Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi

Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species

Ischemic and haemorrhagic complications during percutaneous aortic valve interventions

La réparation valvulaire aortique percutanée a connu d’immense progrès depuis unevingtaine d’années permettant au patient atteint de rétrécissement aortique (RA) serré debénéficier d’un traitement curatif, le plus souvent avec une approche minimaliste sous anesthésielocale associée à une diminution des complications procédurales. Cependant la prise en charge decertaines situations cliniques d’urgence ou de certains patients à haut risque opératoire est encoremal définie et nécessite une évaluation précise des complications ischémiques et hémorragiquesde la procédure percutanée.Dans la première partie de la thèse nous avons confirmé que certaines situations cliniquescomplexes urgentes telles qu’un état de choc cardiogénique secondaire à un RA serré, ou lanécessité d’une chirurgie extracardiaque urgente constituent encore une zone grise où letraitement optimal du RA n'est pas clair et nécessite de plus amples investigations. Dans le choccardiogénique ou la chirurgie extracardiaque urgente, le risque de complications hémorragiqueset surtout ischémiques et la mortalité à court terme restent très élevés. En cas de choccardiogénique, les complications sont principalement reliées au timing de la valvuloplastieaortique (BAV). En cas de chirurgie extracardiaque urgente, la BAV systématique n’améliore pasle pronostic par rapport au traitement médical.Dans la deuxième partie de la thèse, chez des patients à risque intermédiaire ou élevécontre indiqué à l’accès transfémoral pour un TAVI, nous avons comparé les deux voiesalternatives extrathoraciques les plus utilisées : axillaire et carotidienne. Celles ci font jeu égal enterme de complications ischémiques et de mortalité mais l’accès carotidien semble avoir plus decomplications hémorragiques en particulier locales.La troisième et dernière partie de la thèse nous a permis d’apprécier l’incidenceimportante de microbleeds au cours de la procédure TAVI. Leur apparition semble être reliéeavec la durée de la procédure et l’absence de correction du déficit en facteur Willebrand acquislors du RA ; ces lésions n’ont pas de retentissement sur l’évolution neurologique à court terme(6mois). Des études sont en cours pour mieux préciser le lien entre risque hémorragique cérébral,anomalie du facteur vWF et dispositif cardiaque valvulaire ou d’assistance.Ischemic and haemorrhagic complications during percutaneous aortic valve interventionsPercutaneous aortic valve repair including balloon aortic valvuloplasty (BAV) and TAVI has experienced significant improvements over the past twenty years, allowing patients with severe aortic stenosis (SAS) to benefit from a curative treatment, mostly with a minimalist approach under local anesthesia associated with a drastic reduction of procedural complications.However, the management of specific clinical emergency situations or of high-risk patients is still poorly explored and requires an accurate assessment of the ischemic and hemorrhagic complications of percutaneous procedures.In the first part of this thesis, we confirmed that some urgent complex clinical situations such as cardiogenic shock secondary to SAS, or the need for urgent extracardiac surgery in SAS patients still constitute a grey zone where the optimal treatment is unclear and requires further investigations. During cardiogenic shock or urgent extracardiac surgery, the risk of hemorrhagic and especially ischemic complications and short-term mortality remain very high. During cardiogenic shock, complications are mainly related to the timing of the BAV. When urgent extracardiac surgery is required, routine BAV does not improve the prognosis of SAS patients compared to medical treatment.In the second part of this thesis, we compared the axillary and carotid access in intermediate or high-risk patients contraindicated to transfemoral route for TAVI. These accesses have similar rates of ischemic complications and mortality, but carotid artery has more local hemorrhagic complications.The third and final part of this thesis analyse the significant incidence of microbleeds during the TAVI procedure. Their appearance seems to be related to the duration of the procedure and the lack of correction of the von Willebrand factor deficiency acquired during SAS; these lesions have no impact on the neurological evolution in the short term.Studies are underway to better define the link between the risk of cerebral hemorrhage, the vWF factor and cardiac valvular or circulatory assist device

