Targeted genome editing technology can correct the sickle cell disease mutation of the β-globin gene in hematopoietic stem cells. This correction supports production of red blood cells that synthesize normal hemoglobin proteins. Here, we demonstrate that Transcription Activator-Like Effector Nucleases (TALENs) and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 nuclease system can target DNA sequences around the sickle-cell mutation in the β-globin gene for site-specific cleavage and facilitate precise correction when a homologous donor template is codelivered. Several pairs of TALENs and multiple CRISPR guide RNAs were evaluated for both on-target and off-target cleavage rates. Delivery of the CRISPR/Cas9 components to CD34+ cells led to over 18% gene modification in vitro. Additionally, we demonstrate the correction of the sickle cell disease mutation in bone marrow derived CD34+ hematopoietic stem and progenitor cells from sickle cell disease patients, leading to the production of wild-type hemoglobin. These results demonstrate correction of the sickle mutation in patient-derived CD34+ cells using CRISPR/Cas9 technology.

We have investigated the in vivo pathogenic properties of two molecularly cloned strains of human immunodeficiency virus type 1 (HIV-1), HIV-1NL4-3 and HIV-1JR-CSF, in human fetal thymus/liver implants in severe combined immunodeficient mice. Studies comparing their in vivo replication kinetics and abilities to induce CD4+ thymocyte depletion were performed. HIV-1NL4-3 replicated in vivo with faster kinetics and induced greater levels of CD4+ thymocyte depletion than did HIV-1JR-CSF. These results demonstrate that different viral isolates have different pathogenic properties in this system. In the SCID-hu model, this pathogenesis most likely occurs in the absence of an immune response. Therefore, we investigated whether the absence of immune selection resulted in extensive genetic variation and the generation of viral quasispecies. To this end, DNA corresponding to the fourth variable domain region of the viral envelope gp120 protein recovered from biopsy samples at 6 weeks postinfection was sequenced. Little genetic variation was noted in either HIV-1JR-CSF- or HIV-1NL4-3-infected implants. The mutation levels demonstrated in both viral strains were more reflective of the acute rather than the chronic phase of HIV-1 infection in humans. These results suggest that the SCID-hu mouse model can be used to study the in vivo pathogenicity of different HIV-1 isolates in the absence of host immune selective pressures.

BACKGROUND

Social media technologies offer new approaches to HIV prevention and promotion of testing. We examined the efficacy of the Harnessing Online Peer Education (HOPE) social media intervention to increase HIV testing among men who have sex with men (MSM) in Peru.

METHODS

In this cluster randomised controlled trial, Peruvian MSM from Greater Lima (including Callao) who had sex with a man in the past 12 months, were 18 years of age or older, were HIV negative or serostatus unknown, and had a Facebook account or were willing to create one (N=556) were randomly assigned (1:1) by concealed allocation to join intervention or control groups on Facebook for 12 weeks. For the intervention, Peruvian MSM were trained and assigned to be HIV prevention mentors (peer-leaders) to participants in Facebook groups. The interventions period lasted 12 weeks. Participants in control groups received an enhanced standard of care, including standard offline HIV prevention available in Peru and participation in Facebook groups (without peer leaders) that provided study updates and HIV testing information. After accepting a request to join the groups, continued participation was voluntary. Participants also completed questionnaires on HIV risk behaviours and social media use at baseline and 12 week follow-up. The primary outcome was the number of participants who received a free HIV test at a local community clinic. The facebook groups were analysed as clusters to account for intracluster correlations. This trial is registered with ClinicalTrials.gov, number NCT01701206.

RESULTS

Of 49 peer-leaders recruited, 34 completed training and were assigned at random to the intervention Facebook groups. Between March 19, 2012, and June 11, 2012, and Sept 26, 2012, and Dec 19, 2012, 556 participants were randomly assigned to intervention groups (N=278) or control groups (N=278); we analyse data for 252 and 246. 43 participants (17%) in the intervention group and 16 (7%) in the control groups got tested for HIV (adjusted odds ratio 2·61, 95% CI 1·55–4·38). No adverse events were reported.

CONCLUSIONS

Development of peer-mentored social media communities seemed to be an efficacious method to increase HIV testing among high-risk populations in Peru. Results suggest that the HOPE social media intervention could improve HIV testing rates among MSM in Peru.

BACKGROUND

National Institute of Mental Health.

