cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5122546.v1
title: Supplementary Material for: The GTPase Function of YvcJ and Its Subcellular Relocalization Are Dependent on Growth Conditions in Bacillus subtilis

description: We have recently shown that the <i>Bacillus subtilis</i> GTPase YvcJ is involved in the phosphorylation of an unidentified cellular component and that the deletion of <i>yvcJ</i> induced a decrease in competence efficiency. In this paper, we report that growth conditions influence both the YvcJ-dependent phosphorylation event and the localization of this protein. More precisely, we have observed that YvcJ can be localized in the cell either as a helical-like pattern or as foci close to the poles and the septa depending on growth phase and on growth medium. In addition, we show that the mutation of the catalytic lysine residue (K22) located in the Walker A motif of YvcJ, and necessary for its GTPase activity, induces a decrease in competence efficiency similar to that observed for the <i>yvcJ</i> null mutant. This mutation also inhibits the YvcJ-dependent phosphorylation event. Furthermore, a phylogenetic analysis of the YvcJ homologues shows that this protein is ancient in Bacteria (being possibly present in their last common ancestor) and has been conserved in a number of major bacterial phyla, suggesting that this protein has an important function in this domain of life. To sum up, even if the precise cellular role of this ancient protein remains unknown, our data show that the GTPase activity of <i>B. subtilis</i> YvcJ and its function in the phosphorylation of a cellular component are influenced by the growth conditions, and are important for the effect of YvcJ on competence efficiency.
DOI: 10.6084/m9.figshare.5122531
title: Supplementary Material for: Fluorofenidone Attenuates Tubulointerstitial Fibrosis by Inhibiting TGF-β1-Induced Fibroblast Activation

description: <i>Background:</i> Novel therapeutic agents are urgently needed to combat renal fibrosis. The purpose of this study was to assess, using complete unilateral ureteral obstruction (UUO) in rats, whether fluorofenidone (AKF-PD) [1-(3-fluorophenyl)-5-methyl-2-(1H)-pyridone] inhibits renal fibrosis, and to determine whether it exerts its inhibitory function on renal fibroblast activation. <i>Methods:</i> Sprague-Dawley rats were randomly divided into 3 groups: sham operation, UUO and UUO/AKF-PD (500 mg/kg/day). Renal function, tubulointerstitium damage index score, extracellular matrix (ECM) deposition, and the expressions of TGF-β<sub>1</sub>, collagen III, α-SMA, p-Smad2, p-Smad3, p-ERK1/2, p-JNK and p-p38 were measured. In addition, the expressions of α-SMA, fibronectin, CTGF, p-Smad2/3, p-ERK1/2, p-p38 and p-JNK were measured in TGF-β<sub>1</sub>-stimulated normal rat renal fibroblasts (NRK-49F). <i>Results:</i> AKF-PD treatment significantly attenuated tubulointerstitium damage, ECM deposition, the expressions of TGF-β<sub>1</sub>, collagen III, α-SMA, p-ERK1/2, p-p38 and p-JNK in vivo. In vitro, AKF-PD dose-dependently inhibited expressions of α-SMA, fibronectin and CTGF. Furthermore, AKF-PD did not inhibit Smad2/3 phosphorylation or nuclear accumulation, but rather attenuated ERK, p38 and JNK activation. <i>Conclusion:</i> AKF-PD treatment inhibits the progression of renal interstitial fibrosis in obstructed kidneys; this is potentially achieved by suppressing fibroblast activation. Therefore, AKF-PD is a special candidate for the treatment of renal fibrosis.
DOI: 10.6084/m9.figshare.5122534.v1
title: Supplementary Material for: Development of Mu Rhythm in Infants and Preschool Children

