cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121091
title: Supplementary Material for: Dynamic Nucleotide Mutation Gradients and Control Region Usage in Squamate Reptile Mitochondrial Genomes

description: Gradients of nucleotide bias and substitution rates occur in vertebrate mitochondrial genomes due to the asymmetric nature of the replication process. The evolution of these gradients has previously been studied in detail in primates, but not in other vertebrate groups. From the primate study, the strengths of these gradients are known to evolve in ways that can substantially alter the substitution process, but it is unclear how rapidly they evolve over evolutionary time or how different they may be in different lineages or groups of vertebrates. Given the importance of mitochondrial genomes in phylogenetics and molecular evolutionary research, a better understanding of how asymmetric mitochondrial substitution gradients evolve would contribute key insights into how this gradient evolution may mislead evolutionary inferences, and how it may also be incorporated into new evolutionary models. Most snake mitochondrial genomes have an additional interesting feature, 2 nearly identical control regions, which vary among different species in the extent that they are used as origins of replication. Given the expanded sampling of complete snake genomes currently available, together with 2 additional snakes sequenced in this study, we reexamined gradient strength and CR usage in alethinophidian snakes as well as several lizards that possess dual CRs. Our results suggest that nucleotide substitution gradients (and corresponding nucleotide bias) and CR usage is highly labile over the ∼200 m.y. of squamate evolution, and demonstrates greater overall variability than previously shown in primates. The evidence for the existence of such gradients, and their ability to evolve rapidly and converge among unrelated species suggests that gradient dynamics could easily mislead phylogenetic and molecular evolutionary inferences, and argues strongly that these dynamics should be incorporated into phylogenetic models.
DOI: 10.6084/m9.figshare.5121094
title: Supplementary Material for: Welche Funktionen erfüllen Zwangssymptome? – Ergebnisse einer Analyse im stationären Setting

description: <i>Einleitung:</i> Zwangssymptome kÖnnen verschiedene intrapsychische und interpersonelle FunktionalitÄten, d.h. unterschiedliche ZweckmÄßigkeiten oder Sinnhaftigkeiten fÜr den Betroffenen besitzen, die bei einer erfolgreichen Psychotherapie berÜcksichtigt werden sollten. Die vorliegende Studie verfolgte das Ziel, erstmals anhand einer Stichprobe stationÄrer Patienten die im Rahmen kognitiver Verhaltenstherapie erarbeiteten FunktionalitÄten systematisch zu erfassen und auf ZusammenhÄnge mit soziodemografischen und klinischen Variablen hin zu untersuchen. <i>Material und Methoden:</i> Die Behandlungsberichte aller von 2001–2008 stationÄr in unserem Hause behandelten Patienten mit der Erstdiagnose ZwangsstÖrung wurden in die Erhebung aufgenommen. 168 Berichte (63%) enthielten explizite Angaben Über die jeweiligen FunktionalitÄten der StÖrung, welche mittels qualitativer Inhaltsanalyse unter deduktiver Kategorienbildung systematisch ausgewertet wurden. Die erhobenen Funktionen wurden auf ZusammenhÄnge mit Alter, Geschlecht, Erkrankungs- und Behandlungsdauer untersucht. <i>Ergebnis:</i> Bei mehr als der HÄlfte der Patienten (57,7%) waren ≥2 FunktionalitÄten vertreten; insgesamt wurde den ZwÄngen etwas hÄufiger eine intrapsychische FunktionalitÄt zugeschrieben als eine interpersonelle. Am hÄufigsten (53,7%) dienten ZwÄnge der Emotionsregulation; der Wunsch nach Autonomie und Abgrenzung stellte die hÄufigste interpersonelle FunktionalitÄt dar (42,1%). Keine der gefundenen 11 FunktionalitÄten war mit lÄngerer Erkrankungsdauer oder hÄufigeren BehandlungsabbrÜchen assoziiert. Allerdings ließen sich ZusammenhÄnge zwischen einzelnen Subgruppen von Zwangssymptomen und bestimmten FunktionalitÄten feststellen. <i>Schlussfolgerung:</i> Die Ergebnisse verweisen auf eine große Bandbreite an FunktionalitÄten, wobei dem BedÜrfnis nach Regulation aversiver Emotionen und Autonomie ein besonderer Stellenwert zukommt.
DOI: 10.6084/m9.figshare.5121100.v1
title: Supplementary Material for: Expression of a Hypoxia-Associated Protein, Carbonic Anhydrase-9, Correlates with Malignant Phenotypes of Gastric Carcinoma

