cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16752079.v1
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.
DOI: 10.6084/m9.figshare.21286786
title: Dynamics of methylated cell-free DNA in the urine of non-small cell lung cancer patients

description: High levels of methylated DNA in urine represent an emerging biomarker for non-small cell lung cancer (NSCLC) detection and are the subject of ongoing research. This study aimed to investigate the circadian variation of urinary cell-free DNA (cfDNA) abundance and methylation levels of cancer-associated genes in NSCLC patients. In this prospective study of 23 metastatic NSCLC patients with active disease, patients were asked to collect six urine samples during the morning, afternoon, and evening of two subsequent days. Urinary cfDNA concentrations and methylation levels of <i>CDO1, SOX17</i>, and <i>TAC1</i> were measured at each time point. Circadian variation and between- and within-subject variability were assessed using linear mixed models. Variability was estimated using the Intraclass Correlation Coefficient (ICC), representing reproducibility. No clear circadian patterns could be recognized for cfDNA concentrations or methylation levels across the different sampling time points. Significantly lower cfDNA concentrations were found in males (<i>p</i>=0.034). For cfDNA levels, the between- and within-subject variability were comparable, rendering an ICC of 0.49. For the methylation markers, ICCs varied considerably, ranging from 0.14 to 0.74. Test reproducibility could be improved by collecting multiple samples per patient. In conclusion, there is no preferred collection time for NSCLC detection in urine using methylation markers, but single measurements should be interpreted carefully, and serial sampling may increase test performance. This study contributes to the limited understanding of cfDNA dynamics in urine and the continued interest in urine-based liquid biopsies for cancer diagnostics.
DOI: 10.6084/m9.figshare.21286786.v1
title: Dynamics of methylated cell-free DNA in the urine of non-small cell lung cancer patients

description: High levels of methylated DNA in urine represent an emerging biomarker for non-small cell lung cancer (NSCLC) detection and are the subject of ongoing research. This study aimed to investigate the circadian variation of urinary cell-free DNA (cfDNA) abundance and methylation levels of cancer-associated genes in NSCLC patients. In this prospective study of 23 metastatic NSCLC patients with active disease, patients were asked to collect six urine samples during the morning, afternoon, and evening of two subsequent days. Urinary cfDNA concentrations and methylation levels of <i>CDO1, SOX17</i>, and <i>TAC1</i> were measured at each time point. Circadian variation and between- and within-subject variability were assessed using linear mixed models. Variability was estimated using the Intraclass Correlation Coefficient (ICC), representing reproducibility. No clear circadian patterns could be recognized for cfDNA concentrations or methylation levels across the different sampling time points. Significantly lower cfDNA concentrations were found in males (<i>p</i>=0.034). For cfDNA levels, the between- and within-subject variability were comparable, rendering an ICC of 0.49. For the methylation markers, ICCs varied considerably, ranging from 0.14 to 0.74. Test reproducibility could be improved by collecting multiple samples per patient. In conclusion, there is no preferred collection time for NSCLC detection in urine using methylation markers, but single measurements should be interpreted carefully, and serial sampling may increase test performance. This study contributes to the limited understanding of cfDNA dynamics in urine and the continued interest in urine-based liquid biopsies for cancer diagnostics.
DOI: 10.6084/m9.figshare.16870639
title: An investigation into DNA methylation patterns associated with risk preference in older individuals

