Third Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Aarhus, Denmark, August 29-31, 2001

This booklet contains the proceedings of the Third Workshop on Practical Use of Coloured Petri Nets and the CPN Tools, August 29-31, 2001. The workshop is organised by the CPN group at Department of Computer Science, University of Aarhus, Denmark. The papers are also available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop01

Actuation, Sensing And Control For Micro Bio Robots

The continuing trend in miniaturization of technology, advancements in micro and nanofabrication and improvements in high-resolution imaging has enabled micro- and meso-scale robots that have many applications. They can be used for micro-assembly, directed drug delivery, microsurgery and high-resolution measurement. In order to create microrobots, microscopic sensors, actuators and controllers are needed. Unique challenges arise when building microscale robots. For inspiration, we look toward highly capable biological organisms, which excel at these length scales. In this dissertation we develop technologies that combine biological components and synthetic components to create actuation, sensing and assembly onboard microrobots. For actuation, we study the dynamics of synthetic micro structures that have been integrated with single-cell biological organisms to provide un-tethered onboard propulsion to the microrobot. For sensing, we integrate synthetically engineered sensor cells to enable a system capable of detecting a change in the local environment, then storing and reporting the information. Furthermore, we develop a bottom-up fabrication method using a macroscopic magnetic robot to direct the assembly of inorganic engineered micro structures. We showcase the capability of this assembly method by demonstrating highly-specified, predictable assembly of microscale building blocks in a semi-autonomous experiment. These magnetic robots can be used to program the assembly of passive building blocks, with the building blocks themselves having the potential to be arbitrarily complex. We extend the magnetic robot actuation work to consider control algorithms for multiple robots by exploiting spatial gradients of magnetic fields. This thesis makes contributions toward actuation, sensing and control of autonomous micro systems and provides technologies that will lead to the development of swarms of microrobots with a suite of manipulation and sensing capabilities working together to sense and modify the environment

Understanding Corrosion in Modular Acetabular Tapers: Retrieval Analysis, In Vitro Testing and Cell-Material Interactions

Modular metal-on-metal acetabular tapers comprise two overarching design categories: a titanium shell and a metal/ceramic/polymer liner pair, or a dual-mobility articulation design with an added polymeric insert containing a freely rotating femoral head. Both designs often include a metal-on-metal (MoM) or modular dual-mobility (MDM) shell-liner interfaces, which is prone to corrosion and associated local effects. The goals of this dissertation were to document and distinguish between corrosion modes at this modular junction, to design in vitro test methods to characterize mechanical modes, and to examine their interactions with macrophages, which represent a critical part of the immune response. Through retrieval analysis, we established that MoM acetabular tapers are less susceptible to mechanically-assisted corrosion (MAC). Retrieved CoCrMo liners revealed a prevalence of chemically driven corrosion damage modes (intergranular corrosion (IGC), pitting, phase boundary corrosion (PBC)) over mechanically-driven ones (fretting corrosion, large-scale wear, stress cracking). Importantly, corrosion was detected outside engagement regions, where no physical interfacial contact can occur, or tight crevice exists. Cellular remnants were also identified within these tight crevice-like taper surfaces, which fit a narrow size distribution similar to macrophages. In vitro testing revealed that contact areas between shell-liner pairs remained a fraction of the total taper surface area, which translated to low currents (under 1µA) generated over a short-term incremental cyclic loading test. An electrochemical impedance spectroscopy (EIS)-based method was used to examine resulting impedance changes in retrieved CoCrMo liner surfaces associated with specific surface features, associated with IGC, oxide deposits and PBC. Indeed, surface impedance was correlated to the type of surface damage. Impedance analysis proved to be a valuable tool for identifying corrosion modes and adds a quantitative method to the retrieval analysis paradigm. Finally, we developed assays to examine macrophage viability outcomes in response to different corrosion and fretting corrosion stimuli. Ongoing fretting corrosion, and the associated debris generation and negative potential shifts seemed to be the most influential factors on macrophage mortality. In a separate study, where CoCrMo alloy was corroded at high anodic potentials to generate ions and debris, we found macrophage mortality was affected in a dose-dependent manner, primarily by chromium ions in culture media, whereas solid cobalt oxide debris particles killed macrophages in a proximity-dependent manner. A sublethal dose (LD50) of metal ions was found to induce a weak proinflammatory response, measured by cytokine (TNF-α, interleukin (IL)-1β, IFN-γ and IL-27) and chemokine expression, at 24 h. We also detected comparable levels of IL-13, which is a known mediator of the anti-inflammatory M2 phenotype in macrophages. With the results described in this study, we can conclude that chemically driven corrosion modes dominate acetabular taper corrosion over mechanical modes. Corrosion byproducts might also initiate adverse local reactions by inducing cell death and activation of macrophages. Thus, MoM acetabular junctions represent a significant factor in total hip arthroplasty outcomes. Since MDM device usage is on the rise owing to its excellent outcomes in high dislocation risk patients, understanding possible corrosion and associated phagocytic responses proves to be crucial in ensuring satisfactory patient outcomes and to make prudent decisions during surgical planning in terms of device and material choices

