cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12651257
title: Supplementary Material for: Intra-Amniotic Sildenafil Treatment Promotes Lung Growth and Attenuates Vascular Remodeling in an Experimental Model of Congenital Diaphragmatic Hernia

description: <b><i>Background:</i></b> Defective lung development resulting in lung hypoplasia and an attenuated and hypermuscularized pulmonary vasculature contributes to significant postnatal mortality in congenital diaphragmatic hernia (CDH). We hypothesize that deficient embryonic pulmonary blood flow contributes to defective lung development in CDH, which may therefore be ameliorated via enhancement of embryonic pulmonary blood flow. <b><i>Methods:</i></b> The mouse nitrofen model of CDH was utilized to measure embryonic pulmonary blood flow by in utero intracardiac injection of FITC-labeled tomato lectin and color-flow Doppler ultrasound. The effect of prenatal intra-amniotic treatment with sildenafil on survival, lung growth, and vascular morphology in the nitrofen model was determined. <b><i>Results:</i></b> Nitrofen-treated embryos exhibited decreased blood flow in the lung periphery compared to controls, and intra-amniotic sildenafil significantly improved embryonic pulmonary blood flow. Similar to nitrofen alone, pups delivered after nitrofen treatment and intra-amniotic injection of dextrose control exhibited respiratory distress and never survived beyond 6 h. Intra-amniotic sildenafil ameliorated respiratory distress in nitrofen-treated pups and improved postnatal survival to 82%. Following intra-amniotic sildenafil treatment at embryonic day (E)10.5, nitrofen-treated P0 lungs were larger with increased left lobe weight, reduced small pulmonary arterial wall muscularization, and increased airway branching complexity compared to controls. Intra-amniotic sildenafil treatment later at E15.5 also resulted in improved survival, lung growth, and attenuation of vascular remodeling in nitrofen-treated embryos. <b><i>Conclusions:</i></b> Defective embryonic pulmonary blood flow may contribute to lung maldevelopment in CDH. Enhancement of embryonic pulmonary blood flow via intra-amniotic sildenafil results in lung growth and attenuation of pulmonary vascular remodeling and may have therapeutic potential for CDH.
DOI: 10.6084/m9.figshare.12651101
title: Supplementary Material for: Prescriptive Reference Standards of Third-Trimester Cerebroplacental Ratio and Its Physiological Determinants

description: <b><i>Objective:</i></b> To construct valid reference standards reflecting optimal cerebroplacental ratio and to explore its physiological determinants. <b><i>Methods:</i></b> A cohort of 391 low-risk pregnancies of singleton pregnancies of nonmalformed fetuses without maternal medical conditions and with normal perinatal outcomes was created. Doppler measurements of the middle cerebral artery and umbilical artery were performed at 24–42 weeks. Reference standards were produced, and the influence of physiological determinants was explored by nonparametric quantile regression. The derived standards were validated in a cohort of 200 low-risk pregnancies. <b><i>Results:</i></b> Maternal body mass index was significantly associated with the 5th centile of the cerebroplacental ratio. For each additional unit of body mass index, the 5th centile was on average 0.014 lower. The derived 5th, 10th, and 50th centiles selected in the validation cohort were 5, 9.5, and 51% of the measurements. <b><i>Conclusions:</i></b> This study provides methodologically sound prescriptive standards and suggests that maternal body mass index is a determinant of a cutoff commonly used for decision-making.
DOI: 10.6084/m9.figshare.12651257.v1
title: Supplementary Material for: Intra-Amniotic Sildenafil Treatment Promotes Lung Growth and Attenuates Vascular Remodeling in an Experimental Model of Congenital Diaphragmatic Hernia

