An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research

Chemical Diversity and Complexity of Scotch Whisky as Revealed by High-Resolution Mass Spectrometry

Scotch Whisky is an important product, both culturally and economically. Chemically, Scotch Whisky is a complex mixture, which comprises thousands of compounds, the nature of which are largely unknown. Here, we present a thorough overview of the chemistry of Scotch Whisky as observed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Eighty-five whiskies, representing the majority of Scotch Whisky produced and sold, were analyzed by untargeted high-resolution mass spectrometry. Thousands of chemical formulae were assigned for each sample based on parts-per-billion mass accuracy of FT-ICR MS spectra. For the first time, isotopic fine structure analysis was used to confirm the assignment of high molecular weight CHOS species in Scotch Whisky. The assigned spectra were compared using a number of visualization techniques, including van Krevelen diagrams, double bond equivalence (DBE) plots, as well as heteroatomic compound class distributions. Additionally, multivariate analysis, including PCA and OPLS-DA, was used to interpret the data, with key compounds identified for discriminating between types of whisky (blend or malt) or maturation wood type. FT-ICR MS analysis of Scotch Whisky was shown to be of significant potential in further understanding of the complexity of mature spirit drinks and as a tool for investigating the chemistry of the maturation processes. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13361-016-1513-y) contains supplementary material, which is available to authorized users

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research

Chronic fatigue syndrome in patients diagnosed with malignant neoplasm

Wstęp i cele: Zespołem przewlekłego zmęczenia określa się długotrwałe odczuwanie osłabienia przez chorych, związane z obecnością nowotworu lub leczeniem przeciwnowotworowym. Występuje u 70-100% pacjentów poddanych chemioterapii, immunoterapii, radioterapii, a także leczeniu chirurgicznemu. Wystąpienie ZPZ może być związane z obecnością zaawansowanej choroby nowotworowej, jej leczeniem, brakiem aktywności fizycznej, ale także współistnieć z chorobami układu krążenia, oddechowego, niewydolności narządów, wyniszczeniem nowotworowym, depresją. Najprostszą formą oceny zmęczenia jest badanie jego natężenia. Do oceny najlepiej posłużyć się linearną skalą numeryczną (NRS). Przy rozpoznaniu łagodnego stopnia postępowanie opiera się na edukacji chorych celem zmiany trybu życia, żywienia. Przy nasilonym stopniu podejmuje się leczenie odwracalnych przyczyn ZPZ, ewentualnie należy rozważyć postępowanie farmakologiczne. Materiał i metody: Zastosowano metodę przeglądową literatury. Wnioski: Objawy ZPZ mogą się różnić u poszczególnych osób, mogą mieć różną postać.Introduction and aim: Chronic fatigue syndrome (CFS) is determined as prolonged fatigue sensation in patients which is evoked by cancer or cancer treatment. It occurs in 70-100% of patients undergoing chemotherapy, immunotherapy, radiotherapy and surgical treatment. CFS occurrence may be associated with the presence of advanced cancer, its treatment, lack of physical activity, but also coexisting cardiovascular or respiratory diseases, organ failure, cancer cachexia, depression. The simplest form of fatigue evaluation is to measure its intensity with a linear numerical scale. When a mild CFS is detected, the conduct is based on patient education on lifestyle and nutrition. Severe CFS requires treatment of reversible causes of CFS or pharmacotherapy may be considered. Material and methods: The literature review method was used. Conclusion: Symptoms of CFS may vary from person to person, and may vary in appearance

Funkcjonalności ADAS bazujące na zawodach DARPA Urban Challange

Advance driver assistance systems (ADAS) have been commonly introduced in modern car fleet on the roads nowadays. Current computer techniques allow to test and verify even quite complex algorithms used by sophisticated ADAS in real-time simulations. Systems can be tested according to already existing norms or standards e.g. ISO or any other test protocols – like proposed NCAP or NHTSA tests. Every such a test has limitations and conditions that would not be present in the real world, like only one target car. In 2007 the 3rd edition of DARPA Grand Challenge known as DARPA Urban Challenge (DUC) took place. During competition fully autonomous vehicles needed to complete safe driving along realistic urban area respecting all standard US traffic rules and taking into account existing in reality other road players. Based on requirements of DUC a series of test protocols of computer simulation have been proposed. Virtual fully autonomous vehicle has been controlled by the series of split out single action ADAS systems for easier analysis of the car behaviour, at the early test phase. Although It has successfully completed test run, developed own control algorithms needs further optimization.Zaawansowane systemy wspomagające kierowcę (Advance Driver Assistance Systems - ADAS) odnajdują powszechne zastosowanie we współczesnych samochodach. Aktualne techniki komputerowe pozwalają na wykonywanie testów i weryfikacji nawet skomplikowanych algorytmów, użytych w złożonych systemach ADAS, w symulacjach czasu rzeczywistego. Systemy takie mogą być testowane zgodnie z istniejącymi normami i standardami (na przykład: ISO) oraz protokołami (na przykład zaproponowane przez NCAP lub NHTSA). Każdy z tych testów ma jednak pewne ograniczenia, które nie są możliwe do spełnienia w przypadku fizycznych testów, jak chociażby tylko jeden dodatkowy samochód jako monitorowany obiekt. W 2007r. odbyła się trzecia edycja DARPA Grand Challenge, znana także jako DARPA Urban Challenge (DUC). Podczas zawodów, w pełni autonomiczne samochody miały za zadanie bezpiecznie ukończyć przejazd po realistycznym terenie miejskim z uwzględnieniem zarówno wszystkich przepisów ruchu drogowego (USA) jak i innych (fizycznie występujących w teście) uczestników ruchu. Opierając się o wymagania DUC wykonana została zaproponowana seria symulacji komputerowych. W pełni autonomiczny, wirtualny pojazd, kontrolowany był przez serię rozdzielonych, niezależnych i jednozadaniowych systemów ADAS dla łatwiejszej analizy zachowania samochodu we wczesnej fazie testów. Pomimo udanego ukończenia przejazdu testowego, algorytmy sterujące samochodem wymagają dalszej optymalizacji

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved “ab-initio” docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance “gap” was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements