Domains of Physical Activity in Relation to Stiffness Index in the General Population.

Background Regular exercise training represents an important modifier of arterial stiffness (AS). Therefore, sex‐specific relations between domains of physical activity (PA; commuting, domestic, and leisure‐time PA, including active sport and occupational PA) with AS were investigated. Methods and Results Stiffness index by digital photoplethysmography was investigated in 12 650 subjects from the GHS (Gutenberg Health Study). Self‐reported PA was evaluated by the “Short Questionnaire to Assess Health‐Enhancing Physical Activity” and reported as activity score peer week, being a combined measure of duration, frequency, and intensity of PA. Multivariable linear regression analysis demonstrat…

Home treatment of patients with low-risk pulmonary embolism with the oral factor Xa inhibitor rivaroxaban: Rationale and design of the HoT-PE Trial

SummaryPulmonary embolism (PE) is a potentially life-threatening acute cardiovascular syndrome. However, more than 95 % of patients are haemodynamically stable at presentation, and among them are patients at truly low risk who may qualify for immediate or early discharge. The Home Treatment of Pulmonary Embolism (HoT-PE) study is a prospective international multicentre single-arm phase 4 management (cohort) trial aiming to determine whether home treatment of acute lowrisk PE with the oral factor Xa inhibitor rivaroxaban is feasible, effective, and safe. Patients with confirmed PE, who have no right ventricular dysfunction or free floating thrombi in the right atrium or ventricle, are eligib…

Comparison between splines and fractional polynomials for multivariable model building with continuous covariates: a simulation study with continuous response

In observational studies, many continuous or categorical covariates may be related to an outcome. Various spline-based procedures or the multivariable fractional polynomial (MFP) procedure can be used to identify important variables and functional forms for continuous covariates. This is the main aim of an explanatory model, as opposed to a model only for prediction. The type of analysis often guides the complexity of the final model. Spline-based procedures and MFP have tuning parameters for choosing the required complexity. To compare model selection approaches, we perform a simulation study in the linear regression context based on a data structure intended to reflect realistic biomedica…

Coupled variable selection for regression modeling of complex treatment patterns in a clinical cancer registry.

For determining a manageable set of covariates potentially influential with respect to a time-to-event endpoint, Cox proportional hazards models can be combined with variable selection techniques, such as stepwise forward selection or backward elimination based on p-values, or regularized regression techniques such as component-wise boosting. Cox regression models have also been adapted for dealing with more complex event patterns, for example, for competing risks settings with separate, cause-specific hazard models for each event type, or for determining the prognostic effect pattern of a variable over different landmark times, with one conditional survival model for each landmark. Motivat…

Sequential (epi)genetic changes during liver cancer development and progression

The Impact of Age on the Association Between Physical Activity and White Matter Integrity in Cognitively Healthy Older Adults

Cognition emerges from coordinated processing among distributed cortical brain regions, enabled through interconnected white matter networks. Cortical disconnection caused by age-related decline in white matter integrity (WMI) is likely to contribute to age-related cognitive decline. Physical activity (PA) has been suggested to have beneficial effects on white matter structure. However, its potential to counteract age-related decline in WMI is not yet well established. The present explorative study analyzed if PA was associated with WMI in cognitively healthy older adults and if this association was modulated by age. Forty-four cognitively healthy older individuals (aged 60–88 years) with d…

ERK3/MAPK6 controls IL-8 production and chemotaxis

ERK3 is a ubiquitously expressed member of the atypical mitogen activated protein kinases (MAPKs) and the physiological significance of its short half-life remains unclear. By employing gastrointestinal 3D organoids, we detect that ERK3 protein levels steadily decrease during epithelial differentiation. ERK3 is not required for 3D growth of human gastric epithelium. However, ERK3 is stabilized and activated in tumorigenic cells, but deteriorates over time in primary cells in response to lipopolysaccharide (LPS). ERK3 is necessary for production of several cellular factors including interleukin-8 (IL-8), in both, normal and tumorigenic cells. Particularly, ERK3 is critical for AP-1 signaling…

Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data

International audience; Technical variation plays an important role in microarray-based gene expression studies, and batch effects explain a large proportion of this noise. It is therefore mandatory to eliminate technical variation while maintaining biological variability. Several strategies have been proposed for the removal of batch effects, although they have not been evaluated in large-scale longitudinal gene expression data. In this study, we aimed at identifying a suitable method for batch effect removal in a large study of microarray-based longitudinal gene expression. Monocytic gene expression was measured in 1092 participants of the Gutenberg Health Study at baseline and 5-year fol…

Stagewise pseudo-value regression for time-varying effects on the cumulative incidence

In a competing risks setting, the cumulative incidence of an event of interest describes the absolute risk for this event as a function of time. For regression analysis, one can either choose to model all competing events by separate cause-specific hazard models or directly model the association between covariates and the cumulative incidence of one of the events. With a suitable link function, direct regression models allow for a straightforward interpretation of covariate effects on the cumulative incidence. In practice, where data can be right-censored, these regression models are implemented using a pseudo-value approach. For a grid of time points, the possibly unobserved binary event s…

Additional file 9 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 9: Web Table 1B. Differentially expressed genes 4 h after exposure to low dose ionizing radiation (0.05 Gray).

The Prevalence of Amblyopia in Germany

Amblyopia is a condition in which reduced visual acuity is not directly caused by an organic defect (1). Amblyopia can develop when an infant or small child suffers from strabismus. Although both eyes are healthy, different images are formed on each fovea centralis (where vision is sharpest) and on other corresponding locations on the retina; this is in contrast to individuals without strabismus. To prevent double vision the child’s brain suppresses the image produced by one eye. Complete visual ability cannot develop in this eye during the sensitive phase of visual development (2). Approximately half of amblyopia cases (3) are caused by uncorrected higher refractive errors, which are frequ…

Vorsorge statt Nachsorge - Strukturierte Früherkennung von Leberfibrose und Leberzirrhose durch Screening der Allgemeinbevölkerung mit Hilfe des SEAL Programmes

Regularized Regression Incorporating Network Information: Simultaneous Estimation of Covariate Coefficients and Connection Signs

We develop an algorithm that incorporates network information into regression settings. It simultaneously estimates the covariate coefficients and the signs of the network connections (i.e. whether the connections are of an activating or of a repressing type). For the coefficient estimation steps an additional penalty is set on top of the lasso penalty, similarly to Li and Li (2008). We develop a fast implementation for the new method based on coordinate descent. Furthermore, we show how the new methods can be applied to time-to-event data. The new method yields good results in simulation studies concerning sensitivity and specificity of non-zero covariate coefficients, estimation of networ…

Alterations in Circulating miRNA Levels following Early-Stage Estrogen Receptor-Positive Breast Cancer Resection in Post-Menopausal Women

INTRODUCTION: Circulating microRNAs (miRNAs) exhibit remarkable stability and may serve as biomarkers in several clinical cancer settings. The aim of this study was to investigate changes in the levels of specific circulating miRNA following breast cancer surgery and evaluate whether these alterations were also observed in an independent data set.METHODS: Global miRNA analysis was performed on prospectively collected serum samples from 24 post-menopausal women with estrogen receptor-positive early-stage breast cancer before surgery and 3 weeks after tumor resection using global LNA-based quantitative real-time PCR (qPCR).RESULTS: Numbers of specific miRNAs detected in the samples ranged fro…

[IC‐P‐029]: GAUSSIAN MARKOV RANDOM FIELDS FOR ASSESSING INTERMODAL REGIONAL ASSOCIATIONS IN PRODROMAL ALZHEIMER's DISEASE

Association of ocular, cardiovascular, morphometric and lifestyle parameters with retinal nerve fibre layer thickness.