3D-printed simulator for nasopharyngeal swab collection for COVID-19

Introduction: Testing for COVID-19 is a cornerstone of pandemic control. If conducted inappropriately, nasopharyngeal swab collection can be painful and preanalytical sample collection errors may lead to false negative results. Our objective was to develop a realistic and easily available synthetic simulator for nasopharyngeal swab collection.Materials and methods: The nasopharyngeal swab collection simulator was designed through different development steps: segmentation, computer-aided design (CAD), and 3D printing. The model was 3D printed using PolyJet technology, which allows multi-material printing using hard and soft materials.Results: The simulator splits in the parasagittal plane close to the septum to allow better visualization and understanding of nasal cavity landmarks. The model is able to simulate the softness and texture of different structural elements. The simulator allows the user to conduct realistic nasopharyngeal swab collection. A colored pad on the posterior wall of the nasopharynx provides real-time feedback to the user. The simulator also permits incorrect swab insertion, which is of obvious benefit from a training perspective. Comprehensive 3D files for printing and full instructions for manufacturing the simulator is freely available online via an open access link.Conclusion: In the context of the COVID-19 pandemic, we developed a nasopharyngeal swab collection simulator which can be produced by 3D printing via an open access link, which offers complete operating instructions

Belgique

Nihoul Pierre, Bombois Thomas, Dupont Nicolas, Vandevenne François, Debry Jean-Thierry. Belgique. In: Annuaire international de justice constitutionnelle, 29-2013, 2014. Pluralisme des garanties et des juges et droits fondamentaux - Les droits culturels. pp. 659-688

Belgique

Nihoul Pierre, Bombois Thomas, Dupont Nicolas, Vandevenne François, Debry Jean-Thierry. Belgique. In: Annuaire international de justice constitutionnelle, 30-2014, 2015. Juges constitutionnels et doctrine - Constitutions et transitions. pp. 663-694

La Cour constitutionnelle - Chronique de jurisprudence 2013

En 2012, la Cour a rendu cent soixante-six arrêts. Elle clôt ainsi définitivement deux cent dix-sept affaires. En outre, deux affaires ont été définitivement clôturées par ordonnance et une autre par la voie d’un avis publié au Moniteur belge. - Durant cette même année, la Cour fut saisie de deux cent soixante-deux affaires nouvelles

Prognostic Value of Aortic Valve Area by Doppler Echocardiography in Patients With Severe Asymptomatic Aortic Stenosis

International audienceBackground-The aim of this study was to evaluate the relationship between aortic valve area (AVA) obtained by Doppler echocardiography and outcome in patients with severe asymptomatic aortic stenosis and to define a specific threshold of AVA for identifying asymptomatic patients at very high risk based on their clinical outcome. Methods and Results-We included 199 patients with asymptomatic severe aortic stenosis (AVA 0.6 cm(2) (hazard ratio 3.39; 95% CI 1.80-6.40; P<0.0001). Conclusions-Patients with severe asymptomatic aortic stenosis and AVA <= 0.6 cm(2) displayed an important increase in the risk of adverse events during short-term follow-up. Further studies are needed to determine whether elective aortic valve replacement improves outcome in this high-risk subgroup of patients

Prognostic significance of left ventricular concentric remodelling in patients with aortic stenosis

International audienceBackground. - Four patterns of left ventricular (LV) geometry (normal, concentric remodelling, concentric hypertrophy and eccentric hypertrophy) have been described in aortic stenosis (AS). Although LV concentric remodelling (LVCR), characterized by normal LV mass despite increased LV wall thickness, is frequently observed in AS, its prognostic implication has been not specifically studied. Aim. - We aimed to assess, using echocardiography, the prognostic implication of LVCR in asymptomatic or minimally symptomatic patients with AS. Methods. - Overall, 331 patients (mean age 73 +/- 13 years; 45% women) with AS (aortic valve area 50% were enrolled. The endpoints were mortality with conservative management and mortality with conservative and/or surgical management. Results. - Sixty-three (19%) patients died under conservative management (follow-up 29 1 months). The highest risk of mortality under conservative management compared with patients with normal LV geometry was observed for LVCR (adjusted hazard ratio [HR]: 3.53, 95% confidence interval [CI]: 1.19-10.46; P = 0.023), followed by concentric LVH (adjusted HR: 2.97, 95% CI: 1.02-8.60; P = 0.045). Aortic valve replacement was performed in 96 patients (29%) during the entire follow-up (37 +/- 1 months); 72 (22%) patients died. Only LVCR remained independently associated with an increased risk of mortality when surgical management during the entire follow-up was considered (adjusted HR: 2.93, 95% CI: 1.19-7.23; P = 0.020). Conclusions. - Among the patterns of LV geometry in AS, LVCR portends the worst outcome. Patients with LVCR and AS have a considerable increased risk of mortality, regardless of clinical management. (C) 2016 Elsevier Masson SAS. All rights reserved