Monosomal karyotype in acute myeloid leukemia: a better indicator of poor prognosis than a complex karyotype.

PURPOSE: To investigate the prognostic value of various cytogenetic components of a complex karyotype in acute myeloid leukemia (AML). PATIENTS AND METHODS: Cytogenetics and overall survival (OS) were analyzed in 1,975 AML patients age 15 to 60 years. RESULTS: Besides AML with normal cytogenetics (CN) and core binding factor (CBF) abnormalities, we distinguished 733 patients with cytogenetic abnormalities. Among the latter subgroup, loss of a single chromosome (n = 109) conferred negative prognostic impact (4-year OS, 12%; poor outcome). Loss of chromosome 7 was most common, but outcome of AML patients with single monosomy -7 (n = 63; 4-year OS, 13%) and other single autosomal monosomies (n = 46; 4-year OS, 12%) did not differ. Structural chromosomal abnormalities influenced prognosis only in association with a single autosomal monosomy (4-year OS, 4% for very poor v 24% for poor). We derived a monosomal karyotype (MK) as a predictor for very poor prognosis of AML that refers to two or more distinct autosomal chromosome monosomies (n = 116; 4-year OS, 3%) or one single autosomal monosomy in the presence of structural abnormalities (n = 68; 4-year OS, 4%). In direct comparisons, MK provides significantly better prognostic prediction than the traditionally defined complex karyotype, which considers any three or more or five or more clonal cytogenetic abnormalities, and also than various individual specific cytogenetic abnormalities (eg, del[5q], inv[3]/t[3;3]) associated with very poor outcome. CONCLUSION: MK enables (in addition to CN and CBF) the prognostic classification of two new aggregates of cytogenetically abnormal AML, the unfavorable risk MK-negative category (4-year OS, 26% +/- 2%) and the highly unfavorable risk MK-positive category (4-year OS, 4% +/- 1%).

Analysis, modelling and visualisation of spatiotemporal data for urban studies

The proportion of population living in or around cites is more important than ever. Urban sprawl and car dependence have taken over the pedestrian-friendly compact city. Environmental problems like air pollution, land waste or noise, and health problems are the result of this still continuing process. The urban planners have to find solutions to these complex problems, and at the same time insure the economic performance of the city and its surroundings. At the same time, an increasing quantity of socio-economic and environmental data is acquired. In order to get a better understanding of the processes and phenomena taking place in the complex urban environment, these data should be analysed. Numerous methods for modelling and simulating such a system exist and are still under development and can be exploited by the urban geographers for improving our understanding of the urban metabolism. Modern and innovative visualisation techniques help in communicating the results of such models and simulations. This thesis covers several methods for analysis, modelling, simulation and visualisation of problems related to urban geography. The analysis of high dimensional socio-economic data using artificial neural network techniques, especially self-organising maps, is showed using two examples at different scales. The problem of spatiotemporal modelling and data representation is treated and some possible solutions are shown. The simulation of urban dynamics and more specifically the traffic due to commuting to work is illustrated using multi-agent micro-simulation techniques. A section on visualisation methods presents cartograms for transforming the geographic space into a feature space, and the distance circle map, a centre-based map representation particularly useful for urban agglomerations. Some issues on the importance of scale in urban analysis and clustering of urban phenomena are exposed. A new approach on how to define urban areas at different scales is developed, and the link with percolation theory established. Fractal statistics, especially the lacunarity measure, and scale laws are used for characterising urban clusters. In a last section, the population evolution is modelled using a model close to the well-established gravity model. The work covers quite a wide range of methods useful in urban geography. Methods should still be developed further and at the same time find their way into the daily work and decision process of urban planners. La part de personnes vivant dans une région urbaine est plus élevé que jamais et continue à croître. L'étalement urbain et la dépendance automobile ont supplanté la ville compacte adaptée aux piétons. La pollution de l'air, le gaspillage du sol, le bruit, et des problèmes de santé pour les habitants en sont la conséquence. Les urbanistes doivent trouver, ensemble avec toute la société, des solutions à ces problèmes complexes. En même temps, il faut assurer la performance économique de la ville et de sa région. Actuellement, une quantité grandissante de données socio-économiques et environnementales est récoltée. Pour mieux comprendre les processus et phénomènes du système complexe "ville", ces données doivent être traitées et analysées. Des nombreuses méthodes pour modéliser et simuler un tel système existent et sont continuellement en développement. Elles peuvent être exploitées par le géographe urbain pour améliorer sa connaissance du métabolisme urbain. Des techniques modernes et innovatrices de visualisation aident dans la communication des résultats de tels modèles et simulations. Cette thèse décrit plusieurs méthodes permettant d'analyser, de modéliser, de simuler et de visualiser des phénomènes urbains. L'analyse de données socio-économiques à très haute dimension à l'aide de réseaux de neurones artificiels, notamment des cartes auto-organisatrices, est montré à travers deux exemples aux échelles différentes. Le problème de modélisation spatio-temporelle et de représentation des données est discuté et quelques ébauches de solutions esquissées. La simulation de la dynamique urbaine, et plus spécifiquement du trafic automobile engendré par les pendulaires est illustrée à l'aide d'une simulation multi-agents. Une section sur les méthodes de visualisation montre des cartes en anamorphoses permettant de transformer l'espace géographique en espace fonctionnel. Un autre type de carte, les cartes circulaires, est présenté. Ce type de carte est particulièrement utile pour les agglomérations urbaines. Quelques questions liées à l'importance de l'échelle dans l'analyse urbaine sont également discutées. Une nouvelle approche pour définir des clusters urbains à des échelles différentes est développée, et le lien avec la théorie de la percolation est établi. Des statistiques fractales, notamment la lacunarité, sont utilisées pour caractériser ces clusters urbains. L'évolution de la population est modélisée à l'aide d'un modèle proche du modèle gravitaire bien connu. Le travail couvre une large panoplie de méthodes utiles en géographie urbaine. Toutefois, il est toujours nécessaire de développer plus loin ces méthodes et en même temps, elles doivent trouver leur chemin dans la vie quotidienne des urbanistes et planificateurs.

