cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11449671.v1
title: Supplementary tables from Transposable elements have contributed human regulatory regions that are activated upon bacterial infection

description: Transposable elements (TEs) are increasingly recognized as important contributors to mammalian regulatory systems. For instance, they have been shown to play a role in the human interferon response, but their involvement in other mechanisms of immune cell activation remains poorly understood. Here, we investigated the profile of accessible chromatin enhanced in stimulated human macrophages using ATAC-Seq to assess the role of different TE subfamilies in regulating gene expression following an immune response. We found that both previously identified and new repeats belonging to the MER44, THE1, Tigger3 and MLT1 families provide 14 subfamilies that are enriched in differentially accessible chromatin and found near differentially expressed genes. These TEs also harbour binding motifs for several candidate transcription factors, including important immune regulators AP-1 and NF-kB, present in 96% of accessible MER44B and 83% of THE1C instances, respectively. To more directly assess their regulatory potential, we evaluated their presence in regions putatively affecting gene expression, as defined by quantitative trait locus analysis, and found that repeats are also contributing to accessible elements near QTLs. Together, these results suggest that a number of TE families have contributed to the regulation of gene expression in the context of the immune response to infection in humans.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
DOI: 10.6084/m9.figshare.11449482
title: Three-dimensional anatomy of mesophyll cells in rice leaf tissue by serial section light microscopy

description: 2D sections of rice (<i>Oryza sativa</i> L.) mesophyll cells are complex and the cell interior contains a large volume of chloroplasts. Furthermore, the structure of chloroplasts changes in response to salt stress. In this study, we used a 3D reconstruction method based on serial section light microscopy to analyze a wide range of structures in leaf tissues and compared the intracellular structure of mesophyll cells of rice under normal and salt-treated conditions. The 3D reconstructed models revealed that mesophyll cells appeared as ellipsoid discs with several lobes around the cell periphery, with the volumes showing no significant difference between control and salt-treated plants. The chloroplast structure in the whole mesophyll cell was altered under salt stress, showing a reduced coverage area, whereas their volumes did not differ between treatments. These findings suggest that 3D reconstruction based on serial light micrographs can reveal the morphology of cells and chloroplasts in plant tissue.
DOI: 10.6084/m9.figshare.11448795
title: Metadata record for: The Chieti Affective Action Videos database, a resource for the study of emotions in psychology

description: This dataset contains key characteristics about the data described in the Data Descriptor The Chieti Affective Action Videos database, a resource for the study of emotions in psychology. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11448795.v1
title: Metadata record for: The Chieti Affective Action Videos database, a resource for the study of emotions in psychology

description: This dataset contains key characteristics about the data described in the Data Descriptor The Chieti Affective Action Videos database, a resource for the study of emotions in psychology. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11448795.v2
title: Metadata record for: The Chieti Affective Action Videos database, a resource for the study of emotions in psychology

description: This dataset contains key characteristics about the data described in the Data Descriptor The Chieti Affective Action Videos database, a resource for the study of emotions in psychology. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11448741
title: Monolayer LAMMPS Trajectory

description: This is the trajectory file meant to work with the <b>monolayer</b> example folder of d-SEAMS. Check Github to navigate the source code in the browser. The filename needs to be preserved to run without any changes.
DOI: 10.6084/m9.figshare.11448768
title: Quasi-1D Nanotube LAMMPS Trajectory

description: This is the trajectory file meant to work with the <b>iceNanotube</b> example folder of d-SEAMS. Check Github to navigate the source code in the browser. The filename needs to be preserved to run without any changes.
DOI: 10.6084/m9.figshare.11448741.v1
title: Monolayer LAMMPS Trajectory

description: This is the trajectory file meant to work with the <b>monolayer</b> example folder of d-SEAMS. Check Github to navigate the source code in the browser. The filename needs to be preserved to run without any changes.
DOI: 10.6084/m9.figshare.11448720
title: CHILL+ LAMMPS Trajectory

description: This is the trajectory file meant to work with the <b>chillPlus</b> example folder of d-SEAMS. Check Github to navigate the source code in the browser. The filename needs to be preserved to run without any changes.
DOI: 10.6084/m9.figshare.11448717
title: Systematic metadata analysis of brown rot fungi gene expression data reveals the genes involved in Fenton’s reaction and wood decay process