description: Mu rhythm is an idling rhythm that originates in the sensorimotor cortex during rest. The frequency of mu rhythm, which is well established in adults, is 8–12 Hz, whereas the limited results available from children suggest a frequency as low as 5.4 Hz at 6 months of age, which gradually increases to the adult value. Understanding the normal development of mu rhythm has important theoretical and clinical implications since we still know very little about this signal in infants and how it develops with age. We measured mu rhythm over the left hemisphere using a pediatric magnetoencephalography (MEG) system in 25 infants (11–47 weeks), 18 preschool children (2–5 years) and 6 adults (20–39 years) for two 5-min sessions during two intermixed conditions: a rest condition in which the hands were at rest, and a prehension condition in which the subject squeezed a pipette with his/her right hand. In all participants, mu rhythm was present over the frontoparietal area during the rest condition, but was clearly suppressed during the prehension condition. Mu rhythm peak frequency, determined from the amplitude spectra, increased rapidly as a function of age from 2.75 Hz at 11 weeks to 8.25 Hz at 47 weeks (r<sup>2</sup> = 0.83). It increased very slowly during the preschool period (3.1 ± 0.9 years; 8.5 ± 0.54 Hz). The frequency in these children was, however, lower than in adults (10.3 ± 1.2 Hz). Our results show a rapid maturation in spontaneous mu rhythm during the first year of life.
DOI: 10.6084/m9.figshare.5122525
title: Supplementary Material for: Genetic Factors Associated with Age-Related Macular Degeneration

description: Age-related macular degeneration (AMD) is a complex, multifactorial disease associated with environmental and genetic factors. This review emphasizes the clinical impact of the major genetic factors mainly located in the complement factor H gene and on the 10q26 locus, and their current and future implications for the management of AMD.
DOI: 10.6084/m9.figshare.5122528
title: Supplementary Material for: Sensitivity to Lovastatin of <i>Saccharomyces cerevisiae</i> Strains Deleted for Pleiotropic Drug Resistance (<i>PDR)</i> Genes

description: The use of statins is well established in human therapy, and model organisms such as <i>Saccharomyces cerevisiae</i> are commonly used in studies of drug action at molecular and cellular levels. The investigation of the resistance mechanisms towards statins may suggest new approaches to improve therapy based on the use of statins. We investigated the susceptibility to lovastatin of <i>S. cerevisiae</i> strains deleted for <i>PDR</i> genes, responsible for exporting hydrophobic and amphiphilic drugs, such as lovastatin. Strains deleted for the genes tested, <i>PDR1</i>, <i>PDR3</i>, <i>PDR5</i> and <i>SNQ2</i>, exhibited remarkably different phenotypes, with deletion of <i>PDR5</i> causing the highest sensitivity to lovastatin. The study helped clarifying which <i>pdr</i> mutants to use in studies of physiological actions of statins in yeast.
DOI: 10.6084/m9.figshare.5122531.v1
title: Supplementary Material for: Fluorofenidone Attenuates Tubulointerstitial Fibrosis by Inhibiting TGF-β1-Induced Fibroblast Activation

description: <i>Background:</i> Novel therapeutic agents are urgently needed to combat renal fibrosis. The purpose of this study was to assess, using complete unilateral ureteral obstruction (UUO) in rats, whether fluorofenidone (AKF-PD) [1-(3-fluorophenyl)-5-methyl-2-(1H)-pyridone] inhibits renal fibrosis, and to determine whether it exerts its inhibitory function on renal fibroblast activation. <i>Methods:</i> Sprague-Dawley rats were randomly divided into 3 groups: sham operation, UUO and UUO/AKF-PD (500 mg/kg/day). Renal function, tubulointerstitium damage index score, extracellular matrix (ECM) deposition, and the expressions of TGF-β<sub>1</sub>, collagen III, α-SMA, p-Smad2, p-Smad3, p-ERK1/2, p-JNK and p-p38 were measured. In addition, the expressions of α-SMA, fibronectin, CTGF, p-Smad2/3, p-ERK1/2, p-p38 and p-JNK were measured in TGF-β<sub>1</sub>-stimulated normal rat renal fibroblasts (NRK-49F). <i>Results:</i> AKF-PD treatment significantly attenuated tubulointerstitium damage, ECM deposition, the expressions of TGF-β<sub>1</sub>, collagen III, α-SMA, p-ERK1/2, p-p38 and p-JNK in vivo. In vitro, AKF-PD dose-dependently inhibited expressions of α-SMA, fibronectin and CTGF. Furthermore, AKF-PD did not inhibit Smad2/3 phosphorylation or nuclear accumulation, but rather attenuated ERK, p38 and JNK activation. <i>Conclusion:</i> AKF-PD treatment inhibits the progression of renal interstitial fibrosis in obstructed kidneys; this is potentially achieved by suppressing fibroblast activation. Therefore, AKF-PD is a special candidate for the treatment of renal fibrosis.
DOI: 10.6084/m9.figshare.5122516
title: Supplementary Material for: Relative Efficiency of Trend Tests with Misspecified Genetic Models in Stratified Analyses of Case-Control or Cohort Data

