Clustering Plasmodium falciparum Genes to their Functional Roles Using k-means

We developed recently a new and novel Metric Matrics k-means (MMk-means) clustering algorithm to cluster genes to their functional roles with a view of obtaining further knowledge on many P. falciparum genes. To further pursue this aim, in this study, we compare three different k-means algorithms (including MMk-means) results from an in-vitro microarray data (Le Roch et al., Science, 2003) with the classification from an in-vivo microarray data (Daily et al., Nature, 2007) in other to perform a comparative functional classification of P. falciparum genes and further validate the effectiveness of our MMk-means algorithm. Results from this study indicate that the resulting distribution of the comparison of the three algorithms’ in vitro clusters against the in vivo clusters are similar thereby authenticating our MMk-means method and its effectiveness. However, Daily et al. claim that the physiological state (the environmental stress response) of P. falciparum in selected malaria-infected patients observed in one of their clusters can not be found in any in-vitro clusters is not true as our analysis reveal many in-vitro clusters representation in this cluster

Reducing the Time Requirement of k-Means Algorithm

Traditional k-means and most k-means variants are still computationally expensive for large datasets, such as microarray data, which have large datasets with large dimension size d. In k-means clustering, we are given a set of n data points in ddimensional space Rd and an integer k. The problem is to determine a set of k points in Rd, called centers, so as to minimize the mean squared distance from each data point to its nearest center. In this work, we develop a novel k-means algorithm, which is simple but more efficient than the traditional k-means and the recent enhanced k-means. Our new algorithm is based on the recently established relationship between principal component analysis and the k-means clustering. We provided the correctness proof for this algorithm. Results obtained from testing the algorithm on three biological data and six non-biological data (three of these data are real, while the other three are simulated) also indicate that our algorithm is empirically faster than other known k-means algorithms. We assessed the quality of our algorithm clusters against the clusters of a known structure using the Hubert-Arabie Adjusted Rand index (ARIHA). We found that when k is close to d, the quality is good (ARIHA.0.8) and when k is not close to d, the quality of our new k-means algorithm is excellent (ARIHA.0.9). In this paper, emphases are on the reduction of the time requirement of the k-means algorithm and its application to microarray data due to the desire to create a tool for clustering and malaria research. However, the new clustering algorithm can be used for other clustering needs as long as an appropriate measure of distance between the centroids and the members is used. This has been demonstrated in this work on six non-biological data

Costing the supply chain for delivery of ACT and RDTs in the public sector in Benin and Kenya

Studies have shown that supply chain costs are a significant proportion of total programme costs. Nevertheless, the costs of delivering specific products are poorly understood and ballpark estimates are often used to inadequately plan for the budgetary implications of supply chain expenses. The purpose of this research was to estimate the country level costs of the public sector supply chain for artemisinin-based combination therapy (ACT) and rapid diagnostic tests (RDTs) from the central to the peripheral levels in Benin and Kenya.MethodsA micro-costing approach was used and primary data on the various cost components of the supply chain was collected at the central, intermediate, and facility levels between September and November 2013. Information sources included central warehouse databases, health facility records, transport schedules, and expenditure reports. Data from document reviews and semi-structured interviews were used to identify cost inputs and estimate actual costs. Sampling was purposive to isolate key variables of interest. Survey guides were developed and administered electronically. Data were extracted into Microsoft Excel®, and the supply chain cost per unit of ACT and RDT distributed by function and level of system was calculated.ResultsIn Benin, supply chain costs added USD 0.2011 to the initial acquisition cost of ACT and USD 0.3375 to RDTs (normalized to USD 1). In Kenya, they added USD 0.2443 to the acquisition cost of ACT and USD 0.1895 to RDTs (normalized to USD 1). Total supply chain costs accounted for more than 30% of the initial acquisition cost of the products in some cases and these costs were highly sensitive to product volumes. The major cost drivers were found to be labour, transport, and utilities with health facilities carrying the majority of the cost per unit of product. Accurate cost estimates are needed to ensure adequate resources are available for supply chain activities. Product volumes should be considered when costing supply chain functions rather than dollar value. Further work is needed to develop extrapolative costing models that can be applied at country level without extensive micro-costing exercises. This will allow other countries to generate more accurate estimates in the future

