Articles

Tumor inhibitory T cell immunity may be largely a transplantation artifact not necessarily dependent upon a lack of Tregs

There exists a very large literature suggesting that T cells come in a variety of species and that without the action of Tregs tumors would seldom survive inhibition by T cell effectors. We believe that much o...

Authors: Richmond T Prehn and Liisa M Prehn

Multi-scale agent-based modeling on melanoma and its related angiogenesis analysis

Recently, melanoma has become the most malignant and commonly occurring skin cancer. Melanoma is not only the major source (75%) of deaths related to skin cancer, but also it is hard to be treated by the conve...

Authors: Jun Wang, Le Zhang, Chenyang Jing, Gang Ye, Hulin Wu, Hongyu Miao, Yukun Wu and Xiaobo Zhou

Boolean network-based model of the Bcl-2 family mediated MOMP regulation

Mitochondrial outer membrane permeabilization (MOMP) is one of the most important points in the majority of apoptotic signaling cascades and it is controlled by a network of interactions between the members of...

Authors: Tomas Tokar, Zdenko Turcan and Jozef Ulicny

An integrated multidisciplinary model describing initiation of cancer and the Warburg hypothesis

In this paper we propose a chemical physics mechanism for the initiation of the glycolytic switch commonly known as the Warburg hypothesis, whereby glycolytic activity terminating in lactate continues even in ...

Authors: Edward A Rietman, Douglas E Friesen, Philip Hahnfeldt, Robert Gatenby, Lynn Hlatky and Jack A Tuszynski

Tumor necrosis factor receptor superfamily 10B (TNFRSF10B): an insight from structure modeling to virtual screening for designing drug against head and neck cancer

Head and neck cancer (HNC) belongs to a group of heterogeneous disease with distinct patterns of behavior and presentation. TNFRSF10B, a tumor suppressor gene mapped on chromosome 8. Mutation in candidate gene...

Authors: Rana Adnan Tahir, Sheikh Arslan Sehgal, Naureen Aslam Khattak, Jabar Zaman Khan Khattak and Asif Mir

Modelling gene expression profiles related to prostate tumor progression using binary states

Cancer is a complex disease commonly characterized by the disrupted activity of several cancer-related genes such as oncogenes and tumor-suppressor genes. Previous studies suggest that the process of tumor pro...

Authors: Emmanuel Martinez and Victor Trevino

The design of a new truncated and engineered alpha1-antitrypsin based on theoretical studies: an antiprotease therapeutics for pulmonary diseases

Alpha 1- antitrypsin (α1AT) a 54 kDa glycoprotein is a protease inhibitor. In the absence of α1AT, elastase released by lung macrophages, was not inhibited and lead to elastin breakdown and pulmonary problems ...

Authors: Nazanin Pirooznia, Sadegh Hasannia, Seyed Shahriar Arab, Abbas Sahebghadam Lotfi, Mostafa Ghanei and Abbas Shali

Numerical investigation of the effect of cannula placement on thrombosis

Despite the rapid advancement of left ventricular assist devices (LVADs), adverse events leading to deaths have been frequently reported in patients implanted with LVADs, including bleeding, infection, thrombo...

Authors: ChiWei Ong, Socrates Dokos, BeeTing Chan, Einly Lim, Amr Al Abed, NoorAzuanBinAbu Osman, Suhaini Kadiman and Nigel H Lovell

Using allometric procedures to substantiate the plastochrone method for eelgrass leaf growth assessments

Estimation of leaf productivity in eelgrass (Zostera marina L.) is crucial for evaluating the ecological role of this important seagrass species. Although leaf marking techniques are widely used to obtain estimat...

Authors: Héctor Echavarría-Heras, Elena Solana-Arellano, Cecilia Leal-Ramírez and Oscar Castillo

Exploring haemodynamics of haemodialysis using extrema points analysis model

Haemodialysis is a form of renal replacement therapy used to treat patients with end stage renal failure. It is becoming more appreciated that haemodialysis patients exhibit higher rates of multiple end organ ...

Authors: MohamedTarek Eldehni, Aghogho Odudu and ChristopherWilliam McIntyre

Computational simulation of the bone remodeling using the finite element method: an elastic-damage theory for small displacements

The resistance of the bone against damage by repairing itself and adapting to environmental conditions is its most important property. These adaptive changes are regulated by physiological process commonly cal...

Authors: Ahmed Idhammad, Abdelmounaïm Abdali and Noureddine Alaa

A new method to estimate parameters of the growth model for metastatic tumours

Knowledge of natural tumour growth is valuable for understanding tumour biology, optimising screening programs, prognostication, optimal scheduling of chemotherapy, and assessing tumour spread. However, mathem...

