cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7404902
title: Additional file 2: of Differential protein expression in human knee articular cartilage and medial meniscus using two different proteomic methods: a pilot analysis

description: Proteins identified with DDA. Table containing all proteins with at least two unique peptides per protein and present in at least three of the samples that were identified in the DDA analysis. The table further indicates if the protein was found exclusively in articular cartilage, meniscus or in both tissues as well as which proteins that were selected for statistical analysis. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.7404902.v1
title: Additional file 2: of Differential protein expression in human knee articular cartilage and medial meniscus using two different proteomic methods: a pilot analysis

description: Proteins identified with DDA. Table containing all proteins with at least two unique peptides per protein and present in at least three of the samples that were identified in the DDA analysis. The table further indicates if the protein was found exclusively in articular cartilage, meniscus or in both tissues as well as which proteins that were selected for statistical analysis. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.7404911.v1
title: Additional file 3: of Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations

description: Table S2. Genes and loci with significantly difference in logR estimates between the two extreme response groups GR and NR (t-test, FDR p-value
DOI: 10.7284/119881
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1404A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404890
title: Additional file 2: of Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations

description: Table S1. Genes and loci with significantly difference in logR estimates between the two extreme response groups GR and NR (t-test, FDR p-value
DOI: 10.7284/119883
title: Radiometer data collected during research cruise OC1404A using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404890.v1
title: Additional file 2: of Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations

description: Table S1. Genes and loci with significantly difference in logR estimates between the two extreme response groups GR and NR (t-test, FDR p-value
DOI: 10.6084/m9.figshare.7404887
title: Additional file 3: of The effectiveness of patient-centred medical home model versus standard primary care in chronic disease management: protocol for a systematic review and meta-analysis of randomised and non-randomised controlled trials

description: Data extraction form for experimental studies. (XLSX 10Â kb)
DOI: 10.7284/119884
title: Radiometer data collected during research cruise OC1404A using a Biospherical QSR-2200 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404887.v1
title: Additional file 3: of The effectiveness of patient-centred medical home model versus standard primary care in chronic disease management: protocol for a systematic review and meta-analysis of randomised and non-randomised controlled trials

description: Data extraction form for experimental studies. (XLSX 10Â kb)
DOI: 10.7284/119885
title: Rain Gauge data collected during research cruise OC1404A using a RM Young 50202 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119877
title: Singlebeam Echosounder data collected during research cruise OC1404A using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404854
title: Additional file 2: of Identification of Jun loss promotes resistance to histone deacetylase inhibitor entinostat through Myc signaling in luminal breast cancer

description: Table S1. Genes in mouse and human version of Myc signatures. Table S2. A. Upregulated and downregulated genes with FDR of 0% in SAM analysis. B: Entinostat signatures. Table S3. The changes in tumor size of MMTV/Neu tumors treated with entinostat. Table S4. 83 genes which significantly decreased at gene expression and copy number levels with q-value 0% by SAM analysis comparing the untreated samples and the samples resistant while on entinostat. Table S5. Multivariate analysis of each Myc signature accounting for clinical features in METABRIC. (XLSX 74 kb)
DOI: 10.7284/119886
title: Speedlog data collected during research cruise OC1404A using a Furuno DS-50 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404854.v1
title: Additional file 2: of Identification of Jun loss promotes resistance to histone deacetylase inhibitor entinostat through Myc signaling in luminal breast cancer

