Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling.

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.

Serrated polyps of the large intestine: a molecular study comparing sessile serrated adenomas and hyperplastic polyps.

AIMS: To compare the molecular profile of a series of sessile serrated adenomas (SSAs) and hyperplastic polyps (HPs), in order to distinguish these lesions, SSAs having a potential role in the genesis of serrated adenocarcinomas through a serrated pathway in which methylation plays a key role. METHODS AND RESULTS: Twelve HPs and sixteen SSAs of the right and left colon were investigated for microsatellite instability, DNA mismatch repair genes, p53, p16, and beta-catenin expression, MLH1 and p16 (CDKN2A) gene methylation, and KRAS and BRAF mutations. Both SSAs and HPs were microsatellite stable. MLH1 and MSH2 protein silencing, aberrant cytoplasmic expression and methylation of p16 were found to be exclusive to right-sided SSAs. The MLH1 promoter gene was frequently methylated in right-sided SSAs in contrast with HPs. Abnormal p53 and beta-catenin expression was present in both SSAs and HPs. BRAF and KRAS mutation were mutually exclusive, but KRAS mutation was present only in left-sided SSAs and HPs. CONCLUSIONS: HPs and SSAs may be related lesions. However, at least right-sided SSAs differ from left-sided SSAs and HPs in the occurrence of MLH1 and p16 methylation, supporting the hypothesis that SSAs could be precursors of serrated adenocarcinomas.

Clinical and genetic findings in a large cohort of patients with congenital myopathies due to mutations in the skeletal muscle ryanodine receptor (RYR1) gene

RYR1 mutations are the most common cause of structural congenital myopathies and may exhibit both dominant and recessive inheritance. Histopathological findings are variable and include central cores, multi-minicores, type 1 predominance/ uniformity, fibre type disproportion, increased internal nucleation and fatty and connective tissue. Until recently, diagnostic RYR1 sequencing was limited to mutational hotspots due to the large size of the gene. Since the introduction of full RYR1 sequencing in 2007 we have detected pathogenic mutations in 77 families: 39 had dominant inheritance and 38 recessive inheritance. In some cases with presumably recessive inheritance, only one heterozygous mutation inherited from an asymptomatic parent was identified. Of 28 dominant mutations, 6 were novel; 37 of the 59 recessive mutations were also novel. Dominant mutations were more frequently in recognized hotspot regions, while recessive mutations were distributed throughout the coding sequence. Dominant mutations were predominantly missense, whereas recessive mutations included many nonsense and splice mutations expected to result in reduced RyR1 protein. There was wide clinical variability in patients with both dominant and recessive inheritance. As a group, those with dominant mutations were generally more mildly affected than those with recessive inheritance, who had earlier onset and were weaker with more functional limitations. Extraocular muscle involvement was almost exclusively observed in the recessive group. Bulbar involvement was also more prominent in this group, resulting in a larger number requiring gastrostomy insertion. In conclusion, genomic sequencing of the entire RYR1 leads to the detection of many novel mutations, but may miss large genetic rearrangements in some cases. Assigning pathogenicity to novel mutations is often difficult and interpretation of genetic results in the context of clinical, histological and, increasingly, muscle MRI findings is essential.

Dosing regimen of gentamicin in neonates: evaluation of current guidelines based on a large population pharmacokinetic analysis

