Articles

Epidemic cycling in a multi-strain SIRS epidemic network model

One common observation in infectious diseases caused by multi-strain pathogens is that both the incidence of all infections and the relative fraction of infection with each strain oscillate with time (i.e., so...

Authors: Xu-Sheng Zhang

Random walk of passive tracers among randomly moving obstacles

This study is mainly motivated by the need of understanding how the diffusion behavior of a biomolecule (or even of a larger object) is affected by other moving macromolecules, organelles, and so on, inside a ...

Authors: Matteo Gori, Irene Donato, Elena Floriani, Ilaria Nardecchia and Marco Pettini

Assessing potential countermeasures against the dengue epidemic in non-tropical urban cities

Dengue is a common mosquito-borne viral disease epidemic especially in tropical and sub-tropical regions where water sanitation is not substantially controlled. However, dengue epidemics sometimes occur in non...

Authors: Hiroki Masui, Itsuki Kakitani, Shumpei Ujiyama, Kazuyoshi Hashidate, Masataka Shiono and Kazue Kudo

The organelle of differentiation in embryos: the cell state splitter

The cell state splitter is a membraneless organelle at the apical end of each epithelial cell in a developing embryo. It consists of a microfilament ring and an intermediate filament ring subtending a microtub...

Authors: Natalie K. Gordon and Richard Gordon

Modeling immune response and its effect on infectious disease outbreak dynamics

In recent epidemiological models, immunity is incorporated as a simplified value that determines the capacity of an individual to become infected or to transmit the disease. Moreover, the quality of the immune...

Authors: Jorge Reyes-Silveyra and Armin R. Mikler

A physiologically-based flow network model for hepatic drug elimination III: 2D/3D DLA lobule models

One of the major issues in current pharmaceutical development is potential hepatotoxicity and drug-induced liver damage. This is due to the unique metabolic processes performed in the liver to prevent accumula...

Authors: Vahid Rezania, Dennis Coombe and Jack A. Tuszynski

Modeling glucose and free fatty acid kinetics in glucose and meal tolerance test

Quantitative evaluation of insulin regulation on plasma glucose and free fatty acid (FFA) in response to external glucose challenge is clinically important to assess the development of insulin resistance (Worl...

Authors: Yanjun Li, Carson C. Chow, Amber B. Courville, Anne E. Sumner and Vipul Periwal

Toward precision medicine of breast cancer

In this review, we report on breast cancer’s molecular features and on how high throughput technologies are helping in understanding the dynamics of tumorigenesis and cancer progression with the aim of develop...

Authors: Nicolas Carels, Lizânia Borges Spinassé, Tatiana Martins Tilli and Jack Adam Tuszynski

A mathematical model of tumor growth and its response to single irradiation

Mathematical modeling of biological processes is widely used to enhance quantitative understanding of bio-medical phenomena. This quantitative knowledge can be applied in both clinical and experimental setting...

Authors: Yoichi Watanabe, Erik L. Dahlman, Kevin Z. Leder and Susanta K. Hui

A group matrix representation relevant to scales of measurement of clinical disease states via stratified vectors

Previously, we applied basic group theory and related concepts to scales of measurement of clinical disease states and clinical findings (including laboratory data). To gain a more concrete comprehension, we h...

Authors: Jitsuki Sawamura, Shigeru Morishita and Jun Ishigooka

A cell-centered, agent-based framework that enables flexible environment granularities

Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell’s perspective may offer new insights. Agent-based models lend themselves to model fr...

Authors: Ryan C Kennedy, Glen EP Ropella and C Anthony Hunt

Simulation and qualitative analysis of glucose variability, mean glucose, and hypoglycemia after subcutaneous insulin therapy for stress hyperglycemia

The critically ill can have persistent dysglycemia during the “subacute” recovery phase of their illness because of altered gene expression; it is also not uncommon for these patients to receive continuous ent...

Authors: Richard J. Strilka, Mamie C. Stull, Michael S. Clemens, Stewart C. McCaver and Scott B. Armen

Extracting DNA words based on the sequence features: non-uniform distribution and integrity

DNA sequence can be viewed as an unknown language with words as its functional units. Given that most sequence alignment algorithms such as the motif discovery algorithms depend on the quality of background in...

Authors: Zhi Li, Hongyan Cao, Yuehua Cui and Yanbo Zhang

Numerical simulations of multicomponent ecological models with adaptive methods

The study of dynamic relationship between a multi-species models has gained a huge amount of scientific interest over the years and will continue to maintain its dominance in both ecology and mathematical ecol...

