cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23259716
title: Supplementary Material for: Association between Parenchymal B-Cell Follicles and CT-Proven Enlarged Mediastinal Lymph Nodes in Patients with Pulmonary Fibrosis

description: <b><i>Background:</i></b> Mediastinal lymph node enlargement (MLNE) is a finding described in a subset of patients with idiopathic pulmonary fibrosis (IPF) and other interstitial lung diseases (ILDs) and is associated with accelerated disease progression and increased mortality. The cause of MLNE is still not known. Our hypothesis is that there is an association between MLNE and B-cell follicles in lung tissue, another aspect detectable in the lung tissue of patients with IPF and other ILDs. <b><i>Objectives:</i></b> The aim of this study was to assess if there is an association between MLNE and B-cell follicles in lung tissue in patients with IPF and other ILDs. <b><i>Method:</i></b> Patients having transbronchial cryobiopsies performed as part of an investigation for ILD were included in this prospective observational study. MLNE (smallest diameter ≥10 mm) were assessed in station 7, 4R, and 4L on high-resolution computed tomography scans. B-cell follicles were assessed on haematoxylin-eosin-stained specimens. Lung function, 6-minute walk test, acute exacerbation, and mortality were registered after 2 years. In addition, we investigated if the finding of B-cell follicles was consistent in patients who underwent both surgical lung biopsies (SLBs) and cryobiopsies. <b><i>Results:</i></b> In total, 93 patients were included for analysis (46% diagnosed with IPF, 54% diagnosed with other ILDs). MLNE was found in 26 (60%) of the IPF patients and in 23 (46%) of the non-IPF patients (<i>p</i> = 0.164). Diffusing capacity for carbon monoxide was significantly lower (<i>p</i> = 0.03) in patients with MLNE compared to patients without MLNE. B-cell follicles were found in 11 (26%) of the IPF patients and in 22 (44%) of the non-IPF patients (<i>p</i> = 0.064). Germinal centres were not seen in any of the patients. There was no association between MLNE and B-cell follicles (<i>p</i> = 0.057). No significant difference in change of pulmonary function test was seen at 2-year follow-up when comparing the patients with and without MLNE or B-cell follicles. In 13 patients, both SLBs and cryobiopsies were performed. The presence of B-cell follicles was not consistent when comparing the two different methods. <b><i>Conclusion:</i></b> MLNE is evident in a substantial part of patients with ILD and is associated with lower DLCO at inclusion. We could not demonstrate an association between histological B-cell follicles in biopsies and MLNE. A possible explanation for this is that the cryobiopsies might not have captured the changes we sought.
DOI: 10.6084/m9.figshare.22580863
title: Supplementary Material for: Quincke versus diamond-tip needles for entry in placental laser surgery for twin-to-twin transfusion syndrome

description: \ Introduction: Chorioamnion separation (CAS), preterm prelabor rupture of membranes (PPROM), and preterm delivery (PTD) remain major complications of fetoscopic laser photocoagulation (FLP) for twin-to-twin transfusion syndrome (TTTS). We sought to examine whether use of quincke-tip needles for initial entry in FLP reduces the risk of these complications. Methods: This is a secondary analysis of prospectively collected data from patients that had FLP for TTTS at a single tertiary care center (2011 – 2021). We excluded patients for whom direct trocar entry was used. Patients for whom a quincke-tip needle, versus a diamond-tip needle was used for Seldinger entry were compared. Demographics, ultrasound findings and operative characteristics were compared between groups. Post-operative outcomes and complications (including CAS, PPROM and PTD) were also compared. Multivariate logistic regression models were fit to assess independent risk factors for complications. Results: 386 patients met inclusion criteria; quincke-tip needles were used in 81 (21.0%) cases while diamond-tip needles were used in 305 (79.0%). Rates of CAS (11.1% vs 9.5%, p = 0.67) and PPROM (44.4% vs 41.0%, p = 0.57) were similar between groups. Patients in the quincke-tip group delivered 1.5 weeks earlier than those in the diamond-tip group (30.5 vs 32.0 weeks, p = 0.01). However, these patients were more likely to be delivered for maternal (35.9% vs. 19.0%) and fetal (23.1% vs. 15.3%) indications (p &lt; 0.01). In multivariate analysis, needle type was not identified as an independent risk factor for PPROM. However, quincke-tip needle use was associated with PTD less than 32 weeks (aOR 1.83, 95% CI 1.01 – 2.95, p = 0.046). Discussion/Conclusion: Membrane complications following FLP did not depend on needle type. Earlier delivery in quincke-tip group was likely attributable to higher rates of maternal and fetal delivery indications. The needle chosen for entry is probably best determined by operator preference.
DOI: 10.6084/m9.figshare.22580863.v1
title: Supplementary Material for: Quincke versus diamond-tip needles for entry in placental laser surgery for twin-to-twin transfusion syndrome

