cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7284/106815
title: Multiplexed data collected during research cruise AT21-01 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108599
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT21-01 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108598
title: Expendable Probe data collected during research cruise AT21-01 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106808
title: Multibeam Echosounder data collected during research cruise AT21-01 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106816
title: Multiplexed data collected during research cruise AT21-02 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108601
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT21-02 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111385
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT21-02 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108600
title: Expendable Probe data collected during research cruise AT21-02 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7712756
title: DepMap Datasets for WRN manuscript

description: Cancer Dependency Map (DepMap) data used for analyses in the manuscript "WRN Helicase is a Synthetic Lethal Target in Microsatellite Unstable Cancers" by Chan and Shibue et al. is packaged into an rds file.<br>This rds file contains a list of data matrices. All but one of these matrices ("MUT") have cell lines as rows and genes as columns (gene names are mapped to hgnc symbols). <br>This analysis uses the 18Q4 DepMap release. The latest Broad Institute DepMap data can be accessed at https://depmap.org.<br>Associated code for analysis is available at https://github.com/cancerdatasci/WRN_manuscript, and code and other materials can be accessed from https://depmap.org/WRN/<br>The rds file contains the following datasets:-<b>DRIVE</b>: Gene dependency scores from the Novartis DRIVE RNAi screen[1] processed using the DEMETER2 algorithm[2].<br>-<b>CRISPR</b>: Gene dependency scores from the Achilles CRISPR screen processed using the CERES algorithm[3].<br>-<b>GE</b>: Gene expression data (log2(TPM), protein coding genes only) [4]. <br>-<b>CN</b>: Log2 relative copy number [4].<br>-<b>MUT_HOT</b>: Binary matrix indicating which cell lines have hotspot missense mutations in each gene<br>-<b>MUT_DAM</b>: Binary matrix indicating which cell lines have damaging mutations in each gene<br>-<b>MUT_OTHER</b>: Binary matrix indicating which cell lines have other non-silent mutations in each gene<br>-<b>MUT</b>: Dataframe containing all mutation calls from the DepMap 18Q4 release [4]<br>-<b>RPPA</b>: CCLE protein abundance data using reverse-phase protein array [4].<br><b>References</b>[1] McDonald, E.R., et al., Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening. Cell. 170, 577-592 (2017).<br>[2] McFarland, J.M., et al., Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nat. Commun. 9, 4610 (2018).<br>[3] Meyers, R.M., et al., Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779 (2017).<br>[4] Cancer Cell Line Encyclopedia Consortium, and Genomics of Drug Sensitivity in Cancer Consortium. Pharmacogenomic Agreement between Two Cancer Cell Line Data Sets. Nature. 528, 84–87 (2015).
DOI: 10.7284/106809
title: Multibeam Echosounder data collected during research cruise AT21-02 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106817
title: Multiplexed data collected during research cruise AT21-03 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108603
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT21-03 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7712720.v1
title: Wikidata Constraints Violations - July 2017

description: This dataset contains corrections for Wikidata constraint violations extracted from the July 1st 2018 Wikidata full history dump.<br>The constraints.tsv file contains the list of most of the Wikidata constraint violations considered in this dataset (beware, there could be some discrepancies for type, valueType, itemRequiresClaim and valueRequiresClaim constraints).<br>The other files provide for each constraint type the list of all corrections extracted from the edit history. The format of the file is one line per correction with the following tabbed-separated values:* constraint id,* id of the revision that has solved the constraint violation,* subject, predicate and object of the triple that were violating the constraint (separated by a tab)* the string "-&gt;"* subject, predicate and object of the triple(s) of the correction, each followed by "http://wikiba.se/history/ontology#deletion" if the triple has been removed or "http://wikiba.se/history/ontology#addition" if the triple has been added. Each component of these values is separated by a tab.<br>More detailed explanations are provided in a soon to be published paper<br>
DOI: 10.7284/108602
title: Expendable Probe data collected during research cruise AT21-03 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106810
title: Multibeam Echosounder data collected during research cruise AT21-03 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7712570
title: Supplementary Material for: Kinetics of Hepatic Volume Evolution and Architectural Changes after Major Resection in a Porcine Model

