Viral Load Dynamics in Plasma and Semen When Antiretroviral Therapy Is Initiated During Early HIV-1 Infection.

We assessed human immunodeficiency virus (HIV) load in plasma and semen during primary HIV infection using serial samples of semen and plasma during the first 24 weeks after diagnosis in untreated participants and those who started antiretroviral therapy (ART) immediately at diagnosis. In the absence of treatment, semen viral load was >1000 copies/mL in almost all specimens (83%) collected 2-10 weeks after the estimated date of HIV acquisition and remained >1000 copies/mL in 35% of untreated participants at the last observed time point. Thus, in the absence of ART, semen viral load remained at a level consistent with transmissibility throughout primary infection.

The impact of low-fat and full-fat dairy foods on symptoms of gastroesophageal reflux disease: an exploratory analysis based on a randomized controlled trial.

PURPOSE: Gastroesophageal reflux disease (GERD) is a widely prevalent condition. High consumption of dairy foods and dietary fat are associated with worse GERD symptoms. However, existing data are inconsistent and mostly based on observational studies. The purpose of this exploratory analysis of a randomized controlled trial was to investigate the impact of low-fat and full-fat dairy food consumption on GERD symptoms. METHODS: Seventy-two participants with metabolic syndrome completed a 4-week wash-in diet during which dairy intake was limited to three servings of nonfat milk per week. Participants were then randomized to either continue the limited dairy diet or switch to a diet containing 3.3 servings per day of either low-fat or full-fat milk, yogurt and cheese for 12 weeks. Here, we report intervention effects on the frequency of acid reflux, and the frequency and severity of heartburn, exploratory endpoints assessed by a questionnaire administered before and after the 12-week intervention. RESULTS: In the per-protocol analysis (n = 63), there was no differential intervention effect on a cumulative heartburn score (p = 0.443 for the time by diet interaction in the overall repeated measures analysis of variance). Similarly, the intervention groups did not differentially affect the odds of experiencing acid regurgitation (p = 0.651). The intent-to-treat analyses (n = 72) yielded similar results. CONCLUSION: Our exploratory analyses suggest that, in men and women with the metabolic syndrome, increasing the consumption of either low-fat or full-fat dairy foods to at least three servings per day does not affect common symptoms of GERD, heartburn and acid regurgitation compared to a diet limited in dairy. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02663544, registered on January 26, 2016.

How Well Do Neurologic Symptoms Identify Individuals With Neurosyphilis?

Background: Current guidelines recommend lumbar puncture (LP) in patients with syphilis who have neurologic symptoms. Methods: A total of 81 human immunodeficiency virus (HIV)-uninfected individuals and 385 HIV-infected individuals enrolled in a study of cerebrospinal fluid (CSF) abnormalities in syphilis underwent LP and a structured symptom history, including assessment of headache; stiff neck; photophobia; ocular inflammation; vision, hearing, or sensory loss; or gait incoordination. Neurosyphilis was defined as a reactive CSF-Venereal Disease Research Laboratory (VDRL) test. Association between categorical variables was assessed using χ2, Fisher exact test, or logistic regression. Association between continuous and categorical variables was assessed using Mann-Whitney U test. Results: CSF-VDRL was reactive in 20 (24.7%) HIV-uninfected and 68 (17.7%) HIV-infected (P = .14) individuals. No symptom was more common in HIV-uninfected individuals with neurosyphilis. Among the HIV-infected, the odds of a reactive CSF-VDRL were higher in those with mild or greater severity photophobia (2.0 [95% confidence interval [CI], 1.1-3.8]; P = .03), vision loss (2.3 [1.3-4.1]; P = .003), or gait incoordination (2.4 [1.3-4.4]; P = .006); or moderate or greater severity hearing loss (3.1 [1.3-7.5]; P = .01). Diagnostic specificity of these 4 symptoms for neurosyphilis was high when limited to moderate or greater severity (91.6%-100%); however, the diagnostic sensitivity was low (1.5%-38.1%). Conclusions: Among HIV-infected patients with syphilis, 4 specific neurologic symptoms are more common in those with a reactive CSF-VDRL. Lack of symptoms does not guarantee that the CSF-VDRL is nonreactive, regardless of HIV status.

Transmission of HIV-1 drug resistance mutations within partner-pairs: A cross-sectional study of a primary HIV infection cohort.

