cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17048921
title: Supplementary Material for: Importance of Early Genetic Sequencing in Neonates Admitted to NICU with Recurrent Hypernatremia: Results of a Prospective Cohort Study

description: <b><i>Objectives:</i></b> The genetic characteristics in neonates admitted to the NICU with recurrent hypernatremia remained unknown. We aimed to implement early genetic sequencing to identify possible genetic etiologies, optimize the treatment, and improve the outcome. <b><i>Methods:</i></b> We prospectively performed exome sequencing or targeted panel sequencing on neonates diagnosed with recurrent hypernatremia (plasma sodium ≥150 mEq/L, ≥2 episodes) from January 1, 2016, to June 30, 2020. <b><i>Results:</i></b> Among 22,375 neonates admitted to the NICU, approximately 0.33% (73/22,375) developed hypernatremia. The incidence of hypernatremia &gt;14 days and ≤14 days was 0.03% and 0.3%, respectively. Among 38 neonates who had ≥2 hypernatremia episodes, parents of 28 patients consented for sequencing. Genetic diagnosis was achieved in 25% neonates (7/28). Precision medicine treatment was performed in 85.7% (6/7) of the patients, including hydrochlorothiazide and indomethacin for 57.1% (4/7) with arginine vasopressin receptor 2 (<i>AVPR2</i>) deficiency-associated congenital nephrogenic diabetes insipidus; a special diet of fructose formula for 1 patient with solute carrier family 5 member 1 deficiency-associated congenital glucose-galactose malabsorption (1/7, 14.3%); and kallikrein-inhibiting ointment for 1 patient with serine protease inhibitor of Kazal-type <i>5</i> deficiency-associated Netherton syndrome (1/7, 14.3%). Only hypernatremia onset age (adjusted odds ratio 1.32 [1.01–1.72], <i>p</i> = 0.040) independently predicted the underlying genetic etiology. The risk of a genetic etiology of hypernatremia was 9.0 times higher for neonates with a hypernatremia onset age ≥17.5 days (95% confidence interval, 1.1–73.2; <i>p</i> = 0.038). <b><i>Conclusions:</i></b> Single-gene disorders are common in neonates with recurrent hypernatremia, and &gt;50% of cases are caused by <i>AVPR2</i> deficiency-associated congenital nephrogenic diabetes insipidus. Early genetic testing can aid the diagnosis of unexplained recurrent neonatal hypernatremia and improve therapy and outcome.
DOI: 10.6084/m9.figshare.17048921.v1
title: Supplementary Material for: Importance of Early Genetic Sequencing in Neonates Admitted to NICU with Recurrent Hypernatremia: Results of a Prospective Cohort Study

description: <b><i>Objectives:</i></b> The genetic characteristics in neonates admitted to the NICU with recurrent hypernatremia remained unknown. We aimed to implement early genetic sequencing to identify possible genetic etiologies, optimize the treatment, and improve the outcome. <b><i>Methods:</i></b> We prospectively performed exome sequencing or targeted panel sequencing on neonates diagnosed with recurrent hypernatremia (plasma sodium ≥150 mEq/L, ≥2 episodes) from January 1, 2016, to June 30, 2020. <b><i>Results:</i></b> Among 22,375 neonates admitted to the NICU, approximately 0.33% (73/22,375) developed hypernatremia. The incidence of hypernatremia &gt;14 days and ≤14 days was 0.03% and 0.3%, respectively. Among 38 neonates who had ≥2 hypernatremia episodes, parents of 28 patients consented for sequencing. Genetic diagnosis was achieved in 25% neonates (7/28). Precision medicine treatment was performed in 85.7% (6/7) of the patients, including hydrochlorothiazide and indomethacin for 57.1% (4/7) with arginine vasopressin receptor 2 (<i>AVPR2</i>) deficiency-associated congenital nephrogenic diabetes insipidus; a special diet of fructose formula for 1 patient with solute carrier family 5 member 1 deficiency-associated congenital glucose-galactose malabsorption (1/7, 14.3%); and kallikrein-inhibiting ointment for 1 patient with serine protease inhibitor of Kazal-type <i>5</i> deficiency-associated Netherton syndrome (1/7, 14.3%). Only hypernatremia onset age (adjusted odds ratio 1.32 [1.01–1.72], <i>p</i> = 0.040) independently predicted the underlying genetic etiology. The risk of a genetic etiology of hypernatremia was 9.0 times higher for neonates with a hypernatremia onset age ≥17.5 days (95% confidence interval, 1.1–73.2; <i>p</i> = 0.038). <b><i>Conclusions:</i></b> Single-gene disorders are common in neonates with recurrent hypernatremia, and &gt;50% of cases are caused by <i>AVPR2</i> deficiency-associated congenital nephrogenic diabetes insipidus. Early genetic testing can aid the diagnosis of unexplained recurrent neonatal hypernatremia and improve therapy and outcome.
DOI: 10.25502/dvff-xx49/d
title: Cassava maize intercropping in Nigeria