description: Brown-rot fungi are rapid holocellulose degraders and are the most predominant degraders of coniferous wood products in North America. Brown-rot fungi degrades wood by both enzymatic (plant biomass degrading carbohydrate active enzymes-CAZymes) and non-enzymatic systems (Fenton’s reaction) mechanisms. Identifying the genes and molecular mechanisms involved in Fenton’s reaction would significantly improve our understanding about brown-rot decay. Our present study identifies the common gene expression patterns involved in brown rot decay by performing metadata analysis of fungal transcriptome datasets. We have also analyzed and compared the genome-wide annotations (InterPro and CAZymes) of the selected brown rot fungi. Genes encoding for various oxidoreductases, iron homeostasis, and metabolic enzymes involved in Fenton’s mechanism were found to be significantly expressed among all the brown-rot fungal datasets. Interestingly, a higher number of hemicellulases encoding genes were differentially expressed among all the datasets, while a fewer number of cellulases and peroxidases were expressed (especially haem peroxidase and chloroperoxidase). Apart from these lignocellulose degrading enzymes genes encoding for aldo/keto reductases, 2-nitro dioxygenase, aromatic-ring dioxygenase, dienelactone hydrolase, alcohol dehydrogenase, major facilitator superfamily, cytochrome-P450 monoxygenase, cytochrome b5, and short-chain dehydrogenase were common and differentially up regulated among all the analyzed brown-rot fungal datasets.
DOI: 10.6084/m9.figshare.11448717.v1
title: Systematic metadata analysis of brown rot fungi gene expression data reveals the genes involved in Fenton’s reaction and wood decay process

description: Brown-rot fungi are rapid holocellulose degraders and are the most predominant degraders of coniferous wood products in North America. Brown-rot fungi degrades wood by both enzymatic (plant biomass degrading carbohydrate active enzymes-CAZymes) and non-enzymatic systems (Fenton’s reaction) mechanisms. Identifying the genes and molecular mechanisms involved in Fenton’s reaction would significantly improve our understanding about brown-rot decay. Our present study identifies the common gene expression patterns involved in brown rot decay by performing metadata analysis of fungal transcriptome datasets. We have also analyzed and compared the genome-wide annotations (InterPro and CAZymes) of the selected brown rot fungi. Genes encoding for various oxidoreductases, iron homeostasis, and metabolic enzymes involved in Fenton’s mechanism were found to be significantly expressed among all the brown-rot fungal datasets. Interestingly, a higher number of hemicellulases encoding genes were differentially expressed among all the datasets, while a fewer number of cellulases and peroxidases were expressed (especially haem peroxidase and chloroperoxidase). Apart from these lignocellulose degrading enzymes genes encoding for aldo/keto reductases, 2-nitro dioxygenase, aromatic-ring dioxygenase, dienelactone hydrolase, alcohol dehydrogenase, major facilitator superfamily, cytochrome-P450 monoxygenase, cytochrome b5, and short-chain dehydrogenase were common and differentially up regulated among all the analyzed brown-rot fungal datasets.
DOI: 10.6084/m9.figshare.11448702
title: Nucleation LAMMPS Trajectory

description: This is the trajectory file meant to work with the <b>bulkTogologicalCriterion</b> example folder of d-SEAMS. Check Github to navigate the source code in the browser.The filename needs to be preserved to run without any changes.
DOI: 10.6084/m9.figshare.11448711
title: In plane (2D) RDF LAMMPS Trajectory

description: This is the trajectory file meant to work with the <b>rdf2d-example </b>example folder of d-SEAMS. Check Github to navigate the source code in the browser. The filename needs to be preserved to run without any changes.
DOI: 10.6084/m9.figshare.11448513
title: Datasets_Gómez-Gener et al., 2020_NCOMMS

description: Datasets for the paper: "Drought alters the biogeochemistry of boreal stream networks" by Ll. Gómez-Gener. et al., 2020 in Nature Communications (format= csv).<br>Gómez-Gener, L., Lupon, A., Laudon, H. <i>et al.</i> Drought alters the biogeochemistry of boreal stream networks. <i>Nat Commun</i> 11, 1795 (2020). https://doi.org/10.1038/s41467-020-15496-2<br>
DOI: 10.6084/m9.figshare.11448213
title: “We want to know where the line is”: comparing current planning for future sea-level rise with three core principles of robust decision support approaches

description: Handling uncertainties is a major challenge in climate change adaptation. A variety of robust decision support approaches that aim for better management of uncertainty have recently been emerging and are used in environmental planning. The present study examined to what extent existing processes of planning for future sea-level rise in Sweden utilised similar approaches. Three core principles of robust decision support approaches were identified and used as a tool for analyzing five cases of planning for future sea-level rise in companies and authorities at different levels in society. The results show that planning processes typically do not embrace uncertainties, do not use a bottom-up approach and do not specifically aim for robustness, which points to a discrepancy between current planning paradigms and the core principles of robust decision support approaches.
DOI: 10.6084/m9.figshare.11448213.v1
title: “We want to know where the line is”: comparing current planning for future sea-level rise with three core principles of robust decision support approaches