Authors: Kolade M. Owolabi and Kailash C. Patidar

The effect of parameter variability in the allometric projection of leaf growth rates for eelgrass (Zostera marina L.) II: the importance of data quality control procedures in bias reduction

Eelgrass grants important ecological benefits including a nursery for waterfowl and fish species, shoreline stabilization, nutrient recycling and carbon sequestration. Upon the exacerbation of deleterious anth...

Authors: Héctor Echavarría-Heras, Cecilia Leal-Ramírez, Enrique Villa-Diharce and Nohe R. Cazarez-Castro

Bioengineering thermodynamics of biological cells

Cells are open complex thermodynamic systems. They can be also regarded as complex engines that execute a series of chemical reactions. Energy transformations, thermo-electro-chemical processes and transports ...

Authors: Umberto Lucia

Modeling optimal treatment strategies in a heterogeneous mixing model

Many mathematical models assume random or homogeneous mixing for various infectious diseases. Homogeneous mixing can be generalized to mathematical models with multi-patches or age structure by incorporating c...

Authors: Seoyun Choe and Sunmi Lee

A measure of regularity for polygonal mosaics in biological systems

The quantification of the spatial order of biological patterns or mosaics provides useful information as many properties are determined by the spatial distribution of their constituent elements. These are usua...

Authors: Gabriela Contreras-Figueroa, Luis Hernández-Sandoval and José L. Aragón

A Boolean network model of human gonadal sex determination

Gonadal sex determination (GSD) in humans is a complex biological process that takes place in early stages of embryonic development when the bipotential gonadal primordium (BGP) differentiates towards testes o...

Authors: Osiris Ríos, Sara Frias, Alfredo Rodríguez, Susana Kofman, Horacio Merchant, Leda Torres and Luis Mendoza

A new method for the extraction of fetal ECG from the dependent abdominal signals using blind source separation and adaptive noise cancellation techniques

The electrocardiogram (ECG) is a diagnostic tool that records the electrical activity of the heart, and depicts it as a series of graph-like tracings, or waves. Being able to interpret these details allows dia...

Authors: Abdelghani Ghazdali, Abdelilah Hakim, Amine Laghrib, Nezha Mamouni and Said Raghay

Disc degeneration implies low back pain

Low back pain exerts a tremendous burden on individual patients and society due to its prevalence and ability to cause long-term disability. Contemporary treatment and prevention efforts are stymied by the abs...

Authors: Chang-Jiang Zheng and James Chen

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour

DNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic. MRE11 plays an essential role in repairing DNA by cleaving broken ends through its 3′ to 5′ exonuclease and single-stranded DNA endonuclease act...

Authors: Imen Rekik, Zayneb Chaabene, C. Douglas Grubb, Noureddine Drira, Foued Cheour and Amine Elleuch

Bioelectric memory: modeling resting potential bistability in amphibian embryos and mammalian cells

Bioelectric gradients among all cells, not just within excitable nerve and muscle, play instructive roles in developmental and regenerative pattern formation. Plasma membrane resting potential gradients regula...

Authors: Robert Law and Michael Levin

Deconvolution of the vestibular evoked myogenic potential using the power spectrum of the electromyogram

The vestibular evoked myogenic potential (VEMP) can be modelled reasonably well by convolving two functions: one representing an average motor unit action potential (MUAP), the other representing the temporal ...

Authors: Bernd Lütkenhöner

PDON: Parkinson’s disease ontology for representation and modeling of the Parkinson’s disease knowledge domain

Despite the unprecedented and increasing amount of data, relatively little progress has been made in molecular characterization of mechanisms underlying Parkinson’s disease. In the area of Parkinson’s research...

Authors: Erfan Younesi, Ashutosh Malhotra, Michaela Gündel, Phil Scordis, Alpha Tom Kodamullil, Matt Page, Bernd Müller, Stephan Springstubbe, Ullrich Wüllner, Dieter Scheller and Martin Hofmann-Apitius

Fanconi anemia cells with unrepaired DNA damage activate components of the checkpoint recovery process

The FA/BRCA pathway repairs DNA interstrand crosslinks. Mutations in this pathway cause Fanconi anemia (FA), a chromosome instability syndrome with bone marrow failure and cancer predisposition. Upon DNA damag...

