cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16419226.v2
title: Serum activity of matrix metalloproteinase-2 and -9 is increased in chronic post-stroke individuals: a cross-sectional exploratory study

description: High concentrations of matrix metalloproteinase-2 (MMP-2) and −9 (MMP-9) are associated with inflammation early after stroke. In chronic stages, the elevation of some cytokines is related to the presence of co-morbid conditions in these individuals. In addition to this, some characteristics such as sensorimotor impairment, atrophy, and sedentary lifestyle predispose the system to an inflammatory response. To quantify MMP-2 and −9 serum activity in chronic post-stroke individuals and correlate it with variables of physical activity level, body composition, functional and walking capacity, and with inflammatory biomarkers. Additionally, gelatinase activity was characterized according to motor impairment. Fourteen patients with stroke onset &gt;6 months and seven healthy individuals were enrolled in this study. The clinical assessment included: body composition, measure by bioelectrical impedance analyzer; Fugl-Meyer Motor Assessment Scale; six-minute and ten-meter walk tests, and physical activity level assessed by the StepWatch® Activity Monitor. Blood samples were collected from antecubital vein and serum MMP-2 and −9 activity was analyzed using gelatin Zymography, and the TNFα, IL-6, IL-1β, IL-10 biomarkers using ELISA kits. Chronic post-stroke individuals presented an increased activity of MMP-2 and −9 compared to healthy individuals. Positive correlations with time and steps in low cadence and negative ones with medium cadence and peak activity index were observed. According to the motor impairment, the MMP-2 activity was increased in the mild-moderate group compared to the control group. Increased gelatinases in chronic post-stroke individuals could describe an inflammation process related to the limited capacity of walking in high intensities.
DOI: 10.7910/dvn/r9uhvj
title: Replication Data for: State of ex situ conservation of landrace groups of 25 major crops

description: Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been compre- hensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on aver- age, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation
DOI: 10.6084/m9.figshare.20281272
title: Lyophyllum shimeji draft genome and related files

description: The whole genome analysis data of an ectomycorrhizal fungi, Lyophyllum shimeji. Draft genome assembly (fasta format), gene prediction (gff format), functional annotation (tsv format) and orthologous analysis table with other 17 fungal species are included.
DOI: 10.6084/m9.figshare.20281272.v1
title: Lyophyllum shimeji draft genome and related files

description: The whole genome analysis data of an ectomycorrhizal fungi, Lyophyllum shimeji. Draft genome assembly (fasta format), gene prediction (gff format), functional annotation (tsv format) and orthologous analysis table with other 17 fungal species are included.
DOI: 10.7910/dvn/3zsq0i
title: Replication Data for: Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud

description: Improving crop water use efficiency, the amount of carbon assimilated as biomass per unit of water used by a plant, is of major importance as water for agriculture becomes scarcer. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand remain unknown. These traits were measured in 2019 in a panel of 147 African rice (Oryza glaberrima) genotypes known to be potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly contrasted genotypes in terms of biomass accumulation and transpiration confirmed these associations and suggested that root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency, and its residuals, with links to genes involved in water transport and cell wall patterning. Our data suggest that root–shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.
DOI: 10.7910/dvn/hrajqm
title: Replication Data for: Replication Data for: Pricing Rice Quality Attributes and Returns to Quality Upgrading in Sub-Saharan Africa

description: The study applies parametric and nonparametric estimation methods to determine hedonic prices of rice quality attributes, and a partial equilibrium model to determine the payoff to investing in quality improvement in five countries in Sub-Saharan Africa. Results indicate that consumers are willing to pay price premiums for head rice, slender grains, peak viscosity, parboiled rice, and rice sold in urban markets. However, they strongly discount amylose content, rice with impurities and imported rice. Investing in quality improvement through amylose content reduction leads to net welfare gains with a benefit-cost ratio of 47.86 and internal rate of return of 90%.
DOI: 10.5519/qd.1bk4w0d9
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5281/zenodo.5046388
title: Unsupervised New Physics detection at 40 MHz: Training Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Training dataset, consisting of a cocktail of Standard Model collision events (simulation of LHC 13 TeV proton-proton collisions) pre-filtered by a requirement of a muon or electron with 23 GeV transverse momentum. Data format description available on the data challenge web page: https://mpp-hep.github.io/ADC2021/
description: Several bug fixes in dataset definition
DOI: 10.5281/zenodo.5046428
title: Unsupervised New Physics detection at 40 MHz: Training Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Training dataset, consisting of a cocktail of Standard Model collision events (simulation of LHC 13 TeV proton-proton collisions) pre-filtered by a requirement of a muon or electron with 23 GeV transverse momentum. Data format description available on the data challenge web page: https://mpp-hep.github.io/ADC2021/
description: Several bug fixes in dataset definition
DOI: 10.7910/dvn/vrtlb8
title: Replication Data for: Screening of Rice Germplasm and Processing Methods to Produce Low Glycemic Rice

