Acceleration of Gapped Alignment in BLASTP Using the Mercury System

Protein databases have grown exponentially over the last decade. This exponential growth has made extracting valuable information from these databases increasingly time consuming. This project presents a new method of accelerating a commonly used program for performing similarity searching on protein databases, BLASTP. This project describes the design and implementation of Mercury BLASTP, a customized hardware accelerated variant of BLASTP. This project focuses on the gapped alignment stage of Mercury BLASTP and provides design details and implementation results

Cataclysmic Variables from SDSS II. The Second Year

The first full year of operation following the commissioning year of the Sloan Digital Sky Survey has revealed a wide variety of newly discovered cataclysmic variables. We show the SDSS spectra of forty-two cataclysmic variables observed in 2002, of which thirty-five are new classifications, four are known dwarf novae (CT Hya, RZ Leo, T Leo and BZ UMa), one is a known CV identified from a previous quasar survey (Aqr1) and two are known ROSAT or FIRST discovered CVs (RX J09445+0357, FIRST J102347.6+003841). The SDSS positions, colors and spectra of all forty-two systems are presented. In addition, the results of follow-up studies of several of these objects identify the orbital periods, velocity curves and polarization that provide the system geometry and accretion properties. While most of the SDSS discovered systems are faint (>18th mag) with low accretion rates (as implied from their spectral characteristics), there are also a few bright objects which may have escaped previous surveys due to changes in the mass transfer rate.Comment: Accepted for publication in The Astronomical Journal, Vol. 126, Sep. 2003, 44 pages, 25 figures (now with adjacent captions), AASTeX v5.

Two Rare Magnetic Cataclysmic Variables with Extreme Cyclotron Features Identified in the Sloan Digital Sky Survey

Two newly identified magnetic cataclysmic variables discovered in the Sloan Digital Sky Survey (SDSS), SDSSJ155331.12+551614.5 and SDSSJ132411.57+032050.5, have spectra showing highly prominent, narrow, strongly polarized cyclotron humps with amplitudes that vary on orbital periods of 4.39 and 2.6 hrs, respectively. In the former, the spacing of the humps indicates the 3rd and 4th harmonics in a magnetic field of ~60 MG. The narrowness of the cyclotron features and the lack of strong emission lines imply very low temperature plasmas and very low accretion rates, so that the accreting area is heated by particle collisions rather than accretion shocks. The detection of rare systems like these exemplifies the ability of the SDSS to find the lowest accretion rate close binaries.Comment: Accepted for publication in the Astrophysical Journal, vol. 583, February 1, 2003; slight revisions and additions in response to referee's comments; 17 pages, 6 figures, AASTeX v4.

Depression, Stressful Life Events, and the Impact of Variation in the Serotonin Transporter: Findings from the National Longitudinal Study of Adolescent to Adult Health (Add Health)

BackgroundThe low transcriptionally efficient short-allele of the 5HTTLPR serotonin transporter polymorphism has been implicated to moderate the relationship between the experience of stressful life events (SLEs) and depression. Despite numerous attempts at replicating this observation, results remain inconclusive.MethodsWe examined this relationship in young-adult Non-Hispanic white males and females between the ages of 22 and 26 (n = 4724) participating in the National Longitudinal Study of Adolescent to Adult Health (Add Health) with follow-up information every six years since 1995.ResultsLinear and logistic regression models, corrected for multiple testing, indicated that carriers of one or more of the S-alleles were more sensitive to stress than those with two L-alleles and at a higher risk for depression. This relationship behaved in a dose-response manner such that the risk for depression was greatest among those who reported experiencing higher numbers of SLEs. In post-hoc analyses we were not able to replicate an interaction effect for suicide ideation but did find suggestive evidence that the effects of SLEs and 5HTTLPR on suicide ideation differed for males and females. There were no effects of childhood maltreatment.DiscussionOur results provide partial support for the original hypothesis that 5-HTTLPR genotype interacts with the experience of stressful life events in the etiology of depression during young adulthood. However, even with this large sample, and a carefully constructed a priori analysis plan, the results were still not definitive. For the purposes of replication, characterizing the 5HTTLPR in other large data sets with extensive environmental and depression measures is needed

