cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12459056.v6
title: agnostosDB_dbf02445-20200519

description: The agnostosDB (dbf02445-20200519) is a comprehensive dataset of microbial gene clusters (GCs) from genomes and metagenomes. It contains 5,287,759 GCs and more than 280M genes coming from the bacterial and archaeal Genome Taxonomy Database (GTDB) genomes, and from five large-scale metagenomic projects: 583 marine metagenomes from Tara Oceans expedition (TARA), Malaspina expedition, Ocean Sampling Day (OSD), Global Ocean Sampling Expedition (GOS), complemented with 1,246 metagenomes from the Human Microbiome Project (HMP) phase I and II. The dataset is described in Vanni et al. 2020.<br>Additional and more detailed information about the dataset creation and some of its applications, can be found at https://dark.metagenomics.eu/.Related to the agnostosDB is the agnostos-wf, a snakemake workflow stored in the GitHub repository https://github.com/functional-dark-side/agnostos-wf. The agnostos-wf allows to search the agnostosDB gene cluster HMM profiles and/or to integrate new sequence data (genes/contigs) in it.
DOI: 10.6084/m9.figshare.12459056.v7
title: agnostosDB_dbf02445-20200519

description: The agnostosDB (dbf02445-20200519) is a comprehensive dataset of microbial gene clusters (GCs) from genomes and metagenomes. It contains 5,287,759 GCs and more than 280M genes coming from the bacterial and archaeal Genome Taxonomy Database (GTDB) genomes, and from five large-scale metagenomic projects: 583 marine metagenomes from Tara Oceans expedition (TARA), Malaspina expedition, Ocean Sampling Day (OSD), Global Ocean Sampling Expedition (GOS), complemented with 1,246 metagenomes from the Human Microbiome Project (HMP) phase I and II. The dataset is described in Vanni et al. 2020.<br>Additional and more detailed information about the dataset creation and some of its applications, can be found at https://dark.metagenomics.eu/.Related to the agnostosDB is the agnostos-wf, a snakemake workflow stored in the GitHub repository https://github.com/functional-dark-side/agnostos-wf. The agnostos-wf allows to search the agnostosDB gene cluster HMM profiles and/or to integrate new sequence data (genes/contigs) in it.
DOI: 10.6084/m9.figshare.12458870
title: Gmax database.csv

description: Shear modulus database for clean sands
DOI: 10.6084/m9.figshare.12459056.v8
title: agnostosDB_dbf02445-20200519

description: The agnostosDB (dbf02445-20200519) is a comprehensive dataset of microbial gene clusters (GCs) from genomes and metagenomes. It contains 5,287,759 GCs and more than 280M genes coming from the bacterial and archaeal Genome Taxonomy Database (GTDB) genomes, and from five large-scale metagenomic projects: 583 marine metagenomes from Tara Oceans expedition (TARA), Malaspina expedition, Ocean Sampling Day (OSD), Global Ocean Sampling Expedition (GOS), complemented with 1,246 metagenomes from the Human Microbiome Project (HMP) phase I and II. The dataset is described in Vanni et al. 2020.<br>Additional and more detailed information about the dataset creation and some of its applications, can be found at https://dark.metagenomics.eu/.Related to the agnostosDB is the agnostos-wf, a snakemake workflow stored in the GitHub repository https://github.com/functional-dark-side/agnostos-wf. The agnostos-wf allows to search the agnostosDB gene cluster HMM profiles and/or to integrate new sequence data (genes/contigs) in it.
DOI: 10.6084/m9.figshare.12458870.v1
title: Gmax database.csv

description: Shear modulus database for clean sands
DOI: 10.6084/m9.figshare.12458870.v2
title: Gmax database.csv

description: Shear modulus database for clean sands
DOI: 10.6084/m9.figshare.12458870.v3
title: Gmax database.csv

description: Shear modulus database for clean sands
DOI: 10.6073/pasta/bdddb5767fcd2647f17c3b8feb3e7b39
title: Anaktuvuk River tussock tundra flowering in response to fire severity, 2008-2015

