Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.Comment: 12 pages, 4 figure

PREPARING PUBLICATIONS FOR “COMPUTER SCIENCE” ANNUAL

In this paper we present a short instruction for preparing manuscripts for „Computer Science” annual with the use of LATEX and style csagh.sty

Arena-Rosnav 2.0: A Development and Benchmarking Platform for Robot Navigation in Highly Dynamic Environments

Following up on our previous works, in this paper, we present Arena-Rosnav 2.0 an extension to our previous works Arena-Bench and Arena-Rosnav, which adds a variety of additional modules for developing and benchmarking robotic navigation approaches. The platform is fundamentally restructured and provides unified APIs to add additional functionalities such as planning algorithms, simulators, or evaluation functionalities. We have included more realistic simulation and pedestrian behavior and provide a profound documentation to lower the entry barrier. We evaluated our system by first, conducting a user study in which we asked experienced researchers as well as new practitioners and students to test our system. The feedback was mostly positive and a high number of participants are utilizing our system for other research endeavors. Finally, we demonstrate the feasibility of our system by integrating two new simulators and a variety of state of the art navigation approaches and benchmark them against one another. The platform is openly available at https://github.com/Arena-Rosnav.Comment: 8 pages, 5 figure

Body dysmorphia in common skin diseases: Results of an observational, cross-sectional multi-centre study among dermatological out-patients in 17 European countries

Background Body dysmorphic disorder (BDD) is a common psychiatric disorder associated with high costs for healthcare systems as patients may repeatedly ask for different, often not effective interventions. BDD symptoms are more prevalent in patients with dermatological conditions than the general population, but there are no large sample studies comparing the prevalence of BDD symptoms between patients with dermatological conditions and healthy skin controls. Objectives To compare the prevalence of BDD symptoms between patients with different dermatological conditions and healthy skin controls and to describe sociodemographic, physical and psychological factors associated with BDD symptoms to identify patients who may have a particularly high chance of having this condition. Methods This observational cross-sectional, comparative multi-centre study included 8295 participants: 5487 consecutive patients with different skin diseases (56% female) recruited among dermatological out-patients at 22 clinics in 17 European countries and 2808 healthy skin controls (66% female). All patients were examined by a dermatologist. BDD symptoms were assessed by the Dysmorphic Concern Questionnaire (DCQ). Sociodemographic data, information on psychological factors and physical conditions were collected. Each patient was given a dermatological diagnosis according to ICD-10 by a dermatologist. Results The participation rate of invited dermatological patients was 82.4% on average across all centres. BDD symptoms were five times more prevalent in patients with dermatological conditions than in healthy skin controls (10.5% vs. 2.1%). Patients with hyperhidrosis, alopecia and vitiligo had a more than eleven-fold increased chance (adjusted Odds Ratio (OR) > 11) of having BDD symptoms compared to healthy skin controls, and patients with atopic dermatitis, psoriasis, acne, hidradenitis suppurativa, prurigo and bullous diseases had a more than six-fold increased chance (adjusted OR > 6) of having BDD symptoms. Using a logistic regression model, BDD symptoms were significantly related to lower age, female sex, higher psychological stress and feelings of stigmatisation. Conclusions This study reveals that clinical BDD symptoms are significantly associated with common dermatological diseases. As such symptoms are associated with higher levels of psychological distress and multiple unhelpful consultations, general practitioners and dermatologists should consider BDD and refer patients when identified to an appropriate service for BDD screening and management

Preparing Publications for Computer Science Annual

In this paper we present a short instruction for preparing manuscripts for "Computer Science" annual with the use of LATEX and style csagh.st

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

Abstract: We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems