Theoretical Biology and Medical ModellingThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

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A mechanistic model of infection: why duration and intensity of contacts should be included in models of disease spreadEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The importance of highly connected individuals, so-called super-spreaders, for disease spread seems to be overestimated when a constant per-contact transmission probability is assumed. This holds particularly for diseases with low basic reproduction numbers. Simulations of disease spread should weight contacts by duration and intensity. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - November 17, 2009 Category: Biomedical Science Authors: Timo Smieszek Source Type: journals

Formal kinetics of H1N1 epidemicEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We are probably only at the initial stage of development of the H1N1 epidemic. Increasing the number of H1N1-resistant people in future (e.g. due to vaccination) may influence the dynamics of epidemic development. At present, the development of the epidemic depends only on the number of people in the population who are initially resistant to the virus. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 14, 2009 Category: Biomedical Science Authors: Konstantin Gurevich Source Type: journals

Comparative modeling of DNA and RNA polymerases from Moniliophthora perniciosa mitochondrial plasmidEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: This work contributes to the development of new alternatives for controlling the fungal agent of witches' broom disease. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 9, 2009 Category: Biomedical Science Authors: Bruno AndradeAlex TarantoAristoteles Goes-NetoAngelo Duarte Source Type: journals

Homeostatic mechanisms in dopamine synthesis and release: a mathematical modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Dopaminergic systems must respond robustly to important biological signals such as bursts, while at the same time maintaining homeostasis in the face of normal biological fluctuations in inputs, expression levels, and firing rates. This is accomplished through the cooperative effect of many different homeostatic mechanisms including special properties of tyrosine hydroxylase, the dopamine transporters, and the dopamine autoreceptors. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - September 9, 2009 Category: Biomedical Science Authors: Janet BestH. NijhoutMichael Reed Source Type: journals

Binding site of ABC transporter homology models confirmed by ABCB1 crystal structureEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The human ATP-binding cassette (ABC) transporters ABCB1, ABCC4 and ABCC5 are involved in resistance to chemotherapeutic agents. Here we present molecular models of ABCB1, ABCC4 and ABCC5 by homology based on a wide open inward-facing conformation of Escherichia coli MsbA, which were constructed in order to elucidate differences in the electrostatic and molecular features of their drug recognition conformations. As a quality assurance of the methodology, the ABCB1 model was compared to an ABCB1 X-ray crystal structure, and with published cross-linking and site directed mutagenesis data of ABCB1. Amino acids Ile306 (TMH5), I...
Source: Theoretical Biology and Medical Modelling - September 3, 2009 Category: Biomedical Science Authors: Aina RavnaIngebrigt SylteGeorg Sager Source Type: journals

A model analysis of static stress in the vestibular membranesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Static hoop stress disparities are likely to exist in the vestibular membranes given their complex physical configurations. Such stress disparities may contribute to the development of membrane pathologies as seen in Meniere's Disease. They may also factor in the evolutionary development of other derivative membrane structures such as the saccule, the lagena, and the cochlea found in higher animals. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - August 31, 2009 Category: Biomedical Science Authors: Daniel Pender Source Type: journals

The terrestrial evolution of metabolism and life - by the numbersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The equation models the longevity extending affects of caloric restriction, and shows where those affects wane. The equation models the immortality of some types of cells, and supports the argument for the origins of life being at submarine volcanic vents and black smokers. The equation clarifies how early life had to change to survive drifting to the surface, and what drove mutations in its ascent. The equation does not deal with cause and affect; it deals with variables in the essentials of all life, and treats life as an epiphenomenon of these variables. The equation describes how battery discharge into the...
Source: Theoretical Biology and Medical Modelling - August 26, 2009 Category: Biomedical Science Authors: Gregory O'Kelly Source Type: journals

A tumor cord model for doxorubicin delivery and dose optimization in solid tumorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Drug infusion time has a significant effect on the spatial profile of cell mortality within tumor cord systems. Therefore, extending infusion times (up to 2 hours) and fractionating large doses are two strategies that may preserve or increase anti-tumor activity and reduce cardiotoxicity by decreasing peak plasma concentration. However, even under optimal conditions, doxorubicin may have limited delivery into advanced solid tumors. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - August 8, 2009 Category: Biomedical Science Authors: Steffen Eikenberry Source Type: journals

