Scheduled service network design for integrated planning of rail freight transportation

Cette thèse étudie une approche intégrant la gestion de l’horaire et la conception de réseaux de services pour le transport ferroviaire de marchandises. Le transport par rail s’articule autour d’une structure à deux niveaux de consolidation où l’affectation des wagons aux blocs ainsi que des blocs aux services représentent des décisions qui complexifient grandement la gestion des opérations. Dans cette thèse, les deux processus de consolidation ainsi que l’horaire d’exploitation sont étudiés simultanément. La résolution de ce problème permet d’identifier un plan d’exploitation rentable comprenant les politiques de blocage, le routage et l’horaire des trains, de même que l’habillage ainsi que l’affectation du traffic. Afin de décrire les différentes activités ferroviaires au niveau tactique, nous étendons le réseau physique et construisons une structure de réseau espace-temps comprenant trois couches dans lequel la dimension liée au temps prend en considération les impacts temporels sur les opérations. De plus, les opérations relatives aux trains, blocs et wagons sont décrites par différentes couches. Sur la base de cette structure de réseau, nous modélisons ce problème de planification ferroviaire comme un problème de conception de réseaux de services. Le modèle proposé se formule comme un programme mathématique en variables mixtes. Ce dernie r s’avère très difficile à résoudre en raison de la grande taille des instances traitées et de sa complexité intrinsèque. Trois versions sont étudiées : le modèle simplifié (comprenant des services directs uniquement), le modèle complet (comprenant des services directs et multi-arrêts), ainsi qu’un modèle complet à très grande échelle. Plusieurs heuristiques sont développées afin d’obtenir de bonnes solutions en des temps de calcul raisonnables. Premièrement, un cas particulier avec services directs est analysé. En considérant une cara ctéristique spécifique du problème de conception de réseaux de services directs nous développons un nouvel algorithme de recherche avec tabous. Un voisinage par cycles est privilégié à cet effet. Celui-ci est basé sur la distribution du flot circulant sur les blocs selon les cycles issus du réseau résiduel. Un algorithme basé sur l’ajustement de pente est développé pour le modèle complet, et nous proposons une nouvelle méthode, appelée recherche ellipsoidale, permettant d’améliorer davantage la qualité de la solution. La recherche ellipsoidale combine les bonnes solutions admissibles générées par l’algorithme d’ajustement de pente, et regroupe les caractéristiques des bonnes solutions afin de créer un problème élite qui est résolu de facon exacte à l’aide d’un logiciel commercial. L’heuristique tire donc avantage de la vitesse de convergence de l’algorithme d’ajustement de pente et de la qualité de solution de la recherche ellipsoidale. Les tests numériques illustrent l’efficacité de l’heuristique proposée. En outre, l’algorithme représente une alternative intéressante afin de résoudre le problème simplifié. Enfin, nous étudions le modèle complet à très grande échelle. Une heuristique hybride est développée en intégrant les idées de l’algorithme précédemment décrit et la génération de colonnes. Nous proposons une nouvelle procédure d’ajustement de pente où, par rapport à l’ancienne, seule l’approximation des couts liés aux services est considérée. La nouvelle approche d’ajustement de pente sépare ainsi les décisions associées aux blocs et aux services afin de fournir une décomposition naturelle du problème. Les résultats numériques obtenus montrent que l’algorithme est en mesure d’identifier des solutions de qualité dans un contexte visant la résolution d’instances réelles.

Relation entre la structure et la fonction des artères cérébrales dans l’athérosclérose : impact des traitements cardioprotecteurs

Thèse réalisée en cotutelle avec Dre Christine Des Rosiers

Design, implementation and application of a generic framework for integrated regional land-use modeling

