cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5128366.v1
title: Supplementary Material for: Threshold Levels of Visual Field and Acuity Loss Related to Significant Decreases in the Quality of Life and Emotional States of Patients with Retinitis Pigmentosa

description: <b><i>Introduction:</i></b> Retinitis pigmentosa (RP) is an inherited retinal disorder, characterized by photoreceptor degeneration inducing progressive vision loss. This study evaluates its impact on quality of life (QOL) and emotional states of patients affected by RP. <b><i>Methods:</i></b> A cross-sectional study was conducted on 60 RP patients diagnosed with rod-cone dystrophy and on 20 control subjects. The RP population has been divided into 3 groups according to visual field (VF) and visual acuity (VA) impairments. Concurrently, scores of self-reported QOL (25-item National Eye Institute Visual Functioning Questionnaire) and of the Hospital Anxiety and Depression Scale for anxiety/depression assessments were collected. <b><i>Results:</i></b> For the QOL composite score, we noticed consistent differences between all VF and VA affected groups and their control group. We also found significant differences between both the most affected VF group (VF1: ØVF &lt;20°) and VA group (VA1: VA &lt;0.3) compared to other VF and VA groups. For anxiety/depression scores, consistent differences have been found between the control group and VF1 and VA1, respectively. <b><i>Conclusions:</i></b> This work determines that, for RP patients, a significant QOL and emotional state deterioration correlates with a residual VF diameter below 20° and a VA lower than 0.3. It introduces, for the first time, thresholds to be used in visual restoration or visual preservation therapies to improve QOL of RP patients.
DOI: 10.6084/m9.figshare.5128369.v1
title: Supplementary Material for: Anti-Caries Effect of Arginine-Containing Formulations in vivo: A Systematic Review and Meta-Analysis

description: <b><i>Objective:</i></b> To assess the anti-caries effect of arginine-containing formulations in vivo on caries lesions compared with fluorides or placebo. <b><i>Methods:</i></b> Randomized or quasi-randomized human clinical trials wherein arginine was delivered by any method were considered. The MEDLINE, Web of Science, EMBASE, Cochrane Library, and CBM databases were searched to identify relevant articles published up to December 2014. Grey literature was also searched. Two authors performed data extraction independently and in duplicate using data collection forms. Each included study was assessed using the Cochrane risk of bias assessment tool. <b><i>Results:</i></b> Of the 470 studies screened, 31 full articles were scrutinized and assessed for eligibility. Ten studies (n = 15,546 participants) were selected for final inclusion. The meta-analysis results (n = 7 studies) demonstrated a synergistic effect of arginine when used in conjunction with fluoride on early coronal and root caries compared with placebo or fluoride alone. No specific side effects related to arginine usage were identified. <b><i>Conclusions:</i></b> When used in combination with a calcium compound and fluoride, arginine potentially provides a superior anti-caries effect compared with matched formulations of fluoride alone. However, the level of evidence was downgraded because of risks of bias and potential publication bias. In the future, more high quality, non-industry-supported clinical studies in this research area are required before any definitive recommendations can be made.
DOI: 10.6084/m9.figshare.5128354
title: Supplementary Material for: A Randomised, Double-Blind, Placebo-Controlled Trial of As-Needed Naltrexone in the Treatment of Pathological Gambling

description: <b><i>Background/Aims:</i></b> Effective treatment strategies are needed for the treatment of pathological gambling (PG). The efficacy of as-needed naltrexone was assessed in a single-centre, randomised, double-blind, placebo-controlled trial. <b><i>Methods:</i></b> The participants (n = 101) received either as-needed placebo or naltrexone (50 mg) and psychosocial support for 20 weeks. The primary outcome measure was the severity of PG assessed by the Yale-Brown Obsessive Compulsive Scale adapted for PG (PG-YBOCS). Secondary gambling-related outcome measures included thoughts/urges and behaviour subscales of PG-YBOCS as well as the highest daily expenditure and gambling frequency. In addition, RAND-36 scales of emotional well-being and social functioning were used as outcomes. The results were analysed using the intention-to-treat principle and linear random effects modelling. <b><i>Results:</i></b> No significant treatment group differences were found. In an exploratory analysis, emotional well-being increased in a subgroup of participants with <i>AA</i> genotype of opioid receptor, mu 1 <i>(OPRM1) A118G</i> polymorphism (p = 0.02). <b><i>Conclusion:</i></b> Overall, the as-needed naltrexone may not provide substantial additional benefit for PG patients receiving psychosocial support. Replication by larger scale studies is warranted to further evaluate naltrexone administration schedules for the treatment of PG and the role of <i>OPRM1</i>.
DOI: 10.6084/m9.figshare.5128360.v1
title: Supplementary Material for: Outcome of Isolated Premature Menarche: A Retrospective and Follow-Up Study

