cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26050/wdcc/gcos_ehi_exp_v2
title: Heat stored in the Earth system: Where does the energy go? Version 2

description: Project: GCOS Earth Heat Inventory - A study under the Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory (EHI), and presents an updated international assessment of ocean warming estimates, and new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period 1960-2018. Summary: ‘Heat stored in the Earth system: Where does the energy go?’ contains a consistent long-term Earth system heat inventory over the period 1960-2018. Human-induced atmospheric composition changes cause a radiative imbalance at the top-of-atmosphere which is driving global warming. This Earth Energy Imbalance (EEI) is the most critical number defining the prospects for continued global warming and climate change. Understanding the heat gain of the Earth system from this accumulated heat – and particularly how much and where the heat is distributed in the Earth system - is fundamental to understanding how this affects warming oceans, atmosphere and land, rising temperatures and sea level, and loss of grounded and floating ice, which are fundamental concerns for society. This dataset is based on a study under the Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory, and presents an updated international assessment of ocean warming estimates, and new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period 1960-2018. Changes in version 2: a) uncertainties have been added and updated in the netcdf file b) Ocean heat content &gt; 2000m depth: update of one time series, and thus revised ensemble mean c) Atmospheric heat content: update of the time series as received by experts on the 29/05/2020 d) Available heat cyropshere: update of the time series as received by experts on the 27/05/2020. e) some attributes have been added for more details.
DOI: 10.25934/00001412.0
title: Available IPD datapackage for study 'A Multicenter, Double-Blind, Randomized, Parallel-group Evaluation of LAMICTAL Extended-release Adjunctive Therapy in Subjects With Partial Seizures'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00001412.1
title: IPD datapackage for study 'A Multicenter, Double-Blind, Randomized, Parallel-group Evaluation of LAMICTAL Extended-release Adjunctive Therapy in Subjects With Partial Seizures' and research request: 'Retrospective analysis of placebo arm data in clinical epilepsy trials - GSK data re-load for 5325'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00000160.0
title: Available IPD datapackage for study 'A Multicenter, Double-blind, Randomized, Parallel-group Evaluation of LAMICTAL Extended-Release Adjunctive Therapy in Patients With Primary Generalized Tonic-Clonic Seizures'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25934/00000160.1
title: IPD datapackage for study 'A Multicenter, Double-blind, Randomized, Parallel-group Evaluation of LAMICTAL Extended-Release Adjunctive Therapy in Patients With Primary Generalized Tonic-Clonic Seizures' and research request: 'Retrospective analysis of placebo arm data in clinical epilepsy trials - GSK data re-load for 5325'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5281/zenodo.3953653
title: Comparative evaluation of band-based genotyping methods for Mycobacterium intracellulare and its application for epidemiological analysis

description: <em>Mycobacterium intracellulare</em> is a leading cause of nontuberculous mycobacterial pulmonary disease, with a rapidly increasing prevalence worldwide. This bacterium, commonly distributed in soil and water, is known to be transmitted through the environment rather than between people. Therefore, it is imperative to establish distinguishable genotyping methods to understand the clinical outcome, disease relapses, and epidemiology. Therefore, the present study comprised two steps. First, variable number tandem repetition (VNTR), VNTR-mycobacterial interspersed repetitive units (VNTR-MIRU), repetitive sequence based-PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE) as band-based genotyping methods were performed using 19 <em>M. intracellualre</em> isolated from patients with PD. The comparative results of genotyping techniques and geographical characteristics in this study may provide fundamental information for the epidemiology of <em>M. intracellulare</em>.
DOI: 10.5281/zenodo.3953652
title: Comparative evaluation of band-based genotyping methods for Mycobacterium intracellulare and its application for epidemiological analysis

description: <em>Mycobacterium intracellulare</em> is a leading cause of nontuberculous mycobacterial pulmonary disease, with a rapidly increasing prevalence worldwide. This bacterium, commonly distributed in soil and water, is known to be transmitted through the environment rather than between people. Therefore, it is imperative to establish distinguishable genotyping methods to understand the clinical outcome, disease relapses, and epidemiology. Therefore, the present study comprised two steps. First, variable number tandem repetition (VNTR), VNTR-mycobacterial interspersed repetitive units (VNTR-MIRU), repetitive sequence based-PCR (rep-PCR) and pulsed field gel electrophoresis (PFGE) as band-based genotyping methods were performed using 19 <em>M. intracellualre</em> isolated from patients with PD. The comparative results of genotyping techniques and geographical characteristics in this study may provide fundamental information for the epidemiology of <em>M. intracellulare</em>.
DOI: 10.5281/zenodo.3925439
title: Results files of PRosettac for the following PDBs: 5T35, 6BOY, 6BN7, 6BN8, 6BN9, 6BNB, 6HAX, 6HAY, 6HR2, 6SIS.

