cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10078922
title: Supplementary Material for: Functional Characterization and Pharmacological Evaluation of a Novel <b><i>GLA</i></b> Missense Mutation Found in a Severely Affected Fabry Disease Family

description: <b><i>Background:</i></b> Fabry disease (FD) is a rare X-linked storage disorder resulting from the deficient activity of the lysosomal hydrolase α-galactosidase A (α-Gal A). Here we describe a 23-year-old man with FD possessing a novel mutation in the <i>GLA</i> gene, the evaluation of his family, and the functional characterization of the novel variant. <b><i>Methods:</i></b> Two generations of a family were screened for FD by clinical symptoms and low enzymatic activity. This step was followed by DNA sequencing that showed a novel <i>GLA</i> missense mutation. To confirm the pathogenicity potential of the mutation, we employed site-directed polymerase chain reaction mutagenesis. <i>GLA</i> wild-type and mutant plasmids were transfected into mammalian cells; RNA and proteins were extracted for expression and analysis of enzymatic activity. <b><i>Results:</i></b> The patient presents the variant p.Asn34Asp in the <i>GLA</i> and had several manifestations of FD since adolescence. The investigation of the deficiency of α-Gal A was initiated due to stage 4 of chronic kidney disease. All family members carrying the novel mutation presented early symptoms, including index case’s mother, who received a renal transplant when she was 35 years old. <i>In silico</i> and in vitro analysis confirmed the pathogenic potential of the mutation p.Asn34Asp showing that the enzyme had only 4% of residual activity due to protein misfolding. The ability of the pharmacological chaperone 1-deoxygalactonojirimycin to recover the mutant was confirmed, producing 37.5% of residual activity. <b><i>Conclusion:</i></b> In this work, we present a novel missense mutation in <i>GLA</i> that leads to the production of a catalytically competent α-Gal A, which is degraded before its delivery to the lysosome, promoting severe manifestations of FD, with a very similar disease course in affected men and women.
DOI: 10.6084/m9.figshare.10078925
title: ABG data

description: data for age
DOI: 10.6084/m9.figshare.10078712
title: Supplementary Material for: Association between Nonalcoholic Fatty Liver and Gensini Score in Patients with Coronary Heart Disease: A Cross-Sectional Study

description: <b><i>Introduction:</i></b> Obesity is one of the important risk factors of coronary heart disease (CHD). Nonalcoholic fatty liver disease (NAFLD) is always accompanied by obesity. Therefore, this study was designed to elucidate the relationship between NAFLD and CHD in obese and nonobese populations. <b><i>Methods:</i></b> We conducted a cross-sectional study of 454 Chinese patients diagnosed with CHD. Patients were grouped into non-NAFLD + nonobese, non-NAFLD + obese, NAFLD + nonobese, and NAFLD + obese based on the presence or absence of both NAFLD and obesity. <b><i>Results:</i></b> The mean Gensini score was significantly higher in patients with fatty liver compared to those without. Logistic regression analysis found that fatty liver, uric acid, and blood glucose levels were risk factors for a high Gensini score. <b><i>Conclusions:</i></b> Irrespective of the presence of obesity, NAFLD is a risk factor for CHD, and the clinical effect of nonobese fatty liver (especially in women) should be carefully considered.
DOI: 10.6084/m9.figshare.10078055
title: Supplementary Material for: Evaluation of Retinal Pigment Epithelium and Choroidal Neovascularization in Rats Using Laser-Scanning Optical-Resolution Photoacoustic Microscopy

description: <b><i>Purpose:</i></b> To demonstrate the value of the laser-scanning optical-resolution (LSOR)-photoacoustic (PA) microscopy (PAM) system and the conventional multimodal imaging techniques in the evaluation of laser-induced retinal injury and choroidal neovascularization (CNV) in rats. <b><i>Methods:</i></b> Different degrees of retinal injury were induced using laser photocoagulation. We compared the LSOR-PAM system with conventional imaging techniques in evaluating retinal injury with or without CNV. Six additional rats, treated with an anti-VEGF antibody or immunoglobulin G immediately after photocoagulation, were imaged 7 and 14 days after injection, and CNV lesion areas were compared. <b><i>Results:</i></b> In the retinal injury model, fundus autofluorescence showed well-defined hyperreflection, while the lesion displayed abundant PA signals demonstrating nonuniform melanin distribution in retinal pigment epithelium (RPE). RPE was detected with higher contrast in the PAM B-scan image than optical coherence tomography (OCT). Additionally, the CNV lesion was present with multiple PA signal intensities which distinctly characterized the location and area of CNV as found in fundus fluorescein angiography. Furthermore, the decreased PA signals extending from the CNV lesion were similar to those of the vascular bud in ex vivo imaging, which was invisible in other in vivo images. When treated with anti-VEGF agents, statistically significant differences can be demonstrated by PAM similar to other modalities. <b><i>Conclusions:</i></b> LSOR-PAM can detect the melanin distribution of RPE in laser-induced retinal injury and CNV in rats. PAM imaging provides a potential new tool to evaluate the vitality and functionality of RPE in vivo as well as to monitor the development and treatment of CNV.
DOI: 10.6084/m9.figshare.10078055.v1
title: Supplementary Material for: Evaluation of Retinal Pigment Epithelium and Choroidal Neovascularization in Rats Using Laser-Scanning Optical-Resolution Photoacoustic Microscopy