Authors: Alfredo Rodríguez, Leda Torres, Ulises Juárez, David Sosa, Eugenio Azpeitia, Benilde García-de Teresa, Edith Cortés, Rocío Ortíz, Ana M. Salazar, Patricia Ostrosky-Wegman, Luis Mendoza and Sara Frías

The waiting time problem in a model hominin population

Functional information is normally communicated using specific, context-dependent strings of symbolic characters. This is true within the human realm (texts and computer programs), and also within the biologic...

Authors: John Sanford, Wesley Brewer, Franzine Smith and John Baumgardner

Modeling the energetic cost of cancer as a result of altered energy metabolism: implications for cachexia

Cachexia affects most patients with incurable cancer. We hypothesize that in metastatic cancer the mass of the tumor as well as its level of anaerobic energy metabolism play a critical role in describing its e...

Authors: Douglas E. Friesen, Vickie E. Baracos and Jack A. Tuszynski

Mechanistic-enriched models: integrating transcription factor networks and metabolic deregulation in cancer

In the present paper we will examine methodological frameworks to study complex genetic diseases (e.g. cancer) from the stand point of theoretical-computational biology combining both data-driven and hypothesi...

Authors: Enrique Hernández-Lemus and J. Mario Siqueiros-García

General overview on structure prediction of twilight-zone proteins

Protein structure prediction from amino acid sequence has been one of the most challenging aspects in computational structural biology despite significant progress in recent years showed by critical assessment...

Authors: Bee Yin Khor, Gee Jun Tye, Theam Soon Lim and Yee Siew Choong

Effects of different interchain linkers on biological activity of an anti-prostate cancer single-chain bispecific antibody

A single-chain bispecific antibody (scBsAb; an engineered antibody), has promising clinical applications. Nonetheless, the effect of different interchain linkers on its activity is poorly understood.

Authors: Chao-hui Hao, Qian-he Han, Zhong-jie Shan, Jian-ting Hu, Nan Zhang and Xue-pei Zhang

Annual acknowledgement of manuscript reviewers

The Editors of Theoretical Biology and Medical Modelling would like to thank all the Reviewers who have contributed to the journal in Volume 11 (2014).

Authors: Hiroshi Nishiura, Edward Rietman and Rongling Wu

Proposal of a hybrid approach for tumor progression and tumor-induced angiogenesis

One of the main challenges in cancer modelling is to improve the knowledge of tumor progression in areas related to tumor growth, tumor-induced angiogenesis and targeted therapies efficacy. For this purpose, i...

Authors: Patricio Cumsille, Aníbal Coronel, Carlos Conca, Cristóbal Quiñinao and Carlos Escudero

Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) is an incurable malignancy of mature B-lymphocytes, characterized as being a heterogeneous disease with variable clinical manifestation and survival. Mutational statuses of r...

Authors: María Camila Álvarez-Silva, Sally Yepes, Maria Mercedes Torres and Andrés Fernando González Barrios

Enhancing dendritic cell immunotherapy for melanoma using a simple mathematical model

The immunotherapy using dendritic cells (DCs) against different varieties of cancer is an approach that has been previously explored which induces a specific immune response. This work presents a mathematical ...

Authors: E. Castillo-Montiel, J. C. Chimal-Eguía, J. Ignacio Tello, G. Piñon-Zaráte, M. Herrera-Enríquez and AE. Castell-Rodríguez

Cell cycle progression is regulated by intertwined redox oscillators

The different phases of the eukaryotic cell cycle are exceptionally well-preserved phenomena. DNA decompaction, RNA and protein synthesis (in late G₁ phase) followed by DNA replication (in S phase) and lipid synt...

Authors: Jorgelindo da Veiga Moreira, Sabine Peres, Jean-Marc Steyaert, Erwan Bigan, Loïc Paulevé, Marcel Levy Nogueira and Laurent Schwartz

A novel hypothesis for atherosclerosis as a cholesterol sulfate deficiency syndrome

Despite a vast literature, atherosclerosis and the associated ischemia/reperfusion injuries remain today in many ways a mystery. Why do atheromatous plaques make and store a supply of cholesterol and sulfate w...

Authors: Stephanie Seneff, Robert M. Davidson, Ann Lauritzen, Anthony Samsel and Glyn Wainwright

A control system analysis of the dynamic response of N-methyl-D-aspartate glutamate receptors to alcoholism and alcohol withdrawal

N-methyl-D-Aspartate (NMDA) and its receptors (NMDAR) play a critical role in glutamatergic neurotransmission. Ethanol molecules inhibit these receptors, and if the brain is exposed to ethanol ...

