cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5829633.v1
title: Quantifying an Adherence Path-Specific Effect of Antiretroviral Therapy in the Nigeria PEPFAR Program

description: Since the early 2000s, evidence has accumulated for a significant differential effect of first-line antiretroviral therapy (ART) regimens on human immunodeficiency virus (HIV) viral load suppression. This finding was replicated in our data from the Harvard President’s Emergency Plan for AIDS Relief (PEPFAR) program in Nigeria. Investigators were interested in finding the source of these differences, that is, understanding the mechanisms through which one regimen outperforms another, particularly via adherence. This question can be naturally formulated via mediation analysis with adherence playing the role of a mediator. Existing mediation analysis results, however, have relied on an assumption of no exposure-induced confounding of the intermediate variable, and generally require an assumption of no unmeasured confounding for nonparametric identification. Both assumptions are violated by the presence of drug toxicity. In this article, we relax these assumptions and show that certain path-specific effects remain identified under weaker conditions. We focus on the path-specific effect solely mediated by adherence and not by toxicity and propose an estimator for this effect. We illustrate with simulations and present results from a study applying the methodology to the Harvard PEPFAR data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5829624
title: Bayesian Nonparametric Ordination for the Analysis of Microbial Communities

description: Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU counts across heterogeneous biological samples. In the microbial ecology community, ordination methods are frequently used to investigate latent factors or clusters that capture and describe variations of OTU counts across biological samples. It remains important to evaluate how uncertainty in estimates of each biological sample’s microbial distribution propagates to ordination analyses, including visualization of clusters and projections of biological samples on low-dimensional spaces. We propose a Bayesian analysis for dependent distributions to endow frequently used ordinations with estimates of uncertainty. A Bayesian nonparametric prior for dependent normalized random measures is constructed, which is marginally equivalent to the normalized generalized Gamma process, a well-known prior for nonparametric analyses. In our prior, the dependence and similarity between microbial distributions is represented by latent factors that concentrate in a low-dimensional space. We use a shrinkage prior to tune the dimensionality of the latent factors. The resulting posterior samples of model parameters can be used to evaluate uncertainty in analyses routinely applied in microbiome studies. Specifically, by combining them with multivariate data analysis techniques we can visualize credible regions in ecological ordination plots. The characteristics of the proposed model are illustrated through a simulation study and applications in two microbiome datasets. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5829624.v1
title: Bayesian Nonparametric Ordination for the Analysis of Microbial Communities

description: Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU counts across heterogeneous biological samples. In the microbial ecology community, ordination methods are frequently used to investigate latent factors or clusters that capture and describe variations of OTU counts across biological samples. It remains important to evaluate how uncertainty in estimates of each biological sample’s microbial distribution propagates to ordination analyses, including visualization of clusters and projections of biological samples on low-dimensional spaces. We propose a Bayesian analysis for dependent distributions to endow frequently used ordinations with estimates of uncertainty. A Bayesian nonparametric prior for dependent normalized random measures is constructed, which is marginally equivalent to the normalized generalized Gamma process, a well-known prior for nonparametric analyses. In our prior, the dependence and similarity between microbial distributions is represented by latent factors that concentrate in a low-dimensional space. We use a shrinkage prior to tune the dimensionality of the latent factors. The resulting posterior samples of model parameters can be used to evaluate uncertainty in analyses routinely applied in microbiome studies. Specifically, by combining them with multivariate data analysis techniques we can visualize credible regions in ecological ordination plots. The characteristics of the proposed model are illustrated through a simulation study and applications in two microbiome datasets. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5829318
title: Argonaute2 and LaminB modulate gene expression by controlling chromatin topology

description: Code and supplemental data Nazer et al 2018 PLOS Genetics.<br><br><b>nazer_et_al.zip</b>: contains the code and instructions for regenerating the figures.<br><b><br>nazer_et_al_generated_figures.zip</b>: contains the figures and reports created by running the above code.<br>
DOI: 10.6084/m9.figshare.5829318.v1
title: AGO2 and LaminB

