NLO-QCD corrections to e+ e- --> hadrons in models of TeV-scale gravity

We present results on NLO-QCD corrections to the process e+ e- --> hadrons via photon-, Z- and graviton-exchange in the context of TeV-scale gravity models. The quantitative impact of these QCD corrections for searches of extra dimensions at a Linear Collider is briefly discussed.Comment: 10 pages, LaTeX, using axodraw.st

Magnetic Monopoles, Electric Neutrality and the Static Maxwell-Dirac Equations

We study the full Maxwell-Dirac equations: Dirac field with minimally coupled electromagnetic field and Maxwell field with Dirac current as source. Our particular interest is the static case in which the Dirac current is purely time-like -- the "electron" is at rest in some Lorentz frame. In this case we prove two theorems under rather general assumptions. Firstly, that if the system is also stationary (time independent in some gauge) then the system as a whole must have vanishing total charge, i.e. it must be electrically neutral. In fact, the theorem only requires that the system be {\em asymptotically} stationary and static. Secondly, we show, in the axially symmetric case, that if there are external Coulomb fields then these must necessarily be magnetically charged -- all Coulomb external sources are electrically charged magnetic monopoles

Learning pair-wise gene functional similarity by multiplex gene expression maps

Abstract Background The relationships between the gene functional similarity and gene expression profile, and between gene function annotation and gene sequence have been studied extensively. However, not much work has considered the connection between gene functions and location of a gene's expression in the mammalian tissues. On the other hand, although unsupervised learning methods have been commonly used in functional genomics, supervised learning cannot be directly applied to a set of normal genes without having a target (class) attribute. Results Here, we propose a supervised learning methodology to predict pair-wise gene functional similarity from multiplex gene expression maps that provide information about the location of gene expression. The features are extracted from expression maps and the labels denote the functional similarities of pairs of genes. We make use of wavelet features, original expression values, difference and average values of neighboring voxels and other features to perform boosting analysis. The experimental results show that with increasing similarities of gene expression maps, the functional similarities are increased too. The model predicts the functional similarities between genes to a certain degree. The weights of the features in the model indicate the features that are more significant for this prediction. Conclusions By considering pairs of genes, we propose a supervised learning methodology to predict pair-wise gene functional similarity from multiplex gene expression maps. We also explore the relationship between similarities of gene maps and gene functions. By using AdaBoost coupled with our proposed weak classifier we analyze a large-scale gene expression dataset and predict gene functional similarities. We also detect the most significant single voxels and pairs of neighboring voxels and visualize them in the expression map image of a mouse brain. This work is very important for predicting functions of unknown genes. It also has broader applicability since the methodology can be applied to analyze any large-scale dataset without a target attribute and is not restricted to gene expressions

Vortices, Instantons and Branes

The purpose of this paper is to describe a relationship between the moduli space of vortices and the moduli space of instantons. We study charge k vortices in U(N) Yang-Mills-Higgs theories and show that the moduli space is isomorphic to a special Lagrangian submanifold of the moduli space of k instantons in non-commutative U(N) Yang-Mills theories. This submanifold is the fixed point set of a U(1) action on the instanton moduli space which rotates the instantons in a plane. To derive this relationship, we present a D-brane construction in which the dynamics of vortices is described by the Higgs branch of a U(k) gauge theory with 4 supercharges which is a truncation of the familiar ADHM gauge theory. We further describe a moduli space construction for semi-local vortices, lumps in the CP(N) and Grassmannian sigma-models, and vortices on the non-commutative plane. We argue that this relationship between vortices and instantons underlies many of the quantitative similarities shared by quantum field theories in two and four dimensions.Comment: 32 Pages, 4 Figure

Vacuum Instabilities with a Wrong-Sign Higgs-Gluon-Gluon Amplitude

The recently discovered 125 GeV boson appears very similar to a Standard Model Higgs, but with data favoring an enhanced h to gamma gamma rate. A number of groups have found that fits would allow (or, less so after the latest updates, prefer) that the h-t-tbar coupling have the opposite sign. This can be given meaning in the context of an electroweak chiral Lagrangian, but it might also be interpreted to mean that a new colored and charged particle runs in loops and produces the opposite-sign hGG amplitude to that generated by integrating out the top, as well as a contribution reinforcing the W-loop contribution to hFF. In order to not suppress the rate of h to WW and h to ZZ, which appear to be approximately Standard Model-like, one would need the loop to "overshoot," not only canceling the top contribution but producing an opposite-sign hGG vertex of about the same magnitude as that in the SM. We argue that most such explanations have severe problems with fine-tuning and, more importantly, vacuum stability. In particular, the case of stop loops producing an opposite-sign hGG vertex of the same size as the Standard Model one is ruled out by a combination of vacuum decay bounds and LEP constraints. We also show that scenarios with a sign flip from loops of color octet charged scalars or new fermionic states are highly constrained.Comment: 20 pages, 8 figures; v2: references adde

