A no-thin-air memory model for programming languages

Many hardware and compiler optimisations introduced to speed up single-threaded programs also introduce additional, sometimes surprising, behaviours for concurrent programs with shared mutable state. How many of these extra behaviours occur in practice depends on the combination of the hardware, compiler, runtime, etc. that make up the platform. A memory model, which prescribes what values each read of a concurrent program can read, allows programmers to determine whether a program behaves as expected without having to worry about the details of the platform. However, capturing these behaviours in a memory model without also including undesirable "out-of-thin-air" behaviours that do not occur in practice has proved elusive. The memory model of C and C++ allows out-of-thin-air behaviour, while the Java memory model fails to capture some behaviours that are introduced in practice by compiler optimisations. In this thesis, we propose a memory model that forbids out-of-thin-air behaviour, yet allows the behaviours that do occur. Our memory model follows operational intuitions of how the hardware and compilers operate. We illustrate that it behaves as desired on a series of litmus tests. We show that it captures at least some of the expected behaviours, that it forms an envelope around some common compiler optimisations, and that it is implementable on common hardware using the expected compilation schemes. We also show that it supports some established programming idioms.EPSRC Programme Grant REMS: Rigorous Engineering for Mainstream Systems, EP/K008628/1 Computer Laboratory Premium Research Studentshi

Nano mechanical and microstructural investigation of damage mechanisms in copper wire bonds

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Differential involvement of Ca(2+) channels in survival and neurite outgrowth of cultured embryonic cockroach brain neurons.

Full text: http://jn.physiology.org/content/88/3/1475International audienceThe contribution of voltage-gated calcium channels (VGCC) to the development of cultured embryonic cockroach brain neurons was assessed using pharmacological agents. VGCC currents were recorded using the patch-clamp technique and were found to be blocked dose-dependently by micromolar concentrations of mibefradil. The activation and inactivation properties of the calcium channels enable a sizeable calcium current to flow at rest (about -30 and -20 mV in high-potassium culture media). As expected, the cytoplasmic-free calcium concentration was found to rise when the extracellular potassium concentration was raised from 3 to 15 and 30 mM. The effects of VGCC blockers and calcium chelators were different in fresh and in mature cultures in which the neurons were connected to each other to form a defined network. In fresh cultures, the two non-selective VGCC blockers (verapamil and mibefradil) induced a dose-dependent cell death that was proportional to their blocking effect on I(Ba). This effect could not be prevented by addition of fetal calf serum to the culture medium. A similar effect was obtained using intra- or extracellular calcium chelating agents (10 microM BAPTA-AM or 10 mM EGTA). Quite unexpectedly, blockade of the P/Q-like (omega-Aga WA-sensitive) component of the calcium current by 500 nM of omega-AgaTx IVA had no lethal effect, suggesting that the corresponding channels are not involved in the survival mechanism. As expected from their lack of effect on I(Ba), isradipine, nifedipine, and omega-CgTx GVIA did not induce cell death. When the neurons started growing neurites, their sensitivity to calcium channel blockade by mibefradil decreased, indicating a correlation between neurite outgrowth and resistance to calcium depletion. In mature cultures, the neurons became resistant to mibefradil, verapamil, and BAPTA-AM. However, these agents, as well as omega-AgaTx IVA, had a significant inhibitory effect on the increase in diameter of the connectives that linked adjacent clusters of neurons. This effect has been shown to result, in the case of mibefradil, from an inhibition of neurite outgrowth characterized by a significant reduction of the number of primary neurites and secondary branchings but not to a significant modification of the diameter of individual neurites. These results support the view that, as in vertebrates, calcium influx through VGCC plays an important role in survival and neurite outgrowth of cultured embryonic insect neurons. The differential contribution of the P/Q-like and R-like (omega-Aga WA-sensitive) calcium channels in these processes is discussed

Ocean-Atmosphere Application Scheduling within DIET

In this report, we tackle the problem of scheduling an Ocean-Atmosphere application in an heterogeneous environment. The application is used for long term climate forecast. In this context, we analyzed the execution of an experiment. An experiment is composed of several identical simulations composed of parallel tasks. On homogeneous platforms, we propose a heuristic and its optimizations, all based on the same idea: we divide the processors into disjoint sets, each group executing parallel tasks. On heterogeneous platforms the algorithm presented is applied on subsets of simulations. The computation of the subsets is done greedily and aims at minimizing the execution time by sending each subset on a cluster. We performed experiments on the french research grid \emph{Grid'5000} which exhibited some technical difficulties. We also present some modifications done to the heuristics to minimize the impact of these technical difficulties. Our simulations are then validated by experimentations

