681 research outputs found

    An efficient pseudomedian filter for tiling microrrays

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    <p>Abstract</p> <p>Background</p> <p>Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding sites, detection of methylated DNA and several other applications in several model organisms. These experiments are being conducted at increasingly finer resolutions as the microarray technology enjoys increasingly greater feature densities. The increased densities naturally lead to increased data analysis requirements. Specifically, the most widely employed algorithm for tiling array analysis involves smoothing observed signals by computing pseudomedians within sliding windows, a <it>O</it>(<it>n</it><sup>2</sup>log<it>n</it>) calculation in each window. This poor time complexity is an issue for tiling array analysis and could prove to be a real bottleneck as tiling microarray experiments become grander in scope and finer in resolution.</p> <p>Results</p> <p>We therefore implemented Monahan's HLQEST algorithm that reduces the runtime complexity for computing the pseudomedian of <it>n </it>numbers to <it>O</it>(<it>n</it>log<it>n</it>) from <it>O</it>(<it>n</it><sup>2</sup>log<it>n</it>). For a representative tiling microarray dataset, this modification reduced the smoothing procedure's runtime by nearly 90%. We then leveraged the fact that elements within sliding windows remain largely unchanged in overlapping windows (as one slides across genomic space) to further reduce computation by an additional 43%. This was achieved by the application of skip lists to maintaining a sorted list of values from window to window. This sorted list could be maintained with simple <it>O</it>(log <it>n</it>) inserts and deletes. We illustrate the favorable scaling properties of our algorithms with both time complexity analysis and benchmarking on synthetic datasets.</p> <p>Conclusion</p> <p>Tiling microarray analyses that rely upon a sliding window pseudomedian calculation can require many hours of computation. We have eased this requirement significantly by implementing efficient algorithms that scale well with genomic feature density. This result not only speeds the current standard analyses, but also makes possible ones where many iterations of the filter may be required, such as might be required in a bootstrap or parameter estimation setting. Source code and executables are available at <url>http://tiling.gersteinlab.org/pseudomedian/</url>.</p

    Material Strength Effect in the Shock Compression of Alumina

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    The Hugoniot elastic limits (HEL) of a high-density aluminum oxide ceramic (Lucalox) and a slightly lower-density ceramic (porosity approximately 4%) were determined to be 112±13 and 83±5 kbar, respectively. Above the HEL, the shock-stress-volume Hugoniot curves for both materials are offset by 40 kbar or more above their hydrostatic-pressure-volume curves. These results indicate that shear stresses with magnitudes of about 30–40 kbar persist in aluminum oxide to shock-pressure levels of at least 300 kbar

    Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification

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    A generic DNA microarray design applicable to any species would greatly benefit comparative genomics. We have addressed the feasibility of such a design by leveraging the great feature densities and relatively unbiased nature of genomic tiling microarrays. Specifically, we first divided each Homo sapiens Refseq-derived gene's spliced nucleotide sequence into all of its possible contiguous 25 nt subsequences. For each of these 25 nt subsequences, we searched a recent human transcript mapping experiment's probe design for the 25 nt probe sequence having the fewest mismatches with the subsequence, but that did not match the subsequence exactly. Signal intensities measured with each gene's nearest-neighbor features were subsequently averaged to predict their gene expression levels in each of the experiment's thirty-three hybridizations. We examined the fidelity of this approach in terms of both sensitivity and specificity for detecting actively transcribed genes, for transcriptional consistency between exons of the same gene, and for reproducibility between tiling array designs. Taken together, our results provide proof-of-principle for probing nucleic acid targets with off-target, nearest-neighbor features

    DYNAMIC YIELD STRENGTHS OF LIGHT ARMOR MATERIALS.

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    A Phase-Field Model of Spiral Dendritic Growth

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    Domains of condensed-phase monolayers of chiral molecules exhibit a variety of interesting nonequilibrium structures when formed via pressurization. To model these domain patterns, we add a complex field describing the tilt degree of freedom to an (anisotropic) complex-phase-field solidification model. The resulting formalism allows for the inclusion of (in general, non-reflection symmetric) interactions between the tilt, the solid-liquid interface, and the bond orientation. Simulations demonstrate the ability of the model to exhibit spiral dendritic growth.Comment: text plus Four postscript figure file

    Adoption Issues in DevOps from the Perspective of Continuous Delivery Pipeline

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    DevOps and Continuous Delivery (CD) are the terms that are always related to each other in Software Delivery and Operation Process area. DevOps introduces a significant agile perspective to deliver the software product in short cycle time that will reduce technical debt that is caused by delay. Continuous Delivery is one of the DevOps' practices that enables software organization to release new features and new products rapidly. However, the correct practices are still in ambiguity to the current CD process. This paper investigates the advantages and limitation of DevOps adoption to improve the CD process. A qualitative web survey has been conducted to identify the DevOps and Continuous Delivery advantages and adoption problems. 13 respondents' feedbacks have been collected and analyzed. Based on the survey, there are four significant DevOps' practices that need to be considered and developed as a proper guideline to introduce to practitioners

    Male obesity associated gonadal dysfunction and the role of bariatric surgery

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    Obesity is an ever growing pandemic and a prevalent problem among men of reproductive age that can both cause and exacerbate male-factor infertility by means of endocrine abnormalities, associated comorbidities, and direct effects on the precision and throughput of spermatogenesis. Robust epidemiologic, clinical, genetic, epigenetic, and preclinical data support these findings. Clinical studies on the impact of medically induced weight loss on serum testosterone concentrations and spermatogenesis is promising but may show differential and unsustainable results. In contrast, literature has demonstrated that weight loss after bariatric surgery is correlated with an increase in serum testosterone concentrations that is superior than that obtained with only lifestyle modifications, supporting a further metabolic benefit from surgery that may be specific to the male reproductive system. The data on sperm and semen parameters is controversial to date. Emerging evidence in the burgeoning field of genetics and epigenetics has demonstrated that paternal obesity can affect offspring metabolic and reproductive phenotypes by means of epigenetic reprogramming of spermatogonial stem cells. Understanding the impact of this reprogramming is critical to a comprehensive view of the impact of obesity on subsequent generations. Furthermore, conveying the potential impact of these lifestyle changes on future progeny can serve as a powerful tool for obese men to modify their behavior. Healthcare professionals treating male infertility and obesity need to adapt their practice to assimilate these new findings to better counsel men about the importance of paternal preconception health and the impact of novel non-medical therapeutic interventions. Herein, we summarize the pathophysiology of obesity on the male reproductive system and emerging evidence regarding the potential role of bariatric surgery as treatment of male obesity-associated gonadal dysfunction
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