cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20510041.v1
title: Polymethylation scores for prenatal maternal smoke exposure persist until age 15 and are detected in saliva in the Fragile Families and Child Wellbeing cohort

description: Prenatal maternal smoking is associated with low birthweight, neurological disorders, and asthma in exposed children. DNA methylation signatures can function as biomarkers of prenatal smoke exposure. However, the robustness of DNA methylation signatures across child ages, genetic ancestry groups, or tissues is not clear. Using coefficients from a meta-analysis of prenatal smoke exposure and DNA methylation in newborn cord blood, we created polymethylation scores of saliva DNA methylation from children at ages 9 and 15 in the Fragile Families and Child Wellbeing study. In the full sample at age 9 (n = 753), prenatal smoke exposure was associated with a 0.51 (95%CI: 0.35, 0.66) standard deviation higher polymethylation score. The direction and magnitude of the association was consistent in European and African genetic ancestry samples. In the full sample at age 15 (n = 747), prenatal smoke exposure was associated with a 0.48 (95%CI: 0.32, 0.63) standard deviation higher polymethylation score, and the association was attenuated among the European and Admixed–Latin genetic ancestry samples. The polymethylation score classified prenatal smoke exposure accurately (AUC age 9 = 0.77, age 15 = 0.76). Including the polymethylation score increased the AUC of base model covariates by 5 (95% CI: (2.1, 7.2)) percentage points, while including a single candidate site in the <i>AHRR</i> gene did not (<i>P</i>-value = 0.19). Polymethylation scores for prenatal smoking were portable across genetic ancestries and more accurate than an individual DNA methylation site. Polymethylation scores from saliva samples could serve as robust and practical biomarkers of prenatal smoke exposure.
DOI: 10.6084/m9.figshare.21081667
title: DNA hypermethylation of <i>Kiss1r</i> promoter and reduction of hepatic Kiss1r in female rats with type 2 diabetes

description: Kisspeptin, produced from the brain and peripheral tissues, may constitute an important link in metabolic regulation in response to external cues, such as diet. The kisspeptin system is well described in the brain. However, its function and regulation in the peripheral tissues, especially in relation to metabolic disease and sex differences, remain to be elucidated. As <i>Kiss1</i> and <i>Kiss1r</i>, encoding for kisspeptin and kisspeptin receptors, respectively, are altered by overnutrition/fasting and regulated by DNA methylation during puberty and cancer, epigenetic mechanisms in metabolic disorders are highly probable. In the present study, we experimentally induced type 2 diabetes mellitus (DM2) in female Wistar rats using high-fat diet/streptozocin. We analysed expression and DNA methylation of <i>Kiss1</i> and <i>Kiss1r</i> in the peripheral tissues, using quantitative-reverse-transcription PCR (qRT-PCR) and pyrosequencing. We discovered differential expression of <i>Kiss1</i> and <i>Kiss1r</i> in peripheral organs in DM2 females, as compared with healthy controls, and the profile differed from patterns reported earlier in males. DM2 in females was linked to the increased <i>Kiss1</i> mRNA in the liver and increased <i>Kiss1r</i> mRNA in the liver and adipose tissue. However, <i>Kiss1r</i> promoter was hypermethylated in the liver, suggesting gene silencing. Indeed, the increase in DNA methylation of <i>Kiss1r</i> promoter was accompanied by a reduction in Kiss1r protein, implying epigenetic or translational gene repression. Our results deliver novel evidence for tissue-specific differences in <i>Kiss1</i> and <i>Kiss1r</i> expression in peripheral organs in DM2 females and suggest DNA methylation as a player in regulation of the hepatic kisspeptin system in DM2.
DOI: 10.6084/m9.figshare.21081667.v1
title: DNA hypermethylation of <i>Kiss1r</i> promoter and reduction of hepatic Kiss1r in female rats with type 2 diabetes