description: The search for low glycemic rice to manage type 2 diabetes is of utmost importance due to the increasing trend in diabetic cases and the importance of rice as a staple worldwide. This study aimed to investigate the effect of combinations of rice varieties and processing regimes on human glycemic index (GI), and elucidate the relationship between physicochemical properties of rice and human GI. Parboiled polished rice recorded the lowest human GI. Parboiled unpolished rice, brown parboiled unpolished and brown parboiled polished rice recorded intermediate human GI while non-parboiled polished and non-parboiled unpolished rice recorded the highest human GI. Weak but significant positive correlations were observed for amylose and protein contents of parboiled polished rice and human GI while a negative correlation was observed for human GI and yellowness of parboiled grain. The varieties (ORYLUX 6, NERICA 11 and TOG 6813) identified as low GI after parboiling and polishing can be promoted as a component of improved parboiling technology when the goal is to produce low GI rice for the market.
DOI: 10.5281/zenodo.5070454
title: Unsupervised New Physics detection at 40 MHz: Black Box Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of the signal+background Black Box datasets, containing collision events (simulation of LHC 13 TeV proton-proton collisions) pre-filtered by a requirement of a muon or electron with 23 GeV transverse momentum. Data format description available on the data challenge web page: https://mpp-hep.github.io/ADC2021/
description: Several bug fixes in dataset definition
DOI: 10.5281/zenodo.5070455
title: Unsupervised New Physics detection at 40 MHz: Black Box Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of the signal+background Black Box datasets, containing collision events (simulation of LHC 13 TeV proton-proton collisions) pre-filtered by a requirement of a muon or electron with 23 GeV transverse momentum. Data format description available on the data challenge web page: https://mpp-hep.github.io/ADC2021/
DOI: 10.5281/zenodo.5072068
title: Unsupervised New Physics detection at 40 MHz: Black Box Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of the signal+background Black Box datasets, containing collision events (simulation of LHC 13 TeV proton-proton collisions) pre-filtered by a requirement of a muon or electron with 23 GeV transverse momentum. Data format description available on the data challenge web page: https://mpp-hep.github.io/ADC2021/
description: Several bug fixes in dataset definition
DOI: 10.6084/m9.figshare.16699370
title: Associations between infant sex and DNA methylation across umbilical cord blood, artery, and placenta samples

description: DNA methylation (DNAm) is vulnerable to dysregulation by environmental exposures during epigenetic reprogramming that occurs in embryogenesis. Sexual dimorphism in environmentally induced DNAm dysregulation has been identified and therefore it is important to understand sex-specific DNAm patterns. DNAm at several autosomal sites has been consistently associated with sex in cord blood and placental foetal tissues. However, there is limited research comparing sex-specific DNAm across tissues, particularly differentially methylated regions (DMRs). This study leverages DNAm data measured using the Illumina HumanMethylation450 BeadChip in cord blood (N = 179), placenta (N = 229), and umbilical artery samples (N = 229) in the PRogramming of Intergenerational Stress Mechanisms (PRISM) cohort to identify autosomal DMRs and differentially methylated positions (DMPs). A replication analyses was conducted in an independent cohort (GEO Accession GSE129841). We identified 183, 257, and 419 DMRs and 2119, 2281, and 3405 DMPs (<i>p<sub>Bonferroni</sub></i> &lt; 0.05) in cord blood, placenta, and artery samples, respectively. Thirty-nine DMRs overlapped in all three tissues, overlapping with genes involved in spermatogenesis (<i>NKAPL, PIWIL2 and AURKC</i>) and X–inactivation (<i>LRIF1</i>). In replication analysis, 85% of DMRs overlapped with those identified in PRISM. Overall, DMRs and DMPs had higher methylation levels among females in cord blood and artery samples, but higher methylation levels among males in placenta samples. Further research is necessary to understand biological mechanisms that contribute to differences in sex-specific DNAm signatures across tissues, as well as to determine if sexual dimorphism in the epigenome impacts response to environmental stressors.
DOI: 10.6084/m9.figshare.16699370.v2
title: Associations between infant sex and DNA methylation across umbilical cord blood, artery, and placenta samples

