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Technological advances in underwater video recording are opening novel opportunities for monitoring wild fish. However, extracting data from videos is often challenging. Nevertheless, it has been recently demonstrated that accurate and precise estimates of density for animals (whose normal activities are restricted to a bounded area or home range) can be obtained from counts averaged across a relatively low number of video frames. The method, however, requires that individual detectability (PID, the probability of detecting a given animal provided that it is actually within the area surveyed by a camera) has to be known. Here we propose a Bayesian implementation for estimating PID after combining counts from cameras with counts from any reference method. The proposed framework was demonstrated using Serranus scriba as a case-study, a widely distributed and resident coastal fish. Density and PID were calculated after combining fish counts from unbaited remote underwater video (RUV) and underwater visual censuses (UVC) as reference method. The relevance of the proposed framework is that after estimating PID, fish density can be estimated accurately and precisely at the UVC scale (or at the scale of the preferred reference method) using RUV only. This key statement has been extensively demonstrated using computer simulations yielded by real empirical data. Finally, we provide a simulation tool-kit for comparing the expected precision attainable for different sampling effort and for species with different levels of PID. Overall, the proposed method may contribute to substantially enlarge the spatio-temporal scope of density monitoring programs for many resident fish.

Despite the recognised effectiveness of networks of Marine Protected Areas (MPAs) as a biodiversity conservation instrument, nowadays MPA network design frequently disregards the importance of connectivity patterns. In the case of sedentary marine populations, connectivity stems not only from the stochastic nature of the physical environment that affects early-life stages dispersal, but also from the spawning stock attributes that affect the reproductive output (e.g., passive eggs and larvae) and its survivorship. Early-life stages are virtually impossible to track in the ocean. Therefore, numerical ocean current simulations coupled to egg and larval Lagrangian transport models remain the most common approach for the assessment of marine larval connectivity. Inferred larval connectivity may be different depending on the type of connectivity considered; consequently, the prioritisation of sites for marine populations' conservation might also differ. Here, we introduce a framework for evaluating and designing MPA networks based on the identification of connectivity hotspots using graph theoretic analysis. We use as a case of study a network of open-access areas and MPAs, off Mallorca Island (Spain), and test its effectiveness for the protection of the painted comber Serranus scriba. Outputs from network analysis are used to: (1) identify critical areas for improving overall larval connectivity; (2) assess the impact of species' biological parameters in network connectivity; and (3) explore alternative MPA configurations to improve average network connectivity. Results demonstrate the potential of graph theory to identify non-trivial egg/larval dispersal patterns and emerging collective properties of the MPA network which are relevant for increasing protection efficiency., Comment: 8 figures, 3 tables, 1 Supplementary material (including 4 table; 3 figures and supplementary methods)

Using the approach developed in [V. Azcoiti, G. Di Carlo, A. Galante, V. Laliena, \textit{Phys. Lett.} \textbf{B563}, (2003) 117], we are able to reconstruct the behavior of the massive 1-flavor Schwinger model with a $\theta$ term and a quantized topological charge. We calculate the full dependence of the order parameter with $\theta$. Our results at $\theta = \pi$ are compatible with Coleman's conjecture on the phase diagram of this model., Comment: 8 pages, 8 figures

We study the two-dimensional antiferromagnetic Ising model with a purely imaginary magnetic field, which can be thought of as a toy model for the usual $\theta$ physics. Our motivation is to have a benchmark calculation in a system which suffers from a strong sign problem, so that our results can be used to test Monte Carlo methods developed to tackle such problems. We analyze here this model by means of analytical techniques, computing exactly the first eight cumulants of the expansion of the effective Hamiltonian in powers of the inverse temperature, and calculating physical observables for a large number of degrees of freedom with the help of standard multi-precision algorithms. We report accurate results for the free energy density, internal energy, standard and staggered magnetization, and the position and nature of the critical line, which confirm the mean-field qualitative picture, and which should be quantitatively reliable, at least in the high-temperature regime, including the entire critical line.

We investigate numerically the spectral flow introduced by Adams for the staggered Dirac operator on realistic (quenched) gauge configurations. We obtain clear numerical evidence that the definition works as expected: there is a clear separation between crossings near and far away from the origin, and the topological charge defined through the crossings near the origin agrees, for most configurations, with the one defined through the near-zero modes of large taste-singlet chirality of the staggered Dirac operator. The crossings are much closer to the origin if we improve the Dirac operator used in the definition, and they move towards the origin as we decrease the lattice spacing., Comment: References added. Slight changes to the text

We study the two and three-dimensional Antiferromagnetic Ising Model with an imaginary magnetic field $i\theta$ at $\theta = \pi$. We use a new geometric algorithm which does not present a sign problem. This allows us to perform efficient numerical simulations of this system., Comment: 7 pages, 3 figures, presented at the 31st International Symposium on Lattice Field Theory (Lattice 2013), 29 July - 3 August 2013, Mainz, Germany

In this work we study the two and three-dimensional antiferromagnetic Ising model with an imaginary magnetic field $i\theta$ at $\theta=\pi$. In order to perform numerical simulations of the system we introduce a new geometric algorithm not affected by the sign problem. Our results for the $2D$ model are in agreement with the analytical solutions. We also present new results for the $3D$ model which are qualitatively in agreement with mean-field predictions.

We have developed two methods for handling $b$ quarks in lattice QCD. One uses NRQCD (now improved to include radiative corrections) and the other uses Highly Improved Staggered Quarks (HISQ), extrapolating to the $b$ quark from lighter masses and using multiple lattice spacings to control discretisation errors. Comparison of results for the two different methods gives confidence in estimates of lattice QCD systematic errors, since they are very different in these two cases. Here we show results for heavyonium hyperfine splittings and vector current-current correlator moments using HISQ quarks, to add to earlier results testing the heavy HISQ method with pseudoscalar mesons. We also show the form factor for $B \rightarrow \pi l \nu$ decay at zero recoil using NRQCD $b$ quarks and $u/d$ quarks with physical masses. This allows us to test the soft pion theorem relation ($f_0(q^2_{max})=f_B/f_{\pi}$) accurately and we find good agreement as $M_{\pi} \rightarrow 0$. }, Comment: 5 pages, 3 figures, Proceedings of Lattice2013

We analyze the vacuum structure of a generalized lattice Nambu--Jona-Lasinio model with two flavors of Wilson fermions, such that its continuum action is the most general four-fermion action with 'trivial' color interactions, and having a $SU(2)_V x SU(2)_A$ symmetry in the chiral limit. The phase structure of this model in the space of the two four-fermion couplings shows, in addition to the standard Aoki phases, new phases with $<\bar\psi \gamma_5\psi> != 0$, in close analogy to similar results recently suggested by some of us for lattice QCD with two degenerate Wilson fermions. This result shows how the phase structure of an effective model for low energy QCD cannot be entirely understood from Wilson Chiral Perturbation Theory, based on the standard QCD chiral effective Lagrangian approach., Comment: 24 pages, 3 figures, sent to Nuclear Physics B

We present a new study of the form factors for D -> K semileptonic decay from lattice QCD that allows us to compare the shape of the vector form factor to experiment and, for the first time, to extract V_cs using results from all experimental q^2 bins. The valence quarks are implemented with the Highly Improved Staggered Quark action on MILC configurations that include u, d and s sea quarks. The scalar and vector currents are nonperturbatively normalised and, using phased boundary conditions, we are able to cover the full q^2 range accessible to experiment. Our result is V_cs = 0.963(5)_{expt}(14)_{lattice}. We also demonstrate that the form factors are insensitive to whether the spectator quark is u/d or s, which has implications for other decay channels., Comment: 5 pages, 6 figures

We show results from calculations in full lattice QCD of the mass, leptonic width and radiative decay rate to eta_c of the J/psi meson. These provide few % tests of QCD. Another (1.5%) test comes from comparison of time-moments of the vector charmonium correlator with results derived from the experimental values of R(e+e- to hadrons) in the charm region., Comment: 3 pages, 4 figures, Proceedings of Confinement2012