description: Table S1. Genes in mouse and human version of Myc signatures. Table S2. A. Upregulated and downregulated genes with FDR of 0% in SAM analysis. B: Entinostat signatures. Table S3. The changes in tumor size of MMTV/Neu tumors treated with entinostat. Table S4. 83 genes which significantly decreased at gene expression and copy number levels with q-value 0% by SAM analysis comparing the untreated samples and the samples resistant while on entinostat. Table S5. Multivariate analysis of each Myc signature accounting for clinical features in METABRIC. (XLSX 74 kb)
DOI: 10.7284/119875
title: Water Temperature data collected during research cruise OC1404A using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119887
title: Water Temperature data collected during research cruise OC1404A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119888
title: Transmissometer data collected during research cruise OC1404A using a WET Labs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404818
title: Additional file 9 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Enrichment analysis of miRNA-target interactions among switch genes. The table reports miRNA families found to be enriched in the lists of switch genes, based on the miRNA-target interactions computationally predicted by TargetScan (sheet 1) and experimentally validated by miRTarBase (sheet 2). The miRNA families are sorted according to the increasing p-values. (XLSX 159 kb)
DOI: 10.7284/119889
title: TSG (Thermosalinograph) data collected during research cruise OC1404A using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404812
title: Additional file 8 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Kaplan-Meier survival analysis. The table reports the list of the switch genes, the p-values resulted from log-rank test, and the adjusted p-values (FDR) for multiple testing. The list is sorted by increasing p-values. The file reports the 161 switch genes out of 171, whose expression data were available on TCGA Data Portal Release 10.0 (December 2017). (XLS 10 kb)
DOI: 10.6084/m9.figshare.7404818.v1
title: Additional file 9 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Enrichment analysis of miRNA-target interactions among switch genes. The table reports miRNA families found to be enriched in the lists of switch genes, based on the miRNA-target interactions computationally predicted by TargetScan (sheet 1) and experimentally validated by miRTarBase (sheet 2). The miRNA families are sorted according to the increasing p-values. (XLSX 159 kb)
DOI: 10.6084/m9.figshare.7404812.v1
title: Additional file 8 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Kaplan-Meier survival analysis. The table reports the list of the switch genes, the p-values resulted from log-rank test, and the adjusted p-values (FDR) for multiple testing. The list is sorted by increasing p-values. The file reports the 161 switch genes out of 171, whose expression data were available on TCGA Data Portal Release 10.0 (December 2017). (XLS 10 kb)
DOI: 10.7284/119906
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1404B using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119894
title: Anemometer data collected during research cruise OC1404B using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404797
title: Additional file 7 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Switch genes negatively interacting with four core TFs. The table reports the list of switch genes that are simultaneously anti-correlated with OLIG2, POU3F2, SALL2, and SOX2. (XLSX 7 kb)
DOI: 10.6084/m9.figshare.7404791
title: Additional file 6 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Switch genes functional annotations and molecular type. The table is composed of three sheets reporting: the list of the switch genes in Official Gene symbol together with their GO term annotations provided by BioMart [60], whenever available; an indication of their molecular type (protein coding, non-coding or miRNA) obtained from Ensembl annotations of the human genome (GHCR38 version), whenever available; the list of switch genes characterized by a transcription factor activity. The TFs annotated for nervous system related processes are highlighted in yellow. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.7404797.v1
title: Additional file 7 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Switch genes negatively interacting with four core TFs. The table reports the list of switch genes that are simultaneously anti-correlated with OLIG2, POU3F2, SALL2, and SOX2. (XLSX 7 kb)
DOI: 10.7284/119896
title: Fluorometer data collected during research cruise OC1404B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404785
title: Additional file 1: of Porcine cysticercosis (Taenia solium and Taenia asiatica): mapping occurrence and areas potentially at risk in East and Southeast Asia

description: Table S1. Full search output from the initial literature search. Table S2. List of studies that were identified to provide epidemiological data on porcine cysticercosis. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.7404791.v1
title: Additional file 6 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Switch genes functional annotations and molecular type. The table is composed of three sheets reporting: the list of the switch genes in Official Gene symbol together with their GO term annotations provided by BioMart [60], whenever available; an indication of their molecular type (protein coding, non-coding or miRNA) obtained from Ensembl annotations of the human genome (GHCR38 version), whenever available; the list of switch genes characterized by a transcription factor activity. The TFs annotated for nervous system related processes are highlighted in yellow. (XLSX 87 kb)
DOI: 10.7284/117338
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1404B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404782
title: Additional file 5 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. GBM switch genes identified by SWIM for Schulte et al. dataset [25]. The table reports: the list of the switch genes in Official Gene symbol; the adjusted p-values; the fold-change values; their expression direction (up/down in GSf and tumors). (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7404785.v1
title: Additional file 1: of Porcine cysticercosis (Taenia solium and Taenia asiatica): mapping occurrence and areas potentially at risk in East and Southeast Asia

description: Table S1. Full search output from the initial literature search. Table S2. List of studies that were identified to provide epidemiological data on porcine cysticercosis. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.7404782.v1
title: Additional file 5 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. GBM switch genes identified by SWIM for Schulte et al. dataset [25]. The table reports: the list of the switch genes in Official Gene symbol; the adjusted p-values; the fold-change values; their expression direction (up/down in GSf and tumors). (XLSX 16 kb)
DOI: 10.7284/119897
title: Gyrocompass data collected during research cruise OC1404B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404770
title: Additional file 3 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Roles of nodes in GBM correlation network for Schulte et al. dataset [25]. The table contains the following columns. nodeName: the names of the nodes of the correlation network (Official Gene Symbol); hub: it specifies if the nodes of the heat cartography map are (or are not) local hubs within their community; Region: it specifies the region of the heat cartography map to which each node belongs; Type: it specifies for each node of the heat cartography map its universal role; Kp: values of the clusterphobic coefficient parameter KĎ ; zg: values of the within-module degree parameter zg; APCC: the average of the Pearson correlation coefficients between the expression profiles of a node and those of its interaction partners in the heat cartography map; Degree: the degree for each node in the heat cartography map; Date-Party: if the node of the heat cartography map is either a date or party or fight-club hub or if it is not a local hub in its community. (XLSX 64 kb)
DOI: 10.7284/119899
title: Hygrometer data collected during research cruise OC1404B using a Vaisala HMT300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404770.v1
title: Additional file 3 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. Roles of nodes in GBM correlation network for Schulte et al. dataset [25]. The table contains the following columns. nodeName: the names of the nodes of the correlation network (Official Gene Symbol); hub: it specifies if the nodes of the heat cartography map are (or are not) local hubs within their community; Region: it specifies the region of the heat cartography map to which each node belongs; Type: it specifies for each node of the heat cartography map its universal role; Kp: values of the clusterphobic coefficient parameter KĎ ; zg: values of the within-module degree parameter zg; APCC: the average of the Pearson correlation coefficients between the expression profiles of a node and those of its interaction partners in the heat cartography map; Degree: the degree for each node in the heat cartography map; Date-Party: if the node of the heat cartography map is either a date or party or fight-club hub or if it is not a local hub in its community. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.7404761
title: Additional file 2 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. GBM correlation network for Schulte et al. dataset [25]. The table reports the co-expression network of DEGs identified by SWIM in GBM dataset analyzed in the present study. Source nodes, target nodes and their interaction (Pearson correlation) are listed. (XLSX 1930 kb)
DOI: 10.6084/m9.figshare.7404755
title: Additional file 1 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. GBM differentially expressed genes for Schulte et al. dataset [25]. The table reports the list of the statistically significant (adjusted p-value &lt;0.05) DEGs in Official Gene Symbols identified by SWIM in human GBM dataset analyzed in the present study; the p-values resulted from an unpaired two-tailed Student t-test; the adjusted p-values; the fold-change values; the DEGs expression direction (up/down in GSf and tumors); the percentage of the up- and down-regulated DEGs in a pie chart visualization. (XLSX 76 kb)
DOI: 10.6084/m9.figshare.7404761.v1
title: Additional file 2 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. GBM correlation network for Schulte et al. dataset [25]. The table reports the co-expression network of DEGs identified by SWIM in GBM dataset analyzed in the present study. Source nodes, target nodes and their interaction (Pearson correlation) are listed. (XLSX 1930 kb)
DOI: 10.7284/119898
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1404B using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404755.v1
title: Additional file 1 of SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines

description: Table. GBM differentially expressed genes for Schulte et al. dataset [25]. The table reports the list of the statistically significant (adjusted p-value &lt;0.05) DEGs in Official Gene Symbols identified by SWIM in human GBM dataset analyzed in the present study; the p-values resulted from an unpaired two-tailed Student t-test; the adjusted p-values; the fold-change values; the DEGs expression direction (up/down in GSf and tumors); the percentage of the up- and down-regulated DEGs in a pie chart visualization. (XLSX 76 kb)
DOI: 10.7284/119900
title: Radiometer data collected during research cruise OC1404B using a Biospherical QSR-2200 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119901
title: Rain Gauge data collected during research cruise OC1404B using a RM Young 50202 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/119893
title: Singlebeam Echosounder data collected during research cruise OC1404B using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7404038
title: Raw proteomic data from Age-related response to an acute innate immune challenge in mice: proteomics reveals a telomere maintenance-related cost

description: Ageing is characterized by the impairment of the acute innate immune response and the upregulation of low-grade inflammation, i.e. inflammaging. At the cellular level, telomeres are considered as a marker of biological ageing as their length is progressively eroded in the absence of repair mechanisms. However, the link between telomeres and inflammaging remains underexplored. We aimed to identify proteins that are differentially expressed between age classes in response to an acute inflammatory challenge. We challenged young (two months) and old (12 months) C57BL/6 mice using bacterial lipopolysaccharide (LPS) and measured telomere length and proteomic profiles in splenocytes. In total, 233 out of the 1966 proteins we quantified differed among experimental groups. A hierarchical clustering analysis revealed that nine of those 233 proteins were differently expressed among the experimental groups. Young mice responded to LPS by increasing the expression of proteins involved in the innate immune response, and interestingly, in telomere length maintenance. However, this regulation was impaired at older ages. These results are in agreement with the assumption that the strength of selection declines with age, potentially explaining the maintenance of costly, dysregulated, immune responses at old age. We suggest that the immune response is competing with the telomere maintenance process, highlighting how telomeres reflect the ageing trade-off even in a species where telomere length is not related to lifespan.
DOI: 10.7284/119895
title: Singlebeam Echosounder data collected during research cruise OC1404B using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.26180/5c046f5cf3328
title: participant 32 EEG.zip

description: Participant 32, day 1 and 2 EEG data.