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1.  Prior Human Polyomavirus and Papillomavirus Infection and Incident Lung Cancer: A Nested Case-Control Study 
Cancer causes & control : CCC  2015;26(12):1835-1844.
Purpose
To test whether infection with select human polyomaviruses (HPyV) and human papillomaviruses (HPV) is associated with incident lung cancer.
Methods
We performed a nested case-control study, testing serum from the Carotene and Retinol Efficacy Trial (CARET), conducted 1985–2005, for antibodies to Merkel cell (MCV), KI (KIV), and WU (WUV) HPyVs as well as to six high-risk and two low-risk HPV types. Incident lung cancer cases (n=200) were frequency-matched with controls (n=200) on age, enrollment and blood draw dates, intervention arm assignment, and the number of serum freeze / thaw cycles. Sera were tested using multiplex liquid bead microarray antibody assays. We used logistic regression to assess the association between HPyV and HPV antibodies and lung cancer.
Results
There was no evidence of a positive association between levels of MCV, KIV, or WUV antibodies and incident lung cancer (P-corrected>0.10 for all trend tests; odds ratio (OR) range 0.72 to 1.09, P-corrected>0.10 for all). There was also no evidence for a positive association between HPV 16 or 18 infection and incident lung cancer (P-corrected≥0.10 for all trend tests; OR range 0.25 to 2.54, P>0.05 for all OR>1), but the number of persons with serologic evidence of these infections was small.
Conclusions
Prior infection with any of several types of HPyV or HPV was not associated with subsequent diagnosis of lung cancer. Infection with these viruses likely does not influence a person’s risk of lung cancer in Western smoking populations.
doi:10.1007/s10552-015-0676-3
PMCID: PMC4628600  PMID: 26415892
lung cancer; KI polyomavirus; WU polyomavirus; Merkel cell polyomavirus; HPV
2.  Epidemiology of Human Papillomavirus (HPV) Detected in the Oral Cavity and Fingernails of Mid-Adult Women 
Sexually transmitted diseases  2015;42(12):677-685.
Background
Oral and fingernail human papillomavirus (HPV) detection may be associated with HPV-related carcinoma risk at these non-genital sites and foster transmission to the genitals. We describe the epidemiology of oral and fingernail HPV among mid-adult women.
Methods
Between 2011–2012, 409 women aged 30–50 years were followed for 6 months. Women completed health and behavior surveys and provided self-collected oral, fingernail, and vaginal specimens at enrollment and exit for type-specific HPV DNA testing. Concordance of type-specific HPV detection across anatomic sites was described with kappa statistics. Using generalized estimating equations or exact logistic regression, we measured the univariate associations of various risk factors with type-specific oral and fingernail HPV detection.
Results
Prevalence of detecting HPV in the oral cavity (2.4%) and fingernails (3.8%) was low compared to the vagina (33.1%). Concordance across anatomic sites was poor (kappa<.20 for all comparisons). However, concurrent vaginal infection with the same HPV type (OR=101.0;95%CI: 31.4–748.6) and vaginal HPV viral load (OR per one log10 viral load increase=2.2;95%CI:1.5–5.5) were each associated with fingernail HPV detection. Abnormal Pap history (OR=11.1;95%CI:2.8-infinity), lifetime number of male vaginal sex partners ≥10 (OR vs. 0–3 partners=5.0;95%CI:1.2-infinity), and lifetime number of open-mouth kissing partners ≥16 (OR vs. 0–15 partners=infinity;95%CI:2.6-infinity, by exact logistic regression) were each associated with oral HPV detection.
Conclusions
While our findings support HPV DNA deposition or autoinoculation between anatomic sites in mid-adult women, the rarity of HPV in the oral cavity and fingernails suggests that oral/fingernail HPV does not account for a significant fraction of HPV in genital sites.
doi:10.1097/OLQ.0000000000000362
PMCID: PMC4646722  PMID: 26562696
human papillomavirus; women; oral; fingernail
3.  “Improved” but Not Necessarily Safe: An Assessment of Fecal Contamination of Household Drinking Water in Rural Peru 
The indicator used to measure progress toward the Millennium Development Goal (MDG) for water is access to an improved water supply. However, improved supplies are frequently fecally contaminated in developing countries. We examined factors associated with Escherichia coli contamination of improved water supplies in rural Pisco province, Peru. A random sample of 207 households with at least one child less than 5 years old was surveyed, and water samples from the source and storage container were tested for E. coli contamination. Although over 90% of households used an improved water source, 47% of source and 43% of stored water samples were contaminated with E. coli. Pouring or using a spigot to obtain water from the storage container instead of dipping a hand or object was associated with decreased risk of contamination of stored water (adjusted prevalence ratio [aPR] = 0.58, 95% confidence interval [CI] = 0.42, 0.80). Container cleanliness (aPR = 0.67, 95% CI = 0.45, 1.00) and correct handwashing technique (aPR = 0.62, 95% CI = 0.42, 0.90) were also associated with decreased contamination risk. These findings highlighted the limitations of improved water supplies as an indicator of safe water access. To ensure water safety in the home, household water treatment and improved hygiene, water handling, and storage practices should be promoted.
doi:10.4269/ajtmh.14-0802
PMCID: PMC4559687  PMID: 26195455
4.  Progression of Extrapyramidal Signs in Alzheimer's Disease: Clinical and Neuropathological Correlates 
Journal of Alzheimer's disease : JAD  2015;49(4):1085-1093.