Prior to 2011, uptake of PMTCT in Malawi remained low despite increased access to antiretrovirals. We sought to understand barriers to PMTCT in rural Malawi. Twenty-two HIV-infected pregnant and postpartum women in PMTCT programs were interviewed in Nkhoma, Malawi, between April-May 2010. All women were staged by WHO criteria or CD4 count as ineligible for three-drug treatment by Malawi's HIV Guidelines at the time. The median age was 26 years (range 22-39) and 77% were married. Barriers to accessing PMTCT care included transportation to clinic, stigma in the community leading to avoidance of HIV disclosure, food insecurity, and providers' attitudes towards HIV-infected pregnant women. Given Malawi's transition to Option B+ for PMTCT in which women are initiated on antiretroviral therapy (ART) during pregnancy and continued for life, strategies to improve access and retention will need to address barriers and incorporate facilitators that motivate and retain women in HIV care.

G-protein-coupled receptors (GPCRs) are typically present in a basal, inactive state but, when bound to an agonist, activate downstream signaling cascades. In studying arrestin regulation of opioid receptors in dorsal root ganglia (DRG) neurons, we find that agonists of delta opioid receptors (δORs) activate cofilin through Rho-associated coiled-coil-containing protein kinase (ROCK), LIM domain kinase (LIMK), and β-arrestin 1 (β-arr1) to regulate actin polymerization. This controls receptor function, as assessed by agonist-induced inhibition of voltage-dependent Ca(2+) channels in DRGs. Agonists of opioid-receptor-like receptors (ORL1) similarly influence the function of this receptor through ROCK, LIMK, and β-arr1. Functional evidence of this cascade was demonstrated in vivo, where the behavioral effects of δOR or ORL1 agonists were enhanced in the absence of β-arr1 or prevented by inhibiting ROCK. This pathway allows δOR and ORL1 agonists to rapidly regulate receptor function.

Despite the HIV "test-and-treat" strategy's promise, questions about its clinical rationale, operational feasibility, and ethical appropriateness have led to vigorous debate in the global HIV community. We performed a systematic review of the literature published between January 2009 and May 2012 using PubMed, SCOPUS, Global Health, Web of Science, BIOSIS, Cochrane CENTRAL, EBSCO Africa-Wide Information, and EBSCO CINAHL Plus databases to summarize clinical uncertainties, health service challenges, and ethical complexities that may affect the test-and-treat strategy's success. A thoughtful approach to research and implementation to address clinical and health service questions and meaningful community engagement regarding ethical complexities may bring us closer to safe, feasible, and effective test-and-treat implementation.

BACKGROUND

Next-generation sequencing technologies sequence viruses with ultra-deep coverage, thus promising to revolutionize our understanding of the underlying diversity of viral populations. While the sequencing coverage is high enough that even rare viral variants are sequenced, the presence of sequencing errors makes it difficult to distinguish between rare variants and sequencing errors.

RESULTS

In this article, we present a method to overcome the limitations of sequencing technologies and assemble a diverse viral population that allows for the detection of previously undiscovered rare variants. The proposed method consists of a high-fidelity sequencing protocol and an accurate viral population assembly method, referred to as Viral Genome Assembler (VGA). The proposed protocol is able to eliminate sequencing errors by using individual barcodes attached to the sequencing fragments. Highly accurate data in combination with deep coverage allow VGA to assemble rare variants. VGA uses an expectation-maximization algorithm to estimate abundances of the assembled viral variants in the population. RESULTS on both synthetic and real datasets show that our method is able to accurately assemble an HIV viral population and detect rare variants previously undetectable due to sequencing errors. VGA outperforms state-of-the-art methods for genome-wide viral assembly. Furthermore, our method is the first viral assembly method that scales to millions of sequencing reads.

