cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3483392
title: Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates

description: Epigenome-wide DNA methylation association studies have identified highly replicable genomic loci sensitive to maternal smoking during gestation. The role of inter-individual genetic variation in influencing DNA methylation, leading to the possibility of confounding or bias of such associations, has not been assessed. We investigated whether the DNA methylation levels at the top 10 CpG sites previously associated with exposure to maternal smoking during gestation were associated with individual genetic variation at the genome-wide level. Genome-wide association tests between DNA methylation at the top 10 candidate CpG and genome-wide SNPs were performed in 736 case and control participants of the California Childhood Leukemia Study. Three of the strongest maternal-smoking sensitive CpG sites in newborns were significantly associated with SNPs located proximal to each gene: <i>cg18146737</i> in the <i>GFI1</i> gene with <i>rs141819830</i> (<i>P</i> = 8.2×10<sup>−44</sup>), <i>cg05575921</i> in the <i>AHRR</i> gene with <i>rs148405299</i> (<i>P</i> = 5.3×10<sup>−10</sup>), and <i>cg12803068</i> in the <i>MYO1G</i> gene with <i>rs61087368</i> (<i>P</i> = 1.3×10<sup>−18</sup>). For the <i>GFI1</i> CpG <i>cg18146737</i>, the underlying genetic variation at <i>rs141819830</i> confounded the association between maternal smoking and DNA methylation in our data (the regression coefficient changed from −0.02 [<i>P</i> = 0.139] to −0.03 [<i>P</i> = 0.015] after including the genotype). Our results suggest that further studies using DNA methylation at <i>cg18146737, cg05575921</i>, or <i>cg12803068</i> that aim to assess exposure to maternal smoking during gestation should include genotype at the corresponding SNP. New methods are required for adequate and routine inclusion of genotypic influence on DNA methylation in epigenome-wide association studies to control for potential confounding.
DOI: 10.6084/m9.figshare.3483392.v2
title: Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates

description: Epigenome-wide DNA methylation association studies have identified highly replicable genomic loci sensitive to maternal smoking during gestation. The role of inter-individual genetic variation in influencing DNA methylation, leading to the possibility of confounding or bias of such associations, has not been assessed. We investigated whether the DNA methylation levels at the top 10 CpG sites previously associated with exposure to maternal smoking during gestation were associated with individual genetic variation at the genome-wide level. Genome-wide association tests between DNA methylation at the top 10 candidate CpG and genome-wide SNPs were performed in 736 case and control participants of the California Childhood Leukemia Study. Three of the strongest maternal-smoking sensitive CpG sites in newborns were significantly associated with SNPs located proximal to each gene: <i>cg18146737</i> in the <i>GFI1</i> gene with <i>rs141819830</i> (<i>P</i> = 8.2×10<sup>−44</sup>), <i>cg05575921</i> in the <i>AHRR</i> gene with <i>rs148405299</i> (<i>P</i> = 5.3×10<sup>−10</sup>), and <i>cg12803068</i> in the <i>MYO1G</i> gene with <i>rs61087368</i> (<i>P</i> = 1.3×10<sup>−18</sup>). For the <i>GFI1</i> CpG <i>cg18146737</i>, the underlying genetic variation at <i>rs141819830</i> confounded the association between maternal smoking and DNA methylation in our data (the regression coefficient changed from −0.02 [<i>P</i> = 0.139] to −0.03 [<i>P</i> = 0.015] after including the genotype). Our results suggest that further studies using DNA methylation at <i>cg18146737, cg05575921</i>, or <i>cg12803068</i> that aim to assess exposure to maternal smoking during gestation should include genotype at the corresponding SNP. New methods are required for adequate and routine inclusion of genotypic influence on DNA methylation in epigenome-wide association studies to control for potential confounding.
DOI: 10.6084/m9.figshare.3483392.v1
title: Genetic contribution to variation in DNA methylation at maternal smoking sensitive loci in exposed neonates

