cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7599098
title: Supplementary Material for: Fetuses with Isolated Congenital Heart Defects Show Normal Cerebral and Extracerebral Fluid Volume Growth: A 3D Sonographic Study in the Second and Third Trimester

description: <b><i>Objective:</i></b> The aim of our study is to explore whether the cerebral growth is delayed in fetuses with congenital heart defects (CHD) in the second and early third trimester. <b><i>Methods:</i></b> A prospective cohort study was conducted in 77 CHD cases, with 75 healthy controls. 3D cerebral volume acquisition was performed sequentially. The volumes of the fetal hemicerebrum and extracerebral fluid were compared by linear regression analysis, and the Sylvian fissure was measured. <b><i>Results:</i></b> Between 19 and 32 weeks of gestation, 158 measurements in cases and 183 measurements in controls were performed (mean 2.2/subject). The volume growth of the hemicerebrum (<i>R</i><sup>2</sup> = 0.95 vs. 0.95; <i>p</i> = 0.9) and the extracerebral fluid (<i>R</i><sup>2</sup> = 0.84 vs. 0.82,<i> p</i> = 0.9) were similar. Fetuses with abnormal oxygen delivery to the brain have a slightly smaller brain at 20 weeks of gestation (<i>p</i> = 0.02), but this difference disappeared with advancing gestation. CHD cases demonstrated a slightly shallower Sylvian fissure (mean ratio 0.146 vs. 0.153; <i>p</i> = 0.004). <b><i>Conclusions:</i></b> Our study shows no differences in cerebral growth, studied in an unselected cohort, with successive cases of isolated CHD. Even in the severest CHD cases, cerebral size is similar in the early third trimester. The cause and meaning of a shallower Sylvian fissure is unclear; possibly, it is a marker for delayed cerebral maturation or it might be an expression of decreasing amount of extracerebral fluid.
DOI: 10.6084/m9.figshare.7599095
title: Effects of rapid evolution on species coexistence

description: Data supporting the findings of Hart et al. (2019) Effects of rapid evolution on species coexistence. <i>Proceedings of the National Academy of Sciences, USA</i>.<br>
DOI: 10.7284/134038
title: TSG (Thermosalinograph) data collected during research cruise EN643 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7599089
title: Supplementary Material for: Interleaving Stimulation in Parkinson’s Disease, Tremor, and Dystonia

description: <b><i>Background/Aims:</i></b> Interleaving stimulation (ILS) in deep brain stimulation (DBS) provides individualized stimulation of 2 contacts delivered in alternating order. Currently, limited information on the utility of ILS exists. The aims of this study were to determine the practical applications and outcomes of ILS DBS in Parkinson’s disease (PD), tremor, and dystonia. <b><i>Methods:</i></b> We performed a single-center, unblinded, retrospective chart review of all patients with DBS attempted on ILS at our referral center assessing for rationale and outcomes. <b><i>Results:</i></b> Fifty patients (PD, <i>n</i> = 27; tremor, <i>n</i> = 7; dystonia, <i>n</i> = 16 patients) tried ILS for 2 rationales: management of adverse effects (<i>n</i> = 29) and to improve clinical efficacy (<i>n</i> = 21). A total of 19 patients demonstrated improvement with ILS for adverse effect management predominately for the treatment of dyskinesias (<i>n</i> = 12). In the vast majority of dyskinetic patients, a contact added into the rostral zona incerta with ILS was performed. Nine out of 21 patients demonstrated improved clinical efficacy with ILS with all 6 PD patients who tried ILS for this rationale demonstrating benefit. <b><i>Conclusions:</i></b> In PD, ILS provided benefits for dyskinesias and parkinsonism, with minimal improvement of other adverse effects. In tremor and dystonia, marginal effects in terms of mitigation of adverse effects and improvement of clinical outcomes were evident.
DOI: 10.6084/m9.figshare.7599089.v1
title: Supplementary Material for: Interleaving Stimulation in Parkinson’s Disease, Tremor, and Dystonia

