Quantitative integration of geophysical and hydraulic data : from the local towards the regional scale range

Des progrès significatifs ont été réalisés dans le domaine de l'intégration quantitative des données géophysique et hydrologique l'échelle locale. Cependant, l'extension à de plus grandes échelles des approches correspondantes constitue encore un défi majeur. Il est néanmoins extrêmement important de relever ce défi pour développer des modèles fiables de flux des eaux souterraines et de transport de contaminant. Pour résoudre ce problème, j'ai développé une technique d'intégration des données hydrogéophysiques basée sur une procédure bayésienne de simulation séquentielle en deux étapes. Cette procédure vise des problèmes à plus grande échelle. L'objectif est de simuler la distribution d'un paramètre hydraulique cible à partir, d'une part, de mesures d'un paramètre géophysique pertinent qui couvrent l'espace de manière exhaustive, mais avec une faible résolution (spatiale) et, d'autre part, de mesures locales de très haute résolution des mêmes paramètres géophysique et hydraulique. Pour cela, mon algorithme lie dans un premier temps les données géophysiques de faible et de haute résolution à travers une procédure de réduction déchelle. Les données géophysiques régionales réduites sont ensuite reliées au champ du paramètre hydraulique à haute résolution. J'illustre d'abord l'application de cette nouvelle approche dintégration des données à une base de données synthétiques réaliste. Celle-ci est constituée de mesures de conductivité hydraulique et électrique de haute résolution réalisées dans les mêmes forages ainsi que destimations des conductivités électriques obtenues à partir de mesures de tomographic de résistivité électrique (ERT) sur l'ensemble de l'espace. Ces dernières mesures ont une faible résolution spatiale. La viabilité globale de cette méthode est testée en effectuant les simulations de flux et de transport au travers du modèle original du champ de conductivité hydraulique ainsi que du modèle simulé. Les simulations sont alors comparées. Les résultats obtenus indiquent que la procédure dintégration des données proposée permet d'obtenir des estimations de la conductivité en adéquation avec la structure à grande échelle ainsi que des predictions fiables des caractéristiques de transports sur des distances de moyenne à grande échelle. Les résultats correspondant au scénario de terrain indiquent que l'approche d'intégration des données nouvellement mise au point est capable d'appréhender correctement les hétérogénéitées à petite échelle aussi bien que les tendances à gande échelle du champ hydraulique prévalent. Les résultats montrent également une flexibilté remarquable et une robustesse de cette nouvelle approche dintégration des données. De ce fait, elle est susceptible d'être appliquée à un large éventail de données géophysiques et hydrologiques, à toutes les gammes déchelles. Dans la deuxième partie de ma thèse, j'évalue en détail la viabilité du réechantillonnage geostatique séquentiel comme mécanisme de proposition pour les méthodes Markov Chain Monte Carlo (MCMC) appliquées à des probmes inverses géophysiques et hydrologiques de grande dimension . L'objectif est de permettre une quantification plus précise et plus réaliste des incertitudes associées aux modèles obtenus. En considérant une série dexemples de tomographic radar puits à puits, j'étudie deux classes de stratégies de rééchantillonnage spatial en considérant leur habilité à générer efficacement et précisément des réalisations de la distribution postérieure bayésienne. Les résultats obtenus montrent que, malgré sa popularité, le réechantillonnage séquentiel est plutôt inefficace à générer des échantillons postérieurs indépendants pour des études de cas synthétiques réalistes, notamment pour le cas assez communs et importants où il existe de fortes corrélations spatiales entre le modèle et les paramètres. Pour résoudre ce problème, j'ai développé un nouvelle approche de perturbation basée sur une déformation progressive. Cette approche est flexible en ce qui concerne le nombre de paramètres du modèle et lintensité de la perturbation. Par rapport au rééchantillonage séquentiel, cette nouvelle approche s'avère être très efficace pour diminuer le nombre requis