1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/596B270197FE27DE5FABB598B6210622/S0025557200150892a.pdf/div-class-title-span-class-italic-the-geometry-of-biological-time-span-by-a-t-winfree-pp-544-dm68-corrected-second-printing-1990-isbn-3-540-52528-9-springer-div.pdf

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

to be done in this area. Face recognition is a problem that scarcely clamoured for attention before the computer age but, having surfaced, has involved a wide range of techniques and has attracted the attention of some fine minds (David Mumford was a Fields Medallist in 1974). This singular application of mathematical modelling to a messy applied problem of obvious utility and importance but with no unique solution is a pretty one to share with students: perhaps, returning to the source of our opening quotation, we may invert Duncan's earlier observation, 'There is an art to find the mind's construction in the face!'.

Linear and nonlinear waves, by G. B. Whitham. Pp.636. £50. 1999. ISBN 0 471 35942 4 (Wiley).

Statistical physics of vehicular traffic and some related systems

Random-matrix theories in quantum physics : common concepts

Extraction and Solubilization of Proteins for Proteomic Studies Richard M. Leimgruber Preparation of Bacterial Samples for 2-D PAGE Brian Berg Vandahl, Gunna Christiansen, and Svend Birkelund Preparation of Yeast Samples for 2-D PAGE Joakim Norbeck Preparation of Mammalian Tissue Samples for Two-Dimensional Electrophoresis Frank A. Witzmann Differential Detergent Fractionation of Eukaryotic Cells Melinda L. Ramsby and Gregory S. Makowski Serum or Plasma Sample Preparation for Two-Dimensional Gel Electrophoresis Anthony G. Sullivan, Stephen Russell, Henry Brzeski, Richard I. Somiari, and Craig D. Shriver Preparation of Plant Protein Samples for 2-D PAGE David W. M. Leung Laser-Assisted Microdissection in Proteomic Analyses Darrell L. Ellsworth, Stephen Russell, Brenda Deyarmin, Anthony G. Sullivan, Henry Brzeski, Richard I. Somiari, and Craig D. Shriver Purification of Cellular and Organelle Populations by Fluorescence-Activated Cell Sorting for Proteome Analysis William L. Godfrey, Colette J. Rudd, Sujata Iyer, and Diether Recktenwald Purification of Nucleoli From Lymphoma Cells and Solubilization of Nucleolar Proteins for 2-DE Separation Regis Dieckmann, Yohann Coute, Denis Hochstrasser, Jean-Jacques Diaz, and Jean-Charles Sanchez Prefractionation of Complex Protein Mixture for 2-D PAGE Using Reversed-Phase Liquid Chromatography Volker Badock and Albrecht Otto Fractionation of Complex Proteomes by Microscale Solution Isoelectrofocusing Using ZOOM(TM) IEF Fractionators to Improve Protein Profiling Xun Zuo, Ki-Boom Lee, and David W. Speicher Large-Format 2-D Polyacrylamide Gel Electrophoresis Henry Brzeski, Stephen Russell, Anthony G. Sullivan, Richard I. Somiari, and Craig D. Shiver Analysis of Membrane Proteins by Two-Dimensional Gels MichaelFountoulakis 2-D PAGE of High-Molecular-Mass Proteins Masamichi Oh-Ishi and Tadakazu Maeda Using Ultra-Zoom Gels for High-Resolution Two-Dimensional Polyacrylamide Gel Electrophoresis Sjouke Hoving, Hans Voshol, and Jan van Oostrum NEpHGE and pI Strip Proteomic 2-D Gel Electrophoretic Mapping of Lipid-Rich Membranes Steven E. Pfeiffer, Yoshihide Yamaguchi, Cecilia B. Marta, Rashmi Bansal, and Christopher M. Taylor Silver Staining of 2-D Gels Julia Poland, Thierry Rabilloud, and Pranav Sinha Zn2+ Reverse Staining Technique Carlos Fernandez-Patron Multiplexed Proteomics Technology for the Fluorescence Detection of Glycoprotein Levels and Protein Expression Levels Using Pro-Q(R) Emerald and SYPRO(R) Ruby Dyes Birte Schulenberg and Wayne F. Patton Multiplexed Proteomics Technology for the Fluorescence Detection of Phosphorylation and Protein Expression Levels Using Pro-Q(R) Diamond and SYPRO(R) Ruby Dyes Birte Schulenberg, Terrie Goodman, Thomas H. Steinberg, and Wayne F. Patton Sensitive Quantitative Fluorescence Detection of Proteins in Gels Using SYPRO(R) Ruby Protein Gel Stain Birte Schulenberg, Nancy Ahnert, and Wayne F. Patton Rapid, Sensitive Detection of Proteins in Minigels With Fluorescent Dyes: Coomassie Fluor Orange, SYPRO(R) Orange, SYPRO Red, and SYPRO Tangerine Protein Gel Stains Thomas H. Steinberg, Courtenay R. Hart, and Wayne F. Patton Differential In-Gel Electrophoresis in a High-Throughput Environment Richard I. Somiari, Stephen Russell, Stella B. Somiari, Anthony G. Sullivan, Darrell L. Ellsworth, Henry Brzeski, and Craig D. Shriver Statistical Analysis of 2-D Gel Patterns Francoise Seillier-Moiseiwitsch 2-DE Databases on the World Wide Web Christine Hoogland, Khaled Mostaguir, and Ron D. Appel Computer Analysis of 2-D Images Patricia M. Palagi,