Proceedings of the 26th International Symposium on Theoretical Aspects of Computer Science (STACS'09)

The Symposium on Theoretical Aspects of Computer Science (STACS) is held alternately in France and in Germany. The conference of February 26-28, 2009, held in Freiburg, is the 26th in this series. Previous meetings took place in Paris (1984), Saarbr¨ucken (1985), Orsay (1986), Passau (1987), Bordeaux (1988), Paderborn (1989), Rouen (1990), Hamburg (1991), Cachan (1992), W¨urzburg (1993), Caen (1994), M¨unchen (1995), Grenoble (1996), L¨ubeck (1997), Paris (1998), Trier (1999), Lille (2000), Dresden (2001), Antibes (2002), Berlin (2003), Montpellier (2004), Stuttgart (2005), Marseille (2006), Aachen (2007), and Bordeaux (2008). ..

Data visualizing popular science fiction movies with use of circular hierarchical edge bundling

In this article, a specific type of data visualization method called Circular Hierarchical Edge Bundling has been utilized to investigate a subjective discussion on determining the most commonly observed themes in the popular Sci-Fi Movies. To reflect people’s opinions on the subject, a website (www.dystopia-utopia.com) has been designed to invite larger communities to participate in with filling an online form to deliver their judgments. Data Visualization methods and the research results are elaborated in further details

Resistance is Futile: Physical Science, Systems Biology and Single-Cell Analysis to Understanding the Plastic and Heterogeneous Nature of Melanoma and Their Role in Non-Genetic Drug Resistance

Melanoma is the most deadly form of skin cancer due to its great metastatic potential. Targeted therapy that inhibits the BRAF-V600E driver mutation has shown impressive initial responses in melanoma patients. However, drug resistance, as the universal phenomenon for any cancer therapy, always limits treatment efficacy and compromises outcomes. As the early-step of resistance development, non-genetic mechanisms enable cancer cells to transition into a drug-resistant state in as early as a few days after drug treatment without alteration of the genome. This early mechanism is, to a large extent, due to the heterogeneous and highly plastic nature of tumor cells. Therefore, it imperative to understand the plastic and heterogeneous nature of the melanoma cells in order to identify combination therapies that can overcome resistance. In this thesis, we investigate these two fundamental natures of non-genetic drug resistance using BRAF inhibition of BRAF-mutant melanomas as the model system. These melanoma cells undergo multi-step, reversible drug-induced cell-state transitions from the original sensitive phenotype to a drug-resistant one. We first conducted bulk analysis to characterize the detailed kinetics of the entire transition from drug-sensitive state towards drug-resistant state, revealing expression changes of thousands of genes and extensive chromatin remodeling. A 3-step computational biology approach greatly simplified the complexity and revealed that the whole cell-state transition was controlled by a gene module activated within just the first three days of drug treatment, with the RelA transcription factor driving chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes towards resistance. From there, a detailed mechanism connecting tumor epigenetic plasticity with non-genetic drug resistance was resolved through in-depth molecular biology experiments. The mechanism was validated in clinical patient samples. We further investigated heterogeneity by moving from bulk cellular studies to single-cell analysis. The single-cell view further revealed that two driving forces from both cell-state interconversions and phenotype-specific drug selection control the cell-state transition dynamics. The single-cell studies also pinpointed the signaling network hub, RelA, as the driver molecule of the initiation of the adaptive transition. These two competing driving forces were further quantitatively modeled via a thermodynamic-inspired surprisal analysis and a modified Fokker-Planck-type kinetic model. Finally, using integrated single-cell proteomic and metabolic technology I developed to characterize the early-stage signaling and metabolic changes upon initial drug responses, we further identified two distinct paths connecting drug-sensitive and drug-tolerant states. Melanoma cells exclusively traverse one of the two paths depending on the level of MITF in the drug-naïve cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities and are independently druggable. In total, this thesis combines and synergizes various physical science and systems biology approaches together with several unique single-cell technologies and analysis to obtain a deep and comprehensive understanding of non-genetic drug resistance in cancer. The findings from this thesis provide several novel insights into the rational design of effective combination therapy for overcoming the development of resistance in response to cancer treatments.</p

Image Understanding by Socializing the Semantic Gap

Several technological developments like the Internet, mobile devices and Social Networks have spurred the sharing of images in unprecedented volumes, making tagging and commenting a common habit. Despite the recent progress in image analysis, the problem of Semantic Gap still hinders machines in fully understand the rich semantic of a shared photo. In this book, we tackle this problem by exploiting social network contributions. A comprehensive treatise of three linked problems on image annotation is presented, with a novel experimental protocol used to test eleven state-of-the-art methods. Three novel approaches to annotate, under stand the sentiment and predict the popularity of an image are presented. We conclude with the many challenges and opportunities ahead for the multimedia community

