cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125315
title: Supplementary Material for: Systematic Review of the Epidemiology of Urinary Incontinence and Detrusor Overactivity among Patients with Neurogenic Overactive Bladder

description: <b><i>Background:</i></b> The prevalence and incidence of neurogenic overactive bladder (nOAB) are poorly defined. This systematic literature review identified nOAB epidemiological data and estimated the incidence and prevalence of urinary incontinence (UI) and detrusor overactivity (DO) in patients with multiple sclerosis (MS), spinal cord injury (SCI), Parkinson's disease (PD), stroke and spina bifida. An initial search of MEDLINE, Embase, PubMed, and the Cochrane library was supplemented by an internet search for grey literature and manual searching of the bibliographies of retrieved articles. Additional study selection identified comparable studies for statistical analysis. A descriptive statistical analysis, single-arm meta-analysis and stratified analysis were conducted using predefined criteria. <b><i>Summary:</i></b> Initial selection identified 189 articles containing prevalence data. Secondary selection for statistical analysis identified 39 and 52 articles with prevalence of UI and DO, respectively. Random-effect meta-analysis found the prevalence of UI was 50.9% in patients with MS, 52.3% with SCI, 33.1% with PD and 23.6% with stroke. Spina bifida was excluded due to insufficient data. The prevalence of DO may be biased and artificially elevated because it can only be measured with urodynamic investigations. <b><i>Key Messages:</i></b> A substantial proportion of patients with neurological conditions develop UI that may be attributable to nOAB.
DOI: 10.6084/m9.figshare.5125330.v1
title: Supplementary Material for: Retrotransposons Represent the Most Labile Fraction for Genomic Rearrangements in Polyploid Plant Species

description: Understanding how increased genome size and diversity within polyploid genomes impacts plant evolution and breeding continues to be challenging. Although historical studies by McClintock suggested the importance of transposable elements mediated by polyploidisation on genomic changes, data from plant crosses remain scarce. Despite the absence of a conclusive proof regarding autonomous retrotransposon movement in synthetic allopolyploids, the transposition of retrotransposons and their ubiquitous dispersion in all plant species might explain the positive correlation between the genome size of plants and the prevalence of retrotransposons. Here, we address polyploidisation-mediated rearrangements of retrotransposon-associated sequences and discuss a tendency for a preferential restructuring of large ancestral genomes after polyploidisation. A comparative analysis of the frequency of modifications of retrotransposon-associated sequences in synthetic polyploids with marked differences in genome sizes is presented. Such analyses suggest the absence of a significant difference in the rates of rearrangements despite vast dissimilarities in the retrotransposon copy number between species, which emphasises the high plasticity of this genomic feature. See also the sister article focusing on animals by Arkhipova and Rodriguez in this themed issue.
DOI: 10.6084/m9.figshare.5125306
title: Supplementary Material for: CCR5 and FPR1 Mediate Neutrophil Recruitment in Endotoxin-Induced Lung Injury

description: Recruitment of neutrophils, regarded as a key mechanism in acute lung injury (ALI), is orchestrated by cell adhesion molecules and chemokines. While the importance of cell adhesion molecules has been carefully investigated, little is known about the importance of chemokines and their receptors in the recruitment of neutrophils in models of ALI. Wild-type <i>Ccr2</i><sup><i>-/-</i></sup>,<i> Ccr5</i><sup><i>-/-</i></sup>,<i> Fpr1</i><sup><i>-/-</i></sup> or <i>Fpr2</i><sup><i>-/-</i></sup> mice were exposed to aerosolized lipopolysaccharide and the number of neutrophils in the lung tissue (intravascular, interstitial) and in the bronchoalveolar lavage was quantified. Lack of CCR5 or FPR1, but not CCR2 or FPR2, significantly reduced lung neutrophil infiltration in all compartments. Similarly, blockade of CCR5 or FPR1 with specific antagonists reduced counts of alveolar, interstitial and intravascular neutrophils. Such treatments also inhibited lung edema formation and histological lung tissue alterations, thus underscoring the protective role of CCR5 and FPR1 neutralizing strategies in ALI.
DOI: 10.6084/m9.figshare.5125309
title: Supplementary Material for: Sexual Dimorphism in the Brain of the Monogamous California Mouse (Peromyscus californicus)