description: Epigenome-wide DNA methylation association studies have identified highly replicable genomic loci sensitive to maternal smoking during gestation. The role of inter-individual genetic variation in influencing DNA methylation, leading to the possibility of confounding or bias of such associations, has not been assessed. We investigated whether the DNA methylation levels at the top ten CpG sites previously associated with exposure to maternal smoking during gestation were associated with individual genetic variation at the genome-wide level. Genome-wide association tests between DNA methylation at the top ten candidate CpG and genome-wide SNPs were performed in 736 case and control participants of the California Childhood Leukemia Study. Three of the strongest maternal-smoking sensitive CpG sites in newborns were significantly associated with SNPs located proximal to each gene: <i>cg18146737</i> in the <i>GFI1</i> gene with <i>rs141819830</i> (<i>P</i> = 8.2×10<sup>−44</sup>), <i>cg05575921</i> in the <i>AHRR</i> gene with <i>rs148405299</i> (<i>P</i> = 5.3×10<sup>−10</sup>), and <i>cg12803068</i> in the <i>MYO1G</i> gene with <i>rs61087368</i> (<i>P</i> = 1.3×10<sup>−18</sup>). For the <i>GFI1</i> CpG <i>cg18146737</i>, the underlying genetic variation at <i>rs141819830</i> confounded the association between maternal smoking and DNA methylation in our data [OR changed from 0.89 (0.75–1.06, <i>P</i> = 0.184) to 0.78 (0.63–0.97, <i>P</i> = 0.024) after including the genotype]. Our results suggest that further studies using DNA methylation at <i>cg18146737, cg05575921</i>, or <i>cg12803068</i> that aim to assess exposure to maternal smoking during gestation should include genotype at the corresponding SNP. New methods are required for adequate and routine inclusion of genotypic influence on DNA methylation in epigenome-wide association studies to control for potential confounding.
DOI: 10.6084/m9.figshare.3483146
title: Eye Tracking Pilot Accuracy and Precision Data (30 Participants)

description: This file contains accuracy and precision measurements and raw gaze samples taken from 30 participants in a real-world laboratory setting using Tobii X60, 60Hz Remote Eye Tracker using manufacturer's I-VT filter settings. Stimulus was displayed on a Dell 2209WA flatpanel display monitor at approximately 70cm viewing distance at a resolution of 1680x1050.<br> Accuracy data was calculated against fixations on 9 points distributed across upper, middle, lower, left, center, and right thirds of the display. Precision data was calculated against a single fixation for each participant on a non-moving object of focus centered in the display for three seconds' duration, resulting in 80-150 raw gaze samples per participant, dependent on the speed with which the participant was able to focus and fixate on the object.
DOI: 10.15131/shef.data.3483140
title: Review of diversity and inclusion literature and an evaluation of methodologies and metrics relating to health research: systematic mapping protocol

description: This systematic mapping protocol forms part of a project being undertaken by a multidisciplinary team from the University of Sheffield, which aims to inform and support the focus on diversity and inclusion in Wellcome Trust’s new strategic plan. The review aims to “undertake a systematic and critical review of the evidence base for a positive relationship between a diverse and inclusive health research community and the qualities and impacts of the research they undertake”. This protocol sets out our plan for the review in terms of the literature search and how the retrieved literature will be screened for inclusion in the main review, extracted and then assessed.
DOI: 10.15131/shef.data.3483140.v1
title: Review of diversity and inclusion literature and an evaluation of methodologies and metrics relating to health research: systematic mapping protocol

description: This systematic mapping protocol forms part of a project being undertaken by a multidisciplinary team from the University of Sheffield, which aims to inform and support the focus on diversity and inclusion in Wellcome Trust’s new strategic plan. The review aims to “undertake a systematic and critical review of the evidence base for a positive relationship between a diverse and inclusive health research community and the qualities and impacts of the research they undertake”. This protocol sets out our plan for the review in terms of the literature search and how the retrieved literature will be screened for inclusion in the main review, extracted and then assessed.
DOI: 10.6084/m9.figshare.3483116
title: Shoulder arthroplasty trials are infrequently registered: a systematic review of trials

description: <b>Introduction</b> With the intent of improving transparency in clinical research, the International Committee of Medical Journal Editors (ICMJE) established guidelines in 2005 regarding prospective clinical trial registration. This action worked to address bias related to selective outcome reporting in the medical literature. The objective of this study was to assess and characterize the quality of registration of clinical trials appearing in shoulder arthroplasty-related medical journals. <b>Methods</b> All randomized trials involving human subjects, pertaining to shoulder arthroplasty, published between July 1, 2005 and December 31, 2015, and indexed in either PubMed or SportDISCUS were analyzed. We assessed the prevalence of registration, the timing of registration relative to patient enrollment periods, and the variable rates of orthopedic journal compliance with ICMJE and Food and Drug Administration clinical registration standards for our study. <b>Results</b> Of the 382 articles identified, 345 (90.3%) were excluded due to failure to meet inclusion criteria. From the remaining 37, only 12 (32.4%) studies were found to be registered in a trial registry. Ten (10/12, 83.3%) of these provided their registration information within the body of the article. None of the included studies from ICMJE-recognized journals were registered. From 34 included studies from non-ICMJE recognized journals, 12 (35.3%) were registered. <b>Conclusion</b> The level of compliance with clinical trial registration guidelines in the decade since their release among shoulder arthroplasty trials in orthopedic journals is poor. Given the importance of the issue, the prevalence of the problem, and the fact that many other medical specialties have already made efforts to improve ICMJE compliance, further work on the part of orthopedic surgery journal authors and editors is needed to ensure the publication of unbiased results. <b>Trial Registration: </b>UMIN000022487
DOI: 10.6084/m9.figshare.3483116.v1
title: Shoulder arthroplasty trials are infrequently registered: a systematic review of trials

