cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5127721
title: Supplementary Material for: Associations of Pre-Transplant Prescription Narcotic Use with Clinical Complications after Kidney Transplantation

description: <b><i>Background:</i></b> The impact of narcotic use before kidney transplantation on post-transplant clinical outcomes is not well described. <b><i>Methods:</i></b> We examined integrated national transplant registry, pharmacy records, and Medicare billing claims to follow 16,322 kidney transplant recipients, of whom 28.3% filled a narcotic prescription in the year before transplantation. Opioid analgesic fills were normalized to morphine equivalents (ME) and expressed as mg/kg exposures (approximate quartiles: 0.1-1.7, 1.8-5.4, 5.5-23.7, and ≥23.8 mg/kg, respectively). Post-transplant cardiovascular, respiratory, neurological, accidents, substance abuse, and noncompliance events were identified using diagnosis codes on Medicare billing claims. Adjusted associations of ME level with post-transplant complications were quantified by multivariate Cox regression. <b><i>Results:</i></b> The incidence of complications at 3 years post-transplant among those with the highest pre-transplant ME exposure compared to no use included: ventricular arrhythmias, 1.1 vs. 0.2% (p &lt; 0.001); cardiac arrest, 4.7 vs. 2.7% (p &lt; 0.05); hypotension, 14 vs. 8% (p &lt; 0.0001); hypercapnia, 1.6 vs. 0.9% (p &lt; 0.05); mental status changes, 5.3 vs. 2.7% (p &lt; 0.001); drug abuse/dependence, 7.0 vs. 1.7% (p &lt; 0.0001); alcohol abuse, 1.8 vs. 0.6% (p = 0.0001); accidents, 0.9 vs. 0.3% (p &lt; 0.05); and noncompliance, 3.5 vs. 2.3% (p &lt; 0.05). In multivariate analyses, transplant recipients with the highest level of pre-transplant narcotic use had approximately 2 to 4 times the risks of post-transplant ventricular arrhythmias, mental status changes, drug abuse, alcohol abuse, and accidents compared with non-users, and 35-45% higher risks of cardiac arrest and hypotension. <b><i>Conclusion:</i></b> Although associations may reflect underlying conditions or behaviors, high-level prescription narcotic use before kidney transplantation predicts increased risk of clinical complications after transplantation.
DOI: 10.6084/m9.figshare.5127733
title: Supplementary Material for: Impact of Karyotype Organization on Interlocus Recombination between T Cell Receptor Genes in Equidae

description: The T cell receptor (TCR) genes <i>(TRA</i>, <i>TRB</i>, <i>TRD</i> and <i>TRG)</i> reside in 3 different chromosomal regions. During the maturation of T lymphocytes, the TCR genes are rearranged by site-specific recombination, a process that also predisposes T cells to aberrant rearrangements. Illegitimate recombination between the TCR genes occurs at a low level in healthy individuals, but this frequency may correlate with the risk of lymphoma. The aim of this work was to investigate interlocus recombination in equids. Illegitimate rearrangements were studied in peripheral blood lymphocytes by FISH with painting and BAC probes and by sequencing of PCR products, and the frequencies of recombination were assessed in horses and 4 other equids. The presence of several trans-rearrangement products between the <i>TRA</i> and <i>TRG</i> genes was verified by PCR in all investigated equids. Frequencies of trans-rearrangements in horses are higher than in humans, and colocalization of the TCR genes on the same chromosome increases the incidence of trans-rearrangements between them. The orientation of the TCR genes does not impact interlocus recombination itself but does affect the viability of cells carrying its products and consequently the number of trans-rearrangements observed in lymphocytes.
DOI: 10.6084/m9.figshare.5127736.v1
title: Supplementary Material for: Fucose-Mediated Transcriptional Activation of the <b><i>fcs</i></b> Operon by FcsR in <b><i>Streptococcus pneumoniae</i></b>

