

description: Additional file 4. RNA-seq profiling of Ck137956+/- and Ck137956-/- round spermatids.
DOI: 10.6084/m9.figshare.7446473
title: Additional file 7: of Basal position of two new complete mitochondrial genomes of parasitic Cymothoida (Crustacea: Isopoda) challenges the monophyly of the suborder and phylogeny of the entire order

description: Table S2. Comparison of 17 isopod mitochondrial genomes. (XLSX 13 kb)