cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5603203.v4
title: GWAS of Alzheimer's disease progression score

description: Summary statistics for the three GWAS of 1517 Caucasian ADNI subjects described in Scelsi et al. - "Genetic study of multimodal imaging Alzheimer’s disease progression score implicates novel loci", manuscript under review at BRAIN (submission ID: BRAIN-2017-01752).1) FILE: ADNI_FullSample_gwas_newPC.hippo.assoc.linear; DESCRIPTION: GWAS (chromosomes 1-22) for bilateral hippocampal volume, correcting for age, sex, years of education, PC1-2, number of APOE4 alleles2) FILE: ADNI_FullSample_gwas_newPC.amyloid.assoc.linear; DESCRIPTION: GWAS (chromosomes 1-22) for cortical PET SUVR, correcting for age, sex, years of education, PC1-2, number of APOE4 alleles3) FILE: ADNI_FullSample_gwas_newPC.DPS.amyhippocovar.assoc.linear; DESCRIPTION: GWAS (chromosomes 1-22) for Disease Progression Score (DPS), correcting for age, sex, years of education, PC1-2, number of APOE4 alleles, baseline hippocampal volume, baseline PET SUVR4) FILE: ADNI_FullSample_chrX_newPC.hippo.EDUcovar.xstrat.linear; DESCRIPTION: Sex-stratified (Stouffer's method) association test of chromosome X for bilateral hippocampal volume, correcting for age, years of education, PC1-2, number of APOE4 alleles5) FILE: ADNI_FullSample_chrX_newPC.amyloid.EDUcovar.xstrat.linear; DESCRIPTION: Sex-stratified (Stouffer's method) association test of chromosome X for cortical PET SUVR, correcting for age, years of education, PC1-2, number of APOE4 alleles6) FILE: ADNI_FullSample_chrX_newPC.DPSupdate.amyhippoEDUcovar.xstrat.linear; DESCRIPTION: Sex-stratified (Stouffer's method) association test of chromosome X for DPS, correcting for age, years of education, PC1-2, number of APOE4 alleles, baseline hippocampal volume, baseline PET SUVR
DOI: 10.6084/m9.figshare.5602807.v1
title: Dataset for: Reference Values of Renal Tubular Function Tests Are Dependent On Age And Kidney Function

description: Background: Electrolyte disorders due to tubular disorders are rare, and knowledge about validated clinical diagnostic tools such as tubular function tests is sparse. Reference values for tubular function tests are based on studies with small sample size in young healthy volunteers. Patients with tubular disorders however frequently are older and can have a compromised renal function. We therefore evaluated four tubular function tests in individuals with different ages and renal function. Methods: We performed furosemide, thiazide, furosemide-fludrocortisone and desmopressin tests in healthy individuals aged 18 to 50 years, healthy individuals aged more than 50 years and individuals with compromised renal function. For each tubular function test we included 10 individuals per group. Results: The responses in young healthy individuals were in line with previously reported values in literature. The maximal increase in fractional chloride excretion after furosemide was below the lower limit of young healthy individuals in 5/10 older subjects and in 2/10 patients with compromised renal function. The maximal increase in fractional chloride excretion after thiazide was below the lower limit of young healthy individuals in 6/10 older subjects and in 7/10 patients with compromised renal function. Median maximal urine osmolality after desmopressin was 1002 mosmol/kg H2O in young healthy individuals, 820 mosmol/kg H2O in older subjects and 624 mosmol/kg H2O in patients with compromised renal function. Conclusions: Reference values for tubular function tests obtained in young healthy adults cannot simply be extrapolated to older patients or patients with compromised kidney function. Larger validation studies are needed to define true reference values in these patient categories.
DOI: 10.6084/m9.figshare.5602768
title: Supplementary Material for: Exploring Parental Expectations and Experiences Around “Gentle” and “Standard” Caesarean Section

