Tests of the Equivalence Principle with Neutral Kaons

We test the Principle of Equivalence for particles and antiparticles, using CPLEAR data on tagged K0 and K0bar decays into pi^+ pi^-. For the first time, we search for possible annual, monthly and diurnal modulations of the observables |eta_{+-}| and phi_{+-}, that could be correlated with variations in astrophysical potentials. Within the accuracy of CPLEAR, the measured values of |eta_{+-}| and phi_{+-} are found not to be correlated with changes of the gravitational potential. We analyze data assuming effective scalar, vector and tensor interactions, and we conclude that the Principle of Equivalence between particles and antiparticles holds to a level of 6.5, 4.3 and 1.8 x 10^{-9}, respectively, for scalar, vector and tensor potentials originating from the Sun with a range much greater than the distance Earth-Sun. We also study energy-dependent effects that might arise from vector or tensor interactions. Finally, we compile upper limits on the gravitational coupling difference between K0 and K0bar as a function of the scalar, vector and tensor interaction range.Comment: 15 pages latex 2e, five figures, one style file (cernart.csl) incorporate

Test of CPT Symmetry and Quantum Mechanics with Experimental data from CPLEAR

We use fits to recent published CPLEAR data on neutral kaon decays to $\pi^+\pi^-$ and $\pi e\nu$ to constrain the CPT--violation parameters appearing in a formulation of the neutral kaon system as an open quantum-mechanical system. The obtained upper limits of the CPT--violation parameters are approaching the range suggested by certain ideas concerning quantum gravity.Comment: 9 pages of uuencoded postscript (includes 3 figures

MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes

abstract: Background The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such peptide epitopes has potential applications in vaccine design and in better understanding autoimmune diseases and allergies. However, comprehensive experimental determination of peptide-MHC binding affinities is infeasible due to MHC diversity and the large number of possible peptide sequences. Computational methods trained on the limited experimental binding data can address this challenge. We present the MultiRTA method, an extension of our previous single-type RTA prediction method, which allows the prediction of peptide binding affinities for multiple MHC allotypes not used to train the model. Thus predictions can be made for many MHC allotypes for which experimental binding data is unavailable. Results We fit MultiRTA models for both HLA-DR and HLA-DP using large experimental binding data sets. The performance in predicting binding affinities for novel MHC allotypes, not in the training set, was tested in two different ways. First, we performed leave-one-allele-out cross-validation, in which predictions are made for one allotype using a model fit to binding data for the remaining MHC allotypes. Comparison of the HLA-DR results with those of two other prediction methods applied to the same data sets showed that MultiRTA achieved performance comparable to NetMHCIIpan and better than the earlier TEPITOPE method. We also directly tested model transferability by making leave-one-allele-out predictions for additional experimentally characterized sets of overlapping peptide epitopes binding to multiple MHC allotypes. In addition, we determined the applicability of prediction methods like MultiRTA to other MHC allotypes by examining the degree of MHC variation accounted for in the training set. An examination of predictions for the promiscuous binding CLIP peptide revealed variations in binding affinity among alleles as well as potentially distinct binding registers for HLA-DR and HLA-DP. Finally, we analyzed the optimal MultiRTA parameters to discover the most important peptide residues for promiscuous and allele-specific binding to HLA-DR and HLA-DP allotypes. Conclusions The MultiRTA method yields competitive performance but with a significantly simpler and physically interpretable model compared with previous prediction methods. A MultiRTA prediction webserver is available at http://bordnerlab.org/MultiRTA.The electronic version of this article is the complete one and can be found online at: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-48

Towards Universal Structure-Based Prediction of Class II MHC Epitopes for Diverse Allotypes

The binding of peptide fragments of antigens to class II MHC proteins is a crucial step in initiating a helper T cell immune response. The discovery of these peptide epitopes is important for understanding the normal immune response and its misregulation in autoimmunity and allergies and also for vaccine design. In spite of their biomedical importance, the high diversity of class II MHC proteins combined with the large number of possible peptide sequences make comprehensive experimental determination of epitopes for all MHC allotypes infeasible. Computational methods can address this need by predicting epitopes for a particular MHC allotype. We present a structure-based method for predicting class II epitopes that combines molecular mechanics docking of a fully flexible peptide into the MHC binding cleft followed by binding affinity prediction using a machine learning classifier trained on interaction energy components calculated from the docking solution. Although the primary advantage of structure-based prediction methods over the commonly employed sequence-based methods is their applicability to essentially any MHC allotype, this has not yet been convincingly demonstrated. In order to test the transferability of the prediction method to different MHC proteins, we trained the scoring method on binding data for DRB1*0101 and used it to make predictions for multiple MHC allotypes with distinct peptide binding specificities including representatives from the other human class II MHC loci, HLA-DP and HLA-DQ, as well as for two murine allotypes. The results showed that the prediction method was able to achieve significant discrimination between epitope and non-epitope peptides for all MHC allotypes examined, based on AUC values in the range 0.632–0.821. We also discuss how accounting for peptide binding in multiple registers to class II MHC largely explains the systematically worse performance of prediction methods for class II MHC compared with those for class I MHC based on quantitative prediction performance estimates for peptide binding to class II MHC in a fixed register