description: <b><i>Background:</i></b> Defective lung development resulting in lung hypoplasia and an attenuated and hypermuscularized pulmonary vasculature contributes to significant postnatal mortality in congenital diaphragmatic hernia (CDH). We hypothesize that deficient embryonic pulmonary blood flow contributes to defective lung development in CDH, which may therefore be ameliorated via enhancement of embryonic pulmonary blood flow. <b><i>Methods:</i></b> The mouse nitrofen model of CDH was utilized to measure embryonic pulmonary blood flow by in utero intracardiac injection of FITC-labeled tomato lectin and color-flow Doppler ultrasound. The effect of prenatal intra-amniotic treatment with sildenafil on survival, lung growth, and vascular morphology in the nitrofen model was determined. <b><i>Results:</i></b> Nitrofen-treated embryos exhibited decreased blood flow in the lung periphery compared to controls, and intra-amniotic sildenafil significantly improved embryonic pulmonary blood flow. Similar to nitrofen alone, pups delivered after nitrofen treatment and intra-amniotic injection of dextrose control exhibited respiratory distress and never survived beyond 6 h. Intra-amniotic sildenafil ameliorated respiratory distress in nitrofen-treated pups and improved postnatal survival to 82%. Following intra-amniotic sildenafil treatment at embryonic day (E)10.5, nitrofen-treated P0 lungs were larger with increased left lobe weight, reduced small pulmonary arterial wall muscularization, and increased airway branching complexity compared to controls. Intra-amniotic sildenafil treatment later at E15.5 also resulted in improved survival, lung growth, and attenuation of vascular remodeling in nitrofen-treated embryos. <b><i>Conclusions:</i></b> Defective embryonic pulmonary blood flow may contribute to lung maldevelopment in CDH. Enhancement of embryonic pulmonary blood flow via intra-amniotic sildenafil results in lung growth and attenuation of pulmonary vascular remodeling and may have therapeutic potential for CDH.
DOI: 10.6084/m9.figshare.12651053
title: Supplementary Material for: Azathioprine for Connective Tissue Disease-Associated Interstitial Lung Disease

description: <b><i>Background:</i></b> Immunosuppressive therapy still is the standard treatment for patients with connective tissue disease-associated interstitial lung disease (CTD-ILD). <b><i>Objectives:</i></b> This retrospective study aimed to provide data on the tolerability and efficacy of azathioprine in progressive CTD-ILDs. <b><i>Methods:</i></b> A total of 56 patients with CTD-ILD treated with azathioprine between 2003 and 2014 were included in the study. The patients were assessed every 3 months during follow-up. <b><i>Results:</i></b> The mean treatment duration was 34 months, with a range of 3–105 months. Fifteen patients (27%) discontinued treatment due to side effects, mostly due to elevated liver enzymes, within the first 3 months. Forty-one patients were treated for longer than 3 months, and 27 of those (66%) had stabilization or improvement of pulmonary function during treatment. In patients who remained stable or improved, the mean FVC was 62 ± 17% predicted (% pred) at initiation of treatment and 65 ± 17% pred at the last follow-up visit (<i>p</i> = 0.036), and the mean DLCO was 38 ± 16% pred at initiation of treatment and 39 ± 17% pred at the last follow-up visit (<i>p</i> = 0.06). <b><i>Conclusions:</i></b> Azathioprine can stabilize or improve CTD-ILD. While early drug intolerance is frequent, most patients who have tolerated the drug well achieve long-term stabilization or improvement of lung function.
DOI: 10.6084/m9.figshare.12651101.v1
title: Supplementary Material for: Prescriptive Reference Standards of Third-Trimester Cerebroplacental Ratio and Its Physiological Determinants

description: <b><i>Objective:</i></b> To construct valid reference standards reflecting optimal cerebroplacental ratio and to explore its physiological determinants. <b><i>Methods:</i></b> A cohort of 391 low-risk pregnancies of singleton pregnancies of nonmalformed fetuses without maternal medical conditions and with normal perinatal outcomes was created. Doppler measurements of the middle cerebral artery and umbilical artery were performed at 24–42 weeks. Reference standards were produced, and the influence of physiological determinants was explored by nonparametric quantile regression. The derived standards were validated in a cohort of 200 low-risk pregnancies. <b><i>Results:</i></b> Maternal body mass index was significantly associated with the 5th centile of the cerebroplacental ratio. For each additional unit of body mass index, the 5th centile was on average 0.014 lower. The derived 5th, 10th, and 50th centiles selected in the validation cohort were 5, 9.5, and 51% of the measurements. <b><i>Conclusions:</i></b> This study provides methodologically sound prescriptive standards and suggests that maternal body mass index is a determinant of a cutoff commonly used for decision-making.
DOI: 10.6084/m9.figshare.12650834
title: E. coli PopPUNK Database - complete

description: PopPUNK database which can be used to query any genome and examine its context relative to the E. coli dataset.<br>To use: download both parts, unzip into a single directory named "ecoli_poppunk_db" and run using:<br>poppunk --assign-query --ref-db ecoli_poppunk_db --q-files list_of_genomes.txt --output output_dir<br>**Built using PopPUNK version 1.1.3**
DOI: 10.26181/5f0d4d545f893
title: Circumstances and results of football matches involving Brazil from 9 August 1993 to 31 December 2010

