Phylodynamics of HIV-1 from a Phase-III AIDS Vaccine Trial in North America

In 2003, a phase III placebo-controlled trial (VAX004) of a candidate HIV-1 vaccine (AIDSVAX B/B) was completed in 5,403 volunteers at high risk for HIV-1 infection from North America and the Netherlands. A total of 368 individuals became infected with HIV-1 during the trial. The envelope glycoprotein gene (gp120) from the HIV-1 subtype B viruses infecting 349 patients was sequenced from clinical samples taken as close as possible to the time of diagnosis, rendering a final data set of 1,047 sequences (1,032 from North America and 15 from the Netherlands). Here, we used these data in combination with other sequences available in public databases to assess HIV-1 variation as a function of vaccination treatment, geographic region, race, risk behavior, and viral load. Viral samples did not show any phylogenetic structure for any of these factors, but individuals with different viral loads showed significant differences (P = 0.009) in genetic diversity. The estimated time of emergence of HIV-1 subtype B was 1966–1970. Despite the fact that the number of AIDS cases has decreased in North America since the early 90s, HIV-1 genetic diversity seems to have remained almost constant over time. This study represents one of the largest molecular epidemiologic surveys of viruses responsible for new HIV-1 infections in North America and could help the selection of epidemiologically representative vaccine antigens to include in the next generation of candidate HIV-1 vaccines

Using a Tablet-Based App to Deliver Evidence-Based Practices for Suicidal Patients in the Emergency Department: Pilot Randomized Controlled Trial

BACKGROUND: Emergency departments (EDs) have the potential to provide evidence-based practices for suicide prevention to patients who are acutely suicidal. However, few EDs have adequate time and personnel resources to deliver recommended evidence-based assessment and interventions. To raise the clinical standard of care for patients who are suicidal and seeking psychiatric crisis services in the ED, we developed Jaspr Health, a tablet-based app for direct use by such patients, which enables the delivery of 4 evidence-based practices. OBJECTIVE: This study aims to evaluate the feasibility, acceptability, and effectiveness of Jaspr Health among suicidal adults in EDs. METHODS: Patients who were acutely suicidal and seeking psychiatric crisis services participated in an unblinded pilot randomized controlled trial while in the ED. Participants were randomly assigned to Jaspr Health (n=14) or care as usual (control; n=17) groups. Participants were assessed at baseline, and a 2-hour posttest using self-report measures and a semistructured interview were conducted. RESULTS: Conditions differed significantly at baseline with regard to age but not other demographic variables or baseline measures. On average, participants had been in the ED for 17 hours before enrolling in the study. Over their lifetime, 84% (26/31) of the sample had made a suicide attempt (mean 3.4, SD 6.4) and 61% (19/31) had engaged in nonsuicidal self-injurious behaviors, with an average rate of 8.8 times in the past 3 months. All established feasibility and acceptability criteria were met: no adverse events occurred, participants\u27 app use was high, Jaspr Health app user satisfaction ratings were high, and all participants using Jaspr Health recommended its use for other suicidal ED patients. Comparisons between study conditions provide preliminary support for the effectiveness of the app: participants using Jaspr Health reported a statistically significant increase in receiving 4 evidence-based suicide prevention interventions and overall satisfaction ratings with their ED experience. In addition, significant decreases in distress and agitation, along with significant increases in learning to cope more effectively with current and future suicidal thoughts, were observed among participants using Jaspr Health compared with those receiving care as usual. CONCLUSIONS: Even with limited statistical power, the results showed that Jaspr Health is feasible, acceptable, and clinically effective for use by ED patients who are acutely suicidal and seeking ED-based psychiatric crisis services. TRIAL REGISTRATION: ClinicalTrials.gov NCT03584386; https://clinicaltrials.gov/ct2/show/NCT03584386

Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

During adaptive radiation events, characters can arise multiple times due to parallel evolution, but transfer of traits through hybridization provides an alternative explanation for the same character appearing in apparently non-sister lineages. The signature of hybridization can be detected in incongruence between phylogenies derived from different markers, or from the presence of two divergent versions of a nuclear marker such as ITS within one individual.In this study, we cloned and sequenced ITS regions for 30 species of the genus Rheum, and compared them with a cpDNA phylogeny. Seven species contained two divergent copies of ITS that resolved in different clades from one another in each case, indicating hybridization events too recent for concerted evolution to have homogenised the ITS sequences. Hybridization was also indicated in at least two further species via incongruence in their position between ITS and cpDNA phylogenies. None of the ITS sequences present in these nine species matched those detected in any other species, which provides tentative evidence against recent introgression as an explanation. Rheum globulosum, previously indicated by cpDNA to represent an independent origin of decumbent habit, is indicated by ITS to be part of clade of decumbent species, which acquired cpDNA of another clade via hybridization. However decumbent and glasshouse morphology are confirmed to have arisen three and two times, respectively.These findings suggested that hybridization among QTP species of Rheum has been extensive, and that a role of hybridization in diversification of Rheum requires investigation

