An architecture for adaptive replication-based multimedia streaming in P2P networks

This PhD thesis addresses the issue of scalable media streaming in large-scale networking environments. Multimedia streaming is one of the largest sink of network resources and this trend is still growing as testified by the success of services like Skype, Netflix, Spotify and Popcorn Time (BitTorrent-based). In traditional client-server solutions, when the number of consumers increases, the server becomes the bottleneck. To overcome this problem, the Content-Delivery Network (CDN) model was invented. In CDN model, the server copies the media content to some CDN servers, which are located in different strategic locations on the network. However, they require heavy infrastructure investment around the world, which is too expensive. Peer-to-peer (P2P) solutions are another way to achieve the same result. These solutions are naturally scalable, since each peer can act as both a receiver and a forwarder. Most of the proposed streaming solutions in P2P networks focus on routing scenarios to achieve scalability. However, these solutions cannot work properly in video-on-demand (VoD) streaming, when resources of the media server are not sufficient. Replication is a solution that can be used in these situations. This thesis specifically provides a family of replication-based media streaming protocols, which are scalable, efficient and reliable in P2P networks. First, it provides SCALESTREAM, a replication-based streaming protocol that adaptively replicates media content in different peers to increase the number of consumers that can be served in parallel. The adaptiveness aspect of this solution relies on the fact that it takes into account different constraints like bandwidth capacity of peers to decide when to add or remove replicas. SCALESTREAM routes media blocks to consumers over a tree topology, assuming a reliable network composed of homogenous peers in terms of bandwidth. Second, this thesis proposes RESTREAM, an extended version of SCALESTREAM that addresses the issues raised by unreliable networks composed of heterogeneous peers. Third, this thesis proposes EAGLEMACAW, a multiple-tree replication streaming protocol in which two distinct trees, named EAGLETREE and MACAWTREE, are built in a decentralized manner on top of an underlying mesh network. These two trees collaborate to serve consumers in an efficient and reliable manner. The EAGLETREE is in charge of improving efficiency, while the MACAWTREE guarantees reliability. Finally, this thesis provides TURBOSTREAM, a hybrid replication-based streaming protocol in which a tree overlay is built on top of a mesh overlay network. Both these overlays cover all peers of the system and collaborate to improve efficiency and low-latency in streaming media to consumers. This protocol is implemented and tested in a real networking environment using PlanetLab Europe testbed composed of peers distributed in different places in Europe.

Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 Are Identified in Individuals with Congenital Hypogonadotropic Hypogonadism.

Congenital hypogonadotropic hypogonadism (CHH) and its anosmia-associated form (Kallmann syndrome [KS]) are genetically heterogeneous. Among the >15 genes implicated in these conditions, mutations in FGF8 and FGFR1 account for ∼12% of cases; notably, KAL1 and HS6ST1 are also involved in FGFR1 signaling and can be mutated in CHH. We therefore hypothesized that mutations in genes encoding a broader range of modulators of the FGFR1 pathway might contribute to the genetics of CHH as causal or modifier mutations. Thus, we aimed to (1) investigate whether CHH individuals harbor mutations in members of the so-called "FGF8 synexpression" group and (2) validate the ability of a bioinformatics algorithm on the basis of protein-protein interactome data (interactome-based affiliation scoring [IBAS]) to identify high-quality candidate genes. On the basis of sequence homology, expression, and structural and functional data, seven genes were selected and sequenced in 386 unrelated CHH individuals and 155 controls. Except for FGF18 and SPRY2, all other genes were found to be mutated in CHH individuals: FGF17 (n = 3 individuals), IL17RD (n = 8), DUSP6 (n = 5), SPRY4 (n = 14), and FLRT3 (n = 3). Independently, IBAS predicted FGF17 and IL17RD as the two top candidates in the entire proteome on the basis of a statistical test of their protein-protein interaction patterns to proteins known to be altered in CHH. Most of the FGF17 and IL17RD mutations altered protein function in vitro. IL17RD mutations were found only in KS individuals and were strongly linked to hearing loss (6/8 individuals). Mutations in genes encoding components of the FGF pathway are associated with complex modes of CHH inheritance and act primarily as contributors to an oligogenic genetic architecture underlying CHH.

Hidden branches: developments in root system architecture.

The root system is fundamentally important for plant growth and survival because of its role in water and nutrient uptake. Therefore, plants rely on modulation of root system architecture (RSA) to respond to a changing soil environment. Although RSA is a highly plastic trait and varies both between and among species, the basic root system morphology and its plasticity are controlled by inherent genetic factors. These mediate the modification of RSA, mostly at the level of root branching, in response to a suite of biotic and abiotic factors. Recent progress in the understanding of the molecular basis of these responses suggests that they largely feed through hormone homeostasis and signaling pathways. Novel factors implicated in the regulation of RSA in response to the myriad endogenous and exogenous signals are also increasingly isolated through alternative approaches such as quantitative trait locus analysis.

