cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5123596
title: Supplementary Material for: Review and Recommendations for Zero-Inflated Count Regression Modeling of Dental Caries Indices in Epidemiological Studies

description: Over the past 5–10 years, zero-inflated (ZI) count regression models have been increasingly applied to the analysis of dental caries indices (e.g. DMFT, dfms). The main reason for that is linked to the broad decline in children’s caries experience, such that dmf and DMF indices more frequently generate low or even zero counts. This article specifically reviews the application of ZI Poisson and ZI negative binomial regression models to dental caries, with emphasis on the description of the models and the interpretation of fitted model results given the study goals. The review finds that interpretations provided in the published caries research are often imprecise or inadvertently misleading, particularly with respect to failing to discriminate between inference for the class of susceptible persons defined by such models and inference for the sampled population in terms of overall exposure effects. Recommendations are provided to enhance the use as well as the interpretation and reporting of results of count regression models when applied to epidemiological studies of dental caries.
DOI: 10.6084/m9.figshare.5123608.v1
title: Supplementary Material for: Plasma Endothelin-1 and Vascular Endothelial Growth Factor Levels and Their Relationship to Hemodynamics in Idiopathic Pulmonary Fibrosis

description: <b><i>Background:</i></b> Pulmonary hypertension (PH) is associated with a poor prognosis in idiopathic pulmonary fibrosis (IPF). Endothelin-1 (ET-1) and vascular endothelial growth factor (VEGF) are important in both fibrosis and vascular remodeling. <b><i>Objectives:</i></b> We sought to determine the relationship between ET-1 and VEGF levels and hemodynamics in patients with IPF. We hypothesized that higher levels of ET-1 and VEGF would be associated with higher pulmonary artery pressures (PAP) and pulmonary vascular resistance (PVR) in patients with IPF. <b><i>Methods:</i></b> We performed a cross-sectional analysis of 52 adults with IPF enrolled in a prospective cohort with available clinical data, platelet-free plasma, and hemodynamics. ET-1 and VEGF levels were measured via immunoassay. The associations of ET-1 and VEGF with PAP and PVR were examined using generalized additive models adjusted for age, gender, race/ethnicity, and forced vital capacity (% predicted). <b><i>Results:</i></b> Sixteen of 52 (30.8%) had PH (mean PAP ≥25 mm Hg). After multivariable adjustment, higher ET-1 levels were significantly associated with higher systolic (p = 0.01), diastolic (p = 0.02), and mean (p = 0.01) PAP and possibly higher PVR (p = 0.09). There were no significant associations between VEGF levels and hemodynamics. <b><i>Conclusions:</i></b> Higher levels of ET-1 were associated with higher PAP and possibly higher PVR in participants with IPF. In a subgroup of patients, ET-1 may be a contributor to pulmonary vascular disease burden in IPF.
DOI: 10.6084/m9.figshare.5123590
title: Supplementary Material for: A Population-Based Study of Fish Allergy in the Philippines, Singapore and Thailand

description: <b><i>Background:</i></b> Fish allergy is the third most common food allergy after milk and egg in parts of Europe, but there is little data about prevalence in South East Asia where it is an important part of regular diets. <b><i>Objective:</i></b> We aimed to obtain an estimate of the population prevalence of fish allergy among older children in the Philippines, Singapore and Thailand. <b><i>Methods:</i></b> The population prevalence of fish allergy in 14- to 16-year-old children in the 3 countries was evaluated using a structured written questionnaire which was distributed to students of randomly selected secondary schools. An extended questionnaire to determine convincing fish allergy on the basis of typical clinical manifestations within 2 h of ingestion was administered to those with positive responses. <b><i>Results:</i></b> From acohort of 25,842 students, responses were 81.1% in the Philippines (n = 11,434), 67.9% in Singapore (n = 6,498) and 80.2% (n = 2,034) in Thailand. Using criteria for convincing food allergy, fish allergy was much higher in the Philippines [2.29%, 95% confidence interval (CI) 2.02–2.56] than in Singapore (0.26%, 95% CI 0.14–0.79) and Thailand (0.29%, 95% CI 0.06–0.52). Weighted multiple logistic regression analyses showed that compared to the Philippines, prevalence rates were lower in Singapore [odds ratio (OR) 0.40, 95% CI 0.27–0.60, p &lt; 0.0001] and Thailand (OR 0.13, 95% CI 0.05–0.33, p &lt; 0.0001). Females were more likely to have fish allergy compared to males for all children combined (OR 1.32, 95% CI 1.11–1.58, p = 0.002). Most allergies appeared mild, as only 28% of cases sought medical consultation at the time of the reaction and 31.2% of cases reported continued exposure despite allergic symptoms. <b><i>Conclusion:</i></b> Fish allergy in late childhood is more common in the Philippines compared to Singapore and Thailand. Differences in food processing, dietary habits and other cultural practices might be important risk factors for the development of fish allergy in these populations.
DOI: 10.6084/m9.figshare.5123593
title: Supplementary Material for: A Two-Step Hanging Maneuver for a Complete Resection of Couinaud’s Segment I

