Scalar models for the generalized Chaplygin gas and the structure formation constraints

The generalized Chaplygin gas model represents an attempt to unify dark matter and dark energy. It is characterized by a fluid with an equation of state $p = - A/\rho^\alpha$. It can be obtained from a generalization of the DBI action for a scalar, tachyonic field. At background level, this model gives very good results, but it suffers from many drawbacks at perturbative level. We show that, while for background analysis it is possible to consider any value for $\alpha$, the perturbative analysis must be restricted to positive values of $\alpha$. This restriction can be circumvented if the origin of the generalized Chaplygin gas is traced back to a self-interacting scalar field, instead of the DBI action. But, in doing so, the predictions coming from formation of large scale structures reduce the generalized Chaplygin gas model to a kind of quintessence model, and the unification scenario is lost, if the scalar field is the canonical one. However, if the unification condition is imposed from the beginning as a prior, the model may remain competitive. More interesting results, concerning the unification program, are obtained if a non-canonical self-interacting scalar field, inspired by Rastall's theory of gravity, is imposed. In this case, an agreement with the background tests is possible.Comment: Latex file, 25 pages, 33 figures in eps format. New section on scalar models. Accepted for publication in Gravitation&Cosmolog

Confirmation de QTL et validation de marqueurs SNPs associés à la résistance du niébé à Colletotrichum capsici, agent responsable de la maladie des taches brunes

Le niébé (Vigna unguiculata (L.) Walp.) est une légumineuse à graine très importante et constitue la principale source de protéines végétales pour l’alimentation des populations d’Afrique Subsaharienne. Sa production au Burkina Faso est entravée par la maladie des taches brunes provoquée par un champignon, Colletotrichum capsici (Syd.) Butler et Bisby. C’est dans la perspective d’accroître la productivité du niébé que nous avons entrepris de renforcer la lutte variétale contre cet agent pathogène. L’identification de marqueurs SNPs (Single Nucleotide Polymorphism) et QTL liés à la résistance à la maladie des taches brunes a été entrepris à partir d’une population biparentale F2 issus du croisement entre la variété sensible Tiligré et celle résistante KN-1. L’analyse QTL de la résistance du niébé à C. capsici à partir de la méthode ICIM add. a permis de confirmer et de valider respectivement un QTL majeur dénommé qBBDR2.1 et 9 marqueurs SNPs convertis, lesquels ont été cartographiés sur le chromosome Vu02 du niébé. Ce QTL dominant a présenté des effets additifs élevés liés aux allèles favorables de KN-1 et des valeurs de PVE de l’ordre de 51,50% et 55,33%, respectivement aux 21ème et 28ème JAI. English title: Confirmation of QTL mapping and validation of SNPs markers associated to cowpea resistance to Colletotrichum capsici, causal agent of brown blotch disease Cowpea (Vigna unguiculata (L.)Walp.) is one of the most important grain legume crops and constitutes the main source of plant protein for people food in sub-Saharan Africa. Cowpea production in Burkina Faso is constrained by brown blotch disease caused by a fungal,  Colletotrichum capsici (Syd.) Butler and Bisby. In order to increase cowpea productivity we initiated a project to enhance host plant resistance to control the pathogen. The identification of SNP (Single Nucleotide Polymorphism) markers and QTL associated with brown blotch disease resistance was undertaken from a bi-parental F2 population resulting from a cross between the sensitive variety Tiligre and the resistant KN-1 to the disease. QTL analysis of cowpea resistance to C. capsici using the ICIM add method. Allowed to confirm and validate respectively a major QTL named qBBDR2.1 and 9 converted SNP markers, which were mapped on cowpea chromosome Vu02. This dominant QTL showed higher additive effects associated to alleles from KN-1 and PVE values of 51.50% and 55.33% respectively at 21 and 28 days after inoculatio

Acceptability and efficacy of intra-rectal quinine alkaloids as a pre-transfer treatment of non-per os malaria in peripheral health care facilities in Mopti, Mali