description: DNA methylation (DNAm) is vulnerable to dysregulation by environmental exposures during epigenetic reprogramming that occurs in embryogenesis. Sexual dimorphism in environmentally induced DNAm dysregulation has been identified and therefore it is important to understand sex-specific DNAm patterns. DNAm at several autosomal sites has been consistently associated with sex in cord blood and placental foetal tissues. However, there is limited research comparing sex-specific DNAm across tissues, particularly differentially methylated regions (DMRs). This study leverages DNAm data measured using the Illumina HumanMethylation450 BeadChip in cord blood (N = 179), placenta (N = 229), and umbilical artery samples (N = 229) in the PRogramming of Intergenerational Stress Mechanisms (PRISM) cohort to identify autosomal DMRs and differentially methylated positions (DMPs). A replication analyses was conducted in an independent cohort (GEO Accession GSE129841). We identified 183, 257, and 419 DMRs and 2119, 2281, and 3405 DMPs (<i>p<sub>Bonferroni</sub></i> &lt; 0.05) in cord blood, placenta, and artery samples, respectively. Thirty-nine DMRs overlapped in all three tissues, overlapping with genes involved in spermatogenesis (<i>NKAPL, PIWIL2 and AURKC</i>) and X–inactivation (<i>LRIF1</i>). In replication analysis, 85% of DMRs overlapped with those identified in PRISM. Overall, DMRs and DMPs had higher methylation levels among females in cord blood and artery samples, but higher methylation levels among males in placenta samples. Further research is necessary to understand biological mechanisms that contribute to differences in sex-specific DNAm signatures across tissues, as well as to determine if sexual dimorphism in the epigenome impacts response to environmental stressors.
DOI: 10.6084/m9.figshare.17086305.v1
title: Exploring the impact of night shift work on methylation of circadian genes

description: Night shift work is associated with increased breast cancer risk, but the molecular mechanisms are not well-understood. The objective of this study was to explore the relationship between night shift work parameters (current status, duration/years, and intensity) and methylation in circadian genes as a potential mechanism underlying the carcinogenic effects of night shift work. A cross-sectional study was conducted among 74 female healthcare employees (n = 38 day workers, n = 36 night shift workers). The Illumina Infinium MethylationEPIC beadchip was applied to DNA extracted from blood samples to measure methylation using a candidate gene approach at 1150 CpG loci across 22 circadian genes. Linear regression models were used to examine the association between night shift work parameters and continuous methylation measurements (β-values) for each CpG site. The false-discovery rate (q = 0.2) was used to account for multiple comparisons. Compared to day workers, current night shift workers demonstrated hypermethylation in the 5ʹUTR region of <i>CSNK1E</i> (q = 0.15). Individuals that worked night shifts for ≥10 years exhibited hypomethylation in the gene body of <i>NR1D1</i> (q = 0.08) compared to those that worked &lt;10 years. Hypermethylation in the gene body of <i>ARNTL</i> was also apparent in those who worked ≥3 consecutive night shifts a week (q = 0.18). These findings suggest that night shift work is associated with differential methylation in core circadian genes, including <i>CSNK1E, NR1D1</i> and <i>ARNTL</i>. Future, larger-scale studies with long-term follow-up and detailed night shift work assessment are needed to confirm and expand on these findings.
DOI: 10.6084/m9.figshare.16699370.v1
title: Associations between infant sex and DNA methylation across umbilical cord blood, artery, and placenta samples

