cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35078/wythmi
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Teófilo Otoni| Município: Nanuque

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.5519/qd.xu826pte
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (63 records)
DOI: 10.5281/zenodo.7442039
title: Datasets used in Venice et al., "An evolutionary perspective on fungal human pathogens: the genomes of Scedosporium between environmental challenges and opportunism"

description: This datasets collection includes: - For <em>Scedosporium aurantiacum</em> MUT6114 and <em>S. minutisporum </em>MUT6113: fasta files with assembled genome sequences, and gff files with coordinates of both genes and putative TEs insertions. All these files were generated by the authors of this study. - For <em>S. apiospermum</em> IHEM 14462 and <em>Lomentospora prolificans</em> JHH-5317: gff files containing putative TEs insertions only, since the genomic sequences and the gene models were produced by other authors and deposited in the NCBI database under accession numbers GCF_000732125.1 and GCA_002276285.1, respectively. - For <em>S. apiospermum </em>HDO1<em>, S. aurantiacum</em> WM09.24, <em>S. boydii</em> IHEM23826, <em>S. dehoogii</em> 120008799-01-4,<em> Scedosporium</em> sp. IMV00882 and <em>Scopulariopsis brevicaulis</em> LF580: gff files with coordinates of both genes and putative TEs insertions, since the genomic sequences were produced by other authors and deposited in the NCBI database under accession numbers GCA_002158515.1, GCA_000812075.1, GCA_002221725.1, GCA_002812735.1, GCA_001931805.1 and GCA_017657125.1, respectively.
DOI: 10.5281/zenodo.7442038
title: Datasets used in Venice et al., "An evolutionary perspective on fungal human pathogens: the genomes of Scedosporium between environmental challenges and opportunism"

description: This datasets collection includes: - For <em>Scedosporium aurantiacum</em> MUT6114 and <em>S. minutisporum </em>MUT6113: fasta files with assembled genome sequences, and gff files with coordinates of both genes and putative TEs insertions. All these files were generated by the authors of this study. - For <em>S. apiospermum</em> IHEM 14462 and <em>Lomentospora prolificans</em> JHH-5317: gff files containing putative TEs insertions only, since the genomic sequences and the gene models were produced by other authors and deposited in the NCBI database under accession numbers GCF_000732125.1 and GCA_002276285.1, respectively. - For <em>S. apiospermum </em>HDO1<em>, S. aurantiacum</em> WM09.24, <em>S. boydii</em> IHEM23826, <em>S. dehoogii</em> 120008799-01-4,<em> Scedosporium</em> sp. IMV00882 and <em>Scopulariopsis brevicaulis</em> LF580: gff files with coordinates of both genes and putative TEs insertions, since the genomic sequences were produced by other authors and deposited in the NCBI database under accession numbers GCA_002158515.1, GCA_000812075.1, GCA_002221725.1, GCA_002812735.1, GCA_001931805.1 and GCA_017657125.1, respectively.
DOI: 10.5281/zenodo.7670353
title: Chateau Champs - very long focal length dataset for Structure from Motion algorithms

description: This dataset contains a photogrammetric acquisition (99 images) of a sculpture head located in Château de Champs-sur-Marne, France. The images were taken with the full-frame Canon EOS 5D Mark II and a focal length of 1000mm.
DOI: 10.5281/zenodo.7670352
title: Chateau Champs - very long focal length dataset for Structure from Motion algorithms

description: This dataset contains a photogrammetric acquisition (99 images) of a sculpture head located in Château de Champs-sur-Marne, France. The images were taken with the full-frame Canon EOS 5D Mark II and a focal length of 1000mm.
DOI: 10.6084/m9.figshare.22147904
title: Data_SI_Patterns and drivers of anaerobic sediment nitrogen transformations across thermokarst lakes.xlsx

description: Data for sediment nitrogen transformation rates and microbial properties in thermokarst lakes on the Tibetan Plateau
DOI: 10.6084/m9.figshare.22147904.v1
title: Data_SI_Patterns and drivers of anaerobic sediment nitrogen transformations across thermokarst lakes.xlsx

description: Data for sediment nitrogen transformation rates and microbial properties in thermokarst lakes on the Tibetan Plateau
DOI: 10.6084/m9.figshare.22147904.v2
title: Data_SI_Patterns and drivers of anaerobic sediment nitrogen transformations across thermokarst lakes.xlsx

