Intuitive Visualization and Analysis of Multi-Omics Data and Application to Escherichia coli Carbon Metabolism

Combinations of ‘omics’ investigations (i.e, transcriptomic, proteomic, metabolomic and/or fluxomic) are increasingly applied to get comprehensive understanding of biological systems. Because the latter are organized as complex networks of molecular and functional interactions, the intuitive interpretation of multi-omics datasets is difficult. Here we describe a simple strategy to visualize and analyze multi-omics data. Graphical representations of complex biological networks can be generated using Cytoscape where all molecular and functional components could be explicitly represented using a set of dedicated symbols. This representation can be used i) to compile all biologically-relevant information regarding the network through web link association, and ii) to map the network components with multi-omics data. A Cytoscape plugin was developed to increase the possibilities of both multi-omic data representation and interpretation. This plugin allowed different adjustable colour scales to be applied to the various omics data and performed the automatic extraction and visualization of the most significant changes in the datasets. For illustration purpose, the approach was applied to the central carbon metabolism of Escherichia coli. The obtained network contained 774 components and 1232 interactions, highlighting the complexity of bacterial multi-level regulations. The structured representation of this network represents a valuable resource for systemic studies of E. coli, as illustrated from the application to multi-omics data. Some current issues in network representation are discussed on the basis of this work

Lack of association between right-to-left shunt and cerebral ischemia after adjustment for gender and age

<p>Abstract</p> <p>Introduction</p> <p>A number of studies has addressed the possible association between patent foramen ovale (PFO) and stroke. However, the role of PFO in the pathogenesis of cerebral ischemia has remained controversial and most studies did not analyze patient subgroups stratified for gender, age and origin of stroke.</p> <p>Methods</p> <p>To address the role of PFO for the occurrence of cerebral ischemia, we investigated the prevalence of right-to-left shunt in a large group of patients with acute stroke or TIA. 763 consecutive patients admitted to our hospital with cerebral ischemia were analyzed. All patients were screened for the presence of PFO by contrast-enhanced transcranial Doppler sonography at rest and during Valsalva maneuver. Subgroup analyses were performed in patients stratified for gender, age and origin of stroke.</p> <p>Results</p> <p>A right-to-left shunt was detected in 140 (28%) male and in 114 (42%) female patients during Valsalva maneuver, and in 66 (13%) and 44 (16%) at rest respectively. Patients with right-to-left shunt were younger than those without (<it>P </it>< 0.001). PFO was associated with stroke of unknown origin in male (<it>P </it>= 0.001) but not female patients (<it>P </it>> 0.05). After adjusting for age no significant association between PFO and stroke of unknown origin was found in either group.</p> <p>Conclusion</p> <p>Our findings argue against paradoxical embolization as a major cause of cerebral ischemia in patients with right-to-left shunt. Our data demonstrate substantial gender-and age-related differences that should be taken into account in future studies.</p

S3-TM: scalable streaming short text matching

Micro-blogging services have become major venues for information creation, as well as channels of information dissemination. Accordingly, monitoring them for relevant information is a critical capability. This is typically achieved by registering content-based subscriptions with the micro-blogging service. Such subscriptions are long-running queries that are evaluated against the stream of posts. Given the popularity and scale of micro-blogging services like Twitter and Weibo, building a scalable infrastructure to evaluate these subscriptions is a challenge. To address this challenge, we present the S3-TM system for streaming short text matching. S3-TM is organized as a stream processing application, in the form of a data parallel flow graph designed to be run on a data center environment. It takes advantage of the structure of the publications (posts) and subscriptions to perform the matching in a scalable manner, without broadcasting publications or subscriptions to all of the matcher instances. The basic design of S$$^3$$3-TM uses a scoped multicast for publications and scoped anycast for subscriptions. To further improve throughput, we introduce publication routing algorithms that aim at minimizing the scope of the multicasts. First set of algorithms we develop are based on partitioning the word co-occurrence frequency graph, with the aim of routing posts that include commonly co-occurring words to a small set of matchers. While effective, these algorithms fell short in balancing the load. To address this, we develop the SALB algorithm, which provides better load balance by modeling the load more accurately using the word-to-post bipartite graph. We also develop a subscription placement algorithm, called LASP, to group together similar subscriptions, in order to minimize the subscription matching cost. Furthermore, to achieve good scalability for increasing number of nodes, we introduce techniques to handle workload skew. Finally, we introduce load shedding techniques for handling unexpected load spikes with small impact on the accuracy. Our experimental results show that S3-TM is scalable. Furthermore, the SALB algorithm provides more than 2.5× throughput compared to the baseline multicast and outperforms the graph partitioning-based approaches. © 2015, Springer-Verlag Berlin Heidelberg

