Plate-forme de streaming pour les dispositifs mobiles avec adaptation dynamique

Abstract. This paper studies the domain of mobile internet with video streaming services. The internet mobile services are in a moment of expansion and look for the convergence with internet. The mobile internet services' problem is the enormous heterogeneity that exists within the mobile networks, mobile terminals and mobile internet protocols. The reason for this heterogeneity are the heavy restrictions in mobile networks, specifically the limited wide band and the high time of latency, that push developers to make solutions not compatible with internet. We propose a solution with a data base wich keeps all the capabilities of every mobile terminal. With the information from this data base and the particular environment of every user our solution makes a dynamic adaptation of the service, in order to offer the best possible service. The adaptation of the streaming flux is done with a dynamic media encoding process. This process is a great consumer of the processor capacity. From our results we conclude that it is not possible to use intensively the media dynamic encoding. Résumé Cet article traite le domaine d'Internet sur le mobile avec des services de streaming de vidéo. Les services d'Internet sur le mobile sont en pleine expansion et cherchent la convergence avec internet. La problématique des services d'Internet sur le mobile est l'énorme hétérogénéité existant au niveau des réseaux mobiles, des dispositifs mobiles et des protocoles d'Internet sur le mobile. La cause de cette hétérogénéité sont les fortes contraintes des réseaux mobiles au niveau de la bande passante et du temps de latence, qui obligent à créer des solutions non compatibles avec l'Internet. Nous proposons une solution basée sur une base des données avec les capacités de chaque dispositif. Avec les informations de ce base des données et en connaissant les caractéristiques de l'environnement particulier de chaque utilisateur nous faisons une adaptation dynamique des services, de façon à offrir le meilleur service possible. L'adaptation des flux de streaming passe par l'encodage dynamique des média qui est un processus très consommateur de puissance de processeur. Selon nôtres résultats il n'est pas possible de faire un emploi intensif de l'encodage dynamique. Resumen Este proyecto ha sido realizado durante una beca de intercambio Erasmus Mundus en la escuela francesa INSA Lyon en el departamento de informática. El proyecto ha sido llevado a cabo entre este departamento y una empresa privada, 3G-Factory, proveedor de servicios de telefonía móvil. Mi tutor en la escuela INSA Lyon ha sido Vasile-Marian Scuturici y mi tutor en la empresa ha sido Jean-François Hugot. La temática del proyecto se encuentra dentro del campo de las telecomunicaciones y servicios. Más concretamente trata sobre el empleo de la tecnología del streaming en redes de telefonía móvil. Este es un tema de actualidad ya que los primeros servicios de streaming sobre el móvil empiezan a aparecer en el mercado. Sin embrago, la gran heterogeneidad de las redes móviles de datos y de los dispositivos móviles dificultan la implantación de estos servicios para todos los usuarios. El objetivo de este proyecto es primeramente estudiar a fondo el problema, con vistas a ofrecer una posible solución para gestionar esta heterogeneidad, hasta que surja un standard ampliamente aceptado y que la convergencia entre las redes móviles e Internet sea efectiva. La metodología en la consecución de este proyecto es la siguiente: Estudio sobre las tecnologías de streaming existentes (Capítulo 2) Estudio sobre las tecnologías de Internet en el móvil (Capítulo 3) Estudio sobre el streaming en un servicio de telefonía móvil (Capítulo 4) Solución propuesta de una plataforma de streaming que se adapta dinámicamente a las condiciones de la red empleada y al terminal móvil de acceso (Capítulo 5) Validación de la solución por medio de un análisis del desempeño de la codificación dinámica de flujos de streaming (Capítulo 6) Primeramente hay que definir el streaming como una técnica que permite la reproducción de video y audio en tiempo real. Básicamente permite dos usos: el streaming a la demanda (on-demand streaming) y la difusión en directo (live streaming). Esta segunda técnica es más exigente en cuanto a tiempos de latencia. Hay tres disciplinas que entran en juego en el proceso de streaming que hay que tener en cuenta en este estudio: La compresión de datos multimedia, formatos y codecs Los servidores de streaming Los protocolos de streaming Para gestionar la problemática del streaming sobre redes móviles se adapta el uso del standard 3GPP PSS definido por la OMA (Open Mobile Alliance) en cuanto a compresión de datos y protocolos se refier

Spectrum of mutational signatures in T-cell lymphoma reveals a key role for UV radiation in cutaneous T-cell lymphoma

