Knowledge formalization in experience feedback processes : an ontology-based approach

Because of the current trend of integration and interoperability of industrial systems, their size and complexity continue to grow making it more difficult to analyze, to understand and to solve the problems that happen in their organizations. Continuous improvement methodologies are powerful tools in order to understand and to solve problems, to control the effects of changes and finally to capitalize knowledge about changes and improvements. These tools involve suitably represent knowledge relating to the concerned system. Consequently, knowledge management (KM) is an increasingly important source of competitive advantage for organizations. Particularly, the capitalization and sharing of knowledge resulting from experience feedback are elements which play an essential role in the continuous improvement of industrial activities. In this paper, the contribution deals with semantic interoperability and relates to the structuring and the formalization of an experience feedback (EF) process aiming at transforming information or understanding gained by experience into explicit knowledge. The reuse of such knowledge has proved to have significant impact on achieving themissions of companies. However, the means of describing the knowledge objects of an experience generally remain informal. Based on an experience feedback process model and conceptual graphs, this paper takes domain ontology as a framework for the clarification of explicit knowledge and know-how, the aim of which is to get lessons learned descriptions that are significant, correct and applicable

Developing and Modeling Scaffold Free Vascular Constructs

Despite a strong clinical demand for tissue replacement therapies, few tissue-engineered constructs (TECs) have attained FDA approval. Fewer still demonstrate long term viability of implanted cells, with root causes of failure of these devices identified as poor cell retention, poor vascularization, and inflammation following implantation. Focusing on the first two of these issues, we attempt to create a rapidly vascularizable TEC by optimizing a novel vascular implant model developed in our laboratory: the scaffold-free, prevascular endothelial-fibroblast construct (SPEC). The optimization process calls on a hybrid in vivo, in vitro, and in silico approach. We first developed an in vivo temporal model of TEC vascularization by comparing endothelial invasion, cord development, anastomosis, and vessel maturation dynamics of SPECs to avascular grafts such as fibroblast-only spheroids and silicone implants. While the existing microvessel architecture of the SPECs confers an advantage in anastomosis and endothelial infiltration of an implant in the first 12 hours post-implantation, poor lumen patency limits the rate of vessel development in the TECs. Perfusion is apparent at later time points (24-72 h) in both SPECs and fibroblast-only spheroids. Analysis of in vivo vascularization dynamics is augmented by a control flow simulation model which reveals that delayed vascular development coincides with poor accumulation of pro-angiogenic factors such as VEGF. Our in vivo observations drove corrections of our SPEC model, with efforts undertaken to improve lumen formation during the in vitro development period. These approaches include pre-dosing implants with pro-angiogenic factors such as VEGF, inducing endothelial cell realignments in a perfusion chamber, and incorporation of perivascular cells to improve patency of forming tubes. Recombinant human VEGF165 (rhVEGF165) dosing was most consistently associated with increased formation of endothelial-lined lumens, with a dose (ranging from 0-50 ng/mL) and time dependent increase in diameters of these lumens during SPEC formation. Finally, we generated computational models of SPEC formation in a rhVEGF165 field in order to combine our observations of endothelial clustering behavior, SPEC reorganization, and dose/time dependent cord hollowing behavior observed in vitro with existing stochastic models of tissue assembly and cell-cell interface optimization. Through careful control of model parameters, we generated a list of in silico simulations to enable optimization of vascularization response, ultimately resulting in a list of candidate treatments built on the backbone of VEGF pre-dosing. This candidate list can serve as a starting point for future experiments, with a goal of rapid and stable lumen formation and blood perfusion

Comparative evaluation of approaches in T.4.1-4.3 and working definition of adaptive module

The goal of this deliverable is two-fold: (1) to present and compare different approaches towards learning and encoding movements us- ing dynamical systems that have been developed by the AMARSi partners (in the past during the first 6 months of the project), and (2) to analyze their suitability to be used as adaptive modules, i.e. as building blocks for the complete architecture that will be devel- oped in the project. The document presents a total of eight approaches, in two groups: modules for discrete movements (i.e. with a clear goal where the movement stops) and for rhythmic movements (i.e. which exhibit periodicity). The basic formulation of each approach is presented together with some illustrative simulation results. Key character- istics such as the type of dynamical behavior, learning algorithm, generalization properties, stability analysis are then discussed for each approach. We then make a comparative analysis of the different approaches by comparing these characteristics and discussing their suitability for the AMARSi project

