cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12024480.v1
title: Nucleoporin TPR (translocated promoter region, nuclear basket protein) upregulation alters MTOR-HSF1 trails and suppresses autophagy induction in ependymoma

description: Children with ependymoma have high mortality rates because ependymoma is resistant to conventional therapy. Genomic and transcriptomic studies have identified potential targets as significantly altered genes in ependymoma patients. Although several candidate oncogenes in ependymoma were recently reported, the detailed mechanisms for the roles of these candidate oncogenes in ependymoma progression remain unclear. Here, we report an oncogenic role of the nucleoporin TPR (translocated promoter region, nuclear basket protein) in regulating <i>HSF1</i> (heat shock transcription factor 1) mRNA trafficking, maintaining MTORC1 activity to phosphorylate ULK1, and preventing macroautophagy/autophagy induction in ependymoma. High expression of TPR were associated with increased <i>HSF1</i> and <i>HSPA/HSP70</i> expression in ependymoma patients. In an ependymoma mouse xenograft model, MTOR inhibition by rapamycin therapeutically suppressed TPR expression and reduced tumor size <i>in vivo</i>. Together, these results suggest that TPR may act as a biomarker for ependymoma, and pharmacological interventions targeting TPR-HSF1-MTOR may have therapeutic potential for ependymoma treatment. <b>Abbreviations</b>: ATG: autophagy related; BECN1: beclin 1; BSA: bovine serum albumin; CQ: chloroquine; DMSO: dimethyl sulfoxide; GEO: gene expression omnibus; GFP: green fluorescence protein; HSF1: heat shock transcription factor 1; HSPA/HSP70: heat shock protein family A (Hsp70); LMNB1: lamin B1; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MAPK: mitogen-activated protein kinase; MAPK8/JNK: mitogen-activated protein kinase 8; MTORC1: mechanistic target of rapamycin kinase complex 1; NPC: nuclear pore complex; NUP: nucleoporin; PBS: phosphate-buffered saline; q-PCR: quantitative real time PCR; SDS: sodium dodecyl sulfate; SQSTM1: sequestosome 1; STED: stimulated emission depletion microscopy; STX17: syntaxin 17; TCGA: the cancer genome atlas; TPR: translocated promoter region, nuclear basket protein; ULK1: unc-51 like autophagy activating kinase 1.
DOI: 10.6084/m9.figshare.12024489.v1
title: Data on spine density, spine clustering, and RAM performance

description: This file set contains 5 data files. These are:<b> Data availability statement_Craig et al.docx </b>(ReadMe file in .docx file format), <b>Craig et al_spine density_spine clustering_RAM performance.xlsx</b> in .xlsx file format, <b>counting and clustering macro.ijm</b> in .ijm file format, <b>Segment processing macro.ijm</b> in .ijm file format, and <b>Segments list.csv</b> in .csv file format.<br> Data file <b>Craig et al_spine density_spine clustering_RAM performance.xlsx, </b>contains numerical data for spine density, spine clustering, and Radial-arm maze (RAM) performance.<br> The two macro files <b>counting and clustering macro.ijm</b> and <b>Segment processing macro.ijm, </b>were used to count spines then calculate spine density and clustering, and to process a cropped segment, respectively.<br> The file<b> Segments list.csv</b>, provides the list of dendritic segments used for spine density and clustering analysis.<br> For more information on the contents of each data file, please refer to <b>Data availability statement_Craig et al.docx</b>
DOI: 10.6084/m9.figshare.12024447
title: Supplementary Material for: Is Bigger Really Better? Comparison of Ultraportable Handheld Ultrasound with Standard Point-of-Care Ultrasound for Evaluating Safe Site Identification and Image Quality prior to Pleurocentesis

