cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4737229.v1
title: Bayesian semiparametric reproductive dispersion mixed models for non-normal longitudinal data: estimation and case influence analysis

description: Semiparametric reproductive dispersion mixed model (SPRDMM) is a natural extension of the reproductive dispersion model and the semiparametric mixed model. In this paper, we relax the normality assumption of random effects in SPRDMM and use a truncated and centred Dirichlet process prior to specify random effects, and present the Bayesian P-spline to approximate the smoothing unknown function. A hybrid algorithm combining the block Gibbs sampler and the Metropolis–Hastings algorithm is implemented to sample observations from the posterior distribution. Also, we develop Bayesian case deletion influence measure for SPRDMM based on the <i>φ</i>-divergence and present those computationally feasible formulas. Several simulation studies and a real example are presented to illustrate the proposed methodologies.
DOI: 10.6084/m9.figshare.4737235.v1
title: A risk scoring system to predict coronary stent thrombosis

description: <b>Objective:</b> Stent thrombosis (ST) is a potentially life-threatening complication of percutaneous coronary intervention (PCI). We aimed to develop a scoring system to predict the risk of ST following PCI. <b>Research design and methods:</b> Odds ratios (ORs) for risk factors associated with ST were identified from a meta-analysis based on a systematic literature review, and through consensus expert opinion (Delphi–RAND method). The combined ORs were used to calculate risk scores for acute (within 24 hours), early (within 30 days) and late (31 days to 1 year) ST. Risk scores were validated against patient-level data from the TRITON-TIMI 38 study. Twenty risk factors were identified. <b>Results:</b> The most highly predictive factor for early and late ST was “incomplete duration of dual antiplatelet therapy”. Derived total risk scores ranged from 0 to 22 for acute and early ST, and from 0 to 20 for late ST. Increasing scores were associated with an increasing risk of ST when applied to trial data. Model discrimination was 0.60 (<i>p</i> = .0028), 0.67 (<i>p</i> p <b>Conclusion:</b> Our weighted scoring system may help to stratify ST risk and individualize antiplatelet therapy in patients undergoing PCI.
DOI: 10.6084/m9.figshare.4737313.v3
title: Open tools for biological data integration – hands on example with InterMine

description: Slides for an InterMine training session presented at EMBL-EBI's "Introduction to Omics data integration" training course. Provides hands-on examples of querying genes and gene lists, as well as filtering, enriching, and using InterMine's data visualisations and webservices.
DOI: 10.6084/m9.figshare.4737181
title: hCINAP expression in colorectal cancer

description: The authors declare that the data analysis processes supporting the findings of this study are available within the article and its Supplementary Information files. The TCGA gene expression profile data, as recomputed based on gencode v23, were downloaded from UCSC Xena (http://xena.ucsc.edu/). The TCGA clinical data were downloaded from the GDC Data Portal (https://gdc-portal.nci.nih.gov/), with accession number phs000178.v9.p8 in dbGap. Supplementary Information: For analyzing the <i>hCINAP</i> expression in CRC, we downloaded the recomputed TCGA gene expression datasets for COAD and READ cancer types from the UCSC Xena (http://xena.ucsc.edu/). The gene model was based on gencode v23, and the expression unit is TPM (Transcript per million). The clinical data were downloaded from the GDC Data Portal (https://gdc-portal.nci.nih.gov/). For differential expression analysis, we compiled a selected sample set, including 367 tumor- and 51 normal-samples, in which each sample has information available for clinical variables such as gender, age and race (Supplementary Table1). For expression analysis by pathological stages, we only used those tumor samples with stage information (Supplementary Table1). The dataset used for profiling gene expression by CRC subtypes was compiled based on the results of consensus molecular subtypes (CMSs) described previously [PMID: 26457759] , containing 265 tumor samples (Supplementary Table1).
DOI: 10.6084/m9.figshare.4737232.v1
title: Res in IBS 9mar17.sav