Background
Extrapyramidal signs (EPS) are frequent in Alzheimer's disease (AD) and core manifestation of related diseases, i.e., dementia with Lewy bodies and Parkinson's disease; furthermore, Lewy bodies and AD-type pathology occur in all three conditions.
Objective
To identify clusters of EPS progression over time and their clinical and neuropathological correlates.
Methods
3,502 AD patients with longitudinal assessment from the National Alzheimer's Coordinating Center database were included; 394 provided neuropathological data. k-means algorithm was employed to identify clusters of EPS progression and those were compared in terms of cognitive profile, neuropsychiatric features and neuropathological findings.
Results
Three clusters of EPS progression were identified: no/low (n = 1,583), medium (n = 1,259), and high (n = 660) EPS burden. Compared to those with no/low and medium EPS, those with high EPS had greater cognitive and neuropsychiatric impairment, specifically hallucinations. Despite similar AD-pathology across the three clusters, the high EPS cluster had a significantly number of subjects diagnosed with dementia with Lewy bodies.
Conclusions
Cluster analysis of EPS progression over time identified different subgroups of AD patients with distinct clinical and neuropathological features.
doi:10.3233/JAD-150244
PMCID: PMC4779642  PMID: 26599050
Alzheimer's disease; extrapyramidal signs; Lewy bodies; longitudinal studies; K-means clustering
5.  Short-term Natural History of High-Risk Human Papillomavirus Infection in Mid-Adult Women Sampled Monthly (Short title: Short-term HPV Natural History in Mid-Adult Women) 
Characterizing short-term HPV detection patterns and viral load may inform HPV natural history in mid-adult women. From 2011–2012, we recruited women aged 30–50 years. Women submitted monthly self-collected vaginal samples for high-risk HPV DNA testing for 6 months. Positive samples were tested for type-specific HPV DNA load by real-time PCR. HPV type-adjusted linear and Poisson regression assessed factors associated with 1) viral load at initial HPV detection and 2) repeat type-specific HPV detection. One-hundred thirty-nine women (36% of 387 women with ≥4 samples) contributed 243 type-specific HR HPV infections during the study; 54% of infections were prevalent and 46% were incident. Incident (versus prevalent) detection and past pregnancy were associated with lower viral load, whereas current smoking was associated with higher viral load. In multivariate analysis, current smoking was associated with a 40% (95%CI:5%–87%) increase in the proportion of samples that were repeatedly positive for the same HPV type, whereas incident (versus prevalent) detection status and past pregnancy were each associated with a reduction in the proportion of samples repeatedly positive (55%,95%CI:38%–67% and 26%,95%CI:10%–39%, respectively). In a separate multivariate model, each log10 increase in viral load was associated with a 10% (95%CI:4%–16%) increase in the proportion of samples repeatedly positive. Factors associated with repeat HPV detection were similar to those observed in longer-term studies, suggesting that short-term repeat detection may relate to long-term persistence. The negative associations between incident HPV detection and both viral load and repeat detection suggest that reactivation or intermittent persistence was more common than new acquisition.
doi:10.1002/ijc.29602
PMCID: PMC4591913  PMID: 25976733
human papillomavirus; viral load; natural history; women
6.  Pattern of extrapyramidal signs in Alzheimer’s disease 
Journal of neurology  2015;262(11):2548-2556.
Patients with Alzheimer’s disease (AD) often develop extrapyramidal signs (EPS), which increase in frequency as the disease progresses. We aimed to investigate the patterns of presentation of EPS in AD and their correlation with clinical and neuropathological features. 4284 subjects diagnosed with AD from the National Alzheimer’s Coordinating Center (NACC) database with at least one abnormal Unified Parkinson’s Disease Rating Scale (UPDRS) assessment were included. Individuals were assigned to a discovery sample and a sensitivity analysis sample (moderate and mild dementia, respectively) and a subset of subjects provided neuropathological data (n = 284). Individuals from the Washington Heights and Inwood Columbia Aging Project (WHICAP) served as validation sample. Patterns of presentation of EPS were identified employing categorical principal component analysis (CATPCA). Six principal components were identified in both mild and moderate AD samples: (I) hand movements, alternating movements, finger tapping, leg agility (“limbs bradykinesia”); (II) posture, postural instability, arising from chair, gait and body bradykinesia/hypokinesia (“axial”); (III) limb rigidity (“rigidity”); (IV) postural tremor; (V) resting tremor; (VI) speech and facial expression. Similar results were obtained in the WHICAP cohort. Individuals with hallucinations, apathy, aberrant night behaviors and more severe dementia showed higher axial and limb bradykinesia scores. “Limb bradykinesia” component was associated with a neuropathological diagnosis of Lewy body disease and “axial” component with reduced AD-type pathology. Patterns of EPS in AD show distinct clinical and neuropathological correlates; they share a pattern of presentation similar to that seen in Parkinson’s disease, suggesting common pathogenic mechanisms across neurodegenerative diseases.
doi:10.1007/s00415-015-7886-1
PMCID: PMC4776751  PMID: 26338814
Alzheimer’s disease; Extrapyramidal signs; CATPCA; Lewy bodies
7.  Analysis of Liquid Bead Microarray Antibody Assay Data for Epidemiologic Studies of Pathogen-Cancer Associations 
Background
Liquid bead microarray antibody (LBMA) assays are used to assess pathogen-cancer associations. However, studies analyze LBMA data differently, limiting comparability.