description: Flowers were counted from annual photographs of the severe, moderate, and unburned Anaktuvuk River flux tower sites during peak flowering season (6/17-7/20).
DOI: 10.6084/m9.figshare.12458660
title: Test of 3-suture gene sets overlap

description: Comparing groups of genes
DOI: 10.6084/m9.figshare.12458612
title: Metabolite BridgeDb ID Mapping Database (20200610)

description: BridgeDb ID mapping database for metabolites, using HMDB 4.0 (Release of April 2020), ChEBI 186 (Release of April 2020), and Wikidata (10 June 2020) as data sources.
DOI: 10.6084/m9.figshare.12458612.v1
title: Metabolite BridgeDb ID Mapping Database (20200610)

description: BridgeDb ID mapping database for metabolites, using HMDB 4.0 (Release of April 2020), ChEBI 186 (Release of April 2020), and Wikidata (10 June 2020) as data sources.
DOI: 10.6084/m9.figshare.12458591
title: HADDOCK refined models of ACE2 with the bound RBD of SARS-CoV-2 Spike glycoprotein

description: The zip file includes all calculations related to ACE2/RBD of S protein from SARS-CoV-2 performed with HADDOCK. After unzipping the file, two folders appear. These include the models based on the crystal structure 6M0J and the cryo-EM structure 6M17. Each folder has subdirectories variants, ALA_scan, and UniProt, and specifically for 6M17, an additional subdirectory is included, PyMOL_models_6M17. This directory includes additional .pdb and .cif files. The initial .pdb files that were used to produce all reported variants are placed in each folder along with parameter files to reproduce the HADDOCK calculations.
DOI: 10.6084/m9.figshare.12458465
title: Supplementary Material for: The Release of Cyclophilin A from Rapamycin-Stimulated Vascular Smooth Muscle Cells Mediated by Myosin II Activation: Involvement of Apoptosis but Not Autophagy

description: <b><i>Introduction:</i></b> The exocytosis of cyclophilin A (CyPA) by a vesicular pathway in response to reactive oxygen species has been determined. However, other sources of extracellular CyPA remain obscure. <b><i>Objective:</i></b> The aim of this study was to determine the role of autophagy in the secretion of CyPA. <b><i>Methods and Results:</i></b> Rapamycin induced the activation of autophagy and release of CyPA from primary cultured rat aortic smooth muscle cells (RASMCs). However, inhibition of autophagy by knockdown of Atg7 or chloroquine did not affect the rapamycin-induced release of CyPA. With the exception of myosin II activity, rho-associated coiled-coil kinase (ROCK), actin remodelling, and synaptic vesicles were not implicated in the release of rapamycin-induced CyPA. Finally, we confirmed that rapamycin-induced extracellular CyPA originated from apoptotic RASMCs. Furthermore, the decreased activation of myosin II by blebbistatin blocked the release of CyPA from apoptotic RASMCs induced by rapamycin. <b><i>Conclusions:</i></b> Rapamycin induced the release of CyPA from apoptotic RASMCs but did not affect exocytosis through autophagosomes. ROCK, actin remodelling, and synaptic vesicles were not involved in the apoptosis-related release of CyPA. Myosin II activation modulated the apoptosis of vascular smooth muscle cells and the release of CyPA from rapamycin-induced apoptotic cell death.
DOI: 10.6084/m9.figshare.12458465.v1
title: Supplementary Material for: The Release of Cyclophilin A from Rapamycin-Stimulated Vascular Smooth Muscle Cells Mediated by Myosin II Activation: Involvement of Apoptosis but Not Autophagy