We study the two-dimensional Antiferromagnetic Ising Model with an imaginary magnetic field i\theta at \theta=\pi. We use a new geometric algorithm which does not present a sign problem. This allows us to perform efficient numerical simulations of this system., Comment: 7 pages, 3 figures, submitted as a contribution to the 30th International Symposium on Lattice Field Theory, June 24-29, 2012, Cairns, Australia

Recently we studied the B, Bs, D and Ds meson decay constants using various treatments for the heavy quark. For B mesons, we determined fB, fBs, and fBs/fB with NRQCD bottom quarks. We then combined the ratio fBs/fB and another very precise determination from HPQCD for fBs using heavy HISQ quarks, and extracted fB with 2% total errors. We also calculated fD, fDs, and fDs/fD using HISQ charm quarks. Here we review our results and briefly discuss their implications for the determination of the CKM matrix elements |Vcd| and |Vcs|., Comment: 7 pages, 4 figures, and 2 tables. Talk given at Lattice 2012, June 24-29, 2012, Cairns, Australia

We calculate the J/{\psi} mass, leptonic width and radiative decay rate to \gamma \eta_c from lattice QCD including u, d and s quarks in the sea for the first time. We use the Highly Improved Staggered Quark formalism and nonperturbatively normalised vector currents for the leptonic and radiative decay rates. Our results are: M_{J/\psi} -M_{\eta_c} = 116.5(3.2) MeV; \Gamma(J/{\psi} to e^+e^-) = 5.48(16) keV; \Gamma(J/{\psi} to \gamma \eta_c) = 2.49(19) keV. The first two are in good agreement with experiment, with \Gamma(J/{\psi} to e^+e^-) providing a test of a decay matrix element in QCD, independent of CKM uncertainties, to 2%. At the same time results for the time moments of the correlation function can be compared to values from the charm contribution to \Gamma(e^+e^- to hadrons), giving a 1.5% test of QCD. Our results show that an improved experimental error would enable a similarly strong test from \Gamma(J/{\psi} to \gamma \eta_c)., Comment: 20 pages, 16 figures. Added some text plus a figure and two tables comparing the time moments of the charmonium vector correlator to results extracted from experiment for the charm contribution to e^+e^- -> hadrons. This allows a 1.5% test of QCD. Further minor amendments to the text. Version accepted for publication by Physical Review D

In this paper, we discuss the vacuum structure of QCD with two flavors of Wilson fermions, inside the Aoki phase. We provide numerical evidence, coming from HMC simulations in $4^4$, $6^4$ and $8^4$ lattices, supporting a vacuum structure for this model at strong coupling more complex than the one assumed in the standard wisdom, with new vacua where the expectation value of $i\bar\psi\gamma_5\psi$ can take non-zero values, and which can not be connected with the Aoki vacua by parity-flavour symmetry transformations., Comment: 27 pages, 8 figures, 4 tables, v2: 1. Modifies abstract and layout and 2. revises conclusions, v3: Includes new section with discussion on our results and WChPT, other minor modifications, v4: Introduces new section discussing the presence of critical lines within the Aoki phase

We investigate the critical behaviour at theta=pi of the two-dimensional O(3) nonlinear sigma model with topological term on the lattice. Our method is based on numerical simulations at imaginary values of theta, and on scaling transformations that allow a controlled analytic continuation to real values of theta. Our results are compatible with a second order phase transition, with the critical exponent of the SU(2)_1 Wess-Zumino-Novikov-Witten model, for sufficiently small values of the coupling., Comment: Revised version. 24 pages, 7 figures

We determine masses and decay constants of heavy-heavy and heavy-charm pseudoscalar mesons as a function of heavy quark mass using a fully relativistic formalism known as Highly Improved Staggered Quarks for the heavy quark. We are able to cover the region from the charm quark mass to the bottom quark mass using MILC ensembles with lattice spacing values from 0.15 fm down to 0.044 fm. We obtain f_{B_c} = 0.427(6) GeV; m_{B_c} = 6.285(10) GeV and f_{\eta_b} = 0.667(6) GeV. Our value for f_{\eta_b} is within a few percent of f_{\Upsilon} confirming that spin effects are surprisingly small for heavyonium decay constants. Our value for f_{B_c} is significantly lower than potential model values being used to estimate production rates at the LHC. We discuss the changing physical heavy-quark mass dependence of decay constants from heavy-heavy through heavy-charm to heavy-strange mesons. A comparison between the three different systems confirms that the B_c system behaves in some ways more like a heavy-light system than a heavy-heavy one. Finally we summarise current results on decay constants of gold-plated mesons., Comment: 16 pages, 12 figures