BACKGROUND

Our tool VGA is freely available at http://genetics.cs.ucla.edu/vga/

Medical responders to radiological and nuclear disasters currently lack sufficient high-throughput and minimally invasive biodosimetry tools to assess exposure and injury in the affected populations. For this reason, we have focused on developing robust radiation exposure biomarkers in easily accessible biofluids such as urine, serum and feces. While we have previously reported on urine and serum biomarkers, here we assessed perturbations in the fecal metabolome resulting from exposure to external X radiation in vivo. The gastrointestinal (GI) system is of particular importance in radiation biodosimetry due to its constant cell renewal and sensitivity to radiation-induced injury. While the clinical GI symptoms such as pain, bloating, nausea, vomiting and diarrhea are manifested after radiation exposure, no reliable bioindicator has been identified for radiation-induced gastrointestinal injuries. To this end, we focused on determining a fecal metabolomic signature in X-ray irradiated mice. There is overwhelming evidence that the gut microbiota play an essential role in gut homeostasis and overall health. Because the fecal metabolome is tightly correlated with the composition and diversity of the microorganism in the gut, we also performed fecal 16S rRNA sequencing analysis to determine the changes in the microbial composition postirradiation. We used in-house bioinformatics tools to integrate the 16S rRNA sequencing and metabolomic data, and to elucidate the gut integrated ecosystem and its deviations from a stable host-microbiome state that result from irradiation. The 16S rRNA sequencing results indicated that radiation caused remarkable alterations of the microbiome in feces at the family level. Increased abundance of common members of Lactobacillaceae and Staphylococcaceae families, and decreased abundances of Lachnospiraceae, Ruminococcaceae and Clostridiaceae families were found after 5 and 12 Gy irradiation. The metabolomic data revealed statistically significant changes in the microbial-derived products such as pipecolic acid, glutaconic acid, urobilinogen and homogentisic acid. In addition, significant changes were detected in bile acids such as taurocholic acid and 12-ketodeoxycholic acid. These changes may be associated with the observed shifts in the abundance of intestinal microbes, such as R. gnavus , which can transform bile acids.

Pluripotent stem cells (PSCs) may provide a potential source of haematopoietic stem/progenitor cells (HSPCs) for transplantation; however, unknown molecular barriers prevent the self-renewal of PSC-HSPCs. Using two-step differentiation, human embryonic stem cells (hESCs) differentiated in vitro into multipotent haematopoietic cells that had the CD34(+)CD38(-/lo)CD90(+)CD45(+)GPI-80(+) fetal liver (FL) HSPC immunophenotype, but exhibited poor expansion potential and engraftment ability. Transcriptome analysis of immunophenotypic hESC-HSPCs revealed that, despite their molecular resemblance to FL-HSPCs, medial HOXA genes remained suppressed. Knockdown of HOXA7 disrupted FL-HSPC function and caused transcriptome dysregulation that resembled hESC-derived progenitors. Overexpression of medial HOXA genes prolonged FL-HSPC maintenance but was insufficient to confer self-renewal to hESC-HSPCs. Stimulation of retinoic acid signalling during endothelial-to-haematopoietic transition induced the HOXA cluster and other HSC/definitive haemogenic endothelium genes, and prolonged HSPC maintenance in culture. Thus, medial HOXA gene expression induced by retinoic acid signalling marks the establishment of the definitive HSPC fate and controls HSPC identity and function.

The lack of clinical progression in some individuals despite prolonged human immunodeficiency virus type 1 (HIV-1) infection may result from infection with less-pathogenic viral strains. To address this question, we examined the HIV-1 envelope protein from a donor with a low viral burden, stable CD4(+) T-lymphocyte counts, and little evidence of CD8(+) T-cell expansion, activation, or immune activity. To avoid potential changes in envelope function resulting from selection in vitro, envelope clones were constructed by using viral RNA isolated from uncultured peripheral blood mononuclear cells (PBMC). The data showed that recombinant viruses containing envelope sequences derived from RNA isolated from patient PBMC replicated poorly in primary CD4(+) T cells but demonstrated efficient growth in macrophages. The unusual phenotype of these viruses could not be explained solely by differential utilization of coreceptors since the chimeric viruses, as well as an uncloned isolate obtained from the same visit date, can utilize CCR5. In addition, the donor's own cells appeared resistant to infection with chimeric viruses containing autologous envelope sequences. Genotype analysis revealed that the donor was heterozygous for the previously described 32-bp deletion in CCR5 which may be linked with prolonged survival in HIV-1-infected individuals. These data suggest that the changes in envelope sequences confer properties of viral attenuation, which together with the CCR5 +/Delta32 genotype could account for the long-term survival of this patient.

OBJECTIVE

To describe the sociodemographic and sex work characteristics, recent sexual practices, HIV risk perception and testing history, and HIV and syphilis prevalence of Cercado (downtown) and non-Cercado (close urban) male sex workers (MSWs) in Lima, Peru.

METHODS

Eighty-nine MSWs completed a self-administered survey and participated in HIV and syphilis testing.