Land use is a crucial link between human activities and the natural environment and one of the main driving forces of global environmental change. Large parts of the terrestrial land surface are used for agriculture, forestry, settlements and infrastructure. Given the importance of land use, it is essential to understand the multitude of influential factors and resulting land use patterns. An essential methodology to study and quantify such interactions is provided by the adoption of land-use models. By the application of land-use models, it is possible to analyze the complex structure of linkages and feedbacks and to also determine the relevance of driving forces. Modeling land use and land use changes has a long-term tradition. In particular on the regional scale, a variety of models for different regions and research questions has been created. Modeling capabilities grow with steady advances in computer technology, which on the one hand are driven by increasing computing power on the other hand by new methods in software development, e.g. object- and component-oriented architectures. In this thesis, SITE (Simulation of Terrestrial Environments), a novel framework for integrated regional sland-use modeling, will be introduced and discussed. Particular features of SITE are the notably extended capability to integrate models and the strict separation of application and implementation. These features enable efficient development, test and usage of integrated land-use models. On its system side, SITE provides generic data structures (grid, grid cells, attributes etc.) and takes over the responsibility for their administration. By means of a scripting language (Python) that has been extended by language features specific for land-use modeling, these data structures can be utilized and manipulated by modeling applications. The scripting language interpreter is embedded in SITE. The integration of sub models can be achieved via the scripting language or by usage of a generic interface provided by SITE. Furthermore, functionalities important for land-use modeling like model calibration, model tests and analysis support of simulation results have been integrated into the generic framework. During the implementation of SITE, specific emphasis was laid on expandability, maintainability and usability. Along with the modeling framework a land use model for the analysis of the stability of tropical rainforest margins was developed in the context of the collaborative research project STORMA (SFB 552). In a research area in Central Sulawesi, Indonesia, socio-environmental impacts of land-use changes were examined. SITE was used to simulate land-use dynamics in the historical period of 1981 to 2002. Analogous to that, a scenario that did not consider migration in the population dynamics, was analyzed. For the calculation of crop yields and trace gas emissions, the DAYCENT agro-ecosystem model was integrated. In this case study, it could be shown that land-use changes in the Indonesian research area could mainly be characterized by the expansion of agricultural areas at the expense of natural forest. For this reason, the situation had to be interpreted as unsustainable even though increased agricultural use implied economic improvements and higher farmers' incomes. Due to the importance of model calibration, it was explicitly addressed in the SITE architecture through the introduction of a specific component. The calibration functionality can be used by all SITE applications and enables largely automated model calibration. Calibration in SITE is understood as a process that finds an optimal or at least adequate solution for a set of arbitrarily selectable model parameters with respect to an objective function. In SITE, an objective function typically is a map comparison algorithm capable of comparing a simulation result to a reference map. Several map optimization and map comparison methodologies are available and can be combined. The STORMA land-use model was calibrated using a genetic algorithm for optimization and the figure of merit map comparison measure as objective function. The time period for the calibration ranged from 1981 to 2002. For this period, respective reference land-use maps were compiled. It could be shown, that an efficient automated model calibration with SITE is possible. Nevertheless, the selection of the calibration parameters required detailed knowledge about the underlying land-use model and cannot be automated. In another case study decreases in crop yields and resulting losses in income from coffee cultivation were analyzed and quantified under the assumption of four different deforestation scenarios. For this task, an empirical model, describing the dependence of bee pollination and resulting coffee fruit set from the distance to the closest natural forest, was integrated. Land-use simulations showed, that depending on the magnitude and location of ongoing forest conversion, pollination services are expected to decline continuously. This results in a reduction of coffee yields of up to 18% and a loss of net revenues per hectare of up to 14%. However, the study also showed that ecological and economic values can be preserved if patches of natural vegetation are conservated in the agricultural landscape. -----------------------------------------------------------------------

Integrated bioenergy and food production

Rising global energy needs and limited fossil fuel reserves have led to increased use of renewable energies. In Germany, this has entailed massive exploitation of agricultural biomass for biogas generation, associated with unsustainable farming practices. Organic agriculture not only reduces negative environmental impacts, organic farmers were also prime movers in anaerobic digestion (AD) in Germany. This study’s aim was to identify the structure, development, and characteristics of biogas production associated with organic farming systems in order to estimate further development, as well as energetic and associated agronomic potentials. Surveys were conducted among organic farms with AD technology. 144 biogas plants could be included in the analysis. Total installed electrical capacity was 30.8 MWel, accounting for only 0.8% of the total installed electrical capacity in the German biogas sector. Recently, larger plant types (>250 kWel) with increased use of (also purchased) energy crops have emerged. Farmers noticed increases in yields (22% on average) and quality of cash crops in arable farming through integrated biogas production. In conclusion, although the share of AD in organic farming is relatively small it can provide various complementary socio-ecological benefits such as the enhancement of food output through digestate fertilization without additional need for land, while simultaneously reducing greenhouse gas emissions from livestock manures and soils. However, to achieve this eco-functional intensification, AD systems and their management have to be well adapted to farm size and production focus and based primarily on residue biomass.

