Predict collagen hydroxyproline sites using support vector machines.

addresses: School of Biosciences, University of Exeter, Exeter, United Kingdom. [email protected]: Journal ArticleThis is a copy of an article published in the Journal of Computational Biology © 2009 copyright Mary Ann Liebert, Inc.; Journal of Computational Biology is available online at: http://online.liebertpub.com.Collagen hydroxyproline is an important posttranslational modification activity because of its close relationship with various diseases and signaling activities. However, there is no study to date for constructing models for predicting collagen hydroxyproline sites. Support vector machines with two kernel functions (the identity kernel function and the bio-kernel function) have been used for constructing models for predicting collagen hydroxyproline sites in this study. The models are constructed based on 37 sequences collected from NCBI. Peptide data are generated using a sliding window with various sizes to scan the sequences. Fivefold cross-validation is used for model evaluation. The best model has specificity of 70% and sensitivity of 90%

Classification of singular Q-homology planes. I. Structure and singularities

A Q-homology plane is a normal complex algebraic surface having trivial rational homology. We obtain a structure theorem for Q-homology planes with smooth locus of non-general type. We show that if a Q-homology plane contains a non-quotient singularity then it is a quotient of an affine cone over a projective curve by an action of a finite group respecting the set of lines through the vertex. In particular, it is contractible, has negative Kodaira dimension and only one singular point. We describe minimal normal completions of such planes.Comment: improved results from Ph.D. thesis (University of Warsaw, 2009), 25 pages, to appear in Israel J. Mat

The Λp\bf{\Lambda p} interaction studied via femtoscopy in p + Nb reactions at sNN=3.18 GeV\mathbf{\sqrt{s_{NN}}=3.18} ~\mathrm{\bf{GeV}}

We report on the first measurement of $p\Lambda$ and $pp$ correlations via the femtoscopy method in p+Nb reactions at $\mathrm{\sqrt{s_{NN}}=3.18} ~\mathrm{GeV}$, studied with the High Acceptance Di-Electron Spectrometer (HADES). By comparing the experimental correlation function to model calculations, a source size for $pp$ pairs of $r_{0,pp}=2.02 \pm 0.01(\mathrm{stat})^{+0.11}_{-0.12} (\mathrm{sys}) ~\mathrm{fm}$ and a slightly smaller value for $p\Lambda$ of $r_{0,\Lambda p}=1.62 \pm 0.02(\mathrm{stat})^{+0.19}_{-0.08}(\mathrm{sys}) ~\mathrm{fm}$ is extracted. Using the geometrical extent of the particle emitting region, determined experimentally with $pp$ correlations as reference together with a source function from a transport model, it is possible to study different sets of scattering parameters. The $p\Lambda$ correlation is proven sensitive to predicted scattering length values from chiral effective field theory. We demonstrate that the femtoscopy technique can be used as valid alternative to the analysis of scattering data to study the hyperon-nucleon interaction.Comment: 12 pages, 11 figure

Time resolution of the plastic scintillator strips with matrix photomultiplier readout for J-PET tomograph

Recent tests of a single module of the Jagiellonian Positron Emission Tomography system (J-PET) consisting of 30 cm long plastic scintillator strips have proven its applicability for the detection of annihilation quanta (0.511 MeV) with a coincidence resolving time (CRT) of 0.266 ns. The achieved resolution is almost by a factor of two better with respect to the current TOF-PET detectors and it can still be improved since, as it is shown in this article, the intrinsic limit of time resolution for the determination of time of the interaction of 0.511 MeV gamma quanta in plastic scintillators is much lower. As the major point of the article, a method allowing to record timestamps of several photons, at two ends of the scintillator strip, by means of matrix of silicon photomultipliers (SiPM) is introduced. As a result of simulations, conducted with the number of SiPM varying from 4 to 42, it is shown that the improvement of timing resolution saturates with the growing number of photomultipliers, and that the 2 x 5 configuration at two ends allowing to read twenty timestamps, constitutes an optimal solution. The conducted simulations accounted for the emission time distribution, photon transport and absorption inside the scintillator, as well as quantum efficiency and transit time spread of photosensors, and were checked based on the experimental results. Application of the 2 x 5 matrix of SiPM allows for achieving the coincidence resolving time in positron emission tomography of $\approx$ 0.170 ns for 15 cm axial field-of-view (AFOV) and $\approx$ 0.365 ns for 100 cm AFOV. The results open perspectives for construction of a cost-effective TOF-PET scanner with significantly better TOF resolution and larger AFOV with respect to the current TOF-PET modalities.Comment: To be published in Phys. Med. Biol. (26 pages, 17 figures

Observation of Two Resonant Structures in e+e- to pi+ pi- psi(2S) via Initial State Radiation at Belle

The cross section for e+e- to pi+ pi- psi(2S) between threshold and \sqrt{s}=5.5 GeV is measured using 673 fb^{-1} of data on and off the \Upsilon(4S) resonance collected with the Belle detector at KEKB. Two resonant structures are observed in the pi+ pi- psi(2S) invariant mass distribution, one at 4361\pm 9\pm 9 MeV/c2 with a width of 74\pm 15\pm 10 MeV/c2, and another at 4664\pm 11\pm 5 MeV/c2 with a width of 48\pm 15\pm 3 MeV/c2, if the mass spectrum is parameterized with the coherent sum of two Breit-Wigner functions. These values do not match those of any of the known charmonium states.Comment: 10 pages, 5 figures, 2 tables, version to appear in Phys. Rev. Let

Inclusive pion and eta production in p+Nb collisions at 3.5 GeV beam energy

Data on inclusive pion and eta production measured with the dielectron spectrometer HADES in the reaction p+93Nb at a kinetic beam energy of 3.5 GeV are presented. Our results, obtained with the photon conversion method, supplement the rather sparse information on neutral meson production in proton-nucleus reactions existing for this bombarding energy regime. The reconstructed e+e-e+e- transverse-momentum and rapidity distributions are confronted with transport model calculations, which account fairly well for both pi0 and eta production.Comment: 12 pages, 9 figures, submitted to Physical Review

Searching a Dark Photon with HADES

We present a search for the e+e- decay of a hypothetical dark photon, also names U vector boson, in inclusive dielectron spectra measured by HADES in the p (3.5 GeV) + p, Nb reactions, as well as the Ar (1.756 GeV/u) + KCl reaction. An upper limit on the kinetic mixing parameter squared epsilon^{2} at 90% CL has been obtained for the mass range M(U) = 0.02 - 0.55 GeV/c2 and is compared with the present world data set. For masses 0.03 - 0.1 GeV/c^2, the limit has been lowered with respect to previous results, allowing now to exclude a large part of the parameter region favoured by the muon g-2 anomaly. Furthermore, an improved upper limit on the branching ratio of 2.3 * 10^{-6} has been set on the helicity-suppressed direct decay of the eta meson, eta-> e+e-, at 90% CL

An upper limit on hypertriton production in collisions of Ar(1.76 AGeV)+KCl

A high-statistic data sample of Ar(1.76 AGeV)+KCl events recorded with HADES is used to search for a hypertriton signal. An upper production limit per centrality-triggered event of $1.04$ x $10^{-3}$ on the $3\sigma$ level is derived. Comparing this value with the number of successfully reconstructed $\Lambda$ hyperons allows to determine an upper limit on the ratio $N_{_{\Lambda}^3H}/N_{\Lambda}$, which is confronted with statistical and coalescence-type model calculations