Sat, 05 Jul 2008 13:18:05 BST CiteULike: ddcttrl's library [551 articles] http://www.citeulike.org/user/ddcttrl CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/ddcttrl/article/117528 <i>(15 February 2001)</i><br /><br />Special functions, which include the trigonometric functions, have been used for centuries. Their role in the solution of differential equations was exploited by Newton and Leibniz, and the subject of special functions has been in continuous development ever since. In just the past thirty years several new special functions and applications have been discovered. This treatise presents an overview of the area of special functions, focusing primarily on the hypergeometric functions and the associated hypergeometric series. It includes both important historical results and recent developments and shows how these arise from several areas of mathematics and mathematical physics. Particular emphasis is placed on formulas that can be used in computation. The book begins with a thorough treatment of the gamma and beta functions that are essential to understanding hypergeometric functions. Later chapters discuss Bessel functions, orthogonal polynomials and transformations, the Selberg integral and its applications, spherical harmonics, q-series, partitions, and Bailey chains. This clear, authoritative work will be a lasting reference for students and researchers in number theory, algebra, combinatorics, differential equations, applied mathematics, mathematical computing, and mathematical physics. Special Functions George Andrews Richard Askey Ranjan Roy (15 February 2001) 2005-03-08T18:02:51-00:00 2001 Cambridge University Press bessel book special-functions http://www.citeulike.org/user/ddcttrl/article/2931944 <i></i><br /><br />Over the past 20 years, the study of superprocesses has expanded into a major industry and can now be regarded as a central theme in modern probability theory. This book is intended as a rapid introduction to the subject, geared toward graduate students and researchers in stochastic analysis. A variety of different approaches to the superprocesses emerged over the last ten years. Yet no one approach superseded any others. In this book, readers are exposed to a number of different ways of thinking about the processes, and each is used to motivate some key results. The emphasis is on why results are true rather than on rigorous proof. Specific results are given, including extensive references to current literature for their general form. An Introduction to Superprocesses (University Lecture Series) Alison Etheridge 2008-06-26T18:56:42-00:00 American Mathematical Society book branching superprocess http://www.citeulike.org/user/ddcttrl/article/2905743 <i>Physical Review E, Vol. 70, No. 2. (2004), 020901.</i> Molecular discreteness in reaction-diffusion systems yields steady states not seen in the continuum limit Yuichi Togashi Kunihiko Kaneko doi:10.1103/PhysRevE.70.020901 Physical Review E, Vol. 70, No. 2. (2004), 020901. 2008-06-18T15:41:05-00:00 2004 Physical Review E 70 2 020901 American Physical Society molecular reaction-diffusion steady-state stochastic http://www.citeulike.org/user/ddcttrl/article/2903607 <i>Physica A: Statistical and Theoretical Physics, Vol. 186, No. 3-4. (1 August 1992), pp. 441-481.</i><br /><br />We examine some results and techniques of analytic number theory which have application, or potential application, in mathematical physics. We consider inversion formulae for lattice sums, various transformations of infinite series and products, functional equations and scaling relations, with selected applications in electrostatics and statistical mechanics. In the analysis, the Mellin transform and the Riemann zeta function play a key role. Möbius, Mellin, and mathematical physics Barry Ninham Barry Hughes Norman Frankel Lawrence doi:10.1016/0378-4371(92)90210-H Physica A: Statistical and Theoretical Physics, Vol. 186, No. 3-4. (1 August 1992), pp. 441-481. 2008-06-17T23:42:23-00:00 1992 Physica A: Statistical and Theoretical Physics 186 3-4 441 481 integral-transform mellin transform http://www.citeulike.org/user/ddcttrl/article/2873753 <i>(2000)</i><br /><br />int, we begin with a model of diusion in a constant medium, namely we consider the nearest neighbor random walk (X n ) on ZZ, g0.1.ps 61 14 mm q p x 1 x + 1 x with xed probabilities p to jump to the right and q to jump to the left. There are many dierent ways to introduce randomness in the medium and inuence the nature of the diusion taking place. Here are some examples. a) Site randomness: One chooses i.i.d. variables p(x; !), x 2 ZZ, with values in [0; 1], and for a given... Lectures on Random Motions in Random Media A Sznitman (2000) 2008-06-08T17:28:44-00:00 2000 brownian-motion random-media http://www.citeulike.org/user/ddcttrl/article/2775959 <i>(7 May 2008)</i><br /><br />This is a brief review, in relatively non-technical terms, of recent advances in the theory of random field geometry. These advances have provided a collection of explicit new formulae describing mean values of a variety of geometric characteristics of excursion sets of random fields. As well as a review of the theory, we provide brief descriptions of some of the more interesting applications. Some New Random Field Tools for Spatial Analysis Robert Adler (7 May 2008) 2008-05-09T14:13:11-00:00 2008 inference probability random-fields http://www.citeulike.org/user/ddcttrl/article/2745944 <i>Biophys. J., Vol. 87, No. 2. (1 August 2004), pp. 745-753.