The proteomics protocols handbook

One of the major challenges in cancer diagnosis from microarray data is to develop robust classification models which are independent of the analysis techniques used and can combine data from different laboratories. We propose a meta-classification scheme which uses a robust multivariate gene selection procedure and integrates the results of several machine learning tools trained on raw and pattern data. We validate our method by applying it to distinguish diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) on two independent datasets: the HuGeneFL Affmetrixy dataset of Shipp et al. (www. genome. wi. mit. du/MPR/lymphoma) and the Hu95Av2 Affymetrix dataset (DallaFavera's laboratory, Columbia University). Our meta-classification technique achieves higher predictive accuracies than each of the individual classifiers trained on the same dataset and is robust against various data perturbations. We also find that combinations of p53 responsive genes (e.g., p53, PLK1 and CDK2) are highly predictive of the phenotype.

/pdf/a-robust-meta-classification-strategy-for-cancer-diagnosis-1edhq63wpq.pdf

A robust meta-classification strategy for cancer diagnosis from gene expression data

We study the effect of multiplicative noise in dynamical flows arising from the coupling of stochastic processes with intrinsic noise. Situations wherein such systems arise naturally are in chemical or biological oscillators that are coupled to each other in a drive-response configuration. Above a coupling threshold we find that there is a strong correlation between the drive and the response: This is a stochastic analog of the phenomenon of generalised synchronization. Since the dynamical fluctuations are large when there is intrinsic noise, it is necessary to employ measures that are sensitive to correlations between the variables of drive and the response, the permutation entropy, or the mutual information in order to detect the transition to generalized synchrony in such systems.

Generalized synchrony of coupled stochastic processes with multiplicative noise.

Integrable dynamical systems, namely those having as many independent conserved quantities as freedoms, have all Lyapunov exponents equal to zero. Locally, the instantaneous or finite time Lyapunov exponents are nonzero, but owing to a symmetry, their global averages vanish. When the system becomes nonintegrable, this symmetry is broken. A parallel to this phenomenon occurs in mappings which derive from quasiperiodic Schrodinger problems in 1-dimension. For values of the energy such that the eigenstate is extended, the Lyapunov exponent is zero, while if the eigenstate is localized, the Lyapunov exponent becomes negative. This occurs by a breaking of the quasiperiodic symmetry of local Lyapunov exponents, and corresponds to a breaking of a symmetry of the wavefunction in extended and critical states.

Symmetry-breaking in local Lyapunov exponents

The collinear atom-diatom collision system provides one of the simplest instances of chaotic or irregular scattering. Classically, irregular scattering is manifest in the sensitive dependence of post-collision variables on initial conditions, and quantally, in the appearance of a dense spectrum of dynamical resonances. We examine the influence of kinematic factors on such dynamical resonances in collinear (He, H
 2
 +
 ) collisions by computing the transition state spectra for collinear (He, HD+) and (He, DH+) collisions using the time-dependent quantum mechanical approach. The nearest neighbor spacing distributionP(s) and the spectral rigidity Δ3(L) for these resonances suggest that the dynamics is predominantlyirregular for collinear (He, HD+) and predominantlyregular for collinear (He, DH+). These findings are reinforced by a significantly larger “correlation hole” in ensemble averaged survival probability ≪P(t)≫ values for collinear (He, HD+) than for collinear (He,DH+). In addition we have also examined measures of classical chaos through the dependence of the final vibrational action,n
 f, on the initial vibrational phaseφ
 i of the diatom, and Poincare surfaces-of-section. They show that (He, HD+) collisions are partly chaotic over the entire energy range (0–2.78 eV) while (He, DH+) collisions, in contrast, are highly regular at collision energies below the classical threshold for reaction. Above the threshold, the scattering remains regular for initial vibrational statesv=0 and 1 of DH+.

Resonances and chaos in the collinear collision system (He, H 2 + ) and its isotopic variants

We study synchronization in bipartite networks of phase oscillators with general nonlinear coupling and distributed time delays. Phase-locked solutions are shown to arise, where the oscillators in each partition are perfectly synchronized among themselves but can have a phase difference with the other partition, with the phase difference necessarily being either zero or π radians. Analytical conditions for the stability of both types of solutions are obtained and solution branches are explicitly calculated, revealing that the network can have several coexisting stable solutions. With increasing value of the mean delay, the system exhibits hysteresis, phase flips, final state sensitivity, and an extreme form of multistability where the numbers of stable in-phase and antiphase synchronous solutions with distinct frequencies grow without bound. The theory is applied to networks of Landau-Stuart and Rossler oscillators and shown to accurately predict both in-phase and antiphase synchronous behavior in appropriate parameter ranges.

Ramakrishna Ramaswamy

Papers

A robust meta-classification strategy for cancer diagnosis from gene expression data

Generalized synchrony of coupled stochastic processes with multiplicative noise.

Symmetry-breaking in local Lyapunov exponents

Resonances and chaos in the collinear collision system (He, H 2 + ) and its isotopic variants

Bipartite networks of oscillators with distributed delays: Synchronization branches and multistability.