description: This depository includes supplementary files from the manuscript "PRosettaC: Rosetta based modeling of PROTAC mediated ternary complexes". Link for the paper pre-print: https://www.biorxiv.org/content/10.1101/2020.05.27.119354v1 The code for the protocol is available at https://github.com/LondonLab/PRosettaC A web server for applying the protocol by a simple user interface will soon be available at http://prosettac.weizmann.ac.il The files include the final models of the train and test sets from the manuscript as well as the unsuccessful unbound results for seven out of the ten targets. Also included are the input files for the bound results. PDBs of bound structures: 5T35, 6BOY, 6BN7, 6BN8, 6BN9, 6BNB, 6SIS, 6HAX, 6HAY, 6HR2. PDBs of unbound structures: 6HAX, 6HAY, 6HR2, 6BOY, 6BN7, 6BN9, 5T35.
DOI: 10.15161/oar.it/30572
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.5284/1079019
title: Mancetter-Hartshill Roman Pottery Kilns Archive Project

description: Between 1960 and 1977 Kay Hartley conducted excavations near the Warwickshire villages of Mancetter and Hartshill. In 1983 and 1984, further rescue excavations were undertaken by Warwickshire Museum at Mancetter, Cherry Tree Farm. These various excavations investigated a major Roman industrial complex, comprising more than 50 pottery kilns and associated features, including a glass furnace. Following the excavations, a considerable amount of time and effort was put into post-excavation analysis of the mortaria, other pottery and finds. The purpose of this digitisation project has been to secure and make accessible key elements of this archive resource, facilitating and encouraging its study and use, and potentially its further development.
DOI: 10.5281/zenodo.3953725
title: Chlorophyll-a concentrations estimated from particulate absorption coefficients and collocated particulate beam-attenuation coefficients between 620 and 710 nm.

description: This dataset was produced using measurements extracted from the NASA SeaBASS database and collected during three Atlantic Meridional Transect cruises (https://www.amt-uk.org/) and it is described in more details in Graban et al., (2020). The dataset consists of chlorophyll-a concentrations estimated from particulate absorption coefficients (chl-ACS) using the line-height method (Boss et al., 2007) and de-biased using HPLC Total Chlorophyll data (chl-HPLC) as described in Graban et al (2020). The dataset also contains the latitude, longitude, UTC timestamp and the name of the research expeditions during which each point was collected. Finally, the dataset contains the collocated particulate beam-attenuation coefficients at 620 nm to 710 nm interpolated every 2 nm that were used in Graban et al. (2020). To allow the user to assess the accuracy of the chl-ACS data before debiasing, for each cruise separately we also provide plots of the comparison between line height (L=chl-ACS*0.014, see Eq 1 in the paper) and chl-HPLC, parameters and their 95% confidence intervals of the fit to the equation chl-HPLC = a*L^b, plots, median biases (\delta) and robust standard deviations (\sigma) of the relative residuals (i.e., chl-ACS/chl-HPLC-1), as well as the total number of points (N) used in the comparison.<br> <br> References<br> <br> E. S. Boss, R. Collier, G. Larson, K. Fennel, and W. S. Pegau, “Measurements of spectral optical properties and their relation to biogeochemical variables and processes in Crater Lake, Crater Lake National Park, OR,” Hydrobiologia574, 149–159 (2007)." S. Graban, G. Dall'Olmo, S. Goult, and R. Sauzède (2020) "Accurate deep-learning estimation of chlorophyll-a concentration from the spectral particulate beam-attenuation coefficient" Optics Express, https://doi.org/10.1364/OE.397863
DOI: 10.5281/zenodo.3828439
title: Chlorophyll-a concentrations estimated from particulate absorption coefficients and collocated particulate beam-attenuation coefficients between 620 and 710 nm.

