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Even with antiretroviral therapy, children born to HIV-infected (HI) mothers are at a higher risk of early-life infections and morbidities including dental disease. The increased risk of dental caries in HI children suggest immune-mediated changes in oral bacterial communities, however, the impact of perinatal HIV exposure on the oral microbiota remains unclear. We hypothesized that the oral microbiota of HI and perinatally HIV-exposed-but-uninfected (HEU) children will significantly differ from HIV-unexposed-and-uninfected (HUU) children. Saliva samples from 286 child-participants in Nigeria, aged ≤ 6 years, were analyzed using 16S rRNA gene sequencing. Perinatal HIV infection was significantly associated with community composition (HI vs. HUU—p = 0.04; HEU vs. HUU—p = 0.11) however, immune status had stronger impacts on bacterial profiles (p

Background Convergence of tuberculosis (TB) and HIV epidemics is associated with higher morbidity and mortality risks and understanding their distribution across key demographic factors is essential for prevention and control. This analysis examines the prevalence of TB, HIV and TB-HIV coinfection across age and gender in patients with presumptive TB seeking care at the National TB and Leprosy Training Center in Nigeria. Methods Samples from 1603 presumptive pulmonary TB cases who provided informed consent were evaluated with a sequential testing algorithm that included a smear microscopy, cultures in liquid and broth media and then genotyping by Hain line probe assays. HIV was serially tested with two HIV rapid assays and retested with a third assay in non-conclusive samples. Results Twenty-three percent (375/1603) had confirmed pulmonary TB infection, 23.6% (378/1603) were positive for HIV infection and 26.9% (101/375) of the confirmed TB cases were HIV co-infected. Males had a higher prevalence of TB: 27.6% vs. 18.0%, p < .0001; and a lower prevalence of HIV: 19.0% vs. 29.6%, p < .0001. In the age range of 25–29 years, males were twice as likely to have TB (OR = 2.2; 95% confidence interval [CI]: 1.3–3.9, p = 0.0032) while females were five times more likely to have HIV (OR = 4.8; 95% CI: 2.6–8.9, p < .0001). Persons with TB-HIV coinfection were more likely to be young, female and less likely to be married. Conclusion Younger females with a high burden of HIV may be under-diagnosed and under-reported for TB in Nigeria. Community programs for intensified and early detection of TB and HIV targeting younger females are needed in this setting.

Background Human immunodeficiency virus type 1 (HIV-1) subtype has been shown to be associated with disease progression. We compared cognitive function between individuals infected with HIV-1 subtype G and CRF02_AG in Nigeria. Methods For this cross-sectional study, samples were analyzed from 146 antiretroviral-naive participants. Genotypic analysis of plasma HIV RNA was performed by nested polymerase chain reaction of protease and reverse transcriptase genes, and sequences were aligned with curated HIV-1 subtype references. Cognitive status was determined using demographically adjusted T scores and global deficit score (GDS) obtained from a comprehensive neuropsychological test battery. Results A total of 76 (52.1%) participants were infected with CRF02_AG, 48 (32.8%) with subtype G, and 22 (15.1%) with other HIV-1 strains. In a multivariable linear regression adjusting for plasma HIV RNA, CD4 count, and depression score, mean global T score was lower among subtype G-infected compared with CRF02_AG-infected participants (mean difference, -3.0 [95% confidence interval {CI}, -5.2, to -.7]; P = .011). Also, T scores were significantly lower among subtype G- than CRF02_AG-infected participants for the speed of information processing, executive function, and verbal fluency ability domains. Adjusting for similar variables in a logistic regression, the odds of global cognitive impairment (GDS ≥0.5) were 2.2 times higher among subtype G compared with CRF02_AG-infected participants (odds ratio, 2.2 [95% CI, .9-5.4]; P = .078). Conclusions Cognitive performance was significantly worse among antiretroviral-naive individuals with HIV-1 subtype G vs CRF02_AG infection. Further studies are required to characterize the mechanistic basis for these differences.