Using a human cardiovascular-respiratory model to characterize cardiac tamponade and pulsus paradoxusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our modeling study of cardiac tamponade dissects the roles played by septal motion, atrioventricular and right-left ventricular interactions, pulmonary blood pooling, and the depth of respiration. The study fully describes the physiological basis of pulsus paradoxus. Our detailed analysis provides biophysically-based insights helpful for future experimental and clinical study of cardiac tamponade and related pericardial diseases. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - August 5, 2009 Category: Biomedical Science Authors: Deepa RamachandranChuan LuoTony MaJohn Clark Source Type: journals

In silico evidence for the species-specific conservation of mosquito retroposons: Implications as a molecular biomarkerEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We offer evidence to support the species-specific conservation of mosquito retroposons among lower taxa. Our findings suggest that retroposons may therefore constitute a unique biomarker for mosquito species that may be exploited in molecular entomology. Mosquito RST-specific MAbs may possibly permit synthesis of DDT immunoconjugates that could be used to achieve species-tailored toxicity. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 28, 2009 Category: Biomedical Science Authors: Wilson ByarugabaHenry KajumbulaMisaki Wayengera Source Type: journals

Examination of effects of GSK3-[beta] phosphorylation, [beta]-catenin phosphorylation, and [beta]-catenin degradation in kinetics of Wnt signaling pathway using computational methodEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The phosphorylations of [beta]-catenin by kinases other than GSK3[beta] should take place at free unphorphorylated [beta]-catenin instead of the GSK3[beta]-phosphorylated [beta]-catenin *. In order to account for observed enhanced TCF activity, the step of [beta]-catenin dephosphorylation is essential, and the kinetic parameters of [beta]-catenin phosphorylation and degradation need to meet a condition, describing in the text below. These findings should be useful for future experiments. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 21, 2009 Category: Biomedical Science Authors: Ying-Chieh Sun Source Type: journals

Ranking candidate genes in rat models of type 2 diabetesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The very good agreement between CGC gene rankings and manual ratings confirms that CGC is as a reliable tool for interpreting textual information. This, together with the possibility to select many different sub-phenotypes, makes CGC a versatile tool for finding candidate genes. CGC is publicly available at http://ratmap.org/CGC. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 2, 2009 Category: Biomedical Science Authors: Lars AnderssonGreta PetersenFredrik Stahl Source Type: journals

Models of epidemics: when contact repetition and clustering should be includedEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We show that random mixing models provide acceptable estimates of the total outbreak size if the number of contacts per day is high or if the per-contact transmission probability is high, as seen in typical childhood diseases such as measles. In the case of very short infectious periods, for instance, as in Norovirus, models assuming repeating contacts will also behave similarly as random mixing models. If the number of daily contacts or the transmission probability is low, as assumed for MRSA or Ebola, particular consideration should be given to the actual structure of potentially contagious contacts when des...
Source: Theoretical Biology and Medical Modelling - June 28, 2009 Category: Biomedical Science Authors: Timo SmieszekLena FiebigRoland Scholz Source Type: journals

Antimicrobial breakpoint estimation accounting for variability in pharmacokineticsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Compared to traditional methods, our weighted AUC approach gives a more powerful PK/PD link and revealed, through some examples, interesting issues about uniqueness of therapeutic outcome indices and antibiotic resistance problems. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - June 25, 2009 Category: Biomedical Science Authors: Goue Denis Gohore BiJun LiFahima Nekka Source Type: journals

Theoretical study of the Usutu virus helicase 3D structure, by means of computer-aided homology modellingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Background: Usutu virus belongs to the Flaviviridae viral family and constitutes an important pathogen. The viral helicase is an ideal target for inhibitor design, since this enzyme is essential for the survival, proliferation and transmission of the virus. Results: Towards a drug-design approach, the 3D model of the Usutu virus helicase structure has been designed, using conventional homology modelling techniques and the known 3D-structure of the Murray Valley Encephalitis virus helicase, of the same viral family, as template. The model was then subjected to extended molecular dynamics simulations in a periodic box, fille...
Source: Theoretical Biology and Medical Modelling - June 24, 2009 Category: Biomedical Science Authors: Dimitrios Vlachakis Source Type: journals

Computational investigation of epithelial cell dynamic phenotype in vitroEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We documented the causal chains of events, and their relative roles, responsible for simulated cystogenesis. The results stand as an early hypothesis--a theory--of how individual MDCK cell actions give rise to consistently roundish, cystic organoids. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - May 28, 2009 Category: Biomedical Science Authors: Sean KimSunwoo ParkKeith MostovJayanta DebnathC Anthony Hunt Source Type: journals

