Recent omics technologies and their emerging applications for personalised medicine
A major objective of ‘omics’ technologies is to understand genetic causality of complex traits of human diseases. High-throughput omics technologies and their application to medicine open up remarkable opportunities for realising optimised medical treatment for individuals. Because many major breakthrough and discoveries in this field have been driven by the development of new omics technologies, in this review, the authors aim to provide an in-depth description of their underlying principles as a foundation of developing another new omics technology, and to introduce their emerging applications for personali...
Source: IET Systems Biology - May 26, 2017 Category: Biology Source Type: research
Prediction of NSCLC recurrence from microarray data with GEP
This study proposes a new model from GE programming to use microarray datasets for NSCLC recurrence prediction. To this end, the authors also propose a hybrid method to rank and select relevant prognostic genes that are related to NSCLC recurrence prediction. The proposed model was evaluated on real NSCLC microarray datasets and compared with other representational models. The results demonstrated the effectiveness of the proposed model. (Source: IET Systems Biology)
Source: IET Systems Biology - May 26, 2017 Category: Biology Source Type: research
Peripheral arterial disease screening for hemodialysis patients using a fractional-order integrator and transition probability decision-making model
Atherosclerosis and resultant peripheral arterial disease (PAD) are common complications in patients with type 2 diabetes mellitus or end-stage renal disease and in elderly patients. The prevalence of PAD is higher in patients receiving haemodialysis therapy. For early assessment of arterial occlusion using bilateral photoplethysmography (PPG), such as changes in pulse transit time and pulse shape, bilateral timing differences could be used to identify the risk level of PAD. Hence, the authors propose a discrete fractional-order integrator to calculate the bilateral area under the systolic peak (AUSP). These indices indica...
Source: IET Systems Biology - May 4, 2017 Category: Biology Source Type: research
Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD
Rapid developments have been made in synthetic biology within the past two decades, particularly in combination with chemistry, computer science, and other disciplines. Genetic components and internal features have been a main focus of research for synthetic biologists. Logic gates can be applied in various disciplines, but have not yet been used for plasmid design. GenoCAD is a computer-aided design software programme for synthetic biology that can be used to design complex structures. Thus, in this study, the authors analysed a large, commonly used data set containing over 70,000 feature sequences and eventually obtained...
Source: IET Systems Biology - May 4, 2017 Category: Biology Source Type: research
Excluded volume effects in on- and off-lattice reaction–diffusion models
In this study, the authors therefore investigate to which extent on-lattice approximations, the so-called cellular automata models, can be used to simulate reactions and diffusion in the presence of crowding molecules. They show that the diffusion is most severely slowed down in the off-lattice model, since randomly distributed obstacles effectively exclude more volume than those ordered on an artificial grid. Crowded reaction rates can be both increased and decreased by the grid structure and it proves important to model the molecules with realistic sizes when excluded volume is taken into account. The grid artefacts incr...
Source: IET Systems Biology - May 4, 2017 Category: Biology Source Type: research
Peripheral arterial disease screening for hemodialysis patients using a fractional-order integrator and transition probability decision-making model
Atherosclerosis and resultant peripheral arterial disease (PAD) are common complications in patients with type 2 diabetes mellitus or end-stage renal disease and in elderly patients. The prevalence of PAD is higher in patients receiving haemodialysis therapy. For early assessment of arterial occlusion using bilateral photoplethysmography (PPG), such as changes in pulse transit time and pulse shape, bilateral timing differences could be used to identify the risk level of PAD. Hence, the authors propose a discrete fractional-order integrator to calculate the bilateral area under the systolic peak (AUSP). These indices indica...
Source: IET Systems Biology - April 11, 2017 Category: Biology Source Type: research
Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD
Rapid developments have been made in synthetic biology within the past two decades, particularly in combination with chemistry, computer science, and other disciplines. Genetic components and internal features have been a main focus of research for synthetic biologists. Logic gates can be applied in various disciplines, but have not yet been used for plasmid design. GenoCAD is a computer-aided design software programme for synthetic biology that can be used to design complex structures. Thus, in this study, the authors analysed a large, commonly used data set containing over 70,000 feature sequences and eventually obtained...
Source: IET Systems Biology - April 11, 2017 Category: Biology Source Type: research
Increased inflammation in sanctuary sites may explain viral blips in HIV infection
Combined antiretroviral therapy (cART) suppress HIV-1 viral replication, such that viral load in plasma remains below the limit of detection in standard assays. However, intermittent episodes of transient viremia (blips) occur in a set of HIV-patients. Given that follicular hyperplasia occurs during lymphoid inflammation as a normal response to infection, it is hypothesised that when the diameter of the lymph node follicle (LNF) increases and crosses a critical size, a viral blip occurs due to cryptic viremia. To study this hypothesis, a theoretical analysis of a mathematical model is performed to find the conditions for v...