RESULTS

Cercado MSWs had significantly lower median weekly earnings than non-Cercado MSWs (US$43 vs US$72, p=0.04). Most non-Cercado MSWs (81%) reported only insertive anal intercourse with male/transgender partners, while Cercado MSWs primarily reported only insertive (52%) or insertive and receptive (45%) anal intercourse (p=0.03). Consistent condom use was low with insertive and receptive anal intercourse in both subgroups. Among MSWs with recent female partners, condom use with the last partner was lower among Cercado versus non-Cercado MSWs for vaginal sex (37% vs 65%, p=0.04) and anal sex (27% vs 80%, p=0.01). More Cercado than non-Cercado MSWs (57% vs 42%) perceived high HIV risk (p=0.05) and Cercado MSWs had a much higher prevalence than non-Cercado MSWs of HIV (23% vs 4%, p=0.04) and syphilis (22% vs 0%, p=0.02) infections.

CONCLUSIONS

MSWs in Lima are diverse and Cercado MSWs are 'just getting by,' engaging in more risk behaviours, and more likely to have HIV/STIs. Future research should identify, describe and carry out HIV/STI testing with broader groups of MSWs and their client and non-client partners. Prevention efforts should provide HIV/STI risk reduction education for MSWs and related subgroups who are currently not targeted such as female partners.

Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan-cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis-defined CNA signatures are predictive of glycolytic phenotypes, including 18F-fluorodeoxy-glucose (FDG) avidity of patient tumors, and increased proliferation. The primary CNA signature is enriched for p53 mutations and is associated with glycolysis through coordinate amplification of glycolytic genes and other cancer-linked metabolic enzymes. A pan-cancer and cross-species comparison of CNAs highlighted 26 consistently altered DNA regions, containing 11 enzymes in the glycolysis pathway in addition to known cancer-driving genes. Furthermore, exogenous expression of hexokinase and enolase enzymes in an experimental immortalization system altered the subsequent copy number status of the corresponding endogenous loci, supporting the hypothesis that these metabolic genes act as drivers within the conserved CNA amplification regions. Taken together, these results demonstrate that metabolic stress acts as a selective pressure underlying the recurrent CNAs observed in human tumors, and further cast genomic instability as an enabling event in tumorigenesis and metabolic evolution.

BACKGROUND

South Africa has the highest prevalence of Fetal Alcohol Spectrum Disorders (FASD) in the world yet many women have no access to clinic care or to physicians in their communities. The shortage of physicians trained in the diagnosis of FASD is even more severe. Thus there is a need to train community workers to assist in the delivery of health care.

OBJECTIVE

This study reports on the effectiveness of training community workers to screen for a possible diagnosis of a FASD.

METHODS

Community workers in Cape Town, South Africa were trained to screen for FASD in 139, 18-month-old toddlers with prenatal alcohol exposure (PAE). Children were assessed according to the salient characteristics of individuals with PAE using height, weight, head circumference (OFC), philtrum, and lip measurements according to criteria set forth by the Institute of Medicine. Screen-positive children were referred for diagnostic assessment to a pediatrician reliably trained in the diagnosis of FASD.

RESULTS

Of the screen-positive children, 93% received an FASD diagnosis suggesting that the screening procedure was highly sensitive. Diagnoses included 15% with fetal alcohol syndrome (FAS), 23% with Partial FAS, and 62% with Alcohol Related Neurodevelopmental Disorder (ARND, provisional).

CONCLUSIONS

The use of community workers to screen for FASD represents a promising approach to effective diagnosis of children affected by PAE in areas lacking adequate medical resources.

β-Adrenergic signaling can regulate macrophage involvement in several diseases and often produces anti-inflammatory properties in macrophages, which are similar to M2 properties in a dichotomous M1 vs. M2 macrophage taxonomy. However, it is not clear that β-adrenergic-stimulated macrophages may be classified strictly as M2. In this in vitro study, we utilized recently published criteria and transcriptome-wide bioinformatics methods to map the relative polarity of murine β-adrenergic-stimulated macrophages within a wider M1-M2 spectrum. Results show that β-adrenergic-stimulated macrophages did not fit entirely into any one pre-defined category of the M1-M2 spectrum but did express genes that are representative of some M2 side categories. Moreover, transcript origin analysis of genome-wide transcriptional profiles located β-adrenergic-stimulated macrophages firmly on the M2 side of the M1-M2 spectrum and found active suppression of M1 side gene transcripts. The signal transduction pathways involved were mapped through blocking experiments and bioinformatics analysis of transcription factor binding motifs. M2-promoting effects were mediated specifically through β2-adrenergic receptors and were associated with CREB, C/EBPβ, and ATF transcription factor pathways but not with established M1-M2 STAT pathways. Thus, β-adrenergic-signaling induces a macrophage transcriptome that locates on the M2 side of the M1-M2 spectrum but likely accomplishes this effect through a signaling pathway that is atypical for M2-spectrum macrophages.