The Cytoskeleton of Diatoms : Structural and Genomic Analysis

The cytoskeleton is essential for many cellular functions such as cell motility, the control of cell shape and polarity, meiosis, cytokinesis, intracellular transport as well as endo- and exocytosis. The present study analyses the diatom actin and microtubule (MT) cytoskeleton from various sides: visualization through immunolabeling and reporter genes, as well as by in silico genomic analyses. This study presents for the first time immunolabeling of actin, α -tubulin, γ -tubulin as single label or in combinations in Craticula cuspidata. The actin cytoskeleton of this species is divers with a radially arranged fine cortical actin meshwork, a dens dynamic actin network in the deeper cytoplasm without obvious orientation and two thick prominent actin bundles parallel to the raphe. The actin drug, jasplakinolide allowed to gain insight into the dynamics of these structures. The results combined with previous publications indicate that the raphe bundles are highly dynamic structures recovering at a very fast speed after inhibitor treatment. Indicating, that actin filaments contributing to these bundles nucleate all along the raphe simultaneously rather than elongate unidirectional from the cell poles. Co-localization of γ -tubulin and MTs demonstrated the existence of multiple MT organizing centers (MTOCs) on the nuclear surface. MTs radiate out form the MTOCs into the periphery and further towards the cell poles, thus forming a highly symmetrical MT system. Cylindrotheca fusiformis was successfully transformed with the actin reporter, Lifeact-GFP. Expression of this construct allowed the visualization of all actin structures that were also labeled by immunofluorescence, such as the fine, cortical meshwork, the deeper cytoplasmic network and the thick bundles underneath the raphe. Now the experimental tool is available to address questions concerning the dynamics of the actin cytoskeleton and the connection of the actin cytoskeleton to the locomotion process of pennate diatoms. This study focuses also on an in silico genome inventory of actin, actin-related proteins (ARPs) and actin-binding proteins (ABPs) encoded in the genomes of Thalassiosira pseudonana, Thalassiosira oceanica, Phaeodactylum tricornutum, Fragilariopsis cylindrus and Pseudo-nitzschia multiseries. The comparative genomic and phylogenetic study revealed, that most diatoms possess only a single conventional actin and a small set of ARPs and ABPs. Among these are the highly conserved cytoplasmic Arp1 protein and the nuclear Arp4 as well as Arp6. The genomes of the diatoms contain two structurally different homologues of Arp4 that might serve specific functions. All diatom species, examined here lack the ARP2/3-complex, which is essential in most eukaryotes for actin filament branching and plus- end dynamics. Diatoms encode a small set of ABPs, which should be efficient enough to regulate the disassembly of F-actin, the recycling of G-actin, as well as the capping of filaments and their anchoring to membranes. However, none of the sequenced representatives of the Bacillariophyta phylum encode for the essential actin regulating protein profilin. This is the first incidence of organisms not containing profilin. The hypothesis is put forward that disassembled ADP-actin is recycled back to ATP-actin by CAPs, though it remains unclear, how the activated actin is dissociated from CAPs to become available for polymerization at the filament plus-ends. Diatoms possess several multidomain variants of formin. All of them lack the profilin binding domain (FH1) suggesting that they are probably not capable of accelerating plus-end dynamics, a well studied function of formins in most other organisms. It therefore appears that diatoms have developed a novel, yet unknown way of filament growth and regulation of rapid filament elongation. This characteristic seems to have spread among the Stramenopiles, as most Stramenopila predominantly code for formins without a FH1 domain, but in diatoms it is most distinctly expressed

Construction of artificial skin tissue with placode-like structures in well-defined patterns using dielectrophoresis

During embryonic development of animal skin tissue, the skin cells form regular patterns of high cell density (placodes) where hair or feathers will be formed. These placodes are thought to be formed by the aggregation of dermal cells into condensates. The aggregation process is thought to be controlled by a reaction-diffusion mechanism of activator and inhibitor molecules, and involve mechanical forces between cells and cells with the matrix. In this project, placode formation in chicken embryonic skin cells was used as a model system for the study of the mechanism by which the placodes are formed. Artificial aggregates of chicken embryonic skin cells were created by suspending them in a 300 mM low conductivity sorbitol solution and attracting them by positive dielectrophoresis to high field regions within microelectrode arrays by applying a 10 - 20 Vpk-pk 1 MHz signal across the microelectrodes. It was demonstrated that using this method aggregates can be produced in a large variety of patterns and that the distance between the aggregates and aggregate size and shape within the pattern can be controlled effectively. Custom-built image analysis tools were developed in LabVIEW to analyze the patterns formed. The formation of aggregates by dielectrophoresis was followed by an immobilization phase of the resulting patterns inside a gel matrix, forming an artificial skin. Nutrients and oxygen were supplied externally. Long-term incubation of the artificial skin shows that embryonic skin cells in the aggregates were viable and showed behavior similar to that of developing embryonic skin, including further aggregation of the cells and the formation of cell condensates. The domain size was shown to have an influence on the condensation process, with cells in small aggregates forming only one condensate near the centre of the aggregate, and several condensates in larger aggregates. Whilst the distribution of cell condensates within the aggregates in round large aggregates is predominantly random, some line formation could be observed in linear aggregations, indicating some self-organization may be occurring