Hepatitis B: The view from West Africa

The Prevention of Liver Fibrosis and Cancer in Africa (PROLIFICA) study began in 2011 in The Gambia, Sénégal and Nigeria. The study aims to reduce the risk of hepatocellular carcinoma (HCC) in West Africa through the suppression of the Hepatitis B virus (HBV). The biological samples collected allow for the detection of novel liver cancer biomarkers in the hope of improving the diagnostic ability of early disease states. The PROLIFICA platform hopes to improve cancer diagnostics whilst simultaneously providing the training, skills and infrastructure necessary to develop the quality of liver cancer care in West Africa

Isospin influences on particle emission and critical phenomenon in nuclear dissociation

Features of particle emission and critical point behavior are investigated as functions of the isospin of disassembling sources and temperature at a moderate freeze-out density for medium-size Xe isotopes in the framework of isospin dependent lattice gas model. Multiplicities of emitted light particles, isotopic and isobaric ratios of light particles show the strong dependence on the isospin of the dissociation source, but double ratios of light isotope pairs and the critical temperature determined by the extreme values of some critical observables are insensitive to the isospin of the systems. Values of the power law parameter of cluster mass distribution, mean multiplicity of intermediate mass fragments ($IMF$), information entropy ($H$) and Campi's second moment ($S_2$) also show a minor dependence on the isospin of Xe isotopes at the critical point. In addition, the slopes of the average multiplicites of the neutrons ($N_n$), protons ($N_p$), charged particles ($N_{CP}$), and IMFs ($N_{imf}$), slopes of the largest fragment mass number ($A_{max}$), and the excitation energy per nucleon of the disassembling source ($E^*/A$) to temperature are investigated as well as variances of the distributions of $N_n$, $N_p$, $N_{CP}$, $N_{IMF}$, $A_{max}$ and $E^*/A$. It is found that they can be taken as additional judgements to the critical phenomena.Comment: 9 Pages, 8 figure

Parallel computation of 3-D soil-structure interaction in time domain with a coupled FEM/SBFEM approach