The mechanisms that govern the egress of mature thymocytes from the human thymus to the periphery remain understudied yet are of utmost importance to the field of basic immunology, as well as T-cell reconstitution in various immunodeficiencies. We examined the expression and function of sphingosine-1-phosphate (S1P) receptors in human thymocyte egress.

We aimed to determine whether S1P receptors (S1P-Rs) play a role in mature human thymocyte egress and to identify the thymocyte population or populations that express S1P-Rs and respond to S1P by migrating across a concentration gradient.

Human thymocytes were exposed to S1P in Transwell plate migration assays coupled to flow cytometry to evaluate the response to S1P of thymocytes at different stages of maturation. Constitutive S1P-R expression was quantified by means of real-time PCR in sorted thymocyte subsets and flow cytometry. S1P-R1 and Kruppel-like factor 2 expression were monitored after S1P exposure by using flow cytometry and quantitative PCR.

S1P-R1 was the prevalent S1P receptor on mature human thymocytes (CD3(hi)CD27(+)CD69(-)), the population that also demonstrated the greatest response to S1P in migration assays. Pretreatment with FTY720, an S1P-R1 nonselective modulator significantly reduced migration and suggested a role for S1P-R2 in retaining thymocytes in the tissue. Lastly, surface S1P-R1 expression, as well S1PR1 and Kruppel-like factor 2 (KLF2) transcripts, were significantly decreased in mature thymocytes on exposure to S1P.

Mature human thymocytes rely on S1P-R1 to migrate toward S1P. Taken in the context of murine work demonstrating that S1P is required for thymocyte egress to the periphery, our data highlight a new key chemokine for human thymocyte egress.

Stressful life events and daily hassles affect people living with HIV (PLWH). However, capturing stress-related events and cognitive impairment is often plagued with recall biases. Incorporating reliable information technology, such as mobile phones, can be a resourceful method for measuring health behaviors (MHB). We report findings from an MHB pilot study with 32 African American, Latino/Hispanic, and White PLWH from Los Angeles. Participants reported perceived stressors in their daily routines using a smartphone Ecological Momentary Assessment (EMA) application. Participants self-initiated in-the-moment stressful events reports for up to 6 weeks. Stressful event EMAs queried perceived stress levels (1-10 scale) and open-ended text descriptions. Qualitative analysis of participant text responses was completed using grounded thematic coding. Participants reported multiple stressors in their daily routines, impacting activities of daily living or daily functioning. Eliciting input from PLWH via EMA in real time is a novel approach for assessing and identifying sources of stress.

Enfuvirtide (ENF) is a fusion inhibitor that prevents the entry of HIV virions into target cells. Studying the characteristics of viral evolution during treatment and after a treatment interruption can lend insight into the mechanisms of viral evolution and fitness. Although interruption of anti-HIV therapy often results in rapid emergence of an archived "wild-type" virus population, previous work from our group indicates that when only ENF is interrupted, viral gp41 continues to evolve forward and resistance mutations are lost due to back-mutation and remodeling of the envelope protein. To examine the co-evolution of gp120 and gp41 during ENF interruption we extend the Bayesian Hierarchical Phylogenetic model (HPM). Current HPMs enforce conditional independence across all outcomes while biologically all gene regions within a patient should return the same tree unless recombination confers an evolutionary selective advantage. A two-way-interaction HPM is proposed that provides middle ground between these two extremes and allows us to test for differences in evolutionary pressures across gene regions in multiple patients simultaneously. When the model is applied to a well-characterized cohort of HIV-infected patients interrupting ENF we find that across patients, the virus continued to evolve forward in both gene regions. Overall, the hypothesis of independence over dependence between the gene regions is supported. Models that allow for the examination of co-evolution over time will be increasingly important as more therapeutic classes are developed, each of which may impact other through novel and complex mechanisms.

HIV-1-infected persons spontaneously controlling viremia without treatment (SCV) are rare. Sex and race effects on prevalence and outcome are poorly defined, and it is unclear whether SCV qualitatively or quantitatively differs from typical infection. These issues are examined in this article.

