Theoretical Biology and Medical Modelling This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Computational identification of surrogate genes for prostate cancer phases using machine learning and molecular network analysis
Conclusion: We conclude that the surrogate genes we have selected compose an effective classifier of prostate cancer phases, which corresponds to a minimum characterization of cancer phenotypes on the molecular level. Along with their molecular interaction partners, it is fairly to assume that these genes may have important roles in prostate cancer development; particularly, the un-reported genes may bring new insights for the understanding of the molecular mechanisms. Thus our results may serve as a candidate gene set for further functional studies. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - August 23, 2014 Category: Biomedical Science Authors: Rudong LiXiao DongChengcheng MaLei Liu Source Type: research

The homeostatic set point of the hypothalamus-pituitary-thyroid axis ¿ maximum curvature theory for personalized euthyroid targets
Conclusions: In this treatise, we provide evidence supporting a set point-based approach in tailoring euthyroid targets. Rendering FT4 and TSH within the laboratory normal ranges can be clinically suboptimal if these hormone levels are distant from the individualized euthyroid homeostatic set point. This mathematical technique permits the euthyroid set point to be realistically computed using an algorithm readily implementable for computer-aided calculations to facilitate precise targeted dosing of patients in this modern era of personalized medicine. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - August 8, 2014 Category: Biomedical Science Authors: Melvin LeowSimon Goede Source Type: research

The homeostatic set point of the hypothalamus-pituitary-thyroid axis - maximum curvature theory for personalized euthyroid targets
Conclusions: In this treatise, we provide evidence supporting a set point-based approach in tailoring euthyroid targets. Rendering FT4 and TSH within the laboratory normal ranges can be clinically suboptimal if these hormone levels are distant from the individualized euthyroid homeostatic set point. This mathematical technique permits the euthyroid set point to be realistically computed using an algorithm readily implementable for computer-aided calculations to facilitate precise targeted dosing of patients in this modern era of personalized medicine. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - August 8, 2014 Category: Biomedical Science Authors: Melvin LeowSimon Goede Source Type: research

Prospects for developing an accurate diagnostic biomarker panel for low prevalence cancers
Conclusions: A highly accurate blood-based diagnostic panel can be developed from a reasonable number of individual serum biomarkers that are relatively weak classifiers when used singly. A panel constructed as described is advantageous in that a high level of specificity can be forced, accomplishing a prerequisite for screening asymptomatic populations for low-prevalence cancers. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - August 5, 2014 Category: Biomedical Science Authors: Matthew FirpoKenneth BoucherSean Mulvihill Source Type: research

Optimal back-extrapolation method for estimating plasma volume in humans using the indocyanine green dilution method
Conclusions: Based on the more physiological representation of indocyanine green kinetics and greater consistency with previously reported plasma volume values, the new back-extrapolation method is proposed for use when estimating plasma volume using the indocyanine green dilution method. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 22, 2014 Category: Biomedical Science Authors: David PolidoriClarence Rowley Source Type: research

A model of immunohistochemical differences between invasive breast cancers and DCIS lesions tested on a consecutive case series of 1248 patients
Conclusions: The relative rate of tissue invasion differed substantialy among our patients. Differences depended on tumor types, steroid expression phenotypes and age. The dysfunctional ERs in the ER+PgR- phenotype showed slower rates of tissue invasion, suggesting that ligand binding to functional breast tumor ERs, beside promoting the PgR expression, possibly also promotes tumor transition to the invasive phase.In triple-negative tumors, an age dependent premenopausal mechanism possibly acted as an accelerator of tissue invasion, while faster tissue invasion by HER2-overexpressed tumors in older patients possibly depende...
Source: Theoretical Biology and Medical Modelling - June 11, 2014 Category: Biomedical Science Authors: Sven KurbelKsenija Marjanovi¿Branko Dmitrovi¿ Source Type: research

A new flexible plug and play scheme for modeling, simulating, and predicting gastric emptying
Conclusions: A new plug-and-play scheme for biological systems modeling was developed that allows changes to the modeled structure and behavior with reduced programming effort, by abstracting the biological system into a network of smaller sub-systems with independent behavior. In the new scheme, the modeling and simulation becomes an automatic machine readable and executable task. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - June 10, 2014 Category: Biomedical Science Authors: Shaji KrishnanMark van AvesaatFreddy TroostHenk HendriksAlbert de Graaf Source Type: research

Herpes B virus gD interaction with its human receptor ¿ an in silico analysis approach
Conclusion: In this study, we present structural model for the BV gD in a complex with its receptor. Some features predicted by this model can explain previously reported experimental data. This complex model may lead to a better understanding of the function of BV gD and its interaction with receptor and will improve our understanding of the activation of the BV fusion and entry process. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - June 6, 2014 Category: Biomedical Science Authors: Lingke LiZhengliang QiuYan LiFeng LiangHuahu YeYongqin CaiWanfeng GuoYan LiJunjie Yue Source Type: research