description: <b><i>Background and Aims:</i></b> Isolated premature menarche is isolated or recurrent vaginal bleeding in a female in the absence of appropriate secondary sexual characters. <b><i>Methods:</i></b> Retrospective chart review of patients with premature menarche, followed by a telephone questionnaire. Charts of patients evaluated in the Pediatric Endocrine Clinic for premature vaginal bleeding from 1982-2013 were reviewed. <b><i>Results:</i></b> Of 21 patients identified, 17 could be contacted. Five newly diagnosed patients were recruited during the course of the study. The median age at initial presentation was 7 years. Most patients presented with Tanner I sexual development. Some had more advanced breast staging, which regressed later. All had prepubertal baseline and stimulated gonadotropins. Most of the patients reported a single or few episodes of menses. Two reported continuation of irregular bleeding into adulthood. All reported an adult height within the midparental target height. <b><i>Conclusion:</i></b> Premature menarche in the absence of other appropriate secondary sexual characteristics is a benign entity. Most patients have a few isolated episodes of menses that stop spontaneously; some may continue to have periods into adulthood. Unlike true puberty, these patients do not demonstrate advanced skeletal maturation, and the adult height is normal. Fertility appears to be normal.
DOI: 10.6084/m9.figshare.5128351
title: Supplementary Material for: Potential Association of <b><i>INMT</i></b> Nonsynonymous Variant (His46Pro) with Hirschsprung's Disease

description: <b><i>Background:</i></b> Hirschsprung's disease (HSCR) is a congenital disorder which is characterized by the lack of ganglion cells in part of or the entire colon, resulting in intestinal obstruction and other related symptoms. Recently, our group has conducted a genome-wide association study in Korean HSCR cases and controls to identify novel markers in other genes. <b><i>Objectives:</i></b> The present research aimed to further study the potential association of <i>INMT</i> with HSCR by conducting a replication study. <b><i>Methods:</i></b> A total of 15 <i>INMT</i> single nucleotide polymorphisms (SNPs) were analyzed for the association with HSCR in 187 HSCR patients and 283 controls. Analyses were also conducted for subtypes of HSCR (short-segment, long-segment, and total colonic aganglionosis). <b><i>Results:</i></b> A nonsynonymous SNP <i>rs77743549</i> (His46Pro) was significantly associated with the increased risk of HSCR (odds ratio = 1.77; corrected p = 0.002). Furthermore, this <i>rs77743549</i> retained its association with all subtypes of HSCR (p = 0.006-0.002 under the codominant model). A global test showed that <i>rs77743549</i> was associated with the length of aganglionosis (p = 0.00004). <b><i>Conclusion:</i></b> Although further replications and functional evaluations are needed, our study suggests that <i>rs77743549</i> of <i>INMT</i> may be associated with the risk for HSCR and/or the development of the enteric nervous system.
DOI: 10.6084/m9.figshare.5128357.v1
title: Supplementary Material for: Aberrant Placental Villus Expression of miR-486-3p and miR-3074-5p in Recurrent Miscarriage Patients and Uterine Expression of These MicroRNAs during Early Pregnancy in Mice