Influenza A(H5N1) vaccination strategies that improve the speed of the immunological response and cross-clade protection are desired. We compared the immunogenicity of a single 15-μg or 90-μg dose of A/H5N1/Indonesia/05/05 (clade 2) vaccine in adults who were previously primed with A/H5N1/Vietnam/1203/2004 (clade 1) vaccine. High-dose vaccine resulted in significantly higher titers to both clade 1 and 2 antigens. Clade 2 titers were unaffected by the previous dose of clade 1 vaccine. Low-dose priming with a mismatched pandemic influenza A(H5N1) vaccine would improve the rapidity, magnitude, and cross-reactivity of the immunological response following a single high-dose, unadjuvanted, pandemic vaccine.

Introduction Reintroduction of Variola major as an agent of bioterrorism remains a concern. A shortened dosing schedule of Bavarian Nordic's (BN) IMVAMUNE® (modified vaccinia Ankara vaccine against smallpox) was compared to the currently recommended 0- and 28-day schedule for non-inferiority by evaluating the magnitude and kinetics of the immune responses. Methods Subjects were assigned to receive IMVAMUNE or placebo administered subcutaneously on Days 0 and 7, Days 0 and 28, or Day 0. Blood was collected for antibody and cell-mediated immune assays. Subjects were followed for safety for 12 months after last vaccination. Results The primary endpoint of this study was the geometric mean antibody titers (GMT) at 14 days post last vaccination. Of 208 subjects enrolled, 191 received vaccine (Group: 0 + 7, Group: 0 + 28 and Group: 0) and 17 received placebo. Moderate/severe systemic reactogenicity after any vaccination were reported by 31.1%, 25.4%, and 28.6% of the subjects for Group: 0 + 7, Group: 0 + 28, and Group: 0, respectively (Chi-square test, P = 0.77). Based on BN's Plaque Reduction Assay GMTs, Group: 0 + 7 was non-inferior to Group: 0 + 28 at Day 4, 180, and 365 after the second vaccination. On Day 14, Group: 0 + 7 and Group: 0 + 28 GMT were 10.8 (CI: 9.0, 12.9) and 30.2 (CI: 22.1, 41.1), respectively. Based on BN's Enzyme-linked immunosorbent assay, the proportion of subjects with positive titers for Group: 0 + 28 was significantly greater than that for Group: 0 + 7 after second vaccination at Days 4 and 180. By Day 14 after the second dose, the IFN-γ enzyme-linked immunosorbent spot (ELISPOT) responses were similar for Group: 0 + 28 and Group: 0 + 7. Conclusion Overall, a standard dose of IMVAMUNE (0.5 mL of 1 x 108 TCID/mL) administered subcutaneously was safe and well tolerated. A second dose of IMVAMUNE at Day 28 compared to Day 7 provided greater antibody responses and the maximal number of responders. By Day 14 after the second dose, IFN-γ ELISPOT responses were similar for Group: 0 + 28 and Group: 0 + 7.

Background Nigeria is ranked in the top five countries for tuberculosis deaths worldwide. This study investigated the mycobacterial agents associated with presumptive clinical pulmonary tuberculosis (TB) in Nigeria and evaluated the pattern and frequency of mycobacterial infections over twelve calendar months period. Methods Sputum samples from 1,603 consecutive new cases with presumptive diagnosis of TB were collected from August 2010 to July 2011. All sputum samples were incubated for detection of mycobacterial growth and those with positive acid fast bacilli (AFB) growth were tested to detect mycobacterium tuberculosis (MTB) complex and characterized to differentiate between MTB complex species. Cultures suggestive of Non-tuberculous mycobacterial infections (NTM) were sub-cultured and characterized. Results Of the 1,603 patients screened, 444 (28%) culture-positive cases of pulmonary tuberculosis were identified. Of these, 375 (85%) were due to strains of MTB complex (354 cases of M. tuberculosis, 20 M. africanum and one case of M. bovis) and 69 (15%) were due to infection with NTM. In contrast to the MTB complex cases, the NTM cases were more likely to have been diagnosed during the calendar months of the Harmattan dust season (OR = 2.34, 1.28–4.29; p = 0.01), and aged older than 35 years (OR = 2.77, 1.52–5.02, p = 0.0007), but less likely to have AFB identified on their sputum smear (OR = 0.06, 0.02–0.14, p

