Fermi matrix element with isospin breaking

Prompted by the level of accuracy now being achieved in tests of the unitarity of the CKM matrix, we consider the possible modification of the Fermi matrix element for the $\beta$-decay of a neutron, including possible in-medium and isospin violating corrections. While the nuclear modifications lead to very small corrections once the Behrends-Sirlin-Ademollo-Gatto theorem is respected, the effect of the $u-d$ mass difference on the conclusion concerning $V_{ud}$ is no longer insignificant. Indeed, we suggest that the correction to the value of $|V_{ud}|^2 \, + \, |V_{us}|^2 \, + \, |V_{ub}|^2$ is at the level of $10^{-4}$

Effect of Nucleon Structure Variation in Super-allowed Fermi Beta-decay

There is a well known anomaly between the value of the Fermi decay constant extracted from super-allowed Fermi beta-decay of nuclear isotriplets and that required by unitarity of the Cabibbo-Kobayashi-Maskawa matrix. This discrepancy remains at the level of a few tenths of a percent after the most rigorous investigation of conventional nuclear and radiative corrections. Within the framework of the quark-meson coupling model of nuclear matter, which has been previously applied successfully to phenomena such as nuclear saturation and nuclear charge symmetry violation, we show that it is possible to understand a significant fraction of the observed anomaly.Comment: 11 pages with 1 figure and 1 tabl

The role of airway infection in chronic obstructive pulmonary disease

PhDThis. thesis examines the role of respiratory bacterial and viral infection in the natural history of Chronic Obstructive Pulmonary Disease. The rationale for this study is basedu pon previous data demonstratingt hat airway bacterial colonisationi s common in stable COPD and that bacterial and viral pathogens are commonly detected at exacerbations. The methodsu sed have involved the careful characterisationa nd clinical follow up of a cohort of patients with moderate to severe COPD in the stable state and at exacerbation. Sampling of airway and systemic compartments enabled the detection of respiratory pathogens and quantification of inflammation. Comparisons between clinical indices and evidence of infection were performed to determine the relationships between bacterial and viral infections and disease outcomes including lung function decline and exacerbation severity. The findings confirmed that lower airway bacterial colonisation is common in stable COPD and is associated with airway inflammation. They demonstrated for the first time a relationship between the degree of bacterial carriage and the rate of disease progression. This study has also described novel evidence for persistence of respiratorys yncytial virus in the lower airway and associationsw ith inflammation and lung function decline and impaired anti-viral immune responsesT. he combined role of human rhinoviral and bacterial infection at exacerbation has been studied and factors influencing responsesto exacerbationt herapy determinedw ith the importance of early initiation of treatment identified. The findings in this thesis indicate that both viral and bacterial pathogens may play an important role in the natural history of COPD and are therefore targets for potentially novel interventions. This work suggests that viral and bacterial infections and their interactions play an important role in modulating airway inflammation in stable disease and at exacerbation thus impacting on both disease progression and exacerbation severity. This work has provided a rationale for future investigation into the mechanisms underlying susceptibility to infection in this important disease

Model-independent D0−D0ˉD^0-\bar{D^0} mixing and CP violation studies with D0→KS0π+π−D^0 \to K^0_{\rm S}\pi^+\pi^- and D0→KS0K+K−D^0 \to K^0_{\rm S}K^+K^-

Simulation studies are performed to assess the sensitivity of a model-independent analysis of the flavour-tagged decays $D^0 \to K^0_{\rm S}\pi^+\pi^-$ and $D^0 \to K^0_{\rm S}K^+K^-$ to mixing and CP violation. The analysis takes as input measurements of the $D$ decay strong-phase parameters that are accessible in quantum-correlated $D-\bar{D}$ pairs produced at the $\psi(3770)$ resonance. It is shown that the model-independent approach is well suited to the very large data sets expected at an upgraded LHCb experiment, or future high luminosity $e^+e^-$ facility, and that with 100M $K^0_{\rm S}\pi^+\pi^-$ decays a statistical precision of around 0.01 and $0.7^\circ$ is achievable on the CP violation parameters $r_{CP}$ and $a_{CP}$, respectively. Even with this very large sample the systematic uncertainties associated with the strong-phase parameters will not be limiting, assuming that full use is made of the available $\psi(3770)$ data sets of CLEO-c and BES-III. Furthermore, it is demonstrated that large flavour-tagged samples can themselves be exploited to provide information on the strong-phase parameters, a feature that will be beneficial in the measurement of the CKM angle $\gamma/\phi_3$ with $B^- \to DK^-$ decays.Comment: 19 pages, 3 figures. New version fixes typos and incorrect references after journal acceptanc

Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae

Extracytoplasmic solute receptors (ESRs) are important components of solute uptake systems in bacteria, having been studied extensively as parts of ATP binding cassette transporters. Herein we report the first crystal structure of an ESR protein from a functionally characterized electrochemical ion gradient-dependent secondary transporter. This protein, SiaP, forms part of a tripartite ATP-independent periplasmic transporter specific for sialic acid in Haemophilus influenzae. Surprisingly, the structure reveals an overall topology similar to ATP binding cassette ESR proteins, which is not apparent from the sequence, demonstrating that primary and secondary transporters can share a common structural component. The structure of SiaP in the presence of the sialic acid analogue 2,3-didehydro-2-deoxyN-acetylneuraminic acid reveals the ligand bound in a deep cavity with its carboxylate group forming a salt bridge with a highly conserved Arg residue. Sialic acid binding, which obeys simple bimolecular association kinetics as determined by stopped-flow fluorescence spectroscopy, is accompanied by domain closure about a hinge region and the kinking of an alpha-helix hinge component. The structure provides insight into the evolution, mechanism, and substrate specificity of ESR-dependent secondary transporters that are widespread in prokaryotes