Subtyping of Dengue Viruses using Return Time Distribution based Appproach

Dengue virus (DENV) is the causative agent of Dengue Hemorrhagic Fever and Dengue Shock Syndrome, and continues to represent a major public health hazard. DENVs are antigenically classified in four serotypes and each serotype is further divided into respective genotypes. The association between DENV subtypes and the kind & severity of disease caused by them is known. Experimental and computational approaches for subtyping are routinely used for the purpose of diagnosis and treatment of DENV, in addition to the study of phylodynamics. All virus-specific molecular subtyping tools make use of sequence alignments at backend. But as the volume of molecular data increases, alignment-dependent methods become computationally intensive. Hence, the need for alternative efficient approaches for subtyping of viruses becomes apparent. Recently, the concept of Return time distribution (RTD) was proposed and validated for alignment-free clustering and molecular phylogeny. The RTD-based approach is extended here for the subtyping of DENVs. 
Subtyping methodology involves compilation of curated genomic data of known subtypes, computing RTD of these sequences at different levels of k-mers, derivation a distance matrix and clustering. The subtype of the unknown is predicted based on its clustering with known subtypes.
Dataset consisting of 1359 DENV genomes with sequence identity (>92%) were clustered using the RTD based approach at k=5. Serotype specific clades, despite geographical and temporal variation in the dataset, were observed with 100% accuracy. The method was also found to be efficient in terms of time and implementation, apart from accuracy in the subtyping of DENV

Analysis of Next-generation Sequencing Data in Virology - Opportunities and Challenges

Viruses are the most abundant and the smallest organisms, which are relatively simple to sequence. Genome sequence data of viruses for individual species to populations outnumber that of other species. Although this offers an opportunity to study viral diversity at varying levels of taxonomic hierarchy, it also poses challenges for systematic and structured organization of data and its downstream processing. Extensive computational analyses using a number of algorithms and programs have opened exciting opportunities for virus discovery and diagnostics, apart from augmenting our understanding of the intriguing world of viruses. Unravelling evolutionary dynamics of viruses permits improved understanding of phenomena such as quasispecies diversity, role of mutations in host switching and drug resistance, which enables the tangible measurements of genotype and phenotype of viruses. Improved understanding of geno-/serotype diversity in correlation with antigenic diversity will facilitate rational design and development of efficacious vaccines against emerging and re-emerging viruses. Mathematical models developed using the genomic data could be used to predict the spread of viruses due to vector switching and the (re)emergence due to host switching and, thereby, contribute towards designing public health policies for disease management and control

CEP: a conformational epitope prediction server

CEP server () provides a web interface to the conformational epitope prediction algorithm developed in-house. The algorithm, apart from predicting conformational epitopes, also predicts antigenic determinants and sequential epitopes. The epitopes are predicted using 3D structure data of protein antigens, which can be visualized graphically. The algorithm employs structure-based Bioinformatics approach and solvent accessibility of amino acids in an explicit manner. Accuracy of the algorithm was found to be 75% when evaluated using X-ray crystal structures of Ag–Ab complexes available in the PDB. This is the first and the only method available for the prediction of conformational epitopes, which is an attempt to map probable antibody-binding sites of protein antigens

Conversion of Natural Resources through Waste reduction at the Processing Step by Briquetting Technique

India is gifted by nature by way of large quantities of high grade nonferrous mineral resources like barite containing more than 90% barium sulphate. The processing of barite to win chemicals from it requires its carbotherrnic reduction at high temperatures being carried out in rotary furnaces. The powdered charge containing barium sulfide is prone to get damaged due to reverse reaction caused by infiltered oxygen at the end of reduction state. This hampers the yield of water soluble barium sulfide.The paper discusses about the means of achieving favourbale kinetics and high recovery of water soluble barium sulphide in the carbothermic reduction of barite at high temperatures. The reaction rate of reduction step was enhanced many folds by using briquetting technique. Even with barite containing large amnount of harmful impurites, the yield of barium was improved considerably on pilot plant scale, thus achieving better utilisation of natural resoures such as barite and coke

Databases and Algorithms in Allergen Informatics

Allergic diseases are considered as one of the major health problems worldwide due to their increasing prevalence. Advancements in genomic, proteomic, and analytical techniques have resulted in considerable progress in the field of allergology, which has led to accumulation of huge amount of data. Allergen bioinformatics comprises allergen-related data resources and computational methods/tools, which deal with an efficient archival, management, and analysis of allergological data. Significant work has been done in the area of allergen bioinformatics that has proven pivotal for the development and progress of this field. In this chapter, we describe the current status of databases and algorithms, encompassing the field of allergen bioinformatics by examining work carried out thus far with respect to features such as allergens and allergenicity, allergen databases, algorithms/tools for allergen/allergenicity prediction, allergen epitope prediction, and allergenic cross-reactivity assessment. This chapter illustrates concepts and algorithms in allergen bioinformatics, as well as it outlines the key areas for potential development in allergology field

Snail Homing and Mating Search Algorithm: A Novel Bio-Inspired Metaheuristic Algorithm

In this paper, a novel Snail Homing and Mating Search (SHMS) algorithm is proposed. It is inspired from the biological behaviour of the snails. Snails continuously travels to find food and a mate, leaving behind a trail of mucus that serves as a guide for their return. Snails tend to navigate by following the available trails on the ground and responding to cues from nearby shelter homes. The proposed SHMS algorithm is investigated by solving several unimodal and multimodal functions. The solutions are validated using standard statistical tests such as two-sided and pairwise signed rank Wilcoxon test and Friedman rank test. The solution obtained from the SHMS algorithm exhibited superior robustness as well as search space exploration capabilities within the less computational cost. The real-world application of SHMS algorithm is successfully demonstrated in the engineering design domain by solving three cases of design and economic optimization shell and tube heat exchanger problem. The objective function value and other statistical results obtained using SHMS algorithm are compared with other well-known metaheuristic algorithms.Comment: 46 Pages, 11 Figures, 24 Table

A critical review on Vagbhatokta Niruha Basti

Ayurveda is very well known science in this global scenario because of its holistic approach towards positive lifestyle. In Ayurveda for treating any disorder it has two ways to deal with it i.e. Shodhana and Shamana Chikitsa. Out of this Niruha Basti Chikitsa is considered as one of the Shodhana Chikitsa. The word Basti (medicated enema) means bladder. In ancient times bladder of animal is used to conduct this procedure. Hence the procedure is named as Basti Karma. Different types of Niruha Basti are mentioned in Samhitas by using different permutations and combinations of herbs as per the need of action. Due to some traditional mindsets these Niruha Yogas were not widely practiced now a day. So this article aims to review the different combinations of Niruha Basti as told in Ashtanga Hridaya Samhita in order to explore the scientific approach for the benefit of mankind