Next Priority Concept: A new and generic algorithm computing concepts from complex and heterogeneous data

In this article, we present a new data type agnostic algorithm calculating a concept lattice from heterogeneous and complex data. Our NextPriorityConcept algorithm is first introduced and proved in the binary case as an extension of Bordat's algorithm with the notion of strategies to select only some predecessors of each concept, avoiding the generation of unreasonably large lattices. The algorithm is then extended to any type of data in a generic way. It is inspired from pattern structure theory, where data are locally described by predicates independent of their types, allowing the management of heterogeneous data.Comment: 28 pages, 8 figures, 7 algorithm

Développement d’un SIG pour la ville médiévale de Cluny

The Cluny Abbey, the greatest building of European Christendom in the 12th century, has been transformed during its long history. The evolution of the place can be studied thanks to an abundant documentation, through archeological excavations and the study of landscape. The stratigraphic complexity of the successive buildings and the vastness of the territory in relation with its hydrographical system, convinced us to install a SIG database and research system. The Abbey is located at the confluence of two rivers, progressively converted by the monks, in order to obtain an extremely rational use of the water. The installation of a collaborative and interdisciplinary platform, called SIG 4D, dedicated to the history and archeology of the Cluniac landscape, requires the grouping of various types of data, that are often very diverse. The integration of 3D elements and their geolocalization in the geographic system bring technical difficulties which have to be solved. Starting with the documentary study and the excavations, we examine the questions linked to interdisciplinary use of various types of SIG and CAO data, and their dissemination amongst various researchers. Numeric tools offer new possibilities which encourage us to elaborate treatment procedures and data dissemination which are better adapted to the hybrid nature of archeological artifacts and to the study process of the historical traces in architecture and territory.Projet Gunz

ODAS: Open embeddeD Audition System

Artificial audition aims at providing hearing capabilities to machines, computers and robots. Existing frameworks in robot audition offer interesting sound source localization, tracking and separation performance, but involve a significant amount of computations that limit their use on robots with embedded computing capabilities. This paper presents ODAS, the Open embeddeD Audition System framework, which includes strategies to reduce the computational load and perform robot audition tasks on low-cost embedded computing systems. It presents key features of ODAS, along with cases illustrating its uses in different robots and artificial audition applications

Can treatment of malaria be restricted to parasitologically confirmed malaria? A school-based study in Benin in children with and without fever

<p>Abstract</p> <p>Background</p> <p>Applying the switch from presumptive treatment of malaria to new policies of anti-malarial prescriptions restricted to parasitologically-confirmed cases is a still unsolved challenge. Pragmatic studies can provide data on consequences of such a switch. In order to assess whether restricting anti-malarials to rapid diagnostic test (RDT)-confirmed cases in children of between five and 15 years of age is consistent with an adequate management of fevers, a school-based study was performed in Allada, Benin.</p> <p>Methods</p> <p>Children in the index group (with fever and a negative RDT) and the matched control group (without fever and a negative RDT) were not prescribed anti-malarials and actively followed-up during 14 days. Blood smears were collected at each assessment. Self-medication with chloroquine and quinine was assessed with blood spots. Malaria attacks during the follow-up were defined by persistent or recurrent fever concomitant to a positive malaria test.</p> <p>Results</p> <p>484 children were followed-up (242 in each group). At day 3, fever had disappeared in 94% of children from the index group. The incidence of malaria was similar (five cases in the index group and seven cases in the control group) between groups. Self-medication with chloroquine and quinine in this cohort was uncommon.</p> <p>Conclusions</p> <p>Applying a policy of restricting anti-malarials to RDT-confirmed cases is consistent with an adequate management of fevers in this population. Further studies on the management of fever in younger children are of upmost importance.</p

What would PCR assessment change in the management of fevers in a malaria endemic area? A school-based study in Benin in children with and without fever