Medical records of 46 524 persons receiving outpatient care for HIV-1 infection were reviewed. Of these, 29 811 had adequate viremia testing for SCV screening.

SCV was defined as at least three consecutive plasma viremia measurements <50 RNA copies/ml spanning at least 1 year without treatment. SCV loss was defined as at least three consecutive viremia measurements ≥50 RNA copies/ml or one ≥1000 RNA copies/ml. Demographics of persons with SCV were compared with the total population. Viremia and blood CD4 T-cell levels during SCV were compared between demographic subgroups and persons who maintained or lost SCV during observation.

In total, 53 persons (0.18%) met SCV criteria. Prevalence was higher for women versus men and blacks versus whites; these appeared independent. Loss of SCV was observed at 1.22% per year, and significantly associated with viremia 'blips'. Blip magnitudes fit log-normal distributions with means below 50 RNA copies/ml.

Our novel observation of higher SCV prevalence in women and blacks is consistent with prior studies of typical chronic infection. Viremia blips correspond to greater risk of loss of SCV, likely reflecting higher set-point viremia under the limit of detection. Our findings suggest that SCV represents an extreme along a continuum of HIV-1 infection, and not qualitative difference.

Syphilis and human immunodeficiency virus (HIV) coinfection disproportionately affects men who have sex with men (MSM), and the rate of coinfection has been increasing over the last decade. HIV and syphilis coinfection is particularly challenging because the infections interact synergistically thereby increasing the risk of acquisition and transmission as well as accelerating disease progression. Areas covered: This paper reviews and summarizes the epidemiology, pathogenesis, diagnosis, clinical management and prevention of HIV and syphilis coinfection among MSM. Expert commentary: Research does not support a different syphilis treatment for coinfected individuals; however, coinfection may warrant a recommendation for antiretroviral therapy. In order to reverse the epidemic of syphilis and HIV coinfection, there needs to be greater awareness, improved cultural sensitivity among health care providers, improved access to preventative services and increased screening for syphilis and HIV.

Trichomonas vaginalis (Tv) is an extracellular protozoan parasite that causes the most common non-viral sexually transmitted infection: trichomoniasis. While acute symptoms in women may include vaginitis, infections are often asymptomatic, but can persist and are associated with medical complications including increased HIV susceptibility, infertility, pre-term labor, and higher incidence of cervical cancer. Heightened inflammation resulting from Tv infection could account for these complications. Effective cellular immune responses to Tv have not been characterized, and re-infection is common, suggesting a dysfunctional adaptive immune response. Using primary human leukocyte components, we have established an in vitro co-culture system to assess the interaction between Tv and the cells of the human immune system. We determined that in vitro, Tv is able to lyse T-cells and B-cells, showing a preference for B-cells. We also found that Tv lysis of lymphocytes was mediated by contact-dependent and soluble factors. Tv lysis of monocytes is far less efficient, and almost entirely contact-dependent. Interestingly, a common symbiont of Tv, Mycoplasma hominis, did not affect cytolytic activity of the parasite, but had a major impact on cytokine responses. M. hominis enabled more diverse inflammatory cytokine secretion in response to Tv and, of the cytokines tested, Tv strains cleared of M. hominis induced only IL-8 secretion from monocytes. The quality of the adaptive immune response to Tv is therefore likely influenced by Tv symbionts, commensals, and concomitant infections, and may be further complicated by direct parasite lysis of effector immune cells.

Bayesian models are increasingly used to analyze complex multivariate outcome data. However, diagnostics for such models have not been well-developed. We present a diagnostic method of evaluating the fit of Bayesian models for multivariate data based on posterior predictive model checking (PPMC), a technique in which observed data are compared to replicated data generated from model predictions. Most previous work on PPMC has focused on the use of test quantities that are scalar summaries of the data and parameters. However, scalar summaries are unlikely to capture the rich features of multivariate data. We introduce the use of dissimilarity measures for checking Bayesian models for multivariate outcome data. This method has the advantage of checking the fit of the model to the complete data vectors or vector summaries with reduced dimension, providing a comprehensive picture of model fit. An application with longitudinal binary data illustrates the methods.