We present an update of the D meson decay constant f_D using the Highly Improved Staggered Quark (HISQ) action for valence charm and light quarks on MILC N_f = 2+1 lattices. The new determination incorporates HPQCD's improved scale r_1^{N_f = 2+1} = 0.3133(23) fm, accurately retuned bare charm quark masses and data from an ensemble that is more chiral than in our previous calculations. We find f_D = 208.3(3.4) MeV. Combining the new f_D with D -> \mu \nu\ branching fraction data from CLEO-c, we extract the CKM matrix element |V_cd| = 0.223(10)_{exp.}(4)_{lat.}. This value is in excellent agreement with |V_cd| from D semileptonic decays and from neutrino scattering experiments and has comparable total errors. We determine the ratio between semileptonic form factor and decay constant and find [f^{D -> \pi}_+(0) / f_D ]_{lat.} = 3.20(15) GeV^{-1} to be compared with the experimental value of [f^{D -> \pi}_+(0) / f_D ]_{exp.} = 3.19(18) GeV^{-1}. Finally, we mention recent preliminary but already more accurate D -> \mu \nu\ branching fraction measurements from BES III and discuss their impact on precision |V_cd| determinations in the future., Comment: 8 pages, 8 figures, and 5 tables

We investigate numerically the spectral flow introduced by Adams for the staggered Dirac operator on realistic gauge configurations. We study both the unimproved and the HISQ Dirac operators. We compare the spectral flow index with the index obtained by identifying low-lying modes of large chirality., Comment: Talk presented at The XXIX International Conference on Lattice Field Theory - Lattice 2011, July 10-16, 2011, Squaw Valley, Lake Tahoe, California

We present a new and very high statistics study of D and D_s semileptonic decay form factors on the lattice. We work with MILC N_f=2+1 lattices and use the Highly Improved Staggered Action (HISQ) for both the charm and the light valence quarks. We use both scalar and vector currents to determine the form factors f_0(q^2) and f_+(q^2) for a range of D and D_s form factors including those for D to pi and D to K semileptonic decays. By using a phased boundary condition we are able to tune accurately to q^2=0. We also compare the shape in q^2 to that from experiment. We show that the form factors are very insensitive to the spectator quark: D to K and D_s to eta_s form factors are essentially the same, and the same is true for D to pi and D_s to K. This has important implications when considering the corresponding B/B_s processes., Comment: 7 pages, 9 figures, talk given at the XXIX International Symposium on Lattice Field Theory, July 10-16, 2011, Squaw Valley, Lake Tahoe, CA

We give results for the Upsilon spectrum from lattice QCD using an improved version of the NRQCD action for b quarks which includes radiative corrections to kinetic terms at O(v^4) in the velocity expansion. We also include for the first time the effect of up, down, strange and charm quarks in the sea using 'second generation' gluon field configurations from the MILC collaboration. Using the {\Upsilon} 2S - 1S splitting to determine the lattice spacing, we are able to obtain the 1P - 1S splitting to 1.4% and the 3S - 1S splitting to 2.4%. Our improved result for M (Upsilon) - M (eta_b) is 70(9) MeV and we predict M(Upsilon) - M(eta_b') = 35(3) MeV. We also calculate pi, K and eta_s correlators using the Highly Improved Staggered Quark action and perform a chiral and continuum extrapolation to give values for M(eta_s) (0.6893(12) GeV) and f_{eta_s} (0.1819(5) GeV) that allow us to tune the strange quark mass as well as providing an independent and consistent determination of the lattice spacing. Combining the NRQCD and HISQ analyses gives mb/ms = 54.7(2.5) and a value for the heavy quark potential parameter of r_1 = 0.3209(26) fm., Comment: 38 pages, many figures

