RNA-seq transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis

Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix(®) GeneChip(®) Bovine Genome Array platform from the same PBL-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value ≤0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity(®) Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression

Long-Lived Neutralino NLSPs

We investigate the collider signatures of heavy, long-lived, neutral particles that decay to charged particles plus missing energy. Specifically, we focus on the case of a neutralino NLSP decaying to Z and gravitino within the context of General Gauge Mediation. We show that a combination of searches using the inner detector and the muon spectrometer yields a wide range of potential early LHC discoveries for NLSP lifetimes ranging from 10^(-1)-10^5 mm. We further show that events from Z(l+l-) can be used for detailed kinematic reconstruction, leading to accurate determinations of the neutralino mass and lifetime. In particular, we examine the prospects for detailed event study at ATLAS using the ECAL (making use of its timing and pointing capabilities) together with the TRT, or using the muon spectrometer alone. Finally, we also demonstrate that there is a region in parameter space where the Tevatron could potentially discover new physics in the delayed Z(l+l-)+MET channel. While our discussion centers on gauge mediation, many of the results apply to any scenario with a long-lived neutral particle decaying to charged particles.Comment: 31 pages, 12 figure

Renormalization in General Gauge Mediation

We revisit General Gauge Mediation (GGM) in light of the supersymmetric (linear) sigma model by utilizing the current superfield. The current superfield in the GGM is identified with supersymmetric extension of the vector symmetry current of the sigma model while spontaneous breakdown of supersymmetry in the GGM corresponds to soft breakdown of the axial vector symmetry of the sigma model. We first derive the current superfield from the supersymmetric linear sigma model and then compute 2-point functions of the current superfield using the (anti-)commutation relations of the messenger component fields. After the global symmetry are weakly gauged, the 2-point functions of the current superfield are identified with a part of the 2-point functions of the associated vector superfield. We renormalize them by dimensional regularization and show that physical gaugino and sfermion masses of the MSSM are expressed in terms of the wavefunction renormalization constants of the component fields of the vector superfield.Comment: 25 pages, 12 figure

Revealing the footprints of squark gluino production through Higgs search experiments at the Large Hadron Collider at 7 TeV and 14 TeV

The invariant mass distribution of the di-photons from the decay of the lighter scalar Higgs boson(h) to be carefully measured by dedicated h search experiments at the LHC may be distorted by the di-photons associated with the squark-gluino events with much larger cross sections in Gauge Mediated Supersymmetry Breaking (GMSB) models. This distortion if observed by the experiments at the Large Hadron Collider at 7 TeV or 14 TeV, would disfavour not only the standard model but various two Higgs doublet models with comparable h - masses and couplings but without a sector consisting of new heavy particles decaying into photons. The minimal GMSB (mGMSB) model constrained by the mass bound on h from LEP and that on the lightest neutralino from the Tevatron, produce negligible effects. But in the currently popular general GMSB(GGMSB) models the tail of the above distribution may show statistically significant excess of events even in the early stages of the LHC experiments with integrated luminosity insufficient for the discovery of h. We illustrate the above points by introducing several benchmark points in various GMSB models - minimal as well as non-minimal. The same conclusion follows from a detailed parameter scan in a simplified GGMSB model recently employed by the CMS collaboration to interpret their searches in the di-photon + \etslash channel. Other observables like the effective mass distribution of the di-photon + X events may also reveal the presence of new heavy particles beyond the Higgs sector. The contamination of the h mass peak and simple remedies are also discussed.Comment: 23 pages, 7 figures, title and organization of the paper is changed, detailed parameter scan in a simplified GGMSB model is added, conclusions and old numerical results remain unchange

Superpartner spectrum of minimal gaugino-gauge mediation

We evaluate the sparticle mass spectrum in the minimal four-dimensional construction that interpolates between gaugino and ordinary gauge mediation at the weak scale. We find that even in the hybrid case -- when the messenger scale is comparable to the mass of the additional gauge particles -- both the right-handed as well as the left-handed sleptons are lighter than the bino in the low-scale mediation regime. This implies a chain of lepton production and, consequently, striking signatures that may be probed at the LHC already in the near future.Comment: 8 pages, 3 figures; V2: refs and a few comments added; V3 title change

Circulating markers of arterial thrombosis and late-stage age-related macular degeneration: a case-control study.