Chronic pain and substance use disorders occur commonly among HIV-infected persons. Recent CDC guidelines recommend non-pharmacologic approaches over opioid medications for the management of chronic pain. This is particularly relevant for persons with substance use disorders. Structured physical activity may be an effective strategy for pain reduction. We developed a combined cognitive-behavioral therapy (CBT) + exercise intervention to reduce pain, pain-related disability and substance use and improve physical function in older HIV-infected adults with chronic pain and substance use. We employed established CBT protocols for the intervention, and sought feedback from potential end users when developing the exercise component of the intervention. A total of 27 HIV-infected adults ≥ 50 years of age participated in four focus group sessions. Transcripts were analyzed using thematic analysis. Participant demographics: mean age 54 years; male 81%; Hispanic 48%, Black 33%; treated for substance abuse in the past 52%. Exercise was seen as a desirable activity, but many participants expressed barriers to exercise including fear of pain exacerbation, low physical fitness, and lack of availability of perceived safe spaces for HIV-infected persons. Most participants were receptive to exercise for pain reduction, particularly modalities that provide added psychological benefits of reducing stress and anxiety. Exercise for pain management among older HIV-infected adults with chronic pain and substance use was found to be highly acceptable. However, interventions need to be tailored to the unique needs of this population to address their fears and concerns.

Mutational escape of HIV-1 from HIV-1-specific CD8+ T lymphocytes (CTLs) is a major barrier for effective immune control. Each epitope typically is targeted by multiple clones with distinct T cell receptors (TCRs). While the clonal repertoire may be important for containing epitope variation, determinants of its composition are poorly understood. We investigate the clonal repertoire of 29 CTL responses against 23 HIV-1 epitopes longitudinally in nine chronically infected untreated subjects with plasma viremia of <3,000 RNA copies/ml over 17 to 179 weeks. The composition of TCRs targeting each epitope varied considerably in stability over time, although clonal stability (Sorensen index) was not significantly time dependent within this interval. However, TCR stability inversely correlated with epitope variability in the Los Alamos HIV-1 Sequence Database, consistent with TCR evolution being driven by epitope variation. Finally, a robust inverse correlation of TCR breadth against each epitope versus epitope variability further suggested that this variability drives TCR repertoire diversification. In the context of studies demonstrating rapidly shifting HIV-1 sequences in vivo, our findings support a variably dynamic process of shifting CTL clonality lagging in tandem with viral evolution and suggest that preventing escape of HIV-1 may require coordinated direction of the CTL clonal repertoire to simultaneously block escape pathways.IMPORTANCE Mutational escape of HIV-1 from HIV-1-specific CD8+ T lymphocytes (CTLs) is a major barrier to effective immune control. The number of distinct CTL clones targeting each epitope is proposed to be an important factor, but the determinants are poorly understood. Here, we demonstrate that the clonal stability and number of clones for the CTL response against an epitope are inversely associated with the general variability of the epitope. These results show that CTLs constantly lag epitope mutation, suggesting that preventing HIV-1 escape may require coordinated direction of the CTL clonal repertoire to simultaneously block escape pathways.

Preexposure prophylaxis (PrEP) has emerged as a human immunodeficiency virus (HIV) prevention tool for populations at highest risk for HIV infection. Current US Centers for Disease Control and Prevention (CDC) guidelines for identifying PrEP candidates may not be specific enough to identify gay, bisexual, and other men who have sex with men (MSM) at the highest risk for HIV infection. We created an HIV risk score for HIV-negative MSM based on Syndemics Theory to develop a more targeted criterion for assessing PrEP candidacy.

Behavioral risk assessment and HIV testing data were analyzed for HIV-negative MSM attending the Los Angeles LGBT Center between January 2009 and June 2014 (n = 9481). Syndemics Theory informed the selection of variables for a multivariable Cox proportional hazards model. Estimated coefficients were summed to create an HIV risk score, and model fit was compared between our model and CDC guidelines using the Akaike Information Criterion and Bayesian Information Criterion.

Approximately 51% of MSM were above a cutpoint that we chose as an illustrative risk score to qualify for PrEP, identifying 75% of all seroconverting MSM. Our model demonstrated a better overall fit when compared with the CDC guidelines (Akaike Information Criterion Difference = 68) in addition to identifying a greater proportion of HIV infections.

Current CDC PrEP guidelines should be expanded to incorporate substance use, partner-level, and other Syndemic variables that have been shown to contribute to HIV acquisition. Deployment of such personalized algorithms may better hone PrEP criteria and allow providers and their patients to make a more informed decision prior to PrEP use.