cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121562.v1
title: Supplementary Material for: CD22 Regulates Adaptive and Innate Immune Responses of B Cells

description: B cells sense microenvironments through the B cell receptor (BCR) and Toll-like receptors (TLRs). While signals from BCR and TLRs synergize to distinguish self from nonself, inappropriate regulation can result in development of autoimmune disease. Here we show that CD22, an inhibitory co-receptor of BCR, also negatively regulates TLR signaling in B cells. CD22-deficient <i>(Cd22</i><sup>–/–</sup><i>)</i> B cells exhibit hyperactivation in response to ligands of TLRs 3, 4 and 9. Evidence suggests that this results from impaired induction of suppressors of cytokine signaling 1 and 3, well-known suppressors of TLR signaling. Antibody-mediated sequestration of CD22 on wild-type (WT) B cells augments proliferation by TLR ligands. Conversely, expression of CD22 in a <i>Cd22</i><sup>–/–</sup> B cell line blunts responses to TLR ligands. We also show that lipopolysaccharide-induced transcription by nuclear factor-ĸB is inhibited by ectopic expression of CD22 in a TLR4 reporter cell line. Taken together, these results suggest that negative regulation of TLR signaling is an intrinsic property of CD22. Since TLRs and BCR activate B cells through different signaling pathways, and are differentially localized in B cells, CD22 exhibits a broader regulation of receptors that mediate adaptive and innate immune responses of B cells than previously recognized.
DOI: 10.6084/m9.figshare.5121544
title: Supplementary Material for: Laboratory Review: The Role of Gait Analysis in Seniors’ Mobility and Fall Prevention

description: Walking is a complex motor task generally performed automatically by healthy adults. Yet, by the elderly, walking is often no longer performed automatically. Older adults require more attention for motor control while walking than younger adults. Falls, often with serious consequences, can be the result. Gait impairments are one of the biggest risk factors for falls. Several studies have identified changes in certain gait parameters as independent predictors of fall risk. Such gait changes are often too discrete to be detected by clinical observation alone. At the Basel Mobility Center, we employ the GAITRite electronic walkway system for spatial-temporal gait analysis. Although we have a large range of indications for gait analyses and several areas of clinical research, our focus is on the association between gait and cognition. Gait analysis with walking as a single-task condition alone is often insufficient to reveal underlying gait disorders present during normal, everyday activities. We use a dual-task paradigm, walking while simultaneously performing a second cognitive task, to assess the effects of divided attention on motor performance and gait control. Objective quantification of such clinically relevant gait changes is necessary to determine fall risk. Early detection of gait disorders and fall risk permits early intervention and, in the best-case scenario, fall prevention. We and others have shown that rhythmic movement training such as Jaques-Dalcroze eurhythmics, tai chi and social dancing can improve gait regularity and automaticity, thus increasing gait safety and reducing fall risk.
DOI: 10.6084/m9.figshare.5121547
title: Supplementary Material for: Welche Stärken und Schwächen sehen Mütter mit einer gynäkologischen Krebserkrankung und gesunde Väter bei ihren Kindern?

description: <i>Hintergrund:</i> Psychische Erkrankungen bei Eltern werden als Risikofaktor für die psychische Entwicklung von Kindern angesehen. Ob und in welchem Ausmaß dies auch für ernsthafte körperliche Erkrankungen der Eltern gilt, ist bisher seltener untersucht worden. Diese Pilotstudie berichtet über die psychischen Auffälligkeiten von Kindern bei Frauen mit Brust- oder gynäkologischem Krebs. <i>Patienten und Methoden:</i> 19 Paare mit 27 Kindern im Alter zwischen 4 und 16 Jahren beantworteten zu mehreren Messzeitpunkten (T1: innerhalb von 8 Wochen nach Diagnose; T2: 3–5 Monate nach Diagnose; T3: 6 Monate nach T2; T4: 1 Jahr nach T2) einen Fragebogen zu Stärken und Schwächen des Kindes sowie zur eigenen Belastung durch die Erkrankung, dem Ausmaß sozialer Unterstützung sowie der partnerschaftlichen Bewältigung der Erkrankung. Aufgrund der geringen Fallzahlen zu T3 und T4 konzentriert sich die gegenwärtige Untersuchung auf die ersten beiden Messzeitpunkte. <i>Ergebnisse:</i> Zu jedem Messzeitpunkt schätzten beide Eltern die Kinder als überwiegend psychisch unauffällig und prosozial ein. Diejenigen Mütter, die zu T1 stärker durch die Krebserkrankung belastet waren, berichteten zu T2 auch mehr psychische Auffälligkeiten bei ihren Kindern. Dieser prospektive Zusammenhang wurde vollständig über das Ausmaß der partnerschaftlichen Bewältigung der Erkrankung zu T1 mediiert. <i>Diskussion:</i> Sollten diese Ergebnisse repliziert werden, könnten sie darauf hin weisen, dass indizierte Präventionsmaßnahmen bei Familien mit einem krebskranken Elternteil das Erleben einer manifesten psychischen Störung bei betroffenen Kindern und Jugendlichen unter Umständen verhindern. Eine Möglichkeit, die Indikation für eine solche Maßnahme zu stellen, kann in der Einschätzung der individuellen Belastung durch die Krebserkrankung und des Ausmaßes an Unterstützung innerhalb der Partnerschaft liegen.
DOI: 10.6084/m9.figshare.5121553
title: Supplementary Material for: Steroid and Ursodesoxycholic Acid Combination Therapy in Severe Drug-Induced Liver Injury