Particle-Antiparticle Mixing, epsilon_K, Delta Gamma_q, A_SL^q, A_CP(B_d -> psi K_S), A_CP(B_s -> psi phi) and B -> X_{s,d} gamma in the Littlest Higgs Model with T-Parity

We calculate a number of observables related to particle-antiparticle mixing in the Littlest Higgs model with T-parity (LHT). The resulting effective Hamiltonian for Delta F=2 transitions agrees with the one of Hubisz et al., but our phenomenological analysis goes far beyond the one of these authors. In particular, we point out that the presence of mirror fermions with new flavour and CP-violating interactions allows to remove the possible Standard Model (SM) discrepancy between the CP asymmetry S_{psi K_S} and large values of |V_ub| and to obtain for the mass difference Delta M_s < (Delta M_s)_SM as suggested by the recent result by the CDF collaboration. We also identify a scenario in which simultaneously significant enhancements of the CP asymmetries S_{phi psi} and A_SL^q relative to the SM are possible, while satisfying all existing constraints, in particular from the B -> X_s gamma decay and A_CP(B -> X_s gamma) that are presented in the LHT model here for the first time. In another scenario the second, non-SM, value for the angle gamma=-(109+-6) from tree level decays, although unlikely, can be made consistent with all existing data with the help of mirror fermions. We present a number of correlations between the observables in question and study the implications of our results for the mass spectrum and the weak mixing matrix of mirror fermions. In the most interesting scenarios, the latter one turns out to have a hierarchical structure that differs significantly from the CKM one.Comment: 51 pages, 20 figures, 1 table. Extended discussion of the phases in the new mixing matrix V_Hd, some references added or updated, conclusions unchanged. Final version published in JHE

HIV-1 drug resistance mutations emerging on darunavir therapy in PI-naive and -experienced patients in the UK

BACKGROUND: Darunavir is considered to have a high genetic barrier to resistance. Most darunavir-associated drug resistance mutations (DRMs) have been identified through correlation of baseline genotype with virological response in clinical trials. However, there is little information on DRMs that are directly selected by darunavir in clinical settings. OBJECTIVES: We examined darunavir DRMs emerging in clinical practice in the UK. PATIENTS AND METHODS: Baseline and post-exposure protease genotypes were compared for individuals in the UK Collaborative HIV Cohort Study who had received darunavir; analyses were stratified for PI history. A selection analysis was used to compare the evolution of subtype B proteases in darunavir recipients and matched PI-naive controls. RESULTS: Of 6918 people who had received darunavir, 386 had resistance tests pre- and post-exposure. Overall, 2.8% (11/386) of these participants developed emergent darunavir DRMs. The prevalence of baseline DRMs was 1.0% (2/198) among PI-naive participants and 13.8% (26/188) among PI-experienced participants. Emergent DRMs developed in 2.0% of the PI-naive group (4 mutations) and 3.7% of the PI-experienced group (12 mutations). Codon 77 was positively selected in the PI-naive darunavir cases, but not in the control group. CONCLUSIONS: Our findings suggest that although emergent darunavir resistance is rare, it may be more common among PI-experienced patients than those who are PI-naive. Further investigation is required to explore whether codon 77 is a novel site involved in darunavir susceptibility

Quality of data collection in a large HIV observational clinic database in sub-Saharan Africa: implications for clinical research and audit of care

<p>Abstract</p> <p>Background</p> <p>Observational HIV clinic databases are now widely used to answer key questions related to HIV care and treatment, but there has been no systematic evaluation of their quality of data. Our objective was to evaluate the completeness and accuracy of recording of key data HIV items in a large routine observational HIV clinic database.</p> <p>Methods</p> <p>We looked at the number and rate of opportunistic infections (OIs) per 100 person years at risk in the 24 months following antiretroviral therapy (ART) initiation in 559 patients who initiated ART in 2004-2005 and enrolled into a research cohort. We compared this with data in a routine clinic database for the same 559 patients, and a further 1233 patients who initiated ART in the same period. The Research Cohort database was considered as the reference "gold standard" for the assessment of data accuracy. A crude percentage of underreporting of OIs in the clinic database was calculated based on the difference between the OI rates reported in both databases.</p> <p>We reviewed 100 clinic patient medical records to assess the accuracy of recording of key data items of OIs, ART toxicities and ART regimen changes.</p> <p>Results</p> <p>The overall incidence rate per 100 person years at risk for the initial OI in the 559 patients in the research cohort and clinic databases was 24.1 (95% CI: 20.5-28.2) and 13.2 (95% CI: 10.8-16.2) respectively, and 10.4 (95% CI: 9.1-11.9) for the 1233 clinic patients. This represents a 1.8- and 2.3-fold higher rate of events in the research cohort database compared with the same 599 patients and 1233 patients in the routine clinic database, or a 45.1% and 56.8% rate of underreporting, respectively. The combined error rate of missing and incorrect items from the medical records' review was 67% for OIs, 52% for ART-related toxicities, and 83% and 58% for ART discontinuation and modification, respectively.</p> <p>Conclusions</p> <p>There is a high rate of underreporting of OIs in a routine HIV clinic database. This has important implications for the use and interpretation of routine observational databases for research and audit, and highlights the need for regular data validation of these databases.</p

Supersymmetry Without Prejudice

We begin an exploration of the physics associated with the general CP-conserving MSSM with Minimal Flavor Violation, the pMSSM. The 19 soft SUSY breaking parameters in this scenario are chosen so as to satisfy all existing experimental and theoretical constraints assuming that the WIMP is a conventional thermal relic, ie, the lightest neutralino. We scan this parameter space twice using both flat and log priors for the soft SUSY breaking mass parameters and compare the results which yield similar conclusions. Detailed constraints from both LEP and the Tevatron searches play a particularly important role in obtaining our final model samples. We find that the pMSSM leads to a much broader set of predictions for the properties of the SUSY partners as well as for a number of experimental observables than those found in any of the conventional SUSY breaking scenarios such as mSUGRA. This set of models can easily lead to atypical expectations for SUSY signals at the LHC.Comment: 61 pages, 24 figs. Refs., figs, and text added, typos fixed; This version has reduced/bitmapped figs. For a version with better figs please go to http://www.slac.stanford.edu/~rizz

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita

© The Author(s). 2018Background: Southern root-knot nematode Meloidogyne incognita (Kofoid and White, 1919), Chitwood, 1949 is a key pest of agricultural crops. Pasteuria penetrans is a hyperparasitic bacterium capable of suppressing the nematode reproduction, and represents a typical coevolved pathogen-hyperparasite system. Attachment of Pasteuria endospores to the cuticle of second-stage nematode juveniles is the first and pivotal step in the bacterial infection. RNA-Seq was used to understand the early transcriptional response of the root-knot nematode at 8 h post Pasteuria endospore attachment. Results: A total of 52,485 transcripts were assembled from the high quality (HQ) reads, out of which 582 transcripts were found differentially expressed in the Pasteuria endospore encumbered J2 s, of which 229 were up-regulated and 353 were down-regulated. Pasteuria infection caused a suppression of the protein synthesis machinery of the nematode. Several of the differentially expressed transcripts were putatively involved in nematode innate immunity, signaling, stress responses, endospore attachment process and post-attachment behavioral modification of the juveniles. The expression profiles of fifteen selected transcripts were validated to be true by the qRT PCR. RNAi based silencing of transcripts coding for fructose bisphosphate aldolase and glucosyl transferase caused a reduction in endospore attachment as compared to the controls, whereas, silencing of aspartic protease and ubiquitin coding transcripts resulted in higher incidence of endospore attachment on the nematode cuticle. Conclusions: Here we provide evidence of an early transcriptional response by the nematode upon infection by Pasteuria prior to root invasion. We found that adhesion of Pasteuria endospores to the cuticle induced a down-regulated protein response in the nematode. In addition, we show that fructose bisphosphate aldolase, glucosyl transferase, aspartic protease and ubiquitin coding transcripts are involved in modulating the endospore attachment on the nematode cuticle. Our results add new and significant information to the existing knowledge on early molecular interaction between M. incognita and P. penetrans.Peer reviewedFinal Published versio