Objectives: Gentamicin is among the most commonly prescribed antibiotics in newborns, but large interindividual variability in exposure levels exists. Based on a population pharmacokinetic analysis of a cohort of unselected neonates, we aimed to validate current dosing recommendations from a recent reference guideline (Neofax®). Methods: From 3039 concentrations collected in 994 preterm (median gestational age 32.3 weeks, range 24.2-36.5) and 455 term newborns, treated at the University Hospital of Lausanne between 2006 and 2011, a population pharmacokinetic analysis was performed with NONMEM®. Model-based simulations were used to assess the ability of dosing regimens to bring concentrations into targets: trough ≤ 1mg/L and peak ~ 8mg/L. Results: A two-compartment model best characterized gentamicin pharmacokinetics. Model parameters are presented in the table. Body weight, gestational age and postnatal age positively influence clearance, which decreases under dopamine administration. Body weight and gestational age influence the distribution volume. Model based simulations confirm that preterm infants need doses superior to 4 mg/kg, and extended dosage intervals, up to 48 hours for very preterm newborns, whereas most term newborns would achieve adequate exposure under 4 mg/kg q. 24 h. More than 90% of neonates would achieve trough concentrations below 2 mg/L and peaks above 6 mg/L following most recent guidelines. Conclusions: Simulated gentamicin exposure demonstrates good accordance with recent dosing recommendations for target concentration achievement.

Application of a roughness-length representation to parameterize energy loss in 3-D numerical simulations of large rivers

Recent technological advances in remote sensing have enabled investigation of the morphodynamics and hydrodynamics of large rivers. However, measuring topography and flow in these very large rivers is time consuming and thus often constrains the spatial resolution and reach-length scales that can be monitored. Similar constraints exist for computational fluid dynamics (CFD) studies of large rivers, requiring maximization of mesh-or grid-cell dimensions and implying a reduction in the representation of bedform-roughness elements that are of the order of a model grid cell or less, even if they are represented in available topographic data. These ``subgrid'' elements must be parameterized, and this paper applies and considers the impact of roughness-length treatments that include the effect of bed roughness due to ``unmeasured'' topography. CFD predictions were found to be sensitive to the roughness-length specification. Model optimization was based on acoustic Doppler current profiler measurements and estimates of the water surface slope for a variety of roughness lengths. This proved difficult as the metrics used to assess optimal model performance diverged due to the effects of large bedforms that are not well parameterized in roughness-length treatments. However, the general spatial flow patterns are effectively predicted by the model. Changes in roughness length were shown to have a major impact upon flow routing at the channel scale. The results also indicate an absence of secondary flow circulation cells in the reached studied, and suggest simpler two-dimensional models may have great utility in the investigation of flow within large rivers. Citation: Sandbach, S. D. et al. (2012), Application of a roughness-length representation to parameterize energy loss in 3-D numerical simulations of large rivers, Water Resour. Res., 48, W12501, doi: 10.1029/2011WR011284.

Les symbioses industrielles : une nouvelle stratégie pour l'amélioration de l'utilisation des ressources matérielles et énergétiques par les activités économiques

