Estimation of dynamical model parameters taking into account undetectable marker values

BACKGROUND: Mathematical models are widely used for studying the dynamic of infectious agents such as hepatitis C virus (HCV). Most often, model parameters are estimated using standard least-square procedures for each individual. Hierarchical models have been proposed in such applications. However, another issue is the left-censoring (undetectable values) of plasma viral load due to the lack of sensitivity of assays used for quantification. A method is proposed to take into account left-censored values for estimating parameters of non linear mixed models and its impact is demonstrated through a simulation study and an actual clinical trial of anti-HCV drugs. METHODS: The method consists in a full likelihood approach distinguishing the contribution of observed and left-censored measurements assuming a lognormal distribution of the outcome. Parameters of analytical solution of system of differential equations taking into account left-censoring are estimated using standard software. RESULTS: A simulation study with only 14% of measurements being left-censored showed that model parameters were largely biased (from -55% to +133% according to the parameter) with the exception of the estimate of initial outcome value when left-censored viral load values are replaced by the value of the threshold. When left-censoring was taken into account, the relative bias on fixed effects was equal or less than 2%. Then, parameters were estimated using the 100 measurements of HCV RNA available (with 12% of left-censored values) during the first 4 weeks following treatment initiation in the 17 patients included in the trial. Differences between estimates according to the method used were clinically significant, particularly on the death rate of infected cells. With the crude approach the estimate was 0.13 day(-1 )(95% confidence interval [CI]: 0.11; 0.17) compared to 0.19 day(-1 )(CI: 0.14; 0.26) when taking into account left-censoring. The relative differences between estimates of individual treatment efficacy according to the method used varied from 0.001% to 37%. CONCLUSION: We proposed a method that gives unbiased estimates if the assumed distribution is correct (e.g. lognormal) and that is easy to use with standard software

Bacterial Pneumonia among HIV-Infected Patients: Decreased Risk After Tobacco Smoking Cessation. ANRS CO3 Aquitaine Cohort, 2000–2007

BACKGROUND: Bacterial pneumonia is still a substantial cause of morbidity and mortality in HIV-infected patients in the era of combination Antiretroviral Therapy. The benefit of tobacco withdrawal on the risk of bacterial pneumonia has not been quantified in such populations, exposed to other important risk factors such as HIV-related immunodeficiency. Our objective was to estimate the effect of tobacco smoking withdrawal on the risk of bacterial pneumonia among HIV-infected individuals. METHODOLOGY/PRINCIPAL FINDINGS: Patients of the ANRS CO3 Aquitaine Cohort with >or= two visits during 2000-2007 and without bacterial pneumonia at the first visit were included. Former smokers were patients who stopped smoking since >or= one year. We used Cox proportional hazards models adjusted on CD4+ lymphocytes (CD4), gender, age, HIV transmission category, antiretroviral therapy, cotrimoxazole prophylaxis, statin treatment, viral load and previous AIDS diagnosis. 135 cases of bacterial pneumonia were reported in 3336 patients, yielding an incidence of 12 per thousand patient-years. The adjusted hazard of bacterial pneumonia was lower in former smokers (Hazard Ratio (HR): 0.48; P = 0.02) and never smokers (HR: 0.50; P = 0.01) compared to current smokers. It was higher in patients with <200 CD4 cells/microL and in those with 200 to 349 CD4 cells/microL (HR: 2.98 and 1.98, respectively; both P<0.01), but not in those with 350 to 499 CD4 cells/microL (HR: 0.93; P = 0.79), compared to those with >or=500 CD4 cells/microL. The interaction between CD4 cell count and tobacco smoking status was not statistically significant. CONCLUSIONS/SIGNIFICANCE: Smoking cessation dramatically reduces the risk of bacterial pneumonia, whatever the level of immunodeficiency. Smoking cessation interventions should become a key element of the clinical management of HIV-infected individuals

Detection of genes influencing economic traits in three French dairy cattle breeds