description: <i>Background:</i> Drug-induced liver injury (DILI) is the leading cause of acute severe liver disease in Western countries. Treatment strategies for DILI are still not well defined. <i>Aim:</i> We studied the safety and outcomes of steroid/ursodesoxycholic acid (UDCA) combination therapy in DILI patients. <i>Patients, Materials and Methods:</i> 15 consecutive patients with severe DILI were analyzed for clinical, biochemical and histological data. Nine patients were treated with a steroid step-down therapy with reduction of the daily dose over several weeks; 6 patients received a steroid pulse therapy for 3 days. UDCA was administered for several weeks in both groups. <i>Results:</i> Patients without histological signs of preexistent liver damage (n = 10) showed the most favorable clinical course. Bilirubin and serum transaminases dropped to &lt;50% of peak values within 2 weeks, and normalized within 4–8 weeks. In contrast, patients with positive autoimmune antibodies (anti-nuclear antibodies and/or soluble liver antigen) and/or histological features of chronic hepatitis (n = 3) exhibited a slower reduction in bilirubin and serum transaminase levels. These patients were given immunosuppressants (steroids, azathioprine) for a further 6 months. <i>Conclusion:</i> Treatment of severe DILI with corticosteroids (both pulse and step-down therapy) and UDCA appears to be safe, and leads to a more rapid reduction in bilirubin and transaminases after DILI.
DOI: 10.6084/m9.figshare.5121541
title: Supplementary Material for: Tic Disorder: An Unusual Presentation of Neurotoxoplasmosis in a Patient with AIDS

description: Movement disorders have been increasingly recognized in patients with HIV infection and may be due to distinct causes, as opportunistic infections or medication side effects for example. Parkinsonism, tremor and hemichorea have been more frequently noted in association with HIV and opportunistic infections. However, a variety of involuntary movements have already been described. We report a case of neurotoxoplasmosis in a patient with HIV infection who presented with a dystonic tic involving ocular, oral and cervical movements.
DOI: 10.6084/m9.figshare.5121547.v1
title: Supplementary Material for: Welche Stärken und Schwächen sehen Mütter mit einer gynäkologischen Krebserkrankung und gesunde Väter bei ihren Kindern?

description: <i>Hintergrund:</i> Psychische Erkrankungen bei Eltern werden als Risikofaktor für die psychische Entwicklung von Kindern angesehen. Ob und in welchem Ausmaß dies auch für ernsthafte körperliche Erkrankungen der Eltern gilt, ist bisher seltener untersucht worden. Diese Pilotstudie berichtet über die psychischen Auffälligkeiten von Kindern bei Frauen mit Brust- oder gynäkologischem Krebs. <i>Patienten und Methoden:</i> 19 Paare mit 27 Kindern im Alter zwischen 4 und 16 Jahren beantworteten zu mehreren Messzeitpunkten (T1: innerhalb von 8 Wochen nach Diagnose; T2: 3–5 Monate nach Diagnose; T3: 6 Monate nach T2; T4: 1 Jahr nach T2) einen Fragebogen zu Stärken und Schwächen des Kindes sowie zur eigenen Belastung durch die Erkrankung, dem Ausmaß sozialer Unterstützung sowie der partnerschaftlichen Bewältigung der Erkrankung. Aufgrund der geringen Fallzahlen zu T3 und T4 konzentriert sich die gegenwärtige Untersuchung auf die ersten beiden Messzeitpunkte. <i>Ergebnisse:</i> Zu jedem Messzeitpunkt schätzten beide Eltern die Kinder als überwiegend psychisch unauffällig und prosozial ein. Diejenigen Mütter, die zu T1 stärker durch die Krebserkrankung belastet waren, berichteten zu T2 auch mehr psychische Auffälligkeiten bei ihren Kindern. Dieser prospektive Zusammenhang wurde vollständig über das Ausmaß der partnerschaftlichen Bewältigung der Erkrankung zu T1 mediiert. <i>Diskussion:</i> Sollten diese Ergebnisse repliziert werden, könnten sie darauf hin weisen, dass indizierte Präventionsmaßnahmen bei Familien mit einem krebskranken Elternteil das Erleben einer manifesten psychischen Störung bei betroffenen Kindern und Jugendlichen unter Umständen verhindern. Eine Möglichkeit, die Indikation für eine solche Maßnahme zu stellen, kann in der Einschätzung der individuellen Belastung durch die Krebserkrankung und des Ausmaßes an Unterstützung innerhalb der Partnerschaft liegen.
DOI: 10.6084/m9.figshare.5121550.v1
title: Supplementary Material for: Abiotic Stress and Induced DNA Hypomethylation Cause Interphase Chromatin Structural Changes in Rice rDNA Loci