Methods
We generated 10,000 Monte Carlo-type simulations of log-normal antibody distributions (exposure) with 200 cases and 200 controls (outcome). We estimated type I error rates, statistical power, and bias associated with t-tests, logistic regression with a linear exposure and with the exposure dichotomized at 200 units, 400 units, the mean among controls plus two standard deviations, and the value corresponding to the optimal sensitivity and specificity. We also applied these models, and data visualizations (kernel density plots, receiver operating characteristic (ROC) curves, predicted probability plots, and Q-Q plots), to two empirical datasets to assess the consistency of the exposure-outcome relationship.
Results
All strategies had acceptable type I error rates (0.03≤P≤0.048), except for the dichotomization according to optimal sensitivity and specificity, which had a type I error rate of 0.27. Among the remaining methods, logistic regression with a linear predictor (Power=1.00) and t-tests (Power=1.00) had the highest power to detect a mean difference of 1.0 MFI (median fluorescence intensity) on the log scale and were unbiased. Dichotomization methods upwardly biased the risk estimates.
Conclusion
These results indicate that logistic regression with linear predictors and unpaired t-tests are superior to logistic regression with dichotomized predictors for assessing disease associations with LBMA data. Logistic regression with continuous linear predictors and t-tests are preferable to commonly used LBMA dichotomization methods.
doi:10.1016/j.jim.2015.06.007
PMCID: PMC4604026  PMID: 26071614
liquid bead microarray antibody assay; median fluorescence intensity; cut-point; dichotomization; visualization
9.  Risk of Adverse Infant Outcomes Associated with Maternal Tuberculosis in a Low Burden Setting: A Population-Based Retrospective Cohort Study 
Background. Maternal tuberculosis (TB) may be associated with increased risk of adverse infant outcomes. Study Design. We examined the risk of low birth weight (LBW), small for gestational age (SGA), and preterm birth (<37 weeks) associated with maternal TB in a retrospective population-based Washington State cohort using linked infant birth certificate and maternal delivery hospitalization discharge records. We identified 134 women with births between 1987 and 2012 with TB-associated ICD-9 diagnosis codes at hospital delivery discharge and 536 randomly selected women without TB, frequency matched 4 : 1 on delivery year. Multinomial logistic regression analyses were performed to compare the risk of LBW, SGA, and preterm birth between infants born to mothers with and without TB. Results. Infants born to women with TB were 3.74 (aRR 95% CI 1.40–10.00) times as likely to be LBW and 1.96 (aRR 95% CI 0.91–4.22) as likely to be SGA compared to infants born to mothers without TB. Risk of prematurity was similar (aRR 1.01 95% CI 0.39–2.58). Conclusion. Maternal TB is associated with poor infant outcomes even in a low burden setting. A better understanding of the adverse infant outcomes associated with maternal TB, reflecting recent trends in US TB epidemiology, may inform potential targeted interventions in other low prevalence settings.
doi:10.1155/2016/6413713
PMCID: PMC4771913  PMID: 26989338
10.  Absence of an association of human polyomavirus and papillomavirus infection with lung cancer in China: a nested case–control study 
BMC Cancer  2016;16:342.
Background
Studies of human polyomavirus (HPyV) infection and lung cancer are limited and those regarding the association of human papillomavirus (HPV) infection and lung cancer have produced inconsistent results.
Methods
We conducted a nested case–control study to assess the association between incident lung cancer of various histologies and evidence of prior infection with HPyVs and HPVs. We selected serum from 183 cases and 217 frequency matched controls from the Yunnan Tin Miner’s Cohort study, which was designed to identify biomarkers for early detection of lung cancer. Using multiplex liquid bead microarray (LBMA) antibody assays, we tested for antibodies to the VP1 structural protein and small T antigen (ST-Ag) of Merkel cell, KI, and WU HPyVs. We also tested for antibodies against HPV L1 structural proteins (high-risk types 16, 18, 31, 33, 52, and 58 and low-risk types 6 and 11) and E6 and E7 oncoproteins (high risk types 16 and 18). Measures of antibody reactivity were log transformed and analyzed using logistic regression.
Results
We found no association between KIV, WUV, and MCV antibody levels and incident lung cancer (P-corrected for multiple comparisons >0.10 for all trend tests). We also found no association with HPV-16, 18, 31, 33, 52, and 58 seropositivity (P-corrected for multiple comparisons >0.05 for all).
Conclusions
Future studies of infectious etiologies of lung cancer should look beyond HPyVs and HPVs as candidate infectious agents.
Electronic supplementary material
The online version of this article (doi:10.1186/s12885-016-2381-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12885-016-2381-3
PMCID: PMC4888628  PMID: 27246610
Lung cancer; Human polyomavirus; KI polyomavirus; WU polyomavirus; Merkel cell polyomavirus; Human papillomavirus
11.  High Prevalence of Severe Food Insecurity and Malnutrition among HIV-Infected Adults in Senegal, West Africa 
PLoS ONE  2015;10(11):e0141819.
Background
Malnutrition and food insecurity are associated with increased mortality and poor clinical outcomes among people living with HIV/AIDS; however, the prevalence of malnutrition and food insecurity among people living with HIV/AIDS in Senegal, West Africa is unknown. The objective of this study was to determine the prevalence and severity of food insecurity and malnutrition among HIV-infected adults in Senegal, and to identify associations between food insecurity, malnutrition, and HIV outcomes.
Methods
We conducted a cross-sectional study at outpatient clinics in Dakar and Ziguinchor, Senegal. Data were collected using participant interviews, anthropometry, the Household Food Insecurity Access Scale, the Individual Dietary Diversity Scale, and chart review.