An integrated model of soil-canopy spectral radiances, photosynthesis, fluorescence, temperature and energy balance

This paper presents the model SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes), which is a vertical (1-D) integrated radiative transfer and energy balance model. The model links visible to thermal infrared radiance spectra (0.4 to 50 μm) as observed above the canopy to the fluxes of water, heat and carbon dioxide, as a function of vegetation structure, and the vertical profiles of temperature. Output of the model is the spectrum of outgoing radiation in the viewing direction and the turbulent heat fluxes, photosynthesis and chlorophyll fluorescence. A special routine is dedicated to the calculation of photosynthesis rate and chlorophyll fluorescence at the leaf level as a function of net radiation and leaf temperature. The fluorescence contributions from individual leaves are integrated over the canopy layer to calculate top-of-canopy fluorescence. The calculation of radiative transfer and the energy balance is fully integrated, allowing for feedback between leaf temperatures, leaf chlorophyll fluorescence and radiative fluxes. Leaf temperatures are calculated on the basis of energy balance closure. Model simulations were evaluated against observations reported in the literature and against data collected during field campaigns. These evaluations showed that SCOPE is able to reproduce realistic radiance spectra, directional radiance and energy balance fluxes. The model may be applied for the design of algorithms for the retrieval of evapotranspiration from optical and thermal earth observation data, for validation of existing methods to monitor vegetation functioning, to help interpret canopy fluorescence measurements, and to study the relationships between synoptic observations with diurnally integrated quantities. The model has been implemented in Matlab and has a modular design, thus allowing for great flexibility and scalability.

Response of plant-pollinator communities to fire: changes in diversity, abundance and floral reward structure

Globally, plant-pollinator communities are subject to a diverse array of perturbations and in many temperate and semi-arid systems fire is a dominant structuring force. We present a novel and highly integrated approach, which quantifies, in parallel, the response to fire of pollinator communities, floral communities and floral reward structure. Mt Carmel, Israel is a recognised bee-flower biodiversity hotspot, and using a chronosequence of habitats with differing post-fire ages, we follow the changes in plant-pollinator community organisation from immediately following a burn until full regeneration of vegetation. Initially, fire has a catastrophic effect on these communities, however, recovery is rapid with a peak in diversity of both flowers and bees in the first 2 years post-fire, followed by a steady decline over the next 50 years. The regeneration of floral communities is closely matched by that of their principal pollinators. At the community level we quantify, per unit area of habitat, key parameters of nectar and pollen forage known to be of importance in structuring pollinator communities. Nectar Volume, nectar water content, nectar concentration and the diversity of nectar foraging niches are all greatest immediately following fire with a steady decrease as regeneration proceeds. Temporal changes in energy availability for nectar, pollen, total energy (nectar + pollen) and relative importance of pollen to nectar energy show a similar general decline with site age, however, the pattern is less clear owing to the highly patchy distribution of floral resources. Changes in floral reward structure reflect the general shift from annuals (generally low-reward open access flowers) to perennials (mostly high-reward and restricted access flowers) as post-fire regeneration ensues. The impact of fire on floral communities and their associated rewards have clear implications for pollinator community structure and we discuss this and the role of other disturbance factors on these systems.

Model predictive control using dynamic integrated system optimisation and parameter estimation (DISOPE)

DISOPE is a technique for solving optimal control problems where there are differences in structure and parameter values between reality and the model employed in the computations. The model reality differences can also allow for deliberate simplification of model characteristics and performance indices in order to facilitate the solution of the optimal control problem. The technique was developed originally in continuous time and later extended to discrete time. The main property of the procedure is that by iterating on appropriately modified model based problems the correct optimal solution is achieved in spite of the model-reality differences. Algorithms have been developed in both continuous and discrete time for a general nonlinear optimal control problem with terminal weighting, bounded controls and terminal constraints. The aim of this paper is to show how the DISOPE technique can aid receding horizon optimal control computation in nonlinear model predictive control.