description: <b><i>Background:</i></b> A hepatic resection of Couinaud’s segment I is a challenging procedure because it is located deep in the abdominal cavity and surrounded by large blood vessels. A new technique, called the ‘two-step hanging maneuver,’ was applied to completely resect Couinaud’s segment I. <b><i>Methods:</i></b> A 59-year-old male was diagnosed with hepatocellular carcinoma in Couinaud’s segment I. A hanging tape was positioned from the groove between the middle and left hepatic veins to the groove between the right and left Glisson sheaths via the posterior hepatic surface after all short hepatic veins were divided. The liver was split into the left and right hemilivers (step 1). The hanging tape was positioned into the fissure of the ligamentum venosus, then Couinaud’s segment I was completely resected after dividing the liver parenchyma between segments I and IV by hanging the tape medially (step 2). <b><i>Results:</i></b> The operation time was 435 min. No blood transfusions were necessary and there were no complications. <b><i>Conclusion:</i></b> This technique allowed resection of a tumor located in Couinaud’s segment I without mobilization of the tumor and safely divided the liver parenchyma via only an anterior approach.
DOI: 10.6084/m9.figshare.5123596.v1
title: Supplementary Material for: Review and Recommendations for Zero-Inflated Count Regression Modeling of Dental Caries Indices in Epidemiological Studies

description: Over the past 5–10 years, zero-inflated (ZI) count regression models have been increasingly applied to the analysis of dental caries indices (e.g. DMFT, dfms). The main reason for that is linked to the broad decline in children’s caries experience, such that dmf and DMF indices more frequently generate low or even zero counts. This article specifically reviews the application of ZI Poisson and ZI negative binomial regression models to dental caries, with emphasis on the description of the models and the interpretation of fitted model results given the study goals. The review finds that interpretations provided in the published caries research are often imprecise or inadvertently misleading, particularly with respect to failing to discriminate between inference for the class of susceptible persons defined by such models and inference for the sampled population in terms of overall exposure effects. Recommendations are provided to enhance the use as well as the interpretation and reporting of results of count regression models when applied to epidemiological studies of dental caries.
DOI: 10.6084/m9.figshare.5123581
title: Supplementary Material for: SNPs as Supplements in Simple Kinship Analysis or as Core Markers in Distant Pairwise Relationship Tests: When Do SNPs Add Value or Replace Well-Established and Powerful STR Tests?

description: <b><i>Background:</i></b> Genetic tests for kinship testing routinely reach likelihoods that provide virtual proof of the claimed relationship by typing microsatellites – commonly consisting of 12–15 standard forensic short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) have also been applied to kinship testing but these binary markers are required in greater numbers than multiple-allele STRs. However SNPs offer certain advantageous characteristics not found in STRs, including, much higher mutational stability, good performance typing highly degraded DNA, and the ability to be readily up-scaled to very high marker numbers reaching over a million loci. This article outlines kinship testing applications where SNPs markedly improve the genetic data obtained. In particular we explore the minimum number of SNPs that will be required to confirm pairwise relationship claims in deficient pedigrees that typify missing persons’ identification or war grave investigations where commonly few surviving relatives are available for comparison and the DNA is highly degraded. <b><i>Methods: </i></b>We describe the application of SNPs alongside STRs when incomplete profiles or allelic instability in STRs create ambiguous results, we review the use of high density SNP arrays when the relationship claim is very distant, and we outline simulations of kinship analyses with STRs supplemented with SNPs in order to estimate the practical limit of pairwise relationships that can be differentiated from random unrelated pairs from the same population. <b><i>Results:</i></b> The minimum number of SNPs for robust statistical inference of parent-offspring relationships through to those of second cousins (S-3-3) is estimated for both simple, single multiplex SNP sets and for subsets of million-SNP arrays. <b><i>Conclusions:</i></b> There is considerable scope for resolving ambiguous STR results and for improving the statistical power of kinship analysis by adding small-scale SNP sets but where the pedigree is deficient the pairwise relationships must be relatively close. For more distant relationships it is possible to reduce chip-based SNP arrays from the million+ markers down to ∼7,000. However, such numbers indicate that current genotyping approaches will not be able to deliver sufficient data to resolve distant pairwise relationships from the limited DNA typical of the most challenging identification cases.
DOI: 10.6084/m9.figshare.5123587
title: Supplementary Material for: Differences in Cognitive Profile between TIA, Stroke and Elderly Memory Research Subjects: A Comparison of the MMSE and MoCA

