cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5125546.v1
title: Supplementary Material for: Intramural Hematoma Detection by Susceptibility-Weighted Imaging in Intracranial Vertebral Artery Dissection

description: <b><i>Background:</i></b> The radiologic diagnosis of vertebral artery dissection (VAD) depends on characteristic intraluminal findings on angiography and intramural hematoma or a double-lumen sign on high-resolution vessel wall imaging. We aimed to evaluate the accuracy of intramural hematoma sign on susceptibility-weighted imaging (SWI) in VAD. <b><i>Methods:</i></b> We retrospectively analyzed SWI, phase map images and brain computed tomography (CT) of the consecutive patients who suffered an ischemic stroke in the vertebral artery territory from August 2010 to July 2012. We divided the patients into 2 groups: the VAD group and the nondissection group. VAD was diagnosed by conventional catheter angiographic findings (aneurysmal dilatation, pearl-and-string or tapered steno-occlusion) and pathognomonic findings such as intramural hematoma or a double-lumen sign on the source images of TOF-MRA, high-resolution T<sub>1</sub>-weighted MRI or high-resolution T<sub>2</sub>-weighted MRI. Intramural hematoma sign was considered positive if the patient had an eccentric or concentric hypointense signal lesion in the vertebral artery on SWI, a corresponding hyperintense signal on phase map and no evidence of calcification on the brain CT, suggesting blood products other than calcification. Two experienced neuroradiologists blinded to clinical information and angiographic findings were asked to judge for the presence of intramural hematoma sign on SWI. The accuracy of intramural hematoma sign on SWI was evaluated. Phase value, demographic and clinical data were compared between the VAD and the nondissection groups. <b><i>Results:</i></b> Thirty-nine patients were included: 10 in the VAD group and 29 in the non-dissection group. Among the VAD group cases, intramural hematoma sign on SWI was positive in 9 of the 10 VAD cases and in 1 out of the 29 cases in the nondissection group. The intramural hematoma sign on SWI was significantly associated with VAD (p &lt; 0.001), and showed sensitivity of 90% and specificity of 96.6%. Mean phase values of intramural hematomas (n = 9) were all positive and those of calcified lesions (n = 13) were all negative (0.45 radian vs. -0.42 radian, p &lt; 0.001). <b><i>Conclusions:</i></b> The intramural hematoma sign on SWI was significantly associated with VAD and the phase map values were higher in intramural hematomas when compared with atherosclerotic calcifications.
DOI: 10.6084/m9.figshare.5125531.v1
title: Supplementary Material for: Divergence of Repetitive DNA Sequences in the Heterochromatin of Medaka Fishes: Molecular Cytogenetic Characterization of Constitutive Heterochromatin in Two Medaka Species: <b><i>Oryzias hubbsi</i></b> and <b><i>O. celebensis</i></b> (Adrianichthyidae, Beloniformes)

description: The large biarmed chromosomes of <i>Oryzias celebensis</i> [2n = 36, fundamental arm number (FN) = 48] are considered to have resulted from fusions of acrocentric chromosomes in the ancestral karyotype of <i>Oryzias</i>, which is retained in <i>O. hubbsi</i> (2n<i> = </i>48, FN = 48). To understand the molecular evolution of heterochromatin associated with karyotype reorganization in medaka fishes, we cloned 3 and 6 novel families of heterochromatin-related repetitive DNA sequences from <i>O</i>.<i> hubbsi</i> and <i>O. celebensis</i>, respectively, and characterized them using molecular cytogenetics. Two AT-rich repetitive sequences isolated from the genomic DNA of <i>O. hubbsi</i>, a 164-bp satellite DNA (OHU-<i>Rsa</i>I-Scen) and a 177-bp telomere-specific repeat (OHU-<i>Rsa</i>I-Stelo), were shown to be major components of the constitutive heterochromatin of centromeres and telomeres, respectively. A GC-rich 326-bp sequence, named OHU-<i>Alu</i>I-M1, was colocalized with the 18S-28S ribosomal RNA gene cluster to a single autosomal pair of chromosomes and the W chromosome. In <i>O. celebensis</i>, 2 major satellite DNA sequences (the AT-rich 157-bp OCE-<i>Alu</i>I-Scen sequence and the 186-bp OCE-<i>Hin</i>fI-Scen sequence) were identified in the centromeric regions of almost all chromosomes. The 197-bp OCE-<i>Hin</i>fI-S6 sequence was located in the centromeric and distal and/or interstitial heterochromatin of almost all chromosomes, and the 191-bp OCE-<i>Hin</i>fI-S8 sequence was located in 6 pairs of chromosomes. Constitutive heterochromatin on the short arm of large submetacentric chromosome 5 was composed of at least 3 different repetitive sequences: the 171-bp OCE-<i>Alu</i>I-S18 sequence, the 197-bp OCE-<i>Hin</i>fI-S6 sequence and the 172-bp OCE-<i>Hin</i>fI-S11 sequence. All families of repeated sequences showed no nucleotide sequence similarity with each other and high species-specificity among 7 different species. These results suggest that the heterochromatin of <i>O</i>. <i>hubbsi</i> and <i>O</i>. <i>celebensis </i>consists of various types of repetitive sequence and that the sequences evolved independently and were then amplified site-specifically in each lineage after karyotype reorganization occurred in the ancestral karyotype.
DOI: 10.6084/m9.figshare.5125540.v1
title: Supplementary Material for: Kidney Attack: Overdiagnosis of Acute Kidney Injury or Comprehensive Definition of Acute Kidney Syndromes?