description: Global climate change, i.e. higher and more variable temperatures, and a gain in soil salinity are increasing plant stress with direct consequences on crop yield and quality levels. Rice productivity is strongly affected by abiotic stress conditions. The regulation of chromatin structure in response to environmental stress is poorly understood. We investigated the interphase chromatin organization from rice plants in non-stress versus stress conditions. We have used a cytogenetic approach, based on fluorescence in situ hybridization (FISH) with 45S, 5S rDNA and centromeric probes on rice tissue sections. The abiotic stress conditions included cold, heat and mild salinity and were applied during seed germination. In contrast to cold, saline and heat stresses caused extensive decondensation of 45S rDNA chromatin and also an increase in the distance between the 2 homologous 5S rDNA loci. 5-Azacytidine (5-AC), a DNA hypomethylating drug, greatly increased 45S rDNA chromatin decondensation and interestingly was able to induce polarization of centromeres in rice interphase nuclei. The abiotic stresses tested did not perturb the spatial position of centromeres, typically with circular arrangement around the nucleolus. The results suggest a role for chromatin plasticity in a world of climate changes.
DOI: 10.6084/m9.figshare.5121538
title: Supplementary Material for: Cloning and Targeted Disruption of Two Lipopolysaccharide Biosynthesis Genes, <i>kdsA</i> and <i>waaG</i>, of <i>Pseudomonas aeruginosa</i> PAO1 by Site-Directed Mutagenesis

description: The emergence of antibiotic resistance in bacterial pathogens poses a great challenge to public health and emphasizes the need for new antimicrobial targets. The recent development of microbial genomics and the availability of genome sequences allows for the identification of essential genes which could be novel and potential targets for antibacterial drugs. However, these predicted targets need experimental validation to confirm essentiality. Here, we report on experimental validation of a two potential targets in the lipopolysaccharide (LPS) biosynthesis pathway of the pathogen <i>Pseudomonas aeruginosa</i> PAO1 using insertion duplication. Two genes, <i>kdsA</i> and <i>waaG</i>, from LPS encoding proteins 2-dehydro-3-deoxyphosphooctonate aldolase and UDP-glucose (heptosyl) LPS α-1,3-glucosyltransferase were selected as putative target candidates for the gene disruption experiments using plasmid insertion mutagenesis to determine essentiality. The introduction of a selectable ampicillin and kanamycin resistance marker into the chromosome resulted in lack of recovery of antibiotic-resistant colonies suggesting the essentiality of these genes for the survival of <i>P. aeruginosa</i>. Several molecular analyses were carried out in order to confirm the essentiality of these genes. We propose that the above two validated drug targets are essential and can be screened for functional inhibitors for the discovery of novel therapeutic compounds against antibiotic-resistant opportunistic pathogen <i>P. aeruginosa</i>.
DOI: 10.6084/m9.figshare.5121529
title: Supplementary Material for: Gene Expression Profiles of Non-Small Cell Lung Cancer: Survival Prediction and New Biomarkers

