Adaptive stochastic cellular automata: Applications
Qian, S.; Lee, Y. C.; Jones, R. D.; Barnes, C. W.; Flake, G. W.; O'Rourke, M. K.; Lee, K.; Chen, H. H.; Sun, G. Z.; Zhang, Y. Q.; Chen, D.; Giles, C. L.
1990-09-01
The stochastic learning cellular automata model has been applied to the problem of controlling unstable systems. Two example unstable systems studied are controlled by an adaptive stochastic cellular automata algorithm with an adaptive critic. The reinforcement learning algorithm and the architecture of the stochastic CA controller are presented. Learning to balance a single pole is discussed in detail. Balancing an inverted double pendulum highlights the power of the stochastic CA approach. The stochastic CA model is compared to conventional adaptive control and artificial neural network approaches.
Stochastic Nature in Cellular Processes
刘波; 刘圣君; 王祺; 晏世伟; 耿轶钊; SAKATA Fumihiko; GAO Xing-Fa
2011-01-01
The importance of stochasticity in cellular processes is increasingly recognized in both theoretical and experimental studies. General features of stochasticity in gene regulation and expression are briefly reviewed in this article, which include the main experimental phenomena, classification, quantization and regulation of noises. The correlation and transmission of noise in cascade networks are analyzed further and the stochastic simulation methods that can capture effects of intrinsic and extrinsic noise are described.
Scott, Bobby, R., Ph.D.
2003-06-27
OAK - B135 This project final report summarizes modeling research conducted in the U.S. Department of Energy (DOE), Low Dose Radiation Research Program at the Lovelace Respiratory Research Institute from October 1998 through June 2003. The modeling research described involves critically evaluating the validity of the linear nonthreshold (LNT) risk model as it relates to stochastic effects induced in cells by low doses of ionizing radiation and genotoxic chemicals. The LNT model plays a central role in low-dose risk assessment for humans. With the LNT model, any radiation (or genotoxic chemical) exposure is assumed to increase one¡¯s risk of cancer. Based on the LNT model, others have predicted tens of thousands of cancer deaths related to environmental exposure to radioactive material from nuclear accidents (e.g., Chernobyl) and fallout from nuclear weapons testing. Our research has focused on developing biologically based models that explain the shape of dose-response curves for low-dose radiation and genotoxic chemical-induced stochastic effects in cells. Understanding the shape of the dose-response curve for radiation and genotoxic chemical-induced stochastic effects in cells helps to better understand the shape of the dose-response curve for cancer induction in humans. We have used a modeling approach that facilitated model revisions over time, allowing for timely incorporation of new knowledge gained related to the biological basis for low-dose-induced stochastic effects in cells. Both deleterious (e.g., genomic instability, mutations, and neoplastic transformation) and protective (e.g., DNA repair and apoptosis) effects have been included in our modeling. Our most advanced model, NEOTRANS2, involves differing levels of genomic instability. Persistent genomic instability is presumed to be associated with nonspecific, nonlethal mutations and to increase both the risk for neoplastic transformation and for cancer occurrence. Our research results, based on
Stability of Stochastic Neutral Cellular Neural Networks
Chen, Ling; Zhao, Hongyong
In this paper, we study a class of stochastic neutral cellular neural networks. By constructing a suitable Lyapunov functional and employing the nonnegative semi-martingale convergence theorem we give some sufficient conditions ensuring the almost sure exponential stability of the networks. The results obtained are helpful to design stability of networks when stochastic noise is taken into consideration. Finally, two examples are provided to show the correctness of our analysis.
Stochastic Simulations on the Cellular Wave Computers
Ercsey-Ravasz, M.; Roska, T.; Néda, Z.
2006-01-01
The computational paradigm represented by Cellular Neural/nonlinear Networks (CNN) and the CNN Universal Machine (CNN-UM) as a Cellular Wave Computer, gives new perspectives for computational physics. Many numerical problems and simulations can be elegantly addressed on this fully parallelized and analogic architecture. Here we study the possibility of performing stochastic simulations on this chip. First a realistic random number generator is implemented on the CNN-UM, and then as an example...
Stochastic Simulations on the Cellular Wave Computers
Ercsey-Ravasz, M; Neda, Z
2006-01-01
The computational paradigm represented by Cellular Neural/nonlinear Networks (CNN) and the CNN Universal Machine (CNN-UM) as a Cellular Wave Computer, gives new perspectives for computational physics. Many numerical problems and simulations can be elegantly addressed on this fully parallelized and analogic architecture. Here we study the possibility of performing stochastic simulations on this chip. First a realistic random number generator is implemented on the CNN-UM, and then as an example the two-dimensional Ising model is studied by Monte Carlo type simulations. The results obtained on an experimental version of the CNN-UM with 128 * 128 cells are in good agreement with the results obtained on digital computers. Computational time measurements suggests that the developing trend of the CNN-UM chips - increasing the lattice size and the number of local logic memories - will assure an important advantage for the CNN-UM in the near future.
Directed Percolation arising in Stochastic Cellular Automata
Regnault, Damien
2008-01-01
Cellular automata are both seen as a model of computation and as tools to model real life systems. Historically they were studied under synchronous dynamics where all the cells of the system are updated at each time step. Meanwhile the question of probabilistic dynamics emerges: on the one hand, to develop cellular automata which are capable of reliable computation even when some random errors occur; on the other hand, because synchronous dynamics is not a reasonable assumption to simulate re...
Stochastic properties of disturbed Elementary Cellular Automata
Cellular automata are class of simple mathematical systems that generate diverse, often complicated behaviour. Evolution of such a system is given by set of local and deterministic rules. However, in spite of simplicity of 'interactions' it's global behaviour can't be, in general, simply predicted or even can not be predicted in time shorter that time of it's strict evolution. We get as, a systems well known 1-dimensional, Wolfram class automata, and connect it into the reservoir consists of some random source (noise). In our experiment we are interested in: a) numeric verification of ergodicity for such a coupled system. b) finding it's probability distribution and evolution. c) finding some analogous for 'real' quantities and behaviour. d) using the dynamical systems and Markov chains theory to describe the system, and to make any predictions of it's behaviour. (author)
Traffic jam dynamics in stochastic cellular automata
Nagel, K. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Schreckenberg, M. [Univ. Duisburg (Germany)
1995-09-01
Simple models for particles hopping on a grid (cellular automata) are used to simulate (single lane) traffic flow. Despite their simplicity, these models are astonishingly realistic in reproducing start-stop-waves and realistic fundamental diagrams. One can use these models to investigate traffic phenomena near maximum flow. A so-called phase transition at average maximum flow is visible in the life-times of jams. The resulting dynamic picture is consistent with recent fluid-dynamical results by Kuehne/Kerner/Konhaeuser, and with Treiterer`s hysteresis description. This places CA models between car-following models and fluid-dynamical models for traffic flow. CA models are tested in projects in Los Alamos (USA) and in NRW (Germany) for large scale microsimulations of network traffic.
Stochastic Models of Vesicular Sorting in Cellular Organelles
Vagne, Quentin
2016-01-01
The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intra-cellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values leads to fast sorting, but results in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well defined sorted compartments but is exponentially slow. Our results suggests an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components, and highlight the importance of stochastic effects for the steady-state organizati...
Modeling and Analysis of Cellular Networks using Stochastic Geometry: A Tutorial
ElSawy, Hesham
2016-03-22
This paper presents a tutorial on stochastic geometry (SG) based analysis for cellular networks. This tutorial is distinguished by its depth with respect to wireless communication details and its focus on cellular networks. The paper starts by modeling and analyzing the baseband interference in a basic cellular network model. Then, it characterizes signal-tointerference- plus-noise-ratio (SINR) and its related performance metrics. In particular, a unified approach to conduct error probability, outage probability, and rate analysis is presented. Although the main focus of the paper is on cellular networks, the presented unified approach applies for other types of wireless networks that impose interference protection around receivers. The paper then extends the baseline unified approach to capture cellular network characteristics (e.g., frequency reuse, multiple antenna, power control, etc.). It also presents numerical examples associated with demonstrations and discussions. Finally, we point out future research directions.
Stochastic cellular fate decision making by multiple infecting lambda phage.
Matthew L Robb
Full Text Available Bacteriophage lambda is a classic system for the study of cellular decision making. Both experiments and mathematical models have demonstrated the importance of viral concentration in the lysis-lysogeny decision outcome in lambda phage. However, a recent experimental study using single cell and single phage resolution reported that cells with the same viral concentrations but different numbers of infecting phage (multiplicity of infection can have markedly different rates of lysogeny. Thus the decision depends on not only viral concentration, but also directly on the number of infecting phage. Here, we attempt to provide a mechanistic explanation of these results using a simple stochastic model of the lambda phage genetic network. Several potential factors including intrinsic gene expression noise, spatial dynamics and cell-cycle effects are investigated. We find that interplay between the level of intrinsic noise and viral protein decision threshold is a major factor that produces dependence on multiplicity of infection. However, simulations suggest spatial segregation of phage particles does not play a significant role. Cellular image processing is used to re-analyse the original time-lapse movies from the recent study and it is found that higher numbers of infecting phage reduce the cell elongation rate. This could also contribute to the observed phenomena as cellular growth rate can affect transcription rates. Our model further predicts that rate of lysogeny is dependent on bacterial growth rate, which can be experimentally tested. Our study provides new insight on the mechanisms of individual phage decision making. More generally, our results are relevant for the understanding of gene-dosage compensation in cellular systems.
Integrability of a deterministic cellular automaton driven by stochastic boundaries
Prosen, Tomaž; Mejía-Monasterio, Carlos
2016-05-01
We propose an interacting many-body space–time-discrete Markov chain model, which is composed of an integrable deterministic and reversible cellular automaton (rule 54 of Bobenko et al 1993 Commun. Math. Phys. 158 127) on a finite one-dimensional lattice {({{{Z}}}2)}× n, and local stochastic Markov chains at the two lattice boundaries which provide chemical baths for absorbing or emitting the solitons. Ergodicity and mixing of this many-body Markov chain is proven for generic values of bath parameters, implying the existence of a unique nonequilibrium steady state. The latter is constructed exactly and explicitly in terms of a particularly simple form of matrix product ansatz which is termed a patch ansatz. This gives rise to an explicit computation of observables and k-point correlations in the steady state as well as the construction of a nontrivial set of local conservation laws. The feasibility of an exact solution for the full spectrum and eigenvectors (decay modes) of the Markov matrix is suggested as well. We conjecture that our ideas can pave the road towards a theory of integrability of boundary driven classical deterministic lattice systems.
Stochastic Model of Maturation and Vesicular Exchange in Cellular Organelles
Vagne, Quentin
2016-01-01
The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on biochemical maturation of the organelle content by specific enzymes. The relative importance of each mechanism in controlling organelle dynamics remains controversial, in particular for transport through the Golgi apparatus. Using a stochastic model, we show that full maturation of membrane-bound compartments can be seen as the stochastic escape from a steady-state in which export is dominated by vesicular exchange. We show that full maturation can contribute a significant fraction of the total out-flux for small organelles such as endosomes and Golgi cisternae.
The paper considers the problems of existence of quadratic mean almost periodic and global exponential stability for stochastic cellular neural networks with delays. By employing the Holder's inequality and fixed points principle, we present some new criteria ensuring existence and uniqueness of a quadratic mean almost periodic and global exponential stability. These criteria are important in signal processing and the design of networks. Moreover, these criteria are also applied in others stochastic biological neural systems.
Transfer-matrix DMRG for stochastic models: The Domany-Kinzel cellular automaton
Kemper, A.; Schadschneider, A.; Zittartz, J.
2001-01-01
We apply the transfer-matrix DMRG (TMRG) to a stochastic model, the Domany-Kinzel cellular automaton, which exhibits a non-equilibrium phase transition in the directed percolation universality class. Estimates for the stochastic time evolution, phase boundaries and critical exponents can be obtained with high precision. This is possible using only modest numerical effort since the thermodynamic limit can be taken analytically in our approach. We also point out further advantages of the TMRG o...
Hanfeng Kuang; Jinbo Liu; Xi Chen; Jie Mao; Linjie He
2013-01-01
The asymptotic behavior of a class of switched stochastic cellular neural networks (CNNs) with mixed delays (discrete time-varying delays and distributed time-varying delays) is investigated in this paper. Employing the average dwell time approach (ADT), stochastic analysis technology, and linear matrix inequalities technique (LMI), some novel sufficient conditions on the issue of asymptotic behavior (the mean-square ultimate boundedness, the existence of an attractor, and the mean-square ...
Bit-Vectorized GPU Implementation of a Stochastic Cellular Automaton Model for Surface Growth
Kelling, Jeffrey; Gemming, Sibylle
2016-01-01
Stochastic surface growth models aid in studying properties of universality classes like the Kardar--Paris--Zhang class. High precision results obtained from large scale computational studies can be transferred to many physical systems. Many properties, such as roughening and some two-time functions can be studied using stochastic cellular automaton (SCA) variants of stochastic models. Here we present a highly efficient SCA implementation of a surface growth model capable of simulating billions of lattice sites on a single GPU. We also provide insight into cases requiring arbitrary random probabilities which are not accessible through bit-vectorization.
Stochastic fluctuations and distributed control of gene expression impact cellular memory.
Guillaume Corre
Full Text Available Despite the stochastic noise that characterizes all cellular processes the cells are able to maintain and transmit to their daughter cells the stable level of gene expression. In order to better understand this phenomenon, we investigated the temporal dynamics of gene expression variation using a double reporter gene model. We compared cell clones with transgenes coding for highly stable mRNA and fluorescent proteins with clones expressing destabilized mRNA-s and proteins. Both types of clones displayed strong heterogeneity of reporter gene expression levels. However, cells expressing stable gene products produced daughter cells with similar level of reporter proteins, while in cell clones with short mRNA and protein half-lives the epigenetic memory of the gene expression level was completely suppressed. Computer simulations also confirmed the role of mRNA and protein stability in the conservation of constant gene expression levels over several cell generations. These data indicate that the conservation of a stable phenotype in a cellular lineage may largely depend on the slow turnover of mRNA-s and proteins.
Molecular and cellular fundamentals of stochastic radiation action
Description of basic radiobiological processes in order to assess the risk of carcinogenesis due to radiotherapeutic procedures; demonstration of direct radiation-induced damage to DNA and indirect effects due to radiolysis of cellular water; description of repair mechanisms; radiation- induced chromosomal aberrations, genome mutations and disturbances of the cell cycle and their contributions to the carcinogenic effects of radiotherapy.(MG)
Stochastic Cellular Fate Decision Making by Multiple Infecting Lambda Phage
Robb, Matthew L.; Shahrezaei, Vahid
2014-01-01
Bacteriophage lambda is a classic system for the study of cellular decision making. Both experiments and mathematical models have demonstrated the importance of viral concentration in the lysis-lysogeny decision outcome in lambda phage. However, a recent experimental study using single cell and single phage resolution reported that cells with the same viral concentrations but different numbers of infecting phage (multiplicity of infection) can have markedly different rates of lysogeny. Thus t...
Spatial Stochastic Point Models for Reservoir Characterization
Syversveen, Anne Randi
1997-12-31
The main part of this thesis discusses stochastic modelling of geology in petroleum reservoirs. A marked point model is defined for objects against a background in a two-dimensional vertical cross section of the reservoir. The model handles conditioning on observations from more than one well for each object and contains interaction between objects, and the objects have the correct length distribution when penetrated by wells. The model is developed in a Bayesian setting. The model and the simulation algorithm are demonstrated by means of an example with simulated data. The thesis also deals with object recognition in image analysis, in a Bayesian framework, and with a special type of spatial Cox processes called log-Gaussian Cox processes. In these processes, the logarithm of the intensity function is a Gaussian process. The class of log-Gaussian Cox processes provides flexible models for clustering. The distribution of such a process is completely characterized by the intensity and the pair correlation function of the Cox process. 170 refs., 37 figs., 5 tabs.
Stochastic Ordering based Carrier-to-Interference Ratio Analysis for the Shotgun Cellular Systems
Madhusudhanan, Prasanna; Youjian,; Liu,; Brown, Timothy X; Baker, Kenneth R
2011-01-01
A simple analytical tool based on stochastic ordering is developed to compare the distributions of carrier-to-interference ratio at the mobile station of two cellular systems where the base stations are distributed randomly according to certain non-homogeneous Poisson point processes. The comparison is conveniently done by studying only the base station densities without having to solve for the distributions of the carrier-to-interference ratio, that are often hard to obtain.
A Stochastic Cellular Automaton Model of Non-linear Diffusion and Diffusion with Reaction
Brieger, Leesa M.; Bonomi, Ernesto
1991-06-01
This article presents a stochastic cellular automaton model of diffusion and diffusion with reaction. The master equations for the model are examined, and we assess the difference between the implementation in which a single particle at a time moves (asynchronous dynamics) and one implementation in which all particles move simultaneously (synchronous dynamics). Biasing locally each particle's random walk, we alter the diffusion coefficients of the system. By appropriately choosing the biasing function, we can impose a desired non-linear diffusive behaviour in the model. We present an application of this model, adapted to include two diffusing species, two static species, and a chemical reaction in a prototypical simulation of carbonation in concrete.
Pseudo-stochastic signal characterization in wavelet-domain
In this paper we present the method for fast and accurate characterization of pseudo-stochastic signals, which contain a large number of similar but randomly-located fragments. This method allows estimating the statistical characteristics of pseudo-stochastic signal, and it is based on digital signal processing in wavelet-domain. Continuous wavelet transform and the criterion for wavelet scale power density are utilized. We are experimentally implementing this method for the purpose of sand granulometry, and we are estimating the statistical parameters of test sand fractions
de la Cruz, Roberto; Spill, Fabian; Alarcón, Tomás
2016-01-01
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated proliferation rate. Our formulation is based on an age-dependent stochastic process. Cells within the population are characterised by their age. The age-dependent (oxygen-regulated) birth rate is given by a stochastic model of oxygen-dependent cell cycle progression. We then formulate an age-dependent birth-and-death process, which dictates the time evolution of the cell population. The population is under a feedback loop which controls its steady state size: cells consume oxygen which in turns fuels cell proliferation. We show that our stochastic model of cell cycle progression allows for heterogeneity within the cell population induced by stochastic effects. Such heterogeneous behaviour is reflected in variations in the proliferation rate. Within this set-up, we have established...
Non-concave fundamental diagrams and phase transitions in a stochastic traffic cellular automaton
Maerivoet, S.; de Moor, B.
2004-11-01
Within the class of stochastic cellular automata models of traffic flows, we look at the velocity dependent randomization variant (VDR-TCA) whose parameters take on a specific set of extreme values. These initial conditions lead us to the discovery of the emergence of four distinct phases. Studying the transitions between these phases, allows us to establish a rigorous classification based on their tempo-spatial behavioral characteristics. As a result from the system’s complex dynamics, its flow-density relation exhibits a non-concave region in which forward propagating density waves are encountered. All four phases furthermore share the common property that moving vehicles can never increase their speed once the system has settled into an equilibrium.
Stochastic narrow escape in molecular and cellular biology analysis and applications
Holcman, David
2015-01-01
This book covers recent developments in the non-standard asymptotics of the mathematical narrow escape problem in stochastic theory, as well as applications of the narrow escape problem in cell biology. The first part of the book concentrates on mathematical methods, including advanced asymptotic methods in partial equations, and is aimed primarily at applied mathematicians and theoretical physicists who are interested in biological applications. The second part of the book is intended for computational biologists, theoretical chemists, biochemists, biophysicists, and physiologists. It includes a summary of output formulas from the mathematical portion of the book and concentrates on their applications in modeling specific problems in theoretical molecular and cellular biology. Critical biological processes, such as synaptic plasticity and transmission, activation of genes by transcription factors, or double-strained DNA break repair, are controlled by diffusion in structures that have both large and small sp...
Stochastic Characterization of Cast Metal Microstructure
Steinzig, M.
1999-06-01
The major goal of this work is to provide a means to characterize the final structure of a metal that has solidified from a melt. The thermally controlled solidification of a binary alloy, nucleated at isolated sites, is described by the evolution of a probability distribution function (PDF). The relevant equation required for propagating the PDF is developed with variables for grain size and distance to nearest neighbor. The phenomena of nucleation, growth, and impingement of the grains are discussed, and used as the basis for developing rate equations that evolve the PDF. The complementary equations describing global heat and solute transfer are discussed, and coupled with the microstructure evolution equations for grain growth and PDF evolution. The full set of equations is solved numerically and results are compared with experimental data for the plutonium 1 weight percent gallium system. The three principal results of this work are: (1) The formulation of transient evolution equations for the PDF description of nucleation, growth, and impingement of a distribution of grain sizes and locations; (2) Solution of the equations to give a correlation for final average grain size as a function of material parameters, nucleation site density, and cooling rate; and (3) Solution of the equations for final distribution of grain size as a result of the initial random spatial distribution of nucleation sites.
In-Band α-Duplex Scheme for Cellular Networks: A Stochastic Geometry Approach
Alammouri, Ahmad
2016-07-13
In-band full-duplex (FD) communications have been optimistically promoted to improve the spectrum utilization and efficiency. However, the penetration of FD communications to the cellular networks domain is challenging due to the imposed uplink/downlink interference. This paper presents a tractable framework, based on stochastic geometry, to study FD communications in cellular networks. Particularly, we assess the FD communications effect on the network performance and quantify the associated gains. The study proves the vulnerability of the uplink to the downlink interference and shows that FD rate gains harvested in the downlink (up to 97%) come at the expense of a significant degradation in the uplink rate (up to 94%). Therefore, we propose a novel fine-grained duplexing scheme, denoted as -duplex scheme, which allows a partial overlap between the uplink and the downlink frequency bands. We derive the required conditions to harvest rate gains from the -duplex scheme and show its superiority to both the FD and half-duplex (HD) schemes. In particular, we show that the -duplex scheme provides a simultaneous improvement of 28% for the downlink rate and 56% for the uplink rate. Finally, we show that the amount of the overlap can be optimized based on the network design objective.
Strong Attractors in Stochastic Adaptive Networks: Emergence and Characterization
Santos, Augusto Almeida; Krishnan, Ramayya; Moura, José M F
2016-01-01
We propose a family of models to study the evolution of ties in a network of interacting agents by reinforcement and penalization of their connections according to certain local laws of interaction. The family of stochastic dynamical systems, on the edges of a graph, exhibits \\emph{good} convergence properties, in particular, we prove a strong-stability result: a subset of binary matrices or graphs -- characterized by certain compatibility properties -- is a global almost sure attractor of the family of stochastic dynamical systems. To illustrate finer properties of the corresponding strong attractor, we present some simulation results that capture, e.g., the conspicuous phenomenon of emergence and downfall of leaders in social networks.
Kemper, A. [Institut fuer Theoretische Physik, Universitaet zu Koeln, Cologne (Germany). E-mail: kemper@thp.uni-koeln.de; Schadschneider, A. [Institut fuer Theoretische Physik, Universitaet zu Koeln, Cologne (Germany). E-mail: as@thp.uni-koeln.de; Zittartz, J. [Institut fuer Theoretische Physik, Universitaet zu Koeln, Cologne (Germany)
2001-05-18
We apply the transfer-matrix density-matrix renormalization group (TMRG) to a stochastic model, the Domany-Kinzel cellular automaton, which exhibits a non-equilibrium phase transition in the directed percolation universality class. Estimates for the stochastic time evolution, phase boundaries and critical exponents can be obtained with high precision. This is possible using only modest numerical effort since the thermodynamic limit can be taken analytically in our approach. We also point out further advantages of the TMRG over other numerical approaches, such as classical DMRG or Monte Carlo simulations. (author). Letter-to-the-editor.
We apply the transfer-matrix density-matrix renormalization group (TMRG) to a stochastic model, the Domany-Kinzel cellular automaton, which exhibits a non-equilibrium phase transition in the directed percolation universality class. Estimates for the stochastic time evolution, phase boundaries and critical exponents can be obtained with high precision. This is possible using only modest numerical effort since the thermodynamic limit can be taken analytically in our approach. We also point out further advantages of the TMRG over other numerical approaches, such as classical DMRG or Monte Carlo simulations. (author). Letter-to-the-editor
Roh, Min K.; Daigle, Bernie J.; Gillespie, Dan T.; Petzold, Linda R.
2011-12-01
In recent years there has been substantial growth in the development of algorithms for characterizing rare events in stochastic biochemical systems. Two such algorithms, the state-dependent weighted stochastic simulation algorithm (swSSA) and the doubly weighted SSA (dwSSA) are extensions of the weighted SSA (wSSA) by H. Kuwahara and I. Mura [J. Chem. Phys. 129, 165101 (2008)], 10.1063/1.2987701. The swSSA substantially reduces estimator variance by implementing system state-dependent importance sampling (IS) parameters, but lacks an automatic parameter identification strategy. In contrast, the dwSSA provides for the automatic determination of state-independent IS parameters, thus it is inefficient for systems whose states vary widely in time. We present a novel modification of the dwSSA—the state-dependent doubly weighted SSA (sdwSSA)—that combines the strengths of the swSSA and the dwSSA without inheriting their weaknesses. The sdwSSA automatically computes state-dependent IS parameters via the multilevel cross-entropy method. We apply the method to three examples: a reversible isomerization process, a yeast polarization model, and a lac operon model. Our results demonstrate that the sdwSSA offers substantial improvements over previous methods in terms of both accuracy and efficiency.
CellLab-CTS 2015: continuous-time stochastic cellular automaton modeling using Landlab
Tucker, Gregory E.; Hobley, Daniel E. J.; Hutton, Eric; Gasparini, Nicole M.; Istanbulluoglu, Erkan; Adams, Jordan M.; Siddartha Nudurupati, Sai
2016-02-01
CellLab-CTS 2015 is a Python-language software library for creating two-dimensional, continuous-time stochastic (CTS) cellular automaton models. The model domain consists of a set of grid nodes, with each node assigned an integer state code that represents its condition or composition. Adjacent pairs of nodes may undergo transitions to different states, according to a user-defined average transition rate. A model is created by writing a Python code that defines the possible states, the transitions, and the rates of those transitions. The code instantiates, initializes, and runs one of four object classes that represent different types of CTS models. CellLab-CTS provides the option of using either square or hexagonal grid cells. The software provides the ability to treat particular grid-node states as moving particles, and to track their position over time. Grid nodes may also be assigned user-defined properties, which the user can update after each transition through the use of a callback function. As a component of the Landlab modeling framework, CellLab-CTS models take advantage of a suite of Landlab's tools and capabilities, such as support for standardized input and output.
Qian, Hong
2010-12-01
Based on a stochastic, nonlinear, open biochemical reaction system perspective, we present an analytical theory for cellular biochemical processes. The chemical master equation (CME) approach provides a unifying mathematical framework for cellular modeling. We apply this theory to both self-regulating gene networks and phosphorylation-dephosphorylation signaling modules with feedbacks. Two types of bistability are illustrated in mesoscopic biochemical systems: one that has a macroscopic, deterministic counterpart and another that does not. In certain cases, the latter stochastic bistability is shown to be a "ghost" of the extinction phenomenon. We argue the thermal fluctuations inherent in molecular processes do not disappear in mesoscopic cell-sized nonlinear systems; rather they manifest themselves as isogenetic variations on a different time scale. Isogenetic biochemical variations in terms of the stochastic attractors can have extremely long lifetime. Transitions among discrete stochastic attractors spend most of the time in "waiting", exhibit punctuated equilibria. It can be naturally passed to "daughter cells" via a simple growth and division process. The CME system follows a set of nonequilibrium thermodynamic laws that include non-increasing free energy F( t) with external energy drive Q hk ≥0, and total entropy production rate e p =- dF/ dt+ Q hk ≥0. In the thermodynamic limit, with a system's size being infinitely large, the nonlinear bistability in the CME exhibits many of the characteristics of macroscopic equilibrium phase transition.
Elsawy, Hesham
2014-08-01
Using stochastic geometry, we develop a tractable uplink modeling paradigm for outage probability and spectral efficiency in both single and multi-tier cellular wireless networks. The analysis accounts for per user equipment (UE) power control as well as the maximum power limitations for UEs. More specifically, for interference mitigation and robust uplink communication, each UE is required to control its transmit power such that the average received signal power at its serving base station (BS) is equal to a certain threshold ρo. Due to the limited transmit power, the UEs employ a truncated channel inversion power control policy with a cutoff threshold of ρo. We show that there exists a transfer point in the uplink system performance that depends on the following tuple: BS intensity λ, maximum transmit power of UEs Pu, and ρo. That is, when Pu is a tight operational constraint with respect to (w.r.t.) λ and ρo, the uplink outage probability and spectral efficiency highly depend on the values of λ and ρo. In this case, there exists an optimal cutoff threshold ρ*o, which depends on the system parameters, that minimizes the outage probability. On the other hand, when Pu is not a binding operational constraint w.r.t. λ and ρo, the uplink outage probability and spectral efficiency become independent of λ and ρo. We obtain approximate yet accurate simple expressions for outage probability and spectral efficiency, which reduce to closed forms in some special cases. © 2002-2012 IEEE.