BACKGROUND: Transmission of human immunodeficiency virus type 1 (HIV-1) drug resistance mutations, particularly that of minority drug-resistant variants, remains poorly understood. Population-based studies suggest that drug-resistant HIV-1 is less transmissible than drug-susceptible viruses. We compared HIV-1 drug-resistant genotypes among partner-pairs in order to assess the likelihood of transmission of drug resistance mutations and investigate the role of minority variants in HIV transmission. METHODS AND FINDINGS: From 1992-2010, 340 persons with primary HIV-1 infection and their partners were enrolled into observational research studies at the University of Washington Primary Infection Clinic (UWPIC). Out of 50 partner-pairs enrolled, 36 (72%) transmission relationships were confirmed by phylogenetic distance analysis of HIV-1 envelope (env) sequences, and 31 partner-pairs enrolled after 1995 met criteria for this study. Drug resistance mutations in the region of the HIV-1 polymerase gene (pol) that encodes protease and reverse transcriptase were assessed by 454-pyrosequencing. In 25 partner-pairs where the transmission direction could be determined, 12 (48%) transmitters had 1-4 drug resistance mutations (23 total) detected in their HIV-1 populations at a median frequency of 6.0% (IQR 1.5%-98.7%, range 1.0%-99.6%). Of 10 major mutations detected in five transmitters at a frequency >95%, 100% (95% CI 69.2%-100%) were detected in recipients. All of these transmitters were antiretroviral (ARV)-naïve at the time of specimen collection. Fourteen mutations (eight major mutations and six accessory mutations) were detected in nine transmitters at low frequencies (1.0%-11.8%); four of these transmitters had previously received ARV therapy. Two (14% [95% CI 1.8%-42.8%]) G73S accessory mutations were detected in both transmitter and recipient. This number is not significantly different from the number expected based on the observed frequencies of drug-resistant viruses in transmitting partners. Limitations of this study include the small sample size and uncertainties in determining the timing of virus transmission and mutation history. CONCLUSIONS: Drug-resistant majority variants appeared to be commonly transmitted by ARV-naïve participants in our analysis and may contribute significantly to transmitted drug resistance on a population level. When present at low frequency, no major mutation was observed to be shared between partner-pairs; identification of accessory mutations shared within a pair could be due to transmission, laboratory artifact, or apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBECs), and warrants further study.

Results of a randomized controlled trial to increase cervical cancer screening among rural Latinas.

BACKGROUND: Latinas have the highest rates of cervical cancer in the United States and the second highest rate of cervical cancer mortality. One factor in the disparity is the relatively low rate of screening for cervical cancer in this population. METHODS: Eligible women who were out of adherence with cervical cancer screening (>3 years since their last Papanicolaou [Pap] test) were identified via medical record review by a federally qualified local health center. The effects of a low-intensity intervention (video delivered to participants' homes; n = 150) and a high-intensity intervention (video plus a home-based educational session; n = 146) on cervical cancer screening uptake in comparison with a control arm (usual care; n = 147) were investigated. A cost-effectiveness analysis of the interventions was conducted: all intervention costs were calculated, and the incremental cost-effectiveness ratio was computed. Finally, women with positive Pap tests were provided navigation by a community health educator to ensure that they received follow-up care. RESULTS: A total of 443 Latinas participated. Seven months after randomization, significantly more women in the high-intensity arm received a Pap test (53.4%) in comparison with the low-intensity arm (38.7%; P < .001) and the usual-care arm (34.0%; P < .01). The incremental cost-effectiveness ratio for high-intensity women versus the control group amounted to $4.24. Twelve women had positive Pap tests, which encompassed diagnoses ranging from atypical squamous cells of unknown significance to invasive cancer; these women received navigation for follow-up care. CONCLUSIONS: A culturally appropriate, in-home, promotora-led educational intervention was successful in increasing cervical cancer screening among Latinas. Cancer 2017;123:666-674. © 2016 American Cancer Society.

Parasite burden and severity of malaria in Tanzanian children.

