Showing papers by "ETH Zurich published in 2003"

Regulation of Wound Healing by Growth Factors and Cytokines

Abstract: Werner, Sabine, and Richard Grose. Regulation of Wound Healing by Growth Factors and Cytokines. Physiol Rev 83: 835–870, 2003; 10.1152/physrev.00032.2002.—Cutaneous wound healing is a complex proce...

The Reuven Ramaty High-Energy Solar Spectroscopic Imager (Rhessi)

Abstract: RHESSI is the sixth in the NASA line of Small Explorer (SMEX) missions and the first managed in the Principal Investigator mode, where the PI is responsible for all aspects of the mission except the launch vehicle. RHESSI is designed to investigate particle acceleration and energy release in solar flares, through imaging and spectroscopy of hard X-ray/gamma-ray continua emitted by energetic electrons, and of gamma-ray lines produced by energetic ions. The single instrument consists of an imager, made up of nine bi-grid rotating modulation collimators (RMCs), in front of a spectrometer with nine cryogenically-cooled germanium detectors (GeDs), one behind each RMC. It provides the first high-resolution hard X-ray imaging spectroscopy, the first high-resolution gamma-ray line spectroscopy, and the first imaging above 100 keV including the first imaging of gamma-ray lines. The spatial resolution is as fine as ~ 2.3 arc sec with a full-Sun (≳ 1°) field of view, and the spectral resolution is ~ 1–10 keV FWHM over the energy range from soft X-rays (3 keV) to gamma-rays (17 MeV). An automated shutter system allows a wide dynamic range (> 107) of flare intensities to be handled without instrument saturation. Data for every photon is stored in a solid-state memory and telemetered to the ground, thus allowing for versatile data analysis keyed to specific science objectives. The spin-stabilized (~ 15 rpm) spacecraft is Sun-pointing to within ~ 0.2° and operates autonomously. RHESSI was launched on 5 February 2002, into a nearly circular, 38° inclination, 600-km altitude orbit and began observations a week later. The mission is operated from Berkeley using a dedicated 11-m antenna for telemetry reception and command uplinks. All data and analysis software are made freely and immediately available to the scientific community.

The structure of DNA in the nucleosome core

Abstract: The 1.9-A-resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non-histone protein-DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.

Particle-based fluid simulation for interactive applications

Abstract: Realistically animated fluids can add substantial realism to interactive applications such as virtual surgery simulators or computer games. In this paper we propose an interactive method based on Smoothed Particle Hydrodynamics (SPH) to simulate fluids with free surfaces. The method is an extension of the SPH-based technique by Desbrun to animate highly deformable bodies. We gear the method towards fluid simulation by deriving the force density fields directly from the Navier-Stokes equation and by adding a term to model surface tension effects. In contrast to Eulerian grid-based approaches, the particle-based approach makes mass conservation equations and convection terms dispensable which reduces the complexity of the simulation. In addition, the particles can directly be used to render the surface of the fluid. We propose methods to track and visualize the free surface using point splatting and marching cubes-based surface reconstruction. Our animation method is fast enough to be used in interactive systems and to allow for user interaction with models consisting of up to 5000 particles.

Pretreatment of Mice with Streptomycin Provides a Salmonella enterica Serovar Typhimurium Colitis Model That Allows Analysis of Both Pathogen and Host

Abstract: Salmonella enterica subspecies 1 serovar Typhimurium is a principal cause of human enterocolitis. For unknown reasons, in mice serovar Typhimurium does not provoke intestinal inflammation but rather targets the gut-associated lymphatic tissues and causes a systemic typhoid-like infection. The lack of a suitable murine model has limited the analysis of the pathogenetic mechanisms of intestinal salmonellosis. We describe here how streptomycin-pretreated mice provide a mouse model for serovar Typhimurium colitis. Serovar Typhimurium colitis in streptomycin-pretreated mice resembles many aspects of the human infection, including epithelial ulceration, edema, induction of intercellular adhesion molecule 1, and massive infiltration of PMN/CD18(+) cells. This pathology is strongly dependent on protein translocation via the serovar Typhimurium SPI1 type III secretion system. Using a lymphotoxin beta-receptor knockout mouse strain that lacks all lymph nodes and organized gut-associated lymphatic tissues, we demonstrate that Peyer's patches and mesenteric lymph nodes are dispensable for the initiation of murine serovar Typhimurium colitis. Our results demonstrate that streptomycin-pretreated mice offer a unique infection model that allows for the first time to use mutants of both the pathogen and the host to study the molecular mechanisms of enteric salmonellosis.

Bounded Model Checking

Abstract: Symbolic model checking with Binary Decision Diagrams (BDDs) has been successfully used in the last decade for formally verifying finite state systems such as sequential circuits and protocols. Since its introduction in the beginning of the 90's, it has been integrated in the quality assurance process of several major hardware companies. The main bottleneck of this method is that BDDs may grow exponentially, and hence the amount of available memory re- stricts the size of circuits that can be verified efficiently. In this article we survey a technique called Bounded Model Checking (BMC), which uses a propositional SAT solver rather than BDD manipulation techniques. Since its introduction in 1999, BMC has been well received by the industry. It can find many logical er- rors in complex systems that can not be handled by competing techniques, and is therefore widely perceived as a complementary technique to BDD-based model checking. This observation is supported by several independent comparisons that have been published in the last few years.

Repair of bone defects using synthetic mimetics of collagenous extracellular matrices.

Abstract: We have engineered synthetic poly(ethylene glycol) (PEG)-based hydrogels as cell-ingrowth matrices for in situ bone regeneration. These networks contain a combination of pendant oligopeptide ligands for cell adhesion (RGDSP) and substrates for matrix metalloproteinase (MMP) as linkers between PEG chains. Primary human fibroblasts were shown to migrate within these matrices by integrin- and MMP-dependent mechanisms. Gels used to deliver recombinant human bone morphogenetic protein-2 (rhBMP-2) to the site of critical- sized defects in rat crania were completely infiltrated by cells and were remodeled into bony tissue within five weeks. Bone regeneration was dependent on the proteolytic sensitivity of the matrices and their architecture. The cell-mediated proteolytic invasiveness of the gels and entrapment of rhBMP-2 resulted in efficient and highly localized bone regeneration.

Method for generation of homogeneous multicellular tumor spheroids applicable to a wide variety of cell types.

Abstract: Multicellular tumor spheroids (MCTS) are used as organotypic models of normal and solid tumor tissue. Traditional techniques for generating MCTS, such as growth on nonadherent surfaces, in suspension, or on scaffolds, have a number of drawbacks, including the need for manual selection to achieve a homogeneous population and the use of nonphysiological matrix compounds. In this study we describe a mild method for the generation of MCTS, in which individual spheroids form in hanging drops suspended from a microtiter plate. The method has been successfully applied to a broad range of cell lines and shows nearly 100% efficiency (i.e., one spheroid per drop). Using the hepatoma cell line, HepG2, the hanging drop method generated well-rounded MCTS with a narrow size distribution (coefficient of variation [CV] 10% to 15%, compared with 40% to 60% for growth on nonadherent surfaces). Structural analysis of HepG2 and a mammary gland adenocarcinoma cell line, MCF-7, composed spheroids, revealed highly organized, three-dimensional, tissue-like structures with an extensive extracellular matrix. The hanging drop method represents an attractive alternative for MCTS production, because it is mild, can be applied to a wide variety of cell lines, and can produce spheroids of a homogeneous size without the need for sieving or manual selection. The method has applications for basic studies of physiology and metabolism, tumor biology, toxicology, cellular organization, and the development of bioartificial tissue.

Geometric ad-hoc routing: of theory and practice

Abstract: All too often a seemingly insurmountable divide between theory and practice can be witnessed. In this paper we try to contribute to narrowing this gap in the field of ad-hoc routing. In particular we consider two aspects: We propose a new geometric routing algorithm which is outstandingly efficient on practical average-case networks, however is also in theory asymptotically worst-case optimal. On the other hand we are able to drop the formerly necessary assumption that the distance between network nodes may not fall below a constant value, an assumption that cannot be maintained for practical networks. Abandoning this assumption we identify from a theoretical point of view two fundamentamentally different classes of cost metrics for routing in ad-hoc networks.

Climate and the Collapse of Maya Civilization

Abstract: In the anoxic Cariaco Basin of the southern Caribbean, the bulk titanium content of undisturbed sediment reflects variations in riverine input and the hydrological cycle over northern tropical South America. A seasonally resolved record of titanium shows that the collapse of Maya civilization in the Terminal Classic Period occurred during an extended regional dry period, punctuated by more intense multiyear droughts centered at approximately 810, 860, and 910 A.D. These new data suggest that a century-scale decline in rainfall put a general strain on resources in the region, which was then exacerbated by abrupt drought events, contributing to the social stresses that led to the Maya demise.

Environmental exposure assessment of fluoroquinolone antibacterial agents from sewage to soil.