Search for a Technicolor omega_T Particle in Events with a Photon and a b-quark Jet at CDF

If the Technicolor omega_T particle exists, a likely decay mode is omega_T -> gamma pi_T, followed by pi_T -> bb-bar, yielding the signature gamma bb-bar. We have searched 85 pb^-1 of data collected by the CDF experiment at the Fermilab Tevatron for events with a photon and two jets, where one of the jets must contain a secondary vertex implying the presence of a b quark. We find no excess of events above standard model expectations. We express the result of an exclusion region in the M_omega_T - M_pi_T mass plane.Comment: 14 pages, 2 figures. Available from the CDF server (PS with figs): http://www-cdf.fnal.gov/physics/pub98/cdf4674_omega_t_prl_4.ps FERMILAB-PUB-98/321-

Measurement of the B0 anti-B0 oscillation frequency using l- D*+ pairs and lepton flavor tags

The oscillation frequency Delta-md of B0 anti-B0 mixing is measured using the partially reconstructed semileptonic decay anti-B0 -> l- nubar D*+ X. The data sample was collected with the CDF detector at the Fermilab Tevatron collider during 1992 - 1995 by triggering on the existence of two lepton candidates in an event, and corresponds to about 110 pb-1 of pbar p collisions at sqrt(s) = 1.8 TeV. We estimate the proper decay time of the anti-B0 meson from the measured decay length and reconstructed momentum of the l- D*+ system. The charge of the lepton in the final state identifies the flavor of the anti-B0 meson at its decay. The second lepton in the event is used to infer the flavor of the anti-B0 meson at production. We measure the oscillation frequency to be Delta-md = 0.516 +/- 0.099 +0.029 -0.035 ps-1, where the first uncertainty is statistical and the second is systematic.Comment: 30 pages, 7 figures. Submitted to Physical Review

Search for New Particles Decaying to top-antitop in proton-antiproton collisions at squareroot(s)=1.8 TeV

We use 106 \ipb of data collected with the Collider Detector at Fermilab to search for narrow-width, vector particles decaying to a top and an anti-top quark. Model independent upper limits on the cross section for narrow, vector resonances decaying to \ttbar are presented. At the 95% confidence level, we exclude the existence of a leptophobic \zpr boson in a model of topcolor-assisted technicolor with mass M_{\zpr} $<$ 480 \gev for natural width $\Gamma$ = 0.012 M_{\zpr}, and M_{\zpr} $<$ 780 \gev for $\Gamma$ = 0.04 M_{\zpr}.Comment: The CDF Collaboration, submitted to PRL 25-Feb-200

Double Diffraction Dissociation at the Fermilab Tevatron Collider

We present results from a measurement of double diffraction dissociation in $\bar pp$ collisions at the Fermilab Tevatron collider. The production cross section for events with a central pseudorapidity gap of width $\Delta\eta^0>3$ (overlapping $\eta=0$) is found to be $4.43\pm 0.02{(stat)}{\pm 1.18}{(syst) mb}$ [$3.42\pm 0.01{(stat)}{\pm 1.09}{(syst) mb}$] at $\sqrt{s}=1800$ [630] GeV. Our results are compared with previous measurements and with predictions based on Regge theory and factorization.Comment: 10 pages, 4 figures, using RevTeX. Submitted to Physical Review Letter