description: Code and supplemental data for generating the figures in Nazer et al 2018.<br>
DOI: 10.15131/shef.data.5829120
title: Data for paper "Extended discrete element method can evaluate the effect of time dependency and translation of the talus on the estimation of cartilage pressure at the ankle joint"

description: Input kinematics and ankle forces are included as MATLAB file. <br><br>The Extended Discrete Element Method has been used to compute the ankle joint contact pressure distribution. <br>For details email ibenemerito1@sheffield.ac.uk
DOI: 10.15131/shef.data.5829120.v1
title: Data for paper "Extended discrete element method can evaluate the effect of time dependency and translation of the talus on the estimation of cartilage pressure at the ankle joint"

description: Input kinematics and ankle forces are included as MATLAB file. <br><br>The Extended Discrete Element Method has been used to compute the ankle joint contact pressure distribution. <br>For details email ibenemerito1@sheffield.ac.uk
DOI: 10.6084/m9.figshare.5828211
title: Enlargements data.xlsx

description: Enlargements dataset from https://doi.org/10.1007/s10649-017-9788-x<br>Foster, C. (2018). Developing mathematical fluency: Comparing exercises and rich tasks. <i>Educational Studies in Mathematics</i>.<br>
DOI: 10.6084/m9.figshare.5828211.v1
title: Enlargements data.xlsx

description: Enlargements dataset from https://doi.org/10.1007/s10649-017-9788-x<br>Foster, C. (2018). Developing mathematical fluency: Comparing exercises and rich tasks. <i>Educational Studies in Mathematics</i>.<br>
DOI: 10.6084/m9.figshare.5828163
title: Raw data files and mapping file for 'Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms'.

description: Raw data files and mapping file for 'Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms'.
DOI: 10.6084/m9.figshare.5828163.v1
title: Raw data files and mapping file for 'Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms'.

description: Raw data files and mapping file for 'Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms'.
DOI: 10.6084/m9.figshare.5828082
title: Raw data Currents HD.xlsx

description: Data reporting for PLOS Currents Huntington Disease.
DOI: 10.6084/m9.figshare.5828082.v1
title: Raw data Currents HD.xlsx

description: Data reporting for PLOS Currents Huntington Disease.
DOI: 10.6084/m9.figshare.5827770
title: VCRT

description: The Vanderbilt Chest Radiograph Test (VCRT) was designed to be a reliable measure of individual differences in perceptual abilities for radiograph-related decision-making in novices. <br>Sunday, M. A., Donnelly, E., & Gauthier, I. (2017). Individual differences in perceptual abilities in medical imaging: the Vanderbilt Chest Radiograph Test. <i>Cognitive research: principles and implications</i>, <i>2</i>(1), 36.<br>
DOI: 10.6084/m9.figshare.5827695
title: Databook for Nature Energy perspective on coal to gas generation

description: A spreadsheet containing the data used to produce the Figures in the Nature Energy publication - ' Rapid fuel switching from coal to natural gas through effective carbon pricing'<br>
DOI: 10.6084/m9.figshare.5827677
title: Structural coupling data set

description: Structural coupling data describing the architectural dependencies between .java files from various commits of open-source software projects.<br>
DOI: 10.6084/m9.figshare.5827653
title: Coordinates of knots used for geoadditive modelling in Switzerland

description: Coordinates of 100 knots, regularly spaced across Switzerland. These knots are used to compute geoadditive models in the following publication: Guélat J., Kéry M. 2018. Methods in Ecology and Evolution<br>
DOI: 10.6084/m9.figshare.5827635
title: Raw Data and Simulation Code

description: The compressed file "Raw Data and Simulation Code.zip" contains raw data obtained in experiments, a file explaining the data content (readme.pdf), as well as the simulation code (Mathematica notebook) for performing numerical simulations.
DOI: 10.6084/m9.figshare.5827620
title: Supplementary Datasets (1.1-1.8). from Evidence for parent-of-origin effects and interparental conflict in seeds of an ancient flowering plant lineage

description: Supplementary Datasets
DOI: 10.6084/m9.figshare.5827620.v1
title: Supplementary Datasets (1.1-1.8). from Evidence for parent-of-origin effects and interparental conflict in seeds of an ancient flowering plant lineage

