SPAWN: An Iterative, Potentials-Based, Dynamic Scheduling and Partitioning Tool

International audienceMany applications of physics modeling use regular meshes on which computations of highly variable cost can occur. Distributing the underlying cells over manycore architec-tures is a critical load balancing step that should increase the period until another step is required. Graph partitioning tools are known to be very effective for such problems, but they exhibit scalability problems as the number of cores and the number of cells increases. We introduce a dynamic task scheduling approach inspired by physical particles interactions. Our method allows cores to virtually move over a 2D/3D mesh of tasks and uses a Voronoi domain decomposition to balance workload among cores. Displacements of cores are the result of force computations using a carefully chosen pair potential. We evaluate our method against graph partitioning tools and existing task schedulers with a representative physical application, and demonstrate the relevance of our approach

Early calcium increase triggers the formation of olfactory long-term memory in honeybees

<p>Abstract</p> <p>Background</p> <p>Synaptic plasticity associated with an important wave of gene transcription and protein synthesis underlies long-term memory processes. Calcium (Ca²⁺) plays an important role in a variety of neuronal functions and indirect evidence suggests that it may be involved in synaptic plasticity and in the regulation of gene expression correlated to long-term memory formation. The aim of this study was to determine whether Ca²⁺is necessary and sufficient for inducing long-term memory formation. A suitable model to address this question is the Pavlovian appetitive conditioning of the proboscis extension reflex in the honeybee <it>Apis mellifera, </it>in which animals learn to associate an odor with a sucrose reward.</p> <p>Results</p> <p>By modulating the intracellular Ca²⁺concentration ([Ca²⁺]i) in the brain, we show that: (i) blocking [Ca²⁺]i increase during multiple-trial conditioning selectively impairs long-term memory performance; (ii) conversely, increasing [Ca²⁺]i during single-trial conditioning triggers long-term memory formation; and finally, (iii) as was the case for long-term memory produced by multiple-trial conditioning, enhancement of long-term memory performance induced by a [Ca²⁺]i increase depends on <it>de novo </it>protein synthesis.</p> <p>Conclusion</p> <p>Altogether our data suggest that during olfactory conditioning Ca²⁺is both a necessary and a sufficient signal for the formation of protein-dependent long-term memory. Ca²⁺therefore appears to act as a switch between short- and long-term storage of learned information.</p

Resistance of Staphylococcus aureus Recovered from Infected Foreign Body In Vivo to Killing by Antimicrobials

Because persistence of infections associated with prosthetic material despite the use of appropriate antibioticsis a major clinical problem,the antimicrobial susceptibility of bacteria responsible for a chronic subcutaneous tissue cage infection in rat was investigated ex vivo. Three to 6 weeks after the initiation of infection, suspensions of two strains of Staphylococcus aureus recovered from the foreign body surface and surrounding fluid wereexposed to either oxacillin, vancomycin, fleroxacin, gentamicin, or rifampin. The MBCs of these bacteria were markedly elevated, in most cases 128 to >256 times higher than the MBCof batch culture S. aureus in either logarithmic or stationary phase. Kinetic studies showed the bacteria did not growwhen incubated for 2 h in Mueller-Hinton broth, possibly reflecting dormancy. Their killing wasslow and incompleteby all antibioticsat > 8 times their MIC. These data provide direct evidence of a decreased susceptibility of S. aureus to the killing effect of antimicrobials during chronic foreign body infections in viv

Rapid detection of glycopeptide-resistant enterococci: impact on decision-making and costs.

International audienceBACKGROUND: According to French national recommendations, the detection of a patient colonized with glycopeptide-resistant enterococci (GRE) leads to interruption of new admissions and transfer of contact patients (CPs) to another unit or healthcare facility, with weekly screening of CPs. FINDINGS: We evaluated the medical and economic impact of a pragmatic adaptation of national guidelines associated with a real-time PCR (RTP) (Cepheid XpertTM vanA/vanB) as part of the strategy for controlling GRE spread in two medical wards. Screening was previously performed using chromogenic selective medium (CSM). Turn around time (TAT), costs of tests and cost of missed patient days were prospectively collected. In February 2012, the identification of GRE in one patient in the diabetology ward led to the screening of 31 CPs using CSM; one secondary case was identified in a CP already transferred to the Nephrology ward. Awaiting the results of SCM (median TAT, 70.5 h), 41 potential patient days were missed, due to interruption of admissions. The overall cost (screening tests + missing patient.days) was estimated at 14, 302.20 [euro sign]. The secondary case led to screening of 22 CPs in the Nephrology ward using RTP. Because of a short median TAT of 4.6 h, we did not interrupt admissions and patients' transfers. Among 22 CPs, 19 (86%) were negative for vanA, 2 were positive for vanB and 3 had invalid results needing CSM. The overall cost of the strategy was estimated at 870.40 [euro sign] (cost of screening tests only), without missing patient days. CONCLUSION: The rapid PCR test for vanA-positive GRE detection both allowed rapid decision about the best infection control strategy and prevented loss of income due to discontinuation of patient transfers and admissions

