Compositionality, stochasticity and cooperativity in dynamic models of gene regulation

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ode-description. While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first-level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07

Supernova remnant S147 and its associated neutron star(s)

The supernova remnant S147 harbors the pulsar PSR J0538+2817 whose characteristic age is more than an order of magnitude greater than the kinematic age of the system (inferred from the angular offset of the pulsar from the geometric center of the supernova remnant and the pulsar proper motion). To reconcile this discrepancy we propose that PSR J0538+2817 could be the stellar remnant of the first supernova explosion in a massive binary system and therefore could be as old as its characteristic age. Our proposal implies that S147 is the diffuse remnant of the second supernova explosion (that disrupted the binary system) and that a much younger second neutron star (not necessarily manifesting itself as a radio pulsar) should be associated with S147. We use the existing observational data on the system to suggest that the progenitor of the supernova that formed S147 was a Wolf-Rayet star (so that the supernova explosion occurred within a wind bubble surrounded by a massive shell) and to constrain the parameters of the binary system. We also restrict the magnitude and direction of the kick velocity received by the young neutron star at birth and find that the kick vector should not strongly deviate from the orbital plane of the binary system.Comment: 9 pages, 5 figures, revised version accepted for publication in A&

Bioinformatics advances in saliva diagnostics

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart

Statistical inference in a random coefficient panel model

This paper studies the asymptotics of the Weighted Least Squares (WLS) estimator of the autoregressive root in a panel Random Coefficient Autoregression (RCA). We show that, in an RCA context, there is no "unit root problem": the WLS estimator is always asymptotically normal, irrespective of the average value of the autoregressive root, of whether the autoregressive coefficient is random or not, and of the presence and degree of cross dependence. Our simulations indicate that the estimator has good properties, and that confidence intervals have the correct coverage even for sample sizes as small as (N,T)=(10,25). We illustrate our findings through two applications to macroeconomic and financial variables

The meaning of care for older Chinese caregivers : an exploratory model of positive caring

Caring is often a highly personalized and individual activity. Through in-depth and searching interviews with two older care-givers, this study explored the determinants that help to sustain cares in their long-term care role and proposes an explanatory model for sustaining care. Attempts were made to uncover those meanings held by Chinese care-givers in interpreting their roles in a positive way despite the enormous demands placed on them by care-giving or, if they interpreted their care giving negatively, the attitudes that sustained their giving of care. Narrative accounts were obtained through separate interviews (conducted by two experienced social workers) asking open-ended questions guided by prescribed themes (determinants). Content coverage included basic demographic variables: sex, income, education level, religion, age; family responsibility/reciprocity, doing what needs to be done, caring personality, satisfaction and gratification, friendship and company, improved relationship, personal growth and identifying specific rewards of care-giving for self (i.e. the care-giver). The respondents were asked to describe all the above in relation to providing the care as they themselves perceive these domains, then were encouraged to provide a detail explanation for how these domains were encouraging/ discouraging them to continue to care. Similar description and explanation given by the two care-givers were extracted as congruent to the prescribed themes- hence these consistent findings serve to inform the formation of a crude explanatory model for care givers’ commitment to long term care. The study also informs practice in identifying and sustaining good care-givers

Comparison theory and smooth minimal C*-dynamics

We prove that the C*-algebra of a minimal diffeomorphism satisfies Blackadar's Fundamental Comparability Property for positive elements. This leads to the classification, in terms of K-theory and traces, of the isomorphism classes of countably generated Hilbert modules over such algebras, and to a similar classification for the closures of unitary orbits of self-adjoint elements. We also obtain a structure theorem for the Cuntz semigroup in this setting, and prove a conjecture of Blackadar and Handelman: the lower semicontinuous dimension functions are weakly dense in the space of all dimension functions. These results continue to hold in the broader setting of unital simple ASH algebras with slow dimension growth and stable rank one. Our main tool is a sharp bound on the radius of comparison of a recursive subhomogeneous C*-algebra. This is also used to construct uncountably many non-Morita-equivalent simple separable amenable C*-algebras with the same K-theory and tracial state space, providing a C*-algebraic analogue of McDuff's uncountable family of II_1 factors. We prove in passing that the range of the radius of comparison is exhausted by simple C*-algebras.Comment: 30 pages, no figure

Hall Conductivity near the z=2 Superconductor-Insulator Transition in 2D

We analyze here the behavior of the Hall conductivity $\sigma_{xy}$ near a $z=2$ insulator-superconductor quantum critical point in a perpendicular magnetic field. We show that the form of the conductivity is sensitive to the presence of dissipation $\eta$, and depends non-monotonically on $H$ once $\eta$ is weak enough. $\sigma_{xy}$ passes through a maximum at $H \sim \eta T$ in the quantum critical regime, suggesting that the limits $H \to 0$ and $\eta \to 0$ do not commute.Comment: 4 pages, 1 .eps figure, to appear in Phys. Rev.