Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups

We explored the epidemic history of HIV-1 subtype B in the United Kingdom using statistical methods that infer the population history of pathogens from sampled gene sequence data. Phylogenetic analysis of HIV-1 pol gene sequences from Britain showed at least six large transmission chains, indicating a genetically variable, but epidemiologically homogeneous, epidemic among men having sex with men. Through coalescent-based analysis we showed that these chains arose through separate introductions of subtype B strains into the United Kingdom in the early-to-mid 1980s. After an initial period of exponential growth, the rate of spread generally slowed in the early 1990s, which is more likely to correlate with behaviour change than with reduced infectiousness resulting from highly active antiretroviral therapy. Our results provide new insights into the complexity of HIV-1 epidemics that must be considered when developing HIV monitoring and prevention initiatives

A Longitudinal Study Understanding Interpersonal Behavior Changes from Recreation Student to Professional

Personality instrument have been used in college classrooms to help students understand how their interpersonal behaviors will effect their professional work. This investigation assessed 1) how students majoring in commercial recreation have changed in personality over a five year time frame, from traditional college student to practicing professional and 2) which demographic variables have influenced these changes. Forty-six students completed a self-assessment personality inventory, Fundamental Interpersonal Relations OrientationBehavior (FIRO-B). Five years later, the same individuals completed the FIRO-B and demographic questionnaire. Twenty-six responded. The findings suggest a majority of students who changed in personality categories, however, these changes were not statistically significant. Additionally, demographic variables showed no relationship with the changes in personality. These findings indicate the use of personality assessments in undergraduate courses may be a predictor of interpersonal behavior in the professional setting and may be helpful in preparing students to understand their professional style

Inferring pandemic growth rates from sequence data

Using sequence data to infer population dynamics is playing an increasing role in the analysis of outbreaks. The most common methods in use, based on coalescent inference, have been widely used but not extensively tested against simulated epidemics. Here, we use simulated data to test the ability of both parametric and non-parametric methods for inference of effective population size (coded in the popular BEAST package) to reconstruct epidemic dynamics. We consider a range of simulations centred on scenarios considered plausible for pandemic influenza, but our conclusions are generic for any exponentially growing epidemic. We highlight systematic biases in non-parametric effective population size estimation. The most prominent such bias leads to the false inference of slowing of epidemic spread in the recent past even when the real epidemic is growing exponentially. We suggest some sampling strategies that could reduce (but not eliminate) some of the biases. Parametric methods can correct for these biases if the infected population size is large. We also explore how some poor sampling strategies (e.g. that over-represent epidemiologically linked clusters of cases) could dramatically exacerbate bias in an uncontrolled manner. Finally, we present a simple diagnostic indicator, based on coalescent density and which can easily be applied to reconstructed phylogenies, that identifies time-periods for which effective population size estimates are less likely to be biased. We illustrate this with an application to the 2009 H1N1 pandemic

Inhibition of Vaginal Lactobacilli by a Bacteriocin-Like Inhibitor Produced by Enterococcus faecium 62-6: Potential Significance for Bacterial Vaginosis

Objective: Bacterial vaginosis (BV) is characterized by a shift in vaginal tract ecology, which includes a decrease in the concentration and/or prevalence of facultative lactobacilli. Currently, mechanisms which could account for the disappearance of lactobacilli are not well understood. The objective of this study was to determine whether vaginal streptococci/enterococci can produce bacteriocin-like inhibitors antagonistic to vaginal lactobacilli. Methods: Seventy strains of vaginal streptococci or enterococci were tested for antagonistic activities against vaginal lactobacilli using the deferred antagonism technique. Results: One strain, Enterococcus faecium 62-6, which strongly inhibited growth of lactobacilli was selected for further characterization. The spectrum of inhibitory activity of strain 62-6 included Gram-positive organisms from the vaginal environment, although native lactobacilli from the same host were resistant to inhibitor action. Following growth inMRSbroth the strain 62-6 inhibitor was shown to be heat- (100℃, 30 minutes), cold- (4℃, less than 114 days) and pH- (4–7) stable. The sensitivity of inhibitor-containing supernatants to pepsin and α-chymotrypsin suggested an essential proteinaceous component. The inhibitor was sensitive to lipase but resistant to lysozyme. Dialysis of inhibitor-containing culture supernatants suggested a molecular mass greater than 12 000 Da. All physicochemical properties were consistent with its classification as a bacteriocin-like inhibitor. Kinetic assays demonstrated a sharp onset of inhibitor production coinciding with a concentration of 62-6 of 10(7) cfu/ml, suggesting that production may be regulated by quorum sensing. Conclusions: These results may have clinical significance as a novel mechanism to account for the decline of vaginal Lactobacillus populations and contribute to both the establishment and recurrence of BV

Laser Calibration System for Time of Flight Scintillator Arrays

A laser calibration system was developed for monitoring and calibrating time of flight (TOF) scintillating detector arrays. The system includes setups for both small- and large-scale scintillator arrays. Following test-bench characterization, the laser system was recently commissioned in experimental Hall B at the Thomas Jefferson National Accelerator Facility for use on the new Backward Angle Neutron Detector (BAND) scintillator array. The system successfully provided time walk corrections, absolute time calibration, and TOF drift correction for the scintillators in BAND. This showcases the general applicability of the system for use on high-precision TOF detectors.Comment: 11 pages, 11 figure

Reverse immunodynamics : a new method for identifying targets of protective immunity

Despite a dramatic increase in our ability to catalogue variation among pathogen genomes, we have made far fewer advances in using this information to identify targets of protective immunity. Epidemiological models predict that strong immune selection can cause antigenic variants to structure into genetically discordant sets of antigenic types (e.g. serotypes). A corollary of this theory is that targets of immunity may be identified by searching for non-overlapping associations of amino acids among co-circulating antigenic variants. We propose a novel population genetics methodology that combines such predictions with phylogenetic analyses to identify genetic loci (epitopes) under strong immune selection. We apply this concept to the AMA-1 protein of the malaria parasite Plasmodium falciparum and find evidence of epitopes among certain regions of low variability which could render them ideal vaccine candidates. The proposed method can be applied to a myriad of multi-strain pathogens for which vast amounts of genetic data has been collected in recent years