Calibration of structure in a distributed forecasting model for a semiarid flash flood: dynamic surface storage and channel roughness

Flash floods pose a significant danger for life and property. Unfortunately, in arid and semiarid environment the runoff generation shows a complex non-linear behavior with a strong spatial and temporal non-uniformity. As a result, the predictions made by physically-based simulations in semiarid areas are subject to great uncertainty, and a failure in the predictive behavior of existing models is common. Thus better descriptions of physical processes at the watershed scale need to be incorporated into the hydrological model structures. For example, terrain relief has been systematically considered static in flood modelling at the watershed scale. Here, we show that the integrated effect of small distributed relief variations originated through concurrent hydrological processes within a storm event was significant on the watershed scale hydrograph. We model these observations by introducing dynamic formulations of two relief-related parameters at diverse scales: maximum depression storage, and roughness coefficient in channels. In the final (a posteriori) model structure these parameters are allowed to be both time-constant or time-varying. The case under study is a convective storm in a semiarid Mediterranean watershed with ephemeral channels and high agricultural pressures (the Rambla del Albujón watershed; 556 km 2 ), which showed a complex multi-peak response. First, to obtain quasi-sensible simulations in the (a priori) model with time-constant relief-related parameters, a spatially distributed parameterization was strictly required. Second, a generalized likelihood uncertainty estimation (GLUE) inference applied to the improved model structure, and conditioned to observed nested hydrographs, showed that accounting for dynamic relief-related parameters led to improved simulations. The discussion is finally broadened by considering the use of the calibrated model both to analyze the sensitivity of the watershed to storm motion and to attempt the flood forecasting of a stratiform event with highly different behavior.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

The BALTIMOS (BALTEX Integrated Model System) fi eld experiments: A comprehensive atmospheric boundary layer data set for model validation over the open and ice- covered Baltic Sea

A comprehensive atmospheric boundary layer (ABL) data set was collected in eight fi eld experiments (two during each season) over open water and sea ice in the Baltic Sea during 1998–2001 with the primary objective to validate the coupled atmospheric- ice-ocean-land surface model BALTIMOS (BALTEX Integrated Model System). Measurements were taken by aircraft, ships and surface stations and cover the mean and turbulent structure of the ABL including turbulent fl uxes, radiation fl uxes, and cloud conditions. Measurement examples of the spatial variability of the ABL over the ice edge zone and of the stable ABL over open water demonstrate the wide range of ABL conditions collected and the strength of the data set which can also be used to validate other regional models.

Genetic structure of Partamona helleri (Apidae, Meliponini) from Neotropical Atlantic rainforest

Stingless bees of the genus Partamona are distributed from southern Mexico to southern Brazil. This genus has been subject to different approaches to solve questions concerning general biology, taxonomy, systematics and biogeography, but population studies applying molecular techniques are inexistent. We analyzed the genetic structure of P. helleri across its geographic distribution along the coastal Atlantic tropical rainforest in Brazil. Ten mtDNA haplotypes were observed in 47 colonies of P. helleri of which some were exclusive and others shared among geographic sub-groups. Statistical analysis showed high genetic differentiation between geographic areas sampled. Fragmentation of the Atlantic forest during Pleistocene glaciations is discussed as a possible cause of the present haplotype distribution and frequency.

Er:YAl(3)(BO(3))(4) glassy thin films from polymeric precursor and sol-gel methods: Waveguides for integrated optics

This paper presents the characterization of single-mode waveguides for 980 and 1550 nm wavelengths. High quality planar waveguide structure was fabricated from Y(1-x)Er(x)Al(3)(BO(3))(4) multilayer thin films with x = 0.02, 0.05, 0.1, 0.3, and 0.5, prepared through the polymeric precursor and sol-gel methods using spin-coating. The propagation losses of the planar waveguides varying from 0.63 to 0.88 dB/cm were measured at 632.8 and 1550 nm. The photoluminescence spectra and radiative lifetimes of the Er(3+) (4)I(13/2) energy level were measured in waveguiding geometry. For most samples the photoluminescence decay was single exponential with lifetimes in between 640 mu s and 200 mu s, depending on the erbium concentration and synthesis method. These results indicate that Er doped YAl(3)(BO(3))(4) compounds are promising for low loss waveguides. (C) 2009 Elsevier B.V. All fights reserved.