High power density laser estimation using quantitative thermal imaging method

The knowledge of the amplitude and the spatial distribution of an excitation flux is of great interest for the quantification of heat sources. In this work, the development of a non-contact imaging powermeter based on the association of a bolometer with an infrared camera is described. This powermeter allows, thanks to infrared thermographic measurements and image processing methods, the quantitative estimation of the spatial distribution of the power of the flux delivered by a high-power laser. First, the experimental setup used is described. Then, the complete model- ling of the heat transfer within the bolometer using the 3D thermal quadrupole formalism is presented. After that, an inverse method based on the Wiener filter in Fourier-Laplace transform spaces to estimate the spatial distribution of the power flux is described. Finally, power estimation results using two metallic plates as a bolometer are presented and discusse

Role of Anopheles (Cellia) rufipes (Gough, 1910) and other local anophelines in human malaria transmission in the northern savannah of Cameroon: a crosssectional survey

Background As part of a study to determine the impact of insecticide resistance on the effectiveness of longlasting insecticide treated nets (LLINs) in the north of Cameroon, the unexpectedly high density and anthropophilic behaviour of Anopheles rufipes lead us to investigate this species bionomics and role in human malaria parasite transmission. Methods For four consecutive years (2011–2014), annual cross-sectional sampling of adult mosquitoes was conducted during the peak malaria season (September-October) in three health districts in northern Cameroon. Mosquitoes sampled by human landing catch and pyrethrum spray catch methods were morphologically identified, their ovaries dissected for parity determination and Anopheles gambiae siblings were identified by molecular assay. Infection with P. falciparum and blood meal source in residual fauna of indoor resting anopheline mosquitoes were determined by enzyme-linked-immunosorbent assays. Results Anopheles gambiae (sensu lato) (s.l.) comprised 18.4% of mosquitoes collected with An. arabiensis representing 66.27% of the sibling species. The proportion of An. rufipes (2.7%) collected was high with a humanbiting rate ranging between 0.441 and 11.083 bites/person/night (b/p/n) and an anthropophagic rate of 15.36%. Although overall the members of An. gambiae complex were responsible for most of the transmission with entomological inoculation rates (EIR) reaching 1.221 infective bites/person/night (ib/p/n), An. arabiensis and An.coluzzii were the most implicated. The roles of An. funestus, An. pharoensis and An. paludis were minor. Plasmodium falciparum circumsporozoite protein rate in Anopheles rufipes varied from 0.6 to 5.7% with EIR values between 0.010 and 0.481 ib/p/n Conclusions The study highlights the epidemiological role of An. rufipes alongside the members of the An.gambiae complex, and several other sympatric species in human malaria transmission during the wet season in northern Cameroon. For the first time in Cameroon, An. rufipes has been shown to be an important local malaria vector, emphasising the need to review the malaria entomological profile across the country as pre-requisite to effective vector management strategies

Role of Anopheles (Cellia) rufipes (Gough, 1910) and other local anophelines in human malaria transmission in the northern savannah of Cameroon: a crosssectional survey

