Nuclear-modification factor for open-heavy-flavor production at forward rapidity in Cu plus Cu collisions at root s(NN)=200 GeV

Background: Heavy-flavor production in p + p collisions is a good test of perturbative-quantum-chromodynamics (pQCD) calculations. Modification of heavy-flavor production in heavy-ion collisions relative to binary-collision scaling from p + p results, quantified with the nuclear-modification factor (R-AA), provides information on both cold-and hot-nuclear-matter effects. Midrapidity heavy-flavor R-AA measurements at the Relativistic Heavy Ion Collider have challenged parton-energy-loss models and resulted in upper limits on the viscosity-entropy ratio that are near the quantum lower bound. Such measurements have not been made in the forward-rapidity region. Purpose: Determine transverse-momentum (p(T)) spectra and the corresponding R-AA for muons from heavy-flavor meson decay in p + p and Cu + Cu collisions at root s(NN) = 200 GeV and y = 1.65. Method: Results are obtained using the semileptonic decay of heavy-flavor mesons into negative muons. The PHENIX muon-arm spectrometers measure the p(T) spectra of inclusive muon candidates. Backgrounds, primarily due to light hadrons, are determined with a Monte Carlo calculation using a set of input hadron distributions tuned to match measured-hadron distributions in the same detector and statistically subtracted. Results: The charm-production cross section in p + p collisions at root s = 200 GeV, integrated over p(T) and in the rapidity range 1.4 < y < 1.9, is found to be d(sigma e (e) over bar)/dy = 0.139 +/- 0.029 (stat)(-0.058)(+0.051) (syst) mb. This result is consistent with a perturbative fixed-order-plus-next-to-leading-log calculation within scale uncertainties and is also consistent with expectations based on the corresponding midrapidity charm-production cross section measured by PHENIX. The R-AA for heavy-flavor muons in Cu + Cu collisions is measured in three centrality bins for 1 < p(T) < 4 GeV/c. Suppression relative to binary-collision scaling (R-AA < 1) increases with centrality. Conclusions: Within experimental and theoretical uncertainties, the measured charm yield in p + p collisions is consistent with state-of-the-art pQCD calculations. Suppression in central Cu + Cu collisions suggests the presence of significant cold-nuclear-matter effects and final-state energy loss.

Glucocorticoid: Major Factor for Reduced Immunogenicity of 2009 Influenza A (H1N1) Vaccine in Patients with Juvenile Autoimmune Rheumatic Disease

Objective. To assess the immunogenicity and safety of non-adjuvanted influenza A H1N1/2009 vaccine in patients with juvenile autoimmune rheumatic disease (ARD) and healthy controls, because data are limited to the adult rheumatologic population. Method's. A total of 237 patients with juvenile ARD [juvenile systemic lupus erythematosus (JSLE), juvenile idiopathic arthritis (JIA), juvenile dermatomyositis (JDM), juvenile scleroderma, and vasculitis] and 91 healthy controls were vaccinated. Serology for anti-H1N1 was performed by hemagglutination inhibition assay. Seroprotection rate, seroconversion rate, and factor-increase in geometric mean titer (GMT) were calculated. Adverse events were evaluated. Results. Age was comparable in patients and controls (14.8 +/- 3.0 vs 14.6 +/- 3.7 years, respectively; p = 0.47). Three weeks after immunization, seroprotection rate (81.4% vs 95.6%; p = 0.0007), seroconversion rate (74.3 vs 95.6%; p < 0.0001), and the factor-increase in GMT (12.9 vs 20.3; p = 0.012) were significantly lower in patients with juvenile ARD versus controls. Subgroup analysis revealed reduced seroconversion rates in JSLE (p < 0.0001), JIA (p = 0.008), JDM (p = 0.025), and vasculitis (p = 0.017). Seroprotection (p < 0.0001) and GMT (p < 0.0001) were decreased only in JSLE. Glucocorticoid use and lymphopenia were associated with lower seroconversion rates (60.4 vs 82.9%; p = 0.0001; and 55.6 vs 77.2%; p = 0.012). Multivariate logistic regression including diseases, lymphopenia, glucocorticoid, and immunosuppressants demonstrated that only glucocorticoid use (p = 0.012) remained significant. Conclusion. This is the largest study to demonstrate a reduced but adequate immune response to H1N1 vaccine in patients with juvenile ARD. It identified current glucocorticoid use as the major factor for decreased antibody production. The short-term safety results support its routine recommendation for patients with juvenile ARD. ClinicalTrials.gov; NCT01151644. (First Release Nov 15 2011; J Rheumatol 2012;39:167-73; doi:10.3899/jrheum.110721)