BACKGROUND: Severe Plasmodium falciparum malaria is a major cause of death in children. The contribution of the parasite burden to the pathogenesis of severe malaria has been controversial. METHODS: We documented P. falciparum infection and disease in Tanzanian children followed from birth for an average of 2 years and for as long as 4 years. RESULTS: Of the 882 children in our study, 102 had severe malaria, but only 3 had more than two episodes. More than half of first episodes of severe malaria occurred after a second infection. Although parasite levels were higher on average when children had severe rather than mild disease, most children (67 of 102) had high-density infection (>2500 parasites per 200 white cells) with only mild symptoms before severe malaria, after severe malaria, or both. The incidence of severe malaria decreased considerably after infancy, whereas the incidence of high-density infection was similar among all age groups. Infections before and after episodes of severe malaria were associated with similar parasite densities. Nonuse of bed nets, placental malaria at the time of a woman's second or subsequent delivery, high-transmission season, and absence of the sickle cell trait increased severe-malaria risk and parasite density during infections. CONCLUSIONS: Resistance to severe malaria was not acquired after one or two mild infections. Although the parasite burden was higher on average during episodes of severe malaria, a high parasite burden was often insufficient to cause severe malaria even in children who later were susceptible. The diverging rates of severe disease and high-density infection after infancy, as well as the similar parasite burdens before and after severe malaria, indicate that naturally acquired resistance to severe malaria is not explained by improved control of parasite density. (Funded by the National Institute of Allergy and Infectious Diseases and others.).

The role of diet in children's exposure to organophosphate pesticides.

BACKGROUND: Studies suggest that some of the greatest exposure to OPs in children occurs in agricultural communities and various pathways of exposure including the take-home pathway, proximity to orchards, and diet have been explored. However, the importance of the dietary pathway of exposure for children in agricultural communities is not well understood. OBJECTIVES: Our goal was to ascertain whether there were associations between measures of OP exposure and apple juice, fruit, and vegetable consumption across growing seasons by children of farmworkers and non-farmworkers in a rural agricultural setting. METHODS: Study participants were children of farmworker (N=100) or non-farmworker (N=100) households from a longitudinal cohort study. Dietary intake of fruits and vegetables was assessed using a "5-A-Day" abbreviated food frequency questionnaire, and exposure to OPs was characterized using three urinary di-methyl and three di-ethyl metabolite measurements per child for each of three growing seasons. We used generalized estimating equations to examine data. RESULTS: Consumption frequency of fruits and vegetables was similar between children of farmworkers and non-farmworkers and across seasons. There were a few significant trends between dimethyl metabolites (DMAP) and fruit, vegetable or apple juice consumption; however, no clear pattern held across seasons or occupation. One difference was found in vegetable consumption during the harvest season, where the farmworker families showed a significant relationship between vegetable consumption and dimethyl metabolite levels (p=0.002). We also found a significant difference in this relationship between farmworkers and non-farmworkers (p=0.001). No significant trends between fruit and vegetable consumption and diethyl (DEAP) metabolites were found. CONCLUSIONS: Our study shows the importance of considering season and parents' occupation in understanding OP exposure routes among children in an agricultural community. The impact of these factors on dietary OP exposure requires a more thorough analysis of the availability and consumption of produce from different sources including farms using pesticides where parents worked.

Symmetric Directional False Discovery Rate Control.

This research is motivated from the analysis of a real gene expression data that aims to identify a subset of "interesting" or "significant" genes for further studies. When we blindly applied the standard false discovery rate (FDR) methods, our biology collaborators were suspicious or confused, as the selected list of significant genes was highly unbalanced: there were ten times more under-expressed genes than the over-expressed genes. Their concerns led us to realize that the observed two-sample t-statistics were highly skewed and asymmetric, and thus the standard FDR methods might be inappropriate. To tackle this case, we propose a symmetric directional FDR control method that categorizes the genes into "over-expressed" and "under-expressed" genes, pairs "over-expressed" and "under-expressed" genes, defines the p-values for gene pairs via column permutations, and then applies the standard FDR method to select "significant" gene pairs instead of "significant" individual genes. We compare our proposed symmetric directional FDR method with the standard FDR method by applying them to simulated data and several well-known real data sets.

Understanding the impact of colorectal cancer education: a randomized trial of health fairs.

