Basics of collaborative research data management: Requirements for a Schleswig-Holstein state initiative on research data management

Das Papier "Grundlagen eines partnerschaftlichen Forschungsdatenmanagements - Anforderungen an eine schleswig-holsteinische Landesinitiative zum Forschungsdatenmanagement" umreißt die Anforderungen für eine schleswig-holsteinische Landesinitiative zum Forschungsdatenmanagement (FDM-SH). Hierfür wird zunächst das Umfeld, in dem eine solche Initiative entstehen und agieren soll, beschrieben. So beeinflussen sowohl die Eigenheiten der regionalen Forschungslandschaft wie auch die Entwicklungen im Bereich der Nationalen Forschungsdateninfrastruktur (NFDI) die Ausprägungen von Landesinitiativen. Die speziellen Anforderungen werden durch den Vergleich mit anderen Landesinitiativen, die Analyse von spezifischen Umfrageergebnissen aus Schleswig-Holstein sowie die Berücksichtigung der Anforderungen der NFDI gesammelt. Der Ansatz des partnerschaftlichen Forschungsdatenmanagements (FDM) spiegelt das Anliegen Schleswig-Holsteins wider, die Herausforderungen für ein zeitgemäßes FDM vor Ort gemeinsam zu bewältigen und dabei sowohl Know-how zu teilen als auch Ressourcen zu schonen

Structure of Allergens and Structure Based Epitope Predictions

The structure determination of major allergens is a prerequisite for analyzing surface exposed areas of the allergen and for mapping conformational epitopes. These may be determined by experimental methods including crystallographic and NMR-based approaches or predicted by computational methods. In this review we summarize the existing structural information on allergens and their classification in protein fold families. The currently available allergen-antibody complexes are described and the experimentally obtained epitopes compared. Furthermore we discuss established methods for linear and conformational epitope mapping, putting special emphasis on a recently developed approach, which uses the structural similarity of proteins in combination with the experimental cross-reactivity data for epitope prediction

Hard x-ray single-shot spectrometer at the European X-ray Free-Electron Laser

The European X-ray Free-Electron Laser Facility in Germany delivers x-ray pulses with femtosecond pulse duration at a repetition rate of up to 4.5 MHz. The free-electron laser radiation is created by the self-amplified spontaneous emission (SASE) process, whose stochastic nature gives rise to shot-to-shot fluctuations in most beam properties, including spectrum, pulse energy, spatial profile, wavefront, and temporal profile. Each spectrum consisting of many spikes varies in width and amplitude that appear differently within the envelope of the SASE spectrum. In order to measure and study the SASE spectrum, the HIgh REsolution hard X-ray single-shot (HIREX) spectrometer was installed in the photon tunnel of the SASE1 undulator beamline. It is based on diamond gratings, bent crystals as a dispersive element, and a MHz-repetition-rate strip detector. It covers a photon energy range of 3 keV–25 keV and a bandwidth of 0.5% of the SASE beam. The SASE spikes are resolved with 0.15 eV separation using the Si 440 reflection, providing a resolving power of 60 000 at a photon energy of 9.3 keV. The measured SASE bandwidth is 25 eV. In this paper, we discuss the design specifications, installation, and commissioning of the HIREX spectrometer. The spectral results using Si (110), Si (111), and C (110) crystals are presented

Characterization of mutants of a highly cross-reactive calcium-binding protein from Brassica pollen for allergen-specific immunotherapy