d'itérations pour générer des échantillons indépendants à partir de la distribution postérieure bayésienne. - Significant progress has been made with regard to the quantitative integration of geophysical and hydrological data at the local scale. However, extending corresponding approaches beyond the local scale still represents a major challenge, yet is critically important for the development of reliable groundwater flow and contaminant transport models. To address this issue, I have developed a hydrogeophysical data integration technique based on a two-step Bayesian sequential simulation procedure that is specifically targeted towards larger-scale problems. The objective is to simulate the distribution of a target hydraulic parameter based on spatially exhaustive, but poorly resolved, measurements of a pertinent geophysical parameter and locally highly resolved, but spatially sparse, measurements of the considered geophysical and hydraulic parameters. To this end, my algorithm links the low- and high-resolution geophysical data via a downscaling procedure before relating the downscaled regional-scale geophysical data to the high-resolution hydraulic parameter field. I first illustrate the application of this novel data integration approach to a realistic synthetic database consisting of collocated high-resolution borehole measurements of the hydraulic and electrical conductivities and spatially exhaustive, low-resolution electrical conductivity estimates obtained from electrical resistivity tomography (ERT). The overall viability of this method is tested and verified by performing and comparing flow and transport simulations through the original and simulated hydraulic conductivity fields. The corresponding results indicate that the proposed data integration procedure does indeed allow for obtaining faithful estimates of the larger-scale hydraulic conductivity structure and reliable predictions of the transport characteristics over medium- to regional-scale distances. The approach is then applied to a corresponding field scenario consisting of collocated high- resolution measurements of the electrical conductivity, as measured using a cone penetrometer testing (CPT) system, and the hydraulic conductivity, as estimated from electromagnetic flowmeter and slug test measurements, in combination with spatially exhaustive low-resolution electrical conductivity estimates obtained from surface-based electrical resistivity tomography (ERT). The corresponding results indicate that the newly developed data integration approach is indeed capable of adequately capturing both the small-scale heterogeneity as well as the larger-scale trend of the prevailing hydraulic conductivity field. The results also indicate that this novel data integration approach is remarkably flexible and robust and hence can be expected to be applicable to a wide range of geophysical and hydrological data at all scale ranges. In the second part of my thesis, I evaluate in detail the viability of sequential geostatistical resampling as a proposal mechanism for Markov Chain Monte Carlo (MCMC) methods applied to high-dimensional geophysical and hydrological inverse problems in order to allow for a more accurate and realistic quantification of the uncertainty associated with the thus inferred models. Focusing on a series of pertinent crosshole georadar tomographic examples, I investigated two classes of geostatistical resampling strategies with regard to their ability to efficiently and accurately generate independent realizations from the Bayesian posterior distribution. The corresponding results indicate that, despite its popularity, sequential resampling is rather inefficient at drawing independent posterior samples for realistic synthetic case studies, notably for the practically common and important scenario of pronounced spatial correlation between model parameters. To address this issue, I have developed a new gradual-deformation-based perturbation approach, which is flexible with regard to the number of model parameters as well as the perturbation strength. Compared to sequential resampling, this newly proposed approach was proven to be highly effective in decreasing the number of iterations required for drawing independent samples from the Bayesian posterior distribution.