description: <b><i>Background:</i></b> The hepatic volume gain following resection is essential for clinical recovery. Previous studies have focused on cellular regeneration. This study aims to explore the rate of hepatic regeneration of the porcine liver following major resection, highlighting estimates of the early microarchitectural changes that occur during the cellular regeneration. <b><i>Methods:</i></b> Nineteen large white pigs had 75% resection with serial measurements of the hepatic volume, density, blood flow, and architectural changes. <b><i>Results:</i></b> The growth rate initially was 45% per day, then rapidly decreased and was accompanied by a similar pattern of hepatic fat deposition. The architectural changes showed a significant increase in the Ki67 expression (<i>p</i> &lt; 0.0001) in the days following resection with a peak on the 2nd day and nearly normalized on day 7. The expression of CD31 increased significantly on the 2nd and 3rd days compared to the pre-resection samples (<i>p</i> = 0.03). Hepatic artery flow per liver volume remained at baseline ranges during regeneration. Portal flow per liver volume increased after liver resection (<i>p</i> &lt; 0.001), was still elevated on the 1st postoperative day, then decreased. Correlations were significantly negative between the hepatic volume increase on day 3 and the hepatic oxygen consumption and the net lactate production at the end of the procedure (<i>r</i> = –0.82, <i>p</i> = 0.01, and <i>r</i> = –0.70, <i>p</i> = 0.03). <b><i>Conclusion:</i></b> The volume increase in the first days – a fast process – is not explained by cellular proliferation alone. The liver/body weight ratio is back to 50% of the preoperative value after 3 days to close to 100% volume regain on days 10–15.
DOI: 10.7284/106818
title: Multiplexed data collected during research cruise AT21-04 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108604
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT21-04 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17633/rd.brunel.7712540
title: 4000 stories with sentiment analysis dataset

description: This dataset presents 4,000 short stories that have been classified in terms of their emotional content and semantic structure. Emotional content was calculated using the valence, arousal and dominance norms in Warriner et al. (2014). Semantic structure was derived using the doc2vec algorithm, which classifies each text as a 300-place vector. The authors created this dataset as part of a study of the impact of narrative literature on mental health.
DOI: 10.7284/111383
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT21-04 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106811
title: Multibeam Echosounder data collected during research cruise AT21-04 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/106819
title: Multiplexed data collected during research cruise AT21-05 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108477
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT21-05 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/108476
title: Expendable Probe data collected during research cruise AT21-05 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7712468
title: Supplementary Material for: A Rare Case of Localized Argyria on the Face

description: Due to its antibacterial actions, silver sulfadiazine is widely used as a topical agent in the treatment of wounds, including burns. Widespread or prolonged topical application of silver sulfadiazine dressings can lead to argyria including systemic symptoms due to the resorption of silver. Here, we report a patient experiencing localized argyria due to sunlight exposure after topical use of silver sulfadiazine cream on his face.
DOI: 10.7284/106812
title: Multibeam Echosounder data collected during research cruise AT21-05 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109673
title: Multiplexed data collected during research cruise AT22 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109676
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT22 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/111381
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise AT22 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109675
title: Expendable Probe data collected during research cruise AT22 using a Sippican MK12 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.26180/5c6400f45472e
title: Wirasinha.CDD.2019.txt.zip

description: The file contains mouse T cell receptor (TCR) sequences collected by multiplex PCR amplification of cDNA molecules followed by Illumina sequencing. Sequences were aligned to the mouse genome using MIGEC software (see doi: 10.1038/nmeth.2960 for details). Except for the header row, each row contains information about a unique TCR nucleotide sequence. Columns 1-11 contain output from MIGEC software. Columns 12-16 contain information about sample origin, detailed as follows: column 12 "sample_id" is an identifier for the sample of origin; column 13 "chain" specifies the TCR chain ("a" = alpha, "b" = beta); column 14 "genotype" specifies the transgene status of donor mouse ("wt" or "bcl2" to indicate the absence or presence of BCL2-tg expression, respectively); column 15 "tcr_b" specifies the TCR beta chain status of donor mouse ("poly" = C57BL/6 inbred mouse strain); column 16 "mouse" is an identifier of the donor mouse; column 17 "organ" specifies organ of origin (thymus, "gut" = small intestine and spleen); column 18 "subset" specifies the T cell subset of origin ("t_p" = pre-selection thymocytes; "t_1" = Type A IELp; "t_1b" = Type B IELp; "t_r" = thymic T-reg; "t_4" = CD4+ T-conv thymocytes; "t_8" = CD8+ T-conv thymocytes; "g8a" = small intestinal CD8aa+ intraepithelial lymphocytes; "s_r" = splenic T-reg; "s_4" = splenic CD4+ naive T cells and "s_8" = splenic CD8+ naive T cells); column 19 is identical to column 18 except that column 19 shows whether the T-reg sample of origin was a CD25+ ("t_u" and "s_u") or CD25– ("t_d" and "s_d") fraction of a thymic or splenic T-reg population.
DOI: 10.7284/109674
title: Multibeam Echosounder data collected during research cruise AT22 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7712351
title: Supplementary Material for: Possible Association between Cathepsin V and the Development of Placenta Accreta Spectrum Disorders