PURPOSE: The aim of this study was to examine the relation of late-stage age-related macular degeneration (AMD) with markers of systemic atherothrombosis. METHODS: A hospital-based case-control study of AMD was undertaken in London, UK. Cases of AMD (n=81) and controls (n=77) were group matched for age and sex. Standard protocols were used for colour fundus photography and to classify AMD; physical examination included height, weight, history of or treatment for vascular-related diseases and smoking status. Blood samples were taken for measurement of fibrinogen, factor VIIc (FVIIc), factor VIIIc, prothrombin fragment F1.2 (F1.2), tissue plasminogen activator, and von Willebrand factor. Odds ratios from logistic regression analyses of each atherothrombotic marker with AMD were adjusted for age, sex, and established cardiovascular disease risk factors, including smoking, blood pressure, body mass index, and total cholesterol. RESULTS: After adjustment FVIIc and possibly F1.2 were inversely associated with the risk of AMD; per 1 standard deviation increase in these markers the odds ratio were, respectively, 0.62 (95% confidence interval 0.40, 0.95) and 0.71 (0.46, 1.09). None of the other atherothrombotic risk factors appeared to be related to AMD status. There was weak evidence that aspirin is associated with a lower risk of AMD. CONCLUSIONS: This study does not provide strong evidence of associations between AMD and systematic markers of arterial thrombosis, but the potential effects of FVIIc, and F1.2 are worthy of further investigation

Prompt Decays of General Neutralino NLSPs at the Tevatron

Recent theoretical developments have shown that gauge mediation has a much larger parameter space of possible spectra and mixings than previously considered. Motivated by this, we explore the collider phenomenology of gauge mediation models where a general neutralino is the lightest MSSM superpartner (the NLSP), focusing on the potential reach from existing and future Tevatron searches. Promptly decaying general neutralino NLSPs can give rise to final states involving missing energy plus photons, Zs, Ws and/or Higgses. We survey the final states and determine those where the Tevatron should have the most sensitivity. We then estimate the reach of existing Tevatron searches in these final states and discuss new searches (or optimizations of existing ones) that should improve the reach. Finally we comment on the potential for discovery at the LHC.Comment: 41 pages, minor changes, added refs and discussion of previous literatur

Readability estimates for commonly used health-related quality of life surveys

To estimate readability of seven commonly used health-related quality of life instruments: SF-36, HUI, EQ-5D, QWB-SA, HALex, Minnesota Living with Heart Failure Questionnaire (MLHFQ), and the NEI-VFQ-25. The Flesch–Kincaid (F–K) and Flesch Reading Ease (FRE) formulae were used to estimate readability for every item in each measure. The percentage of items that require more than 5 years of formal schooling according to F–K was 50 for the EQ-5D, 53 for the SF-36, 80 for the VFQ-25, 85 for the QWB-SA, 100 for the HUI, HALex, and the MLHFQ. The percentage of items deemed harder than “easy” according to FRE was 50 for the SF-36, 67 for the EQ-5D, 79 for the QWB-SA, 80 for the VFQ-25, 100 for the HUI, HALex, and the MLHFQ. All seven surveys have a substantial number of items with high readability levels that may not be appropriate for the general population

The Higgs as a Probe of Supersymmetric Extra Sectors

We present a general method for calculating the leading contributions to h -> gg and h -> gamma gamma in models where the Higgs weakly mixes with a nearly supersymmetric extra sector. Such mixing terms can play an important role in raising the Higgs mass relative to the value expected in the MSSM. Our method applies even when the extra sector is strongly coupled, and moreover does not require a microscopic Lagrangian description. Using constraints from holomorphy we fix the leading parametric form of the contributions to these Higgs processes, including the Higgs mixing angle dependence, up to an overall coefficient. Moreover, when the Higgs is the sole source of mass for a superconformal sector, we show that even this coefficient is often calculable. For appropriate mixing angles, the contribution of the extra states to h -> gg and h -> gamma gamma can vanish. We also discuss how current experimental limits already lead to non-trivial constraints on such models. Finally, we provide examples of extra sectors which satisfy the requirements necessary to use the holomorphic approximation.Comment: v4: 34 pages, 2 figures, typo corrected and clarification adde

Exactly Marginal Deformations and Global Symmetries

We study the problem of finding exactly marginal deformations of N=1 superconformal field theories in four dimensions. We find that the only way a marginal chiral operator can become not exactly marginal is for it to combine with a conserved current multiplet. Additionally, we find that the space of exactly marginal deformations, also called the "conformal manifold," is the quotient of the space of marginal couplings by the complexified continuous global symmetry group. This fact explains why exactly marginal deformations are ubiquitous in N=1 theories. Our method turns the problem of enumerating exactly marginal operators into a problem in group theory, and substantially extends and simplifies the previous analysis by Leigh and Strassler. We also briefly discuss how to apply our analysis to N=2 theories in three dimensions.Comment: 23 pages, 2 figure