Développement et parallélisation d'algorithmes bioinformatiques pour la reconstruction d'arbres phylogénétiques et de réseaux réticulés

Dans ce mémoire nous abordons de prime abord la reconstruction d'arbres et de réseaux phylogénétiques, à travers deux méthodes d'inférence. Les arbres et les réseaux sont deux supports pour la représentation de l'évolution d'un groupe d'espèces étudiées. Les modèles d'évolution d'espèces qui seront traités sont les suivants : 1) Le modèle arborescent classique qui a longtemps été le seul support formel pour la représentation des relations génétiques entre les espèces. 2) Le modèle en réseau qui permet de représenter des mécanismes phylogénétiques importants pouvant jouer un rôle clé dans l'évolution et pouvant s'expliquer par le phénomène de l'évolution réticulée. Nous nous sommes particulièrement intéressés aux algorithmes d'inférence de réseaux de transferts horizontaux de gènes. Un transfert horizontal de gènes permet à deux espèces de s'échanger, partiellement ou totalement, différents gènes au cours de l'évolution. Le travail effectué sur la reconstruction d'arbres et de réseaux phylogénétiques a mené à la publication de trois articles. Ensuite, nous abordons le problème de réduction du temps d'exécution de différents programmes bioinformatiques. Ce problème a pris de l'ampleur à cause de la croissance du volume de données biologiques et du blocage de la puissance des ordinateurs autour de 3,4GHZ depuis environ deux ans. Nous décrivons un procédé d'accélération des calculs effectués par différents algorithmes d'inférence et de représentation de l'évolution des espèces, en utilisant le parallélisme. Le parallélisme mis en place a été réalisé à travers une librairie standard de passage de messages (Message Passing Interface). Nous montrons les différentes formes de parallélisme, les architectures de systèmes parallèles, quelques environnements qui permettent de supporter l'exécution des applications de façon à exprimer le parallélisme, ainsi que les approches utilisées pour paralléliser différents modèles d'évolution. Les versions parallèles des algorithmes d'évolution ont été développées et installées sur une « grappe » (i.e. cluster) Linux ayant 16 lames possédant chacune deux processeurs et sa propre mémoire.\ud ______________________________________________________________________________ \ud MOTS-CLÉS DE L’AUTEUR : algorithmes d'évolution, arbre phylogénétique, réseau phylogénétique, transferts horizontaux de gènes, programmation parallèle, Message Passing Interface (MPI)

Prevalence and characteristics of accidental perineal tears during childbirth in a communal medical center in Guinea-Conakry: a cross-sectional study

Background: Prevalence studies are still rare in sub-Saharan Africa on perineal tears. We conducted this cross-sectional study in a communal hospital in Guinea-Conakry, with the objective of this study was to determining the prevalence and characteristics of post-obstetric perineal lesions.Methods: All deliveries between March 1st and August 31st, 2014 were reviewed. We included in the analysis all the single deliveries with perineal tears. The Anglo-Saxon classification of perineal tears was used.Results: The prevalence of perineal tears was 5.7% with 5.4% benign lesions and 0.3% severe lesions. We did not register 4th degree lesions. The average age of parturient was 22 years. The majority (96.6%) of parturient had a history of genital mutilation and perineal scarring (60.3%).Conclusions: This prevalence appear low compared to those reported in other studies in Africa and point to the need for more sophisticated studies to have a better estimate of the prevalence of perineal tears in Guinea-Conakry

Fetal death in utero: epidemiological aspects, management and maternal prognosis in the obstetrics and gynecology department of the community medical centre of Ratoma

Background: Fetal death in utero (FDIU) often represents a tragedy badly lived, sometimes incomprehensible. It is considered as a failure of pregnancy's progress and monitoring. It is a frequent problem in obstetrical practice. Objective of study was to contribute to the study of FDIU in the maternity ward of the Ratoma municipal medical center.Methods: This was a prospective study of analytical type conducted over a period of 6 months from 1 January to 30 June 2017.Results: During this study period, we recorded 54 cases of FDIU out of a total of 1256 deliveries, or a frequency of 4.3%. The average age of our patients was 28.5 years with extremes of 16 to 39 years, the most represented age group was 25 to 34 years, with a frequency of 44.4%. The absence of active fetal movement was the main reason for consultation, with a frequency of 51.9%, and housewives were the most affected, with a frequency of 61.1%. The 70.4% of our patients gave birth by vaginal delivery and oxytocin was the most commonly used drug for induction of labor, i.e., 77.8%. The immediate maternal prognosis was 100% favorable and no case of maternal death was recordedConclusions: In-utero fetal death is a frequent obstetrical pathology, the awareness of women for the realization of ANC as well as the early management of risk factors detected during ANC constitutes an element of great importance. Therefore, a regular follow-up of all pregnant women even in the absence of risk factors proves necessary