description: Supplementary Datasets
DOI: 10.25375/uct.5827572
title: Survey of participation capability sufficiency in 4 EIA public participation case studies using evaluative Likert scales

description: This data set presents the non-mandatory responses of 129 stakeholders in four South African Environmental Impact Assessments. the research was conducted between 2014 and 2015. The responses indicate stockholder's self-assessed capabilities for achieving meaningful public participation and reflects their participation experiences.
DOI: 10.6084/m9.figshare.5827494
title: Dictionaries

description: Dictionaries used.
DOI: 10.6084/m9.figshare.5827470
title: PFS数据.sav

description: 105 例 YHJD vs Placebo
DOI: 10.6084/m9.figshare.5827470.v1
title: PFS数据.sav

description: 105 例 YHJD vs Placebo
DOI: 10.6084/m9.figshare.5827452
title: Supplementary Material for: Direct Aspiration Catheter Fracture and Retrieval during Neurothrombectomy

description: <b><i>Background:</i></b> Application of direct aspiration catheters has revolutionized acute stroke care and has led to significant improvement in clinical outcome with a good safety profile. Catheter fracture and retention is a rare but potentially devastating complication. <b><i>Case Description:</i></b> Here we present two cases of acute stroke complicated by aspiration catheter fracture and retention. Successful catheter retrieval and revascularization was achieved in both cases. The stenosis or tortuosity of vascular anatomy appears to be the probable contributor to catheter breakage by anchoring the catheter with resultant fracture at the constraint point from catheter withdrawal tensile stress. <b><i>Conclusion:</i></b> This report describes application of snare devices in retrieving a broken catheter during thrombectomy in the anterior and posterior circulation, and therefore presents a technique that can be safely utilized to address catheter breakage complicating thrombectomy in different vascular anatomic locations.
DOI: 10.6084/m9.figshare.5827434
title: Supplementary Material for: Protein Profile of the Acquired Enamel Pellicle after Rinsing with Whole Milk, Fat-Free Milk, and Water: An in vivo Study

description: This study detected changes in the protein profile of the acquired enamel pellicle (AEP) formed in vivo after rinsing with whole milk, fat-free milk, or water. Nine subjects in good oral condition took part in the study. The acquired pellicle was formed in the morning, for 120 min, after prophylaxis with pumice. Following this, the volunteers rinsed with 10 mL of whole milk, fat-free milk, or deionized water for 30 s, following a blinded crossover protocol. After 60 min, the pellicle was collected with filter paper soaked in 3% citric acid and processed for analysis by liquid chromatography-electrospray ionization tandem mass spectrometry. The obtained tandem mass spectrometry spectra were searched against a human protein database (Swiss-Prot). The proteomic data related to protein quantification were analysed using the PLGS software. A total of 260 proteins were successfully identified in the AEP samples collected from all groups. Forty-nine were common to all 3 groups, while 72, 62, and 49 were specific to the groups rinsing with whole milk, fat-free milk, and water, respectively. Some were typical components of the AEP, such as cystatin-B, cystatin-SN, isoforms of α-amylase, IgA and IgG, lysozyme C, protein S100 A78, histatin-1, proline-rich protein 27, statherin, and lactotransferrin. Other proteins are not commonly described as part of the AEP but could act in defence of the organism against pathogens. Distinct proteomic profiles were found in the AEP after rinsing with whole or fat-free milk, which could have an impact on bacterial adhesion and tooth dissolution. The use of fat-free milk could favourably modulate the adhesion of bacteria to the AEP as well as biofilm formation when compared with whole milk.
DOI: 10.6084/m9.figshare.5827431
title: Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements

description: Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.
DOI: 10.6084/m9.figshare.5827431.v2
title: Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements

description: Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.
DOI: 10.6084/m9.figshare.5827431.v1
title: Evolutionary Conservation of DNA Methylation in CpG Sites within Ultraconserved Noncoding Elements

description: Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.
DOI: 10.6084/m9.figshare.5827425
title: Supplementary Material for: The Effect of a High-Fat Diet on the Development of Abdominal Aortic Aneurysm in a Vascular Hypoperfusion-Induced Animal Model