description: <b><i>Background:</i></b> The Montreal Cognitive Assessment (MoCA) appears more sensitive to mild cognitive impairment (MCI) than the Mini-Mental State Examination (MMSE): over 50% of TIA and stroke patients with an MMSE score of ≥27 (‘normal’ cognitive function) at ≥6 months after index event, score &lt;26 on the MoCA, a cutoff which has good sensitivity and specificity for MCI in this population. We hypothesized that sensitivity of the MoCA to MCI might in part be due to detection of different patterns of cognitive domain impairment. We therefore compared performance on the MMSE and MoCA in subjects without major cognitive impairment (MMSE score of ≥24) with differing clinical characteristics: a TIA and stroke cohort in which frontal/executive deficits were expected to be prevalent and a memory research cohort. <b><i>Methods:</i></b> The MMSE and MoCA were done on consecutive patients with TIA or stroke in a population-based study (Oxford Vascular Study) 6 months or more after the index event and on consecutive subjects enrolled in a memory research cohort (the Oxford Project to Investigate Memory and Ageing). Patients with moderate-to-severe cognitive impairment (MMSE score of &lt;24), dysphasia or inability to use the dominant arm were excluded. <b><i>Results:</i></b> Of 207 stroke patients (mean age ± SD: 72 ± 11.5 years, 54% male), 156 TIA patients (mean age 71 ± 12.1 years, 53% male) and 107 memory research subjects (mean age 76 ± 6.6 years, 46% male), stroke patients had the lowest mean ± SD cognitive scores (MMSE score of 27.7 ± 1.84 and MoCA score of 22.9 ± 3.6), whereas TIA (MMSE score of 28.4 ± 1.7 and MoCA score of 24.9 ± 3.3) and memory subject scores (MMSE score of 28.5 ± 1.7 and MoCA score of 25.5 ± 3.0) were more similar. Rates of MoCA score of &lt;26 in subjects with normal MMSE ( ≥27) were lowest in memory subjects, intermediate in TIA and highest after stroke (34 vs. 48 vs. 67%, p &lt; 0.001). The cerebrovascular patients scored lower than the memory subjects on all MoCA frontal/executive subtests with differences being most marked in visuoexecutive function, verbal fluency and sustained attention (all p &lt; 0.0001) and in stroke versus TIA (after adjustment for age and education). Stroke patients performed worse than TIA patients only on MMSE orientation in contrast to 6/10 subtests of the MoCA. Results were similar after restricting analyses to those with an MMSE score of ≥27. <b><i>Conclusions:</i></b> The MoCA demonstrated more differences in cognitive profile between TIA, stroke and memory research subjects without major cognitive impairment than the MMSE. The MoCA showed between-group differences even in those with normal MMSE and would thus appear to be a useful brief tool to assess cognition in those with MCI, particularly where the ceiling effect of the MMSE is problematic.
DOI: 10.6084/m9.figshare.5123584
title: Supplementary Material for: Effectiveness and Cost-Effectiveness of Dialectical Behaviour Therapy for Self-Harming Patients with Personality Disorder: A Pragmatic Randomised Controlled Trial