description: <b><i>Background:</i></b> Pleural effusions remain a common medical problem which often requires diagnostic pleurocentesis to determine the underlying cause. Pleurocentesis is a frequently performed procedure worldwide with improved safety using ultrasound (US) technology. <b><i>Objectives:</i></b> This prospective, single-center study evaluated the use of an ultraportable handheld (UPHH) US compared with standard point-of-care (SPOC) US in determining a safe site for pleurocentesis. In addition, US image quality and factors impacting on image quality were assessed using both UPHH and SPOC US. <b><i>Methods:</i></b> Paired US assessments were performed by thoracic physicians using UPHH and SPOC US on patients with unilateral pleural effusions to determine a safe site for pleurocentesis (defined as &gt;2 cm of pleural fluid, &gt;2 cm from a solid organ/diaphragm, and &lt;7 cm chest wall depth). Distance measurements for key structures and image quality scores (using a 5-point Likert rating scale) were obtained at the time of US assessment. Factors affecting image quality were analyzed using univariate analysis. <b><i>Results:</i></b> In 52 of the 54 included patients (96.3%), UPHH US was able to identify a safe site for pleurocentesis. Distance measurements between UPHH and SPOC US were not statistically different (all &lt;0.5 cm with values of <i>p</i> &gt; 0.05), but image quality was reduced in UPHH compared with SPOC US by 1 point on a 5-point Likert rating scale (<i>p</i> &lt; 0.002). Increasing body mass index was associated with a reduction in image quality in both UPHH and SPOC US (all <i>p</i> &lt; 0.01). <b><i>Conclusions:</i></b> Although image quality was lower in UPHH than SPOC US, a safe site was found in 96.3% of patients, which suggests that UPHH US may be a useful tool for diagnostic pleuro­centesis when SPOC US is not available (http://www.anzctr.org.au/, Australia New Zealand Clinical Trials Registry, No. ACTRN12618001592235).
DOI: 10.6084/m9.figshare.12024447.v1
title: Supplementary Material for: Is Bigger Really Better? Comparison of Ultraportable Handheld Ultrasound with Standard Point-of-Care Ultrasound for Evaluating Safe Site Identification and Image Quality prior to Pleurocentesis

description: <b><i>Background:</i></b> Pleural effusions remain a common medical problem which often requires diagnostic pleurocentesis to determine the underlying cause. Pleurocentesis is a frequently performed procedure worldwide with improved safety using ultrasound (US) technology. <b><i>Objectives:</i></b> This prospective, single-center study evaluated the use of an ultraportable handheld (UPHH) US compared with standard point-of-care (SPOC) US in determining a safe site for pleurocentesis. In addition, US image quality and factors impacting on image quality were assessed using both UPHH and SPOC US. <b><i>Methods:</i></b> Paired US assessments were performed by thoracic physicians using UPHH and SPOC US on patients with unilateral pleural effusions to determine a safe site for pleurocentesis (defined as &gt;2 cm of pleural fluid, &gt;2 cm from a solid organ/diaphragm, and &lt;7 cm chest wall depth). Distance measurements for key structures and image quality scores (using a 5-point Likert rating scale) were obtained at the time of US assessment. Factors affecting image quality were analyzed using univariate analysis. <b><i>Results:</i></b> In 52 of the 54 included patients (96.3%), UPHH US was able to identify a safe site for pleurocentesis. Distance measurements between UPHH and SPOC US were not statistically different (all &lt;0.5 cm with values of <i>p</i> &gt; 0.05), but image quality was reduced in UPHH compared with SPOC US by 1 point on a 5-point Likert rating scale (<i>p</i> &lt; 0.002). Increasing body mass index was associated with a reduction in image quality in both UPHH and SPOC US (all <i>p</i> &lt; 0.01). <b><i>Conclusions:</i></b> Although image quality was lower in UPHH than SPOC US, a safe site was found in 96.3% of patients, which suggests that UPHH US may be a useful tool for diagnostic pleuro­centesis when SPOC US is not available (http://www.anzctr.org.au/, Australia New Zealand Clinical Trials Registry, No. ACTRN12618001592235).
DOI: 10.6084/m9.figshare.12024375
title: Snapshotted Networks - Gephi file

description: This is a .gexf graph file that contains monthly snapshots of the network of far-right on Telegram over a period from March 2019 to February 2020<br>
DOI: 10.6084/m9.figshare.12024324
title: Supplemental Table 13. Analysis of Genomes published in Matsumoto et al 2019

description: Table containing ANI, MLST, and CSP analysis of the NTM genomes published as part of Matsumoto et al 2019. Supplemental Table 13<br>
DOI: 10.6084/m9.figshare.12024324.v1
title: Supplemental Table 13. Analysis of Genomes published in Matsumoto et al 2019

description: Table containing ANI, MLST, and CSP analysis of the NTM genomes published as part of Matsumoto et al 2019. Supplemental Table 13<br>
DOI: 10.6084/m9.figshare.12024375.v1
title: Snapshotted Networks - Gephi file