description: MicroRNAs (miRNAs) are critical regulators of gene expression; they have emerged as new players in the pathophysiology of reproductive disorders such as preeclampsia and recurrent miscarriage (RM). In this study, miRNA expression profiles were determined by deep sequencing analysis in placental villi obtained from women with RM and with gestational age-matched normal pregnancy (NP). A total of 69 miRNAs were found to be aberrantly expressed in RM. Five of these human <i>(Homo sapiens)</i> miRNAs (hsa-miRNAs), including hsa-miR-3074-5p, -486-3p, -1269b, -6765-3p and -144-3p, were validated by qRT-PCR in 12 RM and 10 NP placental villi. Hsa-miR-3074-5p expression was significantly higher, while hsa-miR-486-3p expression was significantly lower, in RM compared to NP. Subsequently, the expression of mouse <i>(Mus musculus)</i> miR-486-3p (mmu-miR-486-3p) and mmu-miR-3074-5p, which are identical to hsa-miR-486-3p and hsa-miR-3074-5p, respectively, were examined by qRT-PCR in the uterus during early pregnancy. Mmu-miR-486-3p expression was significantly increased during the peri-implantation period, and the levels were significantly higher at implantation than at non-implantation sites. In contrast, the expression of mmu-miR-3074-5p was markedly decreased at implantation compared to non-implantation sites. These data suggest that miR-486-3p and miR-3074-5p may be involved in embryo implantation and that their aberrant expression is associated with RM. Larger studies are warranted to follow up this pilot study.
DOI: 10.6084/m9.figshare.5128363.v1
title: Supplementary Material for: Computational Analysis of Missense Variants of G Protein-Coupled Receptors Involved in the Neuroendocrine Regulation of Reproduction

description: <b><i>Introduction:</i></b> Many missense variants in G protein-coupled receptors (GPCRs) involved in the neuroendocrine regulation of reproduction have been identified by phenotype-driven or large-scale exome sequencing. Computational functional prediction analysis is commonly performed to evaluate their impact on receptor function. <b><i>Methods:</i></b> To assess the performance and outcome of functional prediction analyses for these GPCRs, we performed a statistical analysis of the prediction performance of SIFT and PolyPhen-2 for variants with documented biological function as well as variants retrieved from Ensembl. We obtained missense variants with documented biological function testing from patients with reproductive disorders from a comprehensive literature search. Missense variants from individuals with known reproductive disorders were retrieved from the Human Gene Mutation Database. Missense variants from the general population were retrieved from the Ensembl genome database. <b><i>Results:</i></b> The accuracies of SIFT and PolyPhen-2 were 83 and 85%, respectively. The performance of both prediction tools was greater in predicting loss-of-function variants (SIFT: 92%; PolyPhen-2: 95%) than in predicting variants that did not affect function (SIFT: 54%; PolyPhen-2: 57%). Concordance between SIFT and PolyPhen-2 did not improve accuracy. Surprisingly, approximately half of the variants retrieved from Ensembl were predicted as loss-of-function variants by SIFT (47%) and PolyPhen-2 (54%). <b><i>Conclusion:</i></b> Our findings provide new guidance for interpreting the results and limitations of computational functional prediction analyses for GPCRs and will help to determine which variants require biological function testing. In addition, our findings raise important questions regarding the link between genotype and phenotype in the general population.
DOI: 10.6084/m9.figshare.5128345
title: Supplementary Material for: A Revised Genome Assembly of the Region 5′ to Canine <b><i>SOX9</i></b> Includes the <b><i>RevSex</i></b> Orthologous Region

description: The <i>SOX</i> gene family includes many genes that play a determinant role in several developmental pathways. The <i>SOX9</i> gene has been identified as a major factor in testis development in mammals after it is activated by the <i>SRY</i> gene. However, duplication of the gene itself in some mammalian species, or of a well-delimited upstream ‘<i>RevSex'</i> region in humans, has been shown to result in testis development in the absence of the <i>SRY</i> gene. In the current study, we present an accurate analysis of the genomic organization of the <i>SOX9</i> locus in dogs by both in silico and FISH approaches. Contrary to what is observed in the current dog genome assembly, we found that the genomic organization is quite similar to that reported in humans and other mammalian species, including the position of the <i>RevSex</i> region in respect to <i>SOX9</i>. The analysis of the conserved sequences within this region in 7 mammalian species facilitated the highlighting of a consensus sequence for SRY binding. This new information could help in the identification of evolutionarily conserved elements relevant for <i>SOX9</i> gene regulation, and could provide valid targets for mutation analysis in XY DSD patients.
DOI: 10.6084/m9.figshare.5128342
title: Supplementary Material for: Macronutrient Intake and Inadequacies of Community-Dwelling Older Adults, a Systematic Review