Clustering Plasmodium falciparum Genes to their Functional Roles Using k-means

We developed recently a new and novel Metric Matrics k-means (MMk-means) clustering algorithm to cluster genes to their functional roles with a view of obtaining further knowledge on many P. falciparum genes. To further pursue this aim, in this study, we compare three different k-means algorithms (including MMk-means) results from an in-vitro microarray data (Le Roch et al., Science, 2003) with the classification from an in-vivo microarray data (Daily et al., Nature, 2007) in other to perform a comparative functional classification of P. falciparum genes and further validate the effectiveness of our MMk-means algorithm. Results from this study indicate that the resulting distribution of the comparison of the three algorithms’ in vitro clusters against the in vivo clusters are similar thereby authenticating our MMk-means method and its effectiveness. However, Daily et al. claim that the physiological state (the environmental stress response) of P. falciparum in selected malaria-infected patients observed in one of their clusters can not be found in any in-vitro clusters is not true as our analysis reveal many in-vitro clusters representation in this cluster

Surpoids et obésité dans la population générale de 5 à 19 ans en milieu urbain bamakois (Mali)

Introduction: déterminer la prévalence du surpoids et de l'obésité dans la population âgée de 5 à 19 ans et fournir des données de référence pour de futures études. Méthodes: notre échantillon est issu de la première étude sur les pathologies cardiovasculaires basée sur l'approche STEP de l'Organisation Mondiale de la Santé (OMS) en sélectionnant tous les sujets âgés de 5 à 19 ans. Nous avons utilisé les méthodes de l'OMS et de l'International Obesity Task Force (IOTF) pour déterminer la prévalence du surpoids et de l'obésité dans la population générale. Résultats: la moyenne d'âge était de 11,75 ans ± 4,387 et le sex-ratio M:F était de 0,79. les moyennes pour le poids et la taille étaient de 36,85 kg et 143,48 cm. Selon les critères OMS 1,61% des garçons et 3,28 % des filles étaient en surpoids et 0,92% des garçons contre 1,46% des filles obèses. Selon les critères de l'IOTF 4,10% des garçons et 5,94% des filles étaient en surpoids tandis que 0,72% des garçons et 2,68% des filles étaient obèses. Conclusion: malgré sa faible prévalence le surpoids et l'obésité doivent être régulièrement étudiés pour reconnaître des tendances et prendre des mesures adéquates de prévention. Les 2 méthodes utilisées ont permis d'avoir des données de référence pour de futures études au Mali et ailleurs

Cost-effectiveness of community-based screening and treatment of moderate acute malnutrition in Mali.

IntroductionModerate acute malnutrition (MAM) causes substantial child morbidity and mortality, accounting for 4.4% of deaths and 6.0% of disability-adjusted life years (DALY) lost among children under 5 each year. There is growing consensus on the need to provide appropriate treatment of MAM, both to reduce associated morbidity and mortality and to halt its progression to severe acute malnutrition. We estimated health outcomes, costs and cost-effectiveness of four dietary supplements for MAM treatment in children 6-35 months of age in Mali.MethodsWe conducted a cluster-randomised MAM treatment trial to describe nutritional outcomes of four dietary supplements for the management of MAM: ready-to-use supplementary foods (RUSF; PlumpySup); a specially formulated corn-soy blend (CSB) containing dehulled soybean flour, maize flour, dried skimmed milk, soy oil and a micronutrient pre-mix (CSB++; Super Cereal Plus); Misola, a locally produced, micronutrient-fortified, cereal-legume blend (MI); and locally milled flour (LMF), a mixture of millet, beans, oil and sugar, with a separate micronutrient powder. We used a decision tree model to estimate long-term outcomes and calculated incremental cost-effectiveness ratios (ICERs) comparing the health and economic outcomes of each strategy.ResultsCompared to no MAM treatment, MAM treatment with RUSF, CSB++, MI and LMF reduced the risk of death by 15.4%, 12.7%, 11.9% and 10.3%, respectively. The ICER was US$9821 per death averted (2015 USD) and US$347 per DALY averted for RUSF compared with no MAM treatment.ConclusionMAM treatment with RUSF is cost-effective across a wide range of willingness-to-pay thresholds.Trial registrationNCT01015950

