2,793 research outputs found

    A Faster Circular Binary Segmentation Algorithm for the Analysis of Array CGH Data

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    Motivation: Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number (Olshen {\it et~al}, 2004). The algorithm tests for change-points using a maximal tt-statistic with a permutation reference distribution to obtain the corresponding pp-value. The number of computations required for the maximal test statistic is O(N2),O(N^2), where NN is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster. algorithm. Results: We present a hybrid approach to obtain the pp-value of the test statistic in linear time. We also introduce a rule for stopping early when there is strong evidence for the presence of a change. We show through simulations that the hybrid approach provides a substantial gain in speed with only a negligible loss in accuracy and that the stopping rule further increases speed. We also present the analysis of array CGH data from a breast cancer cell line to show the impact of the new approaches on the analysis of real data. Availability: An R (R Development Core Team, 2006) version of the CBS algorithm has been implemented in the ``DNAcopy\u27\u27 package of the Bioconductor project (Gentleman {\it et~al}, 2004). The proposed hybrid method for the pp-value is available in version 1.2.1 or higher and the stopping rule for declaring a change early is available in version 1.5.1 or higher

    Effect of the Intrinsic Width on the Piezoelectric Force Microscopy of a Single Ferroelectric Domain Wall

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    Intrinsic domain wall width is a fundamental parameter that reflects bulk ferroelectric properties and governs the performance of ferroelectric memory devices. We present closed-form analytical expressions for vertical and lateral piezoelectric force microscopy (PFM) profiles for the conical and disc models of the tip, beyond point charge and sphere approximations. The analysis takes into account the finite intrinsic width of the domain wall, and dielectric anisotropy of the material. These analytical expressions provide insight into the mechanisms of PFM image formation and can be used for quantitative analysis of the PFM domain wall profiles. PFM profile of a realistic domain wall is shown to be the convolution of its intrinsic profile and resolution function of PFM.Comment: 25 pages, 5 figures, 3 tables, 3 Appendices, To be submitted to J. Appl. Phy

    Social Media in South India

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    One of the first ethnographic studies to explore use of social media in the everyday lives of people in Tamil Nadu, Social Media in South India provides an understanding of this subject in a region experiencing rapid transformation. The influx of IT companies over the past decade into what was once a space dominated by agriculture has resulted in a complex juxtaposition between an evolving knowledge economy and the traditions of rural life. While certain class tensions have emerged in response to this juxtaposition, a study of social media in the region suggests that similarities have also transpired, observed most clearly in the blurring of boundaries between work and life for both the old residents and the new. Venkatraman explores the impact of social media at home, work and school, and analyses the influence of class, caste, age and gender on how, and which, social media platforms are used in different contexts. These factors, he argues, have a significant effect on social media use, suggesting that social media in South India, while seeming to induce societal change, actually remains bound by local traditions and practices

    Synthesis, Antiinflammatory and Antimicrobial Activities of Newer Series of 1,3,4-Oxadiazoles.

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    The study of an antimicrobial agent is anything that can kill or inhibit the growth of bacteria such as high heat or radiation or a chemical substance. The antimicrobial agents are broadly classified into antibacterial, antifungal, antiviral, antiprotozoal, antiparasitic and anthelmintics. The antimicrobial agents act by interfering with cell wall synthesis, plasma membrane integrity, nucleic acid synthesis, ribosomal function and folate synthesis. Antibacterial agents are used in relatively low concentrations in or upon the bodies of organisms to prevent or treat specific bacterial diseases without harming the host organism. The most commonly used methods for determination of antimicrobial activity are cylinder plate or cup plate method, turbidimetric or tube assay method and disc diffusion method. Based on these reports, we have planned to synthesize the mannich bases of 1,3,4-oxadiazole derivatives and 2,5-disubstituted-1,3,4-oxadiazole derivatives and screen for antiinflammatory and antimicrobial activities. The 2,5-disubstituted-1,3,4-oxadiazoles and mannich bases of 1,3,4- oxadiazoles shown moderate antibacterial and antifungal activities. Among the ten compounds synthesized only two were tested for antiinflammatory activity and it could show significant action compared to the standard. Hence less information is obtained in terms of antiinflammatory action for the synthesized compounds. On antimicrobial screening, though the compounds could show activities against bacterial and fungal strains but it is less compared to standard. Further research is needed to correlate the 1,3,4-oxadiazole with its antiinflammatory and antimicrobial activities
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