description: Sex differences in behavior and morphology are usually assumed to be stronger in polygynous species compared to monogamous species. A few brain structures have been identified as sexually dimorphic in polygynous rodent species, but it is less clear whether these differences persist in monogamous species. California mice are among the 5% or less of mammals that are considered to be monogamous and as such provide an ideal model to examine sexual dimorphism in neuroanatomy. In the present study we compared the volume of hypothalamic- and limbic-associated regions in female and male California mice for sexual dimorphism. We also used tyrosine hydroxylase (TH) immunohistochemistry to compare the number of dopamine neurons in the ventral tegmental area (VTA) in female and male California mice. Additionally, tract tracing was used to accurately delineate the boundaries of the VTA. The total volume of the sexually dimorphic nucleus of the preoptic area (SDN-POA), the principal nucleus of the bed nucleus of the stria terminalis (BNST), and the posterodorsal medial amygdala (MEA) was larger in males compared to females. In the SDN-POA we found that the magnitude of sex differences in the California mouse were intermediate between the large differences observed in promiscuous meadow voles and rats and the absence of significant differences in monogamous prairie voles. However, the magnitude of sex differences in MEA and the BNST were comparable to polygynous species. No sex differences were observed in the volume of the whole brain, the VTA, the nucleus accumbens or the number of TH-ir neurons in the VTA. These data show that despite a monogamous social organization, sexual dimorphisms that have been reported in polygynous rodents extend to California mice. Our data suggest that sex differences in brain structures such as the SDN-POA persist across species with different social organizations and may be an evolutionarily conserved characteristic of mammalian brains.
DOI: 10.6084/m9.figshare.5125312
title: Supplementary Material for: Assessing the Impact of Population Stratification on Association Studies of Rare Variation

description: <b><i>Aims:</i></b> The study of rare variants, which can potentially explain a great proportion of heritability, has emerged as an important topic in human gene mapping of complex diseases. Although several statistical methods have been developed to increase the power to detect disease-related rare variants, none of these methods address an important issue that often arises in genetic studies: false positives due to population stratification. Using simulations, we investigated the impact of population stratification on false-positive rates of rare-variant association tests. <b><i>Methods:</i></b> We simulated a series of case-control studies assuming various sample sizes and levels of population structure. Using such data, we examined the impact of population stratification on rare-variant collapsing and burden tests of rare variation. We further evaluated the ability of 2 existing methods (principal component analysis and genomic control) to correct for stratification in such rare-variant studies. <b><i>Results:</i></b> We found that population stratification can have a significant influence on studies of rare variants especially when the sample size is large and the population is severely stratified. Our results showed that principal component analysis performed quite well in most situations, while genomic control often yielded conservative results. <b><i>Conclusions:</i></b> Our results imply that researchers need to carefully match cases and controls on ancestry in order to avoid false positives caused by population structure in studies of rare variants, particularly if genome-wide data are not available.
DOI: 10.6084/m9.figshare.5125318
title: Supplementary Material for: A Case of Impaired Tongue Movement in an Elderly Person

description: Medicine
DOI: 10.6084/m9.figshare.5125309.v1
title: Supplementary Material for: Sexual Dimorphism in the Brain of the Monogamous California Mouse (Peromyscus californicus)

description: Sex differences in behavior and morphology are usually assumed to be stronger in polygynous species compared to monogamous species. A few brain structures have been identified as sexually dimorphic in polygynous rodent species, but it is less clear whether these differences persist in monogamous species. California mice are among the 5% or less of mammals that are considered to be monogamous and as such provide an ideal model to examine sexual dimorphism in neuroanatomy. In the present study we compared the volume of hypothalamic- and limbic-associated regions in female and male California mice for sexual dimorphism. We also used tyrosine hydroxylase (TH) immunohistochemistry to compare the number of dopamine neurons in the ventral tegmental area (VTA) in female and male California mice. Additionally, tract tracing was used to accurately delineate the boundaries of the VTA. The total volume of the sexually dimorphic nucleus of the preoptic area (SDN-POA), the principal nucleus of the bed nucleus of the stria terminalis (BNST), and the posterodorsal medial amygdala (MEA) was larger in males compared to females. In the SDN-POA we found that the magnitude of sex differences in the California mouse were intermediate between the large differences observed in promiscuous meadow voles and rats and the absence of significant differences in monogamous prairie voles. However, the magnitude of sex differences in MEA and the BNST were comparable to polygynous species. No sex differences were observed in the volume of the whole brain, the VTA, the nucleus accumbens or the number of TH-ir neurons in the VTA. These data show that despite a monogamous social organization, sexual dimorphisms that have been reported in polygynous rodents extend to California mice. Our data suggest that sex differences in brain structures such as the SDN-POA persist across species with different social organizations and may be an evolutionarily conserved characteristic of mammalian brains.
DOI: 10.6084/m9.figshare.5125312.v1
title: Supplementary Material for: Assessing the Impact of Population Stratification on Association Studies of Rare Variation