Acceptability of contraceptive implants at the maternity ward of the Matam Communal Medical Center

Background: World Health Organization (WHO), defines contraception as "the use of agents, devices, methods or procedures to decrease the likelihood of conception or avoid it". In Africa, only 24% of women of childbearing age have access to a modern contraceptive method. The objective of the study was to determine the frequency of use of the contraceptive implant, to describe the socio-demographic characteristics of the users, to identify the reasons for the choice of the method and to assess the degree of satisfaction of the clients.Methods: The study was conducted at the Matam Communal Medical Center on level 2 of the health pyramid in Guinea. This was a 12-month cross-sectional, descriptive and analytical study (June 2017 to May 2018), including all women admitted for desire for contraception and who agreed to choose the implant as a contraceptive method.Results: The study involved 512 clients. The proportion of female users was 26.21%. The average age was 27.8 years, the main users were women of liberal trade, married, multiparous. The main reasons for choice cited by clients were the effectiveness and long duration of action of the method, i.e. 35.2% and 30.9% respectively. The majority of providers of the method were represented by midwives (73.3%) and the degree of client satisfaction with the method was 97%.Conclusions: The implant is a long-acting method of contraction. It is frequently used at the Communal Medical Center of Matam. Its efficient use would involve effective counselling

Arthropathies Microcristallines : à Propos de 150 Cas au Sénégal

Objectif : Déterminer le profil épidémiologique des cas d’arthropathies microcristallines dans le service de rhumatologie du CHU Aristide Le Dantec. Matériel et méthodes : Il s’agit d’une étude rétrospective menée entre janvier 2002 et décembre 2015 dans le service de rhumatologie du CHU Aristide Le Dantec de Dakar. Nous avions inclus tous les dossiers des patients diagnostiqués pour arthropathies microcristallines selon les critères en vigueur. Résultats : Nous avons colligées 150 cas d’arthropathies microcristallines : 106 cas de gouttes, 37 cas de CCA et 7 cas de rhumatisme apatitique. Les cas de goutte étaient observés chez 92 hommes (86,79%) et 14 femmes (13,21%), d’âge moyen de 55,72 ans (extrême entre 31 et 91 ans). Le délai diagnostique était en moyenne de 11,17 ans (extrême entre 3 jours et 40 ans). L’hyperuricémie était constante et était associé à des facteurs de risque métabolique. Les cas de chondrocalcinose articulaire étaient observés chez 31 femmes (83,8%) et 6 hommes (16,2%) d’âge moyen de 69,05 ans (extrême entre 59 et 91 ans). Le délai diagnostic était de 10,46 ans (extrême entre 1 et 26 ans). Les cas de rhumatisme apatitique étaient constitués uniquement de femme jeune dont l’âge moyen était de 32 ans (extrême entre 29 et 34 ans). Conclusion: L’incidence de cette affection semble être en augmentation dans notre étude où elle est dominée, comme en Occident par la goutte. Le diagnostic des arthropathies microcristallines était tardif et sa présentation clinique et radiologique sévère. Cette sévérité est attribuable en partie au retard diagnostic ce qui est similaire aux formes rapportées chez le noir africain.   Objective: Determine the epidemiological profile of microcrystalline arthropathies in the rheumatology department of the University Hospital of Dakar. Material and methods: This is a retrospective study conducted between January 2002 and December 2015 in the rheumatology department of Aristide Le Dantec University Hospital of Dakar. Microcrystalline arthropathies were diagnosed according to current criteria. Results: We collected 150 cases of microcrystalline arthropathy: 106 cases of gout, 37 cases of CCA and 7 cases of apatitic rheumatism. Cases of gout were observed in 92 men (86.79%) and 14 women (13.21%), with a mean age of 55.72 years (extreme between 31 and 91 years). The diagnostic delay was on average 11.17 years (extreme between 3 days and 40 years). Hyperuricemia was constant and was associated with metabolic risk factors. The cases of articular chondrocalcinosis were observed in 31 women (83.8%) and 6 men (16.2%) with a mean age of 69.05 years (extreme between 59 and 91 years). The diagnostic delay was 10.46 years (extreme between 1 and 26 years). The cases of apatitic rheumatism consisted only of young women whose average age was 32 years (extreme between 29 and 34 years). Conclusion: The incidence of this condition seems to be increasing in our study where it is dominated, as in the West, by gout. The diagnosis of microcrystalline arthropathies was late and its clinical and radiological presentation severe. This severity is partly attributable to the delayed diagnosis, which is similar to the forms reported in black Africans

