Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs

<p>Abstract</p> <p>Background</p> <p>In past number of methods have been developed for predicting subcellular location of eukaryotic, prokaryotic (Gram-negative and Gram-positive bacteria) and human proteins but no method has been developed for mycobacterial proteins which may represent repertoire of potent immunogens of this dreaded pathogen. In this study, attempt has been made to develop method for predicting subcellular location of mycobacterial proteins.</p> <p>Results</p> <p>The models were trained and tested on 852 mycobacterial proteins and evaluated using five-fold cross-validation technique. First SVM (Support Vector Machine) model was developed using amino acid composition and overall accuracy of 82.51% was achieved with average accuracy (mean of class-wise accuracy) of 68.47%. In order to utilize evolutionary information, a SVM model was developed using PSSM (Position-Specific Scoring Matrix) profiles obtained from PSI-BLAST (Position-Specific Iterated BLAST) and overall accuracy achieved was of 86.62% with average accuracy of 73.71%. In addition, HMM (Hidden Markov Model), MEME/MAST (Multiple Em for Motif Elicitation/Motif Alignment and Search Tool) and hybrid model that combined two or more models were also developed. We achieved maximum overall accuracy of 86.8% with average accuracy of 89.00% using combination of PSSM based SVM model and MEME/MAST. Performance of our method was compared with that of the existing methods developed for predicting subcellular locations of Gram-positive bacterial proteins.</p> <p>Conclusion</p> <p>A highly accurate method has been developed for predicting subcellular location of mycobacterial proteins. This method also predicts very important class of proteins that is membrane-attached proteins. This method will be useful in annotating newly sequenced or hypothetical mycobacterial proteins. Based on above study, a freely accessible web server TBpred http://www.imtech.res.in/raghava/tbpred/ has been developed.</p

Bcipep: A database of B-cell epitopes

BACKGROUND: Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases. RESULTS: The current version of Bcipep database contains 3031 entries that include 763 immunodominant, 1797 immunogenic and 471 null-immunogenic epitopes. It covers a wide range of pathogenic organisms like viruses, bacteria, protozoa, and fungi. The database provides a set of tools for the analysis and extraction of data that includes keyword search, peptide mapping and BLAST search. It also provides hyperlinks to various databases such as GenBank, PDB, SWISS-PROT and MHCBN. CONCLUSION: A comprehensive database of B-cell epitopes called Bcipep has been developed that covers information on epitopes from a wide range of pathogens. The Bcipep will be source of information for investigators involved in peptide-based vaccine design, disease diagnosis and research in allergy. It should also be a promising data source for the development and evaluation of methods for prediction of B-cell epitopes. The database is available at

Aerosol characteristics during winter fog at Agra, North India

Simultaneous measurements on physical, chemical and optical properties of aerosols over a tropical semi-arid location, Agra in north India, were undertaken during December 2004. The average concentration of total suspended particulates (TSP) increased by about 1.4 times during intense foggy/hazy days. Concentrations of SO4 2-, NO3 -, NH4 + and Black Carbon (BC) aerosols increased by 4, 2, 3.5 and 1.7 times, respectively during that period. Aerosols were acidic during intense foggy/hazy days but the fog water showed alkaline nature, mainly due to the neutralizing capacity of NH4 aerosols. Trajectory analyses showed that air masses were predominantly from NW direction, which might be responsible for transport of BC from distant and surrounding local sources. Diurnal variation of BC on all days showed a morning and an evening peak that were related to domestic cooking and vehicular emissions, apart from boundary layer changes. OPAC (Optical properties of aerosols and clouds) model was used to compute the optical properties of aerosols. Both OPAC-derived and observed aerosol optical depth (AOD) values showed spectral variation with high loadings in the short wavelengths (&lt;1 μm). AOD value at 0.5 μm wavelength was significantly high during intense foggy/hazy days (1.22) than during clear sky or less foggy/hazy days (0.63). OPAC-derived Single scattering albedo (SSA) was 0.84 during the observational period, indicating significant contribution of absorbing aerosols. However, the BC mass fraction to TSP increased by only 1 during intense foggy/hazy days and thereby did not show any impact on SSA during that period. A large increase was observed in the shortwave (SW) atmospheric (ATM) forcing during intense foggy/hazy days (+75.8 W/m2) than that during clear sky or less foggy/hazy days (+38 W/m2), mainly due to increase in absorbing aerosols. Whereas SW forcing at surface (SUF) increased from -40 W/m2 during clear sky or less foggy/hazy days to -76 W/m2 during intense foggy/hazy days, mainly due to the scattering aerosols like SO4 2-

Bianchi Type-II String Cosmological Models in Normal Gauge for Lyra's Manifold with Constant Deceleration Parameter