description: Kisspeptin, produced from the brain and peripheral tissues, may constitute an important link in metabolic regulation in response to external cues, such as diet. The kisspeptin system is well described in the brain. However, its function and regulation in the peripheral tissues, especially in relation to metabolic disease and sex differences, remain to be elucidated. As <i>Kiss1</i> and <i>Kiss1r</i>, encoding for kisspeptin and kisspeptin receptors, respectively, are altered by overnutrition/fasting and regulated by DNA methylation during puberty and cancer, epigenetic mechanisms in metabolic disorders are highly probable. In the present study, we experimentally induced type 2 diabetes mellitus (DM2) in female Wistar rats using high-fat diet/streptozocin. We analysed expression and DNA methylation of <i>Kiss1</i> and <i>Kiss1r</i> in the peripheral tissues, using quantitative-reverse-transcription PCR (qRT-PCR) and pyrosequencing. We discovered differential expression of <i>Kiss1</i> and <i>Kiss1r</i> in peripheral organs in DM2 females, as compared with healthy controls, and the profile differed from patterns reported earlier in males. DM2 in females was linked to the increased <i>Kiss1</i> mRNA in the liver and increased <i>Kiss1r</i> mRNA in the liver and adipose tissue. However, <i>Kiss1r</i> promoter was hypermethylated in the liver, suggesting gene silencing. Indeed, the increase in DNA methylation of <i>Kiss1r</i> promoter was accompanied by a reduction in Kiss1r protein, implying epigenetic or translational gene repression. Our results deliver novel evidence for tissue-specific differences in <i>Kiss1</i> and <i>Kiss1r</i> expression in peripheral organs in DM2 females and suggest DNA methylation as a player in regulation of the hepatic kisspeptin system in DM2.
DOI: 10.6084/m9.figshare.20343467
title: Whole human genome 5’-mC methylation analysis using long read nanopore sequencing

description: Methylation microarray and bisulphite sequencing are often used to study 5’-methylcytosine (5’-mC) modification of CpG dinucleotides in the human genome. Although both technologies produce trustworthy results, the evaluation of the methylation status of CpG sites suffers from the potential side effects of DNA modification by bisulphite and/or the ambiguity of mapping short reads in repetitive and highly homologous genomic regions, respectively. Nanopore sequencing is an attractive alternative for the study of 5’-mC since it allows sequencing of native DNA molecules, whereas the long reads produced by this technology help to increase the resolution of those genomic regions. In this work, we show that nanopore sequencing with 10X coverage depth, using DNA from a human cell line, produces 5’-mC methylation frequencies consistent with those obtained by 450k microarray, digital restriction enzyme analysis of methylation, and reduced representation bisulphite sequencing. High correlation between methylation frequencies obtained by nanopore sequencing and the other methodologies was also noticeable in either low or high GC content regions, including CpG islands and transcription start sites. We also showed that a minimum of five reads per CpG yields strong correlations (&gt;0.89) in replicate nanopore sequencing runs and an almost uniform linearity of the methylation frequency variation between zero and one. Furthermore, nanopore sequencing was able to correctly display methylation frequency patterns based on genomic annotations of CpG regions. These results demonstrate that nanopore sequencing is a fast, robust, and reliable approach to the study of 5’-mC in the human genome with low coverage depth.
DOI: 10.6084/m9.figshare.20343467.v1
title: Whole human genome 5’-mC methylation analysis using long read nanopore sequencing

description: Methylation microarray and bisulphite sequencing are often used to study 5’-methylcytosine (5’-mC) modification of CpG dinucleotides in the human genome. Although both technologies produce trustworthy results, the evaluation of the methylation status of CpG sites suffers from the potential side effects of DNA modification by bisulphite and/or the ambiguity of mapping short reads in repetitive and highly homologous genomic regions, respectively. Nanopore sequencing is an attractive alternative for the study of 5’-mC since it allows sequencing of native DNA molecules, whereas the long reads produced by this technology help to increase the resolution of those genomic regions. In this work, we show that nanopore sequencing with 10X coverage depth, using DNA from a human cell line, produces 5’-mC methylation frequencies consistent with those obtained by 450k microarray, digital restriction enzyme analysis of methylation, and reduced representation bisulphite sequencing. High correlation between methylation frequencies obtained by nanopore sequencing and the other methodologies was also noticeable in either low or high GC content regions, including CpG islands and transcription start sites. We also showed that a minimum of five reads per CpG yields strong correlations (&gt;0.89) in replicate nanopore sequencing runs and an almost uniform linearity of the methylation frequency variation between zero and one. Furthermore, nanopore sequencing was able to correctly display methylation frequency patterns based on genomic annotations of CpG regions. These results demonstrate that nanopore sequencing is a fast, robust, and reliable approach to the study of 5’-mC in the human genome with low coverage depth.
DOI: 10.5281/zenodo.10849851
title: ERK signaling of invasive cells in mammary organoid

