Traveling-wave Phenomena in a Model of Autocrine Signaling Coupled with Dynamics of the MAPK Cascade

Recently we have revealed a minimal reaction subnetwork in the MAPK (mitogen-activated protein kinase) cascade that is responsible for the emergence of bistable and oscillatory behavior. Here we examine a possible mechanism that provides for the propagation of increased MAPK activity in cell populations by interconnecting the intracellular MAPK subnetwork with the ligand-receptor signaling machinery. Such approach allows for significant reduction of the dimensionality of the parameter space on one hand and the conservation of dynamical complexity of the system on the other hand. The coupled model predicts coexistence of one, two or three different stable steady states, or the coexistence of a stable steady state and periodic solution. We found two robust and physiologically relevant characteristics of the proposed model: (i) There is a very large region of coexistence of at least one stable steady state with non-zero MAPK activity and one steady state with zero MAPK activity in the parameter space. (ii) Spontaneous traveling front waves always switching originally inactive cells into ligand releasing cells emerge in adjacent cell populations, e. g. in healthy and injured tissues. Moreover, the formation of composite traveling front waves and spatial oscillatory patterns of MAPK activity are predicted and discussed.     

Partition coefficients of environmentally important phenols in a supercritical carbon dioxide-water system from cocurrent extraction without analysis of the compressible phase

Partition coefficients of phenol, salicylic acid, and several environmentally important chloro- and nitrophenols in a supercritical CO2-water system were measured using direct cocurrent extraction of aqueous solutions of the individual solutes with CO2. Partitioning data on the nitrophenols and salicylic acid were obtained for the first time. To bypass the troublesome and error-prone analysis of the CO2-rich phase, the present method employed only the solute concentrations in the aqueous phase before and after extraction to determine the partition coefficient. Unlike most previous engineering studies of phenol partitioning in a CO2-water system, the concentrations of phenolic solutes approached infinite dilution in both phases. This makes the results relevant to analytical-scale SFE of environmental water samples with CO2. Because of effective infinite dilution of the solutes, the partition coefficients provide a direct measure of relative CO2-philicity/hydrophilicity of the individual phenols. Compared to the octanol-water partition coefficients of substituted phenols, the CO2-water partition coefficients are more sensitive to substitution in the position neighboring the hydroxyl group.     

Determining link weight system under various objectives for OSPF networks using a Lagrangian relaxation-based approach

An important traffic engineering problem for OSPF networks is the determination of optimal link weights. Certainly, this depends on the traffic engineering objective. Regardless, often a variety of performance measures may be of interest to a network provider due to their impact on the network. In this paper, we consider different objectives and discuss how they impact the determination of the link weights and different performance measures. In particular, we propose a composite objective function; furthermore, we present a Lagrangian relaxation-based dual approach to determine the link weight system. We then consider different performance measures and discuss the effectiveness of different objectives through computational studies of a variety of network topologies. We find that our proposed composite objective function with Lagrangian relaxation-based dual approach is very effective in meeting different performance measures and is computationally very fast.     

ATR artificial brain project: 2004 progress report

This article presents the key assumptions and current status of the ATR Artificial Brain Project being undertaken to create Volitron, a device equipped with circuitry that enables the emergence of thought. Such thought would be recognized from Volitron's specific communication behaviors. The project consists of three complementary themes: psychodynamic architecture, brain-specific evolvable hardware, and the management of brain-building. The psychodynamic architecture is designed to develop automatically, driven by “pleasure” coming from discharges of tension gathered in special tension-accumulating devices. Tension-discharging patterns come first of all from the robot's interactions with its care giver/provider. For the dedicated hardware, we developed qcellular-automata (qCA), in which groups of uniform logic primitives (q-cells) serve as spike-train-processing units, as well as pulsed para-neural networks (PPNN) that can be evolved, using fuzzified signals and a genetic algorithm combined with hill climbing, and converted into qCA. The psychodynamic ideas were tested using three robots: Neko, equipped with a pleasure-driven associator, Miao, equipped with MemeStorms (a special working memory in which conflicting ideas fight for access to the long-term memory and actuators), and Miao+, whose brain is equipped with a growing neural network. This work was presented in part at the 9th International Symposium on Artificial Life and Robotics, Oita, Japan, January 28–30, 2004     

Characterization of Combinatorially Independent Permutation Separability Criteria

