Analysis of Gene Sets Based on the Underlying Regulatory Network

Networks are often used to represent the interactions among genes and proteins. These interactions are known to play an important role in vital cell functions and should be included in the analysis of genes that are differentially expressed. Methods of gene set analysis take advantage of external biological information and analyze a priori defined sets of genes. These methods can potentially preserve the correlation among genes; however, they do not directly incorporate the information about the gene network. In this paper, we propose a latent variable model that directly incorporates the network information. We then use the theory of mixed linear models to present a general inference framework for the problem of testing the significance of subnetworks. Several possible test procedures are introduced and a network based method for testing the changes in expression levels of genes as well as the structure of the network is presented. The performance of the proposed method is compared with methods of gene set analysis using both simulation studies, as well as real data on genes related to the galactose utilization pathway in yeast.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78147/1/cmb.2008.0081.pd

Design, Construction, and Quality Control Guidelines for Stress-Laminated Timber Bridge Decks

DTFH61-90-00067This publication is part of a collection of three booklets of the study "Education and Technology Transfer", under the Timber Bridge Research Program. The other two booklets are: FHWA-RD-92-044 - Corrosion Protection of Steel Hardware Used in Modern Timber Bridges; and FHWA-RD-93-024 - Timber Substructures for Bridge Applications.Under the U.S. National Timber Bridge Initiative Program, sponsored by Congress in 1989 and administered by the United States Department of Agriculture, Forest Service, approximately 130 modern timber bridges are currently in service in 41 participating States. Most of these bridges use stress-laminating technology. Considerable research on stress-laminating technology has been completed in the USA and has provided design, construction, and inspection guidelines for timber bridge decks. Guidelines for the design of stress-laminated timber decks have been published by AASHTO, but they do not provide comprehensive information on materials, construction, and inspection. Therefore, this document presents: (1) background information on timber bridge materials and their quality control; (2) a comprehensive step-by-step design procedure based on the 1991 AASHTO Guide Specification; and (3) guidelines for construction, field monitoring, inspection, and maintenance procedures. Potential fabrication problems are discussed, and an inspection checklist is included

Effects of cover crops on phosphatase activity in a clay arable soil in the UK

The effect of five cover crop species (radish, buckwheat, vetch, phacelia and oat) alongside an un-cropped control, on the activity and persistence of soil acid and alkaline phosphatase activity was investigated. There was no effect on alkaline phosphatase activity at the time of cover crop incorporation (March), but by the point of maturation of the following oat cash crop (June) significant differences were detected, with the greatest activity following an oat cover crop. Acid phosphatase activity showed species-related significant differences at both sampling dates, with the magnitude increasing by June. Again, plots following an oat cover crop showed the greatest activity, followed by phacelia. This has shown that soil phosphatase enzymes are affected by the presence of a cover crop, that this effect is apparently species-dependent – and not dependent on the amount of biomass from the cover crop – and that cover crops could be a potential means to enhance soil phosphorus cycling

Effects of solute Nb atoms and Nb precipitates on isothermal transformation kinetics from austenite to ferrite

Nb is a very important micro-alloying element in low-carbon steels, for grain size refinement and precipitation strengthening, and even a low content of Nb can result in a significant effect on phase transformation kinetics from austenite to ferrite. Solute Nb atoms and Nb precipitates may have different effects on transformation behaviors, and these effects have not yet been fully characterized. This paper examines in detail the effects of solute Nb atoms and Nb precipitates on isothermal transformation kinetics from austenite to ferrite. The mechanisms of the effects have been analyzed using various microscopy techniques. Many solute Nb atoms were found to be segregated at the austenite/ferrite interface and apply a solute drag effect. It has been found that solute Nb atoms have a retardation effect on ferrite nucleation rate and ferrite grain growth rate. The particle pinning effect caused by Nb precipitates is much weaker than the solute drag effect

Time-integrated luminosity recorded by the BABAR detector at the PEP-II e+e- collider

This article is the Preprint version of the final published artcile which can be accessed at the link below.We describe a measurement of the time-integrated luminosity of the data collected by the BABAR experiment at the PEP-II asymmetric-energy e+e- collider at the ϒ(4S), ϒ(3S), and ϒ(2S) resonances and in a continuum region below each resonance. We measure the time-integrated luminosity by counting e+e-→e+e- and (for the ϒ(4S) only) e+e-→μ+μ- candidate events, allowing additional photons in the final state. We use data-corrected simulation to determine the cross-sections and reconstruction efficiencies for these processes, as well as the major backgrounds. Due to the large cross-sections of e+e-→e+e- and e+e-→μ+μ-, the statistical uncertainties of the measurement are substantially smaller than the systematic uncertainties. The dominant systematic uncertainties are due to observed differences between data and simulation, as well as uncertainties on the cross-sections. For data collected on the ϒ(3S) and ϒ(2S) resonances, an additional uncertainty arises due to ϒ→e+e-X background. For data collected off the ϒ resonances, we estimate an additional uncertainty due to time dependent efficiency variations, which can affect the short off-resonance runs. The relative uncertainties on the luminosities of the on-resonance (off-resonance) samples are 0.43% (0.43%) for the ϒ(4S), 0.58% (0.72%) for the ϒ(3S), and 0.68% (0.88%) for the ϒ(2S).This work is supported by the US Department of Energy and National Science Foundation, the Natural Sciences and Engineering Research Council (Canada), the Commissariat à l’Energie Atomique and Institut National de Physique Nucléaire et de Physiquedes Particules (France), the Bundesministerium für Bildung und Forschung and Deutsche Forschungsgemeinschaft (Germany), the Istituto Nazionale di Fisica Nucleare (Italy), the Foundation for Fundamental Research on Matter (The Netherlands), the Research Council of Norway, the Ministry of Education and Science of the Russian Federation, Ministerio de Ciencia e Innovación (Spain), and the Science and Technology Facilities Council (United Kingdom). Individuals have received support from the Marie-Curie IEF program (European Union) and the A.P. Sloan Foundation (USA)

Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV

Results are presented from a search for a W' boson using a dataset corresponding to 5.0 inverse femtobarns of integrated luminosity collected during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV. The W' boson is modeled as a heavy W boson, but different scenarios for the couplings to fermions are considered, involving both left-handed and right-handed chiral projections of the fermions, as well as an arbitrary mixture of the two. The search is performed in the decay channel W' to t b, leading to a final state signature with a single lepton (e, mu), missing transverse energy, and jets, at least one of which is tagged as a b-jet. A W' boson that couples to fermions with the same coupling constant as the W, but to the right-handed rather than left-handed chiral projections, is excluded for masses below 1.85 TeV at the 95% confidence level. For the first time using LHC data, constraints on the W' gauge coupling for a set of left- and right-handed coupling combinations have been placed. These results represent a significant improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe

Search for the standard model Higgs boson decaying into two photons in pp collisions at sqrt(s)=7 TeV

A search for a Higgs boson decaying into two photons is described. The analysis is performed using a dataset recorded by the CMS experiment at the LHC from pp collisions at a centre-of-mass energy of 7 TeV, which corresponds to an integrated luminosity of 4.8 inverse femtobarns. Limits are set on the cross section of the standard model Higgs boson decaying to two photons. The expected exclusion limit at 95% confidence level is between 1.4 and 2.4 times the standard model cross section in the mass range between 110 and 150 GeV. The analysis of the data excludes, at 95% confidence level, the standard model Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The largest excess of events above the expected standard model background is observed for a Higgs boson mass hypothesis of 124 GeV with a local significance of 3.1 sigma. The global significance of observing an excess with a local significance greater than 3.1 sigma anywhere in the search range 110-150 GeV is estimated to be 1.8 sigma. More data are required to ascertain the origin of this excess.Comment: Submitted to Physics Letters

The Effect of Chemical Information on the Spatial Distribution of Fruit Flies: I Model Results

Animal aggregation is a general phenomenon in ecological systems. Aggregations are generally considered as an evolutionary advantageous state in which members derive the benefits of protection and mate choice, balanced by the costs of limiting resources and competition. In insects, chemical information conveyance plays an important role in finding conspecifics and forming aggregations. In this study, we describe a spatio-temporal simulation model designed to explore and quantify the effects of these infochemicals, i.e., food odors and an aggregation pheromone, on the spatial distribution of a fruit fly (Drosophila melanogaster) population, where the lower and upper limit of local population size are controlled by an Allee effect and competition. We found that during the spatial expansion and strong growth of the population, the use of infochemicals had a positive effect on population size. The positive effects of reduced mortality at low population numbers outweighed the negative effects of increased mortality due to competition. At low resource densities, attraction toward infochemicals also had a positive effect on population size during recolonization of an area after a local population crash, by decreasing the mortality due to the Allee effect. However, when the whole area was colonized and the population was large, the negative effects of competition on population size were larger than the positive effects of the reduction in mortality due to the Allee effect. The use of infochemicals thus has mainly positive effects on population size and population persistence when the population is small and during the colonization of an area

Measurement of the Lambda(b) cross section and the anti-Lambda(b) to Lambda(b) ratio with Lambda(b) to J/Psi Lambda decays in pp collisions at sqrt(s) = 7 TeV

The Lambda(b) differential production cross section and the cross section ratio anti-Lambda(b)/Lambda(b) are measured as functions of transverse momentum pt(Lambda(b)) and rapidity abs(y(Lambda(b))) in pp collisions at sqrt(s) = 7 TeV using data collected by the CMS experiment at the LHC. The measurements are based on Lambda(b) decays reconstructed in the exclusive final state J/Psi Lambda, with the subsequent decays J/Psi to an opposite-sign muon pair and Lambda to proton pion, using a data sample corresponding to an integrated luminosity of 1.9 inverse femtobarns. The product of the cross section times the branching ratio for Lambda(b) to J/Psi Lambda versus pt(Lambda(b)) falls faster than that of b mesons. The measured value of the cross section times the branching ratio for pt(Lambda(b)) > 10 GeV and abs(y(Lambda(b))) < 2.0 is 1.06 +/- 0.06 +/- 0.12 nb, and the integrated cross section ratio for anti-Lambda(b)/Lambda(b) is 1.02 +/- 0.07 +/- 0.09, where the uncertainties are statistical and systematic, respectively.Comment: Submitted to Physics Letters

Search for new physics in events with opposite-sign leptons, jets, and missing transverse energy in pp collisions at sqrt(s) = 7 TeV

A search is presented for physics beyond the standard model (BSM) in final states with a pair of opposite-sign isolated leptons accompanied by jets and missing transverse energy. The search uses LHC data recorded at a center-of-mass energy sqrt(s) = 7 TeV with the CMS detector, corresponding to an integrated luminosity of approximately 5 inverse femtobarns. Two complementary search strategies are employed. The first probes models with a specific dilepton production mechanism that leads to a characteristic kinematic edge in the dilepton mass distribution. The second strategy probes models of dilepton production with heavy, colored objects that decay to final states including invisible particles, leading to very large hadronic activity and missing transverse energy. No evidence for an event yield in excess of the standard model expectations is found. Upper limits on the BSM contributions to the signal regions are deduced from the results, which are used to exclude a region of the parameter space of the constrained minimal supersymmetric extension of the standard model. Additional information related to detector efficiencies and response is provided to allow testing specific models of BSM physics not considered in this paper.Comment: Replaced with published version. Added journal reference and DO