Objective. Data on pulmonary tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) complex in Nigeria are limited. We investigated species of MTB complex in TB cases from northern Nigeria. Methods. New TB suspects were enrolled, screened for HIV and their sputum samples were cultured after routine microscopy. Genotypes MTBC and MTBDR plus were used to characterize the MTB complex species and their resistance to isoniazid and rifampicin. Results. Of the 1,603 patients enrolled, 375 (23%) had MTB complex infection: 354 (94.4%) had Mycobacterium tuberculosis; 20 (5.3%) had Mycobacterium africanum; and one had Mycobacterium bovis (0.3%). Cases were more likely to be male (AOR = 1.87, 95% CI : 1.42–2.46; ), young (AOR = 2.03, 95% CI : 1.56–2.65; ) and have HIV (AOR = 1.43, 95% CI : 1.06–1.92; ). In 23 patients (6.1%), the mycobacterium was resistant to at least one drug, and these cases were more likely to have HIV and prior TB treatment (AOR = 3.62, 95% CI : 1.51–8.84; ; AOR : 4.43; 95% CI : 1.71–11.45 resp.), compared to cases without any resistance. Conclusion. Mycobacterium tuberculosis remained the predominant specie in TB in this setting followed by Mycobacterium africanum while Mycobacterium bovis was rare. The association of TB drug resistance with HIV has implications for TB treatment.

DNA vaccines are cost-effective and versatile, though intracellular delivery has been challenging in humans. Alternative delivery modalities such as electroporation have demonstrated improved immune responses, but are painful. In this single-center, double-blind, medical device trial, we evaluated the safety and tolerability of Easy Vax™ dermal electroporation system, alone (without DNA) in healthy adults. Three randomized protocol doses were administered to 10 subjects (80% white, 60% female, mean age: 32.1 years) in each of two areas (total of six doses). Two subjects complained of shooting pain, burning and/or tingling when doses were administered to the forearm region, but not the lateral deltoid regions. Subsequent doses for the remaining eight subjects were restricted to the deltoid regions only. Tolerability pain scores never exceeded 3 of 10 in the 11-Point Pain Rating scale, and 12 of 100 in the Visual Analog Scale (VAS), and lower in follow-up evaluations (P < 0.0001), with no significant difference between the three dosing protocols. Electrical properties of the skin, measured automatically by the device, showed no correlation between pain intensity and skin conductance. In conclusion, the Easy Vax™ electroporation device is safe and well tolerated when administered over the lateral deltoid skin regions in healthy volunteers.

Hepatitis C virus (HCV) has a lower prevalence in children and knowledge is limited regarding the natural outcome of HCV infection in children.To study the risk factors of HCV acquisition and predictors of persistence in Egyptian children.Children, 1-9 years of age, were evaluated for acquisition of HCV (anti-HCV positive regardless of viraemia) and persistence of HCV (anti-HCV and HCV-RNA positive) at two paediatric hepatology clinics in Cairo at enrollment and at 3 monthly intervals. Spontaneous clearance of HCV was defined as ≥ two positive anti-HCV antibody tests with negative HCV-RNA at least 6 months apart.Over a 33-month-period a total of 226 children9 years of age were screened for HCV antibodies. Of those, 146 (65%) were anti-HCV positive of which 87 (60%) were HCV-RNA positive. The HCV acquisition was more likely to occur in older children (P = 0.003) with comorbid conditions (P0.01) compared to anti-HCV negative children. In a multivariate logistic regression analysis, the highest risk factors for HCV acquisition were surgical interventions [odds ratio (OR): 4.7] and blood transfusions (OR: 2.3). The highest risk factor for HCV persistence was dental treatment (OR: 16.9) and male gender (OR: 7.5). HCV persistence was also strongly associated with elevated baseline alanine aminotransaminase (ALT) levels (OR: 4.9) and fluctuating aspartate aminotransferase (AST) levels (OR: 8.1).Although surgical interventions and blood transfusion are significant risk factors for HCV acquisition in Egyptian children, dental treatment remains the highest risk factor for HCV chronic persistence in children.