description: <i>Background/Aims:</i> Genetic single-nucleotide polymorphism (SNP) data are often analyzed using trend tests that rely on a specific assumption about the way that disease frequency varies across genotypes, but the validity of this assumption is not typically known. We explore the relative efficiency of trend tests in which the assumed model may or may not correspond to the true genetic model. <i>Methods:</i> We derive formulae for the asymptotic relative efficiencies (AREs) comparing tests that assume different genetic models. We consider both unstratified and stratified tests, using both case-control and cohort data. We illustrate these formulae using realistic parameters and compare the calculated AREs to simulated relative efficiencies in finite samples. <i>Results:</i> The AREs are identical for unstratified tests using case-control and cohort data, but differ for stratified tests. Loss of efficiency can be substantial, given specific combinations of high-risk allele frequencies, disease frequencies, and assumed versus actual genetic models. Given reasonably large sample sizes, asymptotic calculations align well with finite sample simulations of relative efficiency. <i>Conclusions:</i> ARE is a useful estimate of the relative efficiency of statistics using different underlying genetic models. ARE calculations reveal that additive gene doses, which are most commonly used, lead to large losses in power in some settings.
DOI: 10.6084/m9.figshare.5122519
title: Supplementary Material for: Polymorphism in a Human Chromosome-Specific Interstitial Telomere-Like Sequence at 22q11.2

description: Interstitial telomeric sequences (ITSs) are common in human. We previously reported the presence of an ITS at 22q11.2 which is in the vicinity of the genomically unstable region involved in 22q11 rearrangements. Recently, we studied the molecular status of the ITS 22q11.2 in the normal population. The amplification of an ITS at 22q11.2 showed different patterns ranging from 1–4 kb, confirming the highly polymorphic nature of this sequence. The linkage analysis of the ITS at 22q11.2 in members of 10 different families demonstrated a strong relation between offspring and parents. In contrast, the study of a DiGeorge case and his 2 parents revealed the presence of a novel allele probably inherited from the father. These results open an avenue for the use of this sequence as an allelic marker, and its implication in 22q11.2-related pathogenesis.
DOI: 10.6084/m9.figshare.5122522
title: Supplementary Material for: Relationship between Stage of Kidney Disease and Incident Heart Failure in Older Adults