description: Live-cell imaging of HMT3522 T4-2 invasive mammary epithelial cell line, with fluorescent ERKTR cell signaling reporter and nuclear reporter, to extract trajectory pairs of ERKTR to nuclear cross-correlation as a measure of ERK signaling activity. Datasets X and Y capture ERK signaling state at t and t+1 respectively, while test_obs contains test trajectories and inds_test_starts contains the indices of starting times of test trajectories.
DOI: 10.5281/zenodo.10849852
title: ERK signaling of invasive cells in mammary organoid

description: Live-cell imaging of HMT3522 T4-2 invasive mammary epithelial cell line, with fluorescent ERKTR cell signaling reporter and nuclear reporter, to extract trajectory pairs of ERKTR to nuclear cross-correlation as a measure of ERK signaling activity. Datasets X and Y capture ERK signaling state at t and t+1 respectively, while test_obs contains test trajectories and inds_test_starts contains the indices of starting times of test trajectories.
DOI: 10.6084/m9.figshare.23849370
title: TCGA survival genomic data and pathway information

description: TCGA survival genomic data (LUAD, KIRP and HNSCC) and pathway information (GO-CC, KEGG).
DOI: 10.6084/m9.figshare.23849370.v2
title: TCGA survival genomic data and pathway information

description: TCGA survival genomic data (LUAD, ESCA and HNSCC) and pathway information (GO-CC, KEGG).
DOI: 10.5281/zenodo.10849920
title: Historia del Rey Transparente - AmadissigloXX

description: AmadissigloXX. Base de datos de las reescrituras modernas de los libros de caballerías y del Don Quijote (dir. Elisabetta Sarmati)

Ficha de: Rosa Montero, "Historia del Rey Transparente", 2005.

Se ofrecen dos ficheros:



formato JSON: contiene los metadatos asociados a la obra (autor, fuente, año de publicación, idioma, sinopsis del argumento, anotaciones, fuentes caballerescas, bibliografía crítica, enlaces externos)

formato XML: contiene la base de datos completa con indicación de la versión.
DOI: 10.5281/zenodo.10849921
title: Historia del Rey Transparente - AmadissigloXX

description: AmadissigloXX. Base de datos de las reescrituras modernas de los libros de caballerías y del Don Quijote (dir. Elisabetta Sarmati)

Ficha de: Rosa Montero, "Historia del Rey Transparente", 2005.

Se ofrecen dos ficheros:



formato JSON: contiene los metadatos asociados a la obra (autor, fuente, año de publicación, idioma, sinopsis del argumento, anotaciones, fuentes caballerescas, bibliografía crítica, enlaces externos)

formato XML: contiene la base de datos completa con indicación de la versión.
DOI: 10.5281/zenodo.10849945
title: El rapto del Santo Grial - AmadissigloXX

description: AmadissigloXX. Base de datos de las reescrituras modernas de los libros de caballerías y del Don Quijote (dir. Elisabetta Sarmati)

Ficha de: Paloma Díaz-Mas, "El rapto del Santo Grial", 1984.

Se ofrecen dos ficheros:



formato JSON: contiene los metadatos asociados a la obra (autor, fuente, año de publicación, idioma, sinopsis del argumento, anotaciones, fuentes caballerescas, bibliografía crítica, enlaces externos)

formato XML: contiene la base de datos completa con indicación de la versión.
DOI: 10.5281/zenodo.10849946
title: El rapto del Santo Grial - AmadissigloXX

description: AmadissigloXX. Base de datos de las reescrituras modernas de los libros de caballerías y del Don Quijote (dir. Elisabetta Sarmati)

Ficha de: Paloma Díaz-Mas, "El rapto del Santo Grial", 1984.

Se ofrecen dos ficheros:



formato JSON: contiene los metadatos asociados a la obra (autor, fuente, año de publicación, idioma, sinopsis del argumento, anotaciones, fuentes caballerescas, bibliografía crítica, enlaces externos)

formato XML: contiene la base de datos completa con indicación de la versión.
DOI: 10.5281/zenodo.10835760
title: NovaScope - Minimal Test Run Dataset

description: This is a small (1.14GB) test run dataset consisting of a subset of the (shallow) full liver section data published with the NovaScope protocol. This dataset is meant to be used to test the sanity of the pipeline, without necessarily offering a biologically meaningful interpretation. 

The dataset includes input 1st-seq and 2nd-seq data, along with the spatial barcode layout file. It does not contain histological images.
DOI: 10.5281/zenodo.10835761
title: NovaScope - Minimal Test Run Dataset

description: This is a small (1.14GB) test run dataset consisting of a subset of the (shallow) full liver section data published with the NovaScope protocol. This dataset is meant to be used to test the sanity of the pipeline, without necessarily offering a biologically meaningful interpretation. 