Rôle de l'exercice dans l'approche multidisciplinaire de la lombalgie chronique

RÉSUMÉ L'exercice est utilisé dans le traitement de la lombalgie depuis plus de cent ans. La recherche dans ce domaine a commencé au milieu du XXème siècle puis s'est développée exponentiellement jusqu'à nos jours. La première étude de cette thèse a eu pour but de passer en revue cette abondante littérature scientifique. Il en est ressorti que l'exercice est un moyen efficace de prévention primaire et secondaire de la lombalgie. En tant que modalité de traitement, l'exercice permet de diminuer l'incapacité et la douleur et d'améliorer la condition physique et le statut professionnel des patients lombalgiques subaigus et chroniques. Parmi les caractéristiques de l'exercice, la supervision est essentielle. Des investigations ultérieures sont nécessaires afin d'identifier des sous-groupes de patients répondant favorablement à d'autres caractéristiques de l'exercice. L'exercice est souvent utilisé dans l'optique de maintenir les résultats obtenus à la suite d'un traitement, bien que peu d'études s'y soient penchées. La deuxième partie de cette thèse a eu pour objectifs d'évaluer l'efficacité d'un programme d'exercice (PE) suivi par des patients lombalgiques chroniques ayant complété une restauration fonctionnelle multidisciplinaire (RFM), en comparaison avec le suivi classique (SC) consistant simplement à encourager les patients à adopter un quotidien aussi actif que possible par la suite. Les résultats ont montré que les améliorations obtenues au terme de RFM étaient maintenues par les deux groupes à un an de suivi. Bien qu'aucune différence n'ait été obtenue entre les deux groupes, seul le groupe PE améliorait significativement l'incapacité et l'endurance isométrique des muscles du tronc. Une analyse économique a ensuite été réalisée afin d'évaluer la rentabilité de PE. L'évaluation de la qualité de vie des patients au terme de RFM et à un an de suivi permettait d'estimer les années de vie ajustées par leur qualité (QALYs) gagnées par chaque groupe. Les coûts directs (visites chez le médecin, spécialiste, physio, autres) et indirects (jours d'absence au travail) étaient estimés avant RFM et à un an de suivi à l'aide d'un agenda. Aucune différence significative n'était obtenue entre les groupes. Une mince différence de QALYs en faveur de PE ne se traduisait néanmoins pas en bénéfices mesurables. La recherche future devrait s'attacher à identifier un ou des sous-groupe(s) de patients pour lesquels SC ne permet pas de maintenir à long terme les améliorations obtenues au terme de RFM, et pour lesquels l'efficacité thérapeutique et la rentabilité économique de PE pourraient être accrues. ABSTRACT Exercise is used to treat low back pain for over a hundred years. Research in this area began in the mid-twentieth century and then grew exponentially until nowadays. The first study of this thesis was aimed to review this abundant scientific literature. It showed that exercise is effective in the primary and secondary prevention of low back pain. As a modality of treatment, exercise can reduce disability and pain and improve physical fitness and professional status of patients with subacute and chronic low back pain. Among different exercise characteristics, supervision is essential. Further investigations are needed to identify subgroups of patients responding positively to other characteristics of exercise. Exercise is often used as a post-treatment modality in order to maintain results over time, although only a few studies addressed this issue directly. The purpose of the second part of this thesis was to evaluate the effectiveness of an exercise program (EP) for patients with chronic low back pain who completed a functional multidisciplinary rehabilitation (FMR), compared to the routine follow-up (RF) which simply consisted of encouraging patients to adopt an active daily life thereafter. The results showed that improvements obtained at the end of FMR were maintained by both groups at one year follow-up. Although no difference was obtained between both groups, only the EP group significantly improved disability and isometric endurance of trunk muscles. An economic analysis was then carried out to assess the cost-effectiveness of EP. Based on the evaluation of patients' quality of life after FMR and at one year follow-up, an estimation of adjusted life years for their quality (QALYs) gained by each group was done. Direct costs (physician, specialist, physiotherapist, other therapists visits) and indirect costs (days off work) were measured before FMR and at one year follow-up using a cost diary. No significant difference was obtained between both groups. A slight difference in QALYs in favour of EP did yet not translate into measurable benefits. Future research should focus on identifying subgroups of patients for which RF is insufficient to reach long-term improvements after FMR, and for which the therapeutic effectiveness and cost-effectiveness of EP could be increased.

Ultra-high pressure liquid chromatography-mass spectrometry for plant metabolomics: a systematic comparison of high-resolution quadrupole-time-of-flight and single stage Orbitrap mass spectrometers.

The response of Arabidopsis to stress caused by mechanical wounding was chosen as a model to compare the performances of high resolution quadrupole-time-of-flight (Q-TOF) and single stage Orbitrap (Exactive Plus) mass spectrometers in untargeted metabolomics. Both instruments were coupled to ultra-high pressure liquid chromatography (UHPLC) systems set under identical conditions. The experiment was divided in two steps: the first analyses involved sixteen unwounded plants, half of which were spiked with pure standards that are not present in Arabidopsis. The second analyses compared the metabolomes of mechanically wounded plants to unwounded plants. Data from both systems were extracted using the same feature detection software and submitted to unsupervised and supervised multivariate analysis methods. Both mass spectrometers were compared in terms of number and identity of detected features, capacity to discriminate between samples, repeatability and sensitivity. Although analytical variability was lower for the UHPLC-Q-TOF, generally the results for the two detectors were quite similar, both of them proving to be highly efficient at detecting even subtle differences between plant groups. Overall, sensitivity was found to be comparable, although the Exactive Plus Orbitrap provided slightly lower detection limits for specific compounds. Finally, to evaluate the potential of the two mass spectrometers for the identification of unknown markers, mass and spectral accuracies were calculated on selected identified compounds. While both instruments showed excellent mass accuracy (<2.5ppm for all measured compounds), better spectral accuracy was recorded on the Q-TOF. Taken together, our results demonstrate that comparable performances can be obtained at acquisition frequencies compatible with UHPLC on Q-TOF and Exactive Plus MS, which may thus be equivalently used for plant metabolomics.