description: <i>Background/Aims:</i> Gastric cancers are characterized by a heterogeneously hypoxic environment. Hypoxia might stimulate the malignant potential of cancer cells. The purpose of our study was to clarify the significance of hypoxia in gastric carcinoma by evaluating the expression of a hypoxic marker, namely carbonic anhydrase-9 (CA-9). <i>Methods:</i> A total of 265 patients who had undergone a resection of the primary tumor and were confirmed histologically to have sporadic gastric cancer were enrolled in this study. We evaluated the immunohistochemical expression of CA-9 in the paraffin-embedded specimens of 265 gastric adenocarcinomas. <i>Results:</i> The CA-9 expression was positive in 88 (33%) of 265 gastric carcinomas. The CA-9 expression level was significantly high in cases of type 4 carcinoma (60%, p &lt; 0.001) and diffuse type carcinoma (41%, p &lt; 0.001), and significantly correlated with the invasion depth (p &lt; 0.001), lymph node metastasis (p &lt; 0.001) and lymphatic invasion p = 0.002). The prognosis for CA-9-positive patients was significantly poorer than that of CA-9-negative patients (p = 0.003, log-rank). <i>Conclusion:</i> Hypoxia might be associated with aggressive tumor phenotypes of gastric carcinomas. The hypoxic marker CA-9 may be a useful prognostic indicator.
DOI: 10.6084/m9.figshare.5121091.v1
title: Supplementary Material for: Dynamic Nucleotide Mutation Gradients and Control Region Usage in Squamate Reptile Mitochondrial Genomes

description: Gradients of nucleotide bias and substitution rates occur in vertebrate mitochondrial genomes due to the asymmetric nature of the replication process. The evolution of these gradients has previously been studied in detail in primates, but not in other vertebrate groups. From the primate study, the strengths of these gradients are known to evolve in ways that can substantially alter the substitution process, but it is unclear how rapidly they evolve over evolutionary time or how different they may be in different lineages or groups of vertebrates. Given the importance of mitochondrial genomes in phylogenetics and molecular evolutionary research, a better understanding of how asymmetric mitochondrial substitution gradients evolve would contribute key insights into how this gradient evolution may mislead evolutionary inferences, and how it may also be incorporated into new evolutionary models. Most snake mitochondrial genomes have an additional interesting feature, 2 nearly identical control regions, which vary among different species in the extent that they are used as origins of replication. Given the expanded sampling of complete snake genomes currently available, together with 2 additional snakes sequenced in this study, we reexamined gradient strength and CR usage in alethinophidian snakes as well as several lizards that possess dual CRs. Our results suggest that nucleotide substitution gradients (and corresponding nucleotide bias) and CR usage is highly labile over the ∼200 m.y. of squamate evolution, and demonstrates greater overall variability than previously shown in primates. The evidence for the existence of such gradients, and their ability to evolve rapidly and converge among unrelated species suggests that gradient dynamics could easily mislead phylogenetic and molecular evolutionary inferences, and argues strongly that these dynamics should be incorporated into phylogenetic models.
DOI: 10.6084/m9.figshare.5121082
title: Supplementary Material for: Therapieplanung mithilfe des Interviews zur operationalisierten Fertigkeitsdiagnostik (OFD)

description: <i>Hintergrund: </i>In der Verhaltenstherapie wird sowohl mit stÖrungsspezifischen als auch mit diagnoseÜbergreifenden Interventionen gearbeitet. Letztere dienen oft dem Aufbau spezieller Fertigkeiten wie sozialer Kompetenz oder Emotionsregulation. Mit dem Interview «Operationalisierte Fertigkeitsdiagnostik zur Therapieplanung» (OFD) lassen sich sieben Fertigkeiten in vier Lebensbereichen erfassen: ProblemlÖsen, soziale Kompetenz, StressbewÄltigung, Emotionsregulation, EntspannungsfÄhigkeit, Selbstwirksamkeit, Selbstwert. <i>Patienten und Methoden: </i>In der vorliegenden Studie wurde die psychometrische QualitÄt des Interviews an einer klinischen Stichprobe (N = 111) ÜberprÜft. <i>Ergebnisse: </i>Die Ergebnisse einer frÜheren, nichtklinischen Studie ließen sich weitgehend bestÄtigen. Es ergaben sich gute ReliabilitÄten. Konfirmatorische Faktorenanalysen bestÄtigten grÖßtenteils die Struktur des Interviews. Etablierte FragebÖgen belegen weitgehend dessen ValiditÄt. ZusÄtzlich erwiesen sich die BeurteilerÜbereinstimmung und die ÄnderungssensitivitÄt als gut. <i>Schlussfolgerung: </i>Das OFD ist ein valides Instrument zur differenzierten Erfassung von Fertigkeiten, das zur Indikationsstellung eingesetzt werden kann.
DOI: 10.6084/m9.figshare.5121085
title: Supplementary Material for: Highly Conserved Asp-204 and Gly-776 Are Important for Activity of the Quinoprotein Glucose Dehydrogenase of <i>Escherichia coli</i> and for Mineral Phosphate Solubilization