Role-based Data Management

Database systems build an integral component of today’s software systems and as such they are the central point for storing and sharing a software system’s data while ensuring global data consistency at the same time. Introducing the primitives of roles and their accompanied metatype distinction in modeling and programming languages, results in a novel paradigm of designing, extending, and programming modern software systems. In detail, roles as modeling concept enable a separation of concerns within an entity. Along with its rigid core, an entity may acquire various roles in different contexts during its lifetime and thus, adapts its behavior and structure dynamically during runtime. Unfortunately, database systems, as important component and global consistency provider of such systems, do not keep pace with this trend. The absence of a metatype distinction, in terms of an entity’s separation of concerns, in the database system results in various problems for the software system in general, for the application developers, and finally for the database system itself. In case of relational database systems, these problems are concentrated under the term role-relational impedance mismatch. In particular, the whole software system is designed by using different semantics on various layers. In case of role-based software systems in combination with relational database systems this gap in semantics between applications and the database system increases dramatically. Consequently, the database system cannot directly represent the richer semantics of roles as well as the accompanied consistency constraints. These constraints have to be ensured by the applications and the database system loses its single point of truth characteristic in the software system. As the applications are in charge of guaranteeing global consistency, their development requires more effort in data management. Moreover, the software system’s data management is distributed over several layers, which results in an unstructured software system architecture. To overcome the role-relational impedance mismatch and bring the database system back in its rightful position as single point of truth in a software system, this thesis introduces the novel and tripartite RSQL approach. It combines a novel database model that represents the metatype distinction as first class citizen in a database system, an adapted query language on the database model’s basis, and finally a proper result representation. Precisely, RSQL’s logical database model introduces Dynamic Data Types, to directly represent the separation of concerns within an entity type on the schema level. On the instance level, the database model defines the notion of a Dynamic Tuple that combines an entity with the notion of roles and thus, allows for dynamic structure adaptations during runtime without changing an entity’s overall type. These definitions build the main data structures on which the database system operates. Moreover, formal operators connecting the query language statements with the database model data structures, complete the database model. The query language, as external database system interface, features an individual data definition, data manipulation, and data query language. Their statements directly represent the metatype distinction to address Dynamic Data Types and Dynamic Tuples, respectively. As a consequence of the novel data structures, the query processing of Dynamic Tuples is completely redesigned. As last piece for a complete database integration of a role-based notion and its accompanied metatype distinction, we specify the RSQL Result Net as result representation. It provides a novel result structure and features functionalities to navigate through query results. Finally, we evaluate all three RSQL components in comparison to a relational database system. This assessment clearly demonstrates the benefits of the roles concept’s full database integration