description: In this study, we explore the impact of fucose on the transcriptome of <i>S. pneumoniae</i> D39. The expression of various genes and operons, including the fucose uptake PTS and utilization operon (<i>fcs</i> operon) was altered in the presence of fucose. By means of quantitative RT-PCR and β-galactosidase analysis, we demonstrate the role of the transcriptional regulator FcsR, present upstream of the <i>fcs</i> operon, as a transcriptional activator of the <i>fcs</i> operon. We also predict a 19-bp putative FcsR regulatory site (5′-ATTTGAACATTATTCAAGT-3′) in the promoter region of the <i>fcs</i> operon. The functionality of this predicted FcsR regulatory site was further confirmed by promoter-truncation experiments, where deletion of half of the FscR regulatory site or full deletion led to the abolition of expression of the <i>fcs</i> operon.
DOI: 10.6084/m9.figshare.5127724
title: Supplementary Material for: Are Group Psychotherapeutic Treatments Effective for Patients with Schizophrenia? A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Different psychotherapeutic treatments for schizophrenia are delivered in groups. However, little is known about the effectiveness of these group therapies for people with schizophrenia across different treatments with varying therapeutic orientations. This review aimed to (1) estimate the effect of different group psychotherapeutic treatments for schizophrenia and (2) explore whether any overall ‘group effect' is moderated by treatment intensity, diagnostic homogeneity and therapeutic orientation. <b><i>Methods:</i></b> A systematic search of randomised controlled trials exploring the effectiveness of group psychotherapeutic treatments for people with schizophrenia was conducted. Random-effect meta-analyses on endpoint symptom scores compared group psychotherapeutic treatments with treatment as usual and active sham groups. Findings on social functioning were described narratively, and meta-regression analyses on group characteristics were carried out. <b><i>Results:</i></b> Thirty-four eligible trials were included. A weak-to-moderate significant between-group difference in favour of group psychotherapeutic treatments was found for negative symptom scores (standard mean difference = -0.37, 95% confidence interval -0.60, -0.14; p &lt; 0.01, I<sup>2</sup> = 59.8%) only when compared to treatment as usual and not to active sham groups. Improved social functioning was reported as a treatment outcome in the majority of studies compared to treatment as usual. The ‘group effect' on negative symptoms was positively related to ‘treatment intensity' (β = 0.32, standard error = 0.121; p &lt; 0.05). <b><i>Conclusion:</i></b> Group psychotherapeutic treatments can improve negative symptoms and social functioning deficits in the treatment of schizophrenia. The effect occurs across different treatments and appears to be non-specific. Future research should identify the underlying mechanisms for the positive effect of participating in groups and explore how they can be maximised to increase the therapeutic benefit.
DOI: 10.6084/m9.figshare.5127727
title: Supplementary Material for: Genetic and Phenotypic Characteristics of <b><i>Staphylococcus aureus</i></b> Isolates from Cystic Fibrosis Patients in Austria

description: <b><i>Background:</i></b> Cystic fibrosis (CF) is the most common life-limiting inherited disease in Caucasian populations. While pathological changes can be seen in various organs, morbidity and mortality are mainly related to the respiratory tract, with patients suffering from chronic bronchopulmonary infections with characteristic pathogens including <i>Staphylococcus aureus.</i><b><i>Objectives:</i></b> To date, there is only very limited data on the genetic and phenotypic characteristics of <i>S. aureus </i>in CF patients. Therefore, in our study, we characterized 58 <i>S. aureus </i>isolates collected from CF patients in Austria by <i>spa </i>typing, DNA microarray profiling, as well as antimicrobial susceptibility testing in order to determine common genomic and antimicrobial resistance features. The tested strain collection exhibited high genomic diversity. <b><i>Results:</i></b> The 58 isolates were assigned to 16 clonal complexes and 48 <i>spa </i>types and differed greatly regarding their virulence and resistance gene profiles. The predominant clonal complexes were MLST CC30 (22%), CC15 (16%), CC45 (14%), and CC5 (12%), complexes that are highly prevalent worldwide among <i>S. aureus</i> strains isolated from humans colonized or infected with <i>S. aureus.</i> DNA microarray profiles showed a wide variety of genes encoding antimicrobial resistance and virulence factors such as various leukocidins, haemolysins, enterotoxins, exfoliative toxins, toxic shock syndrome toxin, as well as genes involved in adhesion and immune evasion. <b><i>Conclusions:</i></b> While a large number of strains exhibited resistance to one or several antimicrobial agents, methicillin-resistant <i>S. aureus</i> was found at a low prevalence of 3% (n = 2) only. The two methicillin-resistant <i>S. aureus</i> isolates were assigned to CC152/t355 (SCC<i>mec</i>V) and CC5/t001 (SCC<i>mec</i>I). This is the first study to genetically characterize <i>S. aureus</i> isolates in CF patients in Austria.
DOI: 10.6084/m9.figshare.5127718
title: Supplementary Material for: Delays in Manual Reaching Are Associated with Impaired Functional Abilities in Early Dementia Patients