description: <b><i>Introduction:</i></b> The exocytosis of cyclophilin A (CyPA) by a vesicular pathway in response to reactive oxygen species has been determined. However, other sources of extracellular CyPA remain obscure. <b><i>Objective:</i></b> The aim of this study was to determine the role of autophagy in the secretion of CyPA. <b><i>Methods and Results:</i></b> Rapamycin induced the activation of autophagy and release of CyPA from primary cultured rat aortic smooth muscle cells (RASMCs). However, inhibition of autophagy by knockdown of Atg7 or chloroquine did not affect the rapamycin-induced release of CyPA. With the exception of myosin II activity, rho-associated coiled-coil kinase (ROCK), actin remodelling, and synaptic vesicles were not implicated in the release of rapamycin-induced CyPA. Finally, we confirmed that rapamycin-induced extracellular CyPA originated from apoptotic RASMCs. Furthermore, the decreased activation of myosin II by blebbistatin blocked the release of CyPA from apoptotic RASMCs induced by rapamycin. <b><i>Conclusions:</i></b> Rapamycin induced the release of CyPA from apoptotic RASMCs but did not affect exocytosis through autophagosomes. ROCK, actin remodelling, and synaptic vesicles were not involved in the apoptosis-related release of CyPA. Myosin II activation modulated the apoptosis of vascular smooth muscle cells and the release of CyPA from rapamycin-induced apoptotic cell death.
DOI: 10.6084/m9.figshare.12458438
title: Supplementary Material for: Are Genetic Variants Associated with the Location of Cerebral Arterial Lesions in Stroke Patients?

description: <b><i>Background:</i></b> Genetic variants may play a role in determining the location of cerebral atherosclerosis. We aimed to investigate the association between <i>RNF213</i>, <i>MMP2</i>, and genetic polymorphisms linked to vascular tortuosity with the location of cerebral arterial atherosclerosis. <b><i>Methods:</i></b> A prospective case-control study was conducted on patients with ischemic stroke and age- and sex-matched stroke-free controls. The stroke patients were categorized into those with intracranial artery atherosclerosis (ICAS), extracranial artery atherosclerosis (ECAS), and small vessel occlusion (SVO). Six single nucleotide polymorphisms (SNPs) including rs2118181 (<i>FBN1</i>), rs2179357 (<i>SLC2A10</i>), rs1036095 (<i>TGFBR2</i>), rs243865 (<i>MMP2</i>), rs1800470 (<i>TGFB1</i>), and rs112735431 (<i>RNF213</i>) were analyzed with the TaqMan Genotyping Assay, and the distribution of genotypes across groups was compared. <b><i>Results:</i></b> None of the 6 SNPs were associated with stroke on comparing the 449 stroke patients (71 with ECAS, 169 with ICAS, and 209 with SVO) to the 447 controls. In the subgroup analysis, the adjusted odds ratios (aORs) for age and sex indicated a significant association between rs112735431 and ICAS in the allele comparison analysis and in the additive and dominant model analyses. rs112735431 was associated with anterior circulation involvement and increased burden of cerebral atherosclerosis. rs2179357 was significantly associated with ICAS in the recessive model analysis, and rs1800470 was significantly associated with ECAS in the recessive model analysis when compared to controls. <b><i>Conclusion:</i></b> rs112735431 was associated with ICAS and increased atherosclerosis burden in Korean stroke patients. Further studies are needed to elucidate the role of rs112735431 and to confirm the association of rs2179357 and rs1800470 with cerebral atherosclerosis.
DOI: 10.6084/m9.figshare.12458444
title: Analysis-Experiment-1_Acceptance.pdf

description: Statistical analysis of the response variable "Acceptance" from Experiment 1 using R software. PDF output performed using Rmarkdown.<br>
DOI: 10.6084/m9.figshare.12458444.v1
title: Analysis-Experiment-1_Acceptance.pdf

description: Statistical analysis of the response variable "Acceptance" from Experiment 1 using R software. PDF output performed using Rmarkdown.<br>
DOI: 10.6073/pasta/5220b9fc1fb4c013d59afde6cffb71a4
title: Leaf area index (LAI) recorded from a N, P and N+P fertilization experiment at the 2007 Anaktuvuk River fire scar during the 2016-2019 growing seasons