Authors: Esmaeil Mehrara, Eva Forssell-Aronsson, Viktor Johanson, Lars Kölby, Ragnar Hultborn and Peter Bernhardt

How to interpret the transmissibility of novel influenza A(H7N9): an analysis of initial epidemiological data of human cases from China

As the human infections with novel influenza A(H7N9) virus have been reported from several different provinces in China, the pandemic potential of the virus has been questioned. The presence of human-to-human ...

Authors: Hiroshi Nishiura, Kenji Mizumoto and Keisuke Ejima

Determination of the optimal tubulin isotype target as a method for the development of individualized cancer chemotherapy

As microtubules are essential for cell growth and division, its constituent protein β-tubulin has been a popular target for various treatments, including cancer chemotherapy. There are several isotypes of huma...

Authors: Siamak Ravanbakhsh, Melissa Gajewski, Russell Greiner and Jack A Tuszynski

Development of a three-dimensional model of the human respiratory system for dosimetric use

Determining the fate of inhaled contaminants in the human respiratory system has challenged scientists for years. Human and animal studies have provided some data, but there is a paucity of data for toxic contami...

Authors: Jacky A Rosati Rowe, Ray Burton, George McGregor, Rob McCauley, Wei Tang and Richard Spencer

Mathematical models for the Notch and Wnt signaling pathways and the crosstalk between them during somitogenesis

Somitogenesis is a fundamental characteristic feature of development in various animal embryos. Molecular evidence has proved that the Notch and Wnt pathways play important roles in regulating the process of s...

Authors: Hong-yan Wang, Yan-xin Huang, Yun-feng Qi, Yu Zhang, Yong-li Bao, Lu-guo Sun, Li-hua Zheng, Yu-wei Zhang, Zhi-qiang Ma and Yu-xin Li

Is it possible to stabilize a thermophilic protein further using sequences and structures of mesophilic proteins: a theoretical case study concerning DgAS

Incorporating structural elements of thermostable homologs can greatly improve the thermostability of a mesophilic protein. Despite the effectiveness of this method, applying it is often hampered. First, it re...

Authors: Ming Liu, Hongqiu He and Jiguo Su

Structural mimicry between SLA/LP and Rickettsia surface antigens as a driver of autoimmune hepatitis: insights from an in silico study

Autoimmune hepatitis (AIH) is a chronic, progressive liver disease, characterized by continuing hepatocellular inflammation and necrosis. A subgroup of AIH patients presents specific autoantibodies to soluble ...

Authors: Alessandro Paiardini and Stefano Pascarella

Development of global consensus sequence of HCV glycoproteins involved in viral entry

HCV affects >170 million people worldwide and is a leading cause of liver diseases such as hepatocellular carcinoma. Each year, Pakistan reports hundreds of cases and now it has become a serious health issue. ...

Authors: Sobia Idrees, Usman A Ashfaq and Natasha Idrees

Agent-based modeling of competence phenotype switching in Bacillus subtilis

It is a fascinating phenomenon that in genetically identical bacteria populations of Bacillus subtilis, a distinct DNA uptake phenotype called the competence phenotype may emerge in 10–20% of the population. Many...

Authors: Suzy M Stiegelmeyer and Morgan C Giddings

Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase

bla_VEB-1 is an integron-located extended-spectrum β-lactamase gene initially detected in Escherichia coli and Pseudomonas aeruginosa strains from south-east Asia. Several recent studies have reported that VEB-1-p...

Authors: Abdelmonaem Messaoudi, Hatem Belguith and Jeannette Ben Hamida

Experimental designs for a Benign Paroxysmal Positional Vertigo model

The pathology of the Benign Paroxysmal Positional Vertigo (BPPV) is detected by a clinician through maneuvers consisting of a series of consecutive head turns that trigger the symptoms of vertigo in patient. A...

Authors: Santiago Campos-Barreiro and Jesús López-Fidalgo

Effect of blood protein concentrations on drug-dosing regimes: practical guidance

In this article the importance of blood proteins for drug dosing regimes is discussed. A simple mathematical model is presented for estimating recommended drug doses when the concentration of blood proteins is...

Authors: Konstantin G Gurevich

Stochastic time‐concentration activity models for cytotoxicity in 3D brain cell cultures

In vitro aggregating brain cell cultures containing all types of brain cells have been shown to be useful for neurotoxicological investigations. The cultures are used for the detection of nervous system‐specific ...

Authors: Maria Renner, Marie-Gabrielle Zurich and Annette Kopp-Schneider

Toll-like receptor 9 interaction with CpG ODN – An in silico analysis approach

Toll-like receptor 9 (TLR9) recognises unmethylated CpG DNA and activates a signalling cascade, leading to the production of inflammatory cytokines such as TNF-α, IL-1, IL-6 and IL-12 via the adaptor protein M...

