Predicting promoters in phage genomes using machine learning models

The renewed interest in phages as antibacterial agents has led to the exponentially growing number of sequenced phage genomes. Therefore, the development of novel bioinformatics methods to automate and facilitate phage genome annotation is of utmost importance. The most difficult step of phage genome annotation is the identification of promoters. As the existing methods for predicting promoters are not well suited for phages, we used machine learning models for locating promoters in phage genomes. Several models were created, using different algorithms and datasets, which consisted of known phage promoter and non-promoter sequences. All models showed good performance, but the ANN model provided better results for the smaller dataset (92% of accuracy, 89% of precision and 87% of recall) and the SVM model returned better results for the larger dataset (93% of accuracy, 91% of precision and 80% of recall). Both models were applied to the genome of Pseudomonas phage phiPsa17 and were able to identify both types of promoters, host and phage, found in phage genomes.This study was supported by the Portuguese Foundation for Science andTechnology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit and theProject POCI-01-0145-FEDER-029628. This work was also supported by BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fundunder the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

Targeting HIV-1 Env gp140 to LOX-1 Elicits Immune Responses in Rhesus Macaques.

Improved antigenicity against HIV-1 envelope (Env) protein is needed to elicit vaccine-induced protective immunity in humans. Here we describe the first tests in non-human primates (NHPs) of Env gp140 protein fused to a humanized anti-LOX-1 recombinant antibody for delivering Env directly to LOX-1-bearing antigen presenting cells, especially dendritic cells (DC). LOX-1, or 1ectin-like oxidized low-density lipoprotein (LDL) receptor-1, is expressed on various antigen presenting cells and endothelial cells, and is involved in promoting humoral immune responses. The anti-LOX-1 Env gp140 fusion protein was tested for priming immune responses and boosting responses in animals primed with replication competent NYVAC-KC Env gp140 vaccinia virus. Anti-LOX-1 Env gp140 vaccination elicited robust cellular and humoral responses when used for either priming or boosting immunity. Co-administration with Poly ICLC, a TLR3 agonist, was superior to GLA, a TLR4 agonist. Both CD4+ and CD8+ Env-specific T cell responses were elicited by anti-LOX-1 Env gp140, but in particular the CD4+ T cells were multifunctional and directed to multiple epitopes. Serum IgG and IgA antibody responses induced by anti-LOX-1 Env gp140 against various gp140 domains were cross-reactive across HIV-1 clades; however, the sera neutralized only HIV-1 bearing sequences most similar to the clade C 96ZM651 Env gp140 carried by the anti-LOX-1 vehicle. These data, as well as the safety of this protein vaccine, justify further exploration of this DC-targeting vaccine approach for protective immunity against HIV-1

Precision measurement of charged pion and kaon differential cross sections in electron-positron annihilation at Q = 10.52 GeV

Measurements of inclusive differential cross sections for charged pion and kaon production in electron-positron annihilation have been carried out at a center-of-mass energy of Q = 10.52 GeV. The measurements were performed with the Belle detector at the KEKB electron-positron collider using a data sample containing 113 million e+e- -> qqbar events, where q={u,d,s,c}. We present charge-integrated differential cross sections d\sigma_h+-/dz for h+- = pi+-, K+- as a function of the relative hadron energy z = 2*E_h / sqrt{s} from 0.2 to 0.98. The combined statistical and systematic uncertainties for pi+- (K+-) are 4% (4%) at z ~ 0.6 and 15% (24%) at z ~ 0.9. The cross sections are the first measurements of the z-dependence of pion and kaon production for z > 0.7 as well as the first precision cross section measurements at a center-of-mass energy far below the Z^0 resonance used by the experiments at LEP and SLC.Comment: 7 pages, 3 figures. Ancillary file including all cross section and uncertainty values with 10 pages, 5 figure

Measurement of the CP Violation Parameters in B0 -> pi+ pi- Decays

We present a measurement of the time-dependent charge-parity (CP) violation parameters in B0 -> pi+ pi- decays. The results are obtained from the final data sample containing 772 million BBbar pairs collected at the Upsilon(4S) resonance with the Belle detector at the KEKB asymmetric-energy e+e- collider. We obtain the CP violation parameters Acp = +0.33 +/- 0.06 (stat) +/- 0.03 (syst) and Scp = -0.64 +/- 0.08 (stat) +/- 0.03 (syst), where Acp and Scp represent the direct and mixing-induced CP asymmetry, respectively. Using an isospin analysis including results from other Belle measurements, we find 23.8 < phi2 < 66.8 degrees is disfavored at the 1 sigma level, where phi2 is one of the three interior angles of the CKM unitarity triangle related to B_{u,d} decays.Comment: 16 pages, 5 figures, CKM2012 conference paper, Submitted to PR