description: This dataset was produced using measurements extracted from the NASA SeaBASS database and collected during three Atlantic Meridional Transect cruises (https://www.amt-uk.org/) and it is described in more details in Graban et al., (2020). The dataset consists of chlorophyll-a concentrations estimated from particulate absorption coefficients (chl-ACS) using the line-height method (Boss et al., 2007) and de-biased using HPLC Total Chlorophyll data (chl-HPLC) as described in Graban et al (2020). The dataset also contains the latitude, longitude, UTC timestamp and the name of the research expeditions during which each point was collected. Finally, the dataset contains the collocated particulate beam-attenuation coefficients at 620 nm to 710 nm interpolated every 2 nm that were used in Graban et al. (2020). To allow the user to assess the accuracy of the chl-ACS data before debiasing, for each cruise separately we also provide plots of the comparison between line height (L=chl-ACS*0.014, see Eq 1 in the paper) and chl-HPLC, parameters and their 95% confidence intervals of the fit to the equation chl-HPLC = a*L^b, plots, median biases (\delta) and robust standard deviations (\sigma) of the relative residuals (i.e., chl-ACS/chl-HPLC-1), as well as the total number of points (N) used in the comparison.<br> <br> References<br> <br> E. S. Boss, R. Collier, G. Larson, K. Fennel, and W. S. Pegau, “Measurements of spectral optical properties and their relation to biogeochemical variables and processes in Crater Lake, Crater Lake National Park, OR,” Hydrobiologia574, 149–159 (2007)." S. Graban, G. Dall'Olmo, S. Goult, and R. Sauzède (2020) "Accurate deep-learning estimation of chlorophyll-a concentration from the spectral particulate beam-attenuation coefficient" Optics Express, https://doi.org/10.1364/OE.397863
DOI: 10.25550/1-jvrw
title: MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip

description: **BACKGROUND:** The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex and involves the contribution of genetic and environmental factors. Although many candidate genes have been identified, the regulation and interaction of these genes in CL/P remain unclear. In addition, the contribution of microRNAs (miRNAs), non-coding RNAs that regulate the expression of multiple genes, to the etiology of CL/P is largely unknown. **METHODS:** To identify the signatures of causative biological pathways for human CL/P, we conducted a systematic literature review for human CL/P candidate genes and subsequent bioinformatics analyses. Functional enrichment analyses of the candidate CL/P genes were conducted using the pathway databases GO and KEGG. The miRNA-mediated post-transcriptional regulation of the CL/P candidate genes was analyzed with miRanda, PITA, and TargetScan, and miRTarbase. Genotype-phenotype association analysis was conducted using GWAS. The functional significance of the candidate miRNAs was evaluated experimentally in cell proliferation and target gene regulation assays in human lip fibroblasts. **RESULTS:** Through an extensive search of the main biomedical databases, we mined 177 genes with mutations or association/linkage reported in individuals with CL/P, and considered them as candidate genes for human CL/P. The genotype-phenotype association study revealed that mutations in 12 genes (ABCA4, ADAM3A, FOXE1, IRF6, MSX2, MTHFR, NTN1, PAX7, TP63, TPM1, VAX1, and WNT9B) were significantly associated with CL/P. In addition, our bioinformatics analysis predicted 16 microRNAs (miRNAs) to be post-transcriptional regulators of CL/P genes. To validate the bioinformatics results, the top six candidate miRNAs (miR-124-3p, miR-369-3p, miR-374a-5p, miR-374b-5p, miR-497-5p, and miR-655-3p) were evaluated by cell proliferation/survival assays and miRNA-gene regulation assays in cultured human lip fibroblasts. We found that miR-497-5p and miR-655-3p significantly suppressed cell proliferation in these cells. Furthermore, the expression of the predicted miRNA-target genes was significantly downregulated by either miR-497-5p or miR-655-3p mimic. **CONCLUSION:** Expression of miR-497-5p and miR-655-3p suppresses cell proliferation through the regulation of human CL/P-candidate genes. This study provides insights into the role of miRNAs in the etiology of CL/P and suggests possible strategies for the diagnosis of CL/P. **REFERENCE DATABASES:** - [http://geneontology.org](http://geneontology.org) - [https://www.genome.jp/kegg](https://www.genome.jp/kegg)
DOI: 10.25550/1-hw9a
title: MicroRNA-124-3p suppresses mouse lip mesenchymal cell proliferation through the regulation of genes associated with cleft lip in the mouse.

description: **BACKGROUND:** Cleft lip (CL), one of the most common congenital birth defects, shows considerable geographic and ethnic variation, with contribution of both genetic and environmental factors. Mouse genetic studies have identified several CL-associated genes. However, it remains elusive how these CL-associated genes are regulated and involved in CL. Environmental factors may regulate these genes at the post-transcriptional level through the regulation of non-coding microRNAs (miRNAs). In this study, we sought to identify miRNAs associated with CL in mice. **RESULTS:** Through a systematic literature review and a Mouse Genome Informatics (MGI) database search, we identified 55 genes that were associated with CL in mice. Subsequent bioinformatic analysis of these genes predicted that a total of 33 miRNAs target multiple CL-associated genes, with 20 CL-associated genes being potentially regulated by multiple miRNAs. To experimentally validate miRNA function in cell proliferation, we conducted cell proliferation/viability assays for the selected five candidate miRNAs (miR-124-3p, let-7a-5p, let-7b-5p, let-7c-5p, and let-7d-5p). Overexpression of miR-124-3p, but not of the others, inhibited cell proliferation through suppression of CL-associated genes in cultured mouse embryonic lip mesenchymal cells (MELM cells) isolated from the developing mouse lip region. By contrast, miR-124-3p knockdown had no effect on MELM cell proliferation. This miRNA-gene regulatory mechanism was mostly conserved in O9-1 cells, an established cranial neural crest cell line. Expression of miR-124-3p was low in the maxillary processes at E10.5, when lip mesenchymal cells proliferate, whereas it was greatly increased at later developmental stages, suggesting that miR-124-3p expression is suppressed during the proliferation phase in normal palate development. **CONCLUSIONS:** Our findings indicate that upregulated miR-124-3p inhibits cell proliferation in cultured lip cells through suppression of CL-associated genes. These results will have a significant impact, not only on our knowledge about lip morphogenesis, but also on the development of clinical approaches for the diagnosis and prevention of CL.
DOI: 10.25550/1-jvtj
title: MicroRNA-374a, -4680, and -133b suppress cell proliferation through the regulation of genes associated with human cleft palate in cultured human palate cells.