Challenges in Characterizing and Controlling Complex Cellular Systems
Wikswo, John
2011-03-01
Multicellular dynamic biological processes such as developmental differentiation, wound repair, disease, aging, and even homeostasis can be represented by trajectories through a phase space whose extent reflects the genetic, post-translational, and metabolic complexity of the process - easily extending to tens of thousands of dimensions. Intra- and inter-cellular sensing and regulatory systems and their nested, redundant, and non-linear feed-forward and feed-back controls create high-dimensioned attractors in this phase space. Metabolism provides free energy to drive non-equilibrium processes and dynamically reconfigure attractors. Studies of single molecules and cells provide only minimalist projections onto a small number of axes. It may be difficult to infer larger-scale emergent behavior from linearized experiments that perform only small amplitude perturbations on a limited number of the dimensions. Complete characterization may succeed for bounded component problems, such as an individual cell cycle or signaling cascade, but larger systems problems will require a coarse-grained approach. Hence a new experimental and analytical framework is needed. Possibly one could utilize high-amplitude, multi-variable driving of the system to infer coarse-grained, effective models, which in turn can be tested by their ability to control systems behavior. Navigation at will between attractors in a high-dimensioned dynamical system will provide not only detailed knowledge of the shape of attractor basins, but also measures of underlying stochastic events such as noise in gene expression or receptor binding and how both affect system stability and robustness. Needed for this are wide-bandwidth methods to sense and actuate large numbers of intracellular and extracellular variables and automatically and rapidly infer dynamic control models. The success of this approach may be determined by how broadly the sensors and actuators can span the full dimensionality of the phase space
Full text: The Bauschinger effect refers to an observed asymmetry in the forward and reverse loading curves of a metal or an alloy. Typically, the absolute value of the yield stress in reverse loading is lower than the maximum stress imposed on the initial, forward loading. This difference arises from either the presence of a back stress or from the greater strength of obstacles opposing dislocation motion in the forward than in the reverse direction. Thus, the Bauschinger effect contributes to the phenomena referred to as kinematic hardening. In particular dispersion hardened systems, containing strong, non-shearable particles that offer obstacles to dislocation motion, will often exhibit a large kinematic hardening component. When a material is described as a group of parallel elements (a composite) having variable yield stresses and or Young's moduli, kinematic hardening of type KI, is observed when the first element to yield on forward loading is the first element to yield on reverse loading. Kinematic hardening types KII and KIII result when the order of relaxation of the elements is different from the order of their initial yielding. The reverse loading curves for types KII and KIII hardening generally exhibit inflection points at the initiation of yielding on reverse loading. In previous work, a micromechanics model, with a detailed description of the microstructure, was employed to model the effects of plastic inhomogeneity and duplicate the loading and unloading trends observed experimentally. Trends predicted by the model corresponded well to some of the expectations derived from observation, e.g. the effects related to the inclusions of different phases, however in some cases the correlation depended on the assignment of unrealistic properties to microstructural constituents. In the current work, the material is modeled as an array of coupled elements with varying stiffnesses and strengths. A stochastic cellular automaton is then used to simulate the
Stochastic similarities between hydroclimatic processes for variability characterization
Dimitriadis, Panayiotis; Markonis, Yannis; Iliopoulou, Theano; Gournari, Naya; Deligiannis, Ilias; Kastis, Paris; Nasika, Xristina; Lerias, Eleutherios; Moustakis, Yannis; Petsiou, Amalia; Sotiriadou, Alexia; Stefanidis, Eleutherios; Tyrogiannis, Vassilis; Feloni, Elisavet; Koutsoyiannis, Demetris
2016-04-01
The most important hydroclimatic processes such as temperature, dew point, wind, precipitation and river discharges are investigated for their stochastic behaviour on annual scale through several historical records. We investigate the stochastic similarities between them in terms of long-term persistence and we comment on their statistical variability giving emphasis on the last period. Acknowledgement: This research is conducted within the frame of the undergraduate course "Stochastic Methods in Water Resources" of the National Technical University of Athens (NTUA). The School of Civil Engineering of NTUA provided moral support for the participation of the students in the Assembly.
Stochastic simulation of radium-223 dichloride therapy at the sub-cellular level.
Gholami, Y; Zhu, X; Fulton, R; Meikle, S; El-Fakhri, G; Kuncic, Z
2015-08-01
Radium-223 dichloride ((223)Ra) is an alpha particle emitter and a natural bone-seeking radionuclide that is currently used for treating osteoblastic bone metastases associated with prostate cancer. The stochastic nature of alpha emission, hits and energy deposition poses some challenges for estimating radiation damage. In this paper we investigate the distribution of hits to cells by multiple alpha particles corresponding to a typical clinically delivered dose using a Monte Carlo model to simulate the stochastic effects. The number of hits and dose deposition were recorded in the cytoplasm and nucleus of each cell. Alpha particle tracks were also visualized. We found that the stochastic variation in dose deposited in cell nuclei ([Formula: see text]40%) can be attributed in part to the variation in LET with pathlength. We also found that [Formula: see text]18% of cell nuclei receive less than one sigma below the average dose per cell ([Formula: see text]15.4 Gy). One possible implication of this is that the efficacy of cell kill in alpha particle therapy need not rely solely on ionization clustering on DNA but possibly also on indirect DNA damage through the production of free radicals and ensuing intracellular signaling. PMID:26216391
Maerivoet, S; Immers, B; De Moor, B; Maerivoet, Sven; Logghe, Steven; Immers, Ben; Moor, Bart De
2005-01-01
In this paper, we describe a relation between a microscopic traffic cellular automaton (TCA) model (i.e., the stochastic TCA model of Nagel and Schreckenberg) and the macroscopic first-order hydrodynamic model of Lighthill, Whitham, and Richards (LWR). The innovative aspect of our approach, is that we explicitly derive the LWR's fundamental diagram directly from the STCA's rule set, by assuming a stationarity condition that converts the STCA's rules into a set of linear inequalities. In turn, these constraints define the shape of the fundamental diagram, which is then specified to the LWR model. Application of our methodology to a simulation case study, allows us to compare the tempo-spatial behavior of both models. Our results indicate that, in the presence of noise, the capacity flows in the derived fundamental diagram are overestimations of those of the STCA model. Directly specifying the STCA's capacity flows to the LWR fundamental diagram, effectively remedies most of the mismatches between both approach...
3D printed cellular solid outperforms traditional stochastic foam in long-term mechanical response.
Maiti, A; Small, W; Lewicki, J P; Weisgraber, T H; Duoss, E B; Chinn, S C; Pearson, M A; Spadaccini, C M; Maxwell, R S; Wilson, T S
2016-01-01
3D printing of polymeric foams by direct-ink-write is a recent technological breakthrough that enables the creation of versatile compressible solids with programmable microstructure, customizable shapes, and tunable mechanical response including negative elastic modulus. However, in many applications the success of these 3D printed materials as a viable replacement for traditional stochastic foams critically depends on their mechanical performance and micro-architectural stability while deployed under long-term mechanical strain. To predict the long-term performance of the two types of foams we employed multi-year-long accelerated aging studies under compressive strain followed by a time-temperature-superposition analysis using a minimum-arc-length-based algorithm. The resulting master curves predict superior long-term performance of the 3D printed foam in terms of two different metrics, i.e., compression set and load retention. To gain deeper understanding, we imaged the microstructure of both foams using X-ray computed tomography, and performed finite-element analysis of the mechanical response within these microstructures. This indicates a wider stress variation in the stochastic foam with points of more extreme local stress as compared to the 3D printed material, which might explain the latter's improved long-term stability and mechanical performance. PMID:27117858
3D printed cellular solid outperforms traditional stochastic foam in long-term mechanical response
Maiti, A.; Small, W.; Lewicki, J. P.; Weisgraber, T. H.; Duoss, E. B.; Chinn, S. C.; Pearson, M. A.; Spadaccini, C. M.; Maxwell, R. S.; Wilson, T. S.
2016-04-01
3D printing of polymeric foams by direct-ink-write is a recent technological breakthrough that enables the creation of versatile compressible solids with programmable microstructure, customizable shapes, and tunable mechanical response including negative elastic modulus. However, in many applications the success of these 3D printed materials as a viable replacement for traditional stochastic foams critically depends on their mechanical performance and micro-architectural stability while deployed under long-term mechanical strain. To predict the long-term performance of the two types of foams we employed multi-year-long accelerated aging studies under compressive strain followed by a time-temperature-superposition analysis using a minimum-arc-length-based algorithm. The resulting master curves predict superior long-term performance of the 3D printed foam in terms of two different metrics, i.e., compression set and load retention. To gain deeper understanding, we imaged the microstructure of both foams using X-ray computed tomography, and performed finite-element analysis of the mechanical response within these microstructures. This indicates a wider stress variation in the stochastic foam with points of more extreme local stress as compared to the 3D printed material, which might explain the latter’s improved long-term stability and mechanical performance.
3D printed cellular solid outperforms traditional stochastic foam in long-term mechanical response
Maiti, A.; Small, W.; Lewicki, J. P.; Weisgraber, T. H.; Duoss, E. B.; Chinn, S. C.; Pearson, M. A.; Spadaccini, C. M.; Maxwell, R. S.; Wilson, T. S.
2016-01-01
3D printing of polymeric foams by direct-ink-write is a recent technological breakthrough that enables the creation of versatile compressible solids with programmable microstructure, customizable shapes, and tunable mechanical response including negative elastic modulus. However, in many applications the success of these 3D printed materials as a viable replacement for traditional stochastic foams critically depends on their mechanical performance and micro-architectural stability while deployed under long-term mechanical strain. To predict the long-term performance of the two types of foams we employed multi-year-long accelerated aging studies under compressive strain followed by a time-temperature-superposition analysis using a minimum-arc-length-based algorithm. The resulting master curves predict superior long-term performance of the 3D printed foam in terms of two different metrics, i.e., compression set and load retention. To gain deeper understanding, we imaged the microstructure of both foams using X-ray computed tomography, and performed finite-element analysis of the mechanical response within these microstructures. This indicates a wider stress variation in the stochastic foam with points of more extreme local stress as compared to the 3D printed material, which might explain the latter’s improved long-term stability and mechanical performance. PMID:27117858
Multiscale study for stochastic characterization of shale samples
Tahmasebi, Pejman; Javadpour, Farzam; Sahimi, Muhammad; Piri, Mohammad
2016-03-01
Characterization of shale reservoirs, which are typically of low permeability, is very difficult because of the presence of multiscale structures. While three-dimensional (3D) imaging can be an ultimate solution for revealing important complexities of such reservoirs, acquiring such images is costly and time consuming. On the other hand, high-quality 2D images, which are widely available, also reveal useful information about shales' pore connectivity and size. Most of the current modeling methods that are based on 2D images use limited and insufficient extracted information. One remedy to the shortcoming is direct use of qualitative images, a concept that we introduce in this paper. We demonstrate that higher-order statistics (as opposed to the traditional two-point statistics, such as variograms) are necessary for developing an accurate model of shales, and describe an efficient method for using 2D images that is capable of utilizing qualitative and physical information within an image and generating stochastic realizations of shales. We then further refine the model by describing and utilizing several techniques, including an iterative framework, for removing some possible artifacts and better pattern reproduction. Next, we introduce a new histogram-matching algorithm that accounts for concealed nanostructures in shale samples. We also present two new multiresolution and multiscale approaches for dealing with distinct pore structures that are common in shale reservoirs. In the multiresolution method, the original high-quality image is upscaled in a pyramid-like manner in order to achieve more accurate global and long-range structures. The multiscale approach integrates two images, each containing diverse pore networks - the nano- and microscale pores - using a high-resolution image representing small-scale pores and, at the same time, reconstructing large pores using a low-quality image. Eventually, the results are integrated to generate a 3D model. The methods
Weak Characterizations of Stochastic Integrability and Dudley's Theorem in Infinite Dimensions
Ondreját, Martin; Veraar, M.
2014-01-01
Roč. 27, č. 4 (2014), s. 1350-1374. ISSN 0894-9840 R&D Projects: GA ČR GAP201/10/0752 Institutional support: RVO:67985556 Keywords : stochastic integration in Banach spaces * almost sure limit theorems * Dudley representation theorem * universal representation theorem * weak characterization of stochastic integrability * Doob representation theorem Subject RIV: BA - General Mathematics Impact factor: 0.857, year: 2014 http://library.utia.cas.cz/separaty/2013/SI/ondrejat-0392394.pdf
Chattopadhyay, Arpan; Błaszczyszyn, Bartłomiej; Altman, Eitan
2016-01-01
We consider location-dependent opportunistic bandwidth sharing between static and mobile downlink users in a cellular network. Each cell has some fixed number of static users. Mobile users enter the cell, move inside the cell for some time and then leave the cell. In order to provide higher data rate to mobile users, we propose to provide higher bandwidth to the mobile users at favourable times and locations, and provide higher bandwidth to the static users in other times. We formulate the pr...
Stochastic Characterization of Flutter using Historical Wind Tunnel Data
Heeg, Jennifer
2007-01-01
Methods for predicting the onset of flutter during an experiment are traditionally applied treating the data as deterministic values. Uncertainty and variation in the data is often glossed over by using best-fit curves to represent the information. This paper applies stochastic treatments to wind tunnel data obtained for the Piezoelectric Aeroelastic Response Tailoring Investigation model. These methods include modal amplitude tracking, modal frequency tracking and several applications of the flutter margin method. The flutter margin method was developed by Zimmerman and Weissenburger, and extended by Poirel, Dunn and Porter to incorporate uncertainty. Much of the current work follows the future work recommendations of Poirel, Dunn and Porter.
Kemper, A.; Schadschneider, A.; Zittartz, J.
2001-05-01
We apply the transfer-matrix density-matrix renormalization group (TMRG) to a stochastic model, the Domany-Kinzel cellular automaton, which exhibits a non-equilibrium phase transition in the directed percolation universality class. Estimates for the stochastic time evolution, phase boundaries and critical exponents can be obtained with high precision. This is possible using only modest numerical effort since the thermodynamic limit can be taken analytically in our approach. We also point out further advantages of the TMRG over other numerical approaches, such as classical DMRG or Monte Carlo simulations.
Tucker, G. E.; Hobley, D. E. J.; Hutton, E.; Gasparini, N. M.; Istanbulluoglu, E.; Adams, J. M.; Nudurupati, S. S.
2015-11-01
CellLab-CTS 2015 is a Python-language software library for creating two-dimensional, continuous-time stochastic (CTS) cellular automaton models. The model domain consists of a set of grid nodes, with each node assigned an integer state-code that represents its condition or composition. Adjacent pairs of nodes may undergo transitions to different states, according to a user-defined average transition rate. A model is created by writing a Python code that defines the possible states, the transitions, and the rates of those transitions. The code instantiates, initializes, and runs one of four object classes that represent different types of CTS model. CellLab-CTS provides the option of using either square or hexagonal grid cells. The software provides the ability to treat particular grid-node states as moving particles, and to track their position over time. Grid nodes may also be assigned user-defined properties, which the user can update after each transition through the use of a callback function. As a component of the Landlab modeling framework, CellLab-CTS models take advantage of a suite of Landlab's tools and capabilities, such as support for standardized input and output.
Murthy, Garimella Rama
2012-01-01
In this research paper, the relationship between finite / countable state space stochastic processes and point processes is explored. Utilizing the known relationship between Poisson processes and continuous time Markov chains, finite / countable state space random processes are related to continuous time Markov Chains. Based on the known results for binary random processes, characterization of auto-correlation function of finite state space random processes is explored. An important characte...
Characterization of ambient air pollution for stochastic health models
Batterman, S.A.
1981-08-01
This research is an analysis of various measures of ambient air pollution useful in cross-sectional epidemiological investigations and rick assessments. The Chestnut Ridge area health effects investigation, which includes a cross-sectional study of respiratory symptoms in young children, is used as a case study. Four large coal-fired electric generating power plants are the dominant pollution sources in this area of western Pennsylvania. The air pollution data base includes four years of sulfur dioxide and five years of total suspended particulate concentrations at seventeen monitors. Some 70 different characterizations of pollution are constructed and tested. These include pollutant concentrations at various percentiles and averaging times, exceedence measures which show the amount of time a specified threshold concentration is exceeded, and several dosage measures which transform non-linear dose-response relationships onto pollutant concentrations.
The 1996 performance assessment (PA) for the Waste Isolation Pilot Plant (WIPP) maintains a separation between stochastic (i.e. aleatory) and subjective (i.e. epistemic) uncertainty, with stochastic uncertainty arising from the possible disruptions that could occur at the WIPP over the 10,000-yr regulatory period specified by the US Environmental Protection Agency (40 CFR 191, 40 CFR 194) and subjective uncertainty arising from an inability to uniquely characterize many of the inputs required in the 1996 WIPP PA. The characterization of stochastic uncertainty is discussed, including drilling intrusion time, drilling location, penetration of excavated/nonexcavated areas of the repository, penetration of pressurized brine beneath the repository, borehole plugging patterns, activity level of waste, and occurrence of potash mining. Additional topics discussed include sampling procedures, generation of individual 10,000-yr futures for the WIPP, construction of complementary cumulative distribution functions (CCDFs), mechanistic calculations carried out to support CCDF construction, the Kaplan/Garrick ordered triple representation for risk, and determination of scenarios and scenario probabilities
HELTON,JON CRAIG; DAVIS,FREDDIE J.; JOHNSON,J.D.
2000-05-19
The 1996 performance assessment (PA) for the Waste Isolation Pilot Plant (WIPP) maintains a separation between stochastic (i.e., aleatory) and subjective (i.e., epistemic) uncertainty, with stochastic uncertainty arising from the possible disruptions that could occur at the WIPP over the 10,000 yr regulatory period specified by the US Environmental Protection Agency (40 CFR 191, 40 CFR 194) and subjective uncertainty arising from an inability to uniquely characterize many of the inputs required in the 1996 WIPP PA. The characterization of stochastic uncertainty is discussed including drilling intrusion time, drilling location penetration of excavated/nonexcavated areas of the repository, penetration of pressurized brine beneath the repository, borehole plugging patterns, activity level of waste, and occurrence of potash mining. Additional topics discussed include sampling procedures, generation of individual 10,000 yr futures for the WIPP, construction of complementary cumulative distribution functions (CCDFs), mechanistic calculations carried out to support CCDF construction the Kaplan/Garrick ordered triple representation for risk and determination of scenarios and scenario probabilities.
Hostetter, Megan
This thesis presents a new type of polypropylene (PP) cellular material fabricated through a simple melt-stretching process. Stochastic honeycombs have an open cell, random honeycomb structure, with webs oriented perpendicular to built-in skins. This process has the advantage that, for example, PP pellets can be turned into a sandwich panel in one step. It was demonstrated that despite the randomness in the web structure, the out-of-plane compressive strength of stochastic honeycombs was repeatable, and exceeded that of commercial PP foams and was comparable to commercial PP honeycombs. The key material properties required to produce an this architecture were shown to be a high melt strength and a high viscosity, branched polymer. The viscosity was shown to affect the total length of the webs in cross-section and the relative partitioning of material through the skin, transition region and webs. Web thickness was affected by the areal density of the polymer during fabrication. Mechanical testing methods were adapted from ASTM standards for honeycombs, and the fabrication method was advanced from a manual to a machine controlled process. Stochastic honeycombs were shown to buckle elastically, plastically, and fracture after the peak strength. Elastic and plastic buckling were dominant at lower densities, and plastic buckling and fracture at higher densities. A thin-plate buckling model for the strength of stochastic honeycombs was developed and verified experimentally. The crystallinity of the polymer affected the tensile strength and stiffness, having a linear effect on the buckling strength. The architecture was composed of webs bound on both sides and webs bound on one side and free on the other. A greater fraction of bound webs increased the strength of the structure in the buckling model. A fabrication study showed that melt-stretching the polymer at higher strain rates increased the connectivity and fraction of bound webs. Additionally, higher density led to a
Progresses in the Analysis of Stochastic 2D Cellular Automata: a Study of Asynchronous 2D Minority
Regnault, Damien; Thierry, Éric
2007-01-01
Cellular automata are often used to model systems in physics, social sciences, biology that are inherently asynchronous. Over the past 20 years, studies have demonstrated that the behavior of cellular automata drastically changed under asynchronous updates. Still, the few mathematical analyses of asynchronism focus on one-dimensional probabilistic cellular automata, either on single examples or on specific classes. As for other classic dynamical systems in physics, extending known methods from one- to two-dimensional systems is a long lasting challenging problem. In this paper, we address the problem of analysing an apparently simple 2D asynchronous cellular automaton: 2D Minority where each cell, when fired, updates to the minority state of its neighborhood. Our experiments reveal that in spite of its simplicity, the minority rule exhibits a quite complex response to asynchronism. By focusing on the fully asynchronous regime, we are however able to describe completely the asymptotic behavior of this dynamics...
Sakr, Ahmed Hamdi; Hossain, Ekram
2014-01-01
While cognitive radio enables spectrum-efficient wireless communication, radio frequency (RF) energy harvesting from ambient interference is an enabler for energy-efficient wireless communication. In this paper, we model and analyze cognitive and energy harvesting-based D2D communication in cellular networks. The cognitive D2D transmitters harvest energy from ambient interference and use one of the channels allocated to cellular users (in uplink or downlink), which is referred to as the D2D c...
Cellular spectroscopy: applications to cancer stem cell characterization
Wiegand, G.; Xin, H.; Anderson, A.; Mullinax, J.; Jaiswal, K.; Wiegand, A.; Avital, Itzhak
2011-02-01
Spectroscopic and light scattering methods were used to gain insight into the existence and characterization of the cancer stem cell. Fundamental technical description of devices used have been reported elsewhere. We included alterations and implementation of these biophotonic instruments as applied to our objectives. We disassociated human tumor and submitted the cells to optical characterization to support our working hypothesis of stem cell origins to cancer and mechanisms. Single cell combined with population based analysis within the Pancreatic cancer system led us to information regarding the polarization state of cells possessing anchor proteins and drug influx pumps. Multispectral imaging combined with flow cytometry enabled us to target rare cells that appear to retain template DNA. rendering them resistant to anti-cancer drug therapy. In this study we describe an optical method that combines high-throughput population pattern and correlates each cell with an individual fluorescent and bright-field image.
Malignant and tuberculous pleural effusions: immunophenotypic cellular characterization
Lucia Maria Zanatta de Aguiar; Leila Antonangelo; Vargas, Francisco S.; Maria Cláudia Nogueira Zerbini; Maria Mirtes Sales; David E. Uip; Paulo Hilário Nascimento Saldiva
2008-01-01
INTRODUCTION AND OBJECTIVES: Tuberculosis and cancer are the main causes of pleural effusion. Pleural involvement is associated with migration of immune cells to the pleural cavity. We sought to characterize the immunophenotype of leukocytes in the pleural effusion and peripheral blood of patients with tuberculosis or malignancy. METHODS: Thirty patients with tuberculosis (14) or malignancy (16) were studied. A control group included 20 healthy blood donors. RESULTS: Malignant phycoerythrin p...
Maria Luisa eGuerriero
2014-10-01
Full Text Available Rhythmic behavior is essential for plants; for example, daily (circadian rhythms control photosynthesis and seasonal rhythms regulate their life cycle. The core of the circadian clock is a genetic network that coordinates the expression of specific clock genes in a circadian rhythm reflecting the 24-hour day/night cycle.Circadian clocks exhibit stochastic noise due to the low copy numbers of clock genes and the consequent cell-to-cell variation: this intrinsic noise plays a major role in circadian clocks by inducing more robust oscillatory behavior. Another source of noise is the environment, which causes variation in temperature and light intensity: this extrinsic noise is part of the requirement for the structural complexity of clock networks.Advances in experimental techniques now permit single-cell measurements and the development of single-cell models. Here we present some modeling studies showing the importance of considering both types of noise in understanding how plants adapt to regular and irregular light variations. Stochastic models have proven useful for understanding the effect of regular variations. By contrast, the impact of irregular variations and the interaction of different noise sources are less studied.
Cellular and Phenotypic Characterization of Canine Osteosarcoma Cell Lines
Marie E. Legare, Jamie Bush, Amanda K. Ashley, Taka Kato, William H. Hanneman
2011-01-01
Full Text Available Canine and human osteosarcoma (OSA have many similarities, with the majority of reported cases occurring in the appendicular skeleton, gender predominance noted, high rate of metastasis at the time of presentation, and a lack of known etiology for this devastating disease. Due to poor understanding of the molecular mechanisms underlying OSA, we have characterized seven different OSA canine cell lines: Abrams, D17, Grey, Hughes, Ingles, Jarques, and Marisco and compared them to U2, a human OSA cell line, for the following parameters: morphology, growth, contact inhibition, migrational tendencies, alkaline phosphatase staining, heterologous tumor growth, double-strand DNA breaks, and oxidative damage. All results demonstrated the positive characteristics of the Abrams cell line for use in future studies of OSA. Of particular interest, the robust growth of a subcutaneous tumor and rapid pulmonary metastasis of the Abrams cell line in an immunocompromised mouse shows incredible potential for the future use of Abrams as a canine OSA model. Further investigations utilizing a canine cell model of OSA, such as Abrams, will be invaluable to understanding the molecular events underlying OSA, pharmaceutical inhibition of metastasis, and eventual prevention of this devastating disease.
A Characterization of Cellular Automata Generated by Idempotents on the Full Shift
Salo, Ville
2012-01-01
In this article, we discuss the family of cellular automata generated by so-called idempotent cellular automata (CA G such that G^2 = G) on the full shift. We prove a characterization of products of idempotent CA, and show examples of CA which are not easy to directly decompose into a product of idempotents, but which are trivially seen to satisfy the conditions of the characterization. Our proof uses ideas similar to those used in the well-known Embedding Theorem and Lower Entropy Factor Theorem in symbolic dynamics. We also consider some natural decidability questions for the class of products of idempotent CA.
Malignant and tuberculous pleural effusions: immunophenotypic cellular characterization
Lucia Maria Zanatta de Aguiar
2008-01-01
Full Text Available INTRODUCTION AND OBJECTIVES: Tuberculosis and cancer are the main causes of pleural effusion. Pleural involvement is associated with migration of immune cells to the pleural cavity. We sought to characterize the immunophenotype of leukocytes in the pleural effusion and peripheral blood of patients with tuberculosis or malignancy. METHODS: Thirty patients with tuberculosis (14 or malignancy (16 were studied. A control group included 20 healthy blood donors. RESULTS: Malignant phycoerythrin pleural effusions showed higher percentages of CD3, CD4, CD3CD45RO, and CD20CD25 lymphocytes and lower percentages of CD3CD25 and CD20HLA-DR when compared to PB lymphocytes. Compared to PB, tuberculous effusions had a higher percentage of lymphocytes that co-expressed CD3, CD4, CD3CD45RO, CD3TCRαβ, CD3CD28, and CD20 and a lower percentage of CD14, CD8 and CD3TCRγδ-positive lymphocytes. Malignant effusions presented higher expression of CD14 whereas tuberculous effusions had higher expression of CD3 and CD3CD95L. Peripheral blood cells from tuberculosis patients showed higher expression of CD14, CD20CD25 and CD3CD95L. Compared with the control cells, tuberculosis and cancer peripheral blood cells presented a lower percentage of CD3CD4 and CD3CD28-positive cells as well as a higher percentage of CD3CD8, CD3CD25 and CD3CD80-positive cells. CONCLUSIONS: Tuberculous and malignant peripheral blood is enriched with lymphocytes with a helper/inducer T cell phenotype, which are mainly of memory cells. CD14-positive cells were more frequently found in malignant effusions, while CD3-positive cells expressing Fas ligand were more frequently found in tuberculous effusions.
Malignant and Tuberculous Pleural Effusions: Immunophenotypic Cellular Characterization
de Aguiar, Lucia Maria Zanatta; Antonangelo, Leila; Vargas, Francisco S.; Zerbini, Maria Cláudia Nogueira; Sales, Maria Mirtes; Uip, David E.; Saldiva, Paulo Hilário Nascimento
2008-01-01
INTRODUCTION AND OBJECTIVES Tuberculosis and cancer are the main causes of pleural effusion. Pleural involvement is associated with migration of immune cells to the pleural cavity. We sought to characterize the immunophenotype of leukocytes in the pleural effusion and peripheral blood of patients with tuberculosis or malignancy. METHODS Thirty patients with tuberculosis (14) or malignancy (16) were studied. A control group included 20 healthy blood donors. RESULTS Malignant phycoerythrin pleural effusions showed higher percentages of CD3, CD4, CD3CD45RO, and CD20CD25 lymphocytes and lower percentages of CD3CD25 and CD20HLA-DR when compared to PB lymphocytes. Compared to PB, tuberculous effusions had a higher percentage of lymphocytes that co-expressed CD3, CD4, CD3CD45RO, CD3TCRαβ, CD3CD28, and CD20 and a lower percentage of CD14, CD8 and CD3TCRγδ-positive lymphocytes. Malignant effusions presented higher expression of CD14 whereas tuberculous effusions had higher expression of CD3 and CD3CD95L. Peripheral blood cells from tuberculosis patients showed higher expression of CD14, CD20CD25 and CD3CD95L. Compared with the control cells, tuberculosis and cancer peripheral blood cells presented a lower percentage of CD3CD4 and CD3CD28-positive cells as well as a higher percentage of CD3CD8, CD3CD25 and CD3CD80-positive cells. CONCLUSIONS Tuberculous and malignant peripheral blood is enriched with lymphocytes with a helper/inducer T cell phenotype, which are mainly of memory cells. CD14-positive cells were more frequently found in malignant effusions, while CD3-positive cells expressing Fas ligand were more frequently found in tuberculous effusions. PMID:18925324
Characterizations and simulations of a class of stochastic processes to model anomalous diffusion
In this paper, we study a parametric class of stochastic processes to model both fast and slow anomalous diffusions. This class, called generalized grey Brownian motion (ggBm), is made up of self-similar with stationary increments processes (H-sssi) and depends on two real parameters α element of (0, 2) and β element of (0, 1]. It includes fractional Brownian motion when α element of (0, 2) and β = 1, and time-fractional diffusion stochastic processes when α = β element of (0, 1). The latter have a marginal probability density function governed by time-fractional diffusion equations of order β. The ggBm is defined through the explicit construction of the underlying probability space. However, in this paper we show that it is possible to define it in an unspecified probability space. For this purpose, we write down explicitly all the finite-dimensional probability density functions. Moreover, we provide different ggBm characterizations. The role of the M-Wright function, which is related to the fundamental solution of the time-fractional diffusion equation, emerges as a natural generalization of the Gaussian distribution. Furthermore, we show that the ggBm can be represented in terms of the product of a random variable, which is related to the M-Wright function, and an independent fractional Brownian motion. This representation highlights the H-sssi nature of the ggBm and provides a way to study and simulate the trajectories. For this purpose, we developed a random walk model based on a finite difference approximation of a partial integro-differential equation of a fractional type
Characterizing pervasive vehicular access to the cellular RAN infrastructure: an urban case study
Uppoor, Sandesh; Fiore, Marco
2015-01-01
Managing user mobility is historically one of the most critical issues in cellular radio access networks (RANs). That task will become an even greater challenge due to cellular users on-board vehicles and networked cars that autonomously access Internet-based services, whose number is expected to grow dramatically in the next few years. There is thus a need to characterize RAN access from/by vehicles in a similar way to what has been done for traditional pedestrian access. In this paper, we p...
Characterization of humoral and cellular immune responses in patients with human papilloma virus
A descriptive and cross-sectional study was carried out in 30 females infected with the human papilloma virus, attended in the office of Immunology of the Specialty Polyclinic belonging to 'Saturnino Lora' Provincial Clinical Surgical Teaching Hospital in Santiago de Cuba, from June 2009 to June 2010, in order to characterize them according to immune response. To evaluate the humoral and cellular immune response rosetting assay and quantification of immunoglobulins were used respectively. Women between 25-36 years of age (40 %) infected with this virus, especially those coming from urban areas, prevailed in the series, and a significant decrease of the cellular response as compared to the humoral response was evidenced
Characterization of positive solution to stochastic competitor-competitor-cooperative model
Partha Sarathi Mandal
2013-04-01
Full Text Available In this article we study a randomized three-dimensional Lotka-Volterra model with competitor-competitor-mutualist interaction. We show the existence, uniqueness, moment boundedness, stochastic boundedness and global asymptotic stability of positive global solutions for this stochastic model. Analytical results are validated by numerical examples.
Cellular electrets polymer is a new ferroelectret material exhibiting large piezoelectricity and has attracted considerable attentions in researches and industries. Property characterization is very important for this material and current investigations are mostly on macroscopic properties. In this work, we conduct nanoscale piezoelectric and ferroelectric characterizations of cellular polypropylene (PP) films using piezoresponse force microscopy (PFM). First, both the single-frequency PFM and dual-frequency resonance-tracking PFM testings were conducted on the cellular PP film. The localized piezoelectric constant d33 is estimated to be 7–11pC/N by correcting the resonance magnification with quality factor and it is about one order lower than the macroscopic value. Next, using the switching spectroscopy PFM (SS-PFM), we studied polarization switching behavior of the cellular PP films. Results show that it exhibits the typical ferroelectric-like phase hysteresis loops and butterfly-shaped amplitude loops, which is similar to that of a poly(vinylidene fluoride) (PVDF) ferroelectric polymer film. However, both the phase and amplitude loops of the PP film are intensively asymmetric, which is thought to be caused by the nonzero remnant polarization after poling. Then, the D-E hysteresis loops of both the cellular PP film and PVDF film were measured by using the same wave form as that used in the SS-PFM, and the results show significant differences. Finally, we suggest that the ferroelectric-like behavior of cellular electrets films should be distinguished from that of typical ferroelectrics, both macroscopically and microscopically
This section contains summaries of research on the detection and characterization of damage in molecular, cellular, and physiological systems. Projects under investigation in this section include: chemical synthesis of nucleic acid derivatives; structural and conformational properties of biological molecules in solution; crystallographic and chemical studies of immunoglobulin structure; instrument design and development for x-ray and neutron scattering studies of biological molecules; and chromobiology and circadian regulation
Kryvohuz, Maksym, E-mail: mkryvohu@uci.edu; Mukamel, Shaul [Chemistry Department, University of California, Irvine, California 92697-2025 (United States)
2015-06-07
Generalized nonlinear response theory is presented for stochastic dynamical systems. Experiments in which multiple measurements of dynamical quantities are used along with multiple perturbations of parameters of dynamical systems are described by generalized response functions (GRFs). These constitute a new type of multidimensional measures of stochastic dynamics either in the time or the frequency domains. Closed expressions for GRFs in stochastic dynamical systems are derived and compared with numerical non-equilibrium simulations. Several types of perturbations are considered: impulsive and periodic perturbations of temperature and impulsive perturbations of coordinates. The present approach can be used to study various types of stochastic processes ranging from single-molecule conformational dynamics to chemical kinetics of finite-size reactors such as biocells.
Kryvohuz, Maksym; Mukamel, Shaul
2015-06-01
Generalized nonlinear response theory is presented for stochastic dynamical systems. Experiments in which multiple measurements of dynamical quantities are used along with multiple perturbations of parameters of dynamical systems are described by generalized response functions (GRFs). These constitute a new type of multidimensional measures of stochastic dynamics either in the time or the frequency domains. Closed expressions for GRFs in stochastic dynamical systems are derived and compared with numerical non-equilibrium simulations. Several types of perturbations are considered: impulsive and periodic perturbations of temperature and impulsive perturbations of coordinates. The present approach can be used to study various types of stochastic processes ranging from single-molecule conformational dynamics to chemical kinetics of finite-size reactors such as biocells. PMID:26049450
Generalized nonlinear response theory is presented for stochastic dynamical systems. Experiments in which multiple measurements of dynamical quantities are used along with multiple perturbations of parameters of dynamical systems are described by generalized response functions (GRFs). These constitute a new type of multidimensional measures of stochastic dynamics either in the time or the frequency domains. Closed expressions for GRFs in stochastic dynamical systems are derived and compared with numerical non-equilibrium simulations. Several types of perturbations are considered: impulsive and periodic perturbations of temperature and impulsive perturbations of coordinates. The present approach can be used to study various types of stochastic processes ranging from single-molecule conformational dynamics to chemical kinetics of finite-size reactors such as biocells
Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.
Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B
2016-01-29
Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. PMID:26350218
Jean-Marc Tulliani
2013-01-01
Full Text Available A modified gel-casting process was developed to produce both dense and highly porous (40% volume yttria tetragonal zirconia polycrystal (Y-TZP using agar, a natural polysaccharide, as gelling agent. A fugitive phase, made of commercial polyethylene spheres, was added to the ceramic suspension before gelling to produce cellular ceramic structures. The characterization of the microstructural features of both dense and cellular ceramics was carried out by FEG SEM analysis of cross-sections produced by focused ion beam. The mechanical properties of the components were characterized at room temperature by nanoindentation tests in continuous stiffness measurement mode, by investigating the direct effect of the presence of residual microporosity. The presence of a diffuse residual microporosity from incomplete gel deaeration resulted in a decay of the bending strength and of the elastic modulus. The mechanical behavior of both dense and cellular zirconia (in terms of elastic modulus, flexural strength, and deformation at rupture was investigated by performing four-point bending tests at the temperature of 1500°C.
Characterization of the cellular response triggered by gold nanoparticle-mediated laser manipulation
Kalies, Stefan; Keil, Sebastian; Sender, Sina; Hammer, Susanne C.; Antonopoulos, Georgios C.; Schomaker, Markus; Ripken, Tammo; Escobar, Hugo Murua; Meyer, Heiko; Heinemann, Dag
2015-11-01
Laser-based transfection techniques have proven high applicability in several cell biologic applications. The delivery of different molecules using these techniques has been extensively investigated. In particular, new high-throughput approaches such as gold nanoparticle-mediated laser transfection allow efficient delivery of antisense molecules or proteins into cells preserving high cell viabilities. However, the cellular response to the perforation procedure is not well understood. We herein analyzed the perforation kinetics of single cells during resonant gold nanoparticle-mediated laser manipulation with an 850-ps laser system at a wavelength of 532 nm. Inflow velocity of propidium iodide into manipulated cells reached a maximum within a few seconds. Experiments based on the inflow of FM4-64 indicated that the membrane remains permeable for a few minutes for small molecules. To further characterize the cellular response postmanipulation, we analyzed levels of oxidative heat or general stress. Although we observed an increased formation of reactive oxygen species by an increase of dichlorofluorescein fluorescence, heat shock protein 70 was not upregulated in laser-treated cells. Additionally, no evidence of stress granule formation was visible by immunofluorescence staining. The data provided in this study help to identify the cellular reactions to gold nanoparticle-mediated laser manipulation.
Ray-based stochastic inversion of prestack seismic data for improved reservoir characterization
Van der Burg, D.; Verdel, A.; Wapenaar, C.P.A.
2009-01-01
Trace inversion for reservoir parameters is affected by angle averaging of seismic data and wavelet distortion on the migration image. In an alternative approach to stochastic trace inversion, the data are inverted prestack before migration using 3D dynamic ray tracing. This choice makes it possible
Stochastic processes in cell biology
Bressloff, Paul C
2014-01-01
This book develops the theory of continuous and discrete stochastic processes within the context of cell biology. A wide range of biological topics are covered including normal and anomalous diffusion in complex cellular environments, stochastic ion channels and excitable systems, stochastic calcium signaling, molecular motors, intracellular transport, signal transduction, bacterial chemotaxis, robustness in gene networks, genetic switches and oscillators, cell polarization, polymerization, cellular length control, and branching processes. The book also provides a pedagogical introduction to the theory of stochastic process – Fokker Planck equations, stochastic differential equations, master equations and jump Markov processes, diffusion approximations and the system size expansion, first passage time problems, stochastic hybrid systems, reaction-diffusion equations, exclusion processes, WKB methods, martingales and branching processes, stochastic calculus, and numerical methods. This text is primarily...
Eichhorn, Ralf; Aurell, Erik
2014-04-01
theory for small deviations from equilibrium, in which a general framework is constructed from the analysis of non-equilibrium states close to equilibrium. In a next step, Prigogine and others developed linear irreversible thermodynamics, which establishes relations between transport coefficients and entropy production on a phenomenological level in terms of thermodynamic forces and fluxes. However, beyond the realm of linear response no general theoretical results were available for quite a long time. This situation has changed drastically over the last 20 years with the development of stochastic thermodynamics, revealing that the range of validity of thermodynamic statements can indeed be extended deep into the non-equilibrium regime. Early developments in that direction trace back to the observations of symmetry relations between the probabilities for entropy production and entropy annihilation in non-equilibrium steady states [5-8] (nowadays categorized in the class of so-called detailed fluctuation theorems), and the derivations of the Bochkov-Kuzovlev [9, 10] and Jarzynski relations [11] (which are now classified as so-called integral fluctuation theorems). Apart from its fundamental theoretical interest, the developments in stochastic thermodynamics have experienced an additional boost from the recent experimental progress in fabricating, manipulating, controlling and observing systems on the micro- and nano-scale. These advances are not only of formidable use for probing and monitoring biological processes on the cellular, sub-cellular and molecular level, but even include the realization of a microscopic thermodynamic heat engine [12] or the experimental verification of Landauer's principle in a colloidal system [13]. The scientific program Stochastic Thermodynamics held between 4 and 15 March 2013, and hosted by The Nordic Institute for Theoretical Physics (Nordita), was attended by more than 50 scientists from the Nordic countries and elsewhere, amongst them
Vladimirov, Igor G
2012-01-01
The paper is concerned with open quantum systems whose Heisenberg dynamics are described by quantum stochastic differential equations driven by external boson fields. The system-field coupling operators are assumed to be quadratic polynomials of the system observables, with the latter satisfying canonical commutation relations. In combination with a cubic system Hamiltonian, this leads to a class of quasilinear quantum stochastic systems which retain algebraic closedness in the evolution of mixed moments of the observables. Although such a system is nonlinear and its quantum state is no longer Gaussian, the dynamics of the moments of any order are amenable to exact analysis, including the computation of their steady-state values. In particular, a generalized criterion is developed for quadratic stability of the quasilinear systems. The results of the paper are applicable to the generation of non-Gaussian quantum states with manageable moments and an optimal design of linear quantum controllers for quasilinear...
Stochastic volatility and stochastic leverage
Veraart, Almut; Veraart, Luitgard A. M.
2009-01-01
This paper proposes the new concept of stochastic leverage in stochastic volatility models.Stochastic leverage refers to a stochastic process which replaces the classical constant correlationparameter between the asset return and the stochastic volatility process. We provide a systematictreatment of stochastic leverage and propose to model the stochastic leverage effect explicitly,e.g. by means of a linear transformation of a Jacobi process. Such models are both analyticallytractable and allo...
Oliveira, Roberto Imbuzeiro
2013-01-01
This paper introduces the concept of random context representations for the transition probabilities of a finite-alphabet stochastic process. Processes with these representations generalize context tree processes (a.k.a. variable length Markov chains), and are proven to coincide with processes whose transition probabilities are almost surely continuous functions of the (infinite) past. This is similar to a classical result by Kalikow about continuous transition probabilities. Existence and un...
Isolation and Characterization of Lactic Acid Bacteria (LAB) Produced Exo cellular Polysaccharide
Isolation and characterization of exo cellular polysaccharide was studied in order to evaluate some parameters in the synthesis of exo polysaccharide (EPS) and improve their production through submerged fermentation processes. Isolation strains Lactobacillus delbrueckii ssp bulgaricus (IS1), Lactococcus lactis ssp cremoris (IS2) and Lactobacillus delbrueckii ssp bulgaricus (IS3) were studied in shake flasks using yeast extract, surfactants and different exposure doses of gamma irradiation.The optimum concentration of (EPS) formation (0.762 g/l) by Lactococcus lactis ssp cremoris (IS2), 3.0 (g/l) yeast extract, 1.72 (g/l) at 0.5 (%) surfactant Triton X-100. Also, EPS (1.842 g/l) was produced when Lactococcus lactis ssp cremoris (IS2) exposed to 0.2 kGy dose level.
Cardona-Felix, Cesar S.; Lara-Gonzalez, Samuel; Brieba, Luis G. (LNLS)
2012-02-08
Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.
Berhanu, P; Kolterman, O G; Baron, A; Tsai, P; Olefsky, J M; Brandenburg, D.
1983-01-01
We photolabeled and characterized insulin receptors in isolated adipocytes from normal human subjects and then studied the cellular fate of the labeled insulin-receptor complexes at physiologic temperatures. The biologically active photosensitive insulin derivative, B2(2-nitro-4-azidophenylacetyl)des-PheB1-insulin (NAPA-DP-insulin) was used to photoaffinity label the insulin receptors, and the specifically labeled cellular proteins were identified by sodium dodecyl sulfate-polyacrylamide gel ...
Phenotypic characterization of the bone marrow stem cells used in regenerative cellular therapy
Regenerative medicine is a novel therapeutic method with broad potential for the treatment of various illnesses, based on the use of bone marrow (BM) stem cells, whose phenotypic characterization is limited. The paper deals with the expression of different cell membrane markers in mononuclear BM cells from 14 patients who underwent autologous cell therapy, obtained by medullary puncture and mobilization to peripheral blood, with the purpose of characterizing the different types of cells present in that heterogeneous cellular population and identifying the adhesion molecules involved in their adhesion. A greater presence was observed of adherent stem cells from the marrow stroma in mononuclear cells obtained directly from the BM; a larger population of CD90+cells in mononuclear cells from CD34-/CD45-peripheral blood with a high expression of molecules CD44 and CD62L, which suggests a greater presence of mesenchymal stem cells (MSC) in mobilized cells from the marrow stroma. The higher levels of CD34+cells in peripheral blood stem cells with a low expression of molecules CD117-and DR-suggests the presence of hematopoietic stem cells, hemangioblasts and progenitor endothelial cells mobilized to peripheral circulation. It was found that mononuclear cells from both the BM and peripheral blood show a high presence of stem cells with expression of adhesion molecule CD44 (MMC marker), probably involved in their migration, settling and differentiation
Characterization of memory states of the Preisach operator with stochastic inputs
The Preisach operator with inputs defined by a Markov process xt is considered. The question we address is: what is the distribution of the random memory state of the Preisach operator at a given time moment t0 in the limit r→∞ of infinitely long input history xt, t0-r≤t≤t0? In order to answer this question, we introduce a Markov chain (called the memory state Markov chain) where the states are pairs (mk,Mk) of elements from the monotone sequences of the local minimum input values mk and the local maximum input values Mk recorded in the memory state and the index k of the elements plays the role of time. We express the transition probabilities of this Markov chain in terms of the transition probabilities of the input stochastic process and show that the memory state Markov chain and the input process generate the same distribution of the memory states. These results are illustrated by several examples of stochastic inputs such as the Wiener and Bernoulli processes and their mixture (we first discuss a discrete version of these processes and then the continuous time and state setting). The memory state Markov chain is then used to find the distribution of the random number of elements in the memory state sequence. We show that this number has the Poisson distribution for the Wiener and Bernoulli processes inputs. In particular, in the discrete setting, the mean value of the number of elements in the memory state scales as lnN, where N is the number of the input states, while the mean time it takes the input to generate this memory state scales as N2 for the Wiener process and as N for the Bernoulli process. A similar relationship between the dimension of the memory state vector and the number of iterations in the numerical realization of the input is shown for the mixture of the Wiener and Bernoulli processes, thus confirming that the memory state Markov chain is an efficient tool for generating the distribution of the Preisach operator memory states
CSI 2264: Characterizing Young Stars in NGC 2264 with Stochastically Varying Light Curves
Stauffer, John; Cody, Ann Marie; Rebull, Luisa; Hillenbrand, Lynne A.; Turner, Neal J.; Carpenter, John; Carey, Sean; Terebey, Susan; Morales-Calderón, María; Alencar, Silvia H. P.; McGinnis, Pauline; Sousa, Alana; Bouvier, Jerome; Venuti, Laura; Hartmann, Lee; Calvet, Nuria; Micela, Giusi; Flaccomio, Ettore; Song, Inseok; Gutermuth, Rob; Barrado, David; Vrba, Frederick J.; Covey, Kevin; Herbst, William; Gillen, Edward; Medeiros Guimarães, Marcelo; Bouy, Herve; Favata, Fabio
2016-03-01
We provide CoRoT and Spitzer light curves and other supporting data for 17 classical T Tauri stars in NGC 2264 whose CoRoT light curves exemplify the “stochastic” light curve class as defined in 2014 by Cody et al. The most probable physical mechanism to explain the optical variability within this light curve class is time-dependent mass accretion onto the stellar photosphere, producing transient hot spots. Where we have appropriate spectral data, we show that the veiling variability in these stars is consistent in both amplitude and timescale with the optical light curve morphology. The veiling variability is also well-correlated with the strength of the He i 6678 Å emission line, predicted by models to arise in accretion shocks on or near the stellar photosphere. Stars with accretion burst light curve morphology also have variable mass accretion. The stochastic and accretion burst light curves can both be explained by a simple model of randomly occurring flux bursts, with the stochastic light curve class having a higher frequency of lower amplitude events. Members of the stochastic light curve class have only moderate mass accretion rates. Their Hα profiles usually have blueshifted absorption features, probably originating in a disk wind. The lack of periodic signatures in the light curves suggests that little of the variability is due to long-lived hot spots rotating into or out of our line of sight; instead, the primary driver of the observed photometric variability is likely to be instabilities in the inner disk that lead to variable mass accretion. Based on data from the Spitzer and CoRoT missions, as well as the Canada-France-Hawaii Telescope (CFHT) MegaCam CCD, and the European Southern Observatory Very Large Telescope, Paranal Chile, under program 088.C-0239. The CoRoT space mission was developed and is operated by the French space agency CNES, with particpiation of ESA’s RSSD and Science Programmes, Austria, Belgium, Brazil, Germany, and Spain
Vorobiev, O.; Ezzedine, S. M.; Antoun, T.; Glenn, L.
2014-12-01
This work describes a methodology used for large scale modeling of wave propagation fromunderground explosions conducted at the Nevada Test Site (NTS) in two different geological settings:fractured granitic rock mass and in alluvium deposition. We show that the discrete nature of rockmasses as well as the spatial variability of the fabric of alluvium is very important to understand groundmotions induced by underground explosions. In order to build a credible conceptual model of thesubsurface we integrated the geological, geomechanical and geophysical characterizations conductedduring recent test at the NTS as well as historical data from the characterization during the undergroundnuclear test conducted at the NTS. Because detailed site characterization is limited, expensive and, insome instances, impossible we have numerically investigated the effects of the characterization gaps onthe overall response of the system. We performed several computational studies to identify the keyimportant geologic features specific to fractured media mainly the joints; and those specific foralluvium porous media mainly the spatial variability of geological alluvium facies characterized bytheir variances and their integral scales. We have also explored common key features to both geologicalenvironments such as saturation and topography and assess which characteristics affect the most theground motion in the near-field and in the far-field. Stochastic representation of these features based onthe field characterizations have been implemented in Geodyn and GeodynL hydrocodes. Both codeswere used to guide site characterization efforts in order to provide the essential data to the modelingcommunity. We validate our computational results by comparing the measured and computed groundmotion at various ranges. This work performed under the auspices of the U.S. Department of Energy by Lawrence LivermoreNational Laboratory under Contract DE-AC52-07NA27344.
Highlights: → The present study focused on deformation behavior and failure mechanisms in lattice structure produced by selective laser melting (SLM). → It is demonstrated that heat treatments can be used to increase the energy absorption of an SLM-processed structure. → An in situ testing procedure was introduced, where local strains were calculated by digital image correlation → Shear failure could be predicted by localization using Tresca strains. → The approach employed provides a means to understand the microstructure-mechanical property-local deformation relationship. - Abstract: Cellular materials are promising candidates for load adapted light-weight structures. Direct manufacturing (DM) tools are effective methods to produce non-stochastic structures. Many DM studies currently focus on optimization of the geometric nature of the structures obtained. The literature available so far reports on the mechanical properties but local deformation mechanisms are not taken into account. In order to fill this gap, the current study addresses the deformation behavior of a lattice structure produced by selective laser melting (SLM) on the local scale by means of a comprehensive experimental in situ approach, including electron backscatter diffraction, scanning electron microscopy and digital image correlation. SLM-processed as well as heat treated lattice structures made from TiAl6V4 alloy were employed for mechanical testing. It is demonstrated that the current approach provides means to understand the microstructure-mechanical property-local deformation relationship to allow for optimization of load adapted lattice structures.
Deoxyribonucleic acid (DNA) contains the genetic information and chemical injury to this macromolecule may have severe biological consequences. We report here the detection of 4 new radiation-induced DNA lesions by using a high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) approach. For that purpose, the characteristic fragmentation of most 2'-deoxy-ribo nucleosides, the loss of 116 Da corresponding to the loss of the 2-deoxyribose moiety, was used in the so-called neutral loss mode of the HPLC-MS/MS. One of the newly detected lesions, named dCyd341 because it is a 2'-deoxycytidine modification exhibiting a molecular weight of 341 Da, was also detected in cellular DNA. Characterization of this modified nucleoside was performed using NMR and exact mass determination of the product obtained by chemical synthesis. A mechanism of formation was then proposed, in which the first event is the H-abstraction at the C4 position of a 2-deoxyribose moiety. Then, the sugar modification produced exhibits a reactive aldehyde that, through reaction with a vicinal cytosine base, gives rise to dCyd341. dCyd341 could be considered as a complex damage since its formation involves a DNA strand break and a cross-link between a damaged sugar residue and a vicinal cytosine base located most probably on the complementary DNA strand. In addition to its characterization, preliminary biological studies revealed that cells are able to remove the lesion from DNA. Repair studies have revealed the ability of cells to excise the lesion. Identification of the repair systems involved could represent an interesting challenge. (author)
Zaccolo Manuela
2008-06-01
Full Text Available Abstract Background A novel fluorescent cAMP analog (8-[Pharos-575]- adenosine-3', 5'-cyclic monophosphate was characterized with respect to its spectral properties, its ability to bind to and activate three main isoenzymes of the cAMP-dependent protein kinase (PKA-Iα, PKA-IIα, PKA-IIβ in vitro, its stability towards phosphodiesterase and its ability to permeate into cultured eukaryotic cells using resonance energy transfer based indicators, and conventional fluorescence imaging. Results The Pharos fluorophore is characterized by a Stokes shift of 42 nm with an absorption maximum at 575 nm and the emission peaking at 617 nm. The quantum yield is 30%. Incubation of the compound to RIIα and RIIβ subunits increases the amplitude of excitation and absorption maxima significantly; no major change was observed with RIα. In vitro binding of the compound to RIα subunit and activation of the PKA-Iα holoenzyme was essentially equivalent to cAMP; RII subunits bound the fluorescent analog up to ten times less efficiently, resulting in about two times reduced apparent activation constants of the holoenzymes compared to cAMP. The cellular uptake of the fluorescent analog was investigated by cAMP indicators. It was estimated that about 7 μM of the fluorescent cAMP analog is available to the indicator after one hour of incubation and that about 600 μM of the compound had to be added to intact cells to half-maximally dissociate a PKA type IIα sensor. Conclusion The novel analog combines good membrane permeability- comparable to 8-Br-cAMP – with superior spectral properties of a modern, red-shifted fluorophore. GFP-tagged regulatory subunits of PKA and the analog co-localized. Furthermore, it is a potent, PDE-resistant activator of PKA-I and -II, suitable for in vitro applications and spatial distribution evaluations in living cells.
Parab, Harshala J; Huang, Jing-Hong; Liu, Ru-Shi [Department of Chemistry, National Taiwan University, Taipei 106, Taiwan (China); Lai, Tsung-Ching; Jan, Yi-Hua; Wang, Jui-Ling; Hsiao, Michael; Chen, Chung-Hsuan [Genomics Research Center, Academia Sinica, Taipei 115, Taiwan (China); Hwu, Yeu-Kuang [Institute of Physics, Academia Sinica, Taipei 115, Taiwan (China); Tsai, Din Ping [Department of Physics, National Taiwan University, Taipei 106, Taiwan (China); Chuang, Shih-Yi; Pang, Jong-Hwei S, E-mail: rsliu@ntu.edu.tw, E-mail: mhsiao@gate.sinica.edu.tw [Graduate Institute of Clinical Medical Sciences, Chang Gung University, Tao-Yuan, Taiwan (China)
2011-09-30
The feasibility of using gold nanoparticles (AuNPs) for biomedical applications has led to considerable interest in the development of novel synthetic protocols and surface modification strategies for AuNPs to produce biocompatible molecular probes. This investigation is, to our knowledge, the first to elucidate the synthesis and characterization of sodium hexametaphosphate (HMP)-stabilized gold nanoparticles (Au-HMP) in an aqueous medium. The role of HMP, a food additive, as a polymeric stabilizing and protecting agent for AuNPs is elucidated. The surface modification of Au-HMP nanoparticles was carried out using polyethylene glycol and transferrin to produce molecular probes for possible clinical applications. In vitro cell viability studies performed using as-synthesized Au-HMP nanoparticles and their surface-modified counterparts reveal the biocompatibility of the nanoparticles. The transferrin-conjugated nanoparticles have significantly higher cellular uptake in J5 cells (liver cancer cells) than control cells (oral mucosa fibroblast cells), as determined by inductively coupled plasma mass spectrometry. This study demonstrates the possibility of using an inexpensive and non-toxic food additive, HMP, as a stabilizer in the large-scale generation of biocompatible and monodispersed AuNPs, which may have future diagnostic and therapeutic applications.
Stochastic volatility and stochastic leverage
Veraart, Almut; Veraart, Luitgard A. M.
models which allow for a stochastic leverage effect: the generalised Heston model and the generalised Barndorff-Nielsen & Shephard model. We investigate the impact of a stochastic leverage effect in the risk neutral world by focusing on implied volatilities generated by option prices derived from our new......This paper proposes the new concept of stochastic leverage in stochastic volatility models. Stochastic leverage refers to a stochastic process which replaces the classical constant correlation parameter between the asset return and the stochastic volatility process. We provide a systematic...... treatment of stochastic leverage and propose to model the stochastic leverage effect explicitly, e.g. by means of a linear transformation of a Jacobi process. Such models are both analytically tractable and allow for a direct economic interpretation. In particular, we propose two new stochastic volatility...
CSI 2264: Characterizing Young Stars in NGC 2264 with Stochastically Varying Light Curves
Stauffer, John; Rebull, Luisa; Hillenbrand, Lynne A; Turner, Neal J; Carpenter, John; Carey, Sean; Terebey, Susan; Morales-Calderon, Maria; Alencar, Silvia H P; McGinnis, Pauline; Sousa, Alana; Bouvier, Jerome; Venuti, Laura; Hartmann, Lee; Calvet, Nuria; Micela, Giusi; Flaccomio, Ettore; Song, Inseok; Gutermuth, Rob; Barrado, David; Vrba, Frederick J; Covey, Kevin; Herbst, William; Gillen, Edward; Guimaraes, Marcelo Medeiros; Bouy, Herve; Favata, Fabio
2016-01-01
We provide CoRoT and Spitzer light curves, as well as broad-band multi-wavelength photometry and high resolution, multi- and single-epoch spectroscopy for 17 classical T Tauris in NGC 2264 whose CoRoT light curves (LCs) exemplify the "stochastic" LC class as defined in Cody et al. (2014). The most probable physical mechanism to explain the optical variability in this LC class is time-dependent mass accretion onto the stellar photosphere, producing transient hot spots. As evidence in favor of this hypothesis, multi-epoch high resolution spectra for a subset of these stars shows that their veiling levels also vary in time and that this veiling variability is consistent in both amplitude and timescale with the optical LC morphology. Furthermore, the veiling variability is well-correlated with the strength of the HeI 6678A emission line, a feature predicted by models to arise in accretion shocks on or near the stellar photosphere. Stars with accretion burst LC morphology (Stauffer et al. 2014) are also attributed...
Hao Lei
2015-12-01
Full Text Available Trip travel time reliability is an important measure of transportation system performance and a key factor affecting travelers’ choices. This paper explores a method for estimating travel time distributions for corridors that contain multiple bottlenecks. A set of analytical equations are used to calculate the number of queued vehicles ahead of a probe vehicle and further capture many important factors affecting travel times: the prevailing congestion level, queue discharge rates at the bottlenecks, and flow rates associated with merges and diverges. Based on multiple random scenarios and a vector of arrival times, the lane-by-lane delay at each bottleneck along the corridor is recursively estimated to produce a route-level travel time distribution. The model incorporates stochastic variations of bottleneck capacity and demand and explains the travel time correlations between sequential links. Its data needs are the entering and exiting flow rates and a sense of the lane-by-lane distribution of traffic at each bottleneck. A detailed vehicle trajectory data-set from the Next Generation SIMulation (NGSIM project has been used to verify that the estimated distributions are valid, and the sources of estimation error are examined.