Stress-Induced Reinstatement of Drug Seeking: 20 Years of Progress

In human addicts, drug relapse and craving are often provoked by stress. Since 1995, this clinical scenario has been studied using a rat model of stress-induced reinstatement of drug seeking. Here, we first discuss the generality of stress-induced reinstatement to different drugs of abuse, different stressors, and different behavioral procedures. We also discuss neuropharmacological mechanisms, and brain areas and circuits controlling stress-induced reinstatement of drug seeking. We conclude by discussing results from translational human laboratory studies and clinical trials that were inspired by results from rat studies on stress-induced reinstatement. Our main conclusions are (1) The phenomenon of stress-induced reinstatement, first shown with an intermittent footshock stressor in rats trained to self-administer heroin, generalizes to other abused drugs, including cocaine, methamphetamine, nicotine, and alcohol, and is also observed in the conditioned place preference model in rats and mice. This phenomenon, however, is stressor specific and not all stressors induce reinstatement of drug seeking. (2) Neuropharmacological studies indicate the involvement of corticotropin-releasing factor (CRF), noradrenaline, dopamine, glutamate, kappa/dynorphin, and several other peptide and neurotransmitter systems in stress-induced reinstatement. Neuropharmacology and circuitry studies indicate the involvement of CRF and noradrenaline transmission in bed nucleus of stria terminalis and central amygdala, and dopamine, CRF, kappa/dynorphin, and glutamate transmission in other components of the mesocorticolimbic dopamine system (ventral tegmental area, medial prefrontal cortex, orbitofrontal cortex, and nucleus accumbens). (3) Translational human laboratory studies and a recent clinical trial study show the efficacy of alpha-2 adrenoceptor agonists in decreasing stress-induced drug craving and stress-induced initial heroin lapse

Dressed for Sex: Red as a Female Sexual Signal in Humans

Background: In many non-human primate species, a display of red by a female serves as a sexual signal to attract male conspecifics. Red is associated with sex and romance in humans, and women convey their sexual interest to men through a variety of verbal, postural, and behavioral means. In the present research, we investigate whether female red ornamentation in non-human primates has a human analog, whereby women use a behavioral display of red to signal their sexual interest to men. Methodology/Principal Findings: Three studies tested the hypothesis that women use red clothing to communicate sexual interest to men in profile pictures on dating websites. In Study 1, women who imagined being interested in casual sex were more likely to display red (but not other colors) on their anticipated web profile picture. In Study 2, women who indicated interest in casual sex were more likely to prominently display red (but not other colors) on their actual web profile picture. In Study 3, women on a website dedicated to facilitating casual sexual relationships were more likely to prominently exhibit red (but not other colors) than women on a website dedicated to facilitating marital relationships. Conclusions/Significance: These results establish a provocative parallel between women and non-human female primates in red signal coloration in the mating game. This research shows, for the first time, a functional use of color in women’s sexual self-presentation, and highlights the need to extend research on color beyond physics, physiology, and preference to psychological functioning

Disruptions in the TFTR tokamak

For a successful reactor, it will be useful to predict the occurrence of disruptions and to understand disruption effects including how a plasma disrupts onto the wall and how reproducibly it does so. Studies of disruptions on TFTR at both high-[beta][sub pol] and high-density have shown that, in both types, a fast growing m/n=1/1 mode plays an important role. In highdensity disruptions, a newly observed fast m/n = 1/1 mode occurs early in the thermal decay phase. For the first time in TFTR q-profile measurements just prior to disruptions have been made. Experimental studies of heat deposition patterns on the first wall of TFTR due to disruptions have provided information on MHD phenomena prior to or during the disruption, how the energy is released to the wall, and the reproducibility of the heat loads from disruptions. This information is important in the design of future devices such as ITER. Several new processes of runaway electron generation are theoretically suggested and their application to TFTR and ITER is considered, together with a preliminary assessment of x-ray data from runaways generated during disruptions