description: <b><i>Background/Aims:</i></b> The study aimed to evaluate molecular changes related to trophoblast adhesion in placenta accreta spectrum (PAS) disorders. <b><i>Methods:</i></b> A retrospective analysis of 10 PAS cases in which both the trophoblast adherent site and the non-adherent site were identified was performed in April 2010 and March 2013. Microarray analysis and reverse transcription polymerase chain reaction (RT-PCR) analyses were performed to extract upregulated genes in the adherent site. Gene expression changes were examined by immunohistochemistry. <b><i>Results:</i></b> Microarray analysis showed that 157 transcripts were &gt; 3-fold upregulated, including the following: a disintegrin and metalloproteinase-28 (ADAM28), 3.10-fold; cathepsin V (CTSV), 3.73-fold; cathepsin S (CTSS), 3.46-fold; and matrix metalloproteinase-19 (MMP19), 3.41-fold. RT-PCR showed relatively high mRNA expressions. On immunohistochemistry, extravillous trophoblast (EVT) at the non-adherent site showed weak or no CTSV expression, whereas EVT that invaded myometrium at the adherent site showed strong expression (histological score, median [min-max], 115.6 [37.6–153.6] vs. 184.8 [56.4–222.8], <i>p</i> &lt; 0.05). MMP19 showed moderate staining, with no difference between the adherent and non-adherent sites. ADAM28 and CTSS showed weak or no staining. <b><i>Discussion:</i></b> This limited study suggests that CTSV may be involved in the pathogenesis of PAS.
DOI: 10.6084/m9.figshare.7712354
title: Table S1: Crossing Cook Strait: terranes of the Marlborough Schist, Kapiti Island and Wellington

description: Full analytical results (U, Th and Pb isotope ratios) and common-Pb-corrected calculated ages.
DOI: 10.7284/109677
title: Multiplexed data collected during research cruise AT23 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7712351.v1
title: Supplementary Material for: Possible Association between Cathepsin V and the Development of Placenta Accreta Spectrum Disorders

description: <b><i>Background/Aims:</i></b> The study aimed to evaluate molecular changes related to trophoblast adhesion in placenta accreta spectrum (PAS) disorders. <b><i>Methods:</i></b> A retrospective analysis of 10 PAS cases in which both the trophoblast adherent site and the non-adherent site were identified was performed in April 2010 and March 2013. Microarray analysis and reverse transcription polymerase chain reaction (RT-PCR) analyses were performed to extract upregulated genes in the adherent site. Gene expression changes were examined by immunohistochemistry. <b><i>Results:</i></b> Microarray analysis showed that 157 transcripts were &gt; 3-fold upregulated, including the following: a disintegrin and metalloproteinase-28 (ADAM28), 3.10-fold; cathepsin V (CTSV), 3.73-fold; cathepsin S (CTSS), 3.46-fold; and matrix metalloproteinase-19 (MMP19), 3.41-fold. RT-PCR showed relatively high mRNA expressions. On immunohistochemistry, extravillous trophoblast (EVT) at the non-adherent site showed weak or no CTSV expression, whereas EVT that invaded myometrium at the adherent site showed strong expression (histological score, median [min-max], 115.6 [37.6–153.6] vs. 184.8 [56.4–222.8], <i>p</i> &lt; 0.05). MMP19 showed moderate staining, with no difference between the adherent and non-adherent sites. ADAM28 and CTSS showed weak or no staining. <b><i>Discussion:</i></b> This limited study suggests that CTSV may be involved in the pathogenesis of PAS.
DOI: 10.6084/m9.figshare.7712354.v1
title: Table S1: Crossing Cook Strait: terranes of the Marlborough Schist, Kapiti Island and Wellington