BACKGROUND Glaucoma is a neurodegenerative disease, leading to thinning of the retinal nerve fibre layer (RNFL). The exact influence of ocular, cardiovascular, morphometric, lifestyle and cognitive factors on RNFL thickness (RNFLT) is unknown and was analysed in a subgroup of the Gutenberg Health Study (GHS). METHODS Global peripapillary RNFLT was measured in 3224 eyes of 1973 subjects (49% female) using spectral-domain optical coherence tomography (SD-OCT). The association of age, sex, ocular, cardiovascular, morphometric, lifestyle and cognitive factors on RNFLT was analysed using Pearson correlation coefficient and fitting a linear mixed model. RESULTS In the univariable analysis highest…

Genetic determinants of ototoxicity during and after childhood cancer treatment: Protocol for the pancarelife study

BACKGROUND: Survival rates after childhood cancer now reach nearly 80% in developed countries. However, treatments that lead to survival and cure can cause serious adverse effects with lifelong negative impacts on survivor quality of life. Hearing impairment is a common adverse effect in children treated with cisplatin-based chemotherapy or cranial radiotherapy. Ototoxicity can extend from high-tone hearing impairment to involvement of speech frequencies. Hearing impairment can impede speech and language and neurocognitive development. Although treatment-related risk factors for hearing loss following childhood cancer treatment have been identified, the individual variability in toxicity of…

The frequent stressor and mental health monitoring-paradigm: a proposal for the operationalization and measurement of resilience and the identification of resilience processes in longitudinal observational studies

Resilience has been defined as the maintenance or quick recovery of mental health during and after times of adversity. How to operationalize resilience and to determine the factors and processes that lead to good long-term mental health outcomes in stressor-exposed individuals is a matter of ongoing debate and of critical importance for the advancement of the field. One of the biggest challenges for implementing an outcome-based definition of resilience in longitudinal observational study designs lies in the fact that real-life adversity is usually unpredictable and that its substantial qualitative as well as temporal variability between subjects often precludes defining circumscribed time …

Microglia are unique tissue phagocytes with high self-renewing capacity

PanCareLIFE

Aims: Survival after cancer diagnosed during childhood or adolescence continues to improve with new treatments and supportive therapies. Optimal long-term care requires that risks to vulnerable organs are clearly defined and translated into guidelines that are implemented into practice. PanCareLIFE is a pan-European consortium that addresses survivorship issues comprising fertility, hearing impairment and quality of life. This article describes the scientific basis of PanCareLIFE's studies.Methods: PanCareLIFE involves 17 partner institutions from eight European countries, with additional 11 data providers from five other countries. Study designs and methods include molecular genetic, cohor…

Additional file 10 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 10: Web Table 1C. Differentially expressed genes 2 h after exposure to high dose ionizing radiation (2 Gray).

Additional file 8 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 8: Web Table 1A. Differentially expressed genes 2 h after exposure to low dose ionizing radiation (0.05 Gray).

Mean Platelet Volume and Arterial Stiffness - Clinical Relationship and Common Genetic Variability

AbstractVessel wall stiffening is an important clinical parameter, but it is unknown whether platelets, key elements in the pathogenesis of arterial thrombosis, are associated with arterial stiffness. The present studies sought to determine whether mean platelet volume (MPV), a potential marker of platelet activation, is linked to vascular elasticity as assessed by the augmentation index (AIx), in 15,010 individuals from the population-based Gutenberg Health Study. Multivariable analysis showed that MPV in both males (β 0.776; 95thCI [0.250;1.16]; p = 0.0024) and females (β 0.881[0.328;1.43]; p = 0.0018) is strongly associated with AIx. Individuals with MPV and AIx above the sex-specific me…

Standalone Smartphone Cognitive Behavioral Therapy–Based Ecological Momentary Interventions to Increase Mental Health: Narrative Review

Background A growing number of psychological interventions are delivered via smartphones with the aim of increasing the efficacy and effectiveness of these treatments and providing scalable access to interventions for improving mental health. Most of the scientifically tested apps are based on cognitive behavioral therapy (CBT) principles, which are considered the gold standard for the treatment of most mental health problems. Objective This review investigates standalone smartphone-based ecological momentary interventions (EMIs) built on principles derived from CBT that aim to improve mental health. Methods We searched the MEDLINE, PsycINFO, EMBASE, and PubMed databases for peer-reviewed …

Disease Burden of Rotavirus Gastroenteritis in Children Residing in Germany: A Retrospective, Hospital-based Surveillance.

Background Representative, population-based epidemiologic data for gastroenteritis caused by rotavirus (RV) are rare. RV vaccines were first licensed in Europe in 2006 and recommended in 5 western federal states in 2008 or thereafter. This study establishes a baseline for assessing the impact of vaccination and delineates the RV disease burden in Germany today. Methods Nationwide data obtained from hospitals for children 0 to 10 years of age and transferred to the Federal Statistical Office were analyzed retrospectively. Acute gastroenteritis cases because of RV were identified by the International Classification of Diseases code (ICD-10) combined with the referring diagnosis-related group …

Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were ass…

Impact of Parkinson's disease risk loci on age at onset

Background The aim of this study was to assess whether recently identified Parkinson's disease (PD) risk genes also influence age at onset in PD. Methods We genotyped 23 single-nucleotide polymorphisms in 1,526 Danish PD patients and performed linear regression analyses with age at onset. The combined impact of PD risk loci on age at onset was assessed by linear regression analyses using a weighted genetic risk score. Results The strongest effects were observed with rs12726330 in GBA (beta = –3.63, P = 2.0 × 10−5) and rs34311866 in TMEM175/GAK (beta = –1.19, P = 4.0 × 10−3), corresponding to a 3.6-y and 1.2-y decrease of age at onset per risk allele, respectively. The weighted genetic risk …

Novel circulating microRNA signature as a potential non-invasive multi-marker test in ER-positive early-stage breast cancer:A case control study

Introduction There are currently no highly sensitive and specific minimally invasive biomarkers for detection of early‐stage breast cancer. MicroRNAs (miRNAs) are present in the circulation and may be unique biomarkers for early diagnosis of human cancers. The aim of this study was to investigate the differential expression of miRNAs in the serum of breast cancer patients and healthy controls. Methods Global miRNA analysis was performed on serum from 48 patients with ER‐positive early‐stage breast cancer obtained at diagnosis (24 lymph node‐positive and 24 lymph node‐negative) and 24 age‐matched healthy controls using LNA‐based quantitative real‐time PCR (qRT‐PCR). A signature of miRNAs was…

Development of Applications for Interactive and Reproducible Research: a Case Study

For a proper understanding of the organization and regulation of gene expression, the computational analysis is an essential component of the scientific workflow, and this is particularly true in the fields of biostatistics and bioinformatics. Interactivity and reproducibility are two highly relevant features to consider when adopting or designing a tool, and often they can not be provided simultaneously.In this work, we address the issue of developing a framework that can provide interactive analysis, in order to allow experimentalists to fully exploit advanced software tools, as well as reproducibility as an internal validation of the analysis steps, by providing the underlying code and d…

Predicting the risk of drug–drug interactions in psychiatric hospitals: a retrospective longitudinal pharmacovigilance study

ObjectivesThe aim was to use routine data available at a patient’s admission to the hospital to predict polypharmacy and drug–drug interactions (DDI) and to evaluate the prediction performance with regard to its usefulness to support the efficient management of benefits and risks of drug prescriptions.DesignRetrospective, longitudinal study.SettingWe used data from a large multicentred pharmacovigilance project carried out in eight psychiatric hospitals in Hesse, Germany.ParticipantsInpatient episodes consecutively discharged between 1 October 2017 and 30 September 2018 (year 1) or 1 January 2019 and 31 December 2019 (year 2).Outcome measuresThe proportion of rightly classified hospital epi…

Network-Constrained Covariate Coefficient and Connection Sign Estimation

Often, variables are linked to each other via a network. When such a network structure is known, this knowledge can be incorporated into regularized regression settings via a network penalty term. However, when the type of interaction via the network is unknown (that is, whether connections are of an activating or a repressing type), the connection signs have to be estimated simultaneously with the covariate coefficients. This can be done with an algorithm iterating a connection sign estimation step and a covariate coefficient estimation step. We develop such an algorithm and show detailed simulation results and an application forecasting event times. The algorithm performs well in a variet…

Targeting prohibitins with chemical ligands inhibits KRAS-mediated lung tumours.