The functional neuroimaging correlates of psychogenic versus organic dystonia.

The neurobiological basis of psychogenic movement disorders remains poorly understood and the management of these conditions difficult. Functional neuroimaging studies have provided some insight into the pathophysiology of disorders implicating particularly the prefrontal cortex, but there are no studies on psychogenic dystonia, and comparisons with findings in organic counterparts are rare. To understand the pathophysiology of these disorders better, we compared the similarities and differences in functional neuroimaging of patients with psychogenic dystonia and genetically determined dystonia, and tested hypotheses on the role of the prefrontal cortex in functional neurological disorders. Patients with psychogenic (n = 6) or organic (n = 5, DYT1 gene mutation positive) dystonia of the right leg, and matched healthy control subjects (n = 6) underwent positron emission tomography of regional cerebral blood flow. Participants were studied during rest, during fixed posturing of the right leg and during paced ankle movements. Continuous surface electromyography and footplate manometry monitored task performance. Averaging regional cerebral blood flow across all tasks, the organic dystonia group showed abnormal increases in the primary motor cortex and thalamus compared with controls, with decreases in the cerebellum. In contrast, the psychogenic dystonia group showed the opposite pattern, with abnormally increased blood flow in the cerebellum and basal ganglia, with decreases in the primary motor cortex. Comparing organic dystonia with psychogenic dystonia revealed significantly greater regional blood flow in the primary motor cortex, whereas psychogenic dystonia was associated with significantly greater blood flow in the cerebellum and basal ganglia (all P < 0.05, family-wise whole-brain corrected). Group × task interactions were also examined. During movement, compared with rest, there was abnormal activation in the right dorsolateral prefrontal cortex that was common to both organic and psychogenic dystonia groups (compared with control subjects, P < 0.05, family-wise small-volume correction). These data show a cortical-subcortical differentiation between organic and psychogenic dystonia in terms of regional blood flow, both at rest and during active motor tasks. The pathological prefrontal cortical activation was confirmed in, but was not specific to, psychogenic dystonia. This suggests that psychogenic and organic dystonia have different cortical and subcortical pathophysiology, while a derangement in mechanisms of motor attention may be a feature of both conditions.

Performance evaluation of MPEG-4 Video encoder on Adres

Actualment un típic embedded system (ex. telèfon mòbil) requereix alta qualitat per portar a terme tasques com codificar/descodificar a temps real; han de consumir poc energia per funcionar hores o dies utilitzant bateries lleugeres; han de ser el suficientment flexibles per integrar múltiples aplicacions i estàndards en un sol aparell; han de ser dissenyats i verificats en un període de temps curt tot i l’augment de la complexitat. Els dissenyadors lluiten contra aquestes adversitats, que demanen noves innovacions en arquitectures i metodologies de disseny. Coarse-grained reconfigurable architectures (CGRAs) estan emergent com a candidats potencials per superar totes aquestes dificultats. Diferents tipus d’arquitectures han estat presentades en els últims anys. L’alta granularitat redueix molt el retard, l’àrea, el consum i el temps de configuració comparant amb les FPGAs. D’altra banda, en comparació amb els tradicionals processadors coarse-grained programables, els alts recursos computacionals els permet d’assolir un alt nivell de paral•lelisme i eficiència. No obstant, els CGRAs existents no estant sent aplicats principalment per les grans dificultats en la programació per arquitectures complexes. ADRES és una nova CGRA dissenyada per I’Interuniversity Micro-Electronics Center (IMEC). Combina un processador very-long instruction word (VLIW) i un coarse-grained array per tenir dues opcions diferents en un mateix dispositiu físic. Entre els seus avantatges destaquen l’alta qualitat, poca redundància en les comunicacions i la facilitat de programació. Finalment ADRES és un patró enlloc d’una arquitectura concreta. Amb l’ajuda del compilador DRESC (Dynamically Reconfigurable Embedded System Compile), és possible trobar millors arquitectures o arquitectures específiques segons l’aplicació. Aquest treball presenta la implementació d’un codificador MPEG-4 per l’ADRES. Mostra l’evolució del codi per obtenir una bona implementació per una arquitectura donada. També es presenten les característiques principals d’ADRES i el seu compilador (DRESC). Els objectius són de reduir al màxim el nombre de cicles (temps) per implementar el codificador de MPEG-4 i veure les diferents dificultats de treballar en l’entorn ADRES. Els resultats mostren que els cícles es redueixen en un 67% comparant el codi inicial i final en el mode VLIW i un 84% comparant el codi inicial en VLIW i el final en mode CGA.

Novel role of a family of major facilitator transporters in biofilm development and virulence of Candida albicans.

