Metabolome Based Reaction Graphs of M. tuberculosis and M. leprae: A Comparative Network Analysis

BACKGROUND: Several types of networks, such as transcriptional, metabolic or protein-protein interaction networks of various organisms have been constructed, that have provided a variety of insights into metabolism and regulation. Here, we seek to exploit the reaction-based networks of three organisms for comparative genomics. We use concepts from spectral graph theory to systematically determine how differences in basic metabolism of organisms are reflected at the systems level and in the overall topological structures of their metabolic networks. METHODOLOGY/PRINCIPAL FINDINGS: Metabolome-based reaction networks of Mycobacterium tuberculosis, Mycobacterium leprae and Escherichia coli have been constructed based on the KEGG LIGAND database, followed by graph spectral analysis of the network to identify hubs as well as the sub-clustering of reactions. The shortest and alternate paths in the reaction networks have also been examined. Sub-cluster profiling demonstrates that reactions of the mycolic acid pathway in mycobacteria form a tightly connected sub-cluster. Identification of hubs reveals reactions involving glutamate to be central to mycobacterial metabolism, and pyruvate to be at the centre of the E. coli metabolome. The analysis of shortest paths between reactions has revealed several paths that are shorter than well established pathways. CONCLUSIONS: We conclude that severe downsizing of the leprae genome has not significantly altered the global structure of its reaction network but has reduced the total number of alternate paths between its reactions while keeping the shortest paths between them intact. The hubs in the mycobacterial networks that are absent in the human metabolome can be explored as potential drug targets. This work demonstrates the usefulness of constructing metabolome based networks of organisms and the feasibility of their analyses through graph spectral methods. The insights obtained from such studies provide a broad overview of the similarities and differences between organisms, taking comparative genomics studies to a higher dimension

Linear Collider Physics Resource Book for Snowmass 2001, 3: Studies of Exotic and Standard Model Physics

This Resource Book reviews the physics opportunities of a next-generation e+e- linear collider and discusses options for the experimental program. Part 3 reviews the possible experiments on that can be done at a linear collider on strongly coupled electroweak symmetry breaking, exotic particles, and extra dimensions, and on the top quark, QCD, and two-photon physics. It also discusses the improved precision electroweak measurements that this collider will make available.This Resource Book reviews the physics opportunities of a next-generation e+e- linear collider and discusses options for the experimental program. Part 3 reviews the possible experiments on that can be done at a linear collider on strongly coupled electroweak symmetry breaking, exotic particles, and extra dimensions, and on the top quark, QCD, and two-photon physics. It also discusses the improved precision electroweak measurements that this collider will make available

Use of a Generalized Additive Model to Investigate Key Abiotic Factors Affecting Microcystin Cellular Quotas in Heavy Bloom Areas of Lake Taihu

Lake Taihu is the third largest freshwater lake in China and is suffering from serious cyanobacterial blooms with the associated drinking water contamination by microcystin (MC) for millions of citizens. So far, most studies on MCs have been limited to two small bays, while systematic research on the whole lake is lacking. To explain the variations in MC concentrations during cyanobacterial bloom, a large-scale survey at 30 sites across the lake was conducted monthly in 2008. The health risks of MC exposure were high, especially in the northern area. Both Microcystis abundance and MC cellular quotas presented positive correlations with MC concentration in the bloom seasons, suggesting that the toxic risks during Microcystis proliferations were affected by variations in both Microcystis density and MC production per Microcystis cell. Use of a powerful predictive modeling tool named generalized additive model (GAM) helped visualize significant effects of abiotic factors related to carbon fixation and proliferation of Microcystis (conductivity, dissolved inorganic carbon (DIC), water temperature and pH) on MC cellular quotas from recruitment period of Microcystis to the bloom seasons, suggesting the possible use of these factors, in addition to Microcystis abundance, as warning signs to predict toxic events in the future. The interesting relationship between macrophytes and MC cellular quotas of Microcystis (i.e., high MC cellular quotas in the presence of macrophytes) needs further investigation