Measurements of the masses and widths of the Σc(2455)0/++\Sigma_{c}(2455)^{0/++} and Σc(2520)0/++\Sigma_{c}(2520)^{0/++} baryons

We present measurements of the masses and decay widths of the baryonic states $\Sigma_{c}(2455)^{0/++}$ and $\Sigma_{c}(2520)^{0/++}$ using a data sample corresponding to an integrated luminosity of 711 fb$^{-1}$ collected with the Belle detector at the KEKB $e^{+}e^{-}$ asymmetric-energy collider operating at the $\Upsilon(4S)$ resonance. We report the mass differences with respect to the $\Lambda_{c}^{+}$ baryon $M(\Sigma_{c}(2455)^{0})-M(\Lambda_{c}^{+}) = 167.29\pm0.01\pm0.02$ MeV/$c^{2}$, $M(\Sigma_{c}(2455)^{++})-M(\Lambda_{c}^{+}) = 167.51\pm0.01\pm0.02$ MeV/$c^{2}$, $M(\Sigma_{c}(2520)^{0})-M(\Lambda_{c}^{+}) = 231.98\pm0.11\pm0.04$ MeV/$c^{2}$, $M(\Sigma_{c}(2520)^{++})-M(\Lambda_{c}^{+}) = 231.99\pm0.10\pm0.02$ MeV/$c^{2}$, and the decay widths $\Gamma(\Sigma_{c}(2455)^{0}) = 1.76\pm0.04^{+0.09}_{-0.21}$ MeV/$c^{2}$, $\Gamma(\Sigma_{c}(2455)^{++}) = 1.84\pm0.04^{+0.07}_{-0.20}$ MeV/$c^{2}$, $\Gamma(\Sigma_{c}(2520)^{0}) = 15.41\pm0.41^{+0.20}_{-0.32}$ MeV/$c^{2}$, $\Gamma(\Sigma_{c}(2520)^{++}) = 14.77\pm0.25^{+0.18}_{-0.30}$ MeV/$c^{2}$, where the first uncertainties are statistical and the second are systematic. The isospin mass splittings are measured to be $M(\Sigma_{c}(2455)^{++})-M(\Sigma_{c}(2455)^{0})=0.22\pm0.01\pm0.01$ MeV/$c^{2}$ and $M(\Sigma_{c}(2520)^{++})-M(\Sigma_{c}(2520)^{0})=0.01\pm0.15\pm0.03$ MeV/$c^{2}$. These results are the most precise to date.Comment: 13 pages, 4 figures, Submitted to PRD(RC

Study of B^0 -> rho^0 rho^0 decays, implications for the CKM angle phi_2 and search for other B^0 decay modes with a four-pion final state

We present a study of the branching fraction of the decay B^0->rho0rho0 and the fraction of longitudinally polarized rho0 mesons in this decay. The results are obtained from the final data sample containing 772 million BBbar pairs collected at the Y(4S) resonance with the Belle detector at the KEKB asymmetric-energy e+e- collider. We find 166 +- 59 B^0 -> rho0 rho0 events (including systematic uncertainties), corresponding to a branching fraction of B(B^0->rho0rho0) = (1.02 +- 0.30 (stat) +- 0.15 (syst)) x 10^{-6} with a significance of 3.4 standard deviations and a longitudinal polarization fraction fL = 0.21^{+0.18}_{-0.22} (stat) +- 0.15 (syst). We use the longitudinal polarization fraction to determine the Cabibbo-Kobayashi-Maskawa matrix angle phi_2 = (84.9 +- 13.5) degrees through an isospin analysis in the B->rhorho system. We furthermore find 149 +- 49 B^0->f0rho0 events, corresponding to B(B^0->f0rho0) x B(f0->pi+pi-) = (0.78 +- 0.22 (stat) +- 0.11 (syst)) x 10^{-6}, with a significance of 3.1 standard deviations. We find no other significant contribution with the same final state, and set upper limits at 90% confidence level on the (product) branching fractions, B(B^0->pi+pi-pi+pi-)rho0pi+pi-)<12.0 x 10^{-6}, B(B^0->f0pi+pi-) x B(f0->pi+pi-) f0f0) x B(f0->pi+pi-)^{2} < 0.2 x 10^{-6}.Comment: 21 pages, 20 figures, conference paper for the 2012th CKM workshop, submitted to PR