description: **BACKGROUND:** Cleft palate (CP) is the second most common congenital birth defect; however, the relationship between CP-associated genes and epigenetic regulation remains largely unknown. In this study, we investigated the contribution of microRNAs (miRNAs) to cell proliferation and regulation of genes involved in CP development. **METHODS:** In order to identify all genes for which mutations or association/linkage have been found in individuals with CP, we conducted a systematic literature search, followed by bioinformatics analyses for these genes. We validated the bioinformatics results experimentally by conducting cell proliferation assays and miRNA-gene regulatory analyses in cultured human palatal mesenchymal cells treated with each miRNA mimic. **RESULTS:** We identified 131 CP-associated genes in the systematic review. The bioinformatics analysis indicated that the CP genes were associated with signaling pathways, microRNAs (miRNAs), metabolic pathways, and cell proliferation. A total 17 miRNAs were recognized as potential modifiers of human CP genes. To validate miRNA function in cell proliferation, a main cause of CP, we conducted cell proliferation/viability assays for the top 11 candidate miRNAs from our bioinformatics analysis. Overexpression of miR-133b, miR-374a-5p, and miR-4680-3p resulted in a more than 30% reduction in cell proliferation activity in human palatal mesenchymal cell cultures. We found that several downstream target CP genes predicted by the bioinformatics analyses were significantly downregulated through induction of these miRNAs (FGFR1, GCH1, PAX7, SMC2, and SUMO1 by miR-133b; ARNT, BMP2, CRISPLD1, FGFR2, JARID2, MSX1, NOG, RHPN2, RUNX2, WNT5A and ZNF236 by miR-374a-5p; and ERBB2, JADE1, MTHFD1 and WNT5A by miR-4680-3p) in cultured cells. **CONCLUSIONS:** Our results indicate that miR-374a-5p, miR-4680-3p, and miR-133b regulate expression of genes that are involved in the etiology of human CP, providing insight into the association between CP-associated genes and potential targets of miRNAs in palate development. **REFERENCE DATABASES:** - [http://geneontology.org](http://geneontology.org) - [https://www.genome.jp/kegg](https://www.genome.jp/kegg)
DOI: 10.25550/1-jvw2
title: Genes and microRNAs associated with mouse cleft palate: A systematic review and bioinformatics analysis

description: **ABSTRACT:** Cleft palate (CP) is the most prevalent craniofacial deformity, with ethnic and geographic variation in prevalence in humans. Mice have been used as an animal model to study the cause(s) of CP by several approaches, including genetic and chemical-induced approaches. Mouse genetic approaches revealed that significant amounts of genes are involved in the CP pathology. The aim of this study was to identify common features of CP-associated genes and to explore the roles of microRNAs (miRNAs) as important post-transcriptional regulators that may be involved in the regulation of CP genes. To generate an accurate list of genes associated with CP, we first conducted systematic literature searches through main databases such as Medline, Embase, and PubMed, as well as other sources such as Scopus and Mouse Genome Informatics. We found that 195 mouse strains with single-gene mutations and 140 mouse strains with compound-gene mutations were reported to have CP. The CP genes were categorized by functions and pathways using the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology annotations, highlighting the contribution of cellular metabolism to CP. A total of 18 miRNAs were involved in the regulation of multiple CP genes. Human genotype-phenotype analysis revealed that variants in five human homologous CP genes (IRF6, FOXE1, VAX1, WNT9B, and GAD1) significantly contributed to the human CP phenotype. Thus, our results suggest that cellular metabolism and miRNAs play an important role in the regulation of genetic pathways and networks crucial for palatal formation. **REFERENCE DATABASES:** - [http://geneontology.org](http://geneontology.org) - [https://www.genome.jp/kegg](https://www.genome.jp/kegg)