description: Handling uncertainties is a major challenge in climate change adaptation. A variety of robust decision support approaches that aim for better management of uncertainty have recently been emerging and are used in environmental planning. The present study examined to what extent existing processes of planning for future sea-level rise in Sweden utilised similar approaches. Three core principles of robust decision support approaches were identified and used as a tool for analyzing five cases of planning for future sea-level rise in companies and authorities at different levels in society. The results show that planning processes typically do not embrace uncertainties, do not use a bottom-up approach and do not specifically aim for robustness, which points to a discrepancy between current planning paradigms and the core principles of robust decision support approaches.
DOI: 10.6084/m9.figshare.11448102
title: Replication Data: Opening the Black Box: A Mixed-Methods Investigation of Social and Psychological Mechanisms Underlying Changes in Financial Behaviour

description: The replication files include the RCT dataset, Stata dofile for preparing the data, and R Code for the causal mediation analysis including sensitivity analyses
DOI: 10.6084/m9.figshare.11448042
title: Table S3. Identification of hub genes in the four strains analyzed in this work from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: <i>Cytohubba</i> results for individual strains, and list of the unique hubs genes found across strains including those located nearby a TE
DOI: 10.6084/m9.figshare.11448042.v1
title: Table S3. Identification of hub genes in the four strains analyzed in this work from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: <i>Cytohubba</i> results for individual strains, and list of the unique hubs genes found across strains including those located nearby a TE
DOI: 10.6084/m9.figshare.11448036
title: Table S4. Genotyping and genome distribution of TEs for each analyzed strain from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Presence/absence of the reference TE insertions and distribution of these TEs regarding nearby genes in the strains analyzed in this work. The expression level of the genes nearby candidate TEs are also given.
DOI: 10.6084/m9.figshare.11448033
title: Table S1. Differentially gene expression results from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Sequencing statistics for all the strains analyzed in this work, and expression values for all differentially expressed genes in each strain. Genes previously reported as oxidative stress responsive genes are also listed.
DOI: 10.6084/m9.figshare.11448036.v1
title: Table S4. Genotyping and genome distribution of TEs for each analyzed strain from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Presence/absence of the reference TE insertions and distribution of these TEs regarding nearby genes in the strains analyzed in this work. The expression level of the genes nearby candidate TEs are also given.
DOI: 10.6084/m9.figshare.11448030
title: Table S2. Gene ontology enrichment analysis from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Significant gene ontology clusters according to DAVID functional annotation tool for pairs of strains and for individual strains
DOI: 10.6084/m9.figshare.11448033.v1
title: Table S1. Differentially gene expression results from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Sequencing statistics for all the strains analyzed in this work, and expression values for all differentially expressed genes in each strain. Genes previously reported as oxidative stress responsive genes are also listed.
DOI: 10.6084/m9.figshare.11448027
title: Table S6. TE family expression analysis from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Differentially expressed TE families and their distribution regarding nearby differentially expressed genes. The analysis of differentially expressed TE families in response to DDT is also given.
DOI: 10.6084/m9.figshare.11448030.v1
title: Table S2. Gene ontology enrichment analysis from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Significant gene ontology clusters according to DAVID functional annotation tool for pairs of strains and for individual strains
DOI: 10.6084/m9.figshare.11448027.v1
title: Table S6. TE family expression analysis from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Differentially expressed TE families and their distribution regarding nearby differentially expressed genes. The analysis of differentially expressed TE families in response to DDT is also given.
DOI: 10.6084/m9.figshare.11448021
title: Table S5. ATAC-seq analysis from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Sequencing statistics and peak analysis for all the strains analyzed in this work.
DOI: 10.6084/m9.figshare.11448021.v1
title: Table S5. ATAC-seq analysis from Transposable elements contribute to the genomic response to insecticides in <i>Drosophila melanogaster</i>

description: Sequencing statistics and peak analysis for all the strains analyzed in this work.
DOI: 10.6084/m9.figshare.11447982
title: Table S1 from Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns

description: The top 10 binding KZNFs, their age as defined by Thomas & Schneider (2011) and the number of binding sites that overlap with both gene promoters and KAP1 binding sites (Imbeault et al., 2017).
DOI: 10.6084/m9.figshare.11447982.v1
title: Table S1 from Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns

description: The top 10 binding KZNFs, their age as defined by Thomas & Schneider (2011) and the number of binding sites that overlap with both gene promoters and KAP1 binding sites (Imbeault et al., 2017).
DOI: 10.6084/m9.figshare.11447655
title: The cost-effectiveness of guideline-driven use of drug-eluting stents: propensity-score matched analysis of a seven-year multicentre experience

description: <b>Background:</b> In routine clinical practice, the implantation of a drug-eluting stent (DES) versus a bare metal stent (BMS) for percutaneous coronary intervention (PCI) has been guided by criteria for appropriate use. The cost-effectiveness (CE) of adopting these guidelines, however, is not clear, and was investigated from the perspective of the Australian healthcare payer. <b>Methods and results:</b> Baseline and 12-month follow-up data of 12,710 PCI patients enrolled in the Melbourne Interventional Group (MIG) registry between 2004 and 2011 were analysed. Costs inputs were derived from a clinical costing database and published sources. Propensity-score-matching was performed for DES and BMS groups within sub-groups. Incremental cost-effectiveness ratios (ICERs) were evaluated for all patients, and sub-groups of patients with ‘0’, 1, 2, or ≥3 indications for a DES. The incremental cost per target vessel revascularization avoided for the overall population was $24,683, and for patients with 0, 1, and 2 indications for a DES was $44,635, $33,335, and $23,788, respectively. However, for those with &gt;3 indications, DES compared with BMS was associated with cost savings. At willingness to pay thresholds of $45,000–$75,000, the probability of cost-effectiveness of DES for the overall cohort was 71–91%, ‘0’ indications, 49–67%, 1 indication, 56–82%, 2 indications, 70–90%, and ≥3 indications, 97–99%. <b>Conclusions:</b> The cost-effectiveness of DES compared with BMS increased with increasing risk profile of patients from those who had 1, 2, to ≥3 indications for a DES. When compared with BMS, DES was least cost effective among patients with ‘0’ indications for a DES. Based on these results, selective use of DES implantation is supported. These findings may be useful for evidence-based clinical decision-making.
DOI: 10.6084/m9.figshare.11447724
title: Proteome database of Acinetobacter baumannii strain SDF

description: A Gram-negative bacterium lacking a flagellum, <i>Acinetobacter baumannii</i> is an opportunistic human pathogen of increasing concern. Specifically, the bacterium belongs to the ESKAPE family of pathogens known to exhibit multidrug resistance to many of the frontline antibiotics in use. Many mysteries remain hidden from view in this pathogenic bacterium, but one interesting line of research could be in deciphering the motility mode of this species. Specifically, lacking a flagellum might not negate motility for this bacterium, given the presence of Type IV pilli on the bacterial surface, which may endow this bacterial species the capability of colonizing new area of tissue during an infection cycle. Such modes of infection need attention as wound left untreated may develop into necrotizing fasciitis due to bacterial motility. This work sought to provide some fundamental proteomic information of <i>A. baumannii </i>strain SDF through parsing the UniProt proteome file of the organism. Analysis through an in-house MATLAB software yields a proteome database comprising protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence. Overall, the presented proteome database should find use in gaining an appreciation of the genetic repertoire of this emerging human pathogen with particular relevance to the use of genetic screen to detect molecular effectors that could serve as targets for drug development. <br><br>
DOI: 10.6084/m9.figshare.11447724.v1
title: Proteome database of Acinetobacter baumannii strain SDF

description: A Gram-negative bacterium lacking a flagellum, <i>Acinetobacter baumannii</i> is an opportunistic human pathogen of increasing concern. Specifically, the bacterium belongs to the ESKAPE family of pathogens known to exhibit multidrug resistance to many of the frontline antibiotics in use. Many mysteries remain hidden from view in this pathogenic bacterium, but one interesting line of research could be in deciphering the motility mode of this species. Specifically, lacking a flagellum might not negate motility for this bacterium, given the presence of Type IV pilli on the bacterial surface, which may endow this bacterial species the capability of colonizing new area of tissue during an infection cycle. Such modes of infection need attention as wound left untreated may develop into necrotizing fasciitis due to bacterial motility. This work sought to provide some fundamental proteomic information of <i>A. baumannii </i>strain SDF through parsing the UniProt proteome file of the organism. Analysis through an in-house MATLAB software yields a proteome database comprising protein name, amino acid sequence, number of residues, molecular weight and nucleotide sequence. Overall, the presented proteome database should find use in gaining an appreciation of the genetic repertoire of this emerging human pathogen with particular relevance to the use of genetic screen to detect molecular effectors that could serve as targets for drug development. <br><br>