RésuméCette thèse traite d'un domaine d'application de l'écologie industrielle, les symbioses industrielles, comme stratégie d'amélioration de la consommation des ressources matérielles et énergétiques et de la gestion des déchets par les activités économiques. Les symbioses industrielles cherchent à créer de nouvelles collaborations directement entre les acteurs économiques d'un territoire dans le but d'échanger de l'information, des matières premières et des déchets, et d'intensifier les mutualisations de services et d'infrastructures possibles entre entreprises voisines. Ces quatre types de collaboration sont représentés schématiquement dans la figure ci-dessous.Dans ce travail, la détection et la mise en oeuvre de symbioses industrielles sont abordées sous plusieurs angles. Les recherches réalisées concernent le développement de procédures de mise en oeuvre s'adressant aux collectivités publiques, aux institutions académiques et aux bureaux de conseil dans le domaine de l'environnement. Les objectifs des procédures sont de créer une dynamique de collaboration et de confiance entre les acteurs économiques et l'administration publique d'un territoire afin de détecter des symbioses industrielles potentielles. Ces procédures requièrent la gestion de grandes quantités d'informations relatives aux flux de matière et d'énergie.Un travail de terrain, réalisé sur les territoires du canton de Genève et de Lausanne Région et utilisé comme études de cas, a permis de mettre en évidence un grand nombre de symbioses industrielles qui existent déjà en Suisse romande. Plusieurs dizaines d'exemples ont été identifiés principalement dans lesdomaines de la gestion de l'eau, de l'énergie, des produits chimiques et des matériaux de construction. La législation suisse autoriserait cependant la concrétisation de nombreuses autres opportunités. Dans cette recherche, celles-ci sont évaluées techniquement, légalement, économiquement et environnementalement. La création d'un référentiel d'évaluation des opportunités permet de déterminer quelles sont les symbioses industrielles techniquement réalisables et pertinentes dans le contexte suisse et dans quels cas celles-ci représenteraient une réelle plus-value par rapport à l'utilisation actuelle de la ressource et aux filières existantes de collecte et de valorisation des déchets.Finalement, un logiciel, SymbioGIS, destiné à soutenir la détection et l'évaluation de symbioses industrielles potentielles a été développé. Il s'agit d'une interface web accessible pour de nombreux utilisateurs, couplée à une interface de systèmes d'information géographique. En plus de la détection de symbioses industrielles, plusieurs fonctionnalités sont proposées pour faciliter la prise en compte des flux de matière et d'énergie dans les problématiques liées à l'aménagement du territoire et au positionnement des activités économiques.En conclusion, cette recherche met en évidence la nécessité de rapprocher les institutions publiques en charge de la protection de l'environnement, de la promotion économique et de l'aménagement du territoire pour favoriser l'essor des symbioses industrielles comme stratégie pour la gestion des ressources matérielles et énergétiques. Elle propose des pistes pour intensifier les collaborations entre ces domaines et accélérer le partage des connaissances liées aux flux de matière et d'énergie et à leur cheminement au sein des activités économiques afin de rendre le système industriel existant en Suisse romande viable à long terme. Parallèlement, elle étudie les possibilités de transposer ces considérations et les procédures et outils développés dans le contexte économique et social de la région Asie-Pacifique, où se trouvent aujourd'hui de nombreuses activités de production.SummaryIndustrial symbioses: A new strategy for improving how economic activities use material and energy resourcesThis thesis focuses on one application of industrial ecology, industrial symbioses, as a strategy for improving how economic activities consume material and energy resources. Industrial symbioses seek to create new collaborations among economic players with the goal of exchanging information, raw materials, and waste directly among area businesses, and to step up the potential pooling of services and infrastructure among neighboring companies.The identification and implementation of industrial symbioses are studied from several angles. The research first examines the development of implementation procedures for government bodies, academic institutions, and environmental consulting services. The purpose of the procedures is to create a dynamic of collaboration and trust between the economic players and the public officials in a region in order to identify potential industrial symbioses. The procedures necessitate managing large amounts of information about material and energy flows.Fieldwork conducted in the canton of Geneva and the Lausanne region, and used as case studies for the research, highlights a great number of industrial symbioses that already exist in French-speaking Switzerland. Several dozen examples are identified, primarily in the areas of water management, energy, chemical products, and building materials; however, Swiss law would permit many others. The research evaluates these opportunities from a technical, legal, economic, and environmental standpoint. By developing an assessment framework it is possible to determine which industrial symbioses are technically feasible and pertinent in Switzerland, and under what circumstances they would represent real added value compared to the current use of the resource and to existing systems for collecting and reusing waste.Lastly, SymbioGIS software was developed to help identify and assess potential industrial symbioses. The program's Web-based interface can be accessed by multiple users and is coupled with an interface that provides geographic information. In addition to identifying industrial symbioses, several program functionalities make it easier to consider material and energy flows with regard to local development issues and siting economic activities.In conclusion, the research highlights the need to bring together public institutions charged with protecting the environment, promoting economic activity, and overseeing development in order to foster the expansion of industrial symbioses as a strategy for managing material and energy resources. It proposes solutions for stepping up collaboration among these players and accelerating the sharing of knowledge about material and energy flows and their paths within economic activities with the goal of making theexisting industrial system in French-speaking Switzerland viable long-term. Also examined were thepossibilities of transposing these considerations and the study's findings about Switzerland to the economic and social context of the Asia-Pacific region, where much production is now located.