description: <i>Background:</i> The relationship between stage of chronic kidney disease (CKD) and incident heart failure (HF) remains unclear. <i>Methods:</i> Of the 5,795 community-dwelling adults ≧65 years in the Cardiovascular Health Study, 5,450 were free of prevalent HF and had baseline estimated glomerular filtration rate (eGFR: ml/min/1.73 m<sup>2</sup>) data. Of these, 898 (16%) had CKD 3A (eGFR 45–59 ml/min/1.73 m<sup>2</sup>) and 242 (4%) had CKD stage ≧3B (eGFR &lt;45 ml/min/1.73 m<sup>2</sup>). Data on baseline proteinuria were not available and 4,310 (79%) individuals with eGFR ≧60 ml/min/1.73 m<sup>2</sup> were considered to have no CKD. Propensity scores estimated separately for CKD 3A and ≧3B were used to assemble two cohorts of 1,714 (857 pairs with CKD 3A and no CKD) and 557 participants (148 CKD ≧3B and 409 no CKD), respectively, balanced on 50 baseline characteristics. <i>Results:</i> During 13 years of follow-up, centrally-adjudicated incident HF occurred in 19, 24 and 38% of pre-match participants without CKD (reference), with CKD 3A [unadjusted hazard ratio (HR) 1.40; 95% confidence interval (CI) 1.20–1.63; p &lt; 0.001] and with CKD ≧3B (HR 3.37; 95% CI 2.71–4.18; p &lt; 0.001), respectively. In contrast, among matched participants, incident HF occurred in 23 and 23% of those with CKD 3A and no CKD, respectively (HR 1.03; 95% CI 0.85–1.26; p = 0.746), and 36 and 28% of those with CKD ≧3B and no CKD, respectively (HR 1.44; 95% CI 1.04–2.00; p = 0.027). <i>Conclusions:</i> Among community-dwelling older adults, CKD is a marker of incident HF regardless of stage; however, CKD ≧3B, not CKD 3A, has a modest independent association with incident HF.
DOI: 10.6084/m9.figshare.5122528.v1
title: Supplementary Material for: Sensitivity to Lovastatin of <i>Saccharomyces cerevisiae</i> Strains Deleted for Pleiotropic Drug Resistance (<i>PDR)</i> Genes

description: The use of statins is well established in human therapy, and model organisms such as <i>Saccharomyces cerevisiae</i> are commonly used in studies of drug action at molecular and cellular levels. The investigation of the resistance mechanisms towards statins may suggest new approaches to improve therapy based on the use of statins. We investigated the susceptibility to lovastatin of <i>S. cerevisiae</i> strains deleted for <i>PDR</i> genes, responsible for exporting hydrophobic and amphiphilic drugs, such as lovastatin. Strains deleted for the genes tested, <i>PDR1</i>, <i>PDR3</i>, <i>PDR5</i> and <i>SNQ2</i>, exhibited remarkably different phenotypes, with deletion of <i>PDR5</i> causing the highest sensitivity to lovastatin. The study helped clarifying which <i>pdr</i> mutants to use in studies of physiological actions of statins in yeast.
DOI: 10.6084/m9.figshare.5122516.v1
title: Supplementary Material for: Relative Efficiency of Trend Tests with Misspecified Genetic Models in Stratified Analyses of Case-Control or Cohort Data

description: <i>Background/Aims:</i> Genetic single-nucleotide polymorphism (SNP) data are often analyzed using trend tests that rely on a specific assumption about the way that disease frequency varies across genotypes, but the validity of this assumption is not typically known. We explore the relative efficiency of trend tests in which the assumed model may or may not correspond to the true genetic model. <i>Methods:</i> We derive formulae for the asymptotic relative efficiencies (AREs) comparing tests that assume different genetic models. We consider both unstratified and stratified tests, using both case-control and cohort data. We illustrate these formulae using realistic parameters and compare the calculated AREs to simulated relative efficiencies in finite samples. <i>Results:</i> The AREs are identical for unstratified tests using case-control and cohort data, but differ for stratified tests. Loss of efficiency can be substantial, given specific combinations of high-risk allele frequencies, disease frequencies, and assumed versus actual genetic models. Given reasonably large sample sizes, asymptotic calculations align well with finite sample simulations of relative efficiency. <i>Conclusions:</i> ARE is a useful estimate of the relative efficiency of statistics using different underlying genetic models. ARE calculations reveal that additive gene doses, which are most commonly used, lead to large losses in power in some settings.
DOI: 10.6084/m9.figshare.5122522.v1
title: Supplementary Material for: Relationship between Stage of Kidney Disease and Incident Heart Failure in Older Adults

