cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6860396
title: Structure-based prediction of West Nile virus-human protein–protein interactions

description: In recent years, West Nile virus (WNV) has posed a great threat to global human health due to its explosive spread. Studying the protein–protein interactions (PPIs) between WNV and human is beneficial for understanding the pathogenesis of WNV and the immune response mechanism of human against WNV infection at the molecular level. In this study, we identified the human target proteins which interact with WNV based on protein structure similarity, and then the interacting pairs were filtered by the subcellular co-localization information. As a result, a network of 3346 interactions was constructed, involving 6 WNV proteins and 1970 human target proteins. To our knowledge, this is the first predicted interactome for WNV-human. By analyzing the topological properties and evolutionary rates of the human target proteins, it was demonstrated that these proteins tend to be the hub and bottleneck proteins in the human PPI network and are more conserved than the non-target ones. Triplet analysis showed that the target proteins are adjacent to each other in the human PPI network, suggesting that these proteins may have similar biological functions. Further, the functional enrichment analysis indicated that the target proteins are mainly involved in virus process, transcription regulation, cell adhesion, and so on. In addition, the common and specific targets were identified and compared based on the networks between WNV-human and Dengue virus II (DENV2)-human. Finally, by combining topological features and existing drug target information, we identified 30 potential anti-WNV human targets, among which 11 ones were reported to be associated with WNV infection. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.6860396.v2
title: Structure-based prediction of West Nile virus-human protein–protein interactions

description: In recent years, West Nile virus (WNV) has posed a great threat to global human health due to its explosive spread. Studying the protein–protein interactions (PPIs) between WNV and human is beneficial for understanding the pathogenesis of WNV and the immune response mechanism of human against WNV infection at the molecular level. In this study, we identified the human target proteins which interact with WNV based on protein structure similarity, and then the interacting pairs were filtered by the subcellular co-localization information. As a result, a network of 3346 interactions was constructed, involving 6 WNV proteins and 1970 human target proteins. To our knowledge, this is the first predicted interactome for WNV-human. By analyzing the topological properties and evolutionary rates of the human target proteins, it was demonstrated that these proteins tend to be the hub and bottleneck proteins in the human PPI network and are more conserved than the non-target ones. Triplet analysis showed that the target proteins are adjacent to each other in the human PPI network, suggesting that these proteins may have similar biological functions. Further, the functional enrichment analysis indicated that the target proteins are mainly involved in virus process, transcription regulation, cell adhesion, and so on. In addition, the common and specific targets were identified and compared based on the networks between WNV-human and Dengue virus II (DENV2)-human. Finally, by combining topological features and existing drug target information, we identified 30 potential anti-WNV human targets, among which 11 ones were reported to be associated with WNV infection. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.25152533.v1
title: Data : HRV in Sedentary and Trained aging horses

description: HRV in Sedentary and Trained aging horses (13 pages/file) : 11 horses/grouppage1 : 7:00-9:00page2 : 9:00-11:00page3 : 11:00-13:00page4 : 13:00-15:00page5 : 15:00-17:00page6 : 17:00-19:00page7 : 19:00-21:00page8 : 21:00-23:00page9 : 23:00-01:00page10 : 01:00-03:00page11 : 03:00-05:00page12 : Day 07:00-18:00page13 : Night 18:00-06:00
DOI: 10.6084/m9.figshare.13152223.v1
title: Additional file 3 of Analysing the meta-interaction between pathways by gene set topological impact analysis

description: Additional file 3. R code for constructing global network. (TXT 2 kb)
DOI: 10.6084/m9.figshare.13152226
title: Additional file 4 of Analysing the meta-interaction between pathways by gene set topological impact analysis

description: Additional file 4: Matrix Data 1. JI matrix for Fig. 2a. (XLS 2 kb)
DOI: 10.6084/m9.figshare.13152226.v1
title: Additional file 4 of Analysing the meta-interaction between pathways by gene set topological impact analysis

description: Additional file 4: Matrix Data 1. JI matrix for Fig. 2a. (XLS 2 kb)
DOI: 10.6084/m9.figshare.8957630
title: Additional file 2: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S2. Differentially expressed genes (DEGs) between the cold treatment and control. FPKM reads per kilobase per million mapped reads. FDR false discovery rate. (XLSX 370 kb)
DOI: 10.6084/m9.figshare.8957645.v1
title: Additional file 5: of De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress

description: Table S5. Lipid metabolism-related genes that were differentially expressed during cold treatment. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.19967697.v1
title: Spatio-temporal process monitoring using exponentially weighted spatial LASSO

description: Spatio-temporal process monitoring (STPM) has received a considerable attention recently due to its broad applications in environment monitoring, disease surveillance, streaming image processing, and more. Because spatio-temporal data often have complicated structure, including latent spatio-temporal data correlation, complex spatio-temporal mean structure, and nonparametric data distribution, STPM is a challenging research problem. In practice, if a spatio-temporal process has a distributional shift (e.g., mean shift) started at a specific time point, then the spatial locations with the shift are usually clustered in small regions. This kind of spatial feature of the shift has not been considered in the existing STPM literature yet. In this paper, we develop a new STPM method that takes into account the spatial feature of the shift in its construction. The new method combines the ideas of exponentially weighted moving average in the temporal domain for online process monitoring and spatial LASSO in the spatial domain for accommodating the spatial feature of a future shift. It can also accommodate the complicated spatio-temporal data structure well. Both simulation studies and a real-data application show that it can provide a reliable and effective tool for different STPM applications.
DOI: 10.6084/m9.figshare.8970698.v1
title: Sequencing quality control for 141 transcriptomes .

description: Sequencing quality control
DOI: 10.6084/m9.figshare.16821925
title: Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic β cells

description: Chronic exposure to high concentrations of circulating palmitic acid and stearic acid leads to impaired β cell function, which accelerates the development of type 2 diabetes. However, differences in the mechanisms underlying this process between these two saturated fatty acids remain largely unknown. In this study, we screened for potential circular RNAs (circRNAs) and their associated regulatory pathways in palmitic acid- and stearic acid-induced mouse β-TC6 cell dysfunction. CircRNA high-throughput sequencing, gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes analysis were performed and co-expression and competing endogenous RNAs (ceRNA) networks were constructed. We identified that four circRNAs that were differentially expressed specifically in β cells exposed to palmitic acid, whereas four circRNAs were differentially expressed specifically in β cells exposed to stearic acid. Seven circRNAs were differentially co-expressed in palmitic acid- and stearic acid-treated β cells. In pathway exploration, we identified the core protein Solute carrier family 2 member 2 (SLc2a2), which is mainly involved in insulin resistance, maturity onset diabetes of the young and type 2 diabetes. The expressions of key circRNAs in β-TC6 cells were validated by Real time quantitative PCR, with a consistent result in high-throughput sequencing. The findings aid our understanding of the mechanisms governing the difference between palmitic acid- and stearic acid-induced β cell dysfunction and provide potential therapeutic targets for developing treatments against long-term high fat diet-induced β cell injury. <b>Abbreviations:</b> Acvr1c: Activin A receptor, type 1C; CeRNA, Competing endogenous RNAs; circRNA, circular RNA; DEcircRNA: Differentially Expressed circular RNA; DEmiRNA: Differentially Expressed microRNA; DEmRNA: Differentially Expressed mRNA; GO: Gene Ontology; HPDHigh Palmitic acid Diet; HSD: High Stearic acid Diet; KEGG: Kyoto Encyclopedia of Genes and Genomes; miRNA: microRNA; ncRNAs: non-coding RNAs; qPCR: Real time quantitative PCRS; FAs: Saturated Fatty Acids; SLc2a2: Solute carrier family 2 member 2; T2D: Type 2 Diabetes
DOI: 10.6084/m9.figshare.16821925.v1
title: Comparative analysis of circRNA expression profile and circRNA-miRNA-mRNA regulatory network between palmitic and stearic acid-induced lipotoxicity to pancreatic β cells