The final publication is available at Springer via http://dx.doi.org/10.1007/s10915-011-9551-xThis paper introduces a parallel algorithm for the scaled boundary finite element method (SBFEM). The application code is designed to run on clusters of computers, and it enables the analysis of large-scale soil-structure-interaction problems, where an unbounded domain has to fulfill the radiation condition for wave propagation to infinity. The main focus of the paper is on the mathematical description and numerical implementation of the SBFEM. In particular, we describe in detail the algorithm to compute the acceleration unit impulse response matrices used in the SBFEM as well as the solvers for the Riccati and Lyapunov equations. Finally, two test cases validate the new code, illustrating the numerical accuracy of the results and the parallel performances. © Springer Science+Business Media, LLC 2011.Jose E. Roman and Enrique S. Quintana-Orti were partially supported by the Spanish Ministerio de Ciencia e Innovacion under grants TIN2009-07519, and TIN2008-06570-C04-01, respectively.Schauer, M.; Román Moltó, JE.; Quintana Orti, ES.; Langer, S. (2012). Parallel computation of 3-D soil-structure interaction in time domain with a coupled FEM/SBFEM approach. Journal of Scientific Computing. 52(2):446-467. doi:10.1007/s10915-011-9551-xS446467522Anderson, E., Bai, Z., Bischof, C., Demmel, J., Dongarra, J., Croz, J.D., Greenbaum, A., Hammarling, S., McKenney, A., Sorensen, D.: LAPACK User’s Guide. Society for Industrial and Applied Mathematics, Philadelphia (1992)Antes, H., Spyrakos, C.: Soil-structure interaction. In: Beskos, D., Anagnotopoulos, S. (eds.) Computer Analysis and Design of Earthquake Resistant Structures, p. 271. Computational Mechanics Publications, Southampton (1997)Appelö, D., Colonius, T.: A high-order super-grid-scale absorbing layer and its application to linear hyperbolic systems. J. Comput. Phys. 228(11), 4200–4217 (2009)Astley, R.J.: Infinite elements for wave problems: a review of current formulations and a assessment of accuracy. Int. J. Numer. Methods Eng. 49(7), 951–976 (2000)Balay, S., Buschelman, K., Eijkhout, V., Gropp, W.D., Kaushik, D., Knepley, M., McInnes, L.C., Smith, B.F., Zhang, H.: PETSc users manual. Tech. Rep. ANL-95/11 - Revision 3.1, Argonne National Laboratory (2010)Benner, P.: Contributions to the numerical solution of algebraic Riccati equations and related eigenvalue problems. Dissertation, Fak. f. Mathematik, TU Chemnitz–Zwickau, Chemnitz, FRG (1997)Benner, P.: Numerical solution of special algebraic Riccati equations via an exact line search method. In: Proc. European Control Conf. ECC 97, Paper 786, BELWARE Information Technology, Waterloo (B) (1997)Benner, P., Quintana-Ortí, E.: Solving stable generalized Lyapunov equations with the matrix sign function. Numer. Algorithms 20(1), 75–100 (1999)Benner, P., Byers, R., Quintana-Ortí, E., Quintana-Ortí, G.: Solving algebraic Riccati equations on parallel computers using Newton’s method with exact line search. Parallel Comput. 26(10), 1345–1368 (2000)Benner, P., Quintana-Ortí, E.S., Quintana-Ortí, G.: Solving linear-quadratic optimal control problems on parallel computers. Optim. Methods Softw. 23(6), 879–909 (2008)Bettess, P.: Infinite Elements. Penshaw Press, Sunderland (1992)Blackford, L.S., Choi, J., Cleary, A., D’Azevedo, E., Demmel, J., Dhillon, I., Dongarra, J., Hammarling, S., Henry, G., Petitet, A., Stanley, K., Walker, D., Whaley, R.C.: ScaLAPACK Users’ Guide. Society for Industrial and Applied Mathematics, Philadelphia (1997)Borsutzky, R.: Braunschweiger Schriften zur Mechanik - Seismic Risk Analysis of Buried Lifelines, vol. 63. Mechanik-Zentrum Technische Universität. Braunschweig (2008)Dongarra, J.J., Whaley, R.C.: LAPACK working note 94: A user’s guide to the BLACS v1.1. Tech. Rep. UT-CS-95-281, Department of Computer Science, University of Tennessee (1995)Engquist, B., Majda, A.: Absorbing boundary conditions for the numerical simulation of waves. Math. Comput. 31(139), 629–651 (1977)Granat, R., Kågström, B.: Algorithm 904: The SCASY library – parallel solvers for Sylvester-type matrix equations with applications in condition estimation, part II. ACM Trans. Math. Softw. 37(3), 33:1–33:4 (2010)Guerrero, D., Hernández, V., Román, J.E.: Parallel SLICOT model reduction routines: The Cholesky factor of Grammians. In: Proceedings of the 15th Triennal IFAC World Congress, Barcelona, Spain (2002)Harr, M.E.: Foundations of Theoretical Soil Mechanics. McGraw-Hill, New York (1966)Hilbert, H., Hughes, T., Taylor, R.: Improved numerical dissipation for time integration algorithms in structural dynamics. Earthquake Eng. Struct. Dyn. 5, 283 (1977)Kleinman, D.: On an iterative technique for Riccati equation computations. IEEE Trans. Autom. Control AC-13, 114–115 (1968)Lehmann, L.: Wave Propagation in Infinite Domains. Springer, Berlin (2006)Lehmann, L., Langer, S., Clasen, D.: Scaled boundary finite element method for acoustics. J. Comput. Acoust. 14(4), 489–506 (2006)Liao, Z.P., Wong, H.L.: A transmitting boundary for the numerical simulation of elastic wave propagation. Soil Dyn. Earthq. Eng. 3(4), 174–183 (1984)Lysmer, J., Kuhlmeyer, R.L.: Finite dynamic model for infinite media. J. Eng. Mech. 95, 859–875 (1969)Meskouris, K., Hinzen, K.G., Butenweg, C., Mistler, M.: Bauwerke und Erdbeben - Grundlagen - Anwendung - Beispiele. Vieweg Teubner, Wiesbaden (2007)MPI Forum: The message passing interface (MPI) standard (1994). http://www.mcs.anl.gov/mpiNewmark, N.: A method of computation for structural dynamics. J. Eng. Mech. Div. 85, 67 (1959)Petersen, C.: Dynamik der Baukonstruktionen. Vieweg/Sohn Verlagsgesellschaft, Braunschweig (2000)Roberts, J.: Linear model reduction and solution of the algebraic Riccati equation by use of the sign function. Int. J. Control 32, 677–687 (1980)Schauer, M., Lehmann, L.: Large scale simulation with scaled boundary finite element method. Proc. Appl. Math. Mech. 9, 103–106 (2009)Wolf, J.: The Scaled Boundary Finite Element Method. Wiley, Chichester (2003)Wolf, J., Song, C.: Finite-Element Modelling of Unbounded Media. Wiley, Chichester (1996

Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya

Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization

Global Search for New Physics with 2.0/fb at CDF

Data collected in Run II of the Fermilab Tevatron are searched for indications of new electroweak-scale physics. Rather than focusing on particular new physics scenarios, CDF data are analyzed for discrepancies with the standard model prediction. A model-independent approach (Vista) considers gross features of the data, and is sensitive to new large cross-section physics. Further sensitivity to new physics is provided by two additional algorithms: a Bump Hunter searches invariant mass distributions for "bumps" that could indicate resonant production of new particles; and the Sleuth procedure scans for data excesses at large summed transverse momentum. This combined global search for new physics in 2.0/fb of ppbar collisions at sqrt(s)=1.96 TeV reveals no indication of physics beyond the standard model.Comment: 8 pages, 7 figures. Final version which appeared in Physical Review D Rapid Communication

Observation of Orbitally Excited B_s Mesons

We report the first observation of two narrow resonances consistent with states of orbitally excited (L=1) B_s mesons using 1 fb^{-1} of ppbar collisions at sqrt{s} = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron. We use two-body decays into K^- and B^+ mesons reconstructed as B^+ \to J/\psi K^+, J/\psi \to \mu^+ \mu^- or B^+ \to \bar{D}^0 \pi^+, \bar{D}^0 \to K^+ \pi^-. We deduce the masses of the two states to be m(B_{s1}) = 5829.4 +- 0.7 MeV/c^2 and m(B_{s2}^*) = 5839.7 +- 0.7 MeV/c^2.Comment: Version accepted and published by Phys. Rev. Let

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

Search for the standard model Higgs boson decaying to a bbˉb\bar{b} pair in events with no charged leptons and large missing transverse energy using the full CDF data set

We report on a search for the standard model Higgs boson produced in association with a vector boson in the full data set of proton-antiproton collisions at $\sqrt{s} = 1.96$ TeV recorded by the CDF II detector at the Tevatron, corresponding to an integrated luminosity of 9.45 fb$^{-1}$. We consider events having no identified charged lepton, a transverse energy imbalance, and two or three jets, of which at least one is consistent with originating from the decay of a $b$ quark. We place 95% credibility level upper limits on the production cross section times standard model branching fraction for several mass hypotheses between 90 and $150 \mathrm{GeV}/c^2$. For a Higgs boson mass of $125 \mathrm{GeV}/c^2$, the observed (expected) limit is 6.7 (3.6) times the standard model prediction.Comment: Accepted by Phys. Rev. Let

Search for the standard model Higgs boson decaying to a bb pair in events with one charged lepton and large missing transverse energy using the full CDF data set

We present a search for the standard model Higgs boson produced in association with a W boson in sqrt(s) = 1.96 TeV p-pbar collision data collected with the CDF II detector at the Tevatron corresponding to an integrated luminosity of 9.45 fb-1. In events consistent with the decay of the Higgs boson to a bottom-quark pair and the W boson to an electron or muon and a neutrino, we set 95% credibility level upper limits on the WH production cross section times the H->bb branching ratio as a function of Higgs boson mass. At a Higgs boson mass of 125 GeV/c2 we observe (expect) a limit of 4.9 (2.8) times the standard model value.Comment: Submitted to Phys. Rev. Lett (v2 contains clarifications suggested by PRL