<p>Abstract</p> <p>Background</p> <p>The acceptability and efficacy of a new kit with a new formulation of quinine alkaloids designed for the intra-rectal administration in the treatment of non-per os malaria was assessed in the peripheral health care system of Mopti, Mali.</p> <p>Methods</p> <p>A single-arm trial was conducted from August 2003 to January 2004. An initial dose of diluted quinine alkaloids (20 mg/kg Quinimax^®) was administered by the intra-rectal route to children with presumptive non per-os malaria at six peripheral heath care centres. The children were then referred to two referral hospitals where standard inpatient care including intravenous route were routinely provided. A malaria thick smear was done at inclusion and a second malaria thick smear after arrival at the referral facility, where a more complete clinical examination and laboratory testing was done to confirm diagnosis. Confirmed cases of severe malaria or others diseases were treated according to national treatment guidelines. Cases of non per-os malaria received a second dose of intra rectal quinine alkaloids. Primary outcome was acceptability of the intra rectal route by children and their parents as well as the ease to handle the kit by health care workers.</p> <p>Results</p> <p>The study included 134 children with a median age of 33 months and 53.7% were male. Most of the children (67%) and 92% of parents or guardians readily accepted the intra-rectal route; 84% of health care workers found the kit easy to use. At the peripheral health care centres, 32% of children had a coma score ≤ 3 and this was reduced to 10% at the referral hospital, following one dose of intra-rectal quinine alkaloids (IRQA). The mean time to availability of oral route treatment was 1.8 ± 1.1 days. Overall, 73% of cases were confirmed severe malaria and for those the case fatality rate was 7.2%.</p> <p>Conclusion</p> <p>IRQA was well accepted by children, their parents/guardians and by the health workers at peripheral health facilities in Mopti, Mali. There was also a quick recovery from deep coma and a reduced case fatality rate in severe malaria.</p

Engaging diverse communities participating in clinical trials: case examples from across Africa

<p>Abstract</p> <p>Background</p> <p>In the advent of increasing international collaborative research involving participants drawn from populations with diverse cultural backgrounds, community engagement becomes very critical for the smooth conduction of the research. The African Malaria Network Trust (AMANET) is a pan-African non-governmental organization that sponsors and technically supports malaria vaccine trials in various African countries.</p> <p>Case description</p> <p>AMANET sponsored phase Ib or IIb clinical trials of several malaria vaccine candidates in various Africa countries. In Burkina Faso, Mali and Tanzania trials of the merozoite surface protein 3 -- in its Long Synthetic Peptide configuration (MSP3 LSP) -- were conducted. In Mali, the apical membrane antigen 1 (AMA1) was tested, while a hybrid of glutamate rich protein (GLURP) and MSP3 (GMZ2) was tested in Gabon. AMANET recognizes the importance of engaging with the communities from which trial participants are drawn, hence community engagement was given priority in all project activities conducted in the various countries.</p> <p>Discussion and evaluation</p> <p>Existing local social systems were used to engage the communities from which clinical trial participants were drawn. This article focuses on community engagement activities employed at various AMANET-supported clinical trial sites in different countries, highlighting subtle differences in the approaches used. The paper also gives some general pros and cons of community engagement.</p> <p>Conclusions</p> <p>Community engagement enables two-way sharing of accurate information and ideas between researchers and researched communities, which helps to create an environment conducive to smooth research activities with enhanced sense of research ownership by the communities.</p

An optimized multi-proxy, multi-site Antarctic ice and gas orbital chronology (AICC2012): 120-800 ka

An accurate and coherent chronological framework is essential for the interpretation of climatic and environmental records obtained from deep polar ice cores. Until now, one common ice core age scale had been developed based on an inverse dating method (Datice), combining glaciological modelling with absolute and stratigraphic markers between 4 ice cores covering the last 50 ka (thousands of years before present) (Lemieux-Dudon et al., 2010). In this paper, together with the companion paper of Veres et al. (2013), we present an extension of this work back to 800 ka for the NGRIP, TALDICE, EDML, Vostok and EDC ice cores using an improved version of the Datice tool. The AICC2012 (Antarctic Ice Core Chronology 2012) chronology includes numerous new gas and ice stratigraphic links as well as improved evaluation of background and associated variance scenarios. This paper concentrates on the long timescales between 120–800 ka. In this framework, new measurements of δ18Oatm over Marine Isotope Stage (MIS) 11–12 on EDC and a complete δ18Oatm record of the TALDICE ice cores permit us to derive additional orbital gas age constraints. The coherency of the different orbitally deduced ages (from δ18Oatm, δO2/N2 and air content) has been verified before implementation in AICC2012. The new chronology is now independent of other archives and shows only small differences, most of the time within the original uncertainty range calculated by Datice, when compared with the previous ice core reference age scale EDC3, the Dome F chronology, or using a comparison between speleothems and methane. For instance, the largest deviation between AICC2012 and EDC3 (5.4 ka) is obtained around MIS 12. Despite significant modifications of the chronological constraints around MIS 5, now independent of speleothem records in AICC2012, the date of Termination II is very close to the EDC3 one