description: Chronic exposure to high concentrations of circulating palmitic acid and stearic acid leads to impaired β cell function, which accelerates the development of type 2 diabetes. However, differences in the mechanisms underlying this process between these two saturated fatty acids remain largely unknown. In this study, we screened for potential circular RNAs (circRNAs) and their associated regulatory pathways in palmitic acid- and stearic acid-induced mouse β-TC6 cell dysfunction. CircRNA high-throughput sequencing, gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes analysis were performed and co-expression and competing endogenous RNAs (ceRNA) networks were constructed. We identified that four circRNAs that were differentially expressed specifically in β cells exposed to palmitic acid, whereas four circRNAs were differentially expressed specifically in β cells exposed to stearic acid. Seven circRNAs were differentially co-expressed in palmitic acid- and stearic acid-treated β cells. In pathway exploration, we identified the core protein Solute carrier family 2 member 2 (SLc2a2), which is mainly involved in insulin resistance, maturity onset diabetes of the young and type 2 diabetes. The expressions of key circRNAs in β-TC6 cells were validated by Real time quantitative PCR, with a consistent result in high-throughput sequencing. The findings aid our understanding of the mechanisms governing the difference between palmitic acid- and stearic acid-induced β cell dysfunction and provide potential therapeutic targets for developing treatments against long-term high fat diet-induced β cell injury.
DOI: 10.6084/m9.figshare.8957762
title: Additional file 2:Â of Differential expression, molecular cloning, and characterization of porcine beta defensin 114

description: Detail information of MS. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.25152947
title: Studentmeal_data.xls

description: 广州学生膳食数据
DOI: 10.6084/m9.figshare.8957762.v1
title: Additional file 2:Â of Differential expression, molecular cloning, and characterization of porcine beta defensin 114

description: Detail information of MS. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.20488452.v1
title: Additional file 5 of Systematic transcriptome profiling of pyroptosis related signature for predicting prognosis and immune landscape in lower grade glioma

description: Additional file 5: Table S4. GSEA analysis results in Risk-H group.
DOI: 10.12751/g-node.zpj6rc
title: Dataset - Marmoset retinal ganglion cell responses to finely structured spatiotemporal white noise

description: Dataset accompanying the manuscript by Zapp et al. 2024: Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina.
description: IsSupplementTo: Zapp SJ, Khani MH, Schreyer HM, Sridhar S, Ramakrishna V, Krüppel S, Mietsch M, Protti DA, Karamanlis D, Gollisch T (2023), Accelerated spike-triggered non-negative matrix factorization reveals coordinated ganglion cell subunit mosaics in the primate retina. In preparation.
DOI: 10.5281/zenodo.10561496
title: Florabank taxonomische lijst van planten in functie van beheermonitoring in Vlaanderen

description: Dit Zenodo archief bevat een taxonomische lijst van vaatplanten, mossen, korstmossen en kranswieren. De Florabank is binnen het Instituut voor Natuur- en Bosonderzoek (INBO) de authentieke bron voor plantensoorten. Om deze lijst ter beschikking te stellen van andere organisaties en gebruikers, wordt de lijst via dit archief als open data gepubliceerd. Meer specifiek, zal de lijst gebruikt worden als afgesproken authentieke bron bij de monitoring van vegetatiedoelen in het kader van de monitoring van natuurbeheerplannen die in Vlaanderen door het Agentschap Natuur en Bos (ANB) worden geëvalueerd. 

De eerste versie van deze lijst betreft een snapshot uit de Florabank  van juni 2023. Alle synoniemen werden uit deze lijst verwijderd.

De lijst bevat de volgende velden:



TaxonGroep: Hogere taxonomische groep waartoe een taxon behoort (vaatplanten, mossen, korstmossen, kranswieren),

NaamWetenschappelijk:  Wetenschappelijke naam inclusief auteur,

NaamNederlands: Populaire naam - Nederlands,

TaxonID: Unieke identificatie binnen de Florabank


Er is enerzijds een Excel versie (.xlsx) van de lijst en anderzijds een .csv bestand. Beide bestanden bevatten dezelfde informatie. Bij het .csv bestand hoort ook een .yml bestand met dezelfde naam. Dit .yml bestand bevat metadata die aangemaakt werden met het git2rdata R package (door de functie git2rdata::write_vc()). Het .csv en .yml bestand kunnen met hetzelfde R package ingelezen worden met de functie git2rdata::read_vc(), maar dit is geen vereiste (ook andere tools kunnen gebruikt worden om deze bestanden in te lezen).
DOI: 10.5281/zenodo.10561497
title: Florabank taxonomische lijst van planten in functie van beheermonitoring in Vlaanderen