Extension of Murray's law using a non-Newtonian model of blood flowEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: It is demonstrated that the entropy generated in all the daughter vessels is greater than the entropy generated in the parent vessel. Furthermore, it is shown that the difference of entropy generation between the parent and daughter vessels is smaller for a non-Newtonian fluid than for a Newtonian fluid. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - May 15, 2009 Category: Biomedical Science Authors: Remi Revellin, Francois Rousset, David Baud and Jocelyn Bonjour Source Type: journals

Scale-free flow of life: on the biology, economics, and physics of the cellEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The present work is intended to demonstrate that most of the paradoxes, controversies, and contradictions accumulated in molecular and cell biology over many years of research can be readily resolved if the cell and living systems in general are re-interpreted within an alternative paradigm of biological organization that is based on the concepts and empirical laws of nonequilibrium thermodynamics. In addition to resolving paradoxes and controversies, the proposed re-conceptualization of the cell and biological organization reveals hitherto unappreciated connections among many seemingly disparate phenomena and observations...
Source: Theoretical Biology and Medical Modelling - May 5, 2009 Category: Biomedical Science Authors: Alexei Kurakin Source Type: journals

FEM-based oxygen consumption and cell viability models for avascular pancreatic isletsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Results of the computational models are, as a first estimate, in good quantitative agreement with existing experimental evidence, and they confirm that during culture, hypoxia is often a problem for non-vascularised islet and can lead to considerable cell death (necrosis), especially in the core region of larger islets. Such models are of considerable interest to improve the function and viability of cultured, transplanted, or encapsulated islets. The present implementation allows convenient extension to true multiphysics applications that solve coupled physics phenomena such as diffusion and consumption with ...
Source: Theoretical Biology and Medical Modelling - April 16, 2009 Category: Biomedical Science Authors: Peter Buchwald Source Type: journals

Theoretical basis for reducing time-lines to the determination of positive Mycobacterium tuberculosis cultures using thymidylate kinase (TMK) assaysEmail this article to a colleague. Save this article to My Clippings. discuss this article 1 CommentDiscuss or comment on this article.
Conclusions: TMKmyc assays may be useful for reducing the time-lines to positive identification of Mycobacterium tuberculosis (M.tb) cultures, thereby accelerating disease diagnosis and drug resistance profiling. Incorporating "chemiluminiscent or fluorescent" strategies may enable "photo-detection of TMKmyc changes" and hence automation of the entire assay. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - March 18, 2009 Category: Biomedical Science Authors: Misaki Wayengera Source Type: journals

Binding of long-chain α-neurotoxin would stabilize the resting state of nAChR: A comparative study with α-conotoxinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: These observations could support the claim that alpha neurotoxins stabilize the nAChR resting state. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - February 11, 2009 Category: Biomedical Science Authors: Adak Nasiripourdori, Bijan Ranjbar and Hossein Naderi-Manesh Source Type: journals

Binding of long-chain alpha-neurotoxin would stabilize the resting state of nAChR: A comparative study with alpha-conotoxinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: These observations could support the claim that alpha neurotoxins stabilize the nAChR resting state. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - February 11, 2009 Category: Biomedical Science Authors: Adak Nasiripourdori, Bijan Ranjbar and Hossein Naderi-manesh Source Type: journals

Mitochondrial concept of leukemogenesis: key role of oxygen-peroxide effectsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The argument described in this article is used to explain the causes of congenital and children's leukemia, and the induction of leukemia by certain agents (vitamin K3, benzene, etc.). Specific research is required to validate the proposals made in this article. This will require accurate and accessible methods for measuring and assessing oxidative stress in different types of cells in general, and in hemopoietic cells in particular, in their different functional states. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - November 11, 2008 Category: Biomedical Science Authors: Boris N Lyu, Sanzhar B Ismailov, Bolat Ismailov and Marina B Lyu Source Type: journals

Feature context-dependency and complexity-reduction in probability landscapes for integrative genomicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: These two advances in our understanding of the properties of probability landscapes not only simplify subsequent cross-correlation analysis in hypothesis-driven model building and testing, but also provide additional insights into the biological gene regulatory problems studied. Furthermore, insights into the nature of individual features and a classification of features according to their minimal context-dependency are achieved. The formal structure proposed contributes to a concrete and tangible basis for attempting to formulate novel mathematical structures for describing gene regulation in eukaryotes on a g...
Source: Theoretical Biology and Medical Modelling - September 10, 2008 Category: Biomedical Science Authors: Annick Lesne and Arndt Benecke Source Type: journals

