Can Directionality of HIV Transmission be Predicted by Next-Generation Sequencing Data?

Background: We evaluated use of phylogenetic methods to predict the direction of human immunodeficiency virus (HIV) transmission. Methods: For 33 pairs of HIV-infected patients (hereafter, "index patients") and their partners who acquired genetically linked HIV infection during the study, samples were collected from partners and index patients close to the time when the partner seroconverted (hereafter, "SC samples"); for 31 pairs, samples collected from the index patient at an earlier time point (hereafter, "early index samples") were also available. Phylogenies were inferred using env next-generation sequences (1 tree per pair/subtype). The direction of transmission (DoT) predicted from each tree was classified as correct or incorrect on the basis of which sequences (those from the index patient or the partner) were closest to the root. DoT was also assessed using maximum parsimony to infer ancestral node states for 100 bootstrap trees. Results: DoT was predicted correctly for both single-pair and subtype-specific trees in 22 pairs (67%) by using SC samples and in 23 pairs (74%) by using early index samples. DoT was predicted incorrectly for 4 pairs (15%) by using SC or early index samples. In the bootstrap analysis, DoT was predicted correctly for 18 pairs (55%) by using SC samples and for 24 pairs (73%) by using early index samples. DoT was predicted incorrectly for 7 pairs (21%) by using SC samples and for 4 pairs (13%) by using early index samples. Conclusions: Phylogenetic methods based solely on the tree topology of HIV env sequences, particularly without consideration of phylogenetic uncertainty, may be insufficient for determining DoT

Higgs and neutrino sector, EDM and epsilon_K in a spontaneously CP and R-parity breaking supersymmetric model

We construct an extension of the supersymmetric standard model where both CP symmetry and R-parity are spontaneously broken. We study the electroweak symmetry breaking sector of the model and find minima consistent with the experimental bounds on Higgs boson masses. Neutrino masses and mixing angles are generated through both seesaw and bilinear R-parity violation. We show that the hierarchical mass pattern is obtained, and mixings are consistent with measured values. Due to the spontaneous CP and R-parity violation, the neutrino sector is CP violating, and we calculate the corresponding phase. We further restrict the parameter space to agree with the limits on the electric dipole moment of the neutron. Finally, we study the CP violation parameter epsilon_K in the kaon system and show that we obtain results consistent with the experimental value.Comment: 13 pages, 7 figures, submitted to EPJ

Search for heavy long-lived charged R-hadrons with the ATLAS detector in 3.2 fb(-1) of proton-proton collision data at root s=13 TeV

A search for heavy long-lived charged R-hadrons is reported using a data sample corresponding to 3.2 fb−1 of proton–proton collisions at √s = 13 TeV collected by the ATLAS experiment at the Large Hadron Collider at CERN. The search is based on observables related to large ionisation losses and slow propagation velocities, which are signatures of heavy charged particles travelling significantly slower than the speed of light. No significant deviations from the expected background are observed. Upper limits at 95% confidence level are provided on the production cross section of long-lived R-hadrons in the mass range from 600 GeV to 2000 GeV and gluino, bottom and top squark masses are excluded up to 1580 GeV, 805 GeV and 890 GeV, respectively

The absolute flux of protons and helium at the top of the atmosphere using IMAX

The cosmic-ray proton and helium spectra from 0.2 GeV nucleon^(-1) to about 200 GeV nucleon^(-1) have been measured with the balloon-borne experiment Isotope Matter-Antimatter Experiment (IMAX) launched from Lynn Lake, Manitoba, Canada, in 1992. IMAX was designed to search for antiprotons and light isotopes using a superconducting magnet spectrometer together with scintillators, a time-of-flight system, and Cherenkov detectors. Using redundant detectors, an extensive examination of the instrument efficiency was carried out. We present here the absolute spectra of protons and helium corrected to the top of the atmosphere and to interstellar space. If demodulated with a solar modulation parameter of Φ = 750 MV, the measured interstellar spectra between 20 and 200 GV can be represented by a power law in rigidity, with (1.42 ± 0.21) × 10^4R^(-2.71±0.04) (m^2 GV s sr)^(-1) for protons and (3.15 ± 1.03) × 10^3R^(-2.79±0.08) (m^2 GV s sr)^(-1) for helium

Molecular Properties and Pharmacokinetic Behavior of Cetirizine, a Zwitterionic H 1 -Receptor Antagonist

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Electroweak measurements in electron–positron collisions at w-boson-pair energies at lep

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