Medizin - Open Access LMU - Teil 20/22 Archiv

Background: Fueled by rapid progress in high-throughput sequencing, the size of public sequence databases doubles every two years. Searching the ever larger and more redundant databases is getting increasingly inefficient. Clustering can help to organize sequences into homologous and functionally similar groups and can improve the speed, sensitivity, and readability of homology searches. However, because the clustering time is quadratic in the number of sequences, standard sequence search methods are becoming impracticable. Results: Here we present a method to cluster large protein sequence databases such as UniProt within days down to 20\%-30\% maximum pairwise sequence identity. kClust owes its speed and sensitivity to an alignment-free prefilter that calculates the cumulative score of all similar 6-mers between pairs of sequences, and to a dynamic programming algorithm that operates on pairs of similar 4-mers. To increase sensitivity further, kClust can run in profile-sequence comparison mode, with profiles computed from the clusters of a previous kClust iteration. kClust is two to three orders of magnitude faster than clustering based on NCBI BLAST, and on multidomain sequences of 20\%-30\% maximum pairwise sequence identity it achieves comparable sensitivity and a lower false discovery rate. It also compares favorably to CD-HIT and UCLUST in terms of false discovery rate, sensitivity, and speed. Conclusions: kClust fills the need for a fast, sensitive, and accurate tool to cluster large protein sequence databases to below 30\% sequence identity. kClust is freely available under GPL at ftp://toolkit.lmb.uni-muenchen.de/pub/kClust/.

Background: GLP-1 is an incretine hormone which gets secreted from intestinal L-cells in response to nutritional stimuli leading to pancreatic insulin secretion and suppression of glucagon release. GLP-1 further inhibits gastric motility and reduces appetite which in conjunction improves postprandial glucose metabolism. Additional vasoprotective effects have been described for GLP-1 in experimental models. Despite these vasoprotective actions, associations between endogenous levels of GLP-1 and cardiovascular disease have yet not been investigated in humans which was the aim of the present study. Methods: GLP-1 serum levels were assessed in a cohort of 303 patients receiving coronary CT-angiography due to typical or atypical chest pain. Results: GLP-1 was found to be positively associated with total coronary plaque burden in a fully adjusted model containing age, sex, BMI, hypertension, diabetes mellitus, smoking, triglycerides, LDL-C (low density lipoprotein cholesterol), hsCRP (high-sensitive C-reactive protein), and eGFR (estimated glomerular filtration rate) (OR: 2.53 (95\% CI: 1.12 - 6.08; p = 0.03). Conclusion: Circulating GLP-1 was found to be positivity associated with coronary atherosclerosis in humans. The clinical relevance of this observation needs further investigations.

We introduce hybrid solar cells with an architecture consisting of an electrodeposited ZnO nanorod array (NRA) coated with a conformal thin layer (< 50 nm) of organic polymer-fullerene blend and a quasi-conformal Ag top contact (Thin/NR). We have compared the performance of Thin/NR cells to conventional hybrid cells in which the same NRAs are completely filled with organic blend (Thick/NR). The Thin/NR design absorbs at least as much light as Thick/NR cells, while charge extraction is significantly enhanced due to the proximity of the electrodes, resulting in a higher current density per unit volume of blend and improved power conversion efficiency. The NRAs need not be periodic or aligned and hence can be made very simply.

Background: While early programs to prevent aggression and violence are widely used, only a few controlled trials of effectiveness of psychoanalytically based prevention programs for preschoolers have been evaluated. This study compares `Faustlos' (a violence prevention program) and `Early Steps' (a psychoanalytically based, whole daycare center intervention to prevent violence) in daycare centers in socioeconomically deprived neighborhoods. Methods/Design: Preschoolers in 14 daycare centers in Frankfurt, Germany, participate in a cluster randomized controlled trial (CRCT). The daycare centers were randomly chosen from a representative baseline survey of all Frankfurt's daycare centers carried out in 2003 (n = 5,300) with the following stratifying factors: children's aggressiveness, hyperactivity, anxiety and socioeconomic status. Additionally, the geographic identification of socioeconomically deprived neighborhoods regarding low-income children was taken from the Frankfurt Municipality Statistics. Children's attachment classification and children's aggressiveness, hyperactivity, anxiety and social competence are measured as outcome criteria before and after 2 years of intervention. The programs in the study aim to reach a high-risk population. Therefore, the combination of a random sampling of daycare centers out of a representative baseline survey in all daycare centers in Frankfurt and the application of official data on the local distribution of low-income children are unique features offered by the EVA study design. Data on preschooler's attachment representations are collected in socioeconomically deprived neighborhoods for the first time.