Diagnostic accuracy of free and total metanephrines in plasma and fractionated metanephrines in urine of patients with pheochromocytoma.

BACKGROUND: Plasma free and urinary metanephrines are recognized biomarkers for the assessment of pheochromocytoma. Plasma total metanephrines with a long half-life may represent another useful biomarker. OBJECTIVE: The aim of this study is to evaluate the diagnostic performances of plasma total metanephrines alone or combined with free metanephrines and fractionated 24-h urinary metanephrines. METHODS: A retrospective, case-control diagnostic test study was conducted between 1999 and 2007 in two university hospitals in Switzerland and two institutions in France. The patients included 46 cases with histologically proven pheochromocytoma, and 181 controls suspected of tumor with negative investigations and 3-year follow-up. None had renal dysfunction. Sensitivity and specificity were compared after expressing each measurement result as a ratio over its upper reference limit, adding the ratios of normetanephrine and metanephrine, and defining cut-off values of 1 or 2 for this sum. RESULTS: Applying a cut-off value of 1, plasma free and total metanephrines and urinary fractionated metanephrines had similar sensitivities of 96% (95% confidence interval, 86-99%), 95% (85-99%), and 95% (84-99%) along with similar specificities of 89% (83-94%), 91% (84-95%), and 86% (80-91%). A cut-off of 2 for the sum of ratios over reference limit improves the specificity, and it can be used for a confirmation test based on another biomarker taken among the three biomarkers. CONCLUSION: All three metanephrine-based tests perform equivalently for diagnosing pheochromocytoma in the absence of renal insufficiency, and can be conveniently associated two by two for confirming/excluding tumor.

Efficiency of flexible derotator in walking cerebral palsy children

Introduction The flexible derotator is one of the therapeutic resources used to combat primary and secondary abnormalities in walking cerebral palsy children. It was developed to reduce abnormal femoral and tibial torsions and lessen the latter's negative functional impact. Objective To determine the effect of wearing a flexible derotator on anatomic and functional parameters in walking cerebral palsy children. Methods We performed a retrospective study of walking cerebral palsy children by gathering data on bone-related parameters (femoral and tibial torsion) and functional parameters (distance and speed gait, and the energy expenditure index (EEI)). Fifteen walking cerebral palsy children were treated with the flexible derotator for one year and 15 untreated walking cerebral palsy children were included as controls. The two groups were compared in terms of the various parameters' change over time between the initial examination (the last examination prior to the start of the study or prior to use of the flexible derotator) and the final examination (after one year of follow-up). Results Right femoral anteversion and right and left external tibial torsion improved. There was a significant increase in distance and speed gait and a decrease in the EEI in walking cerebral palsy children. Conclusion Our retrospective study revealed a significant improvement in functional parameters in children with cerebral palsy, as a result of wearing the flexible derotator for at least 6 hours a day for a year. Bone parameters only improved slightly. Use of the flexible derotator could improve these children's quality of life.

