Variable-free exploration of stochastic models: a gene regulatory network example

Finding coarse-grained, low-dimensional descriptions is an important task in the analysis of complex, stochastic models of gene regulatory networks. This task involves (a) identifying observables that best describe the state of these complex systems and (b) characterizing the dynamics of the observables. In a previous paper [13], we assumed that good observables were known a priori, and presented an equation-free approach to approximate coarse-grained quantities (i.e, effective drift and diffusion coefficients) that characterize the long-time behavior of the observables. Here we use diffusion maps [9] to extract appropriate observables ("reduction coordinates") in an automated fashion; these involve the leading eigenvectors of a weighted Laplacian on a graph constructed from network simulation data. We present lifting and restriction procedures for translating between physical variables and these data-based observables. These procedures allow us to perform equation-free coarse-grained, computations characterizing the long-term dynamics through the design and processing of short bursts of stochastic simulation initialized at appropriate values of the data-based observables.Comment: 26 pages, 9 figure

SPREADSHEET ANALYSIS AND DESIGN

Spreadsheet programs and microcomputers have revolutionized information processing in organizations. Users have adopted spreadsheets to solve problems and circumvent the long delays encountered in dealing with the traditional information services department. A significant number of serious errors have been reported through the misuse of spreadsheet technology. This paper discusses several different contexts for the development of spreadsheet models and presents structured design techniques for these models. The recommended approach to spreadsheet analysis and design encourages the use of a block structure format for the worksheet and introduces Spreadsheet Flow Diagrams as a systems design tool. The objective of this design approach is to reduce the probability and severity of spreadsheet errors, improve auditability and promote greater longevity for spreadsheet models.Information Systems Working Papers Serie

Dark Matter and Pseudo-flat Directions in Weakly Coupled SUSY Breaking Sectors

We consider candidates for dark matter in models of gauge mediated supersymmetry breaking, in which the supersymmetry breaking sector is weakly coupled and calculable. Such models typically contain classically flat directions, that receive one-loop masses of a few TeV. These pseudo-flat directions provide a new mechanism to account for the cold dark matter relic abundance. We discuss also the possibility of heavy gravitino dark matter in such models.Comment: 16 pages, 2 figures. v2: comments, refs adde

A multicenter experience using adipose-derived mesenchymal stem cell therapy for cats with chronic, non-responsive gingivostomatitis.

BackgroundThe ability of mesenchymal stem cells (MSCs) to modulate immune responses inspired a series of clinical trials addressing oral mucosal inflammation. We previously reported on the safety and efficacy of fresh, allogeneic and autologous, adipose-derived mesenchymal stem cells (ASCs) to treat feline gingivostomatitis (FCGS), an oral mucosal inflammatory disease that shares similarities with human oral lichen planus.MethodsTo meet clinical demand and goals for future commercialization, we determined the feasibility of shipping fresh ASCs to distant clinics and extended our pilot studies to expand safety and efficacy data for shipped and non-shipped ASCs in a cohort of 18 FCGS cats enrolled locally and at a few different locations within the USA.ResultsWe found that ASCs retained their viability, phenotype, and function after shipment. ASCs administered systemically resulted in a 72% positive response rate, identical to that noted in our previous studies. Cats that responded to ASC therapy had a significant decrease in circulating globulin concentration and histological evidence of decreased CD3+ T cells and CD20+ B cells in the oral mucosa. Responder cats also had significantly decreased percentages of CD8lo cells in blood prior to and at 3 months post-ASC therapy. CD8lo cells may serve as a potential "predictor" for response to systemic ASC therapy.ConclusionFresh feline ASCs can be successfully shipped and administered to cats with FCGS. ASCs modulate the immune response and demonstrate efficacy for chronic oral mucosal inflammatory lesions that are characterized by CD8+ T cell inflammation and T cell activation. FCGS is a potentially useful naturally occurring large animal model of human oral inflammatory diseases

Exact solution of diffusion limited aggregation in a narrow cylindrical geometry

The diffusion limited aggregation model (DLA) and the more general dielectric breakdown model (DBM) are solved exactly in a two dimensional cylindrical geometry with periodic boundary conditions of width 2. Our approach follows the exact evolution of the growing interface, using the evolution matrix E, which is a temporal transfer matrix. The eigenvector of this matrix with an eigenvalue of one represents the system's steady state. This yields an estimate of the fractal dimension for DLA, which is in good agreement with simulations. The same technique is used to calculate the fractal dimension for various values of eta in the more general DBM model. Our exact results are very close to the approximate results found by the fixed scale transformation approach.Comment: 18 pages RevTex, 6 eps figure

THE DECLINING PRICE OF PERSONAL COMPUTERS THE QUESTION OF WHEN TO INVEST

When should a manager invest in new technology? This paper provides guidelines for deciding when to invest in microcomputers. The authors argue that the technology and marketplace of micros today fits the conditions of the declining cost paradox observed by Eden and Ronen (1988). Under these conditions, a decision to defer purchasing equipment until the future to take advantage of hardware price decreases may lead to higher overall costs. The paper concludes with recommendations for the manager confronted with the decision of when to purchase microcomputer technology.Information Systems Working Papers Serie

SAPT: ligação de hidrogênio ou interação de van der Waals?

It is through the application of an electronic partition approach called Symmetry-Adapted Perturbation Theory (SAPT) that the nature of hydrogen bonds and van der Waals interactions can be unveiled according to the contribution of electrostatic, charge transfer, exchange repulsion, polarization, and dispersion terms. Among these, electrostatic partition governs the formation of the hydrogen bonds, whose energies are arguably high. However, the weakness of the interaction strength is caused by dispersion forces, whose contribution decisively lead to the stabilization of complexes formed via van der Waals interactions

THE DECLINING PRICE OF PERSONAL COMPUTERS THE QUESTION OF WHEN TO INVEST

When should a manager invest in new technology? This paper provides guidelines for deciding when to invest in microcomputers. The authors argue that the technology and marketplace of micros today fits the conditions of the declining cost paradox observed by Eden and Ronen (1988). Under these conditions, a decision to defer purchasing equipment until the future to take advantage of hardware price decreases may lead to higher overall costs. The paper concludes with recommendations for the manager confronted with the decision of when to purchase microcomputer technology.Information Systems Working Papers Serie