The QDR (quinidine drug resistance) family of genes encodes transporters belonging to the MFS (major facilitator superfamily) of proteins. We show that QDR transporters, which are localized to the plasma membrane, do not play a role in drug transport. Hence, null mutants of QDR1, QDR2 and QDR3 display no alterations in susceptibility to azoles, polyenes, echinocandins, polyamines or quinolines, or to cell wall inhibitors and many other stresses. However, the deletion of QDR genes, individually or collectively, led to defects in biofilm architecture and thickness. Interestingly, QDR-lacking strains also displayed attenuated virulence, but the strongest effect was observed with qdr2∆, qdr3∆ and in qdr1/2/3∆ strains. Notably, the attenuated virulence and biofilm defects could be reversed upon reintegration of QDR genes. Transcripts profiling confirmed differential expression of many biofilm and virulence-related genes in the deletion strains as compared with wild-type Candida albicans cells. Furthermore, lipidomic analysis of QDR-deletion mutants suggests massive remodelling of lipids, which may affect cell signalling, leading to the defect in biofilm development and attenuation of virulence. In summary, the results of the present study show that QDR paralogues encoding MFS antiporters do not display conserved functional linkage as drug transporters and perform functions that significantly affect the virulence of C. albicans.

Attenuated asymmetry of functional connectivity in schizophrenia: a high-resolution EEG study.

The interhemispheric asymmetries that originate from connectivity-related structuring of the cortex are compromised in schizophrenia (SZ). Under the assumption that such abnormalities affect functional connectivity, we analyzed its correlate-EEG synchronization-in SZ patients and matched controls. We applied multivariate synchronization measures based on Laplacian EEG and tuned to various spatial scales. Compared to the controls who had rightward asymmetry at a local level (EEG power), rightward anterior and leftward posterior asymmetries at an intraregional level (1st and 2nd order S-estimator), and rightward global asymmetry (hemispheric S-estimator), SZ patients showed generally attenuated asymmetry, the effect being strongest for intraregional synchronization in the alpha and beta bands. The abnormalities of asymmetry increased with the duration of the disease and correlated with the negative symptoms. We discuss the tentative links between these findings and gross anatomical asymmetries, including the cerebral torque and gyrification pattern, in normal subjects and SZ patients.

Imagerie cardiaque non invasive: apport spécifique en clinique des nouvelles modalités (II). Evaluation fonctionnelle [Cardiac imaging: specific clinical role of newly developed non invasive techniques. Part II: functional evaluation].

The non-invasive evaluation of myocardial ischemia is a priority in cardiology. The preferred initial non-invasive test is exercise ECG, because of its high accessibility and its low cost. Stress radionuclide myocardial perfusion imaging or stress echocardiography are now routinely performed, and new non-invasive techniques such as perfusion-MRI, dobutamine stress-MRI or 82rubidium perfusion PET have recently gained acceptance in clinical practice. In the same time, an increasing attention has been accorded to the concept of myocardial viability in the decisional processes in case of ischemic heart failure. In this indication, MRI with late enhancement after intravenous injection of gadolinium and 18F-FDG PET showed an excellent diagnostic accuracy. This article will present these new imaging modalities and their accepted indications.

Identification of novel functional TBP-binding sites and general factor repertoires.

Our current knowledge of the general factor requirement in transcription by the three mammalian RNA polymerases is based on a small number of model promoters. Here, we present a comprehensive chromatin immunoprecipitation (ChIP)-on-chip analysis for 28 transcription factors on a large set of known and novel TATA-binding protein (TBP)-binding sites experimentally identified via ChIP cloning. A large fraction of identified TBP-binding sites is located in introns or lacks a gene/mRNA annotation and is found to direct transcription. Integrated analysis of the ChIP-on-chip data and functional studies revealed that TAF12 hitherto regarded as RNA polymerase II (RNAP II)-specific was found to be also involved in RNAP I transcription. Distinct profiles for general transcription factors and TAF-containing complexes were uncovered for RNAP II promoters located in CpG and non-CpG islands suggesting distinct transcription initiation pathways. Our study broadens the spectrum of general transcription factor function and uncovers a plethora of novel, functional TBP-binding sites in the human genome.

