The Kentucky Noisy Monte Carlo Algorithm for Wilson Dynamical Fermions

We develop an implementation for a recently proposed Noisy Monte Carlo approach to the simulation of lattice QCD with dynamical fermions by incorporating the full fermion determinant directly. Our algorithm uses a quenched gauge field update with a shifted gauge coupling to minimize fluctuations in the trace log of the Wilson Dirac matrix. The details of tuning the gauge coupling shift as well as results for the distribution of noisy estimators in our implementation are given. We present data for some basic observables from the noisy method, as well as acceptance rate information and discuss potential autocorrelation and sign violation effects. Both the results and the efficiency of the algorithm are compared against those of Hybrid Monte Carlo. PACS Numbers: 12.38.Gc, 11.15.Ha, 02.70.Uu Keywords: Noisy Monte Carlo, Lattice QCD, Determinant, Finite Density, QCDSPComment: 30 pages, 6 figure

Solving non-uniqueness in agglomerative hierarchical clustering using multidendrograms

In agglomerative hierarchical clustering, pair-group methods suffer from a problem of non-uniqueness when two or more distances between different clusters coincide during the amalgamation process. The traditional approach for solving this drawback has been to take any arbitrary criterion in order to break ties between distances, which results in different hierarchical classifications depending on the criterion followed. In this article we propose a variable-group algorithm that consists in grouping more than two clusters at the same time when ties occur. We give a tree representation for the results of the algorithm, which we call a multidendrogram, as well as a generalization of the Lance and Williams' formula which enables the implementation of the algorithm in a recursive way.Comment: Free Software for Agglomerative Hierarchical Clustering using Multidendrograms available at http://deim.urv.cat/~sgomez/multidendrograms.ph

An open extensible tool environment for Event-B

Abstract. We consider modelling indispensable for the development of complex systems. Modelling must be carried out in a formal notation to reason and make meaningful conjectures about a model. But formal modelling of complex systems is a difficult task. Even when theorem provers improve further and get more powerful, modelling will remain difficult. The reason for this that modelling is an exploratory activity that requires ingenuity in order to arrive at a meaningful model. We are aware that automated theorem provers can discharge most of the onerous trivial proof obligations that appear when modelling systems. In this article we present a modelling tool that seamlessly integrates modelling and proving similar to what is offered today in modern integrated development environments for programming. The tool is extensible and configurable so that it can be adapted more easily to different application domains and development methods.

Diversity and impact of rare variants in genes encoding the platelet G protein-coupled receptors

Platelet responses to activating agonists are influenced by common population variants within or near G protein-coupled receptor (GPCR) genes that affect receptor activity. However, the impact of rare GPCR gene variants is unknown. We describe the rare single nucleotide variants (SNVs) in the coding and splice regions of 18 GPCR genes in 7,595 exomes from the 1,000-genomes and Exome Sequencing Project databases and in 31 cases with inherited platelet function disorders (IPFDs). In the population databases, the GPCR gene target regions contained 740 SNVs (318 synonymous, 410 missense, 7 stop gain and 6 splice region) of which 70 % had global minor allele frequency (MAF) < 0.05 %. Functional annotation using six computational algorithms, experimental evidence and structural data identified 156/740 (21 %) SNVs as potentially damaging to GPCR function, most commonly in regions encoding the transmembrane and C-terminal intracellular receptor domains. In 31 index cases with IPFDs (Gi-pathway defect n=15; secretion defect n=11; thromboxane pathway defect n=3 and complex defect n=2) there were 256 SNVs in the target regions of 15 stimulatory platelet GPCRs (34 unique; 12 with MAF< 1 % and 22 with MAF≥ 1 %). These included rare variants predicting R122H, P258T and V207A substitutions in the P2Y12 receptor that were annotated as potentially damaging, but only partially explained the platelet function defects in each case. Our data highlight that potentially damaging variants in platelet GPCR genes have low individual frequencies, but are collectively abundant in the population. Potentially damaging variants are also present in pedigrees with IPFDs and may contribute to complex laboratory phenotypes