description: Dataset from N=74 (+30 non-participants) subjects with irritable bowel syndrome (Rome III criteria). Of these, n=54 underwent gut-directed hypnotherapy. <br>Group A (n=37) was assessed pre hypnotherapy (T1) and 10 months post hypnotherapy (T2). Group B (n=37) was assessed as a control group at T2. A subset of group 2 (n=16) received also hypnotherapy, and was examined respectively after 10 months (T3). <br><br>Assessed variables comprise factors of resilience:<br>10 item CDRISC (resilience)<br>BFI-K (neuroticism scale)<br>SWE (self-efficacy)<br>STCI (trait cheerfulness scale)<br>CERQ (adaptive/dysfunctional emotion regulation strategies)<br>FSozU (social support)<br><br>and 2. symptom severity, affective status, and wellbeing<br> <br>HADS (psychological distress)<br>IBS-SSS (IBS severity)<br>quality of life visual analogue scales<br><br>All available scores (raw scores or standardized) from these questionnaires are in the file. <br><br>In Group A at T1, IBS-SSS and resilience measures were not captured. <br>Resilience factors were merged to compound scores unweighted (additional) and weighted based on regression coefficients from PCA. Scores and regression coefficients are in the file. Sensitive data such as diagnoses, socioeconomic variables or birth and examination dates were taken out of the file to safeguard anonymity and patient rights.
DOI: 10.6084/m9.figshare.4737157
title: Is maternal education a social vaccine for childhood malaria infection? A cross-sectional study from war-torn Democratic Republic of Congo

description: In zones of violent conflict in the tropics, social disruption leads to elevated child mortality, of which malaria is the leading cause. Understanding the social determinants of malaria transmission may be helpful to optimize malaria control efforts. We conducted a cross-sectional study of healthy children aged 2 months to 5 years attending well-child and/or immunization visits in the Democratic Republic of Congo (DRC). Six hundred and forty-seven children were tested for malaria antigenemia by rapid diagnostic test and the accompanying parent or legal guardian simultaneously completed a survey questionnaire related to demographics, socioeconomic status, maternal education, as well as bednet use and recent febrile illness. We examined the associations between variables using multivariable logistic regression analysis, chi-squared statistic, Fisher’s exact test, and Spearman’s rank correlation, as appropriate. One hundred and twenty-three out of the 647 (19%) children in the study tested positive for malaria. Higher levels of maternal education were associated with a lower risk of malaria in their children. The prevalence of malaria in children of mothers with no education, primary school, and beyond primary was 41/138 (30%), 41/241 (17%), and 39/262 (15%), respectively (<i>p =</i> 0.001). In a multivariable logistic regression model adjusting for the effect of a child’s age and study site, the following remained significant predictors of malaria antigenemia: maternal education, number of children under five per household, and HIV serostatus. Higher maternal education, through several putative causal pathways, was associated with lower malaria prevalence among children in the DRC. Our findings suggest that maternal education might be an effective ‘social vaccine’ against malaria in the DRC and globally.
DOI: 10.6084/m9.figshare.4737181.v1
title: Data availability for bioinformatics.docx

description: The authors declare that the data analyses processes supporting the findings of this study are available within the article and its Supplementary Information files. TCGA gene expression profile data recomputed based on gencode v23 are downloaded from UCSC Xena (http://xena.ucsc.edu/). The TCGA clinical data are downloaded from GDC Data Portal (https://gdc-portal.nci.nih.gov/, with an accession number of phs000178.v9.p8 in dbGap).
DOI: 10.6084/m9.figshare.4737154
title: Restraint stress differentially regulates inflammation and glutamate receptor gene expression in the hippocampus of C57BL/6 and BALB/c mice