Treatment of large bone defects with the Ilizarov technique.

Between 1985 and 1990 we treated 11 large segmental bone defects (average 6.7 cm) in ten patients with the Ilizarov technique. Open fractures, type III according to Gustilo, represented the largest group (8 of 11 cases). The average delay before the Ilizarov technique was initiated was 8.9 months. The external fixator was usually maintained for 1 year. Bone regeneration was obtained in every case. Consolidation was not fulfilled with this technique in three cases. The complications observed were one refracture, four leg-length discrepancies (average 1.5 cm), and five axial deformities exceeding 5 degrees. No pin-track infection was observed. In our limited series of four type IIIC open fractures treated by the Ilizarov technique, no patients required amputation. The Ilizarov technique is particularly useful in the treatment of large bone defects, without major complications, especially if there is an adequate initial debridement.

Lassa virus entry in antigen presenting cells and evaluation of a novel nanoparticle vaccine platform against arena viruses

Arenaviruses are a large and diverse family of viruses that merit significant attention as causative agents of severe hemorrhagic fevers in humans. Lassa virus (LASV) in Africa and the South American hemorrhagic fever viruses Junin (JUNV), Machupo (MACV), and Guanarito (GTOV) have emerged as important human pathogens and represent serious public health problems in their respective endemic areas. A hallmark of fatal arenaviruses hemorrhagic fevers is a marked immunosuppression of the infected patients. Antigen presenting cells (APCs) such as macrophages and in particular dendritic cells (DCs) are early and preferred targets of arenaviruses infection. Instead of being recognized and presented as foreign antigens by DCs, arenaviruses subvert the normal mechanisms of pathogen recognition, invade DCs and establish a productive infection. Viral replication perturbs the DCs' ability to present antigens and to activate T and B cells, contributing to the marked virus-induced immunosuppression observed in fatal disease. Considering their crucial role in the development of an anti-viral immune response, the mechanisms by which arenaviruses, and in particular LASV, invade DCs are of particular interest. The C-type lectin DC-specific Intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) was recently identified as a potential entry receptor for LASV. The first project of my thesis focused therefore on the investigation of the role of DC-SIGN in LASV entry into primary human DCs. My data revealed that DC-SIGN serves as an attachment factor for LASV on human DCs and can facilitate capture of free virus and subsequent cell entry. However, in contrast to other emerging viruses, of the phlebovirus family, I found that DC-SIGN does likely not function as an authentic entry receptor for LASV. Moreover, I was able to show that LASV enters DCs via an unusually slow pathway that depends on actin, but is independent of clathrin and dynamin. Considering the lack of effective treatments and the limited public health infrastructure in endemic regions, the development of protective vaccines against arenaviruses is an urgent need. To address this issue, the second project of my thesis aimed at the development of a novel recombinant arenavirus vaccine based on a nanoparticle (NPs) platform and its evaluation in a small animal model. During the first phase of the project I designed, produced, and characterized suitable vaccine antigens. In the second phase of the project, I generated antigen-conjugated NPs, developed vaccine formulations, and tested the NPs for their ability to elicit anti-viral T cell responses as well as anti-viral antibodies. I demonstrated that the NPs platform is able to activate both cellular and humoral branches of the adaptive anti-viral immunity, providing proof-of-principle. In sum, my first project will allow, in a long term perspective, a better understanding of the viral pathogenesis and contribute to the development of novel antiviral strategies. The second project will expectidly offer a new treatment option against arenaviruses.

