High-Performance Packet Processing Engines Using Set-Associative Memory Architectures

The emergence of new optical transmission technologies has led to ultra-high Giga bits per second (Gbps) link speeds. In addition, the switch from 32-bit long IPv4 addresses to the 128-bit long IPv6 addresses is currently progressing. Both factors make it hard for new Internet routers and firewalls to keep up with wire-speed packet-processing. By packet-processing we mean three applications: packet forwarding, packet classification and deep packet inspection. In packet forwarding (PF), the router has to match the incoming packet's IP address against the forwarding table. It then directs each packet to its next hop toward its final destination. A packet classification (PC) engine examines a packet header by matching it against a database of rules, or filters, to obtain the best matching rule. Rules are associated with either an ``action'' (e.g., firewall) or a ``flow ID'' (e.g., quality of service or QoS). The last application is deep packet inspection (DPI) where the firewall has to inspect the actual packet payload for malware or network attacks. In this case, the payload is scanned against a database of rules, where each rule is either a plain text string or a regular expression. In this thesis, we introduce a family of hardware solutions that combine the above requirements. These solutions rely on a set-associative memory architecture that is called CA-RAM (Content Addressable-Random Access Memory). CA-RAM is a hardware implementation of hash tables with the property that each bucket of a hash table can be searched in one memory cycle. However, the classic hashing downsides have to be dealt with, such as collisions that lead to overflow and worst-case memory access time. The two standard solutions to the overflow problem are either to use some predefined probing (e.g., linear or quadratic) or to use multiple hash functions. We present new hash schemes that extend both aforementioned solutions to tackle the overflow problem efficiently. We show by experimenting with real IP lookup tables, synthetic packet classification rule sets and real DPI databases that our schemes outperform other previously proposed schemes

ADVANCED HASHING SCHEMES FOR PACKETFORWARDING USING SET ASSOCIATIVEMEMORY ARCHITECTURES

Building a high performance IP packet forwarding (PF) engine remains a challenge due to increasingly stringent throughput requirements and the growing sizes of IP forwarding tables.The router has to match the incoming packet's IP address against the forwarding table.The matching process has to be done in wire speed which is why scalability and low power consumption are features that PF engines must maintain.It is common for PF engines to use hash tables; however, the classic hashing downsides have to be dealt with (e.g., collisions, worst case memory access time, ... etc.).While open addressing hash tables, in general, provide good average case search performance, their memory utilization and worst case performance can degrade quickly due to collisions that leads to bucket overflows.Set associative memory can be used for hardware implementations of hash tables with the property that each bucket of a hash table can be searched in one memory cycle.Hence, PF engine architectures based on associative memory will outperform those based on the conventional Ternary Content Addressable Memory (TCAM) in terms of power and scalability.The two standard solutions to the overflow problem are either to use some sort of predefined probing (e.g., linear or quadratic) or to use multiple hash functions.This work presents two new hash schemes that extend both aforementioned solutions to tackle the overflow problem efficiently.The first scheme is a hash probing scheme that is called Content-based HAsh Probing, or CHAP.CHAP is a probing scheme that is based on the content of the hash table to avoid the classical side effects of predefined hash probing methods (i.e., primary and secondary clustering phenomena) and at the same time reduces the overflow.The second scheme, called Progressive Hashing, or PH, is a general multiple hash scheme that reduces the overflow as well.PH splits the prefixes into groups where each group is assigned one hash function, then reuse some hash functions in a progressive fashion to reduce the overflow.We show by experimenting with real IP lookup tables that both schemes outperform other hashing schemes

Mécanismes et conséquences des mutations

L’identification des mutations à l’origine de maladies génétiques chez l’homme a pris ces dernières années un essor considérable. Il est devenu possible d’établir le spectre des mutations délétères pour une maladie génétique donnée, et des bases de données internationales sont aujourd’hui accessibles via le réseau Internet. Le diagnostic génotypique des maladies héréditaires occupe actuellement une place prépondérante en matière de conseil génétique et de diagnostic prénatal. La connaissance du type de mutation délétère et des mécanismes en cause est essentielle pour déterminer la stratégie de diagnostic moléculaire adaptée à chaque situation. Cet article a pour objectif de présenter les différents types de mutations responsables de maladies génétiques (substitutions nucléotidiques, délétions ou insertions de petite taille, mutations dynamiques, grands remaniements…) et de récapituler les connaissances actuelles concernant les mécanismes moléculaires à l’origine de ces mutations. Leurs conséquences sur l’expression du gène (transcription et maturation du transcrit) et sur la fonction de la protéine sont également abordées dans cet article.The identification of mutations leading to human genetic diseases has grown into an intensive research field during the last few years. Through novel DNA analysis progress, it is now possible to determine the mutational spectrum for a given genetic disease and international databases are now available online. Genetic diagnosis of hereditary diseases has become an essential tool in genetic counselling and prenatal diagnosis. The knowledge of the deleterious mutation type and the molecular associated mechanism is fundamental in order to devise the optimal molecular diagnosis strategy. This review aims to present the various mutation categories involved in genetic diseases (single base-pair substitutions, small deletions or insertions, dynamic mutations, gross DNA lesions…) and to summarize our current knowledge about the main molecular mechanisms responsible for these mutations. Their deleterious consequences on gene expression, including transcription and transcript maturation, and protein loss or gain of function are also discussed in this review