description: Data recording the circumstances and results of the full 'A' international football matches involving Brazil, from 9th of August 1993 to 31st of December 2010, as listed in the Rec.Sport.Soccer Statistics Foundation (RSSSF) database. (FIFA commenced releasing national team rankings in 1993.) Excludes matches from the 1996 and 2003 CONCACAF, in which Brazil fielded their under-23 Olympic squad, three friendly matches not recognised by the opponent's federation, and five matches where Brazil was the lower ranked team. Does not take account of goals outside regulation time.<br>
DOI: 10.6084/m9.figshare.12650810
title: Random assembly for happy belly conda intro tutorial

description: Random assembly for happy belly conda intro tutorial: https://astrobiomike.github.io/unix/conda-intro
DOI: 10.6084/m9.figshare.12650810.v1
title: Random assembly for happy belly conda intro tutorial

description: Random assembly for happy belly conda intro tutorial: https://astrobiomike.github.io/unix/conda-intro
DOI: 10.6084/m9.figshare.12651074.v1
title: Extended Data for A rooted phylogeny resolves early bacterial evolution

description: Extended Data for A rooted phylogeny resolves early bacterial evolution
DOI: 10.6084/m9.figshare.12650749
title: Additional file 6 of Concentrations of persistent organic pollutants in maternal plasma and epigenome-wide placental DNA methylation

description: Additional file 6: Supplementary Tables: Table S1. Characteristics of the study subsample and of the full NICHD fetal Growth Studies – Singletons. Table S2: Description of the maternal plasma persistent organic pollutants concentrations. TableS3: Top-significant adjusted difference (BACON-corrected FDR p-values &lt; 0.05) in placenta DNA methylation associated with maternal POP. Table S4: Differentially methylated regions (DMR) analysis. TableS5: Correlations between DNA methylation at the top differentially methylated CpG sites and gene expression in placenta. Table S6: Significant associations between maternal blood levels of POP and expression of genes near the top significant DNA methylation CpG sites. Table S7: Top 10 pathways of diseases and biological function from IPA. TableS8: IPA Canonical Pathway. Table S9: Network identified by Ingenuity Pathway Analysis. Table S10: Placental cis-eQTL analysis of top-significant (Bacon-adjusted FDR P-value&lt;0.05) CpGs. Table S11: Cis-meQTL analysis of top-significant (Bacon-adjusted FDR P-value&lt;0.05) CpGs. Table S12: Spearman correlation between top differentially methylated CpG sites and neonatal anthropometry. Table S13: Spearman correlation between neonatal anthropometry and gene-expression that were significantly correlated with the methylation on the corresponding CpG sites. Table S14: Comparison with previous EWAS on chemicals. Table S15: Sensibility analysis further adjusted for clinical sites for the CpG sites differentially methylated in the original model.
DOI: 10.6084/m9.figshare.12650749.v1
title: Additional file 6 of Concentrations of persistent organic pollutants in maternal plasma and epigenome-wide placental DNA methylation

description: Additional file 6: Supplementary Tables: Table S1. Characteristics of the study subsample and of the full NICHD fetal Growth Studies – Singletons. Table S2: Description of the maternal plasma persistent organic pollutants concentrations. TableS3: Top-significant adjusted difference (BACON-corrected FDR p-values &lt; 0.05) in placenta DNA methylation associated with maternal POP. Table S4: Differentially methylated regions (DMR) analysis. TableS5: Correlations between DNA methylation at the top differentially methylated CpG sites and gene expression in placenta. Table S6: Significant associations between maternal blood levels of POP and expression of genes near the top significant DNA methylation CpG sites. Table S7: Top 10 pathways of diseases and biological function from IPA. TableS8: IPA Canonical Pathway. Table S9: Network identified by Ingenuity Pathway Analysis. Table S10: Placental cis-eQTL analysis of top-significant (Bacon-adjusted FDR P-value&lt;0.05) CpGs. Table S11: Cis-meQTL analysis of top-significant (Bacon-adjusted FDR P-value&lt;0.05) CpGs. Table S12: Spearman correlation between top differentially methylated CpG sites and neonatal anthropometry. Table S13: Spearman correlation between neonatal anthropometry and gene-expression that were significantly correlated with the methylation on the corresponding CpG sites. Table S14: Comparison with previous EWAS on chemicals. Table S15: Sensibility analysis further adjusted for clinical sites for the CpG sites differentially methylated in the original model.
DOI: 10.6084/m9.figshare.12650622
title: Additional file 1 of Genetic legacy of cultures indigenous to the Northeast Asian coast in mitochondrial genomes of nearly extinct maritime tribes

