cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6247049
title: Experience-dependent neuroplasticity of the developing hypothalamus: integrative epigenomic approaches

description: Augmented maternal care during the first postnatal week promotes life-long stress resilience and improved memory compared with the outcome of routine rearing conditions. Recent evidence suggests that this programming commences with altered synaptic connectivity of stress sensitive hypothalamic neurons. However, the epigenomic basis of the long-lived consequences is not well understood. Here, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to examine the effects of augmented maternal care on DNA cytosine methylation, gene expression, and miRNA expression. A total of 9,439 differentially methylated regions (DMRs) associated with augmented maternal care were identified in male offspring hypothalamus, as well as a modest but significant decrease in global DNA methylation. Differentially methylated and expressed genes were enriched for functions in neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation, as well as known stress response genes. Twenty prioritized genes were identified as highly relevant to the stress resiliency phenotype. This combined unbiased approach enabled the discovery of novel genes and gene pathways that advance our understanding of the epigenomic mechanisms underlying the effects of maternal care on the developing brain.
DOI: 10.6084/m9.figshare.6247049.v2
title: Experience-dependent neuroplasticity of the developing hypothalamus: integrative epigenomic approaches

description: Augmented maternal care during the first postnatal week promotes life-long stress resilience and improved memory compared with the outcome of routine rearing conditions. Recent evidence suggests that this programming commences with altered synaptic connectivity of stress sensitive hypothalamic neurons. However, the epigenomic basis of the long-lived consequences is not well understood. Here, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to examine the effects of augmented maternal care on DNA cytosine methylation, gene expression, and miRNA expression. A total of 9,439 differentially methylated regions (DMRs) associated with augmented maternal care were identified in male offspring hypothalamus, as well as a modest but significant decrease in global DNA methylation. Differentially methylated and expressed genes were enriched for functions in neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation, as well as known stress response genes. Twenty prioritized genes were identified as highly relevant to the stress resiliency phenotype. This combined unbiased approach enabled the discovery of novel genes and gene pathways that advance our understanding of the epigenomic mechanisms underlying the effects of maternal care on the developing brain.
DOI: 10.6084/m9.figshare.6247049.v1
title: Experience-dependent neuroplasticity of the developing hypothalamus: integrative epigenomic approaches

description: Augmented maternal care during the first postnatal week promotes life-long stress resilience and improved memory compared with the outcome of routine rearing conditions. Recent evidence suggests that this programming commences with altered synaptic connectivity of stress sensitive hypothalamic neurons. However, the epigenomic basis of the long-lived consequences is not well understood. Here, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to examine the effects of augmented maternal care on DNA cytosine methylation, gene expression, and miRNA expression. A total of 9,439 differentially methylated regions (DMRs) associated with augmented maternal care were identified in male offspring hypothalamus, as well as a modest but significant decrease in global DNA methylation. Differentially methylated and expressed genes were enriched for functions in neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation, as well as known stress response genes. Twenty prioritized genes were identified as highly relevant to the stress resiliency phenotype. This combined unbiased approach enabled the discovery of novel genes and gene pathways that advance our understanding of the epigenomic mechanisms underlying the effects of maternal care on the developing brain.
DOI: 10.17028/rd.lboro.6246878
title: Data about "Thriving at Work"

description: This is previously unpublished data including bi-variate correlations between Thriving at Work and other person/demographic and outcome variables. Scale reliabilities are also presented. The data is derived from a sample of 121 older (aged 55 years and over) workers from Bulgaria.
DOI: 10.17028/rd.lboro.6246878.v1
title: Data about "Thriving at Work"

description: This is previously unpublished data including bi-variate correlations between Thriving at Work and other person/demographic and outcome variables. Scale reliabilities are also presented. The data is derived from a sample of 121 older (aged 55 years and over) workers from Bulgaria.
DOI: 10.6084/m9.figshare.6246833
title: Revolutions data

description: The data are in long format. 295805 rows x 4 columns as a .csv file. The "dataset" column identifies which dataset it is (e.g., "pop" is pop music); the "year" column identies the year, the "variable" column identifies the variable (e.g., M_Topic1) and "value" is the value of the variable in that year, typically a mean (or a count).
DOI: 10.6084/m9.figshare.6246833.v2
title: Revolutions data