The dataset includes input 1st-seq and 2nd-seq data, along with the spatial barcode layout file. It does not contain histological images.
DOI: 10.5255/ukda-sn-857018
title: Metadata for Automating Universal Credit, 2022-2023

description: Automating Universal Credit studies the automated and digital aspects of Universal Credit (UC), a social security benefit in the UK. Recipients mainly interact with UC staff through an online account, and their monthly entitlement is calculated by an automated, means-testing system that factors their personal circumstances and monthly income if they work. The study used qualitative longitudinal methods, which allowed us to understand how UC claimants experience UC in near real-time, including the systems' unexpected behaviours and errors. The study has achieved two main high-level findings. First, we found that Universal Credit creates temporal mandates by applying a fixed, monthly assessment period of earnings for working claimants. We developed the concept of temporal punitiveness to describe how this monthly period creates problems for claimants who are paid their wages on a weekly/bi-weekly basis; due to the rules of calculation within the system, this misalignment may lead to the loss of entitlement. Likewise, parents have a very narrow timeframe to submit for childcare reimbursement; if parents do not submit within certain parameters, they may not be reimbursed. Second, we argue that administrative burdens may originate at the technical layer that citizens interact with to receive a service. To evidence this argument, we identify how the mechanism for reporting earnings data to UC creates administrative burdens for working UC claimants: we found that several claimants' earnings data reported to UC for the automatic calculation was wrong and thus, claimants needed to start a dispute process with the DWP. A FOI request we submitted to the DWP revealed that this happens to 5-6% of claimants each year. UC’s automated tools function at times as gatekeepers to social security entitlements, raising concerns about the current design of UC as a form of social security.
DOI: 10.60895/redata/hphduj
title: Alignment of several two dinucleotide binding domain flavoproteins

description: Alignment of the sequences of human glutathione reductase, human high-molecular weight thioredoxin reductase, human dihydrolipoamide dehydrogenase, trypanothione reductase from Trypanosoma cruzi, mercuric ion reductase from Pseudomonas aeruginosa, mycothione reductase from Mycobacterium tuberculosis, hypothiocyanous acid reductase from Streptococcus pneumoniae, glutathione amide reductase from Marichromatium gracile, doluble pyridine dinucleotide transhydrogenase from Escherichia coli, thioredoxin glutathione reductase from Schistosoma mansoni, low-molecular-weight thioredoxin reductase from E. coli, alkyl hydroperoxide reductase subunit F from E. coli, Bacillithiol disulfide reductase from Staphylococcus aureus, NADH peroxidase from Enterococcus faecalis, nNADH oxidase from Levilactobacillus brevis, NADH-dependent persulfide reductase from Archaeoglobus fulgidus, coenzyme A disulfide reductase from S. aureus, 2-ketopropyl-coenzyme M reductase/carboxylase from Xanthobacter autotrophicus, human apoptosis inducin factor 1, biphenyl dioxygenase subunit A from Acidovorax sp., rubredoxin reductase from P. aeruginosa, monodehydroascorbate reductase from Deschampsia antarctica, putidaredoxin reductase from P. putida, toluene dioxygenase subunit A from P. putida and 2,4-dienoyl-CoA reductase from E. coli.
DOI: 10.60895/redata/9ylqfe
title: Classical molecular dynamics simulations of human glutathione reductase complexed with NADPH and FAD

description: AMBER topologies, coordinates, input files and output files of MD simulations of the GR:FAD:NADPH complex (homodimeric form) considering Lys-66 in its neutral form and in its protonated form
DOI: 10.5281/zenodo.10840695
title: NovaScope - Shallow Liver Section Dataset
DOI: 10.5281/zenodo.10840696
title: NovaScope - Shallow Liver Section Dataset
DOI: 10.18112/openneuro.ds005040.v1.0.0
title: Political Moralization (PMM)
DOI: 10.6084/m9.figshare.21261238
title: Glutathione imparts stress tolerance against <i>Alternaria brassicicola</i> infection via miRNA mediated gene regulation