A project of QTL detection was carried out in the French Holstein, Normande, and Montbéliarde dairy cattle breeds. This granddaughter design included 1 548 artificial insemination bulls distributed in 14 sire families and evaluated after a progeny-test for 24 traits (production, milk composition, persistency, type, fertility, mastitis resistance, and milking ease). These bulls were also genotyped for 169 genetic markers, mostly microsatellites. The QTL were analysed by within-sire linear regression of daughter yield deviations or deregressed proofs on the probability that the son receives one or the other paternal QTL allele, given the marker information. QTL were detected for all traits, including those with a low heritability. One hundred and twenty QTL with a chromosome-wise significance lower than 3% were tabulated. This threshold corresponded to a 15% false discovery rate. Amongst them, 32 were genome-wise significant. Estimates of their contribution to genetic variance ranged from 6 to 40%. Most substitution effects ranged from 0.6 to 1.0 genetic standard deviation. For a given QTL, only 1 to 5 families out of 14 were informative. The confidence intervals of the QTL locations were large and always greater than 20 cM. This experiment confirmed several already published QTL but most of them were original, particularly for non-production traits

Long-term Immune Response to Hepatitis B Virus Vaccination Regimens in Adults With Human Immunodeficiency Virus 1: Secondary Analysis of a Randomized Clinical Trial.

IMPORTANCE:Data on long-term immune responses to hepatitis B virus (HBV) vaccination in adults with human immunodeficiency virus 1 (HIV-1) infection are scarce.OBJECTIVE:To compare long-term (up to month 42) immune responses to the standard HBV vaccination regimen with a 4-injection intramuscular double-dose regimen and a 4-injection intradermal low-dose regimen.DESIGN, SETTING, AND PARTICIPANTS:The phase 3, open-label, multicenter parallel-group (1:1:1 allocation ratio) randomized clinical trial was conducted from June 28, 2007, to October 23, 2008, at 33 centers in France. Participants included 437 HBV-seronegative adults with HIV-1 and CD4 cell counts of more than 200/μL. Follow-up was extended to September 12, 2012, and data were assessed from February 13, 2015, to January 22, 2016. The analysis was imputed for an intention-to-treat population.INTERVENTIONS:Patients were randomly assigned to receive 3 intramuscular standard-dose (20-μg) injections of recombinant HBV vaccine at weeks 0, 4, and 24 (IM20 × 3 group) (145 participants), 4 intramuscular double-dose (40-μg) injections at weeks 0, 4, 8, and 24 (IM40 × 4 group) (148 participants), or 4 intradermal low-dose (4-μg) injections at weeks 0, 4, 8, and 24 (ID4 × 4 group) (144 participants).MAIN OUTCOMES AND MEASURES:The previously published primary trial end point was the percentage of responders at week 28, defined as patients with hepatitis B surface antibody (HBsAb) levels of at least 10 mIU/mL among patients who received at least 1 vaccine dose. The secondary trial end points included the percentage of responders at months 18, 30, and 42 and the duration of response from week 28. Multiple imputation was used to address missing measurements during the follow-up.RESULTS:Among the 437 patients randomized, 426 received at least 1 dose of vaccine. Of these, 287 were men (67.4%) and they had a mean (SD) age of 42.9 (9.7) years. The percentage of responders at month 42 was 41% (95% CI, 33%-49%) in the IM20 × 3 group, 71% (95% CI, 64%-79%) in the IM40 × 4 group (P < .001 vs the IM20 × 3 group), and 44% (95% CI, 35%-53%) in the ID4 × 4 group (P = .64 vs IM20 × 3 group). Fifteen percent of the patients had HBsAb titers of less than 10 mIU/mL at 33.1 months in the IM40 × 4 group, 8.7 months in the IM20 × 3 group, and 6.8 months in the ID4 × 4 group.CONCLUSIONS AND RELEVANCE:In this follow-up of a trial of adults with HIV-1 infection, the IM40 × 4 regimen of recombinant HBV vaccine improved long-term immune response compared with the standard regimen.TRIAL REGISTRATION:clinicaltrials.gov Identifier: NCT00480792

The adoption of open access scholarly communication in Tanzanian public universities: some Influencing factors

