EFFICIENT AND SCALABLE NETWORK SECURITY PROTOCOLS BASED ON LFSR SEQUENCES

The gap between abstract, mathematics-oriented research in cryptography and the engineering approach of designing practical, network security protocols is widening. Network researchers experiment with well-known cryptographic protocols suitable for different network models. On the other hand, researchers inclined toward theory often design cryptographic schemes without considering the practical network constraints. The goal of this dissertation is to address problems in these two challenging areas: building bridges between practical network security protocols and theoretical cryptography. This dissertation presents techniques for building performance sensitive security protocols, using primitives from linear feedback register sequences (LFSR) sequences, for a variety of challenging networking applications. The significant contributions of this thesis are: 1. A common problem faced by large-scale multicast applications, like real-time news feeds, is collecting authenticated feedback from the intended recipients. We design an efficient, scalable, and fault-tolerant technique for combining multiple signed acknowledgments into a single compact one and observe that most signatures (based on the discrete logarithm problem) used in previous protocols do not result in a scalable solution to the problem. 2. We propose a technique to authenticate on-demand source routing protocols in resource-constrained wireless mobile ad-hoc networks. We develop a single-round multisignature that requires no prior cooperation among nodes to construct the multisignature and supports authentication of cached routes. 3. We propose an efficient and scalable aggregate signature, tailored for applications like building efficient certificate chains, authenticating distributed and adaptive content management systems and securing path-vector routing protocols. 4. We observe that blind signatures could form critical building blocks of privacypreserving accountability systems, where an authority needs to vouch for the legitimacy of a message but the ownership of the message should be kept secret from the authority. We propose an efficient blind signature that can serve as a protocol building block for performance sensitive, accountability systems. All special forms digital signatures—aggregate, multi-, and blind signatures—proposed in this dissertation are the first to be constructed using LFSR sequences. Our detailed cost analysis shows that for a desired level of security, the proposed signatures outperformed existing protocols in computation cost, number of communication rounds and storage overhead

Identification of internalin-A-like virulent proteins in Leishmania donovani

Abstract Background An active immune surveillance and a range of barriers to infection allow the host to effectively eliminate microbial pathogens. However, pathogens may use diverse strategies to subdue such host defences. For instance, one such mechanism is the use of leucine-rich repeat (LRR) proteins by pathogens (microbial) to cause infection. In this study, we aimed at identifying novel virulence factor(s) in Leishmania donovani, based on the possibility of lateral gene transfers of bacterial virulence factor(s) to L. donovani. Methods Rigorous homology searching protocols including Hidden Markov Model (HMM) and BLASTp based searches were employed to detect remote but significant similarities between L. donovani proteins and bacterial virulence factors. Results We found that some L. donovani proteins are similar to internalin-A (Inl-A) protein of Listeria monocytogenes, a surface LRR protein that helps mediate host cell invasion by interacting with E-cadherin on the cell membrane. However, to date, no such invasion mechanism has been reported in Leishmania donovani, the causative agent of visceral leishmaniasis. Moreover, a comparative LRR motif analysis of L. donovani Inl-A-like proteins against the Inl-A protein of L. monocytogenes revealed existence of characteristic consensus LRR regions, suggesting a reliable evolutionary relationship between them. Further, through rigorous three dimensional (3D) modeling of L. donovani Inl-A-like proteins and subsequent molecular docking studies we suggest the probability of human E-cadherin binding with the L. donovani Inl-A-like proteins. Conclusions We have identified three potential candidates (UniProt ID: E9B7L9, E9BMT7 and E9BUL5) of Inl-A-like LRR containing proteins in L. donovani with the help of systematic whole genome sequence analysis. Thus, herein we propose the existence of a novel class of Inl-A-like virulence factor proteins in L. donovani and other Leishmania species based on sequence similarity, phylogenetic analysis and molecular modelling studies in L. donovani

SoccerKDNet: A Knowledge Distillation Framework for Action Recognition in Soccer Videos

Classifying player actions from soccer videos is a challenging problem, which has become increasingly important in sports analytics over the years. Most state-of-the-art methods employ highly complex offline networks, which makes it difficult to deploy such models in resource constrained scenarios. Here, in this paper we propose a novel end-to-end knowledge distillation based transfer learning network pre-trained on the Kinetics400 dataset and then perform extensive analysis on the learned framework by introducing a unique loss parameterization. We also introduce a new dataset named SoccerDB1 containing 448 videos and consisting of 4 diverse classes each of players playing soccer. Furthermore, we introduce an unique loss parameter that help us linearly weigh the extent to which the predictions of each network are utilized. Finally, we also perform a thorough performance study using various changed hyperparameters. We also benchmark the first classification results on the new SoccerDB1 dataset obtaining 67.20% validation accuracy. Apart from outperforming prior arts significantly, our model also generalizes to new datasets easily. The dataset has been made publicly available at: https://bit.ly/soccerdb1Comment: Accepted to 10th Springer PReMI 202

Improvement of alignment accuracy utilizing sequentially conserved motifs

Background: Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In recent times, improvement of existing progressing programs and implementation of new iterative algorithms have made a significant change in this field. Results: We report an alignment algorithm that combines progressive dynamic algorithm, local substructure alignment and iterative refinement to achieve an improved, user-interactive tool. Large-scale benchmarking studies show that this FMALIGN server produces alignments that, aside from preservation of functional and structural conservation, have accuracy comparable to other popular multiple alignment programs. Conclusions: The FMALIGN server allows the user to fix conserved regions in equivalent position in the alignment thereby reducing the chance of global misalignment to a great extent. FMALIGN is available at http://caps.ncbs.res.in/FMALIGN/Home.html