KRAS is one of the most frequently mutated oncogenes in human non-small cell lung cancers (NSCLCs). RAS proteins trigger multiple effector signalling pathways including the highly conserved RAF-MAPK pathway. CRAF, a direct RAS effector protein, is required for KRAS-mediated tumourigenesis. Thus, the molecular mechanisms driving the activation of CRAF are intensively studied. Prohibitin 1 (PHB1) is an evolutionarily conserved adaptor protein and interaction of CRAF with PHB1 at the plasma membrane is essential for CRAF activation. Here, we demonstrate that PHB1 is highly expressed in NSCLC patients and correlates with poor survival. Targeting of PHB1 with two chemical ligands (rocaglamide an…

Morphology and Progression in Primary Varicose Vein Disorder Due to 677C>T and 1298A>C Variants of MTHFR

Background: Clinical assessment and prognostic stratification of primary varicose veins have remained controversial and the molecular pathogenesis is unknown. Previous data have suggested a contribution of the MTHFR (methylenetetrahydrofolate reductase) polymorphism c.677C>T. Methods: We collected blood and vein specimens from 159 consecutive patients undergoing varicose vein surgery, or autologous vein reconstruction for arterial occlusive disease as controls. We compared the frequencies of c.677C>T and another polymorphism of MTHFR, c.1298A>C, with morphology and types of complicated disease. Morphology was recorded as a trunk or perforator type and peripheral congestive complication was …

Myopia and Cognitive Performance: Results From the Gutenberg Health Study.

Purpose To analyze the association between myopia and cognitive performance. Methods A cohort of the population-based Gutenberg Health Study included 3819 eligible enrollees between 40 and 79 years. We used the Tower of London (TOL) test to assess cognitive performance. Myopia was defined as a spherical equivalent (SE) ≤ -0.5 diopters (D) via noncycloplegic autorefractometry. We conducted linear mixed models with the SE as the dependent variable and the age, sex, duration of education, and TOL score as covariates. Results Complete data were available for 3452 participants (90.4%). The mean TOL score was 14.0 ± 3.9 in the myopes versus 12.9 ± 4.0 in the nonmyopes (P < 0.001). The mean TOL sc…

Thrombin generation in cardiovascular disease and mortality – results from the Gutenberg Health Study

Thrombin generation may be a potential tool to improve risk stratification for cardiovascular diseases. The aim of this study was to explore the relation between thrombin generation and cardiovascular risk factors, cardiovascular diseases, and total mortality. For this study, 5,000 subjects from the population-based Gutenberg Health Study were analyzed in a highly standardized setting. Thrombin generation was assessed by the Calibrated Automated Thrombogram method at 1 and 5 pM tissue factor triggers in platelet-poor plasma. Lag time, endogenous thrombin potential, and peak height were derived from the thrombin generation curve. Sex-specific multivariable linear regression analysis adjusted…

Individualizing deep dynamic models for psychological resilience data

ABSTRACTDeep learning approaches can uncover complex patterns in data. In particular, variational autoencoders (VAEs) achieve this by a non-linear mapping of data into a low-dimensional latent space. Motivated by an application to psychological resilience in the Mainz Resilience Project (MARP), which features intermittent longitudinal measurements of stressors and mental health, we propose an approach for individualized, dynamic modeling in this latent space. Specifically, we utilize ordinary differential equations (ODEs) and develop a novel technique for obtaining person-specific ODE parameters even in settings with a rather small number of individuals and observations, incomplete data, an…

Distribution of Anterior Chamber Angle Width and Correlation With Age, Refraction, and Anterior Chamber Depth—The Gutenberg Health Study

PURPOSE Scheimpflug imaging allows quantitative analysis of the width of the anterior chamber angle. We report the population-based distribution of the anterior chamber angle width using this noncontact imaging technique and investigate associated factors. METHODS A population-based cross-sectional study was carried out in Germany. A comprehensive ophthalmologic examination including refraction, biometry, and Scheimpflug imaging was performed. Automated measurement of the anterior chamber angle was performed in each anterior chamber quadrant. Exclusion criteria were previous ocular surgery or inadequate image quality. Association analyses were carried out to determine independently associat…

Platelet micro-RNA expression in type 2 diabetes mellitus

Additional file 2 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 2: Web Figure 7. Shared pathways from low and high dose ionizing radiation experiments. Gy = Gray. Web Figure 8. Pathways only affected in high dose ionizing radiation experiments. Gy = Gray.

Quality of life in Parkinson's disease patients with motor fluctuations and dyskinesias in five European countries.

Little is known about the relationship between specific subtypes of treatment-associated motor complications and different domains of health-related Quality of Life (QoL) in patients with Parkinson's disease (PD). Larger studies that investigate these aspects within a cross-cultural setting are scarce.To assess QoL and its association with on-off fluctuations, peak-dose dyskinesias, biphasic dyskinesias, and off-dystonias in PD patients from five European countries.Data from 817 PD patients were collected cross-sectionally in France, Germany, Italy, Spain, and the UK. QoL was measured with the generic EuroQoL 5-Dimension questionnaire (EQ-5D) and the disease-specific Parkinson's Disease Que…

Polypharmacy and the risk of drug-drug interactions and potentially inappropriate medications in hospital psychiatry.

PURPOSE The aim of this study was to analyze the epidemiology of polypharmacy in hospital psychiatry. Another aim was to investigate predictors of the number of drugs taken and the associated risks of drug-drug interactions and potentially inappropriate medications in the elderly. METHODS Daily prescription data were obtained from a pharmacovigilance project sponsored by the Innovations Funds of the German Federal Joint Committee. RESULTS The study included 47 071 inpatient hospital cases from eight different study centers. The mean number of different drugs during the entire stay was 6.1 (psychotropic drugs = 2.7; others = 3.4). The mean number of drugs per day was 3.8 (psychotropic drugs …

e-Health-based management of patients receiving oral anticoagulation therapy: results from the observational thrombEVAL study

Essentials e-Health based health care by an expert centre may advance management of oral anticoagulation. Outcome of patients was compared between an e-health based coagulation service and regular care. Patients in the coagulation service cohort experienced a significantly better clinical outcome. Lower risk for adverse events was related to anticoagulation-specific and non-specific outcome. SummaryBackground Management of oral anticoagulation (OAC) therapy is essential to minimize adverse events in patients receiving vitamin K-antagonists (VKAs). Data on the effect of e-health-based anticoagulation management systems on the clinical outcome of OAC patients are limited. Objectives To compar…

Deconstructing and reconstructing resilience: a dynamic network approach

Resilience is still often viewed as a unitary personality construct that, as a kind of anti-nosological entity, protects individuals against stress-related mental problems. However, increasing evidence indicates that the maintenance of mental health in the face of adversity results from complex and dynamic processes of adaptation to stressors that involve the activation of several separable protective factors. Such resilience factors can reside at biological, psychological and social levels and may include stable predispositions (such as genotype or personality traits) and malleable properties, skills, capacities or external circumstances (such as gene expression patterns, emotion regulatio…

Pharmacotherapy, drug-drug interactions and potentially inappropriate medication in depressive disorders.