BACKGROUND: Regular screening for colorectal cancer (CRC) reduces morbidity and mortality from this disease. A number of factors play a role in the underutilization of CRC screening; populations with the lowest CRC screening rates are least likely to be aware of the need for screening or have knowledge about screening options. The overall purpose of this project was to assess two methods for increasing knowledge about CRC in a health fair context: one, by using a health educator to provide CRC information at a table, or two, to provide a tour through a giant inflatable, walk-through colon model with physical depictions of healthy tissue, polyps, and CRC. METHODS: We participated in six community health fair events, three were randomized to incorporate the use of the inflatable colon, and three used a standard display table method. We used a pre/post-design to look for changes in knowledge about CRC before and after participating in a health fair. We examined descriptive statistics of participants using frequencies and proportions. McNemar's test for paired binary data was used to test whether there were significant differences in the distribution of correct answer percentage from pre to post and from pre to follow up. Linear regression (GEE) was used to investigate whether there was a significant difference in the change from pre- to post-intervention in the percentage of correct answers on knowledge of tests available to detect CRC and awareness of risk factors for CRC between participants at sites with the inflatable colon compared to participants at sites without the inflatable colon. RESULTS: Participants (n = 273) were recruited at the six health fairs. Participants in health fairs with the inflatable colon had higher knowledge at post-test than participants in health fairs with tabling activities, that is, without the inflatable colon; however, the difference was not significant. One month follow-up after each health fair showed virtually no recollection of information learned at the health fairs. CONCLUSIONS: The use of an inflatable colon may be an innovative way to help people learn about CRC and CRC screening; however, it is not significantly more effective than conventional table display methods. Further research is needed to associate intention to obtain screening after touring the inflatable colon with actual screening. Future research could explore ways to better retain knowledge at long-term follow-up.

Diabetes prevention in Hispanics: report from a randomized controlled trial.

INTRODUCTION: Hispanics are at increased risk of developing type 2 diabetes. Lifestyle interventions are effective in preventing diabetes and restoring glucose regulation. METHODS: We recruited Hispanic men and women (N = 320) who were residents of the Lower Yakima Valley, Washington, aged 18 years or older with hemoglobin A1c (HbA1c) levels higher than 6% to a parallel 2-arm randomized-controlled trial conducted from 2008 through 2012. The trial compared participants in the intervention arm, who received an immediate educational curriculum (n = 166), to participants in the control arm, who received a delayed educational curriculum (n = 154). The home-based curriculum consisted of 5 sessions led by community health workers and was designed to inform participants about diabetes, diabetes treatment, and healthy dietary and physical activity behaviors. Participants were randomly assigned to the intervention and control arms, and analysts were blinded as to participant arm. We evaluated intervention effects on HbA1c levels; frequency (times per week) of fruit and vegetable consumption; and frequency (times per week) of mild, moderate, and strenuous leisure-time physical activity. At baseline, 3 months, and 6 months after randomization, participants completed a questionnaire and provided a blood sample. Analysts were blinded to intervention arm. RESULTS: The immediate intervention group (-0.64% [standard error (SE) 0.10]) showed a significant improvement in HbA1c scores (-37.5%, P = .04) compared with the delayed intervention group (-0.44%, P = .14). No significant changes were seen for dietary end points or changes in physical activity. We did observe a trend of greater increases in frequency of moderate and vigorous physical activity and a smaller increase in mild physical activity in the immediate intervention group than in the delayed intervention group. CONCLUSION: This home-based intervention delivered by CHWs was associated with a clinically and statistically significant reduction in HbA1c levels in Hispanic adults with HbA1c levels higher than 6%.

Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time.

BACKGROUND: Whether unique human immunodeficiency type 1 (HIV) genotypes occur in the genital tract is important for vaccine development and management of drug resistant viruses. Multiple cross-sectional studies suggest HIV is compartmentalized within the female genital tract. We hypothesize that bursts of HIV replication and/or proliferation of infected cells captured in cross-sectional analyses drive compartmentalization but over time genital-specific viral lineages do not form; rather viruses mix between genital tract and blood. METHODS: Eight women with ongoing HIV replication were studied during a period of 1.5 to 4.5 years. Multiple viral sequences were derived by single-genome amplification of the HIV C2-V5 region of env from genital secretions and blood plasma. Maximum likelihood phylogenies were evaluated for compartmentalization using 4 statistical tests. RESULTS: In cross-sectional analyses compartmentalization of genital from blood viruses was detected in three of eight women by all tests; this was associated with tissue specific clades containing multiple monotypic sequences. In longitudinal analysis, the tissues-specific clades did not persist to form viral lineages. Rather, across women, HIV lineages were comprised of both genital tract and blood sequences. CONCLUSIONS: The observation of genital-specific HIV clades only in cross-sectional analysis and an absence of genital-specific lineages in longitudinal analyses suggest a dynamic interchange of HIV variants between the female genital tract and blood.

Adaptive resources allocation CUSUM for binomial count data monitoring with application to COVID-19 hotspot detection.

