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Theoretical biology medical modelling [journal]
- Chromosome congression explained by nanoscale electrostatics. [Editorial]
- Theor Biol Med Model 2014; 11(1):12.
Nanoscale electrostatic microtubule disassembly forces between positively charged molecules in kinetochores and negative charges on plus ends of microtubules have been implicated in poleward chromosome motions and may also contribute to antipoleward chromosome movements. We propose that chromosome congression can be understood in terms of antipoleward nanoscale electrostatic microtubule assembly forces between negatively charged microtubule plus ends and like-charged chromosome arms, acting in conjunction with poleward microtubule disassembly forces. Several other aspects of post-attachment prometaphase chromosome motions, as well as metaphase oscillations, are consistently explained within this framework.
- Modelling effects of internalized antibody: a simple comparative study. [JOURNAL ARTICLE]
- Theor Biol Med Model 2014 Feb 13; 11(1):11.
The modelling framework is proposed to study protection properties of antibodies to neutralize the effects of plant toxin (ricin). The present study extends our previous work by including (i) the model of intracellular transport of toxin to the Endoplasmic Reticulum and (ii) the model of the internalised antibodies (when antibody is delivered directly into the cytosol).Simulation of the receptor-toxin-antibody interaction is implemented by solving the systems of PDEs (advection-diffusion models) or ODEs (rate models) for the underlying transport coupled with mass-action kinetics.As the main application of the enhanced framework we present a comparative study of two kinds (external and internalised) of antibodies. This comparison is based on calculation of the non-dimensional protection factor using the same set of parameters (geometry, binding constants, initial concentrations of species, and total initial amount of the antibody).This research will provide a framework for consistent evaluation and comparison of different types of antibodies for toxicological applications.
- A vector-free ECG interpretation with P, QRS & T waves as unbalanced transitions between stable configurations of the heart electric field during P-R, S-T & T-P segments. [Journal Article, Research Support, Non-U.S. Gov't]
- Theor Biol Med Model 2014.:10.
Since cell membranes are weak sources of electrostatic fields, this ECG interpretation relies on the analogy between cells and electrets. It is here assumed that cell-bound electric fields unite, reach the body surface and the surrounding space and form the thoracic electric field that consists from two concentric structures: the thoracic wall and the heart. If ECG leads measure differences in electric potentials between skin electrodes, they give scalar values that define position of the electric field center along each lead. Repolarised heart muscle acts as a stable positive electric source, while depolarized heart muscle produces much weaker negative electric field. During T-P, P-R and S-T segments electric field is stable, only subtle changes are detectable by skin electrodes.Diastolic electric field forms after ventricular depolarization (T-P segments in the ECG recording). Telediastolic electric field forms after the atria have been depolarized (P-Q segments in the ECG recording). Systolic electric field forms after the ventricular depolarization (S-T segments in the ECG recording). The three ECG waves (P, QRS and T) can then be described as unbalanced transitions of the heart electric field from one stable configuration to the next and in that process the electric field center is temporarily displaced. In the initial phase of QRS, the rapidly diminishing septal electric field makes measured potentials dependent only on positive charges of the corresponding parts of the left and the right heart that lie within the lead axes. If more positive charges are near the "DOWN" electrode than near the "UP" electrode, a Q wave will be seen, otherwise an R wave is expected. Repolarization of the ventricular muscle is dampened by the early septal muscle repolarization that reduces deflection of T waves. Since the "UP" electrode of most leads is near the usually larger left ventricle muscle, T waves are in these leads positive, although of smaller amplitude and longer duration than the QRS wave in the same lead. The proposed interpretation is applied to bundle branch blocks, fascicular (hemi-) blocks and changes during heart muscle ischemia.
- Optimization and enhancement of H&E stained microscopical images by applying bilinear interpolation method on lab color mode. [Journal Article]
- Theor Biol Med Model 2014.:9.
Hematoxylin & Eosin (H&E) is a widely employed technique in pathology and histology to distinguish nuclei and cytoplasm in tissues by staining them in different colors. This procedure helps to ease the diagnosis by enhancing contrast through digital microscopes. However, microscopic digital images obtained from this technique usually suffer from uneven lighting, i.e. poor Koehler illumination. Several off-the-shelf methods particularly established to correct this problem along with some popular general commercial tools have been examined to find out a robust solution.First, the characteristics of uneven lighting in pathological images obtained from the H&E technique are revealed, and then how the quality of these images can be improved by employing bilinear interpolation based approach applied on the channels of Lab color mode is explored without losing any essential detail, especially for the color information of nuclei (hematoxylin stained sections). Second, an approach to enhance the nuclei details that are a fundamental part of diagnosis and crucially needed by the pathologists who work with digital images is demonstrated.Merits of the proposed methodology are substantiated on sample microscopic images. The results show that the proposed methodology not only remedies the deficiencies of H&E microscopical images, but also enhances delicate details.Non-uniform illumination problems in H&E microscopical images can be corrected without compromising crucial details that are essential for revealing the features of tissue samples.