Determination of the T- and CPT-violation parameters in the neutral-kaon system using the Bell-Steinberger relation and data from CPLEAR

Data from the CPLEAR experiment, together with the most recent world averages for some of the neutral-kaon parameters, were constrained with the Bell--Steinberger (or unitarity) relation, allowing the T-violation parameter \ree and the CPT-violation parameter \imd of the neutral-kaon mixing matrix to be determined with an increased accuracy: \ree = (164.9 \pm 2.5)\times 10^{-5}, \imd = ( 2.4 \pm 5.0)\times 10^{-5}. Moreover, the constraint allows the CPT-violation parameter for the neutral-kaon semileptonic decays, \rey, to be determined for the first time. The $\Delta S \neq \Delta Q$ parameters \rexm and \imxp are given with an increased accuracy. The quantity $\mathrm{Re}(y~+~x_-)$, which enters the T-violation CPLEAR asymmetry previously published, is determined to be $(0.2 \pm 0.3)\times 10^{-3}$. The value obtained for \red is in agreement with the one resulting from a previous unconstrained fit and has a slightly smaller error

The neutral kaon decays to π+π−π0\pi^+ \pi^- \pi^0: a detailed analysis of the CPLEAR data

A detailed analysis of neutral kaons decaying to \Pgpp \Pgpm \Pgpz\ is presented based on the complete data set containing half a million events. Time-dependent decay rate asymmetries are measured between initially tagged \PKz\ and \PaKz\ and for different regions of the phase space. These asymmetries, resulting from the interference between the CP-conserving decay amplitude of \PKzL\ and the decay amplitude of \PKzS\ -- either CP-violating or CP-conserving -- allow the determinationof the \PKzS\ parameters \etapmz\ (CP-violating) and \lampmz\ (CP-conserving), and also of the main i sospin components of the \PKzS\ decay amplitude. The branching ratio of \PKzS\ $\rightarrow$ \Pgpp \Pgpm \Pgpz\ (CP-conserving) is deduced directly from \lampmz . In addition, we extract the slope parameters describing the energy dependence of the \PKzL \rightarrow \Pgpp \Pgpm \Pgpz Dalitz plot. The whole set of our results fits well within the current phenomenological picture of the neut ral-kaon system including CP violation and Chiral Perturbation Theory (ChPT)

Measurement of the KL−KSK_{L}-K_{S} mass difference using semileptonic decays of tagged neutral kaons

We report on a new measurement of the \kl--\ks\ mass difference \dm\ using the CPLEAR full data sample of neutral-kaon decays to \semi. The result is \dm = (0.5295 \pm 0.0020_{\stat} \pm 0.0003_{\syst}) \times 10^{10}\ \hbs. It includes earlier data reported in Ref. \cite{deltam1}. A measurement of the \dsdq\ violating parameter \rex\ is also obtained

A determination of the CPT violation parameter Re(δ\delta) from the semileptonic decay of strangeness-tagged neutral kaons

We have improved by two orders of magnitude the limit currently available for the CPT violation parameter \red . To this purpose we have analyzed the full sample of neutral-kaon decays to \semi\ recorded in the CPLEAR experiment, where the strangeness of the neutral kaons was tagged at production and decay time. An appropriate function of the measured decay rates, including information from the analysis of \pip\pim\ decay channel, gives directly \red . The result $\red = (3.0 \pm 3.3_\mathrm{{stat}} \pm 0.6_\mathrm{{syst}}) \times 10^{-4}$ is compatible with zero. Values for the parameters \imd, \rexm and \imxp were also obtained

Measurement of the neutral kaon regeneration amplitude in carbon at momenta below 1 GeV/c

The neutral kaon regeneration amplitude in carbon at momenta between 250 and 750~MeV/$c$ was determined by measuring the interference of inherent and coherently regenerated \PKS\ amplitudes. This interference appears in the rates of initially pure (tagged) \PKz\ and \PaKz\ decaying to \Pgpp\Pgpm\ after crossing a carbon absorber

Dispersion relation analysis of the neutral kaon regeneration amplitude in carbon

We apply a forward dispersion relation to the regeneration amplitude for kaon scattering on \PCtw using all available data. The CPLEAR data at low energies allow the determination of the net contribution from the subthreshold region which turns out to be much smaller than earlier evaluations, solving a long standing puzzle