Structure-Based Approach for the Study of Estrogen Receptor Binding Affinity and Subtype Selectivity

Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpa (hER alpha) and beta (hER beta). Because the levels and relative proportion of hER alpha and hER beta differ significantly in different target cells, selective hER ligands could target specific tissues or pathways regulated by one receptor subtype without affecting the other. To understand the structural and chemical basis by which small molecule modulators are able to discriminate between the two subtypes, we have applied three-dimensional target-based approaches employing a series of potent hER-ligands. Comparative molecular field analysis (CoMFA) studies were applied to a data set of 81 hER modulators, for which binding affinity values were collected for both hER alpha and hER beta. Significant statistical coefficients were obtained (hER alpha, q(2) = 0.76; hER beta, q(2) = 0.70), indicating the internal consistency of the models. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. Five hER crystal structures were used in GRID/PCA investigations to generate molecular interaction fields (MIF) maps. hER alpha and hER beta were separated using one factor. The resulting 3D information was integrated with the aim of revealing the most relevant structural features involved in hER subtype selectivity. The final QSAR and GRID/PCA models and the information gathered from 3D contour maps should be useful for the design or novel hER modulators with improved selectivity.

The Aedes aegypti larval transcriptome: a comparative perspective with emphasis on trypsins and the domain structure of peritrophins

The genome sequence of Aedes aegypti was recently reported. A significant amount of Expressed Sequence Tags (ESTs) were sequenced to aid in the gene prediction process. In the present work we describe an integrated analysis of the genomic and EST data, focusing on genes with preferential expression in larvae (LG), adults (AG) and in both stages (SG). A total of 913 genes (5.4% of the transcript complement) are LG, including ion transporters and cuticle proteins that are important for ion homeostasis and defense. From a starting set of 245 genes encoding the trypsin domain, we identified 66 putative LG, AG, and SG trypsins by manual curation. Phylogenetic analyses showed that AG trypsins are divergent from their larval counterparts (LG), grouping with blood-induced trypsins from Anopheles gambiae and Simulium vittatum. These results support the hypothesis that blood-feeding arose only once, in the ancestral Culicomorpha. Peritrophins are proteins that interlock chitin fibrils to form the peritrophic membrane (PM) that compartmentalizes the food in the midgut. These proteins are recognized by having chitin-binding domains with 6 conserved Cys and may also present mucin-like domains (regions expected to be highly O-glycosylated). PM may be formed by a ring of cells (type 2, seen in Ae. aegypti larvae and Drosophila melanogaster) or by most midgut cells (type 1, found in Ae. aegypti adult and Tribolium castaneum). LG and D. melanogaster peritrophins have more complex domain structures than AG and T. castaneum peritrophins. Furthermore, mucin-like domains of peritrophins from T. castaneum (feeding on rough food) are lengthier than those of adult Ae. aegypti (blood-feeding). This suggests, for the first time, that type 1 and type 2 PM may have variable molecular architectures determined by different peritrophins and/or ancillary proteins, which may be partly modulated by diet.

Manager's task to support integrated autonomy at the workplace : Results from an intervention

A new managerial task arises in today’s working life: to provide conditions for and influence interaction between actors and thus to enable the emergence of organizing structure in tune with a changing environment. We call this the enabling managerial task. The goal of this paper is to study whether training first line managers in the enabling managerial task could lead to changes in the work for the subordinates. This paper presents results from questionnaires answered by the subordinates of the managers before and after the training. The training was organized as a learning network and consisted of eight workshops carried out over a period of one year (September 2009–June 2010), where the managers met with each other and the researchers once a month. Each workshop consisted of three parts, during three and a half hours. The first hour was devoted to joint reflection on a task that had been undertaken since the last workshop; some results were presented from the employee pre-assessments, followed by relevant theory and illuminating practices, finally the managers created new tasks for themselves to undertake during the following month. The subordinates’ answers show positive change in all of the seventeen scales used to assess it. The improvements are significant in scales measuring the relationship between the manager and the employees, as well as in those measuring interaction between employees. It is concluded that the result was a success for all managers that had the possibility of using the training in their management work.