StochKit-FF: Efficient Systems Biology on Multicore Architectures

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.Comment: 14 pages + cover pag

Molecular Clock on a Neutral Network

The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants of the full probability distribution of accumulated mutations in terms of graph properties of the neutral network, and use the formalism to prove overdispersion of the molecular clock. We further show that significant overdispersion arises naturally in evolution when the neutral network is highly sparse, exhibits large global fluctuations in neutrality, and small local fluctuations in neutrality. The results are also relevant for elucidating the topological structure of a neutral network from empirical measurements of the substitution process.Comment: 10 page

Implementation of a Tool to Modify Behavior in a Chronic Disease Management Program

Chronic diseases like diabetes, hypertension, and dyslipidemia continue to be a significant burden on the US health care system. As a result, many healthcare providers are implementing strategies to prevent the incidence of heart disease and other chronic conditions. Among these strategies are proper drug therapy and lifestyle modifications. Behavior change is often the rate-limiting step in the prevention and maintenance of lifestyle modifications. The purpose of this paper is to describe a tool used to guide the progression and assess the effectiveness of a cardiovascular risk reduction program. The tool uses the Transtheoretical Model of Behavior Change to determine the readiness and confidence to change specific lifestyle behaviors pertinent to cardiovascular health. The tool aids the practitioner in developing a patient-centered plan to implement and maintain lifestyle changes and can be tailored to use in any situation requiring a behavior change on the part of the patient

Insulin and IGF-1, but not 17β-estradiol, alter the subcellular localization of MIER1α in MCF7 breast carcinoma cells

Background MIER1α is a transcriptional regulator that interacts with estrogen receptor α and inhibits estrogen-stimulated growth of breast carcinoma cells. Interestingly, analysis of MIER1α subcellular localization in breast samples revealed a stepwise shift from the nucleus to the cytoplasm during progression to invasive carcinoma. Previously, we demonstrated that MIER1α is nuclear in MCF7 cells yet it does not contain a nuclear localization signal. Instead MIER1α is targeted to the nucleus through interaction and co-transport with HDAC 1 and 2. Results In this study, we demonstrate that treatment of MCF7 breast carcinoma cells with either insulin or insulin-like growth factor affects the subcellular localization of MIER1α. Both factors reduce the percentage of cells with nuclear MIER1α from 81 and 89 to 41 and 56 %, respectively. Treatment with 17β-estradiol, on the other hand, had no effect and MIER1α remained nuclear. Conclusions Our data demonstrate that insulin and IGF-1 can contribute to loss of nuclear MIER1α in the MCF7 breast carcinoma cell line

The Ghosts of Bindings Past: Micro-Computed X-Ray Tomography for the Study of Bookbinding

This essay describes the results of a new application of micro-computed X-ray tomography (µCT) to conduct nondestructive investigations of the binding structures of premodern books. This application addresses a twofold challenge in the study of historic bindings and their construction. Few premodern books survive in their original bindings. Moreover, until recently, when books were rebound, the original structures were rarely documented, and the remains were usually discarded. Where original bindings do remain in situ, much of their structure is, by design, hidden. Particulars of construction may be surmised; but without destructive disbinding, little can be proven. µCT enables an exploratory, multilinear approach to codicological investigations that makes bindings accessible in the form of tractable volumetric data

Replicators in Fine-grained Environment: Adaptation and Polymorphism

Selection in a time-periodic environment is modeled via the two-player replicator dynamics. For sufficiently fast environmental changes, this is reduced to a multi-player replicator dynamics in a constant environment. The two-player terms correspond to the time-averaged payoffs, while the three and four-player terms arise from the adaptation of the morphs to their varying environment. Such multi-player (adaptive) terms can induce a stable polymorphism. The establishment of the polymorphism in partnership games [genetic selection] is accompanied by decreasing mean fitness of the population.Comment: 4 pages, 2 figure

Escaping from nonhyperbolic chaotic attractors

We study the noise-induced escape process from chaotic attractors in nonhyperbolic systems. We provide a general mechanism of escape in the low noise limit, employing the theory of large fluctuations. Specifically, this is achieved by solving the variational equations of the auxiliary Hamiltonian system and by incorporating the initial conditions on the chaotic attractor unambiguously. Our results are exemplified with the H{\'e}non and the Ikeda map and can be implemented straightforwardly to experimental data.Comment: replaced with published versio

Programmable models of growth and mutation of cancer-cell populations

In this paper we propose a systematic approach to construct mathematical models describing populations of cancer-cells at different stages of disease development. The methodology we propose is based on stochastic Concurrent Constraint Programming, a flexible stochastic modelling language. The methodology is tested on (and partially motivated by) the study of prostate cancer. In particular, we prove how our method is suitable to systematically reconstruct different mathematical models of prostate cancer growth - together with interactions with different kinds of hormone therapy - at different levels of refinement.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Development and Implementation of a Novel Lifestyle Medicine Advanced Pharmacy Practice Experience Elective

Objective: To develop and implement an Advanced Pharmacy Practice Experience (APPE) to increase student’s awareness and use of lifestyle modifications in chronic disease prevention and management. Design: A five-week APPE was developed that utilized a wide variety of activities, including direct patient care, patient education, case studies, journal clubs and reflective assessment and writing to explore various lifestyle modifications and their relation to chronic disease prevention and management. Conclusion: The novel lifestyle medicine APPE provides students a unique opportunity to advance their knowledge in therapeutic lifestyle changes and expand their understanding of the pharmacist’s role in chronic disease prevention and management