Authors: Carlos A Gutierrez and Mary M Staehle

CT brush and CancerZap!: two video games for computed tomography dose minimization

X-ray dose from computed tomography (CT) scanners has become a significant public health concern. All CT scanners spray x-ray photons across a patient, including those using compressive sensing algorithms. New...

Authors: Graham Alvare and Richard Gordon

Periodicity of varicella-zoster virus in the presence of immune boosting and clinical reinfection with varicella

Clinical reinfection with varicella is normally ignored in mathematical transmission models as it is considered too rare to be important.

Authors: Igor A Korostil, James G Wood and David G Regan

The Spatial Chemical Langevin Equation and Reaction Diffusion Master Equations: moments and qualitative solutions

It has been established that stochastic effects play an important role in spatio-temporal biochemical networks. A popular method of representing such stochastic systems is the Reaction Diffusion Master Equatio...

Authors: Atiyo Ghosh, Andre Leier and Tatiana T Marquez-Lago

Modeling drug resistance in a conjoint normal-tumor setting

In this paper, we modify our previously developed conjoint tumor-normal cell model in order to make a distinction between tumor cells that are responsive to chemotherapy and those that may show resistance.

Authors: Mitra Shojania Feizabadi and Tarynn M Witten

Impact and cost-effectiveness of chlamydia testing in Scotland: a mathematical modelling study

Chlamydia is the most common sexually transmitted bacterial infection in Scotland, and is associated with potentially serious reproductive outcomes, including pelvic inflammatory disease (PID) and tubal factor...

Authors: Katharine J Looker, Lesley A Wallace and Katherine ME Turner

Theoretical perspectives on the infectiousness of Ebola virus disease

Ebola virus disease (EVD) has generated a large epidemic in West Africa since December 2013. This mini-review is aimed to clarify and illustrate different theoretical concepts of infectiousness in order to com...

Authors: Hiroshi Nishiura and Gerardo Chowell

Mathematical and computational modeling in biology at multiple scales

A variety of topics are reviewed in the area of mathematical and computational modeling in biology, covering the range of scales from populations of organisms to electrons in atoms. The use of maximum entropy ...

Authors: Jack A Tuszynski, Philip Winter, Diana White, Chih-Yuan Tseng, Kamlesh K Sahu, Francesco Gentile, Ivana Spasevska, Sara Ibrahim Omar, Niloofar Nayebi, Cassandra DM Churchill, Mariusz Klobukowski and Rabab M Abou El-Magd

Papillomavirus binding factor (PBF) is an intrinsically disordered protein with potential participation in osteosarcoma genesis, in silico evidence

Papillomavirus binding factor (PBF) or zinc finger protein 395 is a transcription factor associated to a poor prognosis in patients with osteosarcoma, an aggressive bone cancer that predominantly affects adole...

Authors: Paola Castillo, Abraham F Cetina, Alfonso Méndez-Tenorio, Lennane Michel Espinoza-Fonseca and Blanca L Barrón

Impact of biodiversity and seasonality on Lyme-pathogen transmission

Lyme disease imposes increasing global public health challenges. To better understand the joint effects of seasonal temperature variation and host community composition on the pathogen transmission, a stage-st...

Authors: Yijun Lou, Jianhong Wu and Xiaotian Wu

Stochastic model for tumor control probability: effects of cell cycle and (a)symmetric proliferation

Estimating the required dose in radiotherapy is of crucial importance since the administrated dose should be sufficient to eradicate the tumor and at the same time should inflict minimal damage on normal cells...

Authors: Andrew Dhawan, Kamran Kaveh, Mohammad Kohandel and Sivabal Sivaloganathan

Erratum to: improvement of design of a surgical interface using an eye tracking device

Authors: Duygun Erol Barkana, Alper Açık, Dilek Goksel Duru and Adil Deniz Duru

Animal evolution and atmospheric pO₂: is there a link between gradual animal adaptation to terrain elevation due to Ural orogeny and survival of subsequent hypoxic periods?

Considering evolution of terrestrial animals as something happening only on flat continental plains seems wrong. Many mountains have arisen and disappeared over the geologic time scale, so in all periods some ...

Authors: Sven Kurbel