Functional analysis of altered channel-activating protease-1 (CAP1) expression in the skin

Summary : The skin is a complex organ that protects the body against entry of pathogens and supplies a relatively dry and impermeable barrier to water loss. This barrier function is mainly provided by the epidermis, which is the outermost layer of the skin. Serine proteases are involved in skin physiology and it is known that mutations or alterations in their expression can lead to skin diseases. In order to investigate the importance of the regulated expression of CAPI/Prss8, a membrane bound serine protease expressed in the epidermis, we developed transgenic mice ectopically expressing CAPI/Prss8 in the skin. These animals exhibited a phenotype characterized by scaly skin, epidermal hypertrophy, inflammation and scratching behavior. This phenotype could be completely abolished in mice lacking the proteinase activated receptor 2 (PAR2) revealing PAR2 as a potential in vivo downstream target of CAP 1 /Prss8. We could also provide evidence of a CAP1 /Prss8 function independent of its catalytic activity. Additionally, mice ectopically expressing PAR2 in the skin developed a skin phenotype very similar to CAPI/Prss8 transgenic animals, supporting the hypothesis of PAR2 activation by CAPI/Prss8. We could furthermore demonstrate an inhibitory effect of the serine protease inhibitor nexin-I on CAPI/Prss8, since nexin-1 transgenic expression negated the skin phenotype observed in CAPI/Prss8 transgenic mice. CAP1/Prss8 and PAR2 transgenic animals, and the understanding of the interaction between CAPl/Prss8 and PAR2, can be helpful in developing potential CAPI/Prss8 and PAR2 inhibitory molecules that may be used as drugs to treat ichthyoses-like skin diseases. Résumé : La peau est un organe complexe qui protège le corps contre l'entrée des pathogènes et forme une barrière imperméable qui empêche la déshydratation. Cette fonction de barrière est surtout fournie par l'épiderme, la couche la plus superficielle de la peau. Le bon fonctionnement de cet organe est permis, entre autres, par les protéases à sérine qui sont des enzymes dont l'altération peut causer des maladies de la peau. Pour étudier l'importance de la régulation de CAP1/Prss8, une protéase à sérine exprimée au niveau de l'épiderme, des souris génétiquement modifiées, dans lesquelles CAP1/Prss8 est exprimé d'une manière ectopique dans la peau, ont été générées. Les animaux transgéniques pour CAP1/Prss8 présentent une peau squameuse, un épiderme hypertrophique, des processus inflammatoires et se grattent. Ce phénotype a pu être complètement guéri lorsque le gène de PAR2, un récepteur qui règle l'activité des cellules de l'épiderme, est inactivé chez la souris. Ceci montre que PAR2 est une cible de CAP1/Prss8 dans le système étudié. Des études expérimentales suggèrent de plus que l'effet de CAP1/Prss8 dans ce modèle ne dépend pas de son activité enzymatique. En dernière analyse, il a été démontré que l'expression transgénique de nexin-1, un inhibiteur des protéases à sérine exprimé dans la peau, a la capacité d'améliorer la peau squameuse et l'épiderme hypertrophique causés par CAP1/Prss8 transgénique. Les animaux transgéniques pour CAP1/Prss8 et PAR2, et la compréhension du mécanisme d'interaction entre eux, pourraient aider à développer et à tester des molécules inhibitrices de CAP1 /Prss8 et PARI qui pourraient alors être utilisées comme médicaments pour traiter des maladies de la peau comme les ichthyoses.

