Comparative study of physiological and pathological autoimmune models

7

Development of a New Framework for Distributed Processing of Geospatial Big Data

Geospatial technology is still facing a lack of “out of the box” distributed processing solutions which are suitable for the amount and heterogeneity of geodata, and particularly for use cases requiring a rapid response. Moreover, most of the current distributed computing frameworks have important limitations hindering the transparent and flexible control of processing (and/or storage) nodes and control of distribution of data chunks. We investigated the design of distributed processing systems and existing solutions related to Geospatial Big Data. This research area is highly dynamic in terms of new developments and the re-use of existing solutions (that is, the re-use of certain modules to implement further specific developments), with new implementations continuously emerging in areas such as disaster management, environmental monitoring and earth observation. The distributed processing of raster data sets is the focus of this paper, as we believe that the problem of raster data partitioning is far from trivial: a number of tiling and stitching requirements need to be addressed to be able to fulfil the needs of efficient image processing beyond pixel level. We attempt to compare the terms Big Data, Geospatial Big Data and the traditional Geospatial Data in order to clarify the typical differences, to compare them in terms of storage and processing backgrounds for different data representations and to categorize the common processing systems from the aspect of distributed raster processing. This clarification is necessary due to the fact that they behave differently on the processing side, and particular processing solutions need to be developed according to their characteristics. Furthermore, we compare parallel and distributed computing, taking into account the fact that these are used improperly in several cases. We also briefly assess the widely-known MapReduce paradigm in the context of geospatial applications. The second half of the article reports on a new processing framework initiative, currently at the concept and early development stages, which aims to be capable of processing raster, vector and point cloud data in a distributed IT ecosystem. The developed system is modular, has no limitations on programming language environment, and can execute scripts written in any development language (e.g. Python, R or C#)

Accurate interaction energies at DFT level by means of an efficient dispersion correction

This paper presents an approach for obtaining accurate interaction energies at the DFT level for systems where dispersion interactions are important. This approach combines Becke and Johnson's [J. Chem. Phys. 127, 154108 (2007)] method for the evaluation of dispersion energy corrections and a Hirshfeld method for partitioning of molecular polarizability tensors into atomic contributions. Due to the availability of atomic polarizability tensors, the method is extended to incorporate anisotropic contributions, which prove to be important for complexes of lower symmetry. The method is validated for a set of eighteen complexes, for which interaction energies were obtained with the B3LYP, PBE and TPSS functionals combined with the aug-cc-pVTZ basis set and compared with the values obtained at CCSD(T) level extrapolated to a complete basis set limit. It is shown that very good quality interaction energies can be obtained by the proposed method for each of the examined functionals, the overall performance of the TPSS functional being the best, which with a slope of 1.00 in the linear regression equation and a constant term of only 0.1 kcal/mol allows to obtain accurate interaction energies without any need of a damping function for complexes close to their exact equilibrium geometry

Mutations in the carboxy-terminal part of IS30 transposase affect the formation and dissolution of (IS30)2 dimer

AbstractThe transposase of IS30 catalyses different transpositional rearrangements via the dimer (IS30)2 intermediate structure. Mutation analysis provides evidence that the C-terminal part of IS30 transposase is required for the formation and dissolution of (IS30)2 dimer. C-terminal mutants are also defective in transpositional fusion; however, this deficiency can be `suppressed' by addition of the final product of site-specific dimerisation, the core (IS30)2 intermediate structure. The transposase part studied shows significant homologies in three highly conserved regions to proteins of IS30-related mobile elements

Functional organization of the inverted repeats of IS30.

The mobile element IS30 has 26-bp imperfect terminal inverted repeats (IRs) that are indispensable for transposition. We have analyzed the effects of IR mutations on both major transposition steps, the circle formation and integration of the abutted ends, characteristic for IS30. Several mutants show strikingly different phenotypes if the mutations are present at one or both ends and differentially influence the transposition steps. The two IRs are equivalent in the recombination reactions and contain several functional regions. We have determined that positions 20 to 26 are responsible for binding of the N-terminal domain of the transposase and the formation of a correct 2-bp spacer between the abutted ends. However, integration is efficient without this region, suggesting that a second binding site for the transposase may exist, possibly within the region from 4 to 11 bp. Several mutations at this part of the IRs, which are highly conserved in the IS30 family, considerably affected both major transposition steps. In addition, positions 16 and 17 seem to be responsible for distinguishing the IRs of related insertion sequences by providing specificity for the transposase to recognize its cognate ends. Finally, we show both in vivo and in vitro that position 3 has a determining role in the donor function of the ends, especially in DNA cleavage adjacent to the IRs. Taken together, the present work provides evidence for a more complex organization of the IS30 IRs than was previously suggested