Articles

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

A second-generation computational modeling of cardiac electrophysiology: response of action potential to ionic concentration changes and metabolic inhibition

Cardiac arrhythmias are becoming one of the major health care problem in the world, causing numerous serious disease conditions including stroke and sudden cardiac death. Furthermore, cardiac arrhythmias are i...

Authors: Nour Eddine Alaa, Hamid Lefraich and Imane El Malki

A mathematical model of dysfunction of the thalamo-cortical loop in schizophrenia

Recent experimental results suggest that impairment of auditory information processing in the thalamo-cortical loop is crucially related to schizophrenia. Large differences between schizophrenia patients and h...

Authors: Nils Rosjat, Svitlana Popovych and Silvia Daun-Gruhn

Growth impairment after TBI of leukemia survivors children: a model- based investigation

Children receiving Total Body Irradiation (TBI) in preparation for Hematopoietic Stem Cell Transplantation (HSCT) are at risk for Growth Hormone Deficiency (GHD), which sometimes severely compromises their Fin...

Authors: Chiara Galletto, Antonio Gliozzi, Daniele Nucera, Nicoletta Bertorello, Eleonora Biasin, Andrea Corrias, Patrizia Chiabotto, Franca Fagioli and Caterina Guiot

Dynamical crises, multistability and the influence of the duration of immunity in a seasonally-forced model of disease transmission

Highly successful strategies to make populations more resilient to infectious diseases, such as childhood vaccinations programs, may nonetheless lead to unpredictable outcomes due to the interplay between seas...

Authors: Mathew P Dafilis, Federico Frascoli, Jodie McVernon, Jane M Heffernan and James M McCaw

Potential new therapeutic modality revealed through agent-based modeling of the neuromuscular junction and acetylcholinesterase inhibition

One of the leading causes of death and illness within the agriculture industry is through unintentionally ingesting or inhaling organophosphate pesticides. OP intoxication directly inhibits acetylcholinesteras...

Authors: Richard R Chapleau, Peter J Robinson, John J Schlager and Jeffery M Gearhart

Mathematical modeling of multi-drugs therapy: a challenge for determining the optimal combinations of antiviral drugs

In the current era of antiviral drug therapy, combining multiple drugs is a primary approach for improving antiviral effects, reducing the doses of individual drugs, relieving the side effects of strong antivi...

Authors: Yoshiki Koizumi and Shingo Iwami

A model to explain specific cellular communications and cellular harmony:- a hypothesis of coupled cells and interactive coupling molecules

The various cell types and their relative numbers in multicellular organisms are controlled by growth factors and related extracellular molecules which affect genetic expression pathways. However, these substa...

Authors: Cyril J Craven

Bayesian approach for the estimation of cyclosporine area under the curve using limited sampling strategies in pediatric hematopoietic stem cell transplantation

The optimal marker for cyclosporine (CsA) monitoring in transplantation patients remains controversial. However, there is a growing interest in the use of the area under the concentration-time curve (AUC), par...

Authors: Sarem Sarem, Jun Li, Olivier Barriere, Catherine Litalien, Yves Théorêt, Anne-Laure Lapeyraque and Fahima Nekka

Dimensional analysis yields the general second-order differential equation underlying many natural phenomena: the mathematical properties of a phenomenon’s data plot then specify a unique differential equation for it

This study uses dimensional analysis to derive the general second-order differential equation that underlies numerous physical and natural phenomena described by common mathematical functions. It eschews assum...

Authors: Gordon R Kepner

Computational identification of surrogate genes for prostate cancer phases using machine learning and molecular network analysis

Prostate cancer is one of the most common malignant diseases and is characterized by heterogeneity in the clinical course. To date, there are no efficient morphologic features or genomic biomarkers that can ch...

Authors: Rudong Li, Xiao Dong, Chengcheng Ma and Lei Liu

Beneficial effects of inhaled NO on apoptotic pneumocytes in pulmonary thromboembolism model

Lung ischemia–reperfusion injury (LIRI) may occur in the region of the affected lung after reperfusion therapy. Inhaled NO may be useful in treating acute and chronic pulmonary thromboembolism (PTE) due to the...

Authors: Chaosheng Deng, Minxia Yang, Qichang Lin, Yuanhua Yang, Zhenguo Zhai, Kaixiong Liu, Haibo Ding, Xiaoming Cao, Zhihua Huang, Lina Zhang and Jianming Zhao

The homeostatic set point of the hypothalamus-pituitary-thyroid axis – maximum curvature theory for personalized euthyroid targets

Despite rendering serum free thyroxine (FT4) and thyrotropin (TSH) within the normal population ranges broadly defined as euthyroidism, many patients being treated for hyperthyroidism and hypothyroidism persis...

Authors: Melvin Khee-Shing Leow and Simon L Goede

Prospects for developing an accurate diagnostic biomarker panel for low prevalence cancers

Early detection screening of asymptomatic populations for low prevalence cancers requires a highly specific test in order to limit the cost and anxiety produced by falsely positive identifications. Most solid ...