Herpes B virus gD interaction with its human receptor - an in silico analysis approach
Conclusion: In this study, we present structural model for the BV gD in a complex with its receptor. Some features predicted by this model can explain previously reported experimental data. This complex model may lead to a better understanding of the function of BV gD and its interaction with receptor and will improve our understanding of the activation of the BV fusion and entry process. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - June 6, 2014 Category: Biomedical Science Authors: Lingke LiZhengliang QiuYan LiFeng LiangHuahu YeYongqin CaiWanfeng GuoYan LiJunjie Yue Source Type: research

Comparison of calculated and experimental power in maximal lactate-steady state during cycling
Conclusions: The difference of 12 W can be explained by the biological variability of V O2max and V Lamax. The knowledge of both parameters, as well as their individual influence on MLSS, could be important for establishing training recommendations, which could lead to either an improvement in V O2max or V Lamax by performing high intensity or low intensity exercise training, respectively. Furthermore the validity of V Lamax -test should be focused in further studies. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - May 27, 2014 Category: Biomedical Science Authors: Thomas HauserJennifer AdamHenry Schulz Source Type: research

On the origins of the mitotic shift in proliferating cell layers
Conclusions: Taken together, our results strongly suggest that the mitotic shift reflects a time-dependent accumulation of shared cellular interfaces over the course of the cell cycle. These results uncover fundamental constraints on the relationship between cell shape and cell division that should be general in adherent, polarized cell layers. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - May 27, 2014 Category: Biomedical Science Authors: William GibsonBoris RubinsteinEmily MeyerJames VeldhuisG BrodlandRadhika NagpalMatthew Gibson Source Type: research

Surface aggregation patterns of LDL receptors near coated pits III: potential effects of combined retrograde membrane flow-diffusion and a polarized-insertion mechanism
Although the process of endocytosis of the low density lipoprotein (LDL) macromolecule and its receptor have been the subject of intense experimental research and modeling, there are still conflicting hypotheses and even conflicting data regarding the way receptors are transported to coated pits, the manner by which receptors are inserted before they aggregate in coated pits, and the display of receptors on the cell surface. At first it was considered that LDL receptors in human fibroblasts are inserted at random locations and then transported by diffusion toward coated pits. But experiments have not ruled out the possibil...
Source: Theoretical Biology and Medical Modelling - May 22, 2014 Category: Biomedical Science Authors: Héctor Echavarria-HerasCecilia Leal-RamirezOscar Castillo Source Type: research

Improving the estimation of the death rate of infected cells from time course data during the acute phase of virus infections: application to acute HIV-1 infection in a humanized mouse model
Background: Mathematical modeling of virus dynamics has provided quantitative insights into viral infections such as influenza, the simian immunodeficiency virus/human immunodeficiency virus, hepatitis B, and hepatitis C. Through modeling, we can estimate the half-life of infected cells, the exponential growth rate, and the basic reproduction number (R0). To calculate R0 from virus load data, the death rate of productively infected cells is required. This can be readily estimated from treatment data collected during the chronic phase, but is difficult to determine from acute infection data. Here, we propose two new models ...
Source: Theoretical Biology and Medical Modelling - May 21, 2014 Category: Biomedical Science Authors: Hiroki IkedaRob de BoerKei SatoSatoru MoritaNaoko MisawaYoshio KoyanagiKazuyuki AiharaShingo Iwami Source Type: research

Analysis of inter-patient variations in tumour growth rate
Conclusion: This method can be used to evaluate the homogeneity of tumour growth kinetics among patients. Homogeneity of post-chemotherapy regrowth pattern of NSCLC suggests that, in contrast to untreated tumours, the remaining resistant cells or stem cells (if exist) might have similar biological characteristics among these patients. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - May 20, 2014 Category: Biomedical Science Authors: Esmaeil MehraraEva Forssell-Aronsson Source Type: research

Mathematical modeling of the effects of glutathione on arsenic methylation
Conclusions: The mathematical model aids in the interpretation of data from recent experimental studies and showsthat the Challenger pathway of arsenic methylation, supplemented by the glutathione effects describedabove, is sufficient to understand and predict recent experimental data. More experimental studiesare needed to explicate the detailed mechanisms of action of glutathione on arsenic methylation.Recent experimental work on the effects of glutathione on arsenic methylation and our modelingstudy suggest that supplements that increase hepatic glutathione production should be considered asstrategies to reduce adverse ...
Source: Theoretical Biology and Medical Modelling - May 16, 2014 Category: Biomedical Science Authors: Sean LawleyJina YunMary GambleMegan HallMichael ReedH Nijhout Source Type: research