Abstract: The behavior of fluoroquinolone antibacterial agents (FQs) during mechanical−biological wastewater treatment was studied by mass flow analysis. In addition, the fate of FQs in agricultural soils after sludge application was investigated. Concentrations of FQs in filtered wastewater (raw sewage, primary, secondary, and tertiary effluents) were determined using solid-phase extraction with mixed phase cation exchange disk cartridges and reversed-phase liquid chromatography with fluorescence detection. FQs in suspended solids, sewage sludge (raw, excess, and anaerobically digested sludge), and sludge-treated soils were determined as described for the aqueous samples but preceded by accelerated solvent extraction. Wastewater treatment resulted in a reduction of the FQ mass flow of 88−92%, mainly due to sorption on sewage sludge. A sludge-wastewater partition coefficient (log Kd ∼ 4) was calculated in the activated sludge reactors with a hydraulic residence time of about 8 h. No significant removal of FQs occur...

Variation in immune defence as a question of evolutionary ecology

Abstract: The evolutionary-ecology approach to studying immune defences has generated a number of hypotheses that help to explain the observed variance in responses. Here, selected topics are reviewed in an attempt to identify the common problems, connections and generalities of the approach. In particular, the cost of immune defence, response specificity, sexual selection, neighbourhood effects and questions of optimal defence portfolios are discussed. While these questions still warrant further investigation, future challenges are the development of synthetic concepts for vertebrate and invertebrate systems and also of the theory that predicts immune responses based on a priori principles of evolutionary ecology.

Wireless sensor networks: a new regime for time synchronization

Abstract: Wireless sensor networks (WSNs) consist of large populations of wirelessly connected nodes, capable of computation, communication, and sensing. Sensor nodes cooperate in order to merge individual sensor readings into a high-level sensing result, such as integrating a time series of position measurements into a velocity estimate. The physical time of sensor readings is a key element in this process called data fusion. Hence, time synchronization is a crucial component of WSNs. We argue that time synchronization schemes developed for traditional networks such as NTP [23] are ill-suited for WSNs and suggest more appropriate approaches.

Compactness results in Symplectic Field Theory

Abstract: This is one in a series of papers devoted to the foundations of Symplectic Field Theory sketched in (4). We prove compactness results for moduli spaces of holomorphic curves arising in Symplectic Field Theory. The theorems generalize Gromov's compactness theorem in (8) as well as compactness theorems in Floer homology theory, (6, 7), and in contact geometry, (9, 19).

Worst-Case optimal and average-case efficient geometric ad-hoc routing

Abstract: In this paper we present GOAFR, a new geometric ad-hoc routing algorithm combining greedy and face routing. We evaluate this algorithm by both rigorous analysis and comprehensive simulation. GOAFR is the first ad-hoc algorithm to be both asymptotically optimal and average-case efficient. For our simulations we identify a network density range critical for any routing algorithm. We study a dozen of routing algorithms and show that GOAFR outperforms other prominent algorithms, such as GPSR or AFR.

The aerodynamics of free-flight maneuvers in Drosophila

Abstract: Using three-dimensional infrared high-speed video, we captured the wing and body kinematics of free-flying fruit flies as they performed rapid flight maneuvers. We then “replayed” the wing kinematics on a dynamically scaled robotic model to measure the aerodynamic forces produced by the wings. The results show that a fly generates rapid turns with surprisingly subtle modifications in wing motion, which nonetheless generate sufficient torque for the fly to rotate its body through each turn. The magnitude and time course of the torque and body motion during rapid turns indicate that inertia, not friction, dominates the flight dynamics of insects.

Predicting crystal structures: the Parrinello-Rahman method revisited.

Abstract: By suitably adapting a recent approach [A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12 562 (2002)]] we develop a powerful molecular dynamics method for the study of pressure-induced structural transformations. We use the edges of the simulation cell as collective variables and define a metadynamics that drives the system away from the local minimum towards a new crystal structure. In contrast to the Parrinello-Rahman method, our approach shows no hysteresis, and crystal structure transformations can occur at the equilibrium pressure. We illustrate the power of the method by studying the pressure-induced diamond to simple hexagonal phase transition in a model of silicon.

Cell-responsive synthetic hydrogels

Abstract: Keywords: Biomaterials ; Cells ; Hydrogels ; Peptides ; Tissue Engineering Reference UPLUT-ARTICLE-2003-003doi:10.1002/adma.200304621 Record created on 2008-05-26, modified on 2017-05-12

Ad hoc-VCG: a truthful and cost-efficient routing protocol for mobile ad hoc networks with selfish agents

Abstract: We introduce a game-theoretic setting for routing in a mobile ad hoc network that consists of greedy, selfish agents who accept payments for forwarding data for other agents if the payments cover their individual costs incurred by forwarding data. In this setting, we propose Ad hoc-VCG, a reactive routing protocol that achieves the design objectives of truthfulness (i.e., it is in the agents' best interest to reveal their true costs for forwarding data) and cost-efficiency (i.e., it guarantees that routing is done along the most cost-efficient path) in a game-theoretic sense by paying to the intermediate nodes a premium over their actual costs for forwarding data packets. We show that the total overpayment (i.e., the sum of all premiums paid) is relatively small by giving a theoretical upper bound and by providing experimental evidence. Our routing protocol implements a variation of the well-known mechanism by Vickrey, Clarke, and Groves in a mobile network setting. Finally, we analyze a very natural routing protocol that is an adaptation of the Packet Purse Model [8] with auctions in our setting and show that, unfortunately, it does not achieve cost-efficiency or truthfulness.

