A method for probabilistic mapping between protein structure and function taxonomies through cross training

<p>Abstract</p> <p>Background</p> <p>Prediction of function of proteins on the basis of structure and vice versa is a partially solved problem, largely in the domain of biophysics and biochemistry. This underlies the need of computational and bioinformatics approach to solve the problem. Large and organized latent knowledge on protein classification exists in the form of independently created protein classification databases. By creating probabilistic maps between classes of structural classification databases (e.g. SCOP <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>) and classes of functional classification databases (e.g. PROSITE <abbrgrp><abbr bid="B2">2</abbr></abbrgrp>), structure and function of proteins could be probabilistically related.</p> <p>Results</p> <p>We demonstrate that PROSITE and SCOP have significant semantic overlap, in spite of independent classification schemes. By training classifiers of SCOP using classes of PROSITE as attributes and vice versa, accuracy of Support Vector Machine classifiers for both SCOP and PROSITE was improved. Novel attributes, 2-D elastic profiles and Blocks were used to improve time complexity and accuracy. Many relationships were extracted between classes of SCOP and PROSITE using decision trees.</p> <p>Conclusion</p> <p>We demonstrate that presented approach can discover new probabilistic relationships between classes of different taxonomies and render a more accurate classification. Extensive mappings between existing protein classification databases can be created to link the large amount of organized data. Probabilistic maps were created between classes of SCOP and PROSITE allowing predictions of structure using function, and vice versa. In our experiments, we also found that functions are indeed more strongly related to structure than are structure to functions.</p

Primary Tuberculosis of the Breast Manifested as Abscess: a Rare Case Report

Primary breast tuberculosis is a rare entity. We are reporting a case of primary breast tuberculosis, which presented as breast abscess. On histopathology, it was diagnosed as breast tuberculosis. Aspiration cytology was not done due breast abscess. Patient was put on anti-tubercular drugs. In follow up, after 3 months patient condition was improved. Key words: breast, abscess, tuberculosis, conservative treatment

Detailed protein sequence alignment based on Spectral Similarity Score (SSS)

BACKGROUND: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. RESULTS: Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. CONCLUSION: An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral Similarity Score (SSS) is an extension to the conventional similarity methods and results indicate that it holds a strong potential for analysis of various biological sequences and structural variations in proteins

Automatic generation of coverage directives targeting signal relationships by statically analyzing RTL

The coverage problem has been a long standing issue in simulation- based veri cation. Coverage metrics are required to track the progress and justify completeness of simulation vectors. This thesis presents a scalable methodology to automatically generate coverage directives which augment line coverage for complete coverage of the RTL. The directives target ambiguity in register relationships derived by statically analyzing behavioral RTL. A Python-based tool has been built on the presented methodology to gener- ates implication properties for coverage. The generated properties for two cores (Amber and V-scale) are instantiated within the testbenches provided with them. Simulation results with all the test programs highlight module instances with high line coverage but uncovered properties. These properties are formally proven to be reachable, thus highlighting coverage holes with the provided tests and the usefulness of our process.Electrical and Computer Engineerin

The Notion of Morality of Death and Human Behaviour

The ethical shame identified with suicide is examined as it is hard to standardize how we conceive it, as well as our method for treating suicide. It befits an inquiry on the inherent holiness of life, and essentially whether it is worth living or not. ”There is but one truly serious philosophical problem and that is suicide. In the words of one great philosopher, Judging whether life is or is not worth living amounts to answering the fundamental question of philosophy (Camus, 1942). Keywords: Suicide, Analysis, Lif

On The Genealogy of Knowledge Management & Automated Systems in Engine Manufacturing Industry & Perception of BS III and BS IV Heavy Vehicle Drivers in Pune, Maharashtra: A Qualitative Study

Knowledge management plays an important role in manufacturing industry, as machinery & other physical equipments are not the main criteria of innovation but the knowledge of employees. In manufacturing industry, there is lack of explicit knowledge, which makes it difficult to utilize the power of data. In this paper, a new feedback approach is used with knowledge dust and pearls approach [1] to solve problems related to time and employee motivation with respect to knowledge management. A questionnaire was designed, and interviews of truck drivers were taken to get a general perspective on sociological factors

Characterization of electrothermal microfluidic tweezers (REP) in bio-relevant media

Rapid electrokinetic patterning (REP) has proven to be a powerful microfluidic tweezer that generates spatially and temporally specified microflow via electrothermal vortices. The ultra-small trapping forces on the scale of femtoNewtons exerted by REP, due to its viscous drag of the vortical flow on the trapped particles, attracts many potential bio-manipulation applications. We report, for the first time, use of isotonic sugar-based media to simulate bio-relevant environment for flow manipulation through REP. A DC field was introduced, in addition to the typical AC field, to enhance the vortical flow induced particle trapping performance. In this work, we study the effects of the magnitude and sign of the DC offset on the vortex characteristics. Results show that addition of the DC component in the electric field has a significant impact on the electrothermal micro-vortex and the electric double layer of the electrodes and the trapped particles. We also observe that an abrupt change in the DC offset destabilized the vortex and washed away some particles as the trap equilibrium re-established. However, the trap remained stable when the step change in the DC offset was smaller than ~500 mV