description: \ Introduction: Chorioamnion separation (CAS), preterm prelabor rupture of membranes (PPROM), and preterm delivery (PTD) remain major complications of fetoscopic laser photocoagulation (FLP) for twin-to-twin transfusion syndrome (TTTS). We sought to examine whether use of quincke-tip needles for initial entry in FLP reduces the risk of these complications. Methods: This is a secondary analysis of prospectively collected data from patients that had FLP for TTTS at a single tertiary care center (2011 – 2021). We excluded patients for whom direct trocar entry was used. Patients for whom a quincke-tip needle, versus a diamond-tip needle was used for Seldinger entry were compared. Demographics, ultrasound findings and operative characteristics were compared between groups. Post-operative outcomes and complications (including CAS, PPROM and PTD) were also compared. Multivariate logistic regression models were fit to assess independent risk factors for complications. Results: 386 patients met inclusion criteria; quincke-tip needles were used in 81 (21.0%) cases while diamond-tip needles were used in 305 (79.0%). Rates of CAS (11.1% vs 9.5%, p = 0.67) and PPROM (44.4% vs 41.0%, p = 0.57) were similar between groups. Patients in the quincke-tip group delivered 1.5 weeks earlier than those in the diamond-tip group (30.5 vs 32.0 weeks, p = 0.01). However, these patients were more likely to be delivered for maternal (35.9% vs. 19.0%) and fetal (23.1% vs. 15.3%) indications (p &lt; 0.01). In multivariate analysis, needle type was not identified as an independent risk factor for PPROM. However, quincke-tip needle use was associated with PTD less than 32 weeks (aOR 1.83, 95% CI 1.01 – 2.95, p = 0.046). Discussion/Conclusion: Membrane complications following FLP did not depend on needle type. Earlier delivery in quincke-tip group was likely attributable to higher rates of maternal and fetal delivery indications. The needle chosen for entry is probably best determined by operator preference.
DOI: 10.6084/m9.figshare.22682602.v1
title: Supplementary Material for: Liver-Expressed Antimicrobial Peptide 2 is a Hepatokine that Predicts Weight Loss and Complete Remission of Type 2 Diabetes Mellitus After Vertical Sleeve Gastrectomy in Japanese Individuals

description: Introduction: Vertical sleeve gastrectomy (VSG) is considered one of the most effective treatments for sustained weight loss and complete remission of type 2 diabetes mellitus (CR-T2DM). Liver-expressed antimicrobial peptide 2 (LEAP2), a ghrelin receptor antagonist peptide, is a metabolic hormone regulated by VSG. However, it is unknown whether LEAP2 can be used to predict the outcomes of VSG. This study aimed to evaluate LEAP2 as a predictive factor for weight loss and CR-T2DM after VSG. Methods: This retrospective study included 39 Japanese participants with obesity who underwent VSG. Serum LEAP2, des-acyl ghrelin (DAG), and other metabolic and anthropometric parameters were studied before and at 12 months after VSG. Receiver operating characteristics (ROC) curve was generated to evaluate predictive score for weight loss with cut-off value of &gt; 50 percent excess weight loss (%EWL). ROC curve was also generated to assess CR-T2DM. Results: Serum LEAP2 levels were significantly higher in participants with body mass index (BMI) 32–50 kg/m2 than in those with normal weight. Participants with BMI &gt; 50 kg/m2 had lower serum LEAP2 concentrations than those with BMI 32–50 kg/m2. VSG caused a significant reduction in serum DAG concentrations, but it did not affect serum LEAP2 concentrations in either male or female participants. Preoperative serum LEAP2 concentration of 2.88 pmol/mL was the optimal cutoff value for predicting weight loss after VSG, with sensitivity of 80.0% and specificity of 75.9%. Preoperative serum LEAP2 level higher than 4.67 pmol/mL predicted CR-T2DM after VSG with sensitivity of 100% and specificity of 58.8%, Discussion/Conclusion: Preoperative serum LEAP2 could predict weight loss and CR-T2DM as outcomes of VSG.
DOI: 10.6084/m9.figshare.20401047
title: Exploring the Relation Between Spatial Abilities and STEM Expertise

