Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources

Computational Analysis Of Differentially Expressed Genes In Mycobacterium Tuberculosis Infection

Tuberculosis remains a serious social and public health problem, affecting millions of people annually, and is reported at the end of 2014 by the World Health 01·ganization as one of the world's deadliest communicable diseases. The most challenging being the multi-drug resistant strains of the mycobacterium. Anothe1· maj01· challenge fmstmting the effective control of this disease, especially in po01· countries, is the long time taken to diagnose it, the standa1·d diagnosis of TB is by miuoscopy, but this does not give any inf01·mation on d1·ug-resistance - the cell culture tests take two weeks, by which time it might have sp1·ead to many othe1· people. In this project, the autho1·s utilized various Statistical and Computational techniques to analyze and discove1· genes that a1·e diffe1·entially exp1·essed in human blood cell (Peripheml blood mononuclea1· cells, PBMCs) subsequent to its stimulation with heat-killed Mycobacterium on comparison with an Roswell Pa1·k Memorial Institute (RPMI) culture medium as a control. Using this in-silico technique, some unique bioma1·kers we1·e discove1·ed which a1·e fm'the1· discussed in details. These bioma1·ken identified as diffe1·entially exp1·essed in the human blood cell will not only enhance om· understanding of the pathogen, but is also a spring boa1·d fo1· the completion of an Electronic hand-held, DNA-Based Tube1-culosis diagnosis device. Om· anticipated new technology is at the intersection of genetics and compute1· science that will be used f01· rapid and early detection of Mycobacterium Tuberculosis infection, a pedect altemative to all existing symptom based diagnostic tool

Measurement of the cross section for the production of a WW boson in association with b−b^- jets in pppp collisions at s=7\sqrt{s}=7 TeV with the ATLAS detector

A measurement is presented of the cross section for the production of a W boson with one or two jets, of which at least one must be a b-jet, in pp collisions at sqrt(s)=7 TeV. Production via top decay is not included in the signal definition. The measurement is based on 35 pb^-1 of data collected with the ATLAS detector at the LHC. The W+b-jet cross section is defined for jets reconstructed with the anti-kt clustering algorithm with transverse momentum above 25 GeV and rapidity within +/-2.1. The b-jets are identified by reconstructing secondary vertices. The fiducial cross section is measured both for the electron and muon decay channel of the W boson and is found to be 10.2 +/- 1.9 (stat) +/- 2.6 (syst) pb for one lepton flavour. The results are compared with next-to-leading order QCD calculations, which predict a cross section smaller than, though consistent with, the measured value.Peer Reviewe

Search for New Physics in the Dijet Mass Distribution using 1 fb−1^{-1} of pppp Collision Data at s=\sqrt{s}=7 TeV collected by the ATLAS Detector

Invariant mass distributions of jet pairs (dijets) produced in LHC proton-proton collisions at a centre-of-mass energy sqrt(s)=7 TeV have been studied using a data set corresponding to an integrated luminosity of 1.0 fb^-1 recorded in 2011 by ATLAS. Dijet masses up to ~4 TeV are observed in the data, and no evidence of resonance production over background is found. Limits are set at 95% CL for several new physics hypotheses: excited quarks are excluded for masses below 2.99 TeV, axigluons are excluded for masses below 3.32 TeV, and colour octet scalar resonances are excluded for masses below 1.92 TeV.Peer Reviewe

Measurement of the top quark pair production cross section in pppp collisions at s=7\sqrt{s}=7 TeV in dilepton final states with ATLAS

A measurement of the production cross section of top quark pairs (ttbar) in proton-proton collisions at a center-of-mass energy of 7 TeV recorded with the ATLAS detector at the Large Hadron Collider is reported. Candidate events are selected in the dilepton topology with large missing transverse energy and at least two jets. Using a data sample corresponding to an integrated luminosity of 35 pb^-1, a ttbar production cross section of 171 +/- 20(stat.) +/- 14(syst.) +8-6(lum.) pb is measured for an assumed top quark mass of 172.5 GeV. A second measurement requiring at least one jet identified as coming from a b quark yields a comparable result, demonstrating that the dilepton final states are consistent with being accompanied by b-quark jets. These measurements are in good agreement with Standard Model predictions.Peer Reviewe