description: <b><i>Aims:</i></b> The study of rare variants, which can potentially explain a great proportion of heritability, has emerged as an important topic in human gene mapping of complex diseases. Although several statistical methods have been developed to increase the power to detect disease-related rare variants, none of these methods address an important issue that often arises in genetic studies: false positives due to population stratification. Using simulations, we investigated the impact of population stratification on false-positive rates of rare-variant association tests. <b><i>Methods:</i></b> We simulated a series of case-control studies assuming various sample sizes and levels of population structure. Using such data, we examined the impact of population stratification on rare-variant collapsing and burden tests of rare variation. We further evaluated the ability of 2 existing methods (principal component analysis and genomic control) to correct for stratification in such rare-variant studies. <b><i>Results:</i></b> We found that population stratification can have a significant influence on studies of rare variants especially when the sample size is large and the population is severely stratified. Our results showed that principal component analysis performed quite well in most situations, while genomic control often yielded conservative results. <b><i>Conclusions:</i></b> Our results imply that researchers need to carefully match cases and controls on ancestry in order to avoid false positives caused by population structure in studies of rare variants, particularly if genome-wide data are not available.
DOI: 10.6084/m9.figshare.5125318.v1
title: Supplementary Material for: A Case of Impaired Tongue Movement in an Elderly Person

description: Medicine
DOI: 10.6084/m9.figshare.5125297
title: Supplementary Material for: Association between Alanine Aminotransferase and Intracerebral Hemorrhage in East Asian Populations

description: <b><i>Background:</i></b> Intracerebral hemorrhage (ICH) and chronic liver disease are relatively common in East Asian countries. However, the relationship between the two diseases is unclear. Thus, we investigated the association between serum alanine aminotransferase (ALT) levels and ICH risk in East Asian populations. <b><i>Methods:</i></b> The East Asian Network for Stroke Prevention enrolled 279,982 participants with ALT measurements from four cohort studies in Korea, Taiwan, Japan and mainland China. Among them, 1,324 ICH events and 493 ICH deaths were observed. Cox's proportional hazard regression analysis was performed in each cohort to estimate the hazard ratio (HR) after adjusting for age, blood pressure, diabetes, total cholesterol, smoking and alcohol intake. Combined HRs were then estimated using pooled analyses with fixed-effects models. <b><i>Results:</i></b> The multivariate-adjusted pooled HRs (with 95% confidence interval, CI) for ICH incidence per 10 IU/l increments of ALT were 1.04 (1.03-1.04) in men and 1.01 (0.98-1.04) in women. Corresponding HRs for ICH mortality were 1.04 (1.02-1.05) in men and 1.04 (1.00-1.08) in women. The pooled HRs for ICH incidence in participants with ALT levels greater than or equal to 50 IU/l compared to those with levels less than 20 IU/l were 1.74 (1.41-2.16) in men and 1.60 (1.06-2.40) in women. The corresponding HRs for ICH mortality were 1.72 (1.21-2.44) in men and 1.63 (0.79-3.36) in women. <b><i>Conclusions:</i></b> An elevated ALT level was independently and significantly associated with an increased risk of ICH in East Asian men, but the association was less prominent in women.
DOI: 10.6084/m9.figshare.5125303
title: Supplementary Material for: Interferon-Induced Proteins with Tetratricopeptide Repeats 1 and 2 Are Cellular Factors That Limit Hepatitis B Virus Replication