High-Q plasmas in the TFTR tokamak

In the Tokamak Fusion Test Reactor, the highest neutron source strength S{sub n} and D-D fusion power gain Q{sub DD} are realized in the neutral-beam fueled and heated supershot'' regime that occurs after extensive wall conditioning to minimize recycling. For the best supershots, S{sub n} increases approximately as P{sub b}{sup 1.8}. The highest-Q shots are characterized by high T{sub e}, T{sub i}, and stored energy highly peaked density profiles, broad T{sub e} profiles, and lower Z{sub eff}. Replacement of critical areas of the graphite limiter tiles with carbon-fiber composite tiles, and improved alignment with the plasma, have mitigated the carbon bloom.'' Wall conditioning by lithium pellet injection prior to the beam pulse reduces carbon influx and particle recycling. Empirically, Q{sub DD} increases with decreasing pre-injection carbon radiation, and increases strongly with density peakedness during the beam pulse. To date the best fusion results are S{sub n} = 5 {times} 10{sup 16} n/s, Q{sub DD} = 1.85 {times} 10{sup {minus}3}, and neutron yield = 4.0 {times} 10{sup 16} n/pulse, obtained at I{sub p} = 1.6 to 1.9 MA and beam energy E{sub b} = 95 to 103 keV, with nearly balanced co- and counter-injected beam power. Computer simulations of supershot plasmas show that typically 50--60% of S{sub n} arises from beam-target reactions, with the remainder divided between beam-beam and thermonuclear reactions, the thermonuclear fraction increasing with P{sub b}. The simulations predict that Q{sub DT} = 0.3 to 0.4 would be obtained for the best present plasma conditions, if half the deuterium neutral beams were to be replaced by tritium beams. Somewhat higher values are calculated if D beams are injected into a predominantly tritium target plasma. The projected central beta of fusion alphas is 0.4--0.6%, a level sufficient for the study of alpha-induced collective effects. 16 refs., 8 figs., 3 tabs

The ITS1-5.8S-ITS2 Sequence Region in the Musaceae: Structure, Diversity and Use in Molecular Phylogeny

Genes coding for 45S ribosomal RNA are organized in tandem arrays of up to several thousand copies and contain 18S, 5.8S and 26S rRNA units separated by internal transcribed spacers ITS1 and ITS2. While the rRNA units are evolutionary conserved, ITS show high level of interspecific divergence and have been used frequently in genetic diversity and phylogenetic studies. In this work we report on the structure and diversity of the ITS region in 87 representatives of the family Musaceae. We provide the first detailed information on ITS sequence diversity in the genus Musa and describe the presence of more than one type of ITS sequence within individual species. Both Sanger sequencing of amplified ITS regions and whole genome 454 sequencing lead to similar phylogenetic inferences. We show that it is necessary to identify putative pseudogenic ITS sequences, which may have negative effect on phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstruction based on ITS sequence showed that the genus Musa is divided into two distinct clades – Callimusa and Australimusa and Eumusa and Rhodochlamys. Most of the intraspecific banana hybrids analyzed contain conserved parental ITS sequences, indicating incomplete concerted evolution of rDNA loci. Independent evolution of parental rDNA in hybrids enables determination of genomic constitution of hybrids using ITS. The observation of only one type of ITS sequence in some of the presumed interspecific hybrid clones warrants further study to confirm their hybrid origin and to unravel processes leading to evolution of their genomes

Phylodynamics of HIV-1 from a Phase III AIDS Vaccine Trial in Bangkok, Thailand

In 2003, a phase III placebo-controlled trial (VAX003) was completed in Bangkok, Thailand. Of the 2,546 individuals enrolled in the trial based on high risk for infection through injection drug use (IDU), we obtained clinical samples and HIV-1 sequence data (envelope glycoprotein gene gp120) from 215 individuals who became infected during the trial. Here, we used these data in combination with other publicly available gp120 sequences to perform a molecular surveillance and phylodynamic analysis of HIV-1 in Thailand.Phylogenetic and population genetic estimators were used to assess HIV-1 gp120 diversity as a function of vaccination treatment, viral load (VL) and CD4(+) counts, to identify transmission clusters and to investigate the timescale and demographics of HIV-1 in Thailand. Three HIV-1 subtypes were identified: CRF01_AE (85% of the infections), subtype B (13%) and CRF15_AE (2%). The Bangkok IDU cohort showed more gp120 diversity than other Asian IDU cohorts and similar diversity to that observed in sexually infected individuals. Moreover, significant differences (P<0.02) in genetic diversity were observed in CRF01_AE IDU with different VL and CD4(+) counts. No phylogenetic structure was detected regarding any of the epidemiological and clinical factors tested, although high proportions (35% to 50%) of early infections fell into clusters, which suggests that transmission chains associated with acute infection play a key role on HIV-1 spread among IDU. CRF01_AE was estimated to have emerged in Thailand in 1984.5 (1983-1986), 3-6 years before the first recognition of symptomatic patients (1989). The relative genetic diversity of the HIV-1 population has remained high despite decreasing prevalence rates since the mid 1990s.Our study and recent epidemiological reports indicate that HIV-1 is still a major threat in Thailand and suggest that HIV awareness and prevention needs to be strengthened to avoid AIDS resurgence