The present study deals with a spatially homogeneous and anisotropic Bianchi-II cosmological models representing massive strings in normal gauge for Lyra's manifold by applying the variation law for generalized Hubble's parameter that yields a constant value of deceleration parameter. The variation law for Hubble's parameter generates two types of solutions for the average scale factor, one is of power-law type and other is of the exponential form. Using these two forms, Einstein's modified field equations are solved separately that correspond to expanding singular and non-singular models of the universe respectively. The energy-momentum tensor for such string as formulated by Letelier (1983) is used to construct massive string cosmological models for which we assume that the expansion ($\theta$) in the model is proportional to the component $\sigma^{1}_{~1}$ of the shear tensor $\sigma^{j}_{i}$. This condition leads to $A = (BC)^{m}$, where A, B and C are the metric coefficients and m is proportionality constant. Our models are in accelerating phase which is consistent to the recent observations. It has been found that the displacement vector $\beta$ behaves like cosmological term $\Lambda$ in the normal gauge treatment and the solutions are consistent with recent observations of SNe Ia. It has been found that massive strings dominate in the decelerating universe whereas strings dominate in the accelerating universe. Some physical and geometric behaviour of these models are also discussed.Comment: 24 pages, 10 figure

Evanescent light-matter Interactions in Atomic Cladding Wave Guides

Alkali vapors, and in particular rubidium, are being used extensively in several important fields of research such as slow and stored light non-linear optics3 and quantum computation. Additionally, the technology of alkali vapors plays a major role in realizing myriad industrial applications including for example atomic clocks magentometers8 and optical frequency stabilization. Lately, there is a growing effort towards miniaturizing traditional centimeter-size alkali vapor cells. Owing to the significant reduction in device dimensions, light matter interactions are greatly enhanced, enabling new functionalities due to the low power threshold needed for non-linear interactions. Here, taking advantage of the mature Complimentary Metal-Oxide-Semiconductor (CMOS) compatible platform of silicon photonics, we construct an efficient and flexible platform for tailored light vapor interactions on a chip. Specifically, we demonstrate light matter interactions in an atomic cladding wave guide (ACWG), consisting of CMOS compatible silicon nitride nano wave-guide core with a Rubidium (Rb) vapor cladding. We observe the highly efficient interaction of the electromagnetic guided mode with the thermal Rb cladding. The nature of such interactions is explained by a model which predicts the transmission spectrum of the system taking into account Doppler and transit time broadening. We show, that due to the high confinement of the optical mode (with a mode area of 0.3{\lambda}2), the Rb absorption saturates at powers in the nW regime.Comment: 10 Pages 4 Figures. 1 Supplementar

The Hubble Constant

I review the current state of determinations of the Hubble constant, which gives the length scale of the Universe by relating the expansion velocity of objects to their distance. There are two broad categories of measurements. The first uses individual astrophysical objects which have some property that allows their intrinsic luminosity or size to be determined, or allows the determination of their distance by geometric means. The second category comprises the use of all-sky cosmic microwave background, or correlations between large samples of galaxies, to determine information about the geometry of the Universe and hence the Hubble constant, typically in a combination with other cosmological parameters. Many, but not all, object-based measurements give $H_0$ values of around 72-74km/s/Mpc , with typical errors of 2-3km/s/Mpc. This is in mild discrepancy with CMB-based measurements, in particular those from the Planck satellite, which give values of 67-68km/s/Mpc and typical errors of 1-2km/s/Mpc. The size of the remaining systematics indicate that accuracy rather than precision is the remaining problem in a good determination of the Hubble constant. Whether a discrepancy exists, and whether new physics is needed to resolve it, depends on details of the systematics of the object-based methods, and also on the assumptions about other cosmological parameters and which datasets are combined in the case of the all-sky methods.Comment: Extensively revised and updated since the 2007 version: accepted by Living Reviews in Relativity as a major (2014) update of LRR 10, 4, 200

Massive stars as thermonuclear reactors and their explosions following core collapse

Nuclear reactions transform atomic nuclei inside stars. This is the process of stellar nucleosynthesis. The basic concepts of determining nuclear reaction rates inside stars are reviewed. How stars manage to burn their fuel so slowly most of the time are also considered. Stellar thermonuclear reactions involving protons in hydrostatic burning are discussed first. Then I discuss triple alpha reactions in the helium burning stage. Carbon and oxygen survive in red giant stars because of the nuclear structure of oxygen and neon. Further nuclear burning of carbon, neon, oxygen and silicon in quiescent conditions are discussed next. In the subsequent core-collapse phase, neutronization due to electron capture from the top of the Fermi sea in a degenerate core takes place. The expected signal of neutrinos from a nearby supernova is calculated. The supernova often explodes inside a dense circumstellar medium, which is established due to the progenitor star losing its outermost envelope in a stellar wind or mass transfer in a binary system. The nature of the circumstellar medium and the ejecta of the supernova and their dynamics are revealed by observations in the optical, IR, radio, and X-ray bands, and I discuss some of these observations and their interpretations.Comment: To be published in " Principles and Perspectives in Cosmochemistry" Lecture Notes on Kodai School on Synthesis of Elements in Stars; ed. by Aruna Goswami & Eswar Reddy, Springer Verlag, 2009. Contains 21 figure