Results
One hundred and nine HIV-1 and/or HIV-2 participants were enrolled. The prevalence of food insecurity was 84.6% in Dakar and 89.5% in Ziguinchor. The prevalence of severe food insecurity was 59.6% in Dakar and 75.4% in Ziguinchor. The prevalence of malnutrition (BMI <18.5) was 19.2% in Dakar and 26.3% in Ziguinchor. Severe food insecurity was associated with missing clinic appointments (p = 0.01) and not taking antiretroviral therapy due to hunger (p = 0.02). Malnutrition was associated with lower CD4 cell counts (p = 0.01).
Conclusions
Severe food insecurity and malnutrition are highly prevalent among HIV-infected adults in both Dakar and Ziguinchor, and are associated with poor HIV outcomes. Our findings warrant further studies to determine the root causes of malnutrition and food insecurity in Senegal, and the short- and long-term impacts of malnutrition and food insecurity on HIV care. Urgent interventions are needed to address the unacceptably high rates of malnutrition and food insecurity in this population.
doi:10.1371/journal.pone.0141819
PMCID: PMC4631507  PMID: 26529509
12.  HIV-1 outcompetes HIV-2 in dually infected Senegalese individuals with low CD4+ cell counts 
AIDS (London, England)  2013;27(15):2441-2450.
Objective
Dual infection with HIV-1 and HIV-2, which is not uncommon in West Africa, has implications for transmission, progression, and antiretroviral therapy (ART). Few studies have examined viral dynamics in this setting. Our objective was to directly compare HIV-1 and HIV-2 viral loads and to examine whether this relationship is associated with CD4+ cell count.
Study design
This is a retrospective analysis of data from observational cohort studies.
Methods
We compared HIV-1 and HIV-2 viral loads from 65 dually infected, ART-naive Senegalese individuals. Participants provided blood, oral fluid, and cervicovaginal lavage (CVL) or semen samples for virologic and immunologic testing. We assessed relationships between HIV-1 and HIV-2 levels using linear regression with generalized estimating equations to account for multiple study visits.
Results
After adjusting for CD4+ cell count, age, sex, and commercial sex work, HIV-1 RNA levels were significantly higher than HIV-2 levels in semen, CVL, and oral fluids. Despite similar peripheral blood mononuclear cell DNA levels among individuals with CD4+ cell counts above 500 cells/µl, individuals with CD4+ cell counts below 500 cells/µl had higher HIV-1 and lower HIV-2 DNA levels. Individuals with high CD4+ cell counts had higher mean HIV-1 plasma RNA viral loads than HIV-2, with HIV-1 levels significantly higher and HIV-2 levels trending toward lower mean viral loads among individuals with low CD4+ cell counts.
Conclusion
Our data are consistent with the hypothesis that with disease progression, HIV-1 outcompetes HIV-2 in dually infected individuals. This finding helps explain differences in prevalence and outcomes between HIV-1, HIV-2, and HIV-dual infection.
doi:10.1097/QAD.0b013e328362e856
PMCID: PMC4043222  PMID: 23665777
HIV dual infection; HIV viral load; HIV-1; HIV-2; Senegal
13.  HIV shedding in the oral cavity: an assessment of HIV type, immunovirologic, demographic and oral factors 
Objective
To quantify the prevalence and burden of HIV type 2 (HIV-2) and HIV-1 RNA in the oral cavity of antiretroviral therapy-naive HIV-infected Senegalese individuals and to identify correlates of oral HIV viral loads.
Design
A cross-sectional study of 163 HIV-1 and 27 HIV-2-infected antiretroviral therapy-naive Senegalese adults.
Methods
Participants received clinical and oral exams and provided blood and oral wash samples for viral load and plasma CD4 count ascertainment. Logistic and interval regression models were used to identify univariate and multivariable associations between presence and level of oral HIV RNA and various immunovirologic, local and demographic factors.
Results
Presence of detectable oral HIV RNA was less common in HIV-2-infected compared with HIV-1-infected study participants (33% vs 67%, OR 0.25, 95% CI 0.11 to 0.59). HIV type was no longer associated with oral shedding of HIV when plasma viral load was considered. Detection of oral HIV RNA was associated with increased plasma viral load in both HIV-1-infected and HIV-2-infected individuals (HIV-1, OR 1.89, 95% CI 1.24 to 2.61; HIV-2, OR 1.93, 95% CI 1.1 to 3.39). Oral HIV-1 detection was also associated with periodontal disease (OR 3.02, 95% CI 1.16 to 7.87).
Conclusions
Oral shedding of HIV-2 RNA is less common than HIV-1 RNA, a likely consequence of lower overall viral burden. Both systemic and local factors may contribute to shedding of HIV in the oral cavity.
doi:10.1136/sextrans-2011-050231
PMCID: PMC4028315  PMID: 22250179
14.  Association of Maternal Smoking during Pregnancy with Infant Hospitalization and Mortality Due to Infectious Diseases 
Background
Maternal smoking is associated with infant respiratory infections and with increased risk of low birthweight (LBW) infants and preterm birth. This study assesses the association of maternal smoking during pregnancy with both respiratory and non-respiratory infectious disease (ID) morbidity and mortality in infants.
Methods
We conducted two retrospective case-control analyses of infants born in Washington State from 1987–2004 using linked birth certificate, death certificate, and hospital discharge records. One assessed morbidity—infants hospitalized due to ID within one year of birth (47,404 cases/48,233 controls). The second assessed mortality—infants who died within one year due to ID (627 cases/2,730 controls).