Surpoids et obésité dans la population au-dessus de 20 ans en milieu urbain bamakois (Mali)

Introduction: il est question dans notre travail d'étudier le SP et l'OB et les facteurs associés dans la population âgée de 20 ans ou plus. Méthodes: notre échantillon a été obtenu à partir d'une enquête sur les pathologies cardiovasculaires dans le District de Bamako et impliquant 2199 sujets de 5-104 ans, en sélectionnant tous les sujets âgés d'au moins 20 ans (1162). Pour chaque sujet, l'IMC, rapport taille / hanche et le tour de taille ont été déterminées. Les données ont été analysées avec SPSS 12. Résultats: l'âge moyen était de 36,86 années, 61,4% étaient des femmes, 49,7% dans le secteur informel et 38,0% avaient réalisé l'enseignement primaire. Facteurs de risque cardiovasculaires étaient l'inactivité physique (72,4%), le tabagisme (12,2%) et hypertension (26,7%). La prévalence de l'obésité était de 8,8 et 14,7% respectivement sur la base de l'indice de masse et le tour de taille. Conclusion: le SP et l'OB sont à prendre en compte dans les mesures de politique sanitaire que dans la pratique quotidienne des professionnels de santé, il est peut-être plus utile d'utiliser plusieurs paramètres pour être à même de bien stratifier nos patients par rapport à leur risque

An urgent need for HIV testing among men who have sex with men and transgender women in Bamako, Mali: Low awareness of HIV infection and viral suppression among those living with HIV

Despite the high HIV prevalence among men who have sex with men (MSM) and transgender women (TGW), there are limited data on progress on their respective HIV antiretroviral treatment (ART) cascades to identify progress and gaps in meeting UNAIDS 90-90-90 targets. We conducted a respondent-driven sampling survey of MSM and TGW in Bamako, Mali from October 2014 to February 2015. We describe the HIV treatment cascade for MSM and TGW, identify correlates of being unaware of HIV-infected status and having unsuppressed viral load levels, and estimate proportion of recent infections. We enrolled 387 MSM and 165 TGW. HIV prevalence was 13.7%. Of those living with HIV, 10.4% were aware of their serostatus, 61.2% of them self-reported being on treatment, and of them, 100% were virally suppressed. In multivariate analysis, factors associated with being unaware of HIV infection included not using free condoms in the last six months (aOR: 5.7, 95% CI: 1.1–29.5) and not having comprehensive knowledge of HIV (aOR: 6.5, 95% CI: 1.4–29.9). Having unsuppressed viral load was associated with identifying as a transgender woman (aOR: 4.8, 95% CI: 1.1–20.7) and not having comprehensive knowledge of HIV (aOR: 6.5, 95% CI: 1.0–40.9). Of the 79 HIV-positive participants, 5.1% had recent infections. While the proportion aware of their HIV status was low despite adjusting for viral load biomarkers, all MSM and TGW on treatment were virally suppressed. Improved testing strategies are urgently needed to achieve the first 90 of the HIV cascade among MSM and TGW in Bamako

Field experiments of Anopheles gambiae attraction to local fruits/seedpods and flowering plants in Mali to optimize strategies for malaria vector control in Africa using attractive toxic sugar bait methods

<p>Abstract</p> <p>Background</p> <p>Based on recent studies in Israel demonstrating that attractive toxic sugar bait (ATSB) methods can be used to decimate local anopheline and culicine mosquito populations, an important consideration is whether the same methods can be adapted and improved to attract and kill malaria vectors in Africa. The ATSB approach uses fruit or flower scent as an attractant, sugar solution as a feeding stimulant, and an oral toxin. The ATSB solutions are either sprayed on vegetation or suspended in simple bait stations, and the mosquitoes ingesting the toxic solutions are killed. As such, this approach targets sugar-feeding female and male mosquitoes. This study examines the attractiveness of African malaria vectors to local fruits/seedpods and flowering plants, key biological elements of the ATSB approach for mosquito control.</p> <p>Methods</p> <p>Three field experiments were conducted at sites in Mali. The attraction of <it>Anopheles gambiae </it>s.l. to 26 different local fruits and seedpods was determined at a site in the semi-arid Bandiagara District of Mali. Wire mesh glue traps with fruits/seedpods suspended on skewers inside were set along a seasonal lagoon. Seven replicates of each fruit/seedpod species were tested, with a water-soaked sponge and a sugar-soaked sponge as controls. The attraction of <it>An. gambiae </it>s.l. to 26 different types of flowering plants was determined at a site near Mopti in Mali. The flowering plants held in a water-filled buried container were tested using the same glue traps, with controls including water only and sugar solution. Six replicates of each selected plant type were tested on transects between rice paddies. Additional studies using CDC light traps were done to determine the relative densities and periodicity of <it>An. gambiae </it>s.l. attraction to branches of the most highly attractive flowering plant, branches without flowers, human odor, and candescent light.</p> <p>Results</p> <p>Of the 26 fruits and seedpods tested, 6 were attractive to <it>An. gambiae </it>s.l. females and males, respectively. Guava (<it>Psidium guajava</it>) and honey melon (<it>Cucumis melo</it>) were the two most attractive fruits for both females and males. Of the 26 flowering plants tested, 9 were significantly attractive for females, and 8 were attractive for males. <it>Acacia macrostachya </it>was the most attractive flowering plant. Periodicity studies using this plant showed peaks of <it>An. gambiae </it>s.l. attraction between 1930 and 2200 h and 0400-0500 h, which differed considerably from the response to human odors, which expectedly peaked at around midnight.</p> <p>Conclusion</p> <p>These field experiments in Mali highlight that female and male <it>An. gambiae </it>s.l. have pronounced differences in attraction for diverse types of indigenous fruits/seedpods and flowering plants. The identification of attractive fruits and seedpods shows that a variety of indigenous and locally abundant natural products could potentially be used as juices to make ATSB solution for mosquito control. As well, the simple methods used to identify the most attractive flowering plants provide valuable insights into the natural history of sugar feeding for <it>An. gambiae </it>s.l. These observations can be used to guide future strategies for employing ATSB methods for malaria vector control in Africa. They also provide a basis for subsequent chemical analysis and development of attractive baits for mosquito control.</p

Contrôle Physicochimique des Feuilles de Lippia chevalieri Moldenke Cultivé

Au Mali, le Malarial 5 qui est un Médicament Traditionnel Amélioré (MTA) produit en partie à base de feuilles de Lippia chevalieri est utilisé pour traiter les symptômes du paludisme simple. Les feuilles de Lippia chevalieri cultivé peuvent être utilisées pour la préparation des MTA lorsqu’elles sont de qualité. La présente étude portée sur le contrôle physicochimique a montré que les feuilles de Lippia chevalieri cultivé ont des teneurs en eau inférieures à 10%, celles des cendres totales un peu élevées et celles des cendres insolubles dans l’acide chlorhydriques à 10% faibles. Les meilleurs rendements des extractions sont obtenus par l’eau par infusion et par décoction. Plusieurs groupes chimiques comprenant entre autres des caroténoïdes, des coumarines, des mucilages, des flavonoïdes ont été révélés. In Mali, Malarial 5, which is an Improved Traditional Medicine (ITM) produced partly from the leaves of Lippia chevalieri, is used to treat the symptoms of uncomplicated malaria. The leaves of cultivated Lippia chevalieri can be used for the preparation of improved traditional medicines because they are of good quality. This paper focuses on the physicochemical control which showsthat the leaves of cultivated Lippia chevalieri contain less than 10% of moisture content. The total ash content was a little higher, and the acid insoluble ash was low. The best yields of extractions are obtained with water through infusion and decoction. Several chemical compounds including carotenoids, coumarins, mucilage, and flavonoids were revealed