Introduction The aim of this study was to describe the number and type of drugs used to treat depressive disorders in inpatient psychiatry and to analyse the determinants of potential drug-drug interactions (pDDI) and potentially inappropriate medication (PIM). Methods Our study was part of a larger pharmacovigilance project funded by the German Innovation Funds. It included all inpatients with a main diagnosis in the group of depressive episodes (F32, ICD-10) or recurrent depressive disorders (F33) discharged from eight psychiatric hospitals in Germany between 1 October 2017 and 30 September 2018 or between 1 January and 31 December 2019. Results The study included 14,418 inpatient cases.…

Identifying Prognostic SNPs in Clinical Cohorts: Complementing Univariate Analyses by Resampling and Multivariable Modeling

Clinical cohorts with time-to-event endpoints are increasingly characterized by measurements of a number of single nucleotide polymorphisms that is by a magnitude larger than the number of measurements typically considered at the gene level. At the same time, the size of clinical cohorts often is still limited, calling for novel analysis strategies for identifying potentially prognostic SNPs that can help to better characterize disease processes. We propose such a strategy, drawing on univariate testing ideas from epidemiological case-controls studies on the one hand, and multivariable regression techniques as developed for gene expression data on the other hand. In particular, we focus on …

Cluster-Localized Sparse Logistic Regression for SNP Data

The task of analyzing high-dimensional single nucleotide polymorphism (SNP) data in a case-control design using multivariable techniques has only recently been tackled. While many available approaches investigate only main effects in a high-dimensional setting, we propose a more flexible technique, cluster-localized regression (CLR), based on localized logistic regression models, that allows different SNPs to have an effect for different groups of individuals. Separate multivariable regression models are fitted for the different groups of individuals by incorporating weights into componentwise boosting, which provides simultaneous variable selection, hence sparse fits. For model fitting, th…

Additional file 3 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 3: Web Figure 9. Predicted downsteam diseases and functions. Web Figure 10. Predicted upstream regulators. LDIR = Low dose of ionizing radiation (0.05 Gray), HDIR = High dose of ionizing radiation (2 Gray).

Depression, Anxiety and Quality of Life in Long-Term Survivors of Malignant Melanoma: A Register-Based Cohort Study

Aim The purpose of the study was to determine anxiety and depression, quality of life, and their determinants in long-term survivors of malignant melanoma. Methods In a state cancer registry a cohort of survivors of malignant melanoma was contacted via the physician registered. Of 1302 contactable patients, 689 (52.2%) completed a questionnaire including the Patient Health Questionnaire with generalized anxiety (GAD-7) and depression (PHQ-9) and the EORTC Quality of Life Questionnaire (EORTC QLQ 30). Based on multiple regression analysis, predictors of quality of life and distress were identified. Comparison data were assessed in two waves of representative face-to-face household surveys of…

Large platelets but not putative endothelial progenitor cells are associated with low strut coverage after drug-eluting stent implantation

Objectives This study assessed whether different subsets of circulating endothelial and putative endothelial progenitor cells (CEC and EPC) correlate with stent strut coverage (SSC) using second generation optical coherence tomography (OCT). Background Due to the lack of imaging modalities with a resolution down to the magnitude of a few cells, the influence of EPC on endothelialisation of drug-eluting stents has not been assessed in patients. Methods In 37 patients, SSC of everolimus-eluting stents was assessed by OCT 5-7months after stent implantation. Different subsets of EPC (CD34(+)KDR(+), CD34(+)KDR(+)CD45(dim), CD133(+), CD3(+)CD31(+)), CEC (CD31(+)CD45(-)CD146(+)), and CD31(+)CD45(-…

Effect of nighttime aircraft noise exposure on endothelial function and stress hormone release in healthy adults.

Aims Aircraft noise disturbs sleep, and long-term exposure has been shown to be associated with increases in the prevalence of hypertension and an overall increased risk for myocardial infarction. The exact mechanisms responsible for these cardiovascular effects remain unclear. Methods and results We performed a blinded field study in 75 healthy volunteers (mean age 26 years), who were exposed at home, in random order, to one control pattern (no noise) and two different noise scenarios [30 or 60 aircraft noise events per night with an average maximum sound pressure level (SPL) of 60 dB(A)] for one night each. We performed polygraphy during each study night. Noise caused a worsening in sleep…

Noise annoyance is associated with depression and anxiety in the general population : the contribution of aircraft noise

BACKGROUND: While noise annoyance has become recognized as an important environmental stressor, its association to mental health has hardly been studied. We therefore determined the association of noise annoyance to anxiety and depression and explored the contribution of diverse environmental sources to overall noise annoyance. PATIENTS AND METHODS: We investigated cross-sectional data of n = 15.010 participants of the Gutenberg Health Study (GHS), a population-based, prospective, single-center cohort study in Mid-Germany (age 35 to 74 years). Noise annoyance was assessed separately for road traffic, aircraft, railways, industrial, neighborhood indoor and outdoor noise ("during the day"; "i…

Genome-wide significant association with seven novel multiple sclerosis risk loci

Objective A recent large-scale study in multiple sclerosis (MS) using the ImmunoChip platform reported on 11 loci that showed suggestive genetic association with MS. Additional data in sufficiently sized and independent data sets are needed to assess whether these loci represent genuine MS risk factors. Methods The lead SNPs of all 11 loci were genotyped in 10 796 MS cases and 10 793 controls from Germany, Spain, France, the Netherlands, Austria and Russia, that were independent from the previously reported cohorts. Association analyses were performed using logistic regression based on an additive model. Summary effect size estimates were calculated using fixed-effect meta-analysis. Results…

Psychological interventions for resilience enhancement in adults

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: To assess the effects of resilience‐enhancing interventions in clinical and non‐clinical populations.

Dabigatran after Short Heparin Anticoagulation for Acute Intermediate-Risk Pulmonary Embolism: Rationale and Design of the Single-Arm PEITHO-2 Study

AbstractPatients with intermediate-risk pulmonary embolism (PE) may, depending on the method and cut-off values used for definition, account for up to 60% of all patients with PE and have an 8% or higher risk of short-term adverse outcome. Although four non-vitamin K-dependent direct oral anticoagulants (NOACs) have been approved for the treatment of venous thromboembolism, their safety and efficacy as well as the optimal anticoagulation regimen using these drugs have not been systematically investigated in intermediate-risk PE. Moreover, it remains unknown how many patients with intermediate-high-risk and intermediate-low-risk PE were included in most of the phase III NOAC trials. The ongo…

Prevalence and risk factors of retinal vein occlusion: the Gutenberg Health Study.

SummaryObjective To determine the age- and sex-specific prevalence and determinants of retinal vein occlusions (RVOs) in a large population-based German cohort. Methods The investigation included 15 010 participants (aged 35–74 years) from the Gutenberg Health Study. We determined the prevalence of RVO (central retinal vein occlusion [CRVO] and branch retinal vein occlusion [BRVO]) for the local population by assessing fundus photographs of 12 954 (86.3%; 49.8% women and 50.2% men) participants. Further, we analyzed the associations of RVO with cardiovascular, anthropometric, and ophthalmic parameters. Results The weighted prevalences of RVO, CRVO, and BRVO were 0.40%, 0.08%, and 0.32%, res…

Additional file 1 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 1: Web Figure 1. Representative measurements of the cell cycle distribution of HOECHST33258-stained fibroblasts by flow cytometry during (A) log-phase growth or (B) after G0/1 synchronization over 14 days for radiation experiments. Web Figure 2. Total number of differentially expressed genes in human fibroblasts from cancer free-controls at 0.25 h, 2 h and 24 h after exposure to low (0.05 Gray (Gy)) or high dose (2Gy) of X-rays compared to unirradiated fibroblasts (N = 3). Web Figure 3. Correlation of RNA quality metrics (RIN, Qbit RNA-concentration), expression variation (PC1–3) and number of aligned reads (aligned reads, aligned reads normalized) for all experiments. The c…

Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Abstract Background Exposure to ionizing radiation induces complex stress responses in cells, which can lead to adverse health effects such as cancer. Although a variety of studies investigated gene expression and affected pathways in human fibroblasts after exposure to ionizing radiation, the understanding of underlying mechanisms and biological effects is still incomplete due to different experimental settings and small sample sizes. Therefore, this study aims to identify the time point with the highest number of differentially expressed genes and corresponding pathways in primary human fibroblasts after irradiation at two preselected time points. Methods Fibroblasts from skin biopsies of…

Non-invasive peripheral vascular function, incident cardiovascular disease, and mortality in the general population

AIMS Evidence suggests that peripheral vascular function is related to cardiovascular disease (CVD) and mortality. We evaluated the associations of noninvasive measures of flow-mediated dilatation and peripheral arterial tonometry with incident CVD and mortality. METHODS AND RESULTS In a post-hoc analysis of the community-based Gutenberg Health Study, median age 55 years (25th/75th percentile 46/65) and 49.5% women, we measured brachial artery flow-mediated dilatation (N = 12,599) and fingertip peripheral arterial tonometry (N = 11,125). After a follow-up of up to 11.7 years, we observed 595 incident CVD events, 106 cardiac deaths, and 860 deaths in total. Survival curves showed decreased e…

Partitioned learning of deep Boltzmann machines for SNP data.

Abstract Motivation Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. Results After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning. We propose a sparse regression approach to coarsely screen…

Reduced-Dose Intravenous Thrombolysis for Acute Intermediate–High-risk Pulmonary Embolism: Rationale and Design of the Pulmonary Embolism International THrOmbolysis (PEITHO)-3 trial

Intermediate-high-risk pulmonary embolism (PE) is characterized by right ventricular (RV) dysfunction and elevated circulating cardiac troponin levels despite apparent hemodynamic stability at presentation. In these patients, full-dose systemic thrombolysis reduced the risk of hemodynamic decompensation or death but increased the risk of life-threatening bleeding. Reduced-dose thrombolysis may be capable of improving safety while maintaining reperfusion efficacy. The Pulmonary Embolism International THrOmbolysis (PEITHO)-3 study (ClinicalTrials.gov Identifier: NCT04430569) is a randomized, placebo-controlled, double-blind, multicenter, multinational trial with long-term follow-up. We will c…

Feasibility and utility of a cognitive screening for risk stratification in hospitalized older patients

OBJECTIVES To determine whether the Mini-Cog can be applied by nursing staff to hospitalized elderly patients for cognitive impairment associated risk stratification. METHODS This explorative prospective multicenter cohort study was carried out among 2522 patients aged 70 and older, hospitalized due to physical illness in eight hospitals in Rhineland-Palatinate, Germany. All patients were asked to conduct the Mini-Cog at the day of admission and were clustered into low-performance, intermediate-performance, and good-performance categories by trained nursing staff and two experienced geronto-psychiatrists as gold standard. Complications in the course of the treatment were monitored. RESULTS …

A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration

Genome-wide association studies have previously identified 23 genetic loci associated with circulating fibrinogen concentration. These studies used HapMap imputation and did not examine the X-chromosome. 1000 Genomes imputation provides better coverage of uncommon variants, and includes indels. We conducted a genome-wide association analysis of 34 studies imputed to the 1000 Genomes Project reference panel and including similar to 120 000 participants of European ancestry (95 806 participants with data on the X-chromosome). Approximately 10.7 million single-nucleotide polymorphisms and 1.2 million indels were examined. We identified 41 genome-wide significant fibrinogen loci ; of which, 18 …

Big Data in Medical Science–a Biostatistical View

Big data” is a universal buzzword in business and science, referring to the retrieval and handling of ever-growing amounts of information. It can be assumed, for example, that a typical hospital generates hundreds of terabytes (1 TB = 1012 bytes) of data annually in the course of patient care (1). For instance, exome sequencing, which results in 5 gigabytes (1 GB = 109 bytes) of data per patient, is on the way to becoming routine (2). The analysis of such enormous volumes of information, i.e., organization and description of the data and the drawing of (scientifically valid) conclusions, can already hardly be accomplished with the traditional tools of computer science and statistics. For ex…

2861Role of glycemic state for the relationship between abdominal obesity and markers of inflammation and hemostasis in the population

What subject matter questions motivate the use of machine learning approaches compared to statistical models for probability prediction?

This is a discussion of the following papers: "Probability estimation with machine learning methods for dichotomous and multicategory outcome: Theory" by Jochen Kruppa, Yufeng Liu, Gerard Biau, Michael Kohler, Inke R. Konig, James D. Malley, and Andreas Ziegler; and "Probability estimation with machine learning methods for dichotomous and multicategory outcome: Applications" by Jochen Kruppa, Yufeng Liu, Hans-Christian Diener, Theresa Holste, Christian Weimar, Inke R. Konig, and Andreas Ziegler.

Pitfalls of hypothesis tests and model selection on bootstrap samples: Causes and consequences in biometrical applications

The bootstrap method has become a widely used tool applied in diverse areas where results based on asymptotic theory are scarce. It can be applied, for example, for assessing the variance of a statistic, a quantile of interest or for significance testing by resampling from the null hypothesis. Recently, some approaches have been proposed in the biometrical field where hypothesis testing or model selection is performed on a bootstrap sample as if it were the original sample. P-values computed from bootstrap samples have been used, for example, in the statistics and bioinformatics literature for ranking genes with respect to their differential expression, for estimating the variability of p-v…

Psychological interventions to foster resilience in healthcare professionals.

Background Resilience can be defined as the maintenance or quick recovery of mental health during or after periods of stressor exposure, which may result from a potentially traumatising event, challenging life circumstances, a critical life transition phase, or physical illness. Healthcare professionals, such as nurses, physicians, psychologists and social workers, are exposed to various work-related stressors (e.g. patient care, time pressure, administration) and are at increased risk of developing mental disorders. This population may benefit from resilience-promoting training programmes. Objectives To assess the effects of interventions to foster resilience in healthcare professionals, t…

On stability issues in deriving multivariable regression models

In many areas of science where empirical data are analyzed, a task is often to identify important variables with influence on an outcome. Most often this is done by using a variable selection strategy in the context of a multivariable regression model. Using a study on ozone effects in children (n = 496, 24 covariates), we will discuss aspects relevant for deriving a suitable model. With an emphasis on model stability, we will explore and illustrate differences between predictive models and explanatory models, the key role of stopping criteria, and the value of bootstrap resampling (with and without replacement). Bootstrap resampling will be used to assess variable selection stability, to d…

PREVALENCE AND ASSOCIATIONS OF MYELINATED RETINAL NERVE FIBERS

PURPOSE To determine the prevalence, ocular, and systemic associations of myelinated retinal nerve fibers (MRNF) in a Caucasian cohort. METHODS The Gutenberg Health Study (GHS) is a population-based, prospective cohort study encompassing 15,010 subjects in Germany. Gutenberg Health Study participants, aged 35 to 74 years, stratified for gender, decades of age, and residence were examined for ophthalmologic and systemic conditions. Optic disc centered and macular photographs were reviewed for the presence of MRNF. RESULTS In 25,728 eyes of 12,906 participants (86.0% of the cohort), the prevalence of MRNF was 0.4%. In a binary logistic regression analysis, MRNF was positively associated with …

Sex-specific differences in genetic and nongenetic determinants of mean platelet volume: results from the Gutenberg Health Study.

