Summing O(β0nαsn+1)O(\beta_0^n \alpha_s^{n+1}) Corrections to Top Quark Decays

Order $\beta_0^n \alpha_s^{n+1}$ QCD corrections to top quark decays into $W^+$ and $H^+$ bosons are computed to all orders in perturbation theory. Predictions for the radiative corrections to the top quark width are compared with the estimates from BLM scale setting procedures. The results of the summation are shown to greatly improve understanding of higher order corrections in the limit $m_W,~m_H \to m_t$, where the BLM scale setting method is known to fail. Attempts to reduce nonperturbative error by substituting the running mass for the pole mass in the expression for the decay are shown to fail in the limit $m_W,~m_H \to m_t$ because of subtleties in the treatment of phase space.Comment: 12 pages, Latex, 5 figures. Uses revtex and epsf macro

Evaluation of phytoremediation potential of Peltophorum pterocarpum (DC.) Heyne Leucaena leucocephala (Lam.) De Wit. and Crotolaria retusa Linn for waste oil contaminated soils

An ecological study was carried out to evaluate remediation potential of three hydrocarbon tolerant species (Peltophorum pterocarpum (DC.) Heyne, Leucaena leucocephala (Lam.) De Wit., and Crotolaria retusa Linn) of Fabaceae plant family in relation to enzyme activity for cleaning up soils contaminated with waste oil hydrocarbon. Biochemical analyses were carried out using classical standard procedures to assess the level of enzyme expression in relation to hydrocarbon index assessment in remediation performance through a holistic test of significance using the PROC ANOVA and Duncan’s New Multiple Range Test (DNMRT) procedures. Enzyme expression, oil removal and organic carbon sequestration of the species and the species treated soils showed that in pre-polluted soil foliar enzyme expression in the order Cr>Ll>Pp was high but reduction in post-polluted and post-phytoremediation soils in the order Cr>Ll>Pp. Generally, among species Peroxidase (POD) was higher in activity and expression than Polyphenoloxidase (PPO). The oil and grease recorded a lower content in the pre-pollution soil which increased in content in post-pollution with increase in pollution. However, the impact of phytoapplication has shown some significant (p<0.05) reduction in L. leucocephala soil in the order Ll<Pp<Cr but higher foliar content among the species in the order Ll>Pp>Cr at low enzyme expression in which P. pterocarpum had higher carbon content in the order Pp>Cr> Ll. The pre-pollution soil had a significantly lower carbon than post-polluted soils. The impact of phytoremediation has shown reduction in carbon content with P. pterocarpum treated soil significantly lower in content in the order Pp<Cr< Ll and higher foliar content in the order Pp>Cr> Ll. Thus by the forgoing trajectories and trend of indigenous enzymes, P. pterocarpum and L. leucocephala can thus be recommended as an integral component in any bioremediation technology package for waste oil polluted terrestrial environment.Keywords: Peroxidase, Polyphenoloxidase, Organic carbon, Oil & grease, Phytoapplicatio

Solution of a hydrodynamic lubrication problem with Maple

A set of partial differential equations, arising in a calculation of hydrodynamic lubricationeffects, was solved using a perturbation technique. All of the algebraic manipulations required to find the solution were performed using Maple. The main challenge was the efficient handling and simplification of very long expression, which was met by the power of Maple's built-in procedures and by algebraic transformations suggested by the solution to the lowest-order approximation. As a result, the solution was obtained to a higher order, with greater reliability, than would otherwise have been possible

An approximate viscous shock layer technique for calculating chemically reacting hypersonic flows about blunt-nosed bodies

An approximate axisymmetric method was developed which can reliably calculate fully viscous hypersonic flows over blunt nosed bodies. By substituting Maslen's second order pressure expression for the normal momentum equation, a simplified form of the viscous shock layer (VSL) equations is obtained. This approach can solve both the subsonic and supersonic regions of the shock layer without a starting solution for the shock shape. The approach is applicable to perfect gas, equilibrium, and nonequilibrium flowfields. Since the method is fully viscous, the problems associated with a boundary layer solution with an inviscid layer solution are avoided. This procedure is significantly faster than the parabolized Navier-Stokes (PNS) or VSL solvers and would be useful in a preliminary design environment. Problems associated with a previously developed approximate VSL technique are addressed before extending the method to nonequilibrium calculations. Perfect gas (laminar and turbulent), equilibrium, and nonequilibrium solutions were generated for airflows over several analytic body shapes. Surface heat transfer, skin friction, and pressure predictions are comparable to VSL results. In addition, computed heating rates are in good agreement with experimental data. The present technique generates its own shock shape as part of its solution, and therefore could be used to provide more accurate initial shock shapes for higher order procedures which require starting solutions