description: This is a .gexf graph file that contains monthly snapshots of the network of far-right on Telegram over a period from March 2019 to February 2020<br>
DOI: 10.6084/m9.figshare.12024312
title: Amphibian Diet

description: Amphibian diet data
DOI: 10.6084/m9.figshare.12024309
title: Reptile_Diet.csv

description: Reptile Diet Dataset
DOI: 10.6084/m9.figshare.12024303
title: Supplemental Table 12. NTM All versus All ST-based Distance Matrix

description: A table containing a distance matrix for the NTM genomes using the PubMLST ST types linked to. Supplemental table 12 <br>
DOI: 10.6084/m9.figshare.12024309.v1
title: Reptile_Diet.csv

description: Reptile Diet Dataset
DOI: 10.6084/m9.figshare.12024303.v1
title: Supplemental Table 12. NTM All versus All ST-based Distance Matrix

description: A table containing a distance matrix for the NTM genomes using the PubMLST ST types linked to. Supplemental table 12 <br>
DOI: 10.6084/m9.figshare.12024312.v1
title: Untitled Item

description: Amphibian diet data
DOI: 10.6084/m9.figshare.12024312.v2
title: Amphibian Diet

description: Amphibian diet data
DOI: 10.6084/m9.figshare.12024312.v4
title: Amphibian Diet

description: Amphibian diet data
DOI: 10.6084/m9.figshare.12024159
title: Supplemental Tables 8 and 9. Analysis of Gupta et al 2018 and Pangenome-Derived Conserved Signature Proteins in NTM Genomes

description: A spreadsheet with tables with the presence and absence of the conserved signature proteins (CSP) identified by Gupta et al 2018 (tab 1) and in a Pangenome run (tab 2) in the NTM genomes, along with the genus predictions of individual genomes from this data. Supplemental tables 8 and 9.<br>
DOI: 10.6084/m9.figshare.12024312.v3
title: Amphibian Diet

description: Amphibian diet data
DOI: 10.6084/m9.figshare.12024144
title: Supplemental Table 7. NTM ST Definitions

description: A table of all MLST definitions from the cited database. The tables includes the locus types, organisms associated with the NTM type, and other information. All PubMLST types generated in this study have a value in column J. Supplementary Table 7.
DOI: 10.6084/m9.figshare.12024159.v1
title: Supplemental Tables 8 and 9. Analysis of Gupta et al 2018 and Pangenome-Derived Conserved Signature Proteins in NTM Genomes

description: A spreadsheet with tables with the presence and absence of the conserved signature proteins (CSP) identified by Gupta et al 2018 (tab 1) and in a Pangenome run (tab 2) in the NTM genomes, along with the genus predictions of individual genomes from this data. Supplemental tables 8 and 9.<br>
DOI: 10.6084/m9.figshare.12024126
title: Supplemental File 6. Pangenome Matchtable

description: The matchtable produced by the Pangenome pipeline for the NTM genomes. Gzipped for size. Supplemental File 6.<br>
DOI: 10.6084/m9.figshare.12024126.v1
title: Supplemental File 6. Pangenome Matchtable

description: The matchtable produced by the Pangenome pipeline for the NTM genomes. Gzipped for size. Supplemental File 6.<br>
DOI: 10.6084/m9.figshare.12024057
title: Supplemental Table 4: NTM Clusters

description: A table of all clusters generated from the MASH ANI, along with various data about the membership of the clusters. The given species or genomsp. name of the cluster is also given<br>
DOI: 10.6084/m9.figshare.12024117
title: Supplemental Table 5. NTM Genomes

description: A table of all genomes used in the study with supporting information include cluster membership, suggested name, and ANI and MLST distances to type strains. Supplementary Table 5.
DOI: 10.6084/m9.figshare.12024057.v1
title: Supplemental Table 4: NTM Clusters

description: A table of all clusters generated from the MASH ANI, along with various data about the membership of the clusters. The given species or genomsp. name of the cluster is also given<br>
DOI: 10.6084/m9.figshare.12024117.v1
title: Supplemental Table 5. NTM Genomes

description: A table of all genomes used in the study with supporting information include cluster membership, suggested name, and ANI and MLST distances to type strains. Supplementary Table 5.
DOI: 10.6084/m9.figshare.12024051
title: Supplemental Tables 2 & 3: NTM Genomes MASH ANI-based Clusters