description: ACAI is a 5 year Bill & Melinda Gates Foundation funded project in 5 countries in Africa (Nigeria and Tanzania) providing tailored agronomic advice to small scale cassava growers in the target countries. The project delivers agronomic solutions to imporve cassava root yield and quality and the necessary knowledge base and applications for accessing this knowledge to cassava scaling partners and ultimately farmers in the target countries while instituting the necessary capacity and skills for national system scientists to engage in transformative cassava agronomy.
DOI: 10.6084/m9.figshare.16786305
title: Suggestion of active 3-chymotrypsin like protease (3CL<sup>Pro</sup>) inhibitors as potential anti-SARS-CoV-2 agents using predictive QSAR model based on the combination of ALASSO with an ANN model

description: The novel severe acute respiratory syndrome coronavirus (SARS CoV-2) was introduced as an epidemic in 2019 and had millions of deaths worldwide. Given the importance of this disease, the recommendation and design of new active compounds are crucial. 3-chymotrypsin-like protease (3 CL<sup>pro</sup>) inhibitors have been identified as potent compounds for treating SARS-CoV-2 disease. So, the design of new 3 CL<sup>pro</sup> inhibitors was proposed using a quantitative structure-activity relationship (QSAR) study. In this context, a powerful adaptive least absolute shrinkage and selection operator (ALASSO) penalized variable selection method with inherent advantages coupled with a nonlinear artificial neural network (ANN) modelling method were used to provide a QSAR model with high interpretability and predictability. After evaluating the accuracy and validity of the developed ALASSO-ANN model, new compounds were proposed using effective descriptors, and the biological activity of the new compounds was predicted. Ligand-receptor (LR) interactions were also performed to confirm the interaction strength of the compounds using molecular docking (MD) study. The pharmacokinetics properties and calculated Lipinski’s rule of five were applied to all proposed compounds. Due to the ease of synthesis of these suggested new compounds, it is expected that they have acceptable pharmacological properties.
DOI: 10.6084/m9.figshare.16786305.v2
title: Suggestion of active 3-chymotrypsin like protease (3CL<sup>Pro</sup>) inhibitors as potential anti-SARS-CoV-2 agents using predictive QSAR model based on the combination of ALASSO with an ANN model

description: The novel severe acute respiratory syndrome coronavirus (SARS CoV-2) was introduced as an epidemic in 2019 and had millions of deaths worldwide. Given the importance of this disease, the recommendation and design of new active compounds are crucial. 3-chymotrypsin-like protease (3 CL<sup>pro</sup>) inhibitors have been identified as potent compounds for treating SARS-CoV-2 disease. So, the design of new 3 CL<sup>pro</sup> inhibitors was proposed using a quantitative structure-activity relationship (QSAR) study. In this context, a powerful adaptive least absolute shrinkage and selection operator (ALASSO) penalized variable selection method with inherent advantages coupled with a nonlinear artificial neural network (ANN) modelling method were used to provide a QSAR model with high interpretability and predictability. After evaluating the accuracy and validity of the developed ALASSO-ANN model, new compounds were proposed using effective descriptors, and the biological activity of the new compounds was predicted. Ligand-receptor (LR) interactions were also performed to confirm the interaction strength of the compounds using molecular docking (MD) study. The pharmacokinetics properties and calculated Lipinski’s rule of five were applied to all proposed compounds. Due to the ease of synthesis of these suggested new compounds, it is expected that they have acceptable pharmacological properties.
DOI: 10.6084/m9.figshare.16786305.v1
title: Suggestion of active 3-chymotrypsin like protease (3CL<sup>Pro</sup>) inhibitors as potential anti-SARS-CoV-2 agents using predictive QSAR model based on the combination of ALASSO with an ANN model

