The openCARP CDE: Concept for and implementation of a sustainable collaborativedevelopment environment for research software

This work describes the setup of an advanced technical infrastructure for collabora-tive software development in large, distributed projects based on GitLab. We presentits customization and extension, additional features and processes like code review,continuous automated testing, DevOps practices, and sustainable life-cycle manage-ment including long-term preservation and citable publishing of software releasesalong with relevant metadata. The collaborative development environment (CDE) iscurrently used for developing the open cardiac simulation software openCARP and anevaluation showcases its capability and utility for collaboration and coordination ofsizeable heterogeneous teams. As such, it could be a suitable and sustainable infras-tructure solution for a wide range of research software projects

Combination of Dacarbazine and Dimethylfumarate Efficiently Reduces Melanoma Lymph Node Metastasis

Dimethylfumarate (DMF) has been shown to reduce melanoma growth and metastasis in animal models. We addressed the question of whether DMF is as effective in its antitumor activity as the US Food and Drug Administration–approved alkylating agent dacarbazine (DTIC). We also tested the possibility of an improved antitumoral effect when both therapeutics were used together. Using our severe combined immunodeficiency (SCID) mouse model, in which xenografted human melanoma cells metastasize from primary skin sites to sentinel nodes, we show that these treatments, alone or in combination, reduce tumor growth at primary sites. Our main finding was that metastasis to sentinel nodes is significantly delayed only in mice treated with a combination of DTIC and DMF. Subsequent experiments were able to show that a combination of DTIC/DMF significantly reduced lymph vessel density in primary tumors as examined by real-time PCR and immunohistochemistry. In addition, DTIC/DMF treatment significantly impaired melanoma cell migration in vitro. In vivo, DTIC/DMF therapy significantly reduced mRNA expression and protein concentration of the promigratory chemokines CXCL2 and CXCL11. In addition, our data suggest that this xenotransplantation model is suitable for preclinical testing of various combinations of antimelanoma agents

Report on the 21th World Congress on Sexual Health “Sexual issues straight from the heart”

W pracy przedstawiono sprawozdanie z XXI Kongresu Światowej Organizacji Zdrowia Seksualnego, który odbył się w 2013 roku w Porto Alegre w Brazylii. Uwzględniono w nim tematykę wystąpień autorów zagranicznych i krajowych. Zwrócono uwagę na wybrane interesujące prezentacje przedstawione w ramach sesji ustnych i plakatowych. Zamieszczono krótkie kalendarium wydarzeń naukowych w zbliżającym się okresie.The paper presents the report on the 21th World Congress on Sexual Health, which took place in Porto Alegre in 2013. The topics presented by foreign as well as domestic authors were included. The attention was paid to the selected interesting poster and oral presentations. The short timetable of the forthcoming scientific events is also included

SuLMaSS - Sustainable Lifecycle Management for Scientific Software

The SuLMaSS project [1] will advance, develop, build, evaluate, and test infrastructure for sustainable lifecycle management of scientific software. The infrastructure is tested and evaluated by an existing cardiac electrophysiology simulation software project, which is currently in the prototype state and will be advanced towards optimal usability and a large and active user community. Thus, SuLMaSS is focused on designing and implementing application-oriented e-research technologies and the impact is three-fold: - Provision of a high quality, user-friendly cardiac electrophysiology simulation software package that accommodates attestable needs of the scientific community. - Delivery of infrastructure components for testing, safe-keeping, referencing, and versioning of all phases of the lifecycle of scientific software. - Serve as a best practice example for sustainable scientific software management. Scientific software development in Germany and beyond shall benefit through both the aforementioned best practice role model and the advanced infrastructure that will, in part, be available for external projects as well. With adding value for the wider scientific cardiac electrophysiology community, the software will be available under an open source license and be provided for a large share of people and research groups that can potentially leverage computational cardiac modeling methods. Institutional infrastructure will be extended to explore, evaluate and establish the basis for research software development regarding testing, usage, maintenance and support. The cardiac electrophysiology simulator will drive and showcase the infrastructure formation, thus serving as a lighthouse project. The developed infrastructure can be used by other scientific software projects in future and aims to support the full research lifecycle from exploration through conclusive analysis and publication, to archival, and sharing of data and source code, thus increasing the quality of research results. Moreover it will foster a community-based collaborative development and improve sustainability of research software. References: [1]­‌‌‌‌‌‌‌‌‌ http://www.dfg.de/dfg_magazin/aus_der_wissenschaft/impulse_fuer_das_digitale_lis_jb17/02_aus_der_foerderung/index.htm

Standing together for reproducibility in large-scale computing: report on reproducibility@XSEDE

This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE). The workshop's discussion-oriented agenda focused on reproducibility in large-scale computational research. Two important themes capture the spirit of the workshop submissions and discussions: (1) organizational stakeholders, especially supercomputer centers, are in a unique position to promote, enable, and support reproducible research; and (2) individual researchers should conduct each experiment as though someone will replicate that experiment. Participants documented numerous issues, questions, technologies, practices, and potentially promising initiatives emerging from the discussion, but also highlighted four areas of particular interest to XSEDE: (1) documentation and training that promotes reproducible research; (2) system-level tools that provide build- and run-time information at the level of the individual job; (3) the need to model best practices in research collaborations involving XSEDE staff; and (4) continued work on gateways and related technologies. In addition, an intriguing question emerged from the day's interactions: would there be value in establishing an annual award for excellence in reproducible research? Overvie

Hemocyanin conformational changes associated with SDS-induced phenol oxidase activation

The enzymatic activity of phenoloxidase is assayed routinely in the presence of SDS. Similar assay conditions elicit phenoloxidase activity in another type 3 copper protein, namely hemocyanin, which normally functions as an oxygen carrier. The nature of the conformational changes induced in type 3 copper proteins by the denaturant SDS is unknown. This comparative study demonstrates that arthropod hemocyanins can be converted from being an oxygen carrier to a form which exhibits phenoloxidase activity by incubation with SDS, with accompanying changes in secondary and tertiary structure. Structural characterisation, using various biophysical methods, suggests that the micellar form of SDS is required to induce optimal conformational transitions in the protein which may result in opening a channel to the di-copper centre allowing bulky phenolic substrates access to the catalytic site

Crystallization and Preliminary Analysis of Crystals of the 24-Meric Hemocyanin of the Emperor Scorpion (Pandinus imperator)

Hemocyanins are giant oxygen transport proteins found in the hemolymph of several invertebrate phyla. They constitute giant multimeric molecules whose size range up to that of cell organelles such as ribosomes or even small viruses. Oxygen is reversibly bound by hemocyanins at binuclear copper centers. Subunit interactions within the multisubunit hemocyanin complex lead to diverse allosteric effects such as the highest cooperativity for oxygen binding found in nature. Crystal structures of a native hemocyanin oligomer larger than a hexameric substructure have not been published until now. We report for the first time growth and preliminary analysis of crystals of the 24-meric hemocyanin (MW = 1.8 MDa) of emperor scorpion (Pandinus imperator), which diffract to a resolution of 6.5 Å. The crystals are monoclinc with space group C 1 2 1 and cell dimensions a = 311.61 Å, b = 246.58 Å and c = 251.10 Å (α = 90.00°, β = 90.02°, γ = 90.00°). The asymmetric unit contains one molecule of the 24-meric hemocyanin and the solvent content of the crystals is 56%. A preliminary analysis of the hemocyanin structure reveals that emperor scorpion hemocyanin crystallizes in the same oxygenated conformation, which is also present in solution as previously shown by cryo-EM reconstruction and small angle x-ray scattering experiments