Background As part of a study to determine the impact of insecticide resistance on the effectiveness of longlasting insecticide treated nets (LLINs) in the north of Cameroon, the unexpectedly high density and anthropophilic behaviour of Anopheles rufipes lead us to investigate this species bionomics and role in human malaria parasite transmission. Methods For four consecutive years (2011–2014), annual cross-sectional sampling of adult mosquitoes was conducted during the peak malaria season (September-October) in three health districts in northern Cameroon. Mosquitoes sampled by human landing catch and pyrethrum spray catch methods were morphologically identified, their ovaries dissected for parity determination and Anopheles gambiae siblings were identified by molecular assay. Infection with P. falciparum and blood meal source in residual fauna of indoor resting anopheline mosquitoes were determined by enzyme-linked-immunosorbent assays. Results Anopheles gambiae (sensu lato) (s.l.) comprised 18.4% of mosquitoes collected with An. arabiensis representing 66.27% of the sibling species. The proportion of An. rufipes (2.7%) collected was high with a humanbiting rate ranging between 0.441 and 11.083 bites/person/night (b/p/n) and an anthropophagic rate of 15.36%. Although overall the members of An. gambiae complex were responsible for most of the transmission with entomological inoculation rates (EIR) reaching 1.221 infective bites/person/night (ib/p/n), An. arabiensis and An.coluzzii were the most implicated. The roles of An. funestus, An. pharoensis and An. paludis were minor. Plasmodium falciparum circumsporozoite protein rate in Anopheles rufipes varied from 0.6 to 5.7% with EIR values between 0.010 and 0.481 ib/p/n Conclusions The study highlights the epidemiological role of An. rufipes alongside the members of the An.gambiae complex, and several other sympatric species in human malaria transmission during the wet season in northern Cameroon. For the first time in Cameroon, An. rufipes has been shown to be an important local malaria vector, emphasising the need to review the malaria entomological profile across the country as pre-requisite to effective vector management strategies

Investigating species composition in the Early Aurignacian of le Piage (France) through collagen fingerprinting (ZooMS) of screen-recovered small bone fragments

In the field of paleoproteomics, ZooMS (Zooarcheology by Mass Spectrometry) has been developed to identify morphologically non-diagnostic animal remains to taxon, offering insights into human subsistence practices. Here, we report new ZooMS analyses of 1,050 Early Aurignacian (ca. 37,000–34,000 cal BP) bone fragments from the site of Le Piage (Lot, France). The studied sample is heavily fragmented and was retrieved through water sieving. In our analysis, we compare the taxonomic identifications of bone remains using traditional morphological attributes with remains identified using ZooMS and discuss the implications of the taxonomic patterns that we uncovered. Our results indicate that, despite small effect sizes, the faunal spectrum identified through ZooMS differs from that obtained through morphological analyses. While reindeer remains the dominant species, bovids and other cervids are more abundantly represented in the ZooMS fraction. Two rare taxa, a hare (Lepus sp.) and a previously unidentified carnivore (Pantherinae/Hyaenidae/Mustelidae), were also identified using ZooMS. In addition, we note an increase of Bos/Bison remains in the sample of spongy fragments that is possibly explained by the use of grease-rich bones and bone portions as fuel. Our work adds new data on patterns of reindeer dominance during the Early Aurignacian and illustrates how ZooMS identifications of screen-recovered fragments can enhance our understanding of Paleolithic subsistence strategies and patterns of site occupation

From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma

<p>Abstract</p> <p>Background</p> <p><it>elicobacter pylori </it>infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach.</p> <p>Results</p> <p>A set of 254 <it>H. pylori </it>genes was used to perform array-based comparative genomic hybridization among 120 French <it>H. pylori </it>strains associated with chronic gastritis (n = 33), duodenal ulcers (n = 27), intestinal metaplasia (n = 17) or gastric extra-nodal marginal zone B-cell MALT lymphoma (n = 43). Hierarchical cluster analyses of the DNA hybridization values allowed us to identify a homogeneous subpopulation of strains that clustered exclusively with <it>cag</it>PAI minus MALT lymphoma isolates. The genome sequence of B38, a representative of this MALT lymphoma strain-cluster, was completed, fully annotated, and compared with the six previously released <it>H. pylori </it>genomes (i.e. J99, 26695, HPAG1, P12, G27 and Shi470). B38 has the smallest <it>H. pylori </it>genome described thus far (1,576,758 base pairs containing 1,528 CDSs); it contains the <it>vacA</it>s2m2 allele and lacks the genes encoding the major virulence factors (absence of <it>cag</it>PAI, <it>bab</it>B, <it>bab</it>C, <it>sab</it>B, and <it>hom</it>B). Comparative genomics led to the identification of very few sequences that are unique to the B38 strain (9 intact CDSs and 7 pseudogenes). Pair-wise genomic synteny comparisons between B38 and the 6 <it>H. pylori </it>sequenced genomes revealed an almost complete co-linearity, never seen before between the genomes of strain Shi470 (a Peruvian isolate) and B38.</p> <p>Conclusion</p> <p>These isolates are deprived of the main <it>H. pylori </it>virulence factors characterized previously, but are nonetheless associated with gastric neoplasia.</p