Spy Game: Verifying a Local Generic Solver in Iris

International audienceWe verify the partial correctness of a "local generic solver", that is, an on-demand, incremental, memoizing least fixed point computation algorithm. The verification is carried out in Iris, a modern breed of concurrent separation logic. The specification is simple: the solver computes the optimal least fixed point of a system of monotone equations. Although the solver relies on mutable internal state for memoization and for "spying", a form of dynamic dependency discovery, it is apparently pure: no side effects are mentioned in its specification. As auxiliary contributions, we provide several illustrations of the use of prophecy variables, a novel feature of Iris; we establish a restricted form of the infinitary conjunction rule; and we provide a specification and proof of Longley's modulus function, an archetypical example of spying

A Simple, Possibly Correct LR Parser for C11

International audienceThe syntax of the C programming language is described in the C11 standard by an ambiguous context-free grammar, accompanied with English prose that describes the concept of " scope " and indicates how certain ambiguous code fragments should be interpreted. Based on these elements, the problem of implementing a compliant C11 parser is not entirely trivial. We review the main sources of difficulty and describe a relatively simple solution to the problem. Our solution employs the well-known technique of combining an LALR(1) parser with a " lexical feedback " mechanism. It draws on folklore knowledge and adds several original aspects , including: a twist on lexical feedback that allows a smooth interaction with lookahead; a simplified and powerful treatment of scopes; and a few amendments in the grammar. Although not formally verified, our parser avoids several pitfalls that other implementations have fallen prey to. We believe that its simplicity, its mostly-declarative nature, and its high similarity with the C11 grammar are strong informal arguments in favor of its correctness. Our parser is accompanied with a small suite of " tricky " C11 programs. We hope that it may serve as a reference or a starting point in the implementation of compilers and analysis tools

Validating LR(1) Parsers

International audienceAn LR(1) parser is a finite-state automaton, equipped with a stack, which uses a combination of its current state and one lookahead symbol in order to determine which action to perform next. We present a validator which, when applied to a context-free grammar G and an automaton A, checks that A and G agree. Validating the parser pro-vides the correctness guarantees required by verified compilers and other high-assurance software that involves parsing. The validation process is independent of which technique was used to construct A. The validator is implemented and proved correct using the Coq proof assistant. As an application, we build a formally-verified parser for the C99 language

Modification des traits racinaires le long d’une succession secondaire sur des talus routiers: implications dans la dynamique des communautés et la protection des sols contre l’érosion

Les traits fonctionnels des plantes varient au cours des successions secondaires végétales. Alors que certains traits ont été largement étudiés, les variations des traits racinaires au cours des successions restent relativement peu documentées. L’objectif de cette étude vise à mieux comprendre en quoi des variations de traits racinaires le long d’une succession secondaire contribuent à la dynamique de communautés végétales méditerranéennes. Pour cela, quinze communautés végétales, âgées de 0 à 69 ans, ont été repérées sur des talus en bordures de routes, dans le nord Montpelliérain. Sur cette chronoséquence, nous nous intéressons à des traits racinaires morphologiques et architecturaux des espèces dominantes, représentant 70% de l’abondance végétale. Nous faisons l’hypothèse que des traits morphologiques des racines fines (< 2 mm) permettent de mieux comprendre les modifications des stratégies d’acquisition et de conservation des ressources en nutriments et en eau. Des traits architecturaux, tels que la présence d’un pivot, de racines traçantes et/ou adventives, permettent d’étudier le rôle des racines dans l’ancrage et la capacité des espèces à coloniser le milieu en réponse aux contraintes topographiques liées à la pente des talus. Dans cette communication, nous présentons (i) la méthode retenue pour l’étude des traits racinaires morphologiques et architecturaux sur des espèces de formes de croissance diverses (herbacées, buissons, arbres) et (ii) discutons des limites et atouts de ces méthodes. Enfin, nous discutons de l’implication de ces traits racinaires dans la capacité des communautés à limiter l’érosion superficielle des talu

The ArT\'eMiS wide-field submillimeter camera: preliminary on-sky performances at 350 microns