Prism adaptation to rightward optical deviation improves postural imbalance in left-hemiparetic patients

AbstractLeft-hemiparetic patients show predominant postural imbalance as compared to right-hemiparetic patients. The right hemisphere is crucial for generating internal maps used for perceptual and premotor processing of spatial information. Predominant postural imbalance with right-brain damage could thus result from a distortion of an internal postural map. Well-known manifestations of distorted internal maps due to right-hemisphere lesions, such as hemineglect, may show improvement following prism adaptation shifting the visual field to the right. We therefore investigated the effect of prism adaptation on postural imbalance in left-hemiparetic patients. Three groups of five patients were either adapted to prisms deviating the visual field to the right or left or exposed to neutral prisms while performing reaching movements of the right arm. Postural imbalance was reduced only following prism adaptation to the right. Thus, brief adaptation (i.e., 3 min) to rightward-shifting prisms can dramatically improve postural imbalance. This result shows that the effect of exposure to prisms that horizontally shift the visual field to the right in a reaching task generalizes to the postural system, and it suggests an interaction between horizontal and vertical reference frames. This also supports the theory that predominant postural imbalance in patients with right-brain damage may be partly related to a distortion of an internal postural map

Investigating the unusually high cell wall digestibility of the old INRA early flint F4 maize inbred line

The old INRA flint early line F4, which belongs to the northern flint group, is typified by its high cell wall digest- ibility which reaches values as high as those observed in several brown-midrib bm3 mutant lines. The F4 line thus appeared as a model that could contribute to the understanding of genetic mechanisms involved in variation of secondary wall traits. Different strategies and results were thus gathered including especially cell wall biochemical and digestibility investigations, expression approaches, QTL investigations, and colocalizations between QTLs and candidate genes. Lignin content was lower in F4 than in other lines, with a tendency to lower p-coumarate content. The Syringyl/Guaiacyl lignin unit ratio was similar in F4 as in other lines, but this ratio was nearly not reduced in F4bm3, conversely to what is observed in bm3 mutants. In comparison with the INRA F2 control line, expressions of three PAL genes including the ZmPAL, of the ZmF5H1 and the ZmCOMT genes were significantly reduced in F4 lignifying ear internodes at early silking stage. In the F7025 x F4 RIL progeny, seven QTLs were shown with favorable alleles (increasing cell wall digestibility) originating from F4. Two strong QTLs were located in bins 1.03 and 2.03 colocalizing with the ZmMYB019 and ZmSWN6 transcription factors, respectively. Orthologs of ZmMYB019 have been shown to be involved in lignin biosynthesis, and the PpMYB8 ortholog was shown to regu- late PAL gene expression in maritime pine. The ZmSWN6 NAC transcription factor is an upstream master regulator of the secondary wall biosynthetic programs. At the other QTL positions, colocalizations were also shown with other secondary wall related ZmMYB, but also with BAHD genes involved in arabinoxylan feruloylation, and with the position of the bm6 mutation. Three QTL positions were shown with favorable alleles originating from F7025, which colocalized with ZmMYB and ZmNAC transcriptions factors. As a tentative conclusion, the F4 unusually high cell wall digestibility is likely greatly related to the altered working of at least two major transcription factors regulating cell wall biosynthesis and assembly

Expression of cell wall related genes in basal and ear internodes of silking brown-midrib-3, caffeic acid O-methyltransferase (COMT) down-regulated, and normal maize plants