We present a new determination of the $B_s$ leptonic decay constant from lattice QCD simulations that use gluon configurations from MILC and a highly improved discretization of the relativistic quark action for both valence quarks. Our result, $f_{B_s} = 0.225(4)$\,GeV, is almost three times more accurate than previous determinations. We analyze the dependence of the decay constant on the heavy quark's mass and obtain the first empirical evidence for the leading $1/\sqrt{m_h}$ dependence predicted by Heavy Quark Effective Theory (HQET). As a check, we use our analysis technique to calculate the $m_{B_s}-m_{\eta_b}/2$ mass difference. Our result agrees with experiment to within errors of $11\,\mathrm{MeV}$ (better than 2%). We discuss how to extend our analysis to other quantities in $B_s$ and $B$ physics, making 2%-precision possible for the first time., Comment: 5 pages, 3 figures

We present a new calculation of the $D \rightarrow \pi, l \nu$ semileptonic form factor $f^{D \rightarrow \pi}_+(q^2)$ at $q^2 = 0$ based on HISQ charm and light valence quarks on MILC $N_f = 2 +1$ lattices. Using methods developed recently for HPQCD's study of $D \rightarrow K, l \nu$ decays, we find $f^{D \rightarrow \pi}_+(0) = 0.666(29)$. This signifies a better than factor of two improvement in errors for this quantity compared to previous calculations. Combining the new result with CLEO-c branching fraction data, we extract the CKM matrix element $|V_{cd}| = 0.225(6)_{exp.}(10)_{lat.}$, where the first error comes from experiment and the second from theory. With a total error of $\sim5.3$\% the accuracy of direct determination of $|V_{cd}|$ from $D$ semileptonic decays has become comparable to (and in good agreement with) that from neutrino scattering. We also check for second row unitarity using this new $|V_{cd}|$, HPQCD's earlier $|V_{cs}|$ and $|V_{cb}|$ from the Fermilab Lattice \& MILC collaborations. We find $|V_{cd}|^2 + |V_{cs}|^2 + |V_{cb}|^2 = 0.976(50)$, improving on the current PDG2010 value., Comment: 7 pages, 7 figures, and 4 tables

We examine the taste structure of eigenvectors of the staggered-fermion Dirac operator. We derive a set of conditions on the eigenvectors of modes with small eigenvalues (near-zero modes), such that staggered fermions reproduce the 't Hooft vertex in the continuum limit. We also show that, assuming these conditions, the correlators of flavor-singlet mesons are free of contributions singular in $1/m$, where $m$ is the quark mass. This conclusion holds also when a single flavor of sea quark is represented by the fourth root of the staggered-fermion determinant. We then test numerically, using the HISQ action, whether these conditions hold on realistic lattice gauge fields. We find that the needed structure does indeed emerge., Comment: 24 pages, 21 figures, v2 clarifies a dependence and matches published version

Using the approach developed in \cite{REFVIC2}, we succeeded in reconstructing the behaviour of the antiferromagnetic Ising model with imaginary magnetic field $i\theta$ for two and three dimensions in the low temperature regime. A mean-field calculation, expected to work well for high dimensions, is also carried out, and the mean-field results coincide qualitatively with those of the two- and three-dimensional Ising model. The mean field analysis reveals also a phase structure more complex than the one expected for $QCD$ with a topological $\theta-$therm., Comment: 21 pages, 15 figures. v2 added affiliation of the authors, corrected typos, largely improved presentation, corrected some plots. To be published in Nuclear Physics B

We present a study of $D \rightarrow K, l \nu$ semileptonic decays on the lattice which employs the HISQ action for both the charm and the light quarks. We work with MILC unquenched $N_f = 2 + 1$ lattices and determine the scalar form factor $f_0(q^2)$. This form factor is obtained from a scalar current matrix element that does not require any operator matching. We find $f^{D \rightarrow K}_0(0) \equiv f^{D \rightarrow K}_+(0) = 0.747(19)$ in the chiral plus continuum limit and hereby improve the theory error on this quantity by a factor of $\sim$4 compared to previous lattice determinations. Combining the new theory result with recent experimental measurements of the product $f^{D \rightarrow K}_+(0) * |V_{cs}| $ from BaBar and CLEO-c leads to a very precise direct determination of the CKM matrix element $|V_{cs}| $, $|V_{cs}| = 0.961(11)(24)$, where the first error comes from experiment and the second is the lattice QCD theory error., Comment: 7 pages, 6 figures, and 1 table. Talk given at Lattice 2010, June 14-19, 2010, Villasimius, Italy