In this paper, we present an efficient statistical method (denoted as 'Adaptive Resources Allocation CUSUM') to robustly and efficiently detect the hotspot with limited sampling resources. Our main idea is to combine the multi-arm bandit (MAB) and change-point detection methods to balance the exploration and exploitation of resource allocation for hotspot detection. Further, a Bayesian weighted update is used to update the posterior distribution of the infection rate. Then, the upper confidence bound (UCB) is used for resource allocation and planning. Finally, CUSUM monitoring statistics to detect the change point as well as the change location. For performance evaluation, we compare the performance of the proposed method with several benchmark methods in the literature and showed the proposed algorithm is able to achieve a lower detection delay and higher detection precision. Finally, this method is applied to hotspot detection in a real case study of county-level daily positive COVID-19 cases in Washington State WA) and demonstrates the effectiveness with very limited distributed samples.

Etiology of Fever and Associated Outcomes Among Adults Receiving Chemotherapy for the Treatment of Solid Tumors in Uganda.

Background: Little is known about the microbiology and outcomes of chemotherapy-associated febrile illness among patients in sub-Saharan Africa. Understanding the microbiology of febrile illness could improve antibiotic selection and infection-related outcomes. Methods: From September 2019 through June 2022, we prospectively enrolled adult inpatients at the Uganda Cancer Institute who had solid tumors and developed fever within 30 days of receiving chemotherapy. Evaluation included blood cultures, malaria rapid diagnostic tests, and urinary lipoarabinomannan testing for tuberculosis. Serum cryptococcal antigen was evaluated in participants with human immunodeficiency virus (HIV). The primary outcome was the mortality rate 40 days after fever onset, which we estimated using Cox proportional hazards models. Results: A total of 104 febrile episodes occurred among 99 participants. Thirty febrile episodes (29%) had ≥1 positive microbiologic result. The most frequently identified causes of infection were tuberculosis (19%) and bacteremia (12%). The prevalence of tuberculosis did not differ by HIV status. The 40-day case fatality ratio was 25%. There was no difference in all-cause mortality based on HIV serostatus, presence of neutropenia, or positive microbiologic results. A universal vital assessment score of >4 was associated with all-cause mortality (hazard ratio, 14.5 [95% confidence interval, 5-42.7]). Conclusions: The 40-day mortality rate among Ugandan patients with solid tumors who developed chemotherapy-associated febrile illness was high, and few had an identified source of infection. Tuberculosis and bacterial bloodstream infections were the leading diagnoses associated with fever. Tuberculosis should be included in the differential diagnosis for patients who develop fever after receiving chemotherapy in tuberculosis-endemic settings, regardless of HIV serostatus.

Iron deficiency protects against severe Plasmodium falciparum malaria and death in young children.

BACKGROUND: Iron supplementation may increase malaria morbidity and mortality, but the effect of naturally occurring variation in iron status on malaria risk is not well studied. METHODS: A total of 785 Tanzanian children living in an area of intense malaria transmission were enrolled at birth, and intensively monitored for parasitemia and illness including malaria for up to 3 years, with an average of 47 blood smears. We assayed plasma samples collected at routine healthy-child visits, and evaluated the impact of iron deficiency (ID) on future malaria outcomes and mortality. RESULTS: ID at routine, well-child visits significantly decreased the odds of subsequent parasitemia (23% decrease, P < .001) and subsequent severe malaria (38% decrease, P = .04). ID was also associated with 60% lower all-cause mortality (P = .04) and 66% lower malaria-associated mortality (P = .11). When sick visits as well as routine healthy-child visits are included in analyses (average of 3 iron status assays/child), ID reduced the prevalence of parasitemia (6.6-fold), hyperparasitemia (24.0-fold), and severe malaria (4.0-fold) at the time of sample collection (all P < .001). CONCLUSIONS: Malaria risk is influenced by physiologic iron status, and therefore iron supplementation may have adverse effects even among children with ID. Future interventional studies should assess whether treatment for ID coupled with effective malaria control can mitigate the risks of iron supplementation for children in areas of malaria transmission.

Genetic drift of HIV populations in culture.