description: <b><i>Purpose:</i></b> To demonstrate the value of the laser-scanning optical-resolution (LSOR)-photoacoustic (PA) microscopy (PAM) system and the conventional multimodal imaging techniques in the evaluation of laser-induced retinal injury and choroidal neovascularization (CNV) in rats. <b><i>Methods:</i></b> Different degrees of retinal injury were induced using laser photocoagulation. We compared the LSOR-PAM system with conventional imaging techniques in evaluating retinal injury with or without CNV. Six additional rats, treated with an anti-VEGF antibody or immunoglobulin G immediately after photocoagulation, were imaged 7 and 14 days after injection, and CNV lesion areas were compared. <b><i>Results:</i></b> In the retinal injury model, fundus autofluorescence showed well-defined hyperreflection, while the lesion displayed abundant PA signals demonstrating nonuniform melanin distribution in retinal pigment epithelium (RPE). RPE was detected with higher contrast in the PAM B-scan image than optical coherence tomography (OCT). Additionally, the CNV lesion was present with multiple PA signal intensities which distinctly characterized the location and area of CNV as found in fundus fluorescein angiography. Furthermore, the decreased PA signals extending from the CNV lesion were similar to those of the vascular bud in ex vivo imaging, which was invisible in other in vivo images. When treated with anti-VEGF agents, statistically significant differences can be demonstrated by PAM similar to other modalities. <b><i>Conclusions:</i></b> LSOR-PAM can detect the melanin distribution of RPE in laser-induced retinal injury and CNV in rats. PAM imaging provides a potential new tool to evaluate the vitality and functionality of RPE in vivo as well as to monitor the development and treatment of CNV.
DOI: 10.6084/m9.figshare.10078052
title: Dopaminergic gene analysis indicates influence of inattention but not IQ in executive dysfunction of Indian ADHD probands

description: Organizational inefficiency and inattention are speculated to be the reason for executive deficit (ED) of ADHD probands. Even with average IQ, probands often perform poorly due to higher inattention. Pharmacotherapy, cognitive behavioural therapy, and counselling provide only symptomatic relief. Several candidate genes showed involvement with ADHD; the most consistent are dopamine receptor 4 (DRD4) and solute carrier family 6 member 3 (SLC6A3). We analyzed association of rarely investigated DRD4 and SLC6A3 variants with ADHD core traits in Indo-Caucasoid probands. ED, inattention, organizational efficiency, and IQ were measured by Barkley Deficit in Executive Functioning-Child & Adolescent scale, DSM-IV-TR, Conners’ Parent Rating Scale-revised, and WISC respectively. Target sites were analyzed by PCR, RFLP, and/or Sanger sequencing of genomic DNA. DRD4 variants mostly affected inattention while SLC6A3 variants showed association with IQ. Few DRD4 and SLC6A3 variants showed dichotomous association with IQ and inattention. DRD4 Exon3 VNTR &gt;4R showed negative impact on all traits excepting IQ. Inattention showed correlation with attention span, organizational efficiency, and ED, while IQ failed to do so. We infer that IQ and attention could be differentially regulated by dopaminergic gene variants affecting functional efficiency in ADHD and the two traits should be considered together for providing better rehabilitation.
DOI: 10.6084/m9.figshare.10078052.v1
title: Dopaminergic gene analysis indicates influence of inattention but not IQ in executive dysfunction of Indian ADHD probands