description: <b>Introduction</b> With the intent of improving transparency in clinical research, the International Committee of Medical Journal Editors (ICMJE) established guidelines in 2005 regarding prospective clinical trial registration. This action worked to address bias related to selective outcome reporting in the medical literature. The objective of this study was to assess and characterize the quality of registration of clinical trials appearing in shoulder arthroplasty-related medical journals. <b>Methods</b> All randomized trials involving human subjects, pertaining to shoulder arthroplasty, published between July 1, 2005 and December 31, 2015, and indexed in either PubMed or SportDISCUS were analyzed. We assessed the prevalence of registration, the timing of registration relative to patient enrollment periods, and the variable rates of orthopedic journal compliance with ICMJE and Food and Drug Administration clinical registration standards for our study. <b>Results</b> Of the 382 articles identified, 345 (90.3%) were excluded due to failure to meet inclusion criteria. From the remaining 37, only 12 (32.4%) studies were found to be registered in a trial registry. Ten (10/12, 83.3%) of these provided their registration information within the body of the article. None of the included studies from ICMJE-recognized journals were registered. From 34 included studies from non-ICMJE recognized journals, 12 (35.3%) were registered. <b>Conclusion</b> The level of compliance with clinical trial registration guidelines in the decade since their release among shoulder arthroplasty trials in orthopedic journals is poor. Given the importance of the issue, the prevalence of the problem, and the fact that many other medical specialties have already made efforts to improve ICMJE compliance, further work on the part of orthopedic surgery journal authors and editors is needed to ensure the publication of unbiased results. <b>Trial Registration: </b>UMIN000022487
DOI: 10.6084/m9.figshare.3483104
title: Controlling Herbicide Resistant Annual Bluegrass Phenotypes with Methiozolin

description: Data and analysis files from glasshouse experiments designed to evaluate methiozolin efficacy for controlling annual bluegrass phenotypes with genetic mutations known to confer resistance to various herbicides.
DOI: 10.6084/m9.figshare.3483089
title: Datasets for testing the performance of a method for PSCPP

description: This file contains four datasets for testing the performance of a method for protein side-chain packing.<br>The first chain of every protein is present in a pdb format; and information about symmetry contacts calculated by WHATIF are also present.
DOI: 10.6084/m9.figshare.3483104.v1
title: Controlling Herbicide Resistant Annual Bluegrass Phenotypes with Methiozolin

description: Data and analysis files from glasshouse experiments designed to evaluate methiozolin efficacy for controlling annual bluegrass phenotypes with genetic mutations known to confer resistance to various herbicides.
DOI: 10.6084/m9.figshare.3483065
title: Dataset for OTP evaluation Article

description: Dataset for health outcome of children aged 6-59 months admitted in Outpatient Therapeutic Programme (OTP) centres in Eastern Zambian District.<br>Study conducted in 2012 - data disseminated in 2016
DOI: 10.6084/m9.figshare.3483065.v1
title: Dataset for OTP evaluation Article

description: Dataset for health outcome of children aged 6-59 months admitted in Outpatient Therapeutic Programme (OTP) centres in Eastern Zambian District.<br>Study conducted in 2012 - data disseminated in 2016
DOI: 10.6084/m9.figshare.3483059
title: scripts

description: The shell scripts and configuration files used in the study.
DOI: 10.6084/m9.figshare.3483059.v1
title: scripts

description: The shell scripts and configuration files used in the study.
DOI: 10.6084/m9.figshare.3483056
title: sequences

description: Sequence alignments of the 48 loci analyzed in the study. Additional trnH-psbA sequences are included but not aligned.
DOI: 10.6084/m9.figshare.3483056.v2
title: sequences

description: Sequence alignments of the 48 loci analyzed in the study. Additional trnH-psbA sequences are included but not aligned.
DOI: 10.6084/m9.figshare.3483056.v1
title: sequences.zip