Performance of Missing Transverse Momentum Reconstruction in Proton-Proton Collisions at 7 TeV with ATLAS

The measurement of missing transverse momentum in the ATLAS detector, described in this paper, makes use of the full event reconstruction and a calibration based on reconstructed physics objects. The performance of the missing transverse momentum reconstruction is evaluated using data collected in pp collisions at a centre-of-mass energy of 7 TeV in 2010. Minimum bias events and events with jets of hadrons are used from data samples corresponding to an integrated luminosity of about 0.3 inverse nb and 600 inverse nb, together with events containing a Z boson decaying to two leptons (electrons or muons) or a W boson decaying to a lepton (electron or muon) and a neutrino, from a data sample corresponding to an integrated luminosity of about 36 inverse pb. An estimate of the systematic uncertainty on the missing transverse momentum scale is presented.Peer Reviewe

Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa

IntroductionEvery year, millions of deaths are associated with the increased spread of antimicrobial resistance genes (ARGs) in bacteria. With the increasing urbanization of the global population, the spread of ARGs in urban bacteria has become a more severe threat to human health.MethodsIn this study, we used metagenome-assembled genomes (MAGs) recovered from 1,153 urban metagenomes in multiple urban locations to investigate the fate and occurrence of ARGs in urban bacteria. Additionally, we analyzed the occurrence of these ARGs on plasmids and estimated the virulence of the bacterial species.ResultsOur results showed that multidrug and glycopeptide ARGs are ubiquitous among urban bacteria. Additionally, we analyzed the deterministic effects of phylogeny on the spread of these ARGs and found ARG classes that have a non-random distribution within the phylogeny of our recovered MAGs. However, few ARGs were found on plasmids and most of the recovered MAGs contained few virulence factors.DiscussionOur results suggest that the observed non-random spreads of ARGs are not due to the transfer of plasmids and that most of the bacteria observed in the study are unlikely to be virulent. Additional research is needed to evaluate whether the ubiquitous and widespread ARG classes will become entirely prevalent among urban bacteria and how they spread among phylogenetically distinct species

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 bb¯ , WW⁎ , τ+τ− , γγ , and ZZ⁎ , 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.) −100+110 (syst.) fb, in agreement with the Standard Model prediction.Peer Reviewe

Measurement of photon–jet transverse momentum correlations in 5.02 TeV Pb + Pb and pppp collisions with ATLAS

Jets created in association with a photon can be used as a calibrated probe to study energy loss in the medium created in nuclear collisions. Measurements of the transverse momentum balance between isolated photons and inclusive jets are presented using integrated luminosities of 0.49 nb$^{-1}$ of Pb+Pb collision data at $\sqrt{s_\mathrm{NN}}=5.02$ TeV and 25 pb$^{-1}$ of $pp$ collision data at $\sqrt{s}=5.02$ TeV recorded with the ATLAS detector at the LHC. Photons with transverse momentum $63.1 31.6$ GeV and pseudorapidity $\left|\eta^\mathrm{jet}\right| 7\pi/8$. Distributions of the per-photon jet yield as a function of $x_\mathrm{J\gamma}$, $(1/N_\gamma)(\mathrm{d}N/\mathrm{d}x_\mathrm{J\gamma})$, are corrected for detector effects via a two-dimensional unfolding procedure and reported at the particle level. In $pp$ collisions, the distributions are well described by Monte Carlo event generators. In Pb+Pb collisions, the $x_\mathrm{J\gamma}$ distribution is modified from that observed in $pp$ collisions with increasing centrality, consistent with the picture of parton energy loss in the hot nuclear medium. The data are compared with a suite of energy-loss models and calculations.Peer Reviewe

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements