A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Distributions associated with general runs and patterns in hidden Markov models

This paper gives a method for computing distributions associated with patterns in the state sequence of a hidden Markov model, conditional on observing all or part of the observation sequence. Probabilities are computed for very general classes of patterns (competing patterns and generalized later patterns), and thus, the theory includes as special cases results for a large class of problems that have wide application. The unobserved state sequence is assumed to be Markovian with a general order of dependence. An auxiliary Markov chain is associated with the state sequence and is used to simplify the computations. Two examples are given to illustrate the use of the methodology. Whereas the first application is more to illustrate the basic steps in applying the theory, the second is a more detailed application to DNA sequences, and shows that the methods can be adapted to include restrictions related to biological knowledge.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS125 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Evolution of Local Microstructures (ELMS): Spatial Instabilities of Coarsening

This work examines the diffusional growth of discrete phase particles dispersed within a matrix. Engineering materials are microstructurally heterogeneous, and the details of the microstructure determine how well that material performs in a given application. Critical to the development of designing multiphase microstructures with long-term stability is the process of Ostwald ripening. Ripening, or phase coarsening, is a diffusion-limited process which arises in polydisperse multiphase materials. Growth and dissolution occur because fluxes of solute, driven by chemical potential gradients at the interfaces of the dispersed phase material, depend on particle size. The kinetics of these processes are "competitive," dictating that larger particles grow at the expense of smaller ones, overall leading to an increase of the average particle size. The classical treatment of phase coarsening was done by Todes, Lifshitz, and Slyozov, (TLS) in the limit of zero volume fraction, V(sub v), of the dispersed phase. Since the publication of TLS theory there have been numerous investigations, many of which sought to describe the kinetic scaling behavior over a range of volume fractions. Some studies in the literature report that the relative increase in coarsening rate at low (but not zero) volume fractions compared to that / 2 1/ 3 predicted by TLS is proportional to V(sub v)(exp 1/2), whereas others suggest V(sub v)(exp 1/3). This issue has been resolved recently by simulation studies at low volume fractions in three dimensions by members of the Rensselaer/MSFC team

Modeling the variations of Dose Rate measured by RAD during the first MSL Martian year: 2012-2014

The Radiation Assessment Detector (RAD), on board Mars Science Laboratory's (MSL) rover Curiosity, measures the {energy spectra} of both energetic charged and neutral particles along with the radiation dose rate at the surface of Mars. With these first-ever measurements on the Martian surface, RAD observed several effects influencing the galactic cosmic ray (GCR) induced surface radiation dose concurrently: [a] short-term diurnal variations of the Martian atmospheric pressure caused by daily thermal tides, [b] long-term seasonal pressure changes in the Martian atmosphere, and [c] the modulation of the primary GCR flux by the heliospheric magnetic field, which correlates with long-term solar activity and the rotation of the Sun. The RAD surface dose measurements, along with the surface pressure data and the solar modulation factor, are analysed and fitted to empirical models which quantitatively demonstrate} how the long-term influences ([b] and [c]) are related to the measured dose rates. {Correspondingly we can estimate dose rate and dose equivalents under different solar modulations and different atmospheric conditions, thus allowing empirical predictions of the Martian surface radiation environment

Tobacco Smoke Augments Porphyromonas gingivalis - Streptococcus gordonii Biofilm Formation

Smoking is responsible for the majority of periodontitis cases in the US and smokers are more susceptible than non-smokers to infection by the periodontal pathogen Porphyromonas gingivalis. P. gingivalis colonization of the oral cavity is dependent upon its interaction with other plaque bacteria, including Streptococcus gordonii. Microarray analysis suggested that exposure of P. gingivalis to cigarette smoke extract (CSE) increased the expression of the major fimbrial antigen (FimA), but not the minor fimbrial antigen (Mfa1). Therefore, we hypothesized that CSE promotes P. gingivalis-S. gordonii biofilm formation in a FimA-dependent manner. FimA total protein and cell surface expression were increased upon exposure to CSE whereas Mfa1 was unaffected. CSE exposure did not induce P. gingivalis auto-aggregation but did promote dual species biofilm formation, monitored by microcolony numbers and depth (both, p<0.05). Interestingly, P. gingivalis biofilms grown in the presence of CSE exhibited a lower pro-inflammatory capacity (TNF-α, IL-6) than control biofilms (both, p<0.01). CSE-exposed P. gingivalis bound more strongly to immobilized rGAPDH, the cognate FimA ligand on S. gordonii, than control biofilms (p<0.001) and did so in a dose-dependent manner. Nevertheless, a peptide representing the Mfa1 binding site on S. gordonii, SspB, completely inhibited dual species biofilm formation. Thus, CSE likely augments P. gingivalis biofilm formation by increasing FimA avidity which, in turn, supports initial interspecies interactions and promotes subsequent high affinity Mfa1-SspB interactions driving biofilm growth. CSE induction of P. gingivalis biofilms of limited pro-inflammatory potential may explain the increased persistence of this pathogen in smokers. These findings may also be relevant to other biofilm-induced infectious diseases and conditions