description: Glutathione (GSH) is well known to play a crucial role in imparting resistance against various pathogen invasions. Nevertheless, the role of GSH in regulating miRNA-mediated defense response is yet to be explored. To decipher the GSH-mediated regulation of miRNA expression during necrotrophic infection in <i>Arabidopsis thaliana</i>, wild-type Col-0 and <i>AtECS1</i>, the transgenic line exhibiting enhanced GSH content, were infected with necrotrophic pathogen <i>Alternaria brassicicola. AtECS1</i> plants exhibited enhanced resistance as compared to wild-type. MiRNA next-generation sequencing (NGS) was performed to compare the miRNA expression in Col-0 and <i>AtECS</i>1 leaves. Under control condition, differentially expressed 96 known miRNAs and 17 novel miRNAs viz. ath-miR8167f, ath-miR1886.3, ath-miR3932b-5p, etc. were identified. However, under infected condition, 73 known and 43 novel differentially expressed miRNAs viz. ath-miR5652, ath-miR160b, ath-miR865-5p, etc. were identified. Functional annotation and enrichment analysis revealed that several miRNAs that target defense-related genes like leucine-rich repeat protein kinase, MYB transcription factors, TCP8, etc. were down regulated in the <i>AtECS1</i> line, which, in turn, relieves the repression of their target gene expression, leading to resistance against infection. Together, the present investigation suggests that GSH plays a decisive role in modulating the miRNA-mediated regulation of defense-related genes during pathogen invasion.
DOI: 10.6084/m9.figshare.21261238.v1
title: Glutathione imparts stress tolerance against <i>Alternaria brassicicola</i> infection via miRNA mediated gene regulation

description: Glutathione (GSH) is well known to play a crucial role in imparting resistance against various pathogen invasions. Nevertheless, the role of GSH in regulating miRNA-mediated defense response is yet to be explored. To decipher the GSH-mediated regulation of miRNA expression during necrotrophic infection in <i>Arabidopsis thaliana</i>, wild-type Col-0 and <i>AtECS1</i>, the transgenic line exhibiting enhanced GSH content, were infected with necrotrophic pathogen <i>Alternaria brassicicola. AtECS1</i> plants exhibited enhanced resistance as compared to wild-type. MiRNA next-generation sequencing (NGS) was performed to compare the miRNA expression in Col-0 and <i>AtECS</i>1 leaves. Under control condition, differentially expressed 96 known miRNAs and 17 novel miRNAs viz. ath-miR8167f, ath-miR1886.3, ath-miR3932b-5p, etc. were identified. However, under infected condition, 73 known and 43 novel differentially expressed miRNAs viz. ath-miR5652, ath-miR160b, ath-miR865-5p, etc. were identified. Functional annotation and enrichment analysis revealed that several miRNAs that target defense-related genes like leucine-rich repeat protein kinase, MYB transcription factors, TCP8, etc. were down regulated in the <i>AtECS1</i> line, which, in turn, relieves the repression of their target gene expression, leading to resistance against infection. Together, the present investigation suggests that GSH plays a decisive role in modulating the miRNA-mediated regulation of defense-related genes during pathogen invasion.
DOI: 10.6084/m9.figshare.20117448.v1
title: Genome-wide identification and expression analysis of the NAC transcription factor family in <i>Saccharum spontaneum</i> under different stresses

description: The <i>NAC</i> (<i>NAM, ATAF1/2</i>, and <i>CUC2</i>) transcription factor family is one of the largest families unique to plants and is involved in plant growth and development, organs, morphogenesis, and stress responses. The <i>NAC</i> family has been identified in many plants. As the main source of resistance genes for sugarcane breeding, the <i>NAC</i> gene family in the wild species <i>Saccharum spontaneum</i> has not been systematically studied. In this study, 115 <i>SsNAC</i> genes were identified in the <i>S. spontaneum</i> genome, and these genes were heterogeneously distributed on 25 chromosomes. Phylogenetic analysis divided the <i>SsNAC</i> family members into 18 subgroups, and the gene structure and conserved motif analysis further supported the phylogenetic classification. Four groups of tandemly duplicated genes and nine pairs of segmentally duplicated genes were detected. The <i>SsNAC</i> gene has different expression patterns at different developmental stages of stems and leaves. Further qRT–PCR analysis showed that drought, low-temperature, salinity, pathogenic fungi, and other stresses as well as abscisic acid (ABA) and methyl jasmonate (MeJA) treatments significantly induced the expression of 12 <i>SsNAC</i> genes, indicating that these genes may play a key role in the resistance of <i>S. spontaneum</i> to biotic and abiotic stresses. In summary, the results from this study provide comprehensive information on the <i>NAC</i> transcription factor family, providing a reference for further functional studies of the <i>SsNAC</i> gene.