From Image-based Motion Analysis to Free-Viewpoint Video

The problems of capturing real-world scenes with cameras and automatically analyzing the visible motion have traditionally been in the focus of computer vision research. The photo-realistic rendition of dynamic real-world scenes, on the other hand, is a problem that has been investigated in the field of computer graphics. In this thesis, we demonstrate that the joint solution to all three of these problems enables the creation of powerful new tools that are benecial for both research disciplines. Analysis and rendition of real-world scenes with human actors are amongst the most challenging problems. In this thesis we present new algorithmic recipes to attack them. The dissertation consists of three parts: In part I, we present novel solutions to two fundamental problems of human motion analysis. Firstly, we demonstrate a novel hybrid approach for markerfree human motion capture from multiple video streams. Thereafter, a new algorithm for automatic non-intrusive estimation of kinematic body models of arbitrary moving subjects from video is detailed. In part II of the thesis, we demonstrate that a marker-free motion capture approach makes possible the model-based reconstruction of free-viewpoint videos of human actors from only a handful of video streams. The estimated 3D videos enable the photo-realistic real-time rendition of a dynamic scene from arbitrary novel viewpoints. Texture information from video is not only applied to generate a realistic surface appearance, but also to improve the precision of the motion estimation scheme. The commitment to a generic body model also allows us to reconstruct a time-varying reflectance description of an actor`s body surface which allows us to realistically render the free-viewpoint videos under arbitrary lighting conditions. A novel method to capture high-speed large scale motion using regular still cameras and the principle of multi-exposure photography is described in part III. The fundamental principles underlying the methods in this thesis are not only applicable to humans but to a much larger class of subjects. It is demonstrated that, in conjunction, our proposed algorithmic recipes serve as building blocks for the next generation of immersive 3D visual media.Die Entwicklung neuer Algorithmen zur optischen Erfassung und Analyse der Bewegung in dynamischen Szenen ist einer der Forschungsschwerpunkte in der computergestützten Bildverarbeitung. Während im maschinellen Bildverstehen das Augenmerk auf der Extraktion von Informationen liegt, konzentriert sich die Computergrafik auf das inverse Problem, die fotorealistische Darstellung bewegter Szenen. In jüngster Vergangenheit haben sich die beiden Disziplinen kontinuierlich angenähert, da es eine Vielzahl an herausfordernden wissenschaftlichen Fragestellungen gibt, die eine gemeinsame Lösung des Bilderfassungs-, des Bildanalyse- und des Bildsyntheseproblems verlangen. Zwei der schwierigsten Probleme, welche für Forscher aus beiden Disziplinen eine große Relevanz besitzen, sind die Analyse und die Synthese von dynamischen Szenen, in denen Menschen im Mittelpunkt stehen. Im Rahmen dieser Dissertation werden Verfahren vorgestellt, welche die optische Erfassung dieser Art von Szenen, die automatische Analyse der Bewegungen und die realistische neue Darstellung im Computer erlauben. Es wid deutlich werden, dass eine Integration von Algorithmen zur Lösung dieser drei Probleme in ein Gesamtsystem die Erzeugung völlig neuartiger dreidimensionaler Darstellungen von Menschen in Bewegung ermöglicht. Die Dissertation ist in drei Teile gegliedert: Teil I beginnt mit der Beschreibung des Entwurfs und des Baus eines Studios zur zeitsynchronen Erfassung mehrerer Videobildströme. Die im Studio aufgezeichneten Multivideosequenzen dienen als Eingabedaten für die im Rahmen dieser Dissertation entwickelten videogestützten Bewegunsanalyseverfahren und die Algorithmen zur Erzeugung dreidimensionaler Videos. Im Anschluß daran werden zwei neu entwickelte Verfahren vorgestellt, die Antworten auf zwei fundamentale Fragen in der optischen Erfassung menschlicher Bewegung geben, die Messung von Bewegungsparametern und die Erzeugung von kinematischen Skelettmodellen. Das erste Verfahren ist ein hybrider Algorithmus zur markierungslosen optischen Messung von Bewegunsgparametern aus Multivideodaten. Der Verzicht auf optische Markierungen wird dadurch ermöglicht, dass zur Bewegungsanalyse sowohl aus den Bilddaten rekonstruierte Volumenmodelle als auch leicht zu erfassende Körpermerkmale verwendet werden. Das zweite Verfahren dient der automatischen Rekonstruktion eines kinematischen Skelettmodells anhand von Multivideodaten. Der Algorithmus benötigt weder optischen Markierungen in der Szene noch a priori Informationen über die Körperstruktur, und ist in gleicher Form auf Menschen, Tiere und Objekte anwendbar. Das Thema das zweiten Teils dieser Arbeit ist ein modellbasiertes Verfahrenzur Rekonstruktion dreidimensionaler Videos von Menschen in Bewegung aus nur wenigen zeitsynchronen Videoströmen. Der Betrachter kann die errechneten 3D Videos auf einem Computer in Echtzeit abspielen und dabei interaktiv einen beliebigen virtuellen Blickpunkt auf die Geschehnisse einnehmen. Im Zentrum unseres Ansatzes steht ein silhouettenbasierter Analyse-durch-Synthese Algorithmus, der es ermöglicht, ohne optische Markierungen sowohl die Form als auch die Bewegung eines Menschen zu erfassen. Durch die Berechnung zeitveränderlicher Oberächentexturen aus den Videodaten ist gewährleistet, dass eine Person aus jedem beliebigen Blickwinkel ein fotorealistisches Erscheinungsbild besitzt. In einer ersten algorithmischen Erweiterung wird gezeigt, dass die Texturinformation auch zur Verbesserung der Genauigkeit der Bewegunsgssch ätzung eingesetzt werden kann. Zudem ist es durch die Verwendung eines generischen Körpermodells möglich, nicht nur dynamische Texturen sondern sogar dynamische Reektionseigenschaften der Körperoberäche zu messen. Unser Reektionsmodell besteht aus einer parametrischen BRDF für jeden Texel und einer dynamischen Normalenkarte für die gesamte Körperoberäche. Auf diese Weise können 3D Videos auch unter völlig neuen simulierten Beleuchtungsbedingungen realistisch wiedergegeben werden. Teil III dieser Arbeit beschreibt ein neuartiges Verfahren zur optischen Messung sehr schneller Bewegungen. Bisher erforderten optische Aufnahmen von Hochgeschwindigkeitsbewegungen sehr teure Spezialkameras mit hohen Bildraten. Im Gegensatz dazu verwendet die hier beschriebene Methode einfache Digitalfotokameras und das Prinzip der Multiblitzfotograe. Es wird gezeigt, dass mit Hilfe dieses Verfahrens sowohl die sehr schnelle artikulierte Handbewegung des Werfers als auch die Flugparameter des Balls während eines Baseballpitches gemessen werden können. Die hochgenau erfaßten Parameter ermöglichen es, die gemessene Bewegung in völlig neuer Weise im Computer zu visualisieren. Obgleich die in dieser Dissertation vorgestellten Verfahren vornehmlich der Analyse und Darstellung menschlicher Bewegungen dienen, sind die grundlegenden Prinzipien auch auf viele anderen Szenen anwendbar. Jeder der beschriebenen Algorithmen löst zwar in erster Linie ein bestimmtes Teilproblem, aber in Ihrer Gesamtheit können die Verfahren als Bausteine verstanden werden, welche die nächste Generation interaktiver dreidimensionaler Medien ermöglichen werden