Evidence regarding the health benefits of carotenoids is controversial. Effects of serum carotenoids and their interactions on mortality have not been examined in a representative sample of US adults. The objective was to examine whether serum carotenoid concentrations predict mortality among US adults. The study consisted of adults aged ≥20 years enrolled in the National Health and Nutrition Examination Survey (NHANES) III, 1988–1994, with measured serum carotenoids and mortality follow-up through 2006 (N=13,293). Outcomes were all-cause, cardiovascular disease (CVD), and cancer mortality. In adjusted Cox proportional hazards models, participants in the lowest total carotenoid quartile (1.75µmol/L). For alpha-carotene, the highest quartile (>0.11µmol/L) had the lowest all-cause mortality rates (P

Background. Noroviruses cause significant morbidity and mortality from acute gastroenteritis in all age groups worldwide. Methods.We conducted 2 phase 1 double-blind, controlled studies of a virus-like particle (VLP) vaccine derived from norovirus GI.1 genotype adjuvanted with monophosphoryl lipid A (MPL) and the mucoadherent chitosan. Healthy subjects 18–49 years of age were randomized to 2 doses of intranasal Norwalk VLP vaccine or controls 21 days apart. Study 1 evaluated 5-, 15-, and 50-μg dosages of Norwalk antigen, and study 2 evaluated 50-and 100-μg dosages. Volunteers recorded symptoms for 7 days after dosing, and safety was followed up for 180 days. Blood samples were collected for serological profile, antibody secreting cells (ASCs), and analysis of ASC homing receptors. Results. The most common symptoms were nasal stuffiness, discharge, and sneezing. No vaccine-related serious adverse events occurred. Norwalk VLP-specific immunoglobulin G and immunoglobulin A antibodies increased 4.8-and 9.1-fold, respectively, for the 100-μg dosage level. All subjects tested who received the 50-or 100-μg vaccine dose developed immunoglobulin A ASCs. These cells expressed molecules associated with homing to mucosal and peripheral lymphoid tissues. Conclusions. The intranasal monovalent adjuvanted Norwalk VLP vaccine was well tolerated and highly immunogenic and is a candidate for additional study. Trial Registration. ClinicalTrials.gov identifier: {"type":"clinical-trial","attrs":{"text":"NCT00806962","term_id":"NCT00806962"}}NCT00806962.

We use the framework of coarsened data to motivate performing sensitivity analysis in the presence of incomplete data. To perform the sensitivity analysis, we specify pattern-mixture models to allow departures from the assumption of coarsening at random, a generalization of missing at random and independent censoring. We apply the concept of coarsening to address potential bias from missing data and interval-censored data in a randomized controlled trial of an herbal treatment for acute hepatitis. Computer code using SAS PROC NLMIXED for fitting the models is provided.