An Optimization-Based Topology Error Detection Method for Power System State Estimation

The paper presents an optimization-based method for topology error detection in power systems. The method utilizes the\ua0residual analysis\ua0in state estimation and minimization of normalized measurement residual, with the application of matrix inverse lemma. The work considers a hybrid measurement configuration, i.e., both SCADA and PMU measurements, for the test systems studied. The proposed method is implemented on the TOMLAB optimization platform under the mixed integer nonlinear programming category. The proposed method has been applied and tested on standard IEEE 14-bus and IEEE 118-bus test systems. The method is designed to be computationally efficient and produces accurate results for single topology error detection. The results from the IEEE 14-bus and IEEE 118-bus test systems have shown that the proposed method produces 100% and 94% accurate results for single topology error detection, respectively. The proposed method performs robustly with the increased measurement uncertainties and inclusion of bad data or gross errors in the measurements. The method has superiority in practical implementation over the meta-heuristics-based optimization methods. The proposed method can be easily implemented and could have potential application in the\ua0energy management systems\ua0of the power system control center

Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases

Glaucoma, the leading cause of irreversible blindness, appears in various forms. Mutations in CYP1B1 result in primary congenital glaucoma (PCG) by an autosomal recessive mode of inheritance while it acts as a modifier locus for primary open angle glaucoma (POAG). We investigated the molecular basis of the variable phenotypes resulting from the defects in CYP1B1 by using subclones of 23 CYP1B1 mutants reported in glaucoma patients, in a cell based system by measuring the dual activity of the enzyme to metabolize both retinol and 17β-estradiol. Most variants linked to POAG showed low steroid metabolism while null or very high retinol metabolism was observed in variants identified in PCG. We examined the translational turnover rates of mutant proteins after the addition of cycloheximide and observed that the levels of enzyme activity mostly corroborated the translational turnover rate. We performed extensive normal mode analysis and molecular-dynamics-simulationsbased structural analyses and observed significant variation of fluctuation in certain segmental parts of the mutant proteins, especially at the B-C and F-G loops, which were previously shown to affect the dynamic behavior and ligand entry/exit properties of the cytochrome P450 family of proteins. Our molecular study corroborates the structural analysis,and suggests that the pathologic state of the carrier of CYP1B1 mutations is determined by the allelic state of the gene. To our knowledge, this is the first attempt to dissect biological activities of CYP1B1 for correlation with congenital and adult onset glaucomas

SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs

Establishment of similarities between proteins is very important for the study of the relationship between sequence, structure and function and for the analysis of evolutionary relationships. Motif-based search methods play a crucial role in establishing the connections between proteins that are particularly useful for distant relationships. This paper reports SCANMOT, a web-based server that searches for similarities between proteins by simultaneous matching of multiple motifs. SCANMOT searches for similar sequences in entire sequence databases using multiple conserved regions and utilizes inter-motif spacing as restraints. The SCANMOT server is available via

Refining multiple sequence alignments with conserved core regions

Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same time preserves the family's overall block model. Large-scale benchmarking studies showed a noticeable improvement of alignment after refinement. This can be inferred from the increased alignment score and enhanced sensitivity for database searching using the sequence profiles derived from refined alignments compared with the original alignments. A standalone version of the program is available by ftp distribution () and will be incorporated into the next release of the Cn3D structure/alignment viewer

Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function

Developmental defects in motile cilia, arising from genetic abnormalities in one or more ciliary genes, can lead to a common ciliopathy known as primary ciliary dyskinesia (PCD). Functional studies in model organisms undertaken to understand PCD or cilia biogenesis have identified 100s of genes regulated by Foxj1, the master regulator of motile ciliogenesis. However, limited systems based studies have been performed to elucidate proteins or network/s crucial to the motile ciliary interactome, although this approach holds promise for identification of multiple cilia-associated genes, which, in turn, could be utilized for screening and early diagnosis of the disease. Here, based on the assumption that FOXJ1-mediated regulatory and signaling networks are representative of the motile cilia interactome, we have constructed and analyzed the gene regulatory and protein–protein interaction network (PPIN) mediated by FOXJ1. The predicted FOXJ1 regulatory network comprises of 424 directly and 148 indirectly regulated genes. Additionally, based on gene ontology analysis, we have associated 17 directly and 6 indirectly regulated genes with possible ciliary roles. Topological and perturbation analyses of the PPIN (6927 proteins, 40,608 interactions) identified 121 proteins expressed in ciliated cells, which interact with multiple proteins encoded by FoxJ1 induced genes (FIG) as important interacting proteins (IIP). However, it is plausible that IIP transcriptionally regulated by FOXJ1 and/or differentially expressed in PCD are likely to have crucial roles in motile cilia. We have found 20 de-regulated topologically important effector proteins in the FOXJ1 regulatory network, among which some (PLSCR1, SSX2IP, ACTN2, CDC42, HSP90AA1, PIAS4) have previously reported ciliary roles. Furthermore, based on pathway enrichment of these proteins and their primary interactors, we have rationalized their possible roles in the ciliary interactome. For instance, 5 among these novel proteins that are involved in cilia associated signaling pathways (like Notch, Wnt, Hedgehog, Toll-like receptor etc.) could be ‘topologically important signaling proteins.’ Therefore, based on this FOXJ1 network study we have predicted important effectors in the motile cilia interactome, which are possibly associated with ciliary biology and/or function and are likely to further our understanding of the pathophysiology in ciliopathies like PCD