TLR9 polymorphisms in African populations: no association with severe malaria, but evidence of cis-variants acting on gene expression

BACKGROUND: During malaria infection the Toll-like receptor 9 (TLR9) is activated through induction with plasmodium DNA or another malaria motif not yet identified. Although TLR9 activation by malaria parasites is well reported, the implication to the susceptibility to severe malaria is not clear. The aim of this study was to assess the contribution of genetic variation at TLR9 to severe malaria. METHODS: This study explores the contribution of TLR9 genetic variants to severe malaria using two approaches. First, an association study of four common single nucleotide polymorphisms was performed on both family- and population-based studies from Malawian and Gambian populations (n>6000 individual). Subsequently, it was assessed whether TLR9 expression is affected by cis-acting variants and if these variants could be mapped. For this work, an allele specific expression (ASE) assay on a panel of HapMap cell lines was carried out. RESULTS: No convincing association was found with polymorphisms in TLR9 for malaria severity, in either Gambian or Malawian populations, using both case-control and family based study designs. Using an allele specific expression assay it was observed that TLR9 expression is affected by cis-acting variants, these results were replicated in a second experiment using biological replicates. CONCLUSION: By using the largest cohorts analysed to date, as well as a standardized phenotype definition and study design, no association of TLR9 genetic variants with severe malaria was found. This analysis considered all common variants in the region, but it is remains possible that there are rare variants with association signals. This report also shows that TLR9 expression is potentially modulated through cis-regulatory variants, which may lead to differential inflammatory responses to infection between individuals

Anaemia in a phase 2 study of a blood stage falciparum malaria vaccine

<p>Abstract</p> <p>Background</p> <p>A Phase 1-2b study of the blood stage malaria vaccine AMA1-C1/Alhydrogel was conducted in 336 children in Donéguébougou and Bancoumana, Mali. In the Phase 2 portion of the study (n = 300), no impact on parasite density or clinical malaria was seen; however, children who received the study vaccine had a higher frequency of anaemia (defined as haemoglobin < 8.5 g/dL) compared to those who received the comparator vaccine (Hiberix). This effect was one of many tested and was not significant after adjusting for multiple comparisons.</p> <p>Methods</p> <p>To further investigate the possible impact of vaccination on anaemia, additional analyses were conducted including patients from the Phase 1 portion of the study and controlling for baseline haemoglobin, haemoglobin types S or C, alpha-thalassaemia, G6PD deficiency, and age. A multiplicative intensity model was used, which generalizes Cox regression to allow for multiple events. Frailty effects for each subject were used to account for correlation of multiple anaemia events within the same subject. Intensity rates were calculated with reference to calendar time instead of time after randomization in order to account for staggered enrollment and seasonal effects of malaria incidence. Associations of anaemia with anti-AMA1 antibody were further explored using a similar analysis.</p> <p>Results</p> <p>A strong effect of vaccine on the incidence of anaemia (risk ratio [AMA1-C1 to comparator (Hiberix)]= 2.01, 95% confidence interval [1.26,3.20]) was demonstrated even after adjusting for baseline haemoglobin, haemoglobinopathies, and age, and using more sophisticated statistical models. Anti-AMA1 antibody levels were not associated with this effect.</p> <p>Conclusions</p> <p>While these additional analyses show a robust effect of vaccination on anaemia, this is an intensive exploration of secondary results and should, therefore, be interpreted with caution. Possible mechanisms of the apparent adverse effect on haemoglobin of vaccination with AMA1-C1/Alhydrogel and implications for blood stage vaccine development are discussed. The potential impact on malaria-associated anaemia should be closely evaluated in clinical trials of AMA1 and other blood stage vaccines in malaria-exposed populations.</p

Assessment of genetic diversity of Burkina Faso sweet grain sorghum using microsatellite markers

Sweet grain sorghum [Sorghum bicolor (L.) Moench] is an under-harvested crop produced mainly for its sweet grains in the pasty stage. Little is known of its genetic diversity remains. This study aims to determine the level and structure of the genetic diversity of sweet grain sorghum from Burkina Faso. Thus, 93 accessions were evaluated using 15 polymorphic microsatellite markers. The analysis revealed 49 alleles in total, 6 rare alleles, an average of 3 alleles per locus, a moderate Nei diversity of 0.474, a low level of heterozygosity (0.031) in the collection and very high Wright's fixation index (Fis) of 0.934. The accessions were organized into three genetic groups: A, B and C. Groups A and B were the farthest, with an Fst and a genetic distance of 0.37 and 0.22, respectively, whereas Groups B and C were the closest, with an Fst (genetic differentiation) of 0.279 and a genetic distance of 0.142. This diversity could be exploited in Burkina Faso sweet grain sorghum breeding programs