Testing allele homogeneity: the problem of nested hypotheses

Background: The evaluation of associations between genotypes and diseases in a case-control framework plays an important role in genetic epidemiology. This paper focuses on the evaluation of the homogeneity of both genotypic and allelic frequencies. The traditional test that is used to check allelic homogeneity is known to be valid only under Hardy-Weinberg equilibrium, a property that may not hold in practice. Results: We first describe the flaws of the traditional (chi-squared) tests for both allelic and genotypic homogeneity. Besides the known problem of the allelic procedure, we show that whenever these tests are used, an incoherence may arise: sometimes the genotypic homogeneity hypothesis is not rejected, but the allelic hypothesis is. As we argue, this is logically impossible. Some methods that were recently proposed implicitly rely on the idea that this does not happen. In an attempt to correct this incoherence, we describe an alternative frequentist approach that is appropriate even when Hardy-Weinberg equilibrium does not hold. It is then shown that the problem remains and is intrinsic of frequentist procedures. Finally, we introduce the Full Bayesian Significance Test to test both hypotheses and prove that the incoherence cannot happen with these new tests. To illustrate this, all five tests are applied to real and simulated datasets. Using the celebrated power analysis, we show that the Bayesian method is comparable to the frequentist one and has the advantage of being coherent. Conclusions: Contrary to more traditional approaches, the Full Bayesian Significance Test for association studies provides a simple, coherent and powerful tool for detecting associations.

Phylogeny of Lundia (Bignoniaceae) based on ndhF and PepC sequences

The circumscription of genera belonging to tribe Bignonieae (Bignoniaceae) has traditionally been complex, with only a few genera having stable circumscriptions in the various classification systems proposed for the tribe. The genus Lundia, for instance, is well characterized by a series of morphological synapomorphies and its circumscription has remained quite stable throughout its history. Despite the stable circumscription of Lundia, the circumscription of species within the genus has remained problematic. This study aims to reconstruct the phylogeny of Lundia in order to refine species circumscriptions, gain a better understanding of relationships between taxa, and identify potential morphological synapomorphies for species and major clades. We sampled 26 accessions representing 13 species of Lundia, and 5 outgroups, and reconstructed the phylogeny of the genus using a chloroplast (ndhF) and a nuclear marker (PepC). Data derived from sequences of the individual loci were analyzed using parsimony and Bayesian inference, and the combined molecular dataset was analyzed with Bayesian methods. The monophyly of Lundia nitidula, a species with a particularly complex circumscription, was tested using Shimodaira-Hasegawa (SH) test and the approximately unbiased test for phylogenetic tree selection (AU test). In addition, 40 morphological characters were mapped onto the tree that resulted from the analysis of the combined molecular dataset in order to identify morphological synapomorphies of individual species and major clades. Lundia and most species currently recognized within the genus were strongly supported as monophyletic in all analyses. One species, Lundia nitidula, was not resolved as monophyletic, but the monophyly of this species was not rejected by the AU and SH tests. Lundia sect. Eriolundia is resolved as paraphyletic in all analyses, while Lundia sect. Eulundia is monophyletic and supported by the same morphological characters traditionally used to circumscribe this section. The phylogeny of Lundia contributed important information for a better circumscription of species and served as basis the taxonomic revision of the genus.