description: A spreadsheet containing 2 tables for the clusters generated from the MASH ANI distances using cutoff of 98% ANI (tab 1; sub-species level) and 95% ANI (tab 2; species level). Supplementary Table 2 and 3.
DOI: 10.6084/m9.figshare.12024030
title: Supplemental Table 11: NTM Genome MASH ANI Distances

description: A distance table showing the MASH ANI distance for all genomes within the NTM genomes. Supplementary Table 11.
DOI: 10.6084/m9.figshare.12024051.v1
title: Supplemental Tables 2 & 3: NTM Genomes MASH ANI-based Clusters

description: A spreadsheet containing 2 tables for the clusters generated from the MASH ANI distances using cutoff of 98% ANI (tab 1; sub-species level) and 95% ANI (tab 2; species level). Supplementary Table 2 and 3.
DOI: 10.6084/m9.figshare.12024024
title: Supplemental Table 10: NTM Pangenome-Based ANI All Versus All Table

description: The results of the Pangenome-based ANI for all the NTM genomes in the pangenome. Supplemental Table 10.<br>
DOI: 10.6084/m9.figshare.12024030.v2
title: Supplemental Table 11: NTM Genome MASH ANI Distances

description: A distance table showing the MASH ANI distance for all genomes within the NTM genomes. Supplementary Table 11.
DOI: 10.6084/m9.figshare.12024030.v1
title: Supplemental Table 10: NTM Genome MASH ANI Distances

description: A distance table showing the MASH ANI distance for all genomes within the NTM genomes. Supplementary Table 10.
DOI: 10.6084/m9.figshare.12024024.v2
title: Supplemental Table 10: NTM Pangenome-Based ANI All Versus All Table

description: The results of the Pangenome-based ANI for all the NTM genomes in the pangenome. Supplemental Table 10.<br>
DOI: 10.6084/m9.figshare.12024024.v1
title: Supplemental Table 9: NTM Pangenome-Based ANI All Versus All Table

description: The results of the Pangenome-based ANI for all the NTM genomes in the pangenome. Supplemental Table 9.<br>
DOI: 10.6084/m9.figshare.12023955
title: Additional file 5 of Transcriptional profiling and physiological roles of Aedes aegypti spermathecal-related genes

description: Additional file 5. Hyperlinked excel spreadsheet with reassembled coding sequences and reads mapped with RPKM&gt;1 from Ae. aegypti virgin and inseminated spermathecomes.
DOI: 10.6084/m9.figshare.12023955.v1
title: Additional file 5 of Transcriptional profiling and physiological roles of Aedes aegypti spermathecal-related genes

description: Additional file 5. Hyperlinked excel spreadsheet with reassembled coding sequences and reads mapped with RPKM&gt;1 from Ae. aegypti virgin and inseminated spermathecomes.
DOI: 10.6084/m9.figshare.12023937
title: Universitary students

description: BataBase of University project of photoprotection prectices in scince students<br>
DOI: 10.6084/m9.figshare.12023937.v1
title: Universitary students

description: BataBase of University project of photoprotection prectices in scince students<br>
DOI: 10.6084/m9.figshare.12023922
title: Additional file 4 of Reasons for previous Cesarean deliveries impact a woman’s independent decision of delivery mode and the success of trial of labor after Cesarean

description: Additional file 4.
DOI: 10.6084/m9.figshare.12023919
title: Additional file 3 of Reasons for previous Cesarean deliveries impact a woman’s independent decision of delivery mode and the success of trial of labor after Cesarean

description: Additional file 3.
DOI: 10.6084/m9.figshare.12023922.v1
title: Additional file 4 of Reasons for previous Cesarean deliveries impact a woman’s independent decision of delivery mode and the success of trial of labor after Cesarean

description: Additional file 4.
DOI: 10.6084/m9.figshare.12023919.v1
title: Additional file 3 of Reasons for previous Cesarean deliveries impact a woman’s independent decision of delivery mode and the success of trial of labor after Cesarean

description: Additional file 3.
DOI: 10.6084/m9.figshare.12023910
title: Additional file 2 of Reasons for previous Cesarean deliveries impact a woman’s independent decision of delivery mode and the success of trial of labor after Cesarean

description: Additional file 2.
DOI: 10.6084/m9.figshare.12023910.v1
title: Additional file 2 of Reasons for previous Cesarean deliveries impact a woman’s independent decision of delivery mode and the success of trial of labor after Cesarean