Hermes Regulates Axon Sorting in the Optic Tract by Post-Trancriptional Regulation of Neuropilin 1.

UNLABELLED: The establishment of precise topographic maps during neural development is facilitated by the presorting of axons in the pathway before they reach their targets. In the vertebrate visual system, such topography is seen clearly in the optic tract (OT) and in the optic radiations. However, the molecular mechanisms involved in pretarget axon sorting are poorly understood. Here, we show in zebrafish that the RNA-binding protein Hermes, which is expressed exclusively in retinal ganglion cells (RGCs), is involved in this process. Using a RiboTag approach, we show that Hermes acts as a negative translational regulator of specific mRNAs in RGCs. One of these targets is the guidance cue receptor Neuropilin 1 (Nrp1), which is sensitive to the repellent cue Semaphorin 3A (Sema3A). Hermes knock-down leads to topographic missorting in the OT through the upregulation of Nrp1. Restoring Nrp1 to appropriate levels in Hermes-depleted embryos rescues this effect and corrects the axon-sorting defect in the OT. Our data indicate that axon sorting relies on Hermes-regulated translation of Nrp1. SIGNIFICANCE STATEMENT: An important mechanism governing the formation of the mature neural map is pretarget axon sorting within the sensory tract; however, the molecular mechanisms involved in this process remain largely unknown. The work presented here reveals a novel function for the RNA-binding protein Hermes in regulating the topographic sorting of retinal ganglion cell (RGC) axons in the optic tract and tectum. We find that Hermes negatively controls the translation of the guidance cue receptor Neuropilin-1 in RGCs, with Hermes knock-down resulting in aberrant growth cone cue sensitivity and axonal topographic misprojections. We characterize a novel RNA-based mechanism by which axons restrict their translatome developmentally to achieve proper targeting.This work was supported by Wellcome Trust Programme Grants (085314) (CEH), European Research Council Advanced Grant (322817) (CEH), a Wellcome Trust Investigator Award (WAH), EMBO Long Term Fellowship (JMC), BBSRC studentship (HH) and Cambridge Gates Trust Scholarship (HH)

Oxidant selection to treat an aged PAH contaminated soil by in situ chemical oxidation.

International audienceThis work is a part of the OXYSOL project aiming at the conception of a global treatment pathway including In Situ Chemical Oxidation to clean up soils of former metallurgical sites. It deals with the selection of the most adapted oxidants. Batch experiments were performed with aged contaminated soil samples of a former steel-making plant to degrade the 16 US EPA PAHs. In this research, hydrogen peroxide, modified Fenton's reaction, potassium permanganate, sodium percarbonate and sodium persulfate were compared at high and moderate doses. Hydrogen peroxide, modified Fenton's reagent, percarbonate and activated persulfate led to a maximum degradation ratio of 45%. A higher ratio (70%) was obtained with a high dose of permanganate. Except for permanganate, increasing oxidant dose did not improve degradation rates, especially with radical-based oxidative systems probably due to radical scavenging. Oxidant doses had an effect on pH that drastically increased or dropped in some cases, which was a drawback. Permanganate efficacy was mainly assigned to its persistence. In all cases, the low availability of PAHs, partly sequestrated in the aged soil, was identified as the most limiting factor for degradation performance. Oxidants were ranked according to their efficiency for PAH oxidation in soils. Efficiency was not correlated to the doses

Editorial : Observing, Modeling and Understanding Processes in Natural and Managed Peatlands

Non peer reviewe

Performing the ‘Mask:’ Kongo Astronauts (Eléonore Hellio and Michel Ekeba) on Postcolonial Entanglements