Authors: Matthew A Firpo, Kenneth M Boucher and Sean J Mulvihill

Optimal back-extrapolation method for estimating plasma volume in humans using the indocyanine green dilution method

The indocyanine green dilution method is one of the methods available to estimate plasma volume, although some researchers have questioned the accuracy of this method.

Authors: David Polidori and Clarence Rowley

An integrated physiology model to study regional lung damage effects and the physiologic response

This work expands upon a previously developed exercise dynamic physiology model (DPM) with the addition of an anatomic pulmonary system in order to quantify the impact of lung damage on oxygen transport and ph...

Authors: David A Shelley, Bryant L Sih and Laurel J Ng

Quantitative indices of autophagy activity from minimal models

A number of cellular- and molecular-level studies of autophagy assessment have been carried out with the help of various biochemical and morphological indices. Still there exists ambiguity for the assessment o...

Authors: Kyungreem Han, Jinwoong Kim and Moo Young Choi

Comparative analysis of human and mouse immunoglobulin variable heavy regions from IMGT/LIGM-DB with IMGT/HighV-QUEST

Immunoglobulin (IG) complementarity determining region (CDR) includes VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3. Of these, VH CDR3 plays a dominant role in recognizing and binding antigens. Three...

Authors: Bin Shi, Long Ma, Xiaoyan He, Xiaomei Wang, Peng Wang, Li Zhou and Xinsheng Yao

A model of immunohistochemical differences between invasive breast cancers and DCIS lesions tested on a consecutive case series of 1248 patients

A previous theoretic model (Tumour Biol 2013;34:1–7.) that breast tumor types differ in the relative rate of tissue invasion was elaborated and developed on a consecutive case series.

Authors: Sven Kurbel, Ksenija Marjanović and Branko Dmitrović

A new flexible plug and play scheme for modeling, simulating, and predicting gastric emptying

In-silico models that attempt to capture and describe the physiological behavior of biological organisms, including humans, are intrinsically complex and time consuming to build and simulate in a computing env...

Authors: Shaji Krishnan, Mark van Avesaat, Freddy J Troost, Henk FJ Hendriks and Albert A de Graaf

Herpes B virus gD interaction with its human receptor - an in silico analysis approach

The glycoprotein D (gD) is essential for Herpes B virus (BV) entry into mammalian cells. Nectin-1, an HSV-1 gD receptor, is found to be the receptor which mediated BV induced cell-cell fusion, while HVEM does ...

Authors: Lingke Li, Zhengliang Qiu, Yan Li, Feng Liang, Huahu Ye, Yongqin Cai, Wanfeng Guo, Yan Li and Junjie Yue

On the origins of the mitotic shift in proliferating cell layers

During plant and animal development, monolayer cell sheets display a stereotyped distribution of polygonal cell shapes. In interphase cells these shapes range from quadrilaterals to decagons, with a robust ave...

Authors: William T Gibson, Boris Y Rubinstein, Emily J Meyer, James H Veldhuis, G Wayne Brodland, Radhika Nagpal and Matthew C Gibson

Comparison of calculated and experimental power in maximal lactate-steady state during cycling

The purpose of this study was the comparison of the calculated (MLSS_C) and experimental power (MLSS_E) in maximal lactate steady-state (MLSS) during cycling.

Authors: Thomas Hauser, Jennifer Adam and Henry Schulz

A combined model of human erythropoiesis and granulopoiesis under growth factor and chemotherapy treatment

Haematotoxicity of conventional chemotherapies often results in delays of treatment or reduction of chemotherapy dose. To ameliorate these side-effects, patients are routinely treated with blood transfusions o...

Authors: Sibylle Schirm, Christoph Engel, Markus Loeffler and Markus Scholz

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 hypothes...

Authors: Héctor Echavarria-Heras, Cecilia Leal-Ramirez and Oscar Castillo

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

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....

Authors: Hiroki Ikeda, Rob J de Boer, Kei Sato, Satoru Morita, Naoko Misawa, Yoshio Koyanagi, Kazuyuki Aihara and Shingo Iwami

Analysis of inter-patient variations in tumour growth rate

Inter-patient variations in tumour growth rate are usually interpreted as biological heterogeneity among patients due to, e.g., genetic variability. However, these variations might be a result of non-exponenti...

Authors: Esmaeil Mehrara and Eva Forssell-Aronsson

Mathematical modeling of the effects of glutathione on arsenic methylation

Arsenic is a major environmental toxin that is detoxified in the liver by biochemical mechanisms that are still under study. In the traditional metabolic pathway, arsenic undergoes two methylation reactions, e...

Authors: Sean D Lawley, Jina Yun, Mary V Gamble, Megan N Hall, Michael C Reed and H Frederik Nijhout

Two-dimensional strain-hardening membrane model for large deformation behavior of multiple red blood cells in high shear conditions

Computational modeling of Red Blood Cell (RBC) flow contributes to the fundamental understanding of microhemodynamics and microcirculation. In order to construct theoretical RBC models, experimental studies on...