There is an increasing interest by doctors and patients in extracorporeal shock wave therapy (ESWT) for chronic plantar fasciopathy (PF), particularly in second generation radial extracorporeal shock wave therapy (RSWT). The present review aims at serving this interest by providing a comprehensive overview on physical and medical definitions of shock waves and a detailed assessment of the quality and significance of the randomized clinical trials published on ESWT and RSWT as it is used to treat chronic PF. Both ESWT and RSWT are safe, effective, and technically easy treatments for chronic PF. The main advantages of RSWT over ESWT are the lack of need for any anesthesia during the treatment and the demonstrated long-term treatment success (demonstrated at both 6 and 12 months after the first treatment using RSWT, compared to follow-up intervals of no more than 12 weeks after the first treatment using ESWT). In recent years, a greater understanding of the clinical outcomes in ESWT and RSWT for chronic PF has arisen in relationship not only in the design of studies, but also in procedure, energy level, and shock wave propagation. Either procedure should be considered for patients 18 years of age or older with chronic PF prior to surgical intervention.

Background: Self stigma among people with mental illness results from multiple cognitive and environmental factors and processes. It can negatively affect adherence to psychiatric services, self esteem, hope, social integration and quality of life of people with mental illness. The purpose of this study was to measure the level of self stigma and its correlates among people with mental illness at Jimma University Specialized Hospital, Psychiatry clinic in southwest Ethiopia. Methods: Facility based cross-sectional study was conducted on 422 consecutive samples of people with mental illness using interviewer administered and pretested internalized stigma of mental illness (ISMI) scale. Data was entered using EPI-DATA and analysis was done using STATA software. Bivariate and multivariate linear regressions were done to identify correlates of self stigma. Results: On a scale ranging from 1 to 4, the mean self stigma score was 2.32 (SD = 0.30). Females had higher self stigma (std. beta = 0.11, P < 0.05) than males. Patients with a history of traditional treatment had higher self stigma (std. beta = 0.11, P < 0.05). There was an inverse relationship between level of education and self-stigma (std. beta = -0.17, P < 0.01). Perceived signs (std. beta = 0.13, P < 0.05) and supernatural causes of mental illness ( std. beta = 0.16, P < 0.01) were positively correlated with self stigma. Higher number of drug side effects were positively correlated (std. beta = 0.15, P < 0.05) while higher self esteem was negatively correlated (std. beta = -0.14, P < 0.01) with self stigma. Conclusions: High feeling of inferiority (alienation) but less agreement with common stereotypes (stereotype endorsement) was found. Female showed higher self stigma than male. History of traditional treatment and higher perceived supernatural explanation of mental illness were associated with higher self stigma. Drug side effects and perceived signs of mental illness were correlated with increased self stigma while education and self esteem decreased self stigma among people with mental illness. Patient empowerment psychosocial interventions and strategies to reduce drug side effects can be helpful in reducing self stigma among people with mental illnesses.

Background: Pyoderma gangrenosum (PG) is a rarely diagnosed ulcerative neutrophilic dermatosis with unknown origin that has been poorly characterized in clinical studies so far. Consequently there have been significant discussions about its associated factors and comorbidities. The aim of our multicenter study was to analyze current data from patients in dermatologic wound care centers in Germany in order to describe associated factors and comorbidities in patients with PG. Methods: Retrospective clinical investigation of patients with PG from dermatologic wound care centers in Germany. Results: We received data from 259 patients with PG from 20 different dermatologic wound care centers in Germany. Of these 142 (54.8\%) patients were female, 117 (45.2\%) were male; with an age range of 21 to 95 years, and a mean of 58 years. In our patient population we found 45.6\% with anemia, 44.8\% with endocrine diseases, 12.4\% with internal malignancies, 9.3\% with chronic inflammatory bowel diseases and 4.3\% with elevated creatinine levels. Moreover 25.5\% of all patients had a diabetes mellitus with some aspects of potential association with the metabolic syndrome. Conclusions: Our study describes one of the world's largest populations with PG. Beside the well-known association with chronic bowel diseases and neoplasms, a potentially relevant new aspect is an association with endocrine diseases, in particular the metabolic syndrome, thyroid dysfunctions and renal disorders. Our findings represent clinically relevant new aspects. This may help to describe the patients' characteristics and help to understand the underlying pathophysiology in these often misdiagnosed patients.