description: Risk preference is a complex trait governed by psycho-social, environmental and genetic determinants. We aimed to examine how an individual’s risk preference associates with their epigenetic profile. Risk preferences were ascertained by asking participants of the Northern Ireland COhort for the Longitudinal study of Ageing to make a series of choices between hypothetical income scenarios. From these, four risk preference categories were derived, ranging from risk-averse to risk-seeking. Illumina’s Infinium High-Density Methylation Assay was used to evaluate the status of 862,927 CpGs. Risk preference and DNA methylation data were obtained for 1,656 individuals. The distribution of single-site DNA methylation levels between risk-averse and risk-seeking individuals was assessed whilst adjusting for age, sex and peripheral white cell counts. In this discovery cohort, 55 CpGs were identified with significantly different levels of methylation (p≤x10<sup>−5</sup>) between risk-averse and risk-seeking individuals when adjusting for the maximum number of covariates. No CpGs were significantly differentially methylated in any of the risk preference groups at an epigenome-wide association level (p&lt;9x10<sup>−8</sup>) following covariate adjustment. Protein-coding genes <i>NWD1</i> and <i>LRP1</i> were among the genes in which the top-ranked dmCpGs were located for all analyses conducted. Mutations in these genes have previously been linked to neurological conditions. Epigenetic modifications have not previously been linked to risk-aversion using a population cohort, but may represent important biomarkers of accumulated, complex determinants of this trait. Several striking results from this study support further analysis of DNA methylation as an important link between measurable biomarkers and health behaviours.
DOI: 10.6084/m9.figshare.16870639.v1
title: An investigation into DNA methylation patterns associated with risk preference in older individuals

description: Risk preference is a complex trait governed by psycho-social, environmental and genetic determinants. We aimed to examine how an individual’s risk preference associates with their epigenetic profile. Risk preferences were ascertained by asking participants of the Northern Ireland COhort for the Longitudinal study of Ageing to make a series of choices between hypothetical income scenarios. From these, four risk preference categories were derived, ranging from risk-averse to risk-seeking. Illumina’s Infinium High-Density Methylation Assay was used to evaluate the status of 862,927 CpGs. Risk preference and DNA methylation data were obtained for 1,656 individuals. The distribution of single-site DNA methylation levels between risk-averse and risk-seeking individuals was assessed whilst adjusting for age, sex and peripheral white cell counts. In this discovery cohort, 55 CpGs were identified with significantly different levels of methylation (p≤x10<sup>−5</sup>) between risk-averse and risk-seeking individuals when adjusting for the maximum number of covariates. No CpGs were significantly differentially methylated in any of the risk preference groups at an epigenome-wide association level (p&lt;9x10<sup>−8</sup>) following covariate adjustment. Protein-coding genes <i>NWD1</i> and <i>LRP1</i> were among the genes in which the top-ranked dmCpGs were located for all analyses conducted. Mutations in these genes have previously been linked to neurological conditions. Epigenetic modifications have not previously been linked to risk-aversion using a population cohort, but may represent important biomarkers of accumulated, complex determinants of this trait. Several striking results from this study support further analysis of DNA methylation as an important link between measurable biomarkers and health behaviours.
DOI: 10.6084/m9.figshare.16870640
title: Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohort

description: Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-foetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study. Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated using robust linear regression (N = 231). Primary analyses focused on metal-miRNA associations in early pregnancy (median: 12.3 weeks gestation). In secondary analyses, we investigated associations with late pregnancy miRNA counts (median: 31.8 weeks gestation) in a subset of participants (N = 184) with paired measures. MiRNA associated with three or more metals (P<sub>FDR</sub>&lt;0.05) were further investigated using Bayesian Kernel Machine Regression (BKMR), an environmental mixture method. Thirty-five miRNA were associated (P<sub>FDR</sub>&lt;0.05) with at least one metal in early pregnancy. One association (an inverse association between cobalt and miR–150-5p) remained statistically significant when evaluating late pregnancy miRNA counts. Eight miRNA (miR–302b-3p, miR–199a-5p, miR–188-5p, miR–138-5p, miR–212-3p, miR–608, miR–1272, miR–19b-3p) were associated with three metals (barium, mercury, and thallium) in early pregnancy, and their predicted target genes were enriched in pathways important for placental development. Results were consistent when using BKMR. Early pregnancy exposure to barium, mercury, and thallium may have short-term impacts on a common set of EV miRNA which target pathways important for placental development.
DOI: 10.6084/m9.figshare.16870640.v2
title: Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohort

description: Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-foetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study. Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated using robust linear regression (N = 231). Primary analyses focused on metal-miRNA associations in early pregnancy (median: 12.3 weeks gestation). In secondary analyses, we investigated associations with late pregnancy miRNA counts (median: 31.8 weeks gestation) in a subset of participants (N = 184) with paired measures. MiRNA associated with three or more metals (P<sub>FDR</sub>&lt;0.05) were further investigated using Bayesian Kernel Machine Regression (BKMR), an environmental mixture method. Thirty-five miRNA were associated (P<sub>FDR</sub>&lt;0.05) with at least one metal in early pregnancy. One association (an inverse association between cobalt and miR–150-5p) remained statistically significant when evaluating late pregnancy miRNA counts. Eight miRNA (miR–302b-3p, miR–199a-5p, miR–188-5p, miR–138-5p, miR–212-3p, miR–608, miR–1272, miR–19b-3p) were associated with three metals (barium, mercury, and thallium) in early pregnancy, and their predicted target genes were enriched in pathways important for placental development. Results were consistent when using BKMR. Early pregnancy exposure to barium, mercury, and thallium may have short-term impacts on a common set of EV miRNA which target pathways important for placental development.
DOI: 10.6084/m9.figshare.16870640.v1
title: Urinary Metals and Maternal Circulating Extracellular Vesicle microRNA in the MADRES Pregnancy Cohort

description: <i>Background</i>: Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-fetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study. <i>Methods</i>: Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated using robust linear regression (N=231). Primary analyses focused on metal-miRNA associations in early pregnancy (median: 12.3 weeks gestation). In secondary analyses, we investigated associations with late pregnancy miRNA counts in a smaller subset of participants (N=184) with paired data in the third trimester (median: 31.8 weeks gestation). MiRNA associated with three or more metals (P<sub>FDR</sub>&lt;0.05) were further investigated using Bayesian Kernel Machine Regression (BKMR), an environmental mixture modeling approach. <i>Results</i>: Thirty-five miRNA were associated (P<sub>FDR</sub>&lt;0.05) with at least one metal in early pregnancy. Only one association (an inverse association between cobalt and miR-150-5p) remained statistically significant when evaluating late pregnancy miRNA counts. Eight miRNA (miR-302b-3p, miR-199a-5p, miR-188-5p, miR-138-5p, miR-212-3p, miR-608, miR-1272, miR-19b-3p) were associated with three different metals (barium, mercury, and thallium) in early pregnancy, and their predicted target genes were enriched in pathways important for placental development. Results were consistent when using BKMR. <i>Conclusions</i>: Early pregnancy exposure to barium, mercury, and thallium may have short-term impacts on a common set of maternal circulating EV miRNA which target pathways important for placental development.
DOI: 10.5281/zenodo.3675159
title: New Physics Mining at the Large Hadron Collider: A -&gt; 4 leptons

description: \(A \to 4\ell\) signal events reconstructed by inclusive single-muon selection. Events are represented as an array of physics-motivated high-level features. Details are given in https://arxiv.org/abs/1811.10276
DOI: 10.5281/zenodo.5046446
title: Unsupervised New Physics detection at 40 MHz: A -&gt; 4 leptons Signal Benchmark Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of A -&gt; 4 leptons decays produced in 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.5046445
title: Unsupervised New Physics detection at 40 MHz: A -&gt; 4 leptons Signal Benchmark Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of A -&gt; 4 leptons decays produced in 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/trwoqe
title: Replication Data for: Assessment of rice threshing technology characteristics for enhanced rice sector development in Senegal