Incorporation of Genetic Pathway Information into Analysis of Multivariate Gene Expression Data

Abstract: Multivariate microarray gene expression data are commonly collected to study the genomic responses under ordered conditions such as over increasing/decreasing dose levels or over time during biological processes. One important question from such multivariate gene expression experiments is to identify genes that show different expression patterns over treatment dosages or over time and pathways that are perturbed during a given biological process. In this paper, we develop a hidden Markov random field model for multivariate expression data in order to identify genes and subnetworks that are related to biological processes, where the dependency of the differential expression patterns of genes on the networks are modeled by a Markov random field. Simulation studies indicated that the method is quite effective in identifying genes and the modified subnetworks and has higher sensitivity than the commonly used procedures that do not use the pathway information, with similar observed false discovery rates. We applied the proposed methods for analysis of a microarray time course gene expression study of TrkA- and TrkB-transfected neuroblastoma cell lines and identified genes and subnetworks on MAPK, focal adhesion and prion disease pathways that may explain cell differentiation in TrkA-transfected cell lines

Toxin Induction and Protein Extraction from Fusariumspp. Cultures for Proteomic Studies

Fusaria are filamentous fungi able to produce different toxins. Fusarium mycotoxins such as deoxynivalenol, nivalenol, T2, zearelenone, fusaric acid, moniliformin, etc... have adverse effects on both human and animal health and some are considered as pathogenicity factors. Proteomic studies showed to be effective for deciphering toxin production mechanisms (Taylor et al., 2008) as well as for identifying potential pathogenic factors (Paper et al., 2007, Houterman et al., 2007) in Fusaria. It becomes therefore fundamental to establish reliable methods for comparing between proteomic studies in order to rely on true differences found in protein expression among experiments, strains and laboratories. The procedure that will be described should contribute to an increased level of standardization of proteomic procedures by two ways. The filmed protocol is used to increase the level of details that can be described precisely. Moreover, the availability of standardized procedures to process biological replicates should guarantee a higher robustness of data, taking into account also the human factor within the technical reproducibility of the extraction procedure

A Markov Random Field Model for Network-based Analysis of Genomic Data

A central problem in genomic research is the identification of genes and pathways involved in diseases and other biological processes. The genes identified or the univariate test statistics are often linked to known biological pathways through gene set enrichment analysis in order to identify the pathways involved. However, most of the procedures for identifying differentially expressed genes do not utilize the known pathway information in the phase of identifying such genes. In this paper, we develop a Markov random field (MRF)-based method for identifying genes and subnetworks that are related to diseases. Such a procedure models the dependency of the differential expression patterns of genes on the networks using a local discrete MRF model. Simulation studies indicated that the method is quite effective in identifying genes and subnetworks that are related to disease and has higher sensitivity and lower false discovery rates than the commonly used procedures that do not use the pathway structure information. Applications to two breast cancer microarray gene expression datasets identified several subnetworks on several of the KEGG transcriptional pathways that are related to breast cancer recurrence or survival due to breast cancer. The proposed MRF-based model efficiently utilizes the known pathway structures in identifying the differentially expressed genes and the subnetworks that might be related to phenotype. As more biological networks are identified and documented in databases, the proposed method should find more applications in identifying the subnetworks that are related to diseases and other biological processes

Analysis of the transcriptional program governing meiosis and gametogenesis in yeast and mammals

