A36 Prevalence of HIV-1 subtypes in Slovenia with an emphasis on molecular and phylogenetic investigation of subtype A

21st International BioInformatics Workshop on Virus Evolution and Molecular EpidemiologyIn Slovenia, a small country in Central Europe, less than 1 per 1,000 inhabitants are estimated to be infected with HIV-1. As in most of the Central and Western European countries, the majority of patients diagnosed with HIV-1 are infected with subtype B. However, due to migration, other subtypes can become more prevalent in the country. The aim of this study was to determine HIV-1 subtypes circulating in Slovenia and to further examine the molecular epidemiology of subtype A. A total of 367 Slovenian HIV-1 sequences were included in the study, representing 58% of all patients diagnosed in Slovenia until the end of the year 2013. Subtype was assigned by employing different HIV subtyping tools coupled with Maximum likelihood phylogenetic analysis. The latter was performed to examine the molecular epidemiology of subtype A as well. Identified clusters of Slovenian subtype A sequences were further analyzed for the determination of the time of the most recent common ancestor (tMRCA) by using Monte Carlo Markov chain (MCMC) method available in BEAST 2.1.3 software. We determined the prevalence of subtype B to be 85.3%, while subtype A was the most prevalent non-B subtype found in 18 patients (4.9%), followed by CRF02_AG (2.4%), subtype C (1.1%), subtypes D, G and CRF01_AE (0.8% each) and subtypes F1 and CRF22_01A1 (0.3% each). Subtypes could not be assigned to 12 sequences (3.3%). The phylogenetic tree obtained by ML analysis of the subtype A and subtype A related recombinants revealed that Slovenian sequences were part of 6 major international clusters. Two clusters consisting only of Slovenian sequences were identified and thus additional MCMC analysis was employed. Results of a Slovenian cluster of 4 subtype A sequences showed a posterior probability value of 1 and a tMRCA between the years 1985 and 2008, with a mean in the year 2001. In conclusion, in a Central European country, where subtype B predominates, the second most common subtype was found to be subtype A. Non-B subtypes were observed in one out of seven patients in Slovenia, a fraction that is not negligible, thus proving importance of surveillance of HIV subtype diversity and corresponding molecular epidemiology of non-B subtypes.publishersversionpublishe

One-health simulation modelling : assessment of control strategies against the spread of influenza between swine and human populations using NAADSM

Simulation models implemented using a range of parameters offer a useful approach to identifying effective disease intervention strategies. The objective of this study was to investigate the effects of key control strategies to mitigate the simultaneous spread of influenza among and between swine and human populations. We used the pandemic H1N1 2009 virus as a case study. The study population included swine herds (488 herds) and households-of-people (29 707 households) within a county in Ontario, Canada. Households were categorized as: (i) rural households with swine workers, (ii) rural households without swine workers and (iii) urban households without swine workers. Seventy-two scenarios were investigated based on a combination of the parameters of speed of detection and control strategies, such as quarantine strategy, effectiveness of movement restriction and ring vaccination strategy, all assessed at three levels of transmissibility of the virus at the swine-human interface. Results showed that the speed of detection of the infected units combined with the quarantine strategy had the largest impact on the duration and size of outbreaks. A combination of fast to moderate speed of the detection (where infected units were detected within 5-10 days since first infection) and quarantine of the detected units alone contained the outbreak within the swine population in most of the simulated outbreaks. Ring vaccination had no added beneficial effect. In conclusion, our study suggests that the early detection (and therefore effective surveillance) and effective quarantine had the largest impact in the control of the influenza spread, consistent with earlier studies. To our knowledge, no study had previously assessed the impact of the combination of different intervention strategies involving the simultaneous spread of influenza between swine and human populations

Detecting Latin-Based Medical Terminology in Croatian Texts

No matter what the main language of texts in the medical domain is, there is always an evidence of the usage of Latin-derived words and formative elements in terminology development. Generally speaking, this usage presents language-specific morpho-semantic behaviors in forming both technical-scientific and common-usage words. Nevertheless, this usage of Latin in Croatian medical texts does not seem consistent due to the fact that diferent mechanisms of word formation may be applied to the same term. In our pursuit to map all the diferent occurrences of the same concept to only one, we propose a model designed within NooJ and based on dictionaries and morphological grammars. Starting from the manual detection of nouns and their variations, we recognize some word formation mechanisms and develop grammars suitable to recognize Latinisms and Croatinized Latin medical terminology

Rate of convergence of truncated stochastic approximation procedures with moving bounds

The paper is concerned with stochastic approximation procedures having three main characteristics: truncations with random moving bounds, a matrix valued random step-size sequence, and a dynamically changing random regression function. We study convergence and rate of convergence. Main results are supplemented with corollaries to establish various sets of sufficient conditions, with the main emphases on the parametric statistical estimation. The theory is illustrated by examples and special cases.Comment: 30 page

Longitudinal double-spin asymmetry and cross section for inclusive jet production in polarized proton collisions at sqrt(s) = 200 GeV