description: Interferon (IFN)-α is able to stimulate many cellular genes and inhibit the replication of various viruses. However, it is unknown whether some IFN-stimulated genes (ISGs) specifically inhibit hepatitis B virus (HBV) replication. Therefore, we attempted to identify ISGs with antiviral activities against HBV. Knockdown of IFN-induced proteins with tetratricopeptide repeats 1 and 2 (IFIT1 and IFIT2) in HepG2.2.15 led to markedly increased HBV replication. Consistently, this effect was verified by transient transfection with a replication-competent HBV clone in HepG2 and Huh7. However, IFN-α stimulation could override the knockdown by siRNAs and enhance the expression of IFIT1 and IFIT2, leading to reduced HBV replication. Silencing of IFIT1 or IFIT2 decreased the expression of the corresponding genes while other ISGs like MxA were not affected. Northern blot analysis showed that IFIT1 and IFIT2 knockdown slightly increased the levels of HBV 3.5, 2.4 and 2.1 kb transcripts, while IFIT1 and IFIT2 overexpression did not change their levels. Consistently, the reporter assays with HBV promoters demonstrated that IFIT1 and IFIT2 differentially but only modestly regulated HBV promoter activity. Thus, IFIT1 and IFIT2 contribute significantly to the regulation of HBV replication, likely at both transcriptional and posttranscriptional steps.
DOI: 10.6084/m9.figshare.5125291
title: Supplementary Material for: Seeing the Wood through the Trees: The Current State of Higher Systematics in the Strepsirhini

description: Strepsirhines comprise 10 living or recently extinct families, ≥50% of extant primate families. Their phylogenetic relationships have been intensively studied, but common topologies have only recently emerged; e.g. all recent reconstructions link the Lepilemuridae and Cheirogaleidae. The position of the indriids, however, remains uncertain, and molecular studies have placed them as the sister to every clade except <i>Daubentonia</i>, the preferred sister group of morphologists. The node subtending Afro-Asian lorisids has been similarly elusive. We probed these phylogenetic inconsistencies using a test data set including 20 strepsirhine taxa and 2 outgroups represented by 3,543 mtDNA base pairs, and 43 selected morphological characters, subjecting the data to maximum parsimony, maximum likelihood and Bayesian inference analyses, and reconstructing topology and node ages jointly from the molecular data using relaxed molecular clock analyses. Our permutations yielded compatible but not identical evolutionary histories, and currently popular techniques seem unable to deal adequately with morphological data. We investigated the influence of morphological characters on tree topologies, and examined the effect of taxon sampling in two experiments: (1) we removed the molecular data only for 5 endangered Malagasy taxa to simulate ‘extinction leaving a fossil record'; (2) we removed both the sequence and morphological data for these taxa. Topologies were affected more by the inclusion of morphological data only, indicating that palaeontological studies that involve inserting a partial morphological data set into a combined data matrix of extant species should be interpreted with caution. The gap of approximately 10 million years between the daubentoniid divergence and those of the other Malagasy families deserves more study. The apparently contemporaneous divergence of African and non-daubentoniid Malagasy families 40-30 million years ago may be related to regional plume-induced uplift followed by a global period of cooling and drying.
DOI: 10.6084/m9.figshare.5125294
title: Supplementary Material for: Human Cardiovascular Disease IBC Chip-Wide Association with Weight Loss and Weight Regain in the Look AHEAD Trial

