cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5120593
title: Supplementary Material for: Induction of Bradykinesia with Pallidal Deep Brain Stimulation in Patients with Cranial-Cervical Dystonia

description: <i>Background:</i> Deep brain stimulation (DBS) of the globus pallidus internus (GPi) is an effective and well-tolerated treatment for idiopathic generalized dystonia. More recently, it has been applied as a treatment for focal and segmental dystonias. This patient population offers an opportunity to study the effects of alteration of pallidal outflow on previously normal limb function. <i>Methods:</i> We sought to retrospectively characterize the extent of novel GPi DBS-induced adverse motor effects in patients with adult-onset cervical and cranial-cervical dystonia using a questionnaire, and compared the findings to dystonia improvement as measured by standard scales. <i>Results:</i> Despite significant improvement in dystonia (65% in mean Burke-Fahn-MarsdenDystonia Rating Scale motor score, p &lt; 0.005, and 59% in mean Toronto Western Spasmodic Torticollis Rating Scale score, p &lt; 0.008), slowing and difficulty with normal motor function was reported in previously nondystonic extremities in 10 of 11 patients. Symptoms were common in both upper and lower extremities and included new difficulties with handwriting (82%), getting up from a chair or in/out of a car (73%), and walking (45%), and were not associated with aberrant lead placement near the internal capsule. <i>Conclusion:</i> Although GPi DBS was shown to be effective in these patients, the influence of GPi DBS on nondystonic body regions deserves further investigation.
DOI: 10.6084/m9.figshare.5120584
title: Supplementary Material for: The Perception of Prominence Patterns

description: The term ‘stress’ is used to refer to the perceptual salience at certain places in strings of syllables, but it has several different referents: (a) relative syllable salience in an utterance; this is syllable-, not word-oriented; (b) stress in a word; this is part of the lexical phonology; (c) stressing of words in utterances for various aspects of propositional and expressive meaning, often called ‘accent(uation)’. Referents <i>b</i> and <i>c</i> are word- and meaning-oriented. In this article, the terms are more stringently defined. ‘Stress’ is only used to refer to a lexical stress position (referent <i>b</i>), i.e. a syllable in a word that becomes the docking place for various types of ‘accent’ to weight words in utterances (referent <i>c</i>). ‘Stress’ has no physical attributes by itself. ‘Prominence’ refers to the patterns of salience in syllable strings (referent <i>a</i>). The article reports results of an experiment in prominence perception of the logatome <i>baba</i>, in which the physical parameters F0, syllabic duration, and overall acoustic energy were systematically varied across the bisyllable. Sixteen German subjects had to indicate, by pressing buttons of a computerized reaction time device, whether the first or the second syllable was more prominent. F0 was a more powerful cue than the other two. Equal syllable duration on a monotone resulted in more first-syllable judgements, which could be counteracted by a slightly falling F0 contour on the second syllable to reach equal response frequencies for the two syllables. This ties in with Lehiste’s earlier findings that F0 movement increases the perception of duration. Extrapolating from the results, a research programme for prominence perception is developed that will eventually shed new light on the investigation into the nature and manifestation of speech rhythm.
DOI: 10.6084/m9.figshare.5120587.v1
title: Supplementary Material for: Antioxidants and Other Micronutrients in Complementary Oncology

description: Many patients being treated for cancer use micronutrient supplements, with the intention to complement their cancer treatment or help them cope with the therapy- and disease-associated side effects. The majority are adding antioxidants without the knowledge of the treating physician. There are many concerns that antioxidants might decrease the effectiveness of chemotherapy, but increasing evidence suggests a benefit when antioxidants are added to conventional cytotoxic therapies. However, it is imperative that physicians explore the use of antioxidant and other micronutrient supplements with their cancer patients and educate them about potentially negative as well as potentially beneficial effects.
DOI: 10.6084/m9.figshare.5120581
title: Supplementary Material for: Glomerular Transcriptome Changes Associated with Lipopolysaccharide-Induced Proteinuria