In conversation with Hanna Hölling, Emilie Magnin, and Valerian Maly, Eléonore Hellio and Michel Ekeba of the collective Kongo Astronauts discuss the origins, ongoing evolution, and potential futures of their multifaceted artistic practice. They explain the circumstances that first brought Hellio, who was born in Paris, to Kinshasa, and relate Ekeba’s first experiments with wearing an astronaut costume that he made of discarded electronics purchased at market. Conservation is figured partly in terms of the astronaut costumes, which are constantly changing through cycles of use and repair, but which also have the potential to be purchased as artworks and conserved as static museum objects. Hellio and Ekeba also discuss the films and photographs they produce, which both propagate and disseminate the live performances that take place in Kinshasa. Finally, conservation is also understood in the collaborative, social practices of Kongo Astronauts, which are taken up, reconfigured, and renewed by the various artists who pass through the collective. Ekeba and Hellio also relate the performative and ritual aspects of their work to traditional Congolese practices that were suppressed by colonial authorities

Factors associated with Autism Spectrum Disorder: a case-control study in the Lebanese population

Background: Genetic factors represent the major etiological contributor in Autism Spectrum Disorders (ASD) but several studies also support the involvement of environmental factors. This last hypothesis is reinforced by the evident increase in the prevalence of this disorder in the last decades. Thus, in our study, we aimed to identify the correlation between factors related to sociodemographic elements, to child and mother’s health and ASD in order to dress a best detailed profile of the patients. Methods: We conducted a case-control study including 64 Lebanese patients with ASD and 67 matched controls recruited from all the Lebanese districts. Our data has been analyzed by SPSS 23.0 and the statistical tests carried out were the Independent Sample t-test and the Chi-Square test. In addition, a multivariate logistic regression analysis has been carried out using variables that showed a p<0.05 in the bivariate analysis. Results: Our findings suggest that consanguinity (OR=4; 95% CI [1.3-12.04]), familial history of ASD (6.7 [1.1- 39.3]), stress during pregnancy (3.6 [1.5 8.2]) and fetal prematurity (6.3 [1.2-33.01]) were significantly associated with increased odds of ASD. However, our results have shown no association between siblings suffering from diseases such as mental retardation, child’s infections and ASD. Conclusion: This pilot study carried out in all the regions of Lebanon allowed us to shed the light on factors associated with ASD which might be preventable

Cyclic Peptides as Protein Kinase Inhibitors: Structure–Activity Relationship and Molecular Modeling

Under-expression or overexpression of protein kinases has been shown to be associated with unregulated cell signal transduction in cancer cells. Therefore, there is major interest in designing protein kinase inhibitors as anticancer agents. We have previously reported [WR]5, a peptide containing alternative arginine (R) and tryptophan (W) residues as a non-competitive c-Src tyrosine kinase inhibitor. A number of larger cyclic peptides containing alternative hydrophobic and positively charged residues [WR]x (x = 6–9) and hybrid cyclic-linear peptides, [R6K]W6 and [R5K]W7, containing R and W residues were evaluated for their protein kinase inhibitory potency. Among all the peptides, cyclic peptide [WR]9 was found to be the most potent tyrosine kinase inhibitor. [WR]9 showed higher inhibitory activity (IC50 = 0.21 μM) than [WR]5, [WR]6, [WR]7, and [WR]8 with IC50 values of 0.81, 0.57, 0.35, and 0.33 μM, respectively, against c-Src kinase as determined by a radioactive assay using [γ-33P]ATP. Consistent with the result above, [WR]9 inhibited other protein kinases such as Abl kinase activity with an IC50 value of 0.35 μM, showing 2.2-fold higher inhibition than [WR]5 (IC50 = 0.79 μM). [WR]9 also inhibited PKCa kinase activity with an IC50 value of 2.86 μM, approximately threefold higher inhibition than [WR]5 (IC50 = 8.52 μM). A similar pattern was observed against Braf, c-Src, Cdk2/cyclin A1, and Lck. [WR]9 exhibited IC50 values of 9 is consistently more potent than other cyclic peptides with a smaller ring size and hybrid cyclic-linear peptides [R6K]W6 and [R5K]W7 against selected protein kinases. Thus, the presence of R and W residues in the ring, ring size, and the number of amino acids in the structure of the cyclic peptide were found to be critical in protein kinase inhibitory potency. We identified three putative binding pockets through automated blind docking of cyclic peptides [WR](5–9). The most populated pocket is located between the SH2, SH3, and N-lobe domains on the opposite side of the ATP binding site. The second putative pocket is formed by the same domains and located on the ATP binding site side of the protein. Finally, a third pocket was identified between the SH2 and SH3 domains. These results are consistent with the non-competitive nature of the inhibition displayed by these molecules. Molecular dynamics simulations of the protein–peptide complexes indicate that the presence of either [WR]5 or [WR]9 affects the plasticity of the protein and in particular the volume of the ATP binding site pocket in different ways. These results suggest that the second pocket is most likely the site where these peptides bind and offer a plausible rationale for the increased affinity of [WR]9