description: Additional file 1 : Table S1. List of mitogenome sequences included in Figures S1-S6.
DOI: 10.6084/m9.figshare.12650622.v1
title: Additional file 1 of Genetic legacy of cultures indigenous to the Northeast Asian coast in mitochondrial genomes of nearly extinct maritime tribes

description: Additional file 1 : Table S1. List of mitogenome sequences included in Figures S1-S6.
DOI: 10.6084/m9.figshare.12650604
title: Additional file 1 of Cabin temperature during prehospital patient transport – a prospective observational study

description: Additional file 1. Additional material showing the temperature plots for all three ambulance vehicles and all four seasons, is available as Additional file 1. The figures are A: HEMS winter, B: HEMS spring, C: HEMS summer, D: HEMS: autumn, E: GA1 winter, F: GA1 spring, G: GA1 summer, H: GA1 autumn, I: GA2 winter, J: GA2 spring, K: GA2 summer, L: GA2 autumn. The asterisk in Fig. G denotes that the graph was truncated at 180 min. The temperature remained essentially unchanged until the end of the mission at 256 min. HEMS: helicopter emergency medical service. GA: ground ambulance.
DOI: 10.6084/m9.figshare.12650604.v1
title: Additional file 1 of Cabin temperature during prehospital patient transport – a prospective observational study

description: Additional file 1. Additional material showing the temperature plots for all three ambulance vehicles and all four seasons, is available as Additional file 1. The figures are A: HEMS winter, B: HEMS spring, C: HEMS summer, D: HEMS: autumn, E: GA1 winter, F: GA1 spring, G: GA1 summer, H: GA1 autumn, I: GA2 winter, J: GA2 spring, K: GA2 summer, L: GA2 autumn. The asterisk in Fig. G denotes that the graph was truncated at 180 min. The temperature remained essentially unchanged until the end of the mission at 256 min. HEMS: helicopter emergency medical service. GA: ground ambulance.
DOI: 10.6084/m9.figshare.12650482
title: Additional file 5 of The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research

description: Additional file 5. Road testing data. Tab 1: Participants’ demographics and general feedback on the guidelines and the E&E preprints. Tab 2: Outcome of each manuscript’s assessment and justifications provided by participants for not including information covered in the ARRIVE guidelines.
DOI: 10.6084/m9.figshare.12650482.v1
title: Additional file 5 of The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research

description: Additional file 5. Road testing data. Tab 1: Participants’ demographics and general feedback on the guidelines and the E&E preprints. Tab 2: Outcome of each manuscript’s assessment and justifications provided by participants for not including information covered in the ARRIVE guidelines.
DOI: 10.6084/m9.figshare.12650476
title: Additional file 3 of The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research

description: Additional file 3. Delphi data. Tabs 1, 2, and 3: Panel members’ scores for each of the ARRIVE items during rounds 1, 2, and 3, along with descriptive statistics. Tab. 4: Qualitative feedback, collected from panel members during round 1, on the importance and the wording of each item. Tab. 5: Additional items suggested for consideration in ARRIVE 2.0; similar suggestions were grouped together before processing. Tab. 6: Justifications provided by panel members for changing an item’s score between round 1 and round 2.
DOI: 10.6084/m9.figshare.12650355
title: Additional file 2 of Cell type-specific genome scans of DNA methylation divergence indicate an important role for transposable elements

description: Additional file 2 metadata table. Excel file (metadata_Col-0_allGenotypes.xlsx) with all sequencing runs that form the basis for our analysis. A CSV version of Additional file 2 can be found in the Gitlab repository [83] at results/tables/metadata/metadata_handcurated_marc.csv.
DOI: 10.6084/m9.figshare.12650355.v1
title: Additional file 2 of Cell type-specific genome scans of DNA methylation divergence indicate an important role for transposable elements

