Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale

Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plantassociated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8–35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature

Variation in Structure and Process of Care in Traumatic Brain Injury: Provider Profiles of European Neurotrauma Centers Participating in the CENTER-TBI Study.

INTRODUCTION: The strength of evidence underpinning care and treatment recommendations in traumatic brain injury (TBI) is low. Comparative effectiveness research (CER) has been proposed as a framework to provide evidence for optimal care for TBI patients. The first step in CER is to map the existing variation. The aim of current study is to quantify variation in general structural and process characteristics among centers participating in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. METHODS: We designed a set of 11 provider profiling questionnaires with 321 questions about various aspects of TBI care, chosen based on literature and expert opinion. After pilot testing, questionnaires were disseminated to 71 centers from 20 countries participating in the CENTER-TBI study. Reliability of questionnaires was estimated by calculating a concordance rate among 5% duplicate questions. RESULTS: All 71 centers completed the questionnaires. Median concordance rate among duplicate questions was 0.85. The majority of centers were academic hospitals (n = 65, 92%), designated as a level I trauma center (n = 48, 68%) and situated in an urban location (n = 70, 99%). The availability of facilities for neuro-trauma care varied across centers; e.g. 40 (57%) had a dedicated neuro-intensive care unit (ICU), 36 (51%) had an in-hospital rehabilitation unit and the organization of the ICU was closed in 64% (n = 45) of the centers. In addition, we found wide variation in processes of care, such as the ICU admission policy and intracranial pressure monitoring policy among centers. CONCLUSION: Even among high-volume, specialized neurotrauma centers there is substantial variation in structures and processes of TBI care. This variation provides an opportunity to study effectiveness of specific aspects of TBI care and to identify best practices with CER approaches

Variation in general supportive and preventive intensive care management of traumatic brain injury: a survey in 66 neurotrauma centers participating in the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study

Abstract Background General supportive and preventive measures in the intensive care management of traumatic brain injury (TBI) aim to prevent or limit secondary brain injury and optimize recovery. The aim of this survey was to assess and quantify variation in perceptions on intensive care unit (ICU) management of patients with TBI in European neurotrauma centers. Methods We performed a survey as part of the Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. We analyzed 23 questions focused on: 1) circulatory and respiratory management; 2) fever control; 3) use of corticosteroids; 4) nutrition and glucose management; and 5) seizure prophylaxis and treatment. Results The survey was completed predominantly by intensivists (n = 33, 50%) and neurosurgeons (n = 23, 35%) from 66 centers (97% response rate). The most common cerebral perfusion pressure (CPP) target was > 60 mmHg (n = 39, 60%) and/or an individualized target (n = 25, 38%). To support CPP, crystalloid fluid loading (n = 60, 91%) was generally preferred over albumin (n = 15, 23%), and vasopressors (n = 63, 96%) over inotropes (n = 29, 44%). The most commonly reported target of partial pressure of carbon dioxide in arterial blood (PaCO2) was 36–40 mmHg (4.8–5.3 kPa) in case of controlled intracranial pressure (ICP) < 20 mmHg (n = 45, 69%) and PaCO2 target of 30–35 mmHg (4–4.7 kPa) in case of raised ICP (n = 40, 62%). Almost all respondents indicated to generally treat fever (n = 65, 98%) with paracetamol (n = 61, 92%) and/or external cooling (n = 49, 74%). Conventional glucose management (n = 43, 66%) was preferred over tight glycemic control (n = 18, 28%). More than half of the respondents indicated to aim for full caloric replacement within 7 days (n = 43, 66%) using enteral nutrition (n = 60, 92%). Indications for and duration of seizure prophylaxis varied, and levetiracetam was mostly reported as the agent of choice for both seizure prophylaxis (n = 32, 49%) and treatment (n = 40, 61%). Conclusions Practice preferences vary substantially regarding general supportive and preventive measures in TBI patients at ICUs of European neurotrauma centers. These results provide an opportunity for future comparative effectiveness research, since a more evidence-based uniformity in good practices in general ICU management could have a major impact on TBI outcome

