Comparative evaluation of automated KingFisher Flex Purification System 96 (ThermoFisher Scientific) and manual QIAamp Viral RNA Mini Kit (Qiagen) extraction methods for SARS-CoV-2

Background: The extraction step of the viral material of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) influences the quality of reverse transcriptase-polymerase chain reaction (RT-PCR) results in diagnosis of coronavirus disease 2019 (COVID-19). The purpose of this cross-sectional study was to evaluate the diagnostic performance of the automated extraction system "KingFisher Flex Purification System 96 (ThermoFisher)" compared to the manual method with the "QIAamp Viral RNA Mini Kit (Qiagen)". Methodology: From October to December 2020, comparative diagnostic evaluation of two methods of SARSCoV-2 RNA extraction methods was conducted on 159 fresh and 120 frozen nasopharyngeal and oropharyngeal specimens collected from travellers and suspected cases or contacts of COVID-19 patients in Burkina Faso. The FastPlexTM Triplex 1-Step COVID 19 Detection Kit (RT-PCR, RNA extraction free) (Precigenome LLC) was used to amplify on the same PCR plate, RNA extracts from manual QIAamp Viral RNA Mini Kit and automated KingFisher Flex Purification System 96 (ThermoFisher) using the QuantStudio5 thermal cycler (Applied Biosystems). Analysis of the diagnostic performance of the SARS-CoV-2 RT-PCR assay following RNA extraction by the two methods was done using an online OpenEpi software. Results: For fresh samples, the study found a slightly higher RT-PCR positivity rate following manual extraction (12.6%) than automated extraction (9.4%). For frozen samples, the positivity rate was far higher for manual (38.33%) than automated extraction method (20.83%). The results show that the performance of the automated extraction was inferior when compared to the manual extraction for both fresh samples (sensitivity 35%, specificity 94.2%) and frozen samples (sensitivity 43.5%, specificity 93.2%). However, using McNemar Chi-square with Yates correction, there was no significant difference in positivity rate of RT-PCR (x2=0.76, p=0.38) between the two extraction methods for the fresh samples, but there was a significant difference (x2=12.9, p= 0.0003) in the extraction of the frozen samples. Conclusion: The results of this study showed that KingFisher Flex Purification System 96 (ThermoFisher) automatic extraction method was less sensitive and specific than QIAamp Viral RNA Mini Kit (Qiagen) manual extraction method. This information can serve as guide to laboratories in the choice of RNA extraction methods to use for RT-PCR detection of SARS-CoV-2

Femmes et hommes face aux grossesses non prévues au Maroc et au Sénégal

Cet article étudie la manière dont les femmes ou les couples gèrent les grossesses non prévues dans les capitales du Maroc et du Sénégal (Rabat et Dakar), deux pays soumis à des règles strictes en matière de sexualité des célibataires. Nous analysons les logiques sociales et individuelles qui prévalent à l'annonce d'une grossesse inattendue et la manière dont se prennent les décisions qui vont aboutir à la poursuite de cette grossesse ou à son interruption. Nous nous basons sur des données qualitatives tirées d'un programme financé par l'Union Européenne entre 2005 et 2009, sur l'usage de la contraception d'urgence dans les villes africaines. Nos résultats montrent qu'en dépit de programmes de planification familiale plus performants dans leur pays, les femmes de Rabat vivent leur entrée en sexualité dans des conditions difficiles. Si à Dakar la chasteté avant le mariage est prônée, le non-respect de cette règle entraîne des sanctions beaucoup moins sévères qu'au Maroc. Le choix de l'avortement en cas de grossesse non prévue évolue avec le cycle de vie des individus et selon le stade de la relation. Une pratique envisageable à un moment donné, ne l'est plus forcément à d'autres moments de la relation. Enfin, dans les deux villes, nos données révèlent une forte implication des familles dans la gestion de la formation des couples et de leur fécondité. Cette tendance apparaît cependant plus exacerbée au Maroc où les familles se mobilisent parfois âprement pour obliger ou interdire un avortement

APOBEC3G variants and protection against HIV-1 infection in Burkina Faso

Studies on host factors, particularly the APOBEC3G gene, have previously found an association with AIDS progression in some populations and against some HIV-1 strains but not others. Our study had two main objectives: firstly, to screen a population from Burkina Faso for three variants of APOBEC3G previously described, and secondly to analyze the effect of these three variants and their haplotypes on HIV-1 infection with Circulating Recombinant Forms (CRFs) present in Burkina Faso. This case control study involved 708 seropositive and seronegative individuals. Genotyping was done by the TaqMan allelic discrimination method. Minor allele frequencies of rs6001417 (p<0.05), rs8177832 (P<0.05), and rs35228531 (P<0.001) were higher in seronegative subjects. The rs6001417 and rs8177832 SNPs were associated with HIV-1 infection in an additive model (P<0.01). Furthermore the SNP rs35228531 was also associated with HIV-1 infection in a dominant model (P<0.001). Odds ratio analysis of genotypes and alleles of the different APOBEC3G variants showed that there is a strong association between the minor genetic variants, genotype of the three SNPs, and HIV-1 status. Haplotype analysis demonstrated that rs6001417, rs8177832, and rs35228531 are in linkage disequilibrium. The haplotype GGT from the rs6001417, rs8177832 and rs35228531 respectively has a protective effect OR = 0.54 [0.43-0.68] with P<0.001. There was also associations between the haplotypes GGC OR = 1.6 [1.1;-2.3] P<0.05, and CGC OR = 5.21 [2.4-11.3] P<0.001, which increase the risk of infection by HIV-1 from almost two (2) to five (5) fold. This study demonstrates an association of rs6001417, rs8177832, and rs35228531 of APOBEC3G with HIV-1 infection in a population from Burkina Faso