description: <i>Background:</i> Global gene expression patterns have recently been characterized in normal glomeruli, but gene expression changes that accompany glomerular disease remain poorly characterized. <i>Method:</i> Here, we mapped global glomerular gene expression profile changes occurring in conjunction with lipopolysaccharide (LPS)-induced proteinuria in mice. <i>Results:</i> We observed dramatic transcriptional reprogramming in glomeruli in response to LPS, representing some 20% of all genes and about 45% of the genes that are normally highly expressed in glomeruli. Bioinformatic analysis revealed significant changes in transcripts encoding proteins involved in the regulation of adherence junctions, actin cytoskeleton and survival in podocytes. In the LPS-treated mice, we observed dysregulation of genes expressed in glomerular endothelial and mesangial cells and in podocytes, there was also a significant decrease in podocyte number. Moreover, collagen α1, α2 (IV) and laminin 10 (laminin α5β1γ1), which are expressed in immature glomeruli, were upregulated in the glomeruli of LPS-treated mice, suggesting remodeling of the glomerular basement membrane and activation of mesangial cells. By superimposing the LPS-induced changes onto GlomNet, a protein-protein interaction network was predicted for podocyte proteins affected by LPS. <i>Conclusions:</i> The detected changes in glomerular gene expression and their involvement in protein interaction networks provide putative markers for early and transient glomerular injury and proteinuria.
DOI: 10.6084/m9.figshare.5120593.v1
title: Supplementary Material for: Induction of Bradykinesia with Pallidal Deep Brain Stimulation in Patients with Cranial-Cervical Dystonia

description: <i>Background:</i> Deep brain stimulation (DBS) of the globus pallidus internus (GPi) is an effective and well-tolerated treatment for idiopathic generalized dystonia. More recently, it has been applied as a treatment for focal and segmental dystonias. This patient population offers an opportunity to study the effects of alteration of pallidal outflow on previously normal limb function. <i>Methods:</i> We sought to retrospectively characterize the extent of novel GPi DBS-induced adverse motor effects in patients with adult-onset cervical and cranial-cervical dystonia using a questionnaire, and compared the findings to dystonia improvement as measured by standard scales. <i>Results:</i> Despite significant improvement in dystonia (65% in mean Burke-Fahn-MarsdenDystonia Rating Scale motor score, p &lt; 0.005, and 59% in mean Toronto Western Spasmodic Torticollis Rating Scale score, p &lt; 0.008), slowing and difficulty with normal motor function was reported in previously nondystonic extremities in 10 of 11 patients. Symptoms were common in both upper and lower extremities and included new difficulties with handwriting (82%), getting up from a chair or in/out of a car (73%), and walking (45%), and were not associated with aberrant lead placement near the internal capsule. <i>Conclusion:</i> Although GPi DBS was shown to be effective in these patients, the influence of GPi DBS on nondystonic body regions deserves further investigation.
DOI: 10.6084/m9.figshare.5120569
title: Supplementary Material for: Genomic drift and copy number variation of chemosensory receptor genes in humans and mice

description: Recent studies about the structural variation of genomic sequences have shown that there is a large amount of copy number variations (CNVs) of genes within species. Analyzing Redon et al.’s (2006) crude data on copy number variable regions (CNVRs), we previously showed that CNVs are particularly high for chemosensory receptor genes in human populations. In this paper, we reanalyzed the CNVs of these genes using more refined data by Perry et al. (2008). The results showed that the extent of CNVs is somewhat lower in this dataset than in the previous one, but that the extent is still substantial for olfactory receptor (OR), vomeronasal receptor (VR), and taste receptor (TR) genes. We also studied the CNVs for chemosensory receptor genes in mice, using CNVR data obtained from inbred strains. It was found that the extent of CNVs is quite substantial but is lower than that for human populations. However, because the mouse data came from inbred strains and might be biased, this conclusion should be regarded as tentative. Despite this reservation, the distribution of gene copy number for the OR gene family was approximately normal in both humans and mice, suggesting that genomic drift caused by random duplication and deletion of genes plays important roles in determining the evolutionary change of chemosensation.
DOI: 10.6084/m9.figshare.5120584.v1
title: Supplementary Material for: The Perception of Prominence Patterns