Structural features of lignin obtained at different alkaline oxidation conditions from sugarcane bagasse

Lignin is a macromolecule frequently obtained as residue during technological processing of biomass. Modifications in chemical structure of lignin generate valuable products, some with particular and unique characteristics. One of the available methods for modification of industrial lignin is oxidation by hydrogen peroxide. In this work, we conducted systematic studies of the oxidation process that were carried out at various pHs and oxidizing agent concentrations. Biophysical, biochemical, structural properties of the oxidized lignin were analyzed by UV spectrophotometry, Fourier transform infrared spectroscopy, scanning electron microscopy and small angle X-ray scattering. Our results reveal that lignin oxidized with 9.1% H(2)O(2) (m/v) at pH 13.3 has the highest fragmentation, oxidation degree and stability. Although this processing condition might be considered quite severe, we have concluded that the stability of the obtained oxidized lignin was greatly increased. Therefore, the identified processing conditions of oxidation may be of practical interest for industrial applications. (C) 2011 Elsevier B.V. All rights reserved.

Phylogeographic Analysis of HIV-1 Subtype C Dissemination in Southern Brazil

The HIV-1 subtype C has spread efficiently in the southern states of Brazil (Rio Grande do Sul, Santa Catarina and Parana). Phylogeographic studies indicate that the subtype C epidemic in southern Brazil was initiated by the introduction of a single founder virus population at some time point between 1960 and 1980, but little is known about the spatial dynamics of viral spread. A total of 135 Brazilian HIV-1 subtype C pol sequences collected from 1992 to 2009 at the three southern state capitals (Porto Alegre, Florianopolis and Curitiba) were analyzed. Maximum-likelihood and Bayesian methods were used to explore the degree of phylogenetic mixing of subtype C sequences from different cities and to reconstruct the geographical pattern of viral spread in this country region. Phylogeographic analyses supported the monophyletic origin of the HIV-1 subtype C clade circulating in southern Brazil and placed the root of that clade in Curitiba (Parana state). This analysis further suggested that Florianopolis (Santa Catarina state) is an important staging post in the subtype C dissemination displaying high viral migration rates from and to the other cities, while viral flux between Curitiba and Porto Alegre (Rio Grande do Sul state) is very low. We found a positive correlation (r(2) = 0.64) between routine travel and viral migration rates among localities. Despite the intense viral movement, phylogenetic intermixing of subtype C sequences from different Brazilian cities is lower than expected by chance. Notably, a high proportion (67%) of subtype C sequences from Porto Alegre branched within a single local monophyletic sub-cluster. These results suggest that the HIV-1 subtype C epidemic in southern Brazil has been shaped by both frequent viral migration among states and in situ dissemination of local clades.

Measurement of Direct Photons in Au plus Au Collisions at root s(NN)=200 GeV

We report the measurement of direct photons at midrapidity in Au + Au collisions at root s(NN) = 200 GeV. The direct photon signal was extracted for the transverse momentum range of 4 GeV/c < pT < 22 GeV/c, using a statistical method to subtract decay photons from the inclusive photon sample. The direct photon nuclear modification factor R-AA was calculated as a function of p(T) for different Au + Au collision centralities using the measured p + p direct photon spectrum and compared to theoretical predictions. R-AA was found to be consistent with unity for all centralities over the entire measured pT range. Theoretical models that account for modifications of initial direct photon production due to modified parton distribution functions in Au and the different isospin composition of the nuclei predict a modest change of R-AA from unity. They are consistent with the data. Models with compensating effects of the quark-gluon plasma on high-energy photons, such as suppression of jet-fragmentation photons and induced-photon bremsstrahlung from partons traversing the medium, are also consistent with this measurement.