Aims: First, the influence of determinants on the waiting times of chronically ill patients in the ambulatory sector is investigated. The determinants are subdivided into four groups: (1) need, (2) socio-economic factors, (3) health system and (4) patient time pressures. Next, the influence of waiting times on the annual number of consultations is examined to assess whether the existing variation in waiting times influences the frequency of medical examinations. The waiting times of chronically ill patients are analysed since regular ambulatory care for this patient group could both improve treatment outcomes and lower costs. Data sources: Individual data from the 2010 Representative Survey conducted by the National Association of Statutory Health Insurance Physicians (KBV) together with regional data from the Federal Office of Construction and Regional Planning. Study design: This is a retrospective observational study. The dependent variables are waiting times in the ambulatory sector and the number of consultations of General Practitioners (GPs) and specialist physicians in the year 2010. The explanatory variables of interest are `need' and `health system' in the first model and `length of waiting times' in the second. Negative binomial models with random effects are used to estimate the incidence rate ratios of increased waiting times and number of consultations. Subsequently, the models are stratified by urban and rural areas. Results: In the pooled regression the factor `privately insured' shortens the waiting time for treatment by a specialist by approximately 28\% (about 3 days) in comparison with members of the statutory health insurance system. The category of insurance has no influence on the number of consultations of GPs. In addition, the regression results stratified by urban and rural areas show that in urban areas the factor `privately insured' reduces the waiting time for specialists by approximately 35\% (about 3.3 days) while in rural areas there is no evidence of statistical influence. In neither of the models, however, does the waiting time have a documentable effect on the number of consultations in the ambulatory sector. Conclusions: In our random sample, characteristics of the health care system have an influence on the waiting time for specialists, but the waiting time has no documentable effect on the number of consultations in the ambulatory sector. In the present analysis this applies to consultations of both GPs and specialists. Nevertheless, it does not rule out the possibility that the length of waiting times might influence the treatment outcomes of certain patient populations.

The recent release of the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) by the American Psychiatric Association has led to much debate. For this forum article, we asked BMC Medicine Editorial Board members who are experts in the field of psychiatry to discuss their personal views on how the changes in DSM-5 might affect clinical practice in their specific areas of psychiatric medicine. This article discusses the influence the DSM-5 may have on the diagnosis and treatment of autism, trauma-related and stressor-related disorders, obsessive-compulsive and related disorders, mood disorders (including major depression and bipolar disorders), and schizophrenia spectrum disorders.

Background: We report on a patient with genetically confirmed overlapping diagnoses of CMT1A and FSHD. This case adds to the increasing number of unique patients presenting with atypical phenotypes, particularly in FSHD. Even if a mutation in one disease gene has been found, further genetic testing might be warranted in cases with unusual clinical presentation. Case presentation: The reported 53 years old male patient suffered from walking difficulties and foot deformities first noticed at age 20. Later on, he developed scapuloperoneal and truncal muscle weakness, along with atrophy of the intrinsic hand and foot muscles, pes cavus, claw toes and a distal symmetric hypoesthesia. Motor nerve conduction velocities were reduced to 20 m/s in the upper extremities, and not educible in the lower extremities, sensory nerve conduction velocities were not attainable. Electromyography showed both, myopathic and neurogenic changes. A muscle biopsy taken from the tibialis anterior muscle showed a mild myopathy with some neurogenic findings and hypertrophic type 1 fibers. Whole-body muscle MRI revealed severe changes in the lower leg muscles, tibialis anterior and gastrocnemius muscles were highly replaced by fatty tissue. Additionally, fatty degeneration of shoulder girdle and straight back muscles, and atrophy of dorsal upper leg muscles were seen. Taken together, the presenting features suggested both, a neuropathy and a myopathy. Patient's family history suggested an autosomal dominant inheritance. Molecular testing revealed both, a hereditary motor and sensory neuropathy type 1A (HMSN1A, also called Charcot-Marie-Tooth neuropathy 1A, CMT1A) due to a PMP22 gene duplication and facioscapulohumeral muscular dystrophy (FSHD) due to a partial deletion of the D4Z4 locus (19 kb). Conclusion: Molecular testing in hereditary neuromuscular disorders has led to the identification of an increasing number of atypical phenotypes. Nevertheless, finding the right diagnosis is crucial for the patient in order to obtain adequate medical care and appropriate genetic counseling, especially in the background of arising curative therapies.

Background: CTL escape mutations have been described during acute hepatitis C in patients who developed chronic disease later on. Our aim was to investigate the mutual relationship between HCV specific CD8+ T cells and evolution of the viral sequence during early acute HCV infection. Results: We sequenced multiple clones of NS3 1406 epitope in 4 HLA-A{*}02 patients with acute hepatitis C genotype 1b infection. Pentamers specific for the variants were used to monitor the corresponding CD8+ T cell response. We observed outgrowth of mutations, which induced only a weak and thus potentially insufficient CD8+ T cell response. In one patient we observed outgrowth of variant epitopes with similarities to a different genotype rather than de novo mutations most probably due to a lack of responsiveness to these likely pre-existing variants. We could show that in acute hepatitis C CTL escape mutations occur much earlier than demonstrated in previous studies. Conclusions: The adaption of the virus to a new host is characterized by a high and rapid variability in epitopes under CD8+ T cell immune pressure. This adaption takes place during the very early phase of acute infection and strikingly some sequences were reduced below the limit of detection at some time points but were detected at high frequency again at later time points. Independent of the observed variability, HCV-specific CD8+ T cell responses decline and no adaption to different or new antigens during the course of infection could be detected.