description: Gram-negative bacteria membrane-bound glucose dehydrogenase (m-GDH) has pyrroloquinoline quinone [PQQ (2,7,9,-tricarboxyl-1H-pyrrolo[2,3-f]quinoline-4,5-dione)] as its prosthetic group, transferring electrons to ubiquinone (UQ) in the membrane. Based on the sequence homology of the C-terminal catalytic domain (151–796 amino acid residues) we have modeled the 3D structure of <i>Escherichia coli</i> GDH. The geometrical parameters of the homology model structure, validated using the Ramachandran plot, revealed 95.8% of residues in the allowed regions and 2.2% of the residues in disallowed regions. From the model, we have identified five different amino acids that are specifically involved in maintaining the PQQ in the correct configuration along with a Ca<sup>2+</sup> ion in the active site, and two amino acids on the surface of the protein that might be involved in UQ binding or transfer of electrons to the UQ. Site-directed mutants R201A, D204A, E217L, E217A, R266Q, R266E, E591L, E591Q, E591K, L712W, L712R, G776K, G776D and G776L lost their GDH activity, while E217Q and G776A retained their function similar to that of wild-type GDH, both in terms of specific activity and mineral phosphate solubilization. Our conclusions are consistent with those previously based on model GDH produced by a different method and using a different template X-ray structure.
DOI: 10.6084/m9.figshare.5121088
title: Supplementary Material for: Genetic Screening in Europe

description: Genetic screening has been defined as any kind of test performed systematically for the early detection or exclusion of a genetic disease, genetic predisposition or resistance to a disease, or to determine whether a person carries a gene variant that may produce disease in his or her offspring. In comparison to ‘genetic testing’, the term ‘genetic screening’ should be reserved for the explicit and systematic application of a diagnostic genetic test across a whole population of asymptomatic people (population screening) or a subset of a population such as pregnant women (prenatal/antenatal screening) or newborn infants (neonatal screening). This survey intends to present the current (2006–2008) status of genetic screening and the organization of genetic screening programmes in selected European countries as a background for future attempts to harmonize standards and procedures of genetic screening, an explicit aim of the European Network of Excellence, EuroGentest (www.eurogentest.org). Our report builds on the first comprehensive assessment of genetic screening programmes in Germany by the European Society of Human Genetics, starting with a workshop of experts in 1999, the production of background documentation in 2000, and a final report in 2003.
DOI: 10.6084/m9.figshare.5121079
title: Supplementary Material for: Standardized Reference Ideogram for Physical Mapping in the Saltwater Crocodile (<i>Crocodylus porosus</i>)

description: Basic cytogenetic data, such as diploid number and general chromosome morphology, are available for many reptilian species. Here we present a detailed cytogenetic examination of the saltwater crocodile (<i>Crocodylus porosus</i>) karyotype, including the creation of the first fully annotated G-band standard ideogram for any crocodilian species. The <i>C. porosus</i> karyotype contains macrochromosomes and has a diploid number of 34. This study presents a detailed description of each chromosome, permitting unambiguous chromosome identification. The fully annotated standardized <i>C. porosus</i> ideogram provides the backbone to a standard nomenclature system which can be used to accurately identify specific band locations. Seven microsatellite containing fosmid clones were fluorescently labeled and used as fluorescent in situ hybridization (FISH) probes for physical localization. Chromosome locations for each of these FISH probes were successfully assigned, demonstrating the utility of the fully annotated ideogram for genome mapping.
DOI: 10.6084/m9.figshare.5121076
title: Supplementary Material for: Induction of GNE in Myofibers after Muscle Injury