Identification of restriction endonuclease with potential ability to cleave the HSV-2 genome: Inherent potential for biosynthetic versus live recombinant microbicidesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Viral genome slicing by way of these bacterially- derived R-M enzymatic peptides may have therapeutic potential in HSV-2 infection; a cofactor for HIV-1 acquisition and transmission. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - August 7, 2008 Category: Biomedical Science Authors: Misaki Wayengera, Henry Kajumbula and Wilson Byarugaba Source Type: journals

Does codon bias have an evolutionary origin?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 30, 2008 Category: Biomedical Science Authors: Jan C Biro Source Type: journals

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 29, 2008 Category: Biomedical Science Authors: Jan C Biro Source Type: journals

The velocity of the arterial pulse wave: a viscous-fluid shock wave in an elastic tubeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Contrary to the theory used for more than fifty years to predict the PWV, it speeds up as arteries become smaller and smaller. Furthermore, an increase in the PWV in small arteries may in some cases be due to decreasing force of myocardial contraction rather than arterial stiffness. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 29, 2008 Category: Biomedical Science Authors: Page R. Painter Source Type: journals

Heterogeneity in multistage carcinogenesis and mixture modelingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Carcinogenesis is commonly described as a multistage process, in which stem cells are transformed into cancer cells via a series of mutations. In this article, we consider extensions of the multistage carcinogenesis model by mixture modeling. This approach allows us to describe population heterogeneity in a biologically meaningful way. We focus on finite mixture models, for which we prove identifiability. These models are applied to human lung cancer data from several birth cohorts. Maximum likelihood estimation does not perform well in this application due to the heavy censoring in our data. We thus use analytic graduatio...
Source: Theoretical Biology and Medical Modelling - July 21, 2008 Category: Biomedical Science Authors: Sandro Gsteiger and Stephan Morgenthaler Source Type: journals

Fractal parameters and vascular networks: facts & artifactsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The fractal dimension Df is likely to be the most promising tool for monitoring the effectiveness of anti-angiogenic therapies in various clinical contexts. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - July 17, 2008 Category: Biomedical Science Authors: Daniele Mancardi, Gianfranco Varetto, Enrico Bucci, Fabrizio Maniero and Caterina Guiot Source Type: journals

Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: A series of ABMs are presented extending from the level of intracellular mechanism to clinically observed behavior in the intensive care setting. The ABMs all utilize cell-level agents that encapsulate specific mechanistic knowledge extracted from in vitro experiments. The execution of the ABMs results in a dynamic representation of the multi-scale conceptual models derived from those experiments. These models represent a qualitative means of integrating basic scientific information on acute inflammation in a multi-scale, modular architecture as a means of conceptual model verification that can potentially be ...
Source: Theoretical Biology and Medical Modelling - May 27, 2008 Category: Biomedical Science Authors: Gary An Source Type: journals

Origin of the blood hyperserotonemia of autismEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The models yields platelet 5-HT concentrations that are consistent with values reported in experimental studies. If the parameters are considered independent, the model predicts that platelet 5-HT levels should be sensitive to changes in the platelet 5-HT uptake rate constant, the proportion of free 5-HT cleared in the liver and lungs, the gut 5-HT production rate and its regulation, and the volume of the gut wall. Linear and non-linear interactions among these and other parameters are specified in the equation, which may facilitate the design and interpretation of experimental studies. (Source: Theoretical Bi...
Source: Theoretical Biology and Medical Modelling - May 22, 2008 Category: Biomedical Science Authors: Skirmantas Janusonis Source Type: journals

A mathematical model of glutathione metabolismEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We show that the glutathione pools in hepatic cells and in the blood are quite insensitive to fluctuations in amino acid input and offer an explanation based on model predictions. In contrast, we show that hepatic glutathione pools are highly sensitive to the level of oxidative stress. The model shows that trisomy 21, an increase in oxidative stress, and subsequent increased transport of GSH precursors by peripheral cells can explain the metabolic profile of Down syndrome. The model also correctly simulates the metabolic profile of autism when oxidative stress is substantially increased, the adenosine concentr...
Source: Theoretical Biology and Medical Modelling - April 28, 2008 Category: Biomedical Science Authors: Michael C Reed, Rachel L Thomas, Jovana Pavisic, S JILL James, Cornelia M Ulrich and H FREDERIK Nijhout Source Type: journals

