PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines

Secondary structure prediction is a crucial task for understanding the variety of protein structures and performed biological functions. Prediction of secondary structures for new proteins using their amino acid sequences is of fundamental importance in bioinformatics. We propose a novel technique to predict protein secondary structures based on position-specific scoring matrices (PSSMs) and physico-chemical properties of amino acids. It is a two stage approach involving multiclass support vector machines (SVMs) as classifiers for three different structural conformations, viz., helix, sheet and coil. In the first stage, PSSMs obtained from PSI-BLAST and five specially selected physicochemical properties of amino acids are fed into SVMs as features for sequence-to-structure prediction. Confidence values for forming helix, sheet and coil that are obtained from the first stage SVM are then used in the second stage SVM for performing structure-to-structure prediction. The two-stage cascaded classifiers (PSP_MCSVM) are trained with proteins from RS126 dataset. The classifiers are finally tested on target proteins of critical assessment of protein structure prediction experiment-9 (CASP9). PSP_MCSVM with brainstorming consensus procedure performs better than the prediction servers like Predator, DSC, SIMPA96, for randomly selected proteins from CASP9 targets. The overall performance is found to be comparable with the current state-of-the art. PSP_MCSVM source code, train-test datasets and supplementary files are available freely in public domain at: http://sysbio.icm.edu.pl/secstruct and http://code.google.com/p/cmater-bioinfo

Eastern Ghats Province (India)-Rayner Complex (Antarctica) accretion: Timing the event

There is consensus that, at 1.0–0.9 Ga, the granulites in the Eastern Ghats Province (EGP), Eastern India, and the Rayner Complex, Antarctica, were parts of a coherently evolved crustal block. Paleogeographic reconstructions suggest that in the Neoproterozoic/Early Paleozoic, India and Antarctica were closely positioned at equatorial latitudes in two periods at 1.0–0.9 Ga and 0.6–0.5 Ga. The question is, in which of these periods did the EGP–India vis-à-vis India–Antarctica accretion occur. Top-to-the-west thrusts juxtaposed the EGP with the Bastar Craton, a part of the Greater India landmass. The eastern fringe of the craton underwent anatexis (750–780 °C; 8–9 kbar) and high deformation strain that demonstrably weakened westward. Zircon in the anatectic migmatites at the EGP margin and in the weakly-deformed and non-migmatite granite in the hinterland in the west yields U–Pb upper intercept ages of 2.5–2.4 Ga whereas titanite, hosted in the leucosome of a metatexite and in a granite, has an age of 502 ± 3 Ma coinciding with the lower intercept ages of zircon discordia lines. The lack of 1.0–0.9 Ga dates in the cratonic margin suggests that the EGP accreted with the Bastar Craton and the Greater India landmass at 0.5 Ga during the Gondwanaland assembly, and not in the Early Neoproterozoic. It is within the realms of possibility that the EGP had already separated from the Rayner Complex during the disintegration of Rodinia, and therefore, the 0.5 Ga accretion of the dismembered EGP with Greater India may not be symptomatic of India–Antarctica accretion, in spite of the proximity of the two landmasses inferred from paleogeographic reconstructions

Balanced Multipath Source Routing ⋆

Abstract. We consider the problem of balancing the traffic load ideally over a wireless multihop network. In previous work, a systematic approach to this task was undertaken, starting with an approximate optimisation method that guarantees a provable congestion performance bound, and then designing a distributed implementation by modifying the DSR protocol. In this paper, the performance of the resulting Balanced Multipath Source Routing (BMSR) protocol is validated in a number of simulated networking scenarios. In particular, we study the effect of irregular network structure on the performance of the protocol, and compare it to the performance of DSR and an idealised shortest-path routing algorithm in setups with several source-destination pairs. For all network scenarios we consider, BMSR outperforms DSR significantly. BMSR is also shown to be more robust than the shortest-path algorithm, in that it can distribute the traffic load more evenly in cases where shortest-path routing is impeded by radio interference between proximate paths.

Encounter based sensor tracking.

This paper addresses the problem of tracking a group of mobile sensors in an environment where there is intermittent or no access to a localization service, such as the Global Positioning System. Example applications include tracking personnel underground or animals under dense tree canopies. We assume that each sensor uses inertial, visual or mechanical odometry to measure its relative movement as a series of displacement vectors. Each displacement vector suffers a small quantity of error which compounds, causing the overall accuracy of the positional estimate to decrease with time. The primary contribution of this paper is a novel offline method of counteracting this error by exploiting opportunistic radio encounters between sensors. We fuse encounter information with the displacement vectors to build a graph that models sensor mobility. We show that two dimensional sensor tracking is equivalent to finding an embedding of this graph in the plane. Finally, using radio, inertial and ground truth trace data, we conduct simulations to observe how the number of anchors, transmission range and radio noise affect the performance of the proposed model. We compare these results to those from a competing model in the literature. © 2012 ACM