description: Full analytical results (U, Th and Pb isotope ratios) and common-Pb-corrected calculated ages.
DOI: 10.7284/109679
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT23 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109678
title: Multibeam Echosounder data collected during research cruise AT23 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109680
title: Multiplexed data collected during research cruise AT24-01 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/109681
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT24-01 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/110975
title: Multiplexed data collected during research cruise AT25 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7712246
title: Supplementary Material for: Maternal Influence and Murine Housing Confound Impact of NLRP1 Inflammasome on Microbiome Composition

description: The NLRP1 inflammasome attenuates inflammatory bowel disease (IBD) progression and colitis-associated tumorigenesis. A possible mechanism postulates that the lack of the NLRP1 inflammasome creates permissive niches in the gut for pathogenic bacteria to flourish, causing dysbiosis and increased IBD susceptibility. To evaluate this hypothesis, we characterized the gut microbiome of wild-type, <i>Nlrp1b–/–</i>, and <i>Asc–/–</i> mice under naïve conditions by sequencing the V3 region of the 16s rRNA gene. For both genetically modified mouse lines, the microbiome composition reflected overrepresentation of bacteria associated with dysbiosis relative to wild-type animals. Measurement of short- and medium-chain fatty acids by mass spectrometry further revealed significant differences between genotypes. However, prior to concluding that the NLRP1 inflammasome plays a role in regulating the composition of the microbiome, we evaluated two additional strategies for cohousing wild-type and <i>Nlrp1b–/–</i> mice: breeding homozygous parents and cohousing at weaning, and breeding from heterozygous parents and cohousing littermates. We found that maternal influence was the greater predictor of microbiome composition rather than genotype. With the rise in microbiome research across disciplines, our study should be viewed as a cautionary example that illustrates the importance of careful breeding and housing strategies when evaluating host-microbiome interactions.
DOI: 10.6084/m9.figshare.7712231
title: Tables S1 to S4 from Ancestral and offspring nutrition interact to affect life-history traits in <i>Drosophila melanogaster</i>

description: Included in file
DOI: 10.6084/m9.figshare.7712234
title: Genetic analysis of KillerRed in <i>C. elegans</i> identifies a shared role of calcium genes in ROS-mediated neurodegeneration

description: In <i>C. elegans</i>, neurodegeneration induced by excitotoxicity or aggregation of misfolded proteins is dependent on genes involved in calcium release from the endoplasmic reticulum. Reactive oxygen species (ROS) can also induce neurodegeneration, but the relationship between ROS-mediated neurodegeneration and calcium has not been established. We activated KillerRed in the GABA neurons of <i>C. elegans</i> to produce ROS that leads to functional loss and structural degeneration of these neurons and demonstrated that the severity of neurodegeneration was dependent on extent of KillerRed activation. To genetically examine the role of calcium in ROS-mediated neurodegeneration, we measured functional neurodegeneration in <i>itr-1</i> (inositol trisphosphate receptor), <i>crt-1</i> (caltreticulin), and <i>unc-68</i> (ryanodine receptor) mutants. Similar to other neurotoxic conditions, neurodegeneration triggered by KillerRed was reduced in <i>itr-1</i> and <i>crt-1</i> mutants. Somewhat unexpectedly, genetic or pharmacological disruption of <i>unc-68</i> had a minimal effect on neurodegeneration. Our results indicate ROS-mediated neurodegeneration occurs through a conserved calcium regulated mechanism and suggest that components of the degeneration process have different sensitivities to ROS.
DOI: 10.7284/110855
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise AT25 using a Hawaii UHDAS instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7712222
title: Characters of repetitive elements in Cissus quadrangularis R2

description: Fastq-files R2 Sequences
DOI: 10.6084/m9.figshare.7712222.v1
title: Characters of repetitive elements in Cissus quadrangularis R2

description: Fastq-files R2 Sequences
DOI: 10.6084/m9.figshare.7712231.v1
title: Tables S1 to S4 from Ancestral and offspring nutrition interact to affect life-history traits in <i>Drosophila melanogaster</i>

description: Included in file