Principal eigenvalue characterization connected with stochastic particle motion in a finite interval
Fethi Bin Muhammad Belgacem
2002-01-01
Full Text Available In this paper, we show that despite their distinction, both the Statonovich and Îto s calculi lead to the same reactive Fokker-Planck equation: ∂p∂t−∂∂x[D∂p∂x−bp]=λmp, (1 describing stochastic dynamics of a particle moving under the influence of an indefinite potential m(x,t, a drift b(x,t, and a constant diffusion D. We treat the periodic-parabolic eigenvalue problem (1 for finite domains having absorbing barriers. We show that under conditions required by the maximum principle, the positive principal eigenvalue λ* (and the negative principal λ* eigenvalue is connected to the probability eigendensity function p(x,t by a Raleigh-Ritz like formulation. In the process, we establish the manner of effect of the drift and any inducing potential on the size of the principal eigenvalue. We show that the degree of convexity of the potential plays a major role in this regard.
Smith, L J
1984-11-01
This study was designed to characterize the biochemical, cellular, and morphologic events produced in mice by butylated hydroxytoluene (BHT) and to relate these events to changes in extracellular angiotensin-converting enzyme (ACE) activity. On Day 1 after the administration of BHT, bronchoalveolar lavage (BAL) ACE activity increased 4-fold (p less than 0.001), its specific activity relative to BAL protein increased 3-fold (p less than 0.001), and both type 1 cell damage and endothelial cell damage were detected by electron microscopy. The early increase in BAL ACE activity preceded changes in plasma ACE levels, BAL cell number, protein, lactate, and lactate dehydrogenase (LDH) activity in both plasma and BAL, and the ACE content of alveolar macrophages. On Day 2, BAL ACE activity increased 9-fold, BAL protein increased 4-fold (p less than 0.001), BAL LDH activity increased 34% (p less than 0.05), and the BAL cell count doubled (p less than 0.01). Changes in each animal's appearance, body weight, wet and dry lung weights, and plasma ACE levels occurred between Days 3 and 5. The BAL differential cell count, which consisted of greater than 95% macrophages in uninjured mice, did not change until Day 5 when there was a small increase in polymorphonuclear leukocytes (PMN). On Day 7, the number of PMN peaked, and some of the other measures of lung injury began returning toward normal. These results indicate that BAL ACE activity is a sensitive, early marker of BHT-induced lung injury, which appears to reflect damage to the cells of the alveolar-capillary barrier. In addition, PMN do not appear to play a major role in this model of lung injury. Because of its effects on angiotensin, bradykinin, and prostaglandins, the early release of ACE from damaged cells may modulate the subsequent injury. PMID:6093659
Characterization of CdTe/CdSe quantum dots-transferrin fluorescent probes for cellular labeling
Highlights: ► A convenient method was designed to assess cell efficiency of QDs probes for cellular labeling. ► The relationship between conjugation methods and effectiveness was evaluated clearly. ► QDs-Tf probe synthesized by EDC coupling had the highest labeling efficiency, followed by electrostatic interaction, and dTf coating. - Abstract: In this paper, we prepared three types of transferrin-quantum dots conjugates (QDs-Tf) using three different methods (electrostatic interaction, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) coupling, denatured transferrin (dTf) coating). Fluorescence emission spectra, surface characteristics, zeta potentials of quantum dots (QDs) and QDs-Tf fluorescent probes were characterized by spectrophotometer, capillary electrophoresis, and dynamic light scattering. Fluorescent imaging of HeLa cells was also performed by QDs and QDs-Tf fluorescent probes. It was found that the fluorescence imaging performances of QDs-Tf probes prepared by electrostatic interaction and EDC coupling were better compared with the one prepared by dTf coating. Then a real-time single cell detection system was established to quantitatively evaluate cell labeling effects of QDs-Tf fluorescent probes. It was found that for cell labeling efficiency, the proportion of cells labeled by quantum dot probes to a group of cells, QDs-Tf probe prepared by EDC coupling showed the highest labeling efficiency (85.55 ± 3.88%), followed by electrostatic interaction (78.86 ± 9.57%), and dTf coating showed the lowest (40.09 ± 10.2%). This efficiency order was confirmed by flow cytometry results. This study demonstrated the relationship between conjugation methods and the resultant QDs-Tf probes and provided a foundation for choosing appropriate QDs-Tf probes in cell labeling.
Characterization of CdTe/CdSe quantum dots-transferrin fluorescent probes for cellular labeling
Guan Liyun; Li Yongqiang; Lin Song; Zhang Mingzhen; Chen Jun; Ma Zhiya [Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Department of Biomedical Engineering, Wuhan, HuBei 430074 (China); Zhao Yuandi, E-mail: zydi@mail.hust.edu.cn [Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Department of Biomedical Engineering, Wuhan, HuBei 430074 (China)
2012-09-05
Highlights: Black-Right-Pointing-Pointer A convenient method was designed to assess cell efficiency of QDs probes for cellular labeling. Black-Right-Pointing-Pointer The relationship between conjugation methods and effectiveness was evaluated clearly. Black-Right-Pointing-Pointer QDs-Tf probe synthesized by EDC coupling had the highest labeling efficiency, followed by electrostatic interaction, and dTf coating. - Abstract: In this paper, we prepared three types of transferrin-quantum dots conjugates (QDs-Tf) using three different methods (electrostatic interaction, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) coupling, denatured transferrin (dTf) coating). Fluorescence emission spectra, surface characteristics, zeta potentials of quantum dots (QDs) and QDs-Tf fluorescent probes were characterized by spectrophotometer, capillary electrophoresis, and dynamic light scattering. Fluorescent imaging of HeLa cells was also performed by QDs and QDs-Tf fluorescent probes. It was found that the fluorescence imaging performances of QDs-Tf probes prepared by electrostatic interaction and EDC coupling were better compared with the one prepared by dTf coating. Then a real-time single cell detection system was established to quantitatively evaluate cell labeling effects of QDs-Tf fluorescent probes. It was found that for cell labeling efficiency, the proportion of cells labeled by quantum dot probes to a group of cells, QDs-Tf probe prepared by EDC coupling showed the highest labeling efficiency (85.55 {+-} 3.88%), followed by electrostatic interaction (78.86 {+-} 9.57%), and dTf coating showed the lowest (40.09 {+-} 10.2%). This efficiency order was confirmed by flow cytometry results. This study demonstrated the relationship between conjugation methods and the resultant QDs-Tf probes and provided a foundation for choosing appropriate QDs-Tf probes in cell labeling.
Flaw tolerance vs. performance: A tradeoff in metallic glass cellular structures
Stochastic cellular structures are prevalent in nature and engineering materials alike. They are difficult to manipulate and study systematically and almost always contain imperfections. To design and characterize various degrees of imperfections in perfect periodic, stochastic and natural cellular structures, we fabricate a broad range of metallic glass cellular structures from perfectly periodic to highly stochastic by using a novel artificial microstructure approach based on thermoplastic replication of metallic glasses. For these cellular structures, precisely controlled imperfections are implemented and their effects on the mechanical response are evaluated. It is found that the mechanical performance of the periodic structures is generally superior to that of the stochastic structures. However, the stochastic structures experience a much higher tolerance to flaws than the periodic structure, especially in the plastic regime. The different flaw tolerance is explained by the stress distribution within the various structures, which leads to an overall 'strain-hardening' behavior of the stochastic structure compared to a 'strain-softening' behavior in the periodic structure. Our findings reveal how structure, 'strain-hardening' and flaw tolerance are microscopically related in structural materials
Lamichhane SP
2015-01-01
Full Text Available Surya P Lamichhane,1 Neha Arya,1,2 Nirdesh Ojha,3 Esther Kohler,1 V Prasad Shastri1,2,41Institute for Macromolecular Chemistry, University of Freiburg, Freiburg, 2Helmholtz Virtual Institute on “Multifunctional Biomaterials for Medicine”, 3Laboratory for Process Technology, Department of Microsystems Engineering, University of Freiburg, Freiburg, 4Centre for Biological Signaling Studies (BIOSS, University of Freiburg, Freiburg, GermanyAbstract: The efficient delivery of chemotherapeutics to the tumor via nanoparticle (NP-based delivery systems remains a significant challenge. This is compounded by the fact that the tumor is highly dynamic and complex environment composed of a plurality of cell types and extracellular matrix. Since glycosaminoglycan (GAG production is altered in many diseases (or pathologies, NPs bearing GAG moieties on the surface may confer some unique advantages in interrogating the tumor microenvironment. In order to explore this premise, in the study reported here poly-lactide-co-glycolide (PLGA NPs in the range of 100–150 nm bearing various proteoglycans were synthesized by a single-step nanoprecipitation and characterized. The surface functionalization of the NPs with GAG moieties was verified using zeta potential measurements and X-ray photoelectron spectroscopy. To establish these GAG-bearing NPs as carriers of therapeutics, cellular toxicity assays were undertaken in lung epithelial adenocarcinoma (A549 cells, human pulmonary microvascular endothelial cells (HPMEC, and renal proximal tubular epithelial cells. In general NPs were well tolerated over a wide concentration range (100–600 µg/mL by all cell types and were taken up to appreciable extents without any adverse cell response in A549 cells and HPMEC. Further, GAG-functionalized PLGA NPs were taken up to different extents in A459 cells and HPMEC. In both cell systems, the uptake of heparin-modified NPs was diminished by 50%–65% in comparison to that of
Chakraborty, B.; Haris, K.
characterize the patchiness of the seafloor (Table 1). The backscatter and bathymetry image blocks having 400 x 400 pixels, were classified according to the degree of seepage based on the backscatter strength as well as fractal dimension (determined using... box-dimension technique). Sample blocks F20 J19 F07 Q19 S23 N25 Seepage type Very high High Moderate Low Very low No Mean Backscatter (dB) -31.58 -34.40 -38.99 -38.96 -43.28 -42...
Stochastic dynamics and irreversibility
Tomé, Tânia
2015-01-01
This textbook presents an exposition of stochastic dynamics and irreversibility. It comprises the principles of probability theory and the stochastic dynamics in continuous spaces, described by Langevin and Fokker-Planck equations, and in discrete spaces, described by Markov chains and master equations. Special concern is given to the study of irreversibility, both in systems that evolve to equilibrium and in nonequilibrium stationary states. Attention is also given to the study of models displaying phase transitions and critical phenomema both in thermodynamic equilibrium and out of equilibrium. These models include the linear Glauber model, the Glauber-Ising model, lattice models with absorbing states such as the contact process and those used in population dynamic and spreading of epidemic, probabilistic cellular automata, reaction-diffusion processes, random sequential adsorption and dynamic percolation. A stochastic approach to chemical reaction is also presented.The textbook is intended for students of ...
Characterization of the emergent properties of a synthetic quasi-cellular system
Lazzerini-Ospri Lorenzo
2012-03-01
Full Text Available Abstract Background The process of solutes entrapment during liposomes formation is interesting for the investigation of the relationship between the formation of compartments and the distribution of molecules inside them; a relevant issue in the studies of the origin of life. Theoretically, when no interactions are supposed among the chemical species to be entrapped, the entrapment is described by a standard Poisson process. But very recent experimental findings show that, for small liposomes (100 nm diameter, the distribution of entrapped molecules is best described by a power-law function. This is of a great importance, as the two random processes give rise to two completely different scenarios. Here we present an in silico stochastic simulation of the encapsulation of a cell-free molecular translation system (the PURE system, obtained following two different entrapment models: a pure Poisson process, and a power-law. The protein synthesis inside the liposomes has been studied in both cases, with the aim to highlight experimental observables that could be measured to assess which model gives a better representation of the real process. Results Firstly, a minimal model for in vitro protein synthesis, based on the PURE system molecular composition, has been formalized. Then, we have designed a reliable experimental simulation where stochastic factors affect the reaction course inside the compartment. To this end, 24 solutes, which represent the PURE system components, have been stochastically distributed among vesicles by following either a Poisson or a power-law distribution. The course of the protein synthesis within each vesicle has been consequently calculated, as a function of vesicle size. Our study can predict translation yield in a population of small liposomes down to the attoliter (10-18 L range. Our results show that the efficiency of protein synthesis peaks at approximately 3·10-16 L (840 nm diam. with a Poisson distribution of
Evaluation of soil characterization technologies using a stochastic, value-of-information approach
The US Department of Energy has initiated an integrated demonstration program to develop and compare new technologies for the characterization of uranium-contaminated soils. As part of this effort, a performance-assessment task was funded in February, 1993 to evaluate the field tested technologies. Performance assessment can be cleaned as the analysis that evaluates a system's, or technology's, ability to meet the criteria specified for performance. Four new technologies were field tested at the Fernald Environmental Management Restoration Co. in Ohio. In the next section, the goals of this performance assessment task are discussed. The following section discusses issues that must be resolved if the goals are to be successfully met. The author concludes with a discussion of the potential benefits to performance assessment of the approach taken. This paper is intended to be the first of a series of documentation that describes the work. Also in this proceedings is a paper on the field demonstration at the Fernald site and a description of the technologies (Tidwell et al, 1993) and a paper on the application of advanced geostatistical techniques (Rautman, 1993). The overall approach is to simply demonstrate the applicability of concepts that are well described in the literature but are not routinely applied to problems in environmental remediation, restoration, and waste management. The basic geostatistical concepts are documented in Clark (1979) and in Issaks and Srivastava (1989). Advanced concepts and applications, along with software, are discussed in Deutsch and Journel (1992). Integration of geostatistical modeling with a decision-analytic framework is discussed in Freeze et al (1992). Information-theoretic and probabilistic concepts are borrowed from the work of Shannon (1948), Jaynes (1957), and Harr (1987). The author sees the task as one of introducing and applying robust methodologies with demonstrated applicability in other fields to the problem at hand
Ohira, Toru
2006-01-01
We present a simple dynamical model to address the question of introducing a stochastic nature in a time variable. This model includes noise in the time variable but not in the "space" variable, which is opposite to the normal description of stochastic dynamics. The notable feature is that these models can induce a "resonance" with varying noise strength in the time variable. Thus, they provide a different mechanism for stochastic resonance, which has been discussed within the normal context ...
Jonathan M Behrendt
Full Text Available The efficient transport of micron-sized beads into cells, via a non-endocytosis mediated mechanism, has only recently been described. As such there is considerable scope for optimization and exploitation of this procedure to enable imaging and sensing applications to be realized. Herein, we report the design, synthesis and characterization of fluorescent microsphere-based cellular delivery agents that can also carry biological cargoes. These core-shell polymer microspheres possess two distinct chemical environments; the core is hydrophobic and can be labeled with fluorescent dye, to permit visual tracking of the microsphere during and after cellular delivery, whilst the outer shell renders the external surfaces of the microspheres hydrophilic, thus facilitating both bioconjugation and cellular compatibility. Cross-linked core particles were prepared in a dispersion polymerization reaction employing styrene, divinylbenzene and a thiol-functionalized co-monomer. These core particles were then shelled in a seeded emulsion polymerization reaction, employing styrene, divinylbenzene and methacrylic acid, to generate orthogonally functionalized core-shell microspheres which were internally labeled via the core thiol moieties through reaction with a thiol reactive dye (DY630-maleimide. Following internal labeling, bioconjugation of green fluorescent protein (GFP to their carboxyl-functionalized surfaces was successfully accomplished using standard coupling protocols. The resultant dual-labeled microspheres were visualized by both of the fully resolvable fluorescence emissions of their cores (DY630 and shells (GFP. In vitro cellular uptake of these microspheres by HeLa cells was demonstrated conventionally by fluorescence-based flow cytometry, whilst MTT assays demonstrated that 92% of HeLa cells remained viable after uptake. Due to their size and surface functionalities, these far-red-labeled microspheres are ideal candidates for in vitro, cellular
Characterizing SMS spam in a large cellular network via mining victim spam reports
Skudlark, Ann
2014-01-01
In this paper a study of SMS messages in a large US based cellular carrier utilizing both customer reported SMS spam and network Call Detail Records (CDRs) is conducted to develop a comprehensive understanding of SMS spam in order to develop strategies and approaches to detect and control SMS spam activity. The analysis provides insights into content classification of spam campaigns as well as spam characteristics based on sending patterns, tenure and geolocation.
Jin, Kelly
2012-01-01
Dinoflagellate bioluminescence represents a dramatic response to mechanical stress found in nature. The cellular mechanisms that govern this pathway, however, are not completely understood. The objective of this thesis is to build and expand from previous studies to explore the mechanosensitive properties of dinoflagellate bioluminescence. Chapter I tests the hypothesis that the signaling pathway involves a stretch-activated component. Chapter I uses two separate, measurable types of biolumin...
Characterization of the Interaction of Lassa Fever Virus with Its Cellular Receptor α-Dystroglycan
Kunz, Stefan; Rojek, Jillian M.; Perez, Mar; Spiropoulou, Christina F.; Oldstone, Michael B. A.
2005-01-01
The cellular receptor for the Old World arenaviruses Lassa fever virus (LFV) and lymphocytic choriomeningitis virus (LCMV) has recently been identified as α-dystroglycan (α-DG), a cell surface receptor that provides a molecular link between the extracellular matrix and the actin-based cytoskeleton. In the present study, we show that LFV binds to α-DG with high affinity in the low-nanomolar range. Recombinant vesicular stomatitis virus pseudotyped with LFV glycoprotein (GP) adopted the recepto...
Characterization of inhibitors of phosphodiesterase 1C on a human cellular system.
Dunkern, Torsten R; Hatzelmann, Armin
2007-09-01
Different inhibitors of the Ca(2+)/calmodulin-stimulated phosphodiesterase 1 family have been described and used for the examination of phosphodiesterase 1 in cellular, organ or animal models. However, the inhibitors described differ in potency and selectivity for the different phosphodiesterase family enzymes, and in part exhibit additional pharmacodynamic actions. In this study, we demonstrate that phosphodiesterase 1C is expressed in the human glioblastoma cell line A172 with regard to mRNA, protein and activity level, and that lower activities of phosphodiesterase 2, phosphodiesterase 3, phosphodiesterase 4 and phosphodiesterase 5 are also present. The identity of the phosphodiesterase 1C activity detected was verified by downregulation of the mRNA and protein through human phosphodiesterase 1C specific small interfering RNA. In addition, the measured K(m) values (cAMP, 1.7 microm; cGMP, 1.3 microm) are characteristic of phosphodiesterase 1C. We demonstrate that treatment with the Ca(2+) ionophore ionomycin increases intracellular Ca(2+) in a concentration-dependent way without affecting cell viability. Under conditions of enhanced intracellular Ca(2+) concentration, a rapid increase in cAMP levels caused by the adenylyl cyclase activator forskolin was abolished, indicating the involvement of Ca(2+)-activated phosphodiesterase 1C. The reduction of forskolin-stimulated cAMP levels was reversed by phosphodiesterase 1 inhibitors in a concentration-dependent way. Using this cellular system, we compared the cellular potency of published phosphodiesterase 1 inhibitors, including 8-methoxymethyl-3-isobutyl-1-methylxanthine, vinpocetine, SCH51866, and two established phosphodiesterase 1 inhibitors developed by Schering-Plough (named compounds 31 and 30). We demonstrate that up to 10 microm 8-methoxymethyl-3-isobutyl-1-methylxanthine and vinpocetine had no effect on the reduction of forskolin-stimulated cAMP levels by ionomycin, whereas the more selective and up to 10
Hanna, A. C.; Moysey, S. M.; Murdoch, L. C.
2014-12-01
Carbon injection projects introduce several operational, management and risk-assessment challenges, including leakage of carbon dioxide through fractures or derelict wells, reactivation of dormant faults, topographic subsidence/uplift, and contamination of existing groundwater resources. In this work we evaluate whether geomechanical measurements can be used within a stochastic estimation framework to characterize physical and geometric parameters of a system undergoing injection.A numerical forward model built in COMSOL Multiphysics is used to solve the equations governing linear poroelasticity to compute the geomechanical signals (e.g. pressure, strain, tilt and displacement) produced during injection given a set of model parameters (e.g. Young's modulus, Poisson's ratio, and permeability). A hybrid Markov Chain Monte Carlo/multiobjective genetic algorithm is then used to iteratively generate a sequence of parameter estimates; distributed high performance computing is used to efficiently evaluate the computationally expensive forward model for each set of parameters. The set of posterior parameter estimates is then used to find the mean and uncertainty of each parameter subject to measurement limitations (noise, model error, spatial/temporal constraints).We find that geomechanical measurements collected within the target formation can be used to accurately and efficiently estimate the physical parameters of the formation. We also observe that measurements taken in an overlying confining unit can be used to estimate the parameters of both the confining unit and target aquifer. This suggests that measurements made in the upper confining unit could mitigate drilling costs as well as reduce the risk of puncturing the confining unit. Using various combinations of synthetic measurements from the confining unit and target aquifer, we have also been able to resolve the geometry and physical parameters of heterogeneities analogous to fluvial gravel lenses and faults
From Complex to Simple: Interdisciplinary Stochastic Models
Mazilu, D. A.; Zamora, G.; Mazilu, I.
2012-01-01
We present two simple, one-dimensional, stochastic models that lead to a qualitative understanding of very complex systems from biology, nanoscience and social sciences. The first model explains the complicated dynamics of microtubules, stochastic cellular highways. Using the theory of random walks in one dimension, we find analytical expressions…
Parzen, Emanuel
2015-01-01
Well-written and accessible, this classic introduction to stochastic processes and related mathematics is appropriate for advanced undergraduate students of mathematics with a knowledge of calculus and continuous probability theory. The treatment offers examples of the wide variety of empirical phenomena for which stochastic processes provide mathematical models, and it develops the methods of probability model-building.Chapter 1 presents precise definitions of the notions of a random variable and a stochastic process and introduces the Wiener and Poisson processes. Subsequent chapters examine
Decentralized stochastic control
Speyer, J. L.
1980-01-01
Decentralized stochastic control is characterized by being decentralized in that the information to one controller is not the same as information to another controller. The system including the information has a stochastic or uncertain component. This complicates the development of decision rules which one determines under the assumption that the system is deterministic. The system is dynamic which means the present decisions affect future system responses and the information in the system. This circumstance presents a complex problem where tools like dynamic programming are no longer applicable. These difficulties are discussed from an intuitive viewpoint. Particular assumptions are introduced which allow a limited theory which produces mechanizable affine decision rules.
Hu, B. L. (Bei-Lok)
1999-01-01
We give a summary of the status of current research in stochastic semiclassical gravity and suggest directions for further investigations. This theory generalizes the semiclassical Einstein equation to an Einstein-Langevin equation with a stochastic source term arising from the fluctuations of the energy-momentum tensor of quantum fields. We mention recent efforts in applying this theory to the study of black hole fluctuations and backreaction problems, linear response of hot flat space, and ...
Schneider, Johannes J
2007-01-01
This book addresses stochastic optimization procedures in a broad manner. The first part offers an overview of relevant optimization philosophies; the second deals with benchmark problems in depth, by applying a selection of optimization procedures. Written primarily with scientists and students from the physical and engineering sciences in mind, this book addresses a larger community of all who wish to learn about stochastic optimization techniques and how to use them.
A High-Precision Micropipette Sensor for Cellular-Level Real-Time Thermal Characterization
Wonseok Chang
2011-09-01
Full Text Available We report herein development of a novel glass micropipette thermal sensor fabricated in a cost-effective manner, which is capable of measuring steady thermal fluctuation at spatial resolution of ~2 µm with an accuracy of ±0.01 °C. We produced and tested various micrometer-sized sensors, ranging from 2 µm to 30 µm. The sensor comprises unleaded low-melting-point solder alloy (Sn-based as a core metal inside a pulled borosilicate glass pipette and a thin film of nickel coating outside, creating a thermocouple junction at the tip. The sensor was calibrated using a thermally insulated calibration chamber, the temperature of which can be controlled with an accuracy of ±0.01 °C, and the thermoelectric power (Seebeck coefficient of the sensor was recorded from 8.46 to 8.86 µV/°C. We have demonstrated the capability of measuring temperatures at a cellular level by inserting our temperature sensor into the membrane of a live retinal pigment epithelium cell subjected to a laser beam with a focal spot of 6 μm. We measured transient temperature profiles and the maximum temperatures were in the range of 38–55 ± 0.5 °C.
Santos Fabio M
2012-07-01
Full Text Available Abstract Background The neural mobilization technique is a noninvasive method that has proved clinically effective in reducing pain sensitivity and consequently in improving quality of life after neuropathic pain. The present study examined the effects of neural mobilization (NM on pain sensitivity induced by chronic constriction injury (CCI in rats. The CCI was performed on adult male rats, submitted thereafter to 10 sessions of NM, each other day, starting 14 days after the CCI injury. Over the treatment period, animals were evaluated for nociception using behavioral tests, such as tests for allodynia and thermal and mechanical hyperalgesia. At the end of the sessions, the dorsal root ganglion (DRG and spinal cord were analyzed using immunohistochemistry and Western blot assays for neural growth factor (NGF and glial fibrillary acidic protein (GFAP. Results The NM treatment induced an early reduction (from the second session of the hyperalgesia and allodynia in CCI-injured rats, which persisted until the end of the treatment. On the other hand, only after the 4th session we observed a blockade of thermal sensitivity. Regarding cellular changes, we observed a decrease of GFAP and NGF expression after NM in the ipsilateral DRG (68% and 111%, respectively and the decrease of only GFAP expression after NM in the lumbar spinal cord (L3-L6 (108%. Conclusions These data provide evidence that NM treatment reverses pain symptoms in CCI-injured rats and suggest the involvement of glial cells and NGF in such an effect.
Characterization of cellular traction forces at the single-molecule level
Dunn, Alexander
2013-03-01
The ability of cells to generate and respond to mechanical cues is an essential aspect of stem cell differentiation, embryonic development, and our senses of touch and hearing. However, our understanding of the roles of mechanical force in cell biology remains in its infancy, due largely to a lack of tools that measure the forces generated by living cells at the molecular scale. Here we describe a new technique termed Molecular Force Microscopy (MFM) that visualizes the forces exerted by single cellular adhesion molecules with nm, pN, and sub-second resolutions. MFM uses novel FRET-based molecular tension sensors that bind to a glass coverslip and present a binding site for integrins, a ubiquitous class of cell adhesion proteins. Cell-generated forces stretch the MFM sensor molecules, resulting in decreased FRET with increasing load that can be imaged at the single-molecule level. Human foreskin fibroblasts adhere to surfaces functionalized with the MFM probes and develop robust focal adhesions. FRET values measured using MFM indicate forces of between 1 and 4 pN per integrin, thus providing the first direct measurement of the tension per integrin molecule necessary to form stable adhesions. The relatively narrow force distribution suggests that mechanical tension is subject to exquisite feedback and control at the molecular level.
A high-precision micropipette sensor for cellular-level real-time thermal characterization.
Shrestha, Ramesh; Choi, Tae-Youl; Chang, Wonseok; Kim, Donsik
2011-01-01
We report herein development of a novel glass micropipette thermal sensor fabricated in a cost-effective manner, which is capable of measuring steady thermal fluctuation at spatial resolution of ∼2 μm with an accuracy of ±0.01 °C. We produced and tested various micrometer-sized sensors, ranging from 2 μm to 30 μm. The sensor comprises unleaded low-melting-point solder alloy (Sn-based) as a core metal inside a pulled borosilicate glass pipette and a thin film of nickel coating outside, creating a thermocouple junction at the tip. The sensor was calibrated using a thermally insulated calibration chamber, the temperature of which can be controlled with an accuracy of ±0.01 °C, and the thermoelectric power (Seebeck coefficient) of the sensor was recorded from 8.46 to 8.86 μV/°C. We have demonstrated the capability of measuring temperatures at a cellular level by inserting our temperature sensor into the membrane of a live retinal pigment epithelium cell subjected to a laser beam with a focal spot of 6 μm. We measured transient temperature profiles and the maximum temperatures were in the range of 38-55 ± 0.5 °C. PMID:22164108
Characterization of the Interaction of Lassa Fever Virus with Its Cellular Receptor α-Dystroglycan
Kunz, Stefan; Rojek, Jillian M.; Perez, Mar; Spiropoulou, Christina F.; Oldstone, Michael B. A.