Transfuzijsko liječenje je postupak kojim se bolesnik liječi krvnim pripravcima priređenim iz ljudske krvi. Liječenje se provodi prema procjeni kliničkog stanja bolesnika,odgovarajućim laboratorijskim pokazateljima i korisnosti liječenja s obzirom na mogućnost pojave neželjene reakcije. Usprkos svim postupcima koji se poduzimaju za što sigurnije transfuzijsko liječenje bolesnika uvijek postoji rizik pojave neželjene transfuzijske reakcije. Oko 1% transfundiranih bolesnika razvije neželjene reakcije na krvne pripravake. Većinom se radi o blagim reakcijama bez kliničkih posljedica. Međutim, neke mogu biti teške i uzrokovati smrt bolesnika. Na učestalost transfuzijskih rekacija utječu metode proizvodnje krvnih pripravaka kao i nadzor bolesnika tijekom transfuzijskog liječenja te model prijavljivanja transfuzijske reakcije. Cilj ovog istraživanja bio je utvrditi učestalost transfuzijskih reakcija u Kliničkom bolničkom centru Zagreb (KBC Zagreb) u razdoblju 2002.-2018. godine. Također,u ovom radu biti će opisan sustav prijavljivanja transfuzijskih reakcija u KBC Zagreb te će se analizirati vrste reakcija prema krvnim pripravcima. U promatranom razdoblju zabilježeno je ukupno 1393 transfuzijske reakcije od kojih je najveći broj febrilnih nehemolitičkih transfuzijskih reakcija te alergijskih reakcija. Reakcije se najčešće javljaju kod eritrocitnih i trombocitnih krvnih pripravaka. Sigurno transfuzijsko liječenje ovisi o složenim, integriranim i međusobno ovisnim postupcima. Nužna je suradnja kliničkih odjela, transfuzijske službe, laboratorija i stručnih službi. Prije transfuzije obvezna je identifikacija bolesnika i pripravka te pravovremena reakcija u slučaju pojave komplikacija

EXtra-Xwiz: A Tool to Streamline Serial Femtosecond Crystallography Workflows at European XFEL

X-ray free electron lasers deliver photon pulses that are bright enough to observe diffraction from extremely small crystals at a time scale that outruns their destruction. As crystals are continuously replaced, this technique is termed serial femtosecond crystallography (SFX). Due to its high pulse repetition rate, the European XFEL enables the collection of rich and extensive data sets, which are suited to study various scientific problems, including ultra-fast processes. The enormous data rate, data complexity, and the nature of the pixelized multimodular area detectors at the European XFEL pose severe challenges to users. To streamline the analysis of the SFX data, we developed the semiautomated pipeline EXtra-Xwiz around the established CrystFEL program suite, thereby processing diffraction patterns on detector frames into structure factors. Here we present EXtra-Xwiz, and we introduce its architecture and use by means of a tutorial. Future plans for its development and expansion are also discussed

Characterization of mutants of a highly cross-reactive calcium-binding protein from Brassica pollen for allergen-specific immunotherapy

Abstract not availableTetiana Garmatiuk, Ines Swoboda, Anna Twardosz-Kropfmüller, Fabio Dall’Antonia, Walter Keller, Mohan B.Singh, Prem L. Bhalla, Takashi Okada, Kinya Toriyama, Milena Weber, Minoo Ghannadan, Wolfgang R. Sperr, Katharina Blatt, Peter Valent, Brigitte Klein, Verena Niederberger, Mirela Curin, Nadja Balic, Susanne Spitzauer and Rudolf Valent

Data reduction activities at European XFEL: early results

The European XFEL is a megahertz repetition-rate facility producing extremely bright and coherent pulses of a few tens of femtoseconds duration. The amount of data generated in the context of user experiments can exceed hundreds of gigabits per second, resulting in tens of petabytes stored every year. These rates and volumes pose significant challenges both for facilities and users thereof. In fact, if unaddressed, extraction and interpretation of scientific content will be hindered, and investment and operational costs will quickly become unsustainable. In this article, we outline challenges and solutions in data reduction

Structure of allergens and structure based epitope predictions

The structure determination of major allergens is a prerequisite for analyzing surface exposed areas of the allergen and for mapping conformational epitopes. These may be determined by experimental methods including crystallographic and NMR-based approaches or predicted by computational methods. In this review we summarize the existing structural information on allergens and their classification in protein fold families. The currently available allergen-antibody complexes are described and the experimentally obtained epitopes compared. Furthermore we discuss established methods for linear and conformational epitope mapping, putting special emphasis on a recently developed approach, which uses the structural similarity of proteins in combination with the experimental cross-reactivity data for epitope prediction