Ahmadou Alioum - Academia.edu (original) (raw)

Papers by Ahmadou Alioum

Statistics in Medicine

ABSTRACT

Depuis les années 1990, de nombreux travaux portent sur l'étude de l'évolution des anticorps anti... more Depuis les années 1990, de nombreux travaux portent sur l'étude de l'évolution des anticorps anti-VIH menantà des tests permettant de distinguer les infections récentes des infections déjà bienétabliesà partir d'un seuléchantillon de sérum. L'incidence peut alorsêtre estiméeà partir de la relation entre la prévalence, l'incidence et la durée de l'infection récente ("période fenêtre"). Cependant, de récents travaux ont montré les limites de cette approche dues essentiellementà une grande variabilité de la "période fenêtre". Nous proposons une approche alternative qui consisteà estimer la distribution du temps d'infection basée sur la valeur des marqueurs virologiques au moment où l'infection est découverte pour la première fois. Dans un premier temps, un modèle pour l'évolution des marqueurs est spécifié et estiméà partir de mesures répétées de marqueurs virologiques de séroconversion. Les paramètres du modèle sont estimésà partir des données d'une cohorte de patients inclus pendant la primo-infection. Dans un second temps, nous utilisons ce modèle pour estimer la distribution des temps d'infection pour les sujets nouvellement diagnostiqués VIH+ et reportés dans le système de surveillance des diagnostics VIH en France. Abstract: In the last decade, interest has been focused on HIV antibody assays and testing strategies that could distinguish recent infections from established infection in a single serum sample. Incidence estimates are obtained by using the relationship between prevalence, incidence and duration of recent infection ("window period"). However, recent works demonstrated limitations of this approach due to variability of the "window period". We propose an alternative approach which consists in estimating the distribution on infection times based on serological marker values at the moment when the infection is first discovered. We propose a model based on the repeated measurements of virological markers of seroconversion for the marker trajectory. The parameters of the model are estimated using data from a cohort of HIV infected patients enrolled during primary infection. We use this model to estimate the distribution of infection times for newly HIV diagnosed subjects reported in the French HIV surveillance system.

Revue d'Épidémiologie et de Santé Publique, 2008

Revue d'Épidémiologie et de Santé Publique, 2004

Revue d'Épidémiologie et de Santé Publique, 2014

Aids, 2011

Many people who are HIV positive are unaware of their infection status. Estimation of the number ... more Many people who are HIV positive are unaware of their infection status. Estimation of the number of people with undiagnosed HIV within a country or region is vital for understanding future need for treatment and for motivating testing programs. We review the available estimation approaches which are in current use. They can be broadly classified into those based on prevalence surveys and those based on reported HIV and AIDS cases. Estimation based on prevalence data requires data from regular prevalence surveys in different population groups together with estimates of the size of these groups. The recommended minimal case reporting data needed to estimate the number of patients with undiagnosed HIV are HIV diagnoses, including CD4 count at diagnosis and whether there has been an AIDS diagnosis in the 3 months before or after HIV diagnosis, and data on deaths in people with HIV. We would encourage all countries to implement several methods that will help develop our understanding of strengths and weaknesses of the various methods.

La Revue de Médecine Interne, 2008

Résultats.-Par rapport aux patients ayant une HTAP idiopathique, les patients ayant une HTAP-SSc ... more Résultats.-Par rapport aux patients ayant une HTAP idiopathique, les patients ayant une HTAP-SSc étaient significativement plus âgés, petits et légers. La pression dans l'oreillette droite (POD), la pression artérielle pulmonaire moyenne et les résistances pulmonaires totales (RPT) étaient significativement plus basses au cours de l'HTAP-SSc. Le TM6 était significativement plus altérée au cours de l'HTAP-SSc (276 ± 100 m vs 318 ± 105 m, p < 0,05) tandis que le TM6 % était similaire (54 ± 19 % vs 59 ± 19 %, p = NS). Au cours de l'HTAP idiopathique, une relation linéaire, quoique faible, existait entre le TM6 % et la POD (R = 0,30, p < 0,05) et les RPT (R = 0,27, p < 0,05). En revanche, aucune relation n'était observée entre le TM6 % et les paramètres hémodynamiques de repos au cours de l'HTAP-SSc. Seule la fréquence cardiaque au repos était significativement (et négativement) corrélée au TM6 % dans cette pathologie (R = 0,46, p < 0,05). Enfin, la réserve chronotropique (fréquence cardiaque à la fin-fréquence cardiaque au début du TM6) était également significativement corrélée au TM6 % (R = 0,54, p < 0,05). Conclusion.-Ce travail suggère que l'utilisation du TM6 % est préférable à la simple valeur absolue TM6 du fait des caractéristiques morphologiques des patients SSc. Il n'y a aucune corrélation entre les données hémodynamiques de repos et le TM6 % au cours de l'HTAP-SSc, contrairement à l'HTAP idiopathique. Une diminution de la réserve chronotopique pourrait jouer un rôle dans la diminution de la tolérance à l'exercice au cours de l'HTAP-SSc.