A modular approach for integrative analysis of large-scale gene-expression and drug-response data

High-throughput technologies are now used to generate more than one type of data from the same biological samples. To properly integrate such data, we propose using co-modules, which describe coherent patterns across paired data sets, and conceive several modular methods for their identification. We first test these methods using in silico data, demonstrating that the integrative scheme of our Ping-Pong Algorithm uncovers drug-gene associations more accurately when considering noisy or complex data. Second, we provide an extensive comparative study using the gene-expression and drug-response data from the NCI-60 cell lines. Using information from the DrugBank and the Connectivity Map databases we show that the Ping-Pong Algorithm predicts drug-gene associations significantly better than other methods. Co-modules provide insights into possible mechanisms of action for a wide range of drugs and suggest new targets for therapy

Thymic selection generates a large T cell pool recognizing a self-peptide in humans.

The low frequency of self-peptide-specific T cells in the human preimmune repertoire has so far precluded their direct evaluation. Here, we report an unexpected high frequency of T cells specific for the self-antigen Melan-A/MART-1 in CD8 single-positive thymocytes from human histocompatibility leukocyte antigen-A2 healthy individuals, which is maintained in the peripheral blood of newborns and adults. Postthymic replicative history of Melan-A/MART-1-specific CD8 T cells was independently assessed by quantifying T cell receptor excision circles and telomere length ex vivo. We provide direct evidence that the large T cell pool specific for the self-antigen Melan-A/MART-1 is mostly generated by thymic output of a high number of precursors. This represents the only known naive self-peptide-specific T cell repertoire directly accessible in humans.

Quantification, self-renewal, and genetic tracing of FL1+ tumor-initiating cells in a large cohort of human gliomas.

Evidence has emerged that the initiation and growth of gliomas is sustained by a subpopulation of cancer-initiating cells (CICs). Because of the difficulty of using markers to tag CICs in gliomas, we have previously exploited more robust phenotypic characteristics, including a specific morphology and intrincic autofluorescence, to identify and isolate a subpopulation of glioma CICs, called FL1(+). The objective of this study was to further validate our method in a large cohort of human glioma and a mouse model of glioma. Seventy-four human gliomas of all grades and the GFAP-V(12)HA-ras B8 mouse model were analyzed for in vitro self-renewal capacity and their content of FL1(+). Nonneoplastic brain tissue and embryonic mouse brain were used as control. Genetic traceability along passages was assessed with microsatellite analysis. We found that FL1(+) cells from low-grade gliomas and from control nonneoplasic brain tissue show a lower level of autofluorescence and undergo a restricted number of cell divisions before dying in culture. In contrast, we found that FL1(+) cells derived from many but not all high-grade gliomas acquire high levels of autofluorescence and can be propagated in long-term cultures. Moreover, FL1(+) cells show a remarkable traceability over time in vitro and in vivo. Our results show that FL1(+) cells can be found in all specimens of a large cohort of human gliomas of different grades and in a model of genetically induced mouse glioma as well as nonneoplastic brain. However, their self-renewal capacity is variable and seems to be dependent on the tumor grade.

Proposition d'un concept de contrôle de gestion pour la division "infrastructure routière" de l'Office fédéral des routes (OFROU)