description: Dit Zenodo archief bevat een taxonomische lijst van vaatplanten, mossen, korstmossen en kranswieren. De Florabank is binnen het Instituut voor Natuur- en Bosonderzoek (INBO) de authentieke bron voor plantensoorten. Om deze lijst ter beschikking te stellen van andere organisaties en gebruikers, wordt de lijst via dit archief als open data gepubliceerd. Meer specifiek, zal de lijst gebruikt worden als afgesproken authentieke bron bij de monitoring van vegetatiedoelen in het kader van de monitoring van natuurbeheerplannen die in Vlaanderen door het Agentschap Natuur en Bos (ANB) worden geëvalueerd. 

De eerste versie van deze lijst betreft een snapshot uit de Florabank  van juni 2023. Alle synoniemen werden uit deze lijst verwijderd.

De lijst bevat de volgende velden:



TaxonGroep: Hogere taxonomische groep waartoe een taxon behoort (vaatplanten, mossen, korstmossen, kranswieren),

NaamWetenschappelijk:  Wetenschappelijke naam inclusief auteur,

NaamNederlands: Populaire naam - Nederlands,

TaxonID: Unieke identificatie binnen de Florabank


Er is enerzijds een Excel versie (.xlsx) van de lijst en anderzijds een .csv bestand. Beide bestanden bevatten dezelfde informatie. Bij het .csv bestand hoort ook een .yml bestand met dezelfde naam. Dit .yml bestand bevat metadata die aangemaakt werden met het git2rdata R package (door de functie git2rdata::write_vc()). Het .csv en .yml bestand kunnen met hetzelfde R package ingelezen worden met de functie git2rdata::read_vc(), maar dit is geen vereiste (ook andere tools kunnen gebruikt worden om deze bestanden in te lezen).
DOI: 10.60893/figshare.jap.24935067
title: Supplement Number 1

description: Elastic constant, electronic structure and related magnetic analysis.
DOI: 10.6084/m9.figshare.25074098
title: PurEst

description: We present PurEst, a statistical framework that uses genome-wide DNA methylation data as the only input to first estimate tumor purity of samples and then adjust DNA methylation values of individual CpGs with respect to tumor purity to better reflect somatic changes in tumor cells and improve biological inference. Here we have added scripts and reference data for calculating tumor purity and adjusting Illumina 450/850K DNA methylation beta values. Updated scripts can be found on https://github.com/StaafLab/PurEst.
DOI: 10.4121/20486157.v2
title: Sea surface temperature data reconstructed by unsaturated alkenone index and foraminiferal Mg/Ca since 4 Ma

description: Sea surface temperature records reconstructed by unsaturated alkenone index and foraminiferal Mg/Ca since 4 Ma from North Atlantic (ODP Site 982, DSDP Site 607); North Pacific (ODP Site 1012); Equatorial Pacific (ODP Sites 846, 1237, 1239); Arabian Sea (ODP Site 722); Indian Ocean (ODP Site 709C) and Southern Ocean (ODP Sites 1082, 1090, 1094).
DOI: 10.5281/zenodo.10572208
title: Dataset for "Bacterial Genome Annotation" and "Identification of AMR genes in an assembled bacterial genome" tutorials

description: This dataset is associated with two Galaxy Training Network tutorials: "Bacterial Genome Annotation" and "Identification of AMR genes in an assembled bacterial genome". It has been generated following the tutorial "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data"
DOI: 10.5281/zenodo.10572209
title: Dataset for "Bacterial Genome Annotation" and "Identification of AMR genes in an assembled bacterial genome" tutorials

description: This dataset is associated with two Galaxy Training Network tutorials: "Bacterial Genome Annotation" and "Identification of AMR genes in an assembled bacterial genome". It has been generated following the tutorial "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data"
DOI: 10.5281/zenodo.10572227
title: Dataset for "Bacterial Genome Annotation" and "Identification of AMR genes in an assembled bacterial genome" tutorials

description: This dataset is associated with two Galaxy Training Network tutorials: "Bacterial Genome Annotation" and "Identification of AMR genes in an assembled bacterial genome". It has been generated following the tutorial "Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data"
DOI: 10.6084/m9.figshare.24968994
title: Piccini et al supplementary Data 1.xlsxPiccini et al. 2024 Supplementary Data