description: <b><i>Background/Aims:</i></b> Interleaving stimulation (ILS) in deep brain stimulation (DBS) provides individualized stimulation of 2 contacts delivered in alternating order. Currently, limited information on the utility of ILS exists. The aims of this study were to determine the practical applications and outcomes of ILS DBS in Parkinson’s disease (PD), tremor, and dystonia. <b><i>Methods:</i></b> We performed a single-center, unblinded, retrospective chart review of all patients with DBS attempted on ILS at our referral center assessing for rationale and outcomes. <b><i>Results:</i></b> Fifty patients (PD, <i>n</i> = 27; tremor, <i>n</i> = 7; dystonia, <i>n</i> = 16 patients) tried ILS for 2 rationales: management of adverse effects (<i>n</i> = 29) and to improve clinical efficacy (<i>n</i> = 21). A total of 19 patients demonstrated improvement with ILS for adverse effect management predominately for the treatment of dyskinesias (<i>n</i> = 12). In the vast majority of dyskinetic patients, a contact added into the rostral zona incerta with ILS was performed. Nine out of 21 patients demonstrated improved clinical efficacy with ILS with all 6 PD patients who tried ILS for this rationale demonstrating benefit. <b><i>Conclusions:</i></b> In PD, ILS provided benefits for dyskinesias and parkinsonism, with minimal improvement of other adverse effects. In tremor and dystonia, marginal effects in terms of mitigation of adverse effects and improvement of clinical outcomes were evident.
DOI: 10.7284/134040
title: Winch data collected during research cruise EN643 using a PHE Endeavor instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7599032
title: posteriors.zip

description: This directory contains summaries of the posterior distributions of parameters estimated by genomegaMap analyses of 10,209 Mycobacterium tuberculosis genomes in D. J. Wilson and The CRyPTIC Consortium (2019) for every coding sequence in the H37Rv reference genome (version 2, genbank accession number NC_000962.2).<br>The following files summarize all coding sequences:summary.csv Each row summarizes the posterior distribution of parameters for the named coding sequence, with column headings CDS coding sequence name Gtheta geometric mean theta (population-scaled mutation rate) Gkappa geometric mean kappa (transition:transversion ratio) Gomega geometric mean omega (dN/dS ratio) Etheta arithmetic mean theta Ekappa arithmetic mean kappa Eomega arithmetic mean omega theta50 median theta kappa50 median kappa Gomega50 median (across codons) geometric mean omega theta2.5 2.5 percentile theta kappa2.5 2.5 percentile kappa Gomega2.5 2.5 percentile (across codons) geometric mean omega theta97.5 97.5 percentile theta kappa97.5 97.5 percentile kappa Gomega97.5 97.5 percentile (across codons) geometric mean omega Eppos arithmetic mean probability of positive selection (omega&gt;1)H37Rv.cds.csv Tab-delimited text file of genbank annotations for H37Rv (NC_000962.2) coding sequencesgenomegaMap.template.xml Template xml file for genomegaMap analysis<br>The following files summarize the posterior distribution of omega (the dN/dS ratio) by coding sequence:Rv----.omega50.txt median omega per codonRv----.omega2.5.txt 2.5 percentile omega per codonRv----.omega97.5.txt 97.5 percentile omega per codonRv----.ppos.txt posterior probability of positive selection (omega&gt;1) per codon<br>
DOI: 10.6084/m9.figshare.7599032.v1
title: posteriors.zip

description: This directory contains summaries of the posterior distributions of parameters estimated by genomegaMap analyses of 10,209 Mycobacterium tuberculosis genomes in D. J. Wilson and The CRyPTIC Consortium (2019) for every coding sequence in the H37Rv reference genome (version 2, genbank accession number NC_000962.2).<br>The following files summarize all coding sequences:summary.csv Each row summarizes the posterior distribution of parameters for the named coding sequence, with column headings CDS coding sequence name Gtheta geometric mean theta (population-scaled mutation rate) Gkappa geometric mean kappa (transition:transversion ratio) Gomega geometric mean omega (dN/dS ratio) Etheta arithmetic mean theta Ekappa arithmetic mean kappa Eomega arithmetic mean omega theta50 median theta kappa50 median kappa Gomega50 median (across codons) geometric mean omega theta2.5 2.5 percentile theta kappa2.5 2.5 percentile kappa Gomega2.5 2.5 percentile (across codons) geometric mean omega theta97.5 97.5 percentile theta kappa97.5 97.5 percentile kappa Gomega97.5 97.5 percentile (across codons) geometric mean omega Eppos arithmetic mean probability of positive selection (omega&gt;1)H37Rv.cds.csv Tab-delimited text file of genbank annotations for H37Rv (NC_000962.2) coding sequencesgenomegaMap.template.xml Template xml file for genomegaMap analysis<br>The following files summarize the posterior distribution of omega (the dN/dS ratio) by coding sequence:Rv----.omega50.txt median omega per codonRv----.omega2.5.txt 2.5 percentile omega per codonRv----.omega97.5.txt 97.5 percentile omega per codonRv----.ppos.txt posterior probability of positive selection (omega&gt;1) per codon<br>
DOI: 10.6084/m9.figshare.7599020
title: codoncounts.zip

