Disjoint motif discovery in biological network using pattern join method
In this study, an efficient pattern-join based algorithm is proposed to discover network motif in biological networks. The performance of the proposed algorithm is evaluated on the transcription regulatory network of Escherichia coli and the protein interaction network of Saccharomyces cerevisiae. The running time of the proposed algorithm outperforms most of the existing algorithms to discover large motifs. (Source: IET Systems Biology)
Source: IET Systems Biology - October 23, 2019 Category: Biology Source Type: research
Sliding mode controller–observer pair for p53 pathway
In this study, a sliding mode control (SMC) based robust non-linear technique is presented for the drug design of a control-oriented p53 model. The control input generated by conventional SMC is discontinuous; however, depending on the physical nature of the system, drug infusion needs to be continuous. Therefore, to obtain a smooth control signal, a dynamic SMC (DSMC) is designed. Moreover, the boundedness of the zero-dynamics is also proved. To make the model-based control design possible, the unknown states of the system are estimated using an equivalent control based, reduced-order sliding mode observer. The robustness...
Source: IET Systems Biology - July 19, 2019 Category: Biology Source Type: research
Mining conditions specific hub genes from RNA-Seq gene-expression data via biclustering and their application to drug discovery
In this study, the authors have introduced a new approach for identifying conditions specific hub genes from the RNA-Seq data using a biclustering algorithm. In the proposed approach, efficient ‘runibic’ biclustering algorithm, the concept of gene co-expression network and concept of protein–protein interaction network have been used for getting better performance. The result shows that the proposed approach extracts biologically significant conditions specific hub genes which play an important role in various biological processes and pathways. These conditions specific hub genes can be used as prognos...
Source: IET Systems Biology - July 19, 2019 Category: Biology Source Type: research
Control strategy design for the anti-HBV mathematical model
In this study, an anti-HBV mathematical model is considered and its control strategy of the drug treatment is designed. Based on the Lyapunov theory, this study derives three main theorems to propose three different control strategies, respectively, for drug treatments $mlpar trpar $m(t) and $nlpar trpar $n(t), such that all states of the anti-HBV model can finally converge to the infection-free equilibrium point $E_1$E1 asymptotically. Especially, the designed drug treatment $mlpar trpar $m(t) or $nlpar trpar $n(t) is not a fixed value, but it is time-varying and dependent on states. In Theorem 1, the single drug treatmen...
Source: IET Systems Biology - July 19, 2019 Category: Biology Source Type: research
Contribution of time delays to p53 oscillation in DNA damage response
Although the oscillatory dynamics of the p53 network have been extensively studied, the understanding of the mechanism of delay-induced oscillations is still limited. In this paper, a comprehensive mathematical model of p53 network is studied, which contains two delayed negative feedback loops. By studying the model with and without explicit delays, the results indicate that the time delay of Mdm2 protein synthesis can well control the pulse shape but cannot induce p53 oscillation alone, while the time delay required for Wip1 protein synthesis induces a Hopf bifurcation to drive p53 oscillation. In addition, the synergy of...
Source: IET Systems Biology - July 19, 2019 Category: Biology Source Type: research
Identification of a time-varying intracellular signalling model through data clustering and parameter selection: application to NF-$kappa $κB signalling pathway induced by LPS in the presence of BFA
Developing a model for a signalling pathway requires several iterations of experimentation and model refinement to obtain an accurate model. However, the implementation of such an approach to model a signalling pathway induced by a poorly-known stimulus can become labour intensive because only limited information on the pathway is available beforehand to formulate an initial model. Therefore, a large number of iterations are required since the initial model is likely to be erroneous. In this work, a numerical scheme is proposed to construct a time-varying model for a signalling pathway induced by a poorly-known stimulus wh...
Source: IET Systems Biology - July 19, 2019 Category: Biology Source Type: research
Hilbert transform-based time-series analysis of the circadian gene regulatory network
In this work, the authors propose the Hilbert transform (HT)-based numerical method to analyse the time series of the circadian rhythms. They demonstrate the application of HT by taking both deterministic and stochastic time series that they get from the simulation of the fruit fly model Drosophila melanogaster and show how to extract the period, construct phase response curves, determine period sensitivity of the parameters to perturbations and build Arnold tongues to identify the regions of entrainment. They also derive a phase model that they numerically simulate to capture whether the circadian time series entrains to ...
Source: IET Systems Biology - July 19, 2019 Category: Biology Source Type: research
Activity assessment of small drug molecules in estrogen receptor using multilevel prediction model
The authors have proposed an efficient multilevel prediction model for better activity assessment to test whether certain chemical compounds can disrupt processes in the human body that may create negative health effects. Here, a computational method (in-silico) is proposed for the quality prediction of drugs in terms of their activity, activity score, potency, and efficacy for estrogen receptors (ERs) by using various physicochemical properties (molecular descriptors). PaDEL-Descriptor is used for features extraction. The ER dataset has 8481 drug molecules where 1084 are active, and 7397 are inactive, and each drug molecu...