Mean platelet volume (MPV), a measure of platelet size, is a potential biological marker of platelet function. To date, a comprehensive analysis including known genetic and nongenetic factors that determine MPV is still lacking. MPV has been evaluated in 15 010 individuals from the population-based Gutenberg Health Study. Genetic information was available for 4175 individuals. Our results showed that age (β, 0.0346; 95% confidence interval [CI], 0.0255 to 0.0436), cardiovascular risk factors (CVRFs) such as smoking (β, 0.178; 95% CI, 0.128 to 0.229), hypertension (β, 0.05; 95% CI, 0.00289 to .0981), and high glucose level (β, 0.00179; 95% CI, 0.0006 to 0.00299) were linked with higher MPV i…

SEAL program – Early detection of liver fibrosis and cirrhosis by screening of the general population

Functional genomics indicate that schizophrenia may be an adult vascular-ischemic disorder

AbstractIn search for the elusive schizophrenia pathway, candidate genes for the disorder from a discovery sample were localized within the energy-delivering and ischemia protection pathway. To test the adult vascular-ischemic (AVIH) and the competing neurodevelopmental hypothesis (NDH), functional genomic analyses of practically all available schizophrenia-associated genes from candidate gene, genome-wide association and postmortem expression studies were performed. Our results indicate a significant overrepresentation of genes involved in vascular function (P&lt;0.001), vasoregulation (that is, perivascular (P&lt;0.001) and shear stress (P&lt;0.01), cerebral ischemia (P&lt;0.001), neurode…

AB1232 RHEUMA-VOR: A PROOF-OF-CONCEPT NETWORK STUDY FOR THE IMPROVEMENT OF RHEUMATOLOGICAL HEALTH CARE THROUGH COORDINATED COOPERATION

Background Rheumatoid arthritis (RA), psoriasis arthritis (PsA) and spondyloarthritis (SpA) are the most common chronic autoimmune rheumatic diseases. For all 3, the so-called “window of opportunity” [1-3] has been identified as the decisive factor affecting the outcome. Objectives The aim of the prospective study is to improve early diagnosis of RA, PsA and SpA and thus positively impact the quality of care for patients with the help of coordinating centers. The primary endpoint is the number of cases with an actual indication for immediate referral to a specialist in proportion to all reported cases. Methods The project establishes a network of the University Medical Center Mainz, the Med…

Health-related quality of life in European childhood cancer survivors: Protocol for a study within PanCareLIFE

Background Survival after childhood cancer has improved to more than 80% during the last few years, leading to an increased number of childhood cancer survivors. Cancer itself, or its treatment, may cause chronic health conditions, including somatic and mental sequelae, which may affect survivors’ health-related quality of life (HRQoL). Objective The project PanCareLIFE aims to establish a large database with comprehensive data on childhood cancer survivors from different European countries, including data on HRQoL. Within PanCareLIFE, this study aims to describe HRQoL in survivors, investigate predictors of HRQoL, and describe the association of HRQoL with hearing and female fertility imp…

Prospective validation of a blood-based 9-miRNA profile for early detection of breast cancer in a cohort of women examined by clinical mammography

Mammography is the predominant screening method for early detection of breast cancer, but has limitations and could be rendered more accurate by combination with a blood-based biomarker profile. Circulating microRNAs (miRNAs) are increasingly recognized as strong biomarkers, and we previously developed a 9-miRNA profile using serum and LNA-based qPCR that effectively stratified patients with early stage breast cancer vs. healthy women. To further develop the test into routine clinical practice, we collected serum of women examined by clinical mammography (N = 197) according to standard operational procedures (SOPs) of the Danish Cancer Biobank. The performance of the circulating 9-miRNA pro…

Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures

Gene expression measurements have successfully been used for building prognostic signatures, i.e for identifying a short list of important genes that can predict patient outcome. Mostly microarray measurements have been considered, and there is little advice available for building multivariable risk prediction models from RNA-Seq data. We specifically consider penalized regression techniques, such as the lasso and componentwise boosting, which can simultaneously consider all measurements and provide both, multivariable regression models for prediction and automated variable selection. However, they might be affected by the typical skewness, mean-variance-dependency or extreme values of RNA-…

Feasibility of sample size calculation for RNA-seq studies

Sample size calculation is a crucial step in study design but is not yet fully established for RNA sequencing (RNA-seq) analyses. To evaluate feasibility and provide guidance, we evaluated RNA-seq sample size tools identified from a systematic search. The focus was on whether real pilot data would be needed for reliable results and on identifying tools that would perform well in scenarios with different levels of biological heterogeneity and fold changes (FCs) between conditions. We used simulations based on real data for tool evaluation. In all settings, the six evaluated tools provided widely different answers, which were strongly affected by FC. Although all tools failed for small FCs, s…

Gene expression patterns underlying parasite-induced alterations in host behaviour and life history

Many parasites manipulate their hosts' phenotype. In particular, parasites with complex life cycles take control of their intermediate hosts' behaviour and life history to increase transmission to their definitive host. The proximate mechanisms underlying these parasite-induced alterations are poorly understood. The cestode Anomotaenia brevis affects the behaviour, life history and morphology of parasitized Temnothorax nylanderi ants and indirectly of their unparasitized nestmates. To gain insights on how parasites alter host phenotypes, we contrast brain gene expression patterns of T. nylanderi workers parasitized with the cestode, their unparasitized nestmates and unparasitized workers fr…

Automatic variable selection for exposure-driven propensity score matching with unmeasured confounders.

Multivariable model building for propensity score modeling approaches is challenging. A common propensity score approach is exposure-driven propensity score matching, where the best model selection strategy is still unclear. In particular, the situation may require variable selection, while it is still unclear if variables included in the propensity score should be associated with the exposure and the outcome, with either the exposure or the outcome, with at least the exposure or with at least the outcome. Unmeasured confounders, complex correlation structures, and non-normal covariate distributions further complicate matters. We consider the performance of different modeling strategies in …

Additional file 5 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 5: Web Figure 12. Comparison of predicted downstream diseases and functions in different data sets.

Visualizing the flow of evidence in network meta-analysis and characterizing mixed treatment comparisons

Network meta-analysis techniques allow for pooling evidence from different studies with only partially overlapping designs for getting a broader basis for decision support. The results are network-based effect estimates that take indirect evidence into account for all pairs of treatments. The results critically depend on homogeneity and consistency assumptions, which are sometimes difficult to investigate. To support such evaluation, we propose a display of the flow of evidence and introduce new measures that characterize the structure of a mixed treatment comparison. Specifically, a linear fixed effects model for network meta-analysis is considered, where the network estimates for two trea…

Additional file 6 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 6: Web Figure 13. Comparison of predicted upstream regulators in different data sets.

Early switch to oral anticoagulation in patients with acute intermediate-risk pulmonary embolism (PEITHO-2) : a multinational, multicentre, single-arm, phase 4 trial

BACKGROUND: Current guidelines recommend a risk-adjusted treatment strategy for the management of acute pulmonary embolism. This is a particular patient category for whom optimal treatment (anticoagulant treatment, reperfusion strategies, and duration of hospitalisation) is currently unknown. We investigated whether treatment of acute intermediate-risk pulmonary embolism with parenteral anticoagulation for a short period of 72 h, followed by a switch to a direct oral anticoagulant (dabigatran), is effective and safe. METHODS: We did a multinational, multicentre, single-arm, phase 4 trial at 42 hospitals in Austria, Belgium, France, Germany, Italy, Netherlands, Romania, Slovenia, and Spain. …

Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis

Development of primary liver cancer is a multistage process. Detailed understanding of sequential epigenetic alterations is largely missing. Here, we performed Infinium Human Methylation 450k BeadChips and RNA-Seq analyses for genome-wide methylome and transcriptome profiling of cirrhotic liver (n = 7), low- (n = 4) and high-grade (n = 9) dysplastic lesions, and early (n = 5) and progressed (n = 3) hepatocellular carcinomas (HCC) synchronously detected in 8 patients with HCC with chronic hepatitis B infection. Integrative analyses of epigenetically driven molecular changes were identified and validated in 2 independent cohorts comprising 887 HCCs. Mitochondrial DNA sequencing was further em…