Variation in neurosurgical management of traumatic brain injury

Background: Neurosurgical management of traumatic brain injury (TBI) is challenging, with only low-quality evidence. We aimed to explore differences in neurosurgical strategies for TBI across Europe. Methods: A survey was sent to 68 centers participating in the Collaborative European Neurotrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study. The questionnaire contained 21 questions, including the decision when to operate (or not) on traumatic acute subdural hematoma (ASDH) and intracerebral hematoma (ICH), and when to perform a decompressive craniectomy (DC) in raised intracranial pressure (ICP). Results: The survey was completed by 68 centers (100%). On average, 10 neurosurgeons work in each trauma center. In all centers, a neurosurgeon was available within 30 min. Forty percent of responders reported a thickness or volume threshold for evacuation of an ASDH. Most responders (78%) decide on a primary DC in evacuating an ASDH during the operation, when swelling is present. For ICH, 3% would perform an evacuation directly to prevent secondary deterioration and 66% only in case of clinical deterioration. Most respondents (91%) reported to consider a DC for refractory high ICP. The reported cut-off ICP for DC in refractory high ICP, however, differed: 60% uses 25 mmHg, 18% 30 mmHg, and 17% 20 mmHg. Treatment strategies varied substantially between regions, specifically for the threshold for ASDH surgery and DC for refractory raised ICP. Also within center variation was present: 31% reported variation within the hospital for inserting an ICP monitor and 43% for evacuating mass lesions. Conclusion: Despite a homogeneous organization, considerable practice variation exists of neurosurgical strategies for TBI in Europe. These results provide an incentive for comparative effectiveness research to determine elements of effective neurosurgical care

Composants d'optique intégrée à coeur de Ta2O5. Application à la séparation et à la rotation d'états de polarisation

Un nouveau procédé de fabrication de guides d'ondes tridimensionnels a été développé en associant la technologie de dépôt de Tâ205 par "Dual Ion Beam Sputtering" DIBS et le procédé sol-gel pour réaliser des matériaux bas indice. Le facteur de forme spécifique des guides d'ondes monomodes réalisés induit une forte sensibilité à l'état de polarisation. Les performances en transmission, le confinement des modes guidés et la densité d'intégration sont alors fonction de l'état de polarisation de la lumière. A partir de ces observations, nous avons étudié un séparateur et un rotateur d'état de polarisation en optique intégrée. L'intégration simultanée de ces deux fonctions permettra la réalisation de composants insensibles à l'état de polarisation. Ces deux fonctions passives ont été optimisées numériquement, fabriquées et testées expérimentalement au laboratoire. Le fonctionnement de ces deux composants est basé sur le couplage de modes en optique guidée. Le taux d'extinction expérimental en sortie des voies du séparateur d'états de polarisation est de -17dB en TE et -10dB en TM pour [lambda] = 1,568 [micro]m. Le taux d'extinction à la polarisation expérimental obtenu pour le rotateur d'état de polarisation est de -16dB (90% d'efficacité de conversion) à [lambda] = 1,558 [micro]m. Cependant les pertes d'insertion de ces composants (-10dB) devront être diminuées pour des applications en télécommunication.AIX-MARSEILLE3-BU Sc.St Jérô (130552102) / SudocSudocFranceF

Conception et élaboration d'un capteur optique à ondes guidées pour la détection d'espèces chimiques

Le travail de thèse a consisté à élaborer un nouveau type de capteur utilisant la technique des "m-lines" pour détecter la variation d'indice de matériaux sensibles aux gaz déposés en couches minces. En effet, la variation de conductivité d'un matériau sensible utilisé dans les capteurs à oxyde métallique s'accompagne d'une modification de son indice de réfraction lorsqu'il est exposé à un gaz. La littérature a permis d'identifier certains matériaux susceptibles d'être sensibles au butane, au propane et à l'ozone. Ces matériaux ont été déposés et caractérisés afin d'optimiser leurs propriétés optiques, morphologiques et leur sensibilité au gaz. Un banc de test a été réalisé pour la mesure de la sensibilité aux gaz en fonction de la concentration de gaz et de la température (jusqu'à 100C). Un démonstrateur de principe de capteur a été développé à l'aide d'un réseau coupleur. La détection optique du butane et du propane, dans la gamme 100 à 1000 ppm a été validée.AIX-MARSEILLE3-BU Sc.St Jérô (130552102) / SudocSudocFranceF