Source: IET Systems Biology - July 26, 2016 Category: Biology Source Type: research
Signalling pathway impact analysis based on the strength of interaction between genes
In this study, the authors used newly developed signalling pathway impact analysis (SPIA) methods, SPIA based on Pearson correlation coefficient (PSPIA), and mutual information (MSPIA), to measure the interaction strength between pairs of genes. In analyses of a colorectal cancer dataset, a lung cancer dataset, and a pancreatic cancer dataset, PSPIA and MSPIA identified more candidate cancer-related pathways than were identified by SPIA. Generally, MSPIA performed better than PSPIA. (Source: IET Systems Biology)
Source: IET Systems Biology - July 26, 2016 Category: Biology Source Type: research
Designing a robust backstepping controller for rehabilitation in Parkinson's disease: a simulation study
In this study, a model of basal ganglia (BG) is applied to develop a deep brain stimulation controller to reduce Parkinson's tremor. Conventionally, one area in BG is stimulated, with no feedback, to control Parkinson's tremor. In this study, a new architecture is proposed to develop feedback controller as well as to stimulate two areas of BG simultaneously. To this end, two controllers are designed and implemented in globus pallidus internal (GPi) and subthalamic nucleus (STN) in the brain. A proportional controller and a backstepping controller are designed and implemented in GPi and STN, respectively. The proposed contr...
Source: IET Systems Biology - July 26, 2016 Category: Biology Source Type: research
Protein sequestration versus Hill-type repression in circadian clock models
Circadian (∼24 h) clocks are self-sustained endogenous oscillators with which organisms keep track of daily and seasonal time. Circadian clocks frequently rely on interlocked transcriptional-translational feedback loops to generate rhythms that are robust against intrinsic and extrinsic perturbations. To investigate the dynamics and mechanisms of the intracellular feedback loops in circadian clocks, a number of mathematical models have been developed. The majority of the models use Hill functions to describe transcriptional repression in a way that is similar to the Goodwin model. Recently, a new class of models wit...
Source: IET Systems Biology - July 26, 2016 Category: Biology Source Type: research
Minimum steering node set of complex networks and its applications to biomolecular networks
In this study, the authors analyse the network structural controllability in notion of the minimum steering node sets (MSSs). They first develop a graph-theoretic algorithm to identify the MSS for a given network and then apply it to several biomolecular networks. Application results show that biomolecules identified in the MSSs play essential roles in corresponding biological processes. Furthermore, the application results indicate that the MSSs can reflect the network dynamics and node importance in controlling the networks better than the MDSs. (Source: IET Systems Biology)
Source: IET Systems Biology - May 24, 2016 Category: Biology Source Type: research
Gene selection approach based on improved swarm intelligent optimisation algorithm for tumour classification
This study presents an improved swarm intelligent optimisation algorithm to select genes for maintaining the diversity of the population. The most essential characteristic of the proposed approach is that it can automatically determine the number of the selected genes. On the basis of the gene selection, the authors construct a variety of the tumour classifiers, including the ensemble classifiers. Four gene datasets are used to evaluate the performance of the proposed approach. The experimental results confirm that the proposed classifiers for tumour classification are indeed effective. (Source: IET Systems Biology)
Source: IET Systems Biology - May 24, 2016 Category: Biology Source Type: research
Non-linear feedback control of the p53 protein–mdm2 inhibitor system using the derivative-free non-linear Kalman filter
It is proven that the model of the p53–mdm2 protein synthesis loop is a differentially flat one and using a diffeomorphism (change of state variables) that is proposed by differential flatness theory it is shown that the protein synthesis model can be transformed into the canonical (Brunovsky) form. This enables the design of a feedback control law that maintains the concentration of the p53 protein at the desirable levels. To estimate the non-measurable elements of the state vector describing the p53–mdm2 system dynamics, the derivative-free non-linear Kalman filter is used. Moreover, to compensate for model...
Source: IET Systems Biology - May 24, 2016 Category: Biology Source Type: research
Retrieving relevant time-course experiments: a study on Arabidopsis microarrays
In this study, the authors address this problem in the context of time-course gene expression experiments from an information retrieval perspective. To this end, they introduce a computational framework that takes a time-course experiment as a query and reports a list of relevant experiments retrieved from a given repository. These retrieved experiments can then be used to associate the environmental factors of query experiment with the findings previously reported. The model is tested using a set of time-course Arabidopsis microarrays. The experimental results show that relevant experiments can be successfully retrieved b...
Source: IET Systems Biology - May 24, 2016 Category: Biology Source Type: research