description: The inbred mouse strains, C57BL/6 and BALB/c have been used widely in preclinical psychiatric research. The differences in stress susceptibility of available strains has provided a useful platform to test pharmacological agents and behavioral responses. Previous brain gene profiling efforts have indicated that the inflammation and immune response gene pathway is the predominant gene network in the differential stress response of BALB/c and C57BL/6 mice. The implication is that a composite stress paradigm that includes a sequence of extended, varied and unpredictable stressors induces inflammation-related genes in the hippocampus. We hypothesized that the regulation of inflammation genes in the brain could constitute a primary stress response and tested this by employing a simple stress protocol, repeated exposure to the same stressor for 10 days, 2 h of restraint per day. We examined stress-induced regulation of 13 proinflammatory cytokine genes in male BALB/c and C57BL/6 mice using quantitative PCR. Elevated cytokine genes included tumor necrosis factor alpha (<i>TNFα</i>), interleukin 6 (<i>IL6</i>), interleukin 10 (<i>IL10</i>), tumor necrosis factor (TNF) super family members and interleukin 1 receptor 1 (<i>IL1R1</i>). In addition, we examined restraint stress-induced regulation of 12 glutamate receptor genes in both strains. Our results show that restraint stress is sufficient to elevate the expression of inflammation-related genes in the hippocampus of both BABLB/c and C57BL/6 mice, but they differ in the genes that are induced and the magnitude of change. Cell types that are involved in this response include endothelial cells and astrocytes.Lay summaryRepeated exposure to a simple restraint stress altered the activities of genes involved in inflammation and the functions of the excitatory neurotransmitter, glutamate. These changes in the hippocampus of the mouse brain showed differences that were dependent on the strain of mice and the length of the stress exposure. The effects of stress on activity of these genes may lead to alterations in behavior. Repeated exposure to a simple restraint stress altered the activities of genes involved in inflammation and the functions of the excitatory neurotransmitter, glutamate. These changes in the hippocampus of the mouse brain showed differences that were dependent on the strain of mice and the length of the stress exposure. The effects of stress on activity of these genes may lead to alterations in behavior.
DOI: 10.6084/m9.figshare.4737157.v1
title: Is maternal education a social vaccine for childhood malaria infection? A cross-sectional study from war-torn Democratic Republic of Congo

description: In zones of violent conflict in the tropics, social disruption leads to elevated child mortality, of which malaria is the leading cause. Understanding the social determinants of malaria transmission may be helpful to optimize malaria control efforts. We conducted a cross-sectional study of healthy children aged 2 months to 5 years attending well-child and/or immunization visits in the Democratic Republic of Congo (DRC). Six hundred and forty-seven children were tested for malaria antigenemia by rapid diagnostic test and the accompanying parent or legal guardian simultaneously completed a survey questionnaire related to demographics, socioeconomic status, maternal education, as well as bednet use and recent febrile illness. We examined the associations between variables using multivariable logistic regression analysis, chi-squared statistic, Fisher’s exact test, and Spearman’s rank correlation, as appropriate. One hundred and twenty-three out of the 647 (19%) children in the study tested positive for malaria. Higher levels of maternal education were associated with a lower risk of malaria in their children. The prevalence of malaria in children of mothers with no education, primary school, and beyond primary was 41/138 (30%), 41/241 (17%), and 39/262 (15%), respectively (<i>p =</i> 0.001). In a multivariable logistic regression model adjusting for the effect of a child’s age and study site, the following remained significant predictors of malaria antigenemia: maternal education, number of children under five per household, and HIV serostatus. Higher maternal education, through several putative causal pathways, was associated with lower malaria prevalence among children in the DRC. Our findings suggest that maternal education might be an effective ‘social vaccine’ against malaria in the DRC and globally.
DOI: 10.6084/m9.figshare.4737163.v1
title: Neonatal outcomes of preterm twins according to mode of birth and presentation

description: <b>Purpose:</b> To compare neonatal outcomes of twins delivered &lt;33 weeks’ gestation in tertiary centers in Canada according to the mode of birth and presentation. <b>Materials and methods:</b> This retrospective cohort from the Canadian Neonatal Network database studied preterm twins born from 24 + 0 to 32 + 6 weeks’ gestation between 2005 and 2012. Twins were grouped by the mode of birth: both vaginal, combined vaginal/cesarean section (CS), and both CS. Additionally, twins were grouped by the mode of presentation: both vertex, vertex/breech, breech/vertex, and both breech. The primary outcome was a composite of mortality or severe neonatal morbidity (severe neurological injury [intraventricular hemorrhage grade 3/4 or periventricular leukomalacia], bronchopulmonary dysplasia, retinopathy of prematurity, and necrotizing enterocolitis). <b>Results:</b> Of the 6636 twins, 1934 (29%) were delivered vaginally, 418 (6%) by combined vaginal birth/CS, and 4284 (65%) were born by CS. The composite did not differ between the groups. However, severe neurological injury was decreased (adjusted odds ratio [AOR], 0.77; 95% confidence interval [CI], 0.61–0.98) and respiratory distress syndrome (AOR, 1.34; 95%CI, 1.15–1.56) was increased when both the twins were delivered by CS. <b>Conclusions:</b> Preterm twin infants born via CS experienced less severe neurological injury when compared to those delivered vaginally, but had an increase in respiratory distress syndrome.
DOI: 10.6084/m9.figshare.4737181.v3
title: hCINAP expression in colorectal cancer