Authors: Swe Soe Ye, Yan Cheng Ng, Justin Tan, Hwa Liang Leo and Sangho Kim

A symmetry model for genetic coding via a wallpaper group composed of the traditional four bases and an imaginary base E: Towards category theory-like systematization of molecular/genetic biology

Previously, we suggested prototypal models that describe some clinical states based on group postulates. Here, we demonstrate a group/category theory-like model for molecular/genetic biology as an alternative ...

Authors: Jitsuki Sawamura, Shigeru Morishita and Jun Ishigooka

Pathway landscapes and epigenetic regulation in breast cancer and melanoma cell lines

Epigenetic variation is a main regulation mechanism of gene expression in various cancer histotypes, and due to its reversibility, the potential impact in therapy can be very relevant.

Authors: Mariama El Baroudi, Dario La Sala, Caterina Cinti and Enrico Capobianco

Application of genetic algorithms and constructive neural networks for the analysis of microarray cancer data

Extracting relevant information from microarray data is a very complex task due to the characteristics of the data sets, as they comprise a large number of features while few samples are generally available. I...

Authors: Rafael Marcos Luque-Baena, Daniel Urda, Jose Luis Subirats, Leonardo Franco and Jose M Jerez

Analysing Twitter and web queries for flu trend prediction

Social media platforms encourage people to share diverse aspects of their daily life. Among these, shared health related information might be used to infer health status and incidence rates for specific condit...

Authors: José Carlos Santos and Sérgio Matos

An extended gene protein/products boolean network model including post-transcriptional regulation

Networks Biology allows the study of complex interactions between biological systems using formal, well structured, and computationally friendly models. Several different network models can be created, dependi...

Authors: Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino and Alessandro Vasciaveo

Improvement of design of a surgical interface using an eye tracking device

Surgical interfaces are used for helping surgeons in interpretation and quantification of the patient information, and for the presentation of an integrated workflow where all available data are combined to en...

Authors: Duygun Erol Barkana and Alper Açık

A flowgraph model for bladder carcinoma

Superficial bladder cancer has been the subject of numerous studies for many years, but the evolution of the disease still remains not well understood. After the tumor has been surgically removed, it may reapp...

Authors: Gregorio Rubio, Belén García-Mora, Cristina Santamaría and José Luis Pontones

Seeking genetic signature of radiosensitivity - a novel method for data analysis in case of small sample sizes

The identification of polymorphisms and/or genes responsible for an organism's radiosensitivity increases the knowledge about the cell cycle and the mechanism of the phenomena themselves, possibly providing th...

Authors: Joanna Zyla, Paul Finnon, Robert Bulman, Simon Bouffler, Christophe Badie and Joanna Polanska

A visual test based on a freeware software for quantifying and displaying night-vision disturbances: study in subjects after alcohol consumption

In this work, we propose the Halo test, a simple visual test based on a freeware software for quantifying and displaying night-vision disturbances perceived by subjects under different experimental conditions,...

Authors: José J Castro, Carolina Ortiz, Antonio M Pozo, Rosario G Anera and Margarita Soler

Advances in bioinformatics and biomedical engineering - special issue of IWBBIO 2013

Authors: Francisco M Ortuño and Ignacio Rojas

Investigation of the essential role of platelet-tumor cell interactions in metastasis progression using an agent-based model

Metastatic tumors are a major source of morbidity and mortality for most cancers. Interaction of circulating tumor cells with endothelium, platelets and neutrophils play an important role in the early stages o...

Authors: Abhineet Uppal, Sean C Wightman, Sabha Ganai, Ralph R Weichselbaum and Gary An

Cosinor-based rhythmometry

A brief overview is provided of cosinor-based techniques for the analysis of time series in chronobiology. Conceived as a regression problem, the method is applicable to non-equidistant data, a major advantage...

Authors: Germaine Cornelissen

Computing limits on medicine risks based on collections of individual case reports

Quantifying a medicine’s risks for adverse effects is crucial in assessing its value as a therapeutic agent. Rare adverse effects are often not detected until after the medicine is marketed and used in large a...

Authors: Ola Caster, G Niklas Norén and I Ralph Edwards

The role of the entorhinal cortex in epileptiform activities of the hippocampus

Temporal lobe epilepsy (TLE) is the commonest type of epilepsy in adults, and the hippocampus is indicated to have a close relationship with TLE. Recent researches also indicate that the entorhinal cortex (EC)...

Authors: Hui Ren, Ye-Jun Shi, Qin-Chi Lu, Pei-Ji Liang and Pu-Ming Zhang

Mathematically optimized cryoprotectant equilibration procedures for cryopreservation of human oocytes

Simple and effective cryopreservation of human oocytes would have an enormous impact on the financial and ethical constraints of human assisted reproduction. Recently, studies have demonstrated the potential f...

Authors: Allyson Fry Davidson, James D Benson and Adam Z Higgins

Chromosome congression explained by nanoscale electrostatics

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...

Authors: L John Gagliardi and Daniel H Shain