description: <b><i>Background/Aims:</i></b> Recent evidence shows that early dementia patients have deficits in manual reaching tasks. It is important to understand the impact of these functional disabilities on their quality of life. The aim of this study was to investigate if there is an association between manual reaching and measures of (instrumental) activities of daily living (IADL) in a group of patients with cognitive complaints. <b><i>Methods:</i></b> The manual reaching performance of 27 patients was assessed in detail with eye and hand tracking devices. Patients were divided into three groups based on self-reported loss of IADL function. Parameters describing hand response and movement times were compared between groups. <b><i>Results:</i></b> Patients with loss of IADL function in ≥1 domain had delayed hand response and hand movement times towards visible targets compared to patients with no loss of IADL function. <b><i>Conclusion:</i></b> Delays in manual reaching movements are related to the degree of loss of IADL function in early dementia patients.
DOI: 10.6084/m9.figshare.5127721.v1
title: Supplementary Material for: Associations of Pre-Transplant Prescription Narcotic Use with Clinical Complications after Kidney Transplantation

description: <b><i>Background:</i></b> The impact of narcotic use before kidney transplantation on post-transplant clinical outcomes is not well described. <b><i>Methods:</i></b> We examined integrated national transplant registry, pharmacy records, and Medicare billing claims to follow 16,322 kidney transplant recipients, of whom 28.3% filled a narcotic prescription in the year before transplantation. Opioid analgesic fills were normalized to morphine equivalents (ME) and expressed as mg/kg exposures (approximate quartiles: 0.1-1.7, 1.8-5.4, 5.5-23.7, and ≥23.8 mg/kg, respectively). Post-transplant cardiovascular, respiratory, neurological, accidents, substance abuse, and noncompliance events were identified using diagnosis codes on Medicare billing claims. Adjusted associations of ME level with post-transplant complications were quantified by multivariate Cox regression. <b><i>Results:</i></b> The incidence of complications at 3 years post-transplant among those with the highest pre-transplant ME exposure compared to no use included: ventricular arrhythmias, 1.1 vs. 0.2% (p &lt; 0.001); cardiac arrest, 4.7 vs. 2.7% (p &lt; 0.05); hypotension, 14 vs. 8% (p &lt; 0.0001); hypercapnia, 1.6 vs. 0.9% (p &lt; 0.05); mental status changes, 5.3 vs. 2.7% (p &lt; 0.001); drug abuse/dependence, 7.0 vs. 1.7% (p &lt; 0.0001); alcohol abuse, 1.8 vs. 0.6% (p = 0.0001); accidents, 0.9 vs. 0.3% (p &lt; 0.05); and noncompliance, 3.5 vs. 2.3% (p &lt; 0.05). In multivariate analyses, transplant recipients with the highest level of pre-transplant narcotic use had approximately 2 to 4 times the risks of post-transplant ventricular arrhythmias, mental status changes, drug abuse, alcohol abuse, and accidents compared with non-users, and 35-45% higher risks of cardiac arrest and hypotension. <b><i>Conclusion:</i></b> Although associations may reflect underlying conditions or behaviors, high-level prescription narcotic use before kidney transplantation predicts increased risk of clinical complications after transplantation.
DOI: 10.6084/m9.figshare.5127727.v1
title: Supplementary Material for: Genetic and Phenotypic Characteristics of <b><i>Staphylococcus aureus</i></b> Isolates from Cystic Fibrosis Patients in Austria

description: <b><i>Background:</i></b> Cystic fibrosis (CF) is the most common life-limiting inherited disease in Caucasian populations. While pathological changes can be seen in various organs, morbidity and mortality are mainly related to the respiratory tract, with patients suffering from chronic bronchopulmonary infections with characteristic pathogens including <i>Staphylococcus aureus.</i><b><i>Objectives:</i></b> To date, there is only very limited data on the genetic and phenotypic characteristics of <i>S. aureus </i>in CF patients. Therefore, in our study, we characterized 58 <i>S. aureus </i>isolates collected from CF patients in Austria by <i>spa </i>typing, DNA microarray profiling, as well as antimicrobial susceptibility testing in order to determine common genomic and antimicrobial resistance features. The tested strain collection exhibited high genomic diversity. <b><i>Results:</i></b> The 58 isolates were assigned to 16 clonal complexes and 48 <i>spa </i>types and differed greatly regarding their virulence and resistance gene profiles. The predominant clonal complexes were MLST CC30 (22%), CC15 (16%), CC45 (14%), and CC5 (12%), complexes that are highly prevalent worldwide among <i>S. aureus</i> strains isolated from humans colonized or infected with <i>S. aureus.</i> DNA microarray profiles showed a wide variety of genes encoding antimicrobial resistance and virulence factors such as various leukocidins, haemolysins, enterotoxins, exfoliative toxins, toxic shock syndrome toxin, as well as genes involved in adhesion and immune evasion. <b><i>Conclusions:</i></b> While a large number of strains exhibited resistance to one or several antimicrobial agents, methicillin-resistant <i>S. aureus</i> was found at a low prevalence of 3% (n = 2) only. The two methicillin-resistant <i>S. aureus</i> isolates were assigned to CC152/t355 (SCC<i>mec</i>V) and CC5/t001 (SCC<i>mec</i>I). This is the first study to genetically characterize <i>S. aureus</i> isolates in CF patients in Austria.
DOI: 10.6084/m9.figshare.5127733.v1
title: Supplementary Material for: Impact of Karyotype Organization on Interlocus Recombination between T Cell Receptor Genes in Equidae