description: Additional file 2 metadata table. Excel file (metadata_Col-0_allGenotypes.xlsx) with all sequencing runs that form the basis for our analysis. A CSV version of Additional file 2 can be found in the Gitlab repository [83] at results/tables/metadata/metadata_handcurated_marc.csv.
DOI: 10.6084/m9.figshare.12650308
title: Additional file 1 of Quality of evidence in a post-Soviet country: evaluation of methodological quality of controlled clinical trials published in national journals from Uzbekistan

description: Additional file 1: Supplementary file 1.
DOI: 10.6084/m9.figshare.12650308.v1
title: Additional file 1 of Quality of evidence in a post-Soviet country: evaluation of methodological quality of controlled clinical trials published in national journals from Uzbekistan

description: Additional file 1: Supplementary file 1.
DOI: 10.6084/m9.figshare.12650292
title: Additional file 7 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 7. Table S4. LEfSe biomarker screening results.
DOI: 10.6084/m9.figshare.12650292.v1
title: Additional file 7 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 7. Table S4. LEfSe biomarker screening results.
DOI: 10.6084/m9.figshare.12650274
title: Additional file 1 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 1. Table S1. Filtering step: removing replicated samples or participants with insufficient number of collections.
DOI: 10.6084/m9.figshare.12650277
title: Additional file 2 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 2. Table S2. Quality control: removing samples with poor taxonomic assignment.
DOI: 10.6084/m9.figshare.12650271
title: Additional file 17 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 17. Table S8. Metadata.
DOI: 10.6084/m9.figshare.12650277.v1
title: Additional file 2 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 2. Table S2. Quality control: removing samples with poor taxonomic assignment.
DOI: 10.6084/m9.figshare.12650268
title: Additional file 16 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 16. Table S7 Summary of microbial correlation with F. nucleatum and enrichment tests.
DOI: 10.6084/m9.figshare.12650271.v1
title: Additional file 17 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 17. Table S8. Metadata.
DOI: 10.6084/m9.figshare.12650274.v1
title: Additional file 1 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 1. Table S1. Filtering step: removing replicated samples or participants with insufficient number of collections.
DOI: 10.6084/m9.figshare.12650268.v1
title: Additional file 16 of Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis

description: Additional file 16. Table S7 Summary of microbial correlation with F. nucleatum and enrichment tests.
DOI: 10.6084/m9.figshare.12650199
title: Additional file 1 of Informative missingness in electronic health record systems: the curse of knowing

description: Additional file 1. R code.
DOI: 10.6084/m9.figshare.12650199.v1
title: Additional file 1 of Informative missingness in electronic health record systems: the curse of knowing

description: Additional file 1. R code.
DOI: 10.6084/m9.figshare.12649811
title: A dataset of DFT energies and forces for carbon allotropes of monolayer graphene, bilayer graphene, graphite, and diamond

description: The dataset consists of energies and forces for monolayer graphene, bilayer graphene, graphite, and diamond in various states, including strained static structures and configurations drawn from ab initio MD trajectories. A total number of 4788 configurations was generated from DFT calculations using the Vienna Ab initio Simulation Package (VASP). The energies and forces are stored in the extended XYZ format. One file for each configuration.
DOI: 10.6084/m9.figshare.12649790
title: Processed QM9 (sparse)

description: Processed dataset (sparse version) used in IncidenceNet
DOI: 10.6084/m9.figshare.12649796
title: Gene database Rhodobacter sphaeroides 2.4.1

description: <i>Rhodobacter sphaeroides</i> is a member of purple bacteria useful for the study of photosynthetic processes under anaerobic conditions. Easy to grow and maintain, the bacterium is useful for studying the role of oxygen tension in affecting photosynthesis. Endowed with two chromosomes of different length, genetic studies have illustrated that loss of genes in the shorter chromosome result in significant auxotrophy that suggests that the shorter chromosome is not a truncated version of the larger one. This work sought to reveal the genetic repertoire of <i>Rhodobacter sphaeroides</i> 2.4.1 through parsing the annotated genome sequence of the bacterium downloaded from Genbank. The gene database so obtained contain gene name, gene function, and gene sequence of all genes in the genome of <i>Rhodobacter sphaeroides</i>, and should find use in a variety of molecular cloning experiments as well as genome editing-based loss of function study seeking to elucidate fundamental mechanisms of photosynthesis in this rather unusual class of bacteria.
DOI: 10.6084/m9.figshare.12649757
title: processed QM9 (dense)

description: Processed dataset (dense graph) used in IncidenceNet