Multinomial Logistic Model for Coinfection Diagnosis Between Arbovirus and Malaria in Kedougou.

In tropical regions, populations continue to suffer morbidity and mortality from malaria and arboviral diseases. In Kedougou (Senegal), these illnesses are all endemic due to the climate and its geographical position. The co-circulation of malaria parasites and arboviruses can explain the observation of coinfected cases. Indeed there is strong resemblance in symptoms between these diseases making problematic targeted medical care of coinfected cases. This is due to the fact that the origin of illness is not obviously known. Some cases could be immunized against one or the other of the pathogens, immunity typically acquired with factors like age and exposure as usual for endemic area. Thus, coinfection needs to be better diagnosed. Using data collected from patients in Kedougou region, from 2009 to 2013, we adjusted a multinomial logistic model and selected relevant variables in explaining coinfection status. We observed specific sets of variables explaining each of the diseases exclusively and the coinfection. We tested the independence between arboviral and malaria infections and derived coinfection probabilities from the model fitting. In case of a coinfection probability greater than a threshold value to be calibrated on the data, long duration of illness and age are mostly indicative of arboviral disease while high body temperature and presence of nausea or vomiting symptoms during the rainy season are mostly indicative of malaria disease.

A Truncation Model for Estimating Species Richness.

We propose a truncation model for the abundance distribution in species richness estimation. This model is inherently semiparametric and incorporates an unknown truncation threshold between rare and abundant observations. Using the conditional likelihood, we derive a class of estimators for the parameters in this model by stepwise maximization. The species richness estimator is given by the integer maximizing the binomial likelihood, given all other parameters in the model. Under regularity conditions, we show that our estimators of the model parameters are asymptotically efficient. We recover Chaos lower bound estimator of species richness when the parametric part of the model is single-component Poisson. Thus our class of estimators strictly generalized the latter. We illustrate the performance of the proposed method in a simulation study, and compare it favorably to other widely-used estimators. We also give an application to estimating the number of distinct vocabulary words in French playwright Molière's Tartuffe.

A pairwise alignment algorithm which favors clusters of blocks.

Pairwise sequence alignments aim to decide whether two sequences are related and, if so, to exhibit their related domains. Recent works have pointed out that a significant number of true homologous sequences are missed when using classical comparison algorithms. This is the case when two homologous sequences share several little blocks of homology, too small to lead to a significant score. On the other hand, classical alignment algorithms, when detecting homologies, may fail to recognize all the significant biological signals. The aim of the paper is to give a solution to these two problems. We propose a new scoring method which tends to increase the score of an alignment when "blocks" are detected. This so-called Block-Scoring algorithm, which makes use of dynamic programming, is worth being used as a complementary tool to classical exact alignments methods. We validate our approach by applying it on a large set of biological data. Finally, we give a limit theorem for the score statistics of the algorithm.

Transmission probabilities of HIV and herpes simplex virus type 2, effect of male circumcision and interaction: a longitudinal study in a township of South Africa.

OBJECTIVES: A synergy between HIV and herpes simplex virus type 2 (HSV-2) infections has been reported in observational studies. The objectives of this study were to estimate the per-sex-act female-to-male transmission probabilities (FtoMTPs) of HIV and HSV-2, the effect of each infection on the FtoMTP of the other and the effect of male circumcision on these FtoMTPs. DESIGN: We used longitudinal data collected during the male circumcision trial conducted in Orange Farm (South Africa). METHODS: Results were obtained by specific mathematical modeling of HIV and HSV-2 statuses of the men as functions of their sexual behavior and male circumcision status. The model took into account an estimation of the HIV and HSV-2 statuses of each of their female partners. Confidence intervals (CI) were estimated using a bootstrap resampling method. RESULTS: The HIV and HSV-2 FtoMTPs, during an unprotected sexual contact for an uncircumcised male in the absence of the other virus in both partners, were 0.0047 (95% CI: 0.0014-0.017) and 0.0067 (95% CI: 0.0028-0.014), respectively. HSV-2 in either partner increased HIV FtoMTP with a relative risk (RR) of 3.0 (95% CI: 1.01-7.3). Conversely, HIV in either partner increased HSV-2 FtoMTP (RR= 2.5; 95% CI: 1.1- 6.3). Male circumcision significantly decreased these probabilities with RRs of 0.24 (95% CI: 0.11-0.44) and 0.59 (95% CI: 0.36-0.91), respectively. CONCLUSION: This study gave the first estimates of HSV-2 per-sex-act FtoMTPs in Africa. It demonstrated a synergy between HIV and HSV-2 infections and a protective effect of male circumcision on HSV-2 acquisition by males.