<p>Abstract</p> <p>Background</p> <p>A recent school-based study in Benin showed that applying a policy of anti-malarial prescriptions restricted to parasitologically-confirmed cases on the management of fever is safe and feasible. Additional PCR data were analysed in order to touch patho-physiological issues, such as the usefulness of PCR in the management of malaria in an endemic area or the triggering of a malaria attack in children with submicroscopic malaria.</p> <p>Methods</p> <p>PCR data were prospectively collected in the setting of an exposed (with fever)/non exposed (without fever) study design. All children had a negative malaria rapid diagnostic test (RDT) at baseline, were followed up to day 14 and did not receive drugs with anti-malarial activity. The index group was defined by children with fever at baseline and the control group by children without fever at baseline. Children with submicroscopic malaria in these two groups were defined by a positive PCR at baseline.</p> <p>Results</p> <p>PCR was positive in 66 (27%) children of the index group and in 104 (44%) children of the control group respectively. The only significant factor positively related to PCR positivity at baseline was the clinical status (control group). When definition of malaria attacks included PCR results, no difference of malaria incidence was observed between the index and control groups, neither in the whole cohort, nor in children with submicroscopic malaria. The rate of undiagnosed malaria at baseline was estimated to 3.7% at baseline in the index group.</p> <p>Conclusions</p> <p>Treating all children with fever and a positive PCR would have led to a significant increase of anti-malarial consumption, with few benefits in terms of clinical events. Non malarial fevers do not or do not frequently trigger malaria attacks in children with submicroscopic malaria.</p

Assessment of Volume Depletion in Children with Malaria

BACKGROUND: The degree of volume depletion in severe malaria is currently unknown, although knowledge of fluid compartment volumes can guide therapy. To assist management of severely ill children, and to test the hypothesis that volume changes in fluid compartments reflect disease severity, we measured body compartment volumes in Gabonese children with malaria. METHODS AND FINDINGS: Total body water volume (TBW) and extracellular water volume (ECW) were estimated in children with severe or moderate malaria and in convalescence by tracer dilution with heavy water and bromide, respectively. Intracellular water volume (ICW) was derived from these parameters. Bioelectrical impedance analysis estimates of TBW and ECW were calibrated against dilution methods, and bioelectrical impedance analysis measurements were taken daily until discharge. Sixteen children had severe and 19 moderate malaria. Severe childhood malaria was associated with depletion of TBW (mean [SD] of 37 [33] ml/kg, or 6.7% [6.0%]) relative to measurement at discharge. This is defined as mild dehydration in other conditions. ECW measurements were normal on admission in children with severe malaria and did not rise in the first few days of admission. Volumes in different compartments (TBW, ECW, and ICW) were not related to hyperlactataemia or other clinical and laboratory markers of disease severity. Moderate malaria was not associated with a depletion of TBW. CONCLUSIONS: Significant hypovolaemia does not exacerbate complications of severe or moderate malaria. As rapid rehydration of children with malaria may have risks, we suggest that fluid replacement regimens should aim to correct fluid losses over 12–24 h

Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein

The emergence of resistance to existing classes of antiretroviral drugs necessitates finding new HIV-1 targets for drug discovery. The viral capsid (CA) protein represents one such potential new target. CA is sufficient to form mature HIV-1 capsids in vitro, and extensive structure-function and mutational analyses of CA have shown that the proper assembly, morphology, and stability of the mature capsid core are essential for the infectivity of HIV-1 virions. Here we describe the development of an in vitro capsid assembly assay based on the association of CA-NC subunits on immobilized oligonucleotides. This assay was used to screen a compound library, yielding several different families of compounds that inhibited capsid assembly. Optimization of two chemical series, termed the benzodiazepines (BD) and the benzimidazoles (BM), resulted in compounds with potent antiviral activity against wild-type and drug-resistant HIV-1. Nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic analyses showed that both series of inhibitors bound to the N-terminal domain of CA. These inhibitors induce the formation of a pocket that overlaps with the binding site for the previously reported CAP inhibitors but is expanded significantly by these new, more potent CA inhibitors. Virus release and electron microscopic (EM) studies showed that the BD compounds prevented virion release, whereas the BM compounds inhibited the formation of the mature capsid. Passage of virus in the presence of the inhibitors selected for resistance mutations that mapped to highly conserved residues surrounding the inhibitor binding pocket, but also to the C-terminal domain of CA. The resistance mutations selected by the two series differed, consistent with differences in their interactions within the pocket, and most also impaired virus replicative capacity. Resistance mutations had two modes of action, either directly impacting inhibitor binding affinity or apparently increasing the overall stability of the viral capsid without affecting inhibitor binding. These studies demonstrate that CA is a viable antiviral target and demonstrate that inhibitors that bind within the same site on CA can have distinct binding modes and mechanisms of action