</i><br /><br />The synaptic signaling network is capable of sophisticated cellular computations. These include the ability to respond selectively to different patterns of input, and to sustain changes in response over long periods. The small volume of the synapse complicates the analysis of signaling because the chemical environment is strongly affected by diffusion and stochasticity. This study is based on an updated version of a previously proposed synaptic signaling circuit (Bhalla and Iyengar, 1999) and analyzes three network computation properties in small volumes: bistability, thresholding, and pattern selectivity. Simulations show that although there are diffusive regimes in which bistability may persist, chemical noise at small volumes overwhelms bistability. In the deterministic situation, the network exhibits a sharp threshold for transition between lower and upper stable states. This transition is broadened and individual runs partition between lower and upper states, when stochasticity is considered. The third network property, pattern selectivity, is severely degraded at synaptic volumes. However, there are regimes in which a process similar to stochastic resonance operates and amplifies pattern selectivity. These results imply that simple scaling of signaling conditions to femtoliter volumes is unlikely, and microenvironments, such as reaction complex formation, may be essential for reliable small-volume signaling. 10.1529/biophysj.104.040501 Signaling in Small Subcellular Volumes. II. Stochastic and Diffusion Effects on Synaptic Network Properties Upinder Bhalla doi:10.1529/biophysj.104.040501 Biophys. J., Vol. 87, No. 2. (1 August 2004), pp. 745-753. 2008-05-02T14:29:33-00:00 2004 Biophys. J. 87 2 745 753 biophys diffusion gene network http://www.citeulike.org/user/ddcttrl/article/1339026 <i>Reviews of Modern Physics, Vol. 70, No. 3. (July 1998), 979.</i><br /><br />The techniques of quantum field theory on a lattice are used to examine the diffusion and reaction processes of particles in a solid; such as vacancies or interstitials; or chemical species of all kinds which move by discrete random hopping processes and react in a prescribed way when they are in proximity. First formulated by Doi in the 1970s; the quantum-field-theoretic solution of the “master equation” of statistical physics allows a systematic investigation of any number of nonequilibrium processes ranging from fluorescence to explosions. By formulating the problem on the points of a space lattice in d dimensions one can control the ultraviolet divergences associated with short-range interactions. For illustrative purposes several models are solved in detail. The authors include as an appendix a chronological list of seminal articles in the field. The uses of quantum field theory in diffusion-limited reactions Daniel Mattis Lawrence Glasser doi:10.1103/RevModPhys.70.979 Reviews of Modern Physics, Vol. 70, No. 3. (July 1998), 979. 2007-05-28T17:44:07-00:00 1998 Reviews of Modern Physics 70 3 979 American Physical Society biophys diffusion field-theory reaction http://www.citeulike.org/user/ddcttrl/article/1314109 <i>PNAS, Vol. 100, No. 5. (4 March 2003), pp. 2374-2379.</i><br /><br />Gene expression has a stochastic component because of the single-molecule nature of the gene and the small number of copies of individual DNA-binding proteins in the cell. We show how the statistics of such systems can be mapped onto quantum many-body problems. The dynamics of a single gene switch resembles the spin-boson model of a two-site polaron or an electron transfer reaction. Networks of switches can be approximately described as quantum spin systems by using an appropriate variational principle. In this way, the concept of frustration for magnetic systems can be taken over into gene networks. The landscape of stable attractors depends on the degree and style of frustration, much as for neural networks. We show the number of attractors, which may represent cell types, is much smaller for appropriately designed weakly frustrated stochastic networks than for randomly connected networks. 