description: Data for sediment nitrogen transformation rates and microbial properties in thermokarst lakes on the Tibetan Plateau
DOI: 10.5519/qd.57wfuymr
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (2992 records)
DOI: 10.5281/zenodo.7670655
title: dataset relate to article: "Functional Characterization of Two Variants at the Intron 6-Exon 7 Boundary of the KCNQ2 Potassium Channel Gene Causing Distinct Epileptic Phenotypes"

description: <strong>Sequencing Analysis performed at Fondazione Besta and carried out as part of the study mentioned at title</strong>
description: Funding: Department of Medicine and Health Science of the University of Molise to MVS, from the Italian Ministry for University and Research (PRIN 2017ALCR7C) to MT and MVS, from the Italian Ministry of Health (Project RF-2019-12370491) to MT and BC, the European Commission H2020 (UNICOM – 875299), and the European Joint Programme on Rare Disease JTC 2020 to MT, and from the Italian Ministry of Health Ricerca Finalizzata Giovani Ricercatori 2016 (Project GR-2016-02363337) to JCD and MVS.
DOI: 10.5281/zenodo.7670654
title: dataset relate to article: "Functional Characterization of Two Variants at the Intron 6-Exon 7 Boundary of the KCNQ2 Potassium Channel Gene Causing Distinct Epileptic Phenotypes"

description: <strong>Sequencing Analysis performed at Fondazione Besta and carried out as part of the study mentioned at title</strong>
description: Funding: Department of Medicine and Health Science of the University of Molise to MVS, from the Italian Ministry for University and Research (PRIN 2017ALCR7C) to MT and MVS, from the Italian Ministry of Health (Project RF-2019-12370491) to MT and BC, the European Commission H2020 (UNICOM – 875299), and the European Joint Programme on Rare Disease JTC 2020 to MT, and from the Italian Ministry of Health Ricerca Finalizzata Giovani Ricercatori 2016 (Project GR-2016-02363337) to JCD and MVS.
DOI: 10.34740/kaggle/dsv/5050865
title: Transport Operational Data of Bangladesh Biman
DOI: 10.5281/zenodo.7670688
title: Dataset related to article "Successful use of perampanel in GABRA1-related myoclonic epilepsy with photosensitivity Epilepsy"

description: Sequencing analyses performed at Fondazione Besta and carried out as part of the study mentioned at title
DOI: 10.5281/zenodo.7670687
title: Dataset related to article "Successful use of perampanel in GABRA1-related myoclonic epilepsy with photosensitivity Epilepsy"

description: Sequencing analyses performed at Fondazione Besta and carried out as part of the study mentioned at title
DOI: 10.6084/m9.figshare.14371485
title: Consensus analysis via weighted gene co-expression network analysis (WGCNA) reveals genes participating in early phase of acute respiratory distress syndrome (ARDS) induced by sepsis

description: The understanding of mechanism during conversion from sepsis to sepsis-related ARDS remains limited. In this study, we collected gene expression matrix from the Gene Expression Omnibus (GEO) database and constructed networks using weighted gene co-expression network analysis (WGCNA) to identify the consensus and opposite modules between sepsis and sepsis-induced ARDS and obtained 27 consensus modules associated with sepsis and sepsis-related ARDS, including one model (160 genes) with opposite correlation and 1 sepsis-ARDS specific model with 34 genes. Differentially expressed genes analysis, functional enrichment and protein-protein interactions analyses of candidate genes were performed; 15 of these genes showed different expressions in sepsis-induced ARDS patients, compared with sepsis patients; genes were enriched in processes associated with ribosome, tissue mechanics and extracellular matrix. Feature selection analysis revealed that three genes, <i>TLCD4, PRSS30P</i>, and <i>ZNF493</i>, showed moderate performance in identifying sepsis-induced ARDS from sepsis. Ribosome-related genes indicate crucial roles in the development of sepsis-induced ARDS.
DOI: 10.6084/m9.figshare.14371485.v1
title: Consensus analysis via weighted gene co-expression network analysis (WGCNA) reveals genes participating in early phase of acute respiratory distress syndrome (ARDS) induced by sepsis