During meiosis a competent diploid cell replicates its DNA once and then undergoes two consecutive divisions followed by haploid gamete differentiation. Important aspects of meiotic development that distinguish it from mitotic growth include a highly increased rate of recombination, formation of the synaptonemal complex that aligns the homologous chromosomes, as well as separation of the homologues and sister chromatids during meiosis I and II without an intervening S-phase. Budding yeast is an excellent model organism to study meiosis and gametogenesis and accordingly, to date it belongs to the best studied eukaryotic systems in this context. Knowledge coming from these studies has provided important insights into meiotic development in higher eukaryotes. This was possible because sporulation in yeast and spermatogenesis in higher eukaryotes are analogous developmental pathways that involve conserved genes. For budding yeast a huge amount of data from numerous genome-scale studies on gene expression and deletion phenotypes of meiotic development and sporulation are available. In contrast, mammalian gametogenesis has not been studied on a large-scale until recently. It was unclear if an expression profiling study using germ cells and testicular somatic control cells that underwent lengthy purification procedures would yield interpretable results. We have therefore carried out a pioneering expression profiling study of male germ cells from Rattus norvegicus using Affymetrix U34A and B GeneChips. This work resulted in the first comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis and gametogenesis. We have identified 1268 differentially expressed genes in germ cells at different developmental stages, which were organized into four distinct expression clusters that reflect somatic, mitotic, meiotic and post-meiotic cell types. This included 293 yet uncharacterized transcripts whose expression pattern suggests that they are involved in spermatogenesis and fertility. A group of 121 transcripts were only expressed in meiotic (spermatocytes) and postmeiotic germ cells (round spermatids) but not in dividing germ cells (spermatogonia), Sertoli cells or two somatic control tissues (brain and skeletal muscle). Functional analysis reveals that most of the known genes in this group fulfill essential functions during meiosis, spermiogenesis (the process of sperm maturation) and fertility. Therefore it is highly possible that some of the �30 uncharacterized transcripts in this group also contribute to these processes. A web-accessible database (called reXbase, which was later on integrated into GermOnline) has been developed for our expression profiling study of mammalian male meiosis, which summarizes annotation information and shows a graphical display of expression profiles of every gene covered in our study. In the budding yeast Saccharomyces cerevisiae entry into meiosis and subsequent progression through sporulation and gametogenesis are driven by a highly regulated transcriptional program activated by signal pathways responding to nutritional and cell-type cues. Abf1p, which is a general transcription factor, has previously been demonstrated to participate in the induction of numerous mitotic as well as early and middle meiotic genes. In the current study we have addressed the question how Abf1p transcriptionally coordinates mitotic growth and meiotic development on a genome-wide level. Because ABF1 is an essential gene we used the temperature-sensitive allele abf1-1. A phenotypical analysis of mutant cells revealed that ABF1 plays an important role in cell separation during mitosis, meiotic development, and spore formation. In order to identify genes whose expression depends on Abf1p in growing and sporulating cells we have performed expression profiling experiments using Affymetrix S98 GeneChips comparing wild-type and abf1-1 mutant cells at both permissive and restrictive temperature. We have identified 504 genes whose normal expression depends on functional ABF1. By combining the expression profiling data with data from genome-wide DNA binding assays (ChIPCHIP) and in silico predictions of potential Abf1p-binding sites in the yeast genome, we were able to define direct target genes. Expression of these genes decreases in the absence of functional ABF1 and whose promotors are bound by Abf1p and/or contain a predicted binding site. Among 352 such bona fide direct target genes we found many involved in ribosome biogenesis, translation, vegetative growth and meiotic developement and therefore could account for the observed growth and sporulation defects of abf1-1 mutant cells. Furthermore, the fact that two members of the septin family (CDC3 and CDC10 ) were found to be direct target genes suggests a novel role for Abf1p in cytokinesis. This was further substantiated by the observation that chitin localization and septin ring formation are perturbed in abf1-1 mutant cells

Assessing skewness, kurtosis and normality in linear mixedmodels

ABSTRACT: Linear mixed models provide a useful tool to fit continuous longitudinal data, with the random effects and error term commonly assumed to have normal distributions. However, this restrictive assumption can result in a lack of robustness and needs to be tested. In this paper, we propose tests for skewness, kurtosis, and normality based on generalized least squares (GLS) residuals. To do it, estimating higher order moments is necessary and an alternative estimation procedure is developed. Compared to other procedures in the literature, our approach provides a closed form expression even for the third and fourth order moments. In addition, no further distributional assumptions on either random effects or error terms are needed to show the consistency of the proposed estimators and tests statistics. Their finite-sample performance is examined in a Monte Carlo study and the methodology is used to examine changes in the life expectancy as well as maternal and infant mortality rate of a sample of OECD countries

The Transient Behavior of Nonlinear Systems

It is shown that the classical perturbation procedure for treating nonlinear systems leads to solutions expressed as Fourier-like series with slowly varying coefficients. These slowly varying coefficients contain the information about the long term behavior of the system. Inconsistently, the classical perturbation procedure expresses these coefficients as power series, a mode of expression which has notoriously poor long term validity. An operational procedure is presented for treating oscillations having slowly variable amplitudes and frequencies. An extension of the usual impedance concepts is presented for expressing the frequency characteristics of both linear and nonlinear elements when oscillations with many frequencies are present simultaneously and when these oscillations vary in both frequency and amplitude. From these methods, a perturbation procedure is devised which permits the behavior of systems to be computed with any order of accuracy, using only the algebraic processes which are characteristic of operational procedures. This procedure avoids expressing its results in terms of the local time. Instead, it expresses them in terms of the fundamental characteristics of the oscillations which axe present. As a consequence, the final solutions have the much desired long term validity and they may be used to obtain asymptotic estimates of the behavior of the system. The method is able to treat systems containing nonlinear perturbing elements and elements which we have described as moderately nonlinear. By means of examples it is shown that it is a straightforward process to treat systems to second order accuracy. This level of accuracy covers a large number of the intercoupling effects that characterize the more sophisticated nonlinear phenomena