10.1073/pnas.2627987100 Stochastic gene expression as a many-body problem Masaki Sasai Peter Wolynes doi:10.1073/pnas.2627987100 PNAS, Vol. 100, No. 5. (4 March 2003), pp. 2374-2379. 2007-05-21T00:08:43-00:00 2003 PNAS 100 5 2374 2379 biophys field-theory gene_expression http://www.citeulike.org/user/ddcttrl/article/2745880 <i>Biophys. J., Vol. 87, No. 2. (1 August 2004), pp. 733-744.</i><br /><br />Many cellular signaling events occur in small subcellular volumes and involve low-abundance molecular species. This context introduces two major differences from mass-action analyses of nondiffusive signaling. First, reactions involving small numbers of molecules occur in a probabilistic manner which introduces scatter in chemical activities. Second, the timescale of diffusion of molecules between subcellular compartments and the rest of the cell is comparable to the timescale of many chemical reactions, altering the dynamics and outcomes of signaling reactions. This study examines both these effects on information flow through four protein kinase regulatory pathways. The analysis uses Monte Carlo simulations in a subcellular volume diffusively coupled to a bulk cellular volume. Diffusion constants and the volume of the subcellular compartment are systematically varied to account for a range of cellular conditions. Each pathway is characterized in terms of the probabilistic scatter in active kinase levels as a measure of "noise" on the pathway output. Under the conditions reported here, most signaling outcomes in a volume below one femtoliter are severely degraded. Diffusion and subcellular compartmentalization influence the signaling chemistry to give a diversity of signaling outcomes. These outcomes may include washout of the signal, reinforcement of signals, and conversion of steady responses to transients. 10.1529/biophysj.104.040469 Signaling in Small Subcellular Volumes. I. Stochastic and Diffusion Effects on Individual Pathways Upinder Bhalla doi:10.1529/biophysj.104.040469 Biophys. J., Vol. 87, No. 2. (1 August 2004), pp. 733-744. 2008-05-02T14:05:10-00:00 2004 Biophys. J. 87 2 733 744 biophys diffusion networks http://www.citeulike.org/user/ddcttrl/article/374350 <i>Biophys J, Vol. 88, No. 2. (February 2005), pp. 828-850.</i><br /><br />We present a self-consistent field approximation approach to the problem of the genetic switch composed of two mutually repressing/activating genes. The protein and DNA state dynamics are treated stochastically and on an equal footing. In this approach the mean influence of the proteomic cloud created by one gene on the action of another is self-consistently computed. Within this approximation a broad range of stochastic genetic switches may be solved exactly in terms of finding the probability distribution and its moments. A much larger class of problems, such as genetic networks and cascades, also remain exactly solvable with this approximation. We discuss, in depth, certain specific types of basic switches used by biological systems and compare their behavior to the expectation for a deterministic switch. Self-consistent proteomic field theory of stochastic gene switches. AM Walczak M Sasai PG Wolynes doi:10.1529/biophysj.104.050666 Biophys J, Vol. 88, No. 2. (February 2005), pp. 828-850. 2005-11-01T00:41:33-00:00 2005 Biophys J 0006-3495 88 2 828 850 biophys field-theory gene network potein stochast http://www.citeulike.org/user/ddcttrl/article/370428 <i>Proc Natl Acad Sci U S A, Vol. 102, No. 13. (29 March 2005), pp. 4771-4776.</i><br /><br />Gene expression noise results in protein number distributions ranging from long-tailed to Gaussian. We show how long-tailed distributions arise from a stochastic model of the constituent chemical reactions and suggest that, in conjunction with cooperative switches, they lead to more sensitive selection of a subpopulation of cells with high protein number than is possible with Gaussian distributions. Single-cell-tracking experiments are presented to validate some of the assumptions of the stochastic simulations. We also examine the effect of DNA looping on the shape of protein distributions. We further show that when switches are incorporated in the regulation of a gene via a feedback loop, the distributions can become bimodal. This might explain the bimodal distribution of certain morphogens during early embryogenesis. Stochastic simulations of the origins and implications of long-tailed distributions in gene expression. S Krishna B Banerjee TV Ramakrishnan GV Shivashankar doi:10.1073/pnas.0406415102 Proc Natl Acad Sci U S A, Vol. 102, No. 13. (29 March 2005), pp. 4771-4776. 2005-10-29T23:21:59-00:00 2005 Proc Natl Acad Sci U S A 0027-8424 102 13 4771 4776 biophys gene_expression http://www.citeulike.org/user/ddcttrl/article/204985 <i>Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2478-2487.