Kinematically complete analysis of the CLAS data on the proton structure Function F2 in a Regge-Dual model

The recently measured inclusive electron-proton cross section in the nucleon resonance region, performed with the CLAS detector at the Thomas Jefferson Laboratory, has provided new data for the nucleon structure function F2 with previously unavailable precision. In this paper we propose a description of these experimental data based on a Regge-dual model for F2. The basic inputs in the model are nonlinear complex Regge trajectories producing both isobar resonances and a smooth background. The model is tested against the experimental data, and the Q2 dependence of the moments is calculated. The fitted model for the structure function (inclusive cross section) is a limiting case of the more general scattering amplitude equally applicable to deeply virtual Compton scattering. The connection between the two is discussed.

Functional interaction between the estrogen receptor and CTF1: analysis of the vitellogenin gene B1 promoter in yeast.

Eukaryotic gene expression depends on a complex interplay between the transcriptional apparatus and chromatin structure. We report here a yeast model system for investigating the functional interaction between the human estrogen receptor (hER) and CTF1, a member of the CTF/NFI transcription factor family. We show that a CTF1-fusion protein and the hER transactivate a synthetic promoter in yeast in a synergistic manner. This interaction requires the proline-rich transactivation domain of CTF1. When the natural estrogen-dependent vitellogenin B1 promoter is tested in yeast, CTF1 and CTF1-fusion proteins are unable to activate transcription, and no synergy is observed between hER, which activates the B1 promoter, and these factors. Chromatin structure analysis on this promoter reveals positioned nucleosomes at -430 to -270 (+/-20 bp) and at -270 to - 100 (+/-20 bp) relative to the start site of transcription. The positions of the nucleosomes remain unchanged upon hormone-dependent transcriptional activation of the promoter, and the more proximal nucleosome appears to mask the CTF/NFI site located at - 101 to -114. We conclude that a functional interaction of hER with the estrogen response element located upstream of a basal promoter occurs in yeast despite the nucleosomal organization of this promoter, whereas the interaction of CTF1 with its target site is apparently precluded by a nucleosome.

Measurement Errors Should Always Be Incorporated in Phylogenetic Comparative Analysis

The evolution of continuous traits is the central component of comparative analyses in phylogenetics, and the comparison of alternative models of trait evolution has greatly improved our understanding of the mechanisms driving phenotypic differentiation. Several factors influence the comparison of models, and we explore the effects of random errors in trait measurement on the accuracy of model selection. We simulate trait data under a Brownian motion model (BM) and introduce different magnitudes of random measurement error. We then evaluate the resulting statistical support for this model against two alternative models: Ornstein-Uhlenbeck (OU) and accelerating/decelerating rates (ACDC). Our analyses show that even small measurement errors (10%) consistently bias model selection towards erroneous rejection of BM in favour of more parameter-rich models (most frequently the OU model). Fortunately, methods that explicitly incorporate measurement errors in phylogenetic analyses considerably improve the accuracy of model selection. Our results call for caution in interpreting the results of model selection in comparative analyses, especially when complex models garner only modest additional support. Importantly, as measurement errors occur in most trait data sets, we suggest that estimation of measurement errors should always be performed during comparative analysis to reduce chances of misidentification of evolutionary processes.