A statistical model for the identification of genes governing the incidence of cancer with ageEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The cancer incidence increases with age. This epidemiological pattern of cancer incidence can be attributed to molecular and cellular processes of individual subjects. Also, the incidence of cancer with ages can be controlled by genes. Here we present a dynamic statistical model for explaining the epidemiological pattern of cancer incidence based on individual genes that regulate cancer formation and progression. We incorporate the mathematical equations of age-specific cancer incidence into a framework for functional mapping aimed at identifying quantitative trait loci (QTLs) for dynamic changes of a complex trait. The ma...
Source: Theoretical Biology and Medical Modelling - April 16, 2008 Category: Biomedical Science Authors: Kiranmoy Das and Rongling Wu Source Type: journals

Functional mapping imprinted quantitative trait loci underlying developmental characteristicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The functional iQTL mapping approach developed here provides a quantitative and testable framework for assessing the interplay between imprinted genes and a developmental process, and will have important implications for elucidating the genetic architecture of imprinted traits. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - March 17, 2008 Category: Biomedical Science Authors: Yuehua Cui, Shaoyu Li and Gengxin Li Source Type: journals

Scaling, growth and cyclicity in biology: a new computational approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: As an example of its implementation, the method is applied to the analysis of human growth curves. The excellent quality of the results (R**2=0.998) demonstrates the usefulness and reliability of the approach. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - February 29, 2008 Category: Biomedical Science Authors: Pier Paolo Delsanto, Antonio S Gliozzi and Caterina Guiot Source Type: journals

Sampling and sensitivity analyses tools (SaSAT) for computational modellingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
SaSAT (Sampling and Sensitivity Analysis Tools) is a user-friendly software package for applying uncertainty and sensitivity analyses to mathematical and computational models of arbitrary complexity and context. The toolbox is built in Matlab, a numerical mathematical software package, and utilises algorithms contained in the Matlab Statistics Toolbox. However, Matlab is not required to use SaSAT as the software package is provided as an executable file with all the necessary supplementary files. The SaSAT package is also designed to work seamlessly with Microsoft Excel but no functionality is forfeited if that software is...
Source: Theoretical Biology and Medical Modelling - February 27, 2008 Category: Biomedical Science Authors: Alexander Hoare, David G Regan and David P Wilson Source Type: journals

Variance in multiplex suspension array assays: a distribution generation machine for multiplex countsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Using larger numbers of microspheres per classifier highlights a fundamental stochastic distribution of bead counts issue complicated by other factors. The more classifiers and the higher the count required per classifier there are, the more apparent the distribution of counts per classifier will be, and the more microspheres are required. Additional problems have been identified. Alternate methods of improving precision and reliability are recommended such as intraplexing and multi-well sample replicates to improve precision and confidence. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - January 28, 2008 Category: Biomedical Science Authors: Brian P. Hanley Source Type: journals

A mathematical model of venous neointimal hyperplasia formationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The proposed model describes the formation of venous neointimal hyperplasia, based on pathogenic mechanisms. The results suggest that interventions aimed at specific growth factors may be successful in prolonging the life of the vascular access, while reducing the costs of vascular access maintenance. The model may also provide indication of when invasive access surveillance to repair stenosis should be undertaken. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - January 23, 2008 Category: Biomedical Science Authors: Paula Budu-Grajdeanu, Richard C Schugart, Avner Friedman, Christopher Valentine, Anil K. Agarwal and Brad H. Rovin Source Type: journals

The Peter Pan paradigmEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genetic and environmental agents that disrupt organogenesis are numerous and well described. Less well established, however, is the role of delay in the developmental processes that yield functionally immature tissues at birth. Evidence is mounting that organs do not continue to develop postnatally in the context of these organogenesis insults, condemning the patient to utilize under developed tissues for adult processes. These poorly differentiated organs may appear histologically normal at birth but with age may deteriorate revealing progressive or adult-onset pathology. The genetic and molecular underpinning of the prop...
Source: Theoretical Biology and Medical Modelling - January 8, 2008 Category: Biomedical Science Authors: J Craig Cohen and Janet E. Larson Source Type: journals

Simulating non-small cell lung cancer with a multiscale agent-based modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our in silico results indicate that, in NSCLC, in the presence of a strong extrinsic chemotactic stimulus, and depending on the cell's location, downstream EGFR-ERK signaling may be processed more efficiently, thereby yielding a migration-dominant cell phenotype and overall, an accelerated spatio-temporal expansion rate. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - December 21, 2007 Category: Biomedical Science Authors: Zhihui Wang, Le Zhang, Jonathan Sagotsky and Thomas S Deisboeck Source Type: journals