Authors: Wei Zhou, Yan Li, Xichun Pan, Yuan Gao, Beiping Li, Zhengliang Qiu, Long Liang, Hong Zhou and Junjie Yue

Modeling the obesity epidemic: social contagion and its implications for control

As an obesity epidemic has grown worldwide, a variety of intervention programs have been considered, but a scientific approach to comparatively assessing the control programs has still to be considered. The pr...

Authors: Keisuke Ejima, Kazuyuki Aihara and Hiroshi Nishiura

Fluctuations in Tat copy number when it counts the most: a possible mechanism to battle the HIV latency

The HIV-1 virus can enter a dormant state and become inactive, which reduces accessibility by antiviral drugs. We approach this latency problem from an unconventional point of view, with the focus on understan...

Authors: Zoran Konkoli and Aldo Jesorka

Molecular docking between the RNA polymerase of the Moniliophthora perniciosa mitochondrial plasmid and Rifampicin produces a highly stable complex

Moniliophthora perniciosa (Stahel) Aime & Phillips-Mora is the causal agent of witches’ broom disease (WBD) in cacao (Theobroma cacao). When the mitochondrial genome of this fungus had been completely sequenced, ...

Authors: Bruno Andrade, Catiane Souza and Aristóteles Góes-Neto

IMGT/Collier-de-Perles: a two-dimensional visualization tool for amino acid domain sequences

IMGT/Collier-de-Perles is a tool that allows the user to analyze and draw two-dimensional graphical representations (or IMGT Collier de Perles) of protein domains (e.g., hydropathy plots). The IMGT/Collier-de-...

Authors: Dimitrios Vlachakis, Christos Feidakis, Vasileios Megalooikonomou and Sophia Kossida

A clinical study of the effects of lead poisoning on the intelligence and neurobehavioral abilities of children

Lead is a heavy metal and important environmental toxicant and nerve poison that can destruction many functions of the nervous system. Lead poisoning is a medical condition caused by increased levels of lead i...

Authors: Shuangxing Hou, Lianfang Yuan, Pengpeng Jin, Bojun Ding, Na Qin, Li Li, Xuedong Liu, Zhongliang Wu, Gang Zhao and Yanchun Deng

A new kink in an old theory of carcinogenesis

According to Berenblum’s two-stage hypothesis, the first stage in carcinogenesis is the production of benign premalignant lesions. Between this initiation stage and the formation of a malignant tumor there is ...

Authors: Richmond T Prehn and Liisa M Prehn

A statistical thin-tail test of predicting regulatory regions in the Drosophila genome

The identification of transcription factor binding sites (TFBSs) and cis-regulatory modules (CRMs) is a crucial step in studying gene expression, but the computational method attempting to distinguish CRMs from N...

Authors: Jian-Jun Shu and Yajing LI

The passage of a diffusible indicator through a microvascular system

The aim. (1) To develop a mathematical model of the passage of a diffusible indicator through microcirculation based on a stochastic description of diffusion and flow; (2) To use Goresky transform of the dilut...

Authors: Victor V Kislukhin

Application of neural oscillators to study the effects of walking speed on rhythmic activations at the ankle

Spinal pattern generators (SPG) are neural networks in the spinal cord that do not require a central input from the brain to generate a motor output. We wanted to determine whether SPG can adapt to the changin...

Authors: Sook-Yee Chong, Heiko Wagner and Arne Wulf

Is intracellular pH a clock for mitosis?

Experiments have shown that the intracellular pH of many cells rises to a maximum at the onset of mitosis, subsequently decreasing 0.3 to 0.5 pH units by the end of mitosis. This result, and observations that ...

Authors: L John Gagliardi and Daniel H Shain

Age and gender dependent heart rate circadian model development and performance verification on the proarrhythmic drug case study

There are two main reasons for drug withdrawals at the various levels of the development path – hepatic and cardiac toxicity. The latter one is mainly connected with the proarrhythmic potency and according to ...

Authors: Kamil Fijorek, Nikunjkumar Patel, Łukasz Klima, Katarzyna Stolarz-Skrzypek, Kalina Kawecka-Jaszcz and Sebastian Polak

Surgical inflammatory stress: the embryo takes hold of the reins again

The surgical inflammatory response can be a type of high-grade acute stress response associated with an increasingly complex trophic functional system for using oxygen. This systemic neuro-immune-endocrine res...