description: <b><i>Background/Aims:</i></b> “Gentle” or “natural” cesarean sections are implemented to improve parental satisfaction. The objective of this study was to investigate whether there is a need for adopting such a gentle approach. <b><i>Methods:</i></b> We recruited those with low-risk pregnancies scheduled for elective cesarean delivery at term. Three questionnaires were administered to both partners: prior to delivery, 2-5 days after delivery, and 6 weeks postpartum. Questionnaires assessed the couple's expectations, fears, and satisfaction prior to and after cesarean section. Additionally, participants attended 2 structured interviews: one prior to delivery and one 6 weeks after delivery. <b><i>Results:</i></b> Fifteen couples underwent a “standard” cesarean section (group 1) and 6 underwent a “gentle” section (group 2). Overall, parental satisfaction with cesarean section was high. However, women in the standard group felt less involved in childbirth and both groups still preferred vaginal delivery in light of eventual future pregnancies. Participants in group 2 showed less fear of childbirth after delivery than prior to delivery. There were no differences in total questionnaire scores between groups or between mothers and partners. <b><i>Conclusion:</i></b> This study shows that there is room for improvement in satisfaction levels around cesarean section, even though satisfaction is generally high. A “gentle” cesarean section may help to achieve this.
DOI: 10.6084/m9.figshare.5602732
title: Genotoxic effects of food contact recycled paperboard extracts on two human hepatic cell lines

description: Food contact paperboards may be a potential source of food contamination as they can release chemicals (intentionally added or not), especially recycled paperboards. This study assessed the <i>in vitro</i> genotoxicity of food contact paperboard samples from a manufacturer, collected at the beginning and at the end of a recycling production chain. Samples were extracted in water to mimic a wet food contact. Different genotoxic endpoints were evaluated in two human hepatic cell lines (HepG2 and HepaRG) using bioassays: γH2AX and p53 activation, primary DNA damage with the comet assay and micronucleus formation. It was found that the samples from the beginning and the end of the production chain induced, with the same potency, γH2AX and p53-ser15 activation and DNA damage with the comet assay. The micronucleus assay was negative with the paperboard extract from the beginning of the chain, whereas positive data were observed for the end paperboard extract. These results indicate that samples from recycled food contact paperboard can induce <i>in vitro</i> genotoxic effects in this study’s experimental conditions.
DOI: 10.6084/m9.figshare.5602720
title: Geochemistry data of Nolans Bore obtained by LA-ICP-MS

description: LAICPMS data of minerals from Nolans Bore.<br>
DOI: 10.6084/m9.figshare.5602732.v2
title: Genotoxic effects of food contact recycled paperboard extracts on two human hepatic cell lines

description: Food contact paperboards may be a potential source of food contamination as they can release chemicals (intentionally added or not), especially recycled paperboards. This study assessed the <i>in vitro</i> genotoxicity of food contact paperboard samples from a manufacturer, collected at the beginning and at the end of a recycling production chain. Samples were extracted in water to mimic a wet food contact. Different genotoxic endpoints were evaluated in two human hepatic cell lines (HepG2 and HepaRG) using bioassays: γH2AX and p53 activation, primary DNA damage with the comet assay and micronucleus formation. It was found that the samples from the beginning and the end of the production chain induced, with the same potency, γH2AX and p53-ser15 activation and DNA damage with the comet assay. The micronucleus assay was negative with the paperboard extract from the beginning of the chain, whereas positive data were observed for the end paperboard extract. These results indicate that samples from recycled food contact paperboard can induce <i>in vitro</i> genotoxic effects in this study’s experimental conditions.
DOI: 10.6084/m9.figshare.5602423
title: Procalcitonin performance in detecting serious and invasive bacterial infections in children with fever without apparent source: a systematic review and meta-analysis

description: <b>Introduction</b>: The management of children with fever without apparent sources (FWAS) is difficult. This study aimed to evaluate the diagnostic accuracy of procalcitonin (PCT) in detecting serious or invasive bacterial infection (SBI or IBI) in children with FWAS. <b>Areas covered</b>: A systematic review of literature from 2007 to 2017 was performed on Medline. Twelve studies were included, involving 7,260 children with FWAS and analyzing the diagnostic performance of PCT. Four meta-analyses were performed to calculate pooled sensitivity, specificity, diagnostic odds ratio, and summary receiver operating characteristic curve for PCT in detecting SBI and IBI, at two different thresholds. Considering IBI, PCT sensitivity and specificity at a threshold of 0.5 ng/mL were 0.82 and 0.86, respectively; at a threshold of 2 ng/mL sensitivity and specificity were 0.61 and 0.94, respectively. In detecting SBI, PCT performance was lower, with 55% sensitivity and 85% specificity at a threshold of 0.5 ng/mL, and 30% sensitivity and 95% specificity at a threshold of 2 ng/mL. <b>Expert commentary</b>: Considering IBI, results showed high diagnostic accuracy for PCT. Conversely, PCT performance in diagnosis of SBI was poor. These findings suggest that PCT level determination could be helpful in detecting meningitis, bacteremia and sepsis in children with FWAS.
DOI: 10.6084/m9.figshare.5602423.v1
title: Procalcitonin performance in detecting serious and invasive bacterial infections in children with fever without apparent source: a systematic review and meta-analysis