description: The authors declare that the data analysis processes supporting the findings of this study are available within the article and its Supplementary Information files. The TCGA gene expression profile data, as recomputed based on gencode v23, were downloaded from UCSC Xena (http://xena.ucsc.edu/). The TCGA clinical data were downloaded from the GDC Data Portal (https://gdc-portal.nci.nih.gov/), with accession number phs000178.v9.p8 in dbGap. Supplementary Information: For analyzing the <i>hCINAP</i> expression in CRC, we downloaded the recomputed TCGA gene expression datasets for COAD and READ cancer types from the UCSC Xena (http://xena.ucsc.edu/). The gene model was based on gencode v23, and the expression unit is TPM (Transcript per million). The clinical data were downloaded from the GDC Data Portal (https://gdc-portal.nci.nih.gov/). For differential expression analysis, we compiled a selected sample set, including 367 tumor- and 51 normal-samples, in which each sample has information available for clinical variables such as gender, age and race (Supplementary Table1). For expression analysis by pathological stages, we only used those tumor samples with stage information (Supplementary Table1). The dataset used for profiling gene expression by CRC subtypes was compiled based on the results of consensus molecular subtypes (CMSs) described previously [PMID: 26457759] , containing 265 tumor samples (Supplementary Table1).
DOI: 10.6084/m9.figshare.4737148
title: An update on the molecular diagnosis of congenital heart disease: focus on loss-of-function mutations

description: <b>Introduction</b>: Congenital heart disease (CHD) is the most common birth defect in humans. In spite of tremendous advance in medical care, CHD is still a major contributor to substantial morbidity and mortality. Aggregating evidence demonstrates that genetic defects play a pivotal role in the pathogenesis of CHD, and an increasing number of genetic mutations have been identified to be responsible for CHD. <b>Areas covered</b>: This paper is restricted to the molecular diagnosis of CHD, and highlights loss-of-function mutations in the genes associated with CHD. The newly-made progress in the molecular genetics of CHD is reviewed in this article. <b>Expert commentary</b>: Heart development is a precisely-coordinated biological process, involving in cellular proliferation, differentiation, migration, and integrated morphogenetic interactions, and interruption of this process predominantly by genetic risk factors leads to CHD. To date, mutations in over 60 genes have been causally linked to CHD, of which most mutations cause a loss-of-function effect. Using next generation sequencing technology and data processing software, new CHD-associated genes will be more easily discovered. Identification of the CHD-causative genes is of significant importance in genetic diagnosis, early prophylaxis and personalized treatment of CHD patients.
DOI: 10.6084/m9.figshare.4737154.v1
title: Restraint stress differentially regulates inflammation and glutamate receptor gene expression in the hippocampus of C57BL/6 and BALB/c mice

description: The inbred mouse strains, C57BL/6 and BALB/c have been used widely in preclinical psychiatric research. The differences in stress susceptibility of available strains has provided a useful platform to test pharmacological agents and behavioral responses. Previous brain gene profiling efforts have indicated that the inflammation and immune response gene pathway is the predominant gene network in the differential stress response of BALB/c and C57BL/6 mice. The implication is that a composite stress paradigm that includes a sequence of extended, varied and unpredictable stressors induces inflammation-related genes in the hippocampus. We hypothesized that the regulation of inflammation genes in the brain could constitute a primary stress response and tested this by employing a simple stress protocol, repeated exposure to the same stressor for 10 days, 2 h of restraint per day. We examined stress-induced regulation of 13 proinflammatory cytokine genes in male BALB/c and C57BL/6 mice using quantitative PCR. Elevated cytokine genes included tumor necrosis factor alpha (<i>TNFα</i>), interleukin 6 (<i>IL6</i>), interleukin 10 (<i>IL10</i>), tumor necrosis factor (TNF) super family members and interleukin 1 receptor 1 (<i>IL1R1</i>). In addition, we examined restraint stress-induced regulation of 12 glutamate receptor genes in both strains. Our results show that restraint stress is sufficient to elevate the expression of inflammation-related genes in the hippocampus of both BABLB/c and C57BL/6 mice, but they differ in the genes that are induced and the magnitude of change. Cell types that are involved in this response include endothelial cells and astrocytes.Lay summaryRepeated exposure to a simple restraint stress altered the activities of genes involved in inflammation and the functions of the excitatory neurotransmitter, glutamate. These changes in the hippocampus of the mouse brain showed differences that were dependent on the strain of mice and the length of the stress exposure. The effects of stress on activity of these genes may lead to alterations in behavior. Repeated exposure to a simple restraint stress altered the activities of genes involved in inflammation and the functions of the excitatory neurotransmitter, glutamate. These changes in the hippocampus of the mouse brain showed differences that were dependent on the strain of mice and the length of the stress exposure. The effects of stress on activity of these genes may lead to alterations in behavior.
DOI: 10.6084/m9.figshare.4737148.v1
title: An update on the molecular diagnosis of congenital heart disease: focus on loss-of-function mutations