Systematic review and meta-analysis of risk factors for survival after lung metastasectomy in colorectal cancer patients

Objective: Resection of lung metastases (LM) from colorectal cancer (CRC)¦is increasingly performed with a curative intent.Most series report small groups¦of patients, and it is currently not possible to identify those CRC patients who¦may benefit the most of surgical management. It is clinically relevant to assess¦risk factors for prolonged survival after this type of procedures.¦Methods: A meta analysis of 24 series published between 2000 and 2011¦which focused on surgical management of LM from CRC and included more¦than 40 patients each, with or without prior resection of in transit liver¦metastases. Random effects were calculated for five variables considered as¦potential prognostic factors.¦Results: A total of 2815 patients who underwent surgery with a curative¦intent were considered in this analysis. Four parameters were associated with¦a decreased survival: 1) a short disease-free interval between primary tumor¦resection and development of LM (HR = 1·59, 95% CI 1·27-1·98); 2) multiple¦LM (HR = 2·04, 95%CI 1·72-2·41); 3) positive hilar/mediastinal lymph nodes¦(HR = 1·65, 95% CI 1·35-2·02); and 4) a high prethoracotomy CEA value (HR¦=1·91, 95% CI 1·57-2·32). By comparison, a history of resected liver metastases¦(HR = 1·36, 95% CI 0·92-2·03) did not achieve statistical significance.¦Conclusion: Risk factors for poor clinical outcome after surgery for lung¦metastases in CRC patients include: 1) synchronous lung metastases; 2) high¦pre-thoracotomy CEA; 3) hilar nodes involvement; and 4) multiple pulmonary¦lesions.

Evolutionary biology: genetics and bisexuality.

A population-genetic model indicates that if there is a gene responsible for homosexual behaviour it can readily spread in populations. The model also predicts widespread bisexuality in humans.

The new EASL guidelines for the management of chronic hepatitis B infection adapted for Swiss physicians.

Since the arrival of several new antivirals and due to the growing molecular and clinical knowledge of hepatitis B virus (HBV) infection, therapy of hepatitis B has become complex. Clinical guidelines aim at streamlining medical attitudes: in this respect, the European Association for the Study of the Liver (EASL) recently issued clinical practice guidelines for the management of chronic hepatitis B. Guidelines made by international experts need however to be adapted to local health care systems. Here, we summarise the EASL guidelines with some minor modifications in order to be compatible with the particular Swiss situation, while discussing in more detail some aspects. Chronic hepatitis B is a complex disease with several phases where host and viral factors interact: the features of this continuous interplay need to be evaluated when choosing the most appropriate treatment. The EASL guidelines recommend, as first-line agents, using the most potent antivirals available with the optimal resistance profile, in order to abate HBV DNA as rapidly and as sustainably as possible. Once therapy has been started, the infection evolves and resistant viral strains may emerge. Rescue therapy needs to be started early with more potent agents lacking cross-resistance.

Decoupled post-glacial history in mutualistic plant-insect interactions: insights from the yellow loosestrife (Lysimachia vulgaris) and its associated oil-collecting bees (Macropis europaea and M-fulvipes)

AimWe take a comparative phylogeographical approach to assess whether three species involved in a specialized oil-rewarding pollination system (i.e. Lysimachia vulgaris and two oil-collecting bees within the genus Macropis) show congruent phylogeographical trajectories during post-glacial colonization processes. Our working hypothesis is that within specialized mutualistic interactions, where each species relies on the co-occurrence of the other for survival and/or reproduction, partners are expected to show congruent evolutionary trajectories, because they are likely to have followed parallel migration routes and to have shared glacial refugia. LocationWestern Palaearctic. MethodsOur analysis relies on the extensive sampling of 104 Western Palaearctic populations (totalling 434, 159 and 74 specimens of Lysimachiavulgaris, Macropiseuropaea and Macropisfulvipes, respectively), genotyped with amplified fragment length polymorphism. Based on this, we evaluated the regional genetic diversity (Shannon diversity and allele rarity index) and genetic structure (assessed using structure, population networks, isolation-by-distance and spatial autocorrelation metrics) of each species. Finally, we compared the general phylogeographical patterns obtained. ResultsContrary to our expectations, the analyses revealed phylogeographical signals suggesting that the investigated organisms demonstrate independent post-glacial trajectories as well as distinct contemporaneous demographic parameters, despite their mutualistic interaction. Main conclusionsThe mutualistic partners investigated here are likely to be experiencing distinct and independent evolutionary dynamics because of their contrasting life-history traits (e.g. dispersal abilities), as well as distinct hubs and migration routes. Such conditions would prevent and/or erase any signature of co-structuring of lineages in space and time. As a result, the lack of phylogeographical congruence driven by differences in life-history traits might have arisen irrespective of the three species having shared similar Pleistocene glacial refugia.