TYPE II DIABETES MELLITUS HAS NO MAJOR INFLUENCE ON PLATELET MICRO–RNA EXPRESSION: RESULTS FROM MICRO–ARRAY PROFILING IN A COHORT OF 60 PATIENTS

Blood platelets represent pro–inflammatory mediators in the development of atherosclerosis. Diabetes mellitus as a major contributor to cardiovascular disease burden induces dysfunctional platelets. Platelets contain abundant miRNAs, which recently have been linked tightly to inflammation. While

Chronic venous insufficiency, cardiovascular disease, and mortality: a population study

Abstract Aims  Evidence regarding the health burden of chronic venous insufficiency (CVI), its clinical determinants, and impact on outcome is scarce. Methods and results  Systematic phenotyping of CVI according to established CEAP (Clinical-Etiologic-Anatomic-Pathophysiologic) classification was performed in 12 423 participants (age range: 40–80 years) of the Gutenberg Health Study from April 2012 to April 2017. Prevalence was calculated age- and sex-specifically. Multivariable Poisson regression models were calculated to evaluate the relation of CVI with cardiovascular comorbidities. Survival analyses were carried out to assess the CVI-associated risk of death. Replication of findings was…

Tailoring sparse multivariable regression techniques for prognostic single-nucleotide polymorphism signatures.

When seeking prognostic information for patients, modern technologies provide a huge amount of genomic measurements as a starting point. For single-nucleotide polymorphisms (SNPs), there may be more than one million covariates that need to be simultaneously considered with respect to a clinical endpoint. Although the underlying biological problem cannot be solved on the basis of clinical cohorts of only modest size, some important SNPs might still be identified. Sparse multivariable regression techniques have recently become available for automatically identifying prognostic molecular signatures that comprise relatively few covariates and provide reasonable prediction performance. For illus…

Association of candidate pharmacogenetic markers with platinum-induced ototoxicity

Genetic association studies suggest a genetic predisposition for cisplatin-induced ototoxicity. Among other candidate genes, thiopurine methyltransferase (TPMT) is considered a critical gene for susceptibility to cisplatin-induced hearing loss in a pharmacogenetic guideline. The PanCareLIFE cross-sectional cohort study evaluated the genetic associations in a large pan-European population and assessed the diagnostic accuracy of the genetic markers. 1,112 pediatric cancer survivors who had provided biomaterial for genotyping were screened for participation in the pharmacogenetic association study. 900 participants qualified for inclusion. Based on the assessment of original audiograms, patien…

PCF11 links alternative polyadenylation to formation and spontaneous regression of neuroblastoma

AbstractDiversification at the transcriptome 3’end is an important and evolutionarily conserved layer of gene regulation associated with differentiation and dedifferentiation processes. However the underlying mechanisms and functional consequences are poorly defined. Here, we identify extensive transcriptome-3’end-alterations in neuroblastoma, a tumour entity with a paucity of recurrent somatic mutations and an unusually high frequency of spontaneous regression. Utilising extensive RNAi-screening we reveal the landscape and drivers of transcriptome-3’end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA) of hundreds of transcripts including…

Comments on "Identifying inconsistency in network meta-analysis: Is the net heat plot a reliable method?"

One of the biggest challenges for network meta‐analysis is inconsistency, which occurs when the direct and indirect evidence conflict. Inconsistency causes problems for the estimation and interpretation of treatment effects and treatment contrasts. Krahn and colleagues proposed the net heat approach as a graphical tool for identifying and locating inconsistency within a network of randomized controlled trials. For networks with a treatment loop, the net heat plot displays statistics calculated by temporarily removing each design one at a time, in turn, and assessing the contribution of each remaining design to the inconsistency. The net heat plot takes the form of a matrix which is displaye…

Usefulness of current candidate genetic markers to identify childhood cancer patients at risk for platinum-induced ototoxicity: Results of the European PanCareLIFE cohort study

Background Irreversible sensorineural hearing loss is a common side effect of platinum treatment with the potential to significantly impair the neurocognitive, social and educational development of childhood cancer survivors. Genetic association studies suggest a genetic predisposition for cisplatin-induced ototoxicity. Among other candidate genes, thiopurine methyltransferase (TPMT) is considered a critical gene for susceptibility to cisplatin-induced hearing loss in the FDA drug label and a pharmacogenetic guideline. The aim of this cross-sectional cohort study was to confirm the genetic associations in a large pan-European population and to evaluate the diagnostic accuracy of the genetic…

Additional file 7 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 7: Gene expression in the "Not a Number" pathways (blue = downregulation, red = upregulation). Web Figure 14. Base excision repair (BER) system. Web Fig. 15. Molecular mechanisms of cancer. Web Fig. 16. Assembly of RNA polymerase III complex. Web Fig. 17. DNA double-strand break repair by homologous recombination. Web Fig. 18. Interleukin 4 (IL-4) signaling. Web Fig. 19. Interleukin 17 (IL-17) signaling. Web Fig. 20. Interleukin 17A (IL-17A) signaling in fibroblasts. Web Fig. 21. Mitochondrial dysfunction. Web Fig. 22. Myc mediated apoptosis signaling. Web Fig. 23.Nucleotide excision repair. Web Fig. 24. Protein ubiquitination. Web Fig. 25. Retinoic acid receptor (RAR) activ…

Prevalence, Phenotype, and Psychosocial Well-Being in Euthyroid/Hypothyroid Thyroid-Associated Orbitopathy.

At the onset of thyroid-associated orbitopathy (TAO), most patients are hyperthyroid, while scarce data are available on euthyroid/hypothyroid TAO. The aim of this study was to assess the prevalence, phenotype, and psychosocial burden of patients with initially euthyroid/hypothyroid TAO.The medical records of 461 consecutive and unselected patients with TAO followed at a specialized joint thyroid-eye clinic were analyzed within this retrospective cross-sectional study. Main outcome measures were the prevalence of initially eu- or hypothyroid TAO as well as ophthalmic signs and symptoms, disease-specific quality of life (QoL), work impairment, and rate of psychotherapy in initially eu-/hypot…

Targeting tumor-initiating cells and compensatory YAP pathway to overcome sorafenib resistance in hepatocellular carcinoma

Abstract 147: The Role of Thrombin Generation in Cardiovascular Disease and Mortality - Results from the Population-based Gutenberg Health Study

Background: Thrombin formation is one of the key enzymatic processes that direct the activity of the hemostatic system. Thrombin generation (TG), a method addressing the overall potential of a given plasma sample to form thrombin, may be a potential tool to improve risk stratification for cardiovascular diseases (CVD). This study aims to explore the relation between TG and cardiovascular risk factors (CVRFs), CVD, and total mortality. Methods: For this study, N=5000 subjects from the population-based Gutenberg Health Study were analyzed in a highly standardized setting. TG was measured by the Calibrated Automated Thrombogram method at 1 and 5 pM tissue factor (TF) trigger in platelet poor …

Molecular cause and functional impact of altered synaptic lipid signaling due to a prg‐1 gene SNP

Loss of plasticity-related gene 1 (PRG-1), which regulates synaptic phospholipid signaling, leads to hyperexcitability via increased glutamate release altering excitation/inhibition (E/I) balance in cortical networks. A recently reported SNP in prg-1 (R345T/ mutPRG-1) affects ~5 million European and US citizens in a monoallelic variant. Our studies show that this mutation leads to a loss-of-PRG-1 function at the synapse due to its inability to control lysophosphatidic acid (LPA) levels via a cellular uptake mechanism which appears to depend on proper glycosylation altered by this SNP. PRG-1 +/ mice, which are animal correlates of human PRG-1 +/mut carriers, showed an altered cortical networ…

Additional file 4 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 4: Web Figure 11. Comparison of affected pathways in different data sets.