2005-01-01
The cellular receptor for the Old World arenaviruses Lassa fever virus (LFV) and lymphocytic choriomeningitis virus (LCMV) has recently been identified as α-dystroglycan (α-DG), a cell surface receptor that provides a molecular link between the extracellular matrix and the actin-based cytoskeleton. In the present study, we show that LFV binds to α-DG with high affinity in the low-nanomolar range. Recombinant vesicular stomatitis virus pseudotyped with LFV glycoprotein (GP) adopted the receptor binding characteristics of LFV and depended on α-DG for infection of cells. Mapping of the binding site of LFV on α-DG revealed that LFV binding required the same domains of α-DG that are involved in the binding of LCMV. Further, LFV was found to efficiently compete with laminin α1 and α2 chains for α-DG binding. Together with our previous studies on receptor binding of the prototypic immunosuppressive LCMV isolate LCMV clone 13, these findings indicate a high degree of conservation in the receptor binding characteristics between the highly human-pathogenic LFV and murine-immunosuppressive LCMV isolates. PMID:15857984
Kunz, Stefan; Rojek, Jillian M; Perez, Mar; Spiropoulou, Christina F; Oldstone, Michael B A
2005-05-01
The cellular receptor for the Old World arenaviruses Lassa fever virus (LFV) and lymphocytic choriomeningitis virus (LCMV) has recently been identified as alpha-dystroglycan (alpha-DG), a cell surface receptor that provides a molecular link between the extracellular matrix and the actin-based cytoskeleton. In the present study, we show that LFV binds to alpha-DG with high affinity in the low-nanomolar range. Recombinant vesicular stomatitis virus pseudotyped with LFV glycoprotein (GP) adopted the receptor binding characteristics of LFV and depended on alpha-DG for infection of cells. Mapping of the binding site of LFV on alpha-DG revealed that LFV binding required the same domains of alpha-DG that are involved in the binding of LCMV. Further, LFV was found to efficiently compete with laminin alpha1 and alpha2 chains for alpha-DG binding. Together with our previous studies on receptor binding of the prototypic immunosuppressive LCMV isolate LCMV clone 13, these findings indicate a high degree of conservation in the receptor binding characteristics between the highly human-pathogenic LFV and murine-immunosuppressive LCMV isolates. PMID:15857984
The objective of this research thesis is to characterize the expression of a mammal gene, called Kin-17, which codes for a protein which has a structural homology with the RecA protein of E. coli. This protein plays a crucial role in the cellular response to irradiations and in mutagenesis. In order to better understand the Kin 17 protein function, the author determined the Kin 17 gene expression profile in tissues and cells in culture. It appears that this expression is ubiquitous and weak. The Kin 17 protein quantity and localisation are also studied. The author suggests that this protein belongs to an intra-nuclear network of proteins required during cell growth, and might influence biological processes related to the cellular cycle. The co-localisation of the protein with the T-antigen is studied by immunofluorescence. The expression profile of different Kin-17 genes in cells after UV irradiation has been studied. The obtained results and observations suggest that the Kin 17 protein intervenes in a biological process which allows a cell to counterbalance toxic effects of UV radiations
Cynthia L Araujo-Palomares
Full Text Available Rho-type GTPases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. In this study, we investigate the role of the CDC-42 - RAC - CDC-24 module in Neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. Double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both GTPases share at least one common essential function. The defects of the GTPase mutants are phenocopied by deletion and conditional alleles of the guanine exchange factor (GEF cdc-24, and in vitro GDP-GTP exchange assays identify CDC-24 as specific GEF for both CDC-42 and RAC. In vivo confocal microscopy shows that this module is organized as membrane-associated cap that covers the hyphal apex. However, the specific localization patterns of the three proteins are distinct, indicating different functions of RAC and CDC-42 within the hyphal tip. CDC-42 localized as confined apical membrane-associated crescent, while RAC labeled a membrane-associated ring excluding the region labeled by CDC42. The GEF CDC-24 occupied a strategic position, localizing as broad apical membrane-associated crescent and in the apical cytosol excluding the Spitzenkörper. RAC and CDC-42 also display distinct localization patterns during branch initiation and germ tube formation, with CDC-42 accumulating at the plasma membrane before RAC. Together with the distinct cellular defects of rac and cdc-42 mutants, these localizations suggest that CDC-42 is more important for polarity establishment, while the primary function of RAC may be maintaining polarity. In summary, this study identifies CDC-24 as essential regulator for RAC and CDC-42 that have common and distinct functions during polarity establishment and maintenance of cell polarity in N. crassa.
Florian, Ehmele; Michael, Kunz
2016-04-01
Several major flood events occurred in Germany in the past 15-20 years especially in the eastern parts along the rivers Elbe and Danube. Examples include the major floods of 2002 and 2013 with an estimated loss of about 2 billion Euros each. The last major flood events in the State of Baden-Württemberg in southwest Germany occurred in the years 1978 and 1993/1994 along the rivers Rhine and Neckar with an estimated total loss of about 150 million Euros (converted) each. Flood hazard originates from a combination of different meteorological, hydrological and hydraulic processes. Currently there is no defined methodology available for evaluating and quantifying the flood hazard and related risk for larger areas or whole river catchments instead of single gauges. In order to estimate the probable maximum loss for higher return periods (e.g. 200 years, PML200), a stochastic model approach is designed since observational data are limited in time and space. In our approach, precipitation is linearly composed of three elements: background precipitation, orographically-induces precipitation, and a convectively-driven part. We use linear theory of orographic precipitation formation for the stochastic precipitation model (SPM), which is based on fundamental statistics of relevant atmospheric variables. For an adequate number of historic flood events, the corresponding atmospheric conditions and parameters are determined in order to calculate a probability density function (pdf) for each variable. This method involves all theoretically possible scenarios which may not have happened, yet. This work is part of the FLORIS-SV (FLOod RISk Sparkassen Versicherung) project and establishes the first step of a complete modelling chain of the flood risk. On the basis of the generated stochastic precipitation event set, hydrological and hydraulic simulations will be performed to estimate discharge and water level. The resulting stochastic flood event set will be used to quantify the
Dai, Yongming; Yao, Qiuying; Wu, Guangyu; Wu, Dongmei; Wu, Lianming; Zhu, Li; Xue, Rong; Xu, Jianrong
2016-07-01
The aim of this study was to evaluate the role of diffusion kurtosis imaging (DKI) in the characterization of clear cell renal cell carcinoma (ccRCC) and to correlate DKI parameters with tumor cellularity. Fifty-nine patients with pathologically diagnosed ccRCCs were evaluated by DKI on a 3-T scanner. Regions of interest were drawn on the maps of the mean diffusion coefficient (MD) and mean diffusion kurtosis (MK). All ccRCCs were histologically graded according to the Fuhrman classification system. Tumor cellularity was measured by the nuclear-to-cytoplasm (N/C) ratio and the number of tumor cell nuclei (NTCN). ccRCCs were classified as grade 1 (n = 23), grade 2 (n = 24), grade 3 (n = 10) and grade 4 (n = 3). Both MD and MK could readily discriminate between normal renal parenchyma and ccRCCs (p 0.05) for both MD and MK. With regard to NTCN, no significant difference was found between any two grades (p > 0.05), and the N/C ratio changed significantly with grade (p correlations were found between MK and MD (r = -0.56, p r = -0.36, p correlated (r = 0.45, p = 0.003). DKI could quantitatively characterize ccRCC with different grades by probing non-Gaussian diffusion properties related to changes in the tumor microenvironment or tissue complexities in the tumor. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27119793
Stochastic transition model for pedestrian dynamics
Schultz, Michael
2012-01-01
The proposed stochastic model for pedestrian dynamics is based on existing approaches using cellular automata, combined with substantial extensions, to compensate the deficiencies resulting of the discrete grid structure. This agent motion model is extended by both a grid-based path planning and mid-range agent interaction component. The stochastic model proves its capabilities for a quantitative reproduction of the characteristic shape of the common fundamental diagram of pedestrian dynamics. Moreover, effects of self-organizing behavior are successfully reproduced. The stochastic cellular automata approach is found to be adequate with respect to uncertainties in human motion patterns, a feature previously held by artificial noise terms alone.
Variance decomposition in stochastic simulators
This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models
Variance decomposition in stochastic simulators
Le Maître, O. P.
2015-06-28
This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.
Variance decomposition in stochastic simulators
Le Maître, O. P.; Knio, O. M.; Moraes, A.
2015-06-01
This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.
Chang, Mou-Hsiung
2015-01-01
The classical probability theory initiated by Kolmogorov and its quantum counterpart, pioneered by von Neumann, were created at about the same time in the 1930s, but development of the quantum theory has trailed far behind. Although highly appealing, the quantum theory has a steep learning curve, requiring tools from both probability and analysis and a facility for combining the two viewpoints. This book is a systematic, self-contained account of the core of quantum probability and quantum stochastic processes for graduate students and researchers. The only assumed background is knowledge of the basic theory of Hilbert spaces, bounded linear operators, and classical Markov processes. From there, the book introduces additional tools from analysis, and then builds the quantum probability framework needed to support applications to quantum control and quantum information and communication. These include quantum noise, quantum stochastic calculus, stochastic quantum differential equations, quantum Markov semigrou...
Azza A. Al-Mahrouki
2014-03-01
Full Text Available Tumor radiation resistance poses a major obstacle in achieving an optimal outcome in radiation therapy. In the current study, we characterize a novel therapeutic approach that combines ultrasound-driven microbubbles with radiation to increase treatment responses in a prostate cancer xenograft model in mice. Tumor response to ultrasound-driven microbubbles and radiation was assessed 24 hours after treatment, which consisted of radiation treatments alone (2 Gy or 8 Gy or ultrasound-stimulated microbubbles only, or a combination of radiation and ultrasound-stimulated microbubbles. Immunohistochemical analysis using in situ end labeling (ISEL and terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL revealed increased cell death within tumors exposed to combined treatments compared with untreated tumors or tumors exposed to radiation alone. Several biomarkers were investigated to evaluate cell proliferation (Ki67, blood leakage (factor VIII, angiogenesis (cluster of differentiation molecule CD31, ceramide-formation, angiogenesis signaling [vascular endothelial growth factor (VEGF], oxygen limitation (prolyl hydroxylase PHD2 and DNA damage/repair (γH2AX. Results demonstrated reduced vascularity due to vascular disruption by ultrasound-stimulated microbubbles, increased ceramide production and increased DNA damage of tumor cells, despite decreased tumor oxygenation with significantly less proliferating cells in the combined treatments. This combined approach could be a feasible option as a novel enhancing approach in radiation therapy.
Ari-Wahjoedi, Bambang; Ginta, Turnad Lenggo; Parman, Setyamartana; Abustaman, Mohd Zikri Ahmad
2014-10-01
Multicellular monolithic ceramic body is a ceramic material which has many gas or liquid passages partitioned by thin walls throughout the bulk material. There are many currently known advanced industrial applications of multicellular ceramics structures i.e. as supports for various catalysts, electrode support structure for solid oxide fuel cells, refractories, electric/electronic materials, aerospace vehicle re-entry heat shields and biomaterials for dental as well as orthopaedic implants by naming only a few. Multicellular ceramic bodies are usually made of ceramic phases such as mullite, cordierite, aluminum titanate or pure oxides such as silica, zirconia and alumina. What make alumina ceramics is excellent for the above functions are the intrinsic properties of alumina which are hard, wear resistant, excellent dielectric properties, resists strong acid and alkali attacks at elevated temperatures, good thermal conductivities, high strength and stiffness as well as biocompatible. In this work the processing technology leading to truly multicellular monolithic alumina ceramic bodies and their characterization are reported. Ceramic slip with 66 wt.% solid loading was found to be optimum as impregnant to the polyurethane foam template. Mullitic ceramic composite of alumina-sodium alumino disilicate-Leucite-like phases with bulk and true densities of 0.852 and 1.241 g cm-3 respectively, pore linear density of ±35 cm-1, linear and bulk volume shrinkages of 7-16% and 32 vol.% were obtained. The compressive strength and elastic modulus of the bioceramics are ≈0.5-1.0 and ≈20 MPa respectively.
Biochemical characterization and cellular effects of CADASIL mutants of NOTCH3.
He Meng
Full Text Available Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL is the best understood cause of dominantly inherited stroke and results from NOTCH3 mutations that lead to NOTCH3 protein accumulation and selective arterial smooth muscle degeneration. Previous studies show that NOTCH3 protein forms multimers. Here, we investigate protein interactions between NOTCH3 and other vascular Notch isoforms and characterize the effects of elevated NOTCH3 on smooth muscle gene regulation. We demonstrate that NOTCH3 forms heterodimers with NOTCH1, NOTCH3, and NOTCH4. R90C and C49Y mutant NOTCH3 form complexes which are more resistant to detergents than wild type NOTCH3 complexes. Using quantitative NOTCH3-luciferase clearance assays, we found significant inhibition of mutant NOTCH3 clearance. In coculture assays of NOTCH function, overexpressed wild type and mutant NOTCH3 significantly repressed NOTCH-regulated smooth muscle transcripts and potently impaired the activity of three independent smooth muscle promoters. Wildtype and R90C recombinant NOTCH3 proteins applied to cell cultures also blocked canonical Notch fuction. We conclude that CADASIL mutants of NOTCH3 complex with NOTCH1, 3, and 4, slow NOTCH3 clearance, and that overexpressed wild type and mutant NOTCH3 protein interfere with key NOTCH-mediated functions in smooth muscle cells.
Billing, Anja M; Ben Hamidane, Hisham; Dib, Shaima S; Cotton, Richard J; Bhagwat, Aditya M; Kumar, Pankaj; Hayat, Shahina; Yousri, Noha A; Goswami, Neha; Suhre, Karsten; Rafii, Arash; Graumann, Johannes
2016-01-01
Mesenchymal stem cells (MSC) are multipotent cells with great potential in therapy, reflected by more than 500 MSC-based clinical trials registered with the NIH. MSC are derived from multiple tissues but require invasive harvesting and imply donor-to-donor variability. Embryonic stem cell-derived MSC (ESC-MSC) may provide an alternative, but how similar they are to ex vivo MSC is unknown. Here we performed an in depth characterization of human ESC-MSC, comparing them to human bone marrow-derived MSC (BM-MSC) as well as human embryonic stem cells (hESC) by transcriptomics (RNA-seq) and quantitative proteomics (nanoLC-MS/MS using SILAC). Data integration highlighted and validated a central role of vesicle-mediated transport and exosomes in MSC biology and also demonstrated, through enrichment analysis, their versatility and broad application potential. Particular emphasis was placed on comparing profiles between ESC-MSC and BM-MSC and assessing their equivalency. Data presented here shows that differences between ESC-MSC and BM-MSC are similar in magnitude to those reported for MSC of different origin and the former may thus represent an alternative source for therapeutic applications. Finally, we report an unprecedented coverage of MSC CD markers, as well as membrane associated proteins which may benefit immunofluorescence-based applications and contribute to a refined molecular description of MSC. PMID:26857143
Multicellular monolithic ceramic body is a ceramic material which has many gas or liquid passages partitioned by thin walls throughout the bulk material. There are many currently known advanced industrial applications of multicellular ceramics structures i.e. as supports for various catalysts, electrode support structure for solid oxide fuel cells, refractories, electric/electronic materials, aerospace vehicle re-entry heat shields and biomaterials for dental as well as orthopaedic implants by naming only a few. Multicellular ceramic bodies are usually made of ceramic phases such as mullite, cordierite, aluminum titanate or pure oxides such as silica, zirconia and alumina. What make alumina ceramics is excellent for the above functions are the intrinsic properties of alumina which are hard, wear resistant, excellent dielectric properties, resists strong acid and alkali attacks at elevated temperatures, good thermal conductivities, high strength and stiffness as well as biocompatible. In this work the processing technology leading to truly multicellular monolithic alumina ceramic bodies and their characterization are reported. Ceramic slip with 66 wt.% solid loading was found to be optimum as impregnant to the polyurethane foam template. Mullitic ceramic composite of alumina-sodium alumino disilicate-Leucite-like phases with bulk and true densities of 0.852 and 1.241 g cm−3 respectively, pore linear density of ±35 cm−1, linear and bulk volume shrinkages of 7-16% and 32 vol.% were obtained. The compressive strength and elastic modulus of the bioceramics are ≈0.5-1.0 and ≈20 MPa respectively
Ari-Wahjoedi, Bambang, E-mail: bambang-ariwahjoedi@petronas.com.my [Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 31750 Tronoh, Perak Darul Ridzuan (Malaysia); Centre for Intelligent Signal and Imaging Research, Universiti Teknologi PETRONAS, Bandar Seri Iskandar (Malaysia); Ginta, Turnad Lenggo [Department of Mechanical Engineering, Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 31750 Tronoh, Perak Darul Ridzuan (Malaysia); Centre for Intelligent Signal and Imaging Research, Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 31750 Tro (Malaysia); Parman, Setyamartana [Department of Mechanical Engineering, Universiti Teknologi PETRONAS, Bandar Seri Iskandar, 31750 Tronoh, Perak Darul Ridzuan (Malaysia); Abustaman, Mohd Zikri Ahmad [Kebabangan Petroleum Operating Company Sdn Bhd, Lvl. 52, Tower 2, PETRONAS Twin Towers, KLCC, 50088 Kuala Lumpur (Malaysia)
2014-10-24
Multicellular monolithic ceramic body is a ceramic material which has many gas or liquid passages partitioned by thin walls throughout the bulk material. There are many currently known advanced industrial applications of multicellular ceramics structures i.e. as supports for various catalysts, electrode support structure for solid oxide fuel cells, refractories, electric/electronic materials, aerospace vehicle re-entry heat shields and biomaterials for dental as well as orthopaedic implants by naming only a few. Multicellular ceramic bodies are usually made of ceramic phases such as mullite, cordierite, aluminum titanate or pure oxides such as silica, zirconia and alumina. What make alumina ceramics is excellent for the above functions are the intrinsic properties of alumina which are hard, wear resistant, excellent dielectric properties, resists strong acid and alkali attacks at elevated temperatures, good thermal conductivities, high strength and stiffness as well as biocompatible. In this work the processing technology leading to truly multicellular monolithic alumina ceramic bodies and their characterization are reported. Ceramic slip with 66 wt.% solid loading was found to be optimum as impregnant to the polyurethane foam template. Mullitic ceramic composite of alumina-sodium alumino disilicate-Leucite-like phases with bulk and true densities of 0.852 and 1.241 g cm{sup −3} respectively, pore linear density of ±35 cm{sup −1}, linear and bulk volume shrinkages of 7-16% and 32 vol.% were obtained. The compressive strength and elastic modulus of the bioceramics are ≈0.5-1.0 and ≈20 MPa respectively.
Synthesis and characterization of xanthan–hydroxyapatite nanocomposites for cellular uptake
In this work xanthan–nanohydroxyapatite (XnHAp) and its equivalent strontium substituted (XnHApSr) were synthesized by the precipitation of nanohydroxyapatite in xanthan aqueous solution, characterized and compared to conventional hydroxyapatite particles (HAp). XnHAp and XnHApSr were less crystalline than HAp, as revealed by X-ray diffraction. Xanthan chains enriched the surface of XnHAp and XnHApSr particles, increasing the zeta potential values from −(7 ± 1) mV, determined for HAp, to −(17 ± 3) mV and −(25 ± 3) mV, respectively. This effect led to high colloidal stability of XnHAp and XnHApSr dispersions and acicular particles (140 ± 10) nm long and (8 ± 2) nm wide, as determined by scanning electron microscopy and atomic force microscopy. XnHAp and XnHApSr particles were added to xanthan hydrogels to produce compatible nanocomposites (XCA/XnHAp and XCA/XnHApSr). Dried nanocomposites presented surface energy, Young's modulus and stress at break values comparable to those determined for bare xanthan matrix. Moreover, adding XnHAp or XnHApSr nanoparticles to xanthan hydrogel did not influence its porous morphology, gel content and swelling ratio. XCA/XnHAp and XCA/XnHApSr composites proved to be suitable for osteoblast growth and particularly XCA/XnHapSr composites induced higher alkaline phosphatase activity. - Highlights: • Hydroxyapatites with or without strontium were prepared in xanthan solution. • Xanthan chains enriched the surface of hydroxyapatite nanoparticles (HAp). • Xanthan modified HAp and xanthan hydrogels formed compatible nanocomposites. • Nanocomposites are suitable for bone mineralization, particularly those with Sr
Synthesis and characterization of xanthan–hydroxyapatite nanocomposites for cellular uptake
Bueno, Vania Blasques; Bentini, Ricardo; Catalani, Luiz Henrique [Instituto de Química, Universidade de São Paulo, P.O. Box 26077, São Paulo, SP 05513-970 (Brazil); Barbosa, Leandro R.S. [Instituto de Física, DFGE, Universidade de São Paulo, São Paulo, 05508-090 SP (Brazil); Petri, Denise Freitas Siqueira, E-mail: dfsp@usp.br [Instituto de Química, Universidade de São Paulo, P.O. Box 26077, São Paulo, SP 05513-970 (Brazil)
2014-04-01
In this work xanthan–nanohydroxyapatite (XnHAp) and its equivalent strontium substituted (XnHApSr) were synthesized by the precipitation of nanohydroxyapatite in xanthan aqueous solution, characterized and compared to conventional hydroxyapatite particles (HAp). XnHAp and XnHApSr were less crystalline than HAp, as revealed by X-ray diffraction. Xanthan chains enriched the surface of XnHAp and XnHApSr particles, increasing the zeta potential values from −(7 ± 1) mV, determined for HAp, to −(17 ± 3) mV and −(25 ± 3) mV, respectively. This effect led to high colloidal stability of XnHAp and XnHApSr dispersions and acicular particles (140 ± 10) nm long and (8 ± 2) nm wide, as determined by scanning electron microscopy and atomic force microscopy. XnHAp and XnHApSr particles were added to xanthan hydrogels to produce compatible nanocomposites (XCA/XnHAp and XCA/XnHApSr). Dried nanocomposites presented surface energy, Young's modulus and stress at break values comparable to those determined for bare xanthan matrix. Moreover, adding XnHAp or XnHApSr nanoparticles to xanthan hydrogel did not influence its porous morphology, gel content and swelling ratio. XCA/XnHAp and XCA/XnHApSr composites proved to be suitable for osteoblast growth and particularly XCA/XnHapSr composites induced higher alkaline phosphatase activity. - Highlights: • Hydroxyapatites with or without strontium were prepared in xanthan solution. • Xanthan chains enriched the surface of hydroxyapatite nanoparticles (HAp). • Xanthan modified HAp and xanthan hydrogels formed compatible nanocomposites. • Nanocomposites are suitable for bone mineralization, particularly those with Sr.
Stochastic gene expression with bursting and positive feedback
Platini, Thierry; Pendar, Hodjat; Kulkarni, Rahul
2012-02-01
Stochasticity (or noise) in the process of gene expression can play a critical role in cellular circuits that control switching between probabilistic cell-fate decisions in diverse organisms. Such circuits often include positive feedback loops as critical elements. In some cases (e.g. HIV-1 viral infections), switching between different cell fates occurs even in the absence of bistability in the underlying deterministic model. To characterize the role of noise in such systems, we analyze a simple gene expression circuit that includes contributions from both transcriptional and translational bursting and positive feedback effects. Using a combination of analytical approaches and stochastic simulations, we explore how the underlying parameters control the corresponding mean and variance in protein distributions.
Stochasticity in the Josephson map
The Josephson map describes nonlinear dynamics of systems characterized by standard map with the uniform external bias superposed. The intricate structures of the phase space portrait of the Josephson map are examined on the basis of the tangent map associated with the Josephson map. Numerical observation of the stochastic diffusion in the Josephson map is examined in comparison with the renormalized diffusion coefficient calculated by the method of characteristic function. The global stochasticity of the Josephson map occurs at the values of far smaller stochastic parameter than the case of the standard map. (author)
Detecting Stochastic Information of Electrocardiograms
Gutíerrez, R M; Guti'errez, Rafael M.; Sandoval, Luis A.
2003-01-01
In this work we present a method to detect, identify and characterize stochastic information contained in an electrocardiogram (ECG). We assume, as it is well known, that the ECG has information corresponding to many different processes related to the cardiac activity. We analyze scaling and Markov processes properties of the detected stochastic information using the power spectrum of the ECG and the Fokker-Planck equation respectively. The detected stochastic information is then characterized by three measures. First, the slope of the power spectrum in a particular range of frequencies as a scaling parameter. Second, an empirical estimation of the drift and diffusion coefficients of the Fokker-Planck equation through the Kramers-Moyal coefficients which define the evolution of the probability distribution of the detected stochastic information.
Stochastic cooling is the damping of betatron oscillations and momentum spread of a particle beam by a feedback system. In its simplest form, a pickup electrode detects the transverse positions or momenta of particles in a storage ring, and the signal produced is amplified and applied downstream to a kicker. The time delay of the cable and electronics is designed to match the transit time of particles along the arc of the storage ring between the pickup and kicker so that an individual particle receives the amplified version of the signal it produced at the pick-up. If there were only a single particle in the ring, it is obvious that betatron oscillations and momentum offset could be damped. However, in addition to its own signal, a particle receives signals from other beam particles. In the limit of an infinite number of particles, no damping could be achieved; we have Liouville's theorem with constant density of the phase space fluid. For a finite, albeit large number of particles, there remains a residue of the single particle damping which is of practical use in accumulating low phase space density beams of particles such as antiprotons. It was the realization of this fact that led to the invention of stochastic cooling by S. van der Meer in 1968. Since its conception, stochastic cooling has been the subject of much theoretical and experimental work. The earliest experiments were performed at the ISR in 1974, with the subsequent ICE studies firmly establishing the stochastic cooling technique. This work directly led to the design and construction of the Antiproton Accumulator at CERN and the beginnings of p anti p colliding beam physics at the SPS. Experiments in stochastic cooling have been performed at Fermilab in collaboration with LBL, and a design is currently under development for a anti p accumulator for the Tevatron
The dynamics of stochastic processes
Basse-O'Connor, Andreas
In the present thesis the dynamics of stochastic processes is studied with a special attention to the semimartingale property. This is mainly motivated by the fact that semimartingales provide the class of the processes for which it is possible to define a reasonable stochastic calculus due to the...... result is obtained and applied. Moreover, martingales indexed by the whole real line is studied and characterized and the thesis is concluded with a study of stationary solutions of the Langevin equation....
Foliated stochastic calculus: Harmonic measures
Catuogno, Pedro J.; Ledesma, Diego S.; Ruffino, Paulo R
2010-01-01
In this article we present an intrinsec construction of foliated Brownian motion via stochastic calculus adapted to foliation. The stochastic approach together with a proposed foliated vector calculus provide a natural method to work on harmonic measures. Other results include a decomposition of the Laplacian in terms of the foliated and basic Laplacians, a characterization of totally invariant measures and a differential equation for the density of harmonic measures.
Identifiability in stochastic models
1992-01-01
The problem of identifiability is basic to all statistical methods and data analysis, occurring in such diverse areas as Reliability Theory, Survival Analysis, and Econometrics, where stochastic modeling is widely used. Mathematics dealing with identifiability per se is closely related to the so-called branch of ""characterization problems"" in Probability Theory. This book brings together relevant material on identifiability as it occurs in these diverse fields.
Stochastic Weighted Fractal Networks
Carletti, Timoteo
2010-01-01
In this paper we introduce new models of complex weighted networks sharing several properties with fractal sets: the deterministic non-homogeneous weighted fractal networks and the stochastic weighted fractal networks. Networks of both classes can be completely analytically characterized in terms of the involved parameters. The proposed algorithms improve and extend the framework of weighted fractal networks recently proposed in (T. Carletti & S. Righi, in press Physica A, 2010)
Plata, J.
2016-01-01
We study the dynamics of a classical nonlinear oscillator subject to noise and driven by a sinusoidal force. In particular, we give an analytical identification of the mechanisms responsible for the supernarrow peaks observed recently in the spectrum of a mechanical realization of the system. Our approach, based on the application of averaging techniques, simulates standard detection schemes used in practice. The spectral peaks, detected in a range of parameters corresponding to the existence of two attractors in the deterministic system, are traced to characteristics already present in the linearized stochastic equations. It is found that, for specific variations of the parameters, the characteristic frequencies near the attractors converge on the driving frequency and, as a consequence, the widths of the peaks in the spectrum are significantly reduced. The implications of the study to the control of the observed coherent response of the system are discussed.
Rajesh Prasad
Full Text Available Papain-like cysteine proteases of malaria parasites degrade haemoglobin in an acidic food vacuole to provide amino acids for intraerythrocytic parasites. These proteases are potential drug targets because their inhibitors block parasite development, and efforts are underway to develop chemotherapeutic inhibitors of these proteases as the treatments for malaria. Plasmodium knowlesi has recently been shown to be an important human pathogen in parts of Asia. We report expression and characterization of three P. knowlesi papain-like proteases, termed knowpains (KP2-4. Recombinant knowpains were produced using a bacterial expression system, and tested for various biochemical properties. Antibodies against recombinant knowpains were generated and used to determine their cellular localization in parasites. Inhibitory effects of the cysteine protease inhibitor E64 were assessed on P. knowlesi culture to validate drug target potential of knowpains. All three knowpains were present in the food vacuole, active in acidic pH, and capable of degrading haemoglobin at the food vacuolar pH (≈5.5, suggesting roles in haemoglobin degradation. The proteases showed absolute (KP2 and KP3 to moderate (KP4 preference for peptide substrates containing leucine at the P2 position; KP4 preferred arginine at the P2 position. While the three knowpains appear to have redundant roles in haemoglobin degradation, KP4 may also have a role in degradation of erythrocyte cytoskeleton during merozoite egress, as it displayed broad substrate specificity and was primarily localized at the parasite periphery. Importantly, E64 blocked erythrocytic development of P. knowlesi, with enlargement of food vacuoles, indicating inhibition of haemoglobin hydrolysis and supporting the potential for inhibition of knowpains as a strategy for the treatment of malaria. Functional expression and characterization of knowpains should enable simultaneous screening of available cysteine protease
Sergey Shityakov
2015-06-01
Full Text Available The objective of the present investigation was to study the ability of sulfobutylether-β-cyclodextrin (SBEβCD to form an inclusion complex with sevoflurane (SEV, a volatile anesthetic with poor water solubility. The inclusion complex was prepared, characterized and its cellular toxicity and blood-brain barrier (BBB permeation potential of the formulated SEV have also been examined for the purpose of controlled drug delivery. The SEV-SBEβCD complex was nontoxic to the primary brain microvascular endothelial (pEND cells at a clinically relevant concentration of sevoflurane. The inclusion complex exhibited significantly higher BBB permeation profiles as compared with the reference substance (propranolol concerning calculated apparent permeability values (Papp. In addition, SEV binding affinity to SBEβCD was confirmed by a minimal Gibbs free energy of binding (ΔGbind value of −1.727 ± 0.042 kcal·mol−1 and an average binding constant (Kb of 53.66 ± 9.24 mM indicating rapid drug liberation from the cyclodextrin amphiphilic cavity.