We report a measurement of the longitudinal double-spin asymmetry A_LL and the differential cross section for inclusive midrapidity jet production in polarized proton collisions at sqrt(s)=200 GeV. The cross section data cover transverse momenta 5 < pT < 50 GeV/c and agree with next-to-leading order perturbative QCD evaluations. The A_LL data cover 5 < pT < 17 GeV/c and disfavor at 98% C.L. maximal positive gluon polarization in the polarized nucleon.Comment: 6 pages, 3 figures. Minor changes from review process in Phys. Rev. Lett. Plain text tables of data in STAR publications may be found at http://www.star.bnl.gov/central/publications

Longitudinal double-spin asymmetry for inclusive jet production in p+p collisions at sqrt(s)=200 GeV

We report a new STAR measurement of the longitudinal double-spin asymmetry A_LL for inclusive jet production at mid-rapidity in polarized p+p collisions at a center-of-mass energy of sqrt(s) = 200 GeV. The data, which cover jet transverse momenta 5 < p_T < 30 GeV/c, are substantially more precise than previous measurements. They provide significant new constraints on the gluon spin contribution to the nucleon spin through the comparison to predictions derived from one global fit of polarized deep-inelastic scattering measurements.Comment: 7 pages, 4 figures + 1 tabl

Identified baryon and meson distributions at large transverse momenta from Au+Au collisions at sNN=200\sqrt{s_{_{NN}}} = 200 GeV

Transverse momentum spectra of $\pi^{\pm}$, $p$ and $\bar{p}$ up to 12 GeV/c at mid-rapidity in centrality selected Au+Au collisions at $\sqrt{s_{_{NN}}} = 200$ GeV are presented. In central Au+Au collisions, both $\pi^{\pm}$ and $p(\bar{p})$ show significant suppression with respect to binary scaling at $p_T >$ 4 GeV/c. Protons and anti-protons are less suppressed than $\pi^{\pm}$, in the range 1.5 $< p_{T} <$6 GeV/c. The $\pi^-/\pi^+$ and $\bar{p}/p$ ratios show at most a weak $p_T$ dependence and no significant centrality dependence. The $p/\pi$ ratios in central Au+Au collisions approach the values in p+p and d+Au collisions at $p_T >$ 5 GeV/c. The results at high $p_T$ indicate that the partonic sources of $\pi^{\pm}$, $p$ and $\bar{p}$ have similar energy loss when traversing the nuclear medium.Comment: 6 pages, 4 figure

System-Size Independence of Directed Flow Measured at the BNL Relativistic Heavy-Ion Collider

We measure directed flow (ν_1) for charged particles in Au+Au and Cu+Cu collisions at √S_(NN)=200 and 62.4 GeV, as a function of pseudorapidity (η), transverse momentum (p_t), and collision centrality, based on data from the STAR experiment. We find that the directed flow depends on the incident energy but, contrary to all available model implementations, not on the size of the colliding system at a given centrality. We extend the validity of the limiting fragmentation concept to ν_1 in different collision systems, and investigate possible explanations for the observed sign change in ν_1(p_t)

Spin alignment measurements of the K∗0(892)K^{*0}(892) and ϕ(1020)\phi(1020) vector mesons at RHIC

We present the first spin alignment measurements for the $K^{*0}(892)$ and $\phi(1020)$ vector mesons produced at mid-rapidity with transverse momenta up to 5 GeV/c at $\sqrt{s_{NN}}$ = 200 GeV at RHIC. The diagonal spin density matrix elements with respect to the reaction plane in Au+Au collisions are $\rho_{00}$ = 0.32 $\pm$ 0.04 (stat) $\pm$ 0.09 (syst) for the $K^{*0}$ ($0.8<p_T<5.0$ GeV/c) and $\rho_{00}$ = 0.34 $\pm$ 0.02 (stat) $\pm$ 0.03 (syst) for the $\phi$ ($0.4<p_T<5.0$ GeV/c), and are constant with transverse momentum and collision centrality. The data are consistent with the unpolarized expectation of 1/3 and thus no evidence is found for the transfer of the orbital angular momentum of the colliding system to the vector meson spins. Spin alignments for $K^{*0}$ and $\phi$ in Au+Au collisions were also measured with respect to the particle's production plane. The $\phi$ result, $\rho_{00}$ = 0.41 $\pm$ 0.02 (stat) $\pm$ 0.04 (syst), is consistent with that in p+p collisions, $\rho_{00}$ = 0.39 $\pm$ 0.03 (stat) $\pm$ 0.06 (syst), also measured in this work. The measurements thus constrain the possible size of polarization phenomena in the production dynamics of vector mesons.Comment: 7 pages, 4 figures. fig.1 updated; one more reference added, one typo corrected, published in PRC.77.06190

Strangelet Search in AuAu Collisions at 200 GeV

We have searched for strangelets in a triggered sample of 61 million central (top 4%) Au+Au collisions at \sNN = 200 GeV near beam rapidities at the STAR detector. We have sensitivity to metastable strangelets with lifetimes of order $\geq 0.1 ns$, in contrast to limits over ten times longer in AGS studies and longer still at the SPS. Upper limits of a few 10^{-6} to 10^{-7} per central Au+Au collision are set for strangelets with mass ${}^{>}_{\sim}30$ GeV/c^{2}.Comment: As publishe