description: Medicine
DOI: 10.6084/m9.figshare.5125528
title: Supplementary Material for: Adult Height and Epigenotype in Children with Silver-Russell Syndrome Treated with GH

description: <b><i>Aims:</i></b> To compare<b> </b>adult heights of GH-treated and GH-untreated patients with Silver-Russell syndrome (SRS) who were epigenotyped. <b><i>Methods:</i></b> This was a nonrandomized retrospective study with matched controls at a single center. Molecular analysis of 32 out of 37 GH-treated patients (16 females) revealed <i>IGF2-H19</i> epimutations in 12 and maternal uniparental disomy of chromosome 7 (matUPD7) in 5 patients; 15 were negative. At start of GH, mean age was 7.2 years and mean height -3.34 standard deviation score (SDS). Mean GH dose used was 51 µg/kg·day, mean duration of therapy was 5.6 years. Puberty was blocked by GnRH analogs in 16 patients. The untreated group comprised 13 individuals (5 females, mean age 6.8 years and mean height -3.34 SDS). End points were adult height and overall height gain. <b><i>Results:</i></b> GH-treated patients reached an adult height of -2.12 ± 0.98 SDS gaining 1.22 SDS in comparison to baseline. Adult height SDS of the untreated was -3.13 ± 1.37 SDS. The matched treated patients were significantly taller than their untreated counterparts. Outcome was dependent on height at start of GH and duration of therapy. Height gain was highest in the shortest patients. <b><i>Conclusions:</i></b> GH improved adult height in SRS to a comparable degree as reported in nonsyndromic SGA children. A trend toward a better outcome in matUPD7 needs confirmation in larger cohorts.
DOI: 10.6084/m9.figshare.5125519
title: Supplementary Material for: Molecular and Gene Network Analysis of Thyroid Transcription Factor 1 <b><i>(TTF1)</i></b> and Enhanced at Puberty <b><i>(EAP1)</i></b> Genes in Patients with GnRH-Dependent Pubertal Disorders

description: <b><i>Background/Aim:</i></b> TTF1 and EAP1 are transcription factors that modulate gonadotropin-releasing hormone expression. We investigated the contribution of <i>TTF1</i> and <i>EAP1</i> genes to central pubertal disorders. <b><i>Patients and Methods:</i></b> 133 patients with central pubertal disorders were studied: 86 with central precocious puberty and 47 with normosmic isolated hypogonadotropic hypogonadism. The coding region of <i>TTF1</i> and <i>EAP1</i> were sequenced. Variations of polyglutamine and polyalanine repeats in EAP1 were analyzed by GeneScan software. Association of <i>TTF1</i> and <i>EAP1</i> to genes implicated in timing of puberty was investigated by meta-network framework GeneMANIA and Cytoscape software. <b><i>Results:</i></b> Direct sequencing of the <i>TTF1</i> did not reveal any mutation or polymorphisms. Four EAP1 synonymous variants were identified with similar frequencies among groups. The most common EAP1 5′-distal polyalanine genotype was the homozygous 12/12, but the genotype 12/9 was identified in 2 central precocious puberty sisters without functional alteration in EAP1 transcriptional activity. TTF1 and EAP1 were connected, via genetic networks, to genes implicated in the control of menarche. <b><i>Conclusion:</i></b> No <i>TTF1 </i>or <i>EAP1 </i>germline mutations were associated with central pubertal disorders. <i>TTF1 </i>and <i>EAP1 </i>may affect puberty by changing expression in response to other members of puberty-associated gene networks, or by differentially affecting the expression of gene components of these networks.
DOI: 10.6084/m9.figshare.5125525
title: Supplementary Material for: Detection Rate of Trisomy 21 in Fetuses with Isolated and Non-Isolated Aberrant Right Subclavian Artery