description: This file contains leaf area index (LAI) measurements from an N, P and N+P fertilization experiment established in the southern section of the 2007 Anaktuvuk River fire in 2016. LAI was recorded using a handheld plant canopy analyzer (LI-COR 2200C; LI-COR, Lincoln, NE, USA) Data spans 4 years from 2016 (when fertilization began) until 2019. Data was recorded once a year at the peak of each growing season.
DOI: 10.6084/m9.figshare.12458096
title: JARVIS-DFT Finite Difference Elastic Constants (JVASP-38848 to JVASP-40901)

description: Contains input/output files for finite difference method based elastic calculations in the JARVIS-DFT.
DOI: 10.6084/m9.figshare.12458111
title: Supplementary data of the snow sheep genome assembly

description: This dataset supplements the results described in the paper, "The first draft genome assembly of Snow sheep (<i>Ovis nivicola</i>)", which is published in the journal, Genome Biology and Evolution. More details are given in the read me file included in the zipped folder.
DOI: 10.6084/m9.figshare.12458126
title: Supplementary Material for: AGO Recommendations for the Diagnosis and Treatment of Patients with Locally Advanced and Metastatic Breast Cancer: Update 2020

description: Medicine
DOI: 10.6084/m9.figshare.12457979
title: Supplementary Material for: Chronic Functional Tremor: Positive Signs in the Management, Including Mirror Therapy

description: Functional tremor (FT) is a common functional neurological symptom disorder (FNSD) and difficult to treat. Diagnosis is often delayed in FNSD, which reinforces maladaptation and chronicity. The presented case, who had suffered from FT for 2 years, demonstrates the value of positive neurological symptoms in the diagnosis and treatment of FNSD, even in a chronic case. The patient improved well during integrated inpatient rehabilitation, which included mirror therapy (MT). He had complete suppressibility of the tremor during distraction, which was shown to him, and reversibility of the FT was emphasized. Due do the suppressibility when focusing on the contralateral arm, we installed MT as part of a combined inpatient neurological-psychotherapeutic rehabilitation treatment lasting 8 weeks. During treatment, some strong emotional themes came up. At the end of rehabilitation, the tremor almost completely subsided. Possible pathomechanisms are discussed. Future studies are recommended for determining the effectiveness of MT in FNSD with one-sided symptoms.
DOI: 10.6084/m9.figshare.12457994
title: Fasta

description: FASTA of all splicing patterns
DOI: 10.6084/m9.figshare.12457973
title: differentially expressed genes and pathways that could result in differences in prognosis between patients with circEPSTI1high/miR-942-5plow OSCC and those with circEPSTI1low/miR-942-5phigh OSCC,

description: differentially expressed genes and pathways that could result in differences in prognosis between patients with circEPSTI1<sup>high</sup>/miR-942-5p<sup>low</sup> OSCC and those with circEPSTI1<sup>low</sup>/miR-942-5p<sup>high </sup>OSCC,
DOI: 10.6084/m9.figshare.12457973.v1
title: differentially expressed genes and pathways that could result in differences in prognosis between patients with circEPSTI1high/miR-942-5plow OSCC and those with circEPSTI1low/miR-942-5phigh OSCC,

description: differentially expressed genes and pathways that could result in differences in prognosis between patients with circEPSTI1<sup>high</sup>/miR-942-5p<sup>low</sup> OSCC and those with circEPSTI1<sup>low</sup>/miR-942-5p<sup>high </sup>OSCC,
DOI: 10.6084/m9.figshare.12457964
title: The expression profile of circRNAs in 3 paired OSCC and OSF tissues, as well as 3 NBM tissues, was investigated by circRNA microarray analysis.