La présente étude propose une méthodologie aboutissant à la conception d'un système de contrôle de gestion pour la division « infrastructure routière » ou « I » de l'Office fédéral des routes (OFROU). La première partie de ce travail situe l'OFROU dans son contexte de réformes et identifie les raisons qui justifient l'implantation d'un système de contrôle de gestion à l'OFROU. La deuxième partie pose les jalons permettant d'établir un contrôle de gestion dans sa division « I ». Elle cherche d'abord à donner une définition du contrôle de gestion dans le secteur public, puis présente un état des lieux du système de gestion existant. Finalement, les systèmes de contrôle de gestion de deux autres offices GMEB, MétéoSuisse et armasuisse immobilier, sont analysés afin d'en tirer des éléments pertinents pouvant servir à la conception du contrôle de gestion à l'OFROU. La troisième propose un contrôle de gestion pour la division « I ». Le travail montre que la réalisation d'un concept de contrôle de gestion pour la division « I » n'est pas évidente. Cette dernière, qui est en train de se mettre en place, manque encore d'expérience pour identifier clairement les éléments clé à insérer dans le système. On observe un grand embarras entre le stade du savoir et celui du savoir faire concret. La méthodologie et l'analyse présentées dans ce travail pourraient contribuer à développer un savoir faire interne aboutissant rapidement à la mise sur pied d'un système de contrôle de gestion pour la division « I ». Die vorliegende Studie schlägt eine Methodik zur Erarbeitung eines Management-Kontrollsystems für die Abteilung « Strasseninfrastruktur » oder « I » des Bundesamts für Strassen (ASTRA) vor. Der erste Teil dieser Arbeit stellt das ASTRA im Spannungsfeld dieser Reformen. Ihre Konsequenzen lassen die Einführung eines Management-Kontrollsystems im ASTRA folgerichtig erscheinen. Im zweiten Teil geht es darum, Wegmarken zu setzen, die die Einführung einer Managementkontrolle in der Abteilung « I » in die richtigen Bahnen lenken. Es wird versucht, eine Begriffsbestimmung der Managementkontrolle im öffentlichen Sektor sowie eine Bestandesaufnahme der bestehenden Systeme vorzunehmen. Schliesslich werden die Management-Kontrollsysteme zweier anderer FLAG-Ämter, MeteoSchweiz und armasuisse immobilier, auf mögliche Nutzen für den Aufbau der Managementkontrolle des ASTRA analysiert. Der dritte Teil beinhaltet einen Vorschlag, wie die Management-Kontrolle für die Abteilung « I » aussehen könnte. Die Arbeit zeigt, dass die Erarbeitung eines Management-Kontrollkonzepts für die Abteilung « I » keine einfache Aufgabe ist. Es fehlt an Erfahrung, um die Schlüsselbausteine des Systems erkennen zu können. Zwischen dem Stadium des Wissens und dem des konkreten Know-hows klafft ein empfindlicher Graben. Methodik und Analyse, wie sie in der vorliegenden Arbeit beschrieben werden, könnten zum Aufbau eines internen Know-hows beitragen, das die rasche Verwirklichung eines Management-Kontrollsystems für die Abteilung « I » erlauben könnte.

Large agminated cellular 'plaque-type' blue nevus surrounding the ear: a case and review.

Large or giant cellular blue nevi are usually congenital and represent a challenge for the physician. Close anatomic structures may be altered by the size of the moles. In this article, we report the case of an uncommon large, agminated, cellular blue nevus of the 'plaque type' in a 42-year-old female. Due to the risks of malignant melanoma development on a large or giant blue nevus, we highlight the importance of proper histopathological diagnosis. Furthermore, because of the possibility that the nevus may invade the bone and cerebral tissues, we discuss the indication of a radiological diagnosis. The accurate correlation to clinical and histopathological findings and appropriate multidisciplinary management can save the lives of patients. © 2013 S. Karger AG, Basel.

The v-y latissimus dorsi musculocutaneous flap in the reconstruction of large posterior chest wall defects.

Posterior chest wall defects are frequently encountered after excision of tumors as a result of trauma or in the setting of wound dehiscence after spine surgery. Various pedicled fasciocutaneous and musculocutaneous flaps have been described for the coverage of these wounds. The advent of perforator flaps has allowed the preservation of muscle function but their bulk is limited. Musculocutaneous flaps remain widely employed. The trapezius and the latissimus dorsi (LD) flaps have been used extensively for upper and middle posterior chest wounds, respectively. Their bulk allows for obliteration of the dead space in deep wounds. The average width of the LD skin paddle is limited to 10-12 cm if closure of the donor site is expected without skin grafting. In 2001 a modification of the skin paddle design was introduced in order to allow large flaps to be raised without requiring grafts or flaps for donor site closure. This V-Y pattern allows coverage of large anterior chest defects after mastectomy. We have modified this flap to allow its use for posterior chest wall defects. We describe the flap design, its indications, and its limitations with three clinical cases. Level of Evidence V This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors at www.springer.com/00266 .