Shityakov, Sergey; Puskás, István; Pápai, Katalin; Salvador, Ellaine; Roewer, Norbert; Förster, Carola; Broscheit, Jens-Albert
2015-01-01
The objective of the present investigation was to study the ability of sulfobutylether-β-cyclodextrin (SBEβCD) to form an inclusion complex with sevoflurane (SEV), a volatile anesthetic with poor water solubility. The inclusion complex was prepared, characterized and its cellular toxicity and blood-brain barrier (BBB) permeation potential of the formulated SEV have also been examined for the purpose of controlled drug delivery. The SEV-SBEβCD complex was nontoxic to the primary brain microvascular endothelial (pEND) cells at a clinically relevant concentration of sevoflurane. The inclusion complex exhibited significantly higher BBB permeation profiles as compared with the reference substance (propranolol) concerning calculated apparent permeability values (Papp). In addition, SEV binding affinity to SBEβCD was confirmed by a minimal Gibbs free energy of binding (ΔGbind) value of -1.727 ± 0.042 kcal·mol-1 and an average binding constant (Kb) of 53.66 ± 9.24 mM indicating rapid drug liberation from the cyclodextrin amphiphilic cavity. PMID:26046323
Reasor, Daniel; Clausen, Jonathan; Aidun, Cyrus
2010-11-01
In small vessels, the cellular nature of blood is of utmost importance. The investigation of the non-Newtonian effects of blood for a complete range of hematocrit values and shear rates requires the direct numerical simulation (DNS) of individual red blood cells (RBCs) immersed in Newtonian blood plasma with hemoglobin within. Consequently, a coarse-grained spectrin-link (SL) RBC membrane model is coupled with a highly scalable lattice-Boltzmann (LB) flow solver to capture RBC dynamics in isolation and in dense suspensions of O(1,000) RBCs at realistic hematocrit values. Validation results include experimental comparisons with results for isolated RBCs tumbling, tank-treading, deforming in the wheel configuration, and parachuting in a microvessel-sized rigid tube. The rheology of blood is analyzed via LB-SL simulations of RBC suspensions at physiological concentrations. The results characterize the effect of the RBC deformation on the viscosity, normal stress differences, and particle pressure. Also, a demonstration of the Fahraeus effect is included which correlates the cell-depleted wall layer thickness with tube diameter for a variety of rigid microvessel-sized tube sizes. Lastly, the Fahraeus--Lindqvist effect is demonstrated using the apparent viscosity obtained from these simulations.
Crisan, Dan
2011-01-01
"Stochastic Analysis" aims to provide mathematical tools to describe and model high dimensional random systems. Such tools arise in the study of Stochastic Differential Equations and Stochastic Partial Differential Equations, Infinite Dimensional Stochastic Geometry, Random Media and Interacting Particle Systems, Super-processes, Stochastic Filtering, Mathematical Finance, etc. Stochastic Analysis has emerged as a core area of late 20th century Mathematics and is currently undergoing a rapid scientific development. The special volume "Stochastic Analysis 2010" provides a sa
Katsuaki Koike
2011-01-01
Sample data in the Earth and environmental sciences are limited in quantity and sampling location and therefore, sophisticated spatial modeling techniques are indispensable for accurate imaging of complicated structures and properties of geomaterials. This paper presents several effective methods that are grouped into two categories depending on the nature of regionalized data used. Type I data originate from plural populations and type II data satisfy the prerequisite of stationarity and have distinct spatial correlations. For the type I data, three methods are shown to be effective and demonstrated to produce plausible results: (1) a spline-based method, (2) a combination of a spline-based method with a stochastic simulation, and (3) a neural network method. Geostatistics proves to be a powerful tool for type II data. Three new approaches of geostatistics are presented with case studies: an application to directional data such as fracture, multi-scale modeling that incorporates a scaling law,and space-time joint analysis for multivariate data. Methods for improving the contribution of such spatial modeling to Earth and environmental sciences are also discussed and future important problems to be solved are summarized.
Shephard, Neil
2005-01-01
Stochastic volatility (SV) is the main concept used in the fields of financial economics and mathematical finance to deal with the endemic time-varying volatility and codependence found in financial markets. Such dependence has been known for a long time, early comments include Mandelbrot (1963) and Officer (1973). It was also clear to the founding fathers of modern continuous time finance that homogeneity was an unrealistic if convenient simplification, e.g. Black and Scholes (1972, p. 416) ...
Saleh Heneidi
Full Text Available Advances in stem cell therapy face major clinical limitations, particularly challenged by low rates of post-transplant cell survival. Hostile host factors of the engraftment microenvironment such as hypoxia, nutrition deprivation, pro-inflammatory cytokines, and reactive oxygen species can each contribute to unwanted differentiation or apoptosis. In this report, we describe the isolation and characterization of a new population of adipose tissue (AT derived pluripotent stem cells, termed Multilineage Differentiating Stress-Enduring (Muse Cells, which are isolated using severe cellular stress conditions, including long-term exposure to the proteolytic enzyme collagenase, serum deprivation, low temperatures and hypoxia. Under these conditions, a highly purified population of Muse-AT cells is isolated without the utilization of cell sorting methods. Muse-AT cells grow in suspension as cell spheres reminiscent of embryonic stem cell clusters. Muse-AT cells are positive for the pluripotency markers SSEA3, TR-1-60, Oct3/4, Nanog and Sox2, and can spontaneously differentiate into mesenchymal, endodermal and ectodermal cell lineages with an efficiency of 23%, 20% and 22%, respectively. When using specific differentiation media, differentiation efficiency is greatly enhanced in Muse-AT cells (82% for mesenchymal, 75% for endodermal and 78% for ectodermal. When compared to adipose stem cells (ASCs, microarray data indicate a substantial up-regulation of Sox2, Oct3/4, and Rex1. Muse-ATs also exhibit gene expression patterns associated with the down-regulation of genes involved in cell death and survival, embryonic development, DNA replication and repair, cell cycle and potential factors related to oncogenecity. Gene expression analysis indicates that Muse-ATs and ASCs are mesenchymal in origin; however, Muse-ATs also express numerous lymphocytic and hematopoietic genes, such as CCR1 and CXCL2, encoding chemokine receptors and ligands involved in stem cell
Foxall, W; Cunningham, C; Mellors, R; Templeton, D; Dyer, K; White, J
2012-02-27
ability to detect evidence for an underground facility using InSAR depends on the displacement sensitivity and spatial resolution of the interferogram, as well as on the size and depth of the facility and the time since its completion. The methodology development described in this report focuses on the exploitation of synthetic aperture radar data that are available commercially from a number of satellite missions. Development of the method involves three components: (1) Evaluation of the capability of InSAR to detect and characterize underground facilities ; (2) inversion of InSAR data to infer the location, depth, shape and volume of a subsurface facility; and (3) evaluation and selection of suitable geomechanical forward models to use in the inversion. We adapted LLNL's general-purpose Bayesian Markov Chain-Monte Carlo procedure, the 'Stochastic Engine' (SE), to carry out inversions to characterize subsurface void geometries. The SE performs forward simulations for a large number of trial source models to identify the set of models that are consistent with the observations and prior constraints. The inverse solution produced by this kind of stochastic method is a posterior probability density function (pdf) over alternative models, which forms an appropriate input to risk-based decision analyses to evaluate subsequent response strategies. One major advantage of a stochastic inversion approach is its ability to deal with complex, non-linear forward models employing empirical, analytical or numerical methods. However, while a geomechanical model must incorporate adequate physics to enable sufficiently accurate prediction of surface displacements, it must also be computationally fast enough to render the large number of forward realizations needed in stochastic inversion feasible. This latter requirement prompted us first to investigate computationally efficient empirical relations and closed-form analytical solutions. However, our evaluation revealed
A stochastic representation of the lithologic units and associated hydrogeologic parameters of the potential high-level nuclear waste repository are developed for use in performance-assessment calculations, including the Total-System Performance Assessment for Yucca Mountain-SNL Second Iteration (TSPA-1993). A simplified lithologic model has been developed based on the physical characteristics of the welded and nonwelded units at Yucca Mountain. Ten hydrogeologic units are developed from site-specific data (lithologic and geophysical logs and core photographs) obtained from the unsaturated and saturated zones. The three-dimensional geostatistical model of the ten hydrogeologic units is based on indicator-coding techniques and improves on the two-dimensional model developed for TSPA91. The hydrogeologic properties (statistics and probability distribution functions) are developed from the results of laboratory tests and in-situ aquifer tests or are derived through fundamental relationships. Hydrogeologic properties for matrix properties, bulk conductivities, and fractures are developed from existing site specific data. Extensive data are available for matrix porosity, bulk density, and matrix saturated conductivity. For other hydrogeologic properties, the data are minimal or nonexistent. Parameters for the properties are developed as beta probability distribution functions. For the model units without enough data for analysis, parameters are developed as analogs to existing units. A relational, analytic approach coupled with bulk conductivity parameters is used to develop fracture parameters based on the smooth-wall-parallel-plate theory. An analytic method is introduced for scaling small-core matrix properties to the hydrogeologic unit scales
Irregular Cellular Learning Automata.
Esnaashari, Mehdi; Meybodi, Mohammad Reza
2015-08-01
Cellular learning automaton (CLA) is a recently introduced model that combines cellular automaton (CA) and learning automaton (LA). The basic idea of CLA is to use LA to adjust the state transition probability of stochastic CA. This model has been used to solve problems in areas such as channel assignment in cellular networks, call admission control, image processing, and very large scale integration placement. In this paper, an extension of CLA called irregular CLA (ICLA) is introduced. This extension is obtained by removing the structure regularity assumption in CLA. Irregularity in the structure of ICLA is needed in some applications, such as computer networks, web mining, and grid computing. The concept of expediency has been introduced for ICLA and then, conditions under which an ICLA becomes expedient are analytically found. PMID:25291810
Dynamic stochastic optimization
Ermoliev, Yuri; Pflug, Georg
2004-01-01
Uncertainties and changes are pervasive characteristics of modern systems involving interactions between humans, economics, nature and technology. These systems are often too complex to allow for precise evaluations and, as a result, the lack of proper management (control) may create significant risks. In order to develop robust strategies we need approaches which explic itly deal with uncertainties, risks and changing conditions. One rather general approach is to characterize (explicitly or implicitly) uncertainties by objec tive or subjective probabilities (measures of confidence or belief). This leads us to stochastic optimization problems which can rarely be solved by using the standard deterministic optimization and optimal control methods. In the stochastic optimization the accent is on problems with a large number of deci sion and random variables, and consequently the focus ofattention is directed to efficient solution procedures rather than to (analytical) closed-form solu tions. Objective an...
Staci L Solin
Full Text Available In this study we describe the molecular and cellular characterization of a zebrafish mutant that develops tumors in the optic pathway. Heterozygous Tg(flk1:RFPis18 transgenic adults develop tumors of the retina, optic nerve and optic tract. Molecular and genetic mapping demonstrate the tumor phenotype is linked to a high copy number transgene array integrated in the lincRNA gene lincRNAis18/Zv9_00007276 on chromosome 3. TALENs were used to isolate a 147 kb deletion allele that removes exons 2-5 of the lincRNAis18 gene. Deletion allele homozygotes are viable and do not develop tumors, indicating loss of function of the lincRNAis18 locus is not the trigger for tumor onset. Optic pathway tumors in the Tg(flk1:RFPis18 mutant occur with a penetrance of 80-100% by 1 year of age. The retinal tumors are highly vascularized and composed of rosettes of various sizes embedded in a fibrous matrix. Immunohistochemical analysis showed increased expression of the glial markers GFAP and BLBP throughout retinal tumors and in dysplastic optic nerve. We performed transcriptome analysis of pre-tumorous retina and retinal tumor tissue and found changes in gene expression signatures of radial glia and astrocytes (slc1a3, activated glia (atf3, blbp, apoeb, proliferating neural progenitors (foxd3, nestin, cdh2, her9/hes1, and glioma markers (S100β, vim. The transcriptome also revealed activation of cAMP, Stat3 and Wnt signal transduction pathways. qRT-PCR confirmed >10-fold overexpression of the Wnt pathway components hbegfa, ascl1a, and insm1a. Together the data indicate Müller glia and/or astrocyte-derived progenitors could contribute to the zebrafish Tg(flk1:RFPis18 optic pathway tumors.
Moore, R; King, N; Alroy, J
1988-06-01
Differences in colonic secretory glycoconjugates (ie, mucin) between normal and ulcerative colitis-prone patients have been noted. Similar differences may occur in a corresponding primate model, the cotton-top tamarin (CTT), Saguinus oedipus, a New World monkey which suffers from spontaneous chronic colitis and colon cancer. Lectin reagents were used to characterize and compare colonic cell surface, cytoplasmic, and secretory glycoconjugates of 9 clinically healthy cotton-top tamarins, 7 colitis-susceptible, cancer-resistant tamarins (Callithrix jacchus, Saguinus fuscicollis), and 8 colitis and cancer-resistant primates (Aotus trivirgatus, Saimiri sciureus, Macaca fascicularis, and Macaca mulatta). Paraffin-embedded colonic sections were labeled with ten different biotinylated lectins and visualized by the avidin-biotin peroxidase (ABC) method. Significant differences were demonstrated in the pattern of lectin staining between the colitis-resistant and colitis-prone groups of primates. The differences were noted with Griffonia simplicifolia-I (GS-I), Dolichos biflorus agglutinin (DBA), peanut agglutinin (PNA) before and after neuraminidase, Ricinus communis agglutinin-I (RCA-I), soybean agglutinin (SBA), Ulex europaeus agglutinin-I (UEA-I), wheat germ agglutinin (WGA), and succinylated WGA (S-WGA). Significant differences between the CTT and phylogenetically related colitis-prone but cancer-resistant tamarins were demonstrated with SBA, UEA-I, and PNA after desialylation with neuraminidase. These results suggest that differences in colonic cellular glycoconjugates between colitis- and cancer-susceptible species versus colitis-susceptible, cancer-resistant species may be associated with risk of cancer. PMID:3132857
Stochastic transition model for pedestrian dynamics
Schultz, Michael
2012-01-01
The proposed stochastic model for pedestrian dynamics is based on existing approaches using cellular automata, combined with substantial extensions, to compensate the deficiencies resulting of the discrete grid structure. This agent motion model is extended by both a grid-based path planning and mid-range agent interaction component. The stochastic model proves its capabilities for a quantitative reproduction of the characteristic shape of the common fundamental diagram of pedestrian dynamics...
Highlights: ► The study presents cloning and characterization of TCP1γ gene from L. donovani. ► TCP1γ is a subunit of T-complex protein-1 (TCP1), a chaperonin class of protein. ► LdTCPγ exhibited differential expression in different stages of promastigotes. ► LdTCPγ co-localized with actin, a cytoskeleton protein. ► The data suggests that this gene may have a role in differentiation/biogenesis. ► First report on this chapronin in Leishmania. -- Abstract: T-complex protein-1 (TCP1) complex, a chaperonin class of protein, ubiquitous in all genera of life, is involved in intracellular assembly and folding of various proteins. The gamma subunit of TCP1 complex (TCP1γ), plays a pivotal role in the folding and assembly of cytoskeleton protein(s) as an individual or complexed with other subunits. Here, we report for the first time cloning, characterization and expression of the TCP1γ of Leishmania donovani (LdTCP1γ), the causative agent of Indian Kala-azar. Primary sequence analysis of LdTCP1γ revealed the presence of all the characteristic features of TCP1γ. However, leishmanial TCP1γ represents a distinct kinetoplastid group, clustered in a separate branch of the phylogenic tree. LdTCP1γ exhibited differential expression in different stages of promastigotes. The non-dividing stationary phase promastigotes exhibited 2.5-fold less expression of LdTCP1γ as compared to rapidly dividing log phase parasites. The sub-cellular distribution of LdTCP1γ was studied in log phase promastigotes by employing indirect immunofluorescence microscopy. The protein was present not only in cytoplasm but it was also localized in nucleus, peri-nuclear region, flagella, flagellar pocket and apical region. Co-localization of LdTCP1γ with actin suggests that, this gene may have a role in maintaining the structural dynamics of cytoskeleton of parasite.
Bhaskar,; Kumari, Neeti [Division of Biochemistry, CSIR-Central Drug Research Institute, Chattar Manzil Palace, PO Box 173, Lucknow (India); Goyal, Neena, E-mail: neenacdri@yahoo.com [Division of Biochemistry, CSIR-Central Drug Research Institute, Chattar Manzil Palace, PO Box 173, Lucknow (India)
2012-12-07
Highlights: Black-Right-Pointing-Pointer The study presents cloning and characterization of TCP1{gamma} gene from L. donovani. Black-Right-Pointing-Pointer TCP1{gamma} is a subunit of T-complex protein-1 (TCP1), a chaperonin class of protein. Black-Right-Pointing-Pointer LdTCP{gamma} exhibited differential expression in different stages of promastigotes. Black-Right-Pointing-Pointer LdTCP{gamma} co-localized with actin, a cytoskeleton protein. Black-Right-Pointing-Pointer The data suggests that this gene may have a role in differentiation/biogenesis. Black-Right-Pointing-Pointer First report on this chapronin in Leishmania. -- Abstract: T-complex protein-1 (TCP1) complex, a chaperonin class of protein, ubiquitous in all genera of life, is involved in intracellular assembly and folding of various proteins. The gamma subunit of TCP1 complex (TCP1{gamma}), plays a pivotal role in the folding and assembly of cytoskeleton protein(s) as an individual or complexed with other subunits. Here, we report for the first time cloning, characterization and expression of the TCP1{gamma} of Leishmania donovani (LdTCP1{gamma}), the causative agent of Indian Kala-azar. Primary sequence analysis of LdTCP1{gamma} revealed the presence of all the characteristic features of TCP1{gamma}. However, leishmanial TCP1{gamma} represents a distinct kinetoplastid group, clustered in a separate branch of the phylogenic tree. LdTCP1{gamma} exhibited differential expression in different stages of promastigotes. The non-dividing stationary phase promastigotes exhibited 2.5-fold less expression of LdTCP1{gamma} as compared to rapidly dividing log phase parasites. The sub-cellular distribution of LdTCP1{gamma} was studied in log phase promastigotes by employing indirect immunofluorescence microscopy. The protein was present not only in cytoplasm but it was also localized in nucleus, peri-nuclear region, flagella, flagellar pocket and apical region. Co-localization of LdTCP1{gamma} with actin suggests
Smirnova, Lena; Harris, Georgina; Leist, Marcel; Hartung, Thomas
2015-01-01
Cellular resilience describes the ability of a cell to cope with environmental changes such as toxicant exposure. If cellular metabolism does not collapse directly after the hit or end in programmed cell death, the ensuing stress responses promote a new homeostasis under stress. The processes of reverting "back to normal" and reversal of apoptosis ("anastasis") have been studied little at the cellular level. Cell types show astonishingly similar vulnerability to most toxicants, except for those that require a very specific target, metabolism or mechanism present only in specific cell types. The majority of chemicals triggers "general cytotoxicity" in any cell at similar concentrations. We hypothesize that cells differ less in their vulnerability to a given toxicant than in their resilience (coping with the "hit"). In many cases, cells do not return to the naive state after a toxic insult. The phenomena of "pre-conditioning", "tolerance" and "hormesis" describe this for low-dose exposures to toxicants that render the cell more resistant to subsequent hits. The defense and resilience programs include epigenetic changes that leave a "memory/scar" - an alteration as a consequence of the stress the cell has experienced. These memories might have long-term consequences, both positive (resistance) and negative, that contribute to chronic and delayed manifestations of hazard and, ultimately, disease. This article calls for more systematic analyses of how cells cope with toxic perturbations in the long-term after stressor withdrawal. A technical prerequisite for these are stable (organotypic) cultures and a characterization of stress response molecular networks. PMID:26536287
Ti-6Al-4V open cellular foams were fabricated by additive manufacturing using electron beam melting (EBM). Foam models were developed from CT-scans of aluminum open cellular foams and embedded in CAD for EBM. These foams were fabricated with solid cell structures as well as hollow cell structures and exhibit tailorable stiffness and strength. The strength in proportion to the measured microindentation hardness is as much as 40% higher for hollow cell (wall) structures in contrast to solid, fully dense EBM fabricated components. Plots of relative stiffness versus relative density were in good agreement with the Gibson-Ashby model for open cellular foam materials. Stiffness or Young's modulus values measured using a resonant frequency-damping analysis technique were found to vary inversely with porosity especially for solid cell wall, open cellular structure foams. These foams exhibit the potential for novel biomedical, aeronautics, and automotive applications.
Robustness of a Cellular Automata Model for the HIV Infection
Figueirêdo, P H; Santos, R M Zorzenon dos
2008-01-01
An investigation was conducted to study the robustness of the results obtained from the cellular automata model which describes the spread of the HIV infection within lymphoid tissues [R. M. Zorzenon dos Santos and S. Coutinho, Phys. Rev. Lett. 87, 168102 (2001)]. The analysis focussed on the dynamic behavior of the model when defined in lattices with different symmetries and dimensionalities. The results illustrated that the three-phase dynamics of the planar models suffered minor changes in relation to lattice symmetry variations and, while differences were observed regarding dimensionality changes, qualitative behavior was preserved. A further investigation was conducted into primary infection and sensitiveness of the latency period to variations of the model's stochastic parameters over wide ranging values. The variables characterizing primary infection and the latency period exhibited power-law behavior when the stochastic parameters varied over a few orders of magnitude. The power-law exponents were app...
The majority of cancer patients experience dramatic weight loss, due to cachexia and consisting of skeletal muscle and fat tissue wasting. Cachexia is a negative prognostic factor, interferes with therapy and worsens the patients' quality of life by affecting muscle function. Mice bearing ectopically-implanted C26 colon carcinoma are widely used as an experimental model of cancer cachexia. As part of the search for novel clinical and basic research applications for this experimental model, we characterized novel cellular and molecular features of C26-bearing mice. A fragment of C26 tumor was subcutaneously grafted in isogenic BALB/c mice. The mass growth and proliferation rate of the tumor were analyzed. Histological and cytofluorometric analyses were used to assess cell death, ploidy and differentiation of the tumor cells. The main features of skeletal muscle atrophy, which were highlighted by immunohistochemical and electron microscopy analyses, correlated with biochemical alterations. Muscle force and resistance to fatigue were measured and analyzed as major functional deficits of the cachectic musculature. We found that the C26 tumor, ectopically implanted in mice, is an undifferentiated carcinoma, which should be referred to as such and not as adenocarcinoma, a common misconception. The C26 tumor displays aneuploidy and histological features typical of transformed cells, incorporates BrdU and induces severe weight loss in the host, which is largely caused by muscle wasting. The latter appears to be due to proteasome-mediated protein degradation, which disrupts the sarcomeric structure and muscle fiber-extracellular matrix interactions. A pivotal functional deficit of cachectic muscle consists in increased fatigability, while the reported loss of tetanic force is not statistically significant following normalization for decreased muscle fiber size. We conclude, on the basis of the definition of cachexia, that ectopically-implanted C26 carcinoma represents
Stochastic superparameterization in quasigeostrophic turbulence
In this article we expand and develop the authors' recent proposed methodology for efficient stochastic superparameterization algorithms for geophysical turbulence. Geophysical turbulence is characterized by significant intermittent cascades of energy from the unresolved to the resolved scales resulting in complex patterns of waves, jets, and vortices. Conventional superparameterization simulates large scale dynamics on a coarse grid in a physical domain, and couples these dynamics to high-resolution simulations on periodic domains embedded in the coarse grid. Stochastic superparameterization replaces the nonlinear, deterministic eddy equations on periodic embedded domains by quasilinear stochastic approximations on formally infinite embedded domains. The result is a seamless algorithm which never uses a small scale grid and is far cheaper than conventional SP, but with significant success in difficult test problems. Various design choices in the algorithm are investigated in detail here, including decoupling the timescale of evolution on the embedded domains from the length of the time step used on the coarse grid, and sensitivity to certain assumed properties of the eddies (e.g. the shape of the assumed eddy energy spectrum). We present four closures based on stochastic superparameterization which elucidate the properties of the underlying framework: a ‘null hypothesis’ stochastic closure that uncouples the eddies from the mean, a stochastic closure with nonlinearly coupled eddies and mean, a nonlinear deterministic closure, and a stochastic closure based on energy conservation. The different algorithms are compared and contrasted on a stringent test suite for quasigeostrophic turbulence involving two-layer dynamics on a β-plane forced by an imposed background shear. The success of the algorithms developed here suggests that they may be fruitfully applied to more realistic situations. They are expected to be particularly useful in providing accurate and
Blaskiewicz, M.
2011-01-01
Stochastic Cooling was invented by Simon van der Meer and was demonstrated at the CERN ISR and ICE (Initial Cooling Experiment). Operational systems were developed at Fermilab and CERN. A complete theory of cooling of unbunched beams was developed, and was applied at CERN and Fermilab. Several new and existing rings employ coasting beam cooling. Bunched beam cooling was demonstrated in ICE and has been observed in several rings designed for coasting beam cooling. High energy bunched beams have proven more difficult. Signal suppression was achieved in the Tevatron, though operational cooling was not pursued at Fermilab. Longitudinal cooling was achieved in the RHIC collider. More recently a vertical cooling system in RHIC cooled both transverse dimensions via betatron coupling.
S K Das
2011-08-01
An earlier developed stochastic model has been applied to describe the relative rate of material loss from the steel surface subjected to simultaneous action of high temperature oxidation involving multiple oxides and mechanical erosion. Different oxide scale growths, namely, nickel, iron and chromium have been treated deterministically and erosion is described using a literature based probabilistic framework. Oxidation is described with a power law (parabolic) approach to quantify the rate of growth of all the three oxide scales. In consonance with the published model, erosion is treated using a probabilistic methodology as spatially random phenomena on the oxide surface. The concept of ‘erosion footprint’ has been incorporated in the present model to characterize the erosion-induced damage on the steel surface. The model has been applied to predict the relative material loss as a function of time resulted from erosion–oxidation interaction pertaining to nickel, iron and chromium oxides in dimensionless form. This investigation is expected to provide a quantitative understanding of relative material loss due to solid particle erosion for oxide scales, (composed of multiple oxides) formed on the steel components of coal-ﬁred boilers.
无
2007-01-01
In this paper, the stochastic flow of mappings generated by a Feller convolution semigroup on a compact metric space is studied. This kind of flow is the generalization of superprocesses of stochastic flows and stochastic diffeomorphism induced by the strong solutions of stochastic differential equations.
Stochastic Averaging and Stochastic Extremum Seeking
Liu, Shu-Jun
2012-01-01
Stochastic Averaging and Stochastic Extremum Seeking develops methods of mathematical analysis inspired by the interest in reverse engineering and analysis of bacterial convergence by chemotaxis and to apply similar stochastic optimization techniques in other environments. The first half of the text presents significant advances in stochastic averaging theory, necessitated by the fact that existing theorems are restricted to systems with linear growth, globally exponentially stable average models, vanishing stochastic perturbations, and prevent analysis over infinite time horizon. The second half of the text introduces stochastic extremum seeking algorithms for model-free optimization of systems in real time using stochastic perturbations for estimation of their gradients. Both gradient- and Newton-based algorithms are presented, offering the user the choice between the simplicity of implementation (gradient) and the ability to achieve a known, arbitrary convergence rate (Newton). The design of algorithms...
Applications of queueing theory to stochastic models of gene expression
Kulkarni, Rahul
2012-02-01
The intrinsic stochasticity of cellular processes implies that analysis of fluctuations (`noise') is often essential for quantitative modeling of gene expression. Recent single-cell experiments have carried out such analysis to characterize moments and entire probability distributions for quantities of interest, e.g. mRNA and protein levels across a population of cells. Correspondingly, there is a need to develop general analytical tools for modeling and interpretation of data obtained from such single-cell experiments. One such approach involves the mapping between models of stochastic gene expression and systems analyzed in queueing theory. The talk will provide an overview of this approach and discuss how theorems from queueing theory (e.g. Little's Law) can be used to derive exact results for general stochastic models of gene expression. In the limit that gene expression occurs in bursts, analytical results can be obtained which provide insight into the effects of different regulatory mechanisms on the noise in protein steady-state distributions. In particular, the approach can be used to analyze the effect of post-transcriptional regulation by non-coding RNAs leading to new insights and experimentally testable predictions.
PRODUCTIVE GOVERNMENT EXPENDITURE IN A STOCHASTICALLY GROWING OPEN ECONOMY
Haijun WANG; Shigeng HU
2007-01-01
This paper employs a stochastic endogenous growth model with productive government expenditure in a small open economy to analyze the optimal fiscal policy.First,a stochastic model of a small open economy is constructed.Second.the equilibrium solutions of the representative agent's stochastic optimization problem are derived.Third,we obtain the equilibrium solutions of the central planner's stochastic optimization problem and the optimal government expenditure policy.Finally,the optimal tax policy is characterized.
Jiao, Yang, E-mail: yang.jiao.2@asu.edu; Chawla, Nikhilesh [Materials Science and Engineering, Arizona State University, Arizona 85287-6206 (United States)
2014-03-07
We present a framework to model and characterize the microstructure of heterogeneous materials with anisotropic inclusions of secondary phases based on the directional correlation functions of the inclusions. Specifically, we have devised an efficient method to incorporate both directional two-point correlation functions S{sub 2} and directional two-point cluster functions C{sub 2} that contain non-trivial topological connectedness information into the simulated annealing microstructure reconstruction procedure. Our framework is applied to model an anisotropic aluminum alloy and the accuracy of the reconstructed structural models is assessed by quantitative comparison with the actual microstructure obtained via x-ray tomography. We show that incorporation of directional clustering information via C{sub 2} significantly improves the accuracy of the reconstruction. In addition, a set of analytical “basis” correlation functions are introduced to approximate the actual S{sub 2} and C{sub 2} of the material. With the proper choice of basis functions, the anisotropic microstructure can be represented by a handful of parameters including the effective linear sizes of the iron-rich and silicon-rich inclusions along three orthogonal directions. This provides a general and efficient means for heterogeneous material modeling that enables one to significantly reduce the data set required to characterize the anisotropic microstructure.