Birth preparedness and complication readiness (BPCR) among pregnant women in hard-to-reach areas in Bangladesh:BPCR in hard-to-reach areas of Bangladesh

Birth preparedness and complication readiness aims to reduce delays in care seeking, promote skilled birth attendance, and facility deliveries. Little is known about birth preparedness practices among populations living in hard-to-reach areas in Bangladesh.To describe levels of birth preparedness and complication readiness among recently delivered women, identify determinants of being better prepared for birth, and assess the impact of greater birth preparedness on maternal and neonatal health practices.A cross-sectional survey with 2,897 recently delivered women was undertaken in 2012 as part of an evaluation trial done in five hard-to-reach districts in rural Bangladesh. Mothers were considered well prepared for birth if they adopted two or more of the four birth preparedness components. Descriptive statistics and multivariable logistic regression were used for analysis.Less than a quarter (24.5%) of women were considered well prepared for birth. Predictors of being well-prepared included: husband's education (OR = 1.3; CI: 1.1-1.7), district of residence, exposure to media in the form of reading a newspaper (OR = 2.2; CI: 1.2-3.9), receiving home visit by a health worker during pregnancy (OR = 1.5; CI: 1.2-1.8), and receiving at least 3 antenatal care visits from a qualified provider (OR = 1.4; CI: 1.0-1.9). Well-prepared women were more likely to deliver at a health facility (OR = 2.4; CI: 1.9-3.1), use a skilled birth attendant (OR = 2.4, CI: 1.9-3.1), practice clean cord care (OR = 1.3, CI: 1.0-1.5), receive post-natal care from a trained provider within two days of birth for themselves (OR = 2.6, CI: 2.0-3.2) or their newborn (OR = 2.6, CI: 2.1-3.3), and seek care for delivery complications (OR = 1.8, CI: 1.3-2.6).Greater emphasis on BPCR interventions tailored for hard to reach areas is needed to improve skilled birth attendance, care seeking for complications and essential newborn care and facilitate reductions in maternal and neonatal mortality in low performing districts in Bangladesh

Professions and the social order: some lessons from Burkina Faso?

The study of professions has been dominated by Anglo-American models, with their focus on a small group of legally-licensed occupations. The field has recently shifted, mainly through studies of European experience, to a wider examination of the social management of expert workers. Very little has been written about developments in Africa and their implications for the way in which we might think about professions. This paper presents a case study of the role and practices of the medical profession in Burkina Faso, which has a relatively open market for the supply of healing services and limited regulation of the suppliers, whether physicians or traditional practitioners. The study returns to classic questions about the extent to which practice is shaped by the nature of occupational niches within the division of labour or to the development of a distinctive moral character among the workers within that niche

Multi-objective Hyper-heuristic Approaches for Space Allocation and Timetabling

Abstract An important issue in multi-objective optimisation is how to ensure that the obtained non-dominated set covers the Pareto front as widely as possible. A number of techniques (e.g. weight vectors, niching, clustering, cellular structures, etc.) have been proposed in the literature for this purpose. In this paper we propose a new approach to address this issue in multi-objective combinatorial optimisation. We explore hyperheuristics, a research area which has gained increasing interest in recent years. A hyper-heuristic can be thought of as a heuristic method which iteratively attempts to select a good heuristic amongst many. The aim of using a hyper-heuristic is to raise the level of generality so as to be able to apply the same solution method to several problems, perhaps at the expense of reduced but still acceptable solution quality when compared to a tailor-made approach. The key is not to solve the problem directly but rather to (iteratively) recommend a suitable heuristic chosen because of its performance. In this paper we investigate a tabu search hyper-heuristic technique. The idea of our multi-objective hyperheuristic approach is to choose, at each iteration during the search, the heuristic that is suitable for the optimisation of a given individual objective. We test the resulting approach on two very different real-world combinatorial optimisation problems: space allocation and timetabling. The results obtained show that the multi-objective hyper-heuristic approach can be successfully developed for these two problems producing solutions of acceptable quality

A simulated annealing based hyperheuristic for determining shipper sizes for storage and transportation

The current drive to reduce packaging waste has led many companies to consider the use of multi-trip containers or shippers in which to transport their products in order to reduce packaging waste. The efficiency of such systems obviously depends on selecting shipper dimensions in such a way as to ensure high volumetric utilisation. As is the case with many practical problems the efficiency/solution quality can be improved if problem specific information is used to enhance the operation of a meta-heuristic solution approach. The problem can be modelled as a p-median problem but is too large to be solved in reasonable time without further modification. Four such modifications, all based on properties of the physical problem, are introduced and incorporated into a hyperheuristic driven simulated annealing solution approach

Besoins thérapeutiques et pratiques d’automédication au Burkina-Faso

info:eu-repo/semantics/publishe