The role of microRNA-binding site polymorphisms in DNA repair genes as risk factors for bladder cancer and breast cancer and their impact on radiotherapy outcomes

MicroRNAs (miRNAs) are involved in post-transcriptional regulation of gene expression through binding to messenger RNAs (mRNA) thereby promoting mRNA degradation or altered translation. A single-nucleotide polymorphism (SNP) located within a miRNA-binding site could thus alter mRNA translation and influence cancer risk and treatment response. The common SNPs located within the 3′-untranslated regions of 20 DNA repair genes were analysed for putative miRNA-binding sites using bioinformatics algorithms, calculating the difference in Gibbs free binding energy (ΔΔG) for each wild-type versus variant allele. Seven SNPs were selected to be genotyped in germ line DNAs both from a bladder cancer case–control series (752 cases and 704 controls) and 202 muscle-invasive bladder cancer radiotherapy cases. The PARP-1 SNP rs8679 was also genotyped in a breast cancer case–control series (257 cases and 512 controls). Without adjustment for multiple testing, multivariate analysis demonstrated an association with increased bladder cancer risk with PARP1 rs8679 (Ptrend = 0.05) while variant homozygotes of PARP1 rs8679 were also noted to have an increased breast cancer risk (P = 0.03). In the radiotherapy cases, carriers of the RAD51 rs7180135 minor allele had improved cancer-specific survival (hazard ratio 0.52, 95% confidence interval 0.31–0.87, P = 0.01). This is the first report of associations between DNA repair gene miRNA-binding site SNPs with bladder and breast cancer risk and radiotherapy outcomes. If validated, these findings may give further insight into the biology of bladder carcinogenesis, allow testing of the RAD51 SNP as a potential predictive biomarker and also reveal potential targets for new cancer treatments

Remodeling the B-model

We propose a complete, new formalism to compute unambiguously B-model open and closed amplitudes in local Calabi-Yau geometries, including the mirrors of toric manifolds. The formalism is based on the recursive solution of matrix models recently proposed by Eynard and Orantin. The resulting amplitudes are non-perturbative in both the closed and the open moduli. The formalism can then be used to study stringy phase transitions in the open/closed moduli space. At large radius, this formalism may be seen as a mirror formalism to the topological vertex, but it is also valid in other phases in the moduli space. We develop the formalism in general and provide an extensive number of checks, including a test at the orbifold point of A_p fibrations, where the amplitudes compute the 't Hooft expansion of Wilson loops in lens spaces. We also use our formalism to predict the disk amplitude for the orbifold C^3/Z_3.Comment: 83 pages, 9 figure

Thermoelectric effects of an Aharonov-Bohm interferometer with an embedded quantum dot in the Kondo regime

Thermoelectric effects are studied in an Aharonov-Bohm (AB) interferometer with an embedded quantum dot in the Kondo regime. The AB flux-dependent transmission probability has an asymmetrical shape arising from the Fano interference between the direct tunneling path and the Kondo-resonant tunneling path through a quantum dot. The sign and magnitude of thermopower can be modulated by the AB flux and the direct tunneling amplitude. In addition, the thermopower is anomalously enhanced by the Kondo correlation in the quantum dot near the Kondo temperature ($T_K$). The Kondo correlation in the quantum dot also leads to crossover behavior in diagonal transport coefficients as a function of temperature. The amplitude of an AB oscillation in electric and thermal conductances is small at temperatures far above $T_K$, but becomes enhanced as the system is cooled below $T_K$. The AB oscillation is strong in the thermopower and Lorenz number within the crossover region near the Kondo temperature.Comment: 16 pages, 10 figure

Questions of fairness and anti-doping in US cycling: The contrasting experiences of professionals and amateurs

The focus of researchers, media and policy on doping in cycling is often limited to the professional level of the sport. However, anti-doping test results since 2001 demonstrate that banned substances are also used by US cyclists at lower levels of the sport, necessitating a broader view of the patterns and motivations of substance use within the sport. In this article, we describe and explain the doping culture that has emerged in domestic US cycling among amateur and semi-professionals. Through analysis of records from sports governing bodies and journalistic reports, we assess the range of violation types and discuss the detection and punishing of riders who were not proven to have intended to cheat but became "collateral damage" in the war on doping. We argue that the phenomenon of doping is more complex than what has been shown to occur in elite sport, as it includes a wider variety of behaviours, situations and motivations. We develop fresh insights by examining cases where doping has been accidental, intrinsically motivated, non-performance enhancing or the result of prescribed medical treatments banned by anti-doping authorities. Such trends call into question the fairness of anti-doping measures, and we discuss the possibility of developing localised solutions to testing and sanctioning amateur athletes