description: <i>Objective:</i> The aim of the present study was to clarify the expression of uridine diphospho-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) protein and mRNA in damaged or regenerating myofibers. <i>Methods:</i> We investigated the muscle expression pattern of GNE protein by immunohistochemistry using a murine model involving intramuscular injection of cardiotoxin (CTX), and the expression level of GNE mRNA by quantitative real-time polymerase chain reaction analysis of damaged or regenerating myofibers that had been collected directly from tissue sections using laser-capture microdissection. <i>Results:</i> The expression of GNE protein was increased in severely damaged myofibers as well as in regenerating myofibers with central nuclei, both of which also showed an increase in the expression of GNE mRNA. In regenerating myofibers, immunoreactivity for GNE protein in nuclei relative to that in the cytoplasm was higher at 7 days than at 4 days after CTX injection. <i>Conclusion:</i> Our findings suggest that GNE expression is induced when myofibers are damaged or regenerating, and that GNE plays a role in muscle regeneration.
DOI: 10.6084/m9.figshare.5121079.v1
title: Supplementary Material for: Standardized Reference Ideogram for Physical Mapping in the Saltwater Crocodile (<i>Crocodylus porosus</i>)

description: Basic cytogenetic data, such as diploid number and general chromosome morphology, are available for many reptilian species. Here we present a detailed cytogenetic examination of the saltwater crocodile (<i>Crocodylus porosus</i>) karyotype, including the creation of the first fully annotated G-band standard ideogram for any crocodilian species. The <i>C. porosus</i> karyotype contains macrochromosomes and has a diploid number of 34. This study presents a detailed description of each chromosome, permitting unambiguous chromosome identification. The fully annotated standardized <i>C. porosus</i> ideogram provides the backbone to a standard nomenclature system which can be used to accurately identify specific band locations. Seven microsatellite containing fosmid clones were fluorescently labeled and used as fluorescent in situ hybridization (FISH) probes for physical localization. Chromosome locations for each of these FISH probes were successfully assigned, demonstrating the utility of the fully annotated ideogram for genome mapping.
DOI: 10.6084/m9.figshare.5121088.v1
title: Supplementary Material for: Genetic Screening in Europe

description: Genetic screening has been defined as any kind of test performed systematically for the early detection or exclusion of a genetic disease, genetic predisposition or resistance to a disease, or to determine whether a person carries a gene variant that may produce disease in his or her offspring. In comparison to ‘genetic testing’, the term ‘genetic screening’ should be reserved for the explicit and systematic application of a diagnostic genetic test across a whole population of asymptomatic people (population screening) or a subset of a population such as pregnant women (prenatal/antenatal screening) or newborn infants (neonatal screening). This survey intends to present the current (2006–2008) status of genetic screening and the organization of genetic screening programmes in selected European countries as a background for future attempts to harmonize standards and procedures of genetic screening, an explicit aim of the European Network of Excellence, EuroGentest (www.eurogentest.org). Our report builds on the first comprehensive assessment of genetic screening programmes in Germany by the European Society of Human Genetics, starting with a workshop of experts in 1999, the production of background documentation in 2000, and a final report in 2003.
DOI: 10.6084/m9.figshare.5121070
title: Supplementary Material for: Yamaguchi Fox-Pigeon Imitation Test: A Rapid Test for Dementia

description: <i>Background/Aims:</i> We herein propose a hand-gesture imitation test, consisting of a simple one-handed sign of a ‘fox’ and a complex two-handed sign of a ‘pigeon’, as a rapid, game-like test for detecting dementia/Alzheimer disease (AD) with low psychological burden. The test measures the visuomotor function, which deteriorates in the early stages of AD. <i>Methods:</i> We examined 88 demented subjects, 19 with mild cognitive impairment (MCI), and 53 normal controls aged 65 years or over. The subjects were classified according to the Clinical Dementia Rating (CDR). <i>Results:</i> The specificity of the test was 94%, and the sensitivity was 58% in CDR 0.5 (MCI), 77% in CDR 1 (mild dementia), 75% in CDR 2 (moderate dementia), and 90% in CDR 3 (severe dementia). The test could be conducted within 1 min and no subjects refused to be tested. <i>Conclusion:</i> This brief hand-gesture imitation test can sensitively evaluate visuomotor deficits in dementia/AD, while some subjects are unaware of their failure or even that their cognitive function is being tested. We herein describe the precise protocol for worldwide use.
DOI: 10.6084/m9.figshare.5121073
title: Supplementary Material for: Molecular Cytogenetic Analysis of Cervical Squamous Cell Carcinoma Cells Demonstrates Discordant Levels of Numerical and Structural Chromosomal Instability and Identifies ‘Selected’ Chromosome Rearrangements