description: <i>Background:</i> The relationship between stage of chronic kidney disease (CKD) and incident heart failure (HF) remains unclear. <i>Methods:</i> Of the 5,795 community-dwelling adults ≧65 years in the Cardiovascular Health Study, 5,450 were free of prevalent HF and had baseline estimated glomerular filtration rate (eGFR: ml/min/1.73 m<sup>2</sup>) data. Of these, 898 (16%) had CKD 3A (eGFR 45–59 ml/min/1.73 m<sup>2</sup>) and 242 (4%) had CKD stage ≧3B (eGFR &lt;45 ml/min/1.73 m<sup>2</sup>). Data on baseline proteinuria were not available and 4,310 (79%) individuals with eGFR ≧60 ml/min/1.73 m<sup>2</sup> were considered to have no CKD. Propensity scores estimated separately for CKD 3A and ≧3B were used to assemble two cohorts of 1,714 (857 pairs with CKD 3A and no CKD) and 557 participants (148 CKD ≧3B and 409 no CKD), respectively, balanced on 50 baseline characteristics. <i>Results:</i> During 13 years of follow-up, centrally-adjudicated incident HF occurred in 19, 24 and 38% of pre-match participants without CKD (reference), with CKD 3A [unadjusted hazard ratio (HR) 1.40; 95% confidence interval (CI) 1.20–1.63; p &lt; 0.001] and with CKD ≧3B (HR 3.37; 95% CI 2.71–4.18; p &lt; 0.001), respectively. In contrast, among matched participants, incident HF occurred in 23 and 23% of those with CKD 3A and no CKD, respectively (HR 1.03; 95% CI 0.85–1.26; p = 0.746), and 36 and 28% of those with CKD ≧3B and no CKD, respectively (HR 1.44; 95% CI 1.04–2.00; p = 0.027). <i>Conclusions:</i> Among community-dwelling older adults, CKD is a marker of incident HF regardless of stage; however, CKD ≧3B, not CKD 3A, has a modest independent association with incident HF.
DOI: 10.6084/m9.figshare.5122525.v1
title: Supplementary Material for: Genetic Factors Associated with Age-Related Macular Degeneration

description: Age-related macular degeneration (AMD) is a complex, multifactorial disease associated with environmental and genetic factors. This review emphasizes the clinical impact of the major genetic factors mainly located in the complement factor H gene and on the 10q26 locus, and their current and future implications for the management of AMD.
DOI: 10.6084/m9.figshare.5122513
title: Supplementary Material for: Functional Genomics of Tick Thioester-Containing Proteins Reveal the Ancient Origin of the Complement System

description: Ticks are important ectoparasites and vectors of multiple human and animal diseases. The obligatory hemophagy of ticks provides a formidable route for parasite transmission from one host to another. Parasite survival inside the tick relies on the ability of a pathogen to escape or inhibit tick immune defenses, but the molecular interactions between the tick and its pathogens remain poorly understood. Here we report that tick genomes are unique in that they contain all known classes of the α<sub>2</sub>-macroglobulin family (α<sub>2</sub>M-F) proteins: α<sub>2</sub>-macroglobulin pan-protease inhibitors, C3 complement components, and insect thioester-containing and macroglobulin-related proteins. By using RNA interference-mediated gene silencing in the hard tick <i>Ixodes ricinus</i> we demonstrated the central role of a C3-like molecule in the phagocytosis of bacteria and revealed nonredundant functions for α<sub>2</sub>M-F proteins. Assessment of α<sub>2</sub>M-F functions in a single organism should significantly contribute to the general knowledge on the evolution and function of the complement system. Importantly, understanding the tick immune mechanisms should provide new concepts for efficient transmission blocking of tick-borne diseases.
DOI: 10.6084/m9.figshare.5122519.v1
title: Supplementary Material for: Polymorphism in a Human Chromosome-Specific Interstitial Telomere-Like Sequence at 22q11.2