description: The data are in long format. 295805 rows x 4 columns as a .csv file. The "dataset" column identifies which dataset it is (e.g., "pop" is pop music); the "year" column identies the year, the "variable" column identifies the variable (e.g., M_Topic1) and "value" is the value of the variable in that year, typically a mean (or a count).
DOI: 10.6084/m9.figshare.6246641
title: Comparative genome analysis of Alkhumra hemorrhagic fever virus with Kyasanur forest disease and tick-borne encephalitis viruses by the <i>in silico</i> approach

description: Alkhumra hemorrhagic fever virus (AHFV), a relatively new member of the Flaviviruses, was discovered in Saudi Arabia 23 years ago. AHFV is classified in the tick-borne encephalitis virus serocomplex, along with the Kyasanur forest disease virus (KFDV) and tick-borne encephalitis virus (TBEV). Currently, very little is known about the pathologies of AHFV. In this study, using the available genome information of AHFV, KFDV and TBEV, we have predicted and compared the following aspects of these viruses: evolution, nucleotide and protein compositions, recombination, codon frequency, substitution rate, N- and O-glycosylation sites, signal peptide and cleavage site, transmembrane region, secondary structure of 5’ and 3’ UTRs and RNA-RNA interactions. Additionally, we have modeled the 3D protease and RNA-dependent RNA polymerase structures for AHFV, KFDV and TBEV. Recombination analysis showed no evidence of recombination in the AHFV genome with that of either KFDV or TBEV, although single break point analysis showed that nucleotide position 7399 (in the NS4B) is a breakpoint location. AHFV, KFDV and TBEV are very similar in terms of codon frequency, the number of transmembrane regions, properties of the polyprotein, RNA-RNA interaction sequences, NS3 protease and NS5 polymerase structures and 5’ UTR structure. Using genome sequences, we showed the similarities between these closely- related viruses on several different areas.
DOI: 10.6084/m9.figshare.6246641.v1
title: Comparative genome analysis of Alkhumra hemorrhagic fever virus with Kyasanur forest disease and tick-borne encephalitis viruses by the <i>in silico</i> approach

description: Alkhumra hemorrhagic fever virus (AHFV), a relatively new member of the Flaviviruses, was discovered in Saudi Arabia 23 years ago. AHFV is classified in the tick-borne encephalitis virus serocomplex, along with the Kyasanur forest disease virus (KFDV) and tick-borne encephalitis virus (TBEV). Currently, very little is known about the pathologies of AHFV. In this study, using the available genome information of AHFV, KFDV and TBEV, we have predicted and compared the following aspects of these viruses: evolution, nucleotide and protein compositions, recombination, codon frequency, substitution rate, N- and O-glycosylation sites, signal peptide and cleavage site, transmembrane region, secondary structure of 5’ and 3’ UTRs and RNA-RNA interactions. Additionally, we have modeled the 3D protease and RNA-dependent RNA polymerase structures for AHFV, KFDV and TBEV. Recombination analysis showed no evidence of recombination in the AHFV genome with that of either KFDV or TBEV, although single break point analysis showed that nucleotide position 7399 (in the NS4B) is a breakpoint location. AHFV, KFDV and TBEV are very similar in terms of codon frequency, the number of transmembrane regions, properties of the polyprotein, RNA-RNA interaction sequences, NS3 protease and NS5 polymerase structures and 5’ UTR structure. Using genome sequences, we showed the similarities between these closely- related viruses on several different areas.
DOI: 10.6084/m9.figshare.6246449
title: GOINS Gen Orient. Inv. Net. P. Falciparum