ArTeMiS is a wide-field submillimeter camera operating at three wavelengths simultaneously (200, 350 and 450 microns). A preliminary version of the instrument equipped with the 350 microns focal plane, has been successfully installed and tested on APEX telescope in Chile during the 2013 and 2014 austral winters. This instrument is developed by CEA (Saclay and Grenoble, France), IAS (France) and University of Manchester (UK) in collaboration with ESO. We introduce the mechanical and optical design, as well as the cryogenics and electronics of the ArTeMiS camera. ArTeMiS detectors are similar to the ones developed for the Herschel PACS photometer but they are adapted to the high optical load encountered at APEX site. Ultimately, ArTeMiS will contain 4 sub-arrays at 200 microns and 2x8 sub-arrays at 350 and 450 microns. We show preliminary lab measurements like the responsivity of the instrument to hot and cold loads illumination and NEP calculation. Details on the on-sky commissioning runs made in 2013 and 2014 at APEX are shown. We used planets (Mars, Saturn, Uranus) to determine the flat-field and to get the flux calibration. A pointing model was established in the first days of the runs. The average relative pointing accuracy is 3 arcsec. The beam at 350 microns has been estimated to be 8.5 arcsec, which is in good agreement with the beam of the 12 m APEX dish. Several observing modes have been tested, like On-The-Fly for beam-maps or large maps, spirals or raster of spirals for compact sources. With this preliminary version of ArTeMiS, we concluded that the mapping speed is already more than 5 times better than the previous 350 microns instrument at APEX. The median NEFD at 350 microns is 600 mJy.s1/2, with best values at 300 mJy.s1/2. The complete instrument with 5760 pixels and optimized settings will be installed during the first half of 2015.Comment: 11 pages, 11 figures. Presented at SPIE Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy VII, June 24, 2014. To be published in Proceedings of SPIE Volume 915

Growth factors in multiple myeloma: a comprehensive analysis of their expression in tumor cells and bone marrow environment using Affymetrix microarrays

<p>Abstract</p> <p>Background</p> <p>Multiple myeloma (MM) is characterized by a strong dependence of the tumor cells on their microenvironment, which produces growth factors supporting survival and proliferation of myeloma cells (MMC). In the past few years, many myeloma growth factors (MGF) have been described in the literature. However, their relative importance and the nature of the cells producing MGF remain unidentified for many of them.</p> <p>Methods</p> <p>We have analysed the expression of 51 MGF and 36 MGF receptors (MGFR) using Affymetrix microarrays throughout normal plasma cell differentiation, in MMC and in cells from the bone marrow (BM) microenvironment (CD14, CD3, polymorphonuclear neutrophils, stromal cells and osteoclasts).</p> <p>Results</p> <p>4/51 MGF and 9/36 MGF-receptors genes were significantly overexpressed in plasmablasts (PPC) and BM plasma cell (BMPC) compared to B cells whereas 11 MGF and 11 MGFR genes were overexpressed in BMPC compared to PPC. 3 MGF genes (AREG, NRG3, Wnt5A) and none of the receptors were significantly overexpressed in MMC versus BMPC. Furthermore, 3/51 MGF genes were overexpressed in MMC compared to the the BM microenvironment whereas 22/51 MGF genes were overexpressed in one environment subpopulation compared to MMC.</p> <p>Conclusions</p> <p>Two major messages arise from this analysis 1) The majority of MGF genes is expressed by the bone marrow environment. 2) Several MGF and their receptors are overexpressed throughout normal plasma cell differentiation. This study provides an extensive and comparative analysis of MGF expression in plasma cell differentiation and in MM and gives new insights in the understanding of intercellular communication signals in MM.</p

Endogenous Retroviruses Transcriptional Modulation After Severe Infection, Trauma and Burn