description: <i>Objectives:</i> Despite the well-defined histological types of non-small cell lung cancer (NSCLC), a given stage is often associated with wide-ranging survival rates and treatment outcomes. This disparity has led to an increased demand for the discovery and identification of new informative biomarkers. <i>Methods:</i> In the current study, we screened 81 NSCLC samples using Illumina® whole-genome gene expression microarrays in an effort to identify differentially expressed genes and new NSCLC biomarkers. <i>Results:</i> We identified novel genes whose expression was upregulated in NSCLC, including SPAG5, POLH, KIF23, and RAD54L, which are associated with mitotic spindle formation, DNA repair, chromosome segregation, and dsDNA break repair, respectively. We also identified several novel genes whose expression was downregulated in NSCLC, including SGCG, NLRC4, MMRN1, and SFTPD, which are involved in extracellular matrix formation, apoptosis, blood vessel leakage, and inflammation, respectively. We found a significant correlation between RNA degradation and survival in adenocarcinoma cases. <i>Conclusions:</i> Even though the follow-up time was too limited to draw final conclusions, we were able to show better prediction p values in a group selection based on molecular profiles compared to histology. The current study also uncovered new candidate biomarker genes that are likely to be involved in diverse processes associated with NSCLC development.
DOI: 10.6084/m9.figshare.5121535
title: Supplementary Material for: Evolution of Atherosclerotic Carotid Plaque Morphology: Do Ulcerated Plaques Heal? A Serial Multidetector CT Angiography Study

description: <i>Background:</i> Atherosclerotic carotid plaque rupture may lead to thromboembolization, causing transient ischemic attack or ischemic stroke. Carotid plaque ulceration on angiography is associated with plaque rupture. Although healing of ruptured plaques has been described in coronary arteries, little is known about the natural development of plaque ulcerations in carotid arteries. We therefore explored the evolution of carotid plaque surface morphology with serial multidetector CT angiography (MDCTA). <i>Methods:</i> From a registry of patients with transient ischemic attack or minor ischemic stroke, we selected 83 patients who had undergone serial MDCTA of the carotid arteries. Arteries subjected to revascularization procedures between the two scans were excluded (n = 11). Plaque surface morphology was classified as smooth, irregular or ulcerated on both baseline and follow-up MDCTA. Progression (i.e. development of irregularities or ulceration) and regression (i.e. disappearance of irregularities or ulceration) in morphology were evaluated. <i>Results:</i> The mean time interval between the MDCTA scans was 21 ± 13 months. At baseline, 28 (18%) arteries were normal, 124 (80%) contained atherosclerotic plaque and 3 (2%) were occluded. Plaque surface morphology was smooth in 86 arteries (55%), irregular in 23 (15%) and ulcerated in 15 (10%). At follow-up, surface morphology was unchanged in 88% of arteries, had progressed in 8% and regressed in 4%. Most importantly, plaque morphology remained unchanged in most ulcerated plaques (10/15; 67%). One ulcerated plaque had progressed, whereas 4 had regressed. New ulcerations had developed in 2 nonulcerated plaques. <i>Conclusion:</i> MDCTA allows evaluation of temporal changes in atherosclerotic carotid plaque morphology. Plaque surface morphology remained unchanged in most arteries. Carotid ulcerations persist for a long time, and may remain a potential source of thromboembolism.
DOI: 10.6084/m9.figshare.5121538.v1
title: Supplementary Material for: Cloning and Targeted Disruption of Two Lipopolysaccharide Biosynthesis Genes, <i>kdsA</i> and <i>waaG</i>, of <i>Pseudomonas aeruginosa</i> PAO1 by Site-Directed Mutagenesis

description: The emergence of antibiotic resistance in bacterial pathogens poses a great challenge to public health and emphasizes the need for new antimicrobial targets. The recent development of microbial genomics and the availability of genome sequences allows for the identification of essential genes which could be novel and potential targets for antibacterial drugs. However, these predicted targets need experimental validation to confirm essentiality. Here, we report on experimental validation of a two potential targets in the lipopolysaccharide (LPS) biosynthesis pathway of the pathogen <i>Pseudomonas aeruginosa</i> PAO1 using insertion duplication. Two genes, <i>kdsA</i> and <i>waaG</i>, from LPS encoding proteins 2-dehydro-3-deoxyphosphooctonate aldolase and UDP-glucose (heptosyl) LPS α-1,3-glucosyltransferase were selected as putative target candidates for the gene disruption experiments using plasmid insertion mutagenesis to determine essentiality. The introduction of a selectable ampicillin and kanamycin resistance marker into the chromosome resulted in lack of recovery of antibiotic-resistant colonies suggesting the essentiality of these genes for the survival of <i>P. aeruginosa</i>. Several molecular analyses were carried out in order to confirm the essentiality of these genes. We propose that the above two validated drug targets are essential and can be screened for functional inhibitors for the discovery of novel therapeutic compounds against antibiotic-resistant opportunistic pathogen <i>P. aeruginosa</i>.
DOI: 10.6084/m9.figshare.5121541.v1
title: Supplementary Material for: Tic Disorder: An Unusual Presentation of Neurotoxoplasmosis in a Patient with AIDS