description: Abstract<br>The spatial distribution of genes in chromosomes seems not to be random. For instance, only 10% of genes are transcribed from bidirectional promoters in humans, and many more are organized into larger clusters. This raises intriguing questions previously asked by different authors. We would like to add a few more questions in this context, related to gene orientation inversions. Does gene orientation (inversion) follow a random pattern? Is it relevant to biological activity somehow? We define a new kind of network coined as the gene orientation inversion network (GOIN). GOIN's complex network encodes short- and long-range patterns of inversion of the orientation of pairs of gene in the chromosome. We selected Plasmodium falciparum as a case of study due to the high relevance of this parasite to public health (causal agent of malaria). We constructed here for the first time all of the GOINs for the genome of this parasite. These networks have an average of 383 nodes (genes in one chromosome) and 1314 links (pairs of gene with inverse orientation). We calculated node centralities and other parameters of these networks. These numerical parameters were used to study different properties of gene inversion patterns, for example, distribution, local communities, similarity to Erdös-Rényi random networks, randomness, and so on. We find clues that seem to indicate that gene orientation inversion does not follow a random pattern. We noted that some gene communities in the GOINs tend to group genes encoding for RIFIN-related proteins in the proteome of the parasite. RIFIN-like proteins are a second family of clonally variant proteins expressed on the surface of red cells infected with Plasmodium falciparum. Consequently, we used these centralities as input of machine learning (ML) models to predict the RIFIN-like activity of 5365 proteins in the proteome of Plasmodium sp. The best linear ML model found discriminates RIFIN-like from other proteins with sensitivity and specificity 70-80% in training and external validation series. All of these results may point to a possible biological relevance of gene orientation inversion not directly dependent on genetic sequence information. This work opens the gate to the use of GOINs as a tool for the study of the structure of chromosomes and the study of protein function in proteome research.<br>J Proteome Res. 2018 Mar 2;17(3):1258-1268. doi: 10.1021/acs.jproteome.7b00861. Epub 2018 Feb 5.Chromosome Gene Orientation Inversion Networks (GOINs) of Plasmodium Proteome.Quevedo-Tumailli VF1,2, Ortega-Tenezaca B1,2,3, González-Díaz H4,5.
DOI: 10.6084/m9.figshare.6246449.v1
title: GOINS Gen Orient. Inv. Net. P. Falciparum

description: Abstract<br>The spatial distribution of genes in chromosomes seems not to be random. For instance, only 10% of genes are transcribed from bidirectional promoters in humans, and many more are organized into larger clusters. This raises intriguing questions previously asked by different authors. We would like to add a few more questions in this context, related to gene orientation inversions. Does gene orientation (inversion) follow a random pattern? Is it relevant to biological activity somehow? We define a new kind of network coined as the gene orientation inversion network (GOIN). GOIN's complex network encodes short- and long-range patterns of inversion of the orientation of pairs of gene in the chromosome. We selected Plasmodium falciparum as a case of study due to the high relevance of this parasite to public health (causal agent of malaria). We constructed here for the first time all of the GOINs for the genome of this parasite. These networks have an average of 383 nodes (genes in one chromosome) and 1314 links (pairs of gene with inverse orientation). We calculated node centralities and other parameters of these networks. These numerical parameters were used to study different properties of gene inversion patterns, for example, distribution, local communities, similarity to Erdös-Rényi random networks, randomness, and so on. We find clues that seem to indicate that gene orientation inversion does not follow a random pattern. We noted that some gene communities in the GOINs tend to group genes encoding for RIFIN-related proteins in the proteome of the parasite. RIFIN-like proteins are a second family of clonally variant proteins expressed on the surface of red cells infected with Plasmodium falciparum. Consequently, we used these centralities as input of machine learning (ML) models to predict the RIFIN-like activity of 5365 proteins in the proteome of Plasmodium sp. The best linear ML model found discriminates RIFIN-like from other proteins with sensitivity and specificity 70-80% in training and external validation series. All of these results may point to a possible biological relevance of gene orientation inversion not directly dependent on genetic sequence information. This work opens the gate to the use of GOINs as a tool for the study of the structure of chromosomes and the study of protein function in proteome research.<br>J Proteome Res. 2018 Mar 2;17(3):1258-1268. doi: 10.1021/acs.jproteome.7b00861. Epub 2018 Feb 5.Chromosome Gene Orientation Inversion Networks (GOINs) of Plasmodium Proteome.Quevedo-Tumailli VF1,2, Ortega-Tenezaca B1,2,3, González-Díaz H4,5.
DOI: 10.6084/m9.figshare.6246419
title: The data set of antibacterial effects of moth-eye film in practical settings.