COMAP Early Science: V. Constraints and Forecasts at z∼3z \sim 3

We present the current state of models for the $z\sim3$ carbon monoxide (CO) line-intensity signal targeted by the CO Mapping Array Project (COMAP) Pathfinder in the context of its early science results. Our fiducial model, relating dark matter halo properties to CO luminosities, informs parameter priors with empirical models of the galaxy-halo connection and previous CO(1-0) observations. The Pathfinder early science data spanning wavenumbers $k=0.051$-$0.62\,$Mpc$^{-1}$ represent the first direct 3D constraint on the clustering component of the CO(1-0) power spectrum. Our 95% upper limit on the redshift-space clustering amplitude $A_{\rm clust}\lesssim70\,\mu$K$^2$ greatly improves on the indirect upper limit of $420\,\mu$K$^2$ reported from the CO Power Spectrum Survey (COPSS) measurement at $k\sim1\,$Mpc$^{-1}$. The COMAP limit excludes a subset of models from previous literature, and constrains interpretation of the COPSS results, demonstrating the complementary nature of COMAP and interferometric CO surveys. Using line bias expectations from our priors, we also constrain the squared mean line intensity-bias product, $\langle{Tb}\rangle^2\lesssim50\,\mu$K$^2$, and the cosmic molecular gas density, $\rho_\text{H2}<2.5\times10^8\,M_\odot\,$Mpc$^{-3}$ (95% upper limits). Based on early instrument performance and our current CO signal estimates, we forecast that the five-year Pathfinder campaign will detect the CO power spectrum with overall signal-to-noise of 9-17. Between then and now, we also expect to detect the CO-galaxy cross-spectrum using overlapping galaxy survey data, enabling enhanced inferences of cosmic star-formation and galaxy-evolution history.Comment: Paper 5 of 7 in series. 17 pages + appendix and bibliography (30 pages total); 15 figures, 6 tables; accepted for publication in ApJ; v3 reflects the accepted version with minor changes and additions to tex

Allosteric Regulation of Fibronectin/α5β1 Interaction by Fibronectin-Binding MSCRAMMs

Citation: Liang, X. W., Garcia, B. L., Visai, L., Prabhakaran, S., Meenan, N. A. G., Potts, J. R., . . . Hook, M. (2016). Allosteric Regulation of Fibronectin/alpha(5)beta(1) Interaction by Fibronectin-Binding MSCRAMMs. Plos One, 11(7), 17. doi:10.1371/journal.pone.0159118Adherence ofmicrobes to host tissues is a hallmark of infectious disease and is often mediated by a class of adhesins termed MSCRAMMs (Microbial Surface Components Recognizing Adhesive Matrix Molecules). Numerous pathogens express MSCRAMMs that specifically bind the heterodimeric human glycoprotein fibronectin (Fn). In addition to roles in adhesion, Fn-binding MSCRAMMs exploit physiological Fn functions. For example, several pathogens can invade host cells by a mechanism whereby MSCRAMM-bound Fn bridges interaction with alpha(5)beta(1) integrin. Here, we investigate two Fn-binding MSCRAMMs, FnBPA (Staphylococcus aureus) and BBK32 (Borrelia burgdorferi) to probe structure-activity relationships of MSCRAMM-induced Fn/alpha(5)beta(1) integrin activation. Circular dichroism, fluorescence resonance energy transfer, and dynamic light scattering techniques uncover a conformational rearrangement of Fn involving domains distant from the MSCRAMM binding site. Surface plasmon resonance experiments demonstrate a significant enhancement of Fn/alpha(5)beta(1) integrin affinity in the presence of FnBPA or BBK32. Detailed kinetic analysis of these interactions reveal that this change in affinity can be attributed solely to an increase in the initial Fn/alpha(5)beta(1) on-rate and that this rate-enhancement is dependent on high-affinity Fn-binding by MSCRAMMs. These data implicate MSCRAMM-induced perturbation of specific intramolecular contacts within the Fn heterodimer resulting in activation by exposing previously cryptic alpha(5)beta(1) interaction motifs. By correlating structural changes in Fn to a direct measurement of increased Fn/alpha(5)beta(1) affinity, this work significantly advances our understanding of the structural basis for the modulation of integrin function by Fn-binding MSCRAMMs