Comparison between detailed digital and conventional soil maps of an area with complex geology

Since different pedologists will draw different soil maps of a same area, it is important to compare the differences between mapping by specialists and mapping techniques, as for example currently intensively discussed Digital Soil Mapping. Four detailed soil maps (scale 1:10.000) of a 182-ha sugarcane farm in the county of Rafard, São Paulo State, Brazil, were compared. The area has a large variation of soil formation factors. The maps were drawn independently by four soil scientists and compared with a fifth map obtained by a digital soil mapping technique. All pedologists were given the same set of information. As many field expeditions and soil pits as required by each surveyor were provided to define the mapping units (MUs). For the Digital Soil Map (DSM), spectral data were extracted from Landsat 5 Thematic Mapper (TM) imagery as well as six terrain attributes from the topographic map of the area. These data were summarized by principal component analysis to generate the map designs of groups through Fuzzy K-means clustering. Field observations were made to identify the soils in the MUs and classify them according to the Brazilian Soil Classification System (BSCS). To compare the conventional and digital (DSM) soil maps, they were crossed pairwise to generate confusion matrices that were mapped. The categorical analysis at each classification level of the BSCS showed that the agreement between the maps decreased towards the lower levels of classification and the great influence of the surveyor on both the mapping and definition of MUs in the soil map. The average correspondence between the conventional and DSM maps was similar. Therefore, the method used to obtain the DSM yielded similar results to those obtained by the conventional technique, while providing additional information about the landscape of each soil, useful for applications in future surveys of similar areas.

Genetic removal of tri-unsaturated fatty acids suppresses developmental and molecular phenotypes of an Arabidopsis tocopherol-deficient mutant. Whole-body mapping of malondialdehyde pools in a complex eukaryote.

Malondialdehyde (MDA) is a small, ubiquitous, and potentially toxic aldehyde that is produced in vivo by lipid oxidation and that is able to affect gene expression. Tocopherol deficiency in the vitamin E2 mutant vte2-1 of Arabidopsis thaliana leads to massive lipid oxidation and MDA accumulation shortly after germination. MDA accumulation correlates with a strong visual phenotype (growth reduction, cotyledon bleaching) and aberrant GST1 (glutathione S-transferase 1) expression. We suppressed MDA accumulation in the vte2-1 background by genetically removing tri-unsaturated fatty acids. The resulting quadruple mutant, fad3-2 fad7-2 fad8 vte2-1, did not display the visual phenotype or the aberrant GST1 expression observed in vte2-1. Moreover, cotyledon bleaching in vte2-1 was chemically phenocopied by treatment of wild-type plants with MDA. These data suggest that products of tri-unsaturated fatty acid oxidation underlie the vte2-1 seedling phenotype, including cellular toxicity and gene regulation properties. Generation of the quadruple mutant facilitated the development of an in situ fluorescence assay based on the formation of adducts of MDA with 2-thiobarbituric acid at 37 degrees C. Specificity was verified by measuring pentafluorophenylhydrazine derivatives of MDA and by liquid chromatography analysis of MDA-2-thiobarbituric acid adducts. Potentially applicable to other organisms, this method allowed the localization of MDA pools throughout the body of Arabidopsis and revealed an undiscovered pool of the compound unlikely to be derived from trienoic fatty acids in the vicinity of the root tip quiescent center.

Synchronization reveals topological scales in complex networks

We study the relationship between topological scales and dynamic time scales in complex networks. The analysis is based on the full dynamics towards synchronization of a system of coupled oscillators. In the synchronization process, modular structures corresponding to well-defined communities of nodes emerge in different time scales, ordered in a hierarchical way. The analysis also provides a useful connection between synchronization dynamics, complex networks topology, and spectral graph analysis.