Milk thistle or its purified extract, silymarin (Silybum marianum), is widely used in treating acute or chronic hepatitis. Although silymarin is hepatoprotective in animal experiments and some human hepatotoxic exposures, its efficacy in ameliorating the symptoms of acute clinical hepatitis remains inconclusive. In this study, our purpose was to determine whether silymarin improves symptoms, signs and laboratory test results in patients with acute clinical hepatitis, regardless of etiology.This is a randomized, placebo-controlled trial in which participants, treating physicians and data management staff were blinded to treatment group. The study was conducted at two fever hospitals in Tanta and Banha, Egypt where patients with symptoms compatible with acute clinical hepatitis and serum alanine aminotransferase (ALT) levels2.5 times the upper limit of normal were enrolled. The intervention consisted of three times daily ingestion of either a standard recommended dose of 140 mg of silymarin (Legalon, MADAUS GmbH, Cologne, Germany), or a vitamin placebo for four weeks with an additional four-week follow-up. The primary outcomes were symptoms and signs of acute hepatitis and results of liver function tests on days 2, 4 and 7 and weeks 2, 4, and 8. Side-effects and adverse events were ascertained by self-report.From July 2003 through October 2005, 105 eligible patients were enrolled after providing informed consent. No adverse events were noted and both silymarin and placebo were well tolerated. Patients randomized to the silymarin group had quicker resolution of symptoms related to biliary retention: dark urine (p=0.013), jaundice (p=0.02) and scleral icterus (p=0.043). There was a reduction in indirect bilirubin among those assigned to silymarin (p=0.012), but other variables including direct bilirubin, ALT and aspartate aminotransferase (AST) were not significantly reduced.Patients receiving silymarin had earlier improvement in subjective and clinical markers of biliary excretion. Despite a modest sample size and multiple etiologies for acute clinical hepatitis, our results suggest that standard recommended doses of silymarin are safe and may be potentially effective in improving symptoms of acute clinical hepatitis despite lack of a detectable effect on biomarkers of the underlying hepatocellular inflammatory process.

In developing countries, hepatitis E (HEV) and hepatitis A (HAV) are the major causes of acute viral hepatitis with similar feco-oral modes of transmission. In contrast to the high seroprevalence of hepatitis A infection, a low seroprevalence of HEV among children in endemic areas has been reported. These data suggest the possibility that silent HEV infection is undiagnosed by the current available methods. Many of the serological tests used for HEV diagnosis have poor specificity and are unable to differentiate among different genotypes of HEV. Moreover, the RT-PCR used for HEV isolation is only valid for a brief period during the acute stage of infection. Cell-mediated immune (CMI) responses are highly sensitive, and long lasting after sub-clinical infections as shown in HCV and HIV. Our objective was to develop a quantitative assay for cell-mediated immune (CMI) responses in HEV infection as a surrogate marker for HEV exposure in silent infection. Quantitative assessment of the CMI responses in HEV will also help us to evaluate the role of CMI in HEV morbidity. In this study, an HEV-specific interferon-gamma (IFN-gamma) ELISPOT assay was optimized to analyze HEV-specific CMI responses. We used peripheral blood mononuclear cells (PBMC) and sera from experimentally infected chimpanzees and from seroconverted and control human subjects to validate the assay. The HEV-specific IFN-gamma ELISPOT responses correlated strongly and significantly with anti-HEV ELISA positive/negative results (rho=0.73, p=0.02). Moreover, fine specificities of HEV-specific T cell responses could be identified using overlapping HEV ORF2 peptides.