description: Sequence alignments of the 48 loci analyzed in the study. Additional trnH-psbA sequences are included but not aligned.
DOI: 10.6084/m9.figshare.3482918
title: Hydrogen shock tube ignition dataset

description: Dataset of hydrogen shock tube ignition delay times, originally collected from the literature by Olm et al. [1], converted to the ChemKED YAML-based format. All original references are included inside the YAML files<br>[1] Olm C, Zsély IG, Pálvölgyi R, Varga T, Nagy T, Curran HJ, et al. Comparison of the performance of several recent hydrogen combustion mechanisms. Combust Flame 2014;161:2219–2234. http://dx.doi.org/10.1016/j.combustflame.2014.03.006.
DOI: 10.6084/m9.figshare.3482918.v1
title: Hydrogen shock tube ignition dataset

description: Dataset of hydrogen shock tube ignition delay times, originally collected from the literature by Olm et al. [1], converted to the ChemKED YAML-based format. All original references are included inside the YAML files<br>[1] Olm C, Zsély IG, Pálvölgyi R, Varga T, Nagy T, Curran HJ, et al. Comparison of the performance of several recent hydrogen combustion mechanisms. Combust Flame 2014;161:2219–2234. http://dx.doi.org/10.1016/j.combustflame.2014.03.006.
DOI: 10.6084/m9.figshare.3482906
title: Selected hydrogen chemical kinetic models

description: This is a collection of previously published chemical kinetic models describing hydrogen oxidation, in Cantera CTI format, as well as some associated metadata. <br>These files were converted to the Cantera format based on original files either made available as supplementary material to published articles or via various websites.
DOI: 10.6084/m9.figshare.3482855
title: JH Survey 3 20160710 EM3+ wav files

description: <br>Panshanger Survey 3 - Blakemore Wood<br>10 July 2016 21:00-22:45<br>Justin A T halls<br>EM3+ 384ksps 16bit<br>Neumic microphone at 5%<br>light cloud, windy, warm<br>Luton:- 9:50pm 16C 82% 1006hPa 5.1m/s SSW Waxing crescent<br>51.799272, -0.107264Third Panshanger survey in the series, based in Thieves Lane carpark<br>and with teams covering Blakemore wood and Lady Hughes Wood. <br>We were located in the NE corner of the wood, in a clearing between<br>the stand of silver birch trees and the Eastern edge of the wood.<br>The Tascam DR05 was located by the path junction just by the exit<br>in the very NE corner of the wood.<br>No Barbastelles observed, mainly Common and Soprano Pips - one very early<br>Soprano at 21:12 but most of them later on. One probable Natterers<br>half way over to the Tascam and some Pip social calling (maybe a Leisler's?)<br>on the way out, just on entering Lady Hughe's Wood.<br>
DOI: 10.6084/m9.figshare.3482855.v1
title: JH Survey 3 20160710 EM3+ wav files

description: <br>Panshanger Survey 3 - Blakemore Wood<br>10 July 2016 21:00-22:45<br>Justin A T halls<br>EM3+ 384ksps 16bit<br>Neumic microphone at 5%<br>light cloud, windy, warm<br>Luton:- 9:50pm 16C 82% 1006hPa 5.1m/s SSW Waxing crescent<br>51.799272, -0.107264Third Panshanger survey in the series, based in Thieves Lane carpark<br>and with teams covering Blakemore wood and Lady Hughes Wood. <br>We were located in the NE corner of the wood, in a clearing between<br>the stand of silver birch trees and the Eastern edge of the wood.<br>The Tascam DR05 was located by the path junction just by the exit<br>in the very NE corner of the wood.<br>No Barbastelles observed, mainly Common and Soprano Pips - one very early<br>Soprano at 21:12 but most of them later on. One probable Natterers<br>half way over to the Tascam and some Pip social calling (maybe a Leisler's?)<br>on the way out, just on entering Lady Hughe's Wood.<br>
DOI: 10.6084/m9.figshare.3482828
title: Tests on Thin Reinforced Concrete Walls Subjected to In-plane and Out-of-plane Cyclic Loading - TW4 (3/4)

description: The present dataset describes an experimental campaign on five thin T-shaped reinforced concrete walls. The tests aimed at assessing the influence of wall thickness on member stability, the role of lap splices on damage distribution and displacement ductility, and the effects of the simultaneous application of out-of-plane loading on the member response.Further data can be downloaded from the links below.<br> If you use the data, please cite: Almeida, J. P., O. Prodan, A. Rosso, and K. Beyer. 2016. Tests on Thin Reinforced Concrete Walls Subjected to in-Plane and out-of-Plane Cyclic Loading. <i>Earthquake Spectra</i>.
DOI: 10.6084/m9.figshare.3482828.v1
title: Tests on Thin Reinforced Concrete Walls Subjected to In-plane and Out-of-plane Cyclic Loading - TW4 (3/4)