A unified framework of immunological and epidemiological dynamics for the spread of viral infections in a simple network-based populationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Future infectious disease research would benefit by striving to not only continue to understand the properties of an invading microbe, or the body's response to infections, but how these properties, jointly, affect the propagation of an infection throughout a population. These initial results offer a refinement to current immuno-epidemiological modelling methodology, and reinforce how coupling principles of immunology with epidemiology can provide insight into a multi-scaled description of an ecological system. Overall, we anticipate these results to as a further step towards articulating an integrated, more r...
Source: Theoretical Biology and Medical Modelling - December 20, 2007 Category: Biomedical Science Authors: David M Vickers and Nathaniel D Osgood Source Type: journals

Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxiaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The predictive power of the constructed model for the key flux distributions, especially central carbon metabolism and glutamate-glutamine cycle fluxes, and its application to hypoxia is promising. The resultant acceptable predictions strengthen the power of such stoichiometric models in the analysis of mammalian cell metabolism. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - December 10, 2007 Category: Biomedical Science Authors: Tunahan Cakir, Selma Alsan, Hale Saybasili, Ata Akin and Kutlu O Ulgen Source Type: journals

Measuring the functional sequence complexity of proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: For future extensions, measures of functional bioinformatics may provide a means to evaluate potential evolving pathways from effects such as mutations, as well as analyzing the internal structural and functional relationships within the 3-D structure of proteins. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - December 6, 2007 Category: Biomedical Science Authors: Kirk K. Durston, David K. Y. Chiu, David L. Abel and Jack T. Trevors Source Type: journals

Inflammation: a way to understanding the evolution of portal hypertensionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Low-grade inflammation, related to prehepatic portal hypertension, switches to high-grade inflammation with the development of severe and life-threatening complications when associated with chronic liver disease. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - November 13, 2007 Category: Biomedical Science Authors: Maria-Angeles Aller, Jorge-Luis Arias, Arturo Cruz and Jaime Arias Source Type: journals

The Proteomic Code: a molecular recognition code for proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Background: The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code. Review The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and c...
Source: Theoretical Biology and Medical Modelling - November 13, 2007 Category: Biomedical Science Authors: Jan C Biro Source Type: journals

Analysis of arterial intimal hyperplasia: review and hypothesisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Two questions should inform the priorities of our research: (1) what controls switch the single cell-layer intimal phenotype into normal hyperplasia? (2) how is normal (benign) hyperplasia maintained? We would be hard-pressed to gain practical insights without scrutinizing our premises. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - October 31, 2007 Category: Biomedical Science Authors: Vladimir M Subbotin Source Type: journals

Coordination of the dynamics of yeast sphingolipid metabolism during the diauxic shiftEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The results indicate that yeast coordinates sphingolipid mediated changes during the diauxic shift through an array of small changes in many genes and enzymes, rather than relying on a strategy involving a few select genes with high sensitivity. This study also highlights a novel approach in coupling data mining with mathematical modeling in order to evaluate specific metabolic pathways. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - October 31, 2007 Category: Biomedical Science Authors: Fernando J Alvarez-Vasquez, Kellie J Sims, Eberhard O Voit and Yusuf A Hannun Source Type: journals

Regular mosaic pattern development: A study of the interplay between lateral inhibition, apoptosis and differential adhesionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Patterning the embryo requires collaboration between multiple mechanisms that operate iteratively. Interlacing these mechanisms into feedback loops not only refines the output patterns, but also increases the robustness of patterning to varying initial cell states. (Source: Theoretical Biology and Medical Modelling)
Source: Theoretical Biology and Medical Modelling - October 31, 2007 Category: Biomedical Science Authors: Gregory J. Podgorski, Mayank Bansal and Nicholas S. Flann Source Type: journals

Hypertabastic Survival ModelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new two-parameter probability distribution called hypertabastic is introduced to model the survival or time-to-event data. A simulation study was carried out to evaluate the performance of the hypertabastic distribution in comparison with popular distributions. We then demonstrate the application of the hypertabastic survival model by applying it to data from two motivating studies. The first one demonstrates the proportional hazards version of the model by applying it to a data set from multiple myeloma study. The second one demonstrates an accelerated failure time version of the model by applying it to data from a rand...
Source: Theoretical Biology and Medical Modelling - October 26, 2007 Category: Biomedical Science Authors: Mohammad A Tabatabai, Zoran Bursac, David K Williams and Karan P Singh Source Type: journals