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

Developpement des systemes de production innovants d’association mais/legumineuses dans la zone subhumide du Mali

Parmi les 3 piliers de l’intégration agriculture-élevage (traction animale, fumure organique, cultures fourragères) diffusés en Afrique de l’Ouest, seules les cultures fourragères ont été peu adoptées. Pourtant, les associations maïs/légumineuses ont l’avantage d’améliorer la production et l’alimentation animale. Elles représentent une alternative dans la gestion des risques et des incertitudes pour les agro-éleveurs, confrontés aux changements globaux (climatiques, pression foncière, dégradation des ressources naturelles). L’objectif de cette étude est de déterminer la contribution des associations maïs/légumineuses dans l’amélioration de la production de maïs grain et le bilan fourrager des exploitations agricoles. Le dispositif en blocs dispersés chez 10 producteurs, a consisté en 3 traitements, T1 (maïs seul), T2 (maïs/ niébé) et T3 (maïs/mucuna) durant 2 campagnes agricoles. En 2013 - 2014, les rendements de maïs grain ont été de 2433 kg/ha et en biomasse 2597 kgMS/ha. Par contre, en 2014 - 2015 les rendements ont été de 1932 kg/ha de maïs grain et de 5134 kgMS/ha de biomasse. Les besoins en matière sèche pour 90 jours de supplémentation ont été de 4,62 UBT en 2013 - 2014 et de 9,13 UBT en 2014 - 2015. Ces résultats montrent la contribution des associations maïs/légumineuses dans l’amélioration du rendement de maïs grain et de fourrages dans la zone subhumide au Mali.Mots clés : légumineuses, maïs, fourrage, Mal

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

Acetylcholinesterase (ace‑1R) target site mutation G119S and resistance to carbamates in Anopheles gambiae (sensu lato) populations from Mali

Open Access Journal; Published online: 05 Jun 2020Background The long-lasting insecticidal nets (LLINs) and indoor residual spraying of insecticide (IRS) are major malaria vector control strategies in Mali. The success of control strategies depends on a better understanding of the status of malaria vectors with respect to the insecticides used. In this study we evaluate the level of resistance of Anopheles gambiae (sensu lato) to bendiocarb and the molecular mechanism that underlies it. Methods Larvae of An. gambiae (s.l.) were collected from breeding habitats encountered in the three study sites and bioassayed with bendiocarb. The ace-1 target site substitution G119S was genotyped using a TaqMan assay. Results The three species of the An. gambiae complex in Mali, i.e. An. arabiensis, An. coluzzii and An. gambiae (s.s.) were found in sympatry in the three surveyed localities with different frequencies. We observed a resistance and suspicious resistance of the three species to bendiocarb with a mortality rate ranging from 37% to 86%. The allelic frequency of the G119S mutation was higher in An. gambiae (s.s.) compared to the other two species; 42.86%, 25.61% and 16.67% respectively in Dangassa, Koula, and Karadié. The allelic frequency of G119S in An. coluzzii ranged from 4.5% to 8.33% and from 1.43% to 21.15% for An. arabiensis. After exposure to bendiocarb, the G119S mutation was found only in survivors. The survival of Anopheles gambiae (s.l) populations from the three surveyed localities was associated with the presence of the mutation. Conclusions The study highlights the implication of G119S mutation in bendiocarb resistance in An. gambiae (s.s.), An. arabiensis and An. coluzzii populations from the three surveyed localities

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

Population Size and Migration of Anopheles gambiae in the Bancoumana Region of Mali and Their Significance for Efficient Vector Control

We present results of two intensive mark-release-recapture surveys conducted during the wet and dry seasons of 2008 in the villages of Fourda and Kenieroba, Mali. The former is a small fishing village by the Niger River with a moderate to high densities of Anopheles gambiae Giles s.s. (Diptera: Culicidae) throughout the year, while the latter is a large agricultural community 2 km inland that experiences strong seasonal fluctuation in An. gambiae densities. We estimate the population size of female An. gambiae in Fourda to be in less than 3,000 during the dry season. We found evidence of large population size and migration from Fourda in Kenieroba during the wet season, but very low numbers and no sign of migrants during the dry season. We suggest that malaria vector control measures aimed at adult mosquitoes might be made more efficient in this region and other seasonal riparian habitats by targeting disruption of mosquito populations by the river during the dry season. This would decrease the size of an already small population, and would be likely to delay the explosive growth in vector numbers in the larger inland villages as rainfall increases

Seasonality and shift in age-specific malaria prevalence and incidence in Binko and Carrière villages close to the lake in Selingué, Mali