We present a framework to model and characterize the microstructure of heterogeneous materials with anisotropic inclusions of secondary phases based on the directional correlation functions of the inclusions. Specifically, we have devised an efficient method to incorporate both directional two-point correlation functions S2 and directional two-point cluster functions C2 that contain non-trivial topological connectedness information into the simulated annealing microstructure reconstruction procedure. Our framework is applied to model an anisotropic aluminum alloy and the accuracy of the reconstructed structural models is assessed by quantitative comparison with the actual microstructure obtained via x-ray tomography. We show that incorporation of directional clustering information via C2 significantly improves the accuracy of the reconstruction. In addition, a set of analytical “basis” correlation functions are introduced to approximate the actual S2 and C2 of the material. With the proper choice of basis functions, the anisotropic microstructure can be represented by a handful of parameters including the effective linear sizes of the iron-rich and silicon-rich inclusions along three orthogonal directions. This provides a general and efficient means for heterogeneous material modeling that enables one to significantly reduce the data set required to characterize the anisotropic microstructure
Li X
2011-12-01
Full Text Available Xiuying Li1, Dan Chen1, Chaoyi Le2, Chunliu Zhu1, Yong Gan1, Lars Hovgaard3, Mingshi Yang41Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; 2University of Toronto Mississauga Campus, Ontario, Canada; 3Oral Formulation Development, Novo Nordisk A/S, Maalov; 4Department of Pharmaceutics and Analytical Chemistry, University of Copenhagen, Copenhagen, DenmarkBackground: The aim of this study was to investigate the intestinal mucus-penetrating properties and intestinal cellular uptake of two types of liposomes modified by Pluronic F127 (PF127.Methods: The two types of liposomes, ie, PF127-inlaid liposomes and PF127-adsorbed liposomes, were prepared by a thin-film hydration method followed by extrusion, in which coumarin 6 was loaded as a fluorescence marker. A modified Franz diffusion cell mounted with the intestinal mucus of rats was used to study the diffusion characteristics of the two types of PF127 liposomes. Cell uptake studies were conducted in Caco-2 cells and analyzed using confocal laser scanning microcopy as well as flow cytometry.Results: The diffusion efficiency of the two types of PF127-modified liposomes through intestinal rat mucus was 5–7-fold higher than that of unmodified liposomes. Compared with unmodified liposomes, PF127-inlaid liposomes showed significantly higher cellular uptake of courmarin 6. PF127-adsorbed liposomes showed a lower cellular uptake. Moreover, and interestingly, the two types of PF127-modified liposomes showed different cellular uptake mechanisms in Caco-2 cells.Conclusion: PF127-inlaid liposomes with improved intestinal mucus-penetrating ability and enhanced cellular uptake might be a potential carrier candidate for oral drug delivery.Keywords: Pluronic F127, mucus-penetrating, particles, liposomes, oral drug delivery
Eslami, Sohrab
This dissertation undertakes the theoretical and experimental developments microcantilevers utilized in Atomic Force Microscopy (AFM) with applications to cellular imaging and characterization. The capability of revealing the inhomogeneties or interior of ultra-small materials has been of most interest to many researchers. However, the fundamental concept of signal and image formation remains unexplored and not fully understood. For his, a semi-empirical nonlinear force model is proposed to show that virtual frequency generation, regarded as the simplest synthesized subsurface probe, occurs optimally when the force is tuned to the van der Waals form. This is the first-time observation of a novel theoretical dynamic multi-frequency force microscopy that has not been already reported. Owing to the broad applications of microcantilevers in the nanoscale imaging and microscopic techniques, there is an essential feeling to study and propose a comprehensive model of such systems. Therefore, in the theoretical part of this dissertation, a distributed-parameters representation modeling of the microcantilever along with a general interaction force comprising of two attractive and repulsive components with general amplitude and power terms is studied. This model is investigated in a general 2D Cartesian coordinate to consider the motions of the probe with a tip mass. There is an excitation at the microcantilever's base such that the end of the beam is subject to the proposed general force. These forces are very sensitive to the amplitude and power terms of these parts; on the other hand, atomic intermolecular force is a function of the distance such that this distance itself is also a function of the interaction force that will result in a nonlinear implicit equation. From a parametric study in the probe-sample excitation, it is shown that the predicted behavior of the generated difference-frequency oscillation amplitude agrees well with experimental measurements. Following
Work fluctuations and stochastic resonance
We study Brownian particle motion in a double-well potential driven by an ac force. This system exhibits the phenomenon of stochastic resonance. Distribution of work done on the system over a drive period in the time asymptotic regime has been calculated. We show that fluctuations in the input energy or work done dominate the mean value. The mean value of work done over a period as a function of noise strength can also be used to characterize stochastic resonance in the system. We also discuss the validity of steady state fluctuation theorems in this particular system
Stochastic models of intracellular calcium signals
Cellular signaling operates in a noisy environment shaped by low molecular concentrations and cellular heterogeneity. For calcium release through intracellular channels–one of the most important cellular signaling mechanisms–feedback by liberated calcium endows fluctuations with critical functions in signal generation and formation. In this review it is first described, under which general conditions the environment makes stochasticity relevant, and which conditions allow approximating or deterministic equations. This analysis provides a framework, in which one can deduce an efficient hybrid description combining stochastic and deterministic evolution laws. Within the hybrid approach, Markov chains model gating of channels, while the concentrations of calcium and calcium binding molecules (buffers) are described by reaction–diffusion equations. The article further focuses on the spatial representation of subcellular calcium domains related to intracellular calcium channels. It presents analysis for single channels and clusters of channels and reviews the effects of buffers on the calcium release. For clustered channels, we discuss the application and validity of coarse-graining as well as approaches based on continuous gating variables (Fokker–Planck and chemical Langevin equations). Comparison with recent experiments substantiates the stochastic and spatial approach, identifies minimal requirements for a realistic modeling, and facilitates an understanding of collective channel behavior. At the end of the review, implications of stochastic and local modeling for the generation and properties of cell-wide release and the integration of calcium dynamics into cellular signaling models are discussed
Stochastic models of intracellular calcium signals
Rüdiger, Sten, E-mail: sten.ruediger@physik.hu-berlin.de
2014-01-10
Cellular signaling operates in a noisy environment shaped by low molecular concentrations and cellular heterogeneity. For calcium release through intracellular channels–one of the most important cellular signaling mechanisms–feedback by liberated calcium endows fluctuations with critical functions in signal generation and formation. In this review it is first described, under which general conditions the environment makes stochasticity relevant, and which conditions allow approximating or deterministic equations. This analysis provides a framework, in which one can deduce an efficient hybrid description combining stochastic and deterministic evolution laws. Within the hybrid approach, Markov chains model gating of channels, while the concentrations of calcium and calcium binding molecules (buffers) are described by reaction–diffusion equations. The article further focuses on the spatial representation of subcellular calcium domains related to intracellular calcium channels. It presents analysis for single channels and clusters of channels and reviews the effects of buffers on the calcium release. For clustered channels, we discuss the application and validity of coarse-graining as well as approaches based on continuous gating variables (Fokker–Planck and chemical Langevin equations). Comparison with recent experiments substantiates the stochastic and spatial approach, identifies minimal requirements for a realistic modeling, and facilitates an understanding of collective channel behavior. At the end of the review, implications of stochastic and local modeling for the generation and properties of cell-wide release and the integration of calcium dynamics into cellular signaling models are discussed.
Vesper, B; Onul, A; Haines III, G; Tarjan, G; Xue, J; Elseth, K; Aydogan, B.; Altman, M.; Roeske, J; Paradise, W; De Vitto, H; Radosevich, J
2013-01-01
There is a lack of understanding of the casual mechanisms behind the observation that some breast adenocarcinomas have identical morphology and comparatively different cellular growth behavior. This is exemplified by a differential response to radiation, chemotherapy, and other biological intervention therapies. Elevated concentrations of the free radical nitric oxide (NO), coupled with the up-regulated enzyme nitric oxide synthase (NOS) which produces NO, are activities which impact tumor gr...
Judith Martín-de León
2016-07-01
Full Text Available This paper describes the processing conditions needed to produce low density nanocellular polymers based on polymethylmethacrylate (PMMA with relative densities between 0.45 and 0.25, cell sizes between 200 and 250 nm and cell densities higher than 1014 cells/cm3. To produce these nanocellular polymers, the foaming parameters of the gas dissolution foaming technique using CO2 as blowing agent have been optimized. Taking into account previous works, the amount of CO2 uptake was maintained constant (31% by weight for all the materials. Foaming parameters were modified between 40 °C and 110 °C for the foaming temperature and from 1 to 5 min for the foaming time. Foaming temperatures in the range of 80 to 100 °C and foaming times of 2 min allow for production of nanocellular polymers with relative densities as low as 0.25. Cellular structure has been studied in-depth to obtain the processing-cellular structure relationship. In addition, it has been proved that the glass transition temperature depends on the cellular structure. This effect is associated with a confinement of the polymer in the cell walls, and is one of the key reasons for the improved properties of nanocellular polymers.
Sakai, H; Yuasa, M; Onuma, H; Takeoka, S; Tsuchida, E
2000-01-01
A series of hemoglobin (Hb)-based O(2) carriers, acellular and cellular types, were synthesized and their physicochemical characteristics were compared. The acellular type includes intramolecularly cross-linked Hb (XLHb), polyoxyethylene (POE)-conjugated pyridoxalated Hb (POE-PLP-Hb), hydroxyethylstarch-conjugated Hb (HES-XLHb), and glutaraldehyde-polymerized XLHb (Poly-XLHb). The cellular type is Hb-vesicles (HbV) of which the surface is modified with POE (POE-HbV). Their particle diameters are 7 +/- 2, 22 +/- 2, 47 +/- 17, 68 +/- 24, and 224 +/- 76 nm, respectively, thus all the materials penetrate across membrane filters with 0.4 microm pore size, though only the POE-HbV cannot penetrate across the filter with 0.2 microm pore size. These characteristics of permeability are important to consider an optimal particle size in microcirculation in vivo. POE-PLP-Hb ([Hb] = 5 g/dL) showed viscosity of 6.1 cP at 332 s(-1) and colloid osmotic pressure (COP) of 70.2 Torr, which are beyond the physiological conditions (human blood, viscosity = 3-4 cP, COP = ca. 25 Torr). XLHb and Poly-XLHb showed viscosities of 1.0 and 1.5 cp, respectively, which are significantly lower than that of blood. COP of POE-HbV is regulated to 20 Torr in 5% human serum albumin (HSA). HES-XLHb and POE-HbV/HSA showed comparable viscosity with human blood. Microscopic observation of human red blood cells (RBC) after mixing blood with POE-PLP-Hb or HES-XLHb disclosed aggregates of RBC, a kind of sludge, indicating a strong interaction with RBC, which is anticipated to modify peripheral blood flow in vivo. On the other hand, XLHb and POE-HbV showed no rouleaux or aggregates of RBC. The acellular Hbs (P(50) = 14-32 Torr) have their specific O(2) affinities determined by their structures, while that of the cellular POE-HbV is regulated by coencapsulating an appropriate amount of an allosteric effector (e.g., P(50) = 18, 32 Torr). These differences in physicochemical characteristics between the acellular
Contreras, Arturo Javier
This dissertation describes a novel Amplitude-versus-Angle (AVA) inversion methodology to quantitatively integrate pre-stack seismic data, well logs, geologic data, and geostatistical information. Deterministic and stochastic inversion algorithms are used to characterize flow units of deepwater reservoirs located in the central Gulf of Mexico. A detailed fluid/lithology sensitivity analysis was conducted to assess the nature of AVA effects in the study area. Standard AVA analysis indicates that the shale/sand interface represented by the top of the hydrocarbon-bearing turbidite deposits generate typical Class III AVA responses. Layer-dependent Biot-Gassmann analysis shows significant sensitivity of the P-wave velocity and density to fluid substitution, indicating that presence of light saturating fluids clearly affects the elastic response of sands. Accordingly, AVA deterministic and stochastic inversions, which combine the advantages of AVA analysis with those of inversion, have provided quantitative information about the lateral continuity of the turbidite reservoirs based on the interpretation of inverted acoustic properties and fluid-sensitive modulus attributes (P-Impedance, S-Impedance, density, and LambdaRho, in the case of deterministic inversion; and P-velocity, S-velocity, density, and lithotype (sand-shale) distributions, in the case of stochastic inversion). The quantitative use of rock/fluid information through AVA seismic data, coupled with the implementation of co-simulation via lithotype-dependent multidimensional joint probability distributions of acoustic/petrophysical properties, provides accurate 3D models of petrophysical properties such as porosity, permeability, and water saturation. Pre-stack stochastic inversion provides more realistic and higher-resolution results than those obtained from analogous deterministic techniques. Furthermore, 3D petrophysical models can be more accurately co-simulated from AVA stochastic inversion results. By
Codd, E F
1968-01-01
Cellular Automata presents the fundamental principles of homogeneous cellular systems. This book discusses the possibility of biochemical computers with self-reproducing capability.Organized into eight chapters, this book begins with an overview of some theorems dealing with conditions under which universal computation and construction can be exhibited in cellular spaces. This text then presents a design for a machine embedded in a cellular space or a machine that can compute all computable functions and construct a replica of itself in any accessible and sufficiently large region of t
Turbulent response in a stochastic regime
The theory for the non-linear, turbulent response in a system with intrinsic stochasticity is considered. It is argued that perturbative Eulerian theories, such as the Direct Interaction Approximation (DIA), are inherently unsuited to describe such a system. The exponentiation property that characterizes stochasticity appears in the Lagrangian picture and cannot even be defined in the Eulerian representation. An approximation for stochastic systems - the Normal Stochastic Approximation - is developed and states that the perturbed orbit functions (Lagrangian fluctuations) behave as normally distributed random variables. This is independent of the Eulerian statistics and, in fact, we treat the Eulerian fluctuations as fixed. A simple model problem (appropriate for the electron response in the drift wave) is subjected to a series of computer experiments. To within numerical noise the results are in agreement with the Normal Stochastic Approximation. The predictions of the DIA for this mode show substantial qualitative and quantitative departures from the observations
Krampera, Mauro; Galipeau, Jacques; Shi, Yufang; Tarte, Karin; Sensebe, Luc
2013-09-01
Cultured mesenchymal stromal cells (MSCs) possess immune regulatory properties and are already used for clinical purposes, although preclinical data (both in vitro and in vivo in animal models) are not always homogeneous and unequivocal. However, the various MSC-based clinical approaches to treat immunological diseases would be significantly validated and strengthened by using standardized immune assays aimed at obtaining shared, reproducible and consistent data. Thus, the MSC Committee of the International Society for Cellular Therapy has decided to put forward for general discussion a working proposal for a standardized approach based on a critical view of literature data. PMID:23602578
Moawia Alghalith
2012-01-01
We present new stochastic differential equations, that are more general and simpler than the existing Ito-based stochastic differential equations. As an example, we apply our approach to the investment (portfolio) model.
Stochastic approximation: invited paper
Lai, Tze Leung
2003-01-01
Stochastic approximation, introduced by Robbins and Monro in 1951, has become an important and vibrant subject in optimization, control and signal processing. This paper reviews Robbins' contributions to stochastic approximation and gives an overview of several related developments.
Stochastic tools in turbulence
Lumey, John L
2012-01-01
Stochastic Tools in Turbulence discusses the available mathematical tools to describe stochastic vector fields to solve problems related to these fields. The book deals with the needs of turbulence in relation to stochastic vector fields, particularly, on three-dimensional aspects, linear problems, and stochastic model building. The text describes probability distributions and densities, including Lebesgue integration, conditional probabilities, conditional expectations, statistical independence, lack of correlation. The book also explains the significance of the moments, the properties of the
Stochastic component mode synthesis
Bah, Mamadou T.; Nair, Prasanth B.; Bhaskar, Atul; Keane, Andy J.
2003-01-01
In this paper, a stochastic component mode synthesis method is developed for the dynamic analysis of large-scale structures with parameter uncertainties. The main idea is to represent each component displacement using a subspace spanned by a set of stochastic basis vectors in the same fashion as in stochastic reduced basis methods [1, 2]. These vectors represent however stochastic modes in contrast to the deterministic modes used in conventional substructuring methods [3]. The Craig-Bampton r...
Miller, D B; Hegele, R A; Wolfe, B M; Huff, M W
1995-03-01
Remnants of triglyceride-rich lipoproteins accumulate in plasma of subjects with type III hyperlipoproteinemia (HLP) due to defective clearance by hepatic receptors. Although most subjects with type III HLP are homozygous for apolipoprotein (apo) E2 (arg158-->cys, R158C), a variant that binds defectively to cell surface receptors, some individuals with type III HLP have rare mutations of apo E. We identified six subjects from three families with type III HLP who had either an apo E3/1 or E4/1 phenotype by isoelectric focusing. Using DNA restriction isotyping with HhaI, all six subjects were determined to have only one apo E allele encoding cys158 and the other encoding arg158. Subsequently, digestion of polymerase chain reaction-amplified portions of exon 4 of the apo E gene with endonucleases HaeIII, TaqI, and Sau3AI demonstrated a second DNA variant that encoded a single amino acid substitution (gly127-->asp, G127D) due to a guanosine-to-adenosine nucleotide change resulting in the apo E1 isoform (G127D, R158C), which had arisen from a parent apo E2 allele. This mutation was confirmed with direct DNA sequencing. Incubation of very low density lipoprotein (VLDL) isolated from hyperlipidemic apo E1 subjects with J774 macrophages resulted in a 7- to 12-fold increase in cellular cholesterol ester compared with VLDL from apo E2/2 subjects. Although heterozygosity for apo E1 alone did not impair the interaction of VLDL with cellular receptors in vitro, its presence in subjects with type III HLP suggests that apo E1, perhaps in combination with secondary factors, may be causative for the dyslipidemia. PMID:7883834
Modeling and analysis of stochastic systems
Kulkarni, Vidyadhar G
2011-01-01
Based on the author's more than 25 years of teaching experience, Modeling and Analysis of Stochastic Systems, Second Edition covers the most important classes of stochastic processes used in the modeling of diverse systems, from supply chains and inventory systems to genetics and biological systems. For each class of stochastic process, the text includes its definition, characterization, applications, transient and limiting behavior, first passage times, and cost/reward models. Along with reorganizing the material, this edition revises and adds new exercises and examples. New to the second edi
Ma Wujun
2010-09-01
Full Text Available Abstract Background Isoprenylcysteine methylesterases (ICME demethylate prenylated protein in eukaryotic cell. Until now, knowledge about their molecular information, localization and expression pattern is largely unavailable in plant species. One ICME in Arabidopsis, encoded by At5g15860, has been identified recently. Over-expression of At5g15860 caused an ABA hypersensitive phenotype in transgenic Arabidopsis plants, indicating that it functions as a positive regulator of ABA signaling. Moreover, ABA induced the expression of this gene in Arabidopsis seedlings. The current study extends these findings by examining the sub-cellular localization, expression profiling, and physiological functions of ICME and two other ICME-like proteins, ICME-LIKE1 and ICME-LIKE2, which were encoded by two related genes At1g26120 and At3g02410, respectively. Results Bioinformatics investigations showed that the ICME and other two ICME-like homologs comprise a small subfamily of carboxylesterase (EC 3.1.1.1 in Arabidopsis. Sub-cellular localization of GFP tagged ICME and its homologs showed that the ICME and ICME-like proteins are intramembrane proteins predominantly localizing in the endoplasmic reticulum (ER and Golgi apparatus. Semi-quantitative and real-time quantitative PCR revealed that the ICME and ICME-like genes are expressed in all examined tissues, including roots, rosette leaves, cauline leaves, stems, flowers, and siliques, with differential expression levels. Within the gene family, the base transcript abundance of ICME-LIKE2 gene is very low with higher expression in reproductive organs (flowers and siliques. Time-course analysis uncovered that both ICME and ICME-like genes are up-regulated by mannitol, NaCl and ABA treatment, with ICME showing the highest level of up-regulation by these treatments. Heat stress resulted in up-regulation of the ICME gene significantly but down-regulation of the ICME-LIKE1 and ICME-LIKE2 genes. Cold and dehydration
Suzuki, Youichi; Chin, Wei-Xin; Han, Qi'En; Ichiyama, Koji; Lee, Ching Hua; Eyo, Zhi Wen; Ebina, Hirotaka; Takahashi, Hirotaka; Takahashi, Chikako; Tan, Beng Hui; Hishiki, Takayuki; Ohba, Kenji; Matsuyama, Toshifumi; Koyanagi, Yoshio; Tan, Yee-Joo; Sawasaki, Tatsuya; Chu, Justin Jang Hann; Vasudevan, Subhash G; Sano, Kouichi; Yamamoto, Naoki
2016-01-01
Dengue virus (DENV) is one of the most important arthropod-borne pathogens that cause life-threatening diseases in humans. However, no vaccine or specific antiviral is available for dengue. As seen in other RNA viruses, the innate immune system plays a key role in controlling DENV infection and disease outcome. Although the interferon (IFN) response, which is central to host protective immunity, has been reported to limit DENV replication, the molecular details of how DENV infection is modulated by IFN treatment are elusive. In this study, by employing a gain-of-function screen using a type I IFN-treated cell-derived cDNA library, we identified a previously uncharacterized gene, C19orf66, as an IFN-stimulated gene (ISG) that inhibits DENV replication, which we named Repressor of yield of DENV (RyDEN). Overexpression and gene knockdown experiments revealed that expression of RyDEN confers resistance to all serotypes of DENV in human cells. RyDEN expression also limited the replication of hepatitis C virus, Kunjin virus, Chikungunya virus, herpes simplex virus type 1, and human adenovirus. Importantly, RyDEN was considered to be a crucial effector molecule in the IFN-mediated anti-DENV response. When affinity purification-mass spectrometry analysis was performed, RyDEN was revealed to form a complex with cellular mRNA-binding proteins, poly(A)-binding protein cytoplasmic 1 (PABPC1), and La motif-related protein 1 (LARP1). Interestingly, PABPC1 and LARP1 were found to be positive modulators of DENV replication. Since RyDEN influenced intracellular events on DENV replication and, suppression of protein synthesis from DENV-based reporter construct RNA was also observed in RyDEN-expressing cells, our data suggest that RyDEN is likely to interfere with the translation of DENV via interaction with viral RNA and cellular mRNA-binding proteins, resulting in the inhibition of virus replication in infected cells. PMID:26735137
A NOTE ON THE STOCHASTIC ROOTS OF STOCHASTIC MATRICES
Qi-Ming HE; Eldon GUNN
2003-01-01
In this paper, we study the stochastic root matrices of stochastic matrices. All stochastic roots of 2×2 stochastic matrices are found explicitly. A method based on characteristic polynomial of matrix is developed to find all real root matrices that are functions of the original 3×3 matrix, including all possible (function) stochastic root matrices. In addition, we comment on some numerical methods for computing stochastic root matrices of stochastic matrices.
Stochastic Lie group integrators
Malham, Simon J A
2007-01-01
We present Lie group integrators for nonlinear stochastic differential equations with non-commutative vector fields whose solution evolves on a smooth finite dimensional manifold. Given a Lie group action that generates transport along the manifold, we pull back the stochastic flow on the manifold to the Lie group via the action, and subsequently pull back the flow to the corresponding Lie algebra via the exponential map. We construct an approximation to the stochastic flow in the Lie algebra via closed operations and then push back to the Lie group and then to the manifold, thus ensuring our approximation lies in the manifold. We call such schemes stochastic Munthe-Kaas methods after their deterministic counterparts. We also present stochastic Lie group integration schemes based on Castell--Gaines methods. These involve using an underlying ordinary differential integrator to approximate the flow generated by a truncated stochastic exponential Lie series. They become stochastic Lie group integrator schemes if...
Miyazawa, Kohtaro; Kanaya, Takashi; Tanaka, Sachi; Takakura, Ikuro; Watanabe, Kouichi; Ohwada, Shyuichi; Kitazawa, Haruki; Rose, Michael T; Sakaguchi, Suehiro; Katamine, Shigeru; Yamaguchi, Takahiro; Aso, Hisashi
2007-03-01
The gastrointestinal tract is thought to be the main site of entry for the pathological isoform of the prion protein (PrP(Sc)). Prion diseases are believed to result from a conformational change of the cellular prion protein (PrP(c)) to PrP(Sc). Therefore, PrP(c) expression is a prerequisite for the infection and spread of the disease to the central nervous system. However, the distribution of PrP(c) in the gut is still a matter of controversy. We therefore investigated the localization of PrP(c) in the bovine and murine small intestine. In cattle, most PrP(c) positive epithelial cells were detected in the duodenum, while a few positive cells were found in the jejunum. PrP(c) was expressed in serotonin producing cells. In bovine Peyer's patches, PrP(c) was distributed in extrafollicular areas, but not in the germinal centre of the jejunum and ileum. PrP(c) was expressed in myeloid lineage cells such as myeloid dendritic cells and macrophages. In mice, PrP(c) was expressed in some epithelial cells throughout the small intestine as well as in cells such as follicular dendritic cell in the germinal centre of Peyer's patches. In this study, we demonstrate that there are a number of differences in the localization of PrP(c) between the murine and bovine small intestines. PMID:17165097
Full text: Photodynamic therapy (PDT) can result in apoptosis and/or necrosis. Several steps in the apoptotic program depend on ATP and the intracellular ATP level is one determinant in the decision between apoptosis and necrosis. Therefore, photochemical damage of cellular targets involved in energy supply might play a crucial role for the mode of cell death being executed. The present study aimed at the characterization of changes in cellular energy supply and the associated cell death modes in response to PDT. Using the human epidermoid carcinoma cell line A431 and aluminum (III) phthalocyanine tetrasulfonate (2.5 μM) as a photosensitizer, we studied the changes in mitochondrial function and intracellular ATP-level after irradiation with different light doses. Employing assays for caspase-3 activation and nuclear fragmentation, 50 % of the cells were found to undergo apoptosis after irradiation with light doses between 2.5 to 3.5 J.cm-2. At light doses above 6 J.cm-2 cells died exclusively by necrosis, indicated by rapid and complete loss of ATP and mitochondrial function and an absence of caspase activation and nuclear fragmentation. With apoptotic cell populations the ATP-level was maintained at near control levels for up to eight hours which was far beyond the onset of morphological changes. These data suggest that necrosis as well as apoptosis can be induced with AIPcS4 mediated PDT and that photo damage in energy supplying cellular targets may influence the mode of cell death. Further, it is speculated that cells undergoing apoptosis after PDT maintain high ATP levels long enough to complete the apoptotic program. (author)
Gal-Mor, Ohad; Suez, Jotham; Elhadad, Dana; Porwollik, Steffen; Leshem, Eyal; Valinsky, Lea; McClelland, Michael; Schwartz, Eliezer; Rahav, Galia
2012-01-01
Enteric fever is an invasive life-threatening systemic disease caused by the Salmonella enterica human-adapted serovars Typhi and Paratyphi. Increasing incidence of infections with Salmonella enterica serovar Paratyphi A and the spreading of its antibiotic-resistant derivates pose a significant health concern in some areas of the world. Herein, we describe a molecular and phenotypic characterization of an S. Paratyphi A strain accounted for a recent paratyphoid outbreak in Nepal that affected...
Saleh Heneidi; Simerman, Ariel A; Erica Keller; Prapti Singh; Xinmin Li; Daniel A Dumesic; Gregorio Chazenbalk
2013-01-01
Advances in stem cell therapy face major clinical limitations, particularly challenged by low rates of post-transplant cell survival. Hostile host factors of the engraftment microenvironment such as hypoxia, nutrition deprivation, pro-inflammatory cytokines, and reactive oxygen species can each contribute to unwanted differentiation or apoptosis. In this report, we describe the isolation and characterization of a new population of adipose tissue (AT) derived pluripotent stem cells, termed Mul...
Ramsey Stochastic Model via Multistage Stochastic Programming
Kaňková, Vlasta
Vol. Part II. České Budějovice: University of South Bohemia in České Budějovice, Faculty of Economy , 2010 - (Houda, M.; Friebelová, J.), s. 328-333 ISBN 978-80-7394-218-2. [28th International Conference on Mathematical Methods in Economics 2010. České Budějovice (CZ), 08.09.2010-10.09.2010] R&D Projects: GA ČR GAP402/10/0956; GA ČR(CZ) GA402/08/0107; GA ČR GAP402/10/1610 Institutional research plan: CEZ:AV0Z10750506 Keywords : Ramsey stochastic model * Multistage stochastic programming * Confidence intervals * Autoregressive sequences * Stability * Empirical estimates Subject RIV: AH - Economics http://library.utia.cas.cz/separaty/2010/E/kankova-ramsey stochastic model via multistage stochastic programming.pdf
Modeling stochasticity in biochemical reaction networks
Constantino, P. H.; Vlysidis, M.; Smadbeck, P.; Kaznessis, Y. N.
2016-03-01
Small biomolecular systems are inherently stochastic. Indeed, fluctuations of molecular species are substantial in living organisms and may result in significant variation in cellular phenotypes. The chemical master equation (CME) is the most detailed mathematical model that can describe stochastic behaviors. However, because of its complexity the CME has been solved for only few, very small reaction networks. As a result, the contribution of CME-based approaches to biology has been very limited. In this review we discuss the approach of solving CME by a set of differential equations of probability moments, called moment equations. We present different approaches to produce and to solve these equations, emphasizing the use of factorial moments and the zero information entropy closure scheme. We also provide information on the stability analysis of stochastic systems. Finally, we speculate on the utility of CME-based modeling formalisms, especially in the context of synthetic biology efforts.
For a detailed study of the plasma structure and the transport characteristics of a stochastized plasma edge at the tokamak TEXTOR the dynamic ergodic divertor (DED) was constructed, by which differently shaped external disturbing fields are statically and dynamically generated. Aim of this thgesis is to study experimentally the radial and poloidal structure of the plasma edge stochastized by the DED disturbing field and to analyze its transport characteristics. For this spatially highly resolved radial profiles of the electron density and temperature were measured by means of radiation-emission spectroscopy on thermal helium at the high- and low-field side of TEXTOR. These experimental results yield a good stating base for the validation and further development of three-dimensional transport codes
Stochastic dynamical models for ecological regime shifts
Møller, Jan Kloppenborg; Carstensen, Jacob; Madsen, Henrik; Andersen, Tom
Ecosystems are influenced by a variety of known and unknown drivers. Unknown drivers should be modeled as noise and it is therefore important to analyze how noise influences the deterministic skeleton of system equations. The deterministic skeleton of stochastic dynamical models contains the...... physical and biological knowledge of the system, and nonlinearities introduced here can generate regime shifts or enhance the probability of regime shifts in the case of stochastic models, typically characterized by a threshold value for the known driver. A simple model for light competition between...... phytoplankton and benthic vegetation with feedback mechanisms is formulated, and it is demonstrated that bistability can occur for specific parameter settings. When stochastic input and stochastic propagation of the states are applied on the system regime shifts occur more frequently, and the threshold...
Verhoosel, C.V.; Gutiérrez, M. A.; Hulshoff, S.J.
