Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis

BACKGROUND: Massive Parallel Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and short non-coding RNAs, e.g. miRNAs. The processing methods used to extract and interpret the information are an important aspect of dealing with the vast amounts of data generated from short read sequencing. Although the number of computational tools for MPS data analysis is constantly growing, their strengths and weaknesses as part of a complex analytical pipe-line have not yet been well investigated. PRIMARY FINDINGS: A benchmark MPS miRNA dataset, resembling a situation in which miRNAs are spiked in biological replication experiments was assembled by merging a publicly available MPS spike-in miRNAs data set with MPS data derived from healthy donor peripheral blood mononuclear cells. Using this data set we observed that short reads counts estimation is strongly under estimated in case of duplicates miRNAs, if whole genome is used as reference. Furthermore, the sensitivity of miRNAs detection is strongly dependent by the primary tool used in the analysis. Within the six aligners tested, specifically devoted to miRNA detection, SHRiMP and MicroRazerS show the highest sensitivity. Differential expression estimation is quite efficient. Within the five tools investigated, two of them (DESseq, baySeq) show a very good specificity and sensitivity in the detection of differential expression. CONCLUSIONS: The results provided by our analysis allow the definition of a clear and simple analytical optimized workflow for miRNAs digital quantitative analysis

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

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Traveling waves in trimer granular lattice I: Bifurcation structure of traveling waves in the unit-cell model

Present paper is the first one in the series devoted to the dynamics of traveling waves emerging in the uncompressed, tri-atomic granular crystals. This work is primarily concerned with the dynamics of one-dimensional periodic granular trimer (tri-atomic) chains in the state of acoustic vacuum. Each unit cell consists of three spherical particles of different masses subject to periodic boundary conditions. Hertzian interaction law governs the mutual interaction of these particles. Under the assumption of zero pre-compression, this interaction is modeled as purely nonlinear, which means the absence of linear force component. The dynamics of such chains is governed by the two system parameters that scale the mass ratios between the particles of the unit cell. Such a system supports two different classes of periodic solutions namely the traveling and standing waves. The primary objective of the present study is the numerical analysis of the bifurcation structure of these solutions with emphasis on the dynamics of traveling waves. In fact, understanding of the bifurcation structure of the traveling wave solutions emerging in the unit-cell granular trimer is rather important and can shed light on the more complex nonlinear wave phenomena emerging in semi-infinite trimer chains. (c) 2016 Elsevier B.V. All rights reserved

Traveling waves in trimer granular lattice II: Asymptotic prediction of weakly attenuated pulses

In the present study we consider the impulsive response of perfectly aligned, uncompressed, tri-atomic (trimer) granular lattice. In this study, we demonstrate that under particular choice of the system parameters - impulsively loaded, trimer granular lattice can support formation of highly localized, weakly attenuated pulses. These pulses are manifested by the completely non-symmetric wave profiles and can be attributed to the special family of solitary like waves forming in the non-homogenous, periodic trimer granular lattice in the state of acoustic vacuum. Using the recently developed analytical procedure based on the singular, multi-scale perturbation analysis, we derive a simplified reduced order model predicting the special regions in the space of the system parameters corresponding to the formation of the weakly attenuated pulses. Predictions of the asymptotical model are found to be in very good agreement with the results of numerical simulations of the full trimer granular lattice. From a practical point of view, these results can have important implications in complex, structural optimization problems of wave manipulation in the repetitive granular metamaterials. (C) 2016 Elsevier B.V. All rights reserved

Query based approach to project staffing

The objective of this package is to automate the various activities associated with project staffing. The package assists the management in the selection of Project team13; for any given project. Statistical and graphical details/ reports are also provided

Consecutive transitions from localized to delocalized transport states in the anharmonic chain of three coupled oscillators

In the present paper, we study the mechanism of formation and bifurcations of highly nonstationary regimes manifested by different energy transport intensities, emerging in an anharmonic trimer model. The basic model under investigation comprises a chain of three coupled anharmonic oscillators subject to localized excitation, where the initial energy is imparted to the first oscillator only. We report the formation of three basic nonstationary transport states traversed by locally excited regimes. These states differ by spatial energy distribution, as well as by the intensity of energy transport along the chain. In the current study, we focus on numerical and analytical investigation of the intricate resonant mechanism governing the inter-state transitions of locally excited regimes. Results of the analytical study are in good agreement with the numerical simulations of the trimer model. Published by AIP Publishing

Not Available

Not AvailableBACKGROUND: Swine brucellosis is a zoonotic disease caused by Brucella suis. The study describes the occurrence of brucellosis in two organized piggeries in Southern India. METHODS: A total of 585 serum samples comprising 575 from pigs and 10 from animal handlers were collected and tested by serological tests and PCR. Tissue samples were collected for isolation of the pathogen. RESULTS: Out of 575 serum samples screened, 236 (41.04%) were positive for brucellosis by both Rose Bengal plate test (RBPT) and indirect ELISA (iELISA) and 47 (8.17) samples showed Brucella DNA amplification by genus specific PCR. The sows those aborted and 19 boars with orchitis were seropositive for brucellosis indicating association of clinical symptoms with brucellosis seropositivity. Two of 10 pig handlers were positive by RBPT and showed significant serum agglutination test (SAT) titres of >1:160 and 1:320. B. suis bvI was isolated and identified by biochemical tests and confirmed by amplification Brucella genus and Bruce ladder PCRs from vaginal and testicular samples. CONCLUSIONS: The introduction of untested breeding boars in the farms might have resulted in the disease transmission and spread. The present study highlighted the diagnosis of B. suis bvI as a cause of abortions in the pigs and occupational exposure to farm personnel.Not Availabl

Not Available

Not AvailableBACKGROUND:Swine brucellosis is a zoonotic disease caused by Brucella suis. The study describes the occurrence of brucellosis in two organized piggeries in Southern India. METHODS:A total of 585 serum samples comprising 575 from pigs and 10 from animal handlers were collected and tested by serological tests and PCR. Tissue samples were collected for isolation of the pathogen. RESULTS:Out of 575 serum samples screened, 236 (41.04%) were positive for brucellosis by both Rose Bengal plate test (RBPT) and indirect ELISA (iELISA) and 47 (8.17) samples showed Brucella DNA amplification by genus specific PCR. The sows those aborted and 19 boars with orchitis were seropositive for brucellosis indicating association of clinical symptoms with brucellosis seropositivity. Two of 10 pig handlers were positive by RBPT and showed significant serum agglutination test (SAT) titres of >1:160 and 1:320. B. suis bvI was isolated and identified by biochemical tests and confirmed by amplification Brucella genus and Bruce ladder PCRs from vaginal and testicular samples. CONCLUSIONS:The introduction of untested breeding boars in the farms might have resulted in the disease transmission and spread. The present study highlighted the diagnosis of B. suis bvI as a cause of abortions in the pigs and occupational exposure to farm personnel.Not Availabl