Cold gas accretion in galaxies

Evidence for the accretion of cold gas in galaxies has been rapidly accumulating in the past years. HI observations of galaxies and their environment have brought to light new facts and phenomena which are evidence of ongoing or recent accretion: 1) A large number of galaxies are accompanied by gas-rich dwarfs or are surrounded by HI cloud complexes, tails and filaments. It may be regarded as direct evidence of cold gas accretion in the local universe. It is probably the same kind of phenomenon of material infall as the stellar streams observed in the halos of our galaxy and M31. 2) Considerable amounts of extra-planar HI have been found in nearby spiral galaxies. While a large fraction of this gas is produced by galactic fountains, it is likely that a part of it is of extragalactic origin. 3) Spirals are known to have extended and warped outer layers of HI. It is not clear how these have formed, and how and for how long the warps can be sustained. Gas infall has been proposed as the origin. 4) The majority of galactic disks are lopsided in their morphology as well as in their kinematics. Also here recent accretion has been advocated as a possible cause. In our view, accretion takes place both through the arrival and merging of gas-rich satellites and through gas infall from the intergalactic medium (IGM). The infall may have observable effects on the disk such as bursts of star formation and lopsidedness. We infer a mean ``visible'' accretion rate of cold gas in galaxies of at least 0.2 Msol/yr. In order to reach the accretion rates needed to sustain the observed star formation (~1 Msol/yr), additional infall of large amounts of gas from the IGM seems to be required.Comment: To appear in Astronomy & Astrophysics Reviews. 34 pages. Full-resolution version available at http://www.astron.nl/~oosterlo/accretionRevie

Biocontrol of larval mosquitoes by Acilius sulcatus (Coleoptera: Dytiscidae)

<p>Abstract</p> <p>Background</p> <p>Problems associated with resistant mosquitoes and the effects on non-target species by chemicals, evoke a reason to find alternative methods to control mosquitoes, like the use of natural predators. In this regard, aquatic coleopterans have been explored less compared to other insect predators. In the present study, an evaluation of the role of the larvae of <it>Acilius sulcatus </it>Linnaeus 1758 (Coleoptera: Dytiscidae) as predator of mosquito immatures was made in the laboratory. Its efficacy under field condition was also determined to emphasize its potential as bio-control agent of mosquitoes.</p> <p>Methods</p> <p>In the laboratory, the predation potential of the larvae of <it>A. sulcatus </it>was assessed using the larvae of <it>Culex quinquefasciatus </it>Say 1823 (Diptera: Culicidae) as prey at varying predator and prey densities and available space. Under field conditions, the effectiveness of the larvae of <it>A. sulcatus </it>was evaluated through augmentative release in ten cemented tanks hosting immatures of different mosquito species at varying density. The dip density changes in the mosquito immatures were used as indicator for the effectiveness of <it>A. sulcatus </it>larvae.</p> <p>Results</p> <p>A single larva of <it>A. sulcatus </it>consumed on an average 34 IV instar larvae of <it>Cx. quinquefasciatus </it>in a 24 h period. It was observed that feeding rate of <it>A. sulcatus </it>did not differ between the light-on (6 a.m. – 6 p.m.), and dark (6 p.m. – 6 a.m.) phases, but decreased with the volume of water i.e., space availability. The prey consumption of the larvae of <it>A. sulcatus </it>differed significantly (P < 0.05) with different prey, predator and volume combinations, revealed through univariate ANOVA. The field study revealed a significant decrease (p < 0.05) in larval density of different species of mosquitoes after 30 days from the introduction of <it>A. sulcatus </it>larvae, while with the withdrawal, a significant increase (p < 0.05) in larval density was noted indicating the efficacy of <it>A. sulcatus </it>in regulating mosquito immatures. In the control tanks, mean larval density did not differ (p > 0.05) throughout the study period.</p> <p>Conclusion</p> <p>the larvae of the dytiscid beetle <it>A. sulcatus </it>proved to be an efficient predator of mosquito immatures and may be useful in biocontrol of medically important mosquitoes.</p