description: Organizational inefficiency and inattention are speculated to be the reason for executive deficit (ED) of ADHD probands. Even with average IQ, probands often perform poorly due to higher inattention. Pharmacotherapy, cognitive behavioural therapy, and counselling provide only symptomatic relief. Several candidate genes showed involvement with ADHD; the most consistent are dopamine receptor 4 (DRD4) and solute carrier family 6 member 3 (SLC6A3). We analyzed association of rarely investigated DRD4 and SLC6A3 variants with ADHD core traits in Indo-Caucasoid probands. ED, inattention, organizational efficiency, and IQ were measured by Barkley Deficit in Executive Functioning-Child & Adolescent scale, DSM-IV-TR, Conners’ Parent Rating Scale-revised, and WISC respectively. Target sites were analyzed by PCR, RFLP, and/or Sanger sequencing of genomic DNA. DRD4 variants mostly affected inattention while SLC6A3 variants showed association with IQ. Few DRD4 and SLC6A3 variants showed dichotomous association with IQ and inattention. DRD4 Exon3 VNTR &gt;4R showed negative impact on all traits excepting IQ. Inattention showed correlation with attention span, organizational efficiency, and ED, while IQ failed to do so. We infer that IQ and attention could be differentially regulated by dopaminergic gene variants affecting functional efficiency in ADHD and the two traits should be considered together for providing better rehabilitation.
DOI: 10.6084/m9.figshare.10076903
title: Supplementary Material for: Toward Preventing Enamel Hypoplasia: Modeling Maternal and Neonatal Biomarkers of Human Calcium Homeostasis

description: <b><i>Aim:</i></b> The aim of this study was to assess biomarkers of calcium homeostasis and tooth development, in mothers during pregnancy and their children at birth, for enamel hypoplasia (EH) in the primary maxillary central incisor teeth. <b><i>Methods:</i></b> Bayesian methodology was used for secondary data analyses from a randomized, controlled trial of prenatal vitamin D<sub>3</sub> supplementation in healthy mothers (<i>N</i> = 350) and a follow-up study of a subset of the children. The biomarkers were serum calcium (Ca), phosphorus (P), intact parathyroid hormone (iPTH), total circulating 25-dihydroxyvitamin D (25(OH)D), and 1,25-dihydroxyvitamin D (1,25(OH)<sub>2</sub>D). The maternal biomarkers were assayed monthly during pregnancy, and the child’s biomarkers were derived from cord blood. Digital images of the child’s 2 teeth were scored for EH using Enamel Defects Index criteria for each of the incisal, middle, and cervical regions for an EH extent score. <b><i>Results:</i></b> The child EH prevalence was 41% (60/145), with most defects present in the incisal and middle tooth regions. Cord blood iPTH and 1,25(OH)<sub>2</sub>D levels were significantly associated with EH extent after controlling for maternal factors. For every 1 pg/mL increase in cord blood iPTH, the EH extent decreased by approximately 6%. For every 10 pg/mL increase in cord blood 1,25(OH)<sub>2</sub>D, the EH extent increased by almost 30% (holding all other terms constant and adjusting for subject-level heterogeneity). The relationship between maternal 25(OH)D and maternal mean iPTH varied significantly by EH extent. <b><i>Conclusion:</i></b> The results suggest possible modifiable relationships of maternal and neonatal factors of calcium homeostasis during pregnancy and at birth for EH, contributing to the frontier of knowledge regarding sound tooth development for dental caries prevention.
DOI: 10.6084/m9.figshare.10076903.v1
title: Supplementary Material for: Toward Preventing Enamel Hypoplasia: Modeling Maternal and Neonatal Biomarkers of Human Calcium Homeostasis

description: <b><i>Aim:</i></b> The aim of this study was to assess biomarkers of calcium homeostasis and tooth development, in mothers during pregnancy and their children at birth, for enamel hypoplasia (EH) in the primary maxillary central incisor teeth. <b><i>Methods:</i></b> Bayesian methodology was used for secondary data analyses from a randomized, controlled trial of prenatal vitamin D<sub>3</sub> supplementation in healthy mothers (<i>N</i> = 350) and a follow-up study of a subset of the children. The biomarkers were serum calcium (Ca), phosphorus (P), intact parathyroid hormone (iPTH), total circulating 25-dihydroxyvitamin D (25(OH)D), and 1,25-dihydroxyvitamin D (1,25(OH)<sub>2</sub>D). The maternal biomarkers were assayed monthly during pregnancy, and the child’s biomarkers were derived from cord blood. Digital images of the child’s 2 teeth were scored for EH using Enamel Defects Index criteria for each of the incisal, middle, and cervical regions for an EH extent score. <b><i>Results:</i></b> The child EH prevalence was 41% (60/145), with most defects present in the incisal and middle tooth regions. Cord blood iPTH and 1,25(OH)<sub>2</sub>D levels were significantly associated with EH extent after controlling for maternal factors. For every 1 pg/mL increase in cord blood iPTH, the EH extent decreased by approximately 6%. For every 10 pg/mL increase in cord blood 1,25(OH)<sub>2</sub>D, the EH extent increased by almost 30% (holding all other terms constant and adjusting for subject-level heterogeneity). The relationship between maternal 25(OH)D and maternal mean iPTH varied significantly by EH extent. <b><i>Conclusion:</i></b> The results suggest possible modifiable relationships of maternal and neonatal factors of calcium homeostasis during pregnancy and at birth for EH, contributing to the frontier of knowledge regarding sound tooth development for dental caries prevention.
DOI: 10.6084/m9.figshare.10075439
title: Amyloid beta (M1-42) HSQC spectrum