description: <b>Introduction</b>: The management of children with fever without apparent sources (FWAS) is difficult. This study aimed to evaluate the diagnostic accuracy of procalcitonin (PCT) in detecting serious or invasive bacterial infection (SBI or IBI) in children with FWAS. <b>Areas covered</b>: A systematic review of literature from 2007 to 2017 was performed on Medline. Twelve studies were included, involving 7,260 children with FWAS and analyzing the diagnostic performance of PCT. Four meta-analyses were performed to calculate pooled sensitivity, specificity, diagnostic odds ratio, and summary receiver operating characteristic curve for PCT in detecting SBI and IBI, at two different thresholds. Considering IBI, PCT sensitivity and specificity at a threshold of 0.5 ng/mL were 0.82 and 0.86, respectively; at a threshold of 2 ng/mL sensitivity and specificity were 0.61 and 0.94, respectively. In detecting SBI, PCT performance was lower, with 55% sensitivity and 85% specificity at a threshold of 0.5 ng/mL, and 30% sensitivity and 95% specificity at a threshold of 2 ng/mL. <b>Expert commentary</b>: Considering IBI, results showed high diagnostic accuracy for PCT. Conversely, PCT performance in diagnosis of SBI was poor. These findings suggest that PCT level determination could be helpful in detecting meningitis, bacteremia and sepsis in children with FWAS.
DOI: 10.6084/m9.figshare.5601934
title: patient reports

description: The evolution of 3 cases of myocardial infarction under homeopathic therapy
DOI: 10.6084/m9.figshare.5601934.v1
title: patient reports

description: The evolution of 3 cases of myocardial infarction under homeopathic therapy
DOI: 10.6084/m9.figshare.5601706
title: Dataset for: Bartlett-type corrections and bootstrap adjustments of likelihood-based inference methods for network meta-analysis

description: In network meta-analyses that synthesize direct and indirect comparison evidence concerning multiple treatments, multivariate random effects models have been routinely used for addressing between-studies heterogeneities. Although their standard inference methods depend on large sample approximations (e.g., restricted maximum likelihood [REML] estimation) for the number of trials synthesized, the numbers of trials are often moderate or small. In these situations, standard estimators cannot be expected to behave in accordance with asymptotic theory; in particular, confidence intervals cannot be assumed to exhibit their nominal coverage probabilities (also, the type-I error probabilities of the corresponding tests cannot be retained). The invalidity issue may seriously influence the overall conclusions of network meta-analyses. In this article, we develop several improved inference methods for network meta-analyses to resolve these problems. We first introduce two efficient likelihood-based inference methods, the likelihood-ratio test–based and efficient score test–based methods, in a general framework of network meta-analysis. Then, to improve the small sample inferences, we developed improved higher-order asymptotic methods using Bartlett-type corrections and bootstrap adjustment methods. The proposed methods adopt Monte Carlo approaches using parametric bootstraps to effectively circumvent complicated analytical calculations of case-by-case analyses and to permit flexible application to various statistical models network meta-analyses. These methods can also be straightforwardly applied to multivariate meta-regression analyses and to tests for the evaluation of inconsistency. In numerical evaluations via simulations, the proposed methods generally performed well compared with the ordinary REML-based inference method. Applications to two network meta-analysis datasets are provided.
DOI: 10.6084/m9.figshare.5601706.v1
title: Dataset for: Bartlett-type corrections and bootstrap adjustments of likelihood-based inference methods for network meta-analysis

description: In network meta-analyses that synthesize direct and indirect comparison evidence concerning multiple treatments, multivariate random effects models have been routinely used for addressing between-studies heterogeneities. Although their standard inference methods depend on large sample approximations (e.g., restricted maximum likelihood [REML] estimation) for the number of trials synthesized, the numbers of trials are often moderate or small. In these situations, standard estimators cannot be expected to behave in accordance with asymptotic theory; in particular, confidence intervals cannot be assumed to exhibit their nominal coverage probabilities (also, the type-I error probabilities of the corresponding tests cannot be retained). The invalidity issue may seriously influence the overall conclusions of network meta-analyses. In this article, we develop several improved inference methods for network meta-analyses to resolve these problems. We first introduce two efficient likelihood-based inference methods, the likelihood-ratio test–based and efficient score test–based methods, in a general framework of network meta-analysis. Then, to improve the small sample inferences, we developed improved higher-order asymptotic methods using Bartlett-type corrections and bootstrap adjustment methods. The proposed methods adopt Monte Carlo approaches using parametric bootstraps to effectively circumvent complicated analytical calculations of case-by-case analyses and to permit flexible application to various statistical models network meta-analyses. These methods can also be straightforwardly applied to multivariate meta-regression analyses and to tests for the evaluation of inconsistency. In numerical evaluations via simulations, the proposed methods generally performed well compared with the ordinary REML-based inference method. Applications to two network meta-analysis datasets are provided.
DOI: 10.6084/m9.figshare.5601679
title: Hepatitis B virus (HBV): serological markers of infection and immunity in a cohort of South African children

description: Children age 6-60 months were recruited as part of the Co-infection in South-African Children (COSAC) study, in Kimberley, South Africa. HIV-negative participants (n=174) were recruited through the Kimberley Respiratory Cohort (KReC). These children were admitted to hospital with a clinical diagnosis of respiratory tract infection between July 2014 and August 2016. HIV-positive children (n=136) were recruited primarily from HIV outpatient clinics, (recruited between September 2009 and July 2016). Children had research blood samples taken at the same time as routine clinical blood tests. We tested all samples for markers of hepatitis B virus (HBV) infection and immunity. HBsAg testing was carried out in Kimberley Hospital, South Africa using the Magnetic parcel chemiluminometric immunoassay (MPCI; Advia Centaur platform). Confirmatory HBsAg testing, together with anti-HBs and anti-HBc testing, was carried out by the microbiology department at Oxford University Hospitals (OUH) NHS Foundation Trust, Oxford, UK (Architect i2000). Ethics approval for this study was obtained from the Ethics Committee of the Faculty of Health Science, University of the Free State, Bloemfontein, South Africa (HIV Study Ref: ETOVS Nr 08/09 and COSAC Study Ref: ECUFS NR 80/2014). Written consent for enrollment into the study was obtained from the child’s parent or guardian.
DOI: 10.6084/m9.figshare.5601682
title: Same Sex Marriage Survey - yes vote on AU National map

description: A data visualisation of the YES vote in the Nov 2017 Same Sex Marriage Survey.<br>##How toTo create this data visualisation, save the csv file, and drag it onto the map at: http://nationalmap.gov.au/.<br>Select between raw number of yes votes, and percent who voted yes. The image shows percent who voted yes.<br>You can scroll and zoom in to Federal electorates. Click on an electorate to see the data for that electorate.<br>ABS data from: Australian Marriage Law Postal Survey 2017 - Response.xls (at abs.gov.au).
DOI: 10.6084/m9.figshare.5601682.v1
title: Same Sex Marriage Survey - yes vote on AU National map

description: A data visualisation of the YES vote in the Nov 2017 Same Sex Marriage Survey.<br>##How toTo create this data visualisation, save the csv file, and drag it onto the map at: http://nationalmap.gov.au/.<br>Select between raw number of yes votes, and percent who voted yes. The image shows percent who voted yes.<br>You can scroll and zoom in to Federal electorates. Click on an electorate to see the data for that electorate.<br>ABS data from: Australian Marriage Law Postal Survey 2017 - Response.xls (at abs.gov.au).
DOI: 10.6084/m9.figshare.5601640
title: Nest-dismantling

description: Data for nest-dismantling manuscript
DOI: 10.6084/m9.figshare.5601652
title: ECG signals (1000 fragments)

description: For research purposes, the ECG signals were obtained from the PhysioNet service (http://www.physionet.org) from the MIT-BIH Arrhythmia database. The created database with ECG signals is described below. 1) The ECG signals were from 45 patients: 19 female (age: 23-89) and 26 male (age: 32-89). 2) The ECG signals contained 17 classes: normal sinus rhythm, pacemaker rhythm, and 15 types of cardiac dysfunctions (for each of which at least 10 signal fragments were collected). 3) All ECG signals were recorded at a sampling frequency of 360 [Hz] and a gain of 200 [adu / mV]. 4) For the analysis, 1000, 10-second (3600 samples) fragments of the ECG signal (not overlapping) were randomly selected. 5) Only signals derived from one lead, the MLII, were used. 6) Data are in mat format (Matlab).
DOI: 10.6084/m9.figshare.5601664
title: ECG signals (744 fragments)