Results
Maternal smoking was associated with both hospitalization (Adjusted Odds Ratio (AOR)=1.52; 95%CI: 1.46, 1.58) and mortality (AOR=1.51; 95%CI: 1.17, 1.96) due to any ID. In subgroup analyses, maternal smoking was associated with hospitalization due to a broad range of ID including both respiratory (AOR=1.69; 95%CI: 1.63, 1.76) and non-respiratory ID (AOR=1.27; 95%CI: 1.20, 1.34). Further stratification by birthweight and gestational age did not appreciably change these estimates. In contrast, there was no association of maternal smoking with ID infant mortality when only LBW infants were considered.
Conclusions
Maternal smoking was associated with a broad range of both respiratory and non-respiratory ID outcomes. Despite attenuation of the mortality association among LBW infants, ID hospitalization was found to be independent of both birthweight and gestational age. These findings suggest that full-term infants of normal weight whose mothers smoked may suffer an increased risk of serious ID morbidity and mortality.
doi:10.1097/INF.0b013e3182704bb5
PMCID: PMC3588859  PMID: 22929173
infant; infectious disease; prenatal exposure; maternal smoking
15.  Sexually Explicit Online Media and Sexual Risk among Men Who Have Sex with Men in the United States 
Archives of sexual behavior  2014;43(4):833-843.
This study aimed to describe sexually explicit online media (SEOM) consumption among men who have sex with men (MSM) in the United States and examine associations between exposure to unprotected anal intercourse (UAI) in SEOM and engagement in both UAI and serodiscordant UAI. MSM in the U.S. who accessed a men-seeking-men website in the past year (N = 1,170) were recruited online for a cross-sectional, Internet-based survey of sexual risk and SEOM consumption. In the three months prior to interview, more than half (57%) of the men reported viewing SEOM one or more times per day and almost half (45%) reported that at least half of the SEOM they viewed portrayed UA. Compared to participants who reported that 0–24% of the SEOM they viewed showed UAI, participants who reported that 25–49%, 50–74%, or 75–100% of the SEOM they viewed portrayed UAI had progressively increasing odds of engaging in UAI and serodiscordant UAI in the past three months. As SEOM has become more ubiquitous and accessible, research should examine causal relations between SEOM consumption and sexual risk-taking among MSM as well as ways to use SEOM for HIV prevention.
doi:10.1007/s10508-013-0238-2
PMCID: PMC4011997  PMID: 24464547
HIV; men who have sex with men (MSM); sexually explicit media; pornography; sexual risk-taking
16.  Deconstructing the differences: a comparison of GBD 2010 and CHERG’s approach to estimating the mortality burden of diarrhea, pneumonia, and their etiologies 
Background
Pneumonia and diarrhea are leading causes of death for children under five (U5). It is challenging to estimate the total number of deaths and cause-specific mortality fractions. Two major efforts, one led by the Institute for Health Metrics and Evaluation (IHME) and the other led by the World Health Organization (WHO)/Child Health Epidemiology Reference Group (CHERG) created estimates for the burden of disease due to these two syndromes, yet their estimates differed greatly for 2010.
Methods
This paper discusses three main drivers of the differences: data sources, data processing, and covariates used for modelling. The paper discusses differences in the model assumptions for etiology-specific estimates and presents recommendations for improving future models.
Results
IHME’s Global Burden of Disease (GBD) 2010 study estimated 6.8 million U5 deaths compared to 7.6 million U5 deaths from CHERG. The proportional differences between the pneumonia and diarrhea burden estimates from the two groups are much larger; GBD 2010 estimated 0.847 million and CHERG estimated 1.396 million due to pneumonia. Compared to CHERG, GBD 2010 used broader inclusion criteria for verbal autopsy and vital registration data. GBD 2010 and CHERG used different data processing procedures and therefore attributed the causes of neonatal death differently. The major difference in pneumonia etiologies modeling approach was the inclusion of observational study data; GBD 2010 included observational studies. CHERG relied on vaccine efficacy studies.
Discussion
Greater transparency in modeling methods and more timely access to data sources are needed. In October 2013, the Bill & Melinda Gates Foundation (BMGF) hosted an expert meeting to examine possible approaches for better estimation. The group recommended examining the impact of data by systematically excluding sources in their models. GBD 2.0 will use a counterfactual approach for estimating mortality from pathogens due to specific etiologies to overcome bias of the methods used in GBD 2010 going forward.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-014-0728-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-014-0728-4
PMCID: PMC4305232  PMID: 25592774
17.  DNA hypermethylation of tumors from non-small cell lung cancer (NSCLC) patients is associated with gender and histologic type 
Background
We previously identified a number of genes which were methylated significantly more frequently in the tumor compared to the non-cancerous lung tissues from non-small cell lung cancer (NSCLC) patients. Detection of methylation profiles of genes in NSCLC could provide insight into differential pathways to malignancy and lead to strategies for better treatment of individuals with NSCLC.
Methods
We determined the DNA methylation status of 27 genes using quantitative MethyLight assays in lung tumor samples from 117 clinically well-characterized NSCLC patients.