Open access is a means for free availability of scholarly content via the internet. It is an emerging opportunity for wider and unlimited access to scholarly literature. Scholarly communication, through open access journals and self-arching, are the two main approaches of open access publishing. However, this mode of scholarly communication is not widely utilised in developing countries such as Tanzania. This article discusses the factors that influence the adoption of open access for scholarly communication in Tanzanian public universities, based on a study conducted in 2008 using a survey questionnaire. A sample of 544 researchers, selected through stratified random sampling from a population of 1 088 researchers and 69 policymakers at six public universities in Tanzania, provided their views. It was evident from the findings that researchers’ internet usage skills and self-efficacy, social influence, performance expectancy, effort expectancy, and the respondents’ general perceptions about open access were the positive factors likely to facilitate open access adoption. The current poor research conditions and researchers’ low internet self-efficacy (such as inadequate information search skills) were cited as the main hindrances for researchers to use open access outlets to access scholarly content. It is therefore recommended that university policies on scholarly communication should be revised to incorporate the use of open access publishing. Furthermore, universities should accelerate the establishment of institutional repositories, advocacy campaigns and training directed at researchers, policymakers, readers and information managers of scholarly content, and the improvement of internet speed through subscription to more bandwidth, so as to meet the demand from the scholarly communit

Alternative methods to analyse the impact of HIV mutations on virological response to antiviral therapy

<p>Abstract</p> <p>Background</p> <p>Principal component analysis (PCA) and partial least square (PLS) regression may be useful to summarize the HIV genotypic information. Without pre-selection each mutation presented in at least one patient is considered with a different weight. We compared these two strategies with the construction of a usual genotypic score.</p> <p>Methods</p> <p>We used data from the ANRS-CO3 Aquitaine Cohort Zephir sub-study. We used a subset of 87 patients with a complete baseline genotype and plasma HIV-1 RNA available at baseline and at week 12. PCA and PLS components were determined with all mutations that had prevalences >0. For the genotypic score, mutations were selected in two steps: 1) p-value < 0.01 in univariable analysis and prevalences between 10% and 90% and 2) backwards selection procedure based on the Cochran-Armitage Test. The predictive performances were compared by means of the cross-validated area under the receiver operating curve (AUC).</p> <p>Results</p> <p>Virological failure was observed in 46 (53%) patients at week 12. Principal components and PLS components showed a good performance for the prediction of virological response in HIV infected patients. The cross-validated AUCs for the PCA, PLS and genotypic score were 0.880, 0.868 and 0.863, respectively. The strength of the effect of each mutation could be considered through PCA and PLS components. In contrast, each selected mutation contributes with the same weight for the calculation of the genotypic score. Furthermore, PCA and PLS regression helped to describe mutation clusters (e.g. 10, 46, 90).</p> <p>Conclusion</p> <p>In this dataset, PCA and PLS showed a good performance but their predictive ability was not clinically superior to that of the genotypic score.</p

PLoS One

Compared to the general population, HIV-infected patients are at higher risk of developing non-AIDS-defining cancers. Chronic HCV infection has also been associated with a higher risk than that of the general population of developing cancers other than hepatocarcinoma. Evaluation of the impact of HCV-related factors on non-AIDS-defining and non HCV-liver (NANL) related cancers among HIV/HCV co-infected patients are scarce. The aim of this study was to identify the impact of HIV/HCV clinical characteristics on NANL related cancers in a large cohort of HIV/HCV-coinfected patients followed from 2005 to 2017. Cox proportional hazards models with delayed entry were used to estimate factors associated with NANL related cancer. Among 1391 patients followed for a median of 5 years, 60 patients developed NANL related cancers, yielding an incidence rate of 8.9 per 1000 person-years (95% CI, [6.6-11.1]). By final multivariable analysis, after adjustment for sex, tobacco or alcohol consumption, baseline CD4 cell count and HCV sustained viral response (SVR), age and a longer duration since HIV diagnosis were independently associated with a higher risk of NANL related cancer (aHR for each additional year 1.10, 95% CI 1.06-1.14, p<0.0001 and 1.06, 95% CI 1.01-1.11, p = 0.02, respectively). Duration of HCV infection, cirrhosis, HCV viral load, genotype and SVR were not associated with the occurrence of NANL related cancer. Among HIV/HCV-coinfected patients, age and the duration of HIV infection were the only characteristics found to be associated with the occurrence of NANL related cancer. In contrast, no association was observed with any HCV-related variables

Impact of the M184V/I Mutation on the Efficacy of Abacavir/Lamivudine/Dolutegravir Therapy in HIV Treatment-Experienced Patients.