description: Movement disorders have been increasingly recognized in patients with HIV infection and may be due to distinct causes, as opportunistic infections or medication side effects for example. Parkinsonism, tremor and hemichorea have been more frequently noted in association with HIV and opportunistic infections. However, a variety of involuntary movements have already been described. We report a case of neurotoxoplasmosis in a patient with HIV infection who presented with a dystonic tic involving ocular, oral and cervical movements.
DOI: 10.6084/m9.figshare.5121523
title: Supplementary Material for: Olfactory Receptor-Related Duplicons Mediate a Microdeletion at 11q13.2q13.4 Associated with a Syndromic Phenotype

description: By array-CGH, we identified a cryptic deletion of about 3.4 Mb involving the chromosomal region 11q13.2q13.4 in a child with speech and developmental delay. Highly homologous segmental duplications related to the well-known olfactory receptor (OR)-containing clusters at 8p and 4p are located at the breakpoints of the imbalance and may be involved in its occurrence. Although these structural features are known to promote recurrent chromosomal rearrangements and previous studies had included the 11q13.2q13.4 deletion region among those considered potentially more unstable, neither deletions nor duplications of this region had been reported until now. Among the deleted genes, <i>SHANK2</i> might play a role in the phenotype of the patient since it encodes a postsynaptic scaffolding protein similar to <i>SHANK3</i>, whose haploinsufficiency is a well-known cause of severe speech delay and autistic-like behavior, and recently deletions and mutations of <i>SHANK2</i> have been described in patients with an autistic spectrum disorder or mental retardation.
DOI: 10.6084/m9.figshare.5121532
title: Supplementary Material for: Systematic Reviews of Topical Fluorides for Dental Caries: A Review of Reporting Practice

description: This paper aims to assess systematic reviews on the caries-preventive effect of topical fluorides, identifying key content and reporting quality issues to be considered by researchers planning a review in this area. Published systematic reviews and meta-analyses of any topical fluoride intervention for caries control were included. Relevant databases were searched (December 2009), along with reference lists of included publications. Thirty-eight reports were identified and assessed. A majority of these focused on the child/adolescent population, fluoride toothpastes, no treatment/placebo comparisons, and had caries increment as the main outcome. Complete reporting of eligibility criteria (PICOS) was uncommon, except in Cochrane reviews. Less than half reported searching multiple sources and only one third reported a search strategy. Duplicate study selection and data extraction was reported in 27 (71%) and 16 (42%) reviews, respectively; quality assessment of included studies was not reported in one third of the reviews. Meta-analysis was reported in 20 (52%) reviews, with six not reporting the methods of synthesis used, 17 formally assessing heterogeneity, and 12 reporting analyses for its exploration. This study shows that some content features have been covered more often than others in existing fluoride reviews, while some relevant features are yet to be addressed. Also, reporting of several methodological aspects are below an acceptable level, except for Cochrane reviews. Current reporting guidelines for systematic reviews of interventions (e.g. PRISMA) and sources of high-quality existing reviews (e.g. The Cochrane Library) should be closely followed to enhance the validity and relevance of future topical fluoride reviews.
DOI: 10.6084/m9.figshare.5121526
title: Supplementary Material for: Genome-Wide DNA Methylation Profiles in Renal Tumors of Various Histological Subtypes and Non-Tumorous Renal Tissues

description: <i>Objective:</i> The aim of this study is to clarify genome-wide DNA methylation profiles in renal tumors of various histological subtypes. <i>Methods:</i> Bacterial artificial chromosome (BAC) array-based methylated CpG island amplification was performed using tissue samples of 17 patients with papillary renal cell carcinomas (RCCs), chromophobe RCCs and oncocytomas, and the results were compared with those from 51 patients with clear cell RCCs. <i>Results:</i> Unsupervised hierarchical clustering analysis based on DNA methylation status clustered type 1 and type 2 papillary RCCs into different subclasses. Although chromophobe RCCs and oncocytomas were clustered into the same subclass, the DNA methylation status of 21 BAC clones was able to discriminate chromophobe RCCs from oncocytomas. The number of BAC clones showing DNA methylation alteration in non-tumorous renal tissue from patients with chromophobe RCCs and oncocytomas was smaller than that from patients with clear cell RCCs. Biphasic accumulation of DNA methylation alterations was observed in non-tumorous renal tissue from all 68 patients, and patients showing such alterations on more BAC clones had a poorer outcome than patients showing them on fewer BAC clones. <i>Conclusions:</i> DNA methylation profiles determining the histological subtypes of renal tumors developing in individual patients and/or patient outcome may be already established in non-tumorous renal tissue at the precancerous stage.