Functional diversity of CD8+ T-cell subsets in chronic infection

Certains pathogènes tels que le virus de l'hépatite C ainsi que le virus de l'immunodéficience humaine sont capables de détourner les mécanismes de défense du système immunitaire adaptatif afin d'établir des infections chroniques chez l'homme. La souche clone-13 du virus de la chorioméningite lymphocytaire est utilisée comme modèle d'études d'infection virale chronique chez la souris. Les raisons qui expliqueraient la persistance de certains virus ne sont pas encore bien définies. Toutefois, il a été montré qu'une exposition prolongée à un environnement inflammatoire ainsi que la présence prolongée de l'antigène sont des facteurs qui vont déclencher un procédé de différentiation particulier des lymphocytes T CD8+. Ces cellules sur-expriment alors des récepteurs inhibiteurs tels que PD-1 tandis que leur capacité à produire des cytokines diminue. Ce procédé de différentiation est appelé « exhaustion » et serait à l'origine de la génération de réponses lymphocytaires non ou peu fonctionnelles entraînant de ce fait la persistance de l'infection. Néanmoins, il a également été démontré que ces lymphocytes maintiennent des fonctions effectrices et qu'ils permettent de limiter la réplication du virus. Afin d'étudier la fonction effectrice résiduelle de ces lymphocytes T, nous avons transféré des cellules provenant de souris infectées chroniquement dans des souris receveuses naïves qui ont à leur tour été infectées avec le virus. Grâce à ces expériences, nous avons démontré que les cellules transférées contiennent des cellules qui sont capables de i) re-proliférer, ii) de protéger les souris contre une infection virale, et de iii) survivre en l'absence d'antigène. Nous avons remarqué que les cellules stimulées de façon chronique maintiennent le même phénotype lorsqu'elles sont transférées dans des souris naïves soumises à une infection virale aiguë. Nous avons de ce fait conclu que les cellules stimulées chroniquement contiennent une sous-population de cellules qui comporte des attributs de cellules T mémoire. D'autre part, nous avons pu identifier le facteur de transcription Tcf-1 comme l'élément essential pour la génération des cellules T ressemblant à des cellules mémoires. D'autre part, nous avons étudié l'impact du niveau de stimulation via le récepteur des cellules T (TCR) sur le phénotype adopté par les lymphocytes T au cours d'une infection chronique. Dans ce but, nous avons généré des souches de virus recombinants qui expriment un épitope modifié de manière à réduire le niveau de stimulation via le TCR. D'autre part, nous avons utilisé un mélange de deux souches virales de manière à moduler spécifiquement la quantité d'un épitope tout en conservant la même charge virale. Nous avons montré que la quantité d'antigène avait plus d'influence sur le phénotype des lymphocytes T que la force d'interaction entre le complexe peptide-CMH et le TCR. De plus, l'apparition de ce phénotype ne semble pas avoir d'impact sur la prolifération des cellules en réponse à une infection primaire ou secondaire. Ainsi, nous proposons un modèle par lequel le procédé d'« exhaustion » des cellules T correspond à une différentiation cellulaire particulière qui est indépendante de la capacité de prolifération des cellules. De manière générale, ces découvertes apportent de nouvelles connaissances sur les sous-catégories de lymphocytes T CD8+ qui sont générés pendant une infection virale chronique. Nous pensons que la réponse effectrice du système immunitaire est maintenue pendant de longues périodes grâce à la présence de cellules par partagent certaines caractéristiques avec des cellules mémoires. L'étude approfondie de ces cellules peut avoir des implications importantes sur l'optimisation des stratégies utilisant l'immunothérapie pour combattre les infections chroniques et cancers.

Shedding light on proteolytic cleavage of CD44: the responsible sheddase and functional significance of shedding.

CD44 is the major cell-surface receptor for hyaluronan, which is implicated in cell-cell and cell-matrix adhesion, cell migration, and signaling. Studies have shown that CD44-dependent migration requires CD44 to be shed from the cell surface and that matrix metalloproteinase-mediated cleavage may provide an underlying mechanism. However, the full spectrum of proteases that may participate in CD44 shedding has yet to be defined. In this issue, Anderegg et al. demonstrate that ADAM10, but not ADAM17 or MMP14, mediates constitutive shedding of CD44 in human melanoma cells and that knockdown of ADAM10 blocks the antiproliferative activity of the soluble proteolytic cleavage product of CD44.

Combined functional and viability cardiac MR imaging in a single breathhold

The combination of cardiac viability and functional information enhances the identification of different heart tissues in the setting of ischemic heart disease. A method has recently been proposed for obtaining black-blood delayed-enhancement (DE) viability images using the stimulated-echo acquisition mode (STEAM) MRI pulse sequence in a single short breathhold. The method was validated against conventional inversion-recovery (IR) DE images for identifying regions of myocardial infarction (MI). The method was based on the acquisition of three consecutive images of the same anatomical slice. One image has T(1)-weighted contrast in which infarction appears bright. The two other images are used to construct an anatomical image of the heart, which is combined with the first image to produce a black-blood viability image. However, using appropriate modulation and demodulation frequencies, the latter two images bear useful information about myocardial deformation that results in a cardiac strain-encoding (SENC) functional image. In this work, a method is proposed for obtaining three consecutive SENC images in a single acquisition that can be combined to produce a composite image of the heart, which shows both functional and viability information. The proposed technique reduces scan time by one-half, compared with separate acquisitions of functional and viability images, and alleviates misregistration problems caused by separate breathholds.