description: The novel severe acute respiratory syndrome coronavirus (SARS CoV-2) was introduced as an epidemic in 2019 and had millions of deaths worldwide. Given the importance of this disease, the recommendation and design of new active compounds are crucial. 3-chymotrypsin-like protease (3 CL<sup>pro</sup>) inhibitors have been identified as potent compounds for treating SARS-CoV-2 disease. So, the design of new 3 CL<sup>pro</sup> inhibitors was proposed using a quantitative structure-activity relationship (QSAR) study. In this context, a powerful adaptive least absolute shrinkage and selection operator (ALASSO) penalized variable selection method with inherent advantages coupled with a nonlinear artificial neural network (ANN) modelling method were used to provide a QSAR model with high interpretability and predictability. After evaluating the accuracy and validity of the developed ALASSO-ANN model, new compounds were proposed using effective descriptors, and the biological activity of the new compounds was predicted. Ligand-receptor (LR) interactions were also performed to confirm the interaction strength of the compounds using molecular docking (MD) study. The pharmacokinetics properties and calculated Lipinski’s rule of five were applied to all proposed compounds. Due to the ease of synthesis of these suggested new compounds, it is expected that they have acceptable pharmacological properties.
DOI: 10.6084/m9.figshare.17019827
title: Coding sequences of MAKER-annotated protein-coding genes

description: Coding sequences of MAKER-annotated protein-coding genes
DOI: 10.6084/m9.figshare.17019827.v1
title: Coding sequences of MAKER-annotated protein-coding genes

description: Coding sequences of MAKER-annotated protein-coding genes
DOI: 10.5281/zenodo.5713585
title: Mutation Testing in the Wild: Findings from GitHub

description: Supplementary material for the articule "Mutation Testing in the Wild: Findings from GitHub" submitted to the Empirical Software Engineering Journal. It includes: Literature_search_for_mutation_tools_2018-2021.xlsx. This document contains the papers found in the search for mutation testing tools performed between 2018 and 2021. Mutation_tools.xlsx: This document includes the 127 mutation testing tools identified in our study along with tables and graphs. Repositories_raw_data.xlsx: All repositories data mined from Github as evidence of use of the top 10 mutation tools analyzed in our study. In addition, tables with calculations and graphs used in our work are included. Search_strings_mutation_tools.xlsx: The search strings used to look for repositories using each mutation tool in Github.
DOI: 10.5281/zenodo.5713584
title: Mutation Testing in the Wild: Findings from GitHub

description: Supplementary material for the articule "Mutation Testing in the Wild: Findings from GitHub" submitted to the Empirical Software Engineering Journal. It includes: Literature_search_for_mutation_tools_2018-2021.xlsx. This document contains the papers found in the search for mutation testing tools performed between 2018 and 2021. Mutation_tools.xlsx: This document includes the 127 mutation testing tools identified in our study along with tables and graphs. Repositories_raw_data.xlsx: All repositories data mined from Github as evidence of use of the top 10 mutation tools analyzed in our study. In addition, tables with calculations and graphs used in our work are included. Search_strings_mutation_tools.xlsx: The search strings used to look for repositories using each mutation tool in Github.
DOI: 10.6084/m9.figshare.17019884
title: Transcripts of MAKER-annotated protein-coding genes

description: Transcripts of MAKER-annotated protein-coding genes
DOI: 10.6084/m9.figshare.17019884.v1
title: Transcripts of MAKER-annotated protein-coding genes

description: Transcripts of MAKER-annotated protein-coding genes
DOI: 10.5525/gla.researchdata.1221
title: Development of an age-dependent micronutrient centile charts and their utility in children with chronic gastrointestinal conditions at risk of deficiencies: A proof-of-concept study
DOI: 10.6084/m9.figshare.17048942
title: Supplementary Material for: Safety and Diagnostic Yield of Radial Probe Endobronchial Ultrasound-Guided Biopsy for Peripheral Lung Lesions in Patients with Idiopathic Pulmonary Fibrosis: A Multicenter Cross-Sectional Study

