A Mathematical Framework for Agent Based Models of Complex Biological Networks

Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis.Comment: To appear in Bulletin of Mathematical Biolog

FACTORS AFFECTING METFORMIN AND CLOMIPHENE’S REPRODUCTIVE EFFICACY IN PCOS WOMEN

Polycystic Ovarian Syndrome (PCOS) is a heterogeneous multifactorial disorder in which the ovarian dysfunction is the main cause of an ovulatory infertility. Metformin and Clomiphene Citrate (CC) are two effective drugs to induce ovulation in these patients. The study aimed to ascertain the effect of obesity, serum insulin and free testosterone levels on fertility success with metformin and CC as first line approaches in PCOS. This clinical study was a retrospective multicenter cohort study conducted in nine gynecology and endocrinology clinics. It included (61) PCOS women, aged (18-32) years, having desire to conceive, and free from the study medications for more than six months. Patients were divided to metformin receiving and CC receiving groups. Main outcomes of measure were; pregnancy rate, and improvement in PCOS as detected by ultrasound on their second visit. Results showed that CC was more effective in non-obese users (P0.05). Overall improvement was affected by Serum Free Testosterone (SFT) in both study groups (P\u3e0.05). Metformin was effective regardless of patient’s SFT levels, while CC was effective in patients with high SFT levels. There was a significant association between obesity and pregnancy rate in metformin users (P0.05). However, CC was less effective than metformin in overall improvement (OR=0.53, P\u3e0.05,) suggesting metformin as the possible drug of choice regardless to obesity, serum insulin and SFT levels

Anisotropies in the Neutrino Fluxes and Heating Profiles in Two-dimensional, Time-dependent, Multi-group Radiation Hydrodynamics Simulations of Rotating Core-Collapse Supernovae

Using the 2D multi-group, flux-limited diffusion version of the code VULCAN/2D, that also incorporates rotation, we have calculated the collapse, bounce, shock formation, and early post-bounce evolutionary phases of a core-collapse supernova for a variety of initial rotation rates. This is the first series of such multi-group calculations undertaken in supernova theory with fully multi-D tools. We find that though rotation generates pole-to-equator angular anisotropies in the neutrino radiation fields, the magnitude of the asymmetries is not as large as previously estimated. Moreover, we find that the radiation field is always more spherically symmetric than the matter distribution, with its plumes and convective eddies. We present the dependence of the angular anisotropy of the neutrino fields on neutrino species, neutrino energy, and initial rotation rate. Only for our most rapidly rotating model do we start to see qualitatively different hydrodynamics, but for the lower rates consistent with the pre-collapse rotational profiles derived in the literature the anisotropies, though interesting, are modest. This does not mean that rotation does not play a key role in supernova dynamics. The decrease in the effective gravity due to the centripetal effect can be quite important. Rather, it means that when a realistic mapping between initial and final rotational profiles and 2D multi-group radiation-hydrodynamics are incorporated into collapse simulations the anisotropy of the radiation fields may be only a secondary, not a pivotal factor, in the supernova mechanism.Comment: Includes 11 low-resolution color figures, accepted to the Astrophysical Journal (June 10, 2005; V. 626); high-resolution figures and movies available from the authors upon reques

Boolean dynamics revisited through feedback interconnections

Boolean models of physical or biological systems describe the global dynamics of the system and their attractors typically represent asymptotic behaviors. In the case of large networks composed of several modules, it may be difficult to identify all the attractors. To explore Boolean dynamics from a novel viewpoint, we will analyse the dynamics emerging from the composition of two known Boolean modules. The state transition graphs and attractors for each of the modules can be combined to construct a new asymptotic graph which will (1) provide a reliable method for attractor computation with partial information; (2) illustrate the differences in dynamical behavior induced by the updating strategy (asynchronous, synchronous, or mixed); and (3) show the inherited organization/structure of the original network’s state transition graph.publishe

A Survey of Bayesian Statistical Approaches for Big Data

The modern era is characterised as an era of information or Big Data. This has motivated a huge literature on new methods for extracting information and insights from these data. A natural question is how these approaches differ from those that were available prior to the advent of Big Data. We present a review of published studies that present Bayesian statistical approaches specifically for Big Data and discuss the reported and perceived benefits of these approaches. We conclude by addressing the question of whether focusing only on improving computational algorithms and infrastructure will be enough to face the challenges of Big Data

Економічна ефективність, еластичність масштабу та ефект масштабу в банківському секторі арабських країн

This study investigates Cost Efficiency, Scale Elasticity and Scale Economies of the Jordanian, Egyptian, Saudi Arabian and Bahraini banking systems. Our sample comprises information on 82 banks operating in the countries under study over 1992-2000. The stochastic frontier and Fourierflexible form are used to estimate cost efficiency, scale elasticity and scale efficiency levels. The cost efficiency averaged around 95% over the 1992-2000 period. Islamic banks are found to be the most cost efficient while investment banks are the least. The cost scale elasticity estimates reveal diseconomies of around five percent and the cost scale inefficiency estimates suggest that banks are 65% scale efficient. У даній роботі вивчаються питання економічної ефективності, еластичності масштабу та ефекту масштабу в банківських секторах Йорданії, Єгипту, Саудівської Аравії та Бахрейну. Під час проведення дослідження використано дані про діяльність 82 банків протягом 1992-2000 рр. З метою оцінки рівнів вищезгаданих змінних у роботі використано метод стохастичної межі та гнучкий ряд Фур’є. Як виявилось, протягом 1992-2000 рр. середній показник економічної ефективності становив понад 95%. Також результати дослідження говорять, що ісламські банки є найбільш ефективними, тоді як продуктивність інвестиційних банків є найнижчою. Результати оцінювання еластичності масштабу вказали на те, що рівень негативних наслідків господарювання становить 5%