</i> Bio-Object, a stochastic simulator for post-transcriptional regulation Nobukazu Ohki Masatoshi Hagiwara doi:10.1093/bioinformatics/bti316 Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2478-2487. 2005-05-19T18:11:35-00:00 2005 Bioinformatics 1367-4803 21 10 2478 2487 Oxford University Press biophys drosphila gene network simulation software http://www.citeulike.org/user/ddcttrl/article/622483 <i>Proc Natl Acad Sci U S A, Vol. 103, No. 19. (9 May 2006), pp. 7304-7309.</i><br /><br />Fluctuations in protein numbers (noise) due to inherent stochastic effects in single cells can have large effects on the dynamic behavior of gene regulatory networks. Although deterministic models can predict the average network behavior, they fail to incorporate the stochasticity characteristic of gene expression, thereby limiting their relevance when single cell behaviors deviate from the population average. Recently, stochastic models have been used to predict distributions of steady-state protein levels within a population but not to predict the dynamic, presteady-state distributions. In the present work, we experimentally examine a system whose dynamics are heavily influenced by stochastic effects. We measure population distributions of protein numbers as a function of time in the Escherichia coli lactose uptake network (lac operon). We then introduce a dynamic stochastic model and show that prediction of dynamic distributions requires only a few noise parameters in addition to the rates that characterize a deterministic model. Whereas the deterministic model cannot fully capture the observed behavior, our stochastic model correctly predicts the experimental dynamics without any fit parameters. Our results provide a proof of principle for the possibility of faithfully predicting dynamic population distributions from deterministic models supplemented by a stochastic component that captures the major noise sources. Predicting stochastic gene expression dynamics in single cells. JT Mettetal D Muzzey JM Pedraza EM Ozbudak A van Oudenaarden doi:10.1073/pnas.0509874103 Proc Natl Acad Sci U S A, Vol. 103, No. 19. (9 May 2006), pp. 7304-7309. 2006-05-11T04:05:09-00:00 2006 Proc Natl Acad Sci U S A 0027-8424 103 19 7304 7309 biophys gene_expression http://www.citeulike.org/user/ddcttrl/article/733336 <i>Biophys. J., Vol. 91, No. 1. (1 July 2006), pp. 84-94.</i><br /><br />The fluctuation-dissipation theorem, one of the central theorems in thermal dynamics, breaks down in out-of-equilibrium systems. The idea of effective temperature coming from the extensions of that theorem has been recently introduced to study glasses and has proved to be a key concept for out-of-equilibrium systems. Gene networks involve stochastic chemical kinetics and are far from equilibrium. This leads us to try to use the notion of effective temperature to study them. To develop this idea, we study a simple birth-death process and a general two-species interacting process using the language of effective temperature. Furthermore, a model of a nonregulatory gene is studied as an example. The effective temperature may serves as an alternative and somewhat more fundamental language to describe the intrinsic-extrinsic noise distinction that has already provided a tool for qualifying gene networks. 10.1529/biophysj.105.074914 Effective Temperature in Stochastic Kinetics and Gene Networks Ting Lu Jeff Hasty Peter Wolynes doi:10.1529/biophysj.105.074914 Biophys. J., Vol. 91, No. 1. (1 July 2006), pp. 84-94. 2006-07-03T19:06:17-00:00 2006 Biophys. J. 91 1 84 94 biophys effective-temperature gene_expression network http://www.citeulike.org/user/ddcttrl/article/1341825 <i>Biophys J, Vol. 91, No. 12. (15 December 2006), pp. 4350-4367.</i><br /><br />We study by Green's Function Reaction Dynamics the effect of the diffusive motion of repressor molecules on the noise in mRNA and protein levels for a gene that is under the control of a repressor. We find that spatial fluctuations due to diffusion can drastically enhance the noise in gene expression. After dissociation from the operator, a repressor can rapidly rebind to the DNA. Our results show that the rebinding trajectories are so short that, on this timescale, the RNA polymerase (RNAP) cannot effectively compete with the repressor for binding to the promoter. As a result, a dissociated repressor molecule will on average rebind many times, before it eventually diffuses away. These rebindings thus lower the effective dissociation rate, and this increases the noise in gene expression. Another consequence of the timescale separation between repressor rebinding and RNAP association is that the effect of spatial fluctuations can be described by a well-stirred, zero-dimensional, model by renormalizing the reaction rates for repressor-DNA (un) binding. Our results thus support the use of well-stirred, zero-dimensional models for describing noise in gene expression. We also show that for a fixed repressor strength, the noise due to diffusion can be minimized by increasing the number of repressors or by decreasing the rate of the open complex formation. Lastly, our results emphasize that power spectra are a highly useful tool for studying the propagation of noise through the different stages of gene expression. Diffusion of transcription factors can drastically enhance the noise in gene expression. JS van Zon MJ Morelli S Tănase-Nicola PR ten Wolde doi:10.1529/biophysj.106.086157 Biophys J, Vol. 91, No. 12. (15 December 2006), pp. 4350-4367. 