EPiK-a Workflow for Electron Tomography in Kepler.

Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility

GAIMS: a powerful gait analysis system satisfying the constraints of clinical routine

GAIM

Diagnosing multiple sclerosis with a gait measuring system, an analysis of the motor fatigue, and machine learning

GAIM

3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography

Transmission electron microscopy allows the collection of multiple views of specimens and their computerized three-dimensional reconstruction and analysis with electron tomography. Here we describe development of methods for automated multi-tilt data acquisition, tilt-series processing, and alignment which allow assembly of electron tomographic data from a greater number of tilt series, yielding enhanced data quality and increasing contrast associated with weakly stained structures. This scheme facilitates visualization of nanometer scale details of fine structure in volumes taken from plastic-embedded samples of biological specimens in all dimensions. As heavy metal-contrasted plastic-embedded samples are less sensitive to the overall dose rather than the electron dose rate, an optimal resampling of the reconstruction space can be achieved by accumulating lower dose electron micrographs of the same area over a wider range of specimen orientations. The computerized multiple tilt series collection scheme is implemented together with automated advanced procedures making collection, image alignment, and processing of multi-tilt tomography data a seamless process. We demonstrate high-quality reconstructions from samples of well-described biological structures. These include the giant Mimivirus and clathrin-coated vesicles, imaged in situ in their normal intracellular contexts. Examples are provided from samples of cultured cells prepared by high-pressure freezing and freeze-substitution as well as by chemical fixation before epoxy resin embedding

SMART SECURITY MANAGEMENT IN SECURE DEVICES

International audienceAmong other threats, secure components are subjected tophysical attacks whose aim is to recover the secret information theystore. Most of the work carried out to protect these components generally consists in developing protections (or countermeasures) taken one byone. But this “countermeasure-centered” approach drastically decreasesthe performance of the chip in terms of power, speed and availability.In order to overcome this limitation, we propose a complementary approach: smart dynamic management of the whole set of countermeasuresembedded in the component. Three main specifications for such management are required in a real world application (for example, a conditionalaccess system for Pay-TV): it has to provide capabilities for the chip todistinguish between attacks and normal use cases (without the help of ahuman being and in a robust but versatile way); it also has to be basedon mechanisms which dynamically find a trade-off between security andperformance; all these mecanisms have to formalized in a way which isclearly understandable by the designer. In this article, a prototype whichenables such security management is described. The solution is based ona double-processor architecture: one processor embeds a representativeset of countermeasures (and mechanisms to define their parameters) andexecutes the application code. The second processor, on the same chip,applies a given security strategy, but without requesting sensitive datafrom the first processor. The chosen strategy is based on fuzzy logic reasoning to enable the designer to describe, using a fairly simple formalism,both the attack paths and the normal use cases. A proof of concept hasbeen proposed for the smart card part of a conditional access for Pay-TV,but it could easily be fine-tuned for other applications

Variation individuelle des paramètres de marche au long d'une distance de 500m chez des personnes atteintes de sclérose en plaques et chez des volontaires sains

Background: we previously demonstrated the usefulness of the Deceleration Index (DI, the ratio between the last 100m of the Timed 500-Meter Walk test –T500MW – and the walking speed - WS – of the Timed 25-Foot Walk Test with a propelled start – T25FW+) to evaluate motor fatigue over a long walking distance in people with multiple sclerosis (pwMS). We also recently designed and internally validated a new gait analysis tool for pwMS (GAIMS) that can measure other relevant gait characteristics than the sole WS, such as ataxia, asymmetry and perhaps spasticity. Aims: (i) To compare various gait characteristics between the last and the first 100m of the T500MW in a population of pwMS and healthy volunteers (HV), (ii) to compare the ratio between the last and the first 100m of the T500MW with the DI, and (iii) their relationship with the EDSS. Methods : Subjects were asked to perform the T25FW+ and the T500MW as part of a multimodal evaluation at the MS Clinic of the CHU of Liège. Their gait characteristics were measured using GAIMS. (i) Paired Student’s t-tests were performed on various gait characteristics extracted during the last and first 100m of the T500MW with .05 as a level of significance, (ii) Spearman correlation coefficient (ρ) was calculated (ii) between these ratio and (iii) subject’s EDSS. Results: Seventy-one pwMS and 129 were enrolled in our study. (i) Significant differences were observed for speed related gait characteristics between the last and first 100m of the T500MW, but also for gait characteristics related to ataxia and precision of foot placement. (ii) A moderate positive correlation was observed between the WS ratio of the last and first 100m of the T500MW and the DI. (iii) The correlation between the DI and the EDSS was weakly negative, while the one between the last and first 100m of the T500MW ratio and the EDSS was moderatly negative. Conclusion: (i) As previously demonstrated, we here confirm that alongside to WS, there are other gait features affected by locomotor fatigue over a long walking distance, (ii) the moderate positive correlation between the DI and the last/first 100m of the T500MW indicates that these measures are not the same and that next to a long distance walking test such as the T500MW, a short one such as the T25FW+ remains useful. (iii) The last/first 100m of the T500MW is better correlated to the EDSS and might be a better predictive tool of pwMS’ neurologic state than the DI