The so-called permutation separability criteria are simple operational conditions that are necessary for separability of mixed states of multipartite systems: (1) permute the indices of the density matrix and (2) check if the trace norm of at least one of the resulting operators is greater than one. If it is greater than one then the state is necessarily entangled. A shortcoming of the permutation separability criteria is that many permutations give rise to equivalent separability criteria. Therefore, we introduce a necessary condition for two permutations to yield independent criteria called combinatorial independence. This condition basically means that the map corresponding to one permutation cannot be obtained by concatenating the map corresponding to the second permutation with a norm-preserving map. We characterize completely combina-torially independent criteria, and determine simple permutations that represent all independent criteria. The representatives can be visualized by means of a simple graphical notation. They are composed of three basic operations: partial transpose, and two types of so-called reshufflings. In particular, for a four-partite system all criteria except one are composed of partial transpose and only one type of reshuffling; the exceptional one requires the second type of reshuffling. Furthermore, we show how to obtain efficiently a simple representative for every permutation. This method allows to check easily if two permutations are Combinatorially equivalent or not.     

Multi-Frame Correspondence Estimation Using Subspace Constraints

When a rigid scene is imaged by a moving camera, the set of all displacements of all points across multiple frames often resides in a low-dimensional linear subspace. Linear subspace constraints have been used successfully in the past for recovering 3D structure and 3D motion information from multiple frames (e.g., by using the factorization method of Tomasi and Kanade (1992, International Journal of Computer Vision, 9:137–154)). These methods assume that the 2D correspondences have been precomputed. However, correspondence estimation is a fundamental problem in motion analysis. In this paper we show how the multi-frame subspace constraints can be used for constraining the 2D correspondence estimation process itself.We show that the multi-frame subspace constraints are valid not only for affine cameras, but also for a variety of imaging models, scene models, and motion models. The multi-frame subspace constraints are first translated from constraints on correspondences to constraints directly on image measurements (e.g., image brightness quantities). These brightness-based subspace constraints are then used for estimating the correspondences, by requiring that all corresponding points across all video frames reside in the appropriate low-dimensional linear subspace.The multi-frame subspace constraints are geometrically meaningful, and are {not} violated at depth discontinuities, nor when the camera-motion changes abruptly. These constraints can therefore replace {heuristic} constraints commonly used in optical-flow estimation, such as spatial or temporal smoothness.     

Diffusion-related implications for langasite resonator operation

Oxygen and gallium diffusivities in langasite were experimentally determined by analysis of diffusion profiles of 18O and 71Ga tracers by SIMS analysis as functions of temperature and doping. Strontium-enhanced diffusivities and activation energies of approximately 1.2+/-0.2 eV confirm the predominant role of oxygen vacancies in controlling the electrical conductivity of langasite at elevated temperature and oxygen partial pressure. The potential impact of high levels of porosity and the use of an oxygen primary ion beam on the accuracy of some of the data is discussed. The gallium diffusivity, with activation energy of 3.13 eV, was found to be more than two orders of magnitude lower than that of oxygen. Surface exchange measurements enabled estimation of gallium loss at elevated temperatures and oxygen partial pressure; the level is not believed to be of major concern for resonator performance.     

Toxicity increases in ice containing monochlorophenols upon photolysis: environmental consequences

The toxic effects of photoproducts formed upon the photolysis of 2- and 4-chlorophenol (CP) frozen solutions in polycrystalline ice phase were determined with a bacterial luminescence test (Vibrio fisheri), and in vitro biomarker assay for dioxin-like effects (inductions of AhR-dependent luciferase in H4IIE-luc cells) and compared to the toxic effects of products of the same photoreaction in aquatic phase. Coupling photoproducts formed in ice samples (3'-chlorobiphenyl-2,4'-diol and 3-chlorobiphenyl-2,2'-diol from 2-CP photolysis and 5-chlorobiphenyl-2,4'-diol from 4-CP photolysis) were found to be more toxic to V. fisheri than parent CPs and elicited significant inductions of dioxin-like effects (the effective concentrations EC50 approximately 3 x 10(-5) mol L(-1) corresponded to known weaker ligands of AhR, such as nonplanar polychlorinated biphenyls or polycyclic aromatic hydrocarbons). To complete the picture, a photoproduct formed from 4-CP (5-chlorobiphenyl-2,4'-diol) was synthesized, and a detailed toxicity assessment with purified compound confirmed the results obtained with irradiated samples. Our findings support a recently proposed model according to which solar radiation can trigger the formation of new types of organic pollutants in polar ice or tropospheric ice cloud particles, presenting possibly greater risk to the environment than the parent compounds.