description: Understanding the technology characteristics desirable to farmers to increase the adoption of improved technologies remains a high-priority research issue in sub-Saharan Africa (SSA). The study aimed to quantify farmers’ demand and assessment of the characteristics of rice threshing technologies to enhance the adoption of innovations in Senegal. A multistage sampling technique was used to collect primary data from 318 rice farmers in the Senegal River Valley. Three indexes (demand, supply and attainment) of technology characteristics were estimated to assess farmers’ perceptions of the characteristics of three threshing techniques (traditional, ASI thresher and combine harvester-thresher). The results showed that of the eleven selected characteristics, time savings (0.95), labour savings (0.94) and grain quality (0.93) were farmers’ key demand. The ASI thresher and combine harvester-thresher met farmers’ needs well in terms of the attributes of grain quality and production capacity. However, users of the traditional technique reported low levels of perceived usefulness, and users of the combine harvester-thresher reported low levels of ease of use. Women labour usefulness is a trade-off for advancement in threshing technologies in pursuance of rice sector improvement, implying that efforts towards developing gender-friendly threshers are required. The variables estimated in this study offer policy considerations for development of the rice production system in Senegal. The originality of this paper is its use of a combination of take-the-best theory, the technology acceptance model and an indexing approach to reveal specific characteristics for the development of best-fit mechanization equipment, mainly improved threshers for rice sector development in SSA.
DOI: 10.5281/zenodo.3675196
title: New Physics Mining at the Large Hadron Collider: LQ -&gt; b tau

description: \(LQ \to b \tau\) signal events reconstructed by inclusive single-muon selection. Events are represented as an array of physics-motivated high-level features. Details are given in https://arxiv.org/abs/1811.10276
DOI: 10.5281/zenodo.5055454
title: Unsupervised New Physics detection at 40 MHz: LQ -&gt; b tau Signal Benchmark Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of Leptoquarks -&gt; b tau decays produced in 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.5055453
title: Unsupervised New Physics detection at 40 MHz: LQ -&gt; b tau Signal Benchmark Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of Leptoquarks -&gt; b tau decays produced in 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: 10.48366/r220872
title: NER Annotations in the OntoNotes Corpus

description: The goal of the project was to annotate a large corpus comprising various genres of text (news, conversational telephone speech, weblogs, usenet newsgroups, broadcast, talk shows) in three languages (English, Chinese, and Arabic) with structural information (syntax and predicate argument structure) and shallow semantics (word sense linked to an ontology and coreference). This comparison focuses only on the NER annotations layer in OntoNotes. The dataset represents diverse genres such as newswire (News), broadcast news (BN), broadcast conversation (BC), telephone conversation (Tele) and web data (Web) in English and Chinese and newswire data in Arabic. Furthermore the dataset is multilingual across English, Chinese and Arabic.
DOI: 10.5281/zenodo.3675190
title: New Physics Mining at the Large Hadron Collider: h^0 -&gt; tau tau

description: \(h^0 \to \tau^+ \tau^-\) signal events reconstructed by inclusive single-muon selection. Events are represented as an array of physics-motivated high-level features. Details are given in https://arxiv.org/abs/1811.10276
DOI: 10.5281/zenodo.5061632
title: Unsupervised New Physics detection at 40 MHz: h^0 -&gt; tau tau Signal Benchmark Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of h^0 -&gt; tau tau decays produced in 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.5061633
title: Unsupervised New Physics detection at 40 MHz: h^0 -&gt; tau tau Signal Benchmark Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of h^0 -&gt; tau tau decays produced in 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.3675178
title: New Physics Mining at the Large Hadron Collider: h+ -&gt; tau nu

description: \(h^\pm \to \tau^\pm \nu\) signal events reconstructed by inclusive single-muon selection. Events are represented as an array of physics-motivated high-level features. Details are given in https://arxiv.org/abs/1811.10276
DOI: 10.5281/zenodo.5061687
title: Unsupervised New Physics detection at 40 MHz: h+ -&gt; tau nu Signal Benchmark Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of h+ -&gt; tau nu decays produced in 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.5061688
title: Unsupervised New Physics detection at 40 MHz: h+ -&gt; tau nu Signal Benchmark Dataset

description: Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of h+ -&gt; tau nu decays produced in 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/