description: This directory contains codon counts analysed by genomegaMap in D. J. Wilson and The CRyPTIC Consortium (2019). The codon counts for a particular coding sequence in the Mycobacterium tuberculosis H37Rv reference genome (version 2, genbank accession number NC_000962.2) are contained in each codoncounts.txt file, where the filename is prefixed by the gene identifier. Each file contains a matrix of integers with no row or column names, where element (row i, column j) of the matrix records the number of genomes exhibiting triplet j at codon position i. Positions are ordered as per NC_000962.2, beginning with the start codon. Terminal stop codons are not included. Triplets are ordered as follows:TTT,TTC,TTA,TTG,TCT,TCC,TCA,TCG,TAT,TAC,TGT,TGC,TGG,CTT,CTC,CTA,CTG,CCT,CCC,CCA,CCG,CAT,CAC,CAA,CAG,CGT,CGC,CGA,CGG,ATT,ATC,ATA,ATG,ACT,ACC,ACA,ACG,AAT,AAC,AAA,AAG,AGT,AGC,AGA,AGG,GTT,GTC,GTA,GTG,GCT,GCC,GCA,GCG,GAT,GAC,GAA,GAG,GGT,GGC,GGA,GGG,---where --- represents any call other than the 61 non-stop codons, including deletions, ambiguous or filtered calls, and premature stop codons. 10,209 genomes were mapped against the H37Rv reference, with details and short read archive accession numbers described in the original paper by The CRyPTIC Consortium and the 100,000 Genomes Project (2018).<br>
DOI: 10.6084/m9.figshare.7599017
title: Supplementary Material for: Inferring Gene-Disease Association by an Integrative Analysis of eQTL Genome-Wide Association Study and Protein-Protein Interaction Data

description: <b><i>Objectives:</i></b> Genome-wide association studies (GWASs) have revealed many candidate SNPs, but the mechanisms by which these SNPs influence diseases are largely unknown. In order to decipher the underlying mechanisms, several methods have been developed to predict disease-associated genes based on the integration of GWAS and eQTL data (e.g., Sherlock and COLOC). A number of studies have also incorporated information from gene networks into GWAS analysis to reprioritize candidate genes. <b><i>Methods:</i></b> Motivated by these two different approaches, we have developed a statistical framework to integrate information from GWAS, eQTL, and protein-protein interaction (PPI) data to predict disease-associated genes. Our approach is based on a hidden Markov random field (HMRF) model, and we called the resulting computational algorithm GeP-HMRF (a GWAS-eQTL-PPI-based HMRF). <b><i>Results:</i></b> We compared the performance of GeP-HMRF with Sherlock, COLOC, and NetWAS methods on 9 GWAS datasets, using the disease-related genes in the MalaCards database as the standard, and found that GeP-HMRF significantly improves the prediction accuracy. We also applied GeP-HMRF to an age-related macular degeneration disease (AMD) dataset. Among the top 50 genes predicted by GeP-HMRF, 7 are reported by the MalaCards database to be AMD-related with an enrichment <i>p</i> value of 3.61 × 10<sup>–119</sup>. Among the top 20 genes predicted by GeP-HMRF, CFHR1, CGHR3, HTRA1, and CFH are AMD-related in the MalaCards database, and another 9 genes are supported by the literature. <b><i>Conclusions:</i></b> We built a unified statistical model to predict disease-related genes by integrating GWAS, eQTL, and PPI data. Our approach outperforms Sherlock, COLOC, and NetWAS in simulation studies and 9 GWAS datasets. Our approach can be generalized to incorporate other molecular trait data beyond eQTL and other interaction data beyond PPI.
DOI: 10.7284/134041
title: Winch data collected during research cruise EN643 using a SMATCO Endeavor SMATCO instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7599017.v1
title: Supplementary Material for: Inferring Gene-Disease Association by an Integrative Analysis of eQTL Genome-Wide Association Study and Protein-Protein Interaction Data