description: This is the underlying data set to describe the results on "Antibacterial effects of nanoimprinted moth-eye film in practical settings".
DOI: 10.6084/m9.figshare.6246419.v1
title: The data set of antibacterial effects of moth-eye film in practical settings.

description: This is the underlying data set to describe the results on "Antibacterial effects of nanoimprinted moth-eye film in practical settings".
DOI: 10.6084/m9.figshare.6244379
title: Inflammation in the pleural cavity following injection of multi-walled carbon nanotubes is dependent on their characteristics and the presence of IL-1 genes

description: Upon inhalation, multi-walled carbon nanotubes (MWCNTs) may reach the subpleura and pleural spaces, and induce pleural inflammation and/or mesothelioma in humans. However, the mechanisms of MWCNT-induced pathology after direct intrapleural injections are still only partly elucidated. In particular, a role of the proinflammatory interleukin-1 (IL-1) cytokines in pleural inflammation has so far not been published. We examined the MWCNT-induced pleural inflammation, gene expression abnormalities, and the modifying role of IL-1α and β cytokines following intrapleural injection of two types of MWCNTs (CNT-1 and CNT-2) compared with crocidolite asbestos in IL-1 wild-type (WT) and IL-1α/β KO (IL1-KO) mice. Histopathological examination of the pleura 28 days post-exposure revealed mesothelial cell hyperplasia, leukocyte infiltration, and fibrosis occurring in the CNT-1 (Mitsui-7)-exposed group. The pleura of these mice also showed the greatest changes in mRNA and miRNA expression levels, closely followed by CNT-2. In addition, the CNT-1-exposed group also presented the greatest infiltrations of leukocytes and proliferation of fibrous tissue. WT mice were more prone to development of sustained inflammation and fibrosis than IL1-KO mice. Prominent differences in genetic and epigenetic changes were also observed between the two genotypes. In conclusion, the fibrotic response to MWCNTs in the pleura depends on the particles’ physico-chemical properties and on the presence or absence of the IL-1 genes. Furthermore, we found that CNT-1 was the most potent inducer of inflammatory responses, followed by CNT-2 and crocidolite asbestos.
DOI: 10.6084/m9.figshare.6244379.v1
title: Inflammation in the pleural cavity following injection of multi-walled carbon nanotubes is dependent on their characteristics and the presence of IL-1 genes

description: Upon inhalation, multi-walled carbon nanotubes (MWCNTs) may reach the subpleura and pleural spaces, and induce pleural inflammation and/or mesothelioma in humans. However, the mechanisms of MWCNT-induced pathology after direct intrapleural injections are still only partly elucidated. In particular, a role of the proinflammatory interleukin-1 (IL-1) cytokines in pleural inflammation has so far not been published. We examined the MWCNT-induced pleural inflammation, gene expression abnormalities, and the modifying role of IL-1α and β cytokines following intrapleural injection of two types of MWCNTs (CNT-1 and CNT-2) compared with crocidolite asbestos in IL-1 wild-type (WT) and IL-1α/β KO (IL1-KO) mice. Histopathological examination of the pleura 28 days post-exposure revealed mesothelial cell hyperplasia, leukocyte infiltration, and fibrosis occurring in the CNT-1 (Mitsui-7)-exposed group. The pleura of these mice also showed the greatest changes in mRNA and miRNA expression levels, closely followed by CNT-2. In addition, the CNT-1-exposed group also presented the greatest infiltrations of leukocytes and proliferation of fibrous tissue. WT mice were more prone to development of sustained inflammation and fibrosis than IL1-KO mice. Prominent differences in genetic and epigenetic changes were also observed between the two genotypes. In conclusion, the fibrotic response to MWCNTs in the pleura depends on the particles’ physico-chemical properties and on the presence or absence of the IL-1 genes. Furthermore, we found that CNT-1 was the most potent inducer of inflammatory responses, followed by CNT-2 and crocidolite asbestos.
DOI: 10.6084/m9.figshare.6244346
title: Hawaii FEF dataset and analysis