description: Prokaryotic richness and diversity increased during Holocene glacier retreat and onset of an Antarctic Lake
DOI: 10.6084/m9.figshare.24968994.v1
title: Piccini et al supplementary Data 1.xlsx

description: Prokaryotic richness and diversity increased during Holocene glacier retreat and onset of an Antarctic Lake
DOI: 10.34740/kaggle/dsv/7486058
title: COVID Vaccination in World (updated daily)
DOI: 10.6084/m9.figshare.14556075
title: <i>Primula veris</i> genome assembly

description: Genome assembly and annotation files for two haploid assemblies of <i>Primula veris</i> (cowslip). This data is associated with the following publication:Potente G, Léveillé-Bourret É, Yousefi N, Choudhury RR, Keller B, Diop SI, Duijsings D, Pirovano W, Lenhard M, Szövényi P, Conti E. Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism. Mol Biol Evol. 2022 Feb 3;39(2):msac035. doi: 10.1093/molbev/msac035.
DOI: 10.6084/m9.figshare.14556075.v1
title: Primula veris genome assembly

description: Genome assembly and annotation files for the two haploid assemblies of Primula veris (cowslip).
DOI: 10.5281/zenodo.10572156
title: Supplementary dataset for "Greenhouse gas emission coverage and reduction potentials based on voluntary targets of major car manufacturers"

description: This dataset contains supplementary information for the paper manuscript "Greenhouse gas emission coverage and reduction potentials based on voluntary targets of major car manufacturers"

This article is based on the Master's thesis written by Jelle Smeets and published on 16 November 2022 at Utrecht University in collaboration with original thesis supervisors dr. Mark Roelfsema and dr. Takeshi Kuramochi. The data consists of the car company reduction target analysis and the GHG emission calculation model that were covered in the main paper.
DOI: 10.5281/zenodo.10572157
title: Supplementary dataset for "Greenhouse gas emission coverage and reduction potentials based on voluntary targets of major car manufacturers"

description: This dataset contains supplementary information for the paper manuscript "Greenhouse gas emission coverage and reduction potentials based on voluntary targets of major car manufacturers"

This article is based on the Master's thesis written by Jelle Smeets and published on 16 November 2022 at Utrecht University in collaboration with original thesis supervisors dr. Mark Roelfsema and dr. Takeshi Kuramochi. The data consists of the car company reduction target analysis and the GHG emission calculation model that were covered in the main paper.
DOI: 10.6084/m9.figshare.24988032
title: Supplementary Material for: Incarcerated small bowel herniation in a stoma mimicking sigmoid end colostomy prolapse

description: Introduction: A stoma prolapse is easy to diagnose by visual examination, and it rarely incarcerates. Therefore, manual reduction is usually performed as soon as the diagnosis is made. In this report, we describe a case of stoma prolapse that could not be reduced manually and ruptured because an incarcerated parastomal hernia occurred in the stoma, mimicking stoma prolapse. Case presentation: A 66-year-old woman underwent total hysterectomy, bilateral salpingo-oophorectomy, pelvic and para-aortic lymphadenectomy, omentectomy, resection of dissemination, and low anterior resection with formation of a sigmoid end colostomy for endometrial cancer with infiltration of the rectum. Fourteen months after the initial operation, she presented with stoma prolapse and multiple episodes of vomiting. The prolapsed stoma was 20 cm in length, appeared swollen and edematous, and was somewhat firm. Although it looked viable, some of the mucosa was darkish red, indicating congestion. Therefore, the diagnosis was sigmoid end colostomy prolapse with an ischemic component. An attempt at manual reduction resulted in rupture, so an emergency laparotomy was performed. Intraoperatively, we found that the ileum was incarcerated in the aperture created where the colostomy had been formed. When the incarcerated ileum was released, the stoma prolapse could be reduced easily. The end colostomy was refashioned in the left upper quadrant of the abdomen. Conclusion: An incarcerated parastomal hernia can mimic stoma prolapse. If the findings differ from those of typical stoma prolapse, imaging should be performed to confirm whether another clinical entity is involved in the stoma prolapse.