description: The processes underlying the karyotype complexity and heterogeneity characteristic of cervical squamous cell carcinoma (SCC) cells are not well understood, nor is it known which chromosome abnormalities provide a selective advantage. We used molecular cytogenetics to quantify for the first time the prevalence of all chromosomal abnormalities detectable in 8 cervical SCC cell lines. Of 225 rearrangements identified, 118 occurred frequently (≧70% metaphases) in one or more lines, indicating selection. Most of these selected rearrangements (107; 48% of the total) were included in published lists of abnormalities detected in independent cell stocks (although their significance was not previously recognised), indicating that they arose early in the establishment of the lines and were therefore most likely to have been present in the original tumours. The 8 cell lines showed 4.7- and 11.0-fold variation in levels of numerical and structural chromosomal instability (N-CIN and S-CIN) respectively, as determined by quantifying non-clonal abnormalities. We observed discordance between N-CIN and S-CIN (p = 0.148), with modal chromosome number showing a strong association with N-CIN (p = 0.007) but not with S-CIN (p = 0.602). These data imply that different mechanisms underlie N-CIN and S-CIN in cervical SCC. Despite ongoing S-CIN, newly arisen in vitro rearrangements were infrequently selected, supporting the view that selection is an important determinant of somatic evolution in malignancy. There was a positive association between numbers of non-clonal and clonal rearrangements (p = 0.002 for non-clonal vs. selected rearrangements), suggesting that factors affecting S-CIN determine the total numbers of rearrangements present in established cervical SCC cells.
DOI: 10.6084/m9.figshare.5121064
title: Supplementary Material for: An Extensive Comparison of Quantitative Trait Loci Mapping Methods

description: <i>Background:</i> The choices of study design and statistical approach for mapping a quantitative trait (QT) are of great importance. Larger sibships and a study design based upon phenotypically extreme siblings can be expected to have a greater statistical power. On the other hand, selected samples and/or deviation from normality can influence the robustness and power. Unfortunately, the effects of violation of multivariate normality assumptions and/or selected samples are only known for a limited number of methods. Some recommendations are available in the literature, but an extensive comparison of robustness and power under several different conditions is lacking. <i>Methods:</i> We compared eight freely available and commonly applied QT mapping methods in a Monte-Carlo simulation study under 36 different models and study designs (three genetic models, three selection schemes, two family structures and the possible effect of deviation from normality). <i>Results:</i> Empirical type I error fractions and empirical power are presented and explained as a whole and for each method separately, followed by a thorough discussion. <i>Conclusions:</i> The results from this extensive comparison could serve as a valuable source for the choice of the study design and the statistical approach for mapping a QT.
DOI: 10.6084/m9.figshare.5121067
title: Supplementary Material for: Using Both Cases and Controls for Testing Hardy-Weinberg Proportions in a Genetic Association Study

description: <i>Objectives:</i> Assessment of the Hardy-Weinberg proportion (HWP) in controls has been widely used as a quality control measure in case-control association studies. However, when the disease being studied is common, controls might not represent the general population, which could result in inaccurate HWP test results. Such results could lead investigators to discard important single-nucleotide polymorphisms (SNPs) that could potentially be causal. In this paper, we showed the inappropriateness of the HWP test in controls and proposed a mixture HWP (mHWP) exact test using a mixture sample that mimics the general population. <i>Methods:</i> The mHWP exact test estimates HWP in a mixture sample that is a combination of both cases and controls proportional to the prevalence of disease. We implemented a re-sampling procedure to construct mixture samples and then obtained the empirical p value of HWP in the general population. Simulation studies were performed to investigate the performance of the proposed mHWP exact test. The method was also applied to a genetic association study of obesity. <i>Results:</i> The results showed that the mHWP exact test is more likely than either the traditional HWP method in controls or the likelihood-based approach to keep causal SNPs for further analysis when the disease is more common. <i>Conclusion:</i> The mHWP exact test using a mixture sample is a better HWP test for case-control genetic association studies than the traditional HWP in controls or the likelihood-based approach, and it will improve our ability to keep causal SNPs in the case-control genetic association studies.