description: The understanding of mechanism during conversion from sepsis to sepsis-related ARDS remains limited. In this study, we collected gene expression matrix from the Gene Expression Omnibus (GEO) database and constructed networks using weighted gene co-expression network analysis (WGCNA) to identify the consensus and opposite modules between sepsis and sepsis-induced ARDS and obtained 27 consensus modules associated with sepsis and sepsis-related ARDS, including one model (160 genes) with opposite correlation and 1 sepsis-ARDS specific model with 34 genes. Differentially expressed genes analysis, functional enrichment and protein-protein interactions analyses of candidate genes were performed; 15 of these genes showed different expressions in sepsis-induced ARDS patients, compared with sepsis patients; genes were enriched in processes associated with ribosome, tissue mechanics and extracellular matrix. Feature selection analysis revealed that three genes, <i>TLCD4, PRSS30P</i>, and <i>ZNF493</i>, showed moderate performance in identifying sepsis-induced ARDS from sepsis. Ribosome-related genes indicate crucial roles in the development of sepsis-induced ARDS.
DOI: 10.6084/m9.figshare.14577490
title: Construction and validation of nomograms for predicting the prognosis of grade 3 endometrial endometrioid adenocarcinoma cancers: a SEER-based study

description: Most cases of endometrial adenocarcinoma (EAC) are diagnosed early and have a good prognosis; however, grade 3 (G3) EACs have poor outcomes. We retrospectively analyzed the data of 11,519 patients with G3 EACs registered between 2004 and 2015 in the Surveillance, Epidemiology, and End Results Program database and constructed a nomogram to guide clinicians in decision-making and accurate prediction of the prognosis. The caret package was used to divide samples into a training set and a validation set. Univariate and multivariate Cox regression analyses were performed, and a nomogram was constructed. A calibration curve was plotted, and a decision curve analysis was performed to verify the accuracy and clinical utility in both cohorts. The Cox regression analysis revealed that age, race, tumor size, number of lymph nodes resected, International Federation of Gynecology and Obstetrics stage, tumor/node stage, and adjuvant therapy were the prognostic factors for G3 EAC, and these were included in the nomogram. The area under the curve values of the training cohort for 1-, 3-, and 5-year were 0.832, 0.798, and 0.784, respectively for the overall survival (OS) group, and 0.858, 0.812, and 0.799, respectively for the cancer specific survival (CSS) group. A nomogram was constructed to predict the survival rate of patients with G3 EACs more accurately. The predictive nomogram will help clinicians manage patients with G3 EACs more effectively in terms of clinical prognosis.
DOI: 10.6084/m9.figshare.14577490.v1
title: Construction and validation of nomograms for predicting the prognosis of grade 3 endometrial endometrioid adenocarcinoma cancers: a SEER-based study

description: Most cases of endometrial adenocarcinoma (EAC) are diagnosed early and have a good prognosis; however, grade 3 (G3) EACs have poor outcomes. We retrospectively analyzed the data of 11,519 patients with G3 EACs registered between 2004 and 2015 in the Surveillance, Epidemiology, and End Results Program database and constructed a nomogram to guide clinicians in decision-making and accurate prediction of the prognosis. The caret package was used to divide samples into a training set and a validation set. Univariate and multivariate Cox regression analyses were performed, and a nomogram was constructed. A calibration curve was plotted, and a decision curve analysis was performed to verify the accuracy and clinical utility in both cohorts. The Cox regression analysis revealed that age, race, tumor size, number of lymph nodes resected, International Federation of Gynecology and Obstetrics stage, tumor/node stage, and adjuvant therapy were the prognostic factors for G3 EAC, and these were included in the nomogram. The area under the curve values of the training cohort for 1-, 3-, and 5-year were 0.832, 0.798, and 0.784, respectively for the overall survival (OS) group, and 0.858, 0.812, and 0.799, respectively for the cancer specific survival (CSS) group. A nomogram was constructed to predict the survival rate of patients with G3 EACs more accurately. The predictive nomogram will help clinicians manage patients with G3 EACs more effectively in terms of clinical prognosis.
DOI: 10.6084/m9.figshare.14779274
title: MicroRNA miR-425 promotes tumor progression by inhibiting Dickkopf-related protein-3 in gastric cancer