SOS An innovative secure system architecture

International audience`Smart On Smart' (SOS) is a project launched in 2008 and funded by the `Agence Nationale pourla Recherche'. This project aims at helping the partnershipformed by Trusted Logic, Viaccess, LIP6, and the CEA-LETI to study aninnovative secure system architecture. This architecture is based on twoparts. The first one called the host system is in charge of the mainapplication and processes the sensitive data. Connected to the host system thesecond part called the audit system is strictly dedicated to thesecurity strategy response of the whole system.The underlying idea is that such an architecture will help to build abetter secure system. For instance it becomes possible to improve theintelligence of the security policy to be able to differentiate a normalerror behaviour from a suspect one. Since the whole system's securityreliability is adjustable it becomes also possible to maximise theperformance when nonsensitive data are processed. Non repeatablebehaviour and response of the system under attack could be alsoprogrammed in order to counter the attacker.One of the main tasks is to define a hardware architecture correspondingto this concept for which a safe boundary has to be established between thetwo systems. The software part and in particular the way thesecurity policy is implemented on the audit system is also a non obvioustask especially because the overhead due to this additional auditsystem has to be the lowest possible in order to be cost-effective.We are building a proof of concept around a pay TV application. Additionalhardware features are used to emulate fault injection attacks for thedemo. We are building the hardware model on an FPGA board provingalso that such an architecture fits an FPGA based system

The Human Papillomavirus E6 Oncogene Represses a Cell Adhesion Pathway and Disrupts Focal Adhesion through Degradation of TAp63β upon Transformation

Cervical carcinomas result from cellular transformation by the human papillomavirus (HPV) E6 and E7 oncogenes which are constitutively expressed in cancer cells. The E6 oncogene degrades p53 thereby modulating a large set of p53 target genes as shown previously in the cervical carcinoma cell line HeLa. Here we show that the TAp63β isoform of the p63 transcription factor is also a target of E6. The p63 gene plays an essential role in skin homeostasis and is expressed as at least six isoforms. One of these isoforms, ΔNp63α, has been found overexpressed in squamous cell carcinomas and is shown here to be constitutively expressed in Caski cells associated with HPV16. We therefore explored the role of p63 in these cells by performing microarray analyses after repression of endogenous E6/E7 expression. Upon repression of the oncogenes, a large set of p53 target genes was found activated together with many p63 target genes related to cell adhesion. However, through siRNA silencing and ectopic expression of various p63 isoforms we demonstrated that TAp63β is involved in activation of this cell adhesion pathway instead of the constitutively expressed ΔNp63α and β. Furthermore, we showed in cotransfection experiments, combined with E6AP siRNA silencing, that E6 induces an accelerated degradation of TAp63β although not through the E6AP ubiquitin ligase used for degradation of p53. Repression of E6 transcription also induces stabilization of endogenous TAp63β in cervical carcinoma cells that lead to an increased concentration of focal adhesions at the cell surface. Consequently, TAp63β is the only p63 isoform suppressed by E6 in cervical carcinoma as demonstrated previously for p53. Down-modulation of focal adhesions through disruption of TAp63β therefore appears as a novel E6-dependent pathway in transformation. These findings identify a major physiological role for TAp63β in anchorage independent growth that might represent a new critical pathway in human carcinogenesis