Modélisation et caractérisation de composants d'optique intégrée réalisés par implantation d'ions titane

Nous étudions, en collaboration avec la société SILIOS Technologies, le potentiel de l implantation d ions titane pour réaliser des composants d optique intégrée. L indice de réfraction de la silice étant ainsi accru, nous développons des guides d ondes d atténuation variant de 0,1 à 0,6 dB/cm, en fonction de la dose implantée et après optimisation du recuit. Leurs indices effectifs augmentent avec la dose. A faible dose, le couplage fibre optique guide atteint 90%. A forte dose, des guides courbes de rayon aussi faible que 500 m transmettent 90% de l énergie. Nos mesures confirment les modélisations. Un adaptateur de mode original assure la transition entre guides à faible et fort confinement. Trois solutions originales peuvent corriger la sensibilité à la polarisation de ces guides : l implantation latérale, l anisotropie artificielle du cœur ou la rotation de l état polarisation. Enfin des filtres spectraux en amplitude et en phase sont synthétisés en guides plans segmentés.AIX-MARSEILLE3-BU Sc.St Jérô (130552102) / SudocSudocFranceF

Optical properties of nanostructured materials: a review

International audienceDepending on the size of the smallest feature, the interaction of light with structured materials can be very different. This fundamental problem is treated by different theories. If first order theories are sufficient to describe the scattering from low roughness surfaces, second order or even higher order theories must be used for high roughness surfaces. Random surface structures can then be designed to distribute the light in different propagation directions. For complex structures such as black silicon, which reflects very little light, the theory needs further development. When the material is periodically structured, we speak about photonic crystals or metamaterials. Different theoretical approaches have been developed and experimental techniques are rapidly progressing. However, some work still remains to understand the full potential of this field. When the material is structured in dimension much smaller than the wavelength, the notion of complex refractive index must be revisited. Plasmon resonance can be excited by a progressing wave on metallic nanoparticles inducing a shaping of the absorption band and of the dispersion of the extinction coefficient. This addresses the problem of the permittivity of such metallic nanoparticles. The coupling between several metallic nanoparticles induces a field enhancement in the surrounding media, which can increase phenomena like scattering, absorption, luminescence, or Raman scattering. For semiconductor nanoparticles, electron confinement also induces a modulated absorption spectra. The refractive index is then modified.The bandgap of the material is changed because of the discretization of the electron energy,which can be controlled by the nanometers size particles. Such quantum dots behave like atoms and become luminescent. The lifetime of the electron in the excited states are much larger than in continuous energy bands. Electrons in coupled quantum dots behave as they do in molecules

Mesure de propriétés thermiques de matériaux diélectriques en couches minces par optique guidée

Nous étudions les propriétés thermiques de matériaux diélectriques en couches minces. Nous utilisons pour cela des techniques d'optique guidée basée sur le coupleur à prisme ("m-lines "). Le coefficient thermo-optique dn/dT est mesuré pour différents matériaux en couches minces. Ces mesures sont appliquées à l'interprétation et la simulation du décalage spectral avec la température de filtres interférentiels. Le coupleur à prisme à réflexion totale, dans un montage à deux faisceaux de type pompe-sonde, permet de détecter, en régime harmonique, des variations d'indice photo-induites dans une couche mince aussi faibles que 10 -8. Ces variations d'indice sont provoquées par léchauffement créé par l'absorption d'une faible partie du faisceau pompe dans la couche. Leur répartition dans la couche est reliée aux propriétés thermiques (conductivité, chaleur spécifique) de celle-ci. Un modèle bidimensionnel de conduction thermique dans le coupleur à prisme a donc été développé, avec un bon accord qualitatif entre les calculs et les mesures. Une comparaison des mesures effectuées sur différents échantillons est également présentée.AIX-MARSEILLE3-BU Sc.St Jérô (130552102) / SudocSudocFranceF