description: Gastric cancer is a prevalent yet heterogeneous disease which ranks as the fifth most common cancer in the world. Dietary habit, genetic background, <i>Helicobacter Pylori</i> infections were the risk factors of gastric cancer. MicroRNA miR-425 is highly expressed in gastric cancer, but little attention has been devoted to the mechanism of miR-425 in tumorigenesis. This study aim to investigate the role of miR-425 in gastric cancer. The expression of miR-425 and Dickkopf-related protein-3(DKK-3) were analyzed by qRT-PCR. Gastric cell line BGC-823 and SGC-7901 were transfected miR-425 inhibitors or NC. Then, cell viability was determined by CCK-8, cell apoptosis and cell cycle were assessed by flow cytometer. Cell migration and cell invasion were analyzed by wound healing and trans-well assays. Luciferase reporter assay was conducted to assess the correlation between miR-425 and DKK-3. Downstream regulators, such as p-ASK1 and p-JNK, were analysis by western blot. Compared with normal gastric epithelium cell line, miR-425 was obviously upregulated in gastric cancer cell lines. MiR-425 inhibitor suppressed the cell viability, cell migration and cell invasion. The Luciferase assay data identified that DKK-3 is a target of miR-425. While miR-425 could lower the expression of DKK-3 which mediate tumorigenesis in a certain way.
DOI: 10.6084/m9.figshare.14779274.v1
title: MicroRNA miR-425 promotes tumor progression by inhibiting Dickkopf-related protein-3 in gastric cancer

description: Gastric cancer is a prevalent yet heterogeneous disease which ranks as the fifth most common cancer in the world. Dietary habit, genetic background, <i>Helicobacter Pylori</i> infections were the risk factors of gastric cancer. MicroRNA miR-425 is highly expressed in gastric cancer, but little attention has been devoted to the mechanism of miR-425 in tumorigenesis. This study aim to investigate the role of miR-425 in gastric cancer. The expression of miR-425 and Dickkopf-related protein-3(DKK-3) were analyzed by qRT-PCR. Gastric cell line BGC-823 and SGC-7901 were transfected miR-425 inhibitors or NC. Then, cell viability was determined by CCK-8, cell apoptosis and cell cycle were assessed by flow cytometer. Cell migration and cell invasion were analyzed by wound healing and trans-well assays. Luciferase reporter assay was conducted to assess the correlation between miR-425 and DKK-3. Downstream regulators, such as p-ASK1 and p-JNK, were analysis by western blot. Compared with normal gastric epithelium cell line, miR-425 was obviously upregulated in gastric cancer cell lines. MiR-425 inhibitor suppressed the cell viability, cell migration and cell invasion. The Luciferase assay data identified that DKK-3 is a target of miR-425. While miR-425 could lower the expression of DKK-3 which mediate tumorigenesis in a certain way.
DOI: 10.6084/m9.figshare.14963793
title: Bioinformatic exploration of the immune related molecular mechanism underlying pulmonary arterial hypertension

description: This study aimed to explore the molecular mechanisms related to immune and hub genes related to pulmonary arterial hypertension (PAH). The differentially expressed genes (DEGs) of GSE15197 were identified as filters with adjusted P value &lt;0.05, and |Log2 fold change|&gt; 1. Biofunctional and pathway enrichment annotation of DEGs indicated that immunity and inflammation may play an important role in the molecular mechanism of PAH. The CIBERSORT algorithm further analyzed the immune cell infiltration characteristics of the PAH and control samples. Subsequently, 16 hub genes were identified from DEGs using the least absolute shrinkage and selection operator (LASSO) algorithm. An immune related gene CX3CR1 was further selected from the intersection results of the 16 hub genes and the top 20 genes with the most adjacent nodes in the protein-protein interaction (PPI) network. GSE113439, GSE48149, and GSE33463 datasets were used to validate and proved CX3CR1 with a remarkable score of AUC to distinguish PAH samples caused by various reasons from the control group.
DOI: 10.6084/m9.figshare.14963793.v1
title: Bioinformatic exploration of the immune related molecular mechanism underlying pulmonary arterial hypertension