description: HSQC spectrum of bacterially expressed 15N labelled Aβ(M1-42) with an Nterminal methionine.<br>
DOI: 10.6084/m9.figshare.10075574
title: Existing physiologically-based kinetic (PBK) models, identified via PubMed searches (with associated EndNote library)

description: For the safety assessment of chemicals, it is important to consider both the intrinsic toxicity and the internal exposure of the chemical. PBK models (also referred to as physiologically-based pharmacokinetic/toxicokinetic (PBPK/TK) models) can provide detailed information on the time-course of chemicals in different organs of the body. This information can be incorporated as part of the safety assessment process and/or used to support read-across predictions during product development. Model parameters and chemical information taken from existing PBK models for “source” chemicals (i.e. those with the relevant data) can be used to inform PBK model development for “target” chemicals (i.e. those lacking the relevant data). This approach was demonstrated successfully by Lu et al (2016; PLOS Computational Biology; DOI:10.1371/journal.pcbi.1004495) who developed a “Knowledgebase” of existing PBK models for 307 unique chemicals. This Knowledgebase included chemical identities, species, life-stage, organs and basic physico-chemical properties of the chemicals (along with the list of published articles and abstracts). Appropriate analogues to use as source chemicals were selected using physico-chemical property information, demonstrating the utility of the approach to assist development of new PBK models. The first step in this process is to identify the existing PBK models. Whilst the original “Knowledgebase” comprised publications from 1977 – 2013, many more models have been published since. More recent research at the United States Environment Protection Agency (US EPA), has involved identification of additional published PBK models, obtained through a search of the PubMed database. The resulting Excel spreadsheet lists existing PBK models (identified via PubMed) for 1,290 individual chemical entities, as recorded in 972 separate publications (up to 2016). The data available in the Excel spreadsheet include chemical name, additional information on the chemical (e.g. isomer, metabolite of another chemical, administration as a mixture etc), species, gender, life-stage, administration route, compartments/organs considered and the PubMed ID number. The associated Endnote library gives the full details of all the references obtained via PubMed (including abstracts); PBK models of interest can be searched via their PubMed ID number. This information is provided as an indication of models available, it does not represent an exhaustive search of all existing models.
DOI: 10.6084/m9.figshare.10075439.v1
title: Amyloid beta (M1-42) HSQC spectrum

description: HSQC spectrum of bacterially expressed 15N labelled Aβ(M1-42) with an Nterminal methionine.<br>
DOI: 10.6084/m9.figshare.10075406
title: Refactoring Community Smells in the Wild: The Practitioner’s Field Manual - Replication Package

description: Community smells have been defined as sub-optimal organizational structures that may lead to social debt. Previous studies have shown that they are highly diffused in both open- and closed-source projects, are perceived as harmful by practitioners, and can even lead to the introduction of technical debt in source code. Despite the presence of this body of research, little is known on the practitioners' perceived prominence of community smells in practice as well as on the strategies adopted to deal with them. This paper aims at bridging this gap by proposing an empirical study in which 76 software practitioners are inquired on (i) the prominence of four well-known community smells, i.e., Organizational Silo, Black Cloud, Lone Wolf, and Radio Silence, in their contexts and ii) the methods they adopted to ``refactor'' them. Our results first reveal that community smells frequently manifest themselves in software projects and, more importantly, there exist specific refactoring practices to deal with each of the considered community smells.<br>
DOI: 10.6084/m9.figshare.10075400
title: Supplementary Material for: The Ability of Different Scoring Systems to Predict Mortality in Chronic Obstructive Pulmonary Disease Patients: A Prospective Cohort Study