Proof‐of‐concept study to establish an in situ method to determine the nature and depth of collagen changes in dentine using Fourier Transform Infra‐Red spectroscopy after sodium hypochlorite irrigation

AIM: To establish a method using Fourier Transform Infra-Red spectroscopy (FTIR) to characterize the nature and depth of changes in dentinal collagen following exposure to sodium hypochlorite (NaOCl) during root canal irrigation in an ex vivo model. METHODOLOGY: Fourier Transform Infra-Red spectroscopy was used to assess the changes in dentinal collagen when the root canal was exposed to NaOCl. The changes in dentinal collagen caused by NaOCl irrigation of root canals in transverse sections of roots, at 0.5 mm from the canal wall and 0.5 mm from the external root surface, were assessed by FTIR. The data were analysed using paired t-test with 5% significance level. RESULTS: Fourier Transform Infra-Red spectroscopy confirmed that NaOCl exposure caused alterations in the chemistry and structure of collagen in dentine. FTIR spectra obtained from dentine surfaces and dentine adjacent to root canals exposed to NaOCl, all consistently showed degradation and conformational change of the collagen structure. FTIR data from the ex vivo model showed that the depth of effect of NaOCl extended to at least 0.5 mm from the canal wall. CONCLUSION: In extracted human teeth, NaOCl caused changes in dentinal collagen that were measurable by FTIR. In an ex vivo model, the depth of effect into dentine extended at least 0.5 mm from the canal wall

A low-lying scalar meson nonet in a unitarized meson model

A unitarized nonrelativistic meson model which is successful for the description of the heavy and light vector and pseudoscalar mesons yields, in its extension to the scalar mesons but for the same model parameters, a complete nonet below 1 GeV. In the unitarization scheme, real and virtual meson-meson decay channels are coupled to the quark-antiquark confinement channels. The flavor-dependent harmonic-oscillator confining potential itself has bound states epsilon(1.3 GeV), S(1.5 GeV), delta(1.3 GeV), kappa(1.4 GeV), similar to the results of other bound-state qqbar models. However, the full coupled-channel equations show poles at epsilon(0.5 GeV), S(0.99 GeV), delta(0.97 GeV), kappa(0.73 GeV). Not only can these pole positions be calculated in our model, but also cross sections and phase shifts in the meson-scattering channels, which are in reasonable agreement with the available data for pion-pion, eta-pion and Kaon-pion in S-wave scattering.Comment: A slightly revised version of Zeitschrift fuer Physik C30, 615 (1986

Stationary solutions of the one-dimensional nonlinear Schroedinger equation: I. Case of repulsive nonlinearity

All stationary solutions to the one-dimensional nonlinear Schroedinger equation under box and periodic boundary conditions are presented in analytic form. We consider the case of repulsive nonlinearity; in a companion paper we treat the attractive case. Our solutions take the form of stationary trains of dark or grey density-notch solitons. Real stationary states are in one-to-one correspondence with those of the linear Schr\"odinger equation. Complex stationary states are uniquely nonlinear, nodeless, and symmetry-breaking. Our solutions apply to many physical contexts, including the Bose-Einstein condensate and optical pulses in fibers.Comment: 11 pages, 7 figures -- revised versio

Guidelines for the Selection of Physical Literacy Measures in Physical Education in Australia

Assessment of physical literacy poses a dilemma of what instrument to use. There is currently no guide regarding the suitability of common assessment approaches. The purpose of this brief communication is to provide a user's guide for selecting physical literacy assessment instruments appropriate for use in school physical education and sport settings. While recommendations regarding specific instruments are not provided, the guide offers information about key attributes and considerations for the use. A decision flow chart has been developed to assist teachers and affiliated school practitioners to select appropriate methods of assessing physical literacy. School PE and sport scenarios are presented to illustrate this process. It is important that practitioners are empowered to select the most appropriate instrument/s to suit their needs