description: This study aimed to explore the molecular mechanisms related to immune and hub genes related to pulmonary arterial hypertension (PAH). The differentially expressed genes (DEGs) of GSE15197 were identified as filters with adjusted P value &lt;0.05, and |Log2 fold change|&gt; 1. Biofunctional and pathway enrichment annotation of DEGs indicated that immunity and inflammation may play an important role in the molecular mechanism of PAH. The CIBERSORT algorithm further analyzed the immune cell infiltration characteristics of the PAH and control samples. Subsequently, 16 hub genes were identified from DEGs using the least absolute shrinkage and selection operator (LASSO) algorithm. An immune related gene CX3CR1 was further selected from the intersection results of the 16 hub genes and the top 20 genes with the most adjacent nodes in the protein-protein interaction (PPI) network. GSE113439, GSE48149, and GSE33463 datasets were used to validate and proved CX3CR1 with a remarkable score of AUC to distinguish PAH samples caused by various reasons from the control group.
DOI: 10.6084/m9.figshare.21070678
title: Additional file and SYSTEM DATA.zip

description: Additional file and System data
DOI: 10.6084/m9.figshare.14546514
title: Comprehensive analysis of N6-methyladenosine -related long non-coding RNAs and immune cell infiltration in hepatocellular carcinoma

description: We aimed to illustrate the influence of N6-methyladenosine (m6A) long non-coding RNAs (lncRNAs) and immune cell infiltration in hepatocellular carcinoma (HCC). The relationship of lncRNAs and m6A was identified through gene expression analysis using PERL and R packages. The Kyoto Encyclopedia of Genes and Genomes gene expression enrichment analysis was performed via gene set enrichment analysis. Lasso regression was utilized to construct prognostic model. Differences in the tumor microenvironment and the immune correlation were analyzed to clarify immune cell infiltration in different clusters and their correlation with the clinical prognosis. Co-expression analysis showed that lncRNA expression was associated closely with m6A. Many lncRNAs were predictive risk factors of prognosis in HCC. m6A-lncRNAs were partially highly expressed in tumor tissue and could be used in a prognostic model to predict HCC prognosis, independent of other clinical characteristics. ‘NOTCH SIGNALING PATHWAY’ was most significantly enriched according to GSEA. CKLF-like MARVEL transmembrane domain-containing member 3 (CMTM3) was overexpressed in tumor tissue. Immune cells, such as activated CD4 memory T cells, CD8 T cells, and follicular helper T cells, highly infiltrated tissues in cluster 2. All related scores were higher in cluster 2, indicating a lower purity of tumor cells and higher density of immune-related cells in the tumor microenvironment. m6A-lncRNAs are closely related to HCC occurrence and progression. Corresponding prognostic models can help predict HCC prognosis. m6A-lncRNAs and the related immune cell infiltration in the tumor microenvironment can provide novel therapeutic targets in HCC that need to be further studied. Graphical Abstract Graphical Abstract
DOI: 10.6084/m9.figshare.14546514.v1
title: Comprehensive analysis of N6-methyladenosine -related long non-coding RNAs and immune cell infiltration in hepatocellular carcinoma

description: We aimed to illustrate the influence of N6-methyladenosine (m6A) long non-coding RNAs (lncRNAs) and immune cell infiltration in hepatocellular carcinoma (HCC). The relationship of lncRNAs and m6A was identified through gene expression analysis using PERL and R packages. The Kyoto Encyclopedia of Genes and Genomes gene expression enrichment analysis was performed via gene set enrichment analysis. Lasso regression was utilized to construct prognostic model. Differences in the tumor microenvironment and the immune correlation were analyzed to clarify immune cell infiltration in different clusters and their correlation with the clinical prognosis. Co-expression analysis showed that lncRNA expression was associated closely with m6A. Many lncRNAs were predictive risk factors of prognosis in HCC. m6A-lncRNAs were partially highly expressed in tumor tissue and could be used in a prognostic model to predict HCC prognosis, independent of other clinical characteristics. ‘NOTCH SIGNALING PATHWAY’ was most significantly enriched according to GSEA. CKLF-like MARVEL transmembrane domain-containing member 3 (CMTM3) was overexpressed in tumor tissue. Immune cells, such as activated CD4 memory T cells, CD8 T cells, and follicular helper T cells, highly infiltrated tissues in cluster 2. All related scores were higher in cluster 2, indicating a lower purity of tumor cells and higher density of immune-related cells in the tumor microenvironment. m6A-lncRNAs are closely related to HCC occurrence and progression. Corresponding prognostic models can help predict HCC prognosis. m6A-lncRNAs and the related immune cell infiltration in the tumor microenvironment can provide novel therapeutic targets in HCC that need to be further studied. Graphical Abstract Graphical Abstract