description: <b><i>Background:</i></b> Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality, therefore the prediction of mortality in COPD patients is crucial. In the current study, the abilities of different categorization systems to predict mortality in stable COPD patients from a prospective cohort were compared. <b><i>Methods:</i></b> The ability to predict mortality was compared in terms of discrimination by Harrell’s C (HC) index and calibration using graphical comparison among the GOLD (Global Initiative for Chronic Obstructive Lung Disease) 2011, GOLD 2017, GOLD grade, BODE (BMI, Airflow Obstruction, Dyspnea, Exercise), updated BODE, BODEx (BMI, Airflow Obstruction, Dyspnea, Exacerbation), e-BODE (Exacerbation and BODE), ADO (Age, Dyspnea, Airflow Obstruction), COPD prognostic index (CPI), and simplified/optimized B-AE-D (BMI, Acute Exacerbation, Dyspnea) indexes. <b><i>Results:</i></b> The study included 520 patients, of whom 63 died during a median 40-month follow-up period. Combined prediction systems exhibited higher discrimination properties than single predictors. The CPI exhibited the highest with a HC of 0.768, followed by the simplified B-AE-D (HC 0.761), ADO (HC 0.760), and optimized B-AE-D (HC 0.756). The BODE and its variants other than the ADO exhibited relatively lower HCs (0.656–0.705), and GOLD exhibited the lowest discrimination ability among the combined indices (HCs 0.628–0.637). Subjective symptom questionnaires such as the modified Medical Research Council (mMRC) scale (HC 0.693) and SGRQ (HC 0.679) exhibited the highest ability to predict mortality among the single indices. <b><i>Conclusion:</i></b> The ADO, simplified B-AE-D, optimized B-AE-D, and GOLD 2017 exhibited good calibration properties, but the CPI did not. The simplified and optimized B-AE-Ds and the ADO index had good discrimination and calibration properties for the prediction of mortality in stable COPD patients.
DOI: 10.6084/m9.figshare.10075400.v1
title: Supplementary Material for: The Ability of Different Scoring Systems to Predict Mortality in Chronic Obstructive Pulmonary Disease Patients: A Prospective Cohort Study

description: <b><i>Background:</i></b> Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality, therefore the prediction of mortality in COPD patients is crucial. In the current study, the abilities of different categorization systems to predict mortality in stable COPD patients from a prospective cohort were compared. <b><i>Methods:</i></b> The ability to predict mortality was compared in terms of discrimination by Harrell’s C (HC) index and calibration using graphical comparison among the GOLD (Global Initiative for Chronic Obstructive Lung Disease) 2011, GOLD 2017, GOLD grade, BODE (BMI, Airflow Obstruction, Dyspnea, Exercise), updated BODE, BODEx (BMI, Airflow Obstruction, Dyspnea, Exacerbation), e-BODE (Exacerbation and BODE), ADO (Age, Dyspnea, Airflow Obstruction), COPD prognostic index (CPI), and simplified/optimized B-AE-D (BMI, Acute Exacerbation, Dyspnea) indexes. <b><i>Results:</i></b> The study included 520 patients, of whom 63 died during a median 40-month follow-up period. Combined prediction systems exhibited higher discrimination properties than single predictors. The CPI exhibited the highest with a HC of 0.768, followed by the simplified B-AE-D (HC 0.761), ADO (HC 0.760), and optimized B-AE-D (HC 0.756). The BODE and its variants other than the ADO exhibited relatively lower HCs (0.656–0.705), and GOLD exhibited the lowest discrimination ability among the combined indices (HCs 0.628–0.637). Subjective symptom questionnaires such as the modified Medical Research Council (mMRC) scale (HC 0.693) and SGRQ (HC 0.679) exhibited the highest ability to predict mortality among the single indices. <b><i>Conclusion:</i></b> The ADO, simplified B-AE-D, optimized B-AE-D, and GOLD 2017 exhibited good calibration properties, but the CPI did not. The simplified and optimized B-AE-Ds and the ADO index had good discrimination and calibration properties for the prediction of mortality in stable COPD patients.
DOI: 10.6084/m9.figshare.10075373
title: company_revenue_TRAIN.csv

description: Company revenue data for RAMP challenge: https://github.com/ramp-kits/fan_revenue_prediction<br>
DOI: 10.6084/m9.figshare.10075367
title: award_notices_RAMP.csv

description: For RAMP challenge: https://github.com/ramp-kits/fan_revenue_prediction<br>
DOI: 10.6084/m9.figshare.10075370
title: company_revenue_TEST.csv

description: RAMP challenge: https://github.com/ramp-kits/fan_revenue_prediction<br>
DOI: 10.6084/m9.figshare.10075373.v2
title: company_revenue_TRAIN.csv

description: Company revenue data for RAMP challenge: https://github.com/ramp-kits/fan_revenue_prediction<br>