description: <b><i>Objectives:</i></b> Genome-wide association studies (GWASs) have revealed many candidate SNPs, but the mechanisms by which these SNPs influence diseases are largely unknown. In order to decipher the underlying mechanisms, several methods have been developed to predict disease-associated genes based on the integration of GWAS and eQTL data (e.g., Sherlock and COLOC). A number of studies have also incorporated information from gene networks into GWAS analysis to reprioritize candidate genes. <b><i>Methods:</i></b> Motivated by these two different approaches, we have developed a statistical framework to integrate information from GWAS, eQTL, and protein-protein interaction (PPI) data to predict disease-associated genes. Our approach is based on a hidden Markov random field (HMRF) model, and we called the resulting computational algorithm GeP-HMRF (a GWAS-eQTL-PPI-based HMRF). <b><i>Results:</i></b> We compared the performance of GeP-HMRF with Sherlock, COLOC, and NetWAS methods on 9 GWAS datasets, using the disease-related genes in the MalaCards database as the standard, and found that GeP-HMRF significantly improves the prediction accuracy. We also applied GeP-HMRF to an age-related macular degeneration disease (AMD) dataset. Among the top 50 genes predicted by GeP-HMRF, 7 are reported by the MalaCards database to be AMD-related with an enrichment <i>p</i> value of 3.61 × 10<sup>–119</sup>. Among the top 20 genes predicted by GeP-HMRF, CFHR1, CGHR3, HTRA1, and CFH are AMD-related in the MalaCards database, and another 9 genes are supported by the literature. <b><i>Conclusions:</i></b> We built a unified statistical model to predict disease-related genes by integrating GWAS, eQTL, and PPI data. Our approach outperforms Sherlock, COLOC, and NetWAS in simulation studies and 9 GWAS datasets. Our approach can be generalized to incorporate other molecular trait data beyond eQTL and other interaction data beyond PPI.
DOI: 10.7284/134043
title: Winch data collected during research cruise EN643 using a Markey DUSH-5 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7598978
title: archaeology.xlsx

description: Archaeology
DOI: 10.7284/133983
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN644 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7599014.v1
title: Table S1.: Clinical data of patients with the ASXL3 pathogenic variants

description: <b>Clinical features of our proband and previously reported patients with the <i>ASXL3</i> pathogenic variants</b>
DOI: 10.6084/m9.figshare.7598978.v1
title: archaeology.xlsx

description: Archaeology
DOI: 10.7284/133998
title: Anemometer data collected during research cruise EN644 using a Gill Windsonic instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7598969
title: Supplementary Material for: Spanish Validation of the GEPARD Questionnaire for the Detection of Psoriatic Arthritis in Argentinian Patients with Psoriasis

description: <b><i>Background/Objective:</i></b> Psoriatic arthritis (PsA) is preceded by psoriasis in approximately 80% of cases. Dermatologists are pivotal for early detection. It is important to have simple tools that allow the detection of PsA in patients with skin psoriasis. The aim of our study was to evaluate the performance of an adapted version of the GEPARD Questionnaire in Spanish in Argentinian patients with psoriasis. <b><i>Methods:</i></b> This is a cross-sectional study. A new Spanish (Argentinian) (GEPARDa) translated version of the original questionnaire (German) was developed and then tested as a diagnostic tool in patients with psoriasis, PsA, osteoarthritis associated to psoriasis, and osteoarthritis, all evaluated by rheumatologists who used the CASPAR criteria. <b><i>Results:</i></b> Eighty-three patients were included (55 [66.3%] women with a mean age of 50.7 years [SD 6.3]). Forty-four patients had PsA (29 [34.9%] patients had previous diagnosis of PsA, and 15 [18%] were newly diagnosed after referral by their dermatologists), and 39 patients were without PsA (18 [21.6%] patients had psoriasis without articular involvement, 6 [7.22%] had psoriasis associated with osteoarthritis, and 15 [18%] had osteoarthritis). An area under the curve of 0.9554 (SD 0.01; 95% CI 0.91–0.99) was calculated considering the CASPAR criteria as the gold standard. With a cutoff of ≥6 the questionnaire showed a sensitivity of 88.64%, a specificity of 89.74%, a positive likelihood ratio of 8.6, and a negative likelihood ratio of 0.12. <b><i>Conclusions:</i></b> The GEPARDa version has proven to be a diagnostic tool with excellent performance so that it can be considered a valid tool for the detection of PsA in Argentinian patients.
DOI: 10.6084/m9.figshare.7599014.v2
title: Table S1.: Clinical data of patients with the ASXL3 pathogenic variants

description: <b>Clinical features of our proband and previously reported patients with the <i>ASXL3</i> pathogenic variants</b>
DOI: 10.6084/m9.figshare.7598969.v1
title: Supplementary Material for: Spanish Validation of the GEPARD Questionnaire for the Detection of Psoriatic Arthritis in Argentinian Patients with Psoriasis