description: <b><i>Background:</i></b> Anorexia of ageing may predispose older adults to under-nutrition and protein energy malnutrition. Studies, however, report a large variation in nutrient inadequacies among community-dwelling older adults. <b><i>Summary:</i></b> This systematic review provides a comprehensive overview of the energy and macronutrient intakes and possible inadequacies in community-dwelling older adults. PubMed and EMBASE were screened up to December 2013; data from national nutrition surveys were added. Forty-six studies were included, following the PRISMA guideline. <b><i>Key Messages:</i></b> Mean daily energy intake was 8.9 MJ in men and 7.3 MJ in women. Mean daily carbohydrate and protein intakes were 46 and 15 En% in men and 47 and 16 En% in women, respectively. Mean daily total fat, saturated fatty acid (SFA), mono-unsaturated fatty acid (MUFA) and poly-unsaturated fatty acid intakes were respectively 34, 13, 13 and 5-6 En%. The carbohydrates and MUFA intakes are below the acceptable macronutrient distribution ranges (AMDR). Fat intake is relatively high, and SFA intake exceeds the upper-AMDR. Based on the estimated average requirement (EAR) cut-point method, 10-12% of older adults do not meet the EAR for protein. To interpret a possible energy imbalance additional information is needed on physical activity, energy expenditure and body weight changes. This systematic review indicates a suboptimal dietary macronutrient distribution and a large variation in nutrient intakes among community-dwelling older adults.
DOI: 10.6084/m9.figshare.5128339
title: Supplementary Material for: Description of the SAGhE Cohort: A Large European Study of Mortality and Cancer Incidence Risks after Childhood Treatment with Recombinant Growth Hormone

description: <b><i>Background:</i></b> The long-term safety of growth hormone treatment is uncertain. Raised risks of death and certain cancers have been reported inconsistently, based on limited data or short-term follow-up by pharmaceutical companies. <b><i>Patients and Methods:</i></b> The SAGhE (Safety and Appropriateness of Growth Hormone Treatments in Europe) study assembled cohorts of patients treated in childhood with recombinant human growth hormone (r-hGH) in 8 European countries since the first use of this treatment in 1984 and followed them for cause-specific mortality and cancer incidence. Expected rates were obtained from national and local general population data. The cohort consisted of 24,232 patients, most commonly treated for isolated growth failure (53%), Turner syndrome (13%) and growth hormone deficiency linked to neoplasia (12%). This paper describes in detail the study design, methods and data collection and discusses the strengths, biases and weaknesses consequent on this. <b><i>Conclusion:</i></b> The SAGhE cohort is the largest and longest follow-up cohort study of growth hormone-treated patients with follow-up and analysis independent of industry. It forms a major resource for investigating cancer and mortality risks in r-hGH patients. The interpretation of SAGhE results, however, will need to take account of the methods of cohort assembly and follow-up in each country.
DOI: 10.6084/m9.figshare.5128330
title: Supplementary Material for: Early Antidepressant Treatment and All-Cause 30-Day Mortality in Patients with Ischemic Stroke