description: <b><i>Objective:</i></b> The purpose of this study was to determine the frequency of chromosomal anomalies among the fetuses with isolated and non-isolated aberrant right subclavian artery (ARSA), and to evaluate the sonographic findings associated with ARSA. <b><i>Methods:</i></b> This is a retrospective study conducted during the period between January 2008 and December 2012 at the maternal fetal medicine units of three different referral centers. <b><i>Results:</i></b> Among the 148 cases of ARSA, 98 were isolated and 50 were associated with cardiac anomalies, extracardiac malformations or soft markers. Trisomy 21 was the only chromosomal anomaly with a prevalence of 6.8% (10/148). The corresponding rate was 6.1% (6/98) and 8% (4/50) for isolated and non-isolated ARSA, respectively. Cardiac anomalies, extracardiac findings and soft markers were detected in 5.4% (8), 10.8% (16) and 24.3% (36) of cases, respectively. Among the 10 fetuses with trisomy 21, 6 were isolated, 4 were associated with soft markers, 2 were associated with fetal growth restriction and 1 was associated with hydrops fetalis. Cardiac anomalies were not observed in any of these fetuses. <b><i>Conclusion:</i></b> The prenatal diagnosis of ARSA should prompt meticulous anatomic survey, and karyotype analysis might be offered even in the absence of associated findings.
DOI: 10.6084/m9.figshare.5125528.v1
title: Supplementary Material for: Adult Height and Epigenotype in Children with Silver-Russell Syndrome Treated with GH

description: <b><i>Aims:</i></b> To compare<b> </b>adult heights of GH-treated and GH-untreated patients with Silver-Russell syndrome (SRS) who were epigenotyped. <b><i>Methods:</i></b> This was a nonrandomized retrospective study with matched controls at a single center. Molecular analysis of 32 out of 37 GH-treated patients (16 females) revealed <i>IGF2-H19</i> epimutations in 12 and maternal uniparental disomy of chromosome 7 (matUPD7) in 5 patients; 15 were negative. At start of GH, mean age was 7.2 years and mean height -3.34 standard deviation score (SDS). Mean GH dose used was 51 µg/kg·day, mean duration of therapy was 5.6 years. Puberty was blocked by GnRH analogs in 16 patients. The untreated group comprised 13 individuals (5 females, mean age 6.8 years and mean height -3.34 SDS). End points were adult height and overall height gain. <b><i>Results:</i></b> GH-treated patients reached an adult height of -2.12 ± 0.98 SDS gaining 1.22 SDS in comparison to baseline. Adult height SDS of the untreated was -3.13 ± 1.37 SDS. The matched treated patients were significantly taller than their untreated counterparts. Outcome was dependent on height at start of GH and duration of therapy. Height gain was highest in the shortest patients. <b><i>Conclusions:</i></b> GH improved adult height in SRS to a comparable degree as reported in nonsyndromic SGA children. A trend toward a better outcome in matUPD7 needs confirmation in larger cohorts.
DOI: 10.6084/m9.figshare.5125519.v1
title: Supplementary Material for: Molecular and Gene Network Analysis of Thyroid Transcription Factor 1 <b><i>(TTF1)</i></b> and Enhanced at Puberty <b><i>(EAP1)</i></b> Genes in Patients with GnRH-Dependent Pubertal Disorders