Results
Hypermethylation was detected in one of more of the genes in 106 (91%) of 117 cases and was detected at high levels (Percentage of Methylation Reference (PMR)≥4%) in 79% of NSCLC cases. Methylation of APC, CCND2, KCNH5 and, RUNX was significantly more frequent in adenocarcinomas compared to squamous cell carcinomas (SCC), while methylation of CDKN2A was more common in SCC. Hypermethylation of KCNH5, KCNH8, and RARB was more frequent in females compared to males. Hypermethylation of APC and CCND2 was inversely associated with proliferation score assessed by Ki-67 level.
Conclusions
Our findings of differential gene hypermethylation frequencies in tumor tissues from patients with adenocarcinoma or squamous cell cancers and in females compared to males suggests that further investigation is warranted in order to more fully understand the potential disparate pathways and/or risk factors for NSCLC associated with histologic type and gender.
doi:10.1016/j.lungcan.2009.11.002
PMCID: PMC2888601  PMID: 19945765
hypermethylation; lung cancer; gender; histology
18.  A community-based cluster randomized survey of noncommunicable disease and risk factors in a peri-urban shantytown in Lima, Peru 
Background
An estimated 863 million people–a third of the world’s urban population–live in slums, yet there is little information on the disease burden in these settings, particularly regarding chronic preventable diseases.
Methods
From March to May 2012, we conducted a cluster randomized survey to estimate the prevalence of noncommunicable diseases (NCDs) and associated risk factors in a peri-urban shantytown north of Lima, Peru. Field workers administered a questionnaire that included items from the WHO World Health Survey and the WHO STEPS survey of chronic disease risk factors. We used logistic regression to assess the associations of NCDs and related risk factors with age and gender. We accounted for sampling weights and the clustered sampling design using statistical survey methods.
Results
A total of 142 adults were surveyed and had a weighted mean age of 36 years (range 18–81). The most prevalent diseases were depression (12%) and chronic respiratory disease (8%), while lifetime prevalence of cancer, arthritis, myocardial infarction, and diabetes were all less than 5%. Fifteen percent of respondents were hypertensive and the majority (67%) was unaware of their condition. Being overweight or obese was common for both genders (53%), but abdominal obesity was more prevalent in women (54% vs. 10% in men, p < 0.001). Thirty-five percent of men binge drank and 34% reported current smoking; these behaviors were less common among women (4% binge drank, p < 0.001; 8% smoked, p = 0.002). Increasing age was associated with an increased risk of abdominal obesity (Odds Ratio (OR) = 1.04, 95% CI = 1.01, 1.07, p = 0.02), hypertension (OR = 1.06, 95% CI = 1.02, 1.10, p = 0.006), arthritis (OR = 1.07, 95% CI = 1.03, 1.11, p < 0.001) and cancer (OR = 1.13, 95% CI = 1.07, 1.20, p < 0.001) in adjusted models. The prevalences of other NCDs and related risk factors were similar when stratified by age or gender.
Conclusions
This study underlines the important burden of noncommunicable disease in informal settlements in Peru and suggests that prevention and treatment interventions could be optimized according to age and gender.
doi:10.1186/1472-698X-14-19
PMCID: PMC4040114  PMID: 24885980
Peru; Slum; Shantytown; Noncommunicable disease
19.  Pregnancy outcomes in women infected with Chlamydia trachomatis: a population‐based cohort study in Washington State 
Sexually Transmitted Infections  2007;83(4):314-318.
Objectives
To measure the risk of preterm delivery, premature rupture of membranes, infant low birth weight and infant mortality, by a population‐based retrospective cohort study using Washington State birth certificate data.
Methods
All women diagnosed with Chlamydia trachomatis infection (n = 851), noted with a check box on the birth certificate from 2003, and a randomly selected sample of women not diagnosed with C trachomatis (n = 3404) were identified. To assess the RR between chlamydia infection and pregnancy outcomes, multivariable logistic regression analysis was used.
Results
Women with chlamydia infection were younger, more likely to be non‐white and had less years of education compared with women without chlamydia. Additionally, they were more likely to have inadequate prenatal care and coinfections with other sexually transmitted infections. After adjusting for age and education, chlamydia‐infected women were at an increased risk of preterm delivery (RR 1.46, 95% CI 1.08 to 1.99) and premature rupture of membranes (RR 1.50, 95% CI 1.03 to 2.17) compared with non‐infected women. However, no increased risk of infant death (RR 1.02, 95% CI 0.37 to 2.80) or low birth weight (RR 1.12, 95% CI 0.74 to 1.68) associated with chlamydia infection was observed.
Conclusion
This study suggests that C trachomatis is associated with an increased risk of preterm delivery and premature rupture of membranes, but not with infant death and low birth weight. Routine screening and opportune treatment for C trachomatis should be considered a necessary part of prenatal care to reduce these adverse pregnancy outcomes.
doi:10.1136/sti.2006.022665
PMCID: PMC2598687  PMID: 17344249
20.  Care-seeking and appropriate treatment for childhood acute respiratory illness: an analysis of Demographic and Health Survey and Multiple Indicators Cluster Survey datasets for high-mortality countries 
BMC Public Health  2014;14:446.
Background
Acute lower respiratory illness (ALRI) is a major global cause of morbidity and mortality among children under 5. Antibiotic treatment for ALRI is inexpensive and decreases case fatality, but care-seeking patterns and appropriate treatment vary widely across countries. This study sought to examine patterns of appropriate treatment and estimate the burden of cases of untreated ALRI in high mortality countries.
Methods
This study used cross-sectional survey data from the Phase 5/Phase 6 DHS and MIC3/MICS4 for 39 countries. We analyzed care-seeking patterns and antibiotic treatment based on country-level trends, and estimated the burden of untreated cases using country-level predictors in a general linear model.