In order to elucidate the vacuum structure of the Aoki phase, we carried out a numerical investigation of QCD with two flavours of Wilson fermions, within the p.d.f. framework and in the absence of external sources. The simulations performed at V = 44 suggest a rich vacuum structure, where the observable $i\bar\psi\gamma_5\psi$ is allowed to take non-zero values of the same order of magnitude than the order parameter of the Aoki phase $i\bar\psi\gamma_5\tau_3\psi$. However, the simulation at higher volumes V = 6^4 suffers from large statistical errors., Comment: 7 pages, talk given at the XXVIII International Symposium on Lattice Field Theory, June 14-19, 2010, Villasimius, Italy. v2 corrects agreements

The current-current correlator method has been used successfully to obtain very accurate results for quark masses and the coupling alpha_s. The calculations were done using Highly Improved Staggered Quarks (HISQ) and heavy-heavy meson correlators. We now extend this work to the significantly more challenging heavy-light case, reporting the first results here. The aim is to determine nonperturbative Z factors for NRQCD heavy-light currents, but first we test the method in the HISQ case where Z=1., Comment: 7 pages. Presented at the XXVIII International Symposium on Lattice Field Theory (Lattice 2010), June 14-19 2010, Villasimius, Italy

We give the first accurate results for $B$ and $B_s$ meson masses from lattice QCD including the effect of $u$, $d$ and $s$ sea quarks, and we improve an earlier value for the $B_c$ meson mass. By using the Highly Improved Staggered Quark action for $u/d$, $s$ and $c$ quarks and NRQCD for the $b$ quarks, we are able to achieve an accuracy in the masses of around 10 MeV. Our results are: $m_B$ = 5.291(18) GeV, $m_{B_s}$ = 5.363(11) GeV and $m_{B_c}$ = 6.280(10) GeV. Note that all QCD parameters here are tuned from other calculations, so these are parameter free tests of QCD against experiment. We also give scalar, $B_{s0}^*$, and axial vector, $B_{s1}$, meson masses. We find these to be slightly below threshold for decay to $BK$ and $B^*K$ respectively., Comment: 22 pages, 19 figures

We present a new study of D semileptonic decays on the lattice which employs the Highly Improved Staggered Quark (HISQ) action for both the charm and the light valence quarks. We work with MILC unquenched $N_f = 2 + 1$ lattices and determine the scalar form factor $f_0(q^2)$ for $D \rightarrow K, l \nu$ semileptonic decays. The form factor is obtained from a scalar current matrix element that does not require any operator matching. We develop a new approach to carrying out chiral/continuum extrapolations of $f_0(q^2)$. The method uses the kinematic "$z$" variable instead of $q^2$ or the kaon energy $E_K$ and is applicable over the entire physical $q^2$ range. We find $f^{D \rightarrow K}_0(0) \equiv f^{D \rightarrow K}_+(0) = 0.747(19)$ in the chiral plus continuum limit and hereby improve the theory error on this quantity by a factor of $\sim$4 compared to previous lattice determinations. Combining the new theory result with recent experimental measurements of the product $f^{D \rightarrow K}_+(0) * |V_{cs}| $ from BaBar and CLEO-c leads to the most precise direct determination of the CKM matrix element $|V_{cs}| $ to date, $|V_{cs}| = 0.961(11)(24)$, where the first error comes from experiment and the second is the lattice QCD theory error. We calculate the ratio $f^{D \rightarrow K}_+(0)/f_{D_s}$ and find $2.986 \pm 0.087$ GeV$^{-1}$ and show that this agrees with experiment., Comment: 23 pages, 31 figures, 11 tables. Added a paragraph in sction VII, and updated with PDG 2010 instead of PDG 2008