Background Concerns have been expressed regarding the adequacy of ethics review systems in developing countries. Limited data are available regarding the structural and functional status of Research Ethics Committees (RECs) in the Middle East. The purpose of this study was to survey the existing RECs in Egypt to better understand their functioning status, perceived resource needs, and challenges. Methods We distributed a self-administered survey tool to Egyptian RECs to collect information on the following domains: general characteristics of the REC, membership composition, ethics training, workload, process of ethics review, perceived challenges to effective functioning, and financial and material resources. We used basic descriptive statistics to evaluate the quantitative data. Results We obtained responses from 67% (12/18) of the identified RECs. Most RECs (10/12) have standard operating procedures and many (7/12) have established policies to manage conflicts of interests. The average membership was 10.3 with a range from 7-19. The predominant member type was physicians (69.5% of all of the REC members) with little lay representation (13.7%). Most RECs met at least once/month and the average number of protocols reviewed per meeting was 3.8 with a range from 1-10. Almost three-quarters of the members from all of the 12 RECs indicated they received some formal training in ethics. Regarding resources, roughly half of the RECs have dedicated capital equipment (e.g., meeting room, computers, office furniture, etc); none of the RECs have a formal operating budget. Perceived challenges included the absence of national research ethics guidelines and national standards for RECs and lack of ongoing training of its members in research ethics. Conclusion Our study documents several areas of strengths and areas for improvements in the operations of Egyptian RECs. Regarding strengths, many of the existing RECs meet frequently, have a majority of members with prior training in research ethics, and have written policies. Regarding areas for improvements, many RECs should strive for a more diverse membership and should receive more financial resources and administrative support personnel. We recommend that RECs include more individuals from the community and develop a continuing educational program for its members. Institutional officials should be aware of the resource capacity needs of their RECs.

Background Chest-x-ray is routinely used in the diagnosis of smear negative tuberculosis (TB). This study assesses the incremental cost per true positive test of a point-of-care digital chest-x-ray, in the diagnosis of pulmonary mycobacterial infections among HIV patients with presumed tuberculosis undetected by smear microscopy. Methods Consecutive patients with clinical suspicion of pulmonary tuberculosis were serially tested for Human immunodeficiency virus (HIV), their sputum examined for Acid Fast Bacilli then cultured in broth and solid media. Cultures characterized as tuberculous (M.tb) and non-tuberculous (NTM) mycobacteria by Hain assays were used as gold standards. A chest-x-ray was classified as: (1) consistent for TB, (2) not consistent for TB and (3) no pathology. Results Of the 1391 suspected cases enrolled, complete data were available for 952 (68%): 753/952 (79%) had negative smear tests while 150/753 (20%) had cultures positive for TB. Of those, 82/150 (55%) had chest-x-ray signs consistent with TB and 29/82 (35%) were positive for HIV. Within the co-infected, 9/29 (31%) had NTM infections. Among all suspects, the cost per positive case detected using smear microscopy test was $52.84; the overall incremental cost per positive case using chest-x-ray in smear negatives was $23.42, and in smear negative, HIV positive patients the cost was $15.77. Conclusion Point-of-care chest-x-ray is a cost-effective diagnostic tool for smear negative HIV positive patients with pulmonary mycobacterial infection. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0675-0) contains supplementary material, which is available to authorized users.

Background and Aims: Outpatient clinical notes are a rich source of information regarding drug safety. However, data in these notes are currently underutilized for pharmacovigilance due to methodological limitations in text mining. Large language models (LLM) like BERT have shown progress in a range of natural language processing tasks but have not yet been evaluated on adverse event detection., Methods: We adapted a new clinical LLM, UCSF BERT, to identify serious adverse events (SAEs) occurring after treatment with a non-steroid immunosuppressant for inflammatory bowel disease (IBD). We compared this model to other language models that have previously been applied to AE detection., Results: We annotated 928 outpatient IBD notes corresponding to 928 individual IBD patients for all SAE-associated hospitalizations occurring after treatment with a non-steroid immunosuppressant. These notes contained 703 SAEs in total, the most common of which was failure of intended efficacy. Out of 8 candidate models, UCSF BERT achieved the highest numerical performance on identifying drug-SAE pairs from this corpus (accuracy 88-92%, macro F1 61-68%), with 5-10% greater accuracy than previously published models. UCSF BERT was significantly superior at identifying hospitalization events emergent to medication use (p < 0.01)., Conclusions: LLMs like UCSF BERT achieve numerically superior accuracy on the challenging task of SAE detection from clinical notes compared to prior methods. Future work is needed to adapt this methodology to improve model performance and evaluation using multi-center data and newer architectures like GPT. Our findings support the potential value of using large language models to enhance pharmacovigilance.