Results
According to this analysis, over 66 million children were not treated with antibiotics for ALRI in 2010. Overall, African countries had a lower proportion of mothers who sought care for a recent episode of ALRI (41% to 86%) relative to Asian countries (75% to 87%). Seeking any care for ALRI was inversely related to seeking public sector care. Treatment with antibiotics ranged from 8% in Nepal to 87% in Jordan, and was significantly associated with urban residence.
Conclusions
Untreated ALRI remains a substantial problem in high mortality countries. In Asia, the large population numbers lead to a high burden of children with untreated ALRI. In Africa, care-seeking behaviors and access to care issues may lead to missed opportunities to treat children with antibiotics.
doi:10.1186/1471-2458-14-446
PMCID: PMC4024183  PMID: 24884919
Acute lower respiratory infection; Antibiotic treatment; Child health; High mortality countries
21.  Technologies for Detecting Falsified and Substandard Drugs in Low and Middle-Income Countries 
PLoS ONE  2014;9(3):e90601.
Falsified and substandard drugs are a global health problem, particularly in low- and middle-income countries (LMIC) that have weak pharmacovigilance and drug regulatory systems. Poor quality medicines have important health consequences, including the potential for treatment failure, development of antimicrobial resistance, and serious adverse drug reactions, increasing healthcare costs and undermining the public's confidence in healthcare systems. This article presents a review of the methods employed for the analysis of pharmaceutical formulations. Technologies for detecting substandard and falsified drugs were identified primarily through literature reviews. Key-informant interviews with experts augmented our methods when warranted. In order to aid comparisons, technologies were assigned a suitability score for use in LMIC ranging from 0–8. Scores measured the need for electricity, need for sample preparation, need for reagents, portability, level of training required, and speed of analysis. Technologies with higher scores were deemed the most feasible in LMICs. We categorized technologies that cost $10,000 USD or less as low cost, $10,000–100,000 USD as medium cost and those greater than $100,000 USD as high cost technologies (all prices are 2013 USD). This search strategy yielded information on 42 unique technologies. Five technologies were deemed both low cost and had feasibility scores between 6–8, and an additional four technologies had medium cost and high feasibility. Twelve technologies were deemed portable and therefore could be used in the field. Many technologies can aid in the detection of substandard and falsified drugs that vary from the simplest of checklists for packaging to the most complex mass spectrometry analyses. Although there is no single technology that can serve all the requirements of detecting falsified and substandard drugs, there is an opportunity to bifurcate the technologies into specific niches to address specific sections within the workflow process of detecting products.
doi:10.1371/journal.pone.0090601
PMCID: PMC3966738  PMID: 24671033
22.  Complex Patterns of Protease Inhibitor Resistance among Antiretroviral Treatment-Experienced HIV-2 Patients from Senegal: Implications for Second-Line Therapy 
Protease inhibitor (PI)-based antiretroviral therapy (ART) can effectively suppress HIV-2 plasma load and increase CD4 counts; however, not all PIs are equally active against HIV-2, and few data exist to support second-line therapy decisions. To identify therapeutic options for HIV-2 patients failing ART, we evaluated the frequency of PI resistance-associated amino acid changes in HIV-2 sequences from a cohort of 43 Senegalese individuals receiving unboosted indinavir (n = 18 subjects)-, lopinavir/ritonavir (n = 4)-, or indinavir and then lopinavir/ritonavir (n = 21)-containing ART. Common protease substitutions included V10I, V47A, I54M, V71I, I82F, I84V, L90M, and L99F, and most patients harbored viruses containing multiple changes. Based on genotypic data, we constructed a panel of 15 site-directed mutants of HIV-2ROD9 containing single- or multiple-treatment-associated amino acid changes in the protease-encoding region of pol. We then quantified the susceptibilities of the mutants to the HIV-2 “active” PIs saquinavir, lopinavir, and darunavir using a single-cycle assay. Relative to wild-type HIV-2, the V47A mutant was resistant to lopinavir (6.3-fold increase in the mean 50% effective concentration [EC50]), the I54M variant was resistant to darunavir and lopinavir (6.2- and 2.7-fold increases, respectively), and the L90M mutant was resistant to saquinavir (3.6-fold increase). In addition, the triple mutant that included I54M plus I84V plus L90M was resistant to all three PIs (31-, 10-, and 3.8-fold increases in the mean EC50 for darunavir, saquinavir, and lopinavir, respectively). Taken together, our data demonstrate that PI-treated HIV-2 patients frequently harbor viruses that exhibit complex patterns of PI cross-resistance. These findings suggest that sequential PI-based regimens for HIV-2 treatment may be ineffective.
doi:10.1128/AAC.00405-13
PMCID: PMC3716120  PMID: 23571535
23.  Validation for Clinical Use of a Novel HIV-2 Plasma RNA Viral Load Assay Using the Abbott m2000 Platform 
Background
Optimal care of persons infected with human immunodeficiency virus type 2 (HIV-2) requires an accurate assessment of HIV-2 plasma viral load (VL), but no clinically-approved quantitative HIV-2 RNA VL assay exists.
Objectives
To validate a novel quantitative HIV-2 RNA assay for clinical and research use.
Study Design
The Abbott m2000sp/rt platform was adapted for quantification of HIV-2 RNA in plasma. Amplification targeted a region of the long terminal repeat conserved in Group A and B HIV-2. Electron microscopy-counted-HIV-2 standards, the WHO/NIBSC HIV-2 International Standard and clinical specimens (N=162) were used to determine the precision, sensitivity, specificity, linear range, accuracy, and clinical performance of the assay.