description: <b><i>Background:</i></b> Radial probe endobronchial ultrasound-guided transbronchial lung biopsy (RP-EBUS-TBLB) is widely used for diagnosis of peripheral lung lesions (PLLs). To date, there have been no reports regarding the clinical outcomes of RP-EBUS-TBLB for PLLs in patients with idiopathic pulmonary fibrosis (IPF). <b><i>Objectives:</i></b> This study was performed between October 2017 and December 2019 to identify the safety and diagnostic performance of RP-EBUS-TBLB in IPF patients. <b><i>Methods:</i></b> Patients were divided into the usual interstitial pneumonia (UIP) group (<i>n</i> = 39, 4%), the probable UIP group (<i>n</i> = 12, 1%), and the noninterstitial lung disease (non-ILD) group (<i>n</i> = 903, 95%). <b><i>Results:</i></b> The diagnostic yield was significantly lower in the UIP group than in the non-ILD group (62% vs. 76%; <i>p</i> = 0.042), but there were no significant differences between the UIP and probable UIP groups (62% vs. 83%; <i>p</i> = 0.293) or the probable UIP and non-ILD groups (83% vs. 76%; <i>p</i> = 0.741). Multivariate logistic analysis showed that the mean diameter of PLLs, positive bronchus sign on CT, and “within the lesion” status on EBUS were independently associated with success of the procedure. Especially, the presence of the UIP pattern on CT (OR, 0.385; 95% CI: 0.172–0.863; <i>p</i> = 0.020) was independently associated with failed diagnosis. Among patients with UIP, “within the lesion” status on EBUS (OR, 25.432; 95% CI: 2.321–278.666; <i>p</i> = 0.008) was shown to be a factor contributing to a successful diagnosis. Overall, there were no significant differences in complication rates among the 3 study groups. <b><i>Conclusion:</i></b> RP-EBUS-TBLB can be performed safely with an acceptable diagnostic yield, even in patients with IPF.
DOI: 10.6084/m9.figshare.17048948
title: Supplementary Material for: Circulating Serum Copper Is Associated with Atherosclerotic Cardiovascular Disease, but Not Venous Thromboembolism: A Prospective Cohort Study

description: <b><i>Background and Objective:</i></b> Serum copper has been linked to the risk of atherosclerotic cardiovascular disease (CVD). However, the potential association between serum copper and venous thromboembolism (VTE) is not known. The principal aim was to evaluate the potential prospective association between serum copper and VTE risk. A secondary aim was to confirm or refute previously reported associations between serum copper and atherosclerotic CVD. <b><i>Methods:</i></b> Serum copper was measured at baseline using atomic absorption spectrometry in 2,492 men aged 42–61 years without a history of VTE in the Kuopio Ischemic Heart Disease prospective cohort study. Cox regression models were used to calculate hazard ratios (HRs) with 95% confidence interval (CI) for VTE. <b><i>Results:</i></b> During a median follow-up of 27.0 years, 166 VTE events occurred. The risk of VTE per 1 standard deviation increase in serum copper in age-adjusted analysis was HR: 1.02; 95% CI: 0.88–1.20, which was attenuated to HR: 0.99; 95% CI: 0.82–1.19, following further adjustment for several established and emerging risk factors. Comparing the top versus bottom tertiles of serum copper, the corresponding adjusted HRs were 1.16 (95% CI: 0.80–1.66) and 1.11 (95% CI: 0.74–1.68), respectively. In 1,901 men without a history of coronary heart disease (CHD), the multivariable-adjusted HR for CHD was 1.32 (95% CI: 1.10–1.59) comparing extreme tertiles of serum copper. <b><i>Conclusion:</i></b> In middle-aged Finnish men, we confirmed previously reported associations between high serum copper levels and increased risk of atherosclerotic CVD, but serum copper was not associated with future VTE risk. Other large-scale prospective studies conducted in women, other age-groups, and other populations are needed to confirm or refute these findings.
DOI: 10.17638/datacat.liverpool.ac.uk/1275
title: Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation
DOI: 10.6084/m9.figshare.17048960
title: Supplementary Material for: Risk of Postoperative Renal Failure in Radical Nephrectomy and Nephroureterectomy: A Validated Risk Prediction Model

description: <b><i>Introduction:</i></b> The study aimed to construct and validate a risk prediction model for incidence of postoperative renal failure (PORF) following radical nephrectomy and nephroureterectomy. <b><i>Methods:</i></b> The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database years 2005–2014 were used for the derivation cohort. A stepwise multivariate logistic regression analysis was conducted, and the final model was validated with an independent cohort from the ACS-NSQIP database years 2015–2017. <b><i>Results:</i></b> In cohort of 14,519 patients, 296 (2.0%) developed PORF. The final 9-factor model included age, gender, diabetes, hypertension, BMI, preoperative creatinine, hematocrit, platelet count, and surgical approach. Model receiver-operator curve analysis provided a C-statistic of 0.79 (0.77, 0.82; <i>p</i> &lt; 0.001), and overall calibration testing <i>R</i><sup>2</sup> was 0.99. Model performance in the validation cohort provided a C-statistic of 0.79 (0.76, 0.81; <i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> PORF is a known risk factor for chronic kidney disease and cardiovascular morbidity, and is a common occurrence after unilateral kidney removal. The authors propose a robust and validated risk prediction model to aid in identification of high-risk patients and optimization of perioperative care.
DOI: 10.15468/akp2m7
title: Nomenclatural notes on Cryptocarya R. Br. (Lauraceae) from Madagascar