description: The term ‘stress’ is used to refer to the perceptual salience at certain places in strings of syllables, but it has several different referents: (a) relative syllable salience in an utterance; this is syllable-, not word-oriented; (b) stress in a word; this is part of the lexical phonology; (c) stressing of words in utterances for various aspects of propositional and expressive meaning, often called ‘accent(uation)’. Referents <i>b</i> and <i>c</i> are word- and meaning-oriented. In this article, the terms are more stringently defined. ‘Stress’ is only used to refer to a lexical stress position (referent <i>b</i>), i.e. a syllable in a word that becomes the docking place for various types of ‘accent’ to weight words in utterances (referent <i>c</i>). ‘Stress’ has no physical attributes by itself. ‘Prominence’ refers to the patterns of salience in syllable strings (referent <i>a</i>). The article reports results of an experiment in prominence perception of the logatome <i>baba</i>, in which the physical parameters F0, syllabic duration, and overall acoustic energy were systematically varied across the bisyllable. Sixteen German subjects had to indicate, by pressing buttons of a computerized reaction time device, whether the first or the second syllable was more prominent. F0 was a more powerful cue than the other two. Equal syllable duration on a monotone resulted in more first-syllable judgements, which could be counteracted by a slightly falling F0 contour on the second syllable to reach equal response frequencies for the two syllables. This ties in with Lehiste’s earlier findings that F0 movement increases the perception of duration. Extrapolating from the results, a research programme for prominence perception is developed that will eventually shed new light on the investigation into the nature and manifestation of speech rhythm.
DOI: 10.6084/m9.figshare.5120569.v1
title: Supplementary Material for: Genomic drift and copy number variation of chemosensory receptor genes in humans and mice

description: Recent studies about the structural variation of genomic sequences have shown that there is a large amount of copy number variations (CNVs) of genes within species. Analyzing Redon et al.’s (2006) crude data on copy number variable regions (CNVRs), we previously showed that CNVs are particularly high for chemosensory receptor genes in human populations. In this paper, we reanalyzed the CNVs of these genes using more refined data by Perry et al. (2008). The results showed that the extent of CNVs is somewhat lower in this dataset than in the previous one, but that the extent is still substantial for olfactory receptor (OR), vomeronasal receptor (VR), and taste receptor (TR) genes. We also studied the CNVs for chemosensory receptor genes in mice, using CNVR data obtained from inbred strains. It was found that the extent of CNVs is quite substantial but is lower than that for human populations. However, because the mouse data came from inbred strains and might be biased, this conclusion should be regarded as tentative. Despite this reservation, the distribution of gene copy number for the OR gene family was approximately normal in both humans and mice, suggesting that genomic drift caused by random duplication and deletion of genes plays important roles in determining the evolutionary change of chemosensation.
DOI: 10.6084/m9.figshare.5120572
title: Supplementary Material for: Copy number variation in the mouse genome: implications for the mouse as a model organism for human disease

description: Individuals within a species have genetic differences which ultimately result in the spectrum of phenotypic variation that we observe. Genetic variation exists at the nucleotide level in the form of single nucleotide polymorphisms (SNPs), and at a structural level as inversions, deletions and amplifications of larger stretches of nucleotides. Profiling of human and mouse genomes has identified numerous genomic segmental copy number variations (CNVs) throughout these genomes. Since inbred mice are widely used laboratory models for the study of both normal and disease biology, it is crucial that we understand the full scope of genetic variation, including CNVs, within these animals. These genetic differences can inform us about the history of a population or species, enlighten us on gene function, and guide our selection of a model system for the study of human disease.
DOI: 10.6084/m9.figshare.5120575
title: Supplementary Material for: Acute Treatment Costs of Stroke in Brazil