description: <b><i>Background:</i></b> Antidepressants, in particular selective serotonin reuptake inhibitors, have been associated with antithrombotic and neuroprotective properties and their more widespread use has been suggested in stroke recovery. However, data are sparse on their effects on the clinical outcome, including mortality, associated with early antidepressant treatment after stroke. We aimed to study all-cause 30-day mortality related to early antidepressant treatment in patients with ischemic stroke. <b><i>Methods:</i></b> We did a population-based follow-up study identifying patients from the Danish Stroke Registry admitted in the former Aarhus County from 2003 to 2010. During this time, initiation of antidepressant treatment during admission was registered in the Danish Stoke Registry. The registry also holds clinical information including stroke type, stroke severity and quality of in-hospital stroke care. Information on vital status and covariates including comorbidities and co-medication was obtained from the following population-based medical registries: the Danish Civil Registration System, Danish Medicines Agency's Medical Register and The Danish National Patients Registry. Information was linked using the unique civil registration number assigned to all Danish residents. Multivariable logistic regression was used to compute the adjusted odds ratio (OR) of 30-day mortality in patients treated with antidepressants during admission as compared to patients not treated. In addition, we did stratified analyses on sex, age, stroke severity and propensity score-matched analyses as well as multiple imputation. <b><i>Results:</i></b> Among 5,070 consecutive first-ever stroke patients without prior antidepressant treatment, 955 (18.8%) started antidepressant treatment during admission with a median time from admission until treatment of 5 days (interquartile range 2-11). The proportion of patients with severe stroke was higher among treated patients as compared to that among non-treated patients. The adjusted OR of 30-day mortality was 0.28 (95% confidence interval (CI) 0.18-0.43) for patients treated during admission as compared to patients not treated during admission. Stratification by stroke severity showed signs of effect modification, stratification by sex and age did not. Included in the propensity score-matched analyses were 1,908 patients matched 1:1. The propensity score-matched adjusted OR of death within 30 days was 0.31 (95% CI 0.19-0.49). <b><i>Conclusion:</i></b> Although early antidepressant treatment was more often started in patients with severe stroke, treatment was associated with significantly lower mortality. This result requires replication in randomized trials; however, it indicates that early start of antidepressant treatment after stroke may be safe and a more routine use may be feasible.
DOI: 10.6084/m9.figshare.5128333
title: Supplementary Material for: HIV Nosode: The Homeopathic Pathogenetic Trial

description: <b><i>Background:</i></b> Deriving clinical indications for the HIV nosode by conducting a double-blind, placebo-controlled homeopathic pathogenetic trial (HPT) with the aim to introduce a new nosode to the profession. <b><i>Method:</i></b> The HPT was conducted in 22 volunteers, 15 of which received HIV nosode in 30c potency pills, while 7 received identical placebo pills orally, once a week, for 4 weeks. The volunteers' symptoms during initial 7 days of run-in period were noted. All symptoms for both groups produced during run-in period were excluded from final analysis. Informed consent form, approval by Ethics Committee, laboratory investigations as well as safety and ethical measures were provided. The volunteers were trained to write data in prescribed diaries, and the data were analyzed. <b><i>Results:</i></b> The HPT of the HIV nosode exhibited qualitatively distinct symptoms, which can be applied in clinical practice. Number of symptoms reported in verum group was 130, in placebo group 60. Quantitative pathogenetic index was 0.285 in verum group, 0.238 in placebo group; qualitative pathogenetic index was 0.1402 in the verum group as compared to placebo (0.0907). Safe use was documented. <b><i>Conclusion:</i></b> This study brought in guiding symptoms, which will help the profession to employ this nosode in practice.
DOI: 10.6084/m9.figshare.5128336
title: Supplementary Material for: Rapid Diagnosis of Imprinting Disorders Involving Copy Number Variation and Uniparental Disomy Using Genome-Wide SNP Microarrays

description: Imprinting disorders, such as Beckwith-Wiedemann syndrome (BWS), Prader-Willi syndrome (PWS) and Angelman syndrome (AS), can be detected via methylation analysis, methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), or other methods. In this study, we applied single nucleotide polymorphism (SNP)-based chromosomal microarray analysis to detect copy number variations (CNVs) and uniparental disomy (UPD) events in patients with suspected imprinting disorders. Of 4 patients, 2 had a 5.25-Mb microdeletion in the 15q11.2q13.2 region, 1 had a 38.4-Mb mosaic UPD in the 11p15.4 region, and 1 had a 60-Mb detectable UPD between regions 14q13.2 and 14q32.13. Although the 14q32.2 region was classified as normal by SNP array for the 14q13 UPD patient, it turned out to be a heterodisomic UPD by short tandem repeat marker analysis. MS-MLPA analysis was performed to validate the variations. In conclusion, SNP-based microarray is an efficient alternative method for quickly and precisely diagnosing PWS, AS, BWS, and other imprinted gene-associated disorders when considering aberrations due to CNVs and most types of UPD.