Source: IET Systems Biology - June 11, 2019 Category: Biology Source Type: research
Robust multi-objective blood glucose control in Type-1 diabetic patient
In this study, an automatic robust multi-objective controller has been proposed for blood glucose (BG) regulation in Type-1 Diabetic Mellitus (T1DM) patient through subcutaneous route. The main objective of this work is to control the BG level in T1DM patient in the presence of unannounced meal disturbances and other external noises with a minimum amount of insulin infusion rate. The multi-objective output-feedback controller with H∞, H2 and pole-placement constraints has been designed using linear matrix inequality technique. The designed controller for subcutaneous insulin delivery was tested on in silico adult an...
Source: IET Systems Biology - June 11, 2019 Category: Biology Source Type: research
Cancer adjuvant chemotherapy prediction model for non-small cell lung cancer
This study aims at building a predictive model to identify who needs ACT treatment and who should avoid it. To this end, the authors propose an innovative method to identify NSCLC-related prognostic genes from microarray gene-expression datasets. They also propose a new model using gene-expression programming algorithm for ACT classification. The proposed model was evaluated on integrated microarray datasets from four institutes and compared with four representative methods: general regression neural network, decision tree, support vector machine and naive Bayes. Evaluation results demonstrated the effectiveness of the pro...
Source: IET Systems Biology - June 11, 2019 Category: Biology Source Type: research
Robust control of HIV infection by antiretroviral therapy: a super-twisting sliding mode control approach
Acquired immune deficiency syndrome is an epidemic infectious disease which is caused by the human immunodeficiency virus (HIV) and that has proliferated across worldwide. It has been a matter of concern for the scientific community to develop an antiretroviral therapy, which will prompt a rapid decline in viral abundance. With this motivation, this study proposes the design of a robust super twisting sliding mode controller based on output information for an uncertain HIV infection model. The control objective is to decrease the concentration of infected CD4+ T cells to a specified level by drug administration using only ...
Source: IET Systems Biology - June 11, 2019 Category: Biology Source Type: research
Effective sampling trajectory optimisation for sensitivity analysis of biological systems
Sensitivity analysis has been widely applied to study the biological systems, including metabolic networks, signalling pathways, and genetic circuits. The Morris method is a kind of screening sensitivity analysis approach, which can fast identify a few key factors from numerous biological parameters and inputs. The parameter or input space is randomly sampled to produce a very limited number of trajectories for the calculation of elementary effects. It is clear that the sampled trajectories are not enough to cover the whole uncertain space, which eventually causes unstable sensitivity measures. This paper presents a novel ...
Source: IET Systems Biology - June 11, 2019 Category: Biology Source Type: research
Modelling and simulation of photosynthetic activities in C3 plants as affected by CO2
CO2 concentration ([CO2]) in a greenhouse may be a limiting factor for plant growth. Current greenhouse CO2 control strategy usually depends on expert experience, which may control [CO2] in a moderate range but cannot make it optimal due to lack of considering plant photochemistry reactions. A state-space kinetic model structure covering major photosynthetic reactions as affected by CO2 is useful for [CO2] control strategy development in a greenhouse because modern control theories are usually based on state-space models. In this work, a state-space kinetic model structure for photosynthesis was built, which describes the ...
Source: IET Systems Biology - June 11, 2019 Category: Biology Source Type: research
MicroRNAs and their target mRNAs as potential biomarkers among smokers and non-smokers with lung adenocarcinoma
Lung adenocarcinoma is one of the major causes of mortality. Current methods of diagnosis can be improved through identification of disease specific biomarkers. MicroRNAs are small non-coding regulators of gene expression, which can be potential biomarkers in various diseases. Thus, the main objective of this study was to gain mechanistic insights into genetic abnormalities occurring in lung adenocarcinoma by implementing an integrative analysis of miRNAs and mRNAs expression profiles in the case of both smokers and non-smokers. Differential expression was analysed by comparing publicly available lung adenocarcinoma sample...
Source: IET Systems Biology - April 30, 2019 Category: Biology Source Type: research
Rehabilitation of the Parkinson's tremor by using robust adaptive sliding mode controller: a simulation study
One of the efficient methods in controlling the Parkinson's tremor is Deep Brain Stimulation (DBS) therapy. The stimulation of Basal Ganglia (BG) by DBS brings no feedback though the existence of feedback reduces the additional stimulatory signal delivered to the brain. So this study offers a new adaptive architecture of a closed-loop control system in which two areas of BG are stimulated simultaneously to decrease the following three indicators: hand tremor, the level of a delivered stimulation signal in the disease condition, and the level of a delivered stimulation signal in health condition to the disease condition. On...
Source: IET Systems Biology - March 22, 2019 Category: Biology Source Type: research