description: The present dataset describes an experimental campaign on five thin T-shaped reinforced concrete walls. The tests aimed at assessing the influence of wall thickness on member stability, the role of lap splices on damage distribution and displacement ductility, and the effects of the simultaneous application of out-of-plane loading on the member response.Further data can be downloaded from the links below.<br> If you use the data, please cite: Almeida, J. P., O. Prodan, A. Rosso, and K. Beyer. 2016. Tests on Thin Reinforced Concrete Walls Subjected to in-Plane and out-of-Plane Cyclic Loading. <i>Earthquake Spectra</i>.
DOI: 10.6084/m9.figshare.3482825
title: NCBI.fungiDBselect.genomeonly.tar.gz

description: Custom genome only database used with IMSA+A.<br>https://github.com/JeremyCoxBMI/IMSA-A <br>This is built from NCBI Genomes database and select FungiDB.org genomes.<br><br>
DOI: 10.6084/m9.figshare.3482825.v1
title: NCBI.fungiDBselect.genomeonly.tar.gz

description: Custom genome only database used with IMSA+A.<br>https://github.com/JeremyCoxBMI/IMSA-A <br>This is built from NCBI Genomes database and select FungiDB.org genomes.<br><br>
DOI: 10.6084/m9.figshare.3482822
title: human.DB.tar.gz

description: Human genome database used with IMSA+A.https://github.com/JeremyCoxBMI/IMSA-A
DOI: 10.6084/m9.figshare.3482822.v1
title: human.DB.tar.gz

description: Human genome database used with IMSA+A.https://github.com/JeremyCoxBMI/IMSA-A
DOI: 10.6084/m9.figshare.3482813
title: Gid-to-taxon lookup table

description: This is the gid-to-taxon table for custom genomes-only database for use with the tool IMSA+A.https://github.com/JeremyCoxBMI/IMSA-A This is originally sourced from NCBI, but is an outdated version of database.<br><br><br>
DOI: 10.6084/m9.figshare.3482813.v1
title: Gid-to-taxon lookup table

description: This is the gid-to-taxon table for custom genomes-only database for use with the tool IMSA+A.https://github.com/JeremyCoxBMI/IMSA-A This is originally sourced from NCBI, but is an outdated version of database.<br><br><br>
DOI: 10.6084/m9.figshare.3482810
title: Metatranscriptome simulated datasets of Microbiota

description: Metatranscriptome simulations of Microbiome samples. Simulations are designed to create challenging conditions for taxonomic analysis.
DOI: 10.6084/m9.figshare.3482810.v1
title: Metatranscriptome simulated datasets of Microbiota

description: Metatranscriptome simulations of Microbiome samples. Simulations are designed to create challenging conditions for taxonomic analysis.
DOI: 10.6084/m9.figshare.3482804
title: GroundBeetles.zip

description: Sample coordinates and genetic distances computed between samples<br>
DOI: 10.6084/m9.figshare.3482804.v1
title: GroundBeetles.zip

description: Sample coordinates and genetic distances computed between samples<br>
DOI: 10.6084/m9.figshare.3482753
title: Table S4

description: Table S4: Primers used in this study
DOI: 10.6084/m9.figshare.3482579
title: First record of a non-pollinating fig wasp (Hymenoptera: Sycophaginae) from Dominican amber, with estimation of the size of its host figs

description: Fig trees and their pollinating fig wasps arose about 75 million years ago in the Cretaceous period. Several other groups of chalcid wasps also utilize figs for larval development, including sycophagines, the putative sister group to pollinating fig wasps. Whereas stone and amber fossil pollinators are known, no fossils representing non-pollinating fig wasp groups have been confirmed previously. Here, we describe the first Sycophaginae from the <i>c</i>.15<i>–</i>20 Ma Dominican amber, <i>Idarnes thanatos</i> sp. nov. Farache, Rasplus, Pereira and Compton, and discuss its relationships within the <i>Idarnes carme</i> species group. Additionally, we use linear regression to compare body size, ovipositor sheaths length, and host fig size data from extant <i>Idarnes</i> species to estimate the size of its host figs. <i>Idarnes thanatos</i> was most likely associated with small to medium sized figs (diameter ≤1.0 cm), that were likely to have been dispersed by birds and primates. The discovery of this close relative of extant non-pollinating fig wasps suggests that early Miocene and modern fig wasp communities may share similar ecological and functional features.