description: The T cell receptor (TCR) genes <i>(TRA</i>, <i>TRB</i>, <i>TRD</i> and <i>TRG)</i> reside in 3 different chromosomal regions. During the maturation of T lymphocytes, the TCR genes are rearranged by site-specific recombination, a process that also predisposes T cells to aberrant rearrangements. Illegitimate recombination between the TCR genes occurs at a low level in healthy individuals, but this frequency may correlate with the risk of lymphoma. The aim of this work was to investigate interlocus recombination in equids. Illegitimate rearrangements were studied in peripheral blood lymphocytes by FISH with painting and BAC probes and by sequencing of PCR products, and the frequencies of recombination were assessed in horses and 4 other equids. The presence of several trans-rearrangement products between the <i>TRA</i> and <i>TRG</i> genes was verified by PCR in all investigated equids. Frequencies of trans-rearrangements in horses are higher than in humans, and colocalization of the TCR genes on the same chromosome increases the incidence of trans-rearrangements between them. The orientation of the TCR genes does not impact interlocus recombination itself but does affect the viability of cells carrying its products and consequently the number of trans-rearrangements observed in lymphocytes.
DOI: 10.6084/m9.figshare.5127709
title: Supplementary Material for: Fasting Plasma Glucose Levels Predict Steroid-Induced Abnormal Glucose Metabolism in Patients with Non-Diabetic Chronic Kidney Disease: A Prospective Cohort Study

description: <b><i>Background/Aims:</i></b> Glucocorticoids-induced abnormal glucose metabolism (AGM) is a common medical problem in patients with non-diabetic chronic kidney disease (CKD). However, little information is available regarding the prediction of steroid-induced AGM in this patient population. <b><i>Methods:</i></b> In this prospective cohort study, we consecutively enrolled 303 non-diabetic CKD patients with fasting plasma glucose (FPG) levels &lt;5.6 mmol/l and normal oral glucose tolerance test (OGTT). OGTT was performed every 3 months during glucocorticoid treatment to identify new-onset AGM, and patients were followed for 12 months post steroid withdrawal. <b><i>Results:</i></b> During 593 person-years, there were 107 incident cases of steroid-induced AGM (18/100 person-year), including 55 (51.4%) diabetes and 52 (48.6%) pre-diabetes. In a multivariate model, each millimole increase per liter in FPG enhanced the risk of AGM by 4.6-fold (hazard ratio 4.58, 95% confidence interval, 2.67-7.83). After adjusting other risk factors, a progressively increased risk of AGM or DM was observed in patients with FPG levels ≥4.8 mmol/l, as compared with those whose levels were ≤4.3 mmol/l (p for trend &lt;0.001). Furthermore, a greater increase in FPG level (≥0.3 mmol/l) during the first 3 months of glucocorticoid treatment was associated with an increased risk for future diabetes. For predicting steroid-induced diabetes, the area under the receiver-operating characteristic curve was 0.90 for the combination of FPG and changes in FPG levels at month 3. <b><i>Conclusion:</i></b> Higher-normal FPG and a greater increase in FPG levels during glucocorticoid treatment may help to identify non-diabetic CKD patients at increased risk of steroid-induced AGM or diabetes.
DOI: 10.6084/m9.figshare.5127715
title: Supplementary Material for: SOX3 Overdosage Permits Normal Sex Development in Females with Random X Inactivation