description: <b><i>Background:</i></b> A primary goal of dialectical behaviour therapy (DBT) is to reduce self-harm, but findings from empirical studies are inconclusive. The aim of this study was to assess the effectiveness and cost-effectiveness of DBT in reducing self-harm in patients with personality disorder. <b><i>Methods:</i></b> Participants with a personality disorder and at least 5 days of self-harm in the previous year were randomised to receive 12 months of either DBT or treatment as usual (TAU). The primary outcome was the frequency of days with self-harm; secondary outcomes included borderline personality disorder symptoms, general psychiatric symptoms, subjective quality of life, and costs of care. <b><i>Results:</i></b> Forty patients each were randomised to DBT and TAU. In an intention-to-treat analysis, there was a statistically significant treatment by time interaction for self-harm (incidence rate ratio 0.91, 95% CI 0.89–0.92, p &lt; 0.001). For every 2 months spent in DBT, the risk of self-harm decreased by 9% relative to TAU. There was no evidence of differences on any secondary outcomes. The economic analysis revealed a total cost of a mean of 5,685 GBP (6,786 EUR) in DBT compared to a mean of 3,754 GBP (4,481 EUR) in TAU, but the difference was not significant (95% CI –603 to 4,599 GBP). Forty-eight per cent of patients completed DBT. They had a greater reduction in self-harm compared to dropouts (incidence rate ratio 0.78, 95% CI 0.76–0.80, p &lt; 0.001). <b><i>Conclusions:</i></b> DBT can be effective in reducing self-harm in patients with personality disorder, possibly incurring higher total treatment costs. The effect is stronger in those who complete treatment. Future research should explore how to improve treatment adherence.
DOI: 10.6084/m9.figshare.5123593.v1
title: Supplementary Material for: A Two-Step Hanging Maneuver for a Complete Resection of Couinaud’s Segment I

description: <b><i>Background:</i></b> A hepatic resection of Couinaud’s segment I is a challenging procedure because it is located deep in the abdominal cavity and surrounded by large blood vessels. A new technique, called the ‘two-step hanging maneuver,’ was applied to completely resect Couinaud’s segment I. <b><i>Methods:</i></b> A 59-year-old male was diagnosed with hepatocellular carcinoma in Couinaud’s segment I. A hanging tape was positioned from the groove between the middle and left hepatic veins to the groove between the right and left Glisson sheaths via the posterior hepatic surface after all short hepatic veins were divided. The liver was split into the left and right hemilivers (step 1). The hanging tape was positioned into the fissure of the ligamentum venosus, then Couinaud’s segment I was completely resected after dividing the liver parenchyma between segments I and IV by hanging the tape medially (step 2). <b><i>Results:</i></b> The operation time was 435 min. No blood transfusions were necessary and there were no complications. <b><i>Conclusion:</i></b> This technique allowed resection of a tumor located in Couinaud’s segment I without mobilization of the tumor and safely divided the liver parenchyma via only an anterior approach.
DOI: 10.6084/m9.figshare.5123581.v1
title: Supplementary Material for: SNPs as Supplements in Simple Kinship Analysis or as Core Markers in Distant Pairwise Relationship Tests: When Do SNPs Add Value or Replace Well-Established and Powerful STR Tests?

description: <b><i>Background:</i></b> Genetic tests for kinship testing routinely reach likelihoods that provide virtual proof of the claimed relationship by typing microsatellites – commonly consisting of 12–15 standard forensic short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) have also been applied to kinship testing but these binary markers are required in greater numbers than multiple-allele STRs. However SNPs offer certain advantageous characteristics not found in STRs, including, much higher mutational stability, good performance typing highly degraded DNA, and the ability to be readily up-scaled to very high marker numbers reaching over a million loci. This article outlines kinship testing applications where SNPs markedly improve the genetic data obtained. In particular we explore the minimum number of SNPs that will be required to confirm pairwise relationship claims in deficient pedigrees that typify missing persons’ identification or war grave investigations where commonly few surviving relatives are available for comparison and the DNA is highly degraded. <b><i>Methods: </i></b>We describe the application of SNPs alongside STRs when incomplete profiles or allelic instability in STRs create ambiguous results, we review the use of high density SNP arrays when the relationship claim is very distant, and we outline simulations of kinship analyses with STRs supplemented with SNPs in order to estimate the practical limit of pairwise relationships that can be differentiated from random unrelated pairs from the same population. <b><i>Results:</i></b> The minimum number of SNPs for robust statistical inference of parent-offspring relationships through to those of second cousins (S-3-3) is estimated for both simple, single multiplex SNP sets and for subsets of million-SNP arrays. <b><i>Conclusions:</i></b> There is considerable scope for resolving ambiguous STR results and for improving the statistical power of kinship analysis by adding small-scale SNP sets but where the pedigree is deficient the pairwise relationships must be relatively close. For more distant relationships it is possible to reduce chip-based SNP arrays from the million+ markers down to ∼7,000. However, such numbers indicate that current genotyping approaches will not be able to deliver sufficient data to resolve distant pairwise relationships from the limited DNA typical of the most challenging identification cases.
DOI: 10.6084/m9.figshare.5123584.v1
title: Supplementary Material for: Effectiveness and Cost-Effectiveness of Dialectical Behaviour Therapy for Self-Harming Patients with Personality Disorder: A Pragmatic Randomised Controlled Trial