description: The csv file contains all participants' scores in each spatial thinking factor. <br> The R script contains the necessary workflow for reproducing the results reported in the paper. <br> All statistical analyses have been performed in R (R Core Team, 2021), using: “tidyverse” (Wickham et al., 2019), “DescTools “(Andri et al., 2022), “gdata (Warnes et al., 2022), “ggstatsplot” (Patil, 2021), “corrplot” (Wei & Simko, 2021), “pcal” (Fonseca & Paulo, 2020) and “effectsize” (Ben-Shachar et al., 2020) packages. Andri S. et mult. al. (2022). DescTools: Tools for Descriptive Statistics. R package version 0.99.45, https://cran.r-project.org/package=DescTools Ben-Shachar, M., Lüdecke, D., & Makowski, D. (2020). effectsize: Estimation of Effect Size Indices and Standardized Parameters. <em>Journal of Open Source Software</em>, 5(56), 2815. https://doi.org/10.21105/joss.02815 Fonseca, P. & Paulo, R. (2020). pcal: Calibration of P-values for Point Null Hypothesis Testing, R package version 1.1.0. https://pedro-teles-fonseca.github.io/pcal/ Patil, I. (2021). Visualizations with statistical details: The 'ggstatsplot' approach. <em>Journal of Open Source Software</em>, 6(61), 3167. https://doi.org/10.21105/joss.03167 R Core Team: R (2021). <em>A language and environment for statistical computing</em>. R Foundation for Statistical Computing, https://www.R-project.org Warnes, G. R. et mult. Al (2022). ‘gdata’: Various R Programming Tools for Data Manipulation Version 2.18.0.1, https://CRAN.R-project.org/package=gdata Wei, T., Simko, V. (2021). R package 'corrplot': Visualization of a Correlation Matrix. (Version 0.92), https://github.com/taiyun/corrplot Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L.D., François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhn, M., Pedersen, T.L., Miller, E., Bache, S.M., Müller, K., Ooms, J., Robinson, D., Seidel, D.P., Spinu, V., Takahashi, K., Vaughan, D., Wilke, C., Woo, K., Yutani, H. (2019). Welcome to the tidyverse, <em>Journal of Open Source Software</em>, 4(43), 1686. https://doi.org/10.21105/joss.01686.
DOI: 10.6084/m9.figshare.20401047.v3
title: Exploring the Relation Between Spatial Abilities and STEM Expertise

description: The csv file contains all participants' scores in each spatial thinking factor. The R script contains the necessary workflow for reproducing the results reported in the paper.
DOI: 10.6084/m9.figshare.22664641
title: Supplementary Material for: Radiogenomic associations clear cell renal cell carcinoma: an exploratory study

description: OBJECTIVES: This study investigates how quantitative texture analysis can be used to non-invasively identify novel radiogenomic correlations with Clear Cell Renal Cell Carcinoma (ccRCC) biomarkers. METHODS: The Cancer Genome Atlas–Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) open-source database was used to identify 190 sets of patient genomic data that had corresponding multiphase contrast-enhanced CT images in The Cancer Imaging Archive (TCIA-KIRC). 2824 radiomic features spanning fifteen texture families were extracted from CT images using a custom-built MATLAB software package. Robust radiomic features with strong inter-scanner reproducibility were selected. Random Forest (RF), AdaBoost, and Elastic Net machine learning (ML) algorithms evaluated the ability of the selected radiomic features to predict the presence of 12 clinically relevant molecular biomarkers identified from literature. ML analysis was repeated with cases stratified by stage (I/II vs. III/IV) and grade (1/2 vs. 3/4). 10-fold cross validation was used to evaluate model performance. RESULTS: Before stratification by tumor grade and stage, radiomics predicted the presence of several biomarkers with weak discrimination (AUC 0.60-0.68). Once stratified, radiomics predicted KDM5C, SETD2, PBRM1, and mTOR mutation status with acceptable to excellent predictive discrimination (AUC ranges from 0.70 to 0.86). CONCLUSIONS: Radiomic texture analysis can potentially identify a variety of clinically relevant biomarkers in patients with ccRCC and may have a prognostic implication.
DOI: 10.6084/m9.figshare.22664641.v1
title: Supplementary Material for: Radiogenomic associations clear cell renal cell carcinoma: an exploratory study