<p>Abstract</p> <p>Background</p> <p>Silage maize is a major forage and energy resource for cattle feeding, and several studies have shown that lignin content and structure are the determining factors in forage maize feeding value. In maize, four natural <it>brown-midrib </it>mutants have modified lignin content, lignin structure and cell wall digestibility. The greatest lignin reduction and the highest cell wall digestibility were observed in the <it>brown-midrib-3 </it>(<it>bm3</it>) mutant, which is disrupted in the caffeic acid <it>O</it>-methyltransferase (COMT) gene.</p> <p>Results</p> <p>Expression of cell wall related genes was investigated in basal and ear internodes of normal, COMT antisens (AS225), and <it>bm3 </it>maize plants of the INRA F2 line. A cell wall macro-array was developed with 651 gene specific tags of genes specifically involved in cell wall biogenesis. When comparing basal (older lignifying) and ear (younger lignifying) internodes of the normal line, all genes known to be involved in constitutive monolignol biosynthesis had a higher expression in younger ear internodes. The expression of the COMT gene was heavily reduced, especially in the younger lignifying tissues of the ear internode. Despite the fact that AS225 transgene expression was driven only in sclerenchyma tissues, COMT expression was also heavily reduced in AS225 ear and basal internodes. COMT disruption or down-regulation led to differential expressions of a few lignin pathway genes, which were all over-expressed, except for a phenylalanine ammonia-lyase gene. More unexpectedly, several transcription factor genes, cell signaling genes, transport and detoxification genes, genes involved in cell wall carbohydrate metabolism and genes encoding cell wall proteins, were differentially expressed, and mostly over-expressed, in COMT-deficient plants.</p> <p>Conclusion</p> <p>Differential gene expressions in COMT-deficient plants highlighted a probable disturbance in cell wall assembly. In addition, the gene expressions suggested modified chronology of the different events leading to cell expansion and lignification with consequences far beyond the phenylpropanoid metabolism. The reduced availability of monolignols and S units in <it>bm3 </it>or AS225 plants led to plants also differing in cell wall carbohydrate, and probably protein, composition. Thus, the deficiency in a key-enzyme of the lignin pathway had correlative effects on the whole cell wall metabolism. Furthermore, the observed differential expression between <it>bm3 </it>and normal plants indicated the possible involvement in the maize lignin pathway of genes which up until now have not been considered to play this role.</p

Maize cell wall degradability, from whole plant to tissue level: different scales of complexity

Today, maize stover can be considered as a model for investigating secondary cell wall formation in grasses with major applications in cattle feeding (forage maize) and green energy production (bioethanol, biogas, etc). Up until now, cell wall formation and cell wall degradability have been considered at the whole plant scale. However, a detailed examination of leaves and internodes has underlined a large diversity of lignified cell types (xylem vessels, parenchyma, sub-epidermal and perivascular sclerenchyma) and significant variations in the organization and / or the composition of these different cell types. In this review, we highlighted several aspects of this complexity and their consequences on valorization processes both in agriculture or industries

Apprivoiser MoReq : pour archiver et conserver l’information

L’objectif de ce document, fondé sur la mise en commun d’expériences multiples, est de fournir à tout responsable d’un projet d’archivage électronique, quel que soit son profil (informaticien, archiviste, responsable métier, juriste…) un guide pratique des questions à poser et des actions à mener pour mettre en place un système cohérent, fiable et assimilable par l’ensemble des acteurs concernés, à l’appui d’une politique d’archivage de l’entreprise

Combined approaches provide an anatomical and transcriptomic fingerprint of maize cell wall digestibility

Understanding cell wall biosynthesis and degradation in grasses has become a major aim in plant biology. Although independent previous reports have focused on specific features that dictate cell wall digestibility, cytological, biochemical, and gene regulation parameters have never been integrated within the same study. Herein, we applied a combination of state-of-the-art technologies and different scales of observation on two maize lines that are characterized by highly contrasted forage digestibility. Comparative image analysis of internode sections allow to get an anatomical fingerprint associated with high digestibility: a thin peripheral rind of lignified parenchyma, small numerous vascular bundles, and low proportion of PeriVascular Sclerenchyma (PVS). This cell type patterning led to enhanced digestibility when internode sections were treated with Celluclast, a commercially cell wall degrading enzyme. At a lower scale of observation, Laser Capture Microdissection (LCM) followed by thioacidolysis of PVS revealed a higher proportion of Syringyl (S) unit lignins in the low digestible line while the high digestible line was p-Hydroxyphenyl (H)-rich. Moreover, cytological observation of internodes of the two lines point out that this difference in composition is associated with a delayed lignification of PVS. At the same time, comparative transcriptomics on internodes indicated differential expression of several genes encoding enzymes along the phenylpropanoid pathway and known cell wall-associated Transcription Factors (TFs). Together, these results give an integrative view of different factors which could aim in designing a maize silage ideotype and provide a novel set of potential regulatory genes controlling lignification in maize