Observation of Stratospheric Ozone Depletion associated with Delta II Rocket Emissions

Ozone, chlorine monoxide, methane, and submicron particulate concentrations were measured in the stratospheric plume wake of a Delta II rocket powered by a combination of solid (NH4ClO4/Al) and liquid (LOX/kerosene) propulsion systems. We apply a simple kinetics model describing the main features of gas-phase chlorine reactions in solid propellant exhaust plumes to derive the abundance of total reactive chlorine in the plume and estimate the associated cumulative ozone loss. Measured ozone loss during two plume encounters (12 and 39 minutes after launch) exceeded the estimate by about a factor of about two. Insofar as only the most significant gas-phase chlorine reactions are included in the calculation, these results suggest that additional plume wake chemical processes or emissions other than reactive chlorine from the Delta II propulsion system affect ozone levels in the plume

Determinants of medication adherence to antihypertensive medications among a Chinese population using Morisky medication adherence scale

&lt;b&gt;Background and objectives&lt;/b&gt; Poor adherence to medications is one of the major public health challenges. Only one-third of the population reported successful control of blood pressure, mostly caused by poor drug adherence. However, there are relatively few reports studying the adherence levels and their associated factors among Chinese patients. This study aimed to study the adherence profiles and the factors associated with antihypertensive drug adherence among Chinese patients.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methods&lt;/b&gt; A cross-sectional study was conducted in an outpatient clinic located in the New Territories Region of Hong Kong. Adult patients who were currently taking at least one antihypertensive drug were invited to complete a self-administered questionnaire, consisting of basic socio-demographic profile, self-perceived health status, and self-reported medication adherence. The outcome measure was the Morisky Medication Adherence Scale (MMAS-8). Good adherence was defined as MMAS scores greater than 6 points (out of a total score of 8 points).&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt; From 1114 patients, 725 (65.1%) had good adherence to antihypertensive agents. Binary logistic regression analysis was conducted. Younger age, shorter duration of antihypertensive agents used, job status being employed, and poor or very poor self-perceived health status were negatively associated with drug adherence.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusion&lt;/b&gt; This study reported a high proportion of poor medication adherence among hypertensive subjects. Patients with factors associated with poor adherence should be more closely monitored to optimize their drug taking behavior

The clustering of massive galaxies at z~0.5 from the first semester of BOSS data

We calculate the real- and redshift-space clustering of massive galaxies at z~0.5 using the first semester of data by the Baryon Oscillation Spectroscopic Survey (BOSS). We study the correlation functions of a sample of 44,000 massive galaxies in the redshift range 0.4<z<0.7. We present a halo-occupation distribution modeling of the clustering results and discuss the implications for the manner in which massive galaxies at z~0.5 occupy dark matter halos. The majority of our galaxies are central galaxies living in halos of mass 10^{13}Msun/h, but 10% are satellites living in halos 10 times more massive. These results are broadly in agreement with earlier investigations of massive galaxies at z~0.5. The inferred large-scale bias (b~2) and relatively high number density (nbar=3e-4 h^3 Mpc^{-3}) imply that BOSS galaxies are excellent tracers of large-scale structure, suggesting BOSS will enable a wide range of investigations on the distance scale, the growth of large-scale structure, massive galaxy evolution and other topics.Comment: 11 pages, 12 figures, matches version accepted by Ap

Optical Propagation and Communication

Contains research objectives and reports on four research projects.National Science Foundation (Grant ECS 85-09143)Maryland Procurement Office (Contract MDA 904-84-C-6037)National Science Foundation (Grant ECS 84-15580)U.S. Army Research Office - Durham (Contract DAAG29-84-K-0095)U.S. Navy - Office of Naval Research (Contract N00014-80-C-0941

IUCN Conservation Status Does Not Predict Glucocortoid Concentrations in Reptiles and Birds

Circulating glucocorticoids (GCs) are the most commonly used biomarkers of stress in wildlife. However, their utility as a tool for identifying and/or managing at-risk species has varied. Here, we took a very broad approach to conservation physiology, asking whether International Union for the Conservation of Nature (IUCN) listing status (concern versus no obvious concern) and/or location within a geographic range (edge versus non-edge) predicted baseline and post-restraint concentrations of corticosterone (CORT) among many species of birds and reptiles. Even though such an approach can be viewed as coarse, we asked in this analysis whether CORT concentrations might be useful to implicate species at risk. Indeed, our effort, relying on HormoneBase, a repository of data on wildlife steroids, complements several other large-scale efforts in this issue to describe and understand GC variation. Using a phylogenetically informed Bayesian approach, we found little evidence that either IUCN status or edge/non-edge location in a geographic distribution were related to GC levels. However, we did confirm patterns described in previous studies, namely that breeding condition and evolutionary relatedness among species predicted some GC variation. Given the broad scope of our work, we are reluctant to conclude that IUCN status and location within a range are unrelated to GC regulation. We encourage future more targeted efforts on GCs in at-risk populations to reveal how factors leading to IUCN listing or the environmental conditions at range edges impact individual performance and fitness, particularly in the mammals, amphibians, and fish species we could not study here because data are currently unavailable