Quonops©, la prévision opérationnelle en acoustique sous-marine sur grille de calcul

National audienceQuonops©, la prévision opérationnelle en acoustique sous-marine sur grille de calcu

Quonops©, la prévision opérationnelle en acoustique sous-marine sur grille de calcul

National audienceQuonops©, la prévision opérationnelle en acoustique sous-marine sur grille de calcu

Cestode infections in non-human primates suggest the existence of zoonotic cycles in the area surrounding the Strasbourg primatology center

Background: Several cases of infections due to Echinococcus multilocularis, Taenia martis and Taenia crassiceps were recently described in various species of captive non-human primates (NHPs) harbored in the Strasbourg Primate Center (SPC). Furthermore, one of the first cases of human cysticercosis due to T. martis was described in the Strasbourg region. These data suggest the existence of zoonotic cycles of tapeworm infections in the direct environment of the SPC. The aim of our study was to assess the prevalence of larval cestode infections among intermediate and definitive hosts in the close neighborhood of the center. We analyzed carnivore mammal fecal samples as well as rodent carcasses, collected inside or near the SPC, using PCR. Furthermore, we performed serology for Echinococcus spp. and Taenia spp. on NHP sera. Results: We found that 14.5% (95% CI [8.6; 20.4]) of 138 carnivore feces were positive for E. multilocularis-DNA, as well as 25% (95% CI [5.5; 57.2]) of 12 rodent carcasses, and 5.1% (95% CI [1.4; 8.7]) for T. martis or T. crassiceps. Of all NHPs tested, 10.1% (95% CI [3.8; 16.4]) were seropositive for Echinococcus spp. and 8.2% (95% CI [1.3; 15.1]) for Taenia spp. Conclusions: Our data support the existence of zoonotic cycles of larval cestode infections in the direct environment of the primatology center affecting NHPs harbored in the SPC, potentially threatening the human population living in this area. Since this zoonotic risk is borne by local wildlife, and given the severity of these infections, it seems necessary to put in place measures to protect captive NHPs, and further studies to better assess the risk to human populations

Compiling python modules to native parallel modules using Pythran and OpenMP annotations

International audienceAbstract-High Performance Computing users traditionally rely on low-level, compiled language such as C or FORTRAN to perform compute-intensive tasks. As a consequence, it is a common situation to have High Performance Computing application written in a high-level language such as Python, calling native routines for compute-intensive tasks. To improve development speed and reduce maintenance costs, using a higher-level language like Python seems attractive. While it is usually associated with low performance, several solutions such as Cython, Numba, Parakeet or Pythran offer to automatically or semi-automatically turn Python functions into native ones. One of the key points required to match the performance of native applications is the ability to write parallel applications. This paper studies the addition of OpenMP directives, a popular model to describe parallelism in C/C++/FORTRAN applications, to Pythran, an automatic compiler from a subset of Python to C++. It shows that scientific Python applications annotated with OpenMP directives can be turned by an automatic compiler into native applications that run within the same order of magnitude than manually-written ones

Compiling python modules to native parallel modules using Pythran and OpenMP annotations

International audienceAbstract-High Performance Computing users traditionally rely on low-level, compiled language such as C or FORTRAN to perform compute-intensive tasks. As a consequence, it is a common situation to have High Performance Computing application written in a high-level language such as Python, calling native routines for compute-intensive tasks. To improve development speed and reduce maintenance costs, using a higher-level language like Python seems attractive. While it is usually associated with low performance, several solutions such as Cython, Numba, Parakeet or Pythran offer to automatically or semi-automatically turn Python functions into native ones. One of the key points required to match the performance of native applications is the ability to write parallel applications. This paper studies the addition of OpenMP directives, a popular model to describe parallelism in C/C++/FORTRAN applications, to Pythran, an automatic compiler from a subset of Python to C++. It shows that scientific Python applications annotated with OpenMP directives can be turned by an automatic compiler into native applications that run within the same order of magnitude than manually-written ones

Exploring the vectorization of Python constructs using Pythran and Boost SIMD

International audienceThe Python language is highly dynamic, most notably due to late binding. As a consequence, programs using Python typically run an order of magnitude slower than their C counterpart. It is also a high level language whose semantic can be made more static without much change from a user point of view in the case of mathematical applications. In that case, the language provides several vectorization opportunities that are studied in this paper, and evaluated in the context of Pythran, an ahead-of-time compiler that turns Python module into C++ meta-program

[Research Paper] Combining Obfuscation and Optimizations in the Real World

International audienceCode obfuscation is the de facto standard to protect intellectual property when delivering code in an unmanaged environment. It relies on additive layers of code tangling techniques, white-box encryption calls and platform-specific or tool-specific countermeasures to make it harder for a reverse engineer to access critical pieces of data or to understand core algorithms. The literature provides plenty of different obfuscation techniques that can be used at compile time to transform data or control flow in order to provide some kind of protection against different reverse engineering scenarii. Scheduling code transformations to optimize a given metric is known as the pass scheduling problem, a problem known to be NP-hard, but solved in a practical way using hard-coded sequences that are generally satisfactory. Adding code obfuscation to the problem introduces two new dimensions. First, as a code obfuscator needs to find a balance between obfuscation and performance, pass scheduling becomes a multi-criteria optimization problem. Second, obfuscation passes transform their inputs in unconventional ways, which means some pass combinations may not be desirable or even valid. This paper highlights several issues met when blindly chaining different kind of obfuscation and optimization passes, emphasizing the need of a formal model to combine them. It proposes a non-intrusive formalism to leverage on sequential pass management techniques. The model is validated on real-world scenarii gathered during the development of an industrial-strength obfuscator on top of the LLVM compiler infrastructure

Coping with change in predation risk across space and time through complementary behavioral responses

Abstract Background Our picture of behavioral management of risk by prey remains fragmentary. This partly stems from a lack of studies jointly analyzing different behavioral responses developed by prey, such as habitat use and fine-scale behavior, although they are expected to complement each other. We took advantage of a simple system on the Kerguelen archipelago, made of a prey species, European rabbit Oryctolagus cuniculus, a predator, feral cat Felis catus, and a mosaic of closed and open foraging patches, allowing reliable assessment of spatio-temporal change in predation risk. We investigated the way such a change triggered individual prey decisions on where, when and how to perform routine activities. Results Rabbit presence and behavior were recorded both day and night in patches with similar foraging characteristics, but contrasted in terms of openness. Cats, individually recognizable, were more active at night and in closed patches, in line with their expected higher hunting success in those conditions. Accordingly, rabbits avoided using closed patches at night and increased their vigilance if they did. Both day and night, rabbits increased their use of closed patches as compared to open patches in windy conditions, thereby probably reducing the thermoregulatory costs expected under such harsh environmental conditions. Conclusions Overall, our data map the landscape of fear in this study system and indicate that prey habitat use and vigilance complement each other. Solely focusing on one or the other tactic may lead to erroneous conclusions regarding the way predation risk triggers prey decisions. Finally, future studies should investigate inter-individual variability in the relative use of these different types of complementary behavioral responses to perceived risk, along with the determinants and outcomes of such tactics