- How robust are the natural history parameters used in chlamydia transmission dynamic models? A systematic review. [Journal Article, Research Support, Non-U.S. Gov't]
- Theor Biol Med Model 2014.:8.
Transmission dynamic models linked to economic analyses often form part of the decision making process when introducing new chlamydia screening interventions. Outputs from these transmission dynamic models can vary depending on the values of the parameters used to describe the infection. Therefore these values can have an important influence on policy and resource allocation. The risk of progression from infection to pelvic inflammatory disease has been extensively studied but the parameters which govern the transmission dynamics are frequently neglected. We conducted a systematic review of transmission dynamic models linked to economic analyses of chlamydia screening interventions to critically assess the source and variability of the proportion of infections that are asymptomatic, the duration of infection and the transmission probability. We identified nine relevant studies in Pubmed, Embase and the Cochrane database. We found that there is a wide variation in their natural history parameters, including an absolute difference in the proportion of asymptomatic infections of 25% in women and 75% in men, a six-fold difference in the duration of asymptomatic infection and a four-fold difference in the per act transmission probability. We consider that much of this variation can be explained by a lack of consensus in the literature. We found that a significant proportion of parameter values were referenced back to the early chlamydia literature, before the introduction of nucleic acid modes of diagnosis and the widespread testing of asymptomatic individuals. In conclusion, authors should use high quality contemporary evidence to inform their parameter values, clearly document their assumptions and make appropriate use of sensitivity analysis. This will help to make models more transparent and increase their utility to policy makers.
- A selection criterion for patterns in reaction-diffusion systems. [Journal Article, Research Support, Non-U.S. Gov't]
- Theor Biol Med Model 2014.:7.
Alan Turing's work in Morphogenesis has received wide attention during the past 60 years. The central idea behind his theory is that two chemically interacting diffusible substances are able to generate stable spatial patterns, provided certain conditions are met. Ever since, extensive work on several kinds of pattern-generating reaction diffusion systems has been done. Nevertheless, prediction of specific patterns is far from being straightforward, and a great deal of interest in deciphering how to generate specific patterns under controlled conditions prevails.Techniques allowing one to predict what kind of spatial structure will emerge from reaction-diffusion systems remain unknown. In response to this need, we consider a generalized reaction diffusion system on a planar domain and provide an analytic criterion to determine whether spots or stripes will be formed. Our criterion is motivated by the existence of an associated energy function that allows bringing in the intuition provided by phase transitions phenomena.Our criterion is proved rigorously in some situations, generalizing well-known results for the scalar equation where the pattern selection process can be understood in terms of a potential. In more complex settings it is investigated numerically. Our work constitutes a first step towards rigorous pattern prediction in arbitrary geometries/conditions. Advances in this direction are highly applicable to the efficient design of Biotechnology and Developmental Biology experiments, as well as in simplifying the analysis of morphogenetic models.
- A model to determine the effect of collagen fiber alignment on heart function post myocardial infarction. [Journal Article, Research Support, N.I.H., Extramural, Research Support, U.S. Gov't, Non-P.H.S.]
- Theor Biol Med Model 2014.:6.
Adverse remodeling of the left ventricle (LV) following myocardial infarction (MI) leads to heart failure. Recent studies have shown that scar anisotropy is a determinant of cardiac function post-MI, however it remains unclear how changes in extracellular matrix (ECM) organization and structure contribute to changes in LV function. The objective of this study is to develop a model to identify potential mechanisms by which collagen structure and organization affect LV function post-MI.A four-region, multi-scale, cylindrical model of the post-MI LV was developed. The mechanical properties of the infarct region are governed by a constitutive equation based on the uncrimping of collagen fibers. The parameters of this constitutive equation include collagen orientation, angular dispersion, fiber stiffness, crimp angle, and density. Parametric variation of these parameters was used to elucidate the relationship between collagen properties and LV function.The mathematical model of the LV revealed several factors that influenced cardiac function post-MI. LV function was maximized when collagen fibers were aligned longitudinally. Increased collagen density was also found to improve stroke volume for longitudinal alignments while increased fiber stiffness decreased stroke volume for circumferential alignments.The results suggest that cardiac function post-MI is best preserved through increased circumferential compliance. Further, this study identifies several collagen fiber-level mechanisms that could potentially regulate both infarct level and organ level mechanics. Improved understanding of the multi-scale relationships between the ECM and LV function will be beneficial in the design of new diagnostic and therapeutic technologies.
- Cost-effective length and timing of school closure during an influenza pandemic depend on the severity. [Journal Article, Research Support, Non-U.S. Gov't]
- Theor Biol Med Model 2014.:5.