Veterinary Research, 2004

The aim of this study was to evaluate the impact of the pre-slaughter process on Salmonella caeca... more The aim of this study was to evaluate the impact of the pre-slaughter process on Salmonella caecal contamination of pigs at slaughter. An observational study was carried out in 2001 on 101 conventional farrow-to-finish pig farms. On each farm, one batch of contemporary pigs was followed from the end of the fattening period until slaughter. The Salmonella bacteriological status of the batches was assessed by environmental samples of faecal material. The serological Salmonella status was obtained on 30 individually identified market-age pigs using an indirect ELISA test. At the slaughterhouse, 25 g of caecal contents were taken from 10 of the identified pigs. Faecal and caecal material were analysed according to a classical bacteriological method. A questionnaire was designed to obtain information about the type of feeding during the fattening period (dry versus wet), the duration of fasting on the farm before leaving for the slaughterhouse, the duration of transport between the farm and the slaughterhouse, the holding time in lairage at the slaughterhouse and loading and unloading conditions on the farm and at the slaughterhouse. To assess the relationships between these factors and the Salmonella caecal status of the pigs and the batches, two logistic models were fitted at the individual and at the batch level, respectively. The first analysis was performed using a random effects logistic regression model. The second analysis was based on a cumulative logit model with a positive caecal rate classified into three classes as the outcome variable. The results showed that the Salmonella status of market-age pigs assessed on the farm either by serological or bacteriological examinations and the time spent in lairage before slaughtering played a crucial role on caecal contamination. In the light of these results, actions should be considered both on the farm and at the slaughterhouse to decrease the risk of Salmonella contamination of the caecal contents.

Veterinary Research, 2007

We did a prospective observational 9-month long study to quantify risk factors of managerial and ... more We did a prospective observational 9-month long study to quantify risk factors of managerial and hygiene practices, pig-health status for Salmonella seroconversion of fattening pigs reared in subclinically infected in French farrow-to-finish farms. During the fattening phase, 2649 pigs belonging to the same batch of contemporary pigs, from 89 conventional farrow-to-finish farms were individually followed and regularly blood sampled on a monthly basis. Farm recruitment was based on the farmer's willingness to cooperate. Pigs status were assessed using an indirect ELISA test. Evolution of the serological status was studied by means of a survival analysis. A Cox proportional-hazards model, taking into account the clustering of animals at farm level, was used to examine the effects of explanatory variables on the time to Salmonella seroconversion of pigs. Applying group level antibiotic treatment to the pigs during the fattening period (Hazard Ratio (HR) = 2.4; 95%CI: 1.7, 3.4) was identified as a risk factor for the Salmonella seroconversion, as the presence of residual Salmonella contamination in the fattening pen before placing the pigs into the pens (HR = 1.9; 95%CI: 1.2, 2.9). Porcine reproductive and respiratory syndrome virus (PRRSV) seropositivity during the fattening period also indicated an increased hazard for seroconversion (HR = 1.6; 95%CI: 1.1, 2.5). The batch size was identified as a risk factor for the Salmonella seroconversion: the higher the number of pigs was in the fattening room followed, the higher was the risk (HR +10 pigs = 1.05 for a 10-pig increment; 95%CI: 1.03, 1.06). The biosecurity measures of wearing specific clothes before entering the facilities (HR = 0.5; 95%CI: 0.3, 0.9) and enclosing the pig farm facilities were protective (HR = 0.4; 95%CI: 0.2, 0.8).

Statistics in Medicine, 2007

Ades and Medley provided the first flexible method for estimating age- and time-specific HIV inci... more Ades and Medley provided the first flexible method for estimating age- and time-specific HIV incidence using HIV prevalence data collected among pregnant women and adjusting for the effect of differential selection between infected and uninfected women. This paper extends the approach proposed by these authors. We used a parametric model that allows the relative inclusion rate to depend on both age, calendar time, and duration of HIV infection. We developed a two dimensional penalized log-likelihood approach for estimating time- and age-specific incidence using a binomial likelihood function and a quadratic roughness penalty which allows smoothing over both age and time. Identifiability of the model parameters and effect of sample size are studied through simulations. The method is illustrated using prenatal HIV testing data recorded from 1995 to 2002 in Abidjan, Côte d&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;Ivoire, to estimate the HIV annual incidence rate among women aged 12-40 year old, from the beginning of the epidemic to 2002. We show that estimated incidence rates are highly dependent on hypotheses made to model the relative inclusion rate. Despite this dependency, the application of the method leads to new and accurate findings on HIV incidence qualitative features in Abidjan. We highlight the relevance of such a method in monitoring the dynamics of HIV epidemic in Africa which is essential for planning vaccine trials and future treatment needs, and for assessment of prevention policy.