description: <i>Background and Purpose:</i> Although stroke is the leading cause of death in Brazil, little information exist on the acute treatment provided for stroke and its associated costs. This study addresses this gap by both clinically and economically characterizing the acute treatment of first-ever intracerebral hemorrhage (ICH) and ischemic stroke (IS) in Brazil. <i>Methods:</i> Retrospective medical chart review using data from two high-volume stroke centers in São Paulo, Brazil. Clinical and resource utilization data for all patients admitted to the stroke centers with a first-ever stroke between January 1, 2006 and May 31, 2007 were collected and the mean acute treatment costs per person were calculated by assigning appropriate unit cost data to all resource use. Cost estimates in Brazilian reals (BRL) were converted to US dollars (USD) using the 2005 purchasing power parity index. National costs of acute treatment for incident strokes were estimated by extrapolation of mean cost estimate per person to national incidence data for the two types of stroke. The mean costs of acute treatment on a national scale were examined in sensitivity analysis. <i>Results:</i> A total of 316 stroke patients were identified and their demographic and clinical characteristics, patterns of care, and outcomes were examined. Mean length of hospital stay was 12.0 ± 8.8 days for ICH and 13.3 ±23.4 days for IS. Ninety-one percent of the ICH patients and 68% of the IS patients were admitted to an intensive care unit (ICU). Mean total costs of initial hospitalization were USD 4,101 (SD ±4,254) for ICH and USD 1,902 (SD ±1,426) for IS. In multivariate analysis, hemorrhagic stroke, development of pneumonia, neurosurgical intervention, stay in ICU, and physical therapy were all significant independent predictors of acute treatment costs. Aggregate national health care expenditures for acute treatment of incident ICH were USD 122.4 million (range 30.8–274.2) and USD 326.9 million for IS (range 82.4–732.2). <i>Conclusion:</i> Acute treatment costs of incident ICH and IS in Brazil are substantial and primarily driven by the intensity of hospital treatment and in-hospital complications. With the expected increase in the incidence of stroke in Brazil over the coming decades, these results emphasize the need for effective preventive and acute medical care.
DOI: 10.6084/m9.figshare.5120581.v1
title: Supplementary Material for: Glomerular Transcriptome Changes Associated with Lipopolysaccharide-Induced Proteinuria

description: <i>Background:</i> Global gene expression patterns have recently been characterized in normal glomeruli, but gene expression changes that accompany glomerular disease remain poorly characterized. <i>Method:</i> Here, we mapped global glomerular gene expression profile changes occurring in conjunction with lipopolysaccharide (LPS)-induced proteinuria in mice. <i>Results:</i> We observed dramatic transcriptional reprogramming in glomeruli in response to LPS, representing some 20% of all genes and about 45% of the genes that are normally highly expressed in glomeruli. Bioinformatic analysis revealed significant changes in transcripts encoding proteins involved in the regulation of adherence junctions, actin cytoskeleton and survival in podocytes. In the LPS-treated mice, we observed dysregulation of genes expressed in glomerular endothelial and mesangial cells and in podocytes, there was also a significant decrease in podocyte number. Moreover, collagen α1, α2 (IV) and laminin 10 (laminin α5β1γ1), which are expressed in immature glomeruli, were upregulated in the glomeruli of LPS-treated mice, suggesting remodeling of the glomerular basement membrane and activation of mesangial cells. By superimposing the LPS-induced changes onto GlomNet, a protein-protein interaction network was predicted for podocyte proteins affected by LPS. <i>Conclusions:</i> The detected changes in glomerular gene expression and their involvement in protein interaction networks provide putative markers for early and transient glomerular injury and proteinuria.
DOI: 10.6084/m9.figshare.5120566
title: Supplementary Material for: Benign copy number changes in clinical cytogenetic diagnostics by array CGH