Authors: Maria-Angeles Aller, Jose-Ignacio Arias, Isabel Prieto, Carlos Gilsanz, Ana Arias, Heping Yang and Jaime Arias

Stem cell biology is population biology: differentiation of hematopoietic multipotent progenitors to common lymphoid and myeloid progenitors

The hematopoietic stem cell (HSC) system is a demand control system, with the demand coming from the organism, since the products of the common myeloid and lymphoid progenitor (CMP, CLP respectively) cells are...

Authors: Marc Mangel and Michael B Bonsall

Effectiveness of antiviral prophylaxis coupled with contact tracing in reducing the transmission of the influenza A (H1N1-2009): a systematic review

During the very early stage of the 2009 pandemic, mass chemoprophylaxis was implemented as part of containment measure. The purposes of the present study were to systematically review the retrospective studies...

Authors: Kenji Mizumoto, Hiroshi Nishiura and Taro Yamamoto

Structural, phylogenetic and docking studies of D-amino acid oxidase activator (DAOA), a candidate schizophrenia gene

Schizophrenia is a neurodegenerative disorder that occurs worldwide and can be difficult to diagnose. It is the foremost neurological disorder leading to suicide among patients in both developed and underdevel...

Authors: Sheikh Arslan Sehgal, Naureen Aslam Khattak and Asif Mir

Review of ‘BipolART’ by D. N. Wheatley (Springer, 2012)

Authors: Paul S Agutter

Comparative modeling and docking studies of p16ink4/Cyclin D1/Rb pathway genes in lung cancer revealed functionally interactive residue of RB1 and its functional partner E2F1

Lung cancer is the major cause of mortality worldwide. Major signalling pathways that could play significant role in lung cancer therapy include (1) Growth promoting pathways (Epidermal Growth Factor Receptor/...

Authors: Syeda Naqsh e Zahra, Naureen Aslam Khattak and Asif Mir

Non-local competition drives both rapid divergence and prolonged stasis in a model of speciation in populations with degenerate resource consumption

The theory of speciation is dominated by adaptationist thinking, with less attention to mechanisms that do not affect species adaptation. Degeneracy – the imperfect specificity of interactions between diverse ...

Authors: Nicholas Atamas, Michael S Atamas, Faina Atamas and Sergei P Atamas

The biochemistry of acetaminophen hepatotoxicity and rescue: a mathematical model

Acetaminophen (N-acetyl-para-aminophenol) is the most widely used over-the-counter or prescription painkiller in the world. Acetaminophen is metabolized in the liver where a toxic byproduct is produced that ca...

Authors: Rotem Ben-Shachar, Yifei Chen, Shishi Luo, Catherine Hartman, Michael Reed and H Frederik Nijhout

Further suggestions on the group-theoretical approach using clinical values

In a previous report, we suggested a prototypal model to describe patient states in a graded vector-like format based on the modulo groups via the psychiatric rating scale. In this article, using other simple ...

Authors: Jitsuki Sawamura, Shigeru Morishita and Jun Ishigooka

p42.3 gene expression in gastric cancer cell and its protein regulatory network analysis

To analyze the p42.3 gene expression in gastric cancer (GC) cell, find the relationship between protein structure and function, establish the regulatory network of p42.3 protein molecule and then to obtain the...

Authors: Jianhua Zhang, Chunlei Lu, Zhigang Shang, Rui Xing, Li Shi and Youyong Lv

A hunter virus that targets both infected cells and HIV free virions: Implications for therapy

The design of ‘hunter’ viruses aimed at destroying human immunodeficiency virus (HIV) infected cells is an active area of research that has produced promising results in vitro. Hunters are designed to target expo...

Authors: Cody Greer and Gisela García-Ramos

On a new law of bone remodeling based on damage elasticity: a thermodynamic approach

Bone tissue is the main element of the human skeleton and is a dynamic tissue that is continuously renewed by bone-resorbing osteoclasts and bone-forming osteoblasts.

Authors: Ahmed Idhammad and Abdelmounaïm Abdali

Cardiac dynamics: a simplified model for action potential propagation

This paper analyzes a new semiphysiological ionic model, used recently to study reexitations and reentry in cardiac tissue [I.R. Cantalapiedra et al, PRE 82 011907 (2010)]. The aim of the model is to reproduce ac...

Authors: Angelina Peñaranda, Inma R Cantalapiedra, Jean Bragard and Blas Echebarria

A critical stress model for cell motility

A detailed theoretical model that combines the conventional viscoelastic continuum description of cell motion with a dynamic active stress is presented. The model describes the ameboid cells movement comprisin...

Authors: Mehrnush Mehrayin, Farhad Farmanzad, Masoud Mozafari, Daryoosh Vashaee and Lobat Tayebi