Arthropathies Microcristallines : à Propos de 150 Cas au Sénégal

Objectif : Déterminer le profil épidémiologique des cas d’arthropathies microcristallines dans le service de rhumatologie du CHU Aristide Le Dantec. Matériel et méthodes : Il s’agit d’une étude rétrospective menée entre janvier 2002 et décembre 2015 dans le service de rhumatologie du CHU Aristide Le Dantec de Dakar. Nous avions inclus tous les dossiers des patients diagnostiqués pour arthropathies microcristallines selon les critères en vigueur. Résultats : Nous avons colligées 150 cas d’arthropathies microcristallines : 106 cas de gouttes, 37 cas de CCA et 7 cas de rhumatisme apatitique. Les cas de goutte étaient observés chez 92 hommes (86,79%) et 14 femmes (13,21%), d’âge moyen de 55,72 ans (extrême entre 31 et 91 ans). Le délai diagnostique était en moyenne de 11,17 ans (extrême entre 3 jours et 40 ans). L’hyperuricémie était constante et était associé à des facteurs de risque métabolique. Les cas de chondrocalcinose articulaire étaient observés chez 31 femmes (83,8%) et 6 hommes (16,2%) d’âge moyen de 69,05 ans (extrême entre 59 et 91 ans). Le délai diagnostic était de 10,46 ans (extrême entre 1 et 26 ans). Les cas de rhumatisme apatitique étaient constitués uniquement de femme jeune dont l’âge moyen était de 32 ans (extrême entre 29 et 34 ans). Conclusion: L’incidence de cette affection semble être en augmentation dans notre étude où elle est dominée, comme en Occident par la goutte. Le diagnostic des arthropathies microcristallines était tardif et sa présentation clinique et radiologique sévère. Cette sévérité est attribuable en partie au retard diagnostic ce qui est similaire aux formes rapportées chez le noir africain.   Objective: Determine the epidemiological profile of microcrystalline arthropathies in the rheumatology department of the University Hospital of Dakar. Material and methods: This is a retrospective study conducted between January 2002 and December 2015 in the rheumatology department of Aristide Le Dantec University Hospital of Dakar. Microcrystalline arthropathies were diagnosed according to current criteria. Results: We collected 150 cases of microcrystalline arthropathy: 106 cases of gout, 37 cases of CCA and 7 cases of apatitic rheumatism. Cases of gout were observed in 92 men (86.79%) and 14 women (13.21%), with a mean age of 55.72 years (extreme between 31 and 91 years). The diagnostic delay was on average 11.17 years (extreme between 3 days and 40 years). Hyperuricemia was constant and was associated with metabolic risk factors. The cases of articular chondrocalcinosis were observed in 31 women (83.8%) and 6 men (16.2%) with a mean age of 69.05 years (extreme between 59 and 91 years). The diagnostic delay was 10.46 years (extreme between 1 and 26 years). The cases of apatitic rheumatism consisted only of young women whose average age was 32 years (extreme between 29 and 34 years). Conclusion: The incidence of this condition seems to be increasing in our study where it is dominated, as in the West, by gout. The diagnosis of microcrystalline arthropathies was late and its clinical and radiological presentation severe. This severity is partly attributable to the delayed diagnosis, which is similar to the forms reported in black Africans