description: Analysis of fungal ITS1 sequence data from the interior of leaves from native Hawaiian plants. <br>
DOI: 10.6084/m9.figshare.6244058
title: Accuracy of TcCO2 monitoring meta-analysis

description: This is the data and a code for an R Markdown document for analyses undertaken in a systematic review and meta-analysis of the agreement between transcutaneous and arterial measurements of CO2.
DOI: 10.6084/m9.figshare.6244058.v2
title: Accuracy of TcCO2 monitoring meta-analysis

description: This is the data and a code for an R Markdown document for analyses undertaken in a systematic review and meta-analysis of the agreement between transcutaneous and arterial measurements of CO2.
DOI: 10.6084/m9.figshare.6243986
title: MOESM3 of ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells

description: Additional file 3: Table S3. Description of phenotype-nucleotide polymorphisms (SNPs) predicted to influence transcription of the human ICR gene.
DOI: 10.6084/m9.figshare.6243986.v1
title: MOESM3 of ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells

description: Additional file 3: Table S3. Description of phenotype-nucleotide polymorphisms (SNPs) predicted to influence transcription of the human ICR gene.
DOI: 10.6084/m9.figshare.6243980
title: Additional file 2: of Muver, a computational framework for accurately calling accumulated mutations

description: Results Files. Zip file containing VCF and TXT formatted muver results for all yeast data sets analyzed. (ZIP 10697Â kb)
DOI: 10.6084/m9.figshare.6243980.v1
title: Additional file 2: of Muver, a computational framework for accurately calling accumulated mutations

description: Results Files. Zip file containing VCF and TXT formatted muver results for all yeast data sets analyzed. (ZIP 10697Â kb)
DOI: 10.6084/m9.figshare.6243974
title: MOESM2 of ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells

description: Additional file 2: Table S2. Predicted transcription factor binding sites within genome evolutionary rate profiling (GERP)-constrained elements.
DOI: 10.6084/m9.figshare.6243974.v1
title: MOESM2 of ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells

description: Additional file 2: Table S2. Predicted transcription factor binding sites within genome evolutionary rate profiling (GERP)-constrained elements.
DOI: 10.6084/m9.figshare.6243956
title: MOESM1 of ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells

description: Additional file 1: Table S1. Sources for eutherian genomes used in genome evolutionary rate profiling (GERP) and chromosomal locations of GERP-constrained elements.
DOI: 10.6084/m9.figshare.6243956.v1
title: MOESM1 of ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells

description: Additional file 1: Table S1. Sources for eutherian genomes used in genome evolutionary rate profiling (GERP) and chromosomal locations of GERP-constrained elements.
DOI: 10.6084/m9.figshare.6243908
title: Additional file 1: of Cost implications of PSA screening differ by age

description: Cost model used for our calculations and a generalizable model for other healthcare systems. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6243908.v1
title: Additional file 1: of Cost implications of PSA screening differ by age

description: Cost model used for our calculations and a generalizable model for other healthcare systems. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6243887
title: Additional file 2: of Profiling microbial strains in urban environments using metagenomic sequencing data

description: Table S1. MetaPhlAn2 output table on the whole MetaSub dataset. Values represent the relative abundances detected for each sample (in the columns). (CSV 16816Â kb)
DOI: 10.6084/m9.figshare.6243887.v1
title: Additional file 2: of Profiling microbial strains in urban environments using metagenomic sequencing data

description: Table S1. MetaPhlAn2 output table on the whole MetaSub dataset. Values represent the relative abundances detected for each sample (in the columns). (CSV 16816Â kb)
DOI: 10.6084/m9.figshare.6243881
title: MOESM1 of Cryopreservation without vitrification suitable for large scale cryopreservation of orchid seeds

description: Additional file 1. Raw data.
DOI: 10.6084/m9.figshare.6243881.v1
title: MOESM1 of Cryopreservation without vitrification suitable for large scale cryopreservation of orchid seeds

description: Additional file 1. Raw data.
DOI: 10.6084/m9.figshare.6243662
title: Additional file 3: of Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

description: A complete table of the enrichment of ORCEL genes. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.6243662.v1
title: Additional file 3: of Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

description: A complete table of the enrichment of ORCEL genes. (XLSX 90 kb)