Randomized And Parallel Algorithms For Distance Matrix Calculations In Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a vital problem in biology. Optimal alignment of multiple sequences becomes impractical even for a modest number of sequences [1] since the general version of the problem is NP-hard. Because of the high time complexity of traditional MSA algorithms, even today's fast computers are not able to solve the problem for large number of sequences. In this paper we present a randomized algorithm to calculate distance matrices, which is a major step in many multiple sequence alignment algorithms. The basic idea employed is sampling (along the lines of [2]). We also illustrate how to parallelize this algorithm. In Section 1 we introduce the problem of multiple sequence alignments. In Section 2 we provide a discussion on various methods that have been employed in the literature for Multiple Sequence Alignment. In this section we also introduce our new sampling approach. We extend our randomized algorithm to the case of non-uniform length sequences as well. We show that our algorithms are amenable to parallelism in Section 3. In Section 4 we back up our claim of speedup and accuracy with empirical data and examples. In Section 5 we provide some concluding remarks.     

Intrauterine infection and preterm labor

Preterm labor is defined as labor that begins before 37 completed weeks of pregnancy. More than 12% of infants born in the USA are preterm. At least 40% of preterm births are associated with intrauterine infection. Toll-like receptors (TLRs) are members of a family of cell-surface proteins responsible for recognition of a diverse spectrum of bacterial, viral and fungal pathogens. TLRs initiate the host innate (i.e. non-adaptive) immune response, inducing a proinflammatory cascade involving cytokines, chemokines, prostaglandins, and other effector molecules that result in the characteristic phenomena of labor, such as uterine contractions and rupture of fetal membranes. These cascades may also be activated by mechanisms that are not primarily infectious but are accompanied by inflammatory responses. Now that the molecular mechanisms linking infection and labor have been, to a large extent, elucidated, the challenge is to identify points of overlap with non-infectious causes of labor and to find intervention strategies that can minimize the negative impact of preterm delivery.     

Fractal network dimension and viscoelastic powerlaw behavior: I. A modeling approach based on a coarse-graining procedure combined with shear oscillatory rheometry

Recent advances in dynamic elastography and biorheology have revealed that the complex shear modulus, G*, of various biological soft tissues obeys a frequency-dependent powerlaw. This viscoelastic powerlaw behavior implies that mechanical properties are communicated in tissue across the continuum of scales from microscopic to macroscopic. For deriving constitutive constants from the dispersion of G* in a biological tissue, a hierarchical fractal model is introduced that accounts for multiscale networks. Effective-media powerlaw constants are derived by a constitutive law based on cross-linked viscoelastic clusters embedded in a rigid environment. The spatial variation of G* is considered at each level of hierarchy by an iterative coarse-graining procedure. The establishment of cross-links in this model network is associated with an increasing fractal dimension and an increasing viscoelastic powerlaw exponent. This fundamental relationship between shear modulus dynamics and fractal dimension of the mechanical network in tissue is experimentally reproduced in phantoms by applying shear oscillatory rheometry to layers of tangled paper strips embedded in agarose gel. Both model and experiments demonstrate the sensitivity of G* to the density of the mechanical network in tissue, corroborating disease-related alterations of the viscoelastic powerlaw exponent in human parenchyma demonstrated by in vivo elastography.     

3D volume assessment techniques and computer-aided design and manufacturing for preoperative fabrication of implants in head and neck reconstruction

Cases in subdisciplines of craniomaxillofacial surgery--corrective jaw surgery, maxillofacial trauma, temporomandibular joint/skull base, jaw reconstruction, and postablative reconstruction-illustrate the ease of use, cost effectiveness, and superior results that can be achieved when using computer-assisted design and 3D volumetric analysis in preoperative surgical planning. This article discusses the materials and methods needed to plan cases, illustrates implementation of guides and implants, and describes postoperative analysis in relation to the virtually planned surgery.     

Team training: a safer future for neurointerventional practice

As medical errors and patient harm mount in today's healthcare arena, healthcare administrators have turned to high efficiency, high reliability, and high risk industries for strategies and guidance. By adopting elements of Crew Resource Management (CRM), healthcare teams have been shown to work more effectively together, allowing for earlier recognition of medical errors and catching them before they cause serious patient harm.     

The United States National Health and Nutrition Examination Survey and the epidemiology of ankylosing spondylitis

Currently available U.S. population-based data for ankylosing spondylitis (AS), spondyloarthritis and inflammatory back pain (IBP) from the nationally representative U.S. National Health and Nutrition Examination Survey (NHANES) include both NHANES I (1971-1975) and NHANES II (1976-1980) surveys. The pelvic radiographs obtained in NHANES I provided U.S. prevalence estimates for radiographic sacroiliitis, an important component of the AS case definition. AS and spondyloarthritis prevalences cannot readily be calculated from NHANES I survey data; however, IBP prevalence (Rudwaleit et al Criteria 7b) can be estimated from NHANES II. The NHANES II estimate for IBP is 0.8% of the adult population ages 25 to 49 years. The prevalence of IBP in the subset of persons with a history of a back pain episode lasting 2 or more weeks was 6.7%. The 2009-2010 NHANES U.S. Inflammatory Back Pain/Spondyloarthritis survey is currently fielded.     

The kinetics of αIIbβ3 activation determines the size and stability of thrombi in mice: implications for antiplatelet therapy

Two major pathways contribute to Ras-proximate-1-mediated integrin activation in stimulated platelets. Calcium and diacyglycerol-regulated guanine nucleotide exchange factor I (CalDAG-GEFI, RasGRP2) mediates the rapid but reversible activation of integrin αIIbβ3, while the adenosine diphosphate receptor P2Y12, the target for antiplatelet drugs like clopidogrel, facilitates delayed but sustained integrin activation. To establish CalDAG-GEFI as a target for antiplatelet therapy, we compared how each pathway contributes to thrombosis and hemostasis in mice. Ex vivo, thrombus formation at arterial or venous shear rates was markedly reduced in CalDAG-GEFI(-/-) blood, even in the presence of exogenous adenosine diphosphate and thromboxane A(2). In vivo, thrombosis was virtually abolished in arterioles and arteries of CalDAG-GEFI(-/-) mice, while small, hemostatically active thrombi formed in venules. Specific deletion of the C1-like domain of CalDAG-GEFI in circulating platelets also led to protection from thrombus formation at arterial flow conditions, while it only marginally increased blood loss in mice. In comparison, thrombi in the micro- and macrovasculature of clopidogrel-treated wild-type mice grew rapidly and frequently embolized but were hemostatically inactive. Together, these data suggest that inhibition of the catalytic or the C1 regulatory domain in CalDAG-GEFI will provide strong protection from athero-thrombotic complications while maintaining a better safety profile than P2Y12 inhibitors like clopidogrel.