Arthropathies Microcristallines: à Propos de 150 cas a Sénégal

Objectif : Les arthropathies microcristallines sont classiquement considérées comme rares en Afrique sub-saharienne où la majorité des études porte sur la goutte. L’objectif de notre étude était de déterminer le profil épidémiologique des cas d’arthropathies microcristallines dans le service de rhumatologie du CHU Aristide Le Dantec. Matériel et méthodes : Il s’agit d’une étude rétrospective menée entre janvier 2002 et décembre 2016 dans le service de rhumatologie du CHU Aristide Le Dantec de Dakar. Nous avions inclus tous les dossiers des patients diagnostiqués pour arthropathies microcristallines selon les critères en vigueur. Résultats : Nous avons colligées 150 cas d’arthropathies microcristallines : 106 cas de gouttes, 37 cas de chondrocalcinose articulaire et 7 cas de rhumatisme apatitique. L’âge moyen des patients était de 58,12 ± 14,12 ans avec des extrêmes entre 31 et 91 ans. Quatre-vingt-douze (86,79%) patients atteints de goutte étaient des hommes et trente et un patients (83,8%) atteints de CCA étaient des femmes. Le délai diagnostique moyen des patients atteints d’arthropathies microcristallines était de 10,71±8,07 ans. La présentation clinique des arthropathies microcristallines était polyarticulaire (63 ; 42%), oligoarticulaire (48 ; 32%) et monoarticulaire (35 ; 23,3%) des cas. Les genoux et les chevilles étaient les articulations les plus touchées avec respectivement 40,7 et 20,7% des cas. L’hyperuricémie était constante et était associée à des facteurs de risque métabolique tel que l’obésité et la dyslipidémie avec respectivement 39,62 et 37,74 % des cas.  Conclusion : L’incidence de cette affection semble être en augmentation dans notre étude où elle est dominée, comme en Occident par la goutte. Le diagnostic des arthropathies microcristallines était tardif et sa présentation clinique et radiologique sévère. Cette sévérité est attribuable en partie au retard diagnostic ce qui est similaire aux formes rapportées chez le noir africain.   Objective: Microcrystalline arthropathies are classically considered rare in sub-Saharan Africa where the majority of studies focus on gout. The objective of our study was to determine the epidemiological profile of cases of microcrystalline arthropathy in the rheumatology department of the University Hospital of Dakar. Material and methods: This is a retrospective study conducted between January 2002 and December 2016 in the rheumatology department of Aristide Le Dantec University Hospital of Dakar. Microcrystalline arthropathies were diagnosed according to current criteria. Results: We collected 150 cases of microcrystalline arthropathies: 106 cases of gout, 37 cases of articular chondrocalcinosis and 7 cases of apatitic rheumatism. The average age of patients was 58.12 ± 14.12 years with extremes between 31 and 91 years. Ninety-two (86.79%) patients with gout were male and thirty-one (83.8%) patients with CCA were female. The average diagnostic delay of patients with microcrystalline arthropathies was 10.71 ± 8.07 years. The clinical presentation of microcrystalline arthropathies was polyarticular (63; 42%), oligoarticular (48; 32%) and monoarticular (35; 23.3%) of the cases. The knees and ankles were the most affected joints with respectively 40.7 and 20.7% of cases. Hyperuricemia was constant and was associated with metabolic risk factors such as obesity and dyslipidemia with respectively 39.62 and 37.74% of cases. Conclusion: The incidence of this condition seems to be increasing in our study where it is dominated, as in the West, by gout. The diagnosis of microcrystalline arthropathies was late and its clinical and radiological presentation severe. This severity is partly attributable to the delayed diagnosis, which is similar to the forms reported in black Africans

Management of pre-eclampsia and its complications in the department of gynecology and obstetrics at Donka national hospital Conakry, Guinea

Background: Vascular-renal syndrome, also known as pre-eclampsia, is a condition specific to pregnancy, usually occurring in the last trimester of pregnancy. Pregnant women are sometimes at risk of unpredictable obstetrical complications such as: hemorrhage, kidney failure, HELLP syndrome, sometimes even brain damage requiring prompt care and multidisciplinary collaboration. Vascular-renal syndromes are the third leading cause of maternal death and also the world's leading cause of perinatal death. Objectives of this study were to analyse the management of vascular-renal syndromes. Calculate their frequency, describe the sociodemographic characteristics of patients, describe the clinical and biological signs of patients, evaluate the maternal-fetal prognosis.Methods: The study was conducted in the department of obstetrics and gynecology of Donka National Hospital. It was a prospective, descriptive, cross-sectional, 6-month study from March 1st to August 31st, 2015, of pregnant women with pre-eclampsia.Results: The study included 217 cases of pre-eclampsia out of a total of 3054 patients, i.e. a proportion of 7.10%. The proportion of pre-eclampsia was high in patients aged between 15 and 19 years, housewife, married, primary. The predisposing factors were primigestitis, obesity and twinkling. The clinic was dominated by headaches and visual disturbances. Severe preeclampsia in 78.49%, eclampsia in 21.65% or simple hypertension in 1.75%. Maternal and fetal complications were dominated by eclampsia 26.26%, PPH (2.63%), eclamptic coma (0.46%), acute fetal distress 27.19%, and fetal death in utero (11.40%). In order to improve maternal and fetal prognosis it is necessary to provide multidisciplinary care, which unfortunately is not always available in our context.Conclusions: Obstetric emergency is a frequent situation for which a better management would improve the maternal-fetal prognosis

Fréquence des néphropathies congénitales au Centre hospitalier universitaire de Donka à Conakry: Frequency of congenital nephropathies in the University Hospital of Donka in Conakry