Statistics in Medicine, 1998

We give up-to-date methods for estimating the age-specific incidence of a disease and for estimat... more We give up-to-date methods for estimating the age-specific incidence of a disease and for estimating the effect of risk factors. We recommend taking age as the basic time scale of the analysis; then, the hazard function can be interpreted as the age-specific incidence of the disease. This choice raises a delayed entry problem. We present three methods: the person-years method; the smoothed Nelson-Aalen estimator, and the penalized likelihood approach. When explanatory variables are available, the Poisson model and the Cox model with delayed entry may be used for estimating relative risks; the penalized likelihood approach can also be used. We apply these methods to estimate the age-specific incidence of dementia using data from a large cohort study, Paquid. This 5-year study followed a random initial sample of 3675 subjects with 190 incident cases of dementia. We compare the estimates based on the three possible methods. The estimated incidences computed separately for men and women cross and it is verified that a non-proportional hazards model for gender holds; women below 75 have a lower risk than men while women above 75 have a higher risk.

Statistics in Medicine, 2012

Prognostic studies often have to deal with two important challenges: (i) separating effects of pr... more Prognostic studies often have to deal with two important challenges: (i) separating effects of predictions on different &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;competing&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; events and (ii) uncertainty about cause of death. Multistate Markov models permit multivariable analyses of competing risks of, for example, mortality versus disease recurrence. On the other hand, relative survival methods help estimate disease-specific mortality risks even in the absence of data on causes of death. In this paper, we propose a new Markov relative survival (MRS) model that attempts to combine these two methodologies. Our MRS model extends the existing multistate Markov piecewise constant intensities model to relative survival modeling. The intensity of transitions leading to death in the MRS model is modeled as the sum of an estimable excess hazard of mortality from the disease of interest and an &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;offset&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; defined as the expected hazard of all-cause &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;natural&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; mortality obtained from relevant life-tables. We evaluate the new MRS model through simulations, with a design based on registry-based prognostic studies of colon cancer. Simulation results show almost unbiased estimates of prognostic factor effects for the MRS model. We also applied the new MRS model to reassess the role of prognostic factors for mortality in a study of colorectal cancer. The MRS model considerably reduces the bias observed with the conventional Markov model that does not permit accounting for unknown causes of death, especially if the &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;true&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39; effects of a prognostic factor on the two types of mortality differ substantially.

Statistics in Medicine, 1995

We present a direct approach for correcting the acquired immunodeficiency syndrome (AIDS) inciden... more We present a direct approach for correcting the acquired immunodeficiency syndrome (AIDS) incidence data for reporting delays, based on a non-parametric method for the analysis of right truncated data. We show that the proposed method when applied for grouped data is equivalent to three other published methods. We give a simple formula for the variance of the estimated AIDS incidence. Both estimator and variance are assessed in a simulation study. It is important for the estimation of AIDS incidence in the last quarter of the period under consideration to use month rather than quarter or half-year as the time unit for the analyses. The method is illustrated using data from the United States Centers for Disease Control.

Rheumatology, 2009

Altered angiogenesis is a characteristic feature in SSc and remains ill-understood. VEGF is belie... more Altered angiogenesis is a characteristic feature in SSc and remains ill-understood. VEGF is believed to play a central role. Serum VEGF is elevated in SSc patients but questions remain concerning the source of circulating VEGF. Here we investigated platelet activation and the role of platelets as a source of VEGF and other angiogenic mediators in this disease. A cohort of 40 patients with SSc was included. Age- and sex-matched healthy subjects and subjects presenting a primary RP were included as controls. Platelets were isolated, activated with thrombin and the secretion of VEGF, platelet derived growth factor, homodimeric form BB (PDGF-BB), TGF-beta1 and angiopoietins-1 and -2 measured. Plasma concentrations of these mediators and the functionality of platelet-derived VEGF were also studied. Platelet activation was assayed by measuring plasma beta-thromboglobulin and expression of P-selectin on platelets. The effect of iloprost on VEGF secretion by platelets was studied. Platelets from SSc patients, in contrast to controls, secreted large amounts of VEGF when activated, but not PDGF-BB, TGF-beta1 or angiopoietins. Increased expression of membrane P-selectin confirmed platelet activation in the patients. Iloprost inhibited VEGF secretion by platelets both in vivo and in vitro, through inhibition of platelet activation. Platelets transport high levels of VEGF in SSc. They may contribute to circulating VEGF because of ongoing activation in the course of the disease. If activated at the contact of injured endothelium, platelets may be important in the altered angiogenesis associated with the disease through the secretion of high levels of VEGF.

PLoS ONE, 2010

Background: Bacterial pneumonia is still a substantial cause of morbidity and mortality in HIV-in... more 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.

PLoS ONE, 2012

We assessed the effect of HIV status disclosure on retention in care from initiation of antiretro... more We assessed the effect of HIV status disclosure on retention in care from initiation of antiretroviral therapy (ART) among HIV-infected children aged 10 years or more in Cote d'Ivoire, Mali and Sénégal.