2007-05-29T21:54:43-00:00 2006 Biophys J 0006-3495 91 12 4350 4367 biophys diffusion gene_expression http://www.citeulike.org/user/ddcttrl/article/2745792 <i>Biophys. J., Vol. 93, No. 2. (15 July 2007), pp. 401-410.</i><br /><br />We present a perfect sampling algorithm that can be applied to the master equation of gene regulatory networks. The method recasts Gillespie's stochastic simulation algorithm (SSA) in the light of Markov chain Monte Carlo methods and combines it with the dominated coupling from the past (DCFTP) algorithm to provide guaranteed sampling from the stationary distribution. We show how the DCFTP-SSA can be generically applied to genetic networks with feedback formed by the interconnection of linear enzymatic reactions and nonlinear Monod- and Hill-type elements. We establish rigorous bounds on the error and convergence of the DCFTP-SSA, as compared to the standard SSA, through a set of increasingly complex examples. Once the building blocks for gene regulatory networks have been introduced, the algorithm is applied to study properly averaged dynamic properties of two experimentally relevant genetic networks: the toggle switch, a two-dimensional bistable system; and the repressilator, a six-dimensional transcriptional oscillator. 10.1529/biophysj.106.099390 Perfect Sampling of the Master Equation for Gene Regulatory Networks Martin Hemberg Mauricio Barahona doi:10.1529/biophysj.106.099390 Biophys. J., Vol. 93, No. 2. (15 July 2007), pp. 401-410. 2008-05-02T13:30:50-00:00 2007 Biophys. J. 93 2 401 410 biophys gene master-equation networks regulatory http://www.citeulike.org/user/ddcttrl/article/2250511 <i>Science, Vol. 319, No. 5861. (18 January 2008), pp. 339-343.</i><br /><br />Many cellular components are present in such low numbers per cell that random births and deaths of individual molecules can cause substantial "noise" in concentrations. But biochemical events do not necessarily occur in single steps of individual molecules. Some processes are greatly randomized when synthesis or degradation occurs in large bursts of many molecules during a short time interval. Conversely, each birth or death of a macromolecule could involve several small steps, creating a memory between individual events. We present a generalized theory for stochastic gene expression, formulating the variance in protein abundance in terms of the randomness of the individual gene expression events. We show that common types of molecular mechanisms can produce gestation and senescence periods that reduce noise without requiring higher abundances, shorter lifetimes, or any concentration-dependent control loops. We also show that most single-cell experimental methods cannot distinguish between qualitatively different stochastic principles, although this in turn makes such methods better suited for identifying which components introduce fluctuations. Characterizing the random events that give rise to noise in concentrations instead requires dynamic measurements with single-molecule resolution. 10.1126/science.1144331 Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression Juan Pedraza Johan Paulsson doi:10.1126/science.1144331 Science, Vol. 319, No. 5861. (18 January 2008), pp. 339-343. 2008-01-18T10:34:03-00:00 2008 Science 319 5861 339 343 biophys gene_expression network noise http://www.citeulike.org/user/ddcttrl/article/2150653 <i>Biophys J (7 December 2007)</i><br /><br />Fluorescent proteins are often used as reporters of transcriptional activity. Here we present a mathematical characterization of a novel fluorescent reporter that was recently engineered to have a short half life (~ 12 min). The advantage of this destabilized protein is that it can track the transient transcriptional response often exhibited by signaling pathways. Our mathematical model takes into account the maturation time and half life of the fluorescent protein. We demonstrate that our characterization allows transient transcript profiles to be inferred from fluorescence data. We also investigate a stochastic version of the model. Our analysis reveals that fluorescence measurements can both underestimate or overestimate fluctuations protein levels that arise from the stochastic nature of biochemical reactions. Mathematical Analysis and Quantification of Fluorescent Proteins as Transcriptional Reporters. Xiao Wang Beverly Errede Timothy C Elston doi:10.1529/biophysj.107.122200 Biophys J (7 December 2007) 2007-12-20T09:11:07-00:00 2007 Biophys J 0006-3495 biophys fluorescence protein http://www.citeulike.org/user/ddcttrl/article/2567082 <i>Proceedings of the National Academy of Sciences (19 March 2008), 0707904105.