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components

AbstractBackgroundPrincipal component analysis (PCA) is frequently useentirely written ind in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.ResultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny fra…

Thyroid-associated orbitopathy is linked to gastrointestinal autoimmunity

Summary Common autoimmune disorders tend to co-exist in the same subjects and cluster in families. The objective of this study was to determine the prevalence of autoimmune co-morbidity in patients with autoimmune thyroid disease (AITD) with and without thyroid-associated orbitopathy (TAO). This was a cross-sectional study conducted at an academic tertiary referral centre. Of 1310 patients with AITD [n = 777 or 59% with Graves' disease (GD) and n = 533, 41% with Hashimoto's thyroiditis (HT)] followed at a specialized joint thyroid–eye out-patient clinic, 176 (13·4%) had an adult type of the autoimmune polyglandular syndrome, 129 (9·8%) type 1 diabetes, 111 (8·5%) coeliac disease, 60 (4·6%) …

Comparison of Different Hypotheses Regarding the Spread of Alzheimer’s Disease Using Markov Random Fields and Multimodal Imaging

Alzheimer’s disease (AD) is characterized by a cascade of pathological processes that can be assessed in vivo using different neuroimaging methods. Recent research suggests a systematic sequence of pathogenic events on a global biomarker level, but little is known about the associations and dependencies of distinct lesion patterns on a regional level. Markov random fields are a probabilistic graphical modeling approach that represent the interaction between individual random variables by an undirected graph. We propose the novel application of this approach to study the interregional associations and dependencies between multimodal imaging markers of AD pathology and to compare different hy…

Additional file 11 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 11: Web Table 1D. Differentially expressed genes 4 h after exposure to high dose ionizing radiation (2 Gray).

Genetic Cell Ablation Reveals Clusters of Local Self-Renewing Microglia in the Mammalian Central Nervous System

SummaryDuring early embryogenesis, microglia arise from yolk sac progenitors that populate the developing central nervous system (CNS), but how the tissue-resident macrophages are maintained throughout the organism’s lifespan still remains unclear. Here, we describe a system that allows specific, conditional ablation of microglia in adult mice. We found that the microglial compartment was reconstituted within 1 week of depletion. Microglia repopulation relied on CNS-resident cells, independent from bone-marrow-derived precursors. During repopulation, microglia formed clusters of highly proliferative cells that migrated apart once steady state was achieved. Proliferating microglia expressed …

Additional file 12 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 12: Web Table 2. Differential expression activity in cellular pathways and involved molecules

Similarities and Differences of Mental Health in Women and Men: A Systematic Review of Findings in Three Large German Cohorts

In Germany, large, population-based cohort studies have been implemented in order to identify risk and protective factors for maintaining health across the life span. The purpose of this systematic review is to analyse findings from three large ongoing cohorts and to identify sex-specific prevalence rates, risk and protective factors for mental health. Published studies from the Cooperative Health Research in the Region Augsburg (KORA), the Study of Health in Pomerania (SHIP) and the Gutenberg Health Study (GHS)), representing the southern, north-eastern and middle parts of Germany, were identified through searches of the databases PubMed and Web of Science. A total of 52 articles was ident…

The experience of physicians in pharmacogenomic clinical decision support within eight German university hospitals.

Aim: The aim of this study was to assess the physicians’ attitude, their knowledge and their experience in pharmacogenomic clinical decision support in German hospitals. Materials &amp; methods: We conducted an online survey to address physicians of 13 different medical specialties across eight German university hospitals. In total, 564 returned questionnaires were analyzed. Results: The remaining knowledge gap, the uncertainty of test reimbursement and the physicians’ lack of awareness of existing pharmacogenomic clinical decision support systems (CDSS) are the major barriers for implementing pharmacogenomic CDSS into German hospitals. Furthermore, pharmacogenomic CDSS are most effective …

Additional file 13 of Comparison of time and dose dependent gene expression and affected pathways in primary human fibroblasts after exposure to ionizing radiation

Additional file 13: Supplement file 1. Settings for comparison analyses in IPA.

Lebervorsorge-Programm SEAL: Screening der Allgemeinbevölkerung zur strukturierten Früherkennung von Leberfibrose und Leberzirrhose

Power of the Wilcoxon–Mann–Whitney test for non‐inferiority in the presence of death‐censored observations

In clinical trials with patients in a critical state, death may preclude measurement of a quantitative endpoint of interest, and even early measurements, for example for intention-to-treat analysis, may not be available. For example, a non-negligible proportion of patients with acute pulmonary embolism will die before 30 day measurements on the efficacy of thrombolysis can be obtained. As excluding such patients may introduce bias, alternative analyses, and corresponding means for sample size calculation are needed. We specifically consider power analysis in a randomized clinical trial setting in which the goal is to demonstrate noninferiority of a new treatment as compared to a reference t…

Screening for Cognitive Impairment in Hospitalized Older Patients

Abstract. This study develops a screening method for older patients based on nursing procedure to predict complications associated with cognitive impairment during a hospital stay. This multicenter diagnostic cohort study among older hospitalized patients was carried out in eight primary-care hospitals. Following admission of the patients, trained nurses conducted a structured interview and the Mini-Cog as gold standard for cognitive status; complications during the hospital stay were also monitored. In a second step, the structured interview combined with the Mini-Cog revealed whether there was any abnormality in the interview, making it possible to validly and reliably as well as sensiti…

Psychological interventions to foster resilience in healthcare students

Background Resilience can be defined as maintaining or regaining mental health during or after significant adversities such as a potentially traumatising event, challenging life circumstances, a critical life transition or physical illness. Healthcare students, such as medical, nursing, psychology and social work students, are exposed to various study- and work-related stressors, the latter particularly during later phases of health professional education. They are at increased risk of developing symptoms of burnout or mental disorders. This population may benefit from resilience-promoting training programmes. Objectives To assess the effects of interventions to foster resilience in healthc…

ideal: an R/Bioconductor package for interactive differential expression analysis

AbstractBackgroundRNA sequencing (RNA-seq) is an ever increasingly popular tool for transcriptome profiling. A key point to make the best use of the available data is to provide software tools that are easy to use but still provide flexibility and transparency in the adopted methods. Despite the availability of many packages focused on detecting differential expression, a method to streamline this type of bioinformatics analysis in a comprehensive, accessible, and reproducible way is lacking.ResultsWe developed the ideal software package, which serves as a web application for interactive and reproducible RNA-seq analysis, while producing a wealth of visualizations to facilitate data interpr…

Intake of Vitamin K Antagonists and Worsening of Cardiac and Vascular Disease: Results From the Population‐Based Gutenberg Health Study

Background Preclinical data have indicated a link between use of vitamin K antagonists ( VKA ) and detrimental effects on vascular structure and function. The objective of the present study was to determine the relationship between VKA intake and different phenotypes of subclinical cardiovascular disease in the population. Methods and Results Clinical and laboratory data, as well as medical–technical examinations were assessed from 15 010 individuals aged 35 to 74 years during a highly standardized 5‐hour visit at the study center of the population‐based Gutenberg Health Study. In total, the study sample comprised 287 VKA users and 14 564 VKA nonusers. Multivariable analysis revealed an in…

Author response: ERK3/MAPK6 controls IL-8 production and chemotaxis

Data from: Gene expression patterns underlying parasite-induced alterations in host behaviour and life history

Many parasites manipulate their hosts’ phenotype. In particular, parasites with complex life cycles take control of their intermediate hosts’ behaviour and life history to increase transmission to their definitive host. The proximate mechanisms underlying these parasite-induced alterations are poorly understood. The cestode Anomotaenia brevis affects the behaviour, life history and morphology of parasitized Temnothorax nylanderi ants and indirectly of their unparasitized nestmates. To gain insights on how parasites alter host phenotypes, we contrast brain gene expression patterns of T. nylanderi workers parasitized with the cestode, their unparasitized nestmates and unparasitized workers fr…