Results
The quantitative linear range of the HIV-2 RNA assay was 10–1,000,000 copies/mL (R2 >0.99), with a limit of detection of 8 copies/mL (95% CI, 5–18 copies/ml). The assay did not cross-react with HIV-1, and quantification of HIV-2 RNA was not affected by the presence of >5 log10 HIV-1 RNA copies/mL. The total standard deviation (SD) and intra- and inter- run SD were 0.095, 0.093 and 0.162, respectively, at nominal inputs of 3.7, 1.7 and 1.0 log10 HIV-2 RNA copies/mL. The HIV-2 WHO/NIBSC International Standard (1000 IU) was shown to contain 152 RNA copies/mL (95% CI 141–163). Overall, HIV-2 RNA was quantified at ≥ 10 copies/mL from 86 (53%) clinical specimens (median, 2.24 log10copies/mL; range 10–16870), and nine specimens (6%) had HIV-2 RNA detected at <10 copies/mL.
Conclusions
We developed and validated a highly-sensitive HIV-2 VL assay that is suitable for clinical and research use.
doi:10.1016/j.jcv.2012.06.024
PMCID: PMC3444162  PMID: 22832059
HIV-2; PCR; Real-time; diagnostic; plasma viral loads
24.  Lower levels of HIV RNA in semen in HIV-2 compared with HIV-1 infection: implications for differences in transmission 
AIDS (London, England)  2006;20(6):895-900.
Background and objectives
HIV-2 infection, in comparison with HIV-1, is characterized by lower plasma viral loads, slower CD4 cell count decline, decreased AIDS-related mortality, and lower rates of mother-to-child and sexual transmission. To gain further insight into why HIV-1 is more readily transmitted as compared with HIV-2, we analyzed semen and plasma HIV RNA levels in HIV-1 and HIV-2-positive men from Senegal.
Design and methods
Twenty-two HIV-1 and 10 HIV-2-infected subjects from the University of Dakar donated semen and blood samples for this analysis. HIV-1 and HIV-2 viral loads in semen and plasma were quantified using type-specific polymerase chain reaction assays.
Results
The mean age of the subjects was 37 and 40 years; mean CD4 cell count was 222 and 276 cells/µl and the mean plasma viral load was 4.7 and 3.0 log10 copies/ml for HIV-1 and HIV-2, respectively (P = 0.002). HIV RNA was detected in semen in 21 of 22 (95%) of HIV-1 and seven of 10 (70%) of HIV-2-infected subjects; P = 0.07). However, the levels of HIV RNA present in semen were markedly different between those with HIV-1 and HIV-2, with a mean of 4.4 log10 copies/ml among those with HIV-1 and a mean of 2.6 log10 copies/ml among those with HIV-2 (P < 0.001). In multivariate analysis, plasma viral load and HIV type, but not CD4 cell count, were independently predictive of semen viral load (P = 0.03, 0.05, 0.48, respectively)
Conclusions
These data suggest that differences in semen viral load between HIV-1 and HIV-2 may be in part responsible for the markedly different transmission rates of these two viruses. In addition, risk of male genital tract shedding strongly correlates with plasma viral loads. Interventions that decrease viral load may help decrease transmission of both HIV-1 and HIV-2.
doi:10.1097/01.aids.0000218554.59531.80
PMCID: PMC3726185  PMID: 16549974
HIV-1; HIV-2; virus shedding; semen; male; Africa; Senegal
25.  Lower levels of HIV-2 than HIV-1 in the female genital tract: correlates and longitudinal assessment of viral shedding 
AIDS (London, England)  2008;22(18):2517-2525.
Background
The differing magnitude of the HIV-1 and HIV-2 epidemics is likely a consequence of differing transmission rates between the two viruses. Similar to other sexually transmitted pathogens, risk of HIV-1 and HIV-2 transmission is likely associated with the presence and amount of HIV in the genital tract. Thus, understanding patterns of, and risk factors for HIV genital tract shedding is critical to effective control of HIV transmission.
Methods
We evaluated HIV DNA and RNA detection in cervicovaginal specimens among 168 HIV-1 and 50 HIV-2-infected women in Senegal, West Africa. In a subset of 31 women (20 with HIV-1, 11 with HIV-2), we conducted a prospective study in which cervicovaginal specimens were taken at 3-day intervals over a 6-week period.
Results
We found significantly lower rates and levels of HIV-2 RNA (58% shedding; 13% with >1000 copies/ml) in the female genital tract than HIV-1 RNA (78% shedding; 40% with >1000 copies/ml) (P =0.005 and 0.005, respectively), and shedding correlated with plasma viral load irrespective of virus type (odds ratio =1.9, 95% confidence interval =1.3–2.8 for each log10 increase in HIV viral RNA). Plasma viral load, not HIV type, was the strongest predictor of genital viral load. Over 80% of closely monitored women, regardless of HIV type, had at least intermittent HIV RNA detection during every 3-day sampling over a 6-week time period.
Conclusion
These data help in explaining the different transmission rates between HIV-1 and HIV-2 and may provide new insights regarding prevention.
doi:10.1097/QAD.0b013e328315cdbc
PMCID: PMC3726195  PMID: 19005275
Africa; cervix; women; HIV-1; HIV-2; Senegal; vagina; virus shedding

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