Context and objective. The real extent of congenital nephropathies is little known in Africa and in particular in Guinea. The objective of this study was to determine the prevalence of congenital nephropathies in the University Hospital of Donka. Methods. This was a descriptive retrospective study enrolling patients admitted for congenital nephropathy at both pediatric and pediatric surgery departments of Donka, between January 1st, 2007 and June 30th, 2012. The parameters of the study were epidemiological, clinical and paraclinical data.  Results. Of 34,448 patients recorded during the period studied, 26 had congenital nephropathies. They encompassed nephroblastoma (n=17), SJPU (n=6), hydronephrosis on left multikystic kidney (n=1), multikystic kidney in ptosis (n=1) and renal ectopia (n=1). Male sex was preponderant (21/26) with a sex ratio of 4.2/1. The 29 day-old to 2 year-old children were more affected. Conclusion. Congenital nephropathies appear less frequently in this hospital probably due to the absence of optimal facilities. The early diagnosis of congenital nephropathies should be made during the antenatal time, which would be a key to a better management of these conditions in affected children. Contexte et objectif. L’ampleur réelle des néphropathies congénitales est peu connue en Afrique et notamment en Guinée. L’objectif de cette étude était de déterminer la fréquence des néphropathies congénitales rencontrées. Méthodes. Cette étude documentaire de type descriptif sur la néphropathie congénitale, a été conduite entre les 1er janvier 2007 et 30 juin 2012, dans les services de pédiatrie et de chirurgie pédiatrique de Donka. Les paramètres d’interet englobaient les données épidémiologiques, cliniques et paracliniques.  Résultats. Parmi les 34.448 dossiers colligés, 26 présentaient une néphropathie congénitale. Il s’agissait des néphroblastomes (n=17), des syndromes de jonction pyélo-urétérale (n=6), d’une hydronéphrose sur rein multikystique gauche (n=1), d’un rein multikystique en ptose (n=1) et d’une ectopie rénale (n=1). Le sexe masculin était prépondérant (21/26) avec un sexe ratio de 4,2/1. Les enfants de 29 jours à 2 ans étaient les plus touchés. Conclusion. Les néphropathies congénitales sont paraissent moins fréquentes dans cette institution hospitalière, à cause du manque d’un plateau technique diagnostique optimal. Le diagnostic précoce des néphropathies congénitales devrait être fait dans la période prénatale ce qui permettrait une meilleure prise en charge des enfants affectés

Use of Viremia to Evaluate the Baseline Case Fatality Ratio of Ebola Virus Disease and Inform Treatment Studies: A Retrospective Cohort Study.

BACKGROUND: The case fatality ratio (CFR) of Ebola virus disease (EVD) can vary over time and space for reasons that are not fully understood. This makes it difficult to define the baseline CFRs needed to evaluate treatments in the absence of randomized controls. Here, we investigate whether viremia in EVD patients may be used to evaluate baseline EVD CFRs. METHODS AND FINDINGS: We analyzed the laboratory and epidemiological records of patients with EVD confirmed by reverse transcription PCR hospitalized in the Conakry area, Guinea, between 1 March 2014 and 28 February 2015. We used viremia and other variables to model the CFR. Data for 699 EVD patients were analyzed. In the week following symptom onset, mean viremia remained stable, and the CFR increased with viremia, V, from 21% (95% CI 16%-27%) for low viremia (V < 104.4 copies/ml) to 53% (95% CI 44%-61%) for intermediate viremia (104.4 ≤ V < 105.2 copies/ml) and 81% (95% CI 75%-87%) for high viremia (V ≥ 105.2 copies/ml). Compared to adults (15-44 y old [y.o.]), the CFR was larger in young children (0-4 y.o.) (odds ratio [OR]: 2.44; 95% CI 1.02-5.86) and older adults (≥ 45 y.o.) (OR: 2.84; 95% CI 1.81-4.46) but lower in children (5-14 y.o.) (OR: 0.46; 95% CI 0.24-0.86). An order of magnitude increase in mean viremia in cases after July 2014 compared to those before coincided with a 14% increase in the CFR. Our findings come from a large hospital-based study in Conakry and may not be generalizable to settings with different case profiles, such as with individuals who never sought care. CONCLUSIONS: Viremia in EVD patients was a strong predictor of death that partly explained variations in CFR in the study population. This study provides baseline CFRs by viremia group, which allow appropriate adjustment when estimating efficacy in treatment studies. In randomized controlled trials, stratifying analysis on viremia groups could reduce sample size requirements by 25%. We hypothesize that monitoring the viremia of hospitalized patients may inform the ability of surveillance systems to detect EVD patients from the different severity strata