description: For research purposes, the ECG signals were obtained from the PhysioNet service (http://www.physionet.org) from the MIT-BIH Arrhythmia database. The created database with ECG signals is described below. 1) The ECG signals were from 29 patients: 15 female (age: 23-89) and 14 male (age: 32-89). 2) The ECG signals contained 17 classes: normal sinus rhythm, pacemaker rhythm, and 15 types of cardiac dysfunctions (for each of which at least 10 signal fragments were collected). 3) All ECG signals were recorded at a sampling frequency of 360 [Hz] and a gain of 200 [adu / mV]. 4) For the analysis, 744, 10-second (3600 samples) fragments of the ECG signal (not overlapping) were randomly selected. 5) Only signals derived from one lead, the MLII, were used. 6) Data are in mat format (Matlab).
DOI: 10.6084/m9.figshare.5601622
title: Data Available for 'Generic Approach to Access Barriers in Dehydrogenation Reactions'

description: Data sources for plotting the figures in the article.In the file name, term 'TSS' means transition state scaling relation; term 'GX' means the Gamma (slope) and Xi (intercept) functions.<br>Please contact Liang Yu at yuliang0719@gmail.com or Frank Abild-Pedersen at abild@slac.stanford.edu to access the unzipping password.
DOI: 10.6084/m9.figshare.5601640.v2
title: Nest-dismantling

description: Data for nest-dismantling manuscript
DOI: 10.6084/m9.figshare.5601580
title: Stipa lagascae leaf transcriptome

description: De novo transcriptome assembly of Stipa lagascae based on leaf RNAseq data (SRA ERR1744604, ERR1744605, ERR1744606, ERR1744607, ERR1744608, ERR1744609, ERR1744610). Trinity v2.4.0 was used for assembly using default parameters, with the exception of the parameters "--min_kmer_cov 2 --normalize_max_read_cov 20" and Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5601580.v1
title: Stipa lagascae leaf transcriptome

description: De novo transcriptome assembly of Stipa lagascae based on leaf RNAseq data (SRA ERR1744604, ERR1744605, ERR1744606, ERR1744607, ERR1744608, ERR1744609, ERR1744610). Trinity v2.4.0 was used for assembly using default parameters, with the exception of the parameters "--min_kmer_cov 2 --normalize_max_read_cov 20" and Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5601574
title: Poa pratensis leaf transcriptome

description: De novo transcriptome assembly of Poa pratensis based on leaf RNAseq data (SRA SRR2984344, SRR2984345, SRR2984348, SRR2984349, SRR2984354, SRR2984356, SRR2984357, SRR2984358, SRR2984359, SRR2984360, SRR2984361, SRR2984362, SRR2984363, SRR2984364, SRR2984365, SRR2984366, SRR2988071, SRR2988083, SRR2989148). Trinity v2.4.0 was used for assembly using default parameters, with the exception of the parameters "--min_kmer_cov 2" and Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5601622.v1
title: Data Available for Comm Chem

description: Data sources for plotting the figures in the article.In the file name, term 'TSS' means transition state scaling relation; term 'GX' means the Gamma (slope) and Xi (intercept) functions.
DOI: 10.6084/m9.figshare.5601640.v1
title: Do hair-crested drongos reduce prospective territory competition by dismantling their nest after breeding? (DATA DEPOSITION)

description: Data for nest-dismantling manuscript
DOI: 10.6084/m9.figshare.5601622.v3
title: Data Available for 'Generic Approach to Access Barriers in Dehydrogenation Reactions'

description: Data sources for plotting the figures in the article.In the file name, term 'TSS' means transition state scaling relation; term 'GX' means the Gamma (slope) and Xi (intercept) functions.<br>Please contact Liang Yu at yuliang0719@gmail.com or Frank Abild-Pedersen at abild@slac.stanford.edu to access the unzipping password.
DOI: 10.6084/m9.figshare.5601565
title: Achnatherum splendens leaf transcriptome

description: De novo transcriptome assembly of Achnatherum splendens based on leaf RNAseq data (SRA SRR3089957, SRR3089983, SRR3089986). Trinity v2.4.0 was used for assembly using default parameters were used, with Trimmomatic for trimming of reads before assembly.<br>
DOI: 10.6084/m9.figshare.5601574.v1
title: Poa pratensis leaf transcriptome

description: De novo transcriptome assembly of Poa pratensis based on leaf RNAseq data (SRA SRR2984344, SRR2984345, SRR2984348, SRR2984349, SRR2984354, SRR2984356, SRR2984357, SRR2984358, SRR2984359, SRR2984360, SRR2984361, SRR2984362, SRR2984363, SRR2984364, SRR2984365, SRR2984366, SRR2988071, SRR2988083, SRR2989148). Trinity v2.4.0 was used for assembly using default parameters, with the exception of the parameters "--min_kmer_cov 2" and Trimmomatic for trimming of reads before assembly.<br>