description: The expression profile of circRNAs in 3 paired OSCC and OSF tissues, as well as 3 NBM tissues, was investigated by circRNA microarray analysis.
DOI: 10.6084/m9.figshare.12457979.v1
title: Supplementary Material for: Chronic Functional Tremor: Positive Signs in the Management, Including Mirror Therapy

description: Functional tremor (FT) is a common functional neurological symptom disorder (FNSD) and difficult to treat. Diagnosis is often delayed in FNSD, which reinforces maladaptation and chronicity. The presented case, who had suffered from FT for 2 years, demonstrates the value of positive neurological symptoms in the diagnosis and treatment of FNSD, even in a chronic case. The patient improved well during integrated inpatient rehabilitation, which included mirror therapy (MT). He had complete suppressibility of the tremor during distraction, which was shown to him, and reversibility of the FT was emphasized. Due do the suppressibility when focusing on the contralateral arm, we installed MT as part of a combined inpatient neurological-psychotherapeutic rehabilitation treatment lasting 8 weeks. During treatment, some strong emotional themes came up. At the end of rehabilitation, the tremor almost completely subsided. Possible pathomechanisms are discussed. Future studies are recommended for determining the effectiveness of MT in FNSD with one-sided symptoms.
DOI: 10.6084/m9.figshare.12457964.v1
title: The expression profile of circRNAs in 3 paired OSCC and OSF tissues, as well as 3 NBM tissues, was investigated by circRNA microarray analysis.

description: The expression profile of circRNAs in 3 paired OSCC and OSF tissues, as well as 3 NBM tissues, was investigated by circRNA microarray analysis.
DOI: 10.6084/m9.figshare.12457454
title: holiday_data.csv

description: The data represents holiday containing Korean new years day, The march 1st independence movement day, and General election day in 2019 and 2020. This data can explain abnormal characteristics in day of week matched time series data.
DOI: 10.6084/m9.figshare.12457430
title: work_top5_hours.csv

description: This data compares hourly population present counts at a set of smallest statistical unit containing the busy workplace in 2019 with those in 2020, for corresponding day of week.
DOI: 10.6084/m9.figshare.12457382
title: michelin(all)_hours.csv

description: This data compares hourly population present counts at a set of smallest statistical units containing Michelin restaurant in 2019 with those in 2020, for corresponding day of week.
DOI: 10.6084/m9.figshare.12457415
title: deptstore_hours.csv

description: This data compares hourly population present counts at a set of smallest statistical unit containing department stores in 2019 with those in 2020, for corresponding day of week.
DOI: 10.6084/m9.figshare.12457376
title: Quantitatively Tracking the Elevation of the Tibetan Plateau since the Cretaceous: Insights from Whole-rock Sr/Y and La/Yb Ratios

description: This dataset composed of compiled data used to reconstruct paleo-elevation of the Tibetan Plateau, crustal densities of subduction and collision zones, and elevation data published by previous studies.
DOI: 10.6084/m9.figshare.12457415.v1
title: deptstore_hours.csv

description: This data compares hourly population present counts at a set of smallest statistical unit containing department stores in 2019 with those in 2020, for corresponding day of week.
DOI: 10.6084/m9.figshare.12457430.v1
title: work_top5_hours.csv

description: This data compares hourly population present counts at a set of smallest statistical unit containing the busy workplace in 2019 with those in 2020, for corresponding day of week.
DOI: 10.6084/m9.figshare.12457370
title: starbucks_hours.csv

description: This data compares hourly population present counts at a set of smallest statistical unit containing Starbucks in 2019 with those in 2020, for corresponding day of week.
DOI: 10.6084/m9.figshare.12457376.v1
title: Quantitatively Tracking the Elevation of the Tibetan Plateau since the Cretaceous: Insights from Whole-rock Sr/Y and La/Yb Ratios

description: This dataset composed of compiled data used to reconstruct paleo-elevation of the Tibetan Plateau, crustal densities of subduction and collision zones, and elevation data published by previous studies.
DOI: 10.6084/m9.figshare.12457370.v1
title: starbucks_hours.csv

description: This data compares hourly population present counts at a set of smallest statistical unit containing Starbucks in 2019 with those in 2020, for corresponding day of week.
DOI: 10.6073/pasta/f7bb960b79bb7d73dc96f9b5f105d4f2
title: Point-frame measurments from a N, P and N+P fertilization experiment at the 2007 Anaktuvuk River fire scar during the 2016-2019 growing seasons