Clustering in complex networks. I. General formalism

We develop a full theoretical approach to clustering in complex networks. A key concept is introduced, the edge multiplicity, that measures the number of triangles passing through an edge. This quantity extends the clustering coefficient in that it involves the properties of two¿and not just one¿vertices. The formalism is completed with the definition of a three-vertex correlation function, which is the fundamental quantity describing the properties of clustered networks. The formalism suggests different metrics that are able to thoroughly characterize transitive relations. A rigorous analysis of several real networks, which makes use of this formalism and the metrics, is also provided. It is also found that clustered networks can be classified into two main groups: the weak and the strong transitivity classes. In the first class, edge multiplicity is small, with triangles being disjoint. In the second class, edge multiplicity is high and so triangles share many edges. As we shall see in the following paper, the class a network belongs to has strong implications in its percolation properties.

Clustering in complex networks. II. Percolation properties

The percolation properties of clustered networks are analyzed in detail. In the case of weak clustering, we present an analytical approach that allows us to find the critical threshold and the size of the giant component. Numerical simulations confirm the accuracy of our results. In more general terms, we show that weak clustering hinders the onset of the giant component whereas strong clustering favors its appearance. This is a direct consequence of the differences in the k-core structure of the networks, which are found to be totally different depending on the level of clustering. An empirical analysis of a real social network confirms our predictions.

Protein-protein interactions between adenovirus DNA polymerase and nuclear factor I mediate formation of the DNA replication preinitiation complex.

The in vitro adenovirus (Ad) DNA replication system provides an assay to study the interaction of viral and host replication proteins with the DNA template in the formation of the preinitiation complex. This initiation system requires in addition to the origin DNA sequences 1) Ad DNA polymerase (Pol), 2) Ad preterminal protein (pTP), the covalent acceptor for protein-primed DNA replication, and 3) nuclear factor I (NFI), a host cell protein identical to the CCAAT box-binding transcription factor. The interactions of these proteins were studied by coimmunoprecipitation and Ad origin DNA binding assays. The Ad Pol can bind to origin sequences only in the presence of another protein which can be either pTP or NFI. While NFI alone can bind to its origin recognition sequence, pTP does not specifically recognize DNA unless Ad Pol is present. Thus, protein-protein interactions are necessary for the targetting of either Ad Pol or pTP to the preinitiation complex. DNA footprinting demonstrated that the Ad DNA site recognized by the pTP.Pol complex was within the first 18 bases at the end of the template which constitutes the minimal origin of replication. Mutagenesis studies have defined the Ad Pol interaction site on NFI between amino acids 68-150, which overlaps the DNA binding and replication activation domain of this factor. A putative zinc finger on the Ad Pol has been mutated to a product that fails to bind the Ad origin sequences but still interacts with pTP. These results indicate that both protein-protein and protein-DNA interactions mediate specific recognition of the replication origin by Ad DNA polymerase.

Option valuation as an expectation in the complex domain: The Black-Scholes case

It is very well known that the first succesful valuation of a stock option was done by solving a deterministic partial differential equation (PDE) of the parabolic type with some complementary conditions specific for the option. In this approach, the randomness in the option value process is eliminated through a no-arbitrage argument. An alternative approach is to construct a replicating portfolio for the option. From this viewpoint the payoff function for the option is a random process which, under a new probabilistic measure, turns out to be of a special type, a martingale. Accordingly, the value of the replicating portfolio (equivalently, of the option) is calculated as an expectation, with respect to this new measure, of the discounted value of the payoff function. Since the expectation is, by definition, an integral, its calculation can be made simpler by resorting to powerful methods already available in the theory of analytic functions. In this paper we use precisely two of those techniques to find the well-known value of a European call

Qualitative analysis of barriers and facilitators encountered by HIV patients in an ART adherence programme.