Funder: Galderma; doi: http://dx.doi.org/10.13039/501100009754Funder: NIHR-BRC Cambridge core grantFunder: National Institute for Health Research; doi: http://dx.doi.org/10.13039/501100000272Funder: NHS EnglandAbstract: T-cell non-Hodgkin’s lymphomas develop following transformation of tissue resident T-cells. We performed a meta-analysis of whole exome sequencing data from 403 patients with eight subtypes of T-cell non-Hodgkin’s lymphoma to identify mutational signatures and associated recurrent gene mutations. Signature 1, indicative of age-related deamination, was prevalent across all T-cell lymphomas, reflecting the derivation of these malignancies from memory T-cells. Adult T-cell leukemia-lymphoma was specifically associated with signature 17, which was found to correlate with the IRF4 K59R mutation that is exclusive to Adult T-cell leukemia-lymphoma. Signature 7, implicating UV exposure was uniquely identified in cutaneous T-cell lymphoma (CTCL), contributing 52% of the mutational burden in mycosis fungoides and 23% in Sezary syndrome. Importantly this UV signature was observed in CD4 + T-cells isolated from the blood of Sezary syndrome patients suggesting extensive re-circulation of these T-cells through skin and blood. Analysis of non-Hodgkin’s T-cell lymphoma cases submitted to the national 100,000 WGS project confirmed that signature 7 was only identified in CTCL strongly implicating UV radiation in the pathogenesis of cutaneous T-cell lymphoma

Multivariate methods for the integrative analysis of multi-omics datasets : TCGAome

The objectives of this project are: evaluate the existing state of the art on a selected public dataset, analyze alternatives to include prior biological knowledge in the analysis and explore different visualization approaches to integrative analysis results.Los objetivos de este proyecto son: evaluar el estado de la técnica existente en una selección de datos públicos, analizar alternativas para incluir el conocimiento biológico previo en el análisis y explorar diferentes enfoques de visualización de los resultados del análisis de integración.Els objectius d'aquest projecte són: avaluar l'estat de la tècnica existent en una selecció de dades públiques, analitzar alternatives per incloure el coneixement biològic previ a l'anàlisi i explorar diferents enfocaments de visualització dels resultats de l'anàlisi d'integració

Multivariate methods for the integrative analysis of multi-omics datasets : TCGAome

The objectives of this project are: evaluate the existing state of the art on a selected public dataset, analyze alternatives to include prior biological knowledge in the analysis and explore different visualization approaches to integrative analysis results.Los objetivos de este proyecto son: evaluar el estado de la técnica existente en una selección de datos públicos, analizar alternativas para incluir el conocimiento biológico previo en el análisis y explorar diferentes enfoques de visualización de los resultados del análisis de integración.Els objectius d'aquest projecte són: avaluar l'estat de la tècnica existent en una selecció de dades públiques, analitzar alternatives per incloure el coneixement biològic previ a l'anàlisi i explorar diferents enfocaments de visualització dels resultats de l'anàlisi d'integració

TRON-Bioinformatics/covigator: v2.2.2

What's Changed ENA 2023 api update by @johausmann in https://github.com/TRON-Bioinformatics/covigator/pull/128 Updated accessor module filters in order to support other viruses Dashboard improvements by @johausmann in https://github.com/TRON-Bioinformatics/covigator/pull/129 v2.2.2 release by @johausmann in https://github.com/TRON-Bioinformatics/covigator/pull/132 Full Changelog: https://github.com/TRON-Bioinformatics/covigator/compare/v2.2.1...v2.2.

TRON-Bioinformatics/covigator-ngs-pipeline: v0.18.1

<h2>What's Changed</h2> <ul> <li>Restored conda compatibility with newer nextflow versions by @johausmann in https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/pull/53</li> <li>Implemented a pipeline mode to perform only the steps for lineage determination or genome generation @johausmann in https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/pull/54</li> <li>Added mamba support and update pangolin lineage determination by @johausmann in https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/pull/61</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/TRON-Bioinformatics/covigator-ngs-pipeline/compare/v0.18.0...v0.18.1</p&gt

Genomic Variability among Field Isolates and Laboratory-Adapted Strains of Leptospira borgpetersenii