description: This file contains point-frame measurements from a N, P and N+P fertilization experiment established in the southern section of the 2007 Anaktuvuk River fire in 2016 at a severely burned site and an unburned site. Pin-vegetation contact was recorded using a 0.75 m2 frame with 41 evenly spaced pin-drop points. Data was collected once during the height of the growing season in 2016 (when fertilization began) 2017, 2018 and 2019. This data was used to measure the impact of fertilization and fire on community composition.
DOI: 10.6084/m9.figshare.12457289
title: Additional file 5 of Distinctions between sex and time in patterns of DNA methylation across puberty

description: Additional file 5: Table S1. All significant model results and relevant annotation information for the effect of 1) sex at T1, 2) sex at T2, 3) time effects 4) follow up models of time-related sites, 5) testosterone effects. Table S2. Genomic context enrichment results. Table S3. Details on kMeans threshold probes for modules identified in the 1) sex analysis and 2) time analysis. Table S4. Gene Ontology enrichment analyses results for probes belonging to gene modules based on kMeans threshold. Table S5. Interaction model results.
DOI: 10.6084/m9.figshare.12457289.v1
title: Additional file 5 of Distinctions between sex and time in patterns of DNA methylation across puberty

description: Additional file 5: Table S1. All significant model results and relevant annotation information for the effect of 1) sex at T1, 2) sex at T2, 3) time effects 4) follow up models of time-related sites, 5) testosterone effects. Table S2. Genomic context enrichment results. Table S3. Details on kMeans threshold probes for modules identified in the 1) sex analysis and 2) time analysis. Table S4. Gene Ontology enrichment analyses results for probes belonging to gene modules based on kMeans threshold. Table S5. Interaction model results.
DOI: 10.6084/m9.figshare.12457268
title: Additional file 1 of Distinctions between sex and time in patterns of DNA methylation across puberty

description: Additional file 1: Fig. S1. Distributions of age, tanner stage, and testosterone in males and females.
DOI: 10.6084/m9.figshare.12457268.v1
title: Additional file 1 of Distinctions between sex and time in patterns of DNA methylation across puberty

description: Additional file 1: Fig. S1. Distributions of age, tanner stage, and testosterone in males and females.
DOI: 10.6084/m9.figshare.12457238
title: Additional file 5 of Draft genome sequence of antimicrobial producing Paenibacillus alvei strain MP1 reveals putative novel antimicrobials

description: Additional file 5: Data 5. MP1_prophage_supplement.
DOI: 10.6084/m9.figshare.12457232
title: Additional file 4 of Draft genome sequence of antimicrobial producing Paenibacillus alvei strain MP1 reveals putative novel antimicrobials

description: Additional file 4: Data 4. DSM29_prophage_supplement.
DOI: 10.6084/m9.figshare.12457238.v1
title: Additional file 5 of Draft genome sequence of antimicrobial producing Paenibacillus alvei strain MP1 reveals putative novel antimicrobials

description: Additional file 5: Data 5. MP1_prophage_supplement.
DOI: 10.6084/m9.figshare.12457223
title: Additional file 3 of Draft genome sequence of antimicrobial producing Paenibacillus alvei strain MP1 reveals putative novel antimicrobials

description: Additional file 3: Data 3. OrthoAni_Paenibacillus_alvei.
DOI: 10.6084/m9.figshare.12457223.v1
title: Additional file 3 of Draft genome sequence of antimicrobial producing Paenibacillus alvei strain MP1 reveals putative novel antimicrobials

description: Additional file 3: Data 3. OrthoAni_Paenibacillus_alvei.
DOI: 10.6084/m9.figshare.12457226
title: Additional file 1 of Variation in breeding practices and geographic isolation drive subpopulation differentiation, contributing to the loss of genetic diversity within dog breed lineages

description: Additional file 1.
DOI: 10.6084/m9.figshare.12457232.v1
title: Additional file 4 of Draft genome sequence of antimicrobial producing Paenibacillus alvei strain MP1 reveals putative novel antimicrobials

description: Additional file 4: Data 4. DSM29_prophage_supplement.