description: <b><i>Background/Aim:</i></b> TTF1 and EAP1 are transcription factors that modulate gonadotropin-releasing hormone expression. We investigated the contribution of <i>TTF1</i> and <i>EAP1</i> genes to central pubertal disorders. <b><i>Patients and Methods:</i></b> 133 patients with central pubertal disorders were studied: 86 with central precocious puberty and 47 with normosmic isolated hypogonadotropic hypogonadism. The coding region of <i>TTF1</i> and <i>EAP1</i> were sequenced. Variations of polyglutamine and polyalanine repeats in EAP1 were analyzed by GeneScan software. Association of <i>TTF1</i> and <i>EAP1</i> to genes implicated in timing of puberty was investigated by meta-network framework GeneMANIA and Cytoscape software. <b><i>Results:</i></b> Direct sequencing of the <i>TTF1</i> did not reveal any mutation or polymorphisms. Four EAP1 synonymous variants were identified with similar frequencies among groups. The most common EAP1 5′-distal polyalanine genotype was the homozygous 12/12, but the genotype 12/9 was identified in 2 central precocious puberty sisters without functional alteration in EAP1 transcriptional activity. TTF1 and EAP1 were connected, via genetic networks, to genes implicated in the control of menarche. <b><i>Conclusion:</i></b> No <i>TTF1 </i>or <i>EAP1 </i>germline mutations were associated with central pubertal disorders. <i>TTF1 </i>and <i>EAP1 </i>may affect puberty by changing expression in response to other members of puberty-associated gene networks, or by differentially affecting the expression of gene components of these networks.
DOI: 10.6084/m9.figshare.5125522
title: Supplementary Material for: Aging Promotes Progression of IgA Nephropathy: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> There has been considerable interest in whether old age is associated with IgA nephropathy (IgAN) progression, which is still controversial. <b><i>Methods:</i></b> We searched multiple databases for studies published from 1980 to 2012. The inclusion criteria were case-control, cohort studies published in any language. The included studies needed to have an older group. IgAN was proven by biopsy. <b><i>Results: </i></b>We included 9 studies with a total of 6,543 patients. The meta-analyses of other risk factors between the older group (&gt;50 years old) and the non-older group (15-50 years old) found significant differences in the presence of hypertension, proteinuria, serum cholesterol levels and baseline renal function. In the overall analysis, compared to the non-older group, older age significantly increased the incidence of developing end-stage renal disease [ESRD; relative risk (RR) random model 1.95; 95% CI: 1.27-3.01]. In the subgroup analyses, we found the age limit and traditional risk factors of IgAN may be the sources of heterogeneity between studies. Moreover, the RR (2.56) of the Asian countries was much higher than the RR (1.11) of the European countries. <b><i>Conclusions:</i></b> This comprehensive review revealed that old age is a real risk factor for IgAN progression to ESRD. The incidence of ESRD in the older IgAN patients was 1.95 times higher than that in the non-older IgAN patients. Moreover, the risk of IgAN progression to ESRD of the older patients in Asia was higher than that of the older patients in Europe.
DOI: 10.6084/m9.figshare.5125510
title: Supplementary Material for: Validity of Discharge Diagnoses in the Surveillance of Stroke

description: <b><i>Background:</i></b> Hospital administrative data have been suggested as a valuable cost-effective tool for providing information about the stroke burden. Nevertheless, the choice of the diagnosis codes has been a critical issue in the development of case ascertainment algorithms. <b><i>Methods:</i></b> In this study, the Minimum Basic Data Set administrative database was used to analyze the accuracy of different ICD-9-CM algorithms based on the neurologist's clinical judgement as the ‘gold standard'. <b><i>Results:</i></b> The most accurate algorithm observed in our study involved the selection of ICD-9-CM codes 430-438 in the primary diagnosis. It yielded a sensitivity of 96.1%, a specificity of 87.5% and a positive predictive value of 82.5%. <b><i>Conclusions:</i></b> The Minimum Basic Data Set is a valuable source to evaluate stroke frequency when using an accurate algorithm to select events.
DOI: 10.6084/m9.figshare.5125513
title: Supplementary Material for: Is It Time to Rethink How Neuropsychological Tests Are Used to Diagnose Mild Forms of HIV-Associated Neurocognitive Disorders? Impact of False-Positive Rates on Prevalence and Power

description: <b><i>Background:</i></b> Between 0 and 48% of normal HIV-uninfected individuals score below threshold neuropsychological test scores for HIV-associated neurocognitive disorders (HAND) or are false positives. There has been little effort to understand the effect of varied interpretations of research criteria for HAND on false-positive frequencies, prevalence and analytic estimates. <b><i>Methods:</i></b> The proportion of normal individuals scoring below Z score thresholds drawn from research criteria for HAND, or false-positive frequencies, was estimated in a normal Kenyan population and a simulated normal population using varied interpretations of research criteria for HAND. We calculated the impact of false-positive frequencies on prevalence estimates and statistical power. <b><i>Results:</i></b> False-positive frequencies of 2-74% were observed for asymptomatic neurocognitive impairment/mild neurocognitive disorder and 0-8% for HIV-associated dementia. False-positive frequencies depended on the definition of an abnormal cognitive domain, Z score thresholds and neuropsychological battery size. Misclassification led to clinically important overestimation of prevalence and dramatic decreases in power. <b><i>Conclusions:</i></b> Minimizing false-positive frequencies is critical to decrease bias in prevalence estimates and minimize reductions in power in studies of association, particularly for mild forms of HAND. We recommend changing the Z score threshold to ≤-1.5 for mild impairment, limiting analysis to 3-5 cognitive domains and using the average Z score to define an abnormal domain.
DOI: 10.6084/m9.figshare.5125516
title: Supplementary Material for: Population-Based Validation of the iScore for Predicting Mortality and Early Functional Outcome in Ischemic Stroke Patients