Background Medication adherence is a complex, dynamic and changing behaviour that is affected by a variety of factors, including the patient's beliefs and life circumstances. Studies have highlighted barriers to medication adherence (e.g., unmanaged side effects or a lack of social support), as well as facilitators of medication adherence (e.g., technical simplicity of treatment and psychological acceptance of the disease). Since August 2004, in Lausanne (Switzerland), physicians have referred patients who are either experiencing or are at risk of experiencing problems with their HIV antiretroviral treatment (ART) to a routine interdisciplinary ART adherence programme. This programme consists of multifactorial intervention including electronic drug monitoring (MEMS(TM)). Objective This study's objective was to identify the barriers and facilitators encountered by HIV patients with suboptimal medication adherence (≤90 % adherence over the study period). Setting The community pharmacy of the Department of Ambulatory Care and Community Medicine in Lausanne (Switzerland). Method The study consisted of a retrospective, qualitative, thematic content analysis of pharmacists' notes that were taken during semi-structured interviews with patients and conducted as part of the ART adherence programme between August 2004 and May 2008. Main outcome measure Barriers and facilitators encountered by HIV patients. Results Barriers to and facilitators of adherence were identified for the 17 included patients. These factors fell into three main categories: (1) cognitive, emotional and motivational; (2) environmental, organisational and social; and (3) treatment and disease. Conclusion The pharmacists' notes revealed that diverse barriers and facilitators were discussed during medication adherence interviews. Indeed, the results showed that the 17 non-adherent patients encountered barriers and benefited from facilitators. Therefore, pharmacists should inquire about all factors, regardless of whether they have a negative or a positive impact on medication adherence, and should consider all dimensions of patient adherence. The simultaneous strengthening of facilitators and better management of barriers may allow healthcare providers to tailor care to a patient's specific needs and support each individual patient in improving his medication-related behaviour.

Analysis of gene expression patterns in animals

During my PhD, my aim was to provide new tools to increase our capacity to analyse gene expression patterns, and to study on a large-scale basis the evolution of gene expression in animals. Gene expression patterns (when and where a gene is expressed) are a key feature in understanding gene function, notably in development. It appears clear now that the evolution of developmental processes and of phenotypes is shaped both by evolution at the coding sequence level, and at the gene expression level.Studying gene expression evolution in animals, with complex expression patterns over tissues and developmental time, is still challenging. No tools are available to routinely compare expression patterns between different species, with precision, and on a large-scale basis. Studies on gene expression evolution are therefore performed only on small genes datasets, or using imprecise descriptions of expression patterns.The aim of my PhD was thus to develop and use novel bioinformatics resources, to study the evolution of gene expression. To this end, I developed the database Bgee (Base for Gene Expression Evolution). The approach of Bgee is to transform heterogeneous expression data (ESTs, microarrays, and in-situ hybridizations) into present/absent calls, and to annotate them to standard representations of anatomy and development of different species (anatomical ontologies). An extensive mapping between anatomies of species is then developed based on hypothesis of homology. These precise annotations to anatomies, and this extensive mapping between species, are the major assets of Bgee, and have required the involvement of many co-workers over the years. My main personal contribution is the development and the management of both the Bgee database and the web-application.Bgee is now on its ninth release, and includes an important gene expression dataset for 5 species (human, mouse, drosophila, zebrafish, Xenopus), with the most data from mouse, human and zebrafish. Using these three species, I have conducted an analysis of gene expression evolution after duplication in vertebrates.Gene duplication is thought to be a major source of novelty in evolution, and to participate to speciation. It has been suggested that the evolution of gene expression patterns might participate in the retention of duplicate genes. I performed a large-scale comparison of expression patterns of hundreds of duplicated genes to their singleton ortholog in an outgroup, including both small and large-scale duplicates, in three vertebrate species (human, mouse and zebrafish), and using highly accurate descriptions of expression patterns. My results showed unexpectedly high rates of de novo acquisition of expression domains after duplication (neofunctionalization), at least as high or higher than rates of partitioning of expression domains (subfunctionalization). I found differences in the evolution of expression of small- and large-scale duplicates, with small-scale duplicates more prone to neofunctionalization. Duplicates with neofunctionalization seemed to evolve under more relaxed selective pressure on the coding sequence. Finally, even with abundant and precise expression data, the majority fate I recovered was neither neo- nor subfunctionalization of expression domains, suggesting a major role for other mechanisms in duplicate gene retention.