Cell-demanded release of VEGF from synthetic, biointeractive cell ingrowth matrices for vascularized tissue growth

Abstract: Local, controlled induction of angiogenesis remains a challenge that limits tissue engineering approaches to replace or restore diseased tissues. We present a new class of bioactive synthetic hydrogel matrices based on poly(ethylene glycol) (PEG) and synthetic peptides that exploits the activity of vascular endothelial growth factor (VEGF) alongside the base matrix functionality for cellular ingrowth, that is, induction of cell adhesion by pendant RGD-containing peptides and provision of cell-mediated remodeling by cross-linking matrix metalloproteinase substrate peptides. By using a Michael-type addition reaction, we incorporated variants of VEGF121 and VEGF165 covalently within the matrix, available for cells as they invade and locally remodel the material. The functionality of the matrix-conjugated VEGF was preserved and was critical for in vitro endothelial cell survival and migration within the matrix environment. Consistent with a scheme of locally restricted availability of VEGF, grafting of these VEGF-modified hydrogel matrices atop the chick chorioallontoic membrane evoked strong new blood vessel formation precisely at the area of graft-membrane contact. When implanted subcutaneously in rats, these VEGF-containing matrices were completely remodeled into native, vascularized tissue. This type of synthetic, biointeractive matrix with integrated angiogenic growth factor activity, presented and released only upon local cellular demand, could become highly useful in a number of clinical healing applications of local therapeutic angiogenesis.

Multi-scale Feature Extraction on Point-Sampled Surfaces

Abstract: We present a new technique for extracting line-type features on point-sampled geometry. Given an unstructured point cloud as input, our method first applies principal component analysis on local neighborhoods to classify points according to the likelihood that they belong to a feature. Using hysteresis thresholding, we then compute a minimum spanning graph as an initial approximation of the feature lines. To smooth out the features while maintaining a close connection to the underlying surface, we use an adaptation of active contour models. Central to our method is a multi-scale classification operator that allows feature analysis at multiple scales, using the size of the local neighborhoods as a discrete scale parameter. This significantly improves the reliability of the detection phase and makes our method more robust in the presence of noise. To illustrate the usefulness of our method, we have implemented a non-photorealistic point renderer to visualize point-sampled surfaces as line drawings of their extracted feature curves.

Shape modeling with point-sampled geometry

Abstract: We present a versatile and complete free-form shape modeling framework for point-sampled geometry. By combining unstructured point clouds with the implicit surface definition of the moving least squares approximation, we obtain a hybrid geometry representation that allows us to exploit the advantages of implicit and parametric surface models. Based on this representation we introduce a shape modeling system that enables the designer to perform large constrained deformations as well as boolean operations on arbitrarily shaped objects. Due to minimum consistency requirements, point-sampled surfaces can easily be re-structured on the fly to support extreme geometric deformations during interactive editing. In addition, we show that strict topology control is possible and sharp features can be generated and preserved on point-sampled objects. We demonstrate the effectiveness of our system on a large set of input models, including noisy range scans, irregular point clouds, and sparsely as well as densely sampled models.

Thermal and mechanical properties of plasticized poly(L‐lactic acid)

Abstract: Acetyl tri-n-butyl citrate (ATBC) and poly(ethyleneglycol)s (PEGs) with different molecular weights (from 400 to 10000) were used in this study to plasticize poly(L-lactic acid) (PLA). The thermal and mechanical properties of the plasticized polymer are reported. Both ATBC and PEG are effective in lowering the glass transition (Tg) of PLA up to a given concentration, where the plasticizer reaches its solubility limit in the polymer (50 wt % in the case of ATBC; 15–30 wt %, depending on molecular weight, in the case of PEG). The range of applicability of PEGs as PLA plasticizers is given in terms of PEG molecular weight and concentration. The mechanical properties of plasticized PLA change with increasing plasticizer concentration. In all PLA/plasticizer systems investigated, when the blend Tg approaches room temperature, a stepwise change in the mechanical properties of the system is observed. The elongation at break drastically increases, whereas tensile strength and modulus decrease. This behavior occurs at a plasticizer concentration that depends on the Tg-depressing efficiency of the plasticizer. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 1731–1738, 2003