description: <b><i>Background/Aims:</i></b> The present study identified genetic predictors of weight change during behavioral weight loss treatment. <b><i>Methods:</i></b> Participants were 3,899 overweight/obese individuals with type 2 diabetes from Look AHEAD, a randomized controlled trial to determine the effects of intensive lifestyle intervention (ILI), including weight loss and physical activity, relative to diabetes support and education, on cardiovascular outcomes. Analyses focused on associations of single nucleotide polymorphisms (SNPs) on the Illumina CARe iSelect (IBC) chip (minor allele frequency &gt;5%; n = 31,959) with weight change at year 1 and year 4, and weight regain at year 4, among individuals who lost ≥3% at year 1. <b><i>Results:</i></b> Two novel regions of significant chip-wide association with year-1 weight loss in ILI were identified (p &lt; 2.96E-06). <i>ABCB11 </i>rs484066 was associated with 1.16 kg higher weight per minor allele at year 1, whereas <i>TNFRSF11A,</i> or<i> RANK,</i> rs17069904 was associated with 1.70 kg lower weight per allele at year 1. <b><i>Conclusions:</i></b> This study, the largest to date on genetic predictors of weight loss and regain, indicates that SNPs within <i>ABCB11</i>, related to bile salt transfer, and <i>TNFRSF11A</i>, implicated in adipose tissue physiology, predict the magnitude of weight loss during behavioral intervention. These results provide new insights into potential biological mechanisms and may ultimately inform weight loss treatment.
DOI: 10.6084/m9.figshare.5125300
title: Supplementary Material for: Efficacy and Tolerability of Benzodiazepines versus Antidepressants in Anxiety Disorders: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Placebo-controlled trials showed that both benzodiazepines (BDZ) and antidepressant drugs (AD) are effective in treating anxiety disorders. However, in the last years a progressive shift in the prescribing pattern from BDZ to newer AD has taken place. The aim of this systematic review and meta-analysis is to analyze whether controlled comparisons support such a shift. <b><i>Methods:</i></b> CINHAL, the Cochrane Library, MEDLINE, PubMed and Web of Science were searched from inception up to December 2012. A total of 22 studies met the criteria for inclusion. They were mostly concerned with tricyclic antidepressants (TCA; 18/22) and involved different anxiety disorders. In order to reduce clinical heterogeneity, only the 10 investigations that dealt with the comparison between TCA and BDZ in panic disorder were submitted to meta-analysis, whereas the remaining papers were individually summarized and critically examined. <b><i>Results:</i></b> According to the systematic review, no consistent evidence emerged supporting the advantage of using TCA over BDZ in treating generalized anxiety disorder (GAD), complex phobias and mixed anxiety-depressive disorders. Indeed, BDZ showed fewer treatment withdrawals and adverse events than AD. In panic disorder with and without agoraphobia our meta-analysis found BDZ treatments more effective in reducing the number of panic attacks than TCA (risk ratio, RR = 1.13; 95% CI = 1.01-1.27). Furthermore, BDZ medications were significantly better tolerated than TCA drugs, causing less discontinuation (RR = 0.40; 95% CI = 0.20-0.57) and side effects (RR = 0.41; 95% CI = 0.34-0.50). As to newer AD, BDZ trials resulted in comparable or greater improvements and fewer adverse events in patients suffering from GAD or panic disorder. <b><i>Conclusions:</i></b> The change in the prescribing pattern favoring newer AD over BDZ in the treatment of anxiety disorders has occurred without supporting evidence. Indeed, the role and usefulness of BDZ need to be reappraised.
DOI: 10.6084/m9.figshare.5125297.v1
title: Supplementary Material for: Association between Alanine Aminotransferase and Intracerebral Hemorrhage in East Asian Populations

description: <b><i>Background:</i></b> Intracerebral hemorrhage (ICH) and chronic liver disease are relatively common in East Asian countries. However, the relationship between the two diseases is unclear. Thus, we investigated the association between serum alanine aminotransferase (ALT) levels and ICH risk in East Asian populations. <b><i>Methods:</i></b> The East Asian Network for Stroke Prevention enrolled 279,982 participants with ALT measurements from four cohort studies in Korea, Taiwan, Japan and mainland China. Among them, 1,324 ICH events and 493 ICH deaths were observed. Cox's proportional hazard regression analysis was performed in each cohort to estimate the hazard ratio (HR) after adjusting for age, blood pressure, diabetes, total cholesterol, smoking and alcohol intake. Combined HRs were then estimated using pooled analyses with fixed-effects models. <b><i>Results:</i></b> The multivariate-adjusted pooled HRs (with 95% confidence interval, CI) for ICH incidence per 10 IU/l increments of ALT were 1.04 (1.03-1.04) in men and 1.01 (0.98-1.04) in women. Corresponding HRs for ICH mortality were 1.04 (1.02-1.05) in men and 1.04 (1.00-1.08) in women. The pooled HRs for ICH incidence in participants with ALT levels greater than or equal to 50 IU/l compared to those with levels less than 20 IU/l were 1.74 (1.41-2.16) in men and 1.60 (1.06-2.40) in women. The corresponding HRs for ICH mortality were 1.72 (1.21-2.44) in men and 1.63 (0.79-3.36) in women. <b><i>Conclusions:</i></b> An elevated ALT level was independently and significantly associated with an increased risk of ICH in East Asian men, but the association was less prominent in women.