PfHRP2 and PfLDH antigen detection for monitoring the efficacy of artemisinin-based combination therapy (ACT) in the treatment of uncomplicated falciparum malaria

<p>Abstract</p> <p>Background</p> <p>An assessment of the accuracy of two malaria rapid diagnostic tests (RDT) for the detection of <it>Plasmodium falciparum </it>histidine-rich protein 2 (<it>Pf</it>HRP2) or <it>Pf </it>lactate dehydrogenase (<it>Pf</it>LDH) was undertaken in children aged between six and 59 months included in an anti-malarial efficacy study in Benin.</p> <p>Methods</p> <p>In Allada (Benin), 205 children aged 6-59 months with falciparum malaria received either artesunate-amodiaquine (ASAQ), artemether-lumefantrine (AL), or sulphadoxine-pyrimethamine (SP). Children included in the study were simultaneously followed by both RDT and high-quality microscopy for up to 42 days.</p> <p>Results</p> <p>At the time of inclusion, <it>Pf</it>HRP2-based tests were positive in 203 children (99%) and <it>Pf</it>LDH-based tests were positive in 204 (99.5%). During follow-up, independent of the treatment received, only 17.3% (28/162) of children effectively cured were negative with the <it>Pf</it>HRP2 RDT at day 3, with a gradual increase in specificity until day 42. The specificity of antigen detection with the <it>Pf</it>LDH test was 87% (141/162) on day 3, and between 92% and 100% on days 7 to 42. A statistical difference was observed between the persistence of <it>Pf</it>HRP2 and <it>Pf</it>LDH antigenaemia during follow-up in children treated with artemisinin-based combination therapy (ACT) but not with SP.</p> <p>Conclusion</p> <p>Although both RDTs are as sensitive as microscopy in detecting true malaria cases, the <it>Pf</it>HRP2 RDT had very low specificity during follow-up until day 28. On the other hand, the <it>Pf</it>LDH test could be used to detect failures and, therefore, to assess anti-malarial efficacy.</p

Polymorphisms in Plasmodium falciparum chloroquine resistance transporter and multidrug resistance 1 genes: parasite risk factors that affect treatment outcomes for P. falciparum malaria after artemether-lumefantrine and artesunate-amodiaquine.

Adequate clinical and parasitologic cure by artemisinin combination therapies relies on the artemisinin component and the partner drug. Polymorphisms in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multidrug resistance 1 (pfmdr1) genes are associated with decreased sensitivity to amodiaquine and lumefantrine, but effects of these polymorphisms on therapeutic responses to artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL) have not been clearly defined. Individual patient data from 31 clinical trials were harmonized and pooled by using standardized methods from the WorldWide Antimalarial Resistance Network. Data for more than 7,000 patients were analyzed to assess relationships between parasite polymorphisms in pfcrt and pfmdr1 and clinically relevant outcomes after treatment with AL or ASAQ. Presence of the pfmdr1 gene N86 (adjusted hazards ratio = 4.74, 95% confidence interval = 2.29 - 9.78, P < 0.001) and increased pfmdr1 copy number (adjusted hazards ratio = 6.52, 95% confidence interval = 2.36-17.97, P < 0.001 : were significant independent risk factors for recrudescence in patients treated with AL. AL and ASAQ exerted opposing selective effects on single-nucleotide polymorphisms in pfcrt and pfmdr1. Monitoring selection and responding to emerging signs of drug resistance are critical tools for preserving efficacy of artemisinin combination therapies; determination of the prevalence of at least pfcrt K76T and pfmdr1 N86Y should now be routine