Introduction to a Biological Systems Science

Biological systems analysis and biodynamic modelling of physiological and biological interrelationships in human body and mammal

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays

<p>Abstract</p> <p>Background</p> <p>Array-based comparative genomic hybridization (aCGH) is a high-throughput method for measuring genome-wide DNA copy number changes. Current aCGH methods have limited resolution, sensitivity and reproducibility. Microarrays for aCGH are available only for a few organisms and combination of aCGH data with expression data is cumbersome.</p> <p>Results</p> <p>We present a novel method of using commercial oligonucleotide expression microarrays for aCGH, enabling DNA copy number measurements and expression profiles to be combined using the same platform. This method yields aCGH data from genomic DNA without complexity reduction at a median resolution of approximately 17,500 base pairs. Due to the well-defined nature of oligonucleotide probes, DNA amplification and deletion can be defined at the level of individual genes and can easily be combined with gene expression data.</p> <p>Conclusion</p> <p>A novel method of gene resolution analysis of copy number variation (graCNV) yields high-resolution maps of DNA copy number changes and is applicable to a broad range of organisms for which commercial oligonucleotide expression microarrays are available. Due to the standardization of oligonucleotide microarrays, graCNV results can reliably be compared between laboratories and can easily be combined with gene expression data using the same platform.</p

How to Win a Hot Dog Eating Contest: Distributed Incremental View Maintenance with Batch Updates

In the quest for valuable information, modern big data applications continuously monitor streams of data. These applications demand low latency stream processing even when faced with high volume and velocity of incoming changes and the user’s desire to ask complex queries. In this paper, we study low-latency incremental computation of complex SQL queries in both local and distributed streaming environments. We develop a technique for the efficient incrementalization of queries with nested aggregates for batch updates. We identify the cases in which batch processing can boost the performance of incremental view maintenance but also demonstrate that tuple-at-a-time processing often can achieve better performance in local mode. Batch updates are essential for enabling distributed incremental view maintenance and amortizing the cost of network communication and synchronization. We show how to derive incremental programs optimized for running on large-scale processing platforms. Our implementation of distributed incremental view maintenance can process tens of million of tuples with few-second latency using hundreds of nodes

Distributed Caching for Processing Raw Arrays

As applications continue to generate multi-dimensional data at exponentially increasing rates, fast analytics to extract meaningful results is becoming extremely important. The database community has developed array databases that alleviate this problem through a series of techniques. In-situ mechanisms provide direct access to raw data in the original format---without loading and partitioning. Parallel processing scales to the largest datasets. In-memory caching reduces latency when the same data are accessed across a workload of queries. However, we are not aware of any work on distributed caching of multi-dimensional raw arrays. In this paper, we introduce a distributed framework for cost-based caching of multi-dimensional arrays in native format. Given a set of files that contain portions of an array and an online query workload, the framework computes an effective caching plan in two stages. First, the plan identifies the cells to be cached locally from each of the input files by continuously refining an evolving R-tree index. In the second stage, an optimal assignment of cells to nodes that collocates dependent cells in order to minimize the overall data transfer is determined. We design cache eviction and placement heuristic algorithms that consider the historical query workload. A thorough experimental evaluation over two real datasets in three file formats confirms the superiority - by as much as two orders of magnitude - of the proposed framework over existing techniques in terms of cache overhead and workload execution time

Evaluation of the effect of prospective biomarker testing on progression-free survival in diffuse large B-cell lymphoma.

Novel treatment regimens combining chemotherapy with targeted agents are being developed for diffuse large B-cell lymphoma (DLBCL). These regimens are expected to show efficacy in biomarker-defined..

Neurophysiology

Contains research objectives and reports on three research projects.National Aeronautics and Space Administration (Grant NsG-496)U.S. Air Force (Aeronautical Systems Division) under Contract AF33 (616)-7783The Teagle Foundation, Inc.National Institutes of Health (Grant MH-04737-03)National Institutes of Health (Grant NB-04897-01)National Science Foundation (Grant G-16526)Bell Telephone Laboratories, Inc

Negative Resistance in Brownian Transport

We prove that negative incremental resistance cannot occur on 1D spaces like the circle or the line; we construct an explicit two-dimensional model on the cylinder, and its collapse into a branched 1D backbone. We derive an accurate numerical method for solving our 2D model, and discuss the relevance of the model to biological ion channels.Comment: 3 separate figure

Neurophysiology

Contains research objectives and reports on one research project.U. S. Air Force Cambridge Research Laboratories under Contract AF19(628)-4147Bell Telephone Laboratories, Inc.National Institutes of Health (Grant MH-04737-04)National Science Foundation (Grant GP-2495)National Institutes of Health (Grant NB-04987-02)The Teagle Foundation, Inc.National Aeronautics and Space Administration (Grant NsG-496)U. S. Air Force (Aeronautical Systems Division) under Contract AF 33(615)-1747National Institutes of Health (Grant NB-04985-01

Neurophysiology

Contains research objectives and reports on nine research projects.The Teagle Foundation, Inc.U.S. Air Force (Aeronautical Systems Division) under Contract AF33(616)-7783Bell Telephone Laboratories, Inc.National Institutes of Health [Grant M-4235-(C1)]National Institutes of Health (Grant B-1865-(C3))National Institutes of Health (Grant MP-4737)National Institutes of Health (Grant B-2480(C1)