Although human endogenous retroviruses (HERVs) expression is a growing subject of interest, no study focused before on specific endogenous retroviruses loci activation in severely injured patients. Yet, HERV reactivation is observed in immunity compromised settings like some cancers and auto-immune diseases. Our objective was to assess the transcriptional modulation of HERVs in burn, trauma and septic shock patients. We analyzed HERV transcriptome with microarray data from whole blood samples of a burn cohort (n = 30), a trauma cohort (n = 105) and 2 septic shock cohorts (n = 28, n = 51), and healthy volunteers (HV, n = 60). We described expression of the 337 probesets targeting HERV from U133 plus 2.0 microarray in each dataset and then we compared HERVs transcriptional modulation of patients compared to healthy volunteers. Although all 4 cohorts contained critically ill patients, the majority of the 337 HERVs was not expressed (around 74% in mean). Each cohort had differentially expressed probesets in patients compared to HV (from 19 to 46). Strikingly, 5 HERVs were in common in all types of severely injured patients, with 4 being up-modulated in patients. We highlighted co-expressed profiles between HERV and nearby CD55 and CD300LF genes as well as autonomous HERV expression. We suggest an inflammatory-specific HERV transcriptional response, and importantly, we introduce that the HERVs close to immunity-related genes might have a role on its expression

CRMP5 Regulates Generation and Survival of Newborn Neurons in Olfactory and Hippocampal Neurogenic Areas of the Adult Mouse Brain

The Collapsin Response Mediator Proteins (CRMPs) are highly expressed in the developing brain, and in adult brain areas that retain neurogenesis, ie: the olfactory bulb (OB) and the dentate gyrus (DG). During brain development, CRMPs are essentially involved in signaling of axon guidance and neurite outgrowth, but their functions in the adult brain remain largely unknown. CRMP5 has been initially identified as the target of auto-antibodies involved in paraneoplasic neurological diseases and further implicated in a neurite outgrowth inhibition mediated by tubulin binding. Interestingly, CRMP5 is also highly expressed in adult brain neurogenic areas where its functions have not yet been elucidated. Here we observed in both neurogenic areas of the adult mouse brain that CRMP5 was present in proliferating and post-mitotic neuroblasts, while they migrate and differentiate into mature neurons. In CRMP5−/− mice, the lack of CRMP5 resulted in a significant increase of proliferation and neurogenesis, but also in an excess of apoptotic death of granule cells in the OB and DG. These findings provide the first evidence that CRMP5 is involved in the generation and survival of newly generated neurons in areas of the adult brain with a high level of activity-dependent neuronal plasticity

Troublesome Heterotopic Ossification after Central Nervous System Damage: A Survey of 570 Surgeries

BACKGROUND: Heterotopic ossification (HO) is a frequent complication after central nervous system (CNS) damage but has seldom been studied. We aimed to investigate features of HO for the first time in a large sample and the rate of early recurrence of HO in terms of the time of surgery. METHODOLOGY/PRINCIPAL FINDINGS: We retrospectively analyzed data from an anonymous prospective survey of patients undergoing surgery between May 1993 and November 2009 in our institution for troublesome HO related to acquired neurological disease. Demographic and HO characteristics and neurological etiologies were recorded. For 357 consecutive patients, we collected data on 539 first surgeries for HO (129 surgeries for multiple sites). During the follow-up, recurrences requiring another surgery appeared in 31 cases (5.8% [31/539]; 95% confidence interval [CI]: 3.8%-7.8%; 27 patients). Most HO requiring surgery occurred after traumatic brain injury (199 patients [55.7%]), then spinal cord injury (86 [24.0%]), stroke (42 [11.8%]) and cerebral anoxia (30 [8.6%]). The hip was the primary site of HO (328 [60.9%]), then the elbow (115 [21.3%]), knee (77 [14.3%]) and shoulder (19 [3.5%]). For all patients, 181 of the surgeries were performed within the first year after the CNS damage, without recurrence of HO. Recurrence was not associated with etiology (p = 0.46), sex (p = 1.00), age at CNS damage (p = 0.2), multisite localization (p = 0.34), or delay to surgery (p = 0.7). CONCLUSIONS/SIGNIFICANCE: In patients with CNS damage, troublesome HO and recurrence occurs most frequently after traumatic brain injury and appears frequently in the hip and elbow. Early surgery for HO is not a factor of recurrence