2006-01-01
The field of fluid-structure interaction is combined with the field of stochastics to perform a stochastic flutter analysis. Various methods to directly incorporate the effects of uncertainties in the flutter analysis are investigated. The panel problem with a supersonic fluid flowing over it is considered as a testcase. The stochastic moments (mean, standard deviation, etc.) of the flutter point are computed by an uncertainty analysis. Sensitivity-based methods are used to determine the stoc...
Bagnoli, Franco
1998-01-01
An introduction to cellular automata (both deterministic and probabilistic) with examples. Definition of deterministic automata, dynamical properties, damage spreading and Lyapunov exponents; probabilistic automata and Markov processes, nonequilibrium phase transitions, directed percolation, diffusion; simulation techniques, mean field. Investigation themes: life, epidemics, forest fires, percolation, modeling of ecosystems and speciation. They represent my notes for the school "Dynamical Mod...
Stochastic quantization in general relativity
The stochastic quantization method of Parisi and Wu is briefly reviewed stressing its formal resemblance to the Einstein-Smoluchowski theory of Brownian motion. In order to make it applicable in the context of General Relativity, we present a generalization of the method to the case of Lorentzian signature of the space-time metric. It is shown that this approach has non-trivial implications even for linear quantum fields in curved space-time, where it introduces preferred quantum states characterized by the analyticity of the Feynman propagator in the mass parameter. Finally we propose a stochastic quantization scheme for the full nonlinear Einstein theory of gravitation. It employs the concept of a metric in field configuration space and is based mathematically on Ito's calculus. Non-trivial implications for the gravitational path integral measure and for perturbation theory are pointed out. (Author)
Giuseppe Crescenzo
2010-01-01
Full Text Available Gilthead sea bream (Sparus aurata L. is one of the most intensively farmed fish spe- cies in the Mediterranean, greatly studied for the relevant economic value, although its sensitivity to Aflatoxin B1 (AFB1 has to be investigated, yet. The aim of this study was to perform an in vitro evalua- tion of cytotoxic potential of AFB1 on S. aurata hepatocytes in order to grade the range of AFB1 toxicity, and the boundary between acute and long-term toxicity. Primary monolayer cultures of hepatocytes from S. aurata juveniles were treated with a wide range of concentrations from 5x103 ng/ml to 2x10 2x10-5 ng/ml of AFB1 for a different period of exposure (24, 48, 72 hours. The cytotoxic activity was characterized by MTT reduction assay. After each exposition hepatocytes were examined for morphologic alterations and apoptosis induction. AFB1 exposure significantly reduced cell viability in a dose- and time-depend- ent manner. Dose-response curves obtained after 24, 48 and 72 hrs revealed that prolonged exposure times lead to a significant increase of the toxicpotencyofAFB toxic potency of AFB AFB1. Ourresultsdemonstratethat Our results demonstrate that S. aurata hepatocytes are highly sensitive to AFB1 exposure. Such scientific findings could provide new insights to investigate the real impact of aflatoxin on marine farmed fish.
Fluctuations as stochastic deformation
Kazinski, P. O.
2008-04-01
A notion of stochastic deformation is introduced and the corresponding algebraic deformation procedure is developed. This procedure is analogous to the deformation of an algebra of observables like deformation quantization, but for an imaginary deformation parameter (the Planck constant). This method is demonstrated on diverse relativistic and nonrelativistic models with finite and infinite degrees of freedom. It is shown that under stochastic deformation the model of a nonrelativistic particle interacting with the electromagnetic field on a curved background passes into the stochastic model described by the Fokker-Planck equation with the diffusion tensor being the inverse metric tensor. The first stochastic correction to the Newton equations for this system is found. The Klein-Kramers equation is also derived as the stochastic deformation of a certain classical model. Relativistic generalizations of the Fokker-Planck and Klein-Kramers equations are obtained by applying the procedure of stochastic deformation to appropriate relativistic classical models. The analog of the Fokker-Planck equation associated with the stochastic Lorentz-Dirac equation is derived too. The stochastic deformation of the models of a free scalar field and an electromagnetic field is investigated. It turns out that in the latter case the obtained stochastic model describes a fluctuating electromagnetic field in a transparent medium.
Phase transitions in a cellular automaton model of a highway on-ramp
Belitsky, Vladimir; Maric, Nevena; Schütz, Gunter M.
2007-09-01
We introduce a lattice gas model for the merging of two single-lane automobile highways. The merging rules for traffic on the two lanes are deterministic, but the inflow on both lanes is stochastic. Analysing the stationary distribution of this stochastic cellular automaton, we find a discontinuous phase transition from a free-flow phase which depends on the initial state of the road to a jammed phase where all memory of the initial state is lost. Inside the jammed phase we identify dynamical phase transitions in the approach to stationarity. Each dynamical phase is characterized by a fixed number of relaxation cycles which is decreasing as one moves deeper into the jammed phase. In each cycle step, the number of 'desperate' drivers who force their way onto the main road when they reach the end of the on-ramp increases until stationarity.
Phase transitions in a cellular automaton model of a highway on-ramp
We introduce a lattice gas model for the merging of two single-lane automobile highways. The merging rules for traffic on the two lanes are deterministic, but the inflow on both lanes is stochastic. Analysing the stationary distribution of this stochastic cellular automaton, we find a discontinuous phase transition from a free-flow phase which depends on the initial state of the road to a jammed phase where all memory of the initial state is lost. Inside the jammed phase we identify dynamical phase transitions in the approach to stationarity. Each dynamical phase is characterized by a fixed number of relaxation cycles which is decreasing as one moves deeper into the jammed phase. In each cycle step, the number of 'desperate' drivers who force their way onto the main road when they reach the end of the on-ramp increases until stationarity
Quantifying synergistic information using intermediate stochastic variables
Quax, Rick; Har-Shemesh, Omri; Sloot, Peter M. A.
2016-01-01
Quantifying synergy among stochastic variables is an important open problem in information theory. Information synergy occurs when multiple sources together predict an outcome variable better than the sum of single-source predictions. It is an essential phenomenon in biology such as in neuronal networks and cellular regulatory processes, where different information flows integrate to produce a single response, but also in social cooperation processes as well as in statistical inference tasks ...
Mark Sokolowski
Full Text Available Long INterspersed Element-1 (LINE-1, L1 is an active retrotransposon that mobilizes using a ribonucleoprotein particle (RNP intermediate composed of the full-length bicistronic L1 mRNA and the two proteins (ORF1p and ORF2p encoded by that mRNA. ORF1p and ORF2p demonstrate cis-preference for their encoding mRNA. Previous studies of ORF1p, purified from bacterial and insect cells demonstrated that this protein forms trimers in vitro. While valuable for understanding ORF1p function, these in vitro approaches do not provide any information on ORF1p self-interaction in the context of mammalian cells. We used a mammalian two-hybrid (M2H system in order to study L1 ORF1p self-interaction in human and mouse cells. We demonstrate that the M2H system successfully detects human and mouse ORF1p self-interactions in transiently transfected mammalian cells. We also generated mouse and human ORF1p-specific antibodies to characterize the expression of ORF1p fusion proteins used in the M2H system. Using these antibodies, we demonstrate that ORF1p interaction in trans leads to the formation of heterodimers that are expected to produce a positive signal in the M2H system. Although the role for L1 ORF1p cis-preference in L1 mobilization is established, the impact of ability of ORF1pto interact in trans on the L1 replication cycle is not known. Furthermore, western blot analysis of ORF1p generated by a full-length L1, wild type ORF1, or a codon-optimized ORF1 expression vector is detected in the nucleus. In contrast, the addition of a tag to the N-terminus of the mouse and human ORF1 proteins can significantly alter the subcellular localization in a tag-specific manner. These data support that nuclear localization of ORF1p may contribute to L1 (and potentially the SINE Alu RNP nuclear access in the host cell.
StochPy: a comprehensive, user-friendly tool for simulating stochastic biological processes.
Timo R Maarleveld
Full Text Available Single-cell and single-molecule measurements indicate the importance of stochastic phenomena in cell biology. Stochasticity creates spontaneous differences in the copy numbers of key macromolecules and the timing of reaction events between genetically-identical cells. Mathematical models are indispensable for the study of phenotypic stochasticity in cellular decision-making and cell survival. There is a demand for versatile, stochastic modeling environments with extensive, preprogrammed statistics functions and plotting capabilities that hide the mathematics from the novice users and offers low-level programming access to the experienced user. Here we present StochPy (Stochastic modeling in Python, which is a flexible software tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions of molecule copy numbers and event waiting times, analyses of stochastic time series, and a range of additional statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with stochastic models of gene expression, cell division, and single-molecule enzyme kinetics. StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy is a comprehensive software package for stochastic simulation of the molecular control networks of living cells. It allows novice and experienced users to study stochastic phenomena in cell biology. The integration with other Python software makes StochPy both a user-friendly and easily extendible simulation tool.
Stochastic simulations of a synthetic bacteria-yeast ecosystem
Biliouris Konstantinos
2012-06-01
Full Text Available Abstract Background The field of synthetic biology has greatly evolved and numerous functions can now be implemented by artificially engineered cells carrying the appropriate genetic information. However, in order for the cells to robustly perform complex or multiple tasks, co-operation between them may be necessary. Therefore, various synthetic biological systems whose functionality requires cell-cell communication are being designed. These systems, microbial consortia, are composed of engineered cells and exhibit a wide range of behaviors. These include yeast cells whose growth is dependent on one another, or bacteria that kill or rescue each other, synchronize, behave as predator-prey ecosystems or invade cancer cells. Results In this paper, we study a synthetic ecosystem comprising of bacteria and yeast that communicate with and benefit from each other using small diffusible molecules. We explore the behavior of this heterogeneous microbial consortium, composed of Saccharomyces cerevisiae and Escherichia coli cells, using stochastic modeling. The stochastic model captures the relevant intra-cellular and inter-cellular interactions taking place in and between the eukaryotic and prokaryotic cells. Integration of well-characterized molecular regulatory elements into these two microbes allows for communication through quorum sensing. A gene controlling growth in yeast is induced by bacteria via chemical signals and vice versa. Interesting dynamics that are common in natural ecosystems, such as obligatory and facultative mutualism, extinction, commensalism and predator-prey like dynamics are observed. We investigate and report on the conditions under which the two species can successfully communicate and rescue each other. Conclusions This study explores the various behaviors exhibited by the cohabitation of engineered yeast and bacterial cells. The way that the model is built allows for studying the dynamics of any system consisting of two
A Stochastic Employment Problem
Wu, Teng
2013-01-01
The Stochastic Employment Problem(SEP) is a variation of the Stochastic Assignment Problem which analyzes the scenario that one assigns balls into boxes. Balls arrive sequentially with each one having a binary vector X = (X[subscript 1], X[subscript 2],...,X[subscript n]) attached, with the interpretation being that if X[subscript i] = 1 the ball…
Stochastic Convection Parameterizations
Teixeira, Joao; Reynolds, Carolyn; Suselj, Kay; Matheou, Georgios
2012-01-01
computational fluid dynamics, radiation, clouds, turbulence, convection, gravity waves, surface interaction, radiation interaction, cloud and aerosol microphysics, complexity (vegetation, biogeochemistry, radiation versus turbulence/convection stochastic approach, non-linearities, Monte Carlo, high resolutions, large-Eddy Simulations, cloud structure, plumes, saturation in tropics, forecasting, parameterizations, stochastic, radiation-clod interaction, hurricane forecasts
Ole Peters; Alexander Adamou
2011-01-01
It is argued that the simple trading strategy of leveraging or deleveraging an investment in the market portfolio cannot outperform the market. Such stochastic market efficiency places strong constraints on the possible stochastic properties of the market. Historical data confirm the hypothesis.
Stochastic and non-stochastic radiation effects
Both the carcinogenic and the mutagenic effects of ionizing radiation are thought to be induced by 'stochastic' mechanisms of action. It is generally accepted that the number of carcinogenic injury is proportional to the radiation dose applied, and that there is no direct relationship between radiation dose and severity of induced injury, so that no threshold dose can be defined. However, the severity of mutagenic effects, resulting for example from cell death or leading to functional disorders or malformations, has been observed to be a function of the radiation dose, so that in principle threshold doses can be defined. These latter effects are called non-stochastic radiation effects. (orig./DG)
Greenwood, Priscilla E
2016-01-01
This book describes a large number of open problems in the theory of stochastic neural systems, with the aim of enticing probabilists to work on them. This includes problems arising from stochastic models of individual neurons as well as those arising from stochastic models of the activities of small and large networks of interconnected neurons. The necessary neuroscience background to these problems is outlined within the text, so readers can grasp the context in which they arise. This book will be useful for graduate students and instructors providing material and references for applying probability to stochastic neuron modeling. Methods and results are presented, but the emphasis is on questions where additional stochastic analysis may contribute neuroscience insight. An extensive bibliography is included. Dr. Priscilla E. Greenwood is a Professor Emerita in the Department of Mathematics at the University of British Columbia. Dr. Lawrence M. Ward is a Professor in the Department of Psychology and the Brain...
Stochastic quantization and gravity
We give a preliminary account of the application of stochastic quantization to the gravitational field. We start in Section I from Nelson's formulation of quantum mechanics as Newtonian stochastic mechanics and only then introduce the Parisi-Wu stochastic quantization scheme on which all the later discussion will be based. In Section II we present a generalization of the scheme that is applicable to fields in physical (i.e. Lorentzian) space-time and treat the free linearized gravitational field in this manner. The most remarkable result of this is the noncausal propagation of conformal gravitons. Moreover the concept of stochastic gauge-fixing is introduced and a complete discussion of all the covariant gauges is given. A special symmetry relating two classes of covariant gauges is exhibited. Finally Section III contains some preliminary remarks on full nonlinear gravity. In particular we argue that in contrast to gauge fields the stochastic gravitational field cannot be transformed to a Gaussian process. (Author)
Stochastic volatility selected readings
Shephard, Neil
2005-01-01
Neil Shephard has brought together a set of classic and central papers that have contributed to our understanding of financial volatility. They cover stocks, bonds and currencies and range from 1973 up to 2001. Shephard, a leading researcher in the field, provides a substantial introduction in which he discusses all major issues involved. General Introduction N. Shephard. Part I: Model Building. 1. A Subordinated Stochastic Process Model with Finite Variance for Speculative Prices, (P. K. Clark). 2. Financial Returns Modelled by the Product of Two Stochastic Processes: A Study of Daily Sugar Prices, 1961-7, S. J. Taylor. 3. The Behavior of Random Variables with Nonstationary Variance and the Distribution of Security Prices, B. Rosenberg. 4. The Pricing of Options on Assets with Stochastic Volatilities, J. Hull and A. White. 5. The Dynamics of Exchange Rate Volatility: A Multivariate Latent Factor ARCH Model, F. X. Diebold and M. Nerlove. 6. Multivariate Stochastic Variance Models. 7. Stochastic Autoregressive...
Stochastic resonance during a polymer translocation process
Mondal, Debasish; Muthukumar, M.
2016-04-01
We have studied the occurrence of stochastic resonance when a flexible polymer chain undergoes a single-file translocation through a nano-pore separating two spherical cavities, under a time-periodic external driving force. The translocation of the chain is controlled by a free energy barrier determined by chain length, pore length, pore-polymer interaction, and confinement inside the donor and receiver cavities. The external driving force is characterized by a frequency and amplitude. By combining the Fokker-Planck formalism for polymer translocation and a two-state model for stochastic resonance, we have derived analytical formulas for criteria for emergence of stochastic resonance during polymer translocation. We show that no stochastic resonance is possible if the free energy barrier for polymer translocation is purely entropic in nature. The polymer chain exhibits stochastic resonance only in the presence of an energy threshold in terms of polymer-pore interactions. Once stochastic resonance is feasible, the chain entropy controls the optimal synchronization conditions significantly.
Stochastic resonance during a polymer translocation process.
Mondal, Debasish; Muthukumar, M
2016-04-14
We have studied the occurrence of stochastic resonance when a flexible polymer chain undergoes a single-file translocation through a nano-pore separating two spherical cavities, under a time-periodic external driving force. The translocation of the chain is controlled by a free energy barrier determined by chain length, pore length, pore-polymer interaction, and confinement inside the donor and receiver cavities. The external driving force is characterized by a frequency and amplitude. By combining the Fokker-Planck formalism for polymer translocation and a two-state model for stochastic resonance, we have derived analytical formulas for criteria for emergence of stochastic resonance during polymer translocation. We show that no stochastic resonance is possible if the free energy barrier for polymer translocation is purely entropic in nature. The polymer chain exhibits stochastic resonance only in the presence of an energy threshold in terms of polymer-pore interactions. Once stochastic resonance is feasible, the chain entropy controls the optimal synchronization conditions significantly. PMID:27083746
Turbulence, Spontaneous Stochasticity and Climate
Eyink, Gregory
Turbulence is well-recognized as important in the physics of climate. Turbulent mixing plays a crucial role in the global ocean circulation. Turbulence also provides a natural source of variability, which bedevils our ability to predict climate. I shall review here a recently discovered turbulence phenomenon, called ``spontaneous stochasticity'', which makes classical dynamical systems as intrinsically random as quantum mechanics. Turbulent dissipation and mixing of scalars (passive or active) is now understood to require Lagrangian spontaneous stochasticity, which can be expressed by an exact ``fluctuation-dissipation relation'' for scalar turbulence (joint work with Theo Drivas). Path-integral methods such as developed for quantum mechanics become necessary to the description. There can also be Eulerian spontaneous stochasticity of the flow fields themselves, which is intimately related to the work of Kraichnan and Leith on unpredictability of turbulent flows. This leads to problems similar to those encountered in quantum field theory. To quantify uncertainty in forecasts (or hindcasts), we can borrow from quantum field-theory the concept of ``effective actions'', which characterize climate averages by a variational principle and variances by functional derivatives. I discuss some work with Tom Haine (JHU) and Santha Akella (NASA-Goddard) to make this a practical predictive tool. More ambitious application of the effective action is possible using Rayleigh-Ritz schemes.
Threshold-Range Scaling of Excitable Cellular Automata
Fisch, R; Griffeath, D; Fisch, Robert; Gravner, Janko; Griffeath, David
1993-01-01
Each cell of a two-dimensional lattice is painted one of k colors, arranged in a "color wheel." The colors advance (0 to k-1 mod k) either automatically or by contact with at least a threshold number of successor colors in a prescribed local neighborhood. Discrete-time parallel systems of this sort in which color 0 updates by contact and the rest update automatically are called Greenberg-Hastings (GH) rules. A system in which all colors update by contact is called a cyclic cellular automaton (CCA). Started from appropriate initial conditions these models generate periodic traveling waves. Started from random configurations the same rules exhibit complex self-organization, typically characterized by nucleation of locally periodic "ram's horns" or spirals. Corresponding random processes give rise to a variety of "forest fire" equilibria that display large-scale stochastic wave fronts. This article describes a framework, theoretically based, but relying on extensive interactive computer graphics experimentation,...
Praet, Jelle; Santermans, Eva; Reekmans, Kristien; de Vocht, Nathalie; Le Blon, Debbie; Hoornaert, Chloé; Daans, Jasmijn; Goossens, Herman; Berneman, Zwi; Hens, Niel; Van der Linden, Annemie; Ponsaerts, Peter
2014-01-01
Preclinical animal studies involving intracerebral (stem) cell grafting are gaining popularity in many laboratories due to the reported beneficial effects of cell grafting on various diseases or traumata of the central nervous system (CNS). In this chapter, we describe a histological workflow to characterize and quantify cellular events following neural and fibroblast(-like) stem cell grafting in healthy and demyelinated CNS tissue. First, we provide standardized protocols to isolate and culture eGFP(+) neural and fibroblast(-like) stem cells from embryonic mouse tissue. Second, we describe flow cytometric procedures to determine cell viability, eGFP transgene expression, and the expression of different stem cell lineage markers. Third, we explain how to induce reproducible demyelination in the CNS of mice by means of cuprizone administration, a validated mouse model for human multiple sclerosis. Fourth, the technical procedures for cell grafting in the CNS are explained in detail. Finally, an optimized and validated workflow for the quantitative histological analysis of cell graft survival and endogenous astroglial and microglial responses is provided. PMID:25173390
Stefani N. Thomas
2013-08-01
Full Text Available Radiation and drug resistance are significant challenges in the treatment of locally advanced, recurrent and metastatic breast cancer that contribute to mortality. Clinically, radiotherapy requires oxygen to generate cytotoxic free radicals that cause DNA damage and allow that damage to become fixed in the genome rather than repaired. However, approximately 40% of all breast cancers have hypoxic tumor microenvironments that render cancer cells significantly more resistant to irradiation. Hypoxic stimuli trigger changes in the cell death/survival pathway that lead to increased cellular radiation resistance. As a result, the development of noninvasive strategies to assess tumor hypoxia in breast cancer has recently received considerable attention. Exosomes are secreted nanovesicles that have roles in paracrine signaling during breast tumor progression, including tumor-stromal interactions, activation of proliferative pathways and immunosuppression. The recent development of protocols to isolate and purify exosomes, as well as advances in mass spectrometry-based proteomics have facilitated the comprehensive analysis of exosome content and function. Using these tools, studies have demonstrated that the proteome profiles of tumor-derived exosomes are indicative of the oxygenation status of patient tumors. They have also demonstrated that exosome signaling pathways are potentially targetable drivers of hypoxia-dependent intercellular signaling during tumorigenesis. This article provides an overview of how proteomic tools can be effectively used to characterize exosomes and elucidate fundamental signaling pathways and survival mechanisms underlying hypoxia-mediated radiation resistance in breast cancer.
Charalambous, Charalambos D.; N. U. Ahmed
2013-01-01
We consider a team game reward, and we derive a stochastic Pontryagin's maximum principle for distributed stochastic differential systems with decentralized noisy information structures. Our methodology utilizes the semi martingale representation theorem, variational methods, and backward stochastic differential equations. Furthermore, we derive necessary and sufficient optimality conditions that characterize team and person-by-person optimality of decentralized strategies. Finally, we apply ...
Stochastic dynamics of macromolecular-assembly networks.
Saiz, Leonor; Vilar, Jose
2006-03-01
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components [1]. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage λ induction switches, which rely on the formation of DNA loops by proteins [2] and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes. [1] L. Saiz and J.M.G. Vilar, submitted (2005). [2] J.M.G. Vilar and L. Saiz, Current Opinion in Genetics & Development, 15, 136-144 (2005).
Stochastic Processes in Electrochemistry.
Singh, Pradyumna S; Lemay, Serge G
2016-05-17
Stochastic behavior becomes an increasingly dominant characteristic of electrochemical systems as we probe them on the smallest scales. Advances in the tools and techniques of nanoelectrochemistry dictate that stochastic phenomena will become more widely manifest in the future. In this Perspective, we outline the conceptual tools that are required to analyze and understand this behavior. We draw on examples from several specific electrochemical systems where important information is encoded in, and can be derived from, apparently random signals. This Perspective attempts to serve as an accessible introduction to understanding stochastic phenomena in electrochemical systems and outlines why they cannot be understood with conventional macroscopic descriptions. PMID:27120701
Stochastic Schroedinger equations
A derivation of Belavkin's stochastic Schroedinger equations is given using quantum filtering theory. We study an open system in contact with its environment, the electromagnetic field. Continuous observation of the field yields information on the system: it is possible to keep track in real time of the best estimate of the system's quantum state given the observations made. This estimate satisfies a stochastic Schroedinger equation, which can be derived from the quantum stochastic differential equation for the interaction picture evolution of system and field together. Throughout the paper we focus on the basic example of resonance fluorescence
Sequential stochastic optimization
Cairoli, Renzo
1996-01-01
Sequential Stochastic Optimization provides mathematicians and applied researchers with a well-developed framework in which stochastic optimization problems can be formulated and solved. Offering much material that is either new or has never before appeared in book form, it lucidly presents a unified theory of optimal stopping and optimal sequential control of stochastic processes. This book has been carefully organized so that little prior knowledge of the subject is assumed; its only prerequisites are a standard graduate course in probability theory and some familiarity with discrete-paramet
Parametric resonance and particle stochastic interactions with a periodic medium
Pinheiro, Mario J
2015-01-01
A non-markovian stochastic model shows the emergence of structures in the medium, a self-organization characterized by a relationship between particle's energy, driven frequency $\\omega$ and a frequency of interaction with the medium $\
Stochastic Physicochemical Dynamics
Tsekov, Roumen
2001-01-01
The monograph considers thermodynamic relaxation in quantum systems, stochastic dynamics of gas molecules, fluctuation stability of thin liquid films, resonant diffusion in modulated solid structures and catalytic kinetics of chemical dissociation.
Stochastic calculus with infinitesimals
Herzberg, Frederik
2013-01-01
Stochastic analysis is not only a thriving area of pure mathematics with intriguing connections to partial differential equations and differential geometry. It also has numerous applications in the natural and social sciences (for instance in financial mathematics or theoretical quantum mechanics) and therefore appears in physics and economics curricula as well. However, existing approaches to stochastic analysis either presuppose various concepts from measure theory and functional analysis or lack full mathematical rigour. This short book proposes to solve the dilemma: By adopting E. Nelson's "radically elementary" theory of continuous-time stochastic processes, it is based on a demonstrably consistent use of infinitesimals and thus permits a radically simplified, yet perfectly rigorous approach to stochastic calculus and its fascinating applications, some of which (notably the Black-Scholes theory of option pricing and the Feynman path integral) are also discussed in the book.
Stochastic processes inference theory
Rao, Malempati M
2014-01-01
This is the revised and enlarged 2nd edition of the authors’ original text, which was intended to be a modest complement to Grenander's fundamental memoir on stochastic processes and related inference theory. The present volume gives a substantial account of regression analysis, both for stochastic processes and measures, and includes recent material on Ridge regression with some unexpected applications, for example in econometrics. The first three chapters can be used for a quarter or semester graduate course on inference on stochastic processes. The remaining chapters provide more advanced material on stochastic analysis suitable for graduate seminars and discussions, leading to dissertation or research work. In general, the book will be of interest to researchers in probability theory, mathematical statistics and electrical and information theory.
Dynamics of Double Stochastic Operators
Saburov, Mansoor
2016-03-01
A double stochastic operator is a generalization of a double stochastic matrix. In this paper, we study the dynamics of double stochastic operators. We give a criterion for a regularity of a double stochastic operator in terms of absences of its periodic points. We provide some examples to insure that, in general, a trajectory of a double stochastic operator may converge to any interior point of the simplex.
Stochastic differential equations and applications
Friedman, Avner
2006-01-01
This text develops the theory of systems of stochastic differential equations, and it presents applications in probability, partial differential equations, and stochastic control problems. Originally published in two volumes, it combines a book of basic theory and selected topics with a book of applications.The first part explores Markov processes and Brownian motion; the stochastic integral and stochastic differential equations; elliptic and parabolic partial differential equations and their relations to stochastic differential equations; the Cameron-Martin-Girsanov theorem; and asymptotic es
Stochastic Resonance in Protein Folding Dynamics.
Davtyan, Aram; Platkov, Max; Gruebele, Martin; Papoian, Garegin A
2016-05-01
Although protein folding reactions are usually studied under static external conditions, it is likely that proteins fold in a locally fluctuating cellular environment in vivo. To mimic such behavior in in vitro experiments, the local temperature of the solvent can be modulated either harmonically or using correlated noise. In this study, coarse-grained molecular simulations are used to investigate these possibilities, and it is found that both periodic and correlated random fluctuations of the environment can indeed accelerate folding kinetics if the characteristic frequencies of the applied fluctuations are commensurate with the internal timescale of the folding reaction; this is consistent with the phenomenon of stochastic resonance observed in many other condensed-matter processes. To test this theoretical prediction, the folding dynamics of phosphoglycerate kinase under harmonic temperature fluctuations are experimentally probed using Förster resonance energy transfer fluorescence measurements. To analyze these experiments, a combination of theoretical approaches is developed, including stochastic simulations of folding kinetics and an analytical mean-field kinetic theory. The experimental observations are consistent with the theoretical predictions of stochastic resonance in phosphoglycerate kinase folding. When combined with an alternative experiment on the protein VlsE using a power spectrum analysis, elaborated in Dave et al., ChemPhysChem 2016, 10.1002/cphc.201501041, the overall data overwhelmingly point to the experimental confirmation of stochastic resonance in protein folding dynamics. PMID:26992148
On orthogonality preserving quadratic stochastic operators
Mukhamedov, Farrukh; Taha, Muhammad Hafizuddin Mohd [Department of Computational and Theoretical Sciences, Faculty of Science International Islamic University Malaysia, P.O. Box 141, 25710 Kuantan, Pahang Malaysia (Malaysia)
2015-05-15
A quadratic stochastic operator (in short QSO) is usually used to present the time evolution of differing species in biology. Some quadratic stochastic operators have been studied by Lotka and Volterra. In the present paper, we first give a simple characterization of Volterra QSO in terms of absolutely continuity of discrete measures. Further, we introduce a notion of orthogonal preserving QSO, and describe such kind of operators defined on two dimensional simplex. It turns out that orthogonal preserving QSOs are permutations of Volterra QSO. The associativity of genetic algebras generated by orthogonal preserving QSO is studied too.
Stochastic processes in muon ionization cooling
Errede, D.; Makino, K.; Berz, M.; Johnstone, C. J.; Van Ginneken, A.
2004-02-01
A muon ionization cooling channel consists of three major components: the magnet optics, an acceleration cavity, and an energy absorber. The absorber of liquid hydrogen contained by thin aluminum windows is the only component which introduces stochastic processes into the otherwise deterministic acceleration system. The scattering dynamics of the transverse coordinates is described by Gaussian distributions. The asymmetric energy loss function is represented by the Vavilov distribution characterized by the minimum number of collisions necessary for a particle undergoing loss of the energy distribution average resulting from the Bethe-Bloch formula. Examples of the interplay between stochastic processes and deterministic beam dynamics are given.
After a brief review of the BRST formalism and of the Parisi-Wu stochastic quantization method we introduce the BRST stochastic quantization scheme. It allows the second quantization of constrained Hamiltonian systems in a manifestly gauge symmetry preserving way. The examples of the relativistic particle, the spinning particle and the bosonic string are worked out in detail. The paper is closed by a discussion on the interacting field theory associated to the relativistic point particle system. 58 refs. (Author)