COMAP Early Science: I. Overview

The CO Mapping Array Project (COMAP) aims to use line intensity mapping of carbon monoxide (CO) to trace the distribution and global properties of galaxies over cosmic time, back to the Epoch of Reionization (EoR). To validate the technologies and techniques needed for this goal, a Pathfinder instrument has been constructed and fielded. Sensitive to CO(1-0) emission from $z=2.4$-$3.4$ and a fainter contribution from CO(2-1) at $z=6$-8, the Pathfinder is surveying $12$ deg$^2$ in a 5-year observing campaign to detect the CO signal from $z\sim3$. Using data from the first 13 months of observing, we estimate $P_\mathrm{CO}(k) = -2.7 \pm 1.7 \times 10^4\mu\mathrm{K}^2 \mathrm{Mpc}^3$ on scales $k=0.051-0.62 \mathrm{Mpc}^{-1}$ - the first direct 3D constraint on the clustering component of the CO(1-0) power spectrum. Based on these observations alone, we obtain a constraint on the amplitude of the clustering component (the squared mean CO line temperature-bias product) of $\langle Tb\rangle^2<49$ $\mu$K$^2$ - nearly an order-of-magnitude improvement on the previous best measurement. These constraints allow us to rule out two models from the literature. We forecast a detection of the power spectrum after 5 years with signal-to-noise ratio (S/N) 9-17. Cross-correlation with an overlapping galaxy survey will yield a detection of the CO-galaxy power spectrum with S/N of 19. We are also conducting a 30 GHz survey of the Galactic plane and present a preliminary map. Looking to the future of COMAP, we examine the prospects for future phases of the experiment to detect and characterize the CO signal from the EoR.Comment: Paper 1 of 7 in series. 18 pages, 16 figures, submitted to Ap

Chemical vapour deposition synthetic diamond: materials, technology and applications

Substantial developments have been achieved in the synthesis of chemical vapour deposition (CVD) diamond in recent years, providing engineers and designers with access to a large range of new diamond materials. CVD diamond has a number of outstanding material properties that can enable exceptional performance in applications as diverse as medical diagnostics, water treatment, radiation detection, high power electronics, consumer audio, magnetometry and novel lasers. Often the material is synthesized in planar form, however non-planar geometries are also possible and enable a number of key applications. This article reviews the material properties and characteristics of single crystal and polycrystalline CVD diamond, and how these can be utilized, focusing particularly on optics, electronics and electrochemistry. It also summarizes how CVD diamond can be tailored for specific applications, based on the ability to synthesize a consistent and engineered high performance product.Comment: 51 pages, 16 figure

Reduced fire severity offers near-term buffer to climate-driven declines in conifer resilience across the western United States

Increasing fire severity and warmer, drier postfire conditions are making forests in the western United States (West) vulnerable to ecological transformation. Yet, the relative importance of and interactions between these drivers of forest change remain unresolved, particularly over upcoming decades. Here, we assess how the interactive impacts of changing climate and wildfire activity influenced conifer regeneration after 334 wildfires, using a dataset of postfire conifer regeneration from 10,230 field plots. Our findings highlight declining regeneration capacity across the West over the past four decades for the eight dominant conifer species studied. Postfire regeneration is sensitive to high-severity fire, which limits seed availability, and postfire climate, which influences seedling establishment. In the near-term, projected differences in recruitment probability between low- and high-severity fire scenarios were larger than projected climate change impacts for most species, suggesting that reductions in fire severity, and resultant impacts on seed availability, could partially offset expected climate-driven declines in postfire regeneration. Across 40 to 42% of the study area, we project postfire conifer regeneration to be likely following low-severity but not high-severity fire under future climate scenarios (2031 to 2050). However, increasingly warm, dry climate conditions are projected to eventually outweigh the influence of fire severity and seed availability. The percent of the study area considered unlikely to experience conifer regeneration, regardless of fire severity, increased from 5% in 1981 to 2000 to 26 to 31% by mid-century, highlighting a limited time window over which management actions that reduce fire severity may effectively support postfire conifer regeneration. © 2023 the Author(s)