Background: Neurofibromatosis type 1 (NF1) is one of the most common genetic disorders causing learning disabilities by mutations in the neurofibromin gene, an important inhibitor of the RAS pathway. In a mouse model of NF1, a loss of function mutation of the neurofibromin gene resulted in increased gamma aminobutyric acid (GABA)-mediated inhibition which led to decreased synaptic plasticity and deficits in attentional performance. Most importantly, these defictis were normalized by lovastatin. This placebo-controlled, double blind, randomized study aimed to investigate synaptic plasticity and cognition in humans with NF1 and tried to answer the question whether potential deficits may be rescued by lovastatin. Methods: In NF1 patients (n = 11; 19-44 years) and healthy controls (HC; n = 11; 19-31 years) paired pulse transcranial magnetic stimulation (TMS) was used to study intracortical inhibition (paired pulse) and synaptic plasticity (paired associative stimulation). On behavioural level the Test of Attentional Performance (TAP) was used. To study the effect of 200 mg lovastatin for 4 days on all these parameters, a placebo-controlled, double blind, randomized trial was performed. Results: In patients with NF1, lovastatin revealed significant decrease of intracortical inhibition, significant increase of synaptic plasticity as well as significant increase of phasic alertness. Compared to HC, patients with NF1 exposed increased intracortical inhibition, impaired synaptic plasticity and deficits in phasic alertness. Conclusions: This study demonstrates, for the first time, a link between a pathological RAS pathway activity, intracortical inhibition and impaired synaptic plasticity and its rescue by lovastatin in humans. Our findings revealed mechanisms of attention disorders in humans with NF1 and support the idea of a potential clinical benefit of lovastatin as a therapeutic option.

Background: Gene perturbation experiments in combination with fluorescence time-lapse cell imaging are a powerful tool in reverse genetics. High content applications require tools for the automated processing of the large amounts of data. These tools include in general several image processing steps, the extraction of morphological descriptors, and the grouping of cells into phenotype classes according to their descriptors. This phenotyping can be applied in a supervised or an unsupervised manner. Unsupervised methods are suitable for the discovery of formerly unknown phenotypes, which are expected to occur in high-throughput RNAi time-lapse screens. Results: We developed an unsupervised phenotyping approach based on Hidden Markov Models (HMMs) with multivariate Gaussian emissions for the detection of knockdown-specific phenotypes in RNAi time-lapse movies. The automated detection of abnormal cell morphologies allows us to assign a phenotypic fingerprint to each gene knockdown. By applying our method to the Mitocheck database, we show that a phenotypic fingerprint is indicative of a gene's function. Conclusion: Our fully unsupervised HMM-based phenotyping is able to automatically identify cell morphologies that are specific for a certain knockdown. Beyond the identification of genes whose knockdown affects cell morphology, phenotypic fingerprints can be used to find modules of functionally related genes.

Background: Students can improve the learning process by developing their own multiple choice questions. If a similar effect occurred when creating OSCE (objective structured clinical examination) stations by themselves it could be beneficial to involve them in the development of OSCE stations. This study investigates the effect of students developing emergency medicine OSCE stations on their test performance. Method: In the 2011/12 winter semester, an emergency medicine OSCE was held for the first time at the Faculty of Medicine at the University of Leipzig. When preparing for the OSCE, 13 students (the intervention group) developed and tested emergency medicine examination stations as a learning experience. Their subsequent OSCE performance was compared to that of 13 other students (the control group), who were parallelized in terms of age, gender, semester and level of previous knowledge using the matched-pair method. In addition, both groups were compared to 20 students who tested the OSCE prior to regular emergency medicine training (test OSCE group). Results: There were no differences between the three groups regarding age (24.3 +/- 2.6; 24.2 +/- 3.4 and 24 +/- 2.3 years) or previous knowledge (29.3 +/- 3.4; 29.3 +/- 3.2 and 28.9 +/- 4.7 points in the multiple choice {[} MC] exam in emergency medicine). Merely the gender distribution differed (8 female and 5 male students in the intervention and control group vs. 3 males and 17 females in the test OSCE group). In the exam OSCE, participants in the intervention group scored 233.4 +/- 6.3 points (mean +/- SD) compared to 223.8 +/- 9.2 points (p < 0.01) in the control group. Cohen's effect size was d = 1.24. The students of the test OSCE group scored 223.2 +/- 13.4 points. Conclusions: Students who actively develop OSCE stations when preparing for an emergency medicine OSCE achieve better exam results.