</i><br /><br />Cis-regulatory control of transcription is the dominant form of regulation of gene expression. Recent experimental results suggest that, in addition to the mean expression level, cell-to-cell variability might also be transcriptionally regulated. Here, we develop a stochastic model of transcriptional regulation that allows us to calculate closed-form analytical expressions for the mean and variance of the protein and mRNA distributions for an arbitrarily complex cis-regulatory motif. Our model allows us to investigate how noise may be transcriptionally regulated independently from the mean expression. We show that our approach is in excellent agreement with stochastic simulations and experiment, and leads to an experimentally testable formula for the noise in gene expression as a function of inducer-molecule concentrations. 10.1073/pnas.0707904105 Transcriptional control of noise in gene expression Alvaro Sanchez Jane Kondev doi:10.1073/pnas.0707904105 Proceedings of the National Academy of Sciences (19 March 2008), 0707904105. 2008-03-20T15:15:36-00:00 2008 Proceedings of the National Academy of Sciences 0707904105 biophys gene intrinsic-noise network transcription http://www.citeulike.org/user/ddcttrl/article/2689148 <i>Proceedings of the National Academy of Sciences (17 April 2008), 0708708105.</i><br /><br />We develop a probabilistic method for analyzing global features of a cellular network under intrinsic statistical fluctuations, which is important when there are finite numbers of molecules. By making a self-consistent mean field approximation of splitting the variables in order to reduce the large number of degrees of freedom, which is reasonable for a not very strongly interacting network, we discovered that the underlying energy landscape of the mitogen-activated protein kinases (MAPKs) signal transduction network (with experimentally measured or inferred parameters such as chemical reaction rate coefficients in the network) is funneled toward a global minimum characterized by the nonequilibrium steady-state fixed point of the system at the end of the signal transduction process. For this system, we also show that the energy landscape is robust against intrinsic fluctuations and random perturbation to the inherent chemical reaction rates. The ratio of the slope versus the roughness of the energy landscape becomes a quantitative measure of robustness and stability of the network. Furthermore, we quantify the dissipation cost of this nonequilibrium system through entropy production, caused by the nonequilibrium flux in the system. We found that a lower dissipation cost corresponds to a more robust network. This least dissipation property might provide a design principle for robust and functional networks. Finally, we find the possibility of bistable and oscillatory-like solutions, which are important for cell fate decisions, upon perturbations. The method described here can be used in a variety of biological networks. 10.1073/pnas.0708708105 Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction Saul Lapidus Bo Han Jin Wang doi:10.1073/pnas.0708708105 Proceedings of the National Academy of Sciences (17 April 2008), 0708708105. 2008-04-18T18:35:19-00:00 2008 Proceedings of the National Academy of Sciences 0708708105 biophys intrinsic-noise networks http://www.citeulike.org/user/ddcttrl/article/2741827 <i>(23 Dec 2005)</i><br /><br />We present a simple method for determining the exact noise power spectra in linear chemical reaction networks. We apply the method to networks which are representative of biochemical processes such as gene expression and signal detection. Our results clarify how noise is transmitted by signal detection motifs, and indicate how to coarse-grain networks by the elimination of fast reactions. Exact results for noise power spectra in linear biochemical reaction networks Patrick Warren Sorin Tanase-Nicola Pieter (23 Dec 2005) 2008-05-01T05:55:34-00:00 2005 biophys http://www.citeulike.org/user/ddcttrl/article/2714291 <i>Journal of Statistical Physics, Vol. 65, No. 5. (1 December 1991), pp. 1173-1206.