description: <b><i>Background:</i></b> A primary goal of dialectical behaviour therapy (DBT) is to reduce self-harm, but findings from empirical studies are inconclusive. The aim of this study was to assess the effectiveness and cost-effectiveness of DBT in reducing self-harm in patients with personality disorder. <b><i>Methods:</i></b> Participants with a personality disorder and at least 5 days of self-harm in the previous year were randomised to receive 12 months of either DBT or treatment as usual (TAU). The primary outcome was the frequency of days with self-harm; secondary outcomes included borderline personality disorder symptoms, general psychiatric symptoms, subjective quality of life, and costs of care. <b><i>Results:</i></b> Forty patients each were randomised to DBT and TAU. In an intention-to-treat analysis, there was a statistically significant treatment by time interaction for self-harm (incidence rate ratio 0.91, 95% CI 0.89–0.92, p &lt; 0.001). For every 2 months spent in DBT, the risk of self-harm decreased by 9% relative to TAU. There was no evidence of differences on any secondary outcomes. The economic analysis revealed a total cost of a mean of 5,685 GBP (6,786 EUR) in DBT compared to a mean of 3,754 GBP (4,481 EUR) in TAU, but the difference was not significant (95% CI –603 to 4,599 GBP). Forty-eight per cent of patients completed DBT. They had a greater reduction in self-harm compared to dropouts (incidence rate ratio 0.78, 95% CI 0.76–0.80, p &lt; 0.001). <b><i>Conclusions:</i></b> DBT can be effective in reducing self-harm in patients with personality disorder, possibly incurring higher total treatment costs. The effect is stronger in those who complete treatment. Future research should explore how to improve treatment adherence.
DOI: 10.6084/m9.figshare.5123575
title: Supplementary Material for: Differential Expression of <b><i>SLC9A9</i></b> and Interacting Molecules in the Hippocampus of Rat Models for Attention Deficit/Hyperactivity Disorder

description: <i>SLC9A9</i> [solute carrier family 9, member 9, also known as Na<sup>+</sup>/H<sup>+</sup> exchanger member 9 (NHE9)], has been implicated in human attention deficit/hyperactivity disorder (ADHD), autism, and rat studies of hyperactivity and inattentiveness. <i>SLC9A9</i> is a membrane protein that regulates the luminal pH of the recycling endosome. We recently reported the interactions of <i>SLC9A9</i> with two molecules: calcineurin homologous protein <i>(CHP)</i> and receptor for activated C-kinase 1 <i>(RACK1)</i>. We also reported two novel <i>SLC9A9</i> mutations and abnormal gene expression profiles in the brains of an inattentive type rat model of ADHD (WKY/NCrl rat). In this study, we further examined the expression and relationship of <i>SLC9A9</i> and 9 additional genes <i>(CHP, RACK1, CaM, PPP3R1, PPP1R10, PKCm, CaMKI, NR2B, PLCb1)</i> that may directly or indirectly interact with <i>SLC9A9</i> in the hippocampus of the WKY/NCrl rat and the spontaneously hypertensive rat (SHR) model of the combined type of ADHD. We found that the expression levels of these genes were significantly correlated, suggesting that they may be coregulated. Principal component analysis identified two main factors that accounted for 94% of the expression variance of the 10 genes. Significant differences were found for both factors across the 3 different rat strains. The two ADHD rat models (WKY/NCrl and SHR), although different from each other in adulthood, showed similar profiles in adolescence. Both models were significantly different from WKY/NHsd control rats at both ages. The expression abnormalities of each gene were evaluated and their roles in cell signaling processes such as calcium signaling and protein phosphorylation are discussed. Our results suggest that abnormalities in <i>SLC9A9</i>-mediated signaling pathways could contribute to the ADHD phenotype of two rat models (WKY/NCrl and SHR/NCrl), and that the perturbation of the <i>SLC9A9</i> network is age-dependent.