description: Abdominal aortic aneurysm (AAA) is a vascular disease characterized by chronic inflammation in the infrarenal aorta. Most cases of AAA remain asymptomatic until rupture, and the mortality rate of patients with AAA rupture is very high. Currently, the relation between dietary habits and AAA development remains unknown. In this study, we evaluated the effects of a high-fat diet on the development of AAA in a vascular hypoperfusion-induced animal model. The risk of AAA rupture and AAA diameter in the high-fat group significantly increased compared with those in the control group. The number and size of adipocytes in the vascular wall in the high-fat group significantly increased as compared with those in the control group. Additionally, the collagen-positive sections in the areas with adipocytes significantly decreased as compared with those without adipocytes. The protein levels of matrix metalloproteinase (MMP)-2, MMP-9, and MMP-12, and macrophage-positive areas in the parts with adipocytes also significantly increased as compared with those without adipocytes. These data suggested that AAA rupture risk increased through accelerating chronic inflammation due to the accumulation of adipocytes in the vascular wall in the high-fat group.
DOI: 10.6084/m9.figshare.5827425.v1
title: Supplementary Material for: The Effect of a High-Fat Diet on the Development of Abdominal Aortic Aneurysm in a Vascular Hypoperfusion-Induced Animal Model

description: Abdominal aortic aneurysm (AAA) is a vascular disease characterized by chronic inflammation in the infrarenal aorta. Most cases of AAA remain asymptomatic until rupture, and the mortality rate of patients with AAA rupture is very high. Currently, the relation between dietary habits and AAA development remains unknown. In this study, we evaluated the effects of a high-fat diet on the development of AAA in a vascular hypoperfusion-induced animal model. The risk of AAA rupture and AAA diameter in the high-fat group significantly increased compared with those in the control group. The number and size of adipocytes in the vascular wall in the high-fat group significantly increased as compared with those in the control group. Additionally, the collagen-positive sections in the areas with adipocytes significantly decreased as compared with those without adipocytes. The protein levels of matrix metalloproteinase (MMP)-2, MMP-9, and MMP-12, and macrophage-positive areas in the parts with adipocytes also significantly increased as compared with those without adipocytes. These data suggested that AAA rupture risk increased through accelerating chronic inflammation due to the accumulation of adipocytes in the vascular wall in the high-fat group.
DOI: 10.6084/m9.figshare.5827398
title: SO_question_48407650.rds

description: A list of shared genes between scaffolds in a metagenome. Example data for a question asked on stackoverflow:<br>
DOI: 10.6084/m9.figshare.5827398.v1
title: SO_question_48407650.rds

description: A list of shared genes between scaffolds in a metagenome. Example data for a question asked on stackoverflow:<br>
DOI: 10.6084/m9.figshare.5827386
title: Supplementary Material for: Effect of Oridonin on Cytochrome P450 Expression and Activities in HepaRG Cell

description: Oridonin, the major terpene found in <i>Rabdosia rubescens</i>, is widely used as a dietary supplement or therapeutic drug. However, the effects of oridonin on major CYP450s are still unclear. As oridonin can enhance the effect of other clinical drugs, in this study, we investigated the influence of oridonin on CYP450s mRNA expression and its impact on activities in human HepaRG cell to evaluate the safety by studying its potential drug interaction. HepaRG cells were cultured with series concentrations of oridonin (1, 5, 10, and 20 μmol/L), and the major CYP450s mRNA and protein expression, as well as enzyme activities were analyzed by real-time polymerase chain reaction, Western blot analysis and UPLC-MS/MS-based metabolite assay. In general, ordonin has induced effects on the major member of CYP450s mRNA and protein expression, as well as on the enzyme activity in human HepaRG cells, especially on CYP3A4 and CYP2C9. To our knowledge, this is the first systematic research about the inductive effects of oridonin on the major member of CYP450s in human cell line. These results may provide at least partly of the basis for potential drug-drug interactions and oridonin should be used with caution to avoid potential risk.