Leptospira borgpetersenii serovar Hardjo colonizes cattle kidneys and may occasionally infect humans and other mammals. Strains belonging to two clonal subtypes (types A and B) with marked differences in their pathogenicity in the hamster experimental model have been described for this serovar. Such differences have been attributed to point mutations in individual genes, although those genes have not yet been characterized. In order to better understand genetic variability among L. borgpetersenii serovar Hardjo isolates, we sequenced and compared the genomes of two laboratory-adapted strains and three abattoir-derived field isolates of L. borgpetersenii serovar Hardjo. Relatively low genetic variability was observed within isolates of the same subtype, with most of the mutations of moderate or high impact found in the laboratory-adapted isolates. In contrast, several differences regarding gene content and genetic variants were observed between the two subtypes. Putative type-specific genes appear to encode proteins associated with functions that are critical for infection. Some of these genes seem to be involved in transcriptional regulation, possibly leading to a distinct regulatory pattern in each type. These results show that changes in regulatory mechanisms, previously suggested to be critical during Leptospira speciation, may occur in L. borgpetersenii. In addition, the bioinformatics methodology used in this study for variant calling can be useful to other groups working with nonmodel prokaryotic organisms such as Leptospira species

CoVigator—A Knowledge Base for Navigating SARS-CoV-2 Genomic Variants

Background: The outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulted in the global COVID-19 pandemic. The urgency for an effective SARS-CoV-2 vaccine has led to the development of the first series of vaccines at unprecedented speed. The discovery of SARS-CoV-2 spike-glycoprotein mutants, however, and consequentially the potential to escape vaccine-induced protection and increased infectivity, demonstrates the persisting importance of monitoring SARS-CoV-2 mutations to enable early detection and tracking of genomic variants of concern. Results: We developed the CoVigator tool with three components: (1) a knowledge base that collects new SARS-CoV-2 genomic data, processes it and stores its results; (2) a comprehensive variant calling pipeline; (3) an interactive dashboard highlighting the most relevant findings. The knowledge base routinely downloads and processes virus genome assemblies or raw sequencing data from the COVID-19 Data Portal (C19DP) and the European Nucleotide Archive (ENA), respectively. The results of variant calling are visualized through the dashboard in the form of tables and customizable graphs, making it a versatile tool for tracking SARS-CoV-2 variants. We put a special emphasis on the identification of intrahost mutations and make available to the community what is, to the best of our knowledge, the largest dataset on SARS-CoV-2 intrahost mutations. In the spirit of open data, all CoVigator results are available for download. The CoVigator dashboard is accessible via covigator.tron-mainz.de. Conclusions: With increasing demand worldwide in genome surveillance for tracking the spread of SARS-CoV-2, CoVigator will be a valuable resource of an up-to-date list of mutations, which can be incorporated into global efforts

Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study

Background: repeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who have atypical clinical presentations, especially in paediatric patients without a previous positive family history. Whole genome sequencing is increasingly used as a first-line test for other rare genetic disorders, and we aimed to assess its performance in the diagnosis of patients with neurological repeat expansion disorders. Methods: we retrospectively assessed the diagnostic accuracy of whole genome sequencing to detect the most common repeat expansion loci associated with neurological outcomes (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) using samples obtained within the National Health Service in England from patients who were suspected of having neurological disorders; previous PCR test results were used as the reference standard. The clinical accuracy of whole genome sequencing to detect repeat expansions was prospectively examined in previously genetically tested and undiagnosed patients recruited in 2013–17 to the 100 000 Genomes Project in the UK, who were suspected of having a genetic neurological disorder (familial or early-onset forms of ataxia, neuropathy, spastic paraplegia, dementia, motor neuron disease, parkinsonian movement disorders, intellectual disability, or neuromuscular disorders). If a repeat expansion call was made using whole genome sequencing, PCR was used to confirm the result. Findings: the diagnostic accuracy of whole genome sequencing to detect repeat expansions was evaluated against 793 PCR tests previously performed within the NHS from 404 patients. Whole genome sequencing correctly classified 215 of 221 expanded alleles and 1316 of 1321 non-expanded alleles, showing 97·3% sensitivity (95% CI 94·2–99·0) and 99·6% specificity (99·1–99·9) across the 13 disease-associated loci when compared with PCR test results. In samples from 11 631 patients in the 100 000 Genomes Project, whole genome sequencing identified 81 repeat expansions, which were also tested by PCR: 68 were confirmed as repeat expansions in the full pathogenic range, 11 were non-pathogenic intermediate expansions or premutations, and two were non-expanded repeats (16% false discovery rate). Interpretation: In our study, whole genome sequencing for the detection of repeat expansions showed high sensitivity and specificity, and it led to identification of neurological repeat expansion disorders in previously undiagnosed patients. These findings support implementation of whole genome sequencing in clinical laboratories for diagnosis of patients who have a neurological presentation consistent with a repeat expansion disorder. Funding: Medical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, and Illumina.</p