description: Additional file 2.
DOI: 10.6084/m9.figshare.12023901
title: Additional file 1 of Reasons for previous Cesarean deliveries impact a woman’s independent decision of delivery mode and the success of trial of labor after Cesarean

description: Additional file 1.
DOI: 10.6084/m9.figshare.12023901.v1
title: Additional file 1 of Reasons for previous Cesarean deliveries impact a woman’s independent decision of delivery mode and the success of trial of labor after Cesarean

description: Additional file 1.
DOI: 10.6084/m9.figshare.12023892
title: Additional file 4 of It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome

description: Additional file 4: Table S3. Metadata and taxonomic classifications.
DOI: 10.6084/m9.figshare.12023892.v1
title: Additional file 4 of It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome

description: Additional file 4: Table S3. Metadata and taxonomic classifications.
DOI: 10.6084/m9.figshare.12023886
title: Additional file 7 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 7: Supplementary Table SIV. Quantitation of a mock community sample with same protein content per organism from Kleiner et al.
DOI: 10.6084/m9.figshare.12023889
title: Additional file 3 of It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome

description: Additional file 3: Table S2. Results from linear discriminant analysis of microbiota composition in male mice.
DOI: 10.6084/m9.figshare.12073278
title: A satellite-derived database for stand-replacing windthrow events in boreal forests of European Russia in 1986–2017

description: The GIS database contains the data of stand-replacing windthrow areas in the forest zone of the European Russia (ER) for the 1986–2017 period, and the ArcGIS 10.1/10.2 and Qgis 3* projects to view and analyze the data. The database contains three shapefiles (.shp), corresponding to three hierarchical levels of the data: • “Elementary damaged area”, that is a single-part polygon of wind-damaged forest; • “Windthrow”, that represent a group of closely spaced forest disturbances, i.e., a multipart polygon, associated with one storm event; • “Storm event track”, that is a cluster of windthrow areas with identical direction and having the same date (or date range) of occurrence, which was most likely induced by one convective or non-convective storm. The key fields ID and storm_ID associates each damaged area with the features in the datasets of windthrows and storm event tracks respectively using one-to-many relation. A single value “‒9999” was used for storing NoData in all fields of the attribute table. All data and projects have WGS 1984 coordinate system (without projection). Delineation of windthrow areas was based on the full archive of Landsat images and two Landsat-derived products on forest cover change, namely the Global Forest Change and the Eastern’ Europe Forest Cover Change. Subsequent verification and analysis of each windthrow was carried out to determine a type of storm events with a degree of event certainty, dates (date ranges) and time (time ranges) of an event, windthrow geometrical characteristics. The database contains 102,747 elementary areas of damaged forest that were combined into 700 windthrow areas caused by 486 convective or non-convective storm events. The database includes stand-replacing windthrow only, which an area &gt; 5 ha or &gt; 25 ha for events caused by tornadoes or other storms, respectively. Additional information contained weather station reports and event description from media sources is also provided.. The compiled database provides a valuable source of spatial and temporal information on windthrows in the ER and can be successfully used both in forestry and severe storm studies.
DOI: 10.6084/m9.figshare.12023883
title: Additional file 2 of It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome

description: Additional file 2: Table S1. Results from linear discriminant analysis of microbiota composition in female mice.
DOI: 10.6084/m9.figshare.12023886.v1
title: Additional file 7 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 7: Supplementary Table SIV. Quantitation of a mock community sample with same protein content per organism from Kleiner et al.
DOI: 10.6084/m9.figshare.12023889.v1
title: Additional file 3 of It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome

description: Additional file 3: Table S2. Results from linear discriminant analysis of microbiota composition in male mice.
DOI: 10.6084/m9.figshare.12023880
title: Additional file 6 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 6: Supplementary Table SIII. Proteins identified and SC quantified in the 27 S. flexneri/S. bongori samples.
DOI: 10.6084/m9.figshare.12023883.v1
title: Additional file 2 of It's the fiber, not the fat: significant effects of dietary challenge on the gut microbiome

description: Additional file 2: Table S1. Results from linear discriminant analysis of microbiota composition in female mice.
DOI: 10.6084/m9.figshare.12023880.v1
title: Additional file 6 of Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

description: Additional file 6: Supplementary Table SIII. Proteins identified and SC quantified in the 27 S. flexneri/S. bongori samples.