description: OBJECTIVES: This study investigates how quantitative texture analysis can be used to non-invasively identify novel radiogenomic correlations with Clear Cell Renal Cell Carcinoma (ccRCC) biomarkers. METHODS: The Cancer Genome Atlas–Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) open-source database was used to identify 190 sets of patient genomic data that had corresponding multiphase contrast-enhanced CT images in The Cancer Imaging Archive (TCIA-KIRC). 2824 radiomic features spanning fifteen texture families were extracted from CT images using a custom-built MATLAB software package. Robust radiomic features with strong inter-scanner reproducibility were selected. Random Forest (RF), AdaBoost, and Elastic Net machine learning (ML) algorithms evaluated the ability of the selected radiomic features to predict the presence of 12 clinically relevant molecular biomarkers identified from literature. ML analysis was repeated with cases stratified by stage (I/II vs. III/IV) and grade (1/2 vs. 3/4). 10-fold cross validation was used to evaluate model performance. RESULTS: Before stratification by tumor grade and stage, radiomics predicted the presence of several biomarkers with weak discrimination (AUC 0.60-0.68). Once stratified, radiomics predicted KDM5C, SETD2, PBRM1, and mTOR mutation status with acceptable to excellent predictive discrimination (AUC ranges from 0.70 to 0.86). CONCLUSIONS: Radiomic texture analysis can potentially identify a variety of clinically relevant biomarkers in patients with ccRCC and may have a prognostic implication.
DOI: 10.6084/m9.figshare.22683235.v1
title: Supplementary Material for: A novel intronic deletion in PDE6B causes autosomal recessive retinitis pigmentosa by interfering with RNA splicing

description: Introduction: Retinitis pigmentosa (RP) is a rare degenerative retinal disease caused by mutations in approximately seventy genes. Currently, despite the availability of large-scale DNA sequencing technologies, ~30-40% of patients still cannot be diagnosed at the molecular level. In this study, we investigate a novel intronic deletion of PDE6B, encoding the beta subunit of phosphodiesterase 6, in association with recessive RP. Methods: Three unrelated consanguineous families were recruited from the North-Western part of Pakistan. Whole exome sequencing was performed for the probands of each family and the data were analyzed according to an in-house computer pipeline. Relevant DNA variants in all available members of these families were assessed through Sanger sequencing. A minigene-based splicing assay was also performed. Results: The clinical phenotype for all patients was compatible with rod cone degeneration, with onset during childhood. Whole exome sequencing revealed a homozygous 18 bp intronic deletion (NM_000283.3: c.1921-20_1921-3del) in PDE6B, which co-segregated with disease in 10 affected individuals. In-vitro splicing tests showed that this deletion causes aberrant RNA splicing of the gene, leading to the in-frame deletion of 6 codons and likely to disease. Discussion/Conclusion: Our findings further expand the mutational spectrum of the PDE6B gene.
DOI: 10.5281/zenodo.8017647
title: Dataset for journal article

description: This is the dataset for journal article.
DOI: 10.5281/zenodo.8017646
title: Dataset for journal article

description: This is the dataset for journal article.
DOI: 10.5517/ccdc.csd.cc2dpcq6
title: CCDC 2225078: Experimental Crystal Structure Determination

description: Related Article: Priya Pandey, Lamiaa Fijahi, Nemo McIntosh, Nicholas Turetta, Marco Bardini, Samuele Giannini, Christian Ruzié, Guillaume Schweicher, David Beljonne, Jerome Cornil, Paolo Samorì, Marta Mas-Torrent, Yves Geerts Yves Geerts, Enrico Modena, Lucia Maini|2023|J.Mater.Chem.C|11|7345|doi:10.1039/D3TC00434A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.22682509.v1
title: Supplementary Material for: Diagnostic gene panel testing in (non)-syndromic patients with cleft lip, alveolus and/or palate in the Netherlands.