description: <b>Introduction</b>: Congenital heart disease (CHD) is the most common birth defect in humans. In spite of tremendous advance in medical care, CHD is still a major contributor to substantial morbidity and mortality. Aggregating evidence demonstrates that genetic defects play a pivotal role in the pathogenesis of CHD, and an increasing number of genetic mutations have been identified to be responsible for CHD. <b>Areas covered</b>: This paper is restricted to the molecular diagnosis of CHD, and highlights loss-of-function mutations in the genes associated with CHD. The newly-made progress in the molecular genetics of CHD is reviewed in this article. <b>Expert commentary</b>: Heart development is a precisely-coordinated biological process, involving in cellular proliferation, differentiation, migration, and integrated morphogenetic interactions, and interruption of this process predominantly by genetic risk factors leads to CHD. To date, mutations in over 60 genes have been causally linked to CHD, of which most mutations cause a loss-of-function effect. Using next generation sequencing technology and data processing software, new CHD-associated genes will be more easily discovered. Identification of the CHD-causative genes is of significant importance in genetic diagnosis, early prophylaxis and personalized treatment of CHD patients.
DOI: 10.6084/m9.figshare.4737181.v2
title: hCINAP expression in colorectal cancer

description: For analyzing the hCINAP gene in CRC, we download the recomputed TCGA gene expression datasets of COAD and READ cancer types, which is based on gencode v23 gene model, from UCSC Xena (http://xena.ucsc.edu/). The clinical data are downloaded from GDC Data Portal (https://gdc-portal.nci.nih.gov/). The expression unit is TPM (Transcript per million).For differential expression analysis, we compile a core sample set in which each sample has information available for clinical variables such as gender, age and race. The core sample set includes 367 tumor samples and 51 normal samples (Supplementary Table1). For expression analysis in different pathological stage, we only use the tumor samples and filter out the samples lack of stage information (Supplementary Table1). The dataset used for profiling gene expression across different CRC subtypes is compiled based on the results of consensus molecular subtypes(CMSs)[citation], containing 265 tumor samples (Supplementary Table1).
DOI: 10.5281/zenodo.3994033
title: Dataset for: Majority of olfactory-receptor neurons have individually neutral effects on behavior

description: <strong>Summary</strong> Animals use olfactory receptors to navigate danger, mates, and food. However, for complex olfactory systems, it is unknown what proportion of olfactory-receptor neurons (ORNs) can individually drive avoidance or attraction. Similarly it is unclear what rules govern behavioral responses to ORN-activity combinations. We used optogenetic analysis in Drosophila to map the behavior elicited by nearly all ORN classes; just one-fifth of ORNs drove either avoidance or attraction. Although wind and hunger are closely linked to olfaction, neither context had much effect on single-ORN-class behavior. Various models have been used to explain the way multiple ORNs combine their behavioral influences, including several simple pooling rules. To assess these, we activated two-way combinations and compared patterns of single- and double-ORN responses: these comparisons were inconsistent with simple pooling. We conclude that the majority of ORN types have neutral behavioral effects individually, but participate in broad, odor-elicited ensembles with potent behavioral effects arising from complex interactions.