Production of Muons from Heavy Flavor Decays at Forward Rapidity in pp and Pb-Pb Collisions at root s(NN)=2.76 TeV

The ALICE Collaboration has measured the inclusive production of muons from heavy-flavor decays at forward rapidity, 2.5 < y < 4, in pp and Pb-Pb collisions at root s(NN) = 2.76 TeV. The p(t)-differential inclusive cross section of muons from heavy-flavor decays in pp collisions is compared to perturbative QCD calculations. The nuclear modification factor is studied as a function of p(t) and collision centrality. A weak suppression is measured in peripheral collisions. In the most central collisions, a suppression of a factor of about 3-4 is observed in 6 < p(t) < 10 GeV/c. The suppression shows no significant p(t) dependence.

Phylodynamics and Dispersal of HRSV Entails Its Permanence in the General Population in between Yearly Outbreaks in Children

Background: Human respiratory syncytial virus (HRSV) is one of the major etiologic agents of respiratory tract infections among children worldwide. Methodology/Principal Findings: Here through a comprehensive analysis of the two major HRSV groups A and B (n = 1983) which comprise of several genotypes, we present a complex pattern of population dynamics of HRSV over a time period of 50 years (1956-2006). Circulation pattern of HRSV revealed a series of expansions and fluctuations of co-circulating lineages with a predominance of HRSVA. Positively selected amino acid substitutions of the G glycoprotein occurred upon population growth of GB3 with a 60-nucleotide insertion (GB3 Insert), while other genotypes acquired substitutions upon both population growth and decrease, thus possibly reflecting a role for immune selected epitopes in linkage to the traced substitution sites that may have important relevance for vaccine design. Analysis evidenced the co-circulation and predominance of distinct HRSV genotypes in Brazil and suggested a year-round presence of the virus. In Brazil, GA2 and GA5 were the main culprits of HRSV outbreaks until recently, when the GB3 Insert became highly prevalent. Using Bayesian methods, we determined the dispersal patterns of genotypes through several inferred migratory routes. Conclusions/Significance: Genotypes spread across continents and between neighboring areas. Crucially, genotypes also remained at any given region for extended periods, independent of seasonal outbreaks possibly maintained by re-infecting the general population.

J/psi Suppression at Forward Rapidity in Pb-Pb Collisions at root s(NN)=2.76 TeV

The ALICE experiment has measured the inclusive J/psi production in Pb-Pb collisions at root s(NN) = 2.76 TeV down to zero transverse momentum in the rapidity range 2.5 < y < 4. A suppression of the inclusive J/psi yield in Pb-Pb is observed with respect to the one measured in pp collisions scaled by the number of binary nucleon-nucleon collisions. The nuclear modification factor, integrated over the 0%-80% most central collisions, is 0.545 +/- 0.032(stat) +/- 0.083dsyst_ and does not exhibit a significant dependence on the collision centrality. These features appear significantly different from measurements at lower collision energies. Models including J/psi production from charm quarks in a deconfined partonic phase can describe our data.

Cold-Nuclear-Matter Effects on Heavy-Quark Production in d+Au Collisions at root S-NN=200 GeV

The PHENIX experiment has measured electrons and positrons at midrapidity from the decays of hadrons containing charm and bottom quarks produced in d + Au and p + p collisions at root S-NN = 200 GeV in the transverse-momentum range 0.85 <= p(T)(e) <= 8.5 GeV/c. In central d + Au collisions, the nuclear modification factor R-dA at 1.5 < p(T) < 5 GeV/c displays evidence of enhancement of these electrons, relative to those produced in p + p collisions, and shows that the mass-dependent Cronin enhancement observed at the Relativistic Heavy Ion Collider extends to the heavy D meson family. A comparison with the neutral-pion data suggests that the difference in cold-nuclear-matter effects on light- and heavy-flavor mesons could contribute to the observed differences between the pi(0) and heavy-flavor-electron nuclear modification factors R-AA. DOI: 10.1103/PhysRevLett.109.242301