Populations of Human Immunodeficiency Virus type 1 (HIV-1) undergo a surprisingly large amount of genetic drift in infected patients despite very large population sizes, which are predicted to be mostly deterministic. Several models have been proposed to explain this phenomenon, but all of them implicitly assume that the process of virus replication itself does not contribute to genetic drift. We developed an assay to measure the amount of genetic drift for HIV populations replicating in cell culture. The assay relies on creation of HIV populations of known size and measurements of variation in frequency of a neutral allele. Using this assay, we show that HIV undergoes approximately ten times more genetic drift than would be expected from its population size, which we defined as the number of infected cells in the culture. We showed that a large portion of the increase in genetic drift is due to non-synchronous infection of target cells. When infections are synchronized, genetic drift for the virus is only 3-fold higher than expected from its population size. Thus, the stochastic nature of biological processes involved in viral replication contributes to increased genetic drift in HIV populations. We propose that appreciation of these effects will allow better understanding of the evolutionary forces acting on HIV in infected patients.

IL28B genotype effects during early treatment with peginterferon and ribavirin in difficult-to-treat hepatitis C virus infection.

BACKGROUND: Mathematical models of hepatitis C virus (HCV) during therapy may elucidate mechanisms of action for antiviral therapy. In genome-wide association studies, IL28B gene polymorphisms are highly predictive of therapeutic clearance of HCV. METHODS: We collected sera from 20 chronically infected HCV participants at 13 points during the first 28 days of therapy. We assessed the presence of the C allele at single-nucleotide polymorphism rs12979860 using the ABI TaqMan allelic discrimination kit. We estimated dynamic parameters from the entire population using the Neumann model for HCV infection. Statistical methods for repeated nonlinear measures compared model parameters by established predictors of response. RESULTS: The frequencies of IL28B genotypes were 6 (C/C), 11 (C/T), and 3 (T/T). The mean log decline in HCV RNA from 0 to 48 hours was more rapid among C/C genotype participants compared with C/T or T/T genotype participants (1.4 vs 0.7; P = .07), and from 2 days to 14 days (1.6 vs 0.7; P = .04). In the multivariate model, the C/C genotype predicted a steeper second-phase decline when adjusted for race (P = .01). CONCLUSIONS: The presence of the C/C genotype at IL28B rs12979860 exerts its antiviral effect by increasing the infected hepatocyte death rate. This suggests that an immune-mediated mechanism is responsible.

Identifying the early post-HIV antibody seroconversion period.

BACKGROUND: Identifying persons with recent human immunodeficiency virus (HIV) antibody seroconversion is useful for treatment, research, and prevention, but the sensitivity and specificity of tests for this purpose are uncertain. METHODS: We used longitudinal specimens panels from 155 persons identified prior to HIV seroconversion to assess antibody-based methods for classifying persons as within 30, 60, or 90 days of seroconversion, including 2 incidence assays, a less-sensitive (LS) enzyme immunoassay (EIA), and the BED assay. RESULTS: Sensitivity and specificity, respectively, for identifying persons within 30 days of seroconversion were: 34%-57% and 98%-100% for 2 standard EIAs (employing a signal-to-cutoff ≤4.0; ≥1.0 defines HIV positive), 84% and 73% for the LS-EIA (≤0.2 cutoff), 88% and 72% for the BED (≤0.2 cutoff), and 43%-58% and 98% (≤3 bands) for 2 Western blot (WB) assays. By area under the receiver operator curves, the best test for identifying persons within 30 days of seroconversion was the number of bands on the Bio-Rad WB (0.90); within 60 days, the LS-EIA and BED (both 0.85); and for persons within 90 days the BED (0.86). CONCLUSIONS: Standard EIAs, Western blots, and HIV incidence assays provide useful information for identifying persons 30 to 90 days after seroconversion.

Rapid detection of hot-spots via tensor decomposition with applications to crime rate data.

In many real-world applications of monitoring multivariate spatio-temporal data that are non-stationary over time, one is often interested in detecting hot-spots with spatial sparsity and temporal consistency, instead of detecting system-wise changes as in traditional statistical process control (SPC) literature. In this paper, we propose an efficient method to detect hot-spots through tensor decomposition, and our method has three steps. First, we fit the observed data into a Smooth Sparse Decomposition Tensor (SSD-Tensor) model that serves as a dimension reduction and de-noising technique: it is an additive model decomposing the original data into: smooth but non-stationary global mean, sparse local anomalies, and random noises. Next, we estimate model parameters by the penalized framework that includes Least Absolute Shrinkage and Selection Operator (LASSO) and fused LASSO penalty. An efficient recursive optimization algorithm is developed based on Fast Iterative Shrinkage Thresholding Algorithm (FISTA). Finally, we apply a Cumulative Sum (CUSUM) Control Chart to monitor model residuals after removing global means, which helps to detect when and where hot-spots occur. To demonstrate the usefulness of our proposed SSD-Tensor method, we compare it with several other methods including scan statistics, LASSO-based, PCA-based, T2-based control chart in extensive numerical simulation studies and a real crime rate dataset.