description: Submicroscopic duplications involving <i>SOX3</i> and/or its flanking regions have been identified in 46,XX individuals both with and without disorders of sex development, raising the question whether <i>SOX3</i> overdosage is sufficient to induce testicular development in genetically female individuals. Here, we report a mother-daughter pair with female phenotypes and random X inactivation. The individuals carry complex X chromosomal rearrangements leading to a copy number gain of genomic regions involving <i>SOX3</i> and its upstream region. The amplified DNA fragments were detected at Xq27. These results provide evidence that <i>SOX3 </i>overdosage permits normal sex development in 46,XX individuals with random X inactivation.
DOI: 10.6084/m9.figshare.5127718.v1
title: Supplementary Material for: Delays in Manual Reaching Are Associated with Impaired Functional Abilities in Early Dementia Patients

description: <b><i>Background/Aims:</i></b> Recent evidence shows that early dementia patients have deficits in manual reaching tasks. It is important to understand the impact of these functional disabilities on their quality of life. The aim of this study was to investigate if there is an association between manual reaching and measures of (instrumental) activities of daily living (IADL) in a group of patients with cognitive complaints. <b><i>Methods:</i></b> The manual reaching performance of 27 patients was assessed in detail with eye and hand tracking devices. Patients were divided into three groups based on self-reported loss of IADL function. Parameters describing hand response and movement times were compared between groups. <b><i>Results:</i></b> Patients with loss of IADL function in ≥1 domain had delayed hand response and hand movement times towards visible targets compared to patients with no loss of IADL function. <b><i>Conclusion:</i></b> Delays in manual reaching movements are related to the degree of loss of IADL function in early dementia patients.
DOI: 10.6084/m9.figshare.5127706
title: Supplementary Material for: Altered Neural Activity in the Anterior and Posterior Insula in Individuals with Problematic Internet Use

description: <b><i>Background:</i></b> Individuals with problematic Internet use (PIU) are known to experience increased craving for immediate monetary reward despite long-term negative consequences. What remains unclear is whether their sensitivity to monetary loss is altered. We investigated neural alterations in brain regions involved in the anticipation of a monetary reward and loss avoidance in order to advance our understanding of the characteristics of PIU. <b><i>Methods:</i></b> A total of 11 adults with PIU and 22 age-matched controls participated in this functional magnetic resonance imaging study. Inside the scanner, participants performed a monetary incentive learning task during which they chose one of two fractal stimuli associated with monetary gain (reward trials) or avoidance of monetary loss (avoidance trials). <b><i>Results:</i></b> We found that, relative to controls, activity in the posterior insula during reward anticipation was greater in participants with PIU, whereas its activity during avoidance anticipation was reduced. No group differences in activation were found during reception phases. <b><i>Conclusions:</i></b> Given the roles of the posterior insula in the cortical representation of somatosensory arousal, our results suggest that individuals with PIU may experience more elaborate somatosensory arousal during the anticipation of monetary reward and yet experience less elaborate somatosensory arousal during the anticipation of loss avoidance compared with typical controls.
DOI: 10.6084/m9.figshare.5127712
title: Supplementary Material for: Microhomology-Mediated Microduplication in the Y Chromosomal Azoospermia Factor a Region in a Male with Mild Asthenozoospermia

description: Y chromosomal azoospermia factor (AZF) regions AZFa, AZFb and AZFc represent hotspots for copy number variations (CNVs) in the human genome; yet the number of reports of AZFa-linked duplications remains limited. Nonallelic homologous recombination has been proposed as the underlying mechanism of CNVs in AZF regions. In this study, we identified a hitherto unreported microduplication in the AZFa region in a Japanese male individual. The 629,812-bp duplication contained 22 of 46 exons of <i>USP9Y</i>, encoding the putative fine tuner of spermatogenesis, together with all exons of 3 other genes/pseudogenes. The breakpoints of the duplication resided in the DNA/TcMar-Tigger repeat and nonrepeat sequences, respectively, and were associated with a 2-bp microhomology, but not with short nucleotide stretches. The breakpoint-flanking regions were not enriched with GC content, palindromes, or noncanonical DNA structures. Semen analysis of the individual revealed a normal sperm concentration and mildly reduced sperm motility. The paternal DNA sample of the individual was not available for genetic analysis. The results indicate that CNVs in AZF regions can be generated by microhomology-mediated break-induced replication in the absence of known rearrangement-inducing DNA features. AZFa-linked microduplications likely permit production of a normal amount of sperm, although the precise clinical consequences of these CNVs await further investigation.