Suppression of high transverse momentum D mesons in central Pb-Pb collisions at root s(NN)=2.76 TeV

The production of the prompt charm mesons D-0, D+, D*(+), and their antiparticles, was measured with the ALICE detector in Pb-Pb collisions at the LHC, at a centre-of-mass energy root s(NN) = 2.76 TeV per nucleon-nucleon collision. The p(t)-differential production yields in the range 2 < p(t) < 16 GeV/c at central rapidity, vertical bar y vertical bar < 0.5, were used to calculate the nuclear modification factor R-AA with respect to a proton-proton reference obtained from the cross section measured at root s = 7 TeV and scaled to root s = 2.76 TeV. For the three meson species, R-AA shows a suppression by a factor 3-4, for transverse momenta larger than 5 GeV/c in the 20% most central collisions. The suppression is reduced for peripheral collisions.

Purification of coagulation factor VIII using chromatographic methods. Direct chromatography of plasma in anion exchange resins

Coagulation factor VIII (FVIII) concentrates are used in the treatment of patients with Hemophilia A. Human FVIII was purified directly from plasma using anion exchange chromatography followed by gel filtration. Three Q-Sepharose resins were tested, resulting in 40% recovery of FVIII activity using Q-Sepharose XL resin, about 80% using Q-Sepharose Fast Flow and 70% using the Q-Sepharose Big Beads. The vitamin K-dependent coagulation factors co-eluted with FVIII from the anion exchange columns. In the second step of purification, when Sepharose 6FF was used, 70% of FVIII activity was recovered free from vitamin K-dependent factors.

Microbiological quality and safety of minimally processed vegetables marketed in Campinas, SP-Brazil, as assessed by traditional and alternative methods

In this study, a total of 172 samples of minimally processed vegetables (MPV) were collected from supermarkets in the city of Campinas, Brazil. The MPV were analyzed using traditional and/or alternative methods for total aerobic mesophilic bacteria, total coliforms, Escherichia coil, coagulase positive staphylococci, Salmonella and Listeria monocytogenes. All the MPV analyzed presented populations of aerobic mesophilic microorganisms and total coliforms were >4 log(10) CFU/g and 1.0-3.4 log(10) CFU/g, respectively. E. coil was enumerated in only 10 samples out of 172 collected, while none of the 172 samples of MPV presented contamination by coagulase positive Staphylococcus (<10(1) CFU/g). Among the four methods used for detection of Salmonella in MPV (Vidas, 1,2 Test, Reveal, and Traditional), when Reveal was used a total of 29 positive samples were reported. For L monocytogenes, the four methods tested (Vidas, Vip, Reveal, and traditional) performed similarly. The presence of Salmonella and L monocytogenes in MPV was confirmed in one (watercress) and two samples (watercress and escarole), respectively. In conclusion, it has been observed that the microbiological quality of MPV commercialized in Campinas is generally satisfactory. Besides, the choice of microbiological method should be based not only on resource and time issues, but also on parameters such as sensitivity and specificity for the specific foods under ahalysis. (C) 2012 Elsevier Ltd. All rights reserved.

Divertor map with freedom of geometry and safety factor profile

An explicit, area-preserving and integrable magnetic field line map for a single-null divertor tokamak is obtained using a trajectory integration method to represent equilibrium magnetic surfaces. The magnetic surfaces obtained from the map are capable of fitting different geometries with freely specified position of the X-point, by varying free model parameters. The safety factor profile of the map is independent of the geometric parameters and can also be chosen arbitrarily. The divertor integrable map is composed of a nonintegrable map that simulates the effect of external symmetry-breaking resonances, so as to generate a chaotic region near the separatrix passing through the X-point. The composed field line map is used to analyze escape patterns (the connection length distribution and magnetic footprints on the divertor plate) for two equilibrium configurations with different magnetic shear profiles at the plasma edge.