description: This dataset contains the digitized treatments in Plazi based on the original journal article van der Werff, Henk (2013): Nomenclatural notes on Cryptocarya R. Br. (Lauraceae) from Madagascar. Candollea 68 (2): 303-306, DOI: 10.15553/c2012v682a14
DOI: 10.23670/irj.2021.113.1.1
title: Динамика живой массы и ее среднесуточный прирост молодняка гусей, M±m, г, (n=36)

description: Международный научно-исследовательский журнал 11(113) 11.2021, №11(113) (2021)
DOI: 10.5281/zenodo.5535599
title: Data Set of Publication on Detecting Violations of Access Control and Information Flow Policies in Data Flow Diagrams

description: This data set contains the evaluation data of our publication on "Detecting Violations of Access Control and Information Flow Policies in Data Flow Diagrams". The data set contains an overview on our implementation, description of the evaluation cases, and the evaluation results. The application to produce this data is available in another data set, which is linked to this data set.
description: This work was supported by the German Research Foundation (DFG) under project number 432576552, HE8596/1-1 (FluidTrust), as well as by funding from the topic Engineering Secure Systems (46.23.03) of the Helmholtz Association (HGF) and by KASTEL Security Research Labs.
DOI: 10.5281/zenodo.5535598
title: Data Set of Publication on Detecting Violations of Access Control and Information Flow Policies in Data Flow Diagrams

description: This data set contains the evaluation data of our publication on "Detecting Violations of Access Control and Information Flow Policies in Data Flow Diagrams". The data set contains an overview on our implementation, description of the evaluation cases, and the evaluation results. The application to produce this data is available in another data set, which is linked to this data set.
description: This work was supported by the German Research Foundation (DFG) under project number 432576552, HE8596/1-1 (FluidTrust), as well as by funding from the topic Engineering Secure Systems (46.23.03) of the Helmholtz Association (HGF) and by KASTEL Security Research Labs.
DOI: 10.6084/m9.figshare.17048969
title: Supplementary Material for: The Lipopolysaccharide Mutant Re-LPS Is a Useful Tool for Detecting LPS Contamination in Rheumatoid Synovial Cell Cultures

description: <b><i>Introduction:</i></b> Lipopolysaccharide (LPS) contamination of commercially available proteins has seriously impeded research on citrullinated fibrinogen (cit-Fb) in rheumatoid synovial cells (RSCs). <b><i>Methods:</i></b> RSCs obtained from 4 rheumatoid arthritis patients who underwent full knee arthroplasty were cultured, stimulated with cit-Fb, and cytokine expression levels were measured. We then evaluated polymyxin-B (PMB), heat inactivation, and rough (R)-type LPS mutants for rapid detection of LPS contamination. <b><i>Results:</i></b> cit-Fb induced expression of <i>CXCL10</i> and <i>IFNB</i> in RSCs via the toll-like receptor. PMB inhibited cit-Fb-mediated CXCL10 gene expression but not protein expression induced by 20 μg/mL cit-Fb. Heat inactivation did not affect LPS-mediated <i>CXCL10</i> or <i>IL-6</i> induction; however, cit-Fb-mediated <i>CXCL10</i>expression was inhibited. Wild-type LPS from <i>Escherichia coli</i> (WT-LPS) strongly induces <i>CXCL10</i> expression, but induction by Ra-LPS was weak, and induction by Rc- and Re-LPS was minimal. Re-LPS suppression of WT-LPS-mediated <i>CXCL10</i> induction in RSCs and peripheral blood monocytes (PBMs) was dose dependent. Furthermore, Re-LPS completely suppressed cit-Fb-mediated <i>CXCL10</i> induction in RSCs and PBMs. <b><i>Conclusion:</i></b> To easily identify LPS contamination during routine experiments, our results suggest that Re-LPS is a better tool for rapid detection of LPS contamination compared to PMB and heat treatment.