We update our previous determination of both the decay constant and the mass of the $D_s$ meson using the Highly Improved Staggered Quark formalism. We include additional results at two finer values of the lattice spacing along with improved determinations of the lattice spacing and improved tuning of the charm and strange quark masses. We obtain $m_{D_s}$ = 1.9691(32) GeV, in good agreement with experiment, and $f_{D_s}$ = 0.2480(25) GeV. Our result for $f_{D_s}$ is 1.6$\sigma$ lower than the most recent experimental average determined from the $D_s$ leptonic decay rate and using $V_{cs}$ from CKM unitarity. Combining our $f_{D_s}$ with the experimental rate we obtain a direct determination of $V_{cs} = 1.010(22)$, or alternatively $0.990 {+0.013 \atop -0.016}$ using a probability distribution for statistical errors for this quantity which vanishes above 1. We also include an accurate prediction of the decay constant of the $\eta_c$, $f_{\eta_c}$ = 0.3947(24) GeV, as a calibration point for other lattice calculations., Comment: 24 pages, 20 figures. Updated to include new experimental results from BaBar, new experimental averages from HFAG and consequent discussion of theory/experiment comparison. Other minor typographical changes. Version accepted by Phys. Rev. D

We extend our earlier lattice-QCD analysis of heavy-quark correlators to smaller lattice spacings and larger masses to obtain new values for the c mass and QCD coupling, and, for the first time, values for the b mass: m_c(3GeV,n_f=4)=0.986(6)GeV, alpha_msb(M_Z,n_f=5)=0.1183(7), and m_b(10GeV,n_f=5)=3.617(25)GeV. These are among the most accurate determinations by any method. We check our results using a nonperturbative determination of the mass ratio m_b(mu,n_f)/m_c(mu,n_f); the two methods agree to within our 1% errors and taken together imply m_b/m_c=4.51(4). We also update our previous analysis of alpha_msb from Wilson loops to account for revised values for r_1 and r_1/a, finding a new value alpha_\msb(M_Z,n_f=5)=0.1184(6); and we update our recent values for light-quark masses from the ratio m_c/m_s. Finally, in the Appendix, we derive a procedure for simplifying and accelerating complicated least-squares fits., Comment: 16 pages, 10 figures, 3 tables

The Vafa-Witten arguments on the realization of parity and flavour symmetries in the QCD vacuum do not apply to two lattice regularizations of QCD which are able to reproduce the chiral anomaly: Wilson fermions and Ginsparg-Wilson fermions. We show here how using the last regularization one can get, from first principles, that the more standard order parameters for these symmetries take a vanishing vacuum expectation value for any number of flavours, if quarks have a non-vanishing mass., Comment: 14 pages. References added

Using NRQCD b quarks and HISQ light, strange and charm quarks we have calculated B meson masses and B^*-B splittings. We quote results for a range of lattice spacings and sea quark masses, enabling controlled extrapolation to the physical point. Since the $b$ quark masses and lattice spacing are fixed from the \Upsilon and other meson masses, this allows accurate, parameter-free tests of B, B_s, and B_c masses against experiment. We can also predict the mass of the B^*_c meson., Comment: 7 pages, 1 table, 5 figures, Contribution to the "XXVII International Symposium on Lattice Field Theory", July 26-31, 2009, Peking University, Beijing, China

We review recent results for B_d and B_s mixing parameters using MILC N_f=2+1 lattices, NRQCD b-quarks and AsqTad light quarks. Latest numbers for decay constants f_B and f_{B_s} are also presented. Combining our lattice results with experimental determinations of the mass differences \Delta M_d and \Delta M_s leads to an important ratio of elements of the CKM matrix, |V_{td}|/|V_{ts}| = 0.214(1)(5) and an updated Standard Model number for the branching fraction Br(B_s -> mu^+ mu^-) = 3.19(19) x 10^{-9}. Preliminary new results for f_{B_s} based on other actions are also described., Comment: 7 pages, 5 figures, contribution to the 27th International Symposium on Lattice Field Theory, Beijing, July 2009