</i><br /><br />Diffusion and reaction in heterogeneous media arise in a host of phenomena in the physical and biological sciences. The determination of the mean survival timet (i.e., inverse trapping rate) and relaxation timesTn, n=1,2,3,... (i.e., inverse eigenvalues), associated with diffusion among partially absorbing, static traps with surface rate constantk are problems of long-standing interest. The limitsk=8 andk=0 correspond to the diffusion-controlled case (i.e., perfect absorbers) and reaction-controlled case (i.e., perfect reflectors), respectively. This paper reviews progress we have made on several basic aspects of this problem: (i) the formulation of rigorous bonding techniques and computational methodologies that enable one to estimate the mean survival time t and principal relaxation timeT1 (ii) the quantitative characterization of the microstructure of nontrivial continuum (i.e., off-lattice) models of heterogeneous media; and (iii) evaluation of t and T1 for the same models. We also describe a rigorous link between the mean survival time t and a different effective parameter of the system, namely the fluid permeability tensork associated with Stokes flow through the same porous medium. Diffusion and reaction among traps: some theoretical and simulation results S Torquato doi:10.1007/BF01049606 Journal of Statistical Physics, Vol. 65, No. 5. (1 December 1991), pp. 1173-1206. 2008-04-24T20:21:31-00:00 1991 Journal of Statistical Physics 65 5 1173 1206 branching diffusion random http://www.citeulike.org/user/ddcttrl/article/2688360 <i>(2005), pp. 735-744.</i> Fourier slice photography Ren Ng doi:10.1145/1186822.1073256 (2005), pp. 735-744. 2008-04-18T16:42:58-00:00 2005 735 744 ACM fouier projection-slice http://www.citeulike.org/user/ddcttrl/article/2688066 <i>Science, Vol. 248, No. 4956. (11 May 1990), pp. 697-704.</i><br /><br />Numerical computation of transforms is now widely practiced in science and industry and has been revolutionized by the development of fast transforms that make feasible computing projects that once could not be contemplated. The article discusses the significance of transforms in numerical work, defines the modern forms of several common transforms and their inverses, gives examples, and describes and gives references to methods of numerical evaluation. 10.1126/science.248.4956.697 Numerical Transforms RN Bracewell doi:10.1126/science.248.4956.697 Science, Vol. 248, No. 4956. (11 May 1990), pp. 697-704. 2008-04-18T14:24:08-00:00 1990 Science 248 4956 697 704 projection-slice transforms http://www.citeulike.org/user/ddcttrl/article/2684326 <i>(2002)</i> Review of the Evaluation of the Potential for Bovine Spongiform Encephalopathy in the United States (2002) 2008-04-17T23:39:39-00:00 2002 bibtex-import bse file-import-08-04-18 harvard phac prion risk http://www.citeulike.org/user/ddcttrl/article/2684325 <i>(2004)</i> Scentific report of the european food safety authority on the BSE surveillance model (BSurvE) established by the community reference Laboratory for TSE (2004) 2008-04-17T23:39:39-00:00 2004 bibtex-import bse bsurve europe file-import-08-04-18 phac prion surveillance http://www.citeulike.org/user/ddcttrl/article/2684324 <i>(2005)</i> Assessment of the Canadian Feed Ban (2005) 2008-04-17T23:39:39-00:00 2005 bibtex-import bse file-import-08-04-18 phac prion risk usda http://www.citeulike.org/user/ddcttrl/article/2684323 <i>(October 2005)</i><br /><br /><P>The two-volume set LNCS 3749 and LNCS 3750 constitutes the refereed proceedings of the 8th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2005, held in Palm Springs, CA, USA, in October 2005.</P> <P>Based on rigorous peer reviews the program committee selected 237 carefully revised full papers from 632 submissions for presentation in two volumes. The first volume includes all the contributions related to image analysis and validation, vascular image segmentation, image registration, diffusion tensor image analysis, image segmentation and analysis, clinical applications - validation, imaging systems - visualization, computer assisted diagnosis, cellular and molecular image analysis, physically-based modeling, robotics and intervention, medical image computing for clinical applications, and biological imaging - simulation and modeling. The second volume collects the papers related to robotics, image-guided surgery and interventions, image registration, medical image computing , structural and functional brain analysis, model-based image analysis, image-guided intervention: simulation, modeling and display, and image segmentation and analysis.