A role for XRCC2 gene polymorphisms in breast cancer risk and survival

Background The XRCC2 gene is a key mediator in the homologous recombination repair of DNA double strand breaks. It is hypothesised that inherited variants in the XRCC2 gene might also affect susceptibility to, and survival from, breast cancer. Methods The study genotyped 12 XRCC2 tagging single nucleotide polymorphisms (SNPs) in 1131 breast cancer cases and 1148 controls from the Sheffield Breast Cancer Study (SBCS), and examined their associations with breast cancer risk and survival by estimating ORs and HRs, and their corresponding 95% CIs. Positive findings were further investigated in 860 cases and 869 controls from the Utah Breast Cancer Study (UBCS) and jointly analysed together with available published data for breast cancer risk. The survival findings were further confirmed in studies (8074 cases) from the Breast Cancer Association Consortium (BCAC). Results The most significant association with breast cancer risk in the SBCS dataset was the XRCC2 rs3218408 SNP (recessive model p=2.3×10−4, minor allele frequency (MAF)=0.23). This SNP yielded an ORrec of 1.64 (95% CI 1.25 to 2.16) in a two-site analysis of SBCS and UBCS, and a meta-ORrec of 1.33 (95% CI 1.12 to 1.57) when all published data were included. This SNP may mark a rare risk haplotype carried by two in 1000 of the control population. Furthermore, the XRCC2 coding R188H SNP (rs3218536, MAF=0.08) was significantly associated with poor survival, with an increased per-allele HR of 1.58 (95% CI 1.01 to 2.49) in a multivariate analysis. This effect was still evident in a pooled meta-analysis of 8781 breast cancer patients from the BCAC (HR 1.19, 95% CI 1.05 to 1.36; p=0.01). Conclusions These findings suggest that XRCC2 SNPs may influence breast cancer risk and survival

Origin of the Local Bubble

We present a new unbiased search for OB associations in the Solar neighbourhood which have hosted the progenitor stars of the core collapse supernovae responsible for the Local Bubble in the interstellar gas. For this purpose we have analyzed a volume complete set (with a diameter of 400 pc) of B stars drawn from the Hipparcos catalogue and the Arivel data base, from which candidate members were selected by a kinematical criterion. After careful dereddening the star colours we have constructed a colour-magnitude diagram and confirmed that the Upper Scorpius, Upper Centaurus Lupus, and Lower Centaurus Crux subgroups of the Sco OB2 association are the youngest nearby OB associations. We dated their ages with theoretical isochrones in the range of 20–30 Myr, in agreement with previous work. We have traced backwards in time the paths of the stars and found that they entered the volume of the present bubble at 10 to 15 Myr ago. We argue that the Local Bubble began to form then and estimate that 14 to 20 supernovae have exploded since. The implied energy input into the ambient medium can be shown to be sufficient to excavate a bubble of the presently observed size

Heavy quarkonium: progress, puzzles, and opportunities

A golden age for heavy quarkonium physics dawned a decade ago, initiated by the confluence of exciting advances in quantum chromodynamics (QCD) and an explosion of related experimental activity. The early years of this period were chronicled in the Quarkonium Working Group (QWG) CERN Yellow Report (YR) in 2004, which presented a comprehensive review of the status of the field at that time and provided specific recommendations for further progress. However, the broad spectrum of subsequent breakthroughs, surprises, and continuing puzzles could only be partially anticipated. Since the release of the YR, the BESII program concluded only to give birth to BESIII; the $B$-factories and CLEO-c flourished; quarkonium production and polarization measurements at HERA and the Tevatron matured; and heavy-ion collisions at RHIC have opened a window on the deconfinement regime. All these experiments leave legacies of quality, precision, and unsolved mysteries for quarkonium physics, and therefore beg for continuing investigations. The plethora of newly-found quarkonium-like states unleashed a flood of theoretical investigations into new forms of matter such as quark-gluon hybrids, mesonic molecules, and tetraquarks. Measurements of the spectroscopy, decays, production, and in-medium behavior of c\bar{c}, b\bar{b}, and b\bar{c} bound states have been shown to validate some theoretical approaches to QCD and highlight lack of quantitative success for others. The intriguing details of quarkonium suppression in heavy-ion collisions that have emerged from RHIC have elevated the importance of separating hot- and cold-nuclear-matter effects in quark-gluon plasma studies. This review systematically addresses all these matters and concludes by prioritizing directions for ongoing and future efforts.Comment: 182 pages, 112 figures. Editors: N. Brambilla, S. Eidelman, B. K. Heltsley, R. Vogt. Section Coordinators: G. T. Bodwin, E. Eichten, A. D. Frawley, A. B. Meyer, R. E. Mitchell, V. Papadimitriou, P. Petreczky, A. A. Petrov, P. Robbe, A. Vair

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio