Current Issue : April - June Volume : 2015 Issue Number : 2 Articles : 6 Articles
This paper presents a hybrid method to extract endocardial contour of the right ventricular (RV) in 4-slices from 3D\nechocardiography dataset. The overall framework comprises four processing phases. In Phase I, the region of interest (ROI) is\nidentified by estimating the cavity boundary. Speckle noise reduction and contrast enhancement were implemented in Phase II as\npreprocessing tasks. In Phase III, the RV cavity region was segmented by generating intensity threshold which was used for once\nfor all frames. Finally, Phase IV is proposed to extract the RV endocardial contour in a complete cardiac cycle using a combination\nof shape-based contour detection and improved radial search algorithm. The proposed method was applied to 16 datasets of 3D\nechocardiography encompassing the RV in long-axis view. The accuracy of experimental results obtained by the proposed method\nwas evaluated qualitatively and quantitatively. It has been done by comparing the segmentation results of RV cavity based on\nendocardial contour extraction with the ground truth.The comparative analysis results show that the proposed method performs\nefficiently in all datasets with overall performance of 95% and the root mean square distances (RMSD) measure in terms of mean\n�± SD was found to be 2.21 �± 0.35mm for RV endocardial contours....
TheAUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins\nupon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three\nof the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two\nadditional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining\nthe disease potential of mutations associated with nonsynonymous single nucleotide polymorphisms (nsSNPs) in human proteins.\nThese five command-line driven tools, as well as all the supporting programs, complement those that run our AUTO-MUTE webbased\nserver. Nevertheless, all the codes have been rewritten and substantially altered for the new portable software, and they\nincorporate several new features based on user feedback. Included among these upgrades is the ability to perform three highly\nrequested tasks: to run ââ?¬Å?big dataââ?¬Â batch jobs; to generate predictions using modified protein data bank (PDB) structures, and\nunpublished personal models prepared using standard PDB file formatting; and to utilize NMR structure files that containmultiple\nmodels....
This paper proposes the use of ultrasonic microscale subarrayed MIMO RADARs to estimate the position of breast cancer nodes.\nThetransmit and receive antenna arrays are divided into subarrays. In order to increase the signal diversity each subarray is assigned\na different waveform from an orthogonal set. High-frequency ultrasonic transducers are used since a breast is considered to be\na superficial structure. Closed form expressions for the optimal Neyman-Pearson detector are derived. The combination of the\nwaveform diversity present in the subarrayed deployment and traditional phased-array RADAR techniques provides promising\nresults....
Background. Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples.\nDegenerate primers that anneal to conserved regions can facilitate amplification of divergent, lowconcentration variants, evenwhen\nthe strain present is unknown. Results. A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping\namplicons across multiple whole genomes is described. The new script, run tiled primers, is part of the PriMux software.\nPrimers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses,\nArenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Each\ngroup is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross\nreactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to\nspecifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo.\nConclusions.This software should help researchers designmultiplex sets of primers for targeted whole genome enrichment prior to\nsequencing to obtain better coverage of lowtiter, divergent viruses.Applications include viral discovery froma complex background\nand improved sensitivity and coverage of rapidly evolving strains or variants in a gene family...
This study aims to design epitope-based peptides for the utility of vaccine development by targeting glycoprotein G and envelope\nprotein F ofNipah virus (NiV) that, respectively, facilitate attachment and fusion ofNiV with host cells.Using various databases and\ntools,immune parameters of conserved sequence(s) fromGand F proteins of different isolates ofNiVwere tested to predict probable\nepitope(s). Binding analyses of the peptides with MHC class-I and class-II molecules, epitope conservancy, population coverage,\nand linear B cell epitope prediction were analyzed. Predicted peptides interacted with seven or more MHC alleles and illustrated\npopulation coverage of more than 99% and 95%, for G and F proteins, respectively. The predicted class-I nonamers, SLIDTSSTI\nand EWISIVPNF, superimposed on the putative decameric B cell epitopes, were also identified as core sequences of the most\nprobable class-II 15-mer peptides GPKVSLIDTSSTITI and EWISIVPNFILVRNT. These peptides were further validated for their\nbinding to specific HLA alleles using in silico docking technique. Our in silico analysis suggested that the predicted epitopes, either\nGPKVSLIDTSSTITI or EWISIVPNFILVRNT, could be a better choice as universal vaccine component against NiV irrespective of\ndifferent isolates which may elicit both humoral and cell-mediated immunity....
Histone deacetylase (HDAC) has a critical function in regulating gene expression. The inhibition of HDAC has developed as an\ninteresting anticancer research area that targets biological processes such as cell cycle, apoptosis, and cell differentiation. In this\nstudy, an HDAC inhibitor that is available commercially, suberoyl anilide hydroxamic acid (SAHA), has been modified to improve\nits efficacy and reduce the side effects of the compound. Hydrophobic cap and zinc-binding group of these compounds were\nsubstituted with boron-based compounds, whereas the linker region was substituted with p-aminobenzoic acid. The molecular\ndocking analysis resulted in 8 ligands with ?G binding value more negative than the standards, SAHA and trichostatin A (TSA). That\nligands were analyzed based on the nature of QSAR, pharmacological properties, and ADME-Tox. It is conducted to obtain a potent\ninhibitor of HDAC class II Homo sapiens.The screening process result gave one best ligand, Nova2 (513246-99-6), which was then\nfurther studied by molecular dynamics simulations....
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