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

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

Emissions from the road traffic of West African cities : assessment of vehicle fleet and fuel consumption

Traffic source emission inventories for the rapidly growing West African urban cities are necessary for better characterization of local vehicle emissions released into the atmosphere of these cities. This study is based on local field measurements in Yopougon (Abidjan, C&ocirc te d&rsquo Ivoire) in 2016 a site representative of anthropogenic activities in West African cities. The measurements provided data on vehicle type and age, traveling time, fuel type, and estimated amount of fuel consumption. The data revealed high traffic flow of personal cars on highways, boulevards, and backstreets, whereas high flows of intra-communal sedan taxis were observed on main and secondary roads. In addition, the highest daily fuel consumption value of 56 L&middot day&minus 1 was recorded for heavy vehicles, while the lowest value of 15 L&middot 1 was recorded for personal cars using gasoline. This study is important for the improvement of uncertainties related to the different databases used to estimate emissions either in national or international reports. This work provides useful information for future studies on urban air quality, climate, and health impact assessments in African cities. It may also be useful for policy makers to support implementation of emission reduction policies in West African cities. Document type: Articl

Etude Comparative Des Produits Issus De La Transformation En Filature Des Fibres De Trois Nouvelles Variétés De Cotonnier

Résumé - Au Mali, comme ailleurs en Afrique, la sélection variétale est à la base du succès de la culture cotonnière. Le coton du Mali est presqu’entièrement exporté ; les fibres issues des variétés cultivées doivent répondre aux exigences du marché en termes de caractéristiques technologiques des fibres, facteurs clés du fonctionnement de la filature. Cette étude comparative a été réalisée sur trois nouvelles variétés de cotonniers A, B et C, issues d’un point d'expérimentation. L'objectif de l'étude est d’identifier les variétés ayant les meilleures performances variétales et industrielles pour la vulgarisation en production commerciale par les sociétés cotonnières. 1 échantillon représentatif de 100g de coton fibre, 20 échantillons de 5 m de rubans de carde, d’étirage et de 10 m de mèches, 30 échantillons de 100 m de fil et 40 échantillons de 500 mm de fil ont été respectivement prélevés par balle de chaque variété et à différentes étapes du processus de transformation par variété. Ces échantillons ont été testés sur des appareils de mesure dans les conditions requises au laboratoire de métrologie textile du CERFITEX, Ségou - Mali.L’analyse de variance (ANOVA) des données relatives aux fibres, rubans, mèches et fils et la comparaison de leurs principales caractéristiques de qualité à celle de la production mondiale avec l’application des USTER STATISTICS 2018 ont montré que les variétés de cotonnier A et B sont nettement meilleures que celle de C. Les performances variétales et industrielles de A et B, meilleures que celles de C sont recommandées à la vulgarisation Mots clés : Coton, caractéristiques technologiques, qualité, fibres, fils. [Comparative Study Of The Products Resulting From The Transformation Into Spinning Of The Fibers Of Three New Varieties Of Cotton]Abstract - In Mali, as elsewhere in Africa, varietal selection is the basis of the success of cotton growing. Cotton from Mali is almost entirely exported; fibers from cultivated varieties must meet market requirements in terms of the technological characteristics of fibers, key factors in the operation of the spinning mill. This comparative study was carried out on three new varieties of cotton A, B and C, from an experimental point. The objective of the study is to identify the varieties with the best varietal and industrial performance for popularization in commercial production by cotton companies. 1 representative sample of 100g of cotton fiber, 20 samples of 5m of carding and drawing slivers and 10m of rovings, 30 samples of 100m of yarn and 40 samples of 500mm of yarn were respectively taken per bale of each variety and at different stages of the transformation process by variety. These samples were tested on measuring devices under the required conditions at the CERFITEX textile metrology laboratory, Ségou - Mali.The analysis of variance (ANOVA) of fiber, sliver, roving and yarn data and the comparison of their main quality characteristics to that of world production with the application of USTER STATISTICS 2018 showed that cotton varieties A and B are clearly better than those of C. The varietal and industrial performances of A and B, better than that of C are recommended for popularisation Keywords : Cotton, technological characteristics, quality, fibres, yarns

From reverse innovation to global innovation in animal health: a review

Reverse innovation refers to learning from or diffusion of innovations developed in low income settings and further translated to industrialized countries. There is lack of consensus regarding terminology, but the idea that innovations in low-income countries are promising for adoption in high-income contexts is not new. However, in healthcare literature globally, the vast majority of publications referring to 'disruptive innovation' were published in the last ten years. To assess the potential of innovative developments and technologies for improving animal health, we initiated a literature review in 2020. We used a combined approach, incorporating targeted searching in PubMed using a key word algorithm with a snowball technique, to identify 120 relevant publications and extract data for qualitative coding. Heterogeneity of articles precluded meta-analysis, quality scoring and risk of bias analysis. We can distinguish technical innovations like new digital devices, diagnostic tests and procedures, and social innovations of intersectoral cooperation. We profile two case studies to describe potential global innovations: an integrated surveillance and response system in Somali Regional State, Ethiopia and a blockchain secured One Health intervention to optimally provide post-exposure prophylaxis for rabies exposed people in West Africa. Innovation follows no borders and can also occur in low-income settings, under constraints of cost, lack of services and infrastructure. Lower administrative and legal barriers may contribute to produce innovations that would not be possible under conditions of high density of regulation. We recommend using the term global innovation, which highlights those emanating from international partnership to solve problems of global implications