Endoplasmic Reticulum Dynamic Structural Changes in Neurons: The Fission-Fusion Phenomena

The endoplasmic reticulum (ER) is crucial for protein synthesis and protein maturation, is involved in cell stress and serves in neurons as the major intracellular Ca2+ store. Neuronal ER forms a continuous network of cisterns and tubules extending from soma to a subset of dendritic spines. The continuity of ER structure is important for maintaining ER basic functions and necessary for proteins and ions to diffuse and equilibrate within its lumen. We show that ER in neurons can undergo rapid fission (=fragmentation) and subsequently fusion. This phenomenon was previously unknown in neurons. Our findings show that ER fission is induced during N-methyl D-aspartate (NMDA) receptor-mediated Ca2+ entry to the cell in murine primary cultures and hippocampal slice cultures. Using different pharmacological approaches, we demonstrate, that ER fission is triggered independently on Ca2+ from ER stores. Subsequently, we show that mild hypothermia, reported to be protective in experimental stroke models, enhances ER fragmentation. Finally, we validate the occurrence of rapid neuronal ER fission in an animal cardiac arrest model of cerebral ischemia. We assessed ER structure using confocal microscopy live cell and tissue imaging, 2-photon laser scanning microscopy and transmission electron microscopy (TEM). The fluorescence imaging was performed on murine primary cultures cotransfected to express cytosolic and ER-specific markers; hippocampal slices from transgenic mice expressing ER-specific marker; as well as in transgenic living animals. To characterize the fission-fusion in a quantitative way, we developed a new data analysis method based on fluorescence recovery after photobleaching (FRAP). Our data show that neuronal ER is a dynamic organelle. We propose a model of ER continuity, where ER is in equilibrium with fission-fusion events. Stimulation of NMDA receptors shifts the equilibrium towards the fragmentation, while inhibiting NMDA receptors promotes the continuous state of ER. We conclude that ER fission-fusion may be of importance in physiology and disease. The molecular machinery regulating the reversible changes in ER morphology remains unknown

The Structure and Function of GLFGs in the Nuclear Pore Complex of Yeast

The nuclear pore complex (NPC) is a large multiprotein complex which perforates the nuclear envelope. The NPC is made up of nuclear pore proteins (Nups), one third of which are phenylalanine-glycine (FG) containing. The NPC has a role in controlling movement of molecules between the nucleus and the cytoplasm. The FG Nups fill the NPC’s centre and regulate translocation. There are many different proposed models of how FG Nups may regulate translocation from them reeling cargo complexes into the NPC to inter FG repeats binding to create a gel-like meshwork into which specific cargo can enter and translocate. Using transmission electron microscopy the glycine-leucine-phenylalanine-glycine (GLFG) domains of Nups are mapped, showing a cytoplasmic bias within the wild type (WT) NPC and also in FG domain deletion mutants. FG deletion mutants have higher percentages of GLFG labelling towards the NPC edge than WT and lower percentages towards the middle than WT. GLFG domain labelling is also observed ‘reaching’ to membrane structures from the NPC. Serial sectioning of individual NPCs confirmed that individual NPCs had different distributions of GLFG labelling, which was on the nucleoplasmic or cytoplasmic side, or on both sides. Mutants which are defective in the nucleotide exchange activity of the RanGEF, Prp20, have a deficiency of the active RanGTP molecular switch. This causes a shift in the GLFG labelling from the cytoplasmic side towards the nucleoplasmic side. Similarly the import of Kap121-dependant import cargo causes a shift from cytoplasmic to nucleoplasmic labelling. This is observed as the cargo reaches the midplane of the NPC. Field emission scanning electron microscopy shows GLFG labelling to be associated with filaments (cytoplasmic, internal and nucleoplasmic) and possibly also the transporter. Finally, a model based on the shift in GLFG labelling is developed. This model suggests that there is a collapse and ‘reel in’ of import cargo as in the reversible collapse model, there is then a restructure of GLFG domains into the nucleoplasm due to potentially passing cargo on