There has been a variation in published opinions toward the effectiveness of school closure which is implemented reactively when substantial influenza transmissions are seen at schools. Parameterizing an age-structured epidemic model using published estimates of the pandemic H1N1-2009 and accounting for the cost effectiveness, we examined if the timing and length of school closure could be optimized.Age-structured renewal equation was employed to describe the epidemic dynamics of an influenza pandemic. School closure was assumed to take place only once during the course of the pandemic, abruptly reducing child-to-child transmission for a fixed length of time and also influencing the transmission between children and adults. Public health effectiveness was measured by reduction in the cumulative incidence, and cost effectiveness was also examined by calculating the incremental cost effectiveness ratio and adopting a threshold of 1.0 × 10⁷ Japanese Yen/life-year.School closure at the epidemic peak appeared to yield the largest reduction in the final size, while the time of epidemic peak was shown to depend on the transmissibility. As the length of school closure was extended, we observed larger reduction in the cumulative incidence. Nevertheless, the cost effectiveness analysis showed that the cost of our school closure scenario with the parameters derived from H1N1-2009 was not justifiable. If the risk of death is three times or greater than that of H1N1-2009, the school closure could be regarded as cost effective.There is no fixed timing and duration of school closure that can be recommended as universal guideline for different types of influenza viruses. The effectiveness of school closure depends on the transmission dynamics of a particular influenza virus strain, especially the virulence (i.e. the infection fatality risk).
- A model of hematopoietic stem cell proliferation under the influence of a chemotherapeutic agent in combination with a hematopoietic inducing agent. [Journal Article, Research Support, Non-U.S. Gov't]
- Theor Biol Med Model 2014.:4.
Hematopoiesis is a complex process that encompasses both pro-mitotic and anti-mitotic stimuli. Pharmacological agents used in chemotherapy have a prominent anti-mitotic effect. The approach of inhibiting cell proliferation is rational with respect to the rapidly dividing malignant cells. However, it poses a serious problem with respect to cell proliferation of cell types required for the 'house-keeping' operations of the human body. One such affected system is hematopoiesis. Chemotherapy induced anemia is an undesired side effect of chemotherapy that can lead to serious complications. Patients exhibiting anemia or leukopenia during chemotherapy are frequently administered a hematopoietic inducing agent that enhances hematopoiesis.In previous work, we derived a mathematical model consisting of a set of delay differential equations that was dependent on the effect of a hematopoietic inducing agent. The aim of the current work was to formulate a mathematical model that captures both the effect of a chemotherapeutic agent in combination with a hematopoietic inducing agent. Steady state solutions and stability analysis of the system of equations is performed and numerical simulations of the stem cell population are provided.Numerical simulations confirm that our mathematical model captures the desired result which is that the use of hematopoietic agents in conjunction with chemotherapeutic agents can decrease the negative secondary effects often experienced by patients.The proposed model indicates that the introduction of hematopoietic inducing agents have clinical potential to offset the deleterious effects of chemotherapy treatment. Furthermore, the proposed model is relevant in that it enhances the understanding of stem cell dynamics and provides insight on the stem cell kinetics.
- Metapopulation epidemic models with heterogeneous mixing and travel behaviour. [Journal Article, Research Support, Non-U.S. Gov't]
- Theor Biol Med Model 2014.:3.
Determining the pandemic potential of an emerging infectious disease and how it depends on the various epidemic and population aspects is critical for the preparation of an adequate response aimed at its control. The complex interplay between population movements in space and non-homogeneous mixing patterns have so far hindered the fundamental understanding of the conditions for spatial invasion through a general theoretical framework. To address this issue, we present an analytical modelling approach taking into account such interplay under general conditions of mobility and interactions, in the simplifying assumption of two population classes.We describe a spatially structured population with non-homogeneous mixing and travel behaviour through a multi-host stochastic epidemic metapopulation model. Different population partitions, mixing patterns and mobility structures are considered, along with a specific application for the study of the role of age partition in the early spread of the 2009 H1N1 pandemic influenza.We provide a complete mathematical formulation of the model and derive a semi-analytical expression of the threshold condition for global invasion of an emerging infectious disease in the metapopulation system. A rich solution space is found that depends on the social partition of the population, the pattern of contacts across groups and their relative social activity, the travel attitude of each class, and the topological and traffic features of the mobility network. Reducing the activity of the less social group and reducing the cross-group mixing are predicted to be the most efficient strategies for controlling the pandemic potential in the case the less active group constitutes the majority of travellers. If instead traveling is dominated by the more social class, our model predicts the existence of an optimal across-groups mixing that maximises the pandemic potential of the disease, whereas the impact of variations in the activity of each group is less important.The proposed modelling approach introduces a theoretical framework for the study of infectious diseases spread in a population with two layers of heterogeneity relevant for the local transmission and the spatial propagation of the disease. It can be used for pandemic preparedness studies to identify adequate interventions and quantitatively estimate the corresponding required effort, as well as in an emerging epidemic situation to assess the pandemic potential of the pathogen from population and early outbreak data.