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

Rabies mortality and morbidity associated with animal bites in Africa: a case for integrated rabies disease surveillance, prevention and control: a scoping review

OBJECTIVE: The objective of this scoping review was to map the current situation and available evidence and gaps on rabies morbidity, mortality, integrated rabies surveillance programmes, and existing prevention and control strategies in Africa. METHODS: We conducted a systematic scoping review following the Joanna Briggs methodology and Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews checklist. Medline, Embase, CINAHL (EBSCOHost), Scopus, Web of Science and rabies web conferences were used to search for peer-reviewed publications between January 1946 and May 2020. Two researchers reviewed the studies and extracted data based on author (year) and region, study design and data collection duration, participants/comparators, interventions, control conditions/exposures and outcomes (rabies mortality and morbidity) and key findings/gaps/challenges. The results were reported narratively using Arksey and O'Malley's methodological framework. RESULTS: Electronic search yielded 2775 records, of which 43 studies were included. A total of 543 714 bite victims were censored through the included studies. Most of the victims were less than 15 years of age. The studies included rabies morbidity (21) and mortality (15) fluctuating in space and time across Africa depending on countries' rabies prevention and control practices (16). Others were surveillance (nine studies); surveillance and prevention (five studies); management and control (seven studies); and surveillance, prevention and control (six studies). We found challenges in rabies reporting, existing dog vaccination programmes and post-exposure prophylaxis availability or compliance. CONCLUSION: This study found challenges for dog rabies control and elimination in Africa and the need for a policy to drive the goal of zero dog-transmitted rabies to humans by 2030.This is an open-access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build on this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated and the use is non-commercial (see http://creativecommons.org/licenses/by-nc/4.0/)

Quantifying uncertainties due to chemistry modelling – evaluation of tropospheric composition simulations in the CAMS model (cycle 43R1)

We report on an evaluation of tropospheric ozone and its precursor gases in three atmospheric chemistry versions as implemented in the European Centre for Medium-Range Weather Forecasts (ECMWF) Integrated Forecasting System (IFS), referred to as IFS(CB05BASCOE), IFS(MOZART) and IFS(MOCAGE). While the model versions were forced with the same overall meteorology, emissions, transport and deposition schemes, they vary largely in their parameterisations describing atmospheric chemistry, including the organics degradation, heterogeneous chemistry and photolysis, as well as chemical solver. The model results from the three chemistry versions are compared against a range of aircraft field campaigns, surface observations, ozone-sondes and satellite observations, which provides quantification of the overall model uncertainty driven by the chemistry parameterisations. We find that they produce similar patterns and magnitudes for carbon monoxide (CO) and ozone (O3), as well as a range of non-methane hydrocarbons (NMHCs), with averaged differences for O3 (CO) within 10&thinsp;% (20&thinsp;%) throughout the troposphere. Most of the divergence in the magnitude of CO and NMHCs can be explained by differences in OH concentrations, which can reach up to 50&thinsp;%, particularly at high latitudes. There are also comparatively large discrepancies between model versions for NO2, SO2 and HNO3, which are strongly influenced by secondary chemical production and loss. Other common biases in CO and NMHCs are mainly attributed to uncertainties in their emissions. This configuration of having various chemistry versions within IFS provides a quantification of uncertainties induced by chemistry modelling in the main CAMS global trace gas products beyond those that are constrained by data assimilation.</p

The Relationship between Population Structure and Aluminum Tolerance in Cultivated Sorghum

Background: Acid soils comprise up to 50% of the world's arable lands and in these areas aluminum (Al) toxicity impairs root growth, strongly limiting crop yield. Food security is thereby compromised in many developing countries located in tropical and subtropical regions worldwide. In sorghum, SbMATE, an Al-activated citrate transporter, underlies the Alt(SB) locus on chromosome 3 and confers Al tolerance via Al-activated root citrate release. Methodology: Population structure was studied in 254 sorghum accessions representative of the diversity present in cultivated sorghums. Al tolerance was assessed as the degree of root growth inhibition in nutrient solution containing Al. A genetic analysis based on markers flanking Alt(SB) and SbMATE expression was undertaken to assess a possible role for Alt(SB) in Al tolerant accessions. In addition, the mode of gene action was estimated concerning the Al tolerance trait. Comparisons between models that include population structure were applied to assess the importance of each subpopulation to Al tolerance. Conclusion/Significance: Six subpopulations were revealed featuring specific racial and geographic origins. Al tolerance was found to be rather rare and present primarily in guinea and to lesser extent in caudatum subpopulations. Alt(SB) was found to play a role in Al tolerance in most of the Al tolerant accessions. A striking variation was observed in the mode of gene action for the Al tolerance trait, which ranged from almost complete recessivity to near complete dominance, with a higher frequency of partially recessive sources of Al tolerance. A possible interpretation of our results concerning the origin and evolution of Al tolerance in cultivated sorghum is discussed. This study demonstrates the importance of deeply exploring the crop diversity reservoir both for a comprehensive view of the dynamics underlying the distribution and function of Al tolerance genes and to design efficient molecular breeding strategies aimed at enhancing Al tolerance.CGIAR[G3007.04]McKnight FoundationFundacao de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG)National Council for Scientific and Technological Development (CNPq