description: <b><i>Background:</i></b> We aimed to determine the accuracy of the iScore for predicting mortality and early disability following ischemic stroke in a French population-based study. <b><i>Methods:</i></b> All patients with acute ischemic stroke were identified among residents of the city of Dijon, France, between 2006 and 2011, using a population-based stroke registry. The 30-day iScore and 1-year iScore were calculated. A logistic regression model was used to assess the performance of the iScore for predicting both 30-day and 1-year mortality, and poor functional outcome at discharge (modified Rankin Scale score of 3-6). The discrimination and calibration of the model were assessed using the c-statistic and the Hosmer-Lemeshow goodness-of-fit test, respectively. <b><i>Results:</i></b> Among the 1,199 ischemic stroke patients recorded, 107 (8.9%) were excluded because at least one item of data was missing. For the remaining 1,092 patients, the c-statistic was 0.85 (95% CI: 0.82-0.89) for 30-day and 0.84 (0.81-0.87) for 1-year mortality, and calibration was good (p = 0.82 and p = 0.96, respectively, for the Hosmer-Lemeshow test). Similar results were found for disability (c-statistic 0.81, 95% CI: 0.79-0.84, and p = 0.45 for the Hosmer-Lemeshow test). <b><i>Conclusion:</i></b> This is the first population-based study to demonstrate the accuracy of the iScore for predicting mortality and early disability in ischemic stroke patients.
DOI: 10.6084/m9.figshare.5125522.v1
title: Supplementary Material for: Aging Promotes Progression of IgA Nephropathy: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> There has been considerable interest in whether old age is associated with IgA nephropathy (IgAN) progression, which is still controversial. <b><i>Methods:</i></b> We searched multiple databases for studies published from 1980 to 2012. The inclusion criteria were case-control, cohort studies published in any language. The included studies needed to have an older group. IgAN was proven by biopsy. <b><i>Results: </i></b>We included 9 studies with a total of 6,543 patients. The meta-analyses of other risk factors between the older group (&gt;50 years old) and the non-older group (15-50 years old) found significant differences in the presence of hypertension, proteinuria, serum cholesterol levels and baseline renal function. In the overall analysis, compared to the non-older group, older age significantly increased the incidence of developing end-stage renal disease [ESRD; relative risk (RR) random model 1.95; 95% CI: 1.27-3.01]. In the subgroup analyses, we found the age limit and traditional risk factors of IgAN may be the sources of heterogeneity between studies. Moreover, the RR (2.56) of the Asian countries was much higher than the RR (1.11) of the European countries. <b><i>Conclusions:</i></b> This comprehensive review revealed that old age is a real risk factor for IgAN progression to ESRD. The incidence of ESRD in the older IgAN patients was 1.95 times higher than that in the non-older IgAN patients. Moreover, the risk of IgAN progression to ESRD of the older patients in Asia was higher than that of the older patients in Europe.
DOI: 10.6084/m9.figshare.5125504
title: Supplementary Material for: Shan Virus: A New Mimivirus Isolated from the Stool of a Tunisian Patient with Pneumonia

description: <b><i>Objective:</i></b> Following the isolation of a Marseillevirus from the stool of a healthy young Senegalese and a Mimivirus from a Tunisian patient with pneumonia, we attempted to isolate other giant viruses of amoebae from a large human stool collection. <b><i>Methods: </i></b>During the period 2010-2011, a total of 1,605 stool samples, including 115 from Tunisian patients with pneumonia, were cultured on amoebae. We used a recently developed high-throughput isolation system to detect amoebae plaque lysis on agar plates; this method allows for the testing of 100 samples per plate per week. The giant virus was identified by sequencing of genes conserved in Megavirales. <b><i>Results:</i></b> A single giant virus, called Shan, was isolated from the stool of a Tunisian patient with pneumonia who responded poorly to antibiotics. This virus has an icosahedral shape typical of members of the family Mimiviridae and a size of 640 ± 10 nm. Phylogenetic analyses showed that Shan virus was classified as a member of Mimivirus lineage C that infects amoebae. <b><i>Conclusion:</i></b> Only one isolate was obtained in this study, suggesting that giant viruses of amoebae are rare in human stool. The isolation of Shan virus from a patient with pneumonia brings into question the etiological role of this virus and its subsequent release in stool.