description: DNA methylation (DNAm) is vulnerable to dysregulation by environmental exposures during epigenetic reprogramming that occurs in embryogenesis. Sexual dimorphism in environmentally induced DNAm dysregulation has been identified and therefore it is important to understand sex-specific DNAm patterns. DNAm at several autosomal sites has been consistently associated with sex in cord blood and placental fetal tissues. However, there is limited research comparing sex-specific DNAm across tissues, particularly differentially methylated regions (DMRs). This study leverages DNAm data measured using the Illumina HumanMethylation450 BeadChip in cord blood (N = 179), placenta (N = 229), and umbilical artery samples (N = 229) in the PRogramming of Intergenerational Stress Mechanisms (PRISM) cohort to identify autosomal DMRs and differentially methylated positions (DMPs). A replication analyses was conducted in an independent cohort (GEO Accession GSE129841). We identified 183, 257, and 419 DMRs and 2119, 2281, and 3405 DMPs (<i>p<sub>Bonferroni</sub></i> &lt; 0.05) in cord blood, placenta, and artery samples, respectively. Thirty-nine DMRs overlapped in all three tissues, overlapping with genes involved in spermatogenesis (<i>NKAPL, PIWIL2, AURKC</i>) and X-inactivation (<i>LRIF1</i>). In replication analysis, 85% of DMRs overlapped with those identified in PRISM. Overall DMRs and DMPs had higher methylation levels among females in cord blood and artery samples, but higher methylation levels among males in placenta samples. Further research is necessary to understand biological mechanisms that contribute to differences in sex-specific DNAm signatures across tissues, as well as to determine if sexual dimorphism in the epigenome impacts response to environmental stressors.
DOI: 10.6084/m9.figshare.17086305
title: Exploring the impact of night shift work on methylation of circadian genes

description: Night shift work is associated with increased breast cancer risk, but the molecular mechanisms are not well-understood. The objective of this study was to explore the relationship between night shift work parameters (current status, duration/years, and intensity) and methylation in circadian genes as a potential mechanism underlying the carcinogenic effects of night shift work. A cross-sectional study was conducted among 74 female healthcare employees (n = 38 day workers, n = 36 night shift workers). The Illumina Infinium MethylationEPIC beadchip was applied to DNA extracted from blood samples to measure methylation using a candidate gene approach at 1150 CpG loci across 22 circadian genes. Linear regression models were used to examine the association between night shift work parameters and continuous methylation measurements (β-values) for each CpG site. The false-discovery rate (q = 0.2) was used to account for multiple comparisons. Compared to day workers, current night shift workers demonstrated hypermethylation in the 5ʹUTR region of <i>CSNK1E</i> (q = 0.15). Individuals that worked night shifts for ≥10 years exhibited hypomethylation in the gene body of <i>NR1D1</i> (q = 0.08) compared to those that worked &lt;10 years. Hypermethylation in the gene body of <i>ARNTL</i> was also apparent in those who worked ≥3 consecutive night shifts a week (q = 0.18). These findings suggest that night shift work is associated with differential methylation in core circadian genes, including <i>CSNK1E, NR1D1</i> and <i>ARNTL</i>. Future, larger-scale studies with long-term follow-up and detailed night shift work assessment are needed to confirm and expand on these findings.
DOI: 10.6084/m9.figshare.16752079
title: Longitudinal change in blood DNA epigenetic signature after smoking cessation

description: Cigarette smoking is associated with epigenetic changes that may be reversible following smoking cessation. Whole blood DNA methylation was evaluated in Framingham Heart Study Offspring (n = 169) and Third Generation (n = 30) cohort participants at two study visits 6 years apart and in Atherosclerosis Risk in Communities (ARIC) study (n = 222) participants at two study visits 20 years apart. Changes in DNA methylation (delta β values) at 483,565 cytosine-phosphate-guanine (CpG) sites and differentially methylated regions (DMRs) were compared between participants who were current, former, or never smokers at both visits (current-current, former-former, never-never, respectively), versus those who quit in the interim (current-former). Interim quitters had more hypermethylation at four CpGs annotated to <i>AHRR</i>, one CpG annotated to <i>F2RL3</i>, and one intergenic CpG (cg21566642) compared with current-current smokers (FDR &lt; 0.02 for all), and two significant DMRs were identified. While there were no significant differentially methylated CpGs in the comparison of interim quitters and former-former smokers, 106 DMRs overlapping with small nucleolar RNA were identified. As compared with all non-smokers, current-current smokers additionally had more hypermethylation at two CpG sites annotated to <i>HIVEP3</i> and <i>TMEM126A</i>, respectively, and another intergenic CpG (cg14339116). Gene transcripts associated with smoking cessation were implicated in immune responses, cell homoeostasis, and apoptosis. Smoking cessation is associated with early reversion of blood DNA methylation changes at CpG sites annotated to <i>AHRR</i> and <i>F2RL3</i> towards those of never smokers. Associated gene expression suggests a role of longitudinal smoking-related DNA methylation changes in immune response processes.