description: Interstitial telomeric sequences (ITSs) are common in human. We previously reported the presence of an ITS at 22q11.2 which is in the vicinity of the genomically unstable region involved in 22q11 rearrangements. Recently, we studied the molecular status of the ITS 22q11.2 in the normal population. The amplification of an ITS at 22q11.2 showed different patterns ranging from 1–4 kb, confirming the highly polymorphic nature of this sequence. The linkage analysis of the ITS at 22q11.2 in members of 10 different families demonstrated a strong relation between offspring and parents. In contrast, the study of a DiGeorge case and his 2 parents revealed the presence of a novel allele probably inherited from the father. These results open an avenue for the use of this sequence as an allelic marker, and its implication in 22q11.2-related pathogenesis.
DOI: 10.6084/m9.figshare.5122504
title: Supplementary Material for: Abgelehnt, ausgeschlossen, ignoriert: Die Wahrnehmung sozialer Zurückweisung und psychische Störungen – eine Übersicht

description: Dieser Artikel gibt eine Übersicht über die Bedeutung von Zurückweisungsempfindlichkeit für subklinische Syndrome und psychische Störungen. Mit Zurückweisungsempfindlichkeit wird die Disposition bezeichnet, in sozialen Situationen davon auszugehen zurückgewiesen zu werden, potenzielle soziale Zurückweisungen vorschnell wahrzunehmen und extrem darauf zu reagieren. Aus 1075 Artikeln wurden 21 extrahiert, die Zurückweisungsempfindlichkeit mit dem Rejection Sensitivity Questionnaire (RSQ) an klinischen und nichtklinischen Stichproben untersuchen und Zusammenhänge zu psychopathologischen Symptomen und psychischen Störungen herstellen. Die Ergebnisse der Forschungsbefunde geben erste Hinweise auf eine störungsübergreifende Bedeutung der Zurückweisungsempfindlichkeit sowohl für die Ätiologie als auch für die Aufrechterhaltung psychischer Probleme. Borderline-Symptome, depressive Symptomatik, soziale Ängste und aggressive Verhaltensweisen gehen mit hohen Werten der Zurückweisungsempfindlichkeit einher, während die Aufmerksamkeitsdefizit-/Hyperaktivitätsstörung (ADHS) und psychotische Symptome nicht mit Zurückweisungsempfindlichkeit korrelieren. Empfehlungen für Forschung und Praxis werden diskutiert.
DOI: 10.6084/m9.figshare.5122507
title: Supplementary Material for: Behandlungsintegrität: Implementierung, Messung, Evaluation und Zusammenhänge zum Therapieerfolg

description: Die Sicherung und Überprüfung der Behandlungsintegrität stellt eine essenzielle Voraussetzung für Wirksamkeitsanalysen in der Psychotherapieforschung dar. Die Behandlungsintegrität liefert wichtige Hinweise darüber, ob eine Behandlung so durchgeführt wurde, wie es intendiert war. Es lassen sich 3 unterschiedliche Aspekte der Behandlungsintegrität unterscheiden. Diese sind Adhärenz, Differenzierbarkeit und Kompetenz. Die vorliegende Arbeit gibt Empfehlungen zur Implementierung, Messung und Evaluation der Behandlungsintegrität. Zudem wird eine Übersicht über empirische Befunde gegeben, die einen Bezug zwischen Behandlungsintegrität und Behandlungserfolg herstellen. Es wird deutlich, dass das methodische Vorgehen, insbesondere bei Messung und Evaluation, heterogen und somit die Vergleichbarkeit der Ergebnisse erschwert ist. Dennoch findet sich für viele Studien ein direkter oder indirekter Zusammenhang zwischen Behandlungsintegrität und Behandlungserfolg. Bei nachfolgenden Studien sollten die vorliegenden Empfehlungen zur Implementierung, Messung und Evaluation der Behandlungsintegrität stärker berücksichtigt werden, um eine bessere Vergleichbarkeit der Studien zu ermöglichen.