Testing AutoTrace: A Machine-learning Approach to Automated Tongue Contour Data Extraction

The Programme and Abstract booklet can be viewed at: http://www.qmu.ac.uk/casl/conf/ultrafest_2013/docs/Ultrafest%20abstract%20booklet.pdfOral Presentationpublished_or_final_versio

Discovery potential of top-partners in a realistic composite Higgs model with early LHC data

Composite Higgs models provide a natural, non-supersymmetric solution to the hierarchy problem. In these models, one or more sets of heavy top-partners are typically introduced. Some of these new quarks can be relatively light, with a mass of a few hundred GeV, and could be observed with the early LHC collision data expected to be collected during 2010. We analyse in detail the collider signatures that these new quarks can produce. We show that final states with two (same-sign) or three leptons are the most promising discovery channels. They can yield a 5 sigma excess over the Standard Model expectation already with the 2010 LHC collision data. Exotic quarks of charge 5/3 are a distinctive feature of this model. We present a new method to reconstruct their masses from their leptonic decay without relying on jets in the final state.Comment: 28 pages 11 Figures 7 Tables, minor changes, added references, matches published versio

Probing Higgs couplings with high p T Higgs production

Possible extensions of the Standard Model predict modifications of the Higgs couplings to gluons and to the SM top quark. The values of these two couplings can, in general, be independent. We discuss a way to measure these interactions by studying the Higgs production at high p T within an effective field theory formalism. We also propose an observable r \ub1 with reduced theoretical errors and suggest its experimental interpretation. \ua9 2014 SISSA

Phenotypic Variation and Bistable Switching in Bacteria

Microbial research generally focuses on clonal populations. However, bacterial cells with identical genotypes frequently display different phenotypes under identical conditions. This microbial cell individuality is receiving increasing attention in the literature because of its impact on cellular differentiation, survival under selective conditions, and the interaction of pathogens with their hosts. It is becoming clear that stochasticity in gene expression in conjunction with the architecture of the gene network that underlies the cellular processes can generate phenotypic variation. An important regulatory mechanism is the so-called positive feedback, in which a system reinforces its own response, for instance by stimulating the production of an activator. Bistability is an interesting and relevant phenomenon, in which two distinct subpopulations of cells showing discrete levels of gene expression coexist in a single culture. In this chapter, we address techniques and approaches used to establish phenotypic variation, and relate three well-characterized examples of bistability to the molecular mechanisms that govern these processes, with a focus on positive feedback.

Quantum Gravity in Everyday Life: General Relativity as an Effective Field Theory

This article is meant as a summary and introduction to the ideas of effective field theory as applied to gravitational systems. Contents: 1. Introduction 2. Effective Field Theories 3. Low-Energy Quantum Gravity 4. Explicit Quantum Calculations 5. ConclusionsComment: 56 pages, 2 figures, JHEP style, Invited review to appear in Living Reviews of Relativit

Dynamic summarization of bibliographic-based data

<p>Abstract</p> <p>Background</p> <p>Traditional information retrieval techniques typically return excessive output when directed at large bibliographic databases. Natural Language Processing applications strive to extract salient content from the excessive data. Semantic MEDLINE, a National Library of Medicine (NLM) natural language processing application, highlights relevant information in PubMed data. However, Semantic MEDLINE implements manually coded schemas, accommodating few information needs. Currently, there are only five such schemas, while many more would be needed to realistically accommodate all potential users. The aim of this project was to develop and evaluate a statistical algorithm that automatically identifies relevant bibliographic data; the new algorithm could be incorporated into a dynamic schema to accommodate various information needs in Semantic MEDLINE, and eliminate the need for multiple schemas.</p> <p>Methods</p> <p>We developed a flexible algorithm named Combo that combines three statistical metrics, the Kullback-Leibler Divergence (KLD), Riloff's RlogF metric (RlogF), and a new metric called PredScal, to automatically identify salient data in bibliographic text. We downloaded citations from a PubMed search query addressing the genetic etiology of bladder cancer. The citations were processed with SemRep, an NLM rule-based application that produces semantic predications. SemRep output was processed by Combo, in addition to the standard Semantic MEDLINE genetics schema and independently by the two individual KLD and RlogF metrics. We evaluated each summarization method using an existing reference standard within the task-based context of genetic database curation.</p> <p>Results</p> <p>Combo asserted 74 genetic entities implicated in bladder cancer development, whereas the traditional schema asserted 10 genetic entities; the KLD and RlogF metrics individually asserted 77 and 69 genetic entities, respectively. Combo achieved 61% recall and 81% precision, with an F-score of 0.69. The traditional schema achieved 23% recall and 100% precision, with an F-score of 0.37. The KLD metric achieved 61% recall, 70% precision, with an F-score of 0.65. The RlogF metric achieved 61% recall, 72% precision, with an F-score of 0.66.</p> <p>Conclusions</p> <p>Semantic MEDLINE summarization using the new Combo algorithm outperformed a conventional summarization schema in a genetic database curation task. It potentially could streamline information acquisition for other needs without having to hand-build multiple saliency schemas.</p

The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex.

We incorporated the non-natural photoreactive amino acid p-benzoyl-L-phenylalanine (Bpa) into the RNA polymerase II (Pol II) surface surrounding the central cleft formed by the Rpb1 and Rpb2 subunits. Photo-cross-linking of preinitiation complexes (PICs) with these Pol II derivatives and hydroxyl-radical cleavage assays revealed that the TFIIF dimerization domain interacts with the Rpb2 lobe and protrusion domains adjacent to Rpb9, while TFIIE cross-links to the Rpb1 clamp domain on the opposite side of the Pol II central cleft. Mutations in the Rpb2 lobe and protrusion domains alter both Pol II-TFIIF binding and the transcription start site, a phenotype associated with mutations in TFIIF, Rpb9 and TFIIB. Together with previous biochemical and structural studies, these findings illuminate the structural organization of the PIC and the network of protein-protein interactions involved in transcription start site selection

Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption

Type 1 interferons (IFN-I) are potent innate antiviral effectors that constrain HIV-1 transmission. However, harnessing these cytokines for HIV-1 cure strategies has been hampered by an incomplete understanding of their antiviral activities at later stages of infection. Here, we characterized the IFN-I sensitivity of 500 clonally derived HIV-1 isolates from the plasma and CD4+ T cells of 26 individuals sampled longitudinally after transmission or after antiretroviral therapy (ART) and analytical treatment interruption. We determined the concentration of IFNα2 and IFNβ that reduced viral replication in vitro by 50% (IC50) and found consistent changes in the sensitivity of HIV-1 to IFN-I inhibition both across individuals and over time. Resistance of HIV-1 isolates to IFN-I was uniformly high during acute infection, decreased in all individuals in the first year after infection, was reacquired concomitant with CD4+ T cell loss, and remained elevated in individuals with accelerated disease. HIV-1 isolates obtained by viral outgrowth during suppressive ART were relatively IFN-I sensitive, resembling viruses circulating just before ART initiation. However, viruses that rebounded after treatment interruption displayed the highest degree of IFNα2 and IFNβ resistance observed at any time during the infection course. These findings indicate a dynamic interplay between host innate responses and the evolving HIV-1 quasispecies, with the relative contribution of IFN-I to HIV-1 control affected by both ART and analytical treatment interruption. Although elevated at transmission, host innate pressures are the highest during viral rebound, limiting the viruses that successfully become reactivated from latency to those that are IFN-I resistant