</P> Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2005: 8th International Conference, Palm Springs, CA, USA, October 26-29, 2005, Proceedings, ... Part II (Lecture Notes in Computer Science) (October 2005) 2008-04-17T23:39:39-00:00 2005 Springer bibtex-import file-import-08-04-18 modelling phac prion vcjd http://www.citeulike.org/user/ddcttrl/article/2684322 <i>(2006)</i> BSE Ongoing Surveillance Plan - US 2006 (2006) 2008-04-17T23:39:38-00:00 2006 bibtex-import bse file-import-08-04-18 phac prion surveillance us usda http://www.citeulike.org/user/ddcttrl/article/2684321 <i>(2006)</i> An Estimate of the Prevalence of BSE in the United States (2006) 2008-04-17T23:39:38-00:00 2006 back-calculation bibtex-import bse bsurve file-import-08-04-18 phac prion surveillance usda http://www.citeulike.org/user/ddcttrl/article/2684320 <i>(2006)</i> Attachment 1: Estimation of BSE Prevalence in Canada (2006) 2008-04-17T23:39:38-00:00 2006 bibtex-import bse canada file-import-08-04-18 phac prion surveillance usda http://www.citeulike.org/user/ddcttrl/article/2684319 <i>(2006)</i> Assessment of Bovine Spongiform Encephalopathy (BSE) risks associated with the importation of certain commodities from BSE minimal risk regions (Canada) (2006) 2008-04-17T23:39:38-00:00 2006 bibtex-import bse file-import-08-04-18 phac prion risk us usda http://www.citeulike.org/user/ddcttrl/article/2684318 <i>(2006)</i> Fourth Session of the Statistics and Risk Assessment Section’s International Expert Advisory Group on Risk Modelling Iterative Risk Assessment Processes for Policy Development Under Conditions of Uncertainty / Emerging Infectious Diseases (2006) 2008-04-17T23:39:38-00:00 2006 bibtex-import disease file-import-08-04-18 phac prion http://www.citeulike.org/user/ddcttrl/article/2684317 <i>(2006)</i> CADTH: Enzyme Technology Reduces Risk of Transmitting Prions Through Contaminated Surgical Instruments (2006) 2008-04-17T23:39:38-00:00 2006 bibtex-import file-import-08-04-18 phac prion http://www.citeulike.org/user/ddcttrl/article/2684316 <i></i> Risks of transmission of variant Creutzfeldt-Jakob disease by blood transfusion (variant Creutzfeldt-Jakob disease, transmission, blood transfusion, infectivity)? 2008-04-17T23:39:38-00:00 bibtex-import cjd file-import-08-04-18 phac prion risk http://www.citeulike.org/user/ddcttrl/article/2684315 <i></i> USDA - APHIS Newsroom 2008-04-17T23:39:38-00:00 bibtex-import bse file-import-08-04-18 phac prion usda vcjd http://www.citeulike.org/user/ddcttrl/article/2684314 <i></i> Statistical Methods for Biostatistics and Related Fields 2008-04-17T23:39:37-00:00 bibtex-import biorefs biostatistical file-import-08-04-18 http://www.citeulike.org/user/ddcttrl/article/2684313 <i></i> RTI International - Scientific Research & Development Institute - Scientific Technologies 2008-04-17T23:39:37-00:00 bibtex-import bse file-import-08-04-18 harvard phac prion risk usda http://www.citeulike.org/user/ddcttrl/article/2684312 <i></i> Terrestrial Animal Health Code - 2006 2008-04-17T23:39:37-00:00 bibtex-import bse file-import-08-04-18 oie phac prion vcjd http://www.citeulike.org/user/ddcttrl/article/2684311 <i></i> Mean-Variance Portfolio Selection with Random Parameters in a Complete Market 2008-04-17T23:39:37-00:00 bibtex-import file-import-08-04-18 fmipw_portfolio http://www.citeulike.org/user/ddcttrl/article/2684310 <i></i> Mathematical Approaches for Emerging and Reemerging Infectious ... - Mathema...Journals, Books & Online Media | Springer 2008-04-17T23:39:37-00:00 bibtex-import diseases file-import-08-04-18 modelling phac http://www.citeulike.org/user/ddcttrl/article/2684309 <i></i> Bovine Spongiform Encephalopathy(BSE) 2008-04-17T23:39:37-00:00 bibtex-import bse file-import-08-04-18 phac prion risk http://www.citeulike.org/user/ddcttrl/article/2684308 <i></i> The exponential distribution: The Good, the Bad and the Ugly: A practical guide to its implementation. 2008-04-17T23:39:37-00:00 bibtex-import file-import-08-04-18 markov risk http://www.citeulike.org/user/ddcttrl/article/2684307 <i></i> EconPapers: Citations to The Role of Learning in Dynamic Portfolio Decisions" 2008-04-17T23:39:37-00:00 bibtex-import file-import-08-04-18 fmipw_portfolio http://www.citeulike.org/user/ddcttrl/article/2684306 <i></i> Data assimilation and the use of satellite data 2008-04-17T23:39:37-00:00 assimilation bibtex-import data file-import-08-04-18 http://www.citeulike.org/user/ddcttrl/article/2684305 <i></i> BSurvE 2008-04-17T23:39:37-00:00 bibtex-import bsurve file-import-08-04-18 phac prion usda http://www.citeulike.org/user/ddcttrl/article/2684304 <i></i> Assessing the risk of vCJD transmission via surgery: an interim review : Department of Health - Publications 2008-04-17T23:39:37-00:00 bibtex-import file-import-08-04-18 phac prion surgery vcjd http://www.citeulike.org/user/ddcttrl/article/2684303 <i></i> Amazon.com: Epidemic Models (Publications of the Newton Institute): Books: Denis Mollison 2008-04-17T23:39:37-00:00 bibtex-import disease epidemic file-import-08-04-18 phac risk http://www.citeulike.org/user/ddcttrl/article/2684302 <i>Scientific and Technical Review, Vol. 22, No. 1. (2003)</i> Risk analysis of prion diseases in animals Scientific and Technical Review, Vol. 22, No. 1. (2003) 2008-04-17T23:39:37-00:00 2003 Scientific and Technical Review 22 1 bibtex-import disease file-import-08-04-18 oie phac prion risk