Visual Analysis of Biomolecular Surfaces

Surface models of biomolecules have become crucially important for the study and understanding of interaction between biomolecules and their environment. We argue for the need for a detailed understanding of biomolecular surfaces by describing several applications in computational and structural biology. We review methods used to model, represent, characterize, and visualize biomolecular surfaces focusing on the role that geometry and topology play in identifying features on the surface. These methods enable the development of efficient computational and visualization tools for studying the function of biomolecules.

Fusion of Multisensor Data:Review and Comparative Analysis

Image fusion is a formal framework which is expressed as means and tools for the alliance of multisensor, multitemporal, and multiresolution data. Multisource data vary in spectral, spatial and temporal resolutions necessitating advanced analytical or numerical techniques for enhanced interpretation capabilities. This paper reviews seven pixel based image fusion techniques - intensity-hue-saturation, brovey, high pass filter (HPF), high pass modulation (HPM), principal component analysis, fourier transform and correspondence analysis.Validation of these techniques on IKONOS data (Panchromatic band at I m spatial resolution and Multispectral 4 bands at 4 in spatial resolution) reveal that HPF and HPM methods synthesises the images closest to those the corresponding multisensors would observe at the high resolution level.

Lectin Microarrays for Glycomic Analysis

Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. Glycocalyx of mammalian cells actively participate in cell-cell, cell-matrix, and cell-pathogen interactions, which impact embryogenesis, growth and development, homeostasis, infection and immunity, signaling, malignancy, and metabolic disorders. Relative to genomics and proteomics, glycomics is just growing out of infancy with great potential in biomedicine for biomarker discovery, diagnosis, and treatment. However, the immense diversity and complexity of glycan structures and their multiple modes of interactions with proteins pose great challenges for development of analytical tools for delineating structure function relationships and understanding glycocode. Several tools are being developed for glycan profiling based on chromatography,m mass spectrometry, glycan microarrays, and glyco-informatics. Lectins, which have long been used in glyco-immunology, printed on a microarray provide a versatile platform for rapid high throughput analysis of glycoforms of biological samples. Herein, we summarize technological advances in lectin microarrays and critically review their impact on glycomics analysis. Challenges remain in terms of expansion to include nonplant derived lectins, standardization for routine clinical use, development of recombinant lectins, and exploration of plant kingdom for discovery of novel lectins.

Vegetation Analysis in Uttara Kannada District Using GIS and Remote Sensing Techniques

Uttara Kannada is the only district in Karnataka, which has a forested area of about 80% and falls in the region of the Western Ghats. It is considered to be a very resourceful in terms of abundant natural resources and constitutes an important district in Karnataka. The forest resources of the district are under pressure as a large portion of the forested area has been converted to non-forestry activities since independence owing to the increased demands from human and animal population resulting in degradation of the forest ecosystem. This has led to poor productivity and regenerative capacity which is evident in the form of barren hill tops, etc in Coastal taluks of Uttara Kannada, entailing regular monitoring of the forest resources very essential. The classification of forest is a prerequisite for managing forest resources. Geographical Information System (GIS), allows the spatial and temporal analysis of the features of interest, and helps in solving the problem of deforestation and associated environmental and ecological problems. Spatial and temporal tools such as GIS and remotely sensed data helps the planners and decision makers in evolving the sustainable strategies for management and conservation of natural resources. Uttara Kannada district was classified on the basis of the land-use using supervised hard classifiers. The land use categories identified were urban area, water bodies, agricultural land, forest cover, and waste land. Further classification was carried out on the basis of forest type. The types of forest categorised were semi-evergreen, evergreen, moist deciduous, dry deciduous, plantations and scrub, thorny and non-forested area. The identified classes were correlated with the ground data collected during field visits. The observed results were compared with the historic data and the changes in the forest cover were analysed. From the assessment made it was clear that there has been a considerable degree of forest loss in certain areas of the district. It was also observed that plantations and social forests have increased drastically over the last fifteen years,and natural forests have declined.

Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences

Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

Flowfield Analysis of Linear Plug Nozzle

Full-length and truncated linear plug nozzle flowfields have been analyzed, using both experimental and computational tools, for pressure ratios ranging from 5 to 72, which include the transition of an open base wake to a closed base wake. A good agreement has been found between computational and experimental results on the plug surface. Considering the deficiencies of the computational tools in predicting base flows associated with truncated plug nozzles, an engineering model to predict the wake structure transition in such flows is proposed. The utility of this model in conjunction with empirical tools for the closed-wake base pressure prediction is established. The model is validated against the experimental results available in open literature.

Examining the Effectiveness of Discriminant Function Analysis and Cluster Analysis in Species Identification of Male Field Crickets Based on Their Calling Songs

Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and identification.

Analysis of Annular Plug Nozzle Flowfield

The flowfields associated with truncated annular plug nozzles of varying lengths are studied both experimentally and using computational tools. The nozzles are designed to observe wake structure transition for the range of pressure ratios considered. A classification of the open wake regime is proposed for comparing and analyzing the plug flowfields. The three-dimensional relief experienced by the annular plug flow leads to greater wave interactions on the plug surface as compared with linear plug flow, resulting in a delayed transition of the base wake. The Reynolds averaged Navier-Stokes based solvers employed in the studies could predict the plug surface flow accurately, whereas they exhibited limitations with regard to plug base flow predictions. Based on the experimental data generated, an empirical model for predicting closed wake base pressure is proposed and compared with other models available in literature.

Streptococcus pneumoniae Genome Database (SPGDB): A database for strain specific comparative analysis of Streptococcus pneumoniae genes and proteins

Streptococcus pneumoniae causes pneumonia, septicemia and meningitis. S. pneumoniae is responsible for significant mortality both in children and in the elderly. In recent years, the whole genome sequencing of various S. pneumoniae strains have increased manifold and there is an urgent need to provide organism specific annotations to the scientific community. This prompted us to develop the Streptococcus pneumoniae Genome Database (SPGDB) to integrate and analyze the completely sequenced and available S. pneumoniae genome sequences. Further, links to several tools are provided to compare the pool of gene and protein sequences, and proteins structure across different strains of S. pneumoniae. SPGDB aids in the analysis of phenotypic variations as well as to perform extensive genomics and evolutionary studies with reference to S. pneumoniae. (C) 2014 Elsevier Inc. All rights reserved.

A survey on compressed domain video analysis techniques

Image and video analysis requires rich features that can characterize various aspects of visual information. These rich features are typically extracted from the pixel values of the images and videos, which require huge amount of computation and seldom useful for real-time analysis. On the contrary, the compressed domain analysis offers relevant information pertaining to the visual content in the form of transform coefficients, motion vectors, quantization steps, coded block patterns with minimal computational burden. The quantum of work done in compressed domain is relatively much less compared to pixel domain. This paper aims to survey various video analysis efforts published during the last decade across the spectrum of video compression standards. In this survey, we have included only the analysis part, excluding the processing aspect of compressed domain. This analysis spans through various computer vision applications such as moving object segmentation, human action recognition, indexing, retrieval, face detection, video classification and object tracking in compressed videos.

Fabrication and Nonlinear Thermomechanical Analysis of SU8 Thermal Actuator

SU8-based micromechanical structures are widely used as thermal actuators in the development of compliant micromanipulation tools. This paper reports the design, nonlinear thermomechanical analysis, fabrication, and thermal actuation of SU8 actuators. The thermomechanical analysis of the actuator incorporates nonlinear temperature-dependent properties of SU8 polymer to accurately model its thermal response during actuation. The designed SU8 thermal actuators are fabricated using surface micromachining techniques and the electrical interconnects are made to them using flip-chip bonding. The issues due to thermal stress during fabrication are discussed and a novel strategy is proposed to release the thermal stress in the fabricated actuators. Subsequent characterization of the actuator using an optical profilometer reveals excellent thermal response, good repeatability, and low hysteresis. The average deflection is similar to 8.5 mu m for an actuation current of similar to 5 mA. The experimentally obtained deflection profile and the tip deflection at different currents are both shown to be in good agreement with the predictions of the nonlinear thermomechanical model. This underscores the need to consider nonlinearities when modeling the response of SU8 thermal actuators. 2015-0087]