We present a program to study D semi-leptonic decay form factors with HISQ charm and light quarks. In this exploratory work, we study $D_s$ to $\eta_s$, $l\nu_l$ semi-leptonic decay on MILC coarse ($20^3\times64$) gauge configurations with 2+1 dynamical flavors. We develop a new method to calculate $f_+(0)$ and $f_0(q^2)$ from scalar current matrix elements, $<\pi|\bar{s}c|D>$, which does not require any operator renormalization. We also determine $f_+(q^2)$ and $f_0(q^2)$ from vector currents with a fully non-perturbative renormalization method., Comment: 7 pages, 3 figures, Talk given at Lattice 2009, July 26-31 2009, Peking University, Beijing, China

By using a single formalism to handle charm, strange and light valence quarks in full lattice QCD for the first time, we are able to determine ratios of quark masses to 1%. For $m_c/m_s$ we obtain 11.85(16), an order of magnitude more precise than the current PDG average. Combined with 1% determinations of the charm quark mass now possible this gives $\bar{m}_s(2{\rm GeV}) =$ 92.4(1.5) MeV. The MILC result for $m_s/m_l = 27.2(3) $ yields $\bar{m}_l(2{\rm GeV})$ = 3.40(7) MeV for the average of $u$ and $d$ quark masses., Comment: 4 pages, 2 figures. Version accepted by Physical Review Letters. Changes include modifying the title, using the MILC value for m_s/m_l which changes slightly the resulting up and down quark masses and their average, adding some references and making other small adjustments to the text for space reasons.

We discuss the status of our ongoing efforts to improve on our calculation of the $D_s$ decay constant. We show preliminary results on the ratio of the charm to the strange quark mass. We also present preliminary results for spectroscopy, decay constants and bottom quark mass obtained by performing calculations with highly improved staggered quarks at masses above the c mass and close to the b mass., Comment: 8 pages. Contribution to 27th International Symposium on Lattice Field Theory, Beijing, China, 2009

We compare three different methods to determine the lattice spacing in lattice QCD and give results from calculations on the MILC ensembles of configurations that include the effect of $u$, $d$ and $s$ sea quarks. It is useful, for ensemble to ensemble comparison, to express the results as giving a physical value for $r_1$, a parameter from the heavy quark potential. Combining the three methods gives a value for $r_1$ in the continuum limit of 0.3133(23)(3) fm. Using the MILC values for $r_0/r_1$, this corresponds to a value for the $r_0$ parameter of 0.4661(38) fm. We also discuss how to use the $\eta_s$ for determining the lattice spacing and tuning the $s$-quark mass accurately, by giving values for $m_{\eta_s}$ (0.6858(40) GeV) and $f_{\eta_s}$ (0.1815(10) GeV)., Comment: 15 pages

The vacuum structure of QCD with two degenerated flavours of Wilson fermions is discussed by means of the p.d.f. (probability distribution function) formalism. Under certain assumptions, either new phases related to Aoki's appear, characterized by a non-vanishing expectation value of the condensate $i\bar\psi_u\gamma_5\psi_u + i\bar\psi_d\gamma_5\psi_d$, enriching the standard picture of the QCD vacuum structure with Wilson fermions; or the eigenvalues of the Dirac-Wilson operator must comply with a non-trivial, infinite set of sum rules, enforcing the currently accepted structure of the Aoki vacuum. The same scenario is analyzed using the Ginsparg-Wilson regularization. In this case, the absence of any parity and/or flavour breaking phase is proved for a non-zero value of the fermion mass., Comment: 7 pages, no figures, to be published in PoS(Lattice'09)

By using the Highly Improved Staggered Quark formalism to handle charm, strange and light valence quarks in full lattice QCD, and NRQCD to handle bottom valence quarks we are able to determine accurately ratios of the B meson vector-pseudoscalar mass splittings, in particular, (m(B*_c)-m(B_c))/(m(B*_s)-m(B_s)). We find this ratio to be 1.15(15), showing the `light' quark mass dependence of this splitting to be very small. Hence we predict m(B_c*) = 6.330(7)(2)(6) GeV where the first two errors are from the lattice calculation and the third from existing experiment. This is the most accurate prediction of a gold-plated hadron mass from lattice QCD to date., Comment: 4 pages, 2 figures