Increase in EPI vaccines coverage after implementation of intermittent preventive treatment of malaria in infant with Sulfadoxine -pyrimethamine in the district of Kolokani, Mali: Results from a cluster randomized control trial

<p>Abstract</p> <p>Background</p> <p>Even though the efficacy of Intermittent Preventive Treatment in infants (IPTi) with Sulfadoxine-Pyrimethamine (SP) against clinical disease and the absence of its interaction with routine vaccines of the Expanded Immunization Programme (EPI) have been established, there are still some concerns regarding the addition of IPTi, which may increase the work burden and disrupt the routine EPI services especially in Africa where the target immunization coverage remains to be met. However IPTi may also increase the adherence of the community to EPI services and improve EPI coverage, once the benefice of strategy is perceived.</p> <p>Methods</p> <p>To assess the impact of IPTi implementation on the coverage of EPI vaccines, 22 health areas of the district of Kolokani were randomized at a 1:1 ratio to either receive IPTi-SP or to serve as a control. The EPI vaccines coverage was assessed using cross-sectional surveys at baseline in November 2006 and after one year of IPTi pilot-implementation in December 2007.</p> <p>Results</p> <p>At baseline, the proportion of children of 9-23 months who were completely vaccinated (defined as children who received BGG, 3 doses of DTP/Polio, measles and yellow fever vaccines) was 36.7% (95% CI 25.3% -48.0%). After one year of implementation of IPTi-SP using routine health services, the proportion of children completely vaccinated rose to 53.8% in the non intervention zone and 69.5% in the IPTi intervention zone (P <0.001).</p> <p>The proportion of children in the target age groups who received IPTi with each of the 3 vaccinations DTP2, DTP3 and Measles, were 89.2% (95% CI 85.9%-92.0%), 91.0% (95% CI 87.6% -93.7%) and 77.4% (95% CI 70.7%-83.2%) respectively. The corresponding figures in non intervention zone were 2.3% (95% CI 0.9% -4.7%), 2.6% (95% CI 1.0% -5.6%) and 1.7% (95% CI 0.4% - 4.9%).</p> <p>Conclusion</p> <p>This study shows that high coverage of the IPTi can be obtained when the strategy is implemented using routine health services and implementation results in a significant increase in coverage of EPI vaccines in the district of Kolokani, Mali.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov <a href="http://www.clinicaltrials.gov/ct2/show/NCT00766662">NCT00766662</a></p

First Detection of Leishmania major DNA in Sergentomyia (Spelaeomyia) darlingi from Cutaneous Leishmaniasis Foci in Mali

Leishmania major complex is the main causative agent of zoonotic cutaneous leishmaniasis (ZCL) in the Old World. Phlebotomus papatasi and Phlebotomus duboscqi are recognized vectors of L. major complex in Northern and Southern Sahara, respectively. In Mali, ZCL due to L. major is an emerging public health problem, with several cases reported from different parts of the country. The main objective of the present study was to identify the vectors of Leishmania major in the Bandiagara area, in Mali. Methodology/Principal Findings: An entomological survey was carried out in the ZCL foci of Bandiagara area. Sandflies were collected using CDC miniature light traps and sticky papers. In the field, live female Phlebotomine sandflies were identified and examined for the presence of promastigotes. The remaining sandflies were identified morphologically and tested for Leishmania by PCR in the ITS2 gene. The source of blood meal of the engorged females was determined using the cyt-b sequence. Out of the 3,259 collected sandflies, 1,324 were identified morphologically, and consisted of 20 species, of which four belonged to the genus Phlebotomus and 16 to the genus Sergentomyia. Leishmania major DNA was detected by PCR in 7 of the 446 females (1.6%), specifically 2 out of 115 Phlebotomus duboscqi specimens, and 5 from 198 Sergentomyia darlingi specimens. Human DNA was detected in one blood-fed female S. darlingi positive for L. major DNA. Conclusion: Our data suggest the possible involvement of P. duboscqi and potentially S. darlingi in the transmission of ZCL in Mali