description: ABSTRACT Objectives Clefts of the lip, alveolus and/or palate (CLA/P) are the most common craniofacial congenital malformations in humans. These oral clefts can be divided into non-syndromic (isolated) and syndromic forms. Many cleft-related syndromes are clinically variable and genetically heterogeneous, making it challenging to distinguish syndromic from non-syndromic cases. Recognition of syndromic/genetic causes is important for personalized tailored care, identification of (unrecognized) co-morbidities and accurate genetic counseling. Therefore, Next Generation Sequencing (NGS) based targeted gene panel testing is increasingly implemented in diagnostics of CLA/P patients. In this retrospective study we assess the yield of NGS gene panel testing in a cohort of CLA/P cases. Methods Whole exome sequencing followed by variant detection and interpretation in an a-priori selected set of genes associated with CLA/P phenotypes was performed in 212 unrelated CLA/P patients after genetic counseling between 2015 and 2020. Medical records including family history and results of additional genetic tests were evaluated. Results In 24 CLA/P cases (11.3 %) a pathogenic genetic variant was identified. Twenty out of these 24 had a genetic syndrome requiring specific monitoring and follow-up. Six of these 24 cases (25%) were presumed to be isolated CLA/P cases prior to testing, corresponding to 2,8% of the total cohort. In eight CLA/P cases (3.8%) without a diagnosis after NGS based gene panel testing, a molecular diagnosis was established by additional genetic analyses (e.g., SNP array, single gene testing, trio WES). Conclusion This study illustrates NGS based gene panel testing as a powerful diagnostic tool in the diagnostic work-up of CLA/P patients. Also, in apparently isolated cases and non- familial cases a genetic diagnose could be identified. Early diagnosis facilitates personalized care for patients and accurate genetic counseling of their families.
DOI: 10.5517/ccdc.csd.cc2f471w
title: CCDC 2238387: Experimental Crystal Structure Determination

description: Related Article: Carlo Andrea Mattei, Vincent Montigaud, Bertrand Lefeuvre, Vincent Dorcet, Gilles Argouarch, Olivier Cador, Boris Le Guennic, Olivier Maury, Claudia Lalli, Yannick Guyot, Stéphan Guy, Cyprien Gindre, Amina Bensalah-Ledoux, François Riobé, Bruno Baguenard, Fabrice Pointillart|2023|J.Mater.Chem.C|11|7299|doi:10.1039/D3TC00858D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f472x
title: CCDC 2238388: Experimental Crystal Structure Determination

description: Related Article: Carlo Andrea Mattei, Vincent Montigaud, Bertrand Lefeuvre, Vincent Dorcet, Gilles Argouarch, Olivier Cador, Boris Le Guennic, Olivier Maury, Claudia Lalli, Yannick Guyot, Stéphan Guy, Cyprien Gindre, Amina Bensalah-Ledoux, François Riobé, Bruno Baguenard, Fabrice Pointillart|2023|J.Mater.Chem.C|11|7299|doi:10.1039/D3TC00858D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f473y
title: CCDC 2238389: Experimental Crystal Structure Determination

description: Related Article: Carlo Andrea Mattei, Vincent Montigaud, Bertrand Lefeuvre, Vincent Dorcet, Gilles Argouarch, Olivier Cador, Boris Le Guennic, Olivier Maury, Claudia Lalli, Yannick Guyot, Stéphan Guy, Cyprien Gindre, Amina Bensalah-Ledoux, François Riobé, Bruno Baguenard, Fabrice Pointillart|2023|J.Mater.Chem.C|11|7299|doi:10.1039/D3TC00858D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7698725
title: Data of Nutrition Knowledge in a Sample of College Students in Jordan

description: This cross-sectional research assessed nutrition knowledge in a sample of college students in Amman, Jordan and its association with food security and other risk factors. An Arabic Nutrition Knowledge Index (ANKI) was developed and validated in 122 college students (study-1). In study-2, the demographics scale, validated ANKI, and Arabic Individual Food Insecurity Experience Scale (FIES) were administered to 470 students from the same university. <strong>Ethical considerations:</strong>This manuscript has been read and approved by all authors. The authors confirm that there are no other persons, who satisfied the criteria for authorship, but are not listed. The order of authors listed in the manuscript has been approved by all of them. They also understand that the Corresponding Author is the sole contact for the Editorial process, and holds the responsibility for communicating with the other author about progress, submissions of revisions and final approval of proofs. Moreover, the authors declare that this manuscript is original, has not been published before, and is not currently being considered for publication elsewhere. Furthermore, all data used in the study is confidential and the lead author has full access to the data reported in the manuscript. We confirm that there are no known conflicts of interest associated with this publication, which did not receive any financial support. Finally, the reporting of this work is compliant with The Code of Ethics of the World Medical Association (Declaration of Helsinki). In addition to that, the protocol of this research is approved by the Institutional Review Board at the University of Jordan, Amman, Jordan (ref no.: 2021-89).
description: this project was not funded