description: A database of apparently benign copy number variants (bCNVs) detected by a Spectral Genomics Inc./PerkinElmer BAC array platform has been maintained through the University of Utah Comparative Genomic Hybridization laboratory since 2005. The target population for this database represents 1,275 patients with abnormal phenotypes, primarily children referred for developmental delay and mental retardation. These bCNVs are independent of any identified copy number abnormality detected. The most common 35 bCNVs observed and their frequencies are reported here, and a subset of ten of the patients studied was evaluated on a new oligonucleotide CNV array set designed by Agilent Technologies. There was a 76% concordance of calls for these 35 bCNVs detected by both array platforms in the same patients. The higher resolution of the Agilent oligonucleotide array compared to the BAC array allowed determination of the precise breakpoints of the observed CNVs, in addition to documentation of additional CNVs of smaller sizes. As expected, observed CNVs and their frequencies were generally consistent with those of other previously published and available databases, including the Database of Genomic Variants (http://projects.tcag.ca/variation/). The availability of these data should assist other clinical laboratories in the evaluation of CNVs of unknown clinical significance.
DOI: 10.6084/m9.figshare.5120557
title: Supplementary Material for: Analysis of 30 Genes (355 SNPS) Related to Energy Homeostasis for Association with Adiposity in European-American and Yup’ik Eskimo Populations

description: <i>Objective:</i> Human adiposity is highly heritable, but few of the genes that predispose to obesity in most humans are known. We tested candidate genes in pathways related to food intake and energy expenditure for association with measures of adiposity. <i>Methods:</i> We studied 355 genetic variants in 30 candidate genes in 7 molecular pathways related to obesity in two groups of adult subjects: 1,982 unrelated European Americans living in the New York metropolitan area drawn from the extremes of their body mass index (BMI) distribution and 593 related Yup’ik Eskimos living in rural Alaska characterized for BMI, body composition, waist circumference, and skin fold thicknesses. Data were analyzed by using a mixed model in conjunction with a false discovery rate (FDR) procedure to correct for multiple testing. <i>Results:</i> After correcting for multiple testing, two single nucleotide polymorphisms (SNPs) in <i>Ghrelin</i> (<i>GHRL</i>) (rs35682 and rs35683) were associated with BMI in the New York European Americans. This association was not replicated in the Yup’ik participants. There was no evidence for gene × gene interactions among genes within the same molecular pathway after adjusting for multiple testing via FDR control procedure. <i>Conclusion:</i> Genetic variation in <i>GHRL</i> may have a modest impact on BMI in European Americans.
DOI: 10.6084/m9.figshare.5120560
title: Supplementary Material for: Skewed Matrilineal Genetic Composition in a Small Wild Chimpanzee Community

description: Maternal kinship is important in primate societies because it affects individual behaviour as well as the sustainability of populations. All members of the Bossou chimpanzee community are descended from 8 individuals (herein referred to as original adults) who were already adults or subadults when field observations were initiated in 1976 and whose genetic relationships were unknown. Sequencing of the control region on the maternally inherited mtDNA revealed that 4 (1 male and 3 females) of the 8 original adults shared an identical haplotype. We investigated the effects of the skewed distribution of mtDNA haplotypes on the following two outcomes. First, we demonstrated that the probability of mtDNA haplotype extinction would be increased under such a skewed composition in a small community. Second, the ratio of potential mating candidates to competitors is likely to decrease if chimpanzees become aware of maternal kinship and avoid incest. We estimated that the magnitude of the decrease in the ratio is 10 times greater in males than in females. Here we demonstrate a scenario in which this matrilineal skewness in a small community accelerates extinction of mtDNA haplotype, which will make it more difficult to find a suitable mate within the community.
DOI: 10.6084/m9.figshare.5120572.v1
title: Supplementary Material for: Copy number variation in the mouse genome: implications for the mouse as a model organism for human disease

description: Individuals within a species have genetic differences which ultimately result in the spectrum of phenotypic variation that we observe. Genetic variation exists at the nucleotide level in the form of single nucleotide polymorphisms (SNPs), and at a structural level as inversions, deletions and amplifications of larger stretches of nucleotides. Profiling of human and mouse genomes has identified numerous genomic segmental copy number variations (CNVs) throughout these genomes. Since inbred mice are widely used laboratory models for the study of both normal and disease biology, it is crucial that we understand the full scope of genetic variation, including CNVs, within these animals. These genetic differences can inform us about the history of a population or species, enlighten us on gene function, and guide our selection of a model system for the study of human disease.