Objective The impact of the M184V/I mutation on the virological failure (VF) rate in HIV-positive patients with suppressed viremia switching to an abacavir/lamivudine/dolutegravir regimen has been poorly evaluated. Method This is an observational study from 5 European HIV cohorts among treatment-experienced adults with ≤50 copies/mL of HIV-1 RNA who switched to abacavir/lamivudine/dolutegravir. Primary outcome was the time to first VF (2 consecutive HIV-1 RNA >50 copies/mL or single HIV-1 RNA >50 copies/mL accompanied by change in antiretroviral therapy [ART]). We also analyzed a composite outcome considering the presence of VF and/or virological blips. We report also the results of an inverse probability weighting analysis on a restricted population with a prior history of VF on any ART regimen to calculate statistics standardized to the disparate sampling population. Results We included 1626 patients (median follow-up, 288.5 days; interquartile range, 154-441). Patients with a genotypically documented M184V/I mutation (n = 137) had a lower CD4 nadir and a longer history of antiviral treatment. The incidence of VF was 29.8 cases (11.2-79.4) per 1000 person-years in those with a previously documented M184V/I, and 13.6 cases (8.4-21.8) in patients without documented M184V/I. Propensity score weighting in a restricted population (n = 580) showed that M184V/I was not associated with VF or the composite endpoint (hazard ratio [HR], 1.27; 95% confidence interval [CI], 0.35-4.59 and HR 1.66; 95% CI, 0.81-3.43, respectively). Conclusions In ART-experienced patients switching to an abacavir/lamivudine/dolutegravir treatment, we observed few VFs and found no evidence for an impact of previously-acquired M184V/I mutation on this outcome. Additional analyses are required to demonstrate whether these findings will remain robust during a longer follow-up

The French national prospective cohort of patients co-infected with HIV and HCV (ANRS CO13 HEPAVIH): Early findings, 2006-2010

<p>Abstract</p> <p>Background</p> <p>In France, it is estimated that 24% of HIV-infected patients are also infected with HCV. Longitudinal studies addressing clinical and public health questions related to HIV-HCV co-infection (HIV-HCV clinical progression and its determinants including genetic dimension, patients' experience with these two diseases and their treatments) are limited. The ANRS CO 13 HEPAVIH cohort was set up to explore these critical questions.</p> <p>To describe the cohort aims and organization, monitoring and data collection procedures, baseline characteristics, as well as follow-up findings to date.</p> <p>Methods</p> <p>Inclusion criteria in the cohort were: age > 18 years, HIV-1 infection, chronic hepatitis C virus (HCV) infection or sustained response to HCV treatment. A standardized medical questionnaire collecting socio-demographic, clinical, biological, therapeutic, histological, ultrasound and endoscopic data is administered at enrolment, then every six months for cirrhotic patients or yearly for non-cirrhotic patients. Also, a self-administered questionnaire documenting socio-behavioral data and adherence to HIV and/or HCV treatments is administered at enrolment and yearly thereafter.</p> <p>Results</p> <p>A total of 1,175 patients were included from January 2006 to December 2008. Their median age at enrolment was 45 years and 70.2% were male. The median CD4 cell count was 442 (IQR: 304-633) cells/μl and HIV RNA plasma viral load was undetectable in 68.8%. Most participants (71.6%) were on HAART. Among the 1,048 HIV-HCV chronically co-infected patients, HCV genotype 1 was predominant (56%) and cirrhosis was present in 25%. As of January, 2010, after a median follow-up of 16.7 months (IQR: 11.3-25.3), 13 new cases of decompensated cirrhosis, nine hepatocellular carcinomas and 20 HCV-related deaths were reported, resulting in a cumulative HCV-related severe event rate of 1.9/100 person-years (95% CI: 1.3-2.5). The rate of HCV-related severe events was higher in cirrhotic patients and those with a low CD4 cells count, but did not differ according to sex, age, alcohol consumption, CDC clinical stage or HCV status.</p> <p>Conclusion</p> <p>The ANRS CO 13 HEPAVIH is a nation-wide cohort using a large network of HIV treatment, infectious diseases and internal medicine clinics in France, and thus is highly representative of the French population living with these two viruses and in care.</p