Assessing the validity of plasma phospholipid fatty acids as biomarkers of dairy fat intake using data from a randomized controlled intervention trial.

BACKGROUND: Plasma phospholipid pentadecanoic acid (C15:0), heptadecanoic acid (C17:0), and trans-palmitoleic acid (trans-C16:1n-7) are correlates of dairy fat intake. However, their relative concentrations may be influenced by other endogenous factors, such as liver fat content, and their validity as biomarkers of dairy fat intake has yet to be established. OBJECTIVES: We investigated whether liver fat content modifies relations between concentrations of C15:0, C17:0, and trans-C16:1n-7 (alone and in combination with iso-C17:0) and known dairy fat intake in the context of a randomized controlled intervention study. We further examined the proportion of dairy fat intake explained by these fatty acids on their own and when considering liver fat content. METHODS: We used data from a 12-wk intervention trial in which participants (n = 62) consumed diets limited in dairy (0.3 g/d of dairy fat), rich in low-fat dairy (8.7 g/d of dairy fat), or rich in full-fat dairy (28.5 g/d of dairy fat). We used linear regression models to examine relations between relative fatty acid concentrations and grams per day of dairy fat intake, liver fat percentage, and their interaction. RESULTS: Only trans-C16:1n-7 in isolation (ß: 0.0004 ± 0.0002, P = 0.03) and combined with iso-C17:0 (ß: 0.002 ± 0.0005, P < 0.0001) were consistently positively associated with dairy fat intake regardless of liver fat content. Trans-C16:1n-7 combined with iso-C17:0 also explained the greatest proportion of variation (35.4%) in dairy fat intake. C15:0 and C17:0 were not associated with dairy fat intake after adjusting for liver fat and were predicted to be higher in relation to increased dairy fat intake only among individuals with elevated liver fat. CONCLUSIONS: The potential for liver fat to affect relative plasma phospholipid concentrations of C15:0 and C17:0 raises questions about their validity as biomarkers of dairy fat intake. Of the fatty acid measures tested, trans-C16:1n-7 combined with iso-C17:0, especially with adjustment of liver fat, age, and sex, may provide the most robust estimate of dairy fat consumption.

Post-prostatic massage fluid/urine as an alternative to semen for studying male genitourinary HIV-1 shedding.

OBJECTIVES: Genitourinary tract samples are required to investigate male HIV-1 infectivity. Because semen collection is often impractical, the acceptability, feasibility and validity of post-prostatic massage fluid/urine (post-PMF/U) was evaluated for studying male genitourinary HIV-1 shedding. METHODS: HIV-1-seropositive men were evaluated after 48 h of sexual abstinence. At each visit, a clinician performed prostatic massage, then post-PMF/U and blood were collected. Participants provided semen specimens 1 week later. An audio computer-assisted self-interview (ACASI) administered after each specimen collection evaluated acceptability, adherence to instructions and recent genitourinary symptoms. HIV-1 RNA was quantified using a real-time PCR assay. Detection and quantitation of HIV-1 RNA and stability over visits were compared for semen, post-PMF/U and blood. RESULTS: Post-PMF/U was successfully obtained at 106 visits (64%) and semen at 136 visits (81%, p<0.001). In ACASI, discomfort was rated higher for post-PMF/U collection (p=0.003), but there was no significant difference in acceptability. Detection of HIV-1 RNA in post-PMF/U was associated with detection in semen (p=0.02). Semen and post-PMF/U HIV-1-RNA levels were correlated (ρ=0.657, p<0.001). Concordance of results at repeat visits was 78.9% for post-PMF/U (κ=0.519, p=0.02) and 89.5% for both blood and semen (κ=0.774, p=0.001). CONCLUSIONS: Although semen collections were more successful, both post-PMF/U and semen collections were acceptable to many participants. HIV-1 RNA detection and levels were closely associated in semen and post-PMF/U, and results were relatively stable across visits. To assess male HIV-1 infectivity, post-PMF/U may represent a valid alternative when semen cannot be obtained.