description: <b><i>Background/Objective:</i></b> Psoriatic arthritis (PsA) is preceded by psoriasis in approximately 80% of cases. Dermatologists are pivotal for early detection. It is important to have simple tools that allow the detection of PsA in patients with skin psoriasis. The aim of our study was to evaluate the performance of an adapted version of the GEPARD Questionnaire in Spanish in Argentinian patients with psoriasis. <b><i>Methods:</i></b> This is a cross-sectional study. A new Spanish (Argentinian) (GEPARDa) translated version of the original questionnaire (German) was developed and then tested as a diagnostic tool in patients with psoriasis, PsA, osteoarthritis associated to psoriasis, and osteoarthritis, all evaluated by rheumatologists who used the CASPAR criteria. <b><i>Results:</i></b> Eighty-three patients were included (55 [66.3%] women with a mean age of 50.7 years [SD 6.3]). Forty-four patients had PsA (29 [34.9%] patients had previous diagnosis of PsA, and 15 [18%] were newly diagnosed after referral by their dermatologists), and 39 patients were without PsA (18 [21.6%] patients had psoriasis without articular involvement, 6 [7.22%] had psoriasis associated with osteoarthritis, and 15 [18%] had osteoarthritis). An area under the curve of 0.9554 (SD 0.01; 95% CI 0.91–0.99) was calculated considering the CASPAR criteria as the gold standard. With a cutoff of ≥6 the questionnaire showed a sensitivity of 88.64%, a specificity of 89.74%, a positive likelihood ratio of 8.6, and a negative likelihood ratio of 0.12. <b><i>Conclusions:</i></b> The GEPARDa version has proven to be a diagnostic tool with excellent performance so that it can be considered a valid tool for the detection of PsA in Argentinian patients.
DOI: 10.7284/134001
title: Anemometer data collected during research cruise EN644 using a Gill Windsonic instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7598963
title: RAxML_tree_files(dataset1 & dataset2)

description: This zip package includes tree files (dataset1 & dataset2) out from RAxML.
DOI: 10.6084/m9.figshare.7598978.v2
title: archaeology.xlsx

description: Archaeology
DOI: 10.6084/m9.figshare.7598960
title: Supplementary Material for: Efficacy and Safety of Topical 3% Diquafosol Ophthalmic Solution for the Treatment of Multifactorial Dry Eye Disease: Meta-Analysis of Randomized Clinical Trials

description: <b><i>Purpose:</i></b> A meta-analysis was performed to evaluate the safety and efficacy of topical 3% diquafosol in treating patients with dry eye disease (DED). <b><i>Methods:</i></b> Nine qualified randomized controlled trials incorporating 1,467 patients were included. Two of the reviewers selected the studies and independently assessed the risk of bias. The outcome measures were Schirmer score, tear film break-up time (TFBUT), rose bengal staining score, and corneal fluorescein staining score. To confirm the effect of diquafosol on dryness after cataract surgery, we performed a subgroup analysis according to the presence or absence of surgery. <b><i>Results:</i></b> We observed statistically significant improvements in scores on the Schirmer test (weighted mean difference 0.74 mm at 4 weeks; 95% CI: 0.24–1.24; <i>I</i><sup>2</sup> = 0%), fluorescein stain, rose bengal stain, and TFBUT after treatment with diquafosol compared with the group using other eye drops. As a result of the subgroup analysis of DED after cataract surgery, diquafosol was found to be more effective than the other eye drops with regard to TFBUT and rose bengal staining. <b><i>Conclusions:</i></b> Topical diquafosol could be an effective treatment for DED, and also for DED after cataract surgery. Further randomized controlled trials with larger sample sizes for the different clinical types of DED are warranted to determine the efficacy and limitations of diquafosol for these different clinical types of DED.
DOI: 10.7284/133984
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN644 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25392/leicester.data.7598942
title: Portion size effect in rats

description: This spreadsheet contains data from a series of experiments that tested the existence of a portion size effect in rats. The portion size effect has been widely replicated in humans but it is not known if it exists in animals. Understanding whether it does exist or not in animals will provide insight into the mechanisms that drive the effect in humans.The experiments were conducted at University of Leicester, UK ('mccutcheon_data.xls') and at Bucknell University ('myers_data.xls'). Data include results from five behavioral experiments which are described in detail in the paper that will accompany the dataset on Biorxiv and submitted for publication (Pinder et al, doi to follow).