Measurement of the Top Quark Mass with the Collider Detector at Fermilab

This report describes a measurement of the top quark mass in \ppbar collisions at a center of mass energy of 1.8 TeV. The data sample was collected with the CDF detector during the 1992--95 collider run at the Fermilab Tevatron, and corresponds to an integrated luminosity of 106 \pb. Candidate $t\bar{t}$ events in the ``lepton+jets'' decay channel provide our most precise measurement of the top quark mass. For each event a top mass is determined by using energy and momentum constraints on the production of the \ttbar pair and its subsequent decay. A likelihood fit to the distribution of reconstructed masses in the data sample gives a top mass in the lepton+jets channel of 176.1\pm 5.1 (stat.)\pm 5.3 (syst.) \gevcc. Combining this result with measurements from the ``all-hadronic'' and ``dilepton'' decay topologies yields a top mass of 176.1\pm 6.6 \gevcc.Comment: 158 pages, 41 figure

Observation of Higgs boson production in association with a top quark pair at the LHC with the ATLAS detector

The observation of Higgs boson production in association with a top quark pair (tt H¯ ), based on the analysis of proton–proton collision data at a centre-of-mass energy of 13 TeV recorded with the ATLAS detector at the Large Hadron Collider, is presented. Using data corresponding to integrated luminosities of up to 79.8 fb−1, and considering Higgs boson decays into b¯ b, W W ∗, τ +τ −, γγ , and Z Z∗, the observed significance is 5.8 standard deviations, compared to an expectation of 4.9 standard deviations. Combined with the tt H¯ searches using a dataset corresponding to integrated luminosities of 4.5 fb−1 at 7 TeV and 20.3 fb−1 at 8 TeV, the observed (expected) significance is 6.3 (5.1) standard deviations. Assuming Standard Model branching fractions, the total tt H¯ production cross section at 13 TeV is measured to be 670 ± 90 (stat.) +110 −100 (syst.) fb, in agreement with the Standard Model prediction

Measurement of the ttbar Production Cross Section in ppbar collisions at sqrt s = 1.96 TeV in the All Hadronic Decay Mode

We report a measurement of the ttbar production cross section using the CDF-II detector at the Fermilab Tevatron. The analysis is performed using 311 pb-1 of ppbar collisions at sqrt(s)=1.96 TeV. The data consist of events selected with six or more hadronic jets with additional kinematic requirements. At least one of these jets must be identified as a b-quark jet by the reconstruction of a secondary vertex. The cross section is measured to be sigma(tbart)=7.5+-2.1(stat.)+3.3-2.2(syst.)+0.5-0.4(lumi.) pb, which is consistent with the standard model prediction.Comment: By CDF collaboratio

Search for chargino-neutralino production in ppbar collisions at sqrt(s) = 1.96 TeV

We present the results of a search for associated production of the chargino and neutralino supersymmetric particles using up to 1.1 fb-1 of integrated luminosity collected by the CDF II experiment at the Tevatron ppbar collider at a center-of-mass energy of 1.96 TeV. The search is conducted by analyzing events with a large transverse momentum imbalance and either three charged leptons or two charged leptons of the same electric charge. The numbers of observed events are found to be consistent with standard model expectations. Upper limits on the production cross section are derived in different theoretical models. In one of these models a lower limit on the mass of the chargino is set at 129 GeV/c^2 at the 95% confidence level.Comment: To be submitted to Phys.Rev.Let

Ex-post Performance Implications of Divergence of Managers’ Perceptions of ‘Distance’ From ‘Reality’ in International Business

Despite much research on “distance”, little attention has been paid to the effect of divergence of managers’ perceptions of distance from reality (i.e. distance divergence) and its implications for firm performance. This knowledge is highly important since managerial perceptions of the firm’s environment do not always coincide with the actual environmental characteristics. Consequently, strategies based on inaccurate data may result in erroneous forecasts, missed opportunities and business failure. Using survey data from senior managers of Swedish exporters and corresponding objective data, this study is a first attempt to explore the ex-post performance implications of “distance divergence” when expanding into foreign markets. Our results demonstrate that the larger the divergence between managers’ perceptions of cultural distance and corresponding “objective” distance, the lower the performance expressed in companies’ sales. However, over/underestimation of cultural distance does not have differential effects on firm performance.“Stiftelsen Olle Hakelius Stipendiefond”, Grant no: 1165001