BACKGROUND: Malaria transmission in Mali is seasonal and peaks at the end of the rainy season in October. This study assessed the seasonal variations in the epidemiology of malaria among children under 10 years of age living in two villages in Selingué: Carrière, located along the Sankarani River but distant from the hydroelectric dam, and Binko, near irrigated rice fields, close to the dam. The aim of this study was to provide baseline data, seasonal pattern and age distribution of malaria incidence in two sites situated close to a lake in Selingué. METHODS: Geographically, Selingué area is located in the basin of Sakanrani and belongs to the district of Yanfolila in the third administrative region of Mali, Sikasso. Two cross-sectional surveys were conducted in October 2010 (end of transmission season) and in July 2011 (beginning of transmission season) to determine the point prevalence of asymptomatic parasitaemia, and anaemia among the children. Cumulative incidence of malaria per month was determined in a cohort of 549 children through active and passive case detection from November 2010 through October 2011. The number of clinical episodes per year was determined among the children in the cohort. Logistic regression was used to determine risk factors for malaria. RESULTS: The prevalence of malaria parasitaemia varied significantly between villages with a strong seasonality in Carrière (52.0–18.9 % in October 2010 and July 2011, respectively) compared with Binko (29.8–23.8 % in October 2010 and July 2011, respectively). Children 6–9 years old were at least twice more likely to carry parasites than children up to 5 years old. For malaria incidence, 64.8–71.9 % of all children experienced at least one episode of clinical malaria in Binko and Carrière, respectively. The peak incidence was observed between August and October (end of the rainy season), but the incidence remained high until December. Surprisingly, the risk of clinical malaria was two- to nine-fold higher among children 5–9 years old compared to younger children. CONCLUSIONS: A shift in the peak of clinical episodes from children under 5–9 years of age calls for expanding control interventions, such as seasonal malaria chemoprophylaxis targeting the peak transmission months

MORBIDITE ET MORTALITE CHEZ LES ENFANTS DE 01 A 59 MOIS HOSPITALISES AU SERVICE DE PEDIATRIE GENERALE DU CHU GABRIEL TOURE DE JANVIER A DECEMBRE 2013

Objectif : Ce travail visait à étudier la morbidité et la mortalité chez les enfants âgés de 01 à 59 mois hospitalisés dans le service de pédiatrie générale du CHU Gabriel Touré. Matériels et Méthodes : Il s’agissait d’une étude rétrospective, descriptive, sur une période de 12 mois allant du 1er janvier au 31 décembre 2013. Résultats : Nous avons inclus 1625 enfants âgés de 01 à 59 mois soit 58% des patients hospitalisés. Le tiers des patients avait moins d’un an. Les garçons représentaient 57 % de notre échantillon avec un sex ratio de 1,33. La majorité des patients (83%) était issu de milieu social défavorisé. Les principaux diagnostics retrouvés étaient le paludisme (45%), les infections respiratoires aiguës (20,30%), et la malnutrition aiguë sévère (20,06%). Les patients guéris représentaient 82,3% et le taux de mortalité était estimé à 3,3%. La majorité des patients décédés était des filles (51%). Les décès étaient plus fréquents en juillet et aout. Les trois principales causes de décès étaient la malnutrition (47%), le paludisme (32%) et les infections respiratoires aigües (19%). Nous avons enregistré 48 sorties contre avis médical (3%) et 81 cas d’évasion (5%). Conclusion : La morbidité et la mortalité en pédiatrie restent préoccupantes dans notre pratique. Elles sont liées à des affections pour la plupart évitables par l’information, l’éducation et la communication

Sources and Mechanisms of Resistance to Sorghum Head Bug, Eurystylus-Immaculatus Odh in West-Africa

Sorghum is one of the most important cereal crops in West Africa, and the head bug, Eurystylus immaculatus Odh. (Hemiptera: Miridae) is the key pest of grain sorghum in this region. A range of sorghum genotypes were evaluated for resistance to sorghum head bug at Sotuba (Mali) and Kamboinse (Burkina Faso). Genotypes CSM 388, IS 14332, Malisor 84-7, Sakoika. S 29 and Kamboinse local were resistant to head bugs. both under natural and headcage screening. Head bug resistant genotypes had a lower percentage of head bug damaged grain. The food quality of head bug damaged grain was very poor and unacceptable. Cultivar non-preference was identified as a component of resistance to head bugs. and CSM 388 was nonpreferred compared to E 35-1. Panicle compactness was positively associated with head bug numbers and grain damage. However, genotypes with loose panicles were also susceptible to bugs. Long glumes